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Turbomole USER`S MANUAL

1. note that the options select and all are complementary lt option gt switch off lt option gt or q uit leave this menu Afterwards you have the possibility to change the criterion to be applied for the selection of modified atomic orbitals MAOs within the following little submenu global criterion for selection of Modified Atomic Orbitals MAOs MAOQs are employed if atomic density eigenvalues exceed a threshold of 1000 specify the appropriate option if you want to use another global criterion for selecting MAOs option status description select by eigenvalues of the atomic density matrices select by occupation numbers lt r gt is the selection threshold DEFAULT 1000 or q uit leave this menu The criterion applied by default is the so called atomic density eigenvalue with a threshold of 0 1 You can switch the criterion to occupation numbers by entering occ If you also want to change the threshold you just have to append its new value to the selection keyword e g occ 2 Finally you can select or disable various options in connection with the computation of shared electron numbers SEN within the following menu 96 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE actual settings for data group shared electron numbers 2 center shared electron numbers will be computed values are printed if absolute value exceeds 0100 3 center shared electron numbers will be computed values are
2. Ansatz 2 is used if ansatz is absent ri2model char char A A or B The r12model flag determines which approximation model is used to calculate the RI MP2 F12 ground state energy Ansatz B is used if r12model is absent comaprox char char F K or T V The comaprox flag determines the method used to approximate the com mutator integrals T fi Approximation T V is used if comaprox is absent cabs char val char svd or cho The cabs flag determines the method used to orthogonalize the orbitals of the CABS basis val is the threshold below which CABS orbitals are removed from the calculation svd 1 0d 08 is used if cabs is absent examp char char noinv fixed or inv with flip or noflip The examp flag determines which methods are used to determine the F12 amplitudes For inv the amplitudes are optimized using the orbital invariant method For fixed and noinv only the diagonal amplitudes are non zero and are either predetermined using the coalescence condi tions fixed or optimized noinv not orbital invariant If char inv the F12 energy contribution is computed using all three methods For open shell calculations noflip supresses the use of spin flipped geminal 18 2 FORMAT OF KEYWORDS AND COMMENTS 321 functions The fixed flip method is used if examp is absent pairenergy char char off or on If char off default the print out of the standard and F12 contribu tions to the pair energies is suppressed
3. CPU time and disk space requirements are thus somewhat smaller than for CC2 properties or gradients 188 CHAPTER 9 RI CC2 For SCF CIS CCS it is recommended to use the modules grad and rdgrad for the calculation of ground state gradients and first order properties 9 3 2 Excited State Properties Gradients and Geometries Also for excited states presently unrelaxed and relaxed first order properties are available in the ricc2 program These are implemented for CCS and CC2 Note that in the unrelaxed case CIS and CCS are not equivalent for excited states first order properties and no first order properties are implemented for CIS in the ricc2 program Orbital unrelaxed first order properties The unrelaxed first order properties are calculated from the variational excited states Lagrangian 114 which for the calculation of unrelaxed properties is composed of the unrelaxed ground state Lagrangian Eq 9 12 and the expression for the excitation energy pm Oee Ent 8 HF H CC Y B A t 6 Ey 9 18 pv EP D HE M1 gt Be ual Fo BV T2 HF u2 where it is assumed that the left and right eigenvectors are normalized such that ap E u tv E 1 and H Ho BV The first order properties are calculated as first derivatives of L CC2 E F t per B with respect to the field strength 8 and are evaluated via a density formalism ur ex OL E E t ne l ur ex vy R l aB z gt D Dor Voa gt
4. ly vhostop iiteger for developers only Radial grid points have a linear scaling parameter see Eq 16 19 and Table 1 in Ref 180 With the following input dft rhostart 50 rhostop 200 one performs a numerical integration for the density and the exchange correlation term for 0 5 0 01 2 0 for given MOs and functional NOTE only molecules with a single atom type can be used The results serve to establish stable optimal values see Figure 1 in Ref 180 Program stops after this testing reference Usage of the reference grid which is a very fine grid with very tight thresholds The default values for the different variables are gridsize 7 radsize 14 fullshell 1 dgrenze 16 18 2 FORMAT OF KEYWORDS AND COMMENTS 279 fgrenze 16 qgrenze 16 fcut 16 Please refer to the corresponding sub keywords for explanation If you want to use the reference grid you have to skip the keyword gridsize and type instead reference Example dft functional b p reference test integ Check if the selected grid is accurate enough for the employed basis set by performing a numerical integration of the norm of all occupied and virtual orbitals Useful for LHF batchsize integer Grid points are sorted into batches which are then processed This increases efficency This should be changed only by developers Default is batchsize 100 fullshell Standard grids have reduced number of spherical grid poi
5. 4 p 7 4188720000 5 6984100000 1 1777211960 54478533555 1 p 22309270117 1 p 43100000000E 01 4 d 3 9738796278 1 4528884813 7s6p5d 6s3p2d 211111 411 41 99343296745 1 6510077975 1 0000000000 1 0000000000 1 0000000000 1 0000000000 1 0000000000 26979695152 46968874449 50905100155 52298161137 1 0000000000 1 0000000000 52799310714E 01 18558319471 00000000000000 00000000000000 00000000000000 4 46615918865523 4 46615918865523 val 4 38784 val 4 46616 cl cl cl cl cl 19 4 TACLs INPUT FOR AN REDFT CALCULATION WITH ECPS 61042908544 24216276510 1 d 87909318337E 01 cl def SVP cl 5 s 10449 827566 1571 7365221 357 12065523 100 25185935 30 812727554 3 s 51 923789434 5 7045760975 2 3508376809 1 s 44605124672 1 os 16848856190 5 p 307 66790569 72 102015515 22 532680262 7 8991765444 2 8767268321 1 p 77459363955 1 p 21037699698 1 d 65000000000 ecp ta def ecp ncore 60 7s5p 6s2p coefficient 12 0179609 42959071631 43497228232 1 0000000000 19708362484E 02 14754727977E 01 66679112875E 01 17228924084 15883786100 10009298909 60841752753 54352153355 1 0000000000 1 0000000000 87801484118E 02 6356335547 1E 01 24016428276 47798866557 38515850005 1 0000000000 1 0000000000 1
6. BIBLIOGRAPHY V N Staroverov G E Scuseria J Tao J P Perdew Comparative as sessment of a new nonempirical density functional Molecules and hydrogen bonded complexes J Chem Phys 119 23 12129 12137 2003 S Grimme Semiempirical hybrid density functional with perturbative second order correlation J Chem Phys 124 034108 2006 A Gorling M Levy Correlation energy functional and its high density limit obtained from a coupling constant perturbation expansion Phys Rev B 47 13105 1993 A Gorling M Levy Exact Kohn Sham scheme based on perturbation theory Phys Rev A 50 196 1994 M K Armbruster F Weigend C van Willen W Klopper Self consistent treatment of spin orbit interactions with efficient hartree fock and density functional methods Phys Chem Chem Phys 10 1748 1756 2008 M K Armbruster W Klopper F Weigend Basis set extensions for two component spin orbit treatments of heavy elements Phys Chem Chem Phys 8 4862 4865 2006 M Reiher A Wolf Exact decoupling of the Dirac Hamiltonian I General theory J Chem Phys 121 2037 2047 2004 M Reiher A Wolf Exact decoupling of the Dirac Hamiltonian II The generalized Douglas Kroll Hess transformation up to arbitrary order J Chem Phys 121 10945 10956 2004 M Reiher Douglas Kroll Hess Theory a relativistic electrons only theory for chemistry Theor Chem Acc 116 241 252 2006
7. M von Arnim R Ahlrichs Geometry optimization in generalized natural internal coordinates J Chem Phys 111 20 9183 9190 1999 P Pulay G Fogarasi F Pang J E Boggs Systematic ab initio gradi ent calculation of molecular geometries force constants and dipole moment derivatives J Am Chem Soc 101 10 2550 2560 1979 M Dolg U Wedig H Stoll H Preu Energy adjusted ab initio pseudopo tentials for the first row transition elements J Chem Phys 86 2 866 872 1986 C C J Roothaan Self consistent field theory for open shells of electronic systems Rev Mod Phys 32 2 179 185 1960 R Ahlrichs F Furche S Grimme Comment on Assessment of exchange correlation functionals Chem Phys Lett 325 1 3 317 321 2000 M Sierka A Hogekamp R Ahlrichs Fast evaluation of the Coulomb po tential for electron densities using multipole accelerated resolution of identity approximation J Chem Phys 118 20 9136 9148 2003 F Weigend A fully direct RI HF algorithm Implementation optimised aux iliary basis sets demonstration of accuracy and efficiency Phys Chem Chem Phys 4 18 4285 4291 2002 R Fletcher Practical Methods of Optimization Unconstrained Optimization Band 1 Wiley New York 1980 T Helgaker Transition state optimizations by trust region image minimiza tion Chem Phys Lett 182 5 503 510 1991 F Jensen Locating transition structu
8. Presently also implemented in the ricc22 module are CCSD and CCSD T and explicitly correlated F12 variants thereof The latter have much faster ba sis set convergence are therefore more efficients We recommend in particular CCSD F12 and CCSD F12 T Excitation energies are only available for conventional CCSD 38 CHAPTER 3 HOW TO RUN TURBOMOLE 3 1 6 Calculation of Molecular Properties See Section 1 4 for the functionality and Section 18 for the required keywords of the modules dscf ridft mpshift escf and ricc2 3 1 7 Modules and Data Flow See Figure 3 1 3 2 Parallel Runs Many of the TURBOMOLE modules are parallelized using the message passing interface MPI for distributed and shared memory machines or with OpenMP or multi threaded techniques for shared memory and multi core machines Generally there are two hardware scenarios which determine the kind of paralleliza tion that is possible to use e On a single node with several CPUs and or cores using the same memory shared memory the user can run all parallelized modules of TURBOMOLE For some modules both shared memory and MPI versions are available but it is recommended not to use the latter ones for performance reasons How to run the parallel TURBOMOLE SMP version on multi core and or multi CPU systems Please see chapter 3 2 1 On a cluster a parallel calculation can be performed using several distinct nodes each one with local memory and di
9. TURBOMOLE Program Package for ab initio Electronic Structure Calculations USER S MANUAL TURBOMOLE Version 6 5 May 15 2013 Contents Preface and General Information 1 1 Contributions and Acknowledgements 1 2 Features of TURBOMOLE ssa pas PA 6 wok ee We ee ee 1 3 How to Quote Usage of TURBOMOLE 0004 1 4 Modules and Their Functionality s gt is osas sa eaaa ai aaas Installation of TURBOMOLE 2 1 Install TURBOMOLE command line version 00 Sertmes TOF each user sos s k entm eie E Hoe ew Oe BOY Setting system type and PATH by hand Testing the installation os oa sac mota a aa t ioe mw 2 2 Installation problems How to solve ooa a 1 1 5 Tools 2 2l 2 1 2 2 13 3 3 1 1 3 1 2 3 1 3 3 1 4 3 1 5 3 1 6 3 1 7 How to Run TURBOMOLE Single Point Calculations Running TURBOMOLE Modules Energy and Gradient Calculations Calculation of Molecular Properties Modules and Data Flaw lt ca 4 6 64 44 0b Goby amp uke 4 32 Parallel Rims secs so goate Bw ew de dee a we Ee eee eae 3 2 1 Running Parallel Jobs SMP case 11 11 13 13 23 25 29 29 29 30 31 31 4 CONTENTS 3 2 2 Running Parallel Jobs MPI case 43 4 Preparing your input file with DEFINE 49 4 0 3 Universally Available Display Commands in DEFINE 50 4 0 4 Specifying Atomic Sets
10. The following basis sets are available on TURBODIR basen which you may in spect to see which other basis sets are supported automatically The corresponding publications can be found here 1 3 SV P or def SV P for routine SCF or DFT Quality is about 6 31G TZVP or def TZVP for accurate SCF or DFT Quality is slightly better than 6 311G TZVPP or def TZVPP for MP2 or close to basis set limit SCF or DFT Comparable to 6 311G 2df QZVP and QZVPP for highly correlated treatments quadruple zeta 3d2flg or 4d2flg beyond Ne 3p2d1f for H These basis sets are available for atoms H Kr and the split valence SV and valence triple TZV basis sets types with ECPs also for Rb Rn except lanthanides 64 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE For calculations with the programs rimp2 and ricc2 optimized auxiliary basis sets are available for the basis sets SV P SVP TZVP TZVPP and QZVPP NEW New sets of basis functions partly identical with those mention above de noted def2 X YZ are available for atoms H Rn 6 The def2 basis sets for 5p and 6p block elements are designed for small core ECPs ECP 28 ECP 46 and ECP 60 For each family SV TZV and QZV we offer two sets of polarisation functions leading to def2 SV P and def2 SVP def2 TZVP and def2 TZVPP def2 QZVP and def2 QZVPP We strongly recommended the new def2 basis since they have been shown to provide consistent accuracy across the peri
11. x y z atom lt i gt F reference point atom no lt i gt Oth T compute Oth moment 1st F compute 1st moment 2nd F compute 2nd moment 3rd F compute 3rd moment PEREN EEPE tee Ni Pete ee Set lt moment gt skip computation of lt moment gt or q uit terminate input 92 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE This menu serves to specify the electrostatic moments to be calculated Oth charge 1ist dipole moment 2nd quadrupole moment 3rd octuple moment The refer ence point is the origin of the coordinate system used in the calculation The value of any calculated moment will be independent of this reference point if all lower moments are zero The default for the reference point is the origin i e the coor dinate system used for the calculation of the moments will be the same as the one in which the atomic coordinates are specified The reference point may be changed by typing point with the three new coordinates appended Alternatively you may choose the coordinates of one of the atoms as reference point by entering atom and the atom index Option potential This option collects all possible quantities related to the electrostatic field created by the molecular charge distribution This includes the following suboptions list of suboptions pot electrostatic potential fld electrostatic field fldgrd electrostatic field gradient shld diamagnetic shielding file file referenc
12. 0 003925 correction 0 003644 total 0 000282 ENERGIES a u Total energy 76 0296831863 Total energy OC corr 76 0297567835 Dielectric energy E 0 0118029468 Diel energy OC corr 0 0118765440 18 2 FORMAT OF KEYWORDS AND COMMENTS 301 The following value is included for downward compatibility Total energy corrected 76 0297199849 The dielectric energy of the system is already included in the total energy OC corr denotes the outlying charge correction The last energy entry gives the total out lying charge corrected energy in the old definition used in TURBOMOLE 5 7 and older versions The Cosmo result file which contains the segment information energies and settings can be set using cosmo_out file filename cosmo Isodensity Cavity This option can be used in HF DFT single point calculations only The cosmo_isodens section defines the settings for the density based cavity setup see also chapter 17 If the cosmo_isodens keyword is given without sub options a scaled iosodensity cavity with default settings will be created Possible options are cosmo_isodens activates the density based cavity setup The default values of nspa and nsph are changed to 162 and 92 respectively This values are superseded by the user defined nspa value of the cosmo section By default the scaled density method is used The atom type dependent density values are read from the radii cosmo file located in TURBODIR par
13. Also all some options which require orbitals as e g the generation and visualization of localized orbitals or some population analysis options and not available for excited states in ricc2 As other modules also ricc2 provides the proper flag to bypass a re calculation of the density and gradient to enter immediately the density analysis routines with a previously calculated density The ricc2 program will then pass the densities found on the interface file for the density analysis routines without further check on the 192 CHAPTER 9 RI CC2 method and state for which they have been evaluated If both ground and excited state densities are found on file both will be passed to the density analysis thereby providing a shortcut to the fanal and the anadens keyword for the analysis of differences between ground and excited state densities The general density analysis option In general ricc2 saves by default all relaved densities generated during a calcula tion in files named ccltd lt type gt lt mult gt lt irrep gt lt number gt where ccltd stands for coupled cluster one electron total density lt type gt is one of mp2 gs MP2 ground state cc2 gs CC2 ground state ccs xs CCS excited state cc2 xs CC2 excited state or adc2 xs ADC 2 excited state and the other entries spec ify multiplicity irreducible representation and the number of the state Having specified the calculation of relaxed densities e g by req
14. for frozen core orbitals data group freeze all orbitals with energies below 3a u are sug gested to be frozen and for the amount of memory to be allocated maxcor These defaults can be confirmed with return or modified if desired Note the amount of memory to be allocated determines the number of multiple passes and thus the efficiency of rimp2 It is also possible to run Rimp2prep directly after define 3 The ricc2 program requires the data group ricc2 mp2 geoopt model mp2 Where the last line should only be included if the calculation of gradients is needed e g in geometry optimizations This can be prepared with define in the menus mp2 or cc2 4 For explicitly correlated MP2 F12 calculations with ricc2 also the data groups rir12 and 1cg is needed 5 Start a single rimp2 calculation with the command ricc2 or rimp2 6 For optimisation of structure parameters at the RI MP2 level use the command jobex level cc2 or jobex ri level mp2 For geometry optimizations with RI JK SCF as reference for RI MP2 with the ridft and ricc2 binaries the additional option rijk has to be given 7 The combination of RI MP2 with RI JK SCF can lead to significant computa tional savings in particular for geometry optimizations for small and medium sized molecules with large basis sets quadruple and beyond or basis sets with diffuse functions e g the aug cc pVXZ basis set families For large molecules with TZVPP or similar basis
15. intdef Definitions of redundant internal coordinates coord Cartesian coordinates for option coordinate grad Cartesian coordinates and gradients as provided and accumulated in subsequent optimization cycles by the various gradient programs for coordinate and gradient 112 CHAPTER 5 STRUCTURE OPTIMIZATIONS hessian Analytical force constant matrix as provided by the force constant pro gram aoforce only if option hessian is specified The data group hessian projected may be used alternatively for this purpose All output will be written to the screen except for option hessian output to data group forceapprox 5 3 12 The m Matrix The m matrix serves to fix position and orientation of your molecule during geometry optimizations It cannot be used to fix internal coordinates The m matrix is a diagonal matrix of dimension 3n where n is the number of atoms Normally m will be initialized as a unit matrix by relax As an example consider you want to restrict an atom to the xy plane You then set the m z matrix element for this atom to zero You can use at most six zero m matrix diagonals for linear molecules only five corresponding to translational and rotational degrees of freedom Note that the condition of the BmB matrix can get worse if positional restrictions are applied to the m matrix m matrix elements violating the molecular point group symmetry will be reset to one Non default settings for m matrix diagona
16. s paper have an underscore _ In the present implementation an sp C atom has the name C 3 instead of C_3 Particularly the bond terms are described with the harmonic potential and the non bonded van der Waals terms with the Lennard Jones potential The partial charges needed for electrostatic nonbond terms are calculated with the Charge Equilibration Modell QEq from Rapp 39 There is no cutoff for the non bonded terms 999 The relaxation procedure distinguishes between molecules wih more than 90 atoms and molecules with less atoms For small molecules it consists of a Newton step followed by a linesearch step For big molecules a quasi Newton relaxation is done The BFGS update of the force constant matric is done 40 41 34 42 Pulay s DIIS procedure is implemented for big molecule to accelarate the optimization 43 33 The coordinates for any single atom can be fixed by placing an f in the third to eighth column of the chemical symbol flag group As an example the following coordinates specify acetone with a fixed carbonyl group coord 2 02693271108611 2 03672551266230 0 00000000000000 1 08247228252865 0 68857387733323 0 00000000000000 2 53154870318830 2 48171472134488 0 00000000000000 1 78063790034738 1 04586399389434 O 00000000000000 2 64348282517094 0 13141435997713 1 68855816889786 2 23779643042546 3 09026673535431 O 00000000000000 2 64348282517094 0 13141435997713 1 68855816889
17. 100 117 353 354 357 358 418 frozen coordinates 221 geometries excited states 187 ground state 185 geometry manipulation of 62 GRAD keywords 304 grad 23 24 36 38 40 42 44 45 47 78 84 100 106 109 110 117 119 121 125 138 156 187 196 263 296 298 303 304 311 335 337 363 364 grad_out 120 gradient 191 gradients excited states 187 ground state 185 hcore 26 Infrared Spectra 218 intcorr 213 intense 25 221 internal coordinates linear combination of 61 manual definition of 60 types of 60 intersections conical 181 jmol 26 job lt cycle gt 100 job last 100 job start 100 jobbsse 56 118 120 JOBEX 123 jobex 25 26 30 35 51 79 82 99 100 102 103 113 118 148 156 176 INDEX 177 319 337 364 c 99 119 dscf 99 energy 99 119 ex 99 gceart 99 119 grad 99 gradient 119 keep 99 1 99 1179 level 99 119 1s 99 119 md 99 mdfile 99 mdmaster 99 mem 119 opt 119 relax 99 119 ri 99 119 rijk 99 setup 119 statpt 99 trans 99 trimer 119 kdg 26 kinetic energy 358 lalp 348 Laplace 175 lbet 348 Leapfrog Verlet algorithm 117 354 Lhfprep 255 lhfprep 26 255 asy 256 k1li 256 num 256 lhfprep lhfprep lhfprep Imo 348 log2egy 26 INDEX log2x 26 LT SOS RI MP2 42 171 mdens 192 mdlog 117 mdmaster 353 mdmaster 117 Mdprep 117 353 354 mdprep 353
18. 114 CHAPTER 5 STRUCTURE OPTIMIZATIONS of an optimizations For optimizations in cartesian space this will be faster by a factor of two for any molecule 5 4 2 How to Perform a UFF Calculation You have to generate cartesian coordinates file coord nothing else You can start an single point calculation calculation by typing uff To start an uff geometry optimization one has to change the number of cycles parameter maxcycle in the block uff in the file control The ouput is the optimized structure file coord the analytical gradient file uffgradient and the analytical cartesian hessian file uffhessianO 0 Furthermore the control file will be modified forceinit on carthess uffhessian file uffhesian0 0 These commands have the effect to inititialize the force constant matric for a geom etry optimization with the hessian one In some cases uff cannot recognize the connectivity then one can specify the con nectivity in the file ufftopology The program will calculate the bond angle tor sion inverison and non bonded terms force field terms based on the connectivity specified in the topology file 5 4 3 The UFF implementation The uff implementation follows the paper by Rapp 7 The energy expression in uff is as follows 5 4 FORCE FIELD CALCULATIONS 115 NB 4 Burr 9 Ku ru On Krix 1 cos 20 linear case Na Krux 1 cos 30 trigonal planar case de 5 Ata 1 cos 40 qu
19. 16 3 HOW TO PERFORM 255 This can be done using define modified grid are not supported and then run odft A more suitable procedure is the following 1 Do a Hartree Fock calculation using dscf 2 Use the script 1hfprep to prepare the control file the old control file will be saved in control hf and the molecular orbitals in mos hf or in alpha hf and beta hf for the spin unrestricted case See 1hfprep help for options Actually LHF can be started from any guessed orbitals but if HF orbitals are used a much faster convergence is expected By default the script 1hfprep will add modify the control file with dft functional lhf gridtype 6 gridsize 3 radsize 3 lhf off diag on num slater off asymptotic dynamic 1 d 3 conj grad conv 1 d 6 maxit 20 output 1 asy 1 slater dtresh 1 d 9 slater region 7 0 0 5 10 0 0 5 corrct region 10 0 0 5 scfdump scfiterlimit 30 scfconv 6 scfdamp start 0 000 step 0 500 min 0 50 scforbitalshift noautomatic correction matrix elements file lhfcg correction alpha matrix elements file lhfcg_alpha correction beta matrix elements file lhfcg_beta 3 Run odft With the LHF potential Rydberg series of virtual orbitals can be obtained To that end diffuse orbital basis sets have to be used and special grids are required gridtype 4 is the most diffuse with special radial scaling gridtype 5 is for very good Rydberg orbitals gridtype 6 default in Lhfprep is the least diffuse o
20. 2 0 0004 50 40 5 control as Input and Output File o soacre or ed Sha 50 A06 Be Prepared so escore s sora ae FR a aa a e SRS 51 4 1 The Geometry Main Menu naaa 92 4 1 1 Description of commands 0 4 54 4 1 2 Internal Coordinate Menu aaa aaa e 57 4 1 38 Manipulating the Geometry 0 62 4 2 The Atomic Attributes Menu 22 0004 62 4 2 1 Description of the commands 65 4 3 Generating MO Start Vectors a 67 4 3 1 The MO Start Vectors Menu 67 4 3 2 Assignment of Occupation Numbers 70 4 3 3 Orbital Specification Menu a ose sasos sese sao 72 4 3 4 Roothaan Parameters gt x a oo eao ea wks p emi wua 73 4 3 5 Start MOs for broken symmetry treatments flip 73 4 4 The General Options Menu aaa 76 4 4 1 Important commands os s s Ta a k a a A e aa e a E S it 44 2 Special adjustments cs ss saosa daoia sra ai ee 83 44 3 Relax Options o cs ma ca 0 48 katido gok Kaom eRe 85 4 4 4 Definition of External Electrostatic Fields 89 AAS Properes smio 2 6k ee gon ae a week Ag G wd anai a 90 5 Calculation of Molecular Structure and Ab Initio Molecular Dy namics 99 5 1 Structure Optimizations using the JOBEX Script 99 Dele Opbione s ms fk ae et ee ie Re ee oe eo ee eS 99 Bl Output eo 4 ea ck pa OES eG EOE Se ek a ew G 100 D2 Program STAUPD go wish Rad a ok Hk Ay ee oe a eee ec ey 101 5 2
21. 42 CHAPTER 3 HOW TO RUN TURBOMOLE this value to about 75 of the physical memory available for your calculations but to at most 16000 megabytes Due to the use of integer 4 arithmetics the ricc2 program is presently limited to 16 Gbytes In the dscf program the OpenMP parallelization covers presently only the Hartree Fock coulomb and exchange contributions to the Fock matrix in fully integral direct mode and is mainly intended to be used in combination with OpenMP parallel runs of ricc2 Nevertheless the OpenMP parallelization can also be used in DFT calculations but the numerical integration for the DFT contribution to the Fock matrix will only use a single thread CPU core and thus the overall speed up will be less good Memory usage is low and dscf will ignore maxcor settings The odft module is parallelized using OpenMP For LHF an almost ideal speedup is obtained because the most expensive part of the calculation is the evaluation of the Fock matrix and of the Slater potential and both of them are well parallelized The calculation of the correction term of the grid will use a single thread Restrictions e In the ricc2 program the parts related to RI MP2 F12 LT SOS RI MP2 or calculation of expectation values for S do not yet use OpenMP paralleliza tion If the OpenMP parallelization is switched on by setting OMP_NUM_THREADS these parts will still be executed sequentially e In the dscf program the DFT part will only b
22. 9 19 0 pq Again R indicates that the real part is taken The unrelaxed excited state proper ties obtained thereby are related in the same way to the total energy of the excited states as the unrelaxed ground state properties to the energy of the ground state and the differences between excited and ground state unrelaxed properties are identical to those identified from the second residues of the quadratic response function For a detailed description of the theory see refs 114 113 the algorithms for the RI CC2 implementation are described in refs 111 12 ref 111 also contains a discussion of the basis set effects and the errors introduced by the RI approximation The calculation of excited state first order properties thus requires the calculation of both the right and left eigenvectors and of the excited state Lagrangian multipliers na The disk space and CPU requirements for solving the equations 9 3 FIRST ORDER PROPERTIES AND GRADIENTS 189 for Ey and pe are about the same as those for the calculation of the excitation energies For the construction of the density matrices in addition some files with O nrootN 2 size are written where nroot is the number of excited states The single substitution parts of the excited states Lagrangian multipliers ter are saved in files named CCNLO s m sxzz For the calculation of first order properties for excited states the keyword exprop must be added with appr
23. A Wolf M Reiher B Hess The generalized Douglas Kroll transformation J Chem Phys 117 9215 9226 2002 M Sierka A Burow J Dobler J Sauer Point defects in CeOz2 and CaF investigated using periodic electrostatic embedded cluster method J Chem Phys 130 17 174710 2009 K N Kudin G E Scuseria A fast multipole method for periodic systems with arbitrary unit cell geometries Chem Phys Lett 283 61 68 1998 P Ewald Die Berechnung optischer und elektrostatischer Gitterpotentiale Ann Phys 64 253 287 1921 BIBLIOGRAPHY 399 74 75 76 77 78 79 80 81 82 83 84 85 J Hepburn G Scoles R Penco A simple but reliable method for the predic tion of intermolecular potentials Chem Phys Lett 36 451 456 1975 R Ahlrichs R Penco G Scoles Intermolecular forces in simple systems Chem Phys 19 119 130 1977 S Grimme Accurate description of van der waals complexes by density func tional theory including empirical corrections J Comput Chem 25 12 1463 1473 2004 S Grimme Semiempirical GGA type density functional constructed with a long range dispersion contribution J Comput Chem 27 15 1787 1799 2006 S Grimme J Antony S Ehrlich H Krieg A consistent and accurate ab initio parametrization of density functional dispersion correction DFT D for the 94 elements H Pu J Chem Phys 132 154104 20
24. Epr nr HF W Ti T 511 HF ag S is aW FPS f W JIHF H X Fue Hal W FPP To HF H2 3 5 F D Ru F D4 9 28 uv from which all PERI CC2 equations including the linear response terms may be derived Note that the dependency on the density couples the CC amplitude and multiplier equations for the ground state solution vector 9 8 2 Computational details SCF calculations To carry out a PE SCF calculation with the DSCF or RIDFT module you have to specify the following in the control file point_charges pe options lt length unit gt lt no MM sites gt lt order k gt lt order pol gt lt length exclude list gt lt list of MM sites exclude list xyz coords multipole mom pol tensor gt length unit specifies the unit for the MM site coordinates use AA or AU no MM sites the amount of MM sites length of the list order k the order of multipoles used 0 point charges 1 dipole moments 2 quadrupole moments 3 octupole moments order pol the treatment of polarizabilities 0 none 1 isotropic 2 anisotropic length exclude list number of elements in the exclude list list of MM sites each MM sites is described on one line entries separated by blanks first entry is the exclude list of with as much elements as defined in the head line If the first element in the exclusion list of one site occurs in the exclude list of another site they do not contribute to each others polarization n
25. Eur J 11 12 3559 3564 2005 P Cortona Self consistently determined properties of solids without band structure calculations Phys Rev B 44 8454 1991 BIBLIOGRAPHY 405 147 148 149 150 151 152 153 154 155 156 157 158 T A Wesolowski A Warshel Frozen density functional approach for ab initio calculations of solvated molecules J Phys Chem 97 8050 1993 T A Wesolowski In J Leszczynski Ed Chemistry Reviews of Current Trends Band 10 Page 1 World Scientific Singapore 2006 Singapore 2006 T A Wesolowski A Warshel Kohn sham equations with constrained elec tron density an iterative evaluation of the ground state electron density of interacting molecules Chem Phys Lett 248 71 1996 S Laricchia E Fabiano F D Sala Frozen density embedding with hybrid functionals J Chem Phys 133 164111 2010 S Laricchia E Fabiano F D Sala Frozen density embedding calcula tions with the orbital dependent localized Hartree Fock Kohn Sham poten tial Chem Phys Lett 518 114 2011 L A Constantin E Fabiano S Laricchia F D Sala Semiclassical neutral atom as a reference system in density functional theory Phys Rev Lett 106 186406 2011 S Laricchia E Fabiano L A Constantin F D Sala Generalized gradient approximations of the noninteracting kinetic energy from the semiclassical atom theory Ration
26. For MP2 calculations in the RI approximation use the ricc2 module The input can be prepared with the cc2 menu in define Alternatively the older rimp2 module and for preparation of its input the tool rimp2prep maybe used The module mpgrad calculates the canonical non RI MP2 energy as well as the energy gradient If only the energy is desired use the keyword mp2energy For all further preparations run the tool mp2prep Excited states with CIS TDHF and TDDFT escf Single point excited state energies for CIS TDHF and TDDFT methods can be calculated using escf Excited state energies gradients and other first order properties are provided by egrad Both modules require well converged ground state orbitals Excited states with second order wavefunction methods ricc2 The module ricc2 calculates MP2 and CC2 ground state energies and CIS identical to CCS CIS D CIS D ADC 2 or CC2 excitation energies using the resolution of the identity RI approximation Also available are spin component scaled SCS and SOS variants of the second order methods CIS D CIS Dx ADC 2 or CC2 Excited state gradients are available at the CCS CIS Dx ADC 2 and CC2 levels and the spin component scaled variants of the latter three methods In addition transition moments and first order properties are available for some of the methods For more details see Section 9 The input can be prepared using the cc2 menu of define CCSD F12 ricc22
27. L wdin Ed Quantum Theory of Atoms Molecules and the Solid State Page 253 Academic Press New York 1966 J Pipek P G Mezey A fast intrinsic localization procedure applicable for ab initio and semiempirical linear combination of atomic orbital wave functions J Chem Phys 90 9 4916 4926 1989 D P Tew W Klopper New correlation factors for explicitly correlated elec tronic wave functions J Chem Phys 123 7 074101 2005 W Klopper B Ruscic D P Tew F A Bischoff S Wolfsegger Atom ization energies from coupled cluster calculations augmented with explicitly correlated perturbation theory Chem Phys 356 1 3 14 24 2009 F A Bischoff S H fener A Gl W Klopper Explicitly correlated second order perturbation theory calculations on molecules containing heavy main group elements Theor Chem Acc 121 1 11 19 2008 S H fener F A Bischoff A Gl W Klopper Slater type geminals in explicitly correlated perturbation theory application to n alkanols and anal ysis of errors and basis set requirements Phys Chem Chem Phys 10 23 3390 3399 2008 402 109 110 111 112 113 114 115 116 117 118 119 BIBLIOGRAPHY O Christiansen H Koch P J rgensen The second order approximate cou pled cluster singles and doubles model CC2 Chem Phys Lett 243 5 6 409 418 1995 W Klopper F R Manby S Ten no E
28. Lagrangian approach to molecular vibrational raman intensities using time dependent hybrid density functional theory J Chem Phys 126 20 201104 2007 F Furche Dichtefunktionalmethoden ftir elektronisch angeregte Molek le Theorie Implementierung Anwendung PhD thesis Universitat Karlsruhe 2002 E R Davidson The iterative calculation of a few of the lowest eigenvalues and corresponding eigenvectors of large real symmetric matrices J Comp Phys 17 1 87 94 1975 F Wang T Ziegler Time dependent density functional theory based on a noncollinear formulation of the exchange correlation potential J Chem Phys 121 24 12191 12196 2004 M K hn F Weigend Phosphorescence energies of organic light emitting diodes from spin flip Tamm Dancoff approximation time dependent density functional theory Chem Phys Chem 12 3331 3336 2011 F Haase R Ahlrichs Semidirect MP2 gradient evaluation on workstation computers The MPGRAD program J Comp Chem 14 8 907 912 1993 F Weigend A Kohn C Hattig Efficient use of the correlation consistent basis sets in resolution of the identity MP2 calculations J Chem Phys 116 8 3175 3183 2001 C L Janssen I M B Nielsen New diagnostics for coupled cluster and Moller Plesset perturbation theory Chem Phys Lett 290 4 6 423 430 1998 I M B Nielsen C L Janssen Double substitution based diagnostics for coupled cluster and Mglle
29. Phys 117 7433 2002 J Chem Phys 121 12772 2004 E XX A fully direct RI HF algorithm Implementation optimised auxiliary basis sets demonstration of accuracy and efficiency F Weigend Phys Chem Chem Phys 4 4285 2002 XXI Geometry optimizations with the coupled cluster model CC2 using the reso lution of the identity approximation C Hattig J Chem Phys 118 7751 2003 XXII Analytic gradients for excited states in the coupled cluster model CC2 employ ing the resolution of the identity approximation A Kohn and C Hattig J Chem Phys 119 5021 2003 XXIII Fast evaluation of the Coulomb potential for electron densities using multipole accelerated resolution of identity approximation M Sierka A Hogekamp and R Ahlrichs J Chem Phys 118 9136 2003 XXIV Nuclear second analytical derivative calculations using auxiliary basis set ex pansion P Deglmann K May F Furche and R Ahlrichs Chem Phys Let ters 384 103 2004 XXV Efficient evaluation of three center two electron integrals over Gaussian func tions R Ahlrichs Phys Chem Chem Phys 6 5119 2004 XXVI Analytical time dependent density functional derivative methods within the RI J approximation an approach to excited states of large molecules D Rap poport and F Furche J Chem Phys 122 064105 2005 XXVII Density functional theory for excited states equilibrium structure and elec tronic spectra F Furche
30. eu and all excitations in IRREP t2g Specify soes alln to calculate the n first excitations in all IRREPS If n is not specified all excitations in all IRREPS will be obtained During an escf run a system independent formatted logfile will be constructed for each IRREP It can be re used in subsequent calculations restart or extension of eigenspace or of rpaconv An escf run can be interrupted by typing touch stop in the working directory general keywords rpacor n The maximum amount of core memory to be allocated for the storage of trial vectors is restricted to n MB If the memory needed exceeds the threshold given by rpacor a multiple pass algorithm will be used However especially for large cases this will increase computation time significantly The default is 200 MB spectrum unit The calculated excitation energies and corresponding oscillator strengths are appended to a file named spectrum Possible values of unit are eV nm and 1 cm or rem If no unit is specified excitation energies are given in a u cdspectrum unit The calculated excitation energies and corresponding rotatory strengths are appended to a file named cdspectrum unit can have the same values as in spectrum 18 2 FORMAT OF KEYWORDS AND COMMENTS 311 start vector generation e Flag for generation of UHF start MOs in a triplet instability calculation The option will become effective only if there are triplet instabilitie
31. geometry in this field To do this an external electrostatic field must be defined explicitly which can be done using command man Note that geofield must also be switched on if any properties are to be evaluated in the presence of an electric field The most prominent example is the calculation of hyperpolarizabilies Take Care due to some inconsistencies in define it is always necessary to switch on the field calculations manually Therefore edit the control file after having finished your define session and enter on after the entries of fields and geofield 4 4 5 Properties The program moloch used for this purpose is currently being revamped and will then be much simpler to use The subsequent description for an older version may not work in all cases sorry for that If you enter prop in the general menu define first will check whether the data group properties does already exist in your control file or in a file referenced therein If this is not the case you will be asked to specify the file on which properties shall be written data group properties has not yet been specified FOR INITIALIZING lt moloch gt KEYWORDS ENTER return WRITE TO CONTROL FILE control DEFAULT OR filename WRITE TO ANOTHER FILE Afterwards you will get the following submenu which allows you to control all pos sible actions of program moloch 4 4 THE GENERAL OPTIONS MENU 91 switch on one or more of the following options lt i gt lt i g
32. lt index gt TO BECOME AN RHF OPEN SHELL CHOOSE SHELLS IN lt list gt TO BECOME UHF ALPHA SHELLS CHOOSE SHELLS IN lt list gt TO BECOME UHF BETA SHELLS CHOOSE SHELLS IN lt list gt TO BECOME EMPTY SHELLS REPEAT THE EXTENDED HUECKEL CALCULATION SAVE OCCUPATION NUMBERS amp GO TO NEXT ITEM GEOMETRY DISPLAY COMMANDS CALCULATE EHT ENERGY FURTHER ADVICE INTEGER INDEX OF MO SHELL ACCORDING TO COMMAND s LIST OF MO SHELL INDICES LIKE 1 5 7 8 11 4 3 GENERATING MO START VECTORS 71 Recommendation Enter 1 to get a list of eht MO energies Then make up your mind on what to do closed shell RHF open shell not allowed for DFT or UHF Look at the examples below RHF UHF ROHF c 1 41 43 45 to define these levels to be doubly occupied a 1 5 alpha levels to be occupied b 1 3 5 beta levels to be occupied Or simply s t or u 1 to get singlet triplet or doublet occupation pattern c 1 41 43 45 levels to be doubly occupied o 42 level 42 should be partially occupied You will then be asked to specify the occupation If there are more open shells you have to repeat since only a single open shell can be specified at a time Watch the headline of the menu which tells you the number of electrons assigned to MOs Description of Commands s list p index c list o index This command gives you a listing of all MOs and their energies as ob tained from the extended Htickel calculation For NH3
33. mdprep 26 MECPopt 27 MECPprep 27 menu atomic attributes 62 65 general 76 77 geometry main 52 geometry menu 54 internal coordinate 57 58 occupation number assignment 70 T1 start vectors 67 68 molecular dynamics 116 353 molecular orbitals binary format 68 MOLOCH keywords 339 moloch 90 93 94 96 97 227 339 MP2 RI 315 Mp2prep 36 164 mp2prep 27 37 164 MP3 315 MP4 315 MPGRAD keywords 312 mpgrad 14 23 24 37 39 40 44 82 100 106 110 119 158 159 161 164 166 191 226 228 230 266 275 289 298 302 313 335 344 419 362 364 MPSHIFT keywords 360 mpshift 14 25 35 38 39 224 226 362 multi core 40 NAO 233 nao 233 natural orbitals atomic 233 transition 234 no weight derivatives 308 nohxx 216 217 not converged 100 120 npoints 216 NTO 234 nto 234 NumForce 25 39 40 176 177 190 221 302 Numforce 24 25 27 44 148 157 176 218 219 302 305 odft 23 38 40 42 250 255 257 294 OMP_NUM_THREADS 40 OpenMP 40 outp 27 PARA_ARCH 40 parallelization multi core 40 OpenMP 40 SMP 40 threads 40 parms in 272 PARNODES 40 PEECM keywords 296 Plane averaged 353 plot coefficient 254 420 plotting data keywords 344 population analysis 346 properties excited states 187 ground state 185 q 49 quasi Newton 104 Raman 25 39 221 raman 27 Raman spectra 221 RDGRAD keywords 304 Rdgrad 291 rdg
34. mvd leads to calculation of relativistic corrections for the SCF total density in case of dscf and ridft for the SCF MP2 density in case of rimp2 and mpgrad and for that of the calculated excited state in case of egrad Quantities calculated are expectation values lt p gt lt pt gt and the Darwin term 1 Z4 p Ra moments yields calculation of electrostatic moments arising from nuclear charges and total electron densities Also without setting this keyword moments up to quadrupole are calculated with respect to reference point 0 0 0 Supported extensions moments lt i gt x1 y1 z1 x2 y2 z2 By integer i the maximum order of moments is specified maximum and de fault is i 3 octopole moments real numbers 2 y z allow for the specification of one or more reference points pop drives the options for population analyses By default a Mulliken PA in the 18 2 FORMAT OF KEYWORDS AND COMMENTS 345 basis of cartesian atomic orbitals CAOs is performed for the total den sity D D leading to Mulliken brutto charges and in case of spin unrestricted calculations also for the spin density D D leading to Mul liken brutto numbers for unpaired electrons Besides total numbers also contributions from s p functions are listed separately Two component wavefunctions only module ridft and only if soghf is set In two component calculations instead of S Sz Sy Sz is written to the out
35. one and two electron energies of all previous SCF iterations Information that will allow you to perform a restart if your calculation aborts will be dumped on data group restartd see also restart scfintunit options Disc space specification for two electron integrals The following suboptions are available and necessary unit integer Fortran unit number for this file Unit numbers 30 31 are recom mended size integer Filespace in megabytes for this file size 0 leads to a fully direct run size is set by a statistics run see statistics DSCF switches to direct mode if the file space is exhausted file char Filename This may also be a complete path name if you want to store the integrals in a special directory Make sure the file is local otherwise integrals are transmitted over the network Thus your data group scfintunit may look like this scfintunit unit 30 size 35 file twoint1 unit 31 size 35 file users work twoint2 Maximal 30 files may be specified in this way scfiterlimit integer Maximum number of SCF iterations default 30 scfmo none file char Input output data group for SCF MOs You can specify none To perform a calculation without a start vector i e use a core Hamil tonian guess file char The file where the MOs are written on output default mos These two options can also be used for uhfmo_alpha and uhfmo_beta to use a core guess and write the molecular orbitals to file
36. ricc2 geoopt model cc2 state al 2 excitations irrep al nexc 2 If the geometry optimization should carried out for the lowest excited state of those for which an excitation energy is requested in excitation one can use alternatively state s1 Since the calculation of unrelaxed and relaxed first order properties can be combined gradient calculations without significant extra costs a request for excited state gra dients will automatically enforce the calculation of the relaxed and unrelaxed dipole moments If the keyword geoopt is used the relaxed dipole moment for the specified 9 3 FIRST ORDER PROPERTIES AND GRADIENTS 191 excited state and wavefunction model will be written to the control file and used in calculations with NumForce for the evaluation of the IR intensities 9 3 3 Visualization of densities and Density analysis As most other programs which allow for the calculation of wavefunctions and densi ties also the ricc2 module is interfaced to wavefunction analysis and visualization toolbox described in chapter 14 From ricc2 module this interface can used in two different ways 1 If through the geoopt keyword in ricc2 a unique method and state has been specified for which the density gradient and properties are evaluated the density analysis and visualization routines will called by default with the orbital relaxed density for this state and method similar as in dscf ridft mpgrad etc 2 The ricc2 program
37. scfconv 7 thize 10000000E 04 19 3 NO2 INPUT FOR AN UNRESTRICTED DFT CALCULATION 371 thime 5 scfdamp start 1 500 step 050 min 100 scfdump scfintunit unit 30 size 2 file work user twoint scfdiis start 0 5 scforbitalshift closedshell 3 drvopt cartesian on basis off global off hessian on dipole on nuclear polarizability interconversion off qconv 1 d 10 maxiter 25 optimize internal on cartesian off global off basis off logarithm coordinateupdate dqmax 0 3 interpolate on statistics 5 forceupdate ahlrichs numgeo 0 mingeo 3 maxgeo 4 modus lt g dq gt dynamic fail 0 1 threig 0 005 reseig 0 005 thrbig 3 0 scale 1 00 damping 0 0 forceinit on diag default energy file energy grad file grad forceapprox file force lock off dft functional b p gridsize m3 last step define end 372 CHAPTER 19 SAMPLE CONTROL FILES File coord coord 00000000000000 00000000000000 1 00494155217173 n 1 85766051386774 00000000000000 50247077608587 1 85766051386774 00000000000000 50247077608587 o intdef definitions of internal coordinates 1 k 1 0000000000000 stre 2 d 1 0000000000000 stre 3 k 1 0000000000000 bend end File basis basis n def SVP n 7s4pid 3s2p1d 5 s 1712 8415853 257 64812677 2 1 val 2 39232 3 1 val 2 39232 2 3 1 val 101 88429 511 31 1 53934125305E 02 40221581118E 01 58 458245853 17931144990 16 198367905 46376317823
38. see below only norm is displayed Densities used are the same as above filenames are generated from those of densities by replacement of d for density by f for field mo list of MO numbers calculation of amplitudes of MOs specified by numbers referring to the numbering obtained e g from the tool eiger in the same format The respective filenames are self explanatory and displayed in the output Note that also in MP2 and excited state calculations the HF DFT ground state orbitals are plotted and not natural MP2 excited orbitals Two component cases The density of the spinors specified by numbers referring to the numbering obtained e g from the file EIGS are visualized By setting the keyword minco also the amplitudes of the spinor parts 18 2 FORMAT OF KEYWORDS AND COMMENTS 351 are calculated whose weights the probability of finding the electron in this part lie above the threshold Imo list of LMO numbers calculation of amplitudes of LMOs previously generated by localize ordered by the corresponding diagonal element of the Fock matrix in the LMO basis nmo list of NMO numbers dens XC calculation of amplitudes of NMOs previously generated by natural orbitals file natural and natural orbital occupation file natural has to be set if additionally to one of the above quantities also the density is to be computed calculation of the Kohn Sham exchange correlation potential It is only vali
39. start vector generation escf will provide the start MOs uhfmo_alpha uhfmo_beta as well as occupa tion numbers alpha shells beta shells for a spin unrestricted calculation with equal numbers of a and 8 electrons pseudo singlet occupation 7 4 4 Vertical Excitation and CD Spectra The calculation of excited states within the TDHF RPA TDDFT approach is en abled by scfinstab rpas for closed shell singlet excitations scfinstab rpat for closed shell triplet excitations and scfinstab urpa for excitations out of spin unrestricted reference states If it is intended to use the TDA instead specify scfinstab ciss for closed shell singlet excitations scfinstab cist for closed shell triplet excitations scfinstab ucis for excitations out of spin unrestricted reference states and 7 4 HOW TO PERFORM 155 scfinstab spinflip for spin flip z component of the total spin changes by 1 excitations out of spin unrestricted reference states For details concerning the theory see ref 89 In practice this functionality can be used for the calculation of triplet singlet quartet doublet excitations see ref 90 also for further information about the implementation It is only available within the TDA in combination with LDA functionals and the HF exchange It is strongly recommended to increase escfiterlimit Next the IRREPs of the excitations need to be defined which is again accomplished
40. states CL Singles approximation TDA Time dependent Hartree Fock method RPA Time dependent density functional methods egrad can be employed in geometry optimization of excited states using jobex see Section 5 1 and in finite difference force constant calcula tions using Numforce Details see 20 requires a converged SCF or DFT run for closed shells mpshift com putes NMR chemical shieldings for all atoms of the molecule at the SCF DFT or MP2 level within the GIAO ansatz and the CPHF SCF approximation From this one gets the NMR chemical shifts by compar ison with the shieldings for the standard compound usually employed for this purpose e g TMS for carbon shifts Note that NMR shielding typically requires more flexible basis sets than necessary for geometries or energies ECPs are not supported in mpshift 21 calculates thermodynamic functions from molecular data in a control file an aoforce or a NumForce run is a necessary prerequisite calculates Raman scattering cross sections from molecular data in a control file an aoforce and an egrad run are a necessary prerequisite Please use the Raman script to run these three steps in an automated way 1 5 Tools Note these tools are very helpful and meaningful for many features of TURBOMOLE This is a brief description of additional TURBOMOLE tools Further information will be available by running the programs with the argument help actual plea
41. statistics on integer off provide a statistics output in each optimization cycle by displaying all 330 CHAPTER 18 KEYWORDS IN THE CONTROL FILE the last integer default setting by define is 5 subsequent coordinates gradient and energy values default on gdiishistory file char the presence of this keyword forces relax to provide informational output about the usage of DIIS for the update of the molecular geometry interconversion options default off special input related to the transformation of atomic coordinates between cartesian and internal coordinate spaces default off Available options are maxiter n maximum number of iterations for the iterative conversion procedure internal cartesian coordinates default 25 qconv convergence criterion for the coordinate conversion default 1 d 10 on off options this switch activates special tasks transform coordinates gradients hessians between spaces of internal cartesian coordinates using the def initions of internal coordinates given in intdef available suboptions are cartesian gt internal coordinate gradient hessian cartesian lt internal coordinatethe direction of the transforma tion is indicated by the direction of the arrow Note specification of interconversion on will override optimize forceupdate method options this data group defines both the method for updating the approximate force constant matrix and some
42. the use of invr may result in better convergence bend bend describes a bond angle It requires three atoms to be specified of which the third one is the atom at the apex outp Out of plane angle outp abcd is the angle between bond a d and plane b c d 4 1 tors linc linp comp ring THE GEOMETRY MAIN MENU 61 Dihedral angle tors abcd is the angle between the planes a b c and b c d This is a special coordinate type to describe the bending of a near linear system linc abcd describes the collinear bending of a b c where the angle is defined as for bend the apex atom appears last in the plane of b c d see also below command linp The system b c d has to be non linear of course This coordinate is similar to linc but describes the bending of a b c perpendicular to the plane b c d These two types of coordinates are in most cases sufficient to describe the bending of near linear systems An example may help you to understand these two coordinate types Consider ketene HzCCO which contains a linear system of three atoms Without symmetry this molecule has 9 degrees of freedom You could choose the four bond lengths two CCH angles and the out of plane angle of the C C bond out of the CHH plane But then two degrees of freedom still remain which cannot be specified using these normal coordinate types You can fix these by using linc and linp The two coordi
43. 0000000000 211111 41 3 exponent 2 0178811 377 378 s f 1345 36 12 p f 378 22 12 d f 104 8 12 end 8806470 7668062 0179609 4253015 2930909 0179609 8839557 7558481 0179609 File auxbasis jbas ta def SVP 3 s 15 52133 7 555743 3 699576 1 s 1 820141 1 s 0 898838 1 s 0 445062 1 s 0 220729 1 s 0 109530 1 p 1 502495 1 p 0 562985 1 p 0 228188 1 p 0 095078 5 8 5 0 35 1 1 1 1 CHAPTER 19 SAMPLE CONTROL FILES 14 5464077 7 2732038 2 0178811 9 9355653 4 9677824 2 0178811 6 3473769 3 1736885 2 0178811 493702989D 00 259256574D 01 523168657D 01 262393615D 01 157711902D 01 200789711D 00 185974307D 00 765184411D 01 0 0 0 0 19 4 TACLs INPUT FOR AN REDFT CALCULATION WITH ECPS 2 d 1 337006 0 599535 1 d 0 280427 4 d 0 133078 1 f 1 1428211 i tf 0 4395465 iS 2 0 1758186 3 g 1 630421 0 747093 0 349040 1 g 0 164143 cl def SVP 8 s 4097 080409 1203 083193 386 280948 135 337690 51 567046 21 261034 9 420135 4 445228 1 os 2 209399 t S 1 141575 1 os 0 604182 Tas 0 322378 4 p 51 8499902611 17 5847835188 190072032D 01 155214344D 01 138946250D 01 895263676D 02 100251139D 00 737448223D 01 276219913D 01 546316580D 02 198054511D 01 530973450D 01 1382352655D 02 107149960D 02 132
44. 05 0 00 0 95 0 00 0 43 0 51 0 00 0 00 O a2b FLIPPING ALPHA TO BETA default b2a FLIPPING BETA TO ALPHA r repeat atom choice As evident from the second column for each Cu atom five localized alpha and four localized beta orbitals were generated which are of d type the sixth column labelled d shows values close to 1 the other columns such close to 0 The six columns at the right show the individual contributions of the six cartesian d functions What has to be done to generate start MOs for the ba case Obviously one of the five localized alpha spin orbitals from the first Cu atom atom label 1 cu has to become a beta spin orbital These five orbitals have the indices 15 18 20 22 23 In order to avoid linear dependencies it is advisable to take the orbital that has no beta analogue This can be found by comparing the contributions of the six d functions In the present example this is the case for the localized alpha orbitals 15 and 18 in contrast to all localized beta orbitals they show significant contributions from dzy One thus enters a2b 15 and after confirming the replacement of original MOs with the generated start MOs one is finally asked It is advisable to modify damping and orbital shift in the following way scfdamp start 5 000 step 0 050 min 0 500 scforbitalshift automatic 1 0 scfiterlimit 999 Do you want to replace the corresponding entries in the control file y which should be confirme
45. 1 000 DAMP UPDATE BY 1 1 lt real gt DEFAULT 0000E 00 SCALE INPUT HESSIAN BY lt real gt DEFAULT 1 000 diagonal offreset offdamp lt r gt damp lt real gt scale lt real gt 4 4 THE GENERAL OPTIONS MENU 89 SCALE INPUT HESSIAN BY lt real gt DE IF IDEI THE OBSERVED ABSOLUTE CHANGE IN ENERGY IS OBEYING THE CONDITION DE gt lt real gt gt 0 DEFAULT NO SCALING DO NOT ALLOW EIGENVALUES OF HESSIAN TO DROP BELOW lt real gt DEFAULT 1000E 02 USE lt real gt AS A RESET VALUE FOR TOO SMALL EIGENVALUES CP min DEFAULT 1000E 02 DO NOT ALLOW EIGENVALUES OF HESSIAN TO BECOME LARGER THAN lt real gt DEFAULT 1000 WITH THE EXCEPTION OF min reset AND max ALL OPTIONS MAY BE DISABLED BY ENTERING lt opt gt lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU allow lt real gt min lt real gt reset lt real gt max lt real gt Initialization of the Hessian Finally there are some options to control the choice of the initial Hessian during your geometry optimization OPTION DESCRIPTION off switch off initialization DEFAULT on cart use analytical cartesian hessian provided by a 2nd derivatives calculation DEFAULT n diag use diagonal matrix with diagonal elements set individually within data groups intdef or basis or global DEFAULT n unit lt r gt use multiple of the unit matrix H lt r gt E DEFAULT n DEFAULT lt r gt 1 000 NOTE THAT TH
46. 10 From these the fourth order energy correction is computed as Eyra tO ual W TO TP TP WT TBF 10 11 u2 Eqs 10 5 and 10 7 10 11 are computational much more complex and de manding than the corresponding doubles equations for the CC2 model If M is a measure for the system size e g the number of atoms the computational costs in terms of floating point operations for CCSD calculations scale as O N If for the same molecule the number of one electron basis functions N is increased the costs scale with O N For RI MP2 and RI CC2 the costs scale with the system size as O N and with the number of basis functions as O N The computational costs for an MP3 calculations are about the same as for one CCSD iteration For MP4 the computational costs are comparable to those for two CCSD iteration plus the costs for the perturbation triples correction see below 208 CHAPTER 10 CCSD CCSD F12 AND CCSD T Explicitly correlated CCSD F12 methods In explicitly correlated CCSD calculations the double excitations into products of virtual orbitals described by Th gt gt aibj taibjTaibj are augmented with double excitations into the explicitly correlated pairfunctions geminals which are described in Sec 8 5 T 7 7 4 Ty 10 12 1 kl Ty 5 2 chl Thit 10 13 a where Tpijlij Qiefi2 kl for the defintion Qi and fiz see Sec 8 5 This en hances dramatically the basis set convergence of CCSD calcul
47. 19 6 ROHF OF TWO OPEN SHELLS 385 Extracts from control for O in D Symmetry HF SCF SVP Triplet sigma in D2h coord 0 0 0 0 1 08597397921317 o 0 0 0 0 1 08597397921317 o symmetry d2h closed shells ag 1 3 2 biu 1 2 2 b2u 1 2 b3u 1 2 open shells type 1 b2g 1 1 b3g 1 1 roothaan 1 a 1 b 2 energy SCF SCFKIN SCFPOT 1 149 4774402750 149 4798706643 298 9573109393 Singlet delta in D2h xx yy component where x b2g and y b3g In D infinity h b2g and b3g combine to eg coord 0 0 0 0 1 08597397921317 o 0 0 0 0 1 08597397921317 o symmetry d2h closed shells ag 1 3 2 biu 1 2 2 b2u 1 2 b3u 1 2 open shells type 1 b2g 1 1 b3g 1 1 roothaan 2 rohf 1b2g 1b3g a 0 b 2 386 CHAPTER 19 SAMPLE CONTROL FILES 1b2g 1b2g a 1b3g 1b3g a energy SCF SCFKIN SCFPOT 1 149 4297623516 149 4298351805 298 8595975321 Il Il e e o o ll ll fo Singlet delta in D2h xy yx component an example of the general type xy singlet where in D2h x b2g and y b3g are of different symmetry In D infinity h b2g and b3g combine to eg see the reference calculation in D3d above coord 0 0 0 0 1 08597397921317 o 0 0 0 0 1 08597397921317 o symmetry d2h closed shells ag 1 3 biu 1 2 b2u 1 b3u 1 open shells type 1 b2g 1 b3g 1 1 roothaan 2 rohf 1b2g 1b3g a i b 2 1b2g 1b2g a 0 b 1b3g 1b3g a 0 b 0 energy SCF SCFKIN SCF
48. 2 p l leads to a NMB set for Ni of 4 s 2 p and 1d functions and for O of 2 s and 1 p functions 18 2 FORMAT OF KEYWORDS AND COMMENTS 347 pop paboon to perform a population analyses based on occupation numbers 142 yielding shared electron numbers SENs and multicenter contributions For this method always the total density is used i e the sum of alpha and beta densities in case of UHF the SCF MP2 density in case of MP2 and the GHF total density for two component GHF The results of such an analysis may depend on the choice of the number of modified atomic orbitals MAOs which can be specified by an additional line without further specification their number is calculated by the method mix see below Note One should carefully read the information concerning MAOs given in the output before looking at the numbers for atomic charges and shared electron numbers mao selection options to specify how MAOs are selected per atom Available options are a for the way of sorting MAOs of each atom eig MAOs are sorted according to their eigenvalue those with largest EW finally are chosen This is the default occ MAOs are sorted according to their occupation note that the number of all occupation is NOT the number of electrons in the system This option is kept rather for historical reasons b for the determination of the number of MAOs fix A fixed number of MAOs is taken for each atom usually t
49. 228 347 pople 268 prediag 283 285 printlevel 315 318 properties 90 339 ramanonly 307 redund_inp 269 redundant 109 220 328 335 response 324 conv 324 fop 324 gradient 324 nosemicano 324 nozpreopt 324 semicano 324 sop 324 thrsemi 324 414 zconv 324 zpreopt 324 response 173 175 187 191 195 324 326 restart 286 restartd 283 286 ricc2 163 165 170 172 175 176 179 180 182 187 190 197 202 205 212 316 317 324 326 adc 2 317 cc2 317 ccs 317 ccsd 317 ccesd t 317 cis 317 cis d 317 cisdinf 317 conv 317 didiag 317 fmtprop 317 geoopt 187 317 gsonly 317 hard_restart 317 intcorr 213 317 iprint 317 lindep 317 maxiter 317 maxred 317 mp2 317 mp3 317 mp4 317 mxdiis 317 nohard_restart 317 norestart 317 oconv 317 restart 317 scs 317 sos 317 INDEX ricore 42 43 46 79 122 123 151 156 219 292 364 ricore_slave 364 ridft 151 156 292 rij 135 291 294 rik 122 135 216 292 294 ripop 292 riri2 162 166 168 170 175 176 205 206 208 319 320 ansatz 320 cabs 320 cabsingles 320 ccsdapprox 320 comaprox 320 corrfac 320 examp 320 pairenergy 320 ri2model 320 ri2orb 320 rirpa 216 rohf 289 290 roothaan 268 290 rpaconv 151 310 311 rpacor 155 156 310 rundimensions 284 scfconv 37 81 152 284 288 309 315 settings for AOFORCE 219 NUMFORCE 219 scfdenapproxl
50. 23988931592086 23988931592086 00000000000000 00000000000000 23988931592086 23988931592086 00000000000000 23988931592086 00000000000000 00000000000000 23988931592086 00000000000000 00000000000000 23988931592086 23988931592086 O 00000000000000 O 00000000000000 141 By default the positions of point charges are specified in atomic units as Cartesian coordinates You can change this by specifying cluster frac for fractional crystal coordinates or cluster ang for Cartesian coordinates in Finally you have to specify the coordinates of the QM cluster along with the sur rounding ECPs representing cationic sites and explicit point charges representing anions This is done in the usual way using the coord keyword coord O 00000000000000 O 00000000000000 O 00000000000000 f 2 86167504097169 2 86167504097169 2 86167504097169 ca 2 86167504097169 2 86167504097169 2 86167504097169 ca 2 86167504097169 2 86167504097169 2 86167504097169 ca 2 86167504097169 2 86167504097169 2 86167504097169 ca 0 00000000000000 5 24009410923923 O 00000000000000 f 5 24009410923923 O 00000000000000 O 00000000000000 f O 00000000000000 5 24009410923923 O 00000000000000 f O 00000000000000 O 00000000000000 5 24009410923923 f 5 24009410923923 O 00000000000000 O 00000000000000 f O 00000000000000 O 00000000000000 5 24009410923923 f 0 00000000000000 5 24009410923923 5 24009410923923 f 5 240094109239
51. 282 284 scfdiis 283 285 scfdump 282 284 286 scfinstab 122 151 311 ciss 309 cist 309 dynpol 309 non real 309 polly 309 INDEX rpas 309 rpat 309 singlet 309 spinflip 309 triplet 309 ucis 309 urpa 309 scfintunit 42 44 151 283 286 289 315 361 file 286 size 286 unit 286 scfiterinfo 286 scfiterlimit 286 scfiterlimit 1 217 scfmo 70 267 268 282 283 286 287 290 361 expanded 287 file 286 format 287 none 69 286 scfconv 287 scfdump 287 scfmo none 69 scforbitalorder 287 scforbitalshift 287 automatic 288 closedshell 288 individual 288 noautomatic 288 scftol 288 315 361 scratch scratch files 361 363 scratch files 288 334 362 seed 355 senex 293 sh_coeffs 359 415 sharedtmpdir 196 soes 151 155 156 310 311 soghf 135 136 229 294 spectrum 156 310 315 spinor 136 start vector generation 154 311 statistics 286 288 289 dscf 123 266 289 dscf parallel 289 363 grad parallel 364 kora 289 mpgrad 164 266 289 314 mpshift 225 off 266 289 polly 289 statpt 101 103 339 bfgs 103 hssfreq 339 hssidiag 339 itrvec 102 339 keeptmode 339 powell 103 radmax 339 radmin 339 threchange 102 thrmax displ 102 thrmaxgrad 102 thrrmsdispl 102 thrrmsgrad 102 tradius 101 339 update 339 sum rules 311 surface hopping 359 suspend off 265 symmetry 151 267 thime 12
52. 50052600809 44171422662 1 s 58731856571 1 0000000000 1 s 18764592253 1 0000000000 3 p 13 571470233 40072398852E 01 2 9257372874 21807045028 79927750754 51294466049 1 p 21954348034 1 0000000000 1 d 1 0000000000 1 0000000000 o def SVP 0 7s4pid 3s2p1d 511 31 1 19 3 NO2 INPUT FOR AN UNRESTRICTED DFT CALCULATION 2266 1767785 340 87010191 77 363135167 21 479644940 6 6589433124 1 s 80975975668 1 s 25530772234 3 p 17 721504317 3 8635505440 1 0480920883 1 p 27641544411 1 d 1 2000000000 end 53431809926E 02 39890039230E 01 17853911985 46427684959 44309745172 1 0000000000 1 0000000000 43394573193E 01 23094120765 51375311064 1 0000000000 1 0000000000 373 374 CHAPTER 19 SAMPLE CONTROL FILES 19 4 TaCl Input for an RI DFT Calculation with ECPs Main File control title operating system unix symmetry d3h coord file coord intdef file coord atoms ta 1 jbas ta def SVP basis ta def SVP ecp ta def ecp cl 2 6 jbas cl def SVP basis cl def SVP pople AQ basis file basis ecp file basis rundimensions dim fock dens 7662 natoms 6 nshell 51 nbf CA0 122 nbf A0 115 dim trafo SA0 lt gt A0 CAO 346 scfmo none file mos none hamilton core guess will be made file mos will be generated by the program scfiterlimit 30 scfconv 6 thize LOOOOO00E 04 thime 5 scfdamp start 900
53. After running define or a TURBOMOLE calculation additional options may ap pear specifying the origin of the MOs 18 2 FORMAT OF KEYWORDS AND COMMENTS 287 expanded These MOs were obtained by projection form another basis set They should not be used for wavefunction analysis scfconv integer The MOs are converged SCF MOs the convergence criterion applied was q07 nteger scfdump integer The MOs are unconverged SCF MOs which were written on this data group after iteration integer The latter three options are mutually ex clusive format format string This specifies the FORTRAN format specification which was used for MO output The standard format is 4d20 14 See data group mo output format Example Your data group scfmo could look like this after a successful TURBOMOLE run scfmo scfconv 7 format 3 1x d19 13 1 al eigenvalue 524127 nsao 6 1234567890123d 01 1234567890123d 00 1234567890123d 01 1234567890123d 01 1234567890123d 00 3 a2 eigenvalue 234810 scforbitalorder on off Order SCF MOs with respect to their energies default on scforbitalshift options To assist convergence either the energies of unoccupied MOs can be shifted to higher energies or in open shell cases the energies of closed shell MOs to lower energies In general a large shift may help to get better convergence Options are noautomatic Automatic virtual shell shift switched off automatic real Automatic virtual shell
54. Again ground states may be spin restricted closed shell or spin unrestricted RI J is available and either full TDDFT TDHF or the TDA can be used For further details we refer to a recent review 79 7 2 Theoretical Background We briefly state the basic working equations in the following as far as required to understand the program output For a more detailed treatment of the theory see refs 80 20 79 81 82 and refs therein The first order frequency dependent response of the density matrix can be expanded as a 2 df Xaivi a ea 2 Yaipa x y 2 7 1 The real expansion coefficients Xai and Ya are conveniently gathered in a super vector X xy 7 2 on L the linear space of products of occupied and virtual ground state MOs yi x p 2 plus their complex conjugates X and Y describe the first order change of the ground state MOs due to an external perturbation which is represented by P Q on L For example if an oscillating electric dipole perturbation along the z axis is applied P Q where u is the electric dipole operator Next we define the 2 x 2 super matrices ewer Aa aN 7 3 where the four index quantities A and B are the so called orbital rotation Hessians Explicit expressions for the standard A and B can be found e g in ref 20 For MGGA functionals the linear response of the paramagnetic current density leads to additional XC kernel matrix elements and sub
55. Chem Phys 111 9183 1999 CC2 excitation energy calculations on large molecules using the resolution of the identity approximation C Hattig and F Weigend J Chem Phys 113 5154 2000 Implementation of RI CC2 for triplet excitation energies with an application to trans azobenzene C Hattig and Kasper Hald Phys Chem Chem Phys 4 2111 2002 First order properties for triplet excited states in the approximated Coupled Cluster model CC2 using an explicitly spin coupled basis C Hattig A Kohn and Kasper Hald J Chem Phys 116 5401 2002 and Vir J Nano Sci Tech 5 2002 Transition moments and excited state first order properties in the coupled cluster model CC2 using the resolution of the identity approximation C Hattig and A K hn J Chem Phys 117 6939 2002 An efficient implementation of second analytical derivatives for density func tional methods P Deglmann F Furche and R Ahlrichs Chem Phys Let ters 362 511 2002 Efficient characterization of stationary points on potential energy surfaces P Deglmann and F Furche J Chem Phys 117 9535 2002 An improved method for density functional calculations of the frequency depen dent optical rotation S Grimme F Furche and R Ahlrichs Chem Phys Letters 361 321 2002 1 3 HOW TO QUOTE USAGE OF TURBOMOLE 17 XIX Adiabatic time dependent density functional methods for excited state prop erties F Furche and R Ahlrichs J Chem
56. DIIS Options are errvec char specifies the kind of error vector to be used two different kind of DIIS algorithms char FDS or SDF or FDS SDF uses FDS SDF as error vector char none no DIIS char sFDs use S 2FDS 2 transposed Further suboptions maxiter integer maximum number of iterations used for extrapolation debug integer debug level default 0 integer 1 print applied DIIS coefficients integer 2 print DIIS matrix and eigenvalues too qscal real scaling factor in DIIS procedure qscal gt 1 implies some damping qscal 1 0 straight DIIS thrd real directs the reduction of qscal to qscal 1 0 no damping in DIIS done if errvec lt thrd Defaults for prediag see above and scfdiis errvec FDS SDF maxiter 5 qscal 1 2 thrd 0 0 this implies DIIS damp ing in all iterations prediag is switched of Recommended errvec sFDs leads to the following defaults qscal 1 2 for SCF runs maxiter 6 and thrd 0 3 prediag is off for DFT runs maxiter 5 and thrd 0 1 prediag is on If you want to switch off prediag put prediag none P Pulay Chem Phys Lett 73 393 1980 P Pulay J Comput Chem 4 556 1982 286 CHAPTER 18 KEYWORDS IN THE CONTROL FILE scfdump Dump SCF restart information onto data group restartd and dump SCF MOs in each iteration onto scfmo scfdump iter Additionally a data block scfiterinfo will be dumped containing accumulated SCF total
57. Dynamics Calculations a ooa a a 116 5 6 Counterpoise Corrections using the JOBBSSE Script 118 50l Options 2 42 24 seisi 84 i i a ap e RR Ae ee we a 119 D02 UPAL 6 daaa pa a Bag e aR Te a dae ee ee a Y 120 6 Hartree Fock and DFT Calculations 121 6 1 Backeround Theory an ee ee Bd me oa ee ee ee KOR 123 6 2 Exchange Correlation Functionals Available 124 6 3 Restricted Open Shell Hartree Fock 04 128 CONTENTS Bol Brief Description e ance gta we He ee a ee Sa ee S T 128 6 8 2 nnep n Shell s cg a eae ae ee ee Ee eee a 128 6 3 3 More Than One Open Shell 2 131 Oia Miscellanous ec ag gee eek ele ee ee ee ee 133 6 4 Two component Hartree Fock and DFT Calculations 135 64 1 Background Theory s gosa oa korso aa we ee Ee BS 135 G42 Howtouse ea 2584 62 b ee bw ba me eee eee 135 6 5 Using the Douglas Kroll Hess DKH Hamiltonian 137 6 6 Periodic Electrostatic Embedded Cluster Method 138 6 6 1 General Information so o soe ea socas u ak de 2 be wae 138 6 6 2 Theoretical Background s s o eseigi dada 138 6 6 3 Calculation Setup ia soe saaa cuia e aea aaa 139 6 7 Empirical Dispersion Correction for DFT Calculations 146 Hartree Fock and DFT Response Calculations Stability Dynamic Response Properties and Excited States 147 7 1 Functionalities of Escf and Egrad a aao a 147 ie Theoretical Background lt a es sici
58. For different ways of selecting MAOs see Section 18 2 18 Generation of localized MOs 1localize enables calculation of localized molec ular orbitals Per default a Boys localization including all occupied MOs is carried out i e the squared distance of charge centers of different LMOs is maximized As output one gets localized MOs written to files 1mos or lalp lbet in UHF cases informations about dominant contributions of canonical MOs to LMOs and about location of LMOs from Mulliken PA are written to standard output 14 1 WAVEFUNCTION ANALYSIS AND MOLECULAR PROPERTIES 229 Natural transition orbitals For excited states calculated at the CIS or CCS level the transition density between the ground and an excited state Eig Wen al dal Ver 14 1 can be brought to a diagonal form through a singular value decomposition SVD of the excitation amplitudes Fia OEV ij VAi 14 2 The columns of the matrices O and V belonging to a certain singular value can be interpreted as pairs of occupied and virtual natural transition orbitals 143 144 and the singular values A are the weights with which this occupied virtual pair contributes to the excitation Usually electronic excitations are dominated by one or at least just a few NTO transitions and often the NTOs provide an easier understanding of transition than the excitation amplitudes Fia in the canonical molecular orbital basis From excitation amplitudes computed with th
59. MP2 F12 calculation with the same basis sets plus that of a conventional CCSD calculation multiplied by 1 Ncags N where N is the number of basis and Neoaps the number of complementary auxiliary basis CABS functions typically Noasps 2 3N If the geminal coefficients are determined by solving Eq 10 16 instead of using fixed amplitudes the costs per CCSD F12 iteration increase to 1 2Ncasgs N the costs for conventional CCSD iteration Irrespective how the geminal coefficients are determined the disc space for CCSD F12 calculations are approximated a factor of 1 2Nce 4ps N larger than the disc space required for a conventional CCSD calculation Note that this increase in the computational costs is by far outweighted by the enhanced basis set convergence In combination with the CCSD F12 approximation and also CCSD F12 CCSD F12a CCSD F12b CCSD 2 m5 and CCSD 2 5 the CPU time for the SP ap proach is only about 20 or less longer than for a conventional CCSD calculation within the same basis set CC calculations with restricted open shell ROHF references The MP2 and all CC calculations for ROHF reference wavefunctions are done by first trans forming to a semi canonical orbital basis which are defined by the eigenvectors of the occupied occupied and virtual virtual blocks of the Fock matrices of alpha and beta spin No spin restrictions are applied in the cluster equations This approach is sometimes also denoted as RO
60. MP2 and CC2 calculations are requested via the options level mp2 and level cc2 respectively To select the correct option s use the explanations you get by calling NumForce h For a review of theory and implementation see refs 137 138 Limitations The aoforce code has presently a number of limitations one should be aware of e It can only handle basis sets up to at most g functions e Point groups with reducible E representations such as Cn and Cna with n gt 3 Sn with n gt 5 or T and Ty e Frozen internal or cartesian coordinates are not recognized aoforce will all ways evaluate the full hessian matrix 220 CHAPTER 12 VIBRATIONAL FREQUENCIES 12 1 Analysis of Normal Modes in Terms of Internal Coordinates A note in advance The analysis of normal modes can at nearly no computational cost always be redone as long as you keep a copy of the file hessian A general prerequisite for this option is that you have defined a set of non redundant coordinates for all 3N 6 3N 5 degrees of freedom of your molecule To make sure that this is the case you should switch off redundant coordinates currently this is only possible by manually removing the data group redundant and also removing the entry redundant on in optimize Run define to generate non redundant coordinates by using the iaut command in the internal coordinate menu or by creating them manually via idef We recommend to use the irem command first to del
61. MP3 F12 MP4 and MP4 F12 are available Presently the implementation of the F12 variants and of connected triple excitations is restricted to ground state energies and the CCSD implementation to ground state and excitation energies Closed shell RHF unrestricted UHF or single determinant restricted ROHF open shell reference wavefunctions can be used for CCSD and CCSD T but no gradients or properties are yet available for these wavefunction models The MP3 and MP4 approximations can currently not be combined with ROHF reference wavefunctions Further limitations no MPI parallelization calculations at these levels can presently only carried out on a single compute node only the OpenMP see Sec 3 2 1 parallelization is available for calculations beyond CC2 use of symmetry restricted to Do and its subgroups for the conventional im plementation no symmetry can be used for the F12 methods Please note that calculations with MP3 MP4 CCSD and methods beyond CCSD re quire considerably more disc space and core memory than MP2 or CC2 calculations See section below for more details and recommendations Note that for the explicitely correlated CCSD variants the explicitely correlated double excita tions are neglected for the calculation of the triples corrections 204 205 Prerequisites MP3 MP4 CCSD and CCSD T calculations with the ricc2 module require the same prerequisites as RI CC2 calculations 1
62. N th step during a transition state search The default is zero and the Hessian is read in or computed in the first step only If the standard Hessian update methods fail it can help to use this keyword Warning This will make the calculation much more time demanding keeptmode Freezing transition vector index hssidiag diagonal hessian elements for diagonal Hessian guess default 0 5 radmax Maximum allowed value for trust radius default 0 3 radmin Minimum allowed value for trust radius default 1 0d 4 18 2 FORMAT OF KEYWORDS AND COMMENTS 339 tradius Initial value for trust radius default tradius radmax 0 3 Convergence criteria threchange threshold for energy change default 1 0d 6 thrmaxdispl threshold for maximal displacement element default 1 0d 3 thrmaxgrad threshold for maximal gradient element default 1 0d 3 thrrmsdispl threshold for RMS of displacement RMS root mean square default 5 0d 4 thrrmsgrad threshold for RMS of gradient default 5 0d 4 All values are in atomic units 18 2 17 Keywords for Module MOLOCH properties specifies the global tasks for program moloch by virtue of the following options properties trace off moments active potential off cowan griffin off localization off population analyses off plot off firstorder off fit off a missing option or a option followed by the flag off will not be taken into account The flag active may be
63. NAC elements along the trajectory 360 CHAPTER 18 KEYWORDS IN THE CONTROL FILE Special caution has to be taken to control problems related to conical intersec tions 186 187 At geometries where conical intersections between the ground and excited state are present DFT often exhibits singlet instabilities which leads to imaginary excitation energies in linear response TDDFT in this case the MD run is terminated This problem can be circumvented by the use of the Tamm Dancoff approximation TDA to TDDFT see 7 In addition an optional keyword for the md_master file can be used gap_threshold lt real gt enforces a switch to the ground state in case the S1 S energy gap drops below lt real gt eV As default a switch to So is enforced if the S TDDFT TDA excitation energy becomes negative Often times if a switch is enforced due to a negative TDA excitation energy the potential energy surface is discontinuous and limited numerical precision of the nuclear forces may lead to a loss of total energy conservation In this case the nuclear velocities are rescaled to obtain a conserved total energy 18 2 20 Keywords for Module MPSHIFT In order to control the program execution you can use the following keywords within the control file csmp2 Switches on the calculation of the MP2 NMR shieldings The required SCF shielding step will be performed in the same run This flag will be set by the script mp2prep traloop n specifie
64. Nina O C Winter Christof H ttig J Chem Phys 134 184101 2011 The MP2 F12 Method in the TURBOMOLE Programm Package Rafal A Ba chorz Florian A Bischoff Andreas Gl Christof H ttig Sebastian H fener Wim Klopper David P Tew J Comput Chem 32 2492 2513 2011 Accurate and efficient approximations to explicitly correlated coupled cluster singles and doubles CCSD F12 Christof H ttig David P Tew Andreas K hn J Chem Phys 132 231102 2010 Large scale polarizability calculations using the approximate coupled cluster model CC2 and MP2 combined with the resolution of the identity approxi mation Daniel H Friese Nina O C Winter Patrick Balzerowski Raffael Schwan Christof H ttig J Chem Phys 136 174106 2012 Basis sets The following tables can be used to find the proper citations of the standard orbital and auxiliary basis sets in the TURBOMOLE basis set library Orbital basis sets elements H Kr H He Li Be B Ne Na Mg Al Ar K Ca Sc Zn Ga Kr SVP SV P q ala a a a ala a a TZVP q b b b b b b b b TZVPP q f f f f f f f t QZVP QZVPP i def2 SV P q j a a j a jla a a def2 SVP q j a a j a j a j a def2 TZVP q fl j f j j jl j f def2 TZVPP q ljlj f j j jl f j f 1 3 HOW TO QUOTE USAGE OF TURBOMOLE 19 Note For H Kr def SV P def SVP are identical with the basis sets without def pref
65. Note that this output is restricted to scalar quantities 302 CHAPTER 18 KEYWORDS IN THE CONTROL FILE thus in case of vectors E field only the norm is plotted Output file suffix is map txt a format compatible with gOpenMol for visualization of vectors v The format is Y Z Ug Vy Vz vec for planes and lines default in these cases In case of a line speci fied by a y see below output is a f x y z for scalars for vectors components and norm are displayed vectors Analogously in case of planes it is a 8 f x y z The output file suffix vec may be visual ized by plotting programs suited for two dimensional plots A command file termed gnuset to get a contour plot by gnuplot is automatically generated cub only for 3D writes out data in Cube format which can be imported by many external visualization programs For 3D grids non default boundarys basis vector directions origin and reso lutions may be specified as follows pointval gridi vector 0 3 0 range 2 2 points 200 grid2 vector 0 0 7 range 1 4 points 300 grid3 vector 1 0 0 range 1 1 points 300 origin 1 1 1 Grid vectors automatically normalized now are 0 1 0 0 0 1 1 0 0 the grid is centered at 1 1 1 and e g for the first direction 200 points are distributed between 2 and 2 Grids of lower dimensionality may be specified in the same line as pointval by typing either geo plane or geo line or geo point The way to
66. OF SCF ENERGY scfconv thi INTEGRAL STORAGE CRITERIA thize thime ints INTEGRAL STORAGE ALLOCATION scfintunit iter MAXIMUM NUMBER OF ITERATIONS scfiterlimit diis DIIS CONVERGENCE ACCELERATION scfdiis damp OPTIONS FOR DAMPING scfdamp shift SHIFTING OF ORBITALS scforbitalshift order ORDERING OF ORBITALS scforbitalorder fermi THERMAL SMEARING OF OCC NUMBERS fermi By the command fermi you can switch on smearing of occupation numbers and thus automatically optimize occupations and spin Menu drv The most important of the derivative menus is the first one which tells the programs which derivatives to calculate This is only necessary for special purposes and you should better not change default options option status description crt T CARTESIAN 1st derivatives sec l T CARTESIAN 2nd derivatives bas F energy derivatives with respect to BASIS SET exponents scaling factors contraction coefficients glb F energy derivative with respect to a GLOBAL scaling factor dip T cartesian 1st derivatives of DIPOLE MOMENT pol T nuclear contribution to POLARIZABILITY fa F SPECTROSCOPIC ANALYSIS only tol 0 100D 06 derivative integral cutoff use lt opt gt for enabling lt opt gt for disabling of logical switches lt amp gt will bring you back to GENERAL MENU without more changes lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU 84 CHAPTER 4 PREPARING YOUR INPUT FILE WITH D
67. Perform a SCF of DFT Calculation 224 13 3 How to Perform a MP2 calculation o sos 6 4 24 26 e eee eee 225 134 Chemical Shifts o e s sosa gd Se hE Re a ba Rw A a Oe G 226 13 5 Other Features and Known Limitations 226 14 Molecular Properties Wavefunction Analysis and Interfaces to Vi sualization Tools 227 14 1 Wavefunction analysis and Molecular Properties 227 14 2 Interfaces to Visualization Tools 2 0004 230 15 Frozen Density Embedding calculations 235 15 1 Backeround Theory sc soared aante 2228 6 Feed hes 235 15 2 Frozen Density Embedding calculations using the FDE script 237 t21 OPONIS rare ee ae he a ee Ye ee 241 15 2 2 FDE with hybrid and orbital dependent functionals 246 Ia How TO OUO ba 4 Po a ane Re eR Ewa oe RE Re oe GG 246 16 Orbital Dependent Kohn Sham Density Functional Theory 249 16 1 Theoretical Background lt 2 2 6 eee eee eee ee 249 16 2 Implementation 2 4 046255886 8554445 2 bed eee Ee a 251 160 0 WP BEX yeo ek eg ee eek Ae ee ee Gow es hk eS 251 16 2 2 LHP 26 ee gawk bee SEG ee CRE ES Oe Dw G 252 16 3 How to PORGHI s aou yoy bk a Re ae A Ae ee wa ee eg 252 16 4 How to plot the exchange potential 2 257 16 5 How GO g ote gt gt s Gk ashi oe dna wie BOE ae a ee we ees 257 17 Treatment of Solvation Effects with Cosmo 259 18 Keywords in the control file 265 AS Taroducthion ea e a a a a a A a ee Ae a Gai a R a 265 18 2 For
68. Single Point Calculations Running TURBOMOLE Modules All calculations are carried out in a similar way First you have to run define to obtain the control file or to add change the keywords you need for your pur pose This can also be done manually with an editor Given a bash and a path to TURBODIR bin arch see installation Chapter 2 you call the appropriate module in the following way e g module dscf nohup dscf gt dscf out amp nohup means that the command is immune to hangups logouts and quits amp runs a background command The output will be written to the file dscf out Several modules write some additional output to the control file For the required keywords see Section 18 The features of TURBOMOLE will be described in the following section 3 1 5 Energy and Gradient Calculations Energy calculations may be carried out at different levels of theory Hartree Fock SCF use modules dscf and grad or ridft and rdgrad to obtain the energy and gradient The energy can be calculated after a define run without any pre vious runs dscf and grad need no further keywords ridft and rdgrad only need the keyword rij The gradient calculation however requires a converged dscf or ridft run Density functional theory DFT calculations are carried out in exactly the same way as Hartree Fock calculations except for the additional keyword dft For DFT calculations with the fast Coulomb approximation you have to use the modules rid
69. This may be helpful to draw mo diagrams If only has been set only the start MOs are dumped and the program quits nirreps will hold the total number of displayed orbitals after the successful run moprint If this keyword is present all occupied orbitals are dumped to standard output Be careful about this option as it can create huge output files in case of many basis functions mo output format format If this line is present the dscf program is forced to output the MOs using the new FORTRAN format format regardless of the format option in data group scfmo Otherwise the input format will be used Example mo output format 3 2x d15 8 natural orbitals This data group will be written after an UHF calculation together with nat ural orbital occupation and contains the natural space orbitals same syntax as scfmo natural orbital occupation This data group will be written after an UHF calculation together with natural orbitals and contains the occupation of natural orbitals syntax as any data group related with orbital occupation information e g closed shells e g a 1 5 2 00000000000000 a 6 1 99949836999366 a 7 1 99687490286069 a 8 1 00000000000000 a 9 00312509713931 a 10 00050163000634 point_charges Specification of position and magnitude of point charges to be included in the Hamiltonian Each point charge is defined in the format 18 2 FORMAT OF KEYWORDS AND COMMENTS 283
70. a converged SCF calculation with the one electron density threshold set to denconv 1 d 5 or less an auxiliary basis defined in the data group cbas if orbitals should be excluded from the correlation treatment the data group freeze has to be set the maximum core memory which the program is allowed to allocate should be defined in the data group maxcor the recommended value is 66 75 of the available physical core memory the data group ricc2 with a specification of the coupled cluster model Calculations with the CCSD F12 and CCSD F12 methods require in addition e the data group rir12 with the definition of the standard approximations for the explicitly correlated contributions see Sec 8 5 for details e the data group 1cg which define the correlation function here it is in par ticular important to choose for F12 calculations the exponent recommended values are 0 9 for cc pVDZ F12 1 0 for cc pVTZ F12 and 1 1 for cc pVQZ F12 basis sets e a complementary auxiliary CABS basis set Furthermore it is recommeded to select in addition an auxiliary JK basis set for the evaluation of the Fock matrix elements The rijk menu of define can be used for this How To Perform a Calculation As presently no gradients are available only single point calculations are possible 1 Select in define within the menu cc the wavefunction model submenu ricc2 frozen core options submenu freeze an auxil
71. a number of additional settings for which it is recommended to invoke the interactive tool mp2prep For geometry optimizations with jobex use nohup jobex level mp2 ri CC2 calculations The entry cc2 leads to a submenu which allows to set a number of keywords essential for calculations with the program ricc2 In particular it allows the assignment of auxiliary basis sets mandatory for ricc2 the specification of frozen orbitals and the definition of a scratch directory and of the maximum core memory usage 2nd analytical derivatives The program aoforce computes force constants and IR and Raman Spectra on SCF and DFT level Analytical second derivative calculations can directly be started from converged SCF or DFT calculations Note that the basis is restricted to d functions and ROHF as well as broken occupation numbers are not allowed For better efficiency in case of larger systems use the keyword maxcor as described in Chapter 12 to reduce computational cost RI will be used if the RI option for DFT has been specified 4 4 THE GENERAL OPTIONS MENU 83 4 4 2 Special adjustments Adjustments described by the following menus are often better done directly in the control file have a look at the keywords in Chapter 18 For common calcula tions just start with the defaults and change keywords directly in control if you encounter problems with your calculation SCF options ENTER SCF OPTION TO BE MODIFIED conv ACCURACY
72. aie Guka ae oe e i e ee O 148 T Implementation soo 2446 245s ai a Be ae ee See a O G 151 GA How to Perigi s a e eos d a ee we BS SE Re ee he So 152 TAI Preliminaries oao sosa mes oae g a Re es 152 7 4 2 Polarizabilities and Optical Rotations 152 TAS sbability Analyse e e te e Ae Babee e E BD Oe 153 7 4 4 Vertical Excitation and CD Spectra 154 7 4 5 Excited State Geometry Optimizations s soaa aa 156 7 4 6 Excited State Force Constant Calculations aa 157 7 4 7 Polarizability Derivatives and Raman Spectra 157 Second order M gller Plesset Perturbation Theory 158 8 1 Functionalities of Mpsrad Rimp2 Rice2 oo e cs sosar ems Sro 158 Bel How toguotE e e na 4 aaa a eG ea E he ee A 159 Ru OMe THEI 2 cde a deh God mY A dod Hee So ara ee ps gt eee a ey 160 8 3 How to Prepare and Perform MP2 Calculations 161 CONTENTS 7 8 4 General Comments on MP2 Calculations Practical Hints 164 8 0 RI MP2 Fil2 Calculationg s e i eogi a 6 eG etn eae ee ee ka eS 166 8 6 LT SOS RI MP2 with O N scaling costs 171 9 Second Order Approximate Coupled Cluster CC2 Calculations 174 9 1 CC2 Ground State Energy Calculations 179 9 2 Calculation of Excitation Energies 204 181 9 3 First Order Properties and Gradients 06 185 9 3 1 Ground State Properties Gradients and Geometries 185 9 3 2 Excited State Properties Gradients
73. also thize statistics thize real Integral storage parameter that determines together with thime the num ber of integrals stored on disc Only integrals larger than real will be stored The default value is real 0 100E 04 RHF ROHF closed shells Specification of MO occupation for RHF e g alg 1 4 2 a2g 1 2 open shells type 1 MO occupation of open shells and number of open shells type 1 here means that there is only a single open shell consisting e g of two MOs b2g 1 1 b3g 1 1 rohf This data group is necessary for ROHF calculations with more than one open shell Example rohf 1 a a a 0 b 0 h h a 1 b 2 a h a 1 b 2 290 CHAPTER 18 KEYWORDS IN THE CONTROL FILE This example is for the 7S state of chromium 3d 4s in symmetry group T Note that for this option being activated roothaan also has to be specified in your control file although its parameter has no meaning in this case For more details see Section 6 3 roothaan UHF For ROHF calculations with only one open shell the Roothaan parameters a and b have to be specified within this data group see also rohf Example roothaan a 3 4 b 3 2 This example is for the 3P ground state of carbon 2p in symmetry group I define recognizes most cases and suggests good Roothaan parameters For further information on ROHF calculations e g with more than one open shell see the sample input in Section 19 6 and the
74. and D Rappoport Ch II of Computational Pho tochemistry Ed by M Olivucci Vol 16 of Computational and Theoretical Chemistry Elsevier Amsterdam 2005 XXVIII Structure optimizations for excited states with correlated second order meth ods CC2 CIS Dx and ADC 2 Christof Hattig Adv Quant Chem 50 37 60 2005 XXIX Distributed memory parallel implementation of energies and gradients for second order Moller Plesset perturbation theory with the resolution of the identity ap proximation Christof Hattig Arnim Hellweg Andreas K hn Phys Chem Chem Phys 8 1159 1169 2006 18 XXX XXXI XXXII XXXIII XXXIV XXXV XXXVI CHAPTER 1 PREFACE AND GENERAL INFORMATION Self consistent treatment of spin orbit interactions with efficient Hartree Fock and density functional methods Markus K Armbruster Florian Weigend Christoph van W llen Wim Klopper Phys Chem Chem Phys 10 1748 1756 2008 Quintuple quality coupled cluster correlation energies with triple basis sets David P Tew Wim Klopper Christian Neiss Christof H ttig Phys Chem Chem Phys 9 921 1930 2007 Benchmarking the performance of spin component scaled CC2 in ground and electronically excited states Arnim Hellweg Sarah A Gr n Christof H ttig Phys Chem Chem Phys 10 4119 4127 2008 Scaled opposite spin CC2 for ground and excited states with fourth order scal ing computational costs
75. and b are the Roothaan parameters numerical constants which depend on the particular configuration of interest 6 3 2 One Open Shell Given are term symbols up to indices depending on actual case and group and a and b coefficients n is the number of electrons in an irrep with degeneracy nir Note that not all cases are Roothaan cases All single electron cases are described by a b 0 6 3 RESTRICTED OPEN SHELL HARTREE FOCK Table 6 1 Roothaan coefficients a and b for cases with de generate orbitals Nir 2 e div groups 7 Coov Doon n f e T 6 a b 3A 35 233 1 2 2 1 2 T TA IT 1 2 0 TA 5 5 0 2 3 3 4 a TI 2A 8 9 8 9 1 njp 3 p O 3 t T O I n f p a b 3P 3 4 3 2 2 1 3 rp 9 20 3 10 IS 0 3 1S 1 2 3 1 2 2p 4 5 4 5 ZP 2 3 0 3P 15 16 9 8 4 2 3 pe 69 80 27 40 TS 3 4 0 5 5 6 2p 24 25 24 25 only irrep g J mainly high spin available n f g a b 1 1 8 2G 0 0 2 1 4 T 2 3 4 3 TA 0 4 3 3 8 4G 8 9 16 9 4 1 2 5A 1 2 5 5 8 4G 24 25 32 25 6 3 4 j 26 27 28 27 TA 8 9 4 9 7 7 8 2G 48 49 48 49 continues on next page 129 130 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS Table 6 1 Roothaan coefficients a and b for cases with de generate orbitals continued d O3 h J mainly high
76. append mode and switches to non append mode Once you have specified your basis set nickname define will look in the standard input file normally control for this basis set If it can not be found there you can switch to the standard basis set library if you did not use a standard input file the standard library will be searched immediately If the basis set cannot be found there you are asked either to enter a new standard library which will be standard only until you leave this menu or another input file where the basis set can be found If you do not know the exact nickname of your basis set you may abbreviate it by so you could enter h DZ to obtain basis sets like h DZ h DZP h DZ special etc define will give you a list of all basis sets whose nicknames match your search string and allows you to choose among them You may also use the command list to obtain a list of all basis sets cataloged bb does essentially the same as b but does not search your default input file for basis sets Instead it will look in the basis set library immediately bl gives you a list of all basis sets assigned so far This command is used to modify basis sets which are already assigned The corresponding submenu is self explanatory but we recommend to change directly the file basis The TURBOMOLE programs normally work with basis sets of 5d functions which means they delete the s component of the full 6d set bp allows to
77. are not allowed Polar izability derivatives have to be projected onto vibrational normal modes to obtain Raman intensities see Chapter 12 for further details Chapter 8 Second order Moller Plesset Perturbation Theory 8 1 Functionalities of MPGRAD RIMP2 and RIcc2 TURBOMOLE offers three possibilities for MP2 calculations A conventional imple mentation 91 mpgrad based on the calculation of four center integrals not further developed for several years and two implementations which use the resolution of the identity RI approximation the implementation from 1997 8 in rimp2 and a new implementation as part the CC2 program 10 ricc2 Functionality of mpgrad e Calculation of MP2 energies and or MP2 gradients for RHF and UHF wave functions e The frozen core approximation possibility to exclude low lying orbitals from the MP2 treatment is implemented only for MP2 energies e Exploitation of symmetry of all point groups e Can be used sequentially or parallel e Can be combined with the COSMO solvation model see chapter 17 for de tails Presently restricted to sequential calculations Functionality of rimp2 e Calculation of MP2 energies and or gradients for RHF and UHF wave func tions within the efficient RI approximation RI MP2 e The frozen core approximation is implemented for both RI MP2 energies and gradients 158 8 1 FUNCTIONALITIES OF MPGRAD RIMP2 RICC2 159 RI MP2 needs optim
78. as an approximation to full TDHF TDDFT by constraining the Y vectors to zero For TDHF the TDA is equivalent to configu ration interaction including all single excitations from the HF reference CIS The TDA is not gauge invariant and does not satisfy the usual sum rules 80 but it is somewhat less affected by stability problems see below For MGGA function als the response of the paramagnetic current density is required to ensure gauge invariance and is included by default Stability analysis of closed shell electronic wavefunctions amounts to computing the lowest eigenvalues of the electric orbital rotation Hessian A B which decomposes into a singlet and a triplet part and of the magnetic orbital rotation Hessian A B Note that A B is diagonal for non hybrid and non MGGA DFT while A B generally is not See refs 85 19 83 for further details 150 CHAPTER 7 HF AND DFT RESPONSE CALCULATIONS Properties of excited states are defined as derivatives of the excited state energy with respect to an external perturbation It is advantageous to consider a fully variational Lagrangian of the excited state energy 20 L X Y 0 C Z W Eqs X Y A X Y O X Y A X Y 1 ia pq Here Egs denotes the ground state energy F and S are the Fock and overlap matrices respectively and indices p q run over all occupied and virtual MOs First L is made stationary with respect to all its parameters The additional Lagrange mu
79. be obtained with the interactive module Freeh results are printed to standard I O Prerequisites 1 Both aoforce and even more Numforce require well converged SCF DFT calculations e g scfconv 8 and jobex ri gcart 4 2 The maximum core memory the program aoforce is allowed to allocate should be defined in the data group maxcor the recommended value is about 50 of the available physical core memory in case of RI calculations subtract the memory specified in ricore 3 To start aoforce in the lowest eigenvalue search mode use the keyword les For its use as well as other keywords dealing with the calculation of only some irreps see the Referenceguide part of this manual 4 Numforce additionally requires the file gradient and will not work if the calculation is not done at a stationary point of the molecular total energy For reliable results always use Numforce with the option central i e central differences and be aware of effects due to the step length option d real default value is 0 02a u It is strongly recommended to use Numforce in DFT calculations only with the option weight derivatives in dft since this provides more accurate gradients and thus frequencies see Section 18 2 9 5 The Numforce script can be run for different levels of theory which means that the binaries it calls have to be specified additionally To perform calculations using the RI approximation call Numforce with the option ri
80. by so called quasi Newton Raph son methods They require the exact gradient vector and an approximation to the Hessian matrix The rate of convergence of the structure optimization depends on anharmonicity of the PES and of the quality of the approximation to the Hessian matrix The optimization procedure implemented in statpt belongs to the family of quasi Newton Raphsod methods 30 It is based on the restricted second order method which employes Hessian shift parameter in order to control the step length and direction This shift parameter is determined by the requirement that the step size should be equal to the actual value of the trust radius tradius and ensures that the shifted Hessian has the correct eigenvalue structure all positive for a minimum search and one negative eigenvalue for a TS search For TS optimization there is another way of describing the same algorithm namely as a minimization on the image potential The latter is known as TRIM Trust Radius Image Minimization 31 For TS optimizations the TRIM method implemented in statpt tries to maximize the energy along one of the Hessian eigenvectors while minimizing it in all other directions Thus one follows one particular eigenvector hereafter called the tran sition vector After computing the Hessian for your guess structure you have to identify which vector to follow For a good TS guess this is the eigenvector with negative eigenvalue or imagin
81. cartesian coordinates of the atoms default coord file coord ufftopology contains a list of the next neighbours of each atom see Section 18 2 4 Some times it is useful to enter the connectivity in the input block nxtnei12 in the file ufftopology by hand not always necessary default ufftopology file ufftopology Beyond this uff reads the force field parameters for the atoms from the file parms in If this file exists in the directory from which one starts an uff calculation the pro gram will use this file if not the program reads the data from the file TURBODIR uff parms in 18 2 FORMAT OF KEYWORDS AND COMMENTS 273 If one wants own atom types one has to add these atoms types in the file parms in For each new atom type one has to specify the natural bond distance the natural bond angle the natural non bond distance the well depth of the Lennard Jones potential the scaling factor the effective charge torsional barriers invoking a pair of sp atoms torsional barriers involving a pair of sp atoms generalized Mulliken Pauling electronegativities the idem potentials characteristic atomic size lower bound of the partial charge upper bound of the partial charge Distances energies and charges are in atomic units and angles are in rad UFF Output Data Blocks coord contains the updated cartesian coordinates of the atoms default coord file coord ufftopology contains the full information of the topo
82. command nohup NumForce ex n gt force out amp where n is the number of the excited state in Cy symmetry In order to determine n it is recommended to perform an escf calculation in C1 symmetry Note that numerical calculation of excited state force constants is likely to fail if there are other states nearby in C1 because the roots may flip when the molecule is distorted Note also that it may be necessary to include higher excited states using exopt see above in C4 calculations of molecules with higher symmetry in order to enforce convergence to the correct state In any case it should be checked that the energy change due to the displacements available in the numforce KraftWerk 1og files is reasonably small For a Numforce run the convergence criteria should be tightened It is recommended to use at least scfconv 8 in all Numforce calculations Other Numforce options such as central d np work in exactly the same way as they do for ground states 7 4 7 Polarizability Derivatives and Raman Spectra Calculations of polarizability derivatives by the egrad program use the same speci fications in the scfinstab data group as polarizability calculations by escf scfinstab polly specifies derivatives of the static polarizability while scfinstab dynpol unit frequency requests derivatives of the dynamical polarizability at the given frequency Note that unlike polarizability calculations multiple frequencies
83. concerned with the coupling between the F12 and conventional amplitudes This is avoided by choosing 2 which corresponds to neglecting EBC Extended Brillouin Condition terms in the Fock matrix elements is the method of computing the matrices B see Ref 99 for details The cost and accuracy increases from A to B It is rec 8 5 RI MP2 F12 CALCULATIONS 169 comaprox cabs examp ri2orb corrfac cabsingles ommended to use B default The energies computed using A are then also printed out in the output is the method for approximately computing the integrals for the operator fiz where the matrix representations of F K or T V are used F K the core Hamiltonian plus Coulomb term is rec ommended and is the default refers to the method of orthogonalising the orbitals in the com plementary auxiliary basis Singular value decomposition svd or Cholesky decomposition cho are available svd is recommended and is the default with a threshold of 1 0d 08 The basis set used for CABS is set from the cc menu refers to the choice of excitation space inv is the orbital invariant merhod of Ref 100 with amplitudes c kl noinv is the orig inal orbital dependent diagonal ijij method of Ref 100 with amplitudes c ij not recommended unless in combination with localised orbitals fixed is the diagonal and orbital invariant rational generator approach of Ref 101 where the F12 ampli tudes are
84. consequence the geometry update more exactly the transformation of the updated internal coordinates into Cartesian ones will fail This may also happen in the course of a geometry optimization if the coordinates run into linear dependency during their optimization imet checks the B matrix and removes linear dependent internal coordinates from your list their status is changed from k or f to d If B is only near singular a warning is issued and the lowest eigenvalue s as well as the corresponding eigenvector s are displayed In this case you should try to find better internal coordinates although this may not always be possible After the command imet there may be too few active plus fixed internal coordinates but certainly not too many because linear dependencies have been eliminated Perhaps you will have to add new ones or better try command iaut or ired in the preceding menu Command imet should be used always after creating internal coordinates with iaut or idef especially after iaut because this command creates usually an overcomplete set of internal coordinates idef idef unfolds a little submenu where you can define internal coordinates manually The exact procedure of the definition will be described below in a separate section 4 1 THE GEOMETRY MAIN MENU 59 ideg a iaut iman a iciaz irem 2 This command gives you the number of symmetry restricted degrees of freedom for the atomic set specified b
85. control variables needed for the force constant up date Options for method none no update steepest descent ms suboptions Murtagh Sargent update dfp suboptions Davidon Fletcher Powell update 18 2 FORMAT OF KEYWORDS AND COMMENTS 331 bfgs suboptions Broyden Fletcher Goldfarb Shanno update dfp bfgs suboptions combined bfgs dfp update schlegel suboptions Schlegel update ahlrichs suboptions Ahlrichs update macro option suboptions if method ms dfp bfgs schlegel ahlrichs numgeo integer number of structures used maxgeo integer maximum number of geometries rank of the update procedure for ahlrichs only ingeo integer minimum number of geometries needed to start update if method ms dfp bfgs maxgeo 2 mingeo 1 as default additional suboptions if method ahlrichs modus char fmode for an explanation see suboptions pulay gi ven below e g ahlrichs numgeo 7 mingeo 3 maxgeo 4 modus lt g dg gt dynamic NOTES if the macro option ahlrichs has been chosen and n numgeo ncycl number of geometries available e if ncycl lt n geometry update by inter extra polation using the last two geometries e if ncycl gt n diagonal update for the hessian by least mean squares fit pulay update for the ge ometry using specified modus fmode see pulay below e if ncycl gt max 5 n 3 and max g lt 0 01 and g lt 0 001 or Hj 4 OVi j diagonal update is replace
86. diagonal excita tions enter with amplitude 0 5 diag or the equivalent of the spin adapted singlet and triplet pair excitations enter as far as possible full Note that the diag method with UMP2 F12 yields a result different to that of fixed MP2 F12 even for identical RHF and UHF determinants However the diag method is somewhat less expensive than the full method Recommendations for orbital and auxiliary basis sets The best orbital basis sets to use for MP2 F12 calculations are probably the cc pVXZ F 12 basis sets specially optimised for MP2 F 12 calculations 98 for the atoms H He B Ne and Al Ar In conjunction with these cc pVXZ F12 basis sets we recommend to use the optimised cc pVXZ F12 sets of Yousaf and Peterson 97 as cabs Furthermore cbas and jkbas basis sets can be selected from the cbasen and jkbasen libraries respectively using the alias cc pVXZ F12 a jkbas is currently not available for He Ne and Ar This alias points to the corresponding aug cc pwCV X 1 Z cbas and aug cc pV X 1 Z jkbas These recommendations are on the side of caution and are likely to be refined as more experience is gained 1 6 107 108 For atoms other than H He B Ne and Al Ar optimised F12 basis sets are not yet available In this case basis sets must be selected and or optimised carefully It is advised to contact the Theoretical Chemistry Group in Karlsruhe for support e mail to klopper kit edue 8 6 Laplace transformed SOS R
87. diagonal force constants by 1 real compare of freset which discards off diagonals completely Only values gt 1 0 will be accepted This option is active only within one relax run and will be disabled automatically by relax This is useful in difficult cases where the non diagonal update has lead to too large non diagonal elements of the hessian offreset reset off diagonal force constants to zero This option will be active for 18 2 FORMAT OF KEYWORDS AND COMMENTS 333 the current optimization cycle only i e it will be removed by relax after having discarded off diagonals allow real optimization cycle specification of a maximum energy change allowed given in mHartree which will be accepted using the actual approximate force constant matrix from forceapprox if this energy change will be exceeded the force constants will be scaled appropriately The default 0 0 means NO action scale real scaling factor for the input hessian default 1 0 threig real lower bound for eigenvalues of the approximate hessian default 0 005 if any eigenvalue drops below threig it will be shifted to a reasonable value defined by reseig realdefault texttt0 005 thrbig real upper bound for eigenvalues of the hessian if any eigenvalue exceeds thrbig it will limited to this value default 1000 0 damping real damp the variable metric update for the hessian by 1 1 real default 0 0 forceinit option specify init
88. effective The default number of grid points for the integration is 60 but may be changed by adding the keyword rirpa and the option npoints n to the control file where n is the number of grid points The computation of the HXX energy can be skipped by adding the option nohxx Effective core potentials ECPs are not presently compatible with the HXX energy as computed in rirpa The nohxx option must therefore be included for systems where ECPs were used to obtain the reference KS orbitals in order to skip the HXX energy calculation and compute solely the correlation energy Recommendations e The direct RPA correlation energy is defined in a Kohn Sham context with out inclusion of exchange integrals and therefore the use of self consistent KS orbitals obtained from semi local functionals is recommended HF orbitals or KS orbitals obtained form hybrid functionals lead to inferior results e Experience has demonstrated that the difference in RPA correlation energies obtained from different semi local functionals is very small much smaller than the inherent error of the method e Like MP2 RIRPA results are known to converge very slowly with increasing basis set size in particular slowly with increasing quantum number of the basis set For reliable results the use of QZVP basis sets or higher is recom mended For non covalently bound systems larger basis sets especially with more diffuse functions are needed e It is recommen
89. experimentally determined structures desy will rec ognize the higher symmetry and symmetrize the molecule properly If symmetry is lower than expected use a larger threshold lt eps gt up to 1 0 is possible susy leads you through the complete subgroup structure if you want to lower symmetry e g to investigate Jahn Teller distortions The molecule is automatically reoriented if necessary Example Ty Dag gt Coy gt Cs You may enter Cartesian atomic coordinates and atomic symbols inter actively After entering an atomic symbol you will be asked for Carte sian coordinates for this type of atom until you enter If you enter amp the atom counter will be decremented and you may re define the last atom but you surely won t make mistakes will you After entering define asks for the next atom type Entering amp here will allow you to re define the last atom type and to leave this mode and return to 4 1 THE GEOMETRY MAIN MENU 55 a file aa file sub the geometry main menu Enter q as atom symbol if you want to use a dummy center without nuclear charge Symmetry equivalent atoms are created immediately after you entered a set of coordinates This is a convenient tool to provide e g rings exploit symmetry group Dyn to create an n membered planar ring by putting an atom on the X axis You may also read atomic coordinates and possibly internal coordi nates from file where file must have the same for
90. for excited states only at the CC2 level 9 3 1 Ground State Properties Gradients and Geometries For CC2 one distinguishes between orbital relaxed and unrelaxed properties Both are calculated as first derivatives of the respective energy with respect to an external field corresponding to the calculated property They differ in the treatment of the SCF orbitals In the orbital relaxed case the external field is formally already 186 CHAPTER 9 RI CC2 included at the SCF stage and the orbitals are allowed to relax in the external field in the orbital unrelaxed case the external field is first applied after the SCF calculation and the orbitals do not respond to the external field Orbital unrelared CC2 properties are calculated as first derivatives of the real part of the unrelaxed Lagrangian 109 LY C 8 HF H CC S t u H H D HF 9 12 H gt buy ua H Fo GV To HF H2 with H Ho 6V where V is the one electron operator describing the external field 8 the field strength and Ho and Fo are the Hamiltonian and Fock operators of the unperturbed system by the expression ur CC F Vy CC2 R 5p yO Voa 9 13 0 pq R P Dial VTE 914 p D a l TE H2 where R indicates that the real part is taken Relared CC2 properties and gradi ents are calculated from the the full variational density including the contributions from the orbital response to the external perturbation which
91. form Ere pa pB Exel 4 pa pal Exel 4 pa Exel ps 15 7 where 64 p 4 pp denotes the Slater determinant which yields the total density pA pp Since such a determinant is not easily available the non additive exchange correlation contribution cannot be determined directly and the non additive exchange correlation term can be approximated as 151 BP pa pp ESO pa pp BSS pal ESO pa 15 8 15 2 FROZEN DENSITY EMBEDDING CALCULATIONS USING THE FDE SCRIPT237 15 2 Frozen Density Embedding calculations using the FDE script The shell script FDE controls and executes automatically FDE calculations The script FDE prepares the input files running define runs the calculations only dscf is supported in the present versiob and combines the results running fdetools Because the FDE equations are coupled sets of one electron equations one for each subsystem full relaxation of the electron densities of both subsystems is obtained by using a freeze and thaw 149 procedure until convergence The converged FDE calculations are store in the subdirectories STEPN SUBSYSTEM_A and STEPN SUBSYSTEM_B where N is the number of the FDE iteration The sub directory ISOLATED_SUBSYSTEM_A and ISOLATED_SUBSYSTEM_B contain instead the calculations for isolated subsystems see also Section 15 2 1 Current functionalities and limitations of FDE are e only C point group e only for closed shell systems that
92. functionals Hartree Fock and RI K Those versions are automatically used when setting PARA_ARCH SMP but can also turned on with PARA_ARCH GA on clusters Due to the explicit usage of shared memory on an SMP system user has to be allowed to use sufficient shared memory e In addition to the usual stack size limit problem make sure that your maximum shared memory you are allowed to use on your system is large enough a few GB or 70 90 percent of the total memory should be sufficient cat proc sys kernel shmmax shows the amount of allowed shared mem ory use sysctl to set new values but you have to be root to do that e the default shared memory that is used is per process for the matrices is 300 MB for heap and 10 MB for stack For large cases this can be too small and an error will be given in the output In order to increase the default values just set paroptions ga_memperproc lt stacksize gt lt heapsize gt stacksize and heapsize have to be given in word i e units of 8 Byte 1 MB is equivalent to 131072 word Note Also in the parallel SMP version the setting for memory namely ricore is the value in MB per process If several processes run on the same node the total sum of Nopy ricore must not be larger than the total memory on that system Please note that this keyword is not a setting for the total amount of memory the TURBOMOLE modules need but only for RI integrals and matrices for ridft and rdgrad Esp
93. g the ground state in case of an absorption spectrum and the hotfcht_data_f inp file from the calcuation of the final state the excited state in case of an absorption spectrum Carefully edit the keywords in the header of the resultant file and run hotFCHT please refer to the hotFCHT documentation for further information Chapter 13 Calculation of NMR Shieldings The program mpshift calculates nuclear magnetic shielding constants using the GIAO Gauge Including Atomic Orbital method At present the following methods are implemented HF SCF the coupled perturbed Hartree Fock CPHF equations in the AO basis are solved using a semi direct iterative algorithm 139 similar to dscf DFT using either non hybrid functionals where no iterations are needed 140 or hybrid functionals where the same algorithm as at the HF SCF level is used MP2 semi direct method see ref 21 13 1 Prerequisites mpshift needs converged MO vectors from a SCF or DFT run dscf or ridft 2 for SCF or DFT calculations no specifications have to be made in the control file 3 it is not possible to run the program in the fully direct mode when doing an SCF MP2 or a DFT using hybrid functionals run so you will have to perform a statistics run of dscf before calling mpshift or just set the size of the twoint file to a non zero value 4 to perform an MP2 calculation of the NMR shieldings you have to prepare the input with mp2prep c 13
94. gradients and properties using egrad is ex actly the same as for an excited state calculation using escf see the previous section Gradients and properties are calculated only for one state at a time By default this is the highest excitation specified by soes only one IRREP is allowed Some times e g close to excited state intersections it may be necessary to include higher excited states in the initial excitation vector calculation to prevent root flipping This is accomplished using exopt n which explicitly enforces treatment of the n th state n must be less or equal the number of states specified in soes After the input for the ground and excited state calculations has been set up an excited state geometry optimization can be started by issuing the command nohup jobex ex amp The option ex forces jobex to call egrad instead of grad or rdgrad if ri is also specified In each geometry step the excitation energy is written on the fourth 7 4 HOW TO PERFORM 157 column in energy and the data group last excitation energy change is up dated Otherwise the excited state optimization proceeds in exactly the same way as a ground state optimization see Chapter 3 1 7 4 6 Excited State Force Constant Calculations Excited state vibrational frequencies can be calculated by numerical differentiation of analytic gradients using Numforce see Chapter 12 A Numforce calculation for an excited state may be started by the
95. gt minimum distance between an active MM site and any QM center in a u treatment is handle by option iskip DEFAULT 0 00 a u iskip 1 2 treatment of too close MM sites 1 zeroing all contributions 2 distribute values to nearest non skipped MM site DEFAULT rmax lt float gt maximum distance between an active MM site and QM center of coordinates in a u sites too far away are skipped zeroed DEFAULT 1000 00 a u nomb no treatment of many body effects between induced dipoles all interac tion tensors on the off diagonal of the response matrix are set to Zero works best with isotropic polarizabilities speeds up calculations especially for large response matrices has reduced accuracy not well tested so far longprint 1 2 3 sets a flag for additional output 1 print all MM site input information 2 additionally print all induced dipoles due to nulcei multipole electron electric filed 3 additionally print response matrix 202 CHAPTER 9 RI CC2 e file lt input file gt specifies a file from which the data group point_charges is read Note that all options which are following on the line the control file are then ignored because reading continues in the input file But here further options can be specified after the point_charges flag The file has to start with point_charges as top line and should be finished with end Limitations with respect to standard SCF computatio
96. gt to x lt real gt K set total energy at t lt real gt to x lt real gt H set kinetic energy at t lt real gt to x lt real gt H set position file lt filename gt at t lt real gt set velocity file lt filename gt at t lt real gt set velocity at t lt real gt random set velocity at t lt real gt zero At some time during the ab initio MD run the user can specify a new value for one of the dynamical variables The old value is discarded Single values are given by x real number Vectors must be read in frog format from file file md_action anneal from t lt real gt anneal from t lt real gt x lt real gt quench from t lt real gt quench from t lt real gt x lt real gt file lt file gt relax at t lt real gt In Simulated Annealing MD the temperature of a run is lowered so as to find minimum energy structures Temperature may be lowered gradually by a small factor each step anneal default factor 0 905 over 100 steps or lowered rapidly by reversing all uphill motion quench default factor 0 8 each step The cooling factors may be changed from the default using x Another option allows the quenching part of the run to be logged to a separate file Alterna tively a standard non dynamical geometry optimization can be carried out in a subdirectory relax 18 2 FORMAT OF KEYWORDS AND COMMENTS 359 md_action free from t lt real gt Finally this instruction turns off any previous action and resumes fr
97. in older TURBOMOLE versions It has been corrected in version 6 2 Note that convergence problems may occur if a frequency is close to an electronic excitation energy This is a consequence of the physical fact that the response diverges at the excitation energies and not a problem of the algorithm Static polarizabilities are calculated most efficiently by specifying scfinstab polly before starting escf 7 4 3 Stability Analysis Stability analysis of spin restricted closed shell ground states is enabled by scfinstab singlet for singlet instabilities scfinstab triplet for triplet instabilities most common and scfinstab non real for non real instabilities After that it is necessary to specify the IRREPs of the electronic Hessian eigen vectors orbital rotations to be considered Without additional knowledge of the system one usually needs to calculate the lowest eigenvalue within every IRREP 154 CHAPTER 7 HF AND DFT RESPONSE CALCULATIONS soes all 1 Positivity of the lowest eigenvalues in all IRREPs is sufficient for stability of the ground state solution If one is interested in say the lowest eigenvalues in IRREPs eg and t2g only one may specify soes eg 1 t2g 1 Triplet instabilities in the totally symmetric IRREP indicate open shell diradical states singlet or triplet In this case start MOs for spin symmetry broken UHF or UKS ground state calculation can be generated by specifying
98. in the fde input file to restart a FDE calculation the FDE script can be inkoved without any parameters To force a calculation from scratch use FDE p 3 scratch 246 CHAPTER 15 FROZEN DENSITY EMBEDDING CALCULATIONS 15 2 2 FDE with hybrid and orbital dependent functionals In order to use local approximations 15 1 and 15 8 with FDE the flag f string must be add to the options of the script Here string denotes the local semilocal approximation to hybrid or orbital dependent exchange correlation potentials in Vemb r All LDA GGA functionals in TURBOMOLE can be considered as approxi mations For example the command FDE p 3 f b lyp can be used to approximate bh lyp or b3 lyp hybrid non additive potentials while the command FDE p 3 f pbe approximates the pbe0 hybrid non additive potentials Other combinations of func tionals are not recommended meta GGA are not supported Finally also calculations with the Local Hartree Fock LHF potential can be per formed In this case the command FDE p 3 f becke exchange can be used to approximate the LHF non additive potential 151 Equivalent command func string fde input option func string 15 3 How to quote e General code and FDE with hybrid functionals Frozen density embedding with hybrid functionals S Laricchia E Fabiano and F Della Sala J Chem Phys 133 164111 2010 and Generalized Gradient Approximations of the Noninteracting Kinetic Ene
99. instability calculations it is thus necessary to specify the IRREPs to be treated soes see below For response calculations the perturbation is automatically subduced into irreducible components The overall speedup compared to C symmetry is approxi mately 1 g where g denotes the point group order For spin restricted closed shell ground states spin symmetry is used to further reduce the dimension of the response and eigenvalue problems by a factor of 2 152 CHAPTER 7 HF AND DFT RESPONSE CALCULATIONS Other features escf and egrad fully support external fields using the keyword electrostatic field specify geofield on in fldopt point charges using the keyword point_charges and effective core potentials using ecp In escf calculations occupied and virtual MOs can be frozen using freeze 7 4 How to Perform The most convenient way to set up an escf or egrad calculation is to use the ex op tion of the last general define menu see Chapter 4 define will automatically provide most of the keywords discussed below A large number of not necessarily realistic sample inputs is contained in the escf and egrad subdirectories of the test suite TURBOTEST directory 7 4 1 Preliminaries All response calculations require a complete set of converged occupied and virtual SCF MOs It is strongly recommended to use well converged MOs since the error in the ground state wavefunction enters linearly in all response prope
100. is 0 90 Default value of maximum fde iterations is 20 Saving options in fde input Subsystem A atomic coordinates and basis set information x y Zz atom basis set ecp 2 5015 0 1705 0 0000 f def2 TZVP none 3 2889 1 3859 0 0000 h def2 TZVP none Subsystem B atomic coordinates and basis set information x y Z atom basis set ecp 4 7 7 e 2 7537 0 0364 0 0000 f def2 TZVP none 1 0191 0 1789 0 0003 h def2 TZVP none Running Isolated subsystems FKK KK K K K 2 FK FK FK FK K K K K K K K K K K OK OK ISOLATED SUBSYSTEM A FKK KK KK K FK FK FK FK FK K K K K K K K K K OK OK OK Done FKK KK KK K 2K FK FK FK FK K K K K K K K K K K OK OK ISOLATED SUBSYSTEM B FKK KK KK K K FK FK FK FK K K K K K K K K K K OK OK Done Saved isolated subsystems data in isolated_energy ks mos_A ks mos_B ks FKK KK K K K FK FK FK FK FK K K K K K OK OK K K 240 FDE step 1 KKK K K FK FK K K K K K FK FK FK FK FK FK OK OK K FDE ENERGY TOTAL SYSTEM FDE BINDING ENERGY Dipole convergence 0 138071 DEEE EEEE EEE E E E E E E E EE E FDE step 2 KKK K K FK FK K K K K K K FK FK FK FK 2K OK K K FDE ENERGY TOTAL SYSTEM FDE BINDING ENERGY Dipole convergence 0 009246 FO k k k kkk kk kk FDE step 3 KKK K K FK FK K K K K K K FK OK FK FK 2K OK KK FDE ENERGY
101. is the nuclei electron interaction E p and E p are the exchange and correlation energy functionals The exchange and correlation functionals normally used in DFT are integrals of some function of the density and possibly the density gradient In addition to pure DFT methods dscf and grad modules support hybrid functionals in which the exchange functional includes the Hartree Fock exchange e g B3 LYP 6 2 Exchange Correlation Functionals Available The following exchange correlation functionals are available e LDAs S VWN PWLDA e GGAs B VWN B LYP B P PBE e MGGA TPSS e hybrid functionals BH LYP B3 LYP PBEO TPSSh e double hybrid functional B2 PLYP energy calculations only For EXX and LHF see Chapter 16 In detail the functional library consists of e The Slater Dirac exchange functional only S 49 50 e The 1980 correlation functional functional V in the paper of Vosko Wilk and Nusair only VWN 51 e A combination of the Slater Dirac exchange and Vosko Wilk and Nusair 1980 functional V correlation functionals S VWN 49 50 51 e The S VWN functional with VWN functional III in the paper This is the same functional form as available in the Gaussian program 49 50 51 e A combination of the Slater Dirac exchange and Perdew Wang 1992 corre lation functionals 49 50 52 e A combination of the Slater Dirac exchange and Becke s 1988 exchange func tionals B88 49 50 53 6
102. j are defined as vig Kl kl fi2 i2r z lij 8 6 B j kl mn kl fi2Qi2 fi fe i Qiofi2 mn 8 7 in the spin orbital formalism m n denote spin orbitals and mn is a two electron determinant f is the Fock operator for electron u and ep is a semi canonical Hartree Fock orbital energy A MP2 F12 calculation is defined through a number of choices concerning the na ture of the geminals f jz and Q12 the geminal excitation space ijkl or ijij and approximations in computing the B matrix GBC EBC T fi2 These choices correspond to keywords in the rir12 data group explained below To run a MP2 F12 calculation one has to select the auxiliary basis sets cbas cabs and optionally jkbas The ricc2 program uses the robust fitting techniques of Ref 95 for the F12 integrals and the cbas basis is used for both the F12 and the usual MP2 Coulomb integrals For the density fitting of the Coulomb and exchange matrices of the Fock matrix the jkbas will be used instead of the cbas basis if it is included in the control file this is recommended and is achieved using the rijk menu in define For the RI approximation of the 3 and 4 electron integrals as sums of 168 CHAPTER 8 2ND ORDER MOLLER PLESSET PERTURB THEORY products of 2 electron integrals intrinsic to the F12 method the complementary auxiliary basis CABS approach is used 96 If define is used to set up the cabs basis the library cabasen is se
103. like babel e use the TURBOMOLE script x2t to convert your xyz file to the TURBOMOLE coord file x2t xyzinputfile gt coord e since input files for TURBOMOLE are always called control each input has to be placed in a different directory Create a new directory and copy the coord file there 3 1 A QUICK AND DIRTY TUTORIAL 35 e call define after specifying the title you get the coord menu just enter a coord to read in the coordinates Use desy to let define determine the point group automatically If you want to do geometry optimizations we recommend to use generalized internal coordinates ired generates them automatically e you may then go through the menus without doing anything just press lt Enter gt or q whatever ends the menu or by confirming the proposed decision of define again by just pressing lt Enter gt This way you get the necessary specifications for a SCF based run with SV P as the default basis set which is roughly 6 31G e for more accurate SCF or DFT calculations choose larger basis sets e g TZVP by entering b all def TZVP or b all def2 TZVP in the basis set menu e ECPs which include scalar relativistic corrections are automatically used beyond Kr e an initial guess for MOs and occupation numbers is provided by eht e for DFT you have to enter dft in the last menu and then enter on e for efficient DFT calculations you best choose the RI approximation by entering ri and providin
104. memory in MB which will be allocated during the RI CC2 run This keyword can be set in define or with the Rimp2prep tool the default is 20 MB maxcor has a large influence on computation times for RI CC2 runs It is recommended to set maxcor to ca 75 85 of the available physical core memory spectrum unit The calculated excitation energies and corresponding oscillator strengths are 316 CHAPTER 18 KEYWORDS IN THE CONTROL FILE appended to a file named spectrum Possible values of unit are eV nm and 1 cm or rem If no unit is specified excitation energies are given in a u cdspectrum unit The calculated excitation energies and corresponding rotatory strengths are appended to a file named cdspectrum unit can have the same values as in spectrum laplace conv 5 The purpose of this data group is twofold It activates the Laplace transformed implementation of SOS MP2 in the ricc2 module if the sos option has been specified in ricc2 and it provides the options to specify the technical details for the numerical Laplace transformation conv Threshold for the numerical integration used for the Laplace transforma tion of orbital energy denominators The grid points for the numerical integration are determined such that is the remaining root mean squared error RMSE of the Laplace transformation is lt 107 By default the threshold is set to the value of conv given in ricc2 see below ri
105. method ahlrichs which provides excellent con vergency in most cases General Boundary Conditions for Update The force constant matrix will only be updated if least mingeo cycles exist The maximum number of cycles used for the update is specified by the parameter maxgeo Normally the default values provided by define need not be changed DEFINE BOUNDARY CONDITIONS FOR UPDATE mingeo lt i gt START UPDATE IF THERE ARE AT LEAST lt i gt CYCLES DEFAULT min 3 maxgeo lt i gt USE LAST lt i gt CYCLES FOR UPDATE DEFAULT max 4 lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU Special Boundary Conditions for Ahlrichs and Pulay Updates For the default update method ahlrichs some additional control parameters are available which can be defined in this menu DEFINE BOUNDARY CONDITIONS FOR AHLRICHS OR PULAY UPDATE modus lt i gt DEFINE MODUS FOR GDIIS PROCEDURE MINIMIZE lt dqldq gt IF lt i gt 0 lt gldq gt IF lt i gt 1 lt glg gt IF lt i gt 2 lt dE gt IF lt i gt 3 DEFAULT lt i gt 1 IGNORE GDIIS IF lt gldq gt lt gldq gt IS LARGER THAN lt r gt DEFAULT lt r gt 0 1 lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU fail lt r gt For detailed description consult Section 5 3 RESTRICT UPDATE TO DIAGONAL ELEMENTS IF METHOD IS BFGS DFP OR MS DEFAULT n DISCARD OFF DIAGONAL ELEMENTS DEFAULT n DAMP OFF DIAGONAL ELEMENTS BY 1 1 lt r gt DEFAULT
106. mn In case of our above example one may enter cu which immediately leads to the following output a def SV P basis and the B P functional were used for the high spin state RELEVANT LMOS FOR ATOM 1 cu ALPHA index occupation energy s p d f dxx dyy dzz dxy dxz dy 15 1 000 0 357 0 01 0 00 0 98 0 20 0 27 0 01 0 50 0 00 O 18 1 000 0 357 0 01 0 00 0 98 0 20 0 27 0 01 0 50 0 00 O 20 1 000 0 335 0 00 0 00 1 00 0 00 0 00 0 00 0 00 1 00 O 22 1 000 0 333 0 01 0 00 0 99 0 13 0 03 0 32 0 00 0 00 0 23 1 000 0 333 0 01 0 00 0 99 0 14 0 03 0 34 0 00 0 00 O BETA 39 1 000 0 326 0 00 0 00 1 00 0 33 0 08 0 09 0 00 0 00 O 41 1 000 0 326 0 00 0 00 1 00 0 33 0 08 0 09 0 00 0 00 O 43 1 000 0 321 0 00 0 00 1 00 0 00 0 00 0 00 0 00 1 00 O 46 1 001 0 318 0 05 0 00 0 95 0 00 0 43 0 51 0 00 0 00 O RELEVANT LMOS FOR ATOM 2 cu ALPHA index occupation energy s p d f dxx dyy dzz dxy dxz dy 16 1 000 0 357 0 01 0 00 0 98 0 20 0 27 0 01 0 50 0 00 O 17 1 000 0 357 0 01 0 00 0 98 0 20 0 27 0 01 0 50 0 00 O 19 1 000 0 335 0 00 0 00 1 00 0 00 0 00 0 00 0 00 1 00 O 21 1 000 0 333 0 01 0 00 0 99 0 13 0 03 0 32 0 00 0 00 0 24 1 000 0 333 0 01 0 00 0 99 0 14 0 03 0 34 0 00 0 00 O BETA 40 1 000 0 326 0 00 0 00 1 00 0 33 0 08 0 09 0 00 0 00 O 42 1 000 0 326 0 00 0 00 1 00 0 33 0 08 0 09 0 00 0 00 O 50 50 00 00 50 50 4 3 GENERATING MO START VECTORS 75 44 1 000 0 321 0 00 0 00 1 00 0 00 0 00 0 00 0 00 1 00 0 45 1 001 0 318 0
107. models as long as there is clear correspondence between the singles parts of the eigenvectors Else the DIIS solver will print the doubles diagnostics in each iteration if the print level is set gt 3 States with large double excitation contributions converge notoriously slow a consequence of the par titioned formulation used in the ricc2 program However the results obtained with second order methods for doubly excited states will anyway be poor It is strongly recommended to use in such situations a higher level method Visualization of excitations An easy way to visualize single excitations is to plot the natural transition orbitals that can be obtained from a singular value de composition of the excitation amplitudes See Sec 14 1 for further details Another but computational more involved possibility is plot the difference density between the ground and the respective excited state This requires however a first order property or gradient calculation for the excited state to obtain the difference density For further details see Sec 9 3 3 9 3 First Order Properties and Gradients For the ground state first order properties expectation values are implemented at the SCF MP2 and CC2 level Note that for the ground state CCS and CIS are equivalent to SCF For excited states first order properties are implemented only at the CCS and CC2 level Gradients are presently only available for the ground state at the MP2 and the CC2 and
108. moments resulting from atomic charges Eisra eE E EEE E E lt option gt switch off lt option gt or q uit leave this menu Here you can activate several optional quantities to be computed along with the Mulliken PA To switch on one or more of these options you must enter the cor responding option keywords e g spdf netto for computation of atomic neto pop ulations and MO contributions to atomic brutto populations The status flags for these tasks will then change from F false to T true To switch off any option you simply have to enter the corresponding keyword preceded by a e g netto for disabling calculation of atomic netto populations After having left the Mulliken PA section you will be asked whether a population analysis based on occupation numbers a modified Roby Davidson PA should be performed by moloch When typing y you will see the following submenu where you can switch on several special options for the PA in the same manner as described above 4 4 THE GENERAL OPTIONS MENU 95 add or delete one or more special options for a population analysis based on occupation numbers option status description compute MO contributions to modified atomic orbital MAO occupation numbers maodump F dump all MAOs onto standard output write MAOs onto a separate file select F write only those MAOs which have been employed in the population analysis all F write all MAOs maofile F
109. not optimised but predetermined using the coalescence conditions default An additional keyword noflip suppresses the use of spin flipped geminals in open shell calculations by de fault spin flipped geminals are used as described in Ref 102 controls which orbitals are used in the F12 energy contribution hf means that semi canonical Hartree Fock orbitals are used default rohf means that ROHF orbitals are used any frozen orbitals will then also implicitly be ROHF For calculations on closed shell systems localised orbitals may be used Both the Boys 103 and Pipek Mezey 104 methods are available for localisation of the orbitals corresponds to the choice of correlation factor fiz in the geminal basis functions R12 results in a calculation using linear rj2 and LCG results in a calculation using the Slater type correlation factor with exponent 1 4 ag 1 represented as a linear combination of six Gaussians see Ref 105 Note that the exponents 0 9 1 0 and 1 1 ag 1 are recommended for use with the cc pVXZ F12 basis sets 98 switches on off the calculation of a second order correction to the Hartree Fock energy by accounting for single excitations into the complementary auxiliary basis set CABS The single excitations into the CABS basis can be computed without extra costs if the CABS Fock matrix elements are required anyway for the F12 cal culation i e for ansatz 2 approximation B or comaprox F K The computation o
110. obsolete If they are still acceptable depends on the changes you made during your present define session They are obviously incorrect if you changed the molecule under consideration but any change in the basis sets or the occupation numbers will make them dangerous too because you might not know some day if they really refer to the basis set which is defined in this control file As a rough guide delete them whenever you have made changes in one of the first three main menus during your define session After that you will reach the last main menu of define which helps you to control the actions of all TURBOMOLE programs The meanings of the various options are explained in more detail in the description of the individual programs therefore only a short explanation will be given here Now have a look at the menu GENERAL MENU SELECT YOUR TOPIC scf SELECT NON DEFAULT SCF PARAMETER mp2 OPTIONS AND DATA GROUPS FOR rimp2 and mpgrad cc OPTIONS AND DATA GROUPS FOR ricc2 ex EXCITED STATE AND RESPONSE OPTIONS prop SELECT TOOLS FOR SCF ORBITAL ANALYSIS drv SELECT NON DEFAULT INPUT PARAMETER FOR EVALUATION OF ANALYTICAL ENERGY DERIVATIVES GRADIENTS FORCE CONSTANTS rex SELECT OPTIONS FOR GEOMETRY UPDATES USING RELAX stp SELECT NON DEFAULT STRUCTURE OPTIMIZATION PARAMETER e DEFINE EXTERNAL ELECTROSTATIC FIELD dft DFT Parameters ri RI Parameters rijk RI JK HF Parameters senex seminumeric exchange paramet
111. obtained with the command func 78 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE SURVEY OF AVAILABLE EXCHANGE CORRELATION ENERGY FUNCTIONALS FUNCTIONAL TYPE EXCHANGE CORRELATION REFERENCES slater dirac LDA S 1 2 exchange s vwn LDA IS VWNCV 1 3 vwn LDA VWNCV 3 s vwn_Gaussian LDA S VWN III 1 3 pwlda LDA IS PW 1 2 4 becke exchange GGA S B88 1 2 5 b lyp GGA S B88 LYP 1 2 6 b vwn GGA S B88 VWNCV 1 3 5 lyp GGA LYP 6 b p GGA S B88 VWN V P86 1 3 5 7 pbe GGA S PBE X PW PBE C 1 2 4 8 tpss MGGA S TPSS X PW TPSS C 1 2 4 14 bh lyp HYB 0 5 S B88 LYP 1 2 5 6 9 0 5HF b3 lyp HYB 0 8S 0 72B88 0 19VWNCV 1 3 5 6 10 0 2HF 0 81LYP b3 lyp_Gaussian HYB 0 8S 0 72B88 0 19VWNCIITI 1 3 5 6 10 0 2HF 0 81LYP pbed HYB 0 75 S PBE X PW PBE C 1 2 4 8 11 0 25HF tpssh HYB 0 9 S TPSS X PW TPSS C 1 2 4 14 15 0 1HF lhf ODFT E EXX 12 13 oep ODFT EXX 18 b97 d GGA B97 refit B97 refit 16 b2 plyp DHYB 0 47 SB88 0 53HF 0 73LYP 0 27PT2 17 Default is b p i e B P86 which is probably best for the whole of Chemistry 27 For main group compounds we recommend b3 lyp note that GAUSSIAN uses partly different implementations 27 The programs dscf and grad are used to carry out conventional DFT treatments i e J and K are
112. of atoms which is allowed for define Hitting lt return gt will bring you back to the internal coordinate menu where you can see the new number of internal coordinates in the headline 62 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE 4 1 3 Manipulating the Geometry Note that the molecular geometry can be modified with the iman command of the internal coordinate menu described earlier if internal coordinates has been defined Another option is to select m in the geometry main menu which provides the following submenu CARTESIAN COORDINATE MANIPULATION MENU move TRANSLATE AND OR ROTATE PART OF THE MOLECULE inert MOVE MOLECULE SO THAT COORDINATE AXES BECOME PRINCIPAL AXES OF INERTIA mback RESTORE PREVIOUS MOLECULAR GEOMETRY dis DISPLAY MOLECULAR GEOMETRY YOU MAY APPEND A QUESTION MARK TO ANY OF THESE COMMANDS FOR FURTHER EXPLANATIONS HIT gt return lt OR USE ANY GEOMETRY COMMAND NOT IN THIS LIST TO TERMINATE THIS MENU UPON TERMINATION THE MOLECULAR SYMMETRY WILL BE ENFORCED ACCORDING TO SYMMETRY GROUP c3v The meaning of the commands inert and mback should be clear command move allows you to manipulate the geometry of your molecule After entering move you will be asked to specify a set of atoms on which the command shall act You can use this to manipulate only a part of your molecule e g if you are building a structure from subunits and you want to adjust their relative arrangement As long as you stay i
113. of the identity approximation Phys Chem Chem Phys 8 10 1159 1169 2006 16 A Hellweg S Gr n C Hattig Benchmarking the performance of spin component scaled CC2 in ground and electronically excited states Phys Chem Chem Phys 10 1159 1169 2008 17 N O C Winter C Hattig Scaled opposite spin CC2 for ground and excited states with fourth order scaling computational costs J Chem Phys 134 184101 2011 18 R Bauernschmitt R Ahlrichs Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory Chem Phys Lett 256 4 5 454 464 1996 19 R Bauernschmitt R Ahlrichs Stability analysis for solutions of the closed shell Kohn Sham equation J Chem Phys 104 22 9047 9052 1996 Ww amp F Furche R Ahlrichs Adiabatic time dependent density functional methods for excited state properties J Chem Phys 117 16 7433 7447 2002 BIBLIOGRAPHY 395 21 22 23 24 25 26 27 28 30 31 32 M Kollwitz J Gauss A direct implementation of the GIAO MBPT 2 method for calculating NMR chemical shifts Application to the naphthale nium and and anthracenium ions Chem Phys Lett 260 5 6 639 646 1996 C van W llen Shared memory parallelization of the TURBOMOLE programs AOFORCE ESCF and EGRAD How to quickly parallelize legacy code J Comp Chem 32 1195 1201 2011
114. of the perturbing operator A similar expression is obtained for the left transition moments The left and right transition moments are then combined to yield the transition strength 1 V V V v Siv T73 Me Mf a 2 Mp 9 23 As for the ground state transitions only the transition strengths oe v are a well defined observables but not the transition moments MY s and MY The single substitution parts of the transition Lagrangian multipliers N yp are saved in files named CCNEO s m wazz To obtain the transition strengths for excitations between excited states the keyword tmexc must be added to the data group excitations Additionally the initial and final states must be given in the same line else the input is same as for the calculation of excitation energies and first order properties ricc2 cc2 excitations irrep al nexc 2 irrep a2 nexc 2 tmexc istates a1l 1 fstates all operators diplen 9 5 Ground State Second order Properties with MP2 and CC2 For closed shell restricted Hartree Fock reference states second order properties for one electron perturbation can be computed at the MP2 and the CC2 level For MP2 second order properties are computed as derivatives of the SCF MP2 total energy This approach include the relaxation of the SCF orbitals in the presence of the perturbation and is restricted to the static i e frequency independent limit 196 CHAPTER 9 RI CC2 For coupled cluster model
115. on off Calculate numerical 2nd derivative of SCF energy with respect to elec trostatic field default off increment for numerical differentiation is edelt edelt real Increment for numerical differentiation default 0 005 fields on off Calculate SCF energy for non zero external electrostatic fields defined in electrostatic field geofield on off Calculate SCF energy for one external field definition and dump dis turbed MOs onto scfmo This enables to evaluate properties or perform geometry optimizations in the presence of an external field Caution don t use the RI approximation for all these calculations since this will lead to non negligible errors incore integer By using this option the two electron integrals are kept in RAM integer spec ifies how many megabytes should be allocated If the integrals exceed the RAM allocated the program reverts to the standard mode Supports all meth ods which process two electron integrals i e SCF and DFT including hybrid functionals RHF and UHF 282 CHAPTER 18 KEYWORDS IN THE CONTROL FILE The following condition must be met scfdenapproxl 1 and rhfshells 1 or 2 It is advisable to set thize as small as possible e g thize 0 1d 08 and to remove the keyword scfdump Note this keyword does not work for parallel runs mo diagram only nirreps integer If this keyword is set the energies and symmetry labels of all occupied MOs will be dumped to this data group
116. opt gt for disabling any interconversion option lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU The options qconv and iter are used in each normal relax run to determine the characteristics of the back transformation of coordinates into the internal space With the other options and interconversion switched on you can force relax to perform only the specified coordinate transformation and write the transformed co ordinates to file control To achieve this enter on to switch to the transformation only mode and one of the last four options e g crtint to specify the desired transformation Updating the Hessian relax provides a variety of methods to generate an updated Hessian every cycle This includes the well known methods such as BFGS DFP or MS update methods as well as some less common procedures option status description none F NO UPDATE STEEPEST DESCENT bfgs F BROYDEN FLETCHER GOLDFARB SHANNO UPDATE dfp F DAVIDON FLETCHER POWELL UPDATE bfgs dfp F COMBINED BFGS DFP UPDATE ms F MURTAGH SARGENT UPDATE schlegel F SCHLEGEL UPDATE diagup F DIAGONAL UPDATE AHLRICHS EHRIG multidim F RANK gt 2 BFGS TYPE UPDATE ahlrichs T MACRO AHLRICHS UPDATE DEFAULT USE lt opt gt FOR ENABLING OPTION lt opt gt AND THUS DISABLING ALL OTHER OPTIONS lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU 88 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE We recommend to use the default
117. pV5Z ce pCWVXZ X D 5 siia aug cc pVXZ PP X D 5 cc pwCVXZ PP X D 5 r T GTa S ET s s DISS VITA a a Auxiliary basis sets for RI MP2 and RI CC2 elements Rb Rn Rb Sr Y Cd In Xe Cs Ba La Hg Tl At Rn def SVP def SV P f m def2 S VP def2 SV P m f f m m f f m m def TZVP def TZVPP f m def2 TZVP def2 TZVPP m def2 QZVP def2 QZVP m aug cc pVXZ PP X D 5 p p p cc pwCVXZ PP X D 5 p p p 1 3 HOW TO QUOTE USAGE OF TURBOMOLE 21 a Fully Optimized Contracted Gaussian Basis Sets for Atoms Li to Kr A Schafer H Horn and R Ahlrichs J Chem Phys 97 2571 1992 b Fully Optimized Contracted Gaussian Basis Sets of Triple Zeta Valence Quality for Atoms Li to Kr A Schafer C Huber and R Ahlrichs J Chem Phys 100 5829 1994 c Auxiliary Basis Sets to Approximate Coulomb Potentials K Eichkorn O Treut ler H Ohm M Haser and R Ahlrichs Chem Phys Letters 242 652 1995 d Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials K Eichkorn F Weigend O Treutler and R Ahlrichs Theor Chem Acc 97 119 1997 e Accurate Coulomb fitting basis sets for H to Rn F Weigend Phys Chem Chem Phys 8 1057 2006 f RI MP2 Optimized Auxiliary Basis Se
118. parametrization of the unitary transformation used in the DKH transformation can be optionally selected by dkhparam integer The possible parametrizations in the DKH transformation are dkhparam 1 Optimum parametrization OPT dkhparam 2 Exponential parametrization EXP dkhparam 3 Square root parametrization SQR dkhparam 4 McWeeny parametrization MCW dkhparam 5 Cayley parametrization CAY Note in particular that the parametrization does not affect the Hamiltonian up to fourth order Therefore as long as you run calculations with DKH Hamiltonians below 5th order you may use any symbol for the parametrization as they would all yield the same results Higher order DKH Hamiltonians depend slightly on the chosen paramterization of the unitary transformations applied in order to decouple the Dirac Hamiltonian but this effect can be neglected For details on the arbitrary order DKH Hamiltonians see Ref 67 for details on the infinite order DKH theory 68 for the implementation and 69 for a conceptual review of DKH theory For details on the different parametrizations of the unitary transformations see 70 138 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS 6 6 Periodic Electrostatic Embedded Cluster Method 6 6 1 General Information The Periodic Electrostatic Embedded Cluster Method PEECM functionality 71 provides electronic embedding of a finite quantum mechanical cluster in a periodic infinite array of poin
119. printed if absolute value exceeds 0100 4 center shared electron numbers will be computed values are printed if absolute value exceeds 0100 add or delete one or more options for the computation of Shared Electron Numbers SEN option status description S22 22 555 ie ee ae a a ee 2c lt r gt T compute 2 center SEN and print if ISEN gt lt r gt DEFAULT 1000E 01 3c lt r gt T compute 3 center SEN and print if ISEN gt lt r gt DEFAULT 1000E 01 4c lt r gt T compute 4 center SEN and print if ISEN gt lt r gt DEFAULT 1000E 01 ee ee ee ee ee nosym F switch off use of symmetry orbs F compute orbital contributions to SEN irreps F compute irrep contributions to SEN ee PaaS a ae aa Se eae ee ee lt option gt switch off lt option gt or q uit leave this menu The procedure for changing the options is the same as described above By default calculation of 2 3 and 4 center SENs will be enabled with thresholds of 0 01 each Option plot This option allows you to prepare the data needed for contour plots of orbital ampli tudes or total electron densities We do not recommend to prepare plotting data this way an easier method with an easier syntax is to generate these data directly by the programs where densities also MP2 or excited ones and Molecular orbitals are calculated This is described in Chapter 14 If you nevertheless want to prepare the input for pl
120. put Additionally a vector file named spinvec txt is written which includes the resulting spinvector for each atom in the system also the direction The following modifications and extensions are supported if the respective commands are written in the same line as pop lall Additional information about pyr py pz and analogous for d and f func tions is displayed lengthy output atoms list of atoms Contributions are plotted only if arising from atoms selected by list thrpl real Contributions smaller than thrpl are not displayed default 0 01 overlapMulliken atomic overlap matrix is displayed nettoMulliken netto populations diagonal elements of Mulliken overlap ma trix are calculated mosum list of MOs Summed Mulliken contributions for a group of molecular orbitals defined by numbers referring to the numbering obtained e g from the tool eiger Note that occupancy of MOs is ignored i e all orbitals are treated as occupied mo list of MOs Mulliken contributions for single MOs defined by numbers independent of whether they are occupied or not If this option is valid one may additionally set dos width real points integer to calculate a simulated density of states by broadening the dis crete energy levels with Gaussians and superimposing them The width of each Gaussian may be set by input default 0 01 a u The resolution number of points may be chosen automatically default values are usually
121. range 10 10 points 2000 origin 0 0 0 and run odft proper The plotting subroutine reads the file Lhfcg contaning the matrix elements of the Correation potential is already generated by a previous run The file tx vec will be generated with four columns distance LHF potential Slater potential Correction potential The procedure to plot the OEP EXX potential is the same In this case the expan sion coefficients see Eq 16 6 are read from the file oepcVx dat cartesian format The file tx vec will be generated with four columns distance EXX potential EXX potential zero 16 5 How to quote e For LHF calculations with odft Efficient localized Hartree Fock methods as effective exact exchange Kohn Sham methods for molecules Fabio Della Sala and Andreas Gorling J Chem Phys 115 5718 2001 and The asymptotic region of the Kohn Sham exchange potential in molecules Fabio Della Sala and Andreas Gorling J Chem Phys 116 5374 2002 e For OEP EXX calculations with odft Numerically stable optimized effective potential method with balanced Gaus sian basis sets Andreas Hefelmann Andreas W G tz Fabio Della Sala and 258 CHAPTER 16 ORBITAL DEPENDENT DFT Andreas Giling J Chem Phys 127 054102 2007 Chapter 17 Treatment of Solvation Effects with COSMO The Conductor like Screening Model 169 COSMO is a continuum solvation model CSM where the solute molecule forms a cavity within the dielectric continuum o
122. results depend on the parameterization of the spin adapted excitation operators This prevents in particular a simple comparison of the results for singlet and triplet excited states if the calculations are carried out in a spin free basis With the biorthogonal representation for singlet spin coupled double excita tions 112 results for T7 also differ largely between the left and right eigenvectors and are not invariant with respect to unitary transformations of the occupied or the virtual orbitals The ricc2 module therefore uses since release 6 5 an alternative double excitation diagnostic which is defined by 7 100 Tj Zi n2 with A Ju E and To dois j asb E inj with Fai and Eaibj in the spin orbital basis They are printed in the summaries for excitation energies under the headings t1 and t2 For spin adapted excitation amplitudes 7 and 7 have to be computed from respective linear combinations for the amplitudes which reproduce the values in the spin orbital basis For ADC 2 which has a symmetric secular matrix with identical left and right normalized eigenvectors J and J2 are identical with the contributions from the singles and doubles parts for the eigenvectors to the trace of the occupied or virtual block of the orbital unrelaxed difference density between the ground and the excited state i e the criterium proposed in ref 12 Compared to the suggestion from ref 12 7 and 72 have the additional advantage of tha
123. step is the definition of the part infinite of point charges field that will be replaced by the explicit quantum mechanical cluster Finally the quantum mechanical cluster together with surrounding ECPs representing cationic sites as well as point charges representing anions is defined and put in place of the point charges The input preparation steps can be summarized as follows 1 Dimensionality of the system is specified by the keyword periodic in the embed section periodic 3 means a bulk three dimensional system periodic 2 denotes a two dimensional surface with an aperiodic z direction 2 Definition of the unit cell of periodic point charges field is specified in the subsections cell and content of the embed section 3 Definition of the values of the point charges by specifying a charge value per species using the subsection charges or a charge value for each point charge using the subsection ch_list Note that only one of the subsections can be defined 4 Definition of the part of point charges field that will be replaced by the QM cluster together with the isolating shell ECPs explicit point charges is spec ified in the subsection cluster of the embed section 5 Definition of the quantum mechanical cluster as well as the surrounding ECPs and anionic point charges is included in the usual coord section The following two examples show the definition of the point charges unit cells Example 1 Ca Fj9 cluster embedded in b
124. strongly recommended to use the weight derivatives option The biggest deviations from the uncorrected results are to be expected if doing gradient calculations for elements heavier than Kr using all electron basis sets and very small grids To use the weight derivatives option add weight derivatives in dft The option point charges in drvopt switches on the evaluation of derivatives with respect to coordinates of point charges The gradients are written to the file point_charge_gradients old gradients will be overwritten 18 2 10 Keywords for Module AOFORCE This module calculates analytically harmonic vibrational frequencies within the HF or RI DFT methods for closed shell and spin unrestricted open shell systems Bro ken occupation numbers would lead to results without any physical meaning Note that RI is only used partially which means that the resulting Hessian is only a very good approximation to exact second derivatives of the RIDFT energy expression Apart from a standard force constant calculation which predicts all allowed and for bidden vibrational transitions it is also possible to specify certain irreps for which the calculation has to be done exclusively or to select only a small number of lowest eigenvalues and eigenvectors that are generated at reduced computational cost General keywords drvopt is the keyword for non default options of gradient and second derivative cal culations Possibilities i
125. sufficient to generate a satisfactory plot or specified by hand The output files dos in case of RHF wave 346 CHAPTER 18 KEYWORDS IN THE CONTROL FILE functions and dos_atb dos_a b dos_alpha dos_beta for UHF cases contain energies first column resulting DOS for the re spective energy second column as well as s p d contributions for the respective energy following columns Example pop mo 23 33 dos atoms 2 3 7 8 leads to Mulliken PA CAO basis for each of the eleven MOs 23 33 regarding only contributions from atoms 2 3 and 7 8 results are written to standard output and generation of file s with the respective simulated density of states pop nbo to perform a natural population analyses 141 The possible options specified in the same line are AO must be provided the CAO case is not implemented tw real Threshold t to circumvent numerical difficulties in computing Ow default tw 1 d 6 idbgl integer Debug level default idbgl 0 ab For UHF cases Print alpha and beta density results short Print only natural electron configuration and summary Example pop nbo AO ab short atoms 1 2 6 leads to a natural population analysis AO basis with printing the results of alpha and beta densities only the electron configuration and the summary for the atoms 1 2 and 6 To change the NMB set for atoms one has to add a nbonmb block in the control file Example nbonmb ni s 4 p 2 d 1 o s
126. switch between the proper 5d 7f set and the Cartesian 6d 10f set This command allows you to specify effective core potentials for some atoms The assignment works exactly like the specification of basis sets see above This one does the same as command ecp but restricted to the basis set library the input file will not be used ecpi gives you some general information about what type of pseudopo tentials is supported For more information we refer to 25 and refer ences therein ecpl gives you a list of all pseudopotentials assigned so far 4 3 GENERATING MO START VECTORS 67 ecprm ecprm allows to remove a pseudopotential assignment from the list This command is useful if you want to perform an all electron calculation after an ECP treatment c Command c assigns a special nuclear charge to an atom This is useful to define dummy centers for counterpoise calculations where you set the nuclear charge to zero m This command allows you to assign non default atomic masses to an atom Use this if you want to analyze isotopic shifts of calculated har monic frequencies The standard masses are those of the natural isotope mix dat dat gives you a list of all data already specified This is again the usual command to leave a menu and write all data to file control or any other output file It is not possible to leave this menu unless basis sets have been specified for all atoms in your molecule If you do not want to use a b
127. tables of Roothaan pa rameters in Section 6 3 Note that this keyword toggles the ROHF mode also for more than one open shell If it is not given the open shell electrons are simply ignored alpha shells and beta shells uhf these two data groups specify the occupation of alpha and beta spin UHF MOs syntax as any data group related with orbital occupation information e g closed shells Example alpha shells a 1 8 1 b 1 2 1 beta shells a 1 7 1 b 1 3 1 directs the program to carry out a UHF run uhf overwrites closed shell occupation specification uhfmo_alpha and uhfmo_beta These two data groups contain the UHF MO vectors for alpha and beta spin respectively same syntax as scfmo tC C J Roothaan Rev Mod Phys 32 1960 179 18 2 FORMAT OF KEYWORDS AND COMMENTS 291 uhfmo_beta see uhfmo_alpha DFT dft functional b p gridsize m3 for DFT calculations one has to specify the functional and the grid for the quadra ture of the exchange correlation part The settings above are default both lines can be left out if the B P86 functional and grid m3 are required Other useful functionals supported are b lyp b3 lyp b3 lyp Gaussian equivalent to the Gaussian98 keyword B3LYP with VWNIII bh lyp s vwn s vwn Gaussian equivalent to the Gaussian98 keyword SVWN with VWNIII tpss tpssh Possible grids are 1 5 and m3 m5 where grid 1 is coarse least accurate and 5 most
128. temperature of 0 0K will turn off wall temperature control returning molecules to the system with the same momentum as when they encountered the barrier constraints angstroms tolerance 0 05 adjpercyc 0 25 type H 0 0 9 1 2 type F C 0 0 1 7 type HC 1 0 1 2 2 3 4 1 0 0 1 1 54 1 1 0 constraints specifies and or automatically generates atomic distance constraints The 18 2 FORMAT OF KEYWORDS AND COMMENTS 357 optional flag angstroms can be used to indicate that data will be entered in Angstroms rather than Bohr tolerance is the convergence criterion for application of constraints All distances must be within tolerance of the specified constraint Additionally the RMS deviation of all constrained distances must be below 2 3 of tolerance adjpercyc is the fraction of the total distance correction to be applied on each constraint iteration type X A const rmaxr commands frog to find the closest A atom to each atom X that is closer than rmax and apply const The first type line above examines each H atom and looks for any 0 atoms within 1 2 A The shortest distance if any is then fixed at 0 9A Similarly the second type line binds each F to the closest C within 1 7A but since const 0 0 that distance is fixed at the current value The third type line attaches H atoms to the appropriate nearby C but at the current average H C distance multiplied by the absolute value of const Explicitly specifie
129. the core part of the ricc2 program C Hattig and F Weigend J Chem Phys 113 2000 5154 for transition moments and excited state first order properties C Hattig and A Kohn J Chem Phys 117 2002 6939 178 CHAPTER 9 RI CC2 e for triplet excited states include C Hattig and K Hald Phys Chem Chem Phys 4 2002 2111 C Hattig A Kohn and K Hald J Chem Phys 116 2002 5401 e for ground state geometry optimizations include C Hattig J Chem Phys 118 2003 7751 e for geometry optimizations for excited states include A Kohn and C Hattig J Chem Phys 119 2003 5021 e for calculations with RI ADC 2 RI CIS D RI CIS D include C Hattig Adv Quant Chem 50 2005 37 e if the parallel version of ricc2 is used include a reference to C Hattig A Hellweg A K hn Phys Chem Chem Phys 8 2006 1159 e for transition moments between excited states M Pabst and A K hn J Chem Phys 129 2008 214101 e for RI MP2 F12 calculations R A Bachorz F A Bischoff A Gl C Hattig S H6fener W Klopper D P Tew J Comput Chem 32 2011 2492 e for O N scaling calculations using the Laplace transformation N O C Winter C Hattig J Chem Phys 134 2011 184101 e for second order properties relaxed or unrelaxed D H Friese N O C Winter P Balzerowski R Schwan C Hattig J Chem Phys 136 2012 174106 Auxiliary basis sets e the appropriate refere
130. the fifth orbital in irrep a1 e g you would enter mo 5a1 Equivalently you can use localized orbitals from a Boys localization procedure or modified atomic orbitals as obtained in a Roby Davidson Ahlrichs Heinzmann population analysis In the latter cases you will not have to enter an irrep label as these orbitals are necessarily in C1 symmetry Instead you will have to enter the index of the orbital to be plotted and for option mao the index of the atom at which it is situated In all cases you will additionally have to specify the plane in which the amplitudes or densities will be monitored To do this you have to declare two vectors which span that plane and the origin of this new coordinate system relative to the one in which the atomic coor dinates are given Furthermore you will have to create a grid of points on this plane The orbital amplitude or electron density will then be calculated for every point in this grid The grid is created by telling define the range to be included along both vectors spanning the plane where the unit in each direction is the length of the corresponding basis vector and the number of points to be calculated in this range It is advantageous to use a wide grid while you test the ranges or planes which give the best results and then to switch to a finer grid for the final calculation Finally input MO vector and output plot data files can be specified In case you do not want to add a new data group a
131. the first order properties will be calculated Default is to compute the components of the dipole and the quadrupole moment The option unrelaxed_only suppress the calcula tion of orbital relaxed first order properties which require solution the CPHF like Z vector equations Default is the calculation of unrelaxed and orbital relaxed first order properties The unrelaxed_only option will be ignored if the calculation of gradients is requested see gradient option below and geoopt in data group ricc2 sop requests the calculation of ground state second order properties as e g dipole polarizabilities The operators flag has to be followed by a comma seperated pair of operators If more pairs are needed they have to be given with additional sop commands Default is to compute all symmetry allowed elements of the dipole dipole polarizability With the 18 2 FORMAT OF KEYWORDS AND COMMENTS 325 freq flag on can specify a frequency default is to compute static po larizabilities The relaxed flag switched from the unrelaxed approach which is used by default to the orbital relaxed approach Note that the orbital relaxed approach can not only be used in the static limit freq 0 0d0 For further restrictions for the computation of second order properties check Chapter 9 5 gradient conv require calculation of geometric gradients In difference to the geoopt keyword in the data group ricc2 this can be used to compute gradients fo
132. the nucleus I and r is the position vector of the electron rela electronic force on nuclei u tive to the nucleus all three components for all nuclei the labels are xnef001 ynef001 znef001 xnef002 etc where the number depends on the order in the coord file specification of states for which transition moments or first order proper ties are to be calculated The default is all i e the calculations will be done for all excited states for which excitation energies have been calcu lated Alternatively one can select a subset of these listed in parentheses e g states ag 3 1 3 5 biu 1 1 3 b2u4 This will select the triplet ag states no 1 3 4 5 and the singlet bj states no 1 2 3 and the singlet which is default if no is found ba state no 4 istates all fstates all The specification of initial and final states for transition properties between excited states is mandatory The syntax is analog to the states option i e either all or a list of of states is required 328 CHAPTER 18 KEYWORDS IN THE CONTROL FILE D2 diagnostic Calculate the double substitution based diagnostics Do cc2_natocc Write MP2 CC2 natural occupation numbers and natural orbitals to a file cgrad 1000 Calculate the error functional dp for the RI approximation of a7 b7 integrals 1 ad 27 exact ab 3 Rt 4 Ea i eh amp ORI and its gradients with respect to exponents and c
133. the output by using the keyword intcorr all instead of intcorr Excitation energies with CCSD Since release V6 5 electronic excitation ener gies can also be computed at the conventional CCSD level For this the data group excitations has be added the same keyword as for CC2 apply The implemen tation is currently restricted to vertical excitation energies no transition moments or properties available and in the closed shell case to singlett excited states Note that for single excitation dominated transitions CCSD is as CC2 correct through second order in H and does not neccessarily more accurate than CC2 It is however for double excitations still correct through first order while CC2 describes double excitations only in a zero order approximation Therefore CCSD results are more robust with respect to double excitation contributions to transitions and are thus usefull to check if CC2 is suitable for a certain problem Chapter 11 Correlation Energies from the Random Phase Approximation Ground state energies within the random phase approximation RPA can be com puted using the rirpa module The resolution of the identity RI approximation is used to approximate the two electron repulsion integrals in the correlation treat ment 133 134 The RI approximation is also employed by default for the compu tation of the Coulomb integrals for the HF HXX energy It is optional to use RI for the HF exchange integrals RIRPA grad
134. to functionals of the first three rungs satisfy the HOMO condition 161 H0MO x bHOMO uomol tS dHOMO 16 4 and the asymptotic relation 164 165 vlr oml vx lom 16 5 where m is the highest occupied orbital which do not have a nodal surface in the asymptotic region along direction r Considering together with condition 16 4 we finally obtain that Ux r will approach 1 r along all directions where y0mo r does not have a nodal surface in the asymptotic region e g this is the case of atoms on directions which belong to the nodal surface of the HOMO the vx r will approach m vx ON m 1 r 16 2 IMPLEMENTATION 251 Both OEP EXX and LHF gives total energies very close to the Hartree Fock one ac tually Euf gt Epxx gt Exp thus without an appropriate correlation functional these methods are not suitable for thermochemistry On the other hand OEP EXX and LHF give very good KS orbital spectra In fact the eigenvalues of the HOMO is very close to the Hartree Fock and to exact ionization potential I P this is in contrast to functional of the first three rungs which underestimate the HOMO en ergy by several eVs In addition a continuum set of bound unoccupied orbitals are obtained Thus OEP EXX or LHF KS orbitals are very good input quantities for computing NMR shielding constants 166 energy levels in hybrid interfaces 167 and TD DFT excitation energies 168 th
135. use is best explained by some examples pointval geo plane gridi vector 0 1 0 range 2 2 points 200 grid2 vector 0 0 1 range 1 4 points 300 origin 1 1 1 Values are calculated at a plane spanned by vectors 0 1 0 and 0 0 1 centered at 1 1 1 18 2 FORMAT OF KEYWORDS AND COMMENTS 353 pointval geo line grid1 vector 0 1 0 range 2 2 points 50 origin 0 0 1 Values are calculated at a line in direction 0 1 0 centered at 0 0 1 Output format as above pointval geo point 753 007 Values are calculated at the two points 7 0 5 0 3 0 and 0 0 0 0 7 0 Plane averaged density can be computed by pointval dens averagez fmt vec gridi vector 1 0 0 range 10 10 points 100 grid2 vector 0 1 0 range 10 10 points 100 grid3 vector 0 0 1 range 20 20 points 200 origin 0 0 0 The generated file td vec will contain the quantity pe avay pvz 18 1 18 2 19 Keywords for Module FROG The ab initio molecular dynamics MD program frog needs a command file named mdmaster The interactive Mdprep program manages the generation of mdmaster and associated files It is always a good idea to let Mdprep check over mdmaster before starting an MD run Mdprep has online help for all menus In this implementation of ab initio MD time is divided into steps of equal duration At Every step the energy and its gradient are calculated and these are used by the frog to work out the new coordinates for the next step along the dy
136. you need the timings option to produce the timing summaries and the newref option to save the cur rent program timings as the new reference The module specifications and short long and r options can be used for selecting the test examples The more specialized options are summarized in the following table Note that most of these options can also be set in the DEFCRIT file see below Operation modes help Prints out the help message and exits list Lists the available test examples clean realclean check dir validate dir val dir 20 4 MODES AND OPTIONS OF THE TTEST SCRIPT 391 Deletes the test directories and summary files for the current architecture given by SYSNAME see Chapter 1 5 Deletes all test directories and protocols Checks the correctness of an existing program test in the directory dir default TESTDIR sysname Useful if new criteria or new references are established Examines the output files in the directory dir default TESTDIR sysname and highlights the positions of the retrieved matches Loading path and naming options loaddir dir 1 dir scriptdir dir ls dir testprog prog x prog dir dir critfile file defcritfile file protfile file output file gprotfile file checkfile file errfile file probfile file timfile file Loading path for the TURBOMOLE binaries default TURBODIR bin sysname Loading pat
137. 1 123 151 289 315 361 416 thize 121 123 151 225 282 289 315 361 title 267 355 tmpdir 44 196 197 314 315 tplot 166 315 traloop 161 164 225 313 360 362 trand 361 trast 361 turbomole 354 twoint 224 uff 114 271 maxcycle 114 uffgradient 271 273 uffhessian 271 273 ufftopology 271 273 uhf 269 290 uhfmo_alpha 154 267 286 290 291 uhfmo_beta 154 267 286 290 userdefined bonds 266 vdw_fit 343 velocity gauge 311 win 349 amp 49 plt 349 NUMFORCE frznuclei 221 frznuclei NUMFORCE 221 actual 25 actual step dscf 266 ADC 2 RE 315 analysis of normal modes internal coordinate 220 AOFORCE keywords 305 INDEX aoforce 14 24 25 39 42 82 84 89 103 106 112 148 218 222 305 335 336 aoforce2g98 25 B matrix 57 58 babel 34 Bend 26 bend 25 Boys localization 349 Broken symmetry 73 bsse_out 120 bsseenergy 118 cbasopt 26 ccisd 192 ccitd 191 ccitd cc2 gs 1a1 001 192 ccitd cc2 xs 3a2 001 192 CC2 24 RI 315 CCLO m ss xxx CCLEO s m xxx CCMEO s m xxx CCNEO s m xxx CCNLO s m xxx CCREO s m xxx CCS RI 315 CCSD 315 CCSD T 315 CCSD T 315 cgnce 26 187 183 193 195 188 183 charge vector 253 CIS 24 RI 315 CIS D 24 RI 315 condition 253 INDEX conjugate gradients 104 control 23 25 33 34 36 49 51 66 69 76 102 166 191 196 19
138. 1 F F Zk 1 tdGk l 2 Broyden Fletcher Goldfarb Shanno BFGS S dq 1 dg 1 dq 1 dG DIE ou 1_ pk ldGk dq tyf S1 FE Fy 3 Davidon Fletcher Powell DFP dg 7 dq t FR laGk dGr 1 sia 1 k _ pk 1 P ee se 1 S1 4 combined method BFGS DFP If S1 lt S 1 S1 and 1 gt 0 perform DFP update otherwise BFGS The meaning of the symbols above is as follows F Hh gt approximate inverse force constant matrix in the k th iteration s q general coordinates in the k th iteration GF gradients in the k th iteration dg gk gt dgk 1 gk gk 1 Zk 1 qgk 1 Fk lggk 1 S1 dqt tdg 7t S 1 dg dee 81 An alternative is to use update algorithms for the hessian H itself Ehrig Ahlrichs Diagonal update for the hessian by means of a least squares fit Hii y Hi hi di with the new estimate h for the diagonal elements obtained by a dG dq O Eld and the error d obtained by the regression 108 CHAPTER 5 STRUCTURE OPTIMIZATIONS Another alternative is to use DIIS like methods structure optimization by direct inversion in the iterative subspace See ref 33 for the description of the algorithm The DIIS procedure can often be applied with good success using static or updated force constant matrices Any of the algorithms mentioned above may be chosen Recommended is the macro option ahlrichs which leads to the following action
139. 1 General Wiformation lt lt ioe 6406 4 48 lt a oe ba Bk eas 101 CONTENTS 5 O22 Hessian MARE 2 gos bg ts die ge os Be eR Bd BOR GER a G 102 529 Finding Minima sece eae s i ee Spake be kee 103 5 2 4 Finding transition states o oo a a 103 Oo Program Relax 2 cee ein ee RR MH Bes oe ee Oe EIRE E 104 Sock PUrp sg c gas ae es he Gee Sa Ae Boe A ee als 104 5 3 2 Optimization of General Coordinates 105 5 3 3 Force Constant Update Algorithms 106 5 3 4 Definition of Internal Coordinates 108 5 3 5 Structure Optimizations Using Internal Coordinates 108 5 3 6 Structure Optimization in Cartesian Coordinates 109 5 3 7 Optimization of Basis Sets SCF only 110 5 3 8 Simultaneous Optimization of Basis Set and Structure 110 5 3 9 Optimization of Structure and a Global Scaling Factor 111 5 3 10 Conversion from Internal to Cartesian Coordinates 111 5 3 11 Conversion of Cartesian Coordinates Gradients and Force Constants to Internals o oo a 111 g3 The Wie WIG e pand haere oo Re a ee ke ee A g 112 5 3 13 Initialization of Force Constant Matrices 112 5 3 14 Look at Results 2 2 4 4 452854452844 408 24S 113 54 Force Field Calculations soci 2 4 poenos gos ba Pee Po we ee T13 DAL Purposes e eperik e a eA eo ee eae 113 5 4 2 How to Perform a UFF Calculation ooo aaa 114 5 4 3 The UFF implementation sooo a 114 5 5 Molecular
140. 10 F Furche D Rappoport Density functional methods for excited states equi librium structure and electronic spectra In M Olivucci Ed Computational Photochemistry Band 16 of Computational and Theoretical Chemistry Kapi tel III Elsevier Amsterdam 2005 F Furche On the density matrix based approach to time dependent density functional theory J Chem Phys 114 14 5982 5992 2001 F Furche K Burke Time dependent density functional theory in quantum chemistry Annual Reports in Computational Chemistry 1 19 30 2005 D Rappoport F Furche Excited states and photochemistry In M A L Marques C A Ullrich F Nogueira A Rubio K Burke E K U Gross Eds Time Dependent Density Functional Theory Kapitel 22 Springer 2005 J E Bates F Furche Harnessing the meta generalized gradient approxi mation for time dependent density functional theory J Chem Phys 137 164105 2012 S Grimme F Furche R Ahlrichs An improved method for density functional calculations of the frecuency dependent optical rotation Chem Phys Lett 361 3 4 321 328 2002 H Weiss R Ahlrichs M Haser A direct algorithm for self consistent field linear response theory and application to Ceo Excitation energies oscillator 400 86 89 90 95 96 BIBLIOGRAPHY strengths and frequency dependent polarizabilities J Chem Phys 99 2 1262 1270 1993 D Rappoport F Furche
141. 14 25 10024 10035 1992 F Weigend M H ser RI MP2 first derivatives and global consistency Theor Chem Acc 97 1 4 331 340 1997 F Weigend M H ser H Patzelt R Ahlrichs RI MP2 Optimized auxiliary basis sets and demonstration of efficiency Chem Phys Letters 294 1 3 143 152 1998 393 394 BIBLIOGRAPHY 10 C Hattig F Weigend CC2 excitation energy calculations on large molecules using the resolution of the identity approximation J Chem Phys 113 13 5154 5161 2000 11 C Hattig K Hald Implementation of RI CC2 for triplet excitation energies with an application to trans azobenzene Phys Chem Chem Phys 4 11 2111 2118 2002 12 C Hattig A Kohn K Hald First order properties for triplet excited states in the approximated coupled cluster model CC2 using an explicitly spin coupled basis J Chem Phys 116 13 5401 5410 2002 13 C Hattig Geometry optimizations with the coupled cluster model CC2 using the resolution of the identity approximation J Chem Phys 118 17 7751 7761 2003 14 A Kohn C Hattig Analytic gradients for excited states in the coupled cluster model CC2 employing the resolution of the identity approximation J Chem Phys 119 10 5021 5036 2003 15 C Hattig A Hellweg A Kohn Distributed memory parallel implementation of energies and gradients for second order Mogller Plesset perturbation theory with the resolution
142. 2 EXCHANGE CORRELATION FUNCTIONALS AVAILABLE 125 e Lee Yang and Parr s correlation functional LYP 54 e The B LYP exchange correlation functional B88 exchange and LYP correla tion functionals 49 50 53 54 e The B VWN exchange correlation functional B88 exchange and VWN V correlation functionals 49 50 53 51 e The B P86 exchange correlation functional B88 exchange VWN V and Perdew s 1986 correlation functionals 49 50 53 51 55 e The Perdew Burke and Ernzerhof PBE exchange correlation functional 49 50 52 56 e The Tao Perdew Staroverov and Scuseria functional Slater Dirac TPSS exchange and Perdew Wang 1992 and TPSS correlation functionals 49 50 52 57 Additionally for all four modules dscf grad ridft and rdgrad following hybrid functionals are available a mixture of Hartree Fock exchange with DFT exchange correlation functionals e The BH LYP exchange correlation functional Becke s half and half exchange in a combination with the LYP correlation functional 49 50 53 54 58 e The B3 LYP exchange correlation functional Becke s three parameter functional with the form 0 85 0 72B88 0 2HF 0 19VWN V 0 81LY P 6 3 where HF denotes the Hartree Fock exchange 49 50 53 54 59 e The B3 LYP exchange correlation functional with VWN functional V in the paper This is the same functional form as available in the Gaussian program e The 1996 hybrid functional o
143. 2 How to Perform a SCF of DFT Calculation All you have to do for running mpshift is typing mpshift at the shell level 224 13 3 HOW TO PERFORM A MP2 CALCULATION 225 The results of a SCF or DFT calculation the trace of the total shielding tensors its anisotropy and the CPHF contribution for each symmetry distinct atom are written into the control file after the keyword nmr lt rhf dft gt shielding constants This data group is write only for mpshift but you can utilize it for graphical rendering of the calculated NMR spectra and for a quick overview of the results A more detailed output with the complete shielding tensors can be found in the output of mpshift so it is recommended to put the output in a file when calling the program 13 3 How to Perform a MP2 calculation To perform an MP2 calculation of the NMR shieldings you have to prepare the input with mp2prep c mpshift will then calculate both the SCF and MP2 shielding constants The result is written into the control file after the keyword nmr mp2 shielding constants The script mp2prep will create the keywords csmp2 thize 10000000E 10 mointunit type intermed unit 61 size 0 file halfint type 1112 unit 63 size 0 file moint 1 type 1122 unit 64 size 0 file moint j type 1212 unit 65 size 0 file moint k type 1212a unit 70 size 0 file moint a type gamma i unit 71 size 0 file gamma 1 type gamma 2 unit 72 size 0 file gamma 2 type dtdb 1 unit 76 size 0 file dtd
144. 2 energy calculations the evaluation of the D diagnostic for details see Sec 9 1 use instead mp2 didiag Note that the calculation of the D diagnostic increases the costs compared to a MP2 energy evaluation by about a factor of three Comments on the Output e Most important output for ricc2 rimp2 and mpgrad are of course MP2 HF energies written standard output and additionally to file energy and MP2 HF gradients written to file gradient 166 CHAPTER 8 2ND ORDER MOLLER PLESSET PERTURB THEORY e Incase of MP2 gradient calculations the modules also calculate the MP2 dipole moment from the MP2 density matrix note that in case of mpgrad frozen core orbital specification is ignored for gradient calculations and thus for MP2 dipole moments Further output contains indications of the suitability of the HF MP2 treatment e As discussed above reliable HF MP2 results are in line with small MP2 cor rections The size of the MP2 correction is characterised by the t amplitudes as evident from the above equations mpgrad by default plots the five largest t amplitudes as well as the five largest norms of t amplitudes for fixed i and j rimp2 does the same upon request if tplot is added to control file More or less than five t amplitudes will be plotted for tplot n where n denotes the number of largest amplitudes to be plotted It is up to the user to decide from these quantities whether the SCF MP2 treatment is suited f
145. 2 option see Chapter 12 for details about Numforce The usage of the Numforce interface for excited states is restricted to C1 symmetry Note using ricc2 in connection with jobex or Numforce requires that the method and the electronic state for which the gradient should be calculated and written to the interface files is specified in the option geoopt see Section 9 3 1 in data group ricc2 see Section 18 2 14 For calculations on excited states this state has in addition to be included in the input for excitation energies in datagroup excitations RI SCF reference wavefunctions The ricc2 program can be used in combina tion with conventional SCF or with the RI J and RI JK approximations for SCF with the exception that the calculation of gradients for reference wavefunctions which employ only the RI J approximation for the Coulomb matrix but 4 index integrals for the exchange matrix is presently not supported The implementation of gradi ents in ricc2 assumes that the reference wavefunction has either been calculated without RI J approximation using dscf or with the RI JK approximation using ridft 177 See Chapter 6 for a discussion of the RI approximations in SCF calculations and 18 2 5 for the required input In geometry optimizations with jobex and for the calculation of force constants and vibrational spectra with NumForce the ricc2 program is used in combination with the RI JK approximation for the Hatree Fock calculation u
146. 2 or RICC2 program modules the RI MP2 program directly prints the B2PLYP energy if this functional has been chosen before if you use the RICC2 program the scaled a 0 27 second order correlation energy must be added manually to the SCF energy in order to maintain consistency of the PT2 and GGA correlation parts it is recommend not to apply the frozen core approximation in the PT2 treatment 128 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS 6 3 Restricted Open Shell Hartree Fock 6 3 1 Brief Description The spin restricted open shell Hartree Fock method ROHF can always be chosen to systems where all unpaired spins are parallel The TURBOMOLE keywords for such a case one open shell triplet ez are open shells type 1 eg 1 1 roothaan 1 a 1 b 2 It can also treat more complicated open shell cases as indicated in the tables below In particular it is possible to calculate the xy Singlet case As a guide for expert users complete ROHF TURBOMOLE input for Og for various CSFs configuration state function is given in Section 19 6 Further examples are collected below The ROHF ansatz for the energy expectation value has a term for interactions of closed shells with closed shells indices k l a term for purely open shell interactions indices m n and a coupling term k m E 2 5 hkk S 2ni Kx k k l m n k m where f is the fractional occupation number of the open shell part 0 lt f lt 1 and a
147. 23 5 24009410923923 O 00000000000000 f 5 24009410923923 5 24009410923923 O 00000000000000 f O 00000000000000 5 24009410923923 5 24009410923923 f O 00000000000000 5 24009410923923 5 24009410923923 f repeated for C az216 F389 end 142 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS This is the standard TURBOMOLE syntax for atomic coordinates The actual dis tinction between QM cluster ECP shell and explicit point charges is made in the atoms section atoms f 1 6 23 basis f def TZVP ca 2 5 basis ca def TZVP ca 24 235 basis none ecp ca ecp 18 hay amp wadt f 236 605 basis none charge 1 00000000 In the example above the F atoms 1 and 6 23 as well Ca atoms 2 5 are defined as QM atoms with def TZVP basis sets The Ca atoms 24 235 are pure ECPs and have no basis functions basis none and F atoms 236 605 are explicit point charges with charge 1 with no basis functions and no ECP This step ends the input definition for the PEECM calculation Example 2 AlsO 2 cluster embedded in a Al203 0001 surface In this example a QM cluster with the composition AlgO 12 surrounded by 9 ECPs representing Al cations is embedded in a two dimensional periodic field of point charges 3 for Al and 2 for O corresponding to the 0001 surface of a Al203 As in the first example the program has to know that this is a two dimensional periodic system and this is specified by the keyword periodic 2 The dimensions of t
148. 337 statpt 24 39 80 99 101 103 118 120 steepest descent 104 STOP 100 stop 100 structure library 55 structure optimization 99 substitution 55 Sysname 30 388 389 sysname 27 30 t2x 27 230 Tblist 389 390 tblist 28 Tbtim 389 tbtim 28 temperature 358 time 117 353 timestep 353 tm2aomix 27 tm2molden 27 230 TmoleX 33 Tors 26 tors 27 transformation Laplace 171 TTEST 387 388 390 TURBOMOLE 11 13 15 18 25 30 33 34 36 40 42 46 49 51 54 65 66 68 76 77 99 102 104 109 118 128 138 142 145 158 159 165 178 216 218 221 230 265 283 421 286 287 291 296 300 301 342 354 362 365 TURBOMOLE installation 29 modules 23 quotation of 13 tools 25 Turbotest 31 twoint 35 44 UFF keywords 271 uff 23 53 102 103 113 114 271 272 uffgradient 114 uffhessian0 0 114 ufftopology 114 272 273 275 nxtn12 272 uhfuse 28 vector function 179 velocity 358 vibration 27 218 Vibrational Frequencies 218 wave function analysis keywords 344 x2t 28 34 51 xxx map 191
149. 356 coord 55 57 106 109 111 139 141 144 221 230 266 271 273 336 coordinateupdate 106 329 dqmax 329 interpolate 329 statistics 329 corrgrad 335 cosmo 298 302 allocate_nps 299 ampran 299 cavity 299 closed 299 open 299 disex 299 epsilon 299 nppa 299 nspa 299 phsran 299 refind 299 routf 299 rsolv 299 use_contcav 299 use_old_amat 299 cosmo_atoms 298 300 cosmo_isodens 301 cosmo_isorad 302 cosmo_out file 301 csconv 360 csconvatom 361 csmp2 225 360 current 354 409 410 curswitchdisengage 156 dcosmo_rs 303 potential file definition 303 denconv 37 152 161 162 164 172 175 176 205 212 275 309 315 dft 36 135 151 217 219 252 275 291 294 305 308 batchsize 279 functional 275 debug 276 dgrenze 279 diffuse 277 fgrenze 279 fullshell 279 functional 291 gridordering 280 gridsize 276 291 gridtype 276 nkk 276 nphi 276 ntheta 276 old_RbCs_xi 277 qgrenze 279 radsize 277 reference 278 rhostart 278 rhostop 278 sgrenze 279 symblock1 279 symblock2 279 test integ 279 weight derivatives 280 dkhorder 137 294 dkhorder 2 137 dkhparam 137 294 dkhparam 1 137 dkhparam 2 137 dkhparam 3 137 INDEX dkhparam 4 137 dkhparam 5 137 drvopt 84 220 304 305 basis on 110 drvtol 84 dsenex 293 ecp 152 266 egrad 106 110 328 335 337 electrostatic field 152 280 2
150. 462 000005796 773764610 496630311 296469569 104536049 779079437 004341011 323050499 045563698 868478537 733071804 664006472 864167213 056100845 381557465 004332162 837586403 115072958 292158127 427564979 8 064809799 0 061230399 m e e m O N A O N A ONAreoOoOQO OaBeOOQ QAOreOO QOrPRrereUUOAOOO 247499466 977437973 390023232 696748018 243290186 246870041 060600400 330662251 749288559 957922935 127140045 749288559 957920074 127141953 749289513 957910538 127161026 558811665 350177050 180959582 558811188 350180149 180958077 558810234 350189686 180938885 143 The above input defines a periodic perfect and infinite two dimensional lattice of point charges corresponding to the 0001 a Al O3 surface In order to use the lattice for PEECM calculation we have to make space for our QM cluster and the surrounding ECP shell This is done by specifying the part of the lattice that is virtually removed from the perfect periodic array of point charges to make space for the cluster The positions of the removed point charges are specified in the subsection cluster of the embed keyword Note that the position of the QM cluster must exactly correspond to the removed part of the crystal otherwise positions of the cluster atoms would overlap with positions of point charges in the periodic lattice 144 CHAPTER 6 HARTREE FOCK AN
151. 5 Use correct b region and slater b region for the beta spin 18 2 7 Keywords for Periodic Electrostatic Embedded Cluster Method The Periodic Electrostatic Embedded Cluster Method PEECM functionality pro vides electronic embedding of a finite quantum mechanical cluster in a periodic infinite array of point charges It is implemented within HF and DFT energy and gradient TURBOMOLE modules dscf grad ridft rdgrad and escf Unlike embed ding within a finite set of point charges the PEEC method always yields the correct electrostatic Madelung potential independent of the electrostatic moments of the point charges field It is also significantly faster than the traditional finite point charges embedding The basic PEECM settings are defined in the embed block It can be redirected to an external file using embed file lt file_name gt Following keywords are used for the PEECM calculation setup periodic Specifies the number of periodic directions Allowed values for number are 3 for a bulk three dimensional system 2 for a two dimensional surface slab and 1 for a one dimensional system Default value is 3 cell 18 2 FORMAT OF KEYWORDS AND COMMENTS 297 Unit cell parameters in a form of six real values a b c a 3 y where a b c are lengths of the appropriate cell vectors a is the angle between vectors b and c 8 is the angle between vectors a and c and y is the angle between vectors a and b Default are atom
152. 565114D 01 271180364D 01 754640511D 01 173603618D 01 140197496D 01 982719736D 00 464178589D 00 369336889D 00 359335506D 01 869599318D 01 379 380 CHAPTER 19 SAMPLE CONTROL FILES 6 49227239618 721211200D 01 2 55889114714 634201864D 01 1 p 1 05118767781 264152293D 01 1 p 437994865757 197670692D 01 4 d 34 705550 548703710D 01 10 704427 619019402D 02 3 568067 337450480D 01 1 249848 905232209D 01 1 d 0 445360 418680075D 01 1 f 1 1872146118 1 0000000 1 g 1 30000000 1 0000000 end 19 5 BASISSET OPTIMIZATION FOR NITROGEN 381 19 5 Basisset optimization for Nitrogen Main File control title Basisset optimization for nitrogen SV P operating system unix symmetry oh uncomment following line to clean the basis file after optimization dump basis set coord file coord user defined bonds file coord pople A0 basis file basis rundimensions dim fock dens 141 natoms 1 nshell1 6 nbf CA0 15 nbf A0Q 14 dim trafo SA0 lt gt AQ CAO 17 rhfshells 2 scfmo none file mos roothaan 1 a i1 b 2 scfiterlimit 60 scfconv 10 thize 0 10000000E 04 thime 5 scfdamp start 1 500 step 0 050 min 0 100 scfdump scfintunit unit 30 size 90 file twoint scfdiis start 0 5 scforbitalshift closedshell 4 drvopt cartesian off optimize basis gt basis on basis on global off hessian on dipole on nuclear polarizability 382 CHAPT
153. 6 1 52084856970468 18187168978374 h 1 75612466223131 00000000000000 18187168978374 h intdef definitions of internal coordinates 1 k 1 0000000000000 stre 4 1 val 1 90084 2 k 1 0000000000000 bend 4 3 1 val 106 27756 1 0000000000000 bend 3 2 1 1 0000000000000 bend 2 4 1 end 368 File basis basis n def SVP n 5 s 1712 8415853 257 64812677 58 458245853 16 198367905 5 0052600809 1 s 58731856571 1 s 18764592253 3 p 13 571470233 2 9257372874 79927750754 1 p 21954348034 1d 1 0000000000 h def SVP h 7s 3 s 13 010701000 1 9622572000 44453796000 1 a8 12194962000 1 p 80000000000 end File mos scfmo 7s4pid expanded 40072398852E 01 3s2p1d 53934125305E 02 40221581118E 01 17931144990 46376317823 44171422662 1 0000000000 1 0000000000 21807045028 51294466049 1 0000000000 1 0000000000 511 19682158000E 01 13796524000 47831935000 1 0000000000 1 0000000000 format 4d20 14 CHAPTER 19 511 31 1 SAMPLE CONTROL FILES 19 2 NH INPUT FOR A RHF CALCULATION 1 al eigenvalue 15633041862301D 02 nsaos 10 98699003163455D 00 47221435341751D 01 55873125006179D 02 26746008768233D 02 20823779196149D 03 14270460008808D 01 58676121352806D 03 29091871198884D 03 2 al eigenvalue 99896275238736D 00 nsaos 10 26412162337482D 00 51846472345
154. 6 294 gdiishistory 330 global 106 111 334 336 globgrad 106 111 335 grad 106 109 111 230 267 319 325 335 337 grad_send_dens 364 grid 97 343 hOhessian 103 hessian 84 106 112 113 305 306 334 hessian projected 84 336 hotfcht 308 incore 42 281 intdef 55 57 108 109 220 266 328 330 334 335 integral_ex 359 interconversion 104 330 maxiter 330 412 on 108 329 330 qconv 330 ironly 307 isopts 307 isosub 307 jbas 123 216 267 292 jkbas 123 162 176 216 292 ke_control 355 358 kramers 136 294 laplace 163 172 198 316 conv 316 last MP2 energy change 334 last SCF energy change 334 last excitation energy change 156 last step relax 266 1cg 162 175 176 205 206 321 les 103 219 307 all 307 lesiterlimit 308 lhf 256 295 localize 228 348 351 mo 349 sweeps 349 thrcont 349 lock off 265 loewdin 341 log 354 log_ history 355 358 m matrix 112 334 mao 342 mao selection 347 marij 123 293 extmax 293 lmaxmom 293 nbinmax 293 precision 293 thrmom 293 INDEX wsindex 293 maxcor 41 42 46 82 161 162 175 176 205 212 215 219 306 312 315 maximum norm of basis set gradient 337 cartesian gradient 337 internal gradient 337 md_action 358 359 md_status 354 357 mo output format 282 287 mo diagram 282 mointunit 161 164 225 313 360 moments 340 344 mop
155. 647 656 1970 P Pulay Convergence acceleration of iterative sequences the case of SCF iteration Chem Phys Lett 73 2 393 398 1980 M P Allen D J Tildesley Computer Simulation of Liquids Oxford Univer sity Press Oxford 1987 K Eichkorn O Treutler H Ohm M Haser R Ahlrichs Auxiliary basis sets to approximate Coulomb potentials erratum 1995 242 283 Chem Phys Lett 242 6 652 660 1995 J A Pople R K Nesbet Self consistent orbitals for radicals J Chem Phys 22 3 571 572 1954 J Cizek J Paldus Stability conditions for solutions of Hartree Fock equations for atomic and molecular systems application to pi electron model of cyclic plyenes J Chem Phys 47 10 3976 3985 1967 BIBLIOGRAPHY 397 48 F Neese F Wennmohs A Hansen U Becker Efficient approximate and 49 50 5l 52 53 54 55 56 57 58 59 60 parallel Hartree Fock and hybrid DFT calculations A chain of spheres algo rithm for the Hartree Fock exchange Chem Phys 356 98 109 2009 P A M Dirac Quantum mechanics of many electron systems Proc Royal Soc London A 123 792 714 733 1929 J C Slater A simplification of the Hartree Fock method Phys Rev 81 3 385 390 1951 S Vosko L Wilk M Nusair Accurate spin dependent electron liquid corre lation energies for local spin density calculations a critical analysis Ca
156. 6497297520000 85463057110000 36497297520000 92802041340000 02725683720000 02729288000000 92802581990000 02725323160000 92800239300000 02729288000000 92802581990000 02725323160000 92802041340000 02725683720000 92800239300000 25351019750000 24028611330000 38337475740000 38337475740000 24028611330000 24028611330000 38337475740000 y w w Pee e oOo 00 0 0 0 0 0 0 0 0 y p w m p w ww w pH PPP PPP PP PB 145 This is the standard TURBOMOLE syntax for atomic coordinates The actual distinc tion between QM cluster and ECP shell is made in the atoms section atoms al 1 8 basis al def SV P o 9 20 basis o def SV P al 21 29 basis none ecp al ecp 10 hay amp wadt In the example above the Al atoms 1 8 and O atoms 9 20 are defined as QM atoms with def SV P basis sets The Al atoms 21 29 are pure ECPs and have no basis functions basis none This step ends the input definition for the PEECM calculation 146 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS 6 7 Empirical Dispersion Correction for DFT Calcula tions Based on an idea that has earlier been proposed for Hartree Fock calculations 74 75 a general empirical dispersion correction has been proposed by Stefan Grimme for density functional calculations 76 A modified version of the approach with extension to more elements and more functionals has been published in ref 77 The most recent implementation 78 is less empirical i e the m
157. 65 19 2 NH Input for a RHF Calculation 2 265 p a 4 8 pepe ee es 366 19 3 NOg input for an unrestricted DFT calculation 370 19 4 TaCls Input for an RI DFT Calculation with ECPs 374 19 5 Basisset optimization for Nitrogen 4 381 19 6 ROHF of Two Open Shells 2 224 ge eee ee es 384 20 The Perl based Test Suite Structure 387 BOD General sa yey ak ea e pa RRS A Be hae ew Ea S 387 20 2 Ruining the tests sea saae eee eRe Ee a a 388 10 CONTENTS 20 3 Taking the timings and benchmarking 389 20 4 Modes and options of the TTEST script 390 Bibliography 393 Index 408 Chapter 1 Preface and General Information 1 1 Contributions and Acknowledgements TURBOMOLE 1 is a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH 1989 2007 TURBOMOLE GmbH since 2007 The following peo ple have made contributions Reinhart Ahlrichs Markus Klaus Armbruster Rafat A Bachorz Michael Bar Hans Peter Baron Riidiger Bauernschmitt Florian A Bischoff Stephan B cker Nathan Crawford Peter Deglmann Fabio Della Sala Michael Diedenhofen Michael Ehrig Karin Eichkorn Simon Elliott Daniel Friese Filipp Furche Andreas G168 Frank Haase Marco Haser Christof Hattig Arnim Hellweg Sebastian H fener Hans Horn Chris tian Huber Uwe Huniar Marco Kattannek Wim Klopper Andreas Kohn Christoph K6lmel Markus Kollwitz Klaus May Paola Nava Christ
158. 7 200 202 217 227 converged 100 coord 34 coordinates frozen 221 core memory 254 cos 197 319 COSMO keywords 298 cosmo 26 175 cosmoprep 26 300 counterpoise calculation 66 CP corrections 118 CPHF 224 css 197 319 debug 254 Define 165 216 define 23 28 34 37 39 49 51 53 58 61 66 70 72 74 76 79 85 88 90 93 94 96 97 101 102 108 109 111 118 119 123 136 152 155 162 167 168 170 176 192 205 213 220 227 233 253 255 265 266 268 286 290 292 309 315 330 365 degrees of freedom 57 dens 192 DIIS 104 329 dist 26 dos_atb 346 dos a b 346 dos_alpha 346 dos_beta 346 DRC 26 DsCF 417 keywords 275 Dscf 291 dscf 14 23 24 30 36 42 44 45 47 68 69 78 100 106 117 119 121 125 137 138 152 163 164 176 191 196 198 206 224 227 228 230 250 255 262 263 266 267 283 288 294 296 298 302 304 343 344 361 364 dummy center 55 edens 192 EGRAD keywords 311 egrad 14 25 37 39 42 100 106 147 148 151 152 156 157 191 221 227 228 230 311 335 343 344 eigenvalue difference 254 Eiger 232 348 eiger 26 energy 113 environment variable OMP_NUM_THREADS 40 PARA ARCH 40 PARNODES 40 ESCF keywords 308 escf 14 24 37 42 81 138 147 151 157 262 296 298 303 308 311 evalgrad 26 extended Hiickel calculation 68 FDE 26 Freeh 39 219 freeh 25 FROG keywords 353 frog 24 39
159. 768D 00 37623729061179D 00 47252329287316D 02 21494050853221D 02 11795673774658D 00 11229203933488D 01 27038186251429D 02 3 al eigenvalue 57101279949392D 00 nsaos 10 35584199011701D 01 96938258881594D 01 70254605702716D 01 44746149963029D 00 40094287741992D 03 51691151834284D 01 19189122068531D 02 56638497851180D 03 1 e eigenvalue 64374209294851D 00 nsaos 9 49313475446075D 00 33757893447603D 00 76142296567409D 04 26407572210452D 00 22619038902975D 00 50035170531670D 05 63021657663245D 04 end 48016374887169D 02 90849517503597D 02 77139882704089D 02 83316086019184D 01 65569041318341D 00 47722350097160D 01 74524664248740D 04 12199166245418D 03 369 370 CHAPTER 19 SAMPLE CONTROL FILES 19 3 NOz2 input for an unrestricted DFT calculation Main File control title NO2 c2v UKS SVP operating system unix symmetry c2v coord file coord intdef file coord atoms n 1 basis n def SVP o 2 3 basis o def SVP pople A0 basis file basis rundimensions dim fock dens 1098 natoms 3 nshell 18 nbf CAO 45 nbf AQ 42 dim trafo SA0 lt gt A0 CAO 85 rhfshells 2 uhfmo_alpha none file alpha uhfmo_beta none file beta none hamilton core guess will be made files alpha and beta will be generated by the program uhf alpha shells al 1 6 1 a2 1 1 bi 1 4 1 b2 I 1 beta shells al 1 5 1 a2 1 1 bi 1 4 CT b2 1 1 scfiterlimit 30
160. 786 1 31008893646566 3 07002878668872 1 68840815751978 1 31008893646566 3 07002878668872 1 68840815751978 4 12184425921830 2 06288409251899 O 00000000000000 end 5 5 Molecular Dynamics Calculations Ab initio molecular dynamics MD can be carried out on the ground and excited state Born Oppenheimer potential hypersurface In addition non adiabatic Tully type Surface Hopping MD can be performed using TDDFT At the start of an MD run the user must specify the initial atomic positions and velocities and give rrpyppypp yraoeda 5 5 MOLECULAR DYNAMICS CALCULATIONS 117 some general instructions for the run This is managed by running the interactive program Mdprep and generating the command file mdmaster If this is successful the MD run itself may be started jobex md Time is then advanced in steps The electronic potential energy and its gradients are calculated quantum mechanically at the required coordinates each timestep as detailed above e g dscf and grad The MD program frog uses the Leapfrog Verlet algorithm 44 to turn the gradients into new atomic positions and velocities The atoms thus undergo classical Newtonian dynamics on the ab initio potential hypersurface Trajectory information is recorded in a log file mdlog It is possible to instruct frog to heat or cool the system use a thermostat for canonical dynamics conserve total energy or read in new positions or velocities the appropriate keywords are described in S
161. 81 embed 139 140 142 143 296 298 cell 298 charges 298 cluster 298 content 298 epsilon 298 lmaxmom 298 periodic 298 potval 298 wsicl 298 end 55 201 267 energy 136 156 267 319 325 escfiterlimit 155 311 esp fit 349 ex_energies 359 excitation 190 excitations 175 176 182 184 188 194 195 213 322 326 bothsides 322 conv 322 exprop 188 322 irrep 322 leftopt 322 preopt 322 spectrum 194 322 thrdiis 322 tmexc 195 322 xgrad 322 exopt 156 157 311 INDEX fermi 83 280 hicrt 280 nue 280 stop 280 tmend 280 tmfac 280 tmstrt 280 firstorder 281 fldopt 152 280 281 1st derivative 281 2nd derivative 281 edelt 281 fields 281 geofield 281 forceapprox 108 112 267 329 333 335 336 format 336 forceconv 306 308 forceinit 53 333 336 diag 333 carthess 334 default 334 individual 334 off 109 333 on 53 109 112 329 333 336 carthess 53 113 336 diag 112 forceiterlimit 306 308 forcestatic 336 forceupdate 109 330 336 ahlrichs 331 indgeo 331 maxgeo 331 numgeo 331 allow 333 bfgs 331 damping 333 dfp 330 411 dfp bfgs 331 diagonal 332 ms 330 offdamp 332 offreset 332 pulay 331 337 fail 332 maxpul 332 minpul 332 modus 332 numpul 332 reseig 333 scale 333 schlegel 331 thrbig 333 threig 333 freeze 152 161 162 164 172 175 176 205 215 312 314 315 gap threshold 360 gdiis 13
162. 878668872 1 68840815751978 4 12184425921830 2 06288409251899 O 00000000000000 end 5 3 7 Optimization of Basis Sets SCF only For this task you have to specify optimize basis on internal off This example would perform only a basis set optimization without accompanying geometry optimization It is possible of course to optimize both simultaneously Just leave out the last line of the example internal off Input data groups are egrad Basis set exponents contraction coefficients scaling factors and their respective gradients as provided and accumulated in subsequent opti mization cycles by one of the programs grad or mpgrad if drvopt basis on has been set basis Description of basis sets used see Section 4 2 Output will be the updated basis on basis and the updated force constant matrix on forceapprox For an example see Section 19 5 5 3 8 Simultaneous Optimization of Basis Set and Structure The optimization of geometry and basis set may be performed simultaneously and requires the specification of optimize internal on or cartesian on basis on and needs as input data groups grad and egrad Output will be on coord basis also on forceapprox updated rrppppoa 5 3 PROGRAM RELAX 111 5 3 9 Optimization of Structure and a Global Scaling Factor Optimization of a global scaling factor is usually not performed in geometry opti mizations It is a special feature for special applicat
163. 9 RI CC2 For calculations with the ricc2 program it is recommended to use the cc2 submenu of the define program to set the data groups denconv freeze cbas maxcor MP2 F12 calculations require in addition the data groups rir12 cabs jkbas and lcg The exponent of the Slater function in the interelectronic distance r12 which appears in the geminals used MP2 F12 is defined in the data group 1cg and should be adapted to the one electron basis set which is used Note that the implementation of non abelian point groups in ricc2 is limited to the electronic ground state but comprises all of the RI MP2 functionality included in ricc2 In the present version ricc2 can for excited states only deal with real abelian point groups C1 Cs C2 Ci Con Cov D2 Don The F12 correction can only be calculated in the C point group How To Perform a Calculation Single point calculations Call the ricc2 program after a converged SCF calculation which can be carried either with the dscf or the ridft program Geometry optimizations and molecular dynamics Invoke jobex with the level CC2 option see Section 5 1 for addi tional options and parameters of the jobex script that might be needed or useful for geometry optimizations and ab initio molecular dynamics calculations Force constants and vibrational frequencies Force constants can be calculated by numerical differentiation of the gradients Invoke for this NumForce with the level CC
164. A TRIPLET EXCITATIONS TDHF OR TDDFT cist off TDA TRIPLET EXCITATIONS CI SINGLES l l l l polly off STATIC POLARIZABILITY l l l dynpol off DYNAMIC POLARIZABILITY single off SINGLET STABILITY ANALYSIS triple off TRIPLET STABILITY ANALYSIS nonrel off NON REAL STABILITY ANALYSIS ENTER lt OPTION gt TO SWITCH ON OFF OPTION OR q TO QUIT 82 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE If you have selected an option e g rpas and quit this menu you will get another menu SELECT IRREP AND NUMBER OF STATES ENTER FOR HELP OR Q TO QUIT amp TO GO BACK This should be self evident MP2 and RI MP2 We recommend to use MP2 together with the RI technique program rimp2 or ricc2 This is more efficient and supports the frozen core option in the gradient calculation The entry mp2 leads to a submenu which allows to set some keywords for MP2 and RI MP2 calculations e g defining frozen orbitals maximum memory usage or assign auxiliary basis sets for RI MP2 calculations etc If you want to use ricc2 you have to use the entry cc2 and the submenu ricc2 in order to assign MP2 as wavefunction model It covers all keywords required for rimp2 calculations Mandatory for rimp2 runs is the specification of the auxiliary basis set using the menu entry cbas Alternatively the rimp2prep tool can be used to set the keywords needed for rimp2 calculations Conventional MP2 calculations with mpgrad require
165. AX GRAD ELEMENT rmsd 5 000000E 04 rmsd threshold for RMS OF DISPL rmsg 5 000000E 04 rmsg threshold for RMS OF GRAD 4 4 THE GENERAL OPTIONS MENU 81 defl set default values OPTIMIZATION refers to int off int INTERNAL coordinates rdn off rdn REDUNDANT INTERNAL coordinates crt on crt CARTESIAN coordinates NOTE options int and crt exclude each other ENTER STATPT OPTIONS TO BE MODIFIED itvc 0 itve change INDEX OF TRANSITION VECTOR updte bfgs updte change method of HESSIAN UPDATE hsfrq 0 hsfrq frequency of HESSIAN CALCULATION kptm 0 kptm FREEZING transition vector INDEX hdiag 5 000000E 01 hdiag change DIAGONAL HESSIAN ELEMENTS rmax 3 000000E 01 rmax change MAX TRUST RADIUS rmin 1 000000E 04 rmin change MIN TRUST RADIUS trad 3 000000E 01 trad change TRUST RADIUS Just lt ENTER gt q or terminate this menu Excited states frequency dependent properties and stability analysis Excited state calculations with RPA or CIS based on HF SCF and TDDFT pro cedures as well as stability analyses SCF or DFT are carried out by the program escf You will need a well converged HF SCF or DFT calculation that were converged to at least scfconv 7 see Section 4 4 2 Details of calculations are specified with the command ex MAIN MENU FOR RESPONSE CALCULATIONS OPTION STATUS DESCRIPTION rpas off RPA SINGLET EXCITATIONS TDHF OR TDDFT ciss off TDA SINGLET EXCITATIONS CI SINGLES rpat off RP
166. CC2 second order properties can similar as the first order properties calculated in orbital unrelaxed or orbital relaxed approach as deriva tives of the of the Lagrange functions in Eqs 9 12 and 9 15 As for MP2 the orbital relaxed calculations are restricted to the static limit Frequency dependent second order properties as e g dipole polarizabilities can be computed with the orbital unrelaxed approach Note that second order properties are currently not yet available in the MPI parallel version or for spin component scaled variants of MP2 and CC2 Furthermore non abelian point groups are not implemented for second order properties In addition to the standard input second order properties require that the data group for the numerical Laplace transformation Laplace and that the sops option in the data group response is set Frequency dependent dipole polarizabilities with the CC2 model are obtained with the input ricc2 cc2 laplace conv 4 response sop operators diplen diplen freq 0 077d0 The frequency has to be given in atomic units Static orbital relaxed polarizabilities are obtained with response sop operators diplen diplen relaxed 9 6 Parallel RI MP2 and RI CC2 Calculations The ricc2 program is partially parallized for distributed memory architectures e g clusters of Linux boxes based on the message passing interface MPI standard In the present version parallel calculations can be carried out for g
167. COMMAND WHICH STARTS WITH THE 3 LETTERS dis IS A DISPLAY COMMAND AVAILABLE DISPLAY COMMANDS ARE disc lt range gt DISPLAY CARTESIAN COORDINATES dist lt real gt DISPLAY DISTANCE LIST disb lt range gt DISPLAY BONDING INFORMATION disa lt range gt DISPLAY BOND ANGLE INFORMATION disi lt range gt DISPLAY VALUES OF INTERNAL COORDINATES disg lt range gt GRAPHICAL DISPLAY OF MOL GEOMETRY lt range gt IS A SET OF ATOMS REFERENCED lt real gt IS AN OPTIONAL DISTANCE THRESHOLD DEFAULT 5 0 AS AN EXAMPLE CONSIDER disc 1 3 6 10 11 WHICH DISPLAYS THE CARTESIAN COORDINATES OF ATOMS 1 3 4 5 6 10 and 11 HIT gt return lt TO CONTINUE OR ENTER ANY DISPLAY COMMAND Of course you may enter each of these display commands directly without entering the general command dis before The option disg needs special adaption to the computational environment however and will normally not be available 4 0 4 Specifying Atomic Sets For many commands in define you will have to specify a set of atoms on which that command shall act There are three ways to do that e You may enter all or none the meaning of which should be clear entering none makes not much sense in most cases however e You may specify a list of atomic indices like 1 or 3 5 6 or 2 4 6 7 8 10 or similar e You may also enter atomic identifiers which means strings of at most eight characters the first two contain the element symbol and the remaining six could be u
168. CONTROL FILE D D on sd plt For mpgrad rimp2 calculations one gets in the RHF case the total density D SCF MP2 on td plt and the MP2 contribution on mp2d plt and in the UHF case one obtains the total density D SCF M P2 D SCF MP2 on td plt the spin density D SCF M P2 D SCF MP2 on td plt and the respective MP2 contributions on files mp2d plt and mp2sd plt For egrad it is similar just replace in the filenames mp2 by e Integration of density if absolute value greater than eps within a sphere origin x y z radius r is performed for pointval integrate z y zr eps By default the origin is at 0 0 0 the radius is chosen large enough to include the whole 3D box and all contributions are regarded eps 0 Data different from total and spin densities are generated by following com binable settings to be written in the same line as statement pointval pot leads to calculation of electrostatic potential arising from electron den sities nuclei and if present constant electric fields and point charges The densities used for calculation of potentials are the same as above the respective filenames are generated from those of densities by replace ment of the d for density by a p for potential By pot eonly only the electronic contribution to the electrostatic potential is calcu lated fld calculation of electric field Note that for 3D default output format plt
169. D COMMENTS 341 molap print molecular orbital contributions to overlap populations netto print atomic netto populations irpspd print contributions of irreducible representations to atomic s p d populations irpmol print contributions of irreducible representations to overlap pop ulations or loewdin to perform a L wdin population analysis options are invalid here A L wdin population analysis is based on decomposing VSDVsS instead of DS in case of a Mulliken PA or paboon momao maodump maofile mao all to perform a population analysis based on occupation numbers the options are not necessary and produce some output data concerning the modified atomic orbitals momao print MO contributions to occupation numbers of modified atomic orbitals MAOs maodump print all MAOs on standard output maofile mao all print all MAOs to file mao This kind of population analysis basically aims at so called shared electron numbers SEN between two or more atoms By default 2 3 and 4 center contributions to the total density are plotted if they are larger than 0 01 electrons Thresholds may be individually chosen as well as the possibility to compute SENs for molecular orbitals shared electron numbers orbitals 2 center threshold real 3 center threshold real 4 center threshold real Results of this kind of PA depend on the choice of MAOs By default all MAOs with eigenvalues of the atomic densi
170. D DFT CALCULATIONS resulting in a nuclear fusion cluster ang Al 0 000012482 5 547518253 9 977437973 Al 2 402141094 6 934402943 8 064809799 Al 2 402144432 4 160642624 10 247499466 Al 4 804287434 5 547518253 9 977437973 Al 2 402250767 6 934336185 11 246870041 Al 0 000005568 8 321288109 10 247499466 Al 2 402137518 9 708164215 9 977437973 Al 4 804294586 8 321288109 10 247499466 0 0 907584429 4 156304836 8 957920074 0 1 517618299 5 483696461 11 127141953 0 0 703624666 6 893717766 11 127161026 0 3 145677090 5 457115650 8 957922935 0 3 990177393 4 265182018 11 127140045 0 0 751026928 7 029124260 8 957910538 0 4 100675106 6 893717766 11 127161026 0 0 743527174 9 617761612 8 957922935 0 1 588027477 8 425827980 11 127140045 0 3 309734344 8 316950798 8 957920074 0 3 919768333 9 644342422 11 127141953 0 5 555326939 7 029124260 8 957910538 Al 4 804400921 11 094982147 11 246870041 Al 0 000008912 2 773757219 8 064809799 Al 2 402049065 6 934336185 11 246870041 Al 4 804400921 2 773690462 11 246870041 Al 2 402136564 4 160642624 7 611351967 Al 0 000013520 8 321288109 7 611351967 Al 0 000008912 11 095048904 8 064809799 Al 7 206440926 6 934402943 8 064809799 Al 4 804286480 8 321288109 7 611351967 end The positions of point charges are specified in as Cartesian coordinates Finally you have to specify the coordinates of the QM cluster along with the sur rounding ECPs This is done in the usual way using the coo
171. EFINE The handling of these options is very simple With the exception of tol all are logical switches which are either true or on active or false or off inactive You can switch between the two states if you enter for example crt to switch calculation of Cartesian first derivatives on or crt to switch it off The options crt sec and bas should provide no problems glb refers to a global scaling factor for all basis set exponents Imagine that you would like to replace your basis set which contains basis functions Xp x 20 y yo z 20 exp n 7 70 by another basis set which contains basis functions Xu x xo y yo z 20 exp any r 70 where a is the same for all primitive basis functions y With command glb you are able to calculate analytical derivatives of the total energy with respect to a and can thus easily determine the optimum a dip enables you to calculate the first derivatives of the electric dipole moment with respect to nuclear displacements which gives you infrared intensities pol allows you to calculate the contribution of the nuclear rearrangement on the electric polariz ability fa finally performs only a frequency analysis which means that aoforce will read the force constant matrix hessian or hessian projected diagonalize it and give you the frequencies and normal modes tol is not a logical switch as the other options in this menu but a
172. ER 19 interconversion off qconv 1 d 7 maxiter 25 optimize internal off cartesian off global off optimize basis gt basis on logarithm basis on logarithm coordinateupdate dqmax 0 3 interpolate on statistics 5 forceupdate SAMPLE CONTROL FILES ahlrichs numgeo 0 mingeo 3 maxgeo 4 modus lt g dq gt dynamic fail 0 6 threig 0 005 forceinit on reseig 0 005 thrbig 3 0 diag default energy file energy grad file gradient optimize basis gt egrad file egradient egrad file egradient forceapprox file forceapprox lock off atoms n 1 basis n def SV P closed shells scale 1 00 damping 0 0 alg 1 2 2 open shells type 1 tlu 1 1 end File coord coord O 00000000000000 O 00000000000000 O 00000000000000 n user defined bonds end File basis 19 5 BASISSET OPTIMIZATION FOR NITROGEN 383 n def SV P n 7s4pid 3s2p1d 511 31 1 use expopt to optimize exponents and contopt to optimize contractions 5 s expopt contopt 1712 8415853 0 53934125305E 02 257 64812677 0 40221581118E 01 58 458245853 0 17931144990 16 198367905 0 46376317823 5 0052600809 0 44171422662 1 s expopt 0 58731856571 1 0000000000 1 s expopt 0 18764592253 1 0000000000 3 p expopt contopt 13 571470233 0 40072398852E 01 2 9257372874 0 21807045028 0 79927750754 0 51294466049 1 p expopt 0 21954348034 1 0000000000 1 d 1 0000000000 1 0000000000 File mos scfmo scfcon
173. ESE OPTIONS ARE MUTUALLY EXCLUSIVE lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU Option off will be used if you have already a good Hessian from a previous calcu lation which may be used cart describes an even better state where you have a Hessian from a calculation of the second derivatives available aoforce The other two options describe real procedures for initialization of the Hessian Default values stretches 0 5 angles 0 2 4 4 4 Definition of External Electrostatic Fields This submenu allows you to calculate first and second numerical derivatives of the energy with respect to an external electric field The first three options should be clear 1st and 2nd are logical switches which are turned on and off the usual way 1st or 1st and delta is the increment for the numerical differentiation that is 90 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE the finite value of the external field which replaces the ideally differential field option status description 1st F numerical 1st derivative dE dField 2nd F numerical 2nd derivative d2E dField2 delta lt real gt increment for numerical differentiation DEFAULT 5000E 02 geofield F geometry optimization with external field man F explicit definition of electrostatic field s geofield gives the possibility to perform a whole geometry optimization under the influence of a finite external field and thus to obtain the distorted minimum
174. F Valeev R12 methods in explicitly correlated molecular electronic structure theory Int Rev Phys Chem 25 3 427 468 2006 C Hattig A Kohn Transition moments and excited state first order proper ties in the second order coupled cluster model CC2 using the resolution of the identity approximation J Chem Phys 117 15 6939 6951 2002 T Helgaker P J rgensen J Olsen Molecular Electronic Structure Theory Wiley New York 2000 O Christiansen P J rgensen C Hattig Response functions from Fourier component variational perturbation theory applied to a time averaged quasienergy Int J Quantum Chem 68 1 1 52 1998 C H ttig P J rgensen Derivation of coupled cluster excited states response functions and multiphoton transition moments between two excited states as derivatives of variational functionals J Chem Phys 109 21 9219 9236 1998 C H ttig O Christiansen P J rgensen Multiphoton transition moments and absorption cross section in coupled cluster response theory employing variational transition moment functionals J Chem Phys 108 20 8331 8354 1998 C H ttig Adv Quant Chem 50 37 60 2005 S Grimme E Ugorodina Calculation of 0 0 excitation energies of organic molecules by CIS D quantum chemical methods Chem Phys 305 223 230 2004 Y M Rhee M Head Gordon Scaled second order perturbation corrections to configuration interaction singles Efficie
175. Fock matrix to allow for level shifting etc See scfdiis below restart dscf twoint Try a dscf restart The program will read the data group restartd which must exist also scfmo has to exist and continue the calculation at the point where it ended before If the additional option twoint is appended the program will read the two electron integrals from the files specified in scfintunit so there will be almost no loss of cpu time All this information is normally provided by the previous dscf run if the keyword scfdump see there was given 284 CHAPTER 18 KEYWORDS IN THE CONTROL FILE restartd data Data provided by a previous dscf run that has been interrupted This keyword is created when scfdump was given rundimensions data is set by define so usually no changes are necessary The dimensions must be greater or equal to those actually required i e you can delete basis functions and keep rundimensions This keyword is not necessary for small cases Example dim fock dens 6072 natoms 6 nshel1 34 nbf CAO 108 nbf A0 98 dim trafo SA0 lt gt A0 CAO 256 rhfshells 1 scfconv integer SCF convergency criterion will be 10 for the energy Gradients will only be evaluated if integer gt 6 scfdamp start lt 500 gt step lt 050 gt min lt 100 gt Damping parameters for SCF iterations in order to reduce oscillations The old Fock operator is added to the current one with weight 0 5 as start i
176. HF or RHF wavefunctions may be used The two component formalism does not support the point group symmetries start wave functions may be transformed to Cl symmetry by define or the script uhfuse For spin orbit treatments two component ECPs suffix 2c are required the use of extended basis sets accounting for the spatial splitting of inner p shells also suffix 2c is recommended see 66 ECPs and basis sets def2 XVP 2c X S TZ QZ are available for Ag I Au At they can be selected within the define session RI J and RI JK auxiliary basis sets of def2 type are of sufficient flexibility for two component treatments they are the same with and without suffix 2c The two component formalism may be most easily prepared and applied in the following way e run define choose Cl symmetry select ECPs and basis sets with suffices 2c for the respective elements The corrresponding auxiliary basis sets are provided automatically e insert soghf in the control file as well as further desired keywords e For open shell molecules it is often helpful to increase the value for scforbital shift closedshell a value of ca 1 0 may serve as a rough recommendation e start the two component calculation with ridft e At the end of the SCF procedure real and imaginary parts of spinors are written to files spinor r and spinor i eigenvalues and spinor occupations are collected in the file EIGS the total energy is added to dat
177. HF UCCSD Note that if a frozen core approximation is used the semicanonical orbitals de pend on whether the block diagonalization of the Fock matrices is done in space of all orbitals or only in the space of the correlated valence orbitals The two ap proaches lead thus to slightly different energies but none of two is more valid or more accurate than the other The ricc2 program uses the former scheme with the block diagonalization done in the space of all molecular orbitals The same scheme is used e g in the CFOUR program suite but other codes as e g the implementation in MOLPRO use a block diagonalization restricted to the active valence space Perturbative triples corrections To achieve ground state energies a high ac curacy which systematically surpasses the acccuracy MP2 and DFT calculations for reaction and binding energies the CCSD model should be combined with a perturba tive correction for connected triples The recommended approach for the correction 210 CHAPTER 10 CCSD CCSD F12 AND CCSD T is the CCSD T model Eccsp r Eccsp EO Eo 10 18 which includes the following two terms 4 2 BS 0229 uel let 7 HE 10 19 H2 5 2 EDD a Ea 10 20 H where the approximate triples amplitudes evaluated as 2 shell T2 HF wee ate 10 21 Ea Ei b Ej c k In the literature one also finds sometimes the approximate triples model CCSD T also denoted as CCSD T CCSD w
178. I MP2 with O N scal ing costs The ricc2 module contains since release 6 1 a first implementation of SOS MP2 which exploits the RI approximation and a Laplace transformation of the orbital energy denominators 1 Ea b Ei j fore nr g Raheem gy ay Wee Kate a ei ta 8 8 0 a 1 to achieve an implementation with O N scaling costs opposed to the conven tional O N scaling implementation In particular for large molecules the Laplace transformed implementation can reduce a lot the computational costs of SOS MP2 calculations without loss in accuracy The Laplace transformed implementation for SOS MP2 calculations is activated with the input laplace conv 5 where the parameter conv is a convergence threshold for the numerical integration in 172 CHAPTER 8 2ND ORDER MOLLER PLESSET PERTURB THEORY Eq 8 8 A value of conv 5 means that the numerical integration will be converged to a root mean squared error of 107 a u Whether the conventional or the Laplace transformed implementation will be more efficient depends firstly on the system size the number of occupied orbitals and secondly on the required accuracy the number of grid points for the numerical integration in Eq 8 8 and can be understood and estimated from the following considerations e The computational costs for the most expensive step in canonical RI MP2 energy calculations for large molecules requires 50 V Nz floating poin
179. IC COORDINATES INTERACTIVELY a lt file gt ADD ATOMIC COORDINATES FROM FILE lt file gt aa lt file gt ADD ATOMIC COORDINATES IN ANGSTROEM UNITS FROM FILE lt file gt sub SUBSTITUTE AN ATOM BY A GROUP OF ATOMS i INTERNAL COORDINATE MENU ired REDUNDANT INTERNAL COORDINATES red_info DISPLAY REDUNDANT INTERNAL COORDINATES ff UFF FORCEFIELD CALCULATION m MANIPULATE GEOMETRY frag DEFINE FRAGMENTS FOR BSSE CALCULATION w lt file gt WRITE MOLECULAR COORDINATES TO FILE lt file gt r lt file gt RELOAD ATOMIC AND INTERNAL COORDINATES FROM FILE lt file gt name CHANGE ATOMIC IDENTIFIERS del DELETE ATOMS dis DISPLAY MOLECULAR GEOMETRY banal CARRY OUT BOND ANALYSIS TERMINATE MOLECULAR GEOMETRY SPECIFICATION AND WRITE GEOMETRY DATA TO CONTROL FILE IF YOU APPEND A QUESTION MARK TO ANY COMMAND AN EXPLANATION OF THAT COMMAND MAY BE GIVEN This menu allows you to build your molecule by defining the Cartesian coordinates interactively ai or by reading the coordinates from an external file a aa The 4 1 THE GEOMETRY MAIN MENU 53 structure can be manipulated by the commands sub m name and del The com mand sy allows you to define the molecular symmetry while desy tries to determine automatically the symmetry group of a given molecule There exists a structure library which contains the Cartesian coordinates of selected molecules e g CH4 These data can be obtained by typing for example a
180. ING YOUR INPUT FILE WITH DEFINE read coord determine symmetry quit main geometry menu 4 1 1 Description of commands Main Geometry Menu In the headline of this menu you can see the current number of atoms and molecular symmetry we use an input for PH as example The commands in this menu will now be described briefly Sy desy susy ai Definition of the Sch nflies symbol of the molecular point group sym metry If you enter only sy define will ask you to enter the symbol but you may also directly enter sy c3v define will symmetrize the geometry according to the new Sch nflies symbol and will create new nuclei if necessary You therefore have to take care that you enter the correct symbol and that your molecule is properly oriented All TURBOMOLE programs require the molecule to be in a standard orien tation depending on its point group For the groups Cn Cnv Cnh Dn Dna and Dna the z axis has to be the main rotational axis secondary twofold rotational axis is always the x axis oy is always the xz plane and cp the xy plane Op is oriented as D4 For Ty the threefold rota tional axis points in direction 1 1 1 and the z axis is one of the twofold axes bisecting one vertex of the tetrahedron desy allows you to determine the molecular symmetry automatically The geometry does not need to be perfectly symmetric for this command to work If there are small deviations from some point group symmetry as they occur in
181. INTERNAL COORDINATES iman lt a gt MANIPULATE GEOMETRY BY CHANGING INTERNAL COORDINATE VALUES imanat lt i gt AS iman BUT STARTING AT INTERNAL COORD NUMBER i ic lt i gt lt x gt CHANGE STATUS OF INTERNAL COORDINATE lt i gt TO lt x gt e g ic 5 d TO MAKE 5TH COORD display OR ic k d irem lt i gt REMOVE INTERNAL COORDINATE lt i gt e g irem d TO REMOVE ALL display COORDS dis ANY DISPLAY COMMAND e g disi OR disc disiat lt i gt AS disi BUT STARTING AT INTERNAL COORD NUMBER i WHERE lt a gt OPTIONAL ATOMIC SET DEFAULT all lt i gt INDEX LIST OF INTERNAL COORDINATE S LIKE 3 6 8 OR lt i gt lt x gt lt x gt STATUS OF INTERNAL COORDINATE k f d OR i ADDING A QUESTION MARK TO ANY COMMAND MAY PROVIDE EXPLANATIONS ENTER COMMAND OR HIT gt return lt TO GET BACK TO GEOMETRY MAIN MENU The parameters in the headline of this menu have the following meanings ideg is the total number of symmetry restricted degrees of freedom k is the number of active internal coordinates specified up to now Only these coordinates are optimized during a geometry optimization f is the number of fixed internal coordinates specified These coordinates will be included in the B matrix see command imet but their values will not be changed during geometry optimization 58 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE d is the number of internal coordinates whose values will only be displayed e g by command dis
182. In order to avoid the generation of points in the problematic intersections all remaining points which are not in the interior of another sphere are projected downwards onto the radius R In the next step a segment grid of NSPH segments per H atom and NSPA segments for the other atoms is projected onto the surface defined by R The basis grid points are associated to the nearest segment grid centers and the segment coordinates are re defined as the center of area of their associated basis grid points while the segment area is the sum of the basis grid areas Segments without basis grid points are discarded In order to ensure nearest neighbor association for the new centers this procedure is repeated once At the end of the cavity construction the intersection seams of the spheres are paved with individual segments which do not hold associated basis grid points Density based Cavity Construction Instead of using atom specific radii the cavity can be defined by the electron density In such an isodensity cavity con struction one can use the same density value for all atoms types or the so called scaled isodensity values In the later approach different densities are used for the different atom types The algorithm implemented in TURBOMOLE uses a marching 261 tetrahedron algorithm for the density based cavity construction In order to assure a smooth density change in the intersection seams of atoms with different isodensity specification thi
183. J Frisch B Mennucci J Tomasi R Cammi V Barone Geometries and properties of excited states in the gas phase and in solution Theory and application of a time dependent density functional theory polar izable continuum model J Chem Phys 124 9 094107 2006 S Sinnecker A Rajendran A Klamt M Diedenhofen F Neese Calcula tion of solvent shifts on electronic g tensors with the Conductor like Screening Model COSMO and its self consistent generalization to real solvents Direct COSMO RS J Phys Chem A 110 2235 2245 2006 F Eckert A Klamt Fast solvent screening via quantum chemistry COSMO RS approach AICHE Journal 48 369 385 2002 A Klamt V Jonas T B rger J C W Lohrenz Refinement and parametrization of COSMO RS J Phys Chem A 102 5074 5085 1998 O Treutler R Ahlrichs Efficient molecular numerical integration schemes J Chem Phys 102 1 346 354 1995 A D Becke A multicenter numerical integration scheme for polyatomic molecules J Chem Phys 88 4 2547 2553 1988 408 182 183 184 185 186 187 BIBLIOGRAPHY R Send F Furche First order nonadiabatic couplings from time dependent hybrid density functional response theory Consistent formalism implemen tation and performance J Phys Chem 132 044107 2010 J C Tully Molecular dynamics with electronic transitions J Chem Phys 93 1061 1990 E Tapavicza I Ta
184. MAT OF KEYWORDS AND COMMENTS freeze implicit core 5 virt 2 313 This will freeze the 5 lowest occupied and 2 highest virtual orbitals alpha and beta count as one in UHF cases Note that degenerate orbitals count twice e representations thrice t representations etc In case of mpgrad frozen orbitals have to be specified manually for rimp2 the preparation tool rimp2prep may be used to specify frozen core orbitals frozen virtuals have to be specified manually Note In case of gradient calculations frozen core orbitals are regarded only by rimp2 but not by mpgrad moreover freezing of virtual orbitals is generally not supported by mpgrad MPGRAD Essential Keywords All essential data groups for mpgrad may be generated by the preparation tool mp2prep apart from maxcor see above these are the following traloop n specifies the number of loops or passes over occupied orbitals n performed in the mpgrad run the more passes the smaller file space requirements but CPU time will go up mointunit type intermed unit 61 type 1111 type 1112 type 1122 type 1212 type 1212a type gamma 1 type gamma 2 type 1212u type 1112u unit 62 unit 63 unit 64 unit 65 unit 70 unit 71 unit 72 unit 73 unit 74 type gamma iu unit 75 size 0 size 0 size 0 size 0 size 0 size 0 size 0 size 0 size 0 size 0 size 0 The data group mointunit specifies e which scratch files are needed e
185. MENU 63 main menus You will enter this menu if all necessary data cannot be read from your input file or if you do not use an input file This menu deals with the specification of basis sets and other data related to the atom type ATOMIC ATTRIBUTE DEFINITION MENU atoms 5 bas 5 ecp 0 b ASSIGN ATOMIC BASIS SETS bb b RESTRICTED TO BASIS SET LIBRARY bl LIST ATOMIC BASIS SETS ASSIGNED bm MODIFY DEFINITION OF ATOMIC BASIS SET bp SWITCH BETWEEN 5d 7f AND 6d 10f lib SELECT BASIS SET LIBRARY ecp ASSIGN EFFECTIVE CORE POTENTIALS ecpb ecp RESTRICTED TO BASIS SET LIBRARY ecpi GENERAL INFORMATION ABOUT EFFECTIVE CORE POTENTIALS ecpl LIST EFFECTIVE CORE POTENTIALS ASSIGNED ecprm REMOVE EFFECTIVE CORE POTENTIAL S Cc ASSIGN NUCLEAR CHARGES IF DIFFERENT FROM DEFAULTS cem ASSIGN NUCLEAR CHARGES FOR EMBEDDING m ASSIGN ATOMIC MASSES IF DIFFERENT FROM DEFAULTS dis DISPLAY MOLECULAR GEOMETRY dat DISPLAY ATOMIC ATTRIBUTES YET ESTABLISHED h EXPLANATION OF ATTRIBUTE DEFINITION SYNTAX TERMINATE THIS SECTION AND WRITE DATA OR DATA REFERENCES TO control GOBACK amp TO GEOMETRY MENU The headline gives you the number of atoms the number of atoms to which basis sets have already been assigned and the number of atoms to which effective core potentials have already been assigned Most of the commands in this menu deal with the specification of basis sets and pseudopotentials Basis sets available
186. NOT USED Memory for RI 200 MB Filename for auxbasis auxbasis ENTER RI OPTION TO BE MODIFIED m CHANGE MEMORY FOR RI f CHANGE FILENAME jkbas ASSIGN AUXILIARY RI JK BASIS SETS on TO SWITCH ON RI Use lt ENTER gt q end or to leave this menu For an explanation of the menu items see Section 4 4 1 RI JK calculations can be carried out with the program ridft Optimization to minima and transition structures using STATPT Structure optimizations can be carried out by the program statpt For minimiza tions no additional keywords are required The default values are assumed which work in most of the cases Structure optimization is performed in internal coordi nates if they have been set Otherwise Cartesian coordinates are used One can switch the optimization in internal coordinates on or off respectively in internal redundant or cartesian coordinates For transition structure optimizations the in dex of transition vector has to be set to an integer value gt 0 0 means structure minimization The value of the index specifies transition vector to follow during the saddle point search Note that Hessian eigenpairs are stored in ascending or der of the eigenvalues i e the eigenpair with the smallest eigenvector has the index 1 The command stp gives CONVERGENCE CRITERIA thre 1 000000E 06 thre threshold for ENERGY CHANGE thrd 1 000000E 03 thrd threshold for MAX DISPL ELEMENT thrg 1 000000E 03 thrg threshold for M
187. OMOLE standard basis sets SVP TZVPP and QZVPP nor the cc pVXZ basis set families with X D T Q 5 6 are designed for correlation treatment of inner shells for this purpose polarisation functions for the inner shells are needed The default selection for frozen core orbitals in Define orbitals below 3 a u are frozen provides a reasonable guess If core orbitals are included in the correlation treatment it is recommended to use basis sets with additional tight correlation functions as e g the cc pwCVXZ and cc pCVXZ basis set families e RI MP2 We strongly recommend the use of auxiliary basis sets optimized for the corresponding MO basis sets Fast RI MP2 calculations with the ricc2 program As pointed out above the ricc2 program includes almost all functionalities of the rimp2 program Be cause of slightly refined batching algorithms screening and symmetry treatment the ricc2 program is usually somewhat faster than rimp2 This is in particular the case when the molecular point group is D p or a subgroups thereof and a significant number of atoms is positioned on symmetry elements e g planar molecules and when because of memory restrictions the rimp2 program needs many passes for the integral evaluation All what is needed for a RI MP2 gradient calculation with the ricc2 program is a ricc2 data group with the entry geoopt model mp2 If you want only the RI MP2 energy for a single point use as option just mp2 To activate in MP
188. PHF equations is again determined by forceiterlimit as shown above The convergence of the macro iterations is strongly influenced by the size of the starting search subspace Generally all guess Hessian eigenvectors cor responding to imaginary frequencies and at least two real ones are used as starting search subspace However it proved to be necessary to use even more vectors in the case of guess Hessians with very large conditioning numbers hesscond 8 0d 5 means that all eigenvalues with the quotient eigenvalue max eigenvalue lower than 0 00008 are added to the starting search subspace Default is 1 0d 4 hotfcht Triggers the generation of input files for hotFCHT program to calculate Franck Condon factors by R Berger and co workers See 12 4 Force constant calculations on the DFT level prove to be numerically reliable only with large integration grids or if one includes the effects of quadrature weights This is done by default to prevent this insert no weight derivatives in dft 18 2 11 Keywords for Module EScF ESCF calculations to perform an escf calculation converged molecular orbitals from a HF DFT or RIDFT calculation are needed The HF DFT or RIDFT method is chosen according to the dft or ridft keywords specified above It is recommended to use well converged orbitals specifying scfconv 7 and denconv 1d 7 for the ground state 18 2 FORMAT OF KEYWORDS AND COMMENTS 309 calculation The input for
189. POT 1 149 4297623501 149 4298391833 298 8596015334 E a E a ma N N N N N ONA O N Be Chapter 20 The Perl based Test Suite Structure 20 1 General Testing the TURBOMOLE modules for correctness and speed is the first task once the coding is completed It is subject to automatization and thus requires a structure which is as simple and flexible as possible In the Perl based test suite this is im plemented by a Perl script TTEST which performs all the testing and benchmarking tasks and resides in the central scripts directory of the TURBOMOLE installation The test examples are located in subdirectories of the TURBOTEST directory grouped according to the modules modules to be tested and a rough short long classifica tion The benchmark suite shows the same directory structure and is rooted in the TURBOBENCH directory The central idea of the Perl based test suite is that only the specific information about an individual test example is included in its local directory along with the in put and reference files This information is stored in the criteria file CRIT which con tains the program calls test criteria and specific reference timings Running the test script creates a new test subdirectory usually called like TESTDIR i786 pc linux gnu where the TURBOMOLE programs are run and the results are summarized in the pro tocol file TESTPROTOKOLL 387 388 CHAPTER 20 PERL BASED TEST SUITE 20 2 Running the tests Starti
190. R TURBOTEST and call TTEST Note Some of the tests are very small and will only pass properly if 2 CPUs are used at maximum Therefore TTEST will not run any test if PARNODES is set to a higher value than 2 If you want to run some of the larger tests with more CPUs you have to edit the DEFCRIT file in TURBOMOLE TURBOTEST and change the defmaxnodes option Linear Algebra Settings The number of CPUs and the algorithm of the linear algebra part of Turbomole depends on the settings of parallel_platform cluster for clusters with TCP IP interconnect Communication is avoided by using an algorithm that includes only one or few CPUs MPP for clusters with fast interconnect like Infiniband or Myrinet Number of CPUs that take part at the calculation of the linear algebra routines depends on the size of the input and the number of nodes that are used SMP all CPUs are used and SCALapack see http www netlib org scalapack routines are involved The scripts in TURBODIR mpirun_scripts automatically set this keyword depend ing on the output of sysname All options can be used on all systems but especially the SMP setting can slow down the calculation if used on a cluster with high latency or small bandwidth Sample simple PBS start script bin sh Name of your run PBS N turbomole Number of nodes to run on PBS 1 nodes 4 Export environment PBS V Set your TURBOMOLE pathes HHHHHHHH ENTER YO
191. TOTAL SYSTEM FDE BINDING ENERGY Dipole convergence 0 004395 CHAPTER 15 FROZEN DENSITY EMBEDDING CALCULATIONS 200 96417090754 Ha 5 865327 mHa 3 680548 kcal mol Damping 0 45 200 96418098234 Ha 5 875401 mHa 3 686870 kcal mol Damping 0 35 200 96418289036 Ha 5 877309 mHa 3 688067 kcal mol Damping 0 25 See embedded susbsystems calculations in STEP3 SUBSYSTEM_A STEP3 SUBSYSTEM_B See total system in STEP3 ENERGY_SYSTEM Sun Mar 25 23 00 21 CEST 2012 Total time 20 secs The final energies are stored in the file fde_energy The directory STEPN ENERGY_SYSTEM contains the total system with density p4 pg this directory can only be used for density analysis 15 2 FROZEN DENSITY EMBEDDING CALCULATIONS USING THE FDE SCRIPT241 15 2 1 Options All the options for the FDE can be specified as commandlines and are described below The options can be also be specified in file fde input which is read by the FDE script If fde input is not present it is created by the FDE script Command lines options overwrites options found in the fde input file Subsystem definition The flag p integer is required or it must be present in the fde input file Equivalent command pos cut integer fde input option pos cut integer Kinetic energy functionals In order to use different GGA approximations of the non additive kinetic potential the flag k string must be used Here string is the acronym used to ide
192. The summary of the RI MP2 F 12 correlation energies is always printed out corrfac char char LCG or R12 The corrfac flag determines which correlation factor is used for the geminal basis LCG requires the data group lcg which contains the in formation regarding exponents and coefficients of the linear combination of Gaussians cabsingles char char off or on The cabsingles flag determines whether or not the single excitations into the CABS basis are computed The CABS singles are computed in any case if the CABS Fock matrix elements are computed anyway for the F12 calculation i e for ansatz 2 or rl2model B or comaprox F K ri2orb char char hf rohf boys or pipek The ri2orb flag controls which orbitals are used for the F12 geminal basis functions With hf the semi canonical Hartree Fock orbitals are used default For ROHF based UMP2 calculations rohf orbitals can be used which also implies that the freeze data group options refer to ROHF rather than semi canonical orbitals For closed shell species lo calised orbitals can be used with either the Boys or Pipek Mezey method For the non semi canonical options the r12orb noinv F 12 energy cor rection is evaluated using active occupied orbitals transformed to the same basis as the orbitals in the geminal function ccsdapprox label defines the approximation to CCSD F12 which will be used if the MP2 F12 calculation is followed by a CCSD or CCSD T calculation The avai
193. UK VA 03 55 gt 07 jCuaCvb cd K pV 10 23 which depending on the implementation and system has formally a 2 3 times larger operation count but allows to avoid the storage and I O bottlenecks by processing 10 1 COMPUTATIONAL DEMANDS 211 the 4 index integrals on the fly without storing them Furthermore integral screen ing techniques can be applied to reduce the operation count for large systems to asymptotic scaling with O N In TURBOMOLE only the latter algorithm is presently implemented For small systems other codes will therefore be faster The other class of expensive contributions are so called ring terms in some publi cations denoted as C and D terms which involve contractions of the doubles am plitudes tai with several 4 index MO integrals with two occupied and two virtual indeces partially evaluated with T dependent MO coefficients For these terms the implementation in TURBOMOLE employs the resolution of the identity or density fitting approximation with the cbas auxiliary basis set to reduce the overhead from integral transformation steps Due this approximation CCSD energies obtained with TURBOMOLe will deviate from those obtained with other coupled cluster programs by a small RI error This error is usually in the same order or smaller the RI error for a RI MP2 calculation for the same system and basis sets The RI approximation is also used to evaluate the 4 index integrals in the MO basis neede
194. UR TURBOMOLE INSTALLATION PATH HERE 48 CHAPTER 3 HOW TO RUN TURBOMOLE export TURBODIR whereis TURBOMOLE HHEHHHEHHHHHHHHHHEHAHHAHHEHHEHEA HAH HAHHEHAH HEHEHE HEH HRS export PATH TURBODIR scripts PATH set locale to C unset LANG unset LC_CTYPE set stack size limit to unlimited ulimit s unlimited Count the number of nodes PBS_L_NODENUMBER wc 1 lt PBS_NODEFILE Check if this is a parallel job if PBS_L_NODENUMBER gt 1 then H H Parallel job Set environment variables for a MPI job export PARA_ARCH MPI export PATH TURBODIR bin sysname PATH export PARNODES expr PBS_L_NODENUMBER else HHH Sequentiel job set the PATH for Turbomole calculations export PATH TURBODIR bin sysname PATH fi VERY important is to tell PBS to change directory to where the input files are cd PBS_O_WORKDIR HHHHHHHH ENTER YOUR JOB HERE HHHHHHHHHHHHHHHHEHHHHRHHHEH HH jobex ri gt jobex out HHHHHHHEHE EE RRR aH HH a Chapter 4 Preparing your input file with DEFINE define is the general interactive input generator of TURBOMOLE During a session with define you will create the control file which controls the actions of all other TURBOMOLE programs During your define session you will be guided through four main menus 1 The geometry main menu This first menu allows you to build your molecule define internal coordinates for geometry optimization
195. a GGA and hybrid functionals are implemented for ground state calculations in the dscf and ridft the odft module considers functionals of the fourth rung Currently exchange only orbital dependent approaches are im plemented in the odft module The EXX KS local potential vEX r can be ob tained using the optimized effective potential OEP method in each self consistent step 157 160 158 159 iee YOY In 6a EELE 6 2 Ea s where ys r r S70 2n 2 Palda pa E Pale is the non interacting density response An effective approximation to the OEP EXX potential is given by the Localized Hartree Fock LHF potential 156 which is given by LEF lt di r dj x Pie Oi Lim er i llr r S n dilt oi r yl HF _ NL r 3 s plr di x x 16 3 where the first term is called Slater potential and the second term correction term If terms i j are neglected in the correction term the Krieger Li Iafrate KLI potential 161 is obtained Note that the Eq 16 3 depends only on occupied orbitals whereas Eq 16 2 depends also on virtual orbitals The LHF total energy is assumed to be the EXX total energy even if LHF is not variational although the deviation from the EXX energy is very small usually below 0 01 The LHF potential is equivalent to the Common Energy Denominator Approximation CEDA 162 and to the Effective Local Potential ELP 163 Both OEP EXX and LHF in contrast
196. a group energy The data groups closed shells alpha shells and beta shells for open shell cases are no longer significant but nevertheless kept in the control file additionally the spinor occupations are diposited in data group spinor 6 5 USING THE DOUGLAS KROLL HESS DKH HAMILTONIAN 137 6 5 Using the Douglas Kroll Hess DKH Hamiltonian For consideration of scalar relativistic effects in all electron calculations the scalar relativistic Douglas Kroll Hess DKH Hamiltonian can be employed in the modules dscf and ridft Please make sure to use an all electron basis set in particular ECPs are not allowed This Hamiltonian is defined up to a certain order in the external potential and is available up to arbitrary order for actual calculations however it is advisable not to go beyond 4th order the parameter settings of the implementation allow to run calculations up to about 10th order in the electron nucleus potential The current implemtation is restricted to single point calculations gradients are not available in Cl symmetry and cannot be used in parallel mode Moreover calculated properties using the DKH density do not take care of the picture change effect The arbitrary order Hamiltonian requires in the control file dkhorder integer where integer specifies the order of the DKH Hamiltonian in the external potential i e for the standard 2nd order DKH Hamiltonian one should use dkhorder 2 The
197. a self consistent implementation of the COSMO RS model the so called Direct COSMO RS DCOSMO RS 177 has been implemented in ridft and dscf COSMO RS COSMO for Real Solvents 178 179 is a predictive method for the calculation of thermodynamic properties of fluids that uses a statistical thermody namics approach based on the results of COSMO SCF calculations for molecules embedded in an electric conductor i e using f 1 The liquid can be imagined as a dense packing of molecules in the perfect conductor the reference state For the statistical thermodynamic procedure this system is broken down to an ensemble of pair wise interacting surface segments The interactions can be expressed in terms of surface descriptors e g the screening charge per segment area ot q at Using the information about the surface polarity o and the interaction energy functional one can obtain the so called o potential ug o T This function gives a measure for the affinity of the system S to a surface of polarity o The system S might be a mixture or a pure solvent at a given temperature T Because the parabolic part of the potential can be described well by the COSMO model we substract this portion form the COSMO RS potential jis o T ws o T 1 Fear The parameter co can be obtained from the curvature of a COSMO RS o potential of a nonpolar substance e g hexane Thus the remaining part of the chemical potential of a compound 7 w
198. a vector is smaller than 107 P the vector is assumed to be zero This threshold is also used to test if a set of vectors is linear dependent The default threshold is 10715 maxiter gives the maximum number of iterations for the solution of the cluster equations eigenvalue problems or response equations default 25 mxdiis is the maximum number of vectors used in the DIIS procedures for CC2 ground state or excitation energies default 10 maxred the maximum dimension of the reduced space in the solution of linear equations default 100 iprint print level by default set to 1 or if given the the value of the printlevel data group fmtprop Fortran print format used to print several results in particular one electron properties and transition moments to standard output 18 2 FORMAT OF KEYWORDS AND COMMENTS 319 geoopt SCS sos specify wavefunction and electronic state for which a geometry opti mization is intended For this model the gradient will be calculated and the energy and gradient will be written onto the data groups energy and grad Required for geometry optimizations using the jobex script Note that in the present version gradients are only available for ground states at the MP2 and CC2 and for excited states at the CC2 level and not for ROHF based open shell calculations Not set by default The default model is CC2 the default electronic state the ground state To obtain gradients for the lowe
199. adratic planar case KIJK 1 cos 40 octahedral case KryK C Cf cos 6 C cos 20 general case Nr 1 gt a Vz 1 cos ngoo cos n Nr X Vo C8 Cf cosw C cos 2w Nnb LIJN TIJN 5 Du 2 wt arg POT D2 ET The Fourier coefficients CF ca c of the general angle terms are evaluated as a function of the natural angle Oo 1 Snee 5 2 2 Asin Oo 2 2 C4 4 CF cos bo 5 3 ci c 2 cos 0o 1 5 4 The expressions in the engery term are Ng Na Nr Ni Nn the numbers of the bond angle torsion inversion and the non bonded terms Kij Kijk forceconstants of the bond and angle terms r TIJ bond distance and natural bond distance of the two atoms I and J 0 0o angle and natural angle for three atoms I J K Ce Ce Ge Fourier coefficients of the general angle terms bo torsion angle and natural torison angle of the atoms J J K L Vo height of the torsion barrier n periodicity of the torsion potential w inversion or out of plane angle at atom I 116 CHAPTER 5 STRUCTURE OPTIMIZATIONS Vo height of the inversion barrier Cit Fourier coefficients of the inversions terms L LIJ distance and natural distance of two non bonded atoms I and J Dry depth of the Lennard Jones potential qr partial charge of atoms J and dielectric constant One major difference in this implementation concerns the atom types The atom types in Rapp
200. alization of the accuracy of the frozen density embedding theory for nonbonded interactions J Chem Theory Comput 7 2439 2011 A Lembarki H Chermette Obtaining a gradient corrected kinetic energy functional from the Perdew Wang exchange functional Phys Rev A 50 5328 1994 S Laricchia E Fabiano F D Sala On the accuracy of frozen density em bedding calculations with hybrid and orbital dependent functionals for non bonded interaction energies J Chem Phys 137 1 014102 2012 F D Sala A Gorling Efficient localized Hartree Fock methods as effective exact exchange Kohn Sham methods for molecules J Chem Phys 115 13 5718 5732 2001 A Gorling Orbital and state dependent functionals in density functional theory J Chem Phys 123 6 062203 2005 S K mmel L Kronik Orbital dependent density functionals Theory and applications Rev Mod Phys 80 1 3 2008 406 159 160 161 162 163 164 165 166 167 168 169 BIBLIOGRAPHY F Della Sala Orbital dependent exact exchange mmethods in density func tional theory In M Springborg Ed Chemical Modelling Applications and Theory Band 7 Pages 115 161 Royal Society of Chemistry 2010 A He elmann A W G tz F Della Sala A G rling Numerically stable optimized effective potential method with balanced gaussian basis sets J Chem Phys 127 5 054102 2007 J B Kriege
201. am potential Chem Phys 391 1 19 26 2011 A Klamt G Sch rmann COSMO A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient J Chem Soc Perkin Trans 2 5 799 805 1993 BIBLIOGRAPHY 407 170 171 172 173 174 175 176 177 178 179 180 181 A Klamt V Jonas Treatment of the outlying charge in continuum solvation models J Chem Phys 105 22 9972 9981 1996 A Klamt Calculation of UV Vis spectra in solution J Phys Chem 100 9 3349 3353 1996 F J Olivares del Valle J Tomasi Electron correlation and solvation effects I Basic formulation and preliminary attempt to include the electron correla tion in the quantum mechanical polarizable continuum model so as to study solvation phenomena Chem Phys 150 2 139 150 1991 J G ngy n Rayleigh Schr dinger perturbation theory for nonlinear Schr dinger equations with linear perturbation Int J Quantum Chem 47 6 469 483 1993 J G ngy n Choosing between alternative MP2 algorithms in the self consistent reaction field theory of solvent effects Chem Phys Lett 241 1 2 51 56 1995 R Cammi B Mennucci J Tomasi Second order M ller Plesset analytical derivatives for the polarizable continuum model using the relaxed density ap proach J Phys Chem A 103 45 9100 9108 1999 G Scalmani M
202. ame as in the first case but Numforce has to be called with the cosmo option If no solvent refractive index refind REAL is given in the cosmo section of the control file the program uses the default 1 3 18 2 FORMAT OF KEYWORDS AND COMMENTS 303 Cosmo in vertical excitations and polarizabilities Cosmo is implemented in escf and will be switched on automatically by the Cosmo keywords of the un derlying SCF calculation The refractive index used for the fast term screening of the vertical excitations needs to be defined in the cosmo section of control file refind REAL DCCOSMO RS The DCOSMO RS model see chapter 17 has been imple mented for restricted and unrestricted DFT and HF energy calculations and gradi ents programs dscf ridft and grad rdgrad In addition to the COSMO settings defined at the beginning of this section the dcosmo_rs keyword has to be set dcosmo_rs file filename pot activates the DCOSMO RS method The file defined in this option con tains the DCOSMO RS o potential and related data examples can be found in the default potentials in the TURBODIR parameter directory If the potential file cannot be found in the local directory of the calculation it will be searched in the TURBODIR parameter directory The following o potential files for pure solvents at 25 C are implemented in the current TTURBOMOLE distribution see parameter subdirectory Water h20_25 pot Ethanol ethanol_25 pot Metha
203. ameter dx real spacing of the marching tetrahedron grid in A default 0 3A all_dens real use one isodensity value for all atom types value in a u The outlying charge correction will be performed with a radii based outer cavity Therfore and for the smoothing of the density changes in the intersection areas of the scaled density method radii are needed as for the standard COSMO cavity Please note The isodensity cavity will be constructed only once at the beginning of the SCF calculation The density constructed from the initial mos will be used file mos or alpha beta in case of unrestricted calculations Because the mos of an initial guess do not provide a good density for the cavity construction it is necessary to provide mos of a converged SCF calculation e g a COSMO calculation with standard cavity We recommend the following three steps perform a standard Cosmo calculation add the isodensity options afterwards and start the calculation a second time 302 CHAPTER 18 KEYWORDS IN THE CONTROL FILE Radii based Isosurface Cavity The cosmo_isorad section defines the radii defined isosurface cavity construction The option uses the algorithm of the isoden sity cavity construction but the objective function used depends on the cosmo radii instead of the electron density The default values of nspa and nsph are changed to 162 and 92 respectively This values are superseded by the user defined nspa value of the cosmo se
204. ample CH3 in the By state from 3a1 1b2 molecule in x z plane closed shells al 1 2 2 bi 1 2 open shells type 1 al 3 1 b2 1 1 roothaan 1 rohf 3ai 3al a 0 b 0 1b2 1b2 a 0 b 0 3a1 1b2 a 1 b 2 132 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS Two open shells This becomes tricky in general and we give only the most important case shell 1 is a Roothaan case see 6 3 2 shell 2 is one electron in an a s MO nir 1 with parallel spin coupling of shells This covers e g the p s 3P states or the dts 6D states of atoms The coupling information is given following the keyword rohf The a b within a shell are taken from above 6 3 2 the cross term shell 1 shell 2 is in this case a l1 always b 2 ifn lt nip b where nir and n refer to shell 1 Example 1 The 4d 5s D state of Nb in symmetry I closed shells a 1 4 2 t1 1 3 2 h 1 2 open shells type 1 a 5 1 h 2 4 5 roothaan 1 rohf 5a 5a 0 b 0 5a 2h 1 b 2 2h 2h 15 16 b 15 8 Example 2 The 4d 5s 7S state of Mo symmetry I see Section 6 3 3 can also be done as follows roothaan 1 rohf 5a 5a a 0 b 0 5a 2h a 1 b 2 2h 2h a 1 b 2 6 3 RESTRICTED OPEN SHELL HARTREE FOCK 133 closed shells a 1 4 2 t1 1 3 2 h 1 2 open shells type 1 a 5 1 h 2 1 The shells 5s and 4d have now been made inequivalent Result is identical to 6 3 3 which is also more efficient Ex
205. ample 3 The 4d 5s 3D state of Ni symmetry I closed shells a 1 3 2 ti 1 2 2 open shells type 1 a 4 1 h 1 9 5 roothaan 1 rohf 4a 4a a 0 b 0 1h ih a 80 81 b 80 81 4a 1h a 1 b 10 9 see basis set catalogue basis SV 3D requires this input and gives the energy you must get 6 3 4 Miscellaneous Valence states Valence states are defined as the weighted average of all CSFs arising from an electronic configuration occupation MO This is identical to the average energy of all Slater determinants _ 2nir n 1 a b __ 2nir 1 n This covers e g the cases n 1 and n 2n 1 p p d d etc since there is only a single CSF which is identical to the average of configurations 134 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS Totally symmetric singlets for 2 or 2n 2 electrons n 2 a 0 b Nir n 2Nir 2 ga eee mir 1 is Nie Nee 3 Nip 1 This covers the 1S states of p pt d d etc Average of high spin states n electrons in MO with degenerate nir nin 4h k 1 1 1 L 1 a Nir 1 n i 2Nir 2k k 1 1 11 1 E Nir 1 n where k max 0 n mr l n 2k 2S spin This covers most of the cases given above A CSF results only if n 1 nir 1 Nir Nir 1 2ni 1 since there is a single high spin CSF in these cases The last equations for a and b can be rewritten in ma
206. ams which use 4 index electron repulsion integrals for RI MP2 and RI CC2 this is partially compensated by the RI approximation The following correlation consistent basis sets are available in the TURBOMOLE basis set library cc pVXZ standard valence X tuple zeta basis sets X D T Q 5 6 available for H He Li Ne Na Ar K Ca Ga Kr cc pV6Z only for H He B Ne Al Ar for Al Ar also the recom mended newer cc pV X d Z sets are available cc pwCVXZ PP weighted core valence x tuple zeta basis sets X D T Q 5 are available for post d main group elements Ga Kr In Xe and Tl Rn also pure valence basis sets cc pVXZ PP are available for these elements but it is not recommended to use them cc pwCVXZ weighted core valence X tuple zeta basis sets X D T Q 5 avail able for H He B Ne Al Ar and Ga Kr for Al Ar also the recommended combination of the cc pV X d Z sets with the core valence functions wC i e the cc pwCV X d Z basis set are available aug diffuse functions for combination with the basis sets cc pVXZ cc pV X d Z cc pwCVXZ cc pV X d Z cc pVXZ PP or cc pwCVXZ PP available for H He B Ne Al Ar with X D 6 and Ga Kr In Xe and Tl Rn with X D 5 cce pVXZ F12 with X D T Q for use with the explicitly correlated F12 variants of wavefunction methods MP2 F12 CCSD F12 etc For calculations with the programs rimp2 and ricc2 optimized auxiliary basis sets are available for mo
207. an be avoided by doing the Hartree Fock calculation in the full point group The input and MO coefficients can then be transformed to a lower point group using define only for the ricc2 calculation Calculations with mpgrad 1 Add denconv 1 d 7 to the control file and perform a dscf run 2 If any orbitals are decided to be excluded from MP2 treatment add data group freeze manually to the control file see also Section 18 2 13 3 For preparation of an mpgrad run use the script Mp2prep mp2prep e g m memory p discspace scratch file directory As an example with the command mp2prep e m 100 p 1000 work an MP2 energy calculation is prepared the amount of available core memory is restricted to 100 MB the MOs are blocked so that integral scratch files located in the directory work do not need more than 1000 Mb The number of blocks i e the number of passes with repeated integral evaluations is writ ten to the control file traloop as well as the specification of scratch files mointunit see Section 18 2 13 Note less disc space means more passes and thus lower efficiency of mpgrad but due the technical limitations discspace should be limited to values lt 16Gb to avoid integer overflow errors Settings obtained by mp2prep may be changed manually You may change the num ber of passes in traloop by editing the control file e g if the originally intended disc space is not available To adapt the size of scratch file
208. an escf calculation can be conveniently generated using the ex menu in define see Section 4 In an escf run one of the following properties can be calculated please note the or in the text do only one thing at a time 1 RPA and time dependent DFT singlet or triplet or spin unrestricted excitation energies HF RI DFT scfinstab rpas or scfinstab rpat or scfinstab urpa 2 TDA for HF CI singles singlet or triplet or spin unrestricted or spin flip exci tation energies HF RI DFT scfinstab ciss or scfinstab cist or scfinstab ucis or scfinstab spinflip 3 Eigenvalues of singlet or triplet or non real stability matrices HF RI DFT RHE scfinstab singlet or scfinstab triplet or scfinstab non real 4 Static polarizability and rotatory dispersion tensors HF RIDFT RHF UHF scfinstab polly 5 Dynamic polarizability and rotatory dispersion tensors HF RI DFT RHF UHF scfinstab dynpol unit list of frequencies where unit can be eV nm rcm default is a u Hartree For example to calculate dynamic polarizabilities at 590 nm and 400 i nm i is the imaginary unit 310 CHAPTER 18 KEYWORDS IN THE CONTROL FILE scfinstab dynpol nm 590 400 i The number and symmetry labels of the excited states to be calculated is controlled by the data group soes Example soes big 17 eu 23 t2g all will yield the 17 lowest excitations in IRREP blg the 23 lowest excitations in IRREP
209. and Geometries 188 9 3 3 Visualization of densities and Density analysis 191 9 3 4 Fast geometry optimizations with RLSCF based gradients 193 94 Transition Moments i pa sae i do oe tee a oh eR a ee A 193 9 4 1 Ground to excited state transition moments 193 9 4 2 Transition moments between excited states 195 9 5 Ground State Second order Properties with MP2 and CC2 195 9 6 Parallel RI MP2 and RI CC2 Calculations 196 9 7 Spin component scaling approaches SCS SOS 197 9 8 Polarizable embedding calculations 0 198 OSI TU o sgt ee a a ee ole Rk a Be ee ee he a 199 9 8 2 Computational details SCF calculations 200 9 8 3 Computational details PERI CC2 calculations 202 10 CCSD CCSD F12 and CCSD T calculations 204 10 1 Characteristics of the Implementation and Computational Demands 206 11 Correlation Energies from the Random Phase Approximation 214 12 Calculation of Vibrational Frequencies and Vibrational Spectra 218 12 1 Analysis of Normal Modes in Terms of Internal Coordinates 220 12 2 Calculation of Raman Spectra e c sos sr e moosi reao ena wa 221 12 3 Vibrational frequencies with fixed atoms using NumForce 221 124 Intertace to hotFCHT e sori a s alae Bow a BOR ee We eee e 222 8 CONTENTS 13 Calculation of NMR Shieldings 224 13 1 Prerequisites o s ce mome e ew ee ee ee ae ee ee 224 13 2 How to
210. and Itanium2 systems IBM Platform MPI formerly known as HP MPI and Platform MPI is used see IBM Platform MPI COSMOlogic ships TURBOMOLE with a licensed IBM Platform MPI TURBOMOLE users do not have to install or license IBM Platform MPI themselves Parallel binaries will run out of the box on the fastest interconnect that is found Infiniband Myrinet TCP IP etc The binaries that initialize MPI and start the parallel binaries mpirun are located in the TURBODIR mpirun_scripts HPMPI directory Note the parallel TURBOMOLE modules except ricc2 need an extra server running in addition to the clients This server is included in the parallel binaries and it will be started automatically but this results in one additional task that usually does not need any CPU time So if you are setting PARNODES to N N 1 tasks will be started If you are using a queuing system or if you give a list of hosts where TURBOMOLE jobs shall run on see below make sure that the number of supplied nodes match PARNODES e g if you are using 4 CPUs via a queuing system make sure that PARNODES is set to 4 In some older versions of the LoadLeveler on IBM systems the total number of tasks must be set to PARNODES 1 except for ricc2 Starting parallel jobs After setting up the parallel environment as described in the previous section par allel jobs can be started just like the serial ones If the input is a serial one it will be prepared
211. arched This library contains the optimised cabs basis sets 97 for the cc pVXZ F12 basis sets of Peterson et al 98 For other basis sets the auxilliary basis in the library cabasen is identical with the auxilliary basis in the library cbas The rir12 data group may be set by choosing the 12 option in the cc menu when running define This command activates the 12 menu where the default options may be changed if desired Orbital basis cc pVTZ F12 Cardinal number LF Recommended exponent 1 0000 Actual exponent 1 0000 INPUT MENU FOR MP2 F12 CALCULATIONS ansatz ri2model comaprox cabs examp ri2orb corrfac cabsingles pairenergy slater end amp ansatz ri2model CHOOSE ANSATZ CHOOSE MODEL COMMUTATOR APPROXIMATION CABS ORTHOGONALIZATION CHOOSE FORMULATION CHOOSE GEMINAL ORBITALS CHOOSE CORRELATION FACTOR CABS SINGLE EXCITATIONS PRINT OUT PAITRENERGIES SLATER EXPONENT 2 1 2 2 B A B F K F K T V svd 1 0D 08 cho svd fixed noflip inv fixed noinv flip noflip hf hf rohf boys pipek LCG R12 LCG on on off off on off 1 0000 write riri2 to file and leave the menu go back leaving rir12 unchanged corresponds to the choice of One Almost all modern MP2 F12 calculations use ansatz 2 default which gives much improved energies over ansatz 1 see Ref 99 for details The principal additional cost of using ansatz 2 over ansatz 1 is
212. are derived from the Lagrangian 113 13 LCA HE H CC X ty l H THF 9 15 M1 X t Hal H F Te HF 2 Fook o gt H2 where F is the Fock operator corresponding to the Hamiltonian of the perturbed system H Ho GV One electron properties are then obtained as vetoo R FI IHE SO fa al V TIIE 9 16 H D hattal TIHE YO Rioja u2 Ho y D V 9 17 pq The calculation of one electron first order properties requires that in addition to the cluster equations also the linear equations for the Lagrangian multipliers t are solved which requires similar resources CPU disk space and memory as the 9 3 FIRST ORDER PROPERTIES AND GRADIENTS 187 calculation of a single excitation energy For orbital relaxed properties also a CPHF like linear equation for the Lagrangian multipliers K needs to be solved and the two electron density has to be build since it is needed to set up the inhomogeneity right hand side The calculation of relaxed properties is therefore somewhat more expensive the operation count for solving the so called Z vector equations is similar to what is needed for an SCF calculation and requires also more disk space to keep intermediates for the two electron density about O 2V 2N N N2 in addition to what is needed for the solution of the cluster equations For ground states orbital relaxed first order properties are standard in the literature The calculation of the gradien
213. art vectors generated or read from file default nstart npre spectrum tmexc This flag switches on the calculation of oscillator strengths for excited state ground state transitions Setting the parameter states all1 is mandatory for the calculation of transition properties in the present version The operators flag can be followed by a list of operators see below for which the transition properties will be calculated Default is to compute the oscillator strengths for all components of the dipole operator This flag switches on the calculation of oscillator strengths for excited state excited state transitions Specifying the initial and final states via istates all and fstates all is mandatory for the calculation of transition properties in the present version The operators flag can be followed by a list of operators see below for which the transition prop erties will be calculated Default is to compute the oscillator strengths for all components of the dipole operator exprop require calculation of first order properties for excited states For the states option see spectrum option above for details for the operators input see below xgrad conv request calculation of the gradient for the total energy of an excited state If no state is specified the gradient will be calculated for the lowest excited state included in the calculation of excitation energies Note that only a single state should be specifie
214. ary NOTE The FDE script supports only basis set in the TURBOMOLE library Equivalent command mono or super fde input option method mono or method super Convergence of the freeze and thaw cycles The script FDE runs a self consistent calculation when a convergence criterion is fulfilled The convergence criterion is the change in the total dipole moment This is a tight convergence criterion as the dipole moment is highly sensitive to small changes in electron density The convergence parameter f for the j th step in the freeze and thaw procedure is computed by means the following expression _ Arl lAr 2 15 10 where f eee e Anl lall i A B 244 CHAPTER 15 FROZEN DENSITY EMBEDDING CALCULATIONS is the difference between the dipole moments of two consecutive steps for the i th subsystem Eq 15 10 allows to consider changes in both subsystems or one of them because of the relaxation of their electron densities By default FDE stops when cf lt 0 005 a u The default value for the convergence criteria can be changed using the flag epsilon real where real is a decimal number The maximum number of freeze and thaw cycles can be specified by max iter integer and the default value is 20 In order to make easy the convergence of the iterative solution of the KSCED coupled equations a damping factor 7 must be used for the matrix elements of the embedding potential Vemb as perturbation to a given subs
215. ary frequency A good comparison of different TS optimization methods is given in 32 Structure optimizations using statpt are controlled by the keyword statpt to be present in the control file It can be set either manually or by using the stp menu of define The type of stationary point optimization depends on the value of itrvec specified as an option within statpt By default itrvec is set to 0 which implies a structure minimization A value itrvec gt 0 implies a transition state optimization using the eigenvalue following TRIM algorithm where the index of the transition vector is specified by itrvec Note that statpt orders eigenvalues 102 CHAPTER 5 STRUCTURE OPTIMIZATIONS and eigenvectors of the Hessian in ascending order shifting six or five in the case of linear molecules zero translation and rotation eigenvalues to the end Note this order differs from that used for vibrational frequencies in the control file where rotational and translational eigenvalues are not shifted By default a structure optimization is converged when all of the following criteria are met e the energy change between two optimization cycles drops below the value given by threchange default 1076 a u e the maximum displacement element drops below the value given by thrmax disp1l default 107 a u e the maximum gradient element drops below the value given by thrmaxgrad default 107 a u e the root mean square of the displacem
216. as calculated in subse quent optimization cycles Entries are accumulated by one of the gradient programs globgrad Global scale factors and gradients as calculated in subsequent optimization cycles Entries are accumulated by the grad or aoforce program corrgrad Allows to augment internal SCF gradients by approximate increments ob tained from treatments e g correlation or relativistic on higher level See the example below corrgrad coordinate increment 1 0 0600 8 0 0850 forceapprox options Approximate force constant matrix as needed for geometry optimization tasks The storage format may be specified by the available options 336 CHAPTER 18 KEYWORDS IN THE CONTROL FILE format format the default format is format 8f10 5 but other 10 digit f10 x for mats e g x 4 6 are possible and will be used after being manually specified within forceapprox See the example below forceapprox format 8f10 4 0 9124 0108 0 3347 0 2101 0 0299 1 3347 0 0076 0 1088 0 0778 0 6515 hessian projected this data block contains the analytical cartesian force constant matrix with translational and rotational combinations projected out as output by the aoforce program and may be used to supply a high quality force constant matrix forceapprox for geometry optimizations specifying forceinit on carthess or interconversion cartesian gt internal hessian RELAX Output Data Groups coord either upd
217. as root or with root permissions 2 1 1 Settings for each user The environmental variable TURBODIR must be set to the directory where TURBOMOLE has been unpacked for example TURBODIR my_disk my_name TURBOMOLE Then the most convenient way to extend your path to the TURBOMOLE scripts and binaries is to source the file Config_turbo_env source TURBODIR Config_turbo_env If you have a csh or tcsh as default login shell use source TURBODIR Config_turbo_env tcsh instead It is recommended to add the two lines given above to your bashrc or profile or wherever you prefer to add your local settings 29 30 CHAPTER 2 INSTALLATION OF TURBOMOLE 2 1 2 Setting system type and PATH by hand Check that the Sysname tool works on your computer TURBODIR scripts sysname should return the name of your system and this should match a bin arch subdi rectory If Sysname does not print out a single string matching a directory name in TURBODIR bin and if one of the existing binary versions does work you can force sysname to print out whatever is set in the environment variable TURBOMOLE_SYSNAME TURBOMOLE_SYSNAME em64t unknown linux gnu Please make sure not to append _mpi or _smp to the string when setting TURBOMOLE_SYSNAME even if you intend to run parallel calculations sysname will append this string au tomatically to the system name if PARA_ARCH is set to MPI or SMP see chapter 3 2 2 how to set up parallel environm
218. asis set for one or more atoms use the basis set nickname none On leaving this menu the data groups atoms and basis will be written to the output file After you finished this menu you will enter the third main menu of define which deals with start vectors and occupation numbers 4 3 Generating MO Start Vectors 4 3 1 The MO Start Vectors Menu This menu serves to define the occupation numbers and to generate the start vectors for HF SCF and DFT calculations They may be constructed from earlier SCF calculations perhaps employing another basis set type use by Hamilton core guess hcore or by an extended H ckel calculation which can be performed automatically eht An occupation of the start orbitals will be proposed and can be modified if desired OCCUPATION NUMBER amp MOLECULAR ORBITAL DEFINITION MENU CHOOSE COMMAND infsao OUTPUT SAO INFORMATION atb Switch for writing MOs in ASCII or binary format eht PROVIDE MOS amp amp OCCUPATION NUMBERS FROM EXTENDED HUECKEL GUESS use lt file gt SUPPLY MO INFORMATION USING DATA FROM lt file gt man MANUAL SPECIFICATION OF OCCUPATION NUMBERS hcore HAMILTON CORE GUESS FOR MOS flip FLIP SPIN OF A SELECTED ATOM amp MOVE BACK TO THE ATOMIC ATTRIBUTES MENU THE COMMANDS use OR eht OR OR q uit TERMINATE THIS MENU FOR EXPLANATIONS APPEND A QUESTION MARK TO ANY COMMAND 68 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE Recommendation You wi
219. ated cartesian coordinates if a successful coordinate update has been performed or cartesian coordinates for input internal coordinates if only a conversion from internal to cartesian coordinates has been performed basis updated basis set exponents basis sets contraction coefficients or scaling fac tors if optimize basis on has been specified global updated global scaling factor for all basis set exponents if optimize global on has been specified forceapprox an approximate force constant matrix to be used in quasi Newton type geom etry optimizations this matrix will be improved in subsequent optimization cycles if one of the variable metric methods forceupdate has been chosen See 5 3 13 and 18 2 15 forcestatic a static i e never updated approximate force constant matrix to be used in 18 2 FORMAT OF KEYWORDS AND COMMENTS 337 DIS type geometry optimizations It will be initialized by relax specifying forceupdate pulay modus lt dq dq gt static The next data groups are output by relax depending on the optimization subject in order to control the convergence of optimization procedures driven by the shell script jobex maximum norm of cartesian gradient real maximum norm of internal gradient real maximum norm of basis set gradient real real is the absolute value of the maximum component of the corresponding gradient Other Input Output data used by RELAX In order to save the ef
220. ation analyses are driven by the keyword pop Without any extension Mulliken population analyses MPA are carried out for all densities present in the respective program e g total and spin densities leading to Mulliken charges and unpaired electrons per atom in RHF UHF type calculations in dscf or ridft SCF MP2 densities in rimp2 or mpgrad excited state densities in egrad Suboptions see Section 18 2 18 also allow for calculation of Mulliken contributions of selectable atoms to selectable MOs including provision of data for graphical output simulated density of states With pop nbo a Natural Population Analysis NPA 141 is done Currently only the resulting charges are calculated With pop paboon a population analyses based on occupation numbers 142 is per formed yielding shared electron numbers SENs and multicenter contributions For this method always the total density is used i e the sum of alpha and beta densities in case of UHF the SCF MP2 density in case of MP2 and the GHF total density for two component GHF Note that the results of such an analysis may de pend on the choice of the number of modified atomic orbitals MAOs By default numbers of MAOs which are reasonable in most cases are taken see Section 18 2 18 Nevertheless it is warmly recommended to carefully read the information concerning MAOs given in the output before looking at the numbers for atomic charges and shared electron numbers
221. ational costs reduced by one third or more compared to calculations with the default settings for these thresholds For geometry optimizations with SOS MP2 we recommend to set conv in laplace to 5 e The spread of the orbital energy denominators depends on the basis sets and the orbitals included in the correlation treatment Most segmented contracted basis sets of triple or higher accuracy as e g the TZVPP and QZVPP basis sets lead to rather high lying anti core orbitals with orbital energies of 10 a u and more 8 6 LT SOS RI MP2 WITH O N SCALING COSTS 173 For the calculation of SOS MP2 valence correlation energies it is recom mended to exclude such orbitals from the correlation treatment see input for freeze in Sec 18 Alternatively one can use general contracted basis sets as e g the cor relation consistent cc pV XZ basis sets But note that general contracted basis sets increase the computational costs for the integral evaluation in the Hartree Fock and for gradient calculations also the CPHF equations and related 4 index integral derivatives Also for the calculation of all electron correlation energies with core valence basis sets which include uncontracted steep functions it is rec ommended to check if extremely high lying anti core orbitals can be ex cluded Note that for large molecules it is recommended to disable for geometry optimiza tions or for gradient or property calculation
222. ations 123 With out any further approximations than those needed for evaluating the neccessary matrix elements this extension of the cluster operator T leads to the CCSD F12 method CCSD F12 is an approximation 124 123 to CCSD F12 which neglects certain computationally demanding higher order contributions of Ty This reduces the computational costs dramatically while the accuracy of CCSD F12 is essen tially identical to that of CCSD F12 125 126 In the CCSD F12 approximation the amplitudes are determined from the equations Qu ual T2 Ty HF 0 10 14 Qi m H To To H T2 2Ty T2 HF 0 10 15 Quy uo F Ty THF 0 10 16 Similar as for MP2 F 12 also for CCSD F12 the coefficients for the doubles excita tions into the geminals ch can be determined from the electronic cusp conditions using the rational generator also known as SP or fixed amplitude approach In this case Eq 10 16 is not solved To account for this the energy is then computed from a Lagrange function as Eccsp F12 sp Lccspri2 HF A CC gt Cpa Pjer 10 17 Ha This is the recommended approach which is used by default if not any other approch has been chosen with the examp option in rir12 see Sec 8 5 for further details on the options for F12 calculations note that the examp noinv option should not be combined with CCSD calculations CCSD F12 SP calculations are computation ally som
223. atto grids i e gridsize 9 ntheta specifies the number of 0 points and nphi specifies the number of points For the fixed Lobatto grid i e gridtype 8 the default value is ntheta 25 and nphi 48 When gridsize 9 is given you have to specify both ntheta and nphi see below otherwise the program will crash The restriction for user defined Lobatto grids is the number of grid points which must not exceed 2000 grid points Example 18 2 FORMAT OF KEYWORDS AND COMMENTS 277 dft gridsize 9 ntheta 30 nphi 60 old_RbCs_xi Original grids had not been carefully optimized for all atoms individ ually This has now been done which let to changes of for Rb and Cs only resulting in minor improvements If you have ongoing projects which have been started with the old grids you should continue using them with the keyword 0ld_RbCs_xi Example dft old_RbCs_xi radsize integer Specifies the number of radial grid points Default values depend on type of atom and grid see keyword gridsize The formula for the radial gridsize is given as number of radial grid points ioffrad radsize 1 5 ioffrad is atom dependent the more shells of electrons the larger ioffrad elements ioffrad elements ioffrad for H He 20 for K Kr 40 for Li Ne 25 for Rb Xe 45 for Na Ar 30 for Cs Lw 50 The radial grid size increases further for finer grids gridsize 1 2 3 4 5 6 7 8 radsize 1 2 3 6 8 10 14 9 If you want to conver
224. automatically for the parallel run The parallel versions of the programs dscf and grad can use an integral statistics file as input which is generated by a parallel statistics run This preparation step is done automatically by the scripts dscf and grad that are called in the parallel version This serial step to determine a task distribution for the later parallel run can be lengthy for larger cases and it is recommended to skip this step and let the programs determine the optimal task distribution dynamically during the parallel execution This can be done by setting the environment variable export SKIP_PARA_STAT yes For the additional mandatory or optional input for parallel runs with the ricc2 program see Section 9 6 46 CHAPTER 3 HOW TO RUN TURBOMOLE MPI case How much memory shall be set In the parallel MPI version both settings for memory namely ricore and maxcor are entries per process If several processes run on the same node the total sum of Nepu ricore maxcor must not be larger than the total memory on that system Please note that both keywords are not settings for the total amount of memory the TURBOMOLE modules need but only for storage of intermediates in case of ricc2 maxcor or RI integrals and matrices for ridft and ricc2 ricore Especially for larger molecules and or basis sets set ricore to a small value of a few hundred MB only Running calculations on different nodes If TURBOMOLE is supposed
225. ave an integer value The default value is 2 condition string2 string In the OEP method two constraints can be applied in the OEP equation This is the HOMO condition and the Charge condition The variable string can have the values none HOMO Charge and both No condition is chosen when none is elected The HOMO condition is chosen when HOMO is elected The Charge condition is chosen when Charge is elected The HOMO condition and the Charge condition are chosen when both is elected The variable string2 is optional and only electable if a spin unrestric ted calculation is performed The variable string2 can have the values alpha and beta If string2 alpha then the condition is defined for the alpha spin channel If string2 beta then the condition is defined for the beta spin channel Both spin channels can have different values Example oep 254 LHF core CHAPTER 16 ORBITAL DEPENDENT DFT condition alpha HOMO condition beta Charge If only one spin channel is defined the other spin channel uses the same condition automatically The default value in any case is string both memory integer Core memory is the amount of main memory given to the OEP cal culation to store the three index integrals calculated during the OEP calculation The core memory amount is given MB The calculation runs as fast as possible if all three index integrals can be stored in the core memory The variable integer must have an integer
226. b 1 type dtdb 2 unit 77 size 0 file dtdb 2 traloop 1 statistics mpshift and starts a statistics run of mpshift by calling mpshift If the resulting disk space requirement exceeds the automatically detected free disk space on your system it will increase traloop and run a statistics run again This will be done as long as your free disk space is not sufficient for the calculation If the mp2prep script fails to run on your system try to use the p option or do the procedure described above by hand Call mp2prep h for more informations about mp2prep 226 CHAPTER 13 SHIELDINGS 13 4 Chemical Shifts NMR shifts are obtained by comparing nuclear shieldings of your test compound with a reference molecule dsuyst ref Oref Ssubst Therefore you have to choose a reference molecule with a well known shift for which you can easily calculate the absolute shielding constant This implies a certainty about the geometry too Furthermore you have to use the very same basis set for corresponding atoms to minimize the basis set influence Keywords for the module Mpshift A list of keyword for the module mpshift can be found in Section 18 2 20 13 5 Other Features and Known Limitations e the mpshift program can be restarted at any stage of computing since all intermediate results are written into the file restartcs In case of an external program abort you have to remove the actual step flag by the command actual r or using an
227. b and iaut see internal coordinate menu Section 4 1 2 If you want to change the standard bond lengths or define more bond lengths because not for all possible combinations of elements a standard length is available you can do that by creating your own file with the non default values and by specifying its full pathname in file sys data The file has the following simple format c h 2 2 h h 2 0 4 1 THE GEOMETRY MAIN MENU 57 The format of the entries is almost arbitrary the two element symbols have to be separated by a bar the new bond distance follows in free format in atomic units If the file cannot be read properly a warning message is displayed This command leaves this first main menu and writes all data generated so far to file The default output file is the file you choose in the first question during your define session usually control Now the data groups coord and intdef will be written to file After leaving this menu you will enter the atomic attributes menu which is described in Section 4 2 4 1 2 Internal Coordinate Menu INTERNAL COORDINATE MENU ideg 6 k 2 f 0 d 0 i 0 imet lt a gt PROVIDE B MATRIX FOR ACTIVE INTERNAL COORDINATES CHECK COMPLETENESS AND NUMERICAL QUALITY AND CHANGE REDUNDANT INTERNALS TO display idef SUB MENU FOR INTERACTIVE DEFINITION OF INTERNAL COORDINATES ideg lt a gt OUTPUT NUMBER OF TOT SYMMETRIC INTERNAL DEGREES OF FREEDOM iaut TRY AUTOMATIC DEFINITION OF
228. basis set especially with diffuse basis functions the N4 steps might become the dominant part of the overall timings In these cases the integral screening in the Hartree Fock part often becomes inefficient The resolution of the identity can be applied here to speed up the calculation of the HF reference wavefunction as well as the solution of the coupled perturbed Hartree Fock CPHF equations in the MP2 or CC2 gradient calculation An additional auxiliary basis denoted jkbas set has to be assigned via the General Options Menu in the define program In the submenu rijk choose on and select your auxiliary basis set Then run the jobex script the additional rijk flag gt jobex level cc2 rijk Note that it is at the moment not possible to perform these calculation parallel because the RI JK approximation is presently not supported in the parallel version of the ridft program 9 4 Transition Moments Transition moments are presently implemented for excitations out of the ground state and for excitations between excited states for the coupled cluster models CCS and CC2 Transition moments for excitations from the ground to an excited state are also available for ADC 2 but use an additional approximation see below Note that for transition moments as for excited state first order properties CCS is not equivalent to CIS and CIS transition moments are not implemented in the ricc2 program 9 4 1 Ground to excited state tran
229. bel gt lt list gt skip orbitals within lt list gt amp ignore input for last label clear Clear all assignments p rint print actual orbital selection for help type or help for quit type or q uit Depending on whether you are in the closed or in the open shell section the com mands of this menu refer only to the corresponding type of orbitals The commands of this menu do not need much explanation lt label gt is the irrep label of one irre ducible representation of the molecular point group e g a1 b2 tig lt list gt is a list of orbital indices within this irrep e g 1 2 4 or 1 8 10 11 p or print will give you the same listing of the orbital occupations as you saw before entering this 4 3 GENERATING MO START VECTORS 73 menu After you leave this submenu you will be back in the occupation numbers main menu 4 3 4 Roothaan Parameters In open shell calculations within the restricted Hartree Fock ansatz ROHF the coupling between the closed and the open shells must be specified using two param eters a and b which depend on the type of the open shell the number of electrons in it the electron configuration but also on the state to be calculated For example there are three states arising from the s p configuration of an atom P 1D 1S which have different values of a and b For the definition of these parameters and their use refer to Roothaan s original paper 26 For simple cases
230. between J and I and the bond between J and K The hybridization of atom J determines wtyp Then the torsion terms follow starting with the number of the torsion terms Each line contains one torsion term I J K L nr JK ttyp 0 OLJK OJKL Here are J J K and L the atom numbers nrjx is the number of the bond between J and K ttyp is the torsion type ttyp 1 J sp K sp ttyp 11 like ttyp 1 but one or both atoms are in Group 16 ttyp 2 J sp K sp or vice versa ttyp 21 like ttyp 2 but one or both atoms are in Group 16 ttyp 22 like ttyp 2 but J or K is next a sp atom ttyp 3 J sp K sp ttyp 9 all other cases is the value of the torsion angle in degree Oryg is the angle value of I J K and jgz is the one for J K L The hybridizations of J and K determine ttyp The inversion terms follow starting with the number of inversion terms e g the pyramidalisation of NH3 In each line is one inversion term I J K L itypl ityp2 ityp3 Wy w2 w3 I J K and L are the atom numbers Atom J is the central one itypl ityp2 ityp3 are the types of the inversions ityp 10 atom I is C and atom L is O ityp 11 like ityp 10 but L is any atom ityp 2 Iis P 18 2 FORMAT OF KEYWORDS AND COMMENTS 275 ityp 3 I is As ityp 4 I is Sb ityp 5 I is Bi ityp 9 all other cases w1 w2 and w3 are the values of the inversion angles in degree The nonbond terms follo
231. binmax wsindex extmax thrmom 8 0 0 20 0 1 0D 18 The following options are available precision specifies precision parameter for the multipole expansions Low lmaxmom thrmom nbinmax wsindex extmax precision MARI J calculations require 1 1076 which is the de fault For higher precision calculations it should be set to 1 1078 1 107 maximum l moment of multipole expansions It should be set to a value equal at least twice the maximum angular momentum of basis functions Default value is 10 and it should probably never be set higher than 18 Threshold for moment summation For highly accurate calcula tions it should be set to 1 10724 number of bins per atom for partitioning of electron densities Default value is 8 and hardly ever needs to be changed minimum separation between bins Only bins separated more than the sum of their extents plus wsindex are considered as far field Default is 0 0 and should be changed only by the experts maximum extent for charge distributions of partitioned densities Extents with values larger then this are set to extmax Hardly ever needs to be changed Seminumeric HF Exchange If the keyword senex is found in the control file ridft performs a Hartree Fock SCF calculation using the seminumerical approximation for HF exchange Standard dft grids can be used for the numerical integration Smaller grids 1 0 and the corresponding m grids m1 m2 have been def
232. bjTaibj 9 4 aibj for a closed shell case in an open shell case an additional spin summation has to be included The cluster amplitudes ta and taibj are obtained as solution of the CC2 cluster equations 109 Qu ml A To HF 0 9 5 Qu u2 H F T2 HF 0 9 6 with H exp T H exp T where py and u2 denote respectively the sets of all singly and doubly excited determinants The residual of the cluster equations Q ta taibj is the so called vector function The recommended reference for the CC2 model is ref 109 the implementation with the resolution of the identity approximation RI CC2 was first described in ref 10 Advantages of the RI approximation For RI CC2 calculations the oper ation count and thereby the CPU and the wall time increases as for RI MP2 calculations approximately with O O V2N where O is the number of occupied and V the number of virtual orbitals and Ny the dimension of the auxiliary basis set for the resolution of the identity Since RI CC2 calculations require the itera tive solution of the cluster equations 9 5 and 9 6 they are about 10 20 times more expensive than MP2 calculations The disk space requirements are approxi mately O 2V N N N2 double precision words The details of the algorithms are described in ref 10 for the error introduced by the RI approximation see refs 92 111 Required input data In addition to the above mentioned prereq
233. c orbitals which are to be selected threshold r means the threshold to be applied for the selection criteria occ or eig default 0 1 Example mao selection threshold 0 09 atom c 1 3 5 nmao 5 method eig threshold 0 1 atom o 2 nmao 3 method man olabel olabel 3 5 18 2 plot fit FORMAT OF KEYWORDS AND COMMENTS 343 option plot is out of fashion to plot quantities on a grid rather use pointval in connection with dscf ridft rimp2 or egrad as described below If nev ertheless plot is active you need grid 1 mo 4aig origin 000000 000000 000000 vector1 1 000000 000000 000000 vector2 000000 1 000000 000000 gridi range 5 000000 5 000000 points 100 grid2 range 5 000000 5 000000 points 100 outfile 4alg to obtain two dimensional plot data of mo 4alg the plane is specified by origin and two vectors with grid range and number of grid points which is written to file dalg Several plots may be obtained 1 2 etc at the same time Use tool konto to visualize the plot Note This is the old fashioned way to plot MOs and densities A new and easier one is to use pointval as described below if fit is active you need vdw_fit shell number_of_gridpoints distance_from_vdW_surface refine value_of_potential shell Each line refers to all atoms the line specifies a spherical layer of grid points around the atoms The number of points and their distance from the van der Waals su
234. can be called in a special analysis mode which allows to analyse densities and combination e g differences of densities evaluated in preceeding ricc2 calculations Default density analysis and visualization As in a single calculations with the ricc2 program one electron densities can be calculated for more than one method and or electronic state the interface to the analysis and visualization routines require the specification of a unique level of cal culation and a unique state This is presently done through the geoopt flag which determines the method state for which results are written to interface files e g control gradient or xxx map In ground state calculations ricc2 will pass to the density analysis routines the correlated total and for UHF based calculations also the spin density and the canonical SCF orbitals from which the SCF spin density is constructed All options described in chapter 14 are available from within the ricc2 program apart from the evaluation of electrostatic moments which would interfere with the calculation of expectation values requested through the fop option in response In excited state calculation ricc2 will pass the excited state total and for UHF based calculation in addition the spin density But no ground state densities and or uncorrelated densities or orbitals Thus for excited states the ricc2 program does in difference to egrad not print out a comparison with the ground state SCF density
235. can be set by the 1hfprep script lhf off diag on off numerical slater off on pot file save load asymptotic dynamic 1 d 3 on off homo 1biu homob 1biu ONLY UNRESTRICTED conj grad conv 1 d 7 maxit 20 output 1 cgasy 1 slater dtresh 1 d 9 slater region 7 0 0 5 10 0 0 5 18 2 FORMAT OF KEYWORDS AND COMMENTS 295 corrct region 10 0 0 5 slater b region 7 0 0 5 10 0 0 5 ONLY UNRESTRICTED corrct b region 10 0 0 5 ONLY UNRESTRICTED correlation func lyp func vwn Explanantion off diag off calculation of the KLI exchange potential off diag on calculation of the LHF exchange potential default numerical slater on the Slater potential is calculated numerically everywhere numerical slater off the Slater potential is calculated using orbital basis set default asymptotic off The exchange potential is just replaced by 1 r in the asymptotic re gion asymptotic on Full asymptotic treatment and use of the numerical Slater in the near asymptotic region asymptotic dynamic 1 d 3 Automatic switching on off to the special asymptotic treatment if the differential density matrix rms is below above 1 d 3 default pot file save the converged Slater and correction potentials for all grid points are saved in the files slater pot and corrct pot respectively pot file load The Slater potential is not calculated but read from slater pot the cor rection potential is instead recalculat
236. cc2 ccs cis mp2 didiag cis d energy only cis dinf adc 2 cc2 ccsd mp3 mp4 ccsd t restart norestart hard_restart nohard_restart 18 2 FORMAT OF KEYWORDS AND COMMENTS 317 conv oconv lindep 15 maxiter 25 mxdiis 10 maxred 100 iprint 1 fmtprop 15 8 geoopt model cc2 state a 2 scs cos 1 2d0 css 0 3333d0 sos gsonly didiag intcorr specifies the ab initio models methods for ground and excited states and the most important parameters and thresholds for the solution of the cluster equations linear response equations or eigenvalue problems If more than one model is given the corresponding calculations are performed successively Note The CCS ground state energy is identical with the SCF reference energy CCS excitation energies are identical to CIS excitation energies The MP2 results is equivalent to the result from the rimp2 module cis dinf denotes the iterative CIS D variant CIS D The option ccsd t request a CCSD calculation with the perturbative triples correction CCSD T and as a side result also the CCSD T energy will be printed mp2 didiag Request the calculation of the D diagnostic in MP2 energy calculations ignored in MP2 gradient calculations Note that the evaluation of the D diagnostic increases the computational costs of the RI MP2 energy calculation roughly by a factor of 3 cis d energy only If the energy only flag is given after the cis d keyword i
237. cc2 and egrad If some of following keywords are set correspond ing operations will be performed in the end of these programs If one desires to skip the MO or density generating step in case of programs dscf ridft rimp2 and mpgrad it is possible to directly jump to the routine performing analyses by typing lt program gt proper Currently the respective keywords have to be inserted in the control file by hand not by define Here we briefly present the functionalities i e the default use of keywords non default suboptions are described in detail in Section 18 2 18 227 228 CHAPTER 14 PROPERTIES AND ANALYSIS AND GRAPHICS Electrostatic moments up to quadrupole moments are calculated by default for the above modules Relativistic corrections mvd leads to calculation of relativistic corrections for the SCF total density in case of dscf and ridft for the SCF MP2 density in case of rimp2 and mpgrad and for that of the calculated excited state in case of egrad Quantities calculated are expectation values lt p gt lt pt gt and the Darwin term gt 1 Za p Ra Note that at least the Darwin term requires an accurate descrip tion of the cusp in the wave function thus the use of basis sets with uncontracted steep basis functions is recommended Moreover note that the results for these quantities are not too reasonable if ECPs are used a respective warning is written to the output Population analyses Popul
238. cf will read the submatrices fde_ZJ mat and fde_KXC mat and add them to the Hamiltonian fde input option frozen 1 15 2 FROZEN DENSITY EMBEDDING CALCULATIONS USING THE FDE SCRIPT243 Parallel calculations If PARA_ARCH SMP and OMP calculation will be performed The flag nth nthreads can be used to specify the number of threads For example with the following command FDE p 3 nth 4 will use 4 threads Equivalent command nthreads integer fde input option nthreads integer Monomolecular and supermolecular basis set approach The p4 and ppg densities can be expanded using the supermolecular or monomolec ular basis set In a supermolecular basis set expansion the basis functions x of both subsystems are employed to expand the subsystem electron densities In a monomolecular basis set expansion instead only basis functions x centered on the atoms in the th subsystem are used to expand the corresponding density Both monomolecular and supermolecular basis set expansion of the electron densities are implemented in FDE with the flag m a monomolecular expansion is performed while for a supermolecular one s is used In the absence of both flags a monomolec ular expansion is performed by default For an accurate calculation of binding energies of weakly interacting molecular sys tems a supermolecular basis set is required to avoid the basis set superposition error Otherwise a very large monomolecular basis set is necess
239. ch explicitly enforces that n th excited state is optimized n must not be larger than the number of states specified in soes nacme 312 CHAPTER 18 KEYWORDS IN THE CONTROL FILE flag to compute Cartesian non adiabatic coupling vectors between the excited state of interest and the ground state 182 This option requires the use of weight derivatives in section dft It is only implemented for C1 symmetry 18 2 13 Keywords for Modules MPGRAD and RIMP2 If an MP2 run is to be performed after the SCF run the SCF run has to be done with at least 1 density convergence denconv 1 d 7 2 energy convergence scfconv 6 Keywords Valid for Both MPGRAD and RIMP2 maxcor n The data group maxcor adjusts the maximum size of core memory n in MB which will be allocated during the MP2 run Recommendation 3 4 of the actual main memory at most If maxcor is not found its value is set to 200 MB mp2energy Calculation of MP2 gradient is omitted only MP2 energy is calculated In connection with this keyword you may also activate the spin component scaled SCS MP2 proposed by Grimme mp2energy SCS with the default values of 6 5 for pS and 1 3 for pT which may be modified this way mp2energy SCS pt vall ps val2 freeze alg 1 2 tiu 1 The data group freeze specifies frozen orbitals in the above syntax by irreducible representations The symmetry independent and for standard applications recommended syntax is 18 2 FOR
240. ch4 or a methane The data files are to be found in the directory TURBODIR structures The library can be extended You can perform a geometry optimization at a force field level to preoptimize the geometry For this purpose the Universal Force Field UFF developed from Rapp et al in 1992 7 has been implemented in the uff module see also Section 5 4 This can also be used to calculate an analytical approximate cartesian Hessian If one does so the start Hessian for the ab initio geometry optimization is this Hessian instead of the diagonal one forceinit on carthess for relax module Recommendation Here is an easy way to get internal coordinates which should work Have coord ready before calling define In the main geometry menu proceed as follows to define redundant internals a coord read coord desy determine symmetry if you expect a higher symmetry repeat with in creased tolerance desy 0 1 you may go up to desy 1 ired get redundant internals quit main geometry menu To define internals a coord read coord desy determine symmetry i go to internal coordinate menu iaut automatic assignment of bends etc q to quit bond analysis imet to get the metric unnecessary internals are marked d now If ideg k in the head line you are done Otherwise this did not work lt enter gt go back to main geometry menu quit main geometry menu To define cartesians a coord desy CHAPTER 4 PREPAR
241. consist of two closed shell subsystems e g weakly interacting closed shell dimers e only total and binding energy calculations no gradients e serial and OMP dscf runs no MPI e monomolecular and supermolecular basis set approach e LDA GGA kinetic energy functionals for weakly interacting systems e full or pure electrostatic embedding e LDA GGA hybrid or orbital dependent exchange correlation potentials e multilevel FDE calculation e energy decompostion e FDE calculation with subsystem B taken frozen In order to perform a FDE calculation the files coord and control for the total system are necessary to take informations on atomic coordinates and basis sets The input file for the total system can be generated as usual with define but no calculation on the total system is required denconv 1 d 7 option should be defined in file control in order to better converge the embedded densities and better describe the dipole moment Given a closed shell supramolecular system with a GGA LDA exchange correlation functional the command FDE p 3 238 CHAPTER 15 FROZEN DENSITY EMBEDDING CALCULATIONS invokes an iterative resolution of the KSCED equations with revAPBEk 152 153 as approximation of the non additive kinetic potential see Eq 15 5 in the monomolec ular basis set approach The two subsystems are defined via an integer m 3 in the example above which identifies the first atom of the subsystem B in the file coor
242. correctly The D diagnostic proposed by Nielsen and Janssen 94 can also be evaluated This analysis can be triggered whenever a response property is calculated e g dipole moment with the keyword D2 diagnostic Note that the calculation of Da requires an additional O N step D2 MP2 CC2 lt 0 15 are in excellent agreement with those of higher order correlation methods for D2 MP2 CC2 gt 0 18 the results should be carefully checked 9 2 Calculation of Excitation Energies With the ricc2 program excitation energies can presently be calculated with the RI variants of the methods CCS CIS CIS D CIS D ADC 2 and CC2 The CC2 excitation energies are obtained by standard coupled cluster linear response theory as eigenvalues of the Jacobian defined as derivative of the vector function with respect to the cluster amplitudes ooz _ Wy _ f ull I Tol m EF mll nF Aw T all mHE ual rn HE me Since the CC2 Jacobian is a non symmetric matrix left and right eigenvectors are different and the right left eigenvectors E E are not orthogonal among them selves but form a biorthonormal basis if properly normalized EE Et Ei ELEY by 9 9 To obtain excitation energies only the right or the left eigenvalue problem needs to be solved but for the calculation of transition strengths and first order properties both left and right eigenvectors are needed see below A second complication that arises f
243. cp 18 ecp cu ecp 18 arep se 5 6 basis se ecp 28 arep dzp jbas se ecp 28 ecp se arep 268 CHAPTER 18 KEYWORDS IN THE CONTROL FILE note the backslash this is necessary For each type of atom one has to specify the basis set and the auxiliary fitting basis for RIDFT calculations the ECP if this is used The files basis ecp and jbas must provide the necessary information under the labels specified in atoms pople char This data group specifies the number of Cartesian components of basis func tions i e 5d and 7f in AO Basis 6d and 10f in CAO Basis for which the SCF calculation should be performed Possible values for char are AO default or CAO If CAO is used which is not recommended a core guess must be used instead of a Hiickel guess see scfmo RHF closed shells Specification of MO occupation for RHF e g alg 1 4 2 a2g 1 2 open shells type 1 MO occupation of open shells and number of open shells type 1 here means that there is only a single open shell consisting e g of two MOs b2g 1 1 b3g 1 1 roothaan 1 a 1 b 2 roothaan Roothaan parameters for the open shell here a triplet case define recognizes most cases and suggests good Roothaan parameters For further information on ROHF calculations see the sample input in Sec tion 19 6 and the tables of Roothaan parameters in Section 6 3 18 2 FORMAT OF KEYWORDS AND COMMENTS 269 UHF uhf directs the program t
244. ction The resulting surface exhibits smoother intersection seams and the segment areas are less diverse than the ones of the standard radii bases cavity construction Because gradients are not implemented the radii based isosurface cavity can be used in single point calculations only cosmo_isorad dx real spacing of the marching tetrahedron grid in A default 0 3A Cosmo in MP2 Calculations The iterative Cosmo PTED scheme see chapter 17 can be used with the mp2cosmo script Options are explained in the help mes sage mp2cosmo h Both MP2 modules Rimp2 and mpgrad can be utilized The control file can be prepared by a normal COSMO SCF input followed by a RIMP2 or mpgrad input The PTE gradients can be switched on by using the cosmo_correlated keyword RiMpP2 only Again a normal SCF Cosmo input followed by a Rimp2 input has to be generated The cosmo_correlated keyword forces dscf to keep the COSMO information needed for the following MP2 calculation and toggles on the COSMO gradient contribution Cosmo in Numerical Frequency Calculations NumForce can handle two types of Cosmo frequency calculations The first uses the normal relaxed COSMO energy and gradient It can be performed with a standard dscf or ridft COSMO input without further settings This is the right method to calculate a Hessian for optimizations The second type which uses the approach described in chapter 17 is implemented for ridft only The input is the s
245. cutoff threshold for the derivative integrals i e integrals below this threshold will be neglected in the derivative calculations Entering will bring you to the second derivative submenu Debug Options for the Derivative Programs The following menu deals only with some debug options for grad Use them with caution each of them can produce lots of useless output 4 4 THE GENERAL OPTIONS MENU 85 disple F display 1e contributions to desired derivatives onlyte F calculate 1e contributions to desired derivatives only debugile F display 1e shell contributions to desired derivatives WARNING this produces large outputs debug2e F display 2e shell contributions to desired derivatives WARNING this produces VERY large outputs debug switch for vibrational analysis force only disable transfer relations gradient only disable virial scaling invariance in basis set optimizations gradient only debugvib F notrans F novirial F use lt opt gt for enabling lt opt gt for disabling option lt opt gt lt amp gt will bring you back to GENERAL MENU without more changes lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU As there is no need to use these options normally and the menu text is self explaining no further description will be given Note that all options are logical switches and may be enabled and disabled the same way as shown for the last menu Entering will bring you to the last derivativ
246. d default 0 05 winv inverse stretch of a weak bond default 0 05 wbnd bond angle involving at least one weak bond default 0 02 wout Out of plane angle for weak bonds default 0 02 wtor dihedral angle for weak bonds default 0 02 wlnc linc coordinate for weak bonds default 0 02 wlnp linp coordinate for weak bonds default 0 02 18 2 FORMAT OF KEYWORDS AND COMMENTS 271 18 2 4 Keywords for Module UFF One has to specify only the Cartesian coordinates data group coord to start a uff run The program uff requires the data groups uff ufftopology uffgradient and uffhessian If these keywords do not exist in the control file the program will generate these data groups The data group uff contains the parameters described below The default values in the control file are 1 1 O maxcycle modus ngeq 111111 iterm 0 10D 07 0 10D 04 econv gconv 0 00 1 10 qtot dfac 0 10D 03 0 10D 04 0 30 epssteep epssearch dqmax 25 0 10 0 00 mxls dhls ahls 1 00 0 00 0 00 alpha beta gamma F F F transform lnumhess 1md The explanation of the variables are as follows maxcycle number of max optimization cycles maxcycle 1 single point calculation modus can have the values 1 or 1 If modus 1 only the topology will be calcu lated ngeq each ngeq cycle the partial charges will be calculated If nqeq 0 then the partial charges are calculated only in the first cycle if the file ufftopology do
247. d as otherwise the prepared spin state might be destroyed during the SCF iterations From this input one may start the SCF HF DFT procedure For recommended choices of DFT functionals and formulae to calculate the coupling parameters from these energy differences please consult the papers of the above mentioned authors For reasons of economy a pre optimization by a pure non hybrid DFT functional is reasonable Important For the converged wave function one should check whether the resulting state is really the desired one This can quite reliably be done by a Mulliken popu lation analysis For this purpose add pop to the control file type ridft proper or dscf proper respectively and check the signs of the calculated numbers of unpaired electrons in the output 00 00 76 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE 4 4 The General Options Menu After you specified all data concerning the molecule you want to examine you are on your way to the last of the four main menus Before reaching it you will perhaps get a message like the following DO YOU WANT TO DELETE DATA GROUPS LIKE energy grad hessian hessian projected last energy change maximum norm of internal gradient dipgrad vibrational normal modes vibrational spectrum cartesianforce interspace LEFT OVER FROM PREVIOUS CALCULATIONS DEFAULT n define has scanned your input file for this session and found some data groups which might have become
248. d integral prescreening and differential density scheme ridft and rdgrad are modules for very efficient calculation of energy and gradient at the Hartree Fock HF and DFT level 45 Both programs employ the Resolution of the Identity approach for computing the electronic Coulomb interaction RI J This approach expands the molecular electron density in a set of atom centered auxiliary functions leading to expressions involving three center ERPs only This 121 122 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS usually leads to a more than tenfold speedup for non hybrid DFT compared to the conventional method based on four center ERI s for example the dscf or grad module The combination of RI J for Coulomb interactions with a case adapted conven tional exchange treatment reduces the scaling behaviour of the conventional ex change evaluation required in HF SCF and hybrid DFT treatments Usage of ridft and rdgrad for HF and hybrid DFT is of advantage as compared to dscf and grad for larger systems where it reduces computational costs significantly The most important special features of the ridft and rdgrad modules are e A very efficient semi core algorithm for energy calculation The most expen sive three center integrals are kept in memory which significantly reduces the computational time for small and middle sized molecules The amount of stored integrals is controlled by simply specifying the amount of free memo
249. d of the supramolecular system with n atoms where the atoms 1 m 1 belong to the subsystem A while the atoms m n to the B one Thus the file coord must contains first all the atoms of the system A and then all the atoms of the system B As an example we report here the FDE p 3 output for the HF dimer FDE Version 1 02 Frozen Density Embedding Main Driver Scf like procedure for closed shell interacting systems dimers program development Savio Laricchia Eduardo Fabiano Fabio Della Sala S Laricchia E Fabiano L A Constantin F Della Sala J Chem Theory Comp 2011 S J L Laricchia E Fabiano F Della Sala Chem Phys 133 164111 2010 A Constantin E Fabiano S Laricchia F Della Sala Phys Rev Lett 106 186406 2011 Ss Laricchia E Fabiano F Della Sala Chem Phys Lett 518 114 2011 Sun Mar 25 23 00 01 CEST 2012 Monomolecular basis set approach Serial calculation will be performed running home fabiods REDO branch64 TURBOMOLE bin em64t unknown linux gnu dscf b lyp exchange correlation potential in KS supermolecular calculation revapbek kinetic energy approximation will be used Default convergence criterion on the system dipole 0 005 Default value of starting damping parameter is 0 45 Default value of step damping parameter is 0 10 15 2 FROZEN DENSITY EMBEDDING CALCULATIONS USING THE FDE SCRIPT239 Default value of maximum damping parameter
250. d simultaneous calculation of gradients for several states is in the present version not possible convergence threshold for norm of residual vectors in eigen value problems is set to 107 If not given a default value is used which is chosen as max 10 107 C 10 where conv refers to the values given in the data group ricc2 preopt convergence threshold used for preoptimization of CC2 eigenvectors is set to 107 Pre P default 3 thrdiis 324 CHAPTER 18 KEYWORDS IN THE CONTROL FILE threshold 10 44 5 for residual norm below which DHS extrapolation is switched on in the modified Davidson algorithm for the non linear CC2 eigenvalue problem default 2 leftopt If the flag leftopt is set the left eigenvectors are computed default is to compute the right eigenvectors for test purposes only bothsides The bothsides flag enforces the calculation of both the left and the right eigenvectors for test purposes only response fop unrelaxed_only operators diplen sop operators diplen diplen freq 0 077d0 gradient conv 6 zconv 6 semicano nosemicano thrsemi 3 In this data group you have to give additional input for the calculation of ground state properties and the solution of response equations fop This flag switches on the calculation of ground state first order prop erties expectation values The operators flag can be followed by a list of operators see below for which
251. d by multidimensional BFGS rank n update for the hessian pulay suboptions try to find an optimal linear combination of the coordinates of the numpul previous optimization cycles as specified by modus see below 332 CHAPTER 18 KEYWORDS IN THE CONTROL FILE Available suboptions are numpul integer number of geometries to be utilized maxpul integer maximum number of geometries minpul integer minimum number of geometries needed to start update modus char fmode char lt g g gt or lt g dq gt or lt dq dq gt defines the quantity to be minimized dq internal coordinate change fmode specifies the force constants to be used only if char lt g dq gt or lt dq dq gt fmode static use static force constants fmode dynamic use updated force constants fail real real defines the threshold for the quantity g dq g dq which defines the angle between gradient vector and coordinate change default 0 1 If pulay is used in connection with a multidimensional BFGS update for the hessian than the default is real 0 0 If eal gt real the pulay update for the geometry is expected to fail and will be ignored For example pulay numpul 4 maxpul 4 minpul 3 modus lt dq dq gt static fail 0 2 options for forceupdate diagonal update only the diagonal force constants update for off diagonals will be suppressed only active if method ms dfp bfgs offdamp real this allows to damp off
252. d constraints are listed by atom index and supercede auto generated constraints A positive third number fixes the constraint at that value while zero fixes the constraint at the current distance and a negative number unsets the constraint The output of frog contains the full list of constrained atom pairs and their current constraints in explicit format User defined instructions allow the user to tell frog to change some aspect of the MD run at some point in time t real number The same format is used for md_status above Here is an example md_action fix total energy from t 2000 0 anneal from t 2500 0 free from t 3000 0 In this example starting from the time 2000 0 a u velocities are to be scaled every step to keep average total energy constant Then from 2500 0 a u gradual cooling 358 CHAPTER 18 KEYWORDS IN THE CONTROL FILE at the default rate annealing is to occur until the time 3000 0a u when free Newtonian dynamics will resume Here are all the possible instructions md_action fix temperature from t lt real gt fix total energy from t lt real gt These commands cause velocities to be scaled so as to keep the average ki netic energy i e quasi temperature or the average total energy approximately constant This is only possible once enough information about run history is available to give reliable statistics Keywords log_history ke_control md_action set temperature at t lt real
253. d for DFT calculations and it works for all exchange correlation func tionals including LHF Note that for hybrid functionals only the Kohn Sham part of the potential will be computed the HF part is a non local operator and can t be plotted For GGA functional the full potential will be computed local and non local terms For line plots the output file is tx vec For UHF calculations the output files are tx vec alpha spin potential and sx vec beta spin potential For a line plot the file has three columns 1 total potential 2 local term or Slater potential for LHF 3 non local terms or Correction term for LHF Output formats may be specified by e g fmt xyz if written to the same line as pointval Supported are XYZ plt map in case of scalars density L MO amplitudes electrostatic potential this format is x y z f x y z In case of vectors components of the vector and its norm are displayed This format is valid for all types of grid 3D plane line points see below it is the default format in case of calculation of values at single points Output file suffix is xyz only for 3D default in this case Data are written to binary files that can be directly read by gOpenMol Note that this output is restricted to scalar quantities thus in case of vectors E field only the norm is plotted Output file suffix is plt only for 3D Data are written to ASCII files that can be imported by e g gOpenMol
254. d for single determinant restricted open shell Hartree Fock ROHF reference wavefunctions cmp Sec 8 3 Note that presently no gradients are available for MP2 and CC2 with ROHF reference wavefunctions The second order models MP2 CIS D CIS D ADC 2 and CC2 can be com bined with a spin component scaling SCS or SOS Not yet available for second order properties For the SOS variants ground state and excitation energies can be computed with O N scaling costs if the Laplace transformation LT keyword Laplace is enabled For calculations with CCSD CCSD T and other higher order models beyond CC2 see Chapter 10 Prerequisites Calculations with the ricc2 module require almost the same prerequisites as RI MP2 calculations 1 a converged SCF calculation with the one electron density convergence thres hold set to denconv 1 d 5 or less 2 an auxiliary basis defined in the data group cbas 3 if orbitals should be excluded from the correlation treatment and excitation processes the data group freeze has to be set 4 the maximum core memory which the program is allowed to allocate should be defined in the data group maxcor the recommended value is 66 75 of the available physical core memory 5 depending on the type of calculations that should be carried out additionally the data groups ricc2 excitations response Laplace rir12 and 1cg have to be set see below and Section 18 2 14 176 CHAPTER
255. d for the perturbative triples corrections Disc space requirements In difference to CC2 and MP2 the CCSD model does no longer allow to avoid the storage of double excitation amplitudes taibj and intermediates of with a similar size Thus also the disc space requirements for the CCSD calculation are larger than for RI MP2 and RI CC2 calculation for the same system For a closed shell CCSD ground state energy calculations the amount of disc space needed can be estimated roughly as Nuisk an race mprrs O N 128 x 1024 MBytes 10 24 where N is the number of basis functions O the number of occupied orbitals and mprrs the number of vectors used in the DIIS procedure by default 10 see Sec 18 2 14 for details For closed shell CCSD T calculations the required disc space is with Naw 57 502N oN 128 x 1024 MBytes 10 25 somewhat larger For calculations with an open shell UHF or ROHF reference wavefunctions the above estimates should be multiplied by factor of 4 Memory requirements The CCSD and CCSD T implementation in Turbo mole uses multi pass algorithms to avoid strictly the need to store any arrays with a size of N or O N or larger as complete array in main memory Therefore the min imum memory requirements are relatively low although is difficult to give accurate estimate for them 212 CHAPTER 10 CCSD CCSD F12 AND CCSD T On should however be aware that if the amount of memory prov
256. d to minimizations It is sometimes necessary to do restart several times including a recomputation of the Hessian before the saddle point can be located Assuming you do find the TS it is always a good idea to recompute the Hessian at this structure It is fairly common especially when using symmetry that at your TS there is a second imaginary frequency This means that you have not found the correct TS The proper procedure is to distort the structure along the extra imaginary normal mode using the tool screwer see Section 1 5 Very often such a distortion requires also lowering the point group symmetry The distortion must be large enough otherwise the next run will come back to the invalid structure 5 3 Program Relax 5 3 1 Purpose relax drives and controls a non linear optimization procedure to locate the minimum or a stationary point of a function f x In TURBOMOLE f is always the electronic energy and the coordinates x will be referred to as general coordinates They include e cartesian atomic coordinates e internal atomic coordinates e exponents contraction coefficients and scaling factors of basis functions e a global scaling factor a common scaling factor for all basis set exponents The optimization employs an iterative procedure based on gradients Vf of the current and if available previous iterations Various procedures can be applied steepest descent Pulay s DIIS quasi Newton conjugate gradien
257. d_send_dens This means that the density matrix is computed by one node and distributed to the other nodes rather than computed by every slave In the parallel version of ridft the first client reads in the keyword ricore from the control file and uses the given memory for the additional RI matrices and for RL integral storage All other clients use the same amount of memory as the first client does although they do not need to store any of those matrices This leads to a better usage of the available memory per node But in the case of a big number of auxiliary basis functions the RI matrices may become bigger than the specified ricore and all clients will use as much memory as those matrices would allocate even if that amount is much larger than the given memory To omit this behavior one can use ricore_slave integer specifying the number of MBs that shall be used on each client For parallel jobex runs one has to specify all the parallel keywords needed for the different parts of the geometry optimization i e those for dscf and grad or those for ridft and rdgrad or those for dscf and mpgrad Chapter 19 Sample control files 19 1 Introduction The file control is the input file for TURBOMOLE which directly or by cross references provides the information necessary for all kinds of runs and tasks control is usu ally generated by define the input generator The following sample control files cover a variety of methods and s
258. ded to exclude all non valence orbitals from RIRPA calculations as neither the TURBOMOLE standard basis sets SVP TZVPP and QZVPP nor the cc pVXZ basis set families with X D T Q 5 6 are designed for correlation treatment of inner shells for this purpose polarisation functions for the inner shells are needed The default selection for frozen core orbitals in Define orbitals below 3 a u are frozen provides a reasonable guess If core orbitals are included in the correlation treatment it is recommended to use basis sets with additional tight correlation functions as e g the cc pwCVXZ and cc pCVXZ basis set families e We recommend the use of auxiliary basis sets optimized for the corresponding MO basis sets The auxiliary basis sets optimized for RI MP2 and RI CC2 are suitable for rirpa 133 correlation energy calculations 217 e For systems with heavy atoms where ECPs are required HXX RIRPA total energies can be computed in two steps RIRPA correlation energies can be obtained using the nohxx option and the HXX energy can then be computed separately for example in ridft if the RI J approximation is used for the HXX Coulomb integrals To compute the HXX energy disable dft in the control file and perform a single SCF iteration by setting scfiterlimit 1 Adding the total energy from ridft and the correlation energy from rirpa together gives HXX RIRPA total energies Note the molecular orbitals are altered by ridft after a single i
259. define sets these parameters automatically If not you have to enter them yourself In this case you will get the following message ROOTHAAN PARAMETERS a AND b COULD NOT BE PROVIDED TYPE IN ROOTHAAN a AND b AS INTEGER FRACTIONS OR ENTER val FOR AN AVERAGE OF STATES CALCULATION OR ENTER amp TO REPEAT OCCUPATION NUMBER ASSIGNMENT Note that not all open shell systems can be handled in this way It is possible to specify a and b for atomic calculations with s p d and d configurations and for calculations on linear molecules with 7 and 6 configurations Furthermore it is possible to do calculations on systems with half filled shells where a 1 b 2 In the literature you may find tabulated values for individual states arising from d configurations but these are not correct Instead these are parameters for an average of all states arising from these configurations You can obtain these values if you enter val on the above question For a detailed description see Section 6 3 4 3 5 Start MOs for broken symmetry treatments flip Broken symmetry treatments suggested by e g Noodleman or Ruiz are a popular tool for the calculation of spin coupling parameters in the framework of DFT As an example one might consider two coupled Cu centers e g for a hypothetical arrangement like this coord 0 0 2 7 0 0 cu 0 0 2 7 0 0 cu 0 0 6 1 0 0 f 0 0 6 10 0 f 2 4 0 0 0 0 f 2 4 0 0 0 0 f end n The high spi
260. defines a periodic perfect and infinite three dimensional lattice of point charges corresponding to the bulk CaF2 structure In order to use this lattice for PEECM calculation we have to make space for our QM cluster and the isolating shell This is done by specifying the part of the lattice that is virtually removed from the perfect periodic array of point charges to make space for the cluster The positions of the removed point charges are specified in the subsection cluster of the embed keyword Note that the position of the QM cluster and the isolating shell must exactly correspond to the removed part of the crystal otherwise positions of the cluster atoms would overlap with positions of point charges in the periodic lattice resulting in a nuclear fusion cluster F 0 00000000000000 0 00000000000000 0 00000000000000 Ca 2 61994465796043 2 61994465796043 2 61994465796043 Ca 2 61994465796043 2 61994465796043 2 61994465796043 Ca 2 61994465796043 2 61994465796043 2 61994465796043 Ca 2 61994465796043 2 61994465796043 2 61994465796043 6 6 PERIODIC ELECTROSTATIC EMBEDDED CLUSTER METHOD oe s Rs Bs 23988931592086 00000000000000 23988931592086 00000000000000 00000000000000 00000000000000 23988931592086 23988931592086 23988931592086 23988931592086 23988931592086 repeated for C az216 F389 end 00000000000000 00000000000000 00000000000000 23988931592086 00000000000000
261. dense We recommend however the use of so called multiple grids m3 m5 SCF iterations with grid 1 3 final energy and gradient with grid 3 5 Usually m3 is fine for large or delicate systems try m4 For a reference calculation with a very fine grid and very tight thresholds use reference as grid specification instead of gridsize xy Note the functionals b3 lyp_Gaussian and s vwn_Gaussian are made available only for comparability with Gaussian The functional VWNIII is much less well founded than VWN5 and the TURBOMOLE team does not recommend the use of VWNIII RI Dscf does not run with the keyword rij you must call the RI modules Ridft and Rdgrad for energy and gradient calculations However it does run with the keyword rik but it will ignore all RI settings and do a conventional non RI Hartree Fock or DFT calculation rij Enforces an RI J calculation if module ridft is used can be used for Hartree Fock as well as for DFT calculations with pure or hybrid functionals 292 CHAPTER 18 KEYWORDS IN THE CONTROL FILE ridft Obsolete keyword use rij instead rik Enforces a RI JK calculation if module ridft is used can be used for Hartree Fock as well as for DFT calculations with pure or hybrid functionals ricore integer Choose the memory core available in megabyte for special arrays in the RI calculation the less memory you give the more integrals are treated directly i e recomputed on the fly in
262. e quit The meaning of the four suboptions pot fld fldgrd and shld will probably present no problems to you For each of them however you will have to specify at which point s this property should be calculated This is accomplished by one or more data groups points in file control After you chose one or more of the above options you will therefore reach the next submenu which deals with the specification of these data groups there are 1 data groups points manipulate data group s points a add another data group m lt integer gt modify lt integer gt th data group m all modify all data groups d lt integer gt delete lt integer gt th data group d all delete all data groups off lt integer gt switch off lt integer gt th data group off all switch off all data groups on lt integer gt switch on lt integer gt th data group on all switch on all data groups s scan through data groups quit The first line informs you how many of these data groups already exist in your control file Each of these data groups may consist of several points at which the properties will be calculated You may now create new data groups delete old 4 4 THE GENERAL OPTIONS MENU 93 ones or simply switch on or off individual data groups without deleting them from control The number of different data groups points as well as the number of points in each of them are not limited However if you use many points you
263. e sponding unrelaxed properties are also automatically evaluated at essentially no ad ditional costs Therefore the calculation of unrelaxed properties can not be switched off when relaxed properties have been requested Again the construction of gradients requires the same variational densities as needed for relaxed one electron properties and the solution of the same equations The construction of the gradient contributions from one and two electron densities and derivative integrals takes approximately the same time as for ground states gradients approx 3 4 SCF iterations and only minor extra disk space The implementation of the excited state gradients for the RI CC2 approach is described in detail in Ref 14 There one can also find some information about the performance of CC2 for structures and vibrational frequencies of excited states For the calculation of an excited state gradient with CC2 at a single point without geometry optimization and if it is not a calculation with NumForce one can use the input ricc2 cc2 excitations irrep al nexc 2 xgrad states al 2 Note that presently it is not possible to compute gradients for more than one excited state in one ricc2 calculation For geometry optimizations or a numerical calculation of the Hessian with NumForce the wavefunction model and the excited state for which the geometry should be optimized have to be specified in the data group ricc2 with the keyword geoopt
264. e behavior of the optimization procedure scale factors of contracted basis functions will not be affected by the logarithm suboption scale ALL basis set exponents will be optimized as scale factors i e contracted blocks and single functions will be treated in the same way if both suboptions scale and logarithm are given the log arithms of the scale factors will be optimized global on off optimize a global scaling factor for all basis set exponents default off NOTES basis and global have to be used exclusively e if o0ptimize has been specified but forceapprox is absent the option forceinit on is switched on by default e specification of the option interconversion on will over ride optimize coordinateupdate options define some variables controlling the update of coordinates Available options are dqmax real maximum allowed total change for update of coordinates The maximum change of individual coordinate will be limited to dqmaz 2 and the col lective change dq will be damped by dgmaz dq dq if dq dq gt ddmax4 default 0 3 interpolate on off calculate geometry update by inter extrapolation of geometries of the last two cycles the interpolate option is always switched on by default but it is only active ANY time if steepest descent update has been cho sen i e forceupdate method none otherwise it will only be activated if the DIIS update for the geometry is expected to fail
265. e executed sequentially by a single thread and the incore option will be ignored if more than one thread is used Semi direct dscf calculations i e if a size larger than 0 is given two electron integral scratch file in scfintunit can not be combined with the OpenMP parallel runs The program will than stop with error message in the first Fock matrix construction Multi thread parallelization of aoforce escf and egrad The parallelization of those modules is described in 22 and is based on fork and Unix sockets Except setting PARNODES which triggers the environment variable SMPCPUS nothing has to be set in addition Alternatively the binaries can be called with smpcpus lt N gt command line option or with the keyword smp_cpus in the control file The total memory used in such parallel calculations is approximately the amount of ricore plus the number of CPUs times maxcor Multi thread parallelization of dscf grad ridft and rdgrad Instead of the default binaries used in the SMP version setting TM_PAR_FORK on will cause the TURBOMOLE scripts to use the multi threaded versions of dscf grad ridft and rdgrad The efficiency of the parallelization is usually similar to the 3 2 PARALLEL RUNS 43 default version Global Arrays parallelization of ridft and rdgrad ridft and rdgrad are parallelized with MPI using the Global Arrays toolkit Different to the MPI version ridft and rdgrad also run in parallel for hybrid
266. e g 1t2g1_a plt 1t2g2_a plt and 1t2g3_a plt contain the amplitutes of the three columns of the first irrep alpha spin of type tag Two component wavefunctions only module ridft and only if soghf is set By default only the density of the chosen spinors is written in files named e g 10a_d plt Visualization of the amplitudes of the different spinor parts is achieved e g by pointval mo 10 12 15 minco real where real is a plotting threshold that may take values between zero and one The corresponding part I of the spinor Re a Im a Re Im will be written to file if NT see below is larger than that threshold Nt tr D S T X Tx T Dw gt Civ Ciu i The filenames consist of the number of the spinor according to file EIGS and an additional number for the respective part of the spinor 1 for Re a 2 for Im a 3 and 4 for the corresponding parts e g 10a_4 p1t for the Im 3 of spinor 10 Localised molecular orbitals If one has generated localized molecular orbitals LMOs see above they can also be visualized pointval lmo 3 6 8 as an example leads to calculation of amplitudes for LMOs 3 6 and 8 The coeff cients are read from file 1mos UHF lalp and 1bet the numbering is due to the output from the localizaton section For an UHF case this means If you included in the localization procedure e g 5 a type orbitals and 3 8 type orbitals then if you are interested in plotting the G type LMOs only you hav
267. e latter using LDA GGA kernels not the hybrid ones 16 2 Implementation Both the OEP EXX and LHF methods can be used in spin restricted closed shell and spin unrestricted open shell ground state calculations Both OEP EXX and LHF are parallelized in the OpenMP mode 16 2 1 OEP EXX In the present implementation the OEP EXX local potential is expanded as 160 VEXX p Ye oe ae 16 6 where gp are gaussian functions representing a new type of auxiliary basis set see directory xbasen Inserting Eq 16 6 into Eq 16 2 a matrix equation is easily obtained for the coefficient cp Actually not all the coefficients cp are independent each other as there are other two conditions to be satisfied the HOMO condition see Eq 16 4 and the charge condition XE ono 1 16 7 P which ensures that v X r approaches 1 r in the asymptotic region Actually Eq 16 6 violates the condition 16 5 on the HOMO nodal surfaces such condition cannot be achieve in any simple basis set expansion Note that for the computation of the final KS Hamiltonian only orbital basis set matrix elements of vEX are required which can be easily computes as three index Coulomb integrals Thus the present OEP EXX implementation is grid free like Hartree Fock but in contrast to all other XC functionals 252 CHAPTER 16 ORBITAL DEPENDENT DFT 16 2 2 LHF In the LHF implementation the exchange potential in Eq 16 3 is computed
268. e new unit It is also possible to use a part of your molecule as substituting unit e g if you have some methyl groups in your molecule you can create further ones by substitution Some attention is required for the specification of this substituting unit because you have to specify the atom which will be deleted upon bond formation too If you enter the filename from which the structure is to be read starting with the file will be taken from the structure library see Section 4 1 Definitions of internal coordinates will be adjusted after substitution but no new internal coordinates are created This command offers a submenu which contains everything related to internal coordinates It is further described in Section 4 1 2 56 frag w file name del banal CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE This command offers a submenu which allows you to manipulate the molecular geometry i e to move and rotate the molecule or parts of it It is further described in Section 4 1 3 Here the fragments will be defined as being used by the jobbsse script in order to do a calculation osing the counter poise correction scheme In this menu up to three monomers can be defined together with their charges and their symmetry When assigning atom numbers to frag ments if x is entered instead of a number the program will request the first and last atoms of a range This will be useful for very large fragments The com
269. e number of frozen orbitals should be checked and if neccessary corrected 5 6 1 Options Given a shell the usage is nohup jobbsse amp This command invokes cp correction and if needed structure optimization using the default program statpt Note that the program needs to know which calculation is being done Structure optimizations using program relax can be performed using relax flag nohup jobbsse opt relax amp nohup means that the command is immune to hangups logouts and quits amp runs a background command jobbsse accepts the following arguments control ling the level of calculation convergence criteria and many more for example nohup jobex gcart 4 amp energy integer converge total energy up to 10 lt integer gt Hartree default 6 gcart integer converge maximum norm of cartesian gradient up to 10 lt integer gt atomic units default 3 c integer perform up to integer cycles default 100 gradient calculate the gradient as well opt optimise the structure relax use the relax program for force relaxation level level define the optimization level level scf dft mp2 or cc2 default is scf Note that the program needs this input If the level is DFT the grid will be automatically set to m4 ri use RI modules ridft and rdgrad fast Coulomb approxi mation instead of dscf and grad as well as rimp2 instead of mpgrad l lt path gt employ programs from directory lt path gt mem i
270. e ricc2 program NTOs and their weights the singular values can be calculated with ricctools E g using the right eigenvectors for the second singlett excited state in irrep 1 ricctools ntos CCREQ 2 1 1 The results for the occupied and virtual NTOs will be stored in files named re spectively ntos_occ and ntos_vir Note that the NTO analysis ignores for the correlated methods CIS D ADC 2 CC2 CCSD etc the double excitation con tributions and correlation contributions to the ground state This is no problem for single excitation dominated transition out of a good single reference ground state in particular if only a qualitative picture is wanted but one has to be aware of these omission when using NTOs for states with large double excitation contributions or when they are used for quantitative comparisons Fit of charges due to the electrostatic potential esp_fit fits point charges at the positions of nuclei to electrostatic potential arising from electric charge dis tribution for UHF cases also for spin density also possible in combination with soghf For this purpose the real electrostatic potential is calculated at spher ical shells of grid points around the atoms By default Bragg Slater radii rgs are taken as shell radii A parametrization very close to that suggested by Kollman a multiple shell model with shells of radii ranging from 1 4 rygw to 2 0 ryaw Tvaw is the van der Waals radius U C Sing
271. e search keyword 1les isopts 6 Sets the number of points for interpolation between the two isotopes compared by the isosub option to six Default value is 21 Keywords for the treatment of only selected nuclear displacement vectors ironly CPHF iteration is done only for distortions that are IR active ramanonly les CPHF iteration is done only for distortions that are Raman active This causes a lowest Hessian eigenvalue search to be performed instead of a complete force constant calculation The lowest eigenvalue search consists of the calculation of a guess Hessian and macro iterations to find the solution vector s for the lowest eigenvalue s In each macro iteration the CPHF equations are solved for the present search vector s les all 1 means that one lowest eigenvalue for each irrep will be determined other numbers of lowest eigenvalues per irrep are admissible too Different numbers of lowest eigenvalues for different irreps are requested by e g les al 3 308 CHAPTER 18 KEYWORDS IN THE CONTROL FILE a2 all b2 1 The convergence criterion of the Davidson iterations for the solution of the CPHF equations as well as the maximal residual norm for the lowest Hessian eigenvalue in the macro iteration are specified by forceconv as explained above The maximum number of macro iterations is specified by lesiterlimit x with the default x 25 The maximum number of iterations for each solution of the C
272. e submenu 4 4 3 Relax Options Program relax has a huge variety of options to control its actions which in program define are grouped together in eight consecutive menus These are only briefly described in the following sections for a more detailed discussion of the underlying algorithms refer to the documentation of program relax see Section 5 3 Only experts should try to change default settings Optimization Methods The first of the relax subgenus deals with the type of optimization to be performed int F INTERNAL coordinates crt F CARTESIAN coordinates bas F BASIS SET exponents scale factors glb F GLOBAL scaling factor use lt opt gt for enabling lt opt gt for disabling option lt opt gt lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU 86 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE You can choose between a geometry optimization in the space of internal coordi nates in this case you will need definitions of internal coordinates of course or in the space of Cartesian coordinates these possibilities are mutually exclusive of course Furthermore optimizations of basis set parameters exponents contraction coefficients and scaling factors or of a global scaling factor is possible these options are also exclusive but can be performed simultaneous to a geometry optimization For the geometry optimization you should normally use internal coordinates as they provide better convergence characte
273. e to type pointval lmo 6 8 Natural molecular orbitals for two component wavefunctions only mod ule ridft and only if soghf is set In two component calculations it is often useful to visualize natural molecular orbitals In contrast to one component calculations the occupation numbers are no longer close to zero one or two but can take any value between zero and two Therefor natural orbitals file natural natural orbital occupation file natural has to be set additionally to soghf also possible via define By setting pointval nmo 9 in control file a gOpenMol compatible file named nmo_9 p1t is written 234 CHAPTER 14 PROPERTIES AND ANALYSIS AND GRAPHICS Natural atomic orbitals If one has generated natural molecular orbitals NAOs see above they can be visualized with the following command in the control file pointval nao 7 9 12 where the numbers of the NAOs are in the output of the population analysis Natural transition orbitals If natural transition orbitals NTOs for electronic excitations are available in files named nto_nocc and nto_vir for respectively the occupied and virtual NTOs plot files for visualizing them can be generated by setting pointval nto 1 5 This will generate plot files for the first five occupied and virtual NTOs The plot file are named nto_vir_n plt where n is the NTO index Non default grids are decribed in detail in Sections 18 2 18 Calculation of the above quantities at
274. ecially for larger molecules and or basis sets set ricore to a small value of a few hundred MB only 3 2 2 Running Parallel Jobs MPI case The parallel version of TURBOMOLE runs on all supported systems e workstation cluster with Ethernet Infiniband Myrinet or other connection e SMP systems e or combinations of SMP and cluster 44 CHAPTER 3 HOW TO RUN TURBOMOLE Setting up the parallel MPI environment In addition to the installation steps described in Section 2 see page 29 you just have to set the variable PARA_ARCH to MPI i e in sh bash ksh syntax export PARA_ARCH MPI This will cause sysname to append the string _mpi to the system name and the scripts like jobex will take the parallel binaries by default To call the parallel versions of the programs ridft rdgrad dscf grad ricc2 or mpgrad from your command line without explicit path expand your PATH environment variable to export PATH TURBODIR bin sysname PATH The usual binaries are replaced now by scripts that prepare the input for a parallel run and start mpirun or poe on IBM automatically The number of CPUs that shall be used can be chosen by setting the environment variable PARNODES export PARNODES 8 The default for PARNODES is 2 Finally the user can set a default scratch directory that must be available on all nodes Writing scratch files to local directories is highly recommended otherwise the scratch files will be written over the n
275. ection 18 2 19 below 118 CHAPTER 5 STRUCTURE OPTIMIZATIONS 5 6 Counterpoise Corrections using the Jobbsse Script The shell script jobbsse controls and executes the automatic calculation of the counterpoise correction as it has been formulated by Boys and Bernadi S F Boys and F Bernardi Mol Phys 19 553 1970 to estimate the Basis Set Superposition Error BSSE For a dimer the cp correction takes the form for the monomers A and B E Eas Ea Ea Eg a EB Where parentheses denote ghost basis sets without electrons or nuclear charges For a timer jobbsse used by default the conventional so called site site functional counterpoise corrections EGpo Easc Exigo Ea Excacy EB Ecs Ec jobbsse works similar as the jobex script it cycles through the SCF DFT and if needed gradient and force relaxation programs and stops if either the maximum number of cycles is reached or the convergence criteria change in the total energy maximum norm of the gradient are fulfilled It does either only energy calculations or a full geometry optimization including up to three fragments By default the executable programs are taken from the load modules library within the TURBOMOLE directory Note that you need to set up the fragments and possibly their symmetries using define in the geometry menu beforehand The general structure of a jobbsse calculation is as follows 1 bsseenergy is invo
276. ed For spin unrestricted calcula tions the corresponding files are sLaterA pot slaterB pot corrctA pot and correctB pot homo allows the user to specify which occupied orbital will not be included in the calculation of correction potential by default the highest occupied orbital is selected homob is for the beta spin correlation func functional a correlation functional can be added to the LHF potential use func lyp for LYP or func vwn for VWN5 correlation For expert users Options for the conjugate gradient algorithm for the computation of the correction 296 CHAPTER 18 KEYWORDS IN THE CONTROL FILE potential rms convergence conj grad conv 1 d 7 maximum number of itera tion maxit 20 output level output 0 3 asymptotic continuation in each iteration cgasy 1 With slater dtresh 1 d 9 default the calculations of the numerical integrals for the Slater potential is performed only if it changes more than 1 d 9 Asymptotic regions specification corrct region Rr Apr 0 Rp Ar basis set correction potential Rp Ar Rp Ap smooth region Rr Ar asymptotic correction Defaults Rp 10 Ap 0 5 slater region Ry An Rp Ah 0 Ry An basis set Slater potential Ry Ayn Ry An smoothing region Ryn Avn Rp Ap numerical Slater Ri AD Rip A r smoothing region 7 Ap 00 asymptotic Slater Note Rp A r lt RF Af Defaults Ry 7 An 0 5 Rp 10 AL 0
277. ed coupled cluster singles and doubles model CCSD F12 with optimally reduced auxiliary basis dependence J Chem Phys 129 201103 2008 C Hattig D P Tew A Kohn Accurate and efficient approximations to explicitly correlated coupled cluster singles and doubles CCSD F12 J Chem Phys 132 231102 2010 T B Adler G Knizia H J Werner J Chem Phys 127 221106 2007 G Knizia T B Adler H J Werner J Chem Phys 130 054104 2009 M Torheyden E F Valeev Phys Chem Chem Phys 10 3410 2008 E F Valeev D Crawford J Chem Phys 128 244113 2008 K D Vogiatzis E C Barnes W Klopper Interference corrected explicitly correlated second order perturbation theory Chem Phys Lett 503 1 3 157 161 2011 H Eshuis J Yarkony F Furche Fast computation of molecular random phase approximation correlation energies using resolution of the identity and imaginary frequency integration J Chem Phys 132 234114 2010 404 134 135 136 137 138 139 140 141 142 143 144 145 146 BIBLIOGRAPHY H Eshuis J E Bates F Furche Electron correlation methods based on the random phase approximation Theor Chem Acc 2012 F Furche Molecular tests of the random phase approximation to the exchange correlation energy functional Phys Rev B 64 195120 2001 F Furche Developing the random phase approximation in
278. ed in the ab initio Kohn Sham perturbation theory KS PT2 by Gorling and Levy 63 64 The mixing is described by two empirical parameters a and a in the following manner Exc DHDF 1 ay Ex GGA a Ex HF 6 6 1 a Ec GGA acEo KS PT2 where Ex GGA is the energy of a conventional exchange functional and Ec GGA is the energy of a correlation functional x HF is the Hartree Fock exchange of the occupied Kohn Sham orbitals and Eco KS PT2 is a Moller Plesset like perturbation correction term based on the KS orbitals Ec KS PT2 aldo alib lj 6 7 g e The method is self consistent only with respect to the first three terms in Eq 6 6 i e first a SCF using a conventional hybrid GGA is performed first Based on these orbitals Ec KS PT2 is evaluated afterwards and added to the total energy For B2 PLYP B88 exchange 53 and LYP correlation 54 are used with the param eters az 0 53 and ae 0 27 Due to the relatively large Fock exchange fraction self interaction error related problems are alleviated in B2 PLYP while unwanted side effects of this reduced account of static correlation are damped or eliminated by the PT2 term How to use B2 PLYP e during preparation of your input with DEFINE select b2 plyp in the DFT menu 6 2 EXCHANGE CORRELATION FUNCTIONALS AVAILABLE 127 carry out a DScF run Prepare and run a RI MP2 calculation with either RIMP
279. ed stop or STOP in the working directory jobex will stop after the present step has terminated You can create stop by the command touch stop The output of the last complete cycle is written to file job last while the output of the running cycle is collected within the file job lt cycle gt where lt cycle gt is the index of the cycle The convergence criteria and their current values are written out at the bottom of the job last file 5 2 PROGRAM STATPT 101 5 2 Program STATPT 5 2 1 General Information Stationary points are places on the potential energy surface PES with a zero gradi ent i e zero first derivatives of the energy with respect to atomic coordinates Two types of stationary points are of special importance to chemists These are minima reactants products intermediates and first order saddle points transition states The two types of stationary points can be characterized by the curvature of the PES at these points At a minimum the Hessian matrix second derivatives of energy with respect to atomic coordinates is positive definite that is the curvature is positive in all directions If there is one and only one negative curvature the stationary point is a transition state TS Because vibrational frequencies are basically the square roots of the curvatures a minimum has all real frequencies and a saddle point has one imaginary vibrational frequency Structure optimizations are most effectively done
280. editor mpshift analyses this file and decides where to continue e ECPs can not be used since the electrons in the ECP cores are not taken into account e molecular point groups that contain reducible e representations are not sup ported Cn Cna with n gt 2 e as in mpgrad basis sets with a contraction that is greater than 10 are currently not supported e PBE and PBEO DFT functionals are not implemented in mpshift Chapter 14 Molecular Properties Wavefunction Analysis and Interfaces to Visualization Tools 14 1 Wavefunction analysis and Molecular Properties Molecular properties electrostatic moments relativistic corrections population anal yses for densities and MOs construction of localized MOs etc can be calculated with the module moloch Note that this program does not support unrestricted open shell input a script called moloch2 can currently be used as a work around type moloch2 help for further information Moreover analyses of densities apart from those calculated from molecular orbitals e g MP2 densities densities of ex cited states are not possible For the current version of moloch we refer to the keywords listed in Section 18 2 17 which partly can also be set by define see also Chapter 4 Note moloch is no longer supported but most functionalities of moloch now are integrated in programs that generate MOs or densities and can be done directly within the modules dscf ridft rimp2 mpgrad ri
281. ee dynam ics This is the default status of an MD run surface_hopping This keyword allows to carry out Tully type fewest switches surface hopping SH 183 This option is only available in combination with TDDFT For the TDDFT surface hopping see Tapavicza et al 2007 184 for the current implementation see Tapavicza et al 2011 185 In the current implementation the surface hopping algorithm only allows switches between the first excited singlet state and the ground state However total energies of higher excited states can be computed during the MD simulation The proper functioning of SH has only been tested for the option md_action fix total energy from t 0 00000000000 To carry out SH dynamics simulations the keyword surface_hopping has to be added to the control and mdmaster file In addition several keywords are required in the control file nacme needed to compute non adiabatic couplings this keyword requires the use of weight derivatives in section dft nac keyword needed to collect Cartesian non adiabatic coupling vectors along the trajectory exopt 1 keyword needed to ensure dynamics starting in S4 ex_energies file ex_energies collects excitation energies along the trajectory integral_ex file integral_ex collects time integration of excitation energies along the trajectory sh_coeffs file sh_coeffs collects amplitudes of the adiabatic states along the trajectory nac_matrix file nac_matrix collects
282. efore the programs terminate the converged vectors are written onto formatted files type IR where type is an abbreviation for the type of response calculation performed cf scfinstab Given these files in the working directory escf and egrad calculations can be restarted or continued e g with a larger number of roots Integral direct algorithm In the iterative method outlined above the super matrices A and B never need to be set up explicitly only the products of A and B with some suitable basis vectors are required These matrix vector products are evaluated very efficiently in the AO basis because the required four index integrals can be computed on the fly and need not be transformed or stored on disk In addition prescreening techniques based on rigorous bounds are straightforward to apply This leads to a low order scaling O N O N for the time determining steps Due to the similarity to ground state fock matrix construction the same keywords are used to control these steps as in semi direct SCF namely thime thize scfintunit see Chapter 6 The same is true for DFT and RI keywords such as dft ridft ricore Point group symmetry escf and egrad can exploit point group symmetry for all finite point groups with up to 99 fold symmetry axes gt symmetry The re sponse and eigenvalue problems 7 4 and 7 7 decompose into separate problems for each IRREP that are solved independently For excited state and
283. en atoms ampran real amplitude of the cavity de symmetrization 300 CHAPTER 18 KEYWORDS IN THE CONTROL FILE phsran real phase of the cavity de symmetrization refind real refractive index used for the calculation of vertical excitations and num frequencies the default 1 3 will be used if not set explicitly use_old_amat uses A matrix setup of TURBOMOLE 5 7 use_contcav in case of disjunct cavities only the largest contiguous cavity will be used and the smaller one s neglected This makes sense if an unwanted inner cavity has been constructed e g in the case of fullerenes Default is to use all cavities If the cosmo keyword is given without further specifications the default parameter are used recommended For the generation of the cavity COSMO also requires the definition of atomic radii User defined values can be provided in Angstrom units in the data group cosmo_atoms e g for a water molecule cosmo_atoms radii in Angstrom units o 1 radius 1 7200 h 2 3 radius 1 3000 If this section is missing in the control file the default values defined in the radii cosmo file located in TURBODIR parameter are used A user defined value supersedes this defaults cosmo and cosmo_atoms can be set interactively with the COSMO input program cosmoprep after the usual generation of the TURBOMOLE input The COSMO energies and total charges are listed in the result section E g SCREENING CHARGE cosmo
284. en for the UFF Hes sian If none of them is found it takes the scaled unit matrix For transition state optimization the exact Hessian has a higher priority than the results of LES The results of LES can be used to obtain an initial Hessian matrix for transition state optimizations involving large molecules where calculation of the full Hessian is too expensive Note that LES calculations for statpt in addition to the les keyword require the following keywords to be added manually in the control file hOhessian nomw The default Hessian update for minimization is bfgs which is likely to remain positive definite The powell update is the default for transition state optimizations since the Hessian can develop a negative curvature as the search progresses 5 2 3 Finding Minima Simply specify the statpt keyword in the control file and run jobex as explained above You can very often speedup the optimization by calculating the initial Hessian matrix using uff 5 2 4 Finding transition states Locating minima on a PES is straightforward In contrast transition state opti mization requires much more input The diagonal guess Hessian will almost never work so you must provide a computed one The Hessian should be computed at your best guess as to what the TS should be The real trick here is to find a good guess for the transition state structure The closer you are the better It is often difficult to guess these structures One wa
285. en format input file for the Molden program Molden is a graphical interface for displaying the molecular density MOs nor mal modes and reaction paths For more information about molden see http www cmbi ru nl molden molden htm1 is a script to query a dihedral angle in a molecular structure e g tors 1 2 3 4 gives the torsional angle of atom 4 out of the plane of atoms 1 2 and 3 28 tbtim tblist uhfuse x2t CHAPTER 1 PREFACE AND GENERAL INFORMATION is used to convert timings output files from TURBOBENCH calculations to IATpXtables for options please type TBTIM help is used to produce summaries of timings from TURBOBENCH calcula tions to ATEX format for options please type TBLIST help transforms the UHF MOs from a given symmetry to another symme try which is C4 by default just enter uhfuse but can be specified e g as Cw by entering uhfuse s c2v Now this functionality is included in the MO definition menu of define program see Sec tion 4 3 1 converts standard xyz files into TURBOMOLE coordinates Chapter 2 Installation of TURBOMOLE 2 1 Install TURBOMOLE command line version Installation requires familiarity with some simple UNIX commands The TURBOMOLE package is generally shipped as one tar file This has to be uncompressed gunzip turbomole_65 tar gz and unpacked tar xvf turbomole_65 tar to produce the whole directory structure Note Do not install or run TURBOMOLE
286. ent You can call TURBOMOLE executables and tools easily from anywhere if you add the corresponding directories to your path kornshell or bash syntax PATH PATH TURBODIR scripts PATH PATH TURBODIR bin sysname Note that sysname is set in back quotes which tells the shell to substitute the entry by the output of sysname Now the TURBOMOLE executables can be called from a directory with the required input files For example to call dscf and save the output TURBODIR bin sysname dscf gt dscf out or if the path is OK simply dscf gt dscf out Executable modules are in the bin arch directory for example Linux modules are in bin em64t unknown linux gnu Tools including jobex are in scripts and auxiliary basis sets are kept in the directories basen jbasen jkbasen cbasen xbasen and cabasen Coordinates for some common chemical fragments are sup plied in structures The documentation and a tutorial can be found in the folder DOC 2 2 INSTALLATION PROBLEMS HOW TO SOLVE 31 2 1 3 Testing the installation In addition some sample calculations are supplied in Turbotest so that the modules can be tested Just run TTEST from this directory to run all tests or TTEST help to get help on how this works cd TURBODIR TURBOTEST TTEST 2 2 Installation problems How to solve Please check your user limits If one or several tests of the test suite fail it is very likely that your user limits for stack
287. ent elements drops below the value given by thrrmsdisp1 default 5 10 a u e the root mean square of the gradient elements drops below the value given by thrrmsgrad defaul t 5 10 4a u The default values for the convergence criteria can be changed using the stp menu of define The necessary keywords are described in Section 18 2 16 below For structure optimization of minima with statpt as relaxation program just use jobex amp TS optimizations are performed by the jobex invokation jobex trans amp 5 2 2 Hessian matrix The choice of the initial Hessian matrix has a great effect on the convergence of the structure optimization At present there are three choices for the Hessian matrix in statpt For minimization a diagonal matrix or approximate Hessian matrix from a forcefield calculation using uff see Section 5 4 can be used For transition state optimizations you have to provide either the exact Hessian or results from the lowest eigenvalue search LES see Section 12 Note also that you can calculate the Hessian with a smaller basis set and or at a lower wavefunction level and use it for higher level structure optimization Usually a Hessian ma trix calculated in a minimal basis using RI DFT is good enough for all methods implemented in TURBOMOLE 5 2 PROGRAM STATPT 103 statpt automatically takes the best choice of the Hessian from the control file For minimizations it first looks for the exact Hessian and th
288. environment In TURBOMOLE only ground state energies computed with the dscf ridft and ricc2 module and electronic excitation properties based on RI CC2 are im plemented The general theory is presented in ref 119 and 120 the PERI CC2 model and the TURBOMOLE implementation is described in ref 121 9 8 1 Theory In the following only the most important ideas are presented and discussed with a focus on the PERI CC2 model The essential concept is the introduction of an environment coupling operator G D GD P DES 9 24 with the electrostatic contribution M K D 2 D OAN Er 9 25 m 1 k 0 pq and the polarization contribution P l DOC DT me Erg 9 26 u 1 pq Here owa are multipole interaction integrals of order k and pi are the induced dipoles which can be obtained from the electric field F and the polarizability a at a site u Because the induced dipoles depend on the electron density and vice versa their computations enter the self consistent part of the HF cycle Introducing G D into standard equations for the HF reference state and the CC2 equations leads to a general PE CC2 formulation To maintain efficiency a further approximation has been introduced which makes the operator only dependent on a CCS like density term These general ideas define the PERI CC2 model and allow to formulate the corresponding Lagrangian expression 200 CHAPTER 9 RI CC2 n T ua 1 Lperi co2 t t
289. equire the keyword marij 4 For RI HF calculations auxiliary bases defined in the data group jkbas are needed This group is created by the rijk menu in define How to Perform a Calculation Single point calculations Call the dscf or ridft program after running define Geometry optimizations and molecular dynamics For HF or DFT calculations using dscf and grad simply invoke jobex For DFT calculations using ridft and rdgrad type jobex ri see Section 5 1 for additional options and parameters for geometry opti mizations and ab initio molecular dynamics calculations 6 1 Background Theory In Hartree Fock theory the energy has the form Egyr h J K Vnue 6 1 where h is the one electron kinetic plus potential energy J is the classical Coulomb repulsion of the electrons K is the exchange energy resulting from the quantum fermion nature of electrons and Vnuc is the nuclear repulsion energy 124 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS In density functional theory the exact Hartree Fock exchange for a single determi nant is replaced by a more general expression the exchange correlation functional which can include terms accounting for both exchange energy and the electron cor relation which is omitted from Hartree Fock theory The DFT energy is expressed as a functional of the molecular electron density p r Eprr p T e Vrele Jlo Ex le Eclo Vnuc 6 2 where Tp is the kinetic energy Vne p
290. ers 4 4 THE GENERAL OPTIONS MENU TT hybno hybrid Noga Diag parameters dsp DFT dispersion correction trunc USE TRUNCATED AUXBASIS DURING ITERATIONS marij MULTIPOLE ACCELERATED RI J dis DISPLAY MOLECULAR GEOMETRY list LIST OF CONTROL FILE amp GO BACK TO OCCUPATION ORBITAL ASSIGNMENT MENU or q END OF DEFINE SESSION This menu serves very different purposes The next subsection deals with commands required to activate and or specify specific methods of calculation The subsequent subsection describes commands used to select non default options Standard SCF calculations do not require special action just leave the menu The final subsection describes the settings for property calculations 4 4 1 Important commands DFT calculations Command dft leads you to the menu STATUS OF DFT_OPTIONS DFT is NOT used functional b p gridsize m3 ENTER DFT OPTION TO BE MODIFIED func TO CHANGE TYPE OF FUNCTIONAL grid TO CHANGE GRIDSIZE on TO SWITCH ON DFT Just lt ENTER gt q or terminate this menu To activate DFT input on and then specify the grid for the quadrature of exchange correlation terms TURBOMOLE offers grids 1 coarse to 7 finest and the multiple grids m3 to m5 4 The latter employ a coarser grid during SCF iterations and grid 3 to grid 5 in the final SCF iteration and the gradient evaluation Default is grid m3 for clusters with more than 50 atoms use m4 The functionals supported are
291. es transition moments etc Currently implemented operators labels are overlap overlap charge operator the integrals evaluated in the AO basis are v diplen dipole operator in length gauge p r v with i x y z the index O indicates dependency on the origin for expectation val ues of charged molecules which in the present version is fixed to 0 0 0 all three components individual components can be specified with the labels xdiplen ydiplen zdiplen dipvel dipole operator in velocity gauge j1 V v all three components individual components can be specified with the labels xdipvel ydipvel zdipvel 18 2 FORMAT OF KEYWORDS AND COMMENTS 327 qudlen angmom nef states all quadrupole operator u r rjv all six components individual components can be specified with the labels xxqudlen xyqudlen xzqudlen yyqudlen yzqudlen zzqudlen If all six components are present the program will automatically give the electronic second moment tensor which involves only the electronic contributions Mj the isotropic second moment a itrM and the anisotropy ly Sals S Mu Mirri 3 M i x i x Furthermore the traceless quadrupole moment 1 2 Oi z Brits f On including nuclear contributions is given angular momentum L v all three components individual components can be specified with the labels xangmom yangmom zangmom di ou v where Zy is the charge of
292. es not exist iterm switch for the different types of force field terms 100000 bond terms will be calculated 010000 angle terms will be calculated 001000 torsion terms will be calculated 000100 inversion terms will be calculated 000010 non bonded van der Waals terms will be calculated 000001 non bonded electrostatic terms will be calculated econv gconv convergence criteria for energy and gradient qtot total charge of the molecule 272 CHAPTER 18 KEYWORDS IN THE CONTROL FILE dfac distance parameter to calculate the topology If the distance between the atoms J and J is less than the sum of the covalent radii of the the atoms multiplied with dfac then there is a bond between IJ and J epssteep if the norm of the gradient is greater than epssteep a deepest descent step will be done epssearch if the norm of the gradient is smaller than epssearch no line search step will be done after the Newton step dqmax max displacement in a u for a coordinate in a relax step mxls dhls ahls parameters of linesearch ahls start value dhis increment mxls number of energy calculations alpha beta gamma modification parameter for the eigenvalues of the Hessian see below f x x alpha beta exp gamma x x transform a switch for the transformation in the principal axis system lnumhess a switch for the numerical Hessian lmd a switch for a MD calculation Input Data Blocks Needed by UFF coord
293. ete all previous definitions of internal coordinates See Section 4 for further details If the molecules point group is not C4 define will set some of the coordinate to status d display or i ignore Use the ic command to change all coordinates to k You can also achieve this by editing in the intdef data group manually The analysis in internal coordinates is switched on by adding a line in the data group drvopt that has the following syntax analysis only intcoord print print level Keywords in square brackets are optional If only is added the program assumes that the file hessian exists and runs only the analysis part of aoforce The program will give the following output controlled by the print level given in parenthesis e diagonal elements of the Hessian in internal coordinates force constants of bonds angles etc print level 0 e complete force constant matrix in internal coordinates print level 2 e normal modes in terms of internal coordinates print level 1 e Potential energy contributions V defined as Via LPL Pya where Li are the elements of the normal coordinate belonging to mode n and F j are the elements of the force constant matrix both expressed in the internal coordinate basis w is the related eigenvalue The program will list the diagonal contributions Ve print level 1 the off diagonal contributions Vp Vp 2V7 print level 2 for up to 10 atoms else print level 10 and the brutt
294. etwork to the same directory where the input is located The path to the local disk can be set with export TURBOTMPDIR scratch username tmjob This setting is automatically recognized by the parallel ridft and ricc2 programs Note e This does not set the path for the integral scratch files for dscf see section below about twoint of keyword scfintunit e In MPI parallel runs the programs attach to the name given in TURBOTMPDIR node specific extension e g scratch username tmjob 001 to avoid clashes between processes that access the same file system The jobs must have the permissions to create these directories Therefore one must not set TURBOTMPDIR to something like scratch which would result in directory names like scratch 001 which can usually not created by jobs running under a standard user id e If you run several different parallel TURBOMOLE jobs on the same node make sure that the settings for TURBOTMPDIR and twoint are not identical other wise the jobs would overwrite each other s scratch files This can for example be done by setting TURBOTMPDIR to a directory name which contains the process id of the job or the queuing system For parallel Numforce jobs with the mfile lt hostfile gt option it is important to delete the tmpdir keyword and to unset TURBOTMPDIR 3 2 PARALLEL RUNS 45 On all systems TURBOMOLE is using the MPI library that has been shipped with your operating system On Linux for PCs
295. eus is omitted in the calculation of the electrostatic potential for these points The output files are termed tp plt sp plt etc Electric fields as derivatives of potentials are calculated by pointval fld The absolute values of electric fields are written to files tf plt sf plt etc For non default grid types and outputs that allow also for displaying of components of electric fields see Section 18 2 18 Exchange correlation potentials Only for DFT Computation of the Kohn Sham exchange correlation potential on a grid pointval xc Canonical molecular orbitals Visualization of molecular orbitals i e genera tion of plt files containing amplitudes of MOs i Ai Rp X ciwo Rp 14 5 or in the two component case Ai Rp X cio Re 14 6 V with T as a part of the coefficient matrix Re a Im a Re 8 Im 8 is achieved e g by pointval mo 10 12 15 This yields amplitudes for MOs spinors 10 12 and 15 on the default grid The numbering of MOs refers to that you get from the first column of the output of the tool Eiger the one for spinors refers to the file EIGS The filenames contain the type of the irreducible representation irrep of the MO the current number within this irrep and in case of UHF calculations also the spin e g 2alg_a plt contains amplitudes for the second alpha spin MO of aj type For more dimensional 14 2 INTERFACES TO VISUALIZATION TOOLS 233 irreps columns are written to separate files
296. evaluated without approximations RI J calculations For non hybrid functionals we strongly recommend the RI J procedure which speeds up calculations by a factor 10 at least as compared to conventional treatments without sacrificing accuracy Command ri gives STATUS OF RI OPTIONS RI IS NOT USED Memory for RI 200 MB Filename for auxbasis auxbasis ENTER RI OPTION TO BE MODIFIED 4 4 THE GENERAL OPTIONS MENU 79 m CHANGE MEMORY FOR RI f CHANGE FILENAME jbas ASSIGN AUXILIARY RI J BASIS SETS on TO SWITCH ON RI Use lt ENTER gt q end or to leave this menu Activate RI J with on and choose with m the memory you can dedicate to store three center integrals Keyword ricore default is 200 MB The more memory the faster the calculation A rough guide put ricore to about 2 3 of the memory of the computer Use OS specific commands top on most UNIX systems during an ridft run to find the actual memory usage and then adjust ricore the keyword in control specifying memory If the option jbas is selected define enters a submenu which allows the assignment of auxiliary basis sets for an explanation of the menu items see Section 4 2 Where available the program will select by default the auxiliary basis sets optimized for the orbital basis used Please note that treatment of systems with diffuse wavefunctions may also require an extension of the auxiliary basis For this cases enlarge the sets of s and p functions wit
297. every iteration jbas file auxbasis Cross reference for the file specifying the auxiliary basis as referenced in atoms We strongly recommend using auxbasis sets optimized for the respec tive MO basis sets e g use SVP or TZVP for the basis and the corresponding auxbasis as provided by define default file auxbasis ripop Calculation of atomic charges according to the s partial wave and atomic dipole moments according to the p partial wave as resulting from the auxbasis representation of the density RI JK If the keyword rik is found in the control file ridft performs a Hartree Fock SCF calculation using the RI approximation for both Coulomb and HF exchange efficient for large basis sets For this purpose needed apart from ricore jkbas file auxbasis Cross reference for the file specifying the JK auxiliary basis as referenced in atoms This group is created by the rijk menu in define MARI J Multipole Accelerated Resolution of Identity J This method partitions the Coulomb interactions in the near and far field parts The calculation of the far field part is performed by application of the multipole expansions and the near field part is eval uated employing the RI J approximation It speeds up calculation of the Coulomb term for large systems It can only be used with the ridft module and requires setting of the ridft keyword marij precision 1 0D 06 1lmaxmom 10 18 2 FORMAT OF KEYWORDS AND COMMENTS 293 n
298. ewhat less expensive that CCSD F12 calculations which solve Eq 10 16 while both approaches are approximately similar accurate for energy differences The SP approach becomes in particular very efficient if combined with the neglect of certain higher order explicitly correlated contributions which have a negligible effect on the energies but increase the costs during the CC iterations The most accurate and recommeded variant is the CCSD F12 approximation 127 which gives essentially identical energies as CCSD F12 Also available are the CCSD F12 Ref 127 CCSD F12a Ref 128 and CCSD F12b Ref 129 approximations as well as the perturbative corrections CCSD 2 p and CCSD 2 pyz see Refs 10 1 COMPUTATIONAL DEMANDS 209 130 131 127 Note that these approximations should only be used with ansatz 2 and the SP approach i e fixed geminal amplitudes For MP3 the approximations F12 and F12 to a full F12 implementation be come identical they include all contributions linear in the coefficients ch The explicitly correlated MP4 method MP4 F12 is defined as fourth order approxima tion to CCSD F12 T Note that MP4 F12 has to be used with the SP or fixed amplitude approache for the geminal coefficients cK MP3 F12 and MP4 F12 are currently only available for closed shell or unrestricted Hartree Fock reference wavefunctions The CPU time for a CCSD F12 calculation is approximately the sum of the CPU time for an
299. exactly by specifying no dbdx last SCF energy change real last MP2 energy change real These keywords depend on the optimization task to be processed and are updated by the corresponding program i g SCF energy m matrix options This data block contains non default specifications for the m matrix diagonals This is of use if some cartesian atomic coordinates shall be kept fixed during optimization Available options are integer real real real atomic index followed by diagonal elements of the m matrix for this atom scratch files The scratch file ftmp allocated by relax can be placed anywhere in your file systems instead of the working directory by referencing its pathname in this data group as follows 18 2 FORMAT OF KEYWORDS AND COMMENTS 335 scratch files relax ftmp path file The first column specifies the program the second column the scratch file and the third column the pathname of the file to be used as scratch file Input Data Blocks Needed by RELAX intdef or redundant Definitions of internal coordinates and optionally values of internal coordi nates val given in a u or degrees or force constant diagonal elements fdiag grad Cartesian coordinates and gradients calculated in subsequent optimization cy cles Entries are accumulated by one of the gradient programs grad mpgrad rimp2 ricc2 egrad etc egrad Basis set exponents scale factors and their gradients
300. excited state transition moments the contributions which are second order in ground state amplitudes i e contain second order ampli tudes or products of first order amplitudes With this approximation the ADC 2 transition moments are only correct to first order i e to the same order to which also the CC2 transition moments are correct and are typically similar to the CC2 results The computational costs for the ADC 2 transition moments are within this approximation much lower than for CC2 since the left and right eigenvectors are identical and no lagrangian multipliers need to be determined The extra costs i e CPU and wall time for the calculations of the transitions moments are similar to the those for two or three iterations of the eigenvalue problem which reduces the total CPU and wall time for the calculation of a spectrum i e excitation energies 9 5 GROUND STATE SECOND ORDER PROPERTIES WITH MP2 AND CC2195 and transition moments by almost a factor of three 9 4 2 Transition moments between excited states For the calculation of transition moments between excited states a set of Lagrangian multipliers has to be determined instead of the M for the ground state transition moments From these Lagrangian multipliers and the left and right eigenvectors one obtaines the right transition moment between two excited states i and f as NT fa A T i M Y TDR D4 B E Vig 9 22 Pq where V are the matrix elements
301. ext follows the MM site coordinates in x y z positions the point charge the dipole moment for k gt 1 x y z component the quadrupole moment for k gt 2 xx xy XZ yy yz zz component the octupole moment for k 3 xxx XXy XXZ XYY XYZ XZZ yyy YYZ yZZ zzz component the polarizability one component for pol order 1 xx xy xz yy yz zz component for pol order 2 9 8 POLARIZABLE EMBEDDING CALCULATIONS 201 An example for a polarizable embedding with coordinates given in A point charges and isotropic polarizabilities point_charges pe AA 6 0 39 39 39 39 39 41 41 41 41 41 1 4 0 2765102481 2 5745845304 3 5776314866 0 038060 15 217717 1 3215071687 2 3519378014 2 8130403183 0 009525 14 094642 0 5595582934 1 2645007691 4 7571719292 0 009509 14 096775 1 5471918244 2 5316479230 2 3240961995 0 009519 14 096312 0 3207417883 4 1501938400 4 4162313889 0 009507 14 096476 1 1080691595 4 922838723099 1 675383825535 0 038060 15 217717 0 9775910525 6 5274614891 2 4474576239 0 009525 14 094642 2 5360480539 4 8923046027 0 6040781123 0 009509 14 096775 0 3630448878 4 6028736791 0 7155647205 0 009519 14 096312 1 2817317422 3 6689143712 2 9344225518 0 009507 14 096476 All values are given in atomic units except coordinates if stated otherwise These data are mandatory In addition you can specify further options on the same line as the point_charges flag These are rmin lt float
302. f convergence is good this weight is then reduced by the step 0 05 in each successive iteration until the minimum of 0 1 is reached These are the default settings of define for closed shell RHF DSCF automatically tries to adjust the weight to optimize convergence but in difficult cases it is recommended to start with a large weight e g 1 5 and to set the minimum to a larger value e g 0 5 scfdebug options Flags for debugging purposes Following options are available vectors integer Output level concerning molecular orbitals integer 0 default means minimal output gt 1 will output all start MOs and all MOs in each iteration density integer Output level concerning difference density matrices debug integer integer gt 0 will dump a lot of information be careful scfdenapproxl integer Direct SCF procedures build the Fock matrix by exploiting information from 18 2 FORMAT OF KEYWORDS AND COMMENTS 285 previous iterations for better efficiency With this keyword information from the last integer iterations will be used This feature is switched on with the default value 20 even if the keyword is absent The user may reduce the number of iterations employed to smaller values e g 10 in cases were numerical stability could become an issue With the value 0 this feature is switched off the Fock matrix is constructed from scratch in each iteration scfdiis options Control block for convergence acceleration via Pulay s
303. f CABS singles cannot be switched off if it is free of costs 170 CHAPTER 8 2ND ORDER MOLLER PLESSET PERTURB THEORY pairenergy controls whether or not the F12 contribution to the MP2 pair energies appear in the output default off Further options corrfac LCG refers to a further data group for the definition of the correlation factor When define is used the default is lcg nlcg 6 slater 1 4000 The nature of the LCG correlation factor may be changed by editing this data group in the control file For example to use a Slater type correlation factor with exponent 1 0 ag represented as a linear combination of three Gaussians use lcg nlcg 3 slater 1 0000 Alternatively the exponents and coefficients of the fit may be given explicitly lcg nlcg 3 expol coef1 expo2 coef2 expo3 coef3 MP2 F12 calculations may be combined with Grimme s SCS approach S Grimme J Chem Phys 118 2003 9095 by inserting scs in ricc2 ricc2 mp2 energy only SCS In this case the SCS parameters cos 6 5 and css 1 3 are used Also individual scaling factors for the same spin and opposite spin contributions may be defined see Section 9 7 For open shell calculations two choices of the examp fixed method are available These are controled by a keyword in the rir12 data group ump2fixed full diag full 8 6 LT SOS RI MP2 WITH O N SCALING COSTS 171 These differ in the treatment of the af block where either only the
304. f Perdew Burke and Ernzerhof with the form 0 75 S PBE X 0 25HF PW PBE C 6 4 where PBE X and PBE C are the Perdew Burke Ernzerhof exchange and correlation functionals and PW is the Perdew Wang correlation functional 49 50 52 56 60 e The TPSSH exchange correlation functional of Staroverov Scuseria Tao and Perdew with the form 0 9 5 TPSS X 0 1HF PW TPSS C 6 5 where HF denotes the Hartree Fock exchange 49 50 52 57 61 126 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS Additionally the Double Hydbrid Functional B2 PLYP can be used for single point energy calculations Note that one has to run an MP2 calculation after the DFT step to get the correct B2 PLYP energy B2 PLYP is a so called double hybrid density functional DHDF 62 that uses in addition to a non local exchange contribution as in conventional hybrid GGAs also a non local perturbation correction for the correlation part Note the following options restrictions in the present version of this method e single point calculations only computed with the DSCF and RIMP2 RICC2 modules e UKS treatment for open shell cases e can be combined with resolution of identity approximation for the SCF step RI JK option e can be combined with the dispersion correction DF T D method sg B2 PLYP 0 55 The non local perturbation correction to the correlation contribution is given by second order perturbation theory The idea is root
305. f permittivity that represents the solvent The charge distribution of the solute polarizes the dielectric medium The response of the medium is described by the generation of screening charges on the cavity surface CSMs usually require the solution of the rather complicated boundary conditions for a dielectric in order to obtain the screening charges COSMO instead uses the much simpler boundary condition of vanishing electrostatic potential for a conductor g 0 This represents an electrostatically ideal solvent with oo The vector of the total electrostatic potential on the cavity surface segments is determined by the solute potential which consist of the electronic and the nuclear part and the vector of the screening charges q pio pe As Aq 0 A is the Coulomb matrix of the screening charge interactions For a conductor the boundary condition 0 defines the screening charges as q ATs To take into account the finite permittivity of real solvents the screening charges are scaled by a factor e l fle ae q fi eja 259 260 CHAPTER 17 TREATMENT OF SOLVATION EFFECTS WITH COSMO The deviation between the COSMO approximation and the exact solution is rather small For strong dielectrics like water it is less than 1 while for non polar sol vents with 2 it may reach 10 of the total screening effects However for weak dielectrics screening effects are small and the absolute erro
306. face atomic units 1 au 29 421 TPa during the corresponding timestep ab initio potential energy gradients x y z H Bohr at t This file can be manipulated with LOG2 tools after the MD run Section 1 5 turbomole file control Where to look for TURBOMOLE keywords grad etc md_status The status of the MD run is a record of the action carried out during the previous MD step along with the duration of that step The format matches that of md_action below Canonical dynamics is supported using the Nos Hoover thermostat This option can be enabled in Mdprep or by the following syntax md_status 18 2 FORMAT OF KEYWORDS AND COMMENTS 355 canonical T 500 t 100 from t 25 0000000000 until t 0 00000000000 Here T specifies the temperature of the thermostat in K 500 K in the ex ample and t specifies the thermostat relaxation time in a u 100 a u in the example It is advisable to choose the thermostat relaxation 2 10 times larger than the time step Note that user defined actions are presently not supported in canonical dynamics mode These are optional keywords seed 123 Integer random number seed title Arbitrary title log_history 100 mdlog P 71 mdlog Q ke_control length 50 response 1 To determine the trends in kinetic energy and total energy average values and overall drifts it is necessary to read the history of energy statistics over the recent MD steps The number of MD steps recorded so
307. far in each log file are therefore kept in the log history entry this is updated by the program each step The length of records needed for reliable statistics and the number of steps over which changes are made to kinetic energy response are specified in ke_control barrier angstroms type elps limits 5 0 10 0 7 5 constant 2 0 springlen 1 0 temperature 300 0 356 CHAPTER 18 KEYWORDS IN THE CONTROL FILE barrier specifies a virtual cavity for simulating condensed phases The op tional flag angstroms can be used to indicate that data will be entered in ngstr ms rather than Bohr type can be one of orth elps or none for orthorhombic ellipsoidal or no barrier the default respectively limits are the x y z sizes of the cavity In this case an ellipsoid with a major axis of 20 along y semi major of 15 on z and minor of 10 A on x constant is the Hooke s Law force constant in atomic units of force H Bohr per length unit Here it is 2 0 H Bohr ngstr m a bastard combination of units springlen is the effective limit to the restorative force of the barrier For this system an atom at 5 into the barrier will feel the same force as at 1 0A temperature denotes the temperature of the cavity walls in Kelvin If the system quasi temperature is below this setpoint particles will be accelerated on their return to the interior Alternately they will be retarded if the system is too warm A
308. fashion will be set to 107tPrsemi If set to tight the semi canonical algorithm will become inefficient if the threshold is to large 326 CHAPTER 18 KEYWORDS IN THE CONTROL FILE the algorithm will become numerical unstable zpreopt threshold for preoptimizating the so called Z vector i e the lagrangian multipliers for orbital coefficients with a preceding RI CPHF calcula tion with the cbas auxiliary basis The RI CPHF equations will be converged to a residual error lt 10 7PTe P Default is zpreopt 4 This preoptimization can reduce significantly the computational costs for the solution of the Z vector equations for large basis sets in particular if they contain diffuse basis functions For calculations on large molecules with small or medium sized basis sets the preoptimization becomes inefficient compared to the large effects of integral screening for the conventional CPHF equations and should be disabled This option is automatically disabled for ricc2 calculations based on foregoing RI JK Hartree Fock calculation nozpreopt disable the preoptimization of the Z vector by a preceding RI CPHF calculation with the cbas basis set Note that the preoptimization is automatically deactivated if the ricc2 calculation is based on a foregoing RLJK Hartree Fock calculation Common options for keywords in the data groups ricc2 response and excitations operators diplen dipvel input of operator labels for first order properti
309. fer from older versions 5 7 and older The use_old_amat option can be used to calculate energies not gradients using the old cavity algo rithm of TURBOMOLE 5 7 The basic COSMO settings are defined in the cosmo and the cosmo_atoms block Example with default values cosmo epsilon infinity nppa 1082 nspa 92 disex 10 0000 rsolv 1 30 routf 0 85 cavity closed ampran 0 1D 04 18 2 FORMAT OF KEYWORDS AND COMMENTS 299 phsran 0 0 refind 1 3 the following options are not used by default allocate_nps 140 use_old_amat use_contcav no_oc epsilon real defines a finite permittivity used for scaling of the screening charges allocate_nps integer skips the COSMO segment statistics run and allocates memory for the given number of segments no_oc skips the outlying charge correction All other parameters affect the generation of the surface and the construction of the A matrix nppa integer number of basis grid points per atom allowed values i 10 x 3 x 4 2 12 32 42 92 nspa integer number of segments per atom allowed values i 10 x 3 x 4 2 12 32 42 92 disex real distance threshold for A matrix elements Angstrom rsolv real distance to outer solvent sphere for cavity construction Angstrom routf real factor for outer cavity construction in the outlying charge correction cavity closed pave intersection seams with segments cavity open leave untidy seams betwe
310. fied a wrong one list is again a list of shell indices in usual syntax amp This command has a different meaning in this menu than in the rest of define Here it will repeat the extended Hiickel calculation perhaps you want to change some Hiickel parameters for the next one will not bring you back to the occupation numbers menu but will terminate the whole occupation number and start vector section and will bring you to the last main menu which is described in Section 4 4 If you want to leave this menu without assigning all electrons in your molecule to shells define will issue a warning and suggest to continue defining occupation numbers You can ignore this warning if you do not want to assign all electrons e Calculates and displays the extended Hiickel total energy of your molecule f f will give you some information about the commands in this menu You may overwrite occupation numbers once given by just redefining the correspond ing shell For example if you choose shells 1 10 as closed shells and afterwards shell no 9 as open shell with any occupation number the open shell will be correctly assigned 4 3 3 Orbital Specification Menu define provides the possibility to assign the occupation numbers of the MOs man ually if you like To do that use the command man in the occupation number main menu and you will arrive at the following submenu lt label gt lt list gt select orbitals within lt list gt lt la
311. fmo Shows HOMO LUMO gap occupation checks if there are holes in the oc cupation and much more reads the gradient file and prints the energies of each cycle versus bond lengths or angles Five operational modes are possible evalgrad prints the energy evalgrad 1 prints the coordinate of atom 1 evalgrad 1 2 prints the distance between atoms 1 and 2 evalgrad 1 2 3 prints the bending angle as defined in Bend evalgrad 1 2 3 4 prints the torsional angle as defined in Tors drives the Frozen Density Embedding calculations prepares the control file for a Hamilton core guess RHF only usage see Section 5 1 is the TURBOMOLE driver for all kinds of optimizations example kdg scfdiis kills a data group here scfdiis in the control file prepares for Localized Hartree Fock calculations by adjusting param eters of the control file converts the file logging an MD trajectory into coordinates in frames appropriate for jmol animation program extracts the energy data KE total energy PE from an MD log file interactive program to prepare for an MD run checking in particular the mdmaster file mdprep is actually a FORTRAN program 1 5 TOOLS MECPprep MECPopt mp2prep Numforce outp raman screwer vibration sdg sysname stati t2x tm2aomix tm2molden tors 27 prepares the input for minimum energy crossing point calculations The subdirectories state1l and state2 will be created Multiplici
312. follows Sx _ Yia 1 7 13 ia where 7 and a label occupied and virtual MOs respectively Thus the squared coefficient of a single electron excitation from orbital 7 to orbital a can be defined as Icial Xi Y a 7 14 escf prints out Cia 100 starting with the largest coefficient until the sum of the coefficients is 0 9 or greater TDA is contained as special case with Y a 0 7 3 IMPLEMENTATION 151 7 3 Implementation Without giving details we discuss features of the implementation in escf and egrad that matter for applications The interested reader is referred to the refs given in the program headers as well as ref 87 Simultaneous vector iteration The solutions of Eqs 7 4 and 7 7 are ex panded in a subspace of L which is iteratively expanded Davidson method 88 The iteration is stopped when the Euclidean norm of the residual vector is smaller than 10 The default for k is 5 which usually gives excitation energies accurate to 8 10 digits and properties accurate to 4 5 digits k can be changed by specifying rpaconv k Several roots i e several excited states or frequencies can be treated simultaneously which is very effective and permits the calculation of whole excita tion spectra and dispersion curves During the iteration the vectors are kept on scratch files vfile_ lt IR gt wfile_ lt IR gt and or rhs_ lt IR gt where IR denotes an IR REP of the point group see below B
313. for the optimization of basis set parameters carthess Data group hessian projected is used 5 3 14 Look at Results The energy file includes the total energy of all cycles of a structure optimization completed so far To get a display of energies and gradients use the UNIX command grep cycle gradient which yields e g H20 cycle 1 SCF energy 76 3432480651 dE dxyz 0 124274 cycle 2 SCF energy 76 3575482860 dE dxyz 0 082663 cycle 3 SCF energy 76 3626983371 dE dxyz 0 033998 cycle 4 SCF energy 76 3633251080 dE dxyz 0 016404 cycle 5 SCF energy 76 3634291559 dE dxyz 0 010640 cycle 6 SCF energy 76 3634910117 dE dxyz 0 000730 This should be self evident To see the current or if the optimization is con verged the final atomic distances use the tool dist Bond angles torsional an gles etc are obtained with the tools bend tors outp etc In the file gradient are the collected cartesian coordinates and corresponding gradients of all cycles The values of the general coordinates and corresponding gradients are an output of relax written to job lt cycle gt of job last within jobex To look at this search for Optimization statistics in job last or job lt cycle gt 5 4 Force Field Calculations 5 4 1 Purpose uff preoptimizes a structure and calculates an analytical Hessian which can be used as a start Hessian in a geometry optimization This will accelerate the convergence
314. fort for conversion of accumulated geometry and gradient data as needed for the force constant update or the DIIS update of the geometry to the optimization space within which the geometry has to be optimized one may specify the keyword oldgrad Then the relax program accumulates all subsequent coordinates and gradient as used in optimization in this data group or a referenced file This overrides the input of old coordinate and gradient data from data blocks grad egrad as accumulated by the grad program degrees 18 2 16 Keywords for Module STATPT statpt itrvec 0 update bfgs hssfreq 0 keeptmode hssidiag 0 5 radmax 0 3 radmin 1 0d 4 338 CHAPTER 18 KEYWORDS IN THE CONTROL FILE tradius 0 3 threchange 1 0d 6 thrmaxdispl 1 0d 3 thrmaxgrad 1 0d 3 thrrmsdispl 5 0d 4 thrrmsgrad 5 0d 4 Only non default values are written in the control file except statpt itrvec 0 Following options are available itrvec Index of the Hessian eigenvector to follow for transition structure search tran sition vector Eigenpairs are sorted in ascending order i e with increasing eigenvalues and start with index 1 The eigenpairs corresponding to transla tions and rotations are shifted to the end For minimization the value 0 has to be specified update Method of hessian update For minimization default is BF GS for TS search default is Powell and none is for no update hssfreq Recompute the full Hessian every
315. ft cross references are given The user normally has to choose only the functional and the grid size see below All other parameters have proven defaults functional name Specification of the functional default is BP86 printed as functional 276 ntheta integer CHAPTER 18 KEYWORDS IN THE CONTROL FILE b p For all possible and useful functionals please refer to page 291 and for definition of the functionals the section 6 2 on page 124 Example default input dft functional b p gridsize integer or minteger Specification of the spherical grid see section 18 2 5 on page 291 De fault is gridsize m3 Example dft gridsize m3 gridtype integer not recommended for use Specification of the mapping of the radial grid Possible values for gridtype are 1 6 but gridtype 4 to 6 is only for the use with functional lhf see page 254 For the definition of gridtype 1 3 please refer to Eq 16 17 and 19 in Ref 180 Example default value dft gridtype 3 debug integer Flag for debugging debug 0 means no debug output default debug 1 means some output debug 2 means a lot more output Be careful nkk integer Specification of the sharpness of the partition function as proposed by Becke 181 default is nkk 3 The usage of nkk makes sense only in the range 1 lt nkk lt 6 Example dft nkk 3 not recommended for use nphi integer Only for user specified Lob
316. ft and rdgrad instead of dscf and grad Be careful dscf and grad ignore RI K flags and will try to do a normal calculation but they will not ignore RI J flags rij and stop with an error message To obtain correct derivatives of the DFT energy expression in grad or rdgrad the program also has to consider derivatives of the quadrature weights this option can be enabled by adding the keyword weight derivatives to the data group dft For a semi direct dscf calculation Hartree Fock or DFT you first have to perform a statistics run If you type 3 1 A QUICK AND DIRTY TUTORIAL 37 MP2 stati dscf nohup dscf gt dscf stat amp the disk space requirement MB of your current thime and thize combina tion will be computed and written to the data group scfintunit size integer see Section 18 2 5 The requirement of other combinations will be computed as well and be written to the output file dscf stat The size of the integral file can be set by the user to an arbitrary but reasonable number The file will be written until it reaches the given size and dscf will continue in direct mode for the remaining integrals Note that TURBOMOLE has no 2GB file size limit MP2 calculations need well converged SCF runs the SCF run has to be done with at least the density convergence denconv 1 d 7 and scfconv 7 as described in Section 18 This applies also to CC2 the spin component scaled variants of MP2 and CC2 and other post HF methods
317. g roughly 3 4 of the memory with m number number in MB your computer has available Auxiliary basis sets are provided automatically In the printout of an ridft run you can check how much is really needed a top statement will tell you if you overplayed your cards e B P86 is the default functional It has a good and stable performance through out the periodic system e for an HF or DFT run without RI you simply enter Inohup dscf gt dscf out amp or for a RI DFT run Inohup ridft gt ridft out amp e for a gradient run you simply enter nohup grad gt grad out amp or nohup rdgrad gt rdgrad out amp e for a geometry optimization simply call jobex for a standard SCF input nohup jobex amp for a standard RI DFT input nohup jobex ri amp e many features such as NMR chemical shifts on SCF and DFT level do not require further modifications of the input just call e g mpshift after the appropriate energy calculation mpshift runs with SCF or DFT using a hybrid functional need a file size of the semi direct file twoint that is non zero 36 CHAPTER 3 HOW TO RUN TURBOMOLE e other features such as post SCF methods need further action on the input using either the last menu of define where one can activate all settings needed for DFT TDDFT MP2 CC2 etc calculations this is the recommended way or tools like Mp2prep or Rimp2prep Please refer to the following pages of this documentation 3 1 4
318. ge results with respect to radial grid size increase radsize in steps of 5 which is convenient see equation above diffuse integer Serves to increase quadrature grids this is recommended in case of very diffuse wavefunctions With the keyword diffuse grids are modified by changing the linear scaling factor of radial grid points and the radial eridsize radsize gt radsize incr E E scal 278 CHAPTER 18 KEYWORDS IN THE CONTROL FILE diffuse integer 1 2 3 4 5 6 incr 1 2 3 4 5 6 scal 1 5 2 0 2 8 4 0 5 0 6 0 For information about the linear scaling parameter see Eq 16 19 and Table 1 in Ref 180 In addition the reduction of spherical grid points near nuclei is sup pressed i e fullshell on is set see page 279 Note the keyword radsize integer overrules the setting of incr for more information see p 277 Recommendation For diffuse cases use gridsize m4 or larger in com bination with diffuse 2 and check the number of electrons for more difficult cases use diffuse 4 In case of doubt verify the calculation with a larger grid i e gridsize 7 The test suite example TURBODIR TURBOTEST dscf short H3P04 DSCF DIFFUSE provides an example of usage this also gives reasonable values for damp ing and orbitalshift to reach convergence in this and similar cases see scfdamp and scforbitalshift p 284 and p 287 Example Recommendation dft gridsize m4 diffuse 2 rhostart integer
319. guration state functions also weighted averages of high spin CSFs see Sec 6 3 for further details The M ller Plesset perturbation theory and coupled cluster functionalities implemented in ricc2 require a single determinant reference state and can thus only deal with high spin open shell cases not averaged e The spins of all nopen unpaired electrons are parallel a spin will be assumed so that the ROHF reference state has the spin multiplicity nopen 1 e There must be only one type of open shells and all orbitals in this shell must have the occupation number 1 e For the single electron case i e doublets the Roothaan parameters are a b 0 for high spin cases with more than one unpaired electron the Roothaan parameters must be set to a 1 and b 2 For non abelian points groups this implies that shells with degenerate orbitals as e g t in point group I must be half filled An average over the different symmetry equivalent or inequivalent high spin determinants that are obtained when a shell of degenerate orbitals is less than or more than half filled is not possible with single point ricc2 calculations For states with less than or more than half filled shells of degenerate orbitals the calculations half to be done in a point group that lifts the degeneracy such that it 164 CHAPTER 8 2ND ORDER MOLLER PLESSET PERTURB THEORY becomes possible to assign integer occupation numbers A symmetry breaking of the orbitals c
320. gy are tolerable it is recommended to use less tight thresholds e g conv 6 or conv 5 for an accuracy of respectively at least 0 01 mH 0 03 kJ mol or 0 1 mH 0 3 kJ mol The settings for conv and oconv have not only an impact on the number of iterations for the solution of the cluster equations but as they determine the thresholds for integral screening also to some extend on the costs for the individual iterations CCSD T energy with a second order correction from the interference corrected MP2 F12 The error introduced from a CCSD T calculation with a finite basis set can be corrected from second order corrections of the the interference corrected MP2 F12 INT MP2 F12 Ref 132 The approximate CCSD T INT F12 at the basis set limit is given from Ecesp tyces Eccspcr X FY leg FP ef 10 26 i lt j From define in the submenu ricc2 select the ccsd t method and add the keyword intcorr ricc2 ccsd t intcorr Then switch on the 12 method approximation A or B inv or fixed The cor rected CCSD T INT F12 energy will be printed in the end of the calculation It is highly recommended to start the CCSD T INT F12 calculation from a converged SCF calculation with symmetry which is transfromed to C4 It is furthermore rec ommended to use Boys localized orbitals in the rir12 submenu A table with the corrected second order pair electron energies and the corresponding interference factors can also be printed in
321. h P A Kollman J Comput Chem 5 2 129 145 1984 is used if the keyword is extended esp_fit kolman 230 CHAPTER 14 PROPERTIES AND ANALYSIS AND GRAPHICS 14 2 Interfaces to Visualization Tools Visualization of Molecular Geometry The tool t2x can be used to convert the atomic coordinates stored in the grad and coord data groups into the xyz format which is supported by most viewers e g jmol http jmol sourceforge net Typing t2x gt opt xyz in a directory containing the control file generates a series of frames using the information of grad Note t2x writes to standard output which here is redirected to a file If you are only interested in the most recent structure type t2x c gt str xyz which only extracts the information on coord Visualization of Densities MOs Electrostatic Potentials and Fields There are several possibilities to visualize molecular orbitals or densities tm2molden simply converts MO and geometry information to molden format The conversion program is interactive and self explanatory The generated file can be visualized using either molden http www cmbi ru nl molden molden htm1 or molekel http www cscs ch molekel For larger systems this may become very time consuming as plotting data values on grids are calculated by the respective pro grams molden molekel It is more efficient to calculate the data for plots MO amplitudes densities etc by TURBOMOLE modules and t
322. h diffuse functions The RI J option is only supported by programs ridft and rdgrad if you use jobex to optimize molecular geometry put nohup jobex ri MARI J option RI J calculations can be done even more efficiently with the Multipole Accelerated RI J MARI J option especially for larger molecules where almost linear scaling is achieved 28 Parameters 1 precision parameter 1 00E 06 2 maximum multipole 1 moment 10 3 maximum number of bins 8 4 minimum separation of bins 0 00 5 maximum allowed extension 20 00 6 threshold for multipole neglect 1 00E 18 Enter the number to change a value or lt return gt to accept all Just rely on the defaults Multiple auxiliary basis sets With the command trunc you can switch on this option Effect a reduced auxiliary or fitting basis to represent the electron density is employed during SCF iterations the final SCF iteration and the gradient are computed with the full auxiliary basis truncated RI ALREADY SWITCHED ON DO YOU WANT TO SWITCH OFF truncation default no 80 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE Note trunc is presently not compatible with marij RI in SCF calculations Considerable savings in CPU times are achieved with the RI technique for both Coulomb J and exchange K terms in SCF calculations the RI JK method 29 provided large basis sets are employed e g TZVPP cc pVTZ or cc pVQZ With rijk you get STATUS OF RI OPTIONS RI IS
323. h for the TURBOMOLE scripts default TURBODIR scripts Tests the given executable prog Name for the local test directory default TESTDIR sysname Name for the local criteria file default CRIT Name for the test suite settings file default DEFCRIT Name for the local protocol file default TESTPROTOKOLL Name for the global protocol file default TESTPROTOKOLL sysname Name for the check protocol file default CHECKPROTOKOLL Name for the local error output file default output err Name for the failed tests list default PROBLEMS sysname Name for the timings file default TIMINGS sysname valfile file Execution options short long restart file r file newref string fileref batchmode errorstop noerrorstop timings notimings runopts 0 CHAPTER 20 PERL BASED TEST SUITE Name for the validation file for run criteria default RUNCRIT val Only short long subdirectories of the test suite will be tested default long short The list of test examples for execution will be read in from file default PROBLEMS sysname Produces new reference timings and writes them to the CRIT file A short description of the refer ence platform is provided by string Produces new reference files Running in batch mode no screen output Stops Does not stop after the first error default noerrorstop Writes Does not w
324. he def2 basis sets j x all electron basis sets for Rb to Xe SVPall SVPPall TZVPall TZVPPall g references for the correlation consistent basis sets cc pVXZ etc can be found e g at http tyr0 chem wsu edu kipeters basis html or https bse pnl gov bse portal Note that most of the correlation consistent basis sets in the basis set library of TURBOMOLE have been downloaded from the latter EMSL web site and therefore users are requested to include in addition to the original scientific reference an appropriate citation see web site in any publications resulting from the use of these basis sets property optimized augmentations def2 SVPD def2 TZVPD def2 TZVPPD def2 QZVPD def2 QZVPPD n x basis sets for Dirac Fock ECPs i e the dhf basis sets o auxiliary basis sets for RI DFT c d e auxiliary basis sets for RI MP2 f k h for Dunning basis sets Further references of papers not from the TURBOMOLE group are given in the bibliog raphy The following publications describe details of the methodology implemented in TURBOMOLE Methods I II HI IV Electronic Structure Calculations on Workstation Computers The Program System TURBOMOLE R Ahlrichs M Bar M Haser H Horn and C K lmel Chem Phys Letters 162 165 1989 Improvements on the Direct SCF Method M Haser and R Ahlrichs J Com put Chem 10 104 1989 Semi direct MP2 Gradient Evaluation on Workstation Com
325. he generalization of SCS and SOS to CC2 for ground and excited states is described in 16 It uses the same scaling factors as proposed for the original SCS and SOS MP2 approaches see below In the ricc2 program we have also implemented SCS and SOS variants of CIS D for excitation energies and of CIS D and ADC 2 for excitation energies and gradi ents which are derived from SCS CC2 and SOS CC2 in exactly the same manner as the unmodified methods can be derived as approximations to CC2 see Sec 9 2 and ref 116 Please note that the SCS CIS D and SOS CIS D approximations obtained in this way and implemented in ricc2 differ from the spin component 198 CHAPTER 9 RI CC2 scaled SCS and SOS CIS D methods proposed by respectively S Grimme and E I Ugorodina in 117 and Y M Rhee and M Head Gordon in 118 A line with scaling factors has to be added in the ricc2 data group ricc2 scs cos 1 2d0 css 0 3333d0 cos denotes the scaling factor for the opposite spin component css the same spin component As an abbreviation scs can be inserted in ricc2 In this case the SCS parameters cos 6 5 and css 1 3 proposed S Grimme S Grimme J Chem Phys 118 2003 9095 are used These parameters are also recommended in 16 for the SCS variants of CC2 CIS D CIS Dx and ADC 2 for ground and excited states Also just sos can be used as a keyword to switch to the SOS MP2 approach proposed by the Head Gordon group
326. he unit cell for the 0001 a AlgO3 surface are given in the subsection cell of the embed keyword The aperiodic direction is always the z direction but you have to specify the unit cell as if it was a 3D periodic system This means that the third dimension of the unit cell must be large enough to enclose the entire surface in this direction The unit cell dimensions are specified in A using cell ang The positions of the point charges in the unit cell are specified as Cartesian coordinates in A content ang The values of point charges for Al and O are given in the subsection charges embed periodic 2 cell angs 4 8043 4 8043 24 0000 90 0000 90 0000 120 0000 content ang Al 2 402142286 1 386878848 5 918076515 Al 0 000013520 0 000003382 7 611351967 6 6 PERIODIC ELECTROSTATIC EMBEDDED CLUSTER METHOD Al 0 000008912 Al 2 402041674 Al 0 000005568 Al 2 402137518 Al 0 000000070 Al 0 000006283 Al 2 402151346 Al 0 000100868 Al 0 000001982 Al 0 000004853 0 731205344 0 743527174 1 588027477 1 471626759 3 309734344 3 919768333 0 740424335 1 651123047 1 698525310 3 133347750 1 658615232 0 814115047 0 930515707 1 494558096 1 517625928 3 142566681 0 751034439 0 703617156 oo o ooo oo ooo ao oo o a RE E E E end charges 0 2 0 Al 3 0 end e 773757219 386946321 000003223 1 386872172 773757935 000005607 1 386879444 N VU O F FN e e O N OF BPNNNN A e 773690
327. hich is obtained by adding only EY to the CCSD energy Usually CCSD T is slightly more accurate than CCSD T although for closed shell or spin unrestricted open shell reference wavefunctions the energies of both models CCSD T and CCSD T model are correct through 4 th order per turbation theory For a ROHF reference however BY contributes already in 4 th order and only the CCSD T model is correct through 4 th order perturbation the ory Integral direct implementation and resolution of the identity approxima tion The computationally most demanding in terms floating point operations steps of a CCSD calculation are related to two kinds of terms One of the most costly steps is the contraction ej gt teigj aclbd 10 22 cd where a b c and d are virtual orbitals For small molecules with large basis sets or basis sets with diffuse functions where integral screening is not effective it is time determing step and can most efficiently be evaluated with a minimal operation count of 50 V where O and V are number of respectively occupied and virtual orbitals if the 4 index integrals ac bd in the MO are precalculated and stored on file before the iterative solution of the coupled cluster equation 10 4 and 10 5 For larger systems however the storage and I O of the integrals ac bd leads to bottlenecks An alternatively this contribution can be evaluated in an integral direct was as tidy 3 teidj Cred 07 05 5 triaj
328. his is the number of shells up to the complete valence shell e g 5 for B Ne 6 for Na Mg etc Exceptions are Elements Sc Y La Ti Zr Hf V Nb Ta for which not all five d shells are included but only 2 3 or 4 respectively This modification leads to better agreement with partial charges calculated by an ESP fit thr lt real gt All MAOs with an eigenvalue larger than lt real gt are chosen de fault is lt real gt 0 1 This and the following two options are not valid in connection with occ max Maximum of numbers calculated from fix and thr 0 1 is taken 348 CHAPTER 18 KEYWORDS IN THE CONTROL FILE mix 2 1 mixture of fix and thr 0 1 This choice gives best agreement statistical with charges from an ESP fit It is the default choice c for additional information about MAOs info Eigenvalues and occupations for each MAO are written to output dump Entire information about each MAO is written to output Lengthy Further for each atom the number of MAOs and the sorting mode can be specified individually in lines below this keyword Example atom 1 3 4 eig 7 leads to choice of the 7 MAOs with largest eigenvalue at atoms 1 3 4 localize enables the generation of localized molecular orbitals LMOs using Boys lo calization By default all occupied orbitals are included localized orbitals are written by default in the AO basis to file s 1mo in case of RHF and lalp and lbet in case of UHF orbitals Note that LMO
329. i but no gradients will be calculated for these coordinates nor will they be included in the geometry optimization i means the number of coordinates which are defined but will be com pletely ignored i e they are not even displayed on the screen and will not be used by any program this is the waste paper basket of define Note that the k plus f must equal the number of degrees of freedom ideg of your molecule if you want to perform a geometry optimization If you have less coordinates than degrees of freedom you will have to specify further ones commands idef or iaut see below if you have more coordinates than degrees of freedom you will have to throw away some of them commands irem or imet see below The commands in this menu allow you to define internal coordinates for your molecule adjust your geometry to special values of these internal coordinates and to control the numeric reliability of the chosen set of internal coordinates In detail the commands act as follows Description of commands imet a This command computes the so called B matrix which is the matrix of the derivatives of the active and fixed internal coordinates with respect to Cartesian coordinates This matrix is used in program relax for the conversion from Cartesian coordinates and gradients to internal ones and vice versa If this matrix is singular or even nearly singular this indicates a linear dependency of your internal coordinate set As a
330. ialization of the approximate force constant matrix Available options are on off this activates or deactivates initialization if on has been set relax will provide an initial force constant matrix as specified by one of the possible initialization options as described below and will store this matrix in data group forceapprox after initialization relax resets forceinit to off diag suboptions provide a diagonal force constant matrix with available suboptions are real this will lead to an assignment of diagonal elements default 1 0 334 CHAPTER 18 KEYWORDS IN THE CONTROL FILE default this will lead to an assignment of initial force constant diagonals depending on the coordinate type individual Provide individual defined force constant diagonals for e internal coordinates supplied in intdef fdiag e a global scale factor global fdiag This does not work for basis set optimization For the correct syntax of fdiag see descriptions of intdef global carthess read a cartesian e g analytical hessian from hessian and use it as a start force constant matrix if optimize internal has been set use its transform in internal coordinate space If large molecules are to be optimized it may be necessary large core memory requirements to deactivate the numerical evaluation of the derivative of the B matrix with respect to cartesian coordi nates which is needed to transform H cart H int
331. ian stability analysis Frequency dependent polarizabilities and optical rotations Vertical electronic excitation energies e Transition moments oscillator and rotatory strengths of electronic excitations UV VIS and CD spectra Spin restricted closed shell and spin unrestricted ground states except for stabil ity analysis are supported The RI J approximation in conjunction with LDA GGA and meta GGA MGGA functionals is implemented for all properties Exci tation energies and transition moments can be computed either within the full time dependent HF TDHF or time dependent DFT TDDFT formalisms or within the Tamm Dancoff approximation TDA Excited state first order properties can be evaluated analytically using egrad They include 147 148 CHAPTER 7 HF AND DFT RESPONSE CALCULATIONS e Gradients of the excited state energy with respect to nuclear positions Excited state equilibrium structures jobex adiabatic excitation energies emission spectra e Exited state densities Charge moments population analysis e Excited state force constants by numerical differentiation of gradients using the script Numforce Moreover analytical gradients of static and frequency dependent polarizabilities are available from egrad Together with vibrational normal modes from the aoforce or Numforce they are used to calculate vibrational Raman intensities Excited state gradients for MGGA functionals are presently unavailable
332. ian Ochsenfeld Holger Ohm Mathias Pabst Holger Patzelt Dmitrij Rappoport Oliver Rubner Ansgar Schafer Uwe Schneider Marek Sierka David P Tew Oliver Treutler Barbara Unterreiner Malte von Arnim Florian Weigend Patrick Weis Horst Weiss Nina Winter 11 12 CHAPTER 1 PREFACE AND GENERAL INFORMATION We acknowledge help from e Michael Dolg University of Stuttgart now University of Cologne e Jiirgen Gauss University of Mainz e Christoph van Wiillen University of Bochum now TU Kaiserslautern e Stefan Brode BASF AG Ludwigshafen e Heinz Schiffer HOECHST AG Frankfurt and financial support by the University of Karlsruhe BASF AG BAYER AG HOECHST AG the DFG and the Fonds der Chemischen Industrie Contact address Abteilung fiir Theoretische Chemie Institut f r Physikalische Chemie Karlsruher Institut fiir Technologie Kaiserstr 12 D 76131 Karlsruhe E mail info turbomole com Web http www turbomole com Support is provided by COSMOlogic GmbH amp Co KG see http www cosmologic de Email turbomole cosmologic de 1 2 FEATURES OF TURBOMOLE 13 1 2 Features of TURBOMOLE TURBOMOLE has been specially designed for UNIX workstations and PCs and effi ciently exploits the capabilities of this type of hardware TURBOMOLE consists of a series of modules their use is facilitated by various tools Outstanding features of TURBOMOLE are e semi direct algorithms with adjustable main memory and disk s
333. iary basis for cbas submenue cbas the amount of main memory option memory and for CCSD F12 calculations in addition 206 CHAPTER 10 CCSD CCSD F12 AND CCSD T the F12 options submenu 12 and a CABS basis submenu cabs By default a CCSD F12 with ansatz 2 and geminal amplitudes fixed by the cusp conditions is performed To switch to the computationally more efficient recommended CCSD F12 approximation add to the input group rir12 the linet ccsdapprox ccsd f12 The auxiliary JK basis must be chosed in menu rijk and the exponent for the correlation function must set by editing the lcg data group of the control file 2 Do an SCF calculations using either the dscf or the ridft module 3 Invoke the ricc2 program on the command line or with a batch script How to quote e for all F12 calculations cite the implementation of RI MP2 F12 in TURBO MOLE The MP2 F12 Method in the TURBOMOLE Programm Package Rafal A Ba chorz Florian A Bischoff Andreas Gl Christof Hattig Sebastian H6fener Wim Klopper David P Tew J Comput Chem 32 2492 2513 2011 e for MP3 F12 and CCSD F12 Quintuple quality coupled cluster correlation energies with triple basis sets David P Tew Wim Klopper Christian Neiss Christof Hattig Phys Chem Chem Phys 9 921 1930 2007 e for MP4 F12 CCSD F12 CCSD F12 T Accurate and efficient approximations to explicitly correlated coupled cluster singles and d
334. ic coordinates and their gradients egrad exponents and scale factors and their gradients globgrad global scale factor and its gradient 2 Input data from force constant program aoforce grad cartesian atomic coordinates and their gradients globgrad global scale factor and its gradient hessian the force constant matrix in the space of cartesian coordinates 3 Output data from program relax coord cartesian atomic coordinates basis exponents and scale factors global global scale factor For structure optimizations the use of redundant internal coordinates is recom mended see Section 4 0 6 Normally internal coordinates are not used for input or output by the electronic structure programs dscf mpgrad etc Instead the coor dinates gradients etc are automatically converted to internal coordinates by relax on input and the updated positions of the nuclei are written in cartesians coordinates to the data group coord Details are explained in the following sections 5 3 3 Force Constant Update Algorithms In a Newton type geometry update procedure often only a crude approximation to the force constant matrix H is available What can be done then is to update F H in each iteration using information about previous coordinates and gradients This constitutes the quasi Newton or variable metric methods of which there are a few variants 5 3 PROGRAM RELAX 107 1 Murtagh Sargent MS Ze Ze k _ ppk
335. ic units and degrees You can specify unit cell parameters in A and degrees using cell ang content label x y z end Content of the unit cell where label is the label of the point charge Content of the unit cell where label is the label of the point charge type and x y z are corresponding Cartesian or fractional crystal coordinates Defaults are Cartesian coordinates and atomic units You can specify Cartesian coordinates in A using content ang and fractional coordinates using content frac Note that Cartesian coordinates assume that the cell vector a is aligned along the x axis and the vector b on the xy plane cluster label x y z end Atomic coordinates of the piece of the crystal to be replaced by the QM cluster and surrounding isolation shell ECPs and explicit point charges where label is the point charge label and x y z are corresponding Cartesian or fractional crystal coordinates Defaults are Cartesian coordinates and atomic units You can spec ify Cartesian coordinates in A using cluster ang and fractional coordinates using cluster frac charges label charge end Values of point charges for each atom type where label is the point charge label and charge specifies charge in atomic units ch_list label charge end Values of point charges for each atom where label is the point charge label and charge specifies charge in atomic units Note that charges and ch_list are mutually exclusive An integer number
336. ided into a sequence of blocks These are expected to have decreasing average force constants i e stretches angle coordinates torsions and weak coordi nates The BB matrix is diagonalized for each block separately after the columns of B were orthogonalized against the columns of B of the the preceding blocks n 3 Generalized natural coordinates Natural internal coordinates are defined first for the remaining cage decoupled coordinates are defined type r a positive real number which is an approximate force constant can be read in for each type of coordinate see below The force constants are used for the definition of the matrix m in BmBt Types of internal coordinates for the definition of m The matrix m is assumed to be a diagonal matrix For each type of coordinate a different value for the force constants m can be read in Types of coordinates are stre bond stretch default 0 5 invr inverse bond stretch default 0 5 bend bond angle default 0 2 outp Out of plane angle default 0 2 tors dihedral or torsional angle default 0 2 linc Special angle coordinate for collinear chains bending of the chain a b c in the plane of b c d default 0 2 linp bending of the chain a b c perpendicular to the plane of b c d default 0 2 wstr stretch of a weak bond i e the bond is assumed to have a very low force constant e g a hydrogen bond or a van der Waals bon
337. ided to the pro gram in the data group maxcor becomes too small compared to O N 128 x 1024 MBytes loops will be broken in many small batches at the cost of increased I O operations and a decrease in performance As mentioned above it is recommended to set maxcor to 66 77 of the physical core memory available for the calculation Important options The options to define the orbital and the auxiliary basis sets the maximum amount allocatable core memory maxcor and the frozen core approximation maxcor have been mentioned above and described in the previous chapters on MP2 and CC2 calculations Apart from this CCSD and CCSD T calculations require very little additional input Relevant are in particular some options in the ricc2 data group ricc2 ccsd ccsd t conv 7 oconv 6 mxdiis 10 maxiter 25 The options ccsd and ccsd t request respectively CCSD and CCSD T calcu lations Since CCSD T requires the cluster amplitudes from a converged CCSD calculation the option ccsd t is implies the ccsd option The number given for mxdiis defines the maximum number of vectors included in the DIIS procedure for the solution of the cluster equations As mentioned above it has some impact on the amount of disc space used by a CCSD calculation Unless disc space becomes a bottleneck it is not recommended to change the default value With maxiter one defines the maximum number of iterations for the solution of the cluster equation
338. idvds3 path10 file10 mpshift jdvdsi pathi1 file11 mpshift jdvds2 path12 file12 mpshift jdvds3 path13 file13 mpshift cshmmat path14 file14 trast trand traloop number stands for traloop start and traloop end Each loop or pass in MP2 chemical shift calculations can be done individually by providing the keywords trast and trand This can be used to do a simple parallelization of the run Create separate inputs for each traloop Add trast lt number gt trand lt number gt in the control files number goes from 1 to the number of traloops Each calculation will create a restart file called restart mpshift To collect all 362 CHAPTER 18 KEYWORDS IN THE CONTROL FILE steps and to do the remaining work copy all restart files to one directory and rename them to restart mpshift number add trast 1 and trand num ber_of_traloops to the control file and start mpshift 18 2 21 Keywords for Parallel Runs On all systems the parallel input preparation is done automatically Details for the parallel installation are given in Section 3 2 2 The following keyword is optional for parallel MPI runs parallel_platform architecture Currently the following parallel platforms are supported SMP for systems with very fast communication all CPUs are used for the linear algebra part Synonyms for SMP are HP V Class SP3 SMP and HP S X Class MPP for systems with fast communication like Fast Ethernet the number of CPUs that wi
339. ients are not yet available Functionality of rirpa e Calculation of RPA energies for RHF and UHF wave functions e The frozen core approximation can be used to exclude low lying occupied or bitals from the RPA treatment for single point energies e RI K for RPA single point energy calculations So far only C symmetry is supported and the program can only be run sequentially Ground State Energy Theory The RPA energy consists of the Hartree Fock exact exchange energy EFF and a correlation energy piece EC RPA rirpa computes Eq 11 1 non selfconsistently from a given set of converged input orbitals The correlation energy 1 C RPA RPA TDARPA E 5 Oe On QI 11 2 n 214 215 is expressed in terms of RPA excitation energies at full coupling QRPA and within the Tamm Dancoff approximation QTPARPA The excitation energies are obtained from time dependent DFT response theory and are eigenvalues of the symplectic eigenvalue problem 135 136 A _ QonA Xon Yon 0 11 3 The super vectors Xo and Yon are defined on the product space Doce X Lyirt and Doce X Lyirt respectively where Loc and Lyirt denote the one particle Hilbert spaces spanned by occupied and virtual static KS molecular orbitals MOs The super operator A B e au contains the so called orbital rotation Hessians A B iajb a i ij ab 2 ia jb 11 5 A Bais a Ei Oi Sab 11 6 i and a denote the energy eige
340. igenvalue problem to generate reasonable start vec tors the eigenvectors are converged in this step only to a remaining residual norm lt preopt 2 pre optimization of the eigenvectors by a robust modified Davidson algorithm see ref 10 using the LINEAR CC RESPONSE SOLVER until the norm of all residuals are below preopt combined with a DIIS extrapolation for roots assumed to be converged below the threshold thrdiis 3 solution of the nonlinear eigenvalue problem with a DIIS algorithm using the DIIS CC RESPONSE SOLVER until the norm of the residuals are below the re quired threshold conv This procedure is usually fairly stable and efficient with the default values for the thresholds But for difficult cases it can be necessary to select tighter thresholds In case of convergence problems the first thing do is to verify that the ground state is not a multireference case by checking the D1 diagnostic If this is not the case the following situations can cause problems in the calculation of excitation energies e almost degenerate roots in the same symmetry class e complex roots break down of the CC approximation close to conical intersec tions e large contributions from double excitations The first two reasons can be identified by running the program with a print level lt 3 It will then print in each iteration the actual estimates for the eigenvalues If some of these are very close or if complex roots appear you should make su
341. ill work on the current input modify it add results read in results from previous modules etc Run a geometry optimization and your resulting coordinates of the minimum struc ture will replace the start structure After that run a frequency analysis and it will calculate the vibrational modes of the minimum structure Run a transition state search and the Hessian of the previous step will be used as input And so on 3 1 3 How to run A brief overview Please note that there is a detailed step by step tutorial located in the DOC directory of your TURBOMOLE installation As mentioned in the section before all TURBOMOLE modules need the control file as input file The control file provides directly or by cross references the information necessary for all kinds of runs and tasks see Section 18 define provides step by step the control file Coordinates atomic attributes e g basis sets MO start vectors and keywords specific for the desired method of calculation We recommend generating a set of Cartesian coordinates for the desired molecule using special molecular design software and converting this set into TURBOMOLE format see Section 19 2 as input for define A straightforward way to perform a TURBOMOLE calculation from scratch is as follows e generate your atomic coordinates by any tool or program you are familiar with e save it as an xyz file which is a standard output format of all programs or use a conversion tool
342. imations to the true harmonic frequencies for such modes for which the mechanical coupling to the embedding environment is negligible In particular the frequencies of stretch modes which involve bonds between the me chanically active subsystem and atoms with frozen coordinates will be strongly affected by this approximation Note e The frznuclei is not compatible with the polyhedral difference algorithm It can only be used with central differences which should be enforced with the central option e If the option frznuclei is switched on the program assumes that the con straints enforced by fixing coordinates remove the six external degrees of free dom for on overall rotation or translation of the system and therefore the hessian matrix is not projected onto the subspace of internal coordinates Fix ing the coordinates of only one or two atoms might does lead to some artifical small but non zero frequencies e Zero point vibrational energies calculated with the frznuclei option are only meaningful for comparison of systems with the same mechanically active atoms and similar embedding as the contributions from the frozen coordinates are not included 12 4 Interface to hotFCHT aoforce supports the generation of input files for the hotFCHT code version 2 0 and later of R Berger and co workers see http fias uni frankfurt de berger group hotFCHT index html1 which allows for the calculation of Franck Condon factors Ju
343. in C3 and TZVP you get e g ORBITAL SYMMETRY ENERGY SHELL CUMULATED CL SHL OCC OP SHL OCC SHELL TYPE DEGENERACY SHELL DEG PER ORBITAL PER ORBITAL 1 tal 15 63244 2 2 0 0000 0 0000 2 2a1 0 99808 2 4 0 0000 0 0000 3 le 0 64406 4 8 0 0000 0 0000 4 3al 0 57085 2 10 0 0000 0 0000 5 2e 0 30375 4 14 0 0000 0 0000 6 4al 0 87046 2 16 0 0000 0 0000 TO CONTINUE ENTER lt return gt This allows you to get the linear combination of basis functions which form the MO index Note that this refers not to the basis set you spec ified but to the extended Hiickel basis index must be a single index not an index list This command allows you to specify closed shells Their occupation will be 2 per MO the total occupation the shell degeneracy which you can obtain by using command s list is a list of shell indices like 1 13 or 1 3 5 7 This command allows you to specify open shells index must be a single shell index not an index list You will then be asked for the number of electrons per MO which shall be contained in this shell For example for a fluorine atom you should choose o n where n is the index of the p shell and an occupation of 5 3 per MO You may enter the 72 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE occupation numbers as simple integers or as integer fractions e g 1 for the s occupation in sodium 5 3 for the p occupation in fluorine v list With this command you can remove an orbital occupation if you spec i
344. ined as well Grids of at least size m3 are recommended for heavy atoms The gridsize can be modified just like in dft calculations The keyword dsenex activates seminumerical gradient calculations An example using the default grid for SCF m1 and grid 5 for gradients default grid 3 looks like this senex dsenex gridsize 5 294 CHAPTER 18 KEYWORDS IN THE CONTROL FILE Two component SCF GHF Self consistent two component calculations e g for spin orbit interactions can be carried out using the module ridft The following keywords are valid soghf enforces two component SCF calculations this option is combinable with rij rik and dft kramers switches on Kramers restricted formalism gdiis enforces DIIS for complex Fock operator Scalar relativistic Douglas Kroll Hess DKH Hamiltonian Scalar relativistic all electron calculations can be done employing the Douglas Kroll Hess DKH Hamiltonian Implemented for modules dscf and ridft dkhorder integer switches on DKH calculation of order integer dkhparam integer selects parameterization of the DKH Hamiltonian Valid values are 1 de fault 2 3 4 and 5 18 2 6 Keywords for Module ODFT For the orbital dependent functionals OEP EXX or LHF run the odft program see Chapter 16 For OEP EXX options see Section 16 3 The options for the LHF potential can be specified in as follows non default options are indicated in square brackets and
345. ion menu fdiag serves for the input of diagonal force constants for the individual in ternal coordinates to initialize forceapprox 5 3 5 Structure Optimizations Using Internal Coordinates This is the default task of relax optimize internal on does not need to be specified You need as input the data groups 5 3 PROGRAM RELAX 109 grad cartesian coordinates and gradients as provided and accumulated in subsequent optimization cycles by the programs grad or rdgrad etc intdef definitions of internal coordinates redundant definitions of redundant coordinates Output will be the updated coordinates on coord and the updated force constant matrix on forceapprox If any non default force constant update option has been chosen relax increments its counting variables lt numgeo gt lt numpul gt within com mand keyword forceupdate If the approximate force constant has been initialized forceinit on relax switches the initialization flag to forceinit off Refer also to the general documentation of TURBOMOLE It is recommended to check cor rectness of your definition of internal coordinates 1 Calculate their values for your cartesian start coordinates using the relax program see Section 5 3 11 or within a define session 2 Have a look at the eigenvectors of the BmB matrix Set some behind keyword intdef if there are any eigenvalues close to zero lt 107 is to be considered bad for small molecules b
346. ion of excitation ener gies is initiated by the data group excitations in which at least the symmetries irreducible representations and the number of the excited states must be given for other options see Section 18 2 14 With the following input the ricc2 program will calculate the lowest two roots states for the symmetries A and B of singlet multiplicity at the CIS CIS D and CC2 level with default convergence thresholds Ground state calculations will be carried out for MP2 needed for the CIS D model and used as start guess for CC2 and CC2 ricc2 Provided that it is not an unrestricted open shell run In this case the wavefunctions will not be spin eigenfunctions and multiplicities are not well defined 9 2 CALCULATION OF EXCITATION ENERGIES 183 cis cis d cc2 excitations irrep al nexc 2 irrep b1 nexc 2 The single substitution parts of the right eigenvectors are stored in files named CCREO s m xzrx where s is the number of the symmetry class irreducible repre sentation m is the multiplicity and zzz the number of the excitation within the symmetry class For the left eigenvectors the single substitution parts are stored in files named CCLEO s m azaz These files can be kept for later restarts Trouble shooting For the iterative second order methods CIS D ADC 2 and CC2 the solution of the nonlinear partitioned eigenvalue problem proceeds usu ally in three steps 1 solution of the CCS CIS e
347. ions by even more special users As reference see 38 To optimize the structure and a global scaling factor specify optimize internal on or cartesian on global on You need as input data groups grad and globgrad the latter contains the global scaling factors and their gradients accumulated in all optimization cycles Out put will be on coord global also on forceapprox updated Note that for optimization of a global scaling factor a larger initial force constant element is rec ommended about 10 0 5 3 10 Conversion from Internal to Cartesian Coordinates Due to translational and rotational degrees of freedom and the non linear dependence of internal coordinates upon cartesian coordinates there is no unique set of cartesian coordinates for a given set of internal coordinates Therefore an iterative procedure is employed to calculate the next local solution for a given cartesian start coordinates This task may be performed using the relax program but it is much easier done within a define session 5 3 11 Conversion of Cartesian Coordinates Gradients and Force Constants to Internals To perform this tasks you have to activate the interconversion mode by interconversion on cartesian gt internal coordinate gradient hessian Note that any combination of the three options showed is allowed The default value is coordinate the two other have to be switched on explicitly if desired You need as input data groups
348. ions in the shell script FDE d or dipole dipole 1 dipole moment each step v or verbose shows more informations save mos save mos 1 save the MOs of both subsystems for each step save matrix save matrix 1 save fde matrices in each step help list all commands coulomb contribution 0 693026 mHa nuclear contribution 3 136544 mHa exchange correlation contribution 1 156390 mHa kinetic contribution 6 989320 mHa where the FDE energy E P the FDE binding energy the embedding energy error AF and the error energy decomposition in its coulomb nuclear exchange correlation and kinetic contributions are reported This output is present at each FDE iteration fde input option err energy 1 Restarting The script FDE checks in the current directory for previous FDE calculations If these are present then the FDE calculation will be restarted from the last iteration found The directories ISOLATED_SUBSYSTEM_A and ISOLATED_SUBSYSTEM_B will be overwritten by the converged calculations from previous run The energy and the orbital from the isolated systems are saved in the current directory in the files isolated_energy ks mos_A ks and mos_B ks Note that a restart is possible only if the same subsystem definition and the same basis set are used e g the same p flag and the s or m flag Other flags e g kinetic and xc functionals and convergence paramters can be instead modified As all the options are saved
349. is sets for one and two component Dirac Fock effec tive core potentials F Weigend and A Baldes J Chem Phys 133 174102 2010 22 CHAPTER 1 PREFACE AND GENERAL INFORMATION Auxiliary basis sets for density fitted correlated wavefunction calculations Weight ed core valence and ECP basis sets for post d elements C Hattig G Schmitz J KoSmann submitted for publication A unpublished 1 4 MODULES AND THEIR FUNCTIONALITY 23 1 4 Modules and Their Functionality For references see Bibliography define uff dscf odft grad ridft and rdgrad mpgrad rimp2 ricc2 interactive input generator which creates the input file control define supports most basis sets in use especially the only fully atom optimized consistent basis sets of SVP and TZV quality 2 3 4 5 6 available for the atoms H Rn excluding lanthanides define determines the molec ular symmetry and internal coordinates allowing efficient geometry opti mization define allows to perform a geometry optimization at a force field level to preoptimize the geometry and to calculate a Cartesian Hessian matrix define sets the keywords necessary for single point calculations and geometry optimizations within a variety of methods There are also many features to manipulate geometries of molecules just try and see how it works performs a geometry optimization at a force field level The Universal Force Field UFF 7 is implemented Beyond
350. ised auxiliary basis sets which are available for all TURBOMOLE standard basis sets SVP TZVP TZVPP QZVPP as well as for the aug ec p wC VXZ X D T Q 5 basis sets series for Al Ar also for the aug cc p wC V X d Z series Exploitation of symmetry of all point groups Can only be used for sequential calculations Can be combined with the COSMO solvation model see chapter 17 for de tails Functionality of ricc2 e Includes all of the above rimp2 functionalities e Runs sequentially and parallel with MPI or OpenMP and supports at the MP2 level all point groups and can in geometry optimizations and vibrational frequency calculations with NumForce combined with RI JK SCF for the Hartre Fock reference calculation e Contains an implementation of explicitly correlated MP2 F12 methods present ly restricted to energies and the C4 point group e Can for open shell calculations be used with UHF and single determinant high spin ROHF reference wavefunctions ROHF MP2 presently limited to ener gies e Energies and gradients for the spin component scaled SCS and SOS MP2 ap proaches including a Laplace transformed implementation of SOS MP2 with O N scaling computation costs e Static polarizabilities currently restricted to closed shell reference wavefunc tions and the sequential and SMP versions cannot yet be combined with spin component scaling see Chapter 9 5 for a description of the input e See Chap
351. ist of all coordinates involved will be displayed and you will be asked to confirm deletion The syntax is simply irem 5 to delete internal coordinate no 5 or irem d to remove all display coordinates Hitting lt return gt will bring you back to the geometry main menu Interactive Definition of Internal Coordinates If you choose idef in the internal coordinate menu you will get the following infor mation ENTER INTERNAL COORDINATE DEFINITION COMMAND lt x gt lt type gt lt indices gt WHERE lt x gt k f d I lt type gt stre invr bend outp tors linc linp comp ring pyrm bipy pris cube octa THESE COMMANDS WILL BE EXPLAINED IN DETAIL IF YOU ENTER lt x gt lt type gt FOR SOME CHOICE OF lt x gt AND lt type gt E G k stre DEFAULT G0 BACK TO INTERNAL MAIN MENU DISPLAY dis The lt x gt means the status see page 57 of the internal coordinate entered k f d i The syntax is k stre 1 2 d tors 3627 f bend 345 i outp 347 9 Note that in the third example atom 5 is the central atom of the angle Specification of available internal coordinates The following types of coordinates are available stre The stre for stretch describes a distance between two atoms It needs only two atomic indices to be given the order of which is arbitrary invr The invr coordinate for inverse r describes an inverse distance The declaration is the same as for stre but in some cases if you are far away from the minimum
352. ith mole fraction x in the mixture Si can be expressed as 263 iw Me H aijig o T Ho g kT In ai lI ua where the combinatorial term Lo g accounts for effects due to the size and shape differences of the molecules in the mixture and a denotes the area of segment t The kT ln z can be skiped for infnited dilution The free energy gained by the solvation process in the DCOSMO RS framework is the sum of the dielectric energy of the COSMO model and the chemical potential described above 1 Ediel RS AORE a foci Euiel foot The factor fp has been introduced to account for the missing solute solvent back polarization The default value is one in the current implementation From the above expression the solvent operator VES can be derived by functional derivative with respect to the electron densityr ARS ghRS fled q m 5 lr r d ne Thus the solvation influence of the COSMO RS model can be viewed as a correction of the COSMO screening charges q The additional charges denoted as ga be obtained from q4 5 A 64 5 where the potential PAES arises from na chemical potential of the solute in the solvent djig rue fool t Fs q q qt In order to get a simple and differentiable representation of the COSMO RS potential us o T we use equally spaced cubic splines An approximate gradient of the method has been implemented DCOSMO RS can be used in SCF energy and gradient calculatio
353. itionally the combinatorial contribution at infinite dilution of the COSMO RS model is given in the output The use of this energy makes sense if the molecule under consideration is different than the used solvent or not component of the solvent mixture respectively To be consistent one should only compare energies containing the same contributions i e same outlying charge correction and with or without combinatorial contribution Please note the COSMO RS contribution of the DCOSMO RS energy depends on the reference state and the COSMO RS parameterization used in the calculation of the chosen COSMO RS potential Therefore the DCOSMO RS energies should not be used in a comparison with the gas phase energy i e the calculation of solvation energies 18 2 9 Keywords for Modules GRAD and RDGRAD Many of the dscf and ridft keywords are also used by grad and rdgrad drvopt This keyword and corresponding options are required in gradient calculations only in special circumstances Just drvopt is fine no options needed to compute deriva tives of the energy with respect to nuclear coordinates within the method specified SCF DFT RIDFT 18 2 FORMAT OF KEYWORDS AND COMMENTS 305 If running a DFT gradient calculation it is possible to include the derivatives of the quadrature weights to get more accurate results In normal cases however those effects are marginal An exception is numerical calculation of frequencies by Numforce where it is
354. ity The second rung of the Jacob s ladder is the generalized gradient approximation GGA in this case the XC energy density depends also on the gradient of the density In the third rung meta GGA an additional variable is used the Kohn Sham kinetic energy density which allows e g to construct self correlation free functionals Functionals in the above rungs can have high accuracy for different class of problems in chemistry and solid state physics but their main limitation is the self interaction error SIE 156 157 158 159 To avoid the SIE the exchange must be treated exactly and this can be achieved by functionals in the fourth rung which depend explicitly on all the occupied KS orbitals In the KS formalism the EXX exact exchange energy is for closed shell systems ns 2 156 157 158 159 occ OCC REXX Ns TLL foc OE r Oh r OE er GES r 16 1 lr r i e the same functional form of the Hartree Fock HF exchange but computed with KS orbitals which are obtained using a self consistent local EXX potential At this point we should recall that hybrid DFT functionals including HF exchange doesn t belong to the KS formalism in hybrid DFT in fact the non local HF jNL 5ng ba r a r a r ri Generalized Kohn Sham equations determining the orbitals exchange operator r r is employed in the self consistent 249 250 CHAPTER 16 ORBITAL DEPENDENT DFT While LDA GGA met
355. ity matrix in analogy to the HF density matrix MP2 corrections of properties like electric moments or atomic populations are ob tained in the same way as for the HF level the HF density matrix is just replaced by the MP2 density matrix The resolution of the identity RI approximation means expansion of products of virtual and occupied orbitals by expansions of so called auxiliary functions Calculation and transformation of four center two electron integrals see above is replaced by that of three center integrals which leads to computational savings of rimp2 compared to mpgrad by a factor of ca 5 small basis sets like SVP to ca 10 large basis sets like TZVPP or more for cc pVQZ basis sets The errors dif ferences to mpgrad of rimp2 in connection with optimised auxliliary basis sets are small and well documented 9 92 The use of the mpgrad modul is recommended rather for reference calculations or if suitable auxiliary basis sets are not available 8 3 How to Prepare and Perform MP2 Calculations Prerequisites Calculations with mpgrad rimp2 or ricc2 require e a converged SCF calculation with the one electron density convergence thres hold set to denconv 1 d 7 or less e the maximum core memory the program is allowed to allocate should be de fined in the data group maxcor in MB the recommended value is ca 3 4 of the available physical core memory at most e orbitals to be excluded from the correlation
356. ix def2 QZVPP and def2 QZVP are identical with QZVPP and QZVP Orbital basis sets elements Rb Rn Rb Sr Y Cd In Cs Ba La Hg Tl At Rn def SVP def SV P de TZVP d d d d d d d j def TZVPP f d f f d f d j def2 SV P j d d j d d j j def2 SVP j d j j d j j j def2 TZVP def2 TZVPP j def2 QZVP def2 QZVP j Auxiliary basis sets for RI DFT Coulomb fitting H kr Rb At Rn def SVP def SV P c d l def TZVP d d 1 def2 universal i 20 CHAPTER 1 PREFACE AND GENERAL INFORMATION Auxiliary basis sets for RI MP2 and RI CC2 elements H Ar H He Li Be B F Ne Na Mg Al Cl Ar SVP SV P f k f f f k f f k TZVP TZVPP fIik f f f k f f k QZVP QZVPP k def2 SV P f k m f f k m f k def2 SVP fi kom f f k m f k def2 TZVP def2 TZVPP f k fim f k m m k aug cc pVXZ X D Q hh h k k h h k h h aug cc pV5Z k k k k k k cc pwCVXZ X D 5 k k k k Note the auxiliary basis sets for the aug cc pV X d Z basis sets for Al Ar are identical with the aug cc pVXZ auxiliary basis sets Auxiliary basis sets for RI MP2 and RI CC2 elements K Kr K Ca Sc Zn Ga Br Kr SVP SV P f f f f k TZVP TZVPP f f f f QZVP QZVPP k def2 SV P m f def2 SVP m f m def2 TZVP def2 TZVPP m f aug cc pVXZ X D Q aug cc
357. ked to generate input files for define which is then used to prepare the control files including occupation numbers initial guess MOs etc for the different ghost and monomer calculations and shell scripts with commands for calculations on these fragments 2 jobbsse cycles over the supermolecular complex and the fragments and com putes the energies and if requested gradients for them Then the counterpoise corrected results are evaluated and written to the standard data groups en ergy and grad 3 For geometry optimizations one of the structure relaxation codes statpt or relax is invoked to update the coordinates and check for convergence If the structure optimization is not converged jobbsse continues with the previous step Note that counterpoise corrected calculations with jobbsse are NOT as black box as ordinary geometry optimizations with jobex The input generated for the frag ments are based on the default occupation numbers obtained from the EHT guess default assignments for the frozen orbitals memory etc Since this might be differ ent from what is needed or even fail it is recommended to let jobbsse stop after the initial setup step using the flag setup and to check carefully the assigned basis 5 6 COUNTERPOISE CORRECTIONS USING THE JOBBSSE SCRIPT 119 sets occupations number and subsystem symmetries In particular for MP2 or CC2 calculations with molecules containing not only the atoms H Ar also th
358. l disks Set in addition to tmpdir the keyword sharedtmpdir to indicate that several pro cesses might share the same local disk The program will than create in s the directory given in tmpdir subdirectories with node specific names Note that at the end of a ricc2 run the scratch directories specified with tmpdir are not guaranteed to be empty To avoid that they will fill your file system you should remove them after the ricc2 calculation is finished Another difference to the parallel HF and DFT gradient programs is that ricc2 will communicate much larger amounts of data between the compute nodes With a fast network interconnection Gigabit or better this should not cause any problems but with slow networks the communication might become the limiting factor for performance or overloading the system If this happens the program can be put into an alternative mode where the communication of integral intermediates is replaced by a reevaluation of the intermediates at the expense of a larger operation count wherever this is feasible Add for this in the control the following data group mpi_param min_comm 9 7 Spin component scaling approaches SCS SOS By introducing individually scaling factors to the same spin and opposite spin con tributions of the correlation energy second order methods can be modified for a hopefully better performance SCS MP2 has first been proposed by S Grimme and SOS MP2 by Y Jung et al see below T
359. lable approximation and corresponding labels are 322 CHAPTER 18 KEYWORDS IN THE CONTROL FILE CCSD F12 ccsd f12 CCSD F12 ccsd f 12 CCSD F12 ccsd f12 CCSD F12b ccsd 12b CCSD 2 m5 ccsd pt2f12 CCSD 2 as ccsd 2 f12 It is recommended that these approximations are only used in combina tion with ansatz 2 and the SP approach i e geminal coefficients fixed by the cusp conditions For CCSD F12b calculations also the CCSD F 12a energies are calculated as a byproduct By default a CCSD F12 calcu lation is carried out but it is recommended that whenever appropriate the computationally more efficient CCSD F12 approximation is used excitations irrep au multiplicity 1 nexc 4 npre 6 nstart 8 irrep bg multiplicity 3 nexc 2 npre 4 nstart 5 spectrum states all operators diplen dipvel tmexc istates all fstates all operators diplen dipvel exprop states all operators qudlen xgrad states ag 3 1 conv 6 thrdiis 2 preopt 3 leftopt bothsides In this data group you have to give additional input for calculations on excited states irrep the irreducible representation multiplicity spin multiplicity 1 for singlet 3 for triplet default singlet not needed for UHF nexc the number of excited states to be calculated within this irrep and for this multiplicity npre the number of roots used in preoptimization steps default npre nexc 18 2 FORMAT OF KEYWORDS AND COMMENTS 323 nstart the number of st
360. lectric quadrupole moment are displayed automatically in the define ex menu If a large number of states is to be calculated it is highly recommended to provide extra memory by specifying rpacor m 156 CHAPTER 7 HF AND DFT RESPONSE CALCULATIONS the integer m being the core memory size in megabytes default is 20 The larger m the more vectors can be processed simultaneously without re calculation of integrals As a rule of thumb m should be ca 90 of the available main memory If RI J is used ridft it is recommended to set ricore to a small value and rpacor to a large value if the number of states is large and vice versa if it is small By specifying spectrum unit and or cdspectrum unit a list of excitation energies and oscillator and or rotatory strengths of the optically allowed transitions is written onto file spectrum and or cdspectrum As above unit specifies the energy unit and may be ev nm 1 cm or a u default The files spectrum and cdspectrum may conveniently be used for further processing e g using a plotting program such as Gnuplot By specifying curswitchdisengage inclusion of the current density response for MGGA calculations is disabled Note that the results of calculations using this flag will no longer be gauge invariant and will differ from results obtained with the standard gauge invariant implementation 7 4 5 Excited State Geometry Optimizations The input for computing excited state
361. led set of equations for the ground state This is done iteratively until convergence is achieved which is controlled with an outer loop as well as some micro iterations for the multiplier and amplitude solver Normally the default options should be fine but they can be changed by modifying the control file Options in ricc2 block in file control ricc2 pe_maxiter lt int gt pe_maxtOiter lt int gt pe_maxl0iter lt int gt 9 8 POLARIZABLE EMBEDDING CALCULATIONS 203 pe_maxiter maximum of macro iterations default 50 pe_maxtOiter maximum of micro iterations in T0 solver default 4 pe_maxl0iter maximum of micro iterations in L0 solver default 4 There are several limitations for the use of PERI CC2 e only ground state energies excitation energies and transition moments are supported no other properties or gradients and so on e no other wave function model than CC2 is supported e no use of symmetry e no MPI parallelization is available but SMP binaries work e open shell systems are not covered Chapter 10 CCSD CCSD F12 and CCSD T calculations The ricc2 module includes also an implementation of the full coupled cluster singles and doubles method CCSD and its explicitly correlated CCSD F12 and CCSD F12 variants CCSD and the F12 variants can be combined with a perturbative correc tion for connected triple excitations CCSD T As perturbative approximations beyond MP2 also the approximations MP3
362. list clean The TTEST script knows several operation modes realclean and validate controlled by its options The run mode is default and means that the test calculations are performed and the results are written to the TESTPROTOKOLL file The check mode differs only in that the programs are not executed but the existing program output is checked against the reference The results of the check are written to the CHECKPROTOKOLL file Calling the test script in the list mode simply lists the test examples that are currently available This allows the user to save the full list to file edit and re use it with the r option The clean and realclean options are for cleaning up the test directories and protocols Finally the validate mode is mainly of use for writing the CRIT files It helps to verify the match patterns provided in the test criteria and shows if it extracts the expected data for comparison with the reference For every output file used for testing the validate option produces a copy with an additional val extension The match strings evaluated for test criteria are highlighted in the output by lt lt lt lt lt and gt gt gt gt gt marks There is a lot of options controlling the behavior of TTESTTesting specific versions of TURBOMOLE modules is provided by loading path options 1 for binaries 1s for scripts and x for a specific executable For benchmarking
363. ll as energy calculations of other wave function models see chapter 9 6 SMP and MPI mpgrad parallel conventional i e non RI MP2 energy and gradient cal culations Please note that RI MP2 is one to two orders of magnitude faster than conventional MP2 so even serial RI MP2 will be faster than parallel MP2 calculations MPI only aoforce parallel Hartree Fock and DFT analytic 2nd derivatives for vi brational frequencies IR spectra generation of Hessian for transition state searches and check for minimum structures SMP only escf parallel TDDFT RPA CIS excited state calculations UV Vis and CD spectra polarizabilities SMP only egrad parallel TDDFT RPA CIS excited state analytic gradients includ ing polarizability derivatives for RAMAN spectra SMP only NumForce this script can used for a trivial parallelization of the numerical displaced coordinates Additional optional keywords for parallel runs with the MPI binaries are described in Chapter 18 However those keywords do not have to be set by the users When using the parallel version of TURBOMOLE scripts are replacing the binaries Those scripts prepare a usual input run the necessary steps and automatically start the parallel programs The users just have to set environment variables see Sec 3 2 2 below To use the OpenMP parallelization only an environment variable needs to be set But to use this parallelization efficiently one should co
364. ll be taken for linear algebra part depends on the size of the matrices Synonyms for MPP are SP3 and linuxcluster cluster for systems with slow communication the linear algebra part will be done on one single node Synonyms for cluster are HP Cluster and every platform that is not known by TURBOMOLE Use this setting if you encounter problems with ScaLAPACK ScaLA PACK routines may print warnings or errors to the master output file lines often start with PD especially if the number of CPUs is large and the size of the matrices is small to medium SGI similar to SMP but here the server task is treated differently the MPI implementation on the SGIs would cause this task to request too much CPU time otherwise If you want to run mpgrad traloop has to be equal to or a multiple of the number of parallel workers For very large parallel runs it may be impossible to allocate the scratch files in the working directory In this case the scratch files option can be specified an example for a dscf run is given below The scratch directory must be accessible from all nodes 18 2 FORMAT OF KEYWORDS AND COMMENTS 363 scratch files dscf dens home dfs cd00 cd03_dens dscf fock home dfs cd00 cd03_fock dscf dfock home dfs cd00 cd03_dfock dscf ddens nome dfs cd00 cd03_ddens dscf xsv nome dfs cd00 cd03_xsv dscf pulay home dfs cd00 cd03_pulay dscf statistics home dfs cd00 cd03_statistics dscf errvec nome dfs cd00 cd03_e
365. ll normally only need to enter eht For the EHT guess define will ask for some specifications and you should always choose the default i e just lt enter gt Of importance is only the molecular charge specified as 0 neutral default 1 or 1 etc Based on the EHT orbital energies define proposes an occupation If you accept you are done if not you get the occupation number assignment menu explained in 4 3 2 Description of Commands infsao Command infsao provides information about the symmetry adapted basis which is used for the SCF calculation To exploit the molecular symmetry as efficiently as possible TURBOMOLE programs do not use the simple basis which you specified during your define session Instead it builds linear combinations of equal basis functions on different but symmetry equivalent atoms This basis is then called the SAO basis Symmetry Adapted Orbital It has the useful property that each basis function transformed to this basis transforms belongs to one irreducible representation of the molecular point group that is the basis reflects the full molecular symmetry as specified by the Sch6nflies symbol infsao gives you a listing of all symmetry adapted basis functions and their constituents either on file or on the screen This may help you if you want to have a closer look at the SCF vectors because the vector which is output by program dscf is written in terms of these SAOs atb Molecular orbitals can be
366. lly The number of CPUs that shall be used can be chosen by setting the environment variable PARNODES export PARNODES 8 The default for PARNODES is 2 NOTE Depending on what you are going to run some care has to be taken that the system settings like memory limits etc will prevent the parallel versions to run See the following sections OpenMP parallelization of dscf odft and ricc2 The OpenMP parallelization does not need any special program startup The bi naries can be invoked in exactly the same manner as for sequential non parallel calculations The only difference is that before the program is started the environ ment variable PARNODES has to be set to the number or threads that should be used by the program the scripts will set OMP_NUM_THREADS to the same value and start the OpenMP binaries The number of threads is essentially the max number of CPU cores the program will try to utilize To exploit e g all eight cores of a machine with two quad core CPUs set export PARNODES 8 for csh and tcsh use setenv PARNODES 8 Presently the OpenMP parallelization of ricc2 comprises all functionalities apart from the recently LT SOS RI MP2 and the calculation of expectation values for 82 Note that the memory specified with maxcor is for OpenMP parallel calculation the maximum amount of memory that will be dynamically allocated by all threads together To use your computational resources efficiently it is recommended to set
367. logy of the molecule and the whole force field terms see below default ufftopology file ufftopology uffgradient contains the accumulated cartesian analytical gradients default uffgradient file uffgradient uffhessian contains the cartesian analytical Hessian default uffhessian file uffhessian0 0 The file ufftopology The topology file ufftopology contains the blocks nxtneil2 nxteneil3 nxtneil4 connectivity angle torsion inversion nonbond and qpartial It starts with uff topology and ends with end The first three blocks nxtneil2 nxtneil3 nxtneil4 have the same form they start with the atom number and the number of its neigh bours in the next line are the numbers of the neighbour atoms Then the connec tivity block follows starting with the number of bond terms Each line contains one bond term I J d BO Here are I and J the number of the atoms d the distance in a u and BO is the bond order The angle terms follow starting with the number of the angle terms In each line is one angle term J I K wtyp 0 nr JI nrg Here are J I and K the atoms number where atom J is in the apex wtyp is the angle type and has the following values 274 CHAPTER 18 KEYWORDS IN THE CONTROL FILE wtyp 1 linear case wtyp 2 trigonal planar case wtyp 3 quadratic planar case wtyp 6 octahedral case wtyp 9 all other cases 0 is the angle value in degree nrj and nryx are the number of the bonds
368. ls of selected atoms have to be specified within data group m matrix as m matrix 1 0 0 0 0 0 0 10 1 0 0 0 0 0 11 1 0 1 0 0 0 5 3 13 Initialization of Force Constant Matrices The most simple initial hessian is a unit matrix However better choices are prefer able For structure optimizations using internal coordinates you may use structural information to set up a diagonal force constant matrix with elements chosen in ac cord to the softness or stiffness of the individual modes For detailed information refer to ref 36 For optimization of basis set parameters less information is avail able When neither data block forceapprox is available nor forceinit on is set the force constant matrix will be initialized as a unit matrix Specifying the force constant initialization key forceinit on diag will lead to diag real Initialization with real as diagonal elements diag default Initial force constant diagonals will be assigned the following default values 5 4 FORCE FIELD CALCULATIONS 113 internal coordinates stretches 0 50 angles 0 20 scaling factors p 1 50 d 3 00 exponents uncontracted 0 15 contracted 10 00 contraction coefficients 100 00 global scaling factor 15 00 cartesian force constants 0 50 diag individual Initial force constant diagonals will be taken from intdef fdiag or global fdiag Similar initialization modes are NOT supported for geometry optimization in cartesian space and
369. lt x gt lt y gt lt z gt lt q gt with lt x gt lt y gt lt z gt being the coordinates and lt q gt its charge e g point_charges thr lt real gt self energy nocheck list 2 2 2 5 5 0 0 2 5 In addition the following optional arguments may be given thr real distance threshold for discarding redundant point charges default value 107 selfenergy if given the selfenergy of the point charge array will will be included in the energy and the gradient nocheck switches off the check for redundant point charges and the default sym metrization This option can significantly speed up the point charge treatment if many of them are involved use only if the point charges are well distributed and symmetry is C1 e g when they stem from proper MM runs list print all point charges in the output default is to print the point charges only if less than 100 charges given prediag concerns the first SCF iteration cycle if start MOs from an EHT guess are used The SCF iteration procedure requires control mechanisms to ensure fast con vergence in TURBOMOLE these are based on orbital energies of the preceeding iteration used for level shifting and damping besides DIIS see below This feature cannot be used in the first iteration if EHT MOs are employed as start since are not available The keyword prediag provides e of the zeroth iteration by diagonalization of occ occ and virt virt part of the first
370. ltipliers Z and W enforce that the MOs satisfy the ground state HF KS equations and are orthonormal Z is the so called Z vector while W turns out to be the excited state energy weighted density matrix Computation of Z and W requires the solution of a single static TDHF TDKS response equation 7 4 also called coupled and perturbed HF KS equation Once the relaxed densities have been computed excited state properties are obtained by simple contraction with derivative integrals in the atomic orbital AO basis Thus computation of excited state gradients is more expensive than that of ground state gradients only by a constant factor which is usually in the range of 1 4 TDHF TDDFT expressions for components of the frequency dependent polarizabil ity amp ag w can also be reformulated as variational polarizability Lagrangians 86 TOP Xa Ya X6 Yg C ZP WP w Xa Ya A wA Xg Yo Xa Yala ual Xo Yp 0 Zier D gt Wasp p ias pqa p lt q 7 12 The stationary point of L w equals to aag w The requirement that L w be stationary with respect to all variational parameters determines the Lagrange multi pliers Z and W P All polarizability components a are processed simultaneously which allows for computation of polarizability derivatives at the computational cost which is only 2 3 higher than for the electronic polarizability itself Within TDDFT and TDHF the X and Y coefficients are normalized as
371. mand w writes your molecular geometry and your internal coor dinates to file Afterwards you will be back in the geometry main menu If the filename entered starts with the structure will be written to the structure library name allows you to change atomic identifiers turning e g oxygen atoms into sulfur atoms After entering the identifier to be changed remember the double quotation marks c ring you will be asked to enter the new one You can use question marks for characters not to be changed e g you enter ring to change c chain to c ring If you do not enter eight characters your input will be filled up with trailing blanks The command del allows you to delete one or more atoms After you entered the atomic list define will show you a list of all atoms con cerned and will ask you to confirm deleting these atoms If any internal coordinate definitions exist which rely on some of the deleted atoms these definitions will be deleted too The command banal allows you to perform a bonding analysis that is define will try to decide which atoms are bonded and which are not according to a table of standard bond lengths which is included in the code of define You must have performed this command before you can use the display commands disb display bonding information or disa display bond angle information The standard bond lengths and the bonding analysis available from these are also needed for the commands su
372. mat as the data group coord in file control The Cartesian coordinates and the definitions of the internal coordinates are read in free format you only have to care for the keywords coord and optionally intdef and important for the end at the end of the file The atomic symbol follows the Cartesian coordinates separated by at least one blank For a description of the internal coordinate definitions refer to 4 1 2 Entering as first character of file will tell define to take file from the structure library The name following the actually does not need to be a filename in this case but rather a search string referenced in the structure library contents file see Section 4 1 same as a but assumes the atomic coordinates to be in A rather than a u This command allows you to replace one atom in your molecule by an other molecule For example if you have methane and you want to create ethane you could just substitute one hydrogen atom by another methane molecule The only requirement to be met by the substituted atom is that it must have exactly one bond partner The substituting molecule must have an atom at the substituting site in the example above it would not be appropriate to use CH3 instead of CH for substi tution Upon substitution two atoms will be deleted and the two ones forming the new bond will be put to a standard distance define will then ask you to specify a dihedral angle between the old and th
373. mat of Keywords and Comments saosaoa a 265 18 2 1 General Keywords 2 22 sc ee daa aa 265 CONTENTS 9 18 2 2 Keywords for System Specification 267 18 2 3 Keywords for redundant internal coordinates in redund_inp 269 18 2 4 Keywords for Module Uff 04 271 18 2 5 Keywords for Modules Dscf and Ridft 275 18 2 6 Keywords for Module ODFT 2 00084 294 18 2 7 Keywords for Periodic Electrostatic Embedded Cluster Method 296 18 2 8 Keywords for Cosmo s re sares erari a tarwa 298 18 2 9 Keywords for Modules Grad and Rdgrad 304 18 2 10 Keywords for Module Aoforce 08 305 18 2 11 Keywords for Module Escf 2 308 18 2 12 Keywords for Module Egrad 2 311 18 2 13 Keywords for Modules Mpgrad and Rimp2 ole 18 2 14 Keywords for Module Rice lt e os s ee ee Cb ronu ossos 315 18 2 15 Keywords for Module Relax oa oaa 328 18 2 16 Keywords for Module Statpt 337 18 2 17 Keywords for Module Moloch 0 4 339 18 2 18 Keywords for wave function analysis and generation of plotting Gat soe ede gig oR eke eae ee pRa ee E a G 344 18 2 19 Keywords for Module Frog 2 353 18 2 20 Keywords for Module Mpshift 360 18 2 21 Keywords for Parallel Runs 2 362 19 Sample control files 365 10 1 Introduction 2 402 6 Shoe bk AG ER A ee we Se es 3
374. n J Phys 58 8 1200 1211 1980 J P Perdew Y Wang Accurate and simple analytic representation of the electron gas correlation energy Phys Rev B 45 23 13244 13249 1992 A D Becke Density functional exchange energy approximation with correct asymptotic behaviour Phys Rev A 38 6 3098 3100 1988 C Lee W Yang R G Parr Development of the Colle Salvetti correlation energy formula into a functional of the electron density Phys Rev B 37 2 785 789 1988 J P Perdew Density functional approximation for the correlation energy of the inhomogenous electron gas Phys Rev B 33 12 8822 8824 1986 J P Perdew K Burke M Ernzerhof Generalized gradient approximation made simple Phys Rev Lett 77 18 3865 3868 1996 J Tao J P Perdew V N Staroverov G E Scuseria Climbing the density functional ladder Nonempirical meta generalized gradient approximation de signed for molecules and solids Phys Rev Lett 91 14 146401 2003 A D Becke A new mixing of Hartree Fock and local density functional the ories J Chem Phys 98 2 1372 1377 1993 A D Becke Density functional thermochemistry HI The role of exact ex change J Chem Phys 98 7 5648 5652 1993 J P Perdew M Ernzerhof K Burke Rationale for mixing exact exchange with density functional approximations J Chem Phys 105 22 9982 9985 1996 398 61 66 69 70 71
375. n can also be appended to charges or ch_list to set the tolerance for charge neutrality violation to 107 default n 5 298 CHAPTER 18 KEYWORDS IN THE CONTROL FILE Additionally the following keywords control the accuracy of PEECM calculation lmaxmom Maximum order of the multipole expansions in periodic fast multipole method PFMM Default value is 25 potval Electrostatic potential at the lattice points resulting from periodic point charges field will be output if this keyword is present Default is not to output wsicl Well separateness criterion for PFMM Default is 3 0 epsilon Minimum accuracy for lattice sums in PFMM Default is 1 0d 8 18 2 8 Keywords for COSMO The Conductor like Screening Model COsMo is a continuum solvation model where the solute molecule forms a cavity within the dielectric continuum of per mittivity epsilon that represents the solvent A brief description of the method is given in chapter 17 The model is currently implemented for SCF energy and gradi ent calculations dscf ridft and grad rdgrad MP2 energy calculations RIMP2 and mpgrad and MP2 gradients RIMP2 and response calculations with escf For simple HF or DFT single point calculations or optimizations with standard set tings we recommend to add the cosmo keyword to the control file and to skip the rest of this section Please note due to improvements in the A matrix and cavity setup the COSMO ener gies and gradients may dif
376. n case a doublet with an excess alpha electron at each Cu atom aa in an obvious notation preserves Dy symmetry while the low spin state ba does 74 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE not For a broken symmetry treatment it is advidsable to calculate the high spin state first and then broken symmetry state s from the energy difference s one may calculate approximate values for the spin spin coupling parameters as described by e g the above authors Access to broken symmetry states usually is possible by the choice of appropriate start MOs followed by an SCF procedure Start MOs may be obtained by first applying a localization procedure to the MOs of the high spin state and then by moving localized alpha orbitals to the beta subset The preparation of broken symmetry start MOs can be done with define semi automatically Prerequisite is a converged wave function for the high spin state in C symmetry that fulfills the aufbau principle If in this case one enters flip in the orbital definition menu define selects the occupied valence orbitals of the system by an orbital energy criterion which one can usually accept unless the system is highly charged and the orbital energies are shifted Next a Boys orbital localization procedure is carried out which depending on the size of the problem may take some time Then the user is asked ENTER INDICES OF ATOMS OR ELEMENT TO BE MANIPULATED example 1 2 3 or
377. n case of the module aoforce are frequency analysis only analysis only to read a complete Hessian from the input file hessian and perform only the frequency analysis 306 CHAPTER 18 KEYWORDS IN THE CONTROL FILE analysis only intcoord print printlevel to perform an analysis of normal modes in terms of internal coordinates Details about this option and the effect of the printlevel default is 0 are given in Section 12 The effect of the keyword only is the same as described above maxcor 50 fixes the RAM memory to be used by the run here 50 MB about 70 of available memory should be fine because maxcor specifies only the memory used to store derivatives of density and Fock matrices as well as the CPHF RHS Default is 200 MB forceconv 7 sets the convergence criterion for the CPHF equations to a residual norm of 1 0d 7 Normally the default value of 1 0d 5 already provides an accuracy of vibrational frequencies of 0 01 cm7 with respect to the values obtained for the convergence limit forceiterlimit 10 fixes the maximum number of Davidson iterations for the solution of the CPHF equations to a value of ten Normal calculations should not need more than eight iterations but as a precaution the default value is 25 nosalc forces the program in case of molecules with C1 symmetry not to use 3N 6 5 symmetry adapted but all 3N cartesian nuclear displacement vectors This option may lead to a moderate speed up f
378. n occupation numbers would lead to results without any physical meaning Note that RI is only used partially which means that the resulting Hessian is only a very good approximation to exact second derivatives of the RIDFT energy expression Apart from a standard force constant calculation which predicts all symmetry allowed and forbidden vibrational transitions it is also possible to specify certain irreps for which the calculation has to be done exclusively or to select only a small number of lowest eigenvalues and eigenvectors that are generated at reduced computational cost Furthermore the Numforce script allows the calculation of second derivatives for all methods for which a program for analytic gradients is available in TURBOMOLE i e the main use of this script is the prediction of vibrational spectra at the MP2 level and for excited states using RI CC2 or TDDFT If force constant calculations result in imaginary frequencies molecular distortions along these normal modes should lower the energy To distort the molecule use the interactive module vibration output of the new coordinates is done to the general input file on newcoord Vibrational frequencies also enable calculation of the molecular partition function and thus prediction of thermodynamic functions at temperatures other than 0 K 218 219 and finite pressure within the assumption of an ideal gas and no coupling between degrees of freedom These functions can
379. n the samples coord and intdef and userdefined bonds contains atom specification type and location and the bonds and internal coordinates convenient for geometry optimizations basis specification of basis sets ecp specification of effective core potentials 18 2 FORMAT OF KEYWORDS AND COMMENTS 267 jbas auxiliary fitting basis for the Coulomb terms in ridft scfmo uhfmo_alpha uhfmo_beta MO vectors of SCF or DFT calculations for RHF or UHF runs natural orbitals natural orbital occupation keywords and data groups set by unrestricted dscf or ridft runs Contain natural MO vector and orbital occupation energy grad energies and gradients of all runs e g for documentation in a geometry opti mizations forceapprox approximate force constant for geometry optimizations The control file must end with this keyword end 18 2 2 Keywords for System Specification General information defining the molecular system nuclear coordinates symmetry basis functions number of occupied MOs etc which are required by every module title give title of run or project here symmetry d4h Sch6nflies symbol of the point group All point groups are supported with the exception of NMR shielding and force constant calculations etc which do not work for groups with complex irreps C3 C3h T etc Use a lower symmetry group in this case atoms Example atoms cu 1 4 basis cu ecp 18 arep jbas cu e
380. n this menu the molecular symmetry needs not be correct so that you can try different movements and or rotations but as soon as you leave it the geometry will be symmetrized according to the present Schonflies symbol After you specified the atomic set to be considered you get the following information INPUT DIRECTION OF MOVEMENT OR LOCATION OF ROTATION AXIS EITHER AS A COORDINATE TRIPLE SEPARATED BY BLANKS OR AS TWO ATOMIC INDICES SEPARATED BY KOMMA OR x OR y OR z OR ENTER ANY DISPLAY COMMAND FIRST OR amp TO GO BACK You can thus specify the direction of movement or the rotational axis in the form 0 0 1 or simply z which both describes the z axis or 1 3256 3 333 0 2218 for an arbitrary axis If you want to specify an axis which is related to your molecule you may also enter two atomic indices which define it After having specified the axis you have to enter the distance of movement and the angle of rotation If you want to perform a simple rotation enter 0 for the distance of movement and if you want to simply move your structure enter 0 for the rotational angle You can leave this menu and return to the geometry main menu by hitting lt return gt or by entering any command of the geometry main menu 4 2 The Atomic Attributes Menu After you specified the molecular geometry and symmetry and wrote this data to file you will encounter the atomic attributes menu which is the second of the four 4 2 THE ATOMIC ATTRIBUTES
381. namical trajectory Both the accuracy of the trajectory and the total computation time thus depend crucially on the time step chosen in Mdprep A bad choice of timestep will result in integration errors and cause fluctuations and drift in the total energy As a general rule of thumb a timestep At should be chosen which is no longer than one tenth of the shortest vibrational period of the system to be simulated 304 CHAPTER 18 KEYWORDS IN THE CONTROL FILE Note that Mdprep will transform velocities so that the total linear and angular momentum is zero Actually for the Leapfrog algorithm initial velocities are At 2 before the starting time The following keywords are vital for frog nsteps 75 Number of MD time steps to be carried out nsteps is decreased by 1 every time frog is run and JOBEX md stops when nsteps reaches 0 natoms 9 Number of atoms in system current file mdlog aa The file containing the current position velocity time and timestep that is the input configuration During an MD run the current information is generally kept at the end of the log file log file mdlog ZZ The file to which the trajectory should be logged i e the output t time a u atomic positions x y z Bohr and symbols at t timestep au At atomic symbols and velocities x y z au at t At 2 kinetic energy H interpolated at t ab initio potential energy H calculated at t and pressure recorded at the barrier sur
382. nates linc 1 3 2 4 and linp 1 3 2 4 where 1 oxygen 2 carbon 3 carbon 4 hydrogen would solve the problem The type comp describes a compound coordinate i e a linear combi nation of primitive internal coordinates This is often used to prevent strong coupling between primitive internal coordinates and to achieve better convergence of the geometry optimization The use of linear com binations rather than primitive coordinates is especially recommended for rings and cages see ref 24 Command iaut uses linear combina tions in most cases After you entered k comp n where n is the number of primitive internal coordinates to be combined you will be asked to enter the type of the co ordinate stre bend Then you will have to enter the weight the coefficient of this primitive coordinate in the linear combination and the atomic indices which define each coordinate The definition of the primitive coordinates is the same as described above for the correspond ing coordinate types It is not possible to combine internal coordinates of different types This type helps you to define special ring coordinates You only have to enter k ring n where n is the ring size Then you will be asked for the atomic indices of all atoms which constitute the ring and which must be entered in the same order as they appear in the ring The maximum number of atoms in the ring is 69 but in most cases the ring size will be limited by the maximum number
383. nce for the auxiliary SVP TZVP and TZVPP basis sets for calculations with RI MP2 RI CC2 and related methods is F Weigend M Haser H Patzelt R Ahlrichs Chem Phys Lett 294 1998 143 e for the auxiliary cc pV XZ cc pV X d Z aug cc pVXZ aug cc pV X d Z basis sets with X D T or Q cite F Weigend A Kohn C Hattig J Chem Phys 116 2001 3175 e for the auxiliary cc pV5Z cc pV 5 d Z aug cc pV5Z aug cc pV 5 d Z cc pwCVXZ with X D T Q 5 and QZVPP basis sets the reference is C Hattig Phys Chem Chem Phys 7 2005 59 66 This reference should also be included if you employ the analytic basis set gradients implemented in the ricc2 program for the optimization of your own auxiliary basis set s e for the auxiliary def2 basis sets from Rb to Rn the reference is A Hellweg C Hattig S Hofener and W Klopper Theor Chem Acc 117 2007 587 597 For more details on the references for the basis sets included in the basis set libraries of the TURBOMOLE distribution see Sec 1 3 and the library files 9 1 CC2 GROUND STATE ENERGY CALCULATIONS 179 9 1 CC2 Ground State Energy Calculations The CC2 ground state energy is similarly to other coupled cluster energies ob tained from the expression Ecc HF H CC HF H exp T HF 9 1 Bsor t tit 2 aj0 Galioy 9 2 iajb where the cluster operator T is expanded as T Ti To with Ti Y oaa 9 3 ai 1 To 5 Ds tai
384. nctional oep As the computation of the OEP functional is completely analytic and grid free any selection of a grid type or size will not influence the OEP calculation in contrast to other density functionals Particular care is instead required to orbital and auxiliary basis set An arbitrary combination of them can lead to very good total energy i e very close to the 16 3 HOW TO PERFORM 253 Hartree Fock one but unphysical OEP potential In the present release we strongly recommend to use the d aug cc p VTZ oep basis set and the corresponding auxiliary basis set directory xbasen The following options can modify the quality time and output of an OEP calculation All the options can be set by define Every option has a reasonable default value so the user does not need to select any of the options below to run a proper OEP calculation oep options Listing of all possible options for the flag oep charge vector integer The Charge condition expansion coefficients in auxiliary basis set repre sentation can be calculated in different kinds The selection of integer 1 will use the following ansatz to calculate the coefficients En if Gp 0 0 if Gp 0 Gp is the integral over a normalized Gaussian auxiliary basis function Ni is the number of auxiliary basis functions with Gp 4 0 The selection of integer 2 will use the following ansatz to calculate the coefficients CP P 0 ifGp 0 The variable integer must h
385. nd it to the queue and check the file mylimits out to find out which limits are set Parallel version The parallel binaries are being started by the mpirun command which often uses ssh to start a process on a remote node The limits for the stack size can not be set by the user in such a case so everything in HOME profile HOME bashrc etc will not help to get rid of the problem To check the limits on a remote node try sh bash ksh syntax ssh lt hostname gt ulimit a If the ssh command gives a lower stack size than unlimited or a large number you have to change the file etc security limits conf on all nodes where the parallel binaries might run and add there the line example for 4GB limit soft stack 4194303 Redo ssh lt hostname gt ulimit a and you should get 4GB stack size limit as it is set in limits conf now Chapter 3 How to Run TURBOMOLE 3 1 A Quick and Dirty Tutorial A detailed tutorial for the usage of TURBOMOLE on the command line can be found in the DOC directory of your TURBOMOLE installation or on the web site of COSMOlogic see http www cosmologic de 3 1 1 Graphical user interface The most likely quickest and easiest way to start using TURBOMOLE is to use the free graphical user interface TmoleX It can be used to import and graphically build molecules select basis sets methods and job tasks submit jobs to the local machine or to remote systems visualize and combine result
386. nd step by egrad see Section 7 4 7 Finally the program intense is used to project the polarizability derivatives onto vibrational normal modes and to compute Raman scattering cross sections which are written out along with vibrational frequencies and normal modes The script Raman can be used to perform all these steps automatically 12 3 Vibrational frequencies with fixed atoms using NumForce The NumForce script provides with the option frznuclei a possibility to do a vi brational analysis with fixed atoms The atoms for which the cartesian coordinates should frozen have to be marked in coord with a f behind the atom type The frozen coordinates will be skipped during the numerical evaluation of the force con stant matrix instead all off diagonal elements of the force constant matrix which refer to one or two frozen coordinates will be set to zero while the diagonale elements for the frozen coordinates will be set to an arbitrarly chosen large value This feature is mainly intended to allow for a vibrational analysis in embbeded clus ter calculations e g for defects in ionic crystals The vibrational analysis uses a kind of frozen phonon approximation which corresponds to setting the masses of the fixed atoms to infinity i e decoupling the fixed atoms mechanically from the me chanically active subsystem The resulting vibrational frequencies will thus only 222 CHAPTER 12 VIBRATIONAL FREQUENCIES provide good approx
387. ne session which means that it will only be modified This may lead to difficulties however because define reads from the input file when entering each main menu and writes the corresponding data when leaving this menu Therefore the input file may be in an ill defined status for the next main menu this will be the case for example if you add or change atoms in the first menu so that the basis set information is wrong in the second menu define takes care of most but not all of these problems For these reasons it is recommended to use a different filename for the input and the output file of the define session if you change the molecule to be investigated In most cases involving only changes in the last three of the four main menus no problem should arise when using the same file as input and output 4 0 6 Be Prepared Atomic Coordinates Molecules and their structures are specified by coordinates of its atoms within the program invariably by Cartesian coordinates in atomic units Angstrom would also do In TURBOMOLE these coordinates are contained in the file coord see Section 19 Sample control files for an example Recommendation We strongly recommend to create the coord file before calling define only for small molecules one should use the interactive input feature of define Set up the molecule by any program you like and write out coordinates in the xyz format XMol format which is supported by most programs Then
388. ng a single test example is simple Change to the test example of your choice and call the TTEST script without arguments The test is started in a subdirectory named TESTDIR sysname where sysname is the current platform name as returned by the Sysname script The tested executable a short description and the test summary are output to the screen Detailed information about the performed com mands and results of all test criteria are found in the TESTPROTOKOLL file in the test subdirectory The default location for the binaries and scripts used for testing is the TURBODIR directory If you like to test some other e g your local version of the TURBOMOLE binaries or scripts you can specify the loading paths by the 1 or 1s options for the binaries and scripts respectively TTEST 1 usr local TURBOMOLE bin i786 pc linux gnu ls usr local TURBOMOLE scripts A specific executable can be chosen by the x option TTEST x usr local TURBOMOLE bin i786 pc linux gnu dscf If a test output is already present e g in the TESTDIR directory you may wish to check the results This is accomplished by calling TTEST in check mode TTEST check TESTDIR which compares the results in TESTDIR with the reference and writes the results to the CHECKPROTOKOLL file in the test directory Testing parts of the TURBOTEST directory structure or the entire test suite at once is performed by calling the TTEST script from the appropriate place The
389. nly for the first Rydberg orbitals 256 CHAPTER 16 ORBITAL DEPENDENT DFT Only gridsize 3 5 can be used no modified grids Use test integ to check if the selected grid is accurate enough for the employed basis set see page 279 The options in the 1hf group are off diag on The LHF exchange potential is computed default off diag off The KLI exchange potential is computed can be selected by lhfprep k1i num slater on the Slater potential is calculated numerically everywhere this is more accurate but quite expensive When ECPs are used turn on this option It can be selected by lhfprep num num slater off the Slater potential is computed using basis sets This leads to very fast calculations but accurate results are obtained only for first row elements or if an uncontracted basis set or a basis set with special additional contractions is used This is the default asymptotic for asymptotic treatment there are three options asymptotic off No asymptotic treatment and no use of the numerical Slater The total exchange potential is just replaced by 1 r in the asymptotic region This method is the fastest one but can be used only for the density matrix convergence or if Rydberg virtual orbitals are of no interest asymptotic on Full asymptotic treatment and use of the numerical Slater in the near asymptotic region It can be selected by lhfprep asy asymptotic dynamic 1 d 3 Automatic switching on off to the s
390. nly for C1 symmetry Note all integrals are kept in memory so this is for atoms and small molecules only 18 2 FORMAT OF KEYWORDS AND COMMENTS 315 tplot Enforces plotting of five largest t amplitudes as well as five largest norms of t amplitudes for fixed pair of occupied orbitals ij By additional integer this number may be changed mp2occ Enforces plotting of all eigenvalues of the MP2 density matrix 18 2 14 Keywords for Module Ricc2 Note that beside the keywords listed below the outcome of the ricc2 program also depends on the settings of most thresholds that influence the integral screening e g denconv scfconv scftol and for the solution of Z vector equation with 4 index integrals for relaxed properties and gradients on the settings for integrals storage in semi direct SCF runs i e thime thize scfintunit For the explanation of these keywords see Section 18 2 5 cbas file auxbasis Auxiliary basis set for RI approximation For details Section 18 2 13 freeze Freeze orbitals in the calculation of correlation and excitation energies For details see Section 18 2 13 printlevel 1 Print level The default value is 1 tmpdir work thisjob Specify a directory for large intermediate files typically three index coulomb integrals and similar intermediates which is different from the directory where the ricc2 program is started maxcor 20 The data group maxcor adjusts the maximum size of core
391. nol methanol_25 pot Tetrahydrofurane thf_25 pot Acetone propanone_25 pot Chloroform chcl13_25 pot Tetrachloromethane ccl4_25 pot Acetonitrile acetonitrile_25 pot Nitromethane nitromethane_25 pot Dimethylsulfoxide dimethylsulfoxide_25 pot Diethylether diethylether_25 pot Hexane hexane_25 pot Cyclohexane cyclohexane_25 pot Benzene benzene_25 pot Toluene toluene_25 pot Aniline aniline_25 pot The DCOSMO RS energies and total charges are listed in the COSMO section of the output 304 CHAPTER 18 KEYWORDS IN THE CONTROL FILE SCREENING CHARGE cosmo 0 012321 correction 0 011808 total 0 000513 correction on the COSMO level ENERGIES a u Total energy 76 4841708454 Outlying charge corr COSMO 0 0006542315 Outlying charge corr DCOSMO RS 0 0011042856 Combinatorial contribution of the solute 0 0017627889 at inf dil in the mixture pure solvent Not included in the total energy above The outlying charge correction cannot be defined straight forward like in the normal Cosmo model Therefore the output shows two corrections that can be added to the Total energy The first one is the correction on the Cosmo level COSMO and the second is the difference of the DCOSMO RS dielectric energy calculated form the corrected and the uncorrected COSMO charges respectively DCOSMO RS The charges are corrected on the COSMO level only The Total energy includes the Ediel rzs defined in section 17 Add
392. ns e In PE SCF computations symmetry cannot be exploited e PE SCF computations do not work in parallel MPI parallelization The energy of a PE SCF calculation printed in the output contains the following terms Epr scr Eom EQM MM es Epol 9 29 Here Eom is the energy of the quantum mechanical method of your choice FQM MM es the electrostatic interaction energy between the QM and the MM region and Epo the energy gain due to the total of induced dipole moments If necessary missing terms can be computed without knowledge of the electron distribution At the moment TURBOMOLE does not offer the possibility to generate the nec essary potentials or to create a potential file from a set of coordinates Embed ding potentials can be obtained from literature or generated by approaches like the LoProp method 122 Atom centered polarizabilities are also available from other methods or from experiment Finally there are some polarizable force fields which in principle can be used for the PE method for example the AMOEBA force field 9 8 3 Computational details PERI CC2 calculations Prepare a normal RI CC2 calculation Note that you have to start from a previous PE SCF run The information for the polarizable embedding is the same as for the SCF case and contained in the data group point_charges pe There are some additional options to control the PERI CC2 calculations As noted in the theory section one has to solve a coup
393. ns level level rijk ex 1 lt path gt ls lt path gt md mdfile file mdscript file keep help 5 1 2 Output CHAPTER 5 STRUCTURE OPTIMIZATIONS converge maximum norm of cartesian gradient up to 10 lt integer gt atomic units default 3 perform up to integer cycles default 20 begin with a direct SCF step begin with a gradient step begin with a force relaxation step use the relax program for force relaxation perform transition state search define the optimization level level scf mp2 cc2 or uff default is scf use RI modules ridft and rdgrad fast Coulomb approxi mation instead of dscf and grad as well as rimp2 instead of mpgrad in connection with level cc2 the RI JK versions of HF and CPHF are switched on perform excited state geometry optimization using egrad employ programs from directory lt path gt load scripts from directory lt path gt a molecular dynamics MD run using frog instead of relax commands for MD run are contained in this file default mdmaster option to execute a shell script before the frog step keep program output from all optimization steps shows a short description of the commands above There will be an output written to file job start which informs you about the current options The convergence is signalled by the file converged otherwise you should find the file not converged within your working directory If jobex finds a file nam
394. ns geometry optimizations with dscf ridft grad and rdgrad Please regard the restriction of the DCOSMO RS energy explained in the keyword section 18 2 8 Because the DCOSMO RS contribution can be considered as a slow term contribution in vertical exitations it does not have to be taken into account in response calculations For the calculation of vertical excitation energies it is recommended to use the mos of a DCOSMO RS calculation in a COSMO response calculation see above 264 CHAPTER 17 TREATMENT OF SOLVATION EFFECTS WITH COSMO Chapter 18 Keywords in the control file 18 1 Introduction The file control is the input file for TURBOMOLE which directly or by cross references provides the information necessary for all kinds of runs and tasks control is usu ally generated by define the input generator This chapter provides a short hand documentation a list of the most important key words the possible parameters for each keyword default values and a brief explanation 18 2 Format of Keywords and Comments TURBOMOLE input is keyword directed Keywords start with a eg title Comments may be given after dummy or by a line starting with these lines are ignored by TURBOMOLE Blank lines are also ignored Keywords may be in any order unless stated otherwise below The sample inputs given below should help to give an idea how the keywords are to be used They are sorted according to program Complete control file
395. nsider a few additional points e g memory usage which are described in Sec 3 2 1 3 2 1 Running Parallel Jobs SMP case The SMP version of TURBOMOLE currently combines three different parallelization schemes which all use shared memory dscf odft and ricc2 are also partially parallelized with OpenMP for appli cations on shared memory in particular multi CPU and multi core machines aoforce escf and egrad are currently parallelized as described in 22 ridft and rdgrad are parallelized with MPI using the Global Arrays toolkit but use shared memory on SMP systems dscf grad ridft and rdgrad using the parallelization of 22 are also included in the default distribution and can optionally be used 3 2 PARALLEL RUNS 41 Setting up the parallel SMP environment In addition to the installation steps described in Section 2 see page 29 you just have to set the variable PARA_ARCH to SMP i e in sh bash ksh syntax export PARA_ARCH SMP This will cause sysname to append the string _smp to the system name and the scripts like jobex will take the parallel binaries by default To call the parallel versions of the programs ridft rdgrad dscf ricc2 aoforce escf or egrad from your command line without explicit path expand your PATH environment variable to export PATH TURBODIR bin sysname PATH The usual binaries are replaced now by scripts that prepare the input for a parallel run and start the job automatica
396. nt and reliable excitation energy methods J Phys Chem A 111 5314 5326 2007 J M Olsen K Aidas J Kongsted Excited states in solution through polar izable embedding J Chem Theory Comput 6 3721 3734 2010 BIBLIOGRAPHY 403 120 121 122 123 124 125 126 127 128 129 130 131 132 133 K Sneskov T Schwabe J Kongsted O Christiansen Scrutinizing the effects of polarization in QM MM excited state calculations J Chem Phys 134 104108 2011 T Schwabe K Sneskov J M Olsen J Kongsted O Christiansen C H ttig PERI CC2 A polarizable embedded RI CC2 method J Chem Theory Com put 8 3274 3283 2012 L Gagliardi R Lindh G Karlstr m Local properties of quantum chemical systems The LoProp approach J Chem Phys 121 4494 5000 2004 D P Tew W Klopper C Neiss C H ttig Quintuple quality coupled cluster correlation energies with triple basis sets Phys Chem Chem Phys 9 1921 1930 2007 H Fliegl C Hattig W Klopper Coupled cluster theory with simplified linear r12 corrections The CCSD R12 model J Chem Phys 122 084107 2005 T Shiozaki M Kamiya S Hirata E F Valeev Explicitly correlated coupled cluster singles and doubles method based on complete diagrammatic equations J Chem Phys 129 071101 2008 A Kohn G W Richings D P Tew Implementation of the full explicitly cor relat
397. nteger Is able to control the memory from outside define Note that if you did not define any memory it is automatically set to 1 GB 120 CHAPTER 5 STRUCTURE OPTIMIZATIONS trimer calculates in case we have a trimer Energy ABC AB C AB AC B AC BC A BC rather than Energy ABC A BC A B AC B C AB C note that the first term neglects the BSSE in the dimer setup Interrupt calculation after the initial setup step to check and possibly correct the control files for the fragments and the supermolecule To continue start jobbsse without the setup option help shows a short description of the commands above 5 6 2 Output There will be an output written to file bsse_out In this file you will find all individual energies computed which were used to calculate the last cp corrected energy The same holds true for the last gradients which are written to grad_out The convergence criteria and their current values are written out at the not converged file For the possible options to control convergence check the subsection for the opti mization program used statpt which is used by default or relax Since for weak complexes the force constants for intra and intermolecular bonds very strongly in magnitude it is recommended to use whenever possible redundant internal coordi nates Chapter 6 Hartree Fock and DFT Calculations Energy and gradient calculations at the Hartree Fock HF and DFT le
398. ntify a given GGA kinetic energy approximation that can be selected among the following functionals e string revapbek generalized gradient approximation with a PBE like en hancement factor obtained using the asymptotic expansions of the semiclas sical neutral atom as reference 152 153 revAPBEk This is the default choice e string 1c94 Perdew Wang PW91 exchange functional reparametrized for kinetic energy by Lembarki and Chermette 154 LC94 e string t f gradient expansion truncated at the zeroth order GEAO corre sponding to the Thomas Fermi functional For example the command FDE p 3 k 1c94 approximates the non additive kinetic contribution to the embedding potential through the functional derivative of LC94 kinetic energy functional A pure electrostatic embedding can be also performed with FDE script where the embedding potential required by a subsystem A to account for the presence of the B one will be merely Vemb T Vex r vsl B 15 9 with v2 r and vy pp r the electrostatic potentials generated respectively by the ext nuclei and electron density of the subsystem B To perform an electrostatic embed ding calculation use 242 CHAPTER 15 FROZEN DENSITY EMBEDDING CALCULATIONS FDE p 3 k electro and can be performed for both Kohn Sham only for LDA GGA exchange correlation functionals and Hartree Fock methods The electrostatic embedding is implemented only for testing purpo
399. nts near nu clei With the keyword fullshell this reduction is suppressed Refer ence grid see keyword reference always has full spherical grids with 1202 points Should be used to checked the influence of spherical grid reduction Example for the usage of fullshe11 dft functional b p gridsize m4 fullshell symblock1 real syabiloek teal for developers only Values of real effects efficiency of the quadrature default is symblock1 0 001 and symblock2 0 001 one can try higher or smaller values xparameter integer not recommended for use Where xparameter default can be sgrenze 8 fgrenze 10 qgrenze 12 dgrenze 12 and fcut 14 These parameters control neglect of near zeros of various quantities With xparameter integer one changes the default integer larger than defaults will increase the numerical ac curacy Tighter threshold are set automatically with keyword scfconv see section 18 2 5 on page 284 280 CHAPTER 18 KEYWORDS IN THE CONTROL FILE weight derivatives Includes the derivatives of quadrature weights to get more accurate re sults Default is that the derivatives of quadrature weights will be not considered see section 18 2 9 on page 305 gridordering Grid points are ordered into batches of neighbouring points This in creases efficiency since now zeros can be skipped for entire batches gridordering is default for serial version not for the parallel one You cannot use weight deri
400. nvalues of canonical occupied and virtual KS MOs rirpa computes so called direct RPA energies only i e no exchange terms are included in Eqs 11 5 and 11 6 In RIRPA the two electron integrals in Eqs 11 5 are approximated by the resolution of the identity approximation In conjunction with a frequency integration this leads to an efficient scheme for the calculation of RPA correlation energies 133 poe W Clw 11 7 w 2n where the integrand contains Naux X Naux quantities only FO ip St m ane Qlw QW 11 8 Naux is the number of auxiliary basis functions The integral is approximated using Clenshaw Curtiss quadrature Prerequisites Calculations with rirpa require e a converged SCF calculation e the maximum core memory the program is allowed to allocate should be de fined in the data group maxcor in MB the recommended value is ca 3 4 of the available physical core memory at most e orbitals to be excluded from the correlation treatment have to be specified in data group freeze 216 CHAPTER 11 RANDOM PHASE APPROXIMATION e an auxiliary basis defined in the data group cbas e an auxiliary basis defined in the data group jbas for the computation of the Coulomb integrals for the Hartree Fock energy e optional an auxiliary basis defined in the data group jkbas for the compu tation of the exchange integrals for the Hartree Fock energy rik should be added to the control file for RI JK to be
401. ny ways the probably most concise form is n n 2 28 n 2f n Re n n 2 2S n 2f n This applies to shells with one electron one hole the high spin couplings of half filled shells and those with one electron more ore less For d d d and d it represents the weighted average of high spin cases F 3P for d d 4F P for d d 6 4 TWO COMPONENT HARTREE FOCK AND DFT CALCULATIONS 135 6 4 Two component Hartree Fock and DFT Calcula tions 6 4 1 Background Theory Two component treatments allow for self consistent calculations including spin orbit interactions These may be particularly important for compounds containing heavy elements additionally to scalar relativistic effects Two component treatments were implemented within the module ridft for RI JK Hartree Fock and RI DFT local gradient corrected and hybrid functionals via effective core potentials describing both scalar and spin orbit relativistic effects The theoretical background and the implementation is described in 65 Two component treatments require the use of complex two component orbitals no 6 vp r instead of real non complex one component orbitals needed for non relativistic or scalar relativistic treatments The Hartree Fock and Kohn Sham equations are now spinor equations with a complex Fock operator Foe Fo ye r vale Peo FOB WEP P r The wavefunction is no longer eigenfunction of the spin opera
402. o carry out a UHF run e g alpha shells alg 1 4 1 a2g 1 1 beta shells alg 1 4 1 a2g 1 1 The specification of MO occupation for UHF uhf overwrites closed shell occupation specification 18 2 3 Keywords for redundant internal coordinates in redund_inp With the parameters in redund_inp the generation of redundant internal coor dinates can be modified All entries have to be made in the control file before invoking the ired option Important options are iprint n print parameter for debug output The larger n is the more output is printed n gt 0 n lt 5 default 0 metric n method for generating and processing of redundant internal coordinates n gt 3 n lt 3 n 0 default 3 Values for the metric option n 1 Delocalized Coordinates The BmBt matrix is diagonalized for the complete set of redundant internal coordinates matrix m is a unit matrix Delocalized Coordinates obtained with a modified matrix m the val ues of m can be defined by user input see below Hybrid Coordinates Natural internal coordinates are defined as in the old iaut option If a cage remains delocalized coordinates as for n 1 are defined for the cage Very simular to the n 1 option but for the remaining cage delocal ized coordinates with modified matrix m are defined as for n 3 270 CHAPTER 18 KEYWORDS IN THE CONTROL FILE n 2 Decoupled coordinates The redundant coordinates are div
403. o contributions 5 Vp print level 1 e Based on these quantities the program will give an assignment of normal modes by listing all internal coordinates with large diagonal or brutto contri butions print level 0 12 2 CALCULATION OF RAMAN SPECTRA 221 Note that for large molecules or complicated topologies the B matrix that is used to transform from Cartesian coordinates into internal coordinates and vice versa may become singular In this case only the normal modes in the internal coordinate basis can be listed 12 2 Calculation of Raman Spectra Vibrational Raman scattering cross sections are computed in the approximation of the polarizability theory from derivatives of the frequency dependent polarizability tensor with respect to normal modes of vibration 5 ku ia w cag w Here a w and y w denote the isotropic part and the anisotropy of the differ entiated polarizability tensor respectively The coefficients c and Ca depend on the scattering geometry and the polarization of the incident and scattered radiation The factor w w go o 4negct 2wy includes the frequency w and the degeneracy g of the vibration c is speed of light and g stands for the dielectric constant of vacuum Computation of Raman spectra with TURBOMOLE is a three step procedure First vibrational frequencies and normal modes are calculated by aoforce Cartesian polarizability derivatives are computed in the seco
404. o use a visualization tool afterwards a way that is described in the following An AIMAI wavefunction file http aim tkgristmill com will be written if you add wfn to control Calculation of data on grids to be used for plots with visualization tools e g gOpenMol available via http www csc fi gopenmol is driven by the keyword pointval This keyword is evaluated by all density matrix generating TURBOMOLE modules i e by dscf ridft rimp2 mpgrad ricc2 see Section 9 3 3 and egrad Note that all of the following quantities may be calculated simultaneusly and that for programs dscf ridft rimp2 and mpgrad the density matrix generating steps may be skipped by typing lt program gt proper Electron densities For the above mentioned programs setting of keyword pointval dens or simply 14 2 INTERFACES TO VISUALIZATION TOOLS 231 pointval yields calculation of densities p Rp X Dyydy Rp oy Rp 14 3 vu dens on an orthogonal grid Rp the size of which is automatically adjusted to the size of the molecule and the resolution is adjusted to yield acceptable gOpenMol plots for specification of non default grid types planes lines and non default output formats see Section 18 2 18 Names of output files are td plt total density UHF a density plus 8 density sd plt spin density a density minus density mp2d plt MP2 density mp2sd plt MP2 spin density ed plt differential density for exci
405. occupation based on the Hiickel calculation may be unreliable if the dif ference of the energies of the HOMO and the LUMO is less than 0 05 a u you will get a warning You will also have to enter this menu for all open shell cases other than doublets With command use you are able to use information about occupied MOs and start vectors from a former calculation on the same molecule file should be the path and name of the control file of this former cal culation of which all data groups related to occupation numbers and vectors will be read As the new generated data will overwrite the ex isting data if both resist in the same directory it is best and in some cases necessary to have the data of the former calculation in another di rectory than the one you started the define session in Then just type use lt path gt control to construct a new SCF vector from the data of the old calculation without changing the old data The data groups closed shells and open shells will be taken for your new calcula tion and the SCF vector from the old calculation will be projected onto the space which is spanned by your present basis set These start vec tors are usually better than the ones you could obtain by an extended Hiickel calculation man allows you to declare occupation numbers or change a previous declaration manually After selecting this command you will get a short information about the current occupation numbers actual closed shell
406. odic table Recommendation Use the same basis set type for all atoms use ECPs beyond Kr since this accounts for scalar relativistic effects New basis sets def2 X YZ MP2 implies RI MP2 and RICC2 exploratory MP2 SVP almost quantitative DFT SV P HF SVP MP2 TZVPP properties HF and DFT TZVPP quantitative DFT TZVP HF TZVPP MP2 QZVPP basis set limit DFT QZVP HF QZVP If you want a better basis than SV P assigned automatically use b all def2 TZVP or another basis The assignment can be checked by b1 Diffuse functions should only be added if really necessary E g for small anions or treatment of excited states use TZVP instead of SVP diffuse This is more accurate and usually faster Only for excited states of small molecules or excited states with a partial Rydberg character add additional diffuse functions e g by using the aug cc pVTZ basis as well as the keyword diffuse for more information see page 277 in the keyword section Old basis sets def XYZ For standard correlated calculations MP2 RI MP2 RI CC2 use the doubly polarized TZVPP or def TZVPP basis Correlation Consistent Dunning Basis Sets Dunning basis sets like cc pVDZ cc pVTZ cc pVQZ are also supported e g by b all cc pVTZ But these basis sets employ generalized contractions for which 4 2 THE ATOMIC ATTRIBUTES MENU 65 TURBOMOLE is not optimized This has in particular strong effects on the perfor mance of all progr
407. oefficients of the auxiliary basis set as specified in the data group cbas The results are written to egrad scaled by the factor given with the keyword cgrad and can be used to optimize auxiliary basis sets for RI MP2 and RI CC2 calculations see Sec tion 1 5 18 2 15 Keywords for Module RELAX optimize options define what kind of nonlinear parameters are to be optimized by relax and specify some control variables for parameter update Available options are internal on off optimize molecular structures in the space of internal coordinates us ing definitions of internal coordinates given in intdef as described in Section 4 1 default on redundant on off optimize molecular structures in redundant internal coordinates using definitions of redundant internal coordinates given in redundant For an optimization in redundant internal coordinates option internal has to be switched on too and option cartesian has to be switched off default on cartesian on off optimize molecular structures in the space of symmetry distinct carte sian coordinates default off basis on off suboptions optimize basis set exponents default off Available suboptions are 18 2 FORMAT OF KEYWORDS AND COMMENTS 329 logarithm exponents of uncontracted basis functions will be optimized after conversion into their logarithms this improves the condition of the approximate force constant matrix obtained by variable metric methods and th
408. omitted For most of these options with the only exceptions of trace and cowan griffin there are additional data groups allowing for more detailed specifications as explained below 340 CHAPTER 18 KEYWORDS IN THE CONTROL FILE moments if moment is active you need moments Oth ist 2nd 3rd point 0 0 0 to compute the Oth 1st 2nd and 3rd moment at the reference point 0 0 0 potential if potential is active you need points 1 pot fld fldgrd shld point 0 0 0 to compute the electrostatic potential pot and or electrostatic field 1d and or electrostatic field gradient fldgrd and or the zeroth order contribu tion to the diamagnetic shielding shld at reference point 0 0 0 localization if localization is active you need boys to perform a boys localization of orbitals with orbital energies gt thresholad 2 Hartrees localize with respect to locxyz x y and z and write resulting orbitals to lmofile Imo At the most sweeps 10000 orbital rotations are performed Non defaults may be specified using the following suboptions lmofile filename locxyz diri dir2 dir3 threshold real sweeps integer population analyses if population analyses is active you need mulliken spdf molap netto irpspd irpmol mommul to perform a Mulliken population analysis The options specify the output data spdf print molecular orbital contributions to atomic s p d populations 18 2 FORMAT OF KEYWORDS AN
409. on each grid point and numerically integrated to obtain orbital basis sets matrix elements In this case the DFT grid is needed but no auxiliary basis set is required The Slater potential can be computed numerically on each grid point as in Eq 16 3 or using a basis set expansion as 156 occ Tay D AN ONST ty 16 8 ole p Here the vector x r contains the basis functions S stands for the corresponding overlap matrix the vector u collects the coefficients representing orbital a and the matrix K represents the non local exchange operator iN in the basis set While the numerical Slater is quite expensive but exact the basis set method is very fast but its accuracy depends on the completeness of the basis set Concerning the correction term Eq 16 3 shows that it depends on the exchange potential itself Thus an iterative procedure is required in each self consistent step this is done using the conjugate gradient method Concerning conditions 16 4 and 16 5 both are satisfied in the present implemen tation KS occupied orbitals are asymptotically continued 164 on the asymptotic grid point r according to 7 er atal he eeo EL e7 PiNIFI IFo 5 16 9 where ro is the reference point not in the asymptotic region 8 2e and Q is the molecular charge A surface around the molecule is used to defined the points ro 16 3 How to Perform OEP EXX To run OEP EXX calculations select dft fu
410. on moments for excitations out of the ground state resembles the calculation of first order properties for excited states In addition to the left and right eigenvectors a set of transition Lagrangian multipliers My has to be determined and some transition density matrices have to be constructed Disk space core memory and CPU time requirements are thus also similar The single substitution parts of the transition Lagrangian multipliers u are saved in files named CCMEO s m aaza To obtain the transition strengths for excitations out of the ground state the keyword spectrum must be added with appropriate options see Section 18 2 14 to the data group excitations else the input is same as for the calculation of excitation energies and first order properties ricc2 cc2 excitations irrep al nexc 2 spectrum states all operators diplen qudlen For the ADC 2 model which is derived by a perturbation expansion of the expres sions for exact states the calculation of transition moments for excitations from the ground to an excited state would require the second order double excitation am plitudes for the ground state wavefunction which would lead to operation counts scaling as O N if no further approximations are introduced On the other hand the second order contributions to the transition moments are usually not expected to be important Therefore the implementation in the ricc2 program neglects in the calculation of the ground to
411. onomical electronic structure method Y Jung R C Lochan A D Dutoi and M Head Gordon J Chem Phys 121 9793 2004 e for SCS MP2 calculations S Grimme J Chem Phys 118 2003 9095 e for RI MP2 polarizabilities Large scale polarizability calculations using the approximate coupled cluster model CC2 and MP2 combined with the resolution of the identity approxi mation Daniel H Friese Nina O C Winter Patrick Balzerowski Raffael Schwan Christof Hattig J Chem Phys 136 174106 2012 8 2 Some Theory Second order Mgller Plesset Perturbation Theory MP2 corrects errors introduced by the mean field ansatz of the Hartree Fock HF theory the perturbation operator is just the difference of the exact and the HF Hamiltonian One straightforward obtains the MP2 energy ab Emp F 5 Ex ij ab J 8 1 iajb with the t amplitudes ab _ _ tj ab 8 2 Ei j Ea p i and j denote occupied a and b virtual orbitals p are the corresponding orbital energies ij ab ij ab ij ba are four center two electron integrals in a com monly used notation 8 3 HOW TO PREPARE AND PERFORM MP2 CALCULATIONS 161 MP2 gradients necessary for optimisation of structure parameters at the MP2 level are calculated as analytical derivatives of the MP2 energy with respect to nuclear coordinates calulation of these derivatives also yields the first order perturbed wave function expressed as MP2 dens
412. opriate options to the data group excitations else the input is same as for the calculation of excitation energies ricc2 cc2 response fop unrelaxed_only operators diplen qudlen excitations irrep al nexc 2 exprop states all operators diplen qudlen Orbital relaxed first order properties and gradients To obtain orbital relaxed first order properties or analytic derivatives gradients the Lagrange functional for the excited state in Eq 9 18 is analogously to the treatment of ground states augmented by the equations for the SCF orbitals and the perturbations is also included in the Fock operator rl Coas Bt 2 68 HE H CC gt B Aw t BE 9 20 py S28 uy H H T HF H YOKO ual ff F T HE Y RE F a Ho Compared to unrelaxed properties the calculation of relaxed properties needs in addition for each excited state the solution of a CPHF equations for the Lagrangian multipliers RED for which the computational costs are similar to those of a Hartree Fock calculation Orbital relaxed properties are requested by adding the flag relaxed to the input line for the exprop option The following is an example for a CC2 single point calculation for orbital relaxed excited state properties ricc2 cc2 excitations 190 CHAPTER 9 RI CC2 irrep al nexc 2 exprop states all relaxed operators diplen qudlen Note that during the calculation of orbital relaxed excited state properties the corr
413. or molecules notedly larger than 1000 basis functions and 100 atoms noproj forces the program not to project out translations and rotations when form ing a basis of symmetry adapted molecular displacements This option may be needed if a Hessian is required that contains translation and rotation contributions e g for coupling the system with low cost methods Output of the unprojected hessian is done on nprhessian format is the same as for con ventional hessian Output of the corresponding eigenvalues and eigenvectors is done analogously on nprvibrational spectrum and nprvibrational normal modes nomw causes the program to diagonalize a not mass weighted hessian Out 18 2 FORMAT OF KEYWORDS AND COMMENTS 307 put is on nprhessian nprvibrational spectrum and nprvibrational normal modes because projection of rotations is not possible in this case isosub This keyword allows to trace back the effects of isotopic substitution on vibrational frequencies The atom s for which isotopic substitution is to be investigated are specified in subsequent lines of the form atom index mass in special isotope e g isosub 3 2 001 5 13 The interpolation then takes place between the mass es specified in atoms or the default mass es if none specified and the mass es in isosub Take care of symmetry equivalent atoms otherwise symmetry analysis will fail This feature can not be used in a lowest eigenvalu
414. or the present problem or not Unfortunately it is not possible to define a threshold which distinguishes a good and a bad MP2 case since the value of indi vidual t amplitudes are not orbital invariant but depend on the orbital basis and thereby under certain circumstances even on the orientation Example the largest norm of t amplitudes for the Cu atom d s good MP2 case amounts to ca 0 06 that of the Ni atom d s bad MP2 case is ca 0 14 e A more descriptive criterion may be derived from the MP2 density matrix The eigenvalues of this matrix reflect the changes in occupation numbers re sulting from the MP2 treatment compared to the SCF density matrix where occupation numbers are either one two for RHF or zero Small changes mean small corrections to HF and thus suitability of the HF MP2 method for the given problem In case of gradient calculations rimp2 displays by default the largest eigenvalue of the MP2 density matrix i e the largest change in oc cupation numbers in All eigenvalues are shown if mp2occ is added to the control file For main group compounds largest changes in occupation numbers of ca 5 or less are typical for d metal compounds somewhat higher values are tolerable e A similar idea is pursued by the Dz and D diagnostics 93 94 which is im plemented in ricc2 D is a diagnostic for strong interactions of the HF reference state with doubly excited determinants
415. orbital selection range al 1 18 a2 1i 1 e 1 13 any further closed shell orbitals to declare DEFAULT y If you answer this question with y you enter the orbital specification menu which will be described in Section 4 3 3 The same procedure applies to the open shell occupation numbers after you finished the closed shell occupations hcore tells programs dscf and ridft to run without a start vector it writes the data group scfmo none to file control dscf or ridft will then start from the core Hamiltonian start vector which is the vector obtained by diagonalizing the one electron Hamiltonian Note that you still have to specify the occupation numbers This concerns only the 70 flip CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE first SCF run however as for the following calculations the converged vector of the previous iteration will be taken A SCF calculation with a core Hamiltonian start vector typically will take 2 3 iterations more than a calculation with an extended Hiickel start vector a calculation with the converged SCF vector of a previous calculation will need even less iterations depending on how large the difference in the geometry between the two calculations is flipping of spins at a selected atom Requirements converged UHF molecular orbitals and no symmetry C1 definewill localize the or bitals assign them to the atoms and give the user the possibility to choose atoms at which alpha
416. orbitals are moved to beta orbitals or vice versa This is useful for spin broken start orbitals but not for spatial symmetry breaking This command as well as use and eht terminates this menu but with out providing a start vector If the keyword scfmo exists in your input file it will be kept unchanged i e the old vector will be taken other wise scfmo none will be inserted into your output file which forces a calculation without start vector to be performed When you leave this menu the data groups closed shells open shells optionally and scfmo will be written to file You will then reach the last of the four main menus the General Menu which is described in Section 4 4 4 3 2 Assignment of Occupation Numbers If an automatic assignment of occupation numbers is not possible or you do not except the occupation numbers generated by the EHT you enter the following menu OCCUPATION lt int gt lt list gt lt list gt lt list gt lt list gt lt list gt ePdcooaewpeoedtwvrers d Nn dis e f lt int gt lt index gt lt list gt lt index gt lt index gt NUMBER ASSIGNMENT MENU e 60 c 0 0 0 CHOOSE UHF SINGLET OCCUPATION CHOOSE UHF TRIPLET OCCUPATION CHOOSE UHF WITH lt int gt UNPAIRED ELECTRONS PRINT MO S FROM EHT IN lt list gt DEFAULT ALL PRINT MO COEFFICIENTS OF SHELL lt index gt CHOOSE SHELLS IN lt list gt TO BECOME CLOSED SHELLS CHOOSE SHELL
417. ost important parameters are computed by first principles and it provides a consistent description across the whole periodic system The first version DFT D1 can be invoked by the keyword o0lddisp in the control file The second version DFT D2 is used if the keyword disp is found For the usage of DFT D3 just add keyword disp3 to the control file Only one of the three keywords is expected to be present If DFT D3 is used the total energy is given by Eprr p3 Exs prr Edisp 6 8 where Exs prr is the usual self consistent Kohn Sham energy as obtained from the chosen functional and Egisp is a dispersion correction given by the sum of two and three body energies Edisp EO E 6 9 with the dominating two body term J CAB BO S Y 5 fan ras 6 10 AB n 6 8 10 AB The first sum runs over all atom pair CA denotes the nth order dispersion coef ficient for atom pair AB rap is their interatomic distance and fa is a damping function Please have look at http toc uni muenster de DFTD3 for more detailed infor mation Chapter 7 Hartree Fock and DFT Response Calculations Stability Dynamic Response Properties and Excited States 7 1 Functionalities of ESCF and EGRAD escf and egrad are designed as efficient tools for response and excited state calcu lations on large molecules escf serves to compute the following properties for HF and KS reference states e Eigenvalues of the electronic Hess
418. otential is calculated at spherical shells of grid points around the atoms By default Bragg Slater radii rgs are taken as shell radii for each atom the number of points is given by 1000 TBa the total number of points is the sum of points for each atom reduced by the number of points of overlapping spheres Non default shells one or more can be specified as follows esp_fit shell 21 si shell 22 s2 Integer numbers 7 define the number of points for the respective shell real numbers s constants added to radii default corresponds to one shell with s 1 0 A parameterization very close to that by Kollman U C Singh P A Kollman J Comput Chem 5 2 129 145 1984 may be obtained by esp_fit kollman Here five shells are placed around each atom with r 1 4 r qw k k 0pm 20pm 40pm 60pm 80pm and r gw are the van der Waals radii of the atoms pointval drives the calculation of space dependent molecular quantities at 3D grids planes lines or single points Without further specifications the values of densities are plotted on a three dimensional grid adapted to the molecular size Data are deposed to output files suffix plt that can be visualized directly with the gOpenMol program In case of RHF dscf ridft calculations you get the total density on file td p1lt for UHF dscf ridft calculations one gets both values for the total density D D on td plt and the spin density 350 CHAPTER 18 KEYWORDS IN THE
419. otting data as needed by moloch using define on activating plot you get the following menu 4 4 THE GENERAL OPTIONS MENU 97 there are 1 data groups grid manipulate data group s grid a add another data group m lt integer gt modify lt integer gt th data group m all modify all data groups d lt integer gt delete lt integer gt th data group d all delete all data groups off lt integer gt switch off lt integer gt th data group off all switch off all data groups on lt integer gt switch on lt integer gt th data group on all switch on all data groups s scan through data groups quit The commands in this menu serve for the manipulation of data groups grid in an analogous way as described for points in the potential section above grid data groups contain the input information necessary to create the plot data by moloch one data group for each plot If you want to add a new data group you will enter this submenu specify the input orbital input density mo lt label gt use occupied molecular orbital lt label gt mo density use one electron density built from the occupied molecular orbitals lmo lt i gt use localized molecular orbital no lt lmo gt mao lt i gt lt k gt use modified atomic orbital no lt i gt centered on atom no lt k gt help explanation of the syntax for lt label gt quit Here you may specify the orbital to be plotted To plot the amplitude of
420. oubles CCSD F12 Christof Hattig David P Tew Andreas Kohn J Chem Phys 132 231102 2010 10 1 Characteristics of the Implementation and Com putational Demands In CCSD the ground state energy is as for CC2 evaluated as Ecc HE H CC HF H exp T HF 10 1 For other avaible approximation and the corresponding input options see Sec 18 2 14 10 1 COMPUTATIONAL DEMANDS 207 where the cluster operator T Ti To consist of linear combination of single and double excitations T J taa l 10 2 ai 1 Th 5 Do bai Tab 10 3 aibj In difference to CC2 the cluster amplitudes tai and taj are determined from equa tions which contain no further approximations apart from the restriction of T to single and double excitations u aH F Qu Hal An 0 10 4 gt Ep 2 A T T2 HF 0 10 5 b where again H exp T1 exp T1 and py and pe are respectively the sets of all singly and doubly excited deter minants For MP3 the energy is computed from the first order amplitudes CaN as EMP3 tot Eur Emp2 Emp3 10 6 HF A A TS HE X tQ ual W TS HE 10 7 H2 with W H F To evaluate the fourth order energy one needs in addition to the first order also the second order amplitudes which are obtained from the solution of the equations uF TO W Tf HF 0 10 8 ual FT W TS HF 0 10 9 uF TP W TS HF 0 10
421. own Using GGA approximations for the kinetic energy functional T T 4 we have Tradd oA pp TSCA 04 pp TOCA pa TOF pp 15 4 and an OT pai pal gGGA dpa r 7 where 24 r 6TECA 5p r The FDE total energy of total system is pat pal r OF pal r 15 5 EPP ISA pp Ts pal Tsloa T351 pal F Vext A B J pa pal Eze 6a PB 15 6 Note that this energy differs from the KS total energy of the total system due to the approximation in Eq 15 4 as well as the approximated kinetic potential see Eq 15 5 which lead to approximated embedded densities 64 pa and pp pg With the current state of the art GGA kinetic approximations the error in the binding energy for weakly interacting systems is close to chemical accuracy Using the Generalized Kohn Sham GKS theory also hybrid exchange correlation functionals can be used in embedding calculations To obtain a practical computa tional method the obtained embedding potential must be approximated by a local expression as shown in Ref 150 This corresponds to performing for each subsys tem hybrid calculations including the interaction with other subsystems through an embedding potential derived at a semilocal level of theory When orbital dependent exchange correlation functionals e g hybrid functional and LHF are considered within the FDE method the embedding potential includes a non additive exchange correlation term of the
422. p erties of excited states at the CIS CIS D ADC 2 and CC2 level using 24 relax statpt frog aoforce escf CHAPTER 1 PREFACE AND GENERAL INFORMATION either a closed shell RHF or a UHF SCF reference function Calculates R12 basis set limit correction for MP2 energies Employs the RI tech nique to approximate two electron integrals Includes as a subset also the functionalities of the rimp2 program 10 11 12 13 14 15 16 17 requires a gradient run by grad rdgrad rimp2 or mpgrad and pro poses a new structure based on the gradient and the approximated force constants The approximated force constants will be updated performs structure optimization using the Trust Radius Image Mini mization algorithm It can be used to find minima or transition struc tures first order saddle points Transition structure searches usually require initial Hessian matrix calculated analytically or the transition vector from the lowest eigenvalue search executes one molecular dynamics MD step Like relax it follows a gradient run these gradients are used as classical Newtonian forces to alter the velocities and coordinates of the nuclei requires a well converged SCF or DFT run by dscf or ridft see keywords and performs an analytic calculation of force constants vi brational frequencies and IR intensities aoforce is also able to calcu late only the lowest Hessian eigenvalues with the corresponding eigen vectors
423. pace require ments e full use of all point groups e efficient integral evaluation e stable and accurate grids for numerical integration e low memory and disk space requirements 1 3 How to Quote Usage of TURBOMOLE Please quote the usage of the program package under consideration of the version number TURBOMOLE V6 5 2013 a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH 1989 2007 TURBOMOLE GmbH since 2007 available from http www turbomole com A LaTeX template could look like this misc TURBOMOLE title TURBOMOLE V6 5 2013 a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH 1989 2007 TURBOMOLE GmbH since 2007 available from tt http www turbomole com Scientific publications require proper citation of methods and procedures employed The output headers of TURBOMOLE modules include the relevant papers One may also use the following connections between method module number in the subsequent list For module ricc2 see also Section 9 CHAPTER 1 PREFACE AND GENERAL INFORMATION e Programs and methods general program structure and features I HF SCF dscf ridft II DFT quadrature dscf ridft escf aoforce IV d m grids RI DFT ridft aoforce escf c d XXIII marij VII escf XXIV aoforce MP2 mpgrad III RI MP2 ricc2 energies and gradients VIII XXIX f and static pola
424. pecial asymptotic treatment if the differential density matrix rms is below above 1 d 3 This is the default pot file save the converged Slater and correction potentials for all grid points are saved in the files slater pot and corrct pot respectively Using pot file load the Slater potential is not calculated but read from slater pot the correction potential is instead recalculated For spin unrestricted calculations the corresponding files are slaterA pot slaterB pot corrctA pot and correctB pot homo allows the user to specify which occupied orbital will not be included in 16 4 HOW TO PLOT THE EXCHANGE POTENTIAL 257 the calculation of correction potential by default the highest occupied orbital is selected This option is useful for those systems where the HOMO of the starting orbitals e g EHT HF is different from the final LHF HOMO homob is for the beta spin correlation func functional a correlation functional can be added to the LHF potential use func lyp for LYP or func vwn for VWN5 correlation For other options see 18 2 6 16 4 How to plot the exchange potential It is recommended to check plots of the exchange potential for both OEP EXX and LHF potential to avoid spurious numerical oscillations which usually originates from too small or too large basis set To plot the LHF potential over a line add to the control file e g for a 2000 points along the z axis pointval xc geo line gridi vector 0 0 1
425. periodic field of point charges surrounding the cluster has the following form NEUC u v 7 p J 2 2 S Dwa f ET PE LEO where UC denotes the unit cell of point charges Dy are elements of the den sity matrix u v are basis functions qk Ry denote charges and positions of point charges and L denote direct lattice vectors of the outer part O It is evaluated using the periodic fast multipole method PFMM 72 which unlike the Ewald method 73 defines the lattice sums entirely in the direct space In general PFMM yields a different electrostatic potential then the Ewald method but the difference is merely a constant shift which depends on the shape of external infinite surface of the solid i e on the way in which the lattice sum converges toward the infinite limit However this constant does not influence relative energies which are the same as obtained using the Ewald method provided that the total charge of the cluster re mains constant Additionally since the electrostatic potential within a solid is not 6 6 PERIODIC ELECTROSTATIC EMBEDDED CLUSTER METHOD 139 a well defined quantity both the absolute total energies and orbital energies have no meaning i e you cannot compare energies of neutral and charged clusters 6 6 3 Calculation Setup There are three key steps in setting up a PEECM calculation In the first step the periodic field of point charges has to be defined by specifying the point charges unit cell Next
426. puters The MP GRAD Program F Haase and R Ahlrichs J Comp Chem 14 907 1993 Efficient Molecular Numerical Integration Schemes O Treutler and R Ahlrichs J Chem Phys 102 346 1995 Stability Analysis for Solutions of the Closed Shell Kohn Sham Equation R Bauernschmitt and R Ahlrichs J Chem Phys 104 9047 1996 16 VI VII VIII IX XI XII XIII XIV XV XVI XVII XVIII CHAPTER 1 PREFACE AND GENERAL INFORMATION Treatment of Electronic Excitations within the Adiabatic Approximation of Time Dependent Density Functional Theory R Bauernschmitt and R Ahlrichs Chem Phys Letters 256 454 1996 Calculation of excitation energies within time dependent density functional the ory using auxiliary basis set expansions R Bauernschmitt M H ser O Treut ler and R Ahlrichs Chem Phys Letters 264 573 1997 RI MP2 first derivatives and global consistency F Weigend and M H ser Theor Chem Acc 97 331 1997 A direct implementation of the GIAO MBPT 2 method for calculating NMR chemical shifts Application to the naphthalenium and anthracenium ions M Kollwitz and J Gauss Chem Phys Letters 260 639 1996 Parallelization of Density Functional and RI Coulomb Approximation in TUR BOMOLE M v Arnim and R Ahlrichs J Comp Chem 19 1746 1998 Geometry optimization in generalized natural internal Coordinates M v Arnim and R Ahlrichs J
427. r Y Li G J Iafrate Construction and application of an accurate local spin polarized kohn sham potential with integer discontinuity Exchange only theory Phys Rev A 45 101 1992 O V Gritsenko E J Baerends Orbital structure of the kohn sham ex change potential and exchange kernel and the field counteracting potential for molecules in an electric field Phys Rev A 64 042506 2001 A F Izmaylov V N Staroverov G E Scuseria E R Davidson G Stoltz E Canc s The effective local potential method Implementation for molecules and relation to approximate optimized effective potential techniques J Chem Phys 126 8 084107 2007 F Della Sala A G rling The asymptotic region of the Kohn Sham exchange potential in molecules J Chem Phys 116 13 5374 5388 2002 F Della Sala A G rling Asymptotic behavior of the Kohn Sham exchange potential Phys Rev Lett 89 033003 2002 W Hieringer F D Sala A G rling Density functional calculations of nmr shielding constants using the localized hartree fock method Chem Phys Lett 383 1 2 115 121 2004 E Fabiano M Piacenza S D Agostino F D Sala Towards an accurate description of the electronic properties of the biphenylthiol gold interface The role of exact exchange J Chem Phys 131 23 234101 2009 F D Sala E Fabiano Accurate singlet and triplet excitation energies using the localized hartree fock kohn sh
428. r Plesset perturbation theory Chem Phys Lett 310 5 6 568 576 1999 F R Manby Density fitting in second order linear r 2 Mgller Plesset pertur bation theory J Chem Phys 119 9 4607 4613 2003 E F Valeev Improving on the resolution of the identity in linear R12 ab initio theories Chem Phys Lett 395 4 6 190 195 2004 BIBLIOGRAPHY 401 97 98 99 100 101 102 103 104 105 106 107 108 K E Yousaf K A Peterson Optimized auxiliary basis sets for explicitly correlated methods J Chem Phys 129 18 184108 2008 K A Peterson T B Adler H J Werner Systematically convergent basis sets for explicitly correlated wavefunctions The atoms H He B Ne and Al Ar J Chem Phys 128 8 084102 2008 W Klopper C C M Samson Explicitly correlated second order M ller Plesset methods with auxiliary basis sets J Chem Phys 116 15 6397 6410 2002 W Klopper W Kutzelnigg M ller Plesset calculations taking care of the correlation cusp Chem Phys Lett 134 1 17 22 1987 S Ten no Explicitly correlated second order perturbation theory Intro duction of a rational generator and numerical quadratures J Chem Phys 121 1 117 129 2004 D P Tew W Klopper Open shell explicitly correlated f12 methods Mol Phys 108 315 325 2010 S F Boys Localized orbitals and localized adjustment functions In P O
429. r ground state excited state transitions are available first order properties for the ground state with SCF CCS MP2 and CC2 and for excited states with CCS CC2 ADC 2 and CIS Dx geometric gradients for the electronic ground state at the MP2 and the CC2 level for electronically excited states at the CIS D ADC 2 and CC2 level second order properties for the ground state with MP2 and CC2 and a closed shell RHF reference wavefunction currently restricted to the sequentical and SMP parallel versions 174 175 gradients for auxiliary basis sets for RI MP2 CC2 etc calculations based on the RI MP2 error functional F12 corrections to RI MP2 MP2 ground state energies can be computed in C symmetry using explicitly correlated two electron basis functions in the framework of the MP2 F12 model 110 106 solvent effects for the methods and states for which orbital relaxed densities are available equilibrium solvent effects can be included in the framework of the cosmomode for details see Chapter 17 All functionalities at the MP2 and CC2 level are implemented for closed shell RHF and open shell UHF reference wavefunctions with the exception of second order propeties Calculations with the method CIS CIS D CIS D and ADC 2 are presently restricted to closed shell RHF and open shell UHF reference wavefunc tions Ground state energies for MP2 MP2 F12 and CC2 and excited state energies for CC2 are also implemente
430. r properties which are obtained as analytic derivatives the total energy Diagnostics Together with the MP2 and or CC2 ground state energy the pro gram evaluates the D diagnostic proposed by Janssen and Nielsen 93 which is defined as Di os max D taiti Amax 5 taitaj 9 7 where Amax M is the largest eigenvalue of a positive definite matrix M For CC2 the D diagnostic will be computed automatically For MP2 is must explictly be requested with the didiag option in the ricc2 data group since for RI MP2 the calculation of D will contribute significantly to the computational costs Large values of D indicate a multireference character of the ground state introduced by strong orbital relaxation effects In difference to the T and S2 diagnostics proposed earlier by Lee and coworkers the D diagnostic is strictly size intensive and can thus be used also for large systems and to compare results for molecules of different size MP2 and CC2 results for geometries and vibrational frequencies are in general in excellent agreement with those of higher order correlation methods if respec tively D MP2 lt 0 015 and D CC2 lt 0 030 93 13 For D MP2 lt 0 040 and 9 2 CALCULATION OF EXCITATION ENERGIES 181 D CC2 lt 0 050 MP2 and or CC2 usually still perform well but results should be carefully checked Larger values of D indicate that MP2 and CC2 are inadequate to describe the ground state of the system
431. r several methods within a loop over models but gradients and energies will not be written to the data groups grad and energy as needed for geometry optimizations Note that in the present version gradients are only available for MP2 and CC2 and only for a closed shell RHF reference convergence threshold for norm of residual vectors in linear response equations is set to 10 If not given in the response data group a default value is used which is chosen as max 107 10 10 where conv and oconv refer to the values given in the data group ricc2 ZCOnV convergence threshold for the norm of the residual vector in the solution of the Z vector equations will be set to 107 79 semicano use semi canonical formulation for the calculation of transition one electron densities Switched on by default The semi canonical formu lation is usually computationally more efficient than the non canonical formulation Exceptions are systems with many nearly degenerate pairs of occupied orbitals which have to be treated in a non canonical way anyway See also explanation for thrsemi below nosemicano use non canonical formulation for the calculation of transition one electron densities Default is to use the semi canonical formulation thrsemi the threshold for the selection of nearly degenerate pairs of occupied orbitals which if contributing to the density have to be treated in a non canonical
432. r therefore typi cally amounts to less than one kcal mol The dielectric energy i e the free electro static energy gained by the solvation process is half of the solute solvent interaction energy 1 Ediet 5 flea ee The total free energy of the solvated molecule is the sum of the energy of the isolated system calculated with the solvated wave function and the dielectric energy E E w Euiet A Cosmo energy calculation starts with the construction of the cavity surface grid Within the SCF procedure the screening charges are calculated in every cycle and the potential generated by these charges is included into the Hamiltonian This ensures a variational optimization of both the molecular orbitals and the screening charges and allows for the evaluation of analytic gradients Radii based Cavity Construction In order to ensure a sufficiently accurate and efficient segmentation of the molecular shaped cavity the COSMO implementation uses a double grid approach and segments of hexagonal pentagonal and triangular shape The cavity construction starts with a union of spheres of radii R RSOLV for all atoms 7 In order to avoid problems with symmetric species the cavity con struction uses de symmetrized coordinates The coordinates are slightly distorted with a co sinus function of amplitude AMPRAN and a phase shift PHSRAN Ini tially a basis grid with NPPA segments per atom is projected onto atomic spheres of radii R RSOLY
433. rad 23 24 36 38 44 47 79 100 106 109 119 121 123 125 138 156 187 263 296 298 303 304 363 364 reference potential 254 RELAX keywords 328 relax 14 24 26 39 53 58 85 87 99 100 104 106 108 109 111 113 118 120 328 330 332 334 337 restart cc 318 RI ADC 2 24 315 RLCC2 24 315 keywords 315 RLCCS 315 RLCIS 24 315 RI CIS D 24 315 RI MP2 315 RI MP2 F12 42 Ricc2 keywords 315 ricc2 13 14 23 26 37 42 44 47 64 65 82 158 167 171 174 182 INDEX 184 185 187 190 194 196 198 204 206 209 227 229 231 315 316 326 335 RIDFT keywords 275 Ridft 291 ridft 14 23 24 35 36 38 44 46 47 69 79 80 100 119 121 123 125 135 138 152 162 163 176 177 191 193 198 206 217 224 227 228 230 231 233 250 262 263 267 291 294 296 298 302 304 343 345 363 364 RIMP2 keywords 312 rimp2 23 24 37 39 64 65 82 100 106 119 158 159 161 162 165 166 174 227 228 230 313 314 317 335 343 344 Rimp2prep 36 162 314 315 rimp2prep 37 rirpa 214 217 Roothaan parameters 73 rpaprof 217 screwer 27 104 scs 170 197 319 SCS ADC 2 24 SCS CC2 24 SCS MP2 197 sdg 27 Simulated Annealing 358 SMP 40 sos 198 SOS ADC 2 24 SOS CC2 24 SOS MP2 197 SOS RI MP2 42 fourth order scaling 171 INDEX spectra Raman 221 spin flipping spins on atoms 70 Stati 123 stati 27 STATPT keywords
434. ratch files dscf dens pathi filet dscf fock path2 file2 dscf dfock path3 file3 dscf ddens path4 file4 dscf statistics path7 file7 dscf errvec path8 file8 dscf oldfock path9 file9 dscf oneint path10 file10 The first column specifies the program type dscf stands for SCF energy cal culations i e the dscf program the second column the scratch file needed by this program and the third column the pathname of the file to be used as scratch file statistics options The following options are allowed off dscf kora Do not perform integrals statistics Perform integrals statistics for dscf see KORA 18 2 FORMAT OF KEYWORDS AND COMMENTS 289 mpgrad see mpgrad polly see POLLY dscf parallel see PARALLEL PROCESSING Options kora dscf parallel grad mpgrad polly will be described in the related chapters If statistics dscf has been given integral prescreening will be performed which is an n4 step and may therefore be time consuming and a table of the number of stored integrals as a function of the two parameters thize and thime will be dumped Afterwards the filespace needed for the cur rent combination of thize and thime will be written to the data group scfintunit and statistics dscf will be replaced by statistics off thime integer Integral storage parameter which is related to the time needed to calculate the integral The larger integer the less integrals will be stored The default value is integer 5 see
435. rd keyword coord 0 00002358760000 10 48329315900000 18 85463057110000 al 4 53939007480000 13 10412613690000 15 24028611330000 al 4 53939638280000 7 86247730390000 19 36497297520000 al 9 07879006320000 10 48329315900000 18 85463057110000 al 6 6 PERIODIC ELECTROSTATIC EMBEDDED CLUSTER METHOD 4 53959732680000 0 00001052200000 4 53938331720000 9 07880357850000 1 71508649490000 2 86788376470000 1 32965829240000 5 94446987180000 7 54034461170000 1 41923561090000 7 74915508620000 1 40506312580000 3 00093786570000 6 25449323900000 7 40729073370000 10 49804944110000 9 07900452260000 0 00001684120000 4 53921616520000 9 07900452260000 4 53938151440000 0 00002554910000 0 00001684120000 13 61820356690000 9 07878826040000 end 13 15 18 15 85428007030000 36268741690000 13 31245694970000 06002818410000 13 13 18 15 15 18 13 20 24164297480000 10399998250000 24151682240000 86247730390000 72496001430000 20 13 15 10 10 13 15 10399998250000 72496001430000 34577677080000 72496001430000 02724227310000 28312353520000 02724227310000 17494056150000 92251179600000 71676368210000 22517102690000 28312353520000 96648359440000 96660974680000 10412613690000 72496001430000 21 19 18 19 16 21 21 16 21 16 21 16 21 16 21 16 21 15 25351019750000 25351019750000 14 14 15 15 14 21 21 25351019750000 3
436. re optimization in internal coordinates redundant on off Structure optimization in redundant coordinates cartesian on off Structure optimization in cartesian coordinates basis on off Optimization of basis set exponents contraction coefficients scaling factors global on off Optimization of global scaling factor for all basis set expo nents Note All options except internal are switched off by default unless they have been activated explicitly by specifying on Some of the options may be used simultaneously e g e internal basis e internal global e cartesian basis Other options have to be used exclusively e g e internal cartesian e basis global 106 CHAPTER 5 STRUCTURE OPTIMIZATIONS The update of the coordinates may be controlled by special options provided in data group coordinateupdate which takes as options dqmax real Maximum total coordinate change default 0 3 interpolate on off Calculate coordinate update by inter extrapolation us ing coordinates and gradients of the last two optimiza tion cycles default interpolate on if possible statistics integer off Display optimization statistics for the integer previ ous optimization cycles Without integer all available information will be displayed off suppresses opti mization statistics The following data blocks are used by program relax 1 Input data from gradient programs grad rdgrad egrad rimp2 mpgrad etc grad cartesian atom
437. re that the 184 CHAPTER 9 RI CC2 DUS procedure is not switched on before the residuals of the eigenvectors are small compared to the differences in the eigenvalues For this thrdiis controlling the DUS extrapolation in the linear solver should be set about one order of magnitude smaller than the smallest difference between two eigenvalues and preopt controlling the switch to the DIIS solver again about one order of magnitude smaller then thrdiis Tighter thresholds or difficult situations can make it necessary to increase the limit for the number of iterations maxiter In rare cases complex roots might persist even with tight convergence thresholds This can happen for CC2 and CIS D close to conical intersections between two states of the same symmetry where CC response can fail due to its non symmetric Jacobian In this case one can try to use instead the ADC 2 model But the nonlinear partitioned form of the eigenvalue problem used in the ricc2 program is not well suited to deal with such situations Diagnostics for double excitations As pointed out in ref 12 the 7T diag nostic or T gt 100 T which is evaluated directly from the squared norm of the single and double excitation part of the eigenvectors T 100 T T T with J gt is ET where the excitation amplitudes are for spin free calculations in a correspoding spin adapted basis which is not necessarily normalized has the disadvantage that the
438. res by mode following A comparison of six methods on the Arg Lennard Jones potential J Chem Phys 102 17 6706 6718 1995 396 33 34 35 36 37 38 39 40 Al 42 43 44 45 BIBLIOGRAPHY P Cs sz r P Pulay Geometry optimization by direct inversion in the iterative subspace J Mol Struct 114 31 34 1984 R Fletcher A new approach to variable metric algorithms Comput J 13 3 317 322 1970 H B Schlegel Optimization of equilibrium geometries and transition struc tures J Comput Chem 3 2 214 218 1982 H B Schlegel Estimating the hessian for gradient type geometry optimiza tions Theor Chim Acta 66 5 333 340 1984 M Ehrig Diplomarbeit Master s thesis Universit t Karlsruhe 1990 T Koga H Kobayashi Exponent optimization by uniform scaling technique J Chem Phys 82 3 1437 1439 1985 A K Rapp W A Goddard III Charge equilibration for molecular dynamics simulations J Phys Chem 95 8 3358 3363 1991 C G Broyden The convergence of a class of double rank minimization algo rithms 1 General considerations J Inst Math Appl 6 1 76 90 1970 D Goldfarb A family of variable metric methods derived by variational means Math Comput 24 109 23 26 1970 D F Shanno Conditioning of quasi newton methods for function minimiza tion Math Comput 24 111
439. rface Bohr are given the default is 1 0 refine one line only smoothing of the layers of grid points around the molecule the real number is used to define isopotential surfaces on which the points of the layers have to lie vdw_radii element_symbol van_d_waals_radius One line per element has to be specified it contains the name of the element and the van der Waals radius in Bohr 344 CHAPTER 18 KEYWORDS IN THE CONTROL FILE 18 2 18 Keywords for wave function analysis and generation of plot ting data Properties of RHF UHF and two component GHF wave functions as well as those of SCF MP2 densities or such from excited state DFT calculations can be directly analyzed within the respective programs dscf ridft mpgrad rimp2 and egrad In case of spin unrestricted calculations results are given for total densities D D and spin densities D D If not explicitly noted otherwise in the following D is the SCF density D SCF in case of dscf and ridft the MP2 corrected density D SCF D MP2 for mpgrad and rimp2 and the entire density of the excited state in case of egrad For modules dscf and ridft the analysis of properties may be directly started by calling dscf proper or ridft proper In case of mpgrad and rimp2 this is possible only if the MP2 density has already been generated i e after a complete run of mpgrad or rimp2 Functionalities of analyses are driven by the following keywords
440. rgy from the Semiclassical Atom Theory Rationalization of the Accuracy of the Frozen Density Embedding Theory for Nonbonded Interaction S Laricchia E Fabiano L A Constantin and F Della Sala J Chem Theory Comput 7 2439 2011 and On the accuracy of frozen density embedding calculations with hybrid and orbital dependent functionals for non bonded interaction energies S Laricchia E Fabiano and F Della Sala J Chem Phys 137 014102 2012 e For FDE with the LHF potential Frozen density embedding calculations with the orbital dependent localized Hartree Fock Kohn Sham potential S Laricchia E Fabiano and F Della Sala Chem Phys Lett 518 114 2011 15 3 HOW TO QUOTE 247 e For the revAPBEk kinetic functional Semiclassical Neutral Atom as a Reference System in Density Functional The ory L A Constantin E Fabiano S Laricchia and F Della Sala Phys Rev Lett 106 186406 2011 248 CHAPTER 15 FROZEN DENSITY EMBEDDING CALCULATIONS Chapter 16 Orbital Dependent Kohn Sham Density Functional Theory 16 1 Theoretical Background Approximations to the exchange correlation XC functional of the Kohn Sham KS Density Functional Theory DFT can be classified by the so called Jacob s ladder The ground on which the ladder lies is the Hartree approximation XC energy is zero and the first rung is the local density approximation LDA in which the XC energy density is a simple local function of the dens
441. rint 282 mp2energy 37 161 312 314 mp2energy SCS 312 mp2energy SCS pt vall ps val2 312 mp2occ 166 315 mp2pair 314 mulliken 340 mvd 228 344 nac 359 nac_matrix 359 nacme 311 natoms 354 natural orbital occupation 267 natural orbital occupation file natural 351 natural orbitals 267 282 occupation 282 natural orbitals file natural 351 newcoord 218 nmr 225 dft 225 mp2 225 rhf 225 INDEX shielding constants 225 nomw 103 306 noproj 306 nosalc 306 nprhessian 306 nprvibrational normal modes 307 nprvibrational spectrum 307 nsteps 354 oep 253 oldgrad 337 open shells 69 70 268 289 operating system 265 optimize 104 105 220 328 330 basis 105 328 logarithm 329 scale 329 cartesian 105 328 global 105 329 internal 105 108 328 334 redundant 105 328 paboon 341 parallel_parameters 363 364 parallel_platform 47 362 pardft 363 path 265 point_charges 152 201 282 point_charges pe 202 points 92 93 97 340 pointval 192 230 231 349 dens 351 fld 232 351 fmt 351 cub 352 map 352 plt 352 txt 352 vec 352 xyz 352 413 geo 234 353 line 353 plane 353 point 353 integrate 350 1mo 233 351 mo 232 351 nao 234 nmo 351 nto 234 pot 232 351 xc 232 351 pop 228 344 346 atoms 346 dos 346 lall 346 mo 346 netto 346 overlap 346 thrpl 346 pop nbo 228 346 pop paboon
442. ristics in most cases Coordinate Updates The next submenu deals with the way relax updates the old coordinates You may choose a maximum change for the coordinates or you can allow coordinate updates by means of extrapolation dqmax lt real gt coordinates are allowed to change by at most lt real gt DEFAULT 0 3000 a u polish perform an interpolation or extrapolation of coordinates DEFAULT y polish disable inter extrapolation lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU These options result in better convergence of your optimization in most cases Interconversion Between Internal and Cartesian Coordinates The interconversion between internal and Cartesian coordinates is not possible di rectly in this direction Instead it is performed iteratively The following options control this conversion 4 4 THE GENERAL OPTIONS MENU 87 option description on switch on interconversion DEFAULT off qconv lt r gt set convergence threshold for interconversion of coordinates to lt r gt DEFAULT lt r gt 1000E 09 iter lt i gt allow at most lt i gt iterations for interconversion of coordinates DEFAULT lt i gt 25 crtint transform cartesian into internal coordinates DEFAULT n intcrt transform internal into cartesian coordinates DEFAULT n grdint transform cartesian into internal gradients DEFAULT n hssint transform cartesian into internal hessian DEFAULT n use lt
443. rite the timings on file for further processing default notimings Sets the conditions under which the test is run default sequential parallel Bibliography 1 R Ahlrichs M Bar M Haser H Horn C K lmel Electronic structure cal culations on workstation computers The program system Turbomole Chem Phys Lett 162 3 165 169 1989 A Sch fer H Horn R Ahlrichs Fully optimized contracted Gaussian basis sets for atoms Li to Kr J Chem Phys 97 4 2571 2577 1992 A Sch fer C Huber R Ahlrichs Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr J Chem Phys 100 8 5829 5835 1994 K Eichkorn F Weigend O Treutler R Ahlrichs Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials Theor Chem Acc 97 1 4 119 124 1997 F Weigend F Furche R Ahlrichs Gaussian basis sets of quadruple zeta va lence quality for atoms H Kr J Chem Phys 119 24 12753 12762 2003 F Weigend R Ahlrichs Balanced basis sets of split valence triple zeta valence and quadruple zeta valence quality for H to Rn Design and assessment of accuracy Phys Chem Chem Phys 7 18 3297 3305 2005 A K Rapp C J Casewit K S Colwell W A Goddard III W M Skiff UFF a full periodic table force field for molecular mechanics and molecular dynamics simulations J Am Chem Soc 1
444. rizabilities XXXVI stability analysis escf V electronic excitations by CIS RPA TD DFT escf VI VII XVIII XX VII excited state structures and properties with CIS RPA TD DFT egrad XIX XXVI XXVII RI CC2 riccQ x singlet XII and triplet excitation energies XIII x transition moments and first order properties of excited states XV and first order properties for triplet states XIV ground state geometry optimizations X XI x excited state geometry optimizations and relaxed properties XXII x parallelization XXIX spin component scaled SCS variants XXXII SOS CC2 amp SOS ADC 2 energies with O N scaling XXXIII x frequency dependent and static polarizabilities XXXVI RI ADC 2 RI CIS D and RI CIS D ricc2 XXVIII analytical second derivatives force fields aoforce XVI XVII RI JK ridft XX NMR chemical shifts mpshift IX MP2 parallel DFT ridft X geometry optimization in redundant internal coordinates relax XI RI integral evaluation XXV explicitly correlated F12 methods for ground state energies ricc2 MP2 F12 XXXIV MP3 F12 XXXV MP4 F12 XXXV CCSD F12 XXXI CCSD F12 XXXV CCSD F12 T XXXI CCSD F12 T XXXV e Orbital and auxiliary basis sets basis sets 1 3 HOW TO QUOTE USAGE OF TURBOMOLE 15 SV SV P SVP DZ a TZV TZVP TZVPP b TZVPP Rb Hg f QZV QZVP QZVPP i x new balanced basis sets with smaller ECPs i e t
445. rom the non symmetric eigenvalue problem is that in the case of close degeneracies within the same irreducible representation symmetry it can happen that instead of two close lying real roots a degenerate complex conjugated pair of excitation energies and eigenvectors is obtained CC2 and also other standard coupled cluster response methods are thus not suited for the description of conical intersections etc For the general theory behind coupled cluster response calculations see e g ref 112 113 or other reviews The ricc2 program exploits that the doubles doubles block of the CC2 Jacobian is diagonal and the linear eigenvalue problem in the singles and doubles space can be reformulated as a non linear eigenvalue problem in single substitution space only ATT t w ACC t ACC t Ayoyy w ASL t AS S E02 WCO B WOR MV V1 182 CHAPTER 9 RI CC2 This allows to avoid the storage of the double substitution part of the eigen or excitation vectors En En The algorithms are described in refs 10 11 about the RI error see ref 111 The solution of the CC2 eigenvalue problem can be started from the solutions of the CCS eigenvalue problem see below or the trial vectors or solutions of a previous CC2 excitation energy calculation The operation count per transformed trial vector for one iteration for the CC2 eigenvalue problem is about 1 3 1 7 times the operation count for one iteration for the cluster equation
446. round state and excitation energies for all wavefunction models available in ricc2 The analytic gradients for RI MP2 and RI CC2 in the ground state and RI CC2 in excited states are also parallized While in general the parallel execution of ricc2 works similar to that of other parallized Turbomole modules as e g dscf and grad there are some important difference concerning in particular the handling of the large scratch files needed for RI CC2 or RI MP2 As the parallel version dscf also the parallel version of ricc2 assumes that the program is started in a directory which is readable and writable on all compute nodes under the same path e g a NFS directory The directory must contain all input files and will at the end of a calculation contain all output 9 7 SPIN COMPONENT SCALING APPROACHES SCS SOS 197 files Large scratch files e g for integral intermediates will be placed under the path specified in the control file with tmpdir see Section 18 2 14 which should point to a directory in a file system with a good performance The parallel version of the ricc2 program can presently account for the following two situations Clusters with single processor nodes and local disks Specify in tmpdir a directory in the file system on the local disk All large files will be places on the nodes in these file systems The local file system must have the same name on all nodes Clusters with multiple e g dual processor nodes and loca
447. rrvec dscf oldfock nome dfs cd00 cd03_oldfock dscf oneint nome dfs cd00 cd03_oneint For all programs employing density functional theory DFT i e dscf gradand ridft rdgrad pardft can be specified pardft tasksize 1000 memdiv 0 The tasksize is the approximate number of points in one DFT task default 1000 and memdiv says whether the nodes are dedicated exclusively to your job mem div 1 or not default memdiv 0 For dscf and grad runs you need a parallel statistics file which has to be generated in advance The filename is specified with 2e ints_shell_statistics file DSCF par stat or 2e ints _shell_statistics file GRAD par stat respectively The statistics files have to be generated with a single node dscf or grad run For a dscf statistics run one uses the keywords statistics dscf parallel 2e ints_shell_statistics file DSCF par stat parallel_parameters maxtask 400 maxdisk 0 dynamic_fraction 0 300000 and for a grad statistics run 364 CHAPTER 18 KEYWORDS IN THE CONTROL FILE statistics grad parallel 2e ints _shell_statistics file GRAD par stat parallel_parameters maxtask 400 maxtask is the maximum number of two electron integral tasks maxdisk defines the maximum task size with respect to mass storage MBytes and dynamic_fraction is the fraction of two electron integral tasks which will be allo cated dynamically For parallel grad and rdgrad runs one can also specify gra
448. rties Thus before starting escf or egrad specify the keywords scfconv 7 denconv 1d 7 in control perform a dscf statistics run if semi direct integral processing is to be used see Chapter 3 1 and re run dscf or ridft dscf gt dscf out amp or ridft gt ridft out amp in case of RI J The above tight convergence criteria are also recommended for excited state geom etry optimizations 7 4 2 Polarizabilities and Optical Rotations The calculation of dynamic polarizabilities is controlled by the keyword scfinstab dynpol unit list of frequencies unit specifies the unit of the following frequencies and may be ev nm 1 cm or a u default The frequencies may be either purely real or purely imaginary For example to calculate dynamic polarizabilities at 590nm and 400i nm i is the imaginary unit specify 7 4 HOW TO PERFORM 153 scfinstab dynpol nm 590 400 i and run escf escf gt escf out amp The resulting polarizabilities and rotatory dispersions are given in a u in the pro gram output escf out in the above example The conversion of the optical rotation in a u to the specific rotation a w in deg dm g cc is given in Eq 15 of ref 84 aly C d w 7 15 where C 1 343 10 4w M with M being the the molar mass in g mol w the frequency in cm 1 and 6 w is 1 3 trace of the electronic rotatory dispersion tensor given in atomic units Please note that w has the wrong sign
449. ry using the keyword ricore e Multipole accelerated RI for Coulomb MARI J linear scaling O V method for large molecules It significantly reduces calculation times for molecules with more than 1000 basis functions All algorithms implemented in dscf grad ridft and rdgrad modules can exploit molecular symmetry for all finite point groups Typically the CPU time is pro portional to 1 Ng where Ng is the order of the nuclear exchange group Another important feature is a parallel implementation using the MPI interface Additionally dscf and ridft modules include the following common features e An UHF implementation 46 with automatic generation of optimal start vec tors by solving the HF instability equations 47 in the AO basis see the keyword scfinstab for detailed information e Occupation number optimization using pseudo Fermi thermal smearing RI techniques can also be used for the Hartree Fock exchange part of the Fock matrix RI HF This is done by the ridft module if the keyword rik is found in the control file In this case ridft performs a Hartree Fock SCF calculation using the RI approximation for both J and K if suitable auxiliary basis sets which differ from that used for fitting of the Coulomb part only are specified This is efficient only for comparably large basis sets like TZVPP cc pVTZ and larger HF exchange can also be calculated seminumerically 48 The calculation of 4c 2e Integrals is
450. s If convergence is not reached within this limit the calculation is stopped Usually 25 iterations should be sufficient for convergence Only in difficult cases with strong correlation effects more iterations are needed It is recommended to increase this limit only if the reason for the strong correlation effects is known Since one reason could also be an input error as e g unreasonable geometries or orbital occupations as a wrong basis set assignment The two parameters conv and oconv define the convergence thresholds for the it erative solution of the cluster equations Convergence is assumed if the change in the energy with respect to the previous iteration has is smaller than 10 Y and the euclidian norm of the residual the so called vector function is smaller than 10 If conv is not given in the data group ricc2 the threshold for changes in the energy is set to value given in denconv by default 1077 If oconv is not given in the data group ricc2 the threshold for the residual norm is by default set to 10 times the threshold changes in the energy With the default settings for 10 1 COMPUTATIONAL DEMANDS 213 these thresholds the energy will thus be converged until changes drop below 1077 Hartree which typically ensures an accuracy of about 1 uH These setting are thus rather tight and conservative even for the calculation of highly accurate reaction en ergies If for your application larger uncertainites for the ener
451. s define and apply job templates export coordinates or the wavefunction to different file formats etc TmoleX includes an own tutorial please see there which functionalites of TURBOMOLE are supported and how it can be used 3 1 2 Before you start TURBOMOLE is different Many programs work in a simple form qcprog input in gt output out The user has to write an input file input in run the binary qcprog and read the sometimes quite lengthy output file output out afterwards The input file will not be changed during the job Different input files can be run in the very same directory TURBOMOLE is NOT of that kind e the input file is always called control having different input files in the same directory is not possible e the control file can contain references to external files like coordinates basis sets molecular orbitals old results 33 34 CHAPTER 3 HOW TO RUN TURBOMOLE the input file does not contain the method level of theory and the kind of job This is driven by the tools and programs you are running on that input and not by the input file itself control file also contains results not just input data e input files are overwritten i e coordinates and orbitals are changed after a calculation e you do not have to write the input file yourself there is an own program called define which does that for you Hence TURBOMOLE is being used as a tool box on your data Each module or script you call w
452. s determine the point group symmetry of the molecule adjust internal coordinates to the desired values and related operations Beyond this one can perform a geometry optimization at a force field level to preoptimize the geometry and calculate a Cartesian analytical Hessian After leaving this menu your molecule to be calculated should be fully specified The atomic attributes menu Here you will have to assign basis sets and or effective core potentials to all atoms The SV P basis is assigned automati cally as default as well as ECPs small core beyond Kr The occupation numbers and start vectors menu In this menu you should choose eht to start from Extended Hiickel MO vectors Then you have to define the number of occupied orbitals in each irreducible representation The general menu The last menu manages a lot of control parameters for all TURBOMOLE programs Most of the menu commands are self explanatory and will only be discussed briefly Typing or q terminates the current menu writes data to control and leads to the next while typing amp goes back to the previous menu 49 50 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE 4 0 3 Universally Available Display Commands in DEFINE There are some commands which may be used at almost every stage of your define session If you build up a complicated molecular geometry you will find the dis command useful It will bring you to the following little submenu ANY
453. s n is the maximum number of structures to be included for the update default is n 4 ncycles lt n geometry update by inter extrapolation using the last 2 geometries ncycles gt n diagonal update for the hessian as described above DIIS like update for the geometry G lt thr BFGS type update of the hessian and quasi Newton update of gener alized coordinates References for the algorithms mentioned above 34 30 35 33 36 37 5 3 4 Definition of Internal Coordinates If structure optimizations are to be performed in the space of internal coordinates optimize internal is the default setting appropriate internal coordinate def initions have to be provided on data block intdef The types available and their definitions are described in Section 4 1 2 For recommendations about the choice of internal coordinates consult ref 24 Nevertheless the structure of intdef will shortly be described The syntax is in free format 1 k 1 00000000 bend 1 2 3 val 1 9500 fdiag 6666 The first items have been explained in Chapter 4 Two additional items val real fdiag real may be supplied for special purposes val serves for the input of values for internal coordinates for the intercon version internal cartesian coordinates it will be read in by relax if the flag for interconversion of coordinates has been activated interconversion on or by the interactive input program define within the geometry spec ificat
454. s add statistics mpgrad to control file and start an mpgrad statistics run with the command mpgrad 4 Start a single mpgrad calculation with the command mpgrad 5 For optimisation of structure parameters at the non RI MP2 level use the command jobex level mp2 Note that the frozen core approximation is ignored in this case 8 4 General Comments on MP2 Calculations Practical Hints Recommendations e It is well known that perturbation theory yields reliable results only if the perturbation is small This is also valid for MP2 which means that MP2 improves HF results only if HF already provides a fairly good solution to the 8 4 GENERAL COMMENTS 165 problem If HF fails e g in case of partially filled d shells MP2 usually will also fail and should not be used in this case e MP2 results are known to converge very slowly with increasing basis sets in particular slowly with increasing l quantum number of the basis set ex pansion Thus for reliable results the use of TZVPP basis sets or higher is recommended When using SVP basis sets a qualitative trend can be expected at the most Basis sets much larger than TZVPP usually do not significantly improve geometries of bonded systems but still can improve the energetic description For non bonded systems larger basis sets especially with more diffuse functions are needed e It is recommended to exclude all non valence orbitals from MP2 calculations as neither the TURB
455. s are provided in Chapter 19 An alphabetical list of all keywords is given in the index 18 2 1 General Keywords operating system unix path lock off suspend off The four keywords above are set by define but are not necessary 265 266 CHAPTER 18 KEYWORDS IN THE CONTROL FILE statistics dscf or statistics mpgrad Only a statistics run will be performed to determine file space requirements as specified for dscf or mpgrad On return the statistics option will be changed to statistics off actual step dscf means current step Keyword and data group as e g dscf is set by every program and removed on successful completion last step relax Keyword and data group as e g relax set by every program on successful com pletion General file cross references coord file coord intdef file coord user defined bonds file coord basis file basis ecp file basis jbas file auxbasis scfmo file mos uhfmo_alpha file alpha uhfmo_beta file beta natural orbitals file natural natural orbital occupation file natural energy file energy grad file gradient forceapprox file forceapprox It is convenient not to include all input in the control file directly and to refer instead to other files providing the corresponding information The above cross references are default settings from define you may use other file names define will create most of these files Examples of these files are given below i
456. s areas are smoothened by a radii based procedure A Matrix Setup The A matrix elements are calculated as the sum of the con tributions of the associated basis grid points of the segments k and l if their distance is below a certain threshold the centers of the segments are used otherwise For all segments that do not have associated basis grid points i e intersection seam segments the segment centers are used The diagonal elements Az that represent the self energy of the segment are calculated via the basis grid points contributions or by using the segment area Akk 3 8 ax if no associated basis grid points exist Outlying charge correction The part of the electron density reaching outside the cavity causes an inconsistency that can be compensated by the outlying charge correction This correction will be performed at the end of a converged SCF or an iterative MP2 calculation and uses an outer surface for the estimation of the energy and charge correction 170 The outer surface is constructed by an outward projection of the spherical part of the surface onto the radius R ROUT F RSOLYV It is recommended to use the corrected values Numerical Frequency Calculation The calculation of harmonic frequencies raises the problem of non equilibrium solvation in the Cosmo framework because the molecular vibrations are on a time scale that do not allow a re orientation of the solvent molecules Therefore the total response of the con
457. s described above but to change 98 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE an existing one you will be asked which one of the specifications you want to modify Chapter 5 Calculation of Molecular Structure and Ab Initio Molecular Dynamics 5 1 Structure Optimizations using the Jobex Script In its normal mode of operation the shell script jobex controls and executes au tomatic optimizations of molecular geometry parameters It will cycle through the direct SCF gradient and force relaxation programs and stop if either the maximum number of cycles is reached or the convergence criteria change in the total energy maximum norm of the gradient are fulfilled By default the executable programs are taken from the load modules library within the TURBOMOLE directory 5 1 1 Options Given a shell the usage is nohup jobex amp This command invokes structure optimization using the default program statpt Structure optimizations using program relax can be performed using relax flag nohup jobex relax amp nohup means that the command is immune to hangups logouts and quits amp runs a background command jobex accepts the following arguments controlling the level of calculation convergence criteria and many more for example nohup jobex gcart 4 amp energy integer converge total energy up to 10 lt integer gt Hartree default 6 99 100 gcart integer c integer dscf grad statpt relax tra
458. s in general the preoptimization for the Z vector equations with the nozpreopt option in the response data group see Sec 18 2 14 Restrictions e The Laplace transformed SOS MP2 implementation is presently only paral lelized with MPI The OpenMP parallelization is not yet recognized by the LT SOS RI MP2 related program parts e It is presently not compatible with the calculation of the D and D diag nostics The respective options will be ignored by program if the Laplace transformed implementation is used Chapter 9 Second Order Approximate Coupled Cluster CC2 Calculations ricc2 is a module for the calculation of excitation energies and response properties at a correlated ab initio level in particular the second order approximate coupled cluster model CC2 109 All calculations employ the resolution of the identity RI approximation for the electron repulsion integrals used in the correlation treatment and the description of excitation processes At present the following functionalities are implemented ground state energies for MP2 and CC2 and spin component scaled variants thereof the MP2 results are identical with those obtained with rimp2 but usually the calculations are somewhat faster excitation energies for the models CIS CCS CIS D CIS D ADC 2 and CC2 transition moments for ground state excited and excited excited state tran sitions for the models CCS and CC2 for ADC 2 only moments fo
459. s in the ground state calculation depending on the number of vectors transformed simultaneously The disk space requirements are about O V N N double precision words per vector in addition to the disk space required for the ground state calculation CCS excitation energies are obtained by the same approach but here double sub stitutions are excluded from the expansion of the excitation or eigenvectors and the ground state amplitudes are zero Therefore the CCS Jacobian dQ CCS Aw oo ui H m HF 9 10 is a symmetric matrix and left and right eigenvectors are identical and form an orthonormal basis The configuration interaction singles CIS excitation energies are identical to the CCS excitation energies The operation count for a RI CIS calculation is O ON N per iteration and transformed trial vector The second order perturbative correction CIS D to the CIS excitation energies is calculated from the expression wel VCIS 4 yl BOIS Aeff MP1 CIS RCTS 9 11 Note that tM are the first order double substitution amplitudes from which also the MP2 ground state energy is calculated the first order single substitution am plitudes vanish for a Hartree Fock reference due to the Brillouin theorem The operation count for a RI CIS D calculation is similar to that of a single iteration for the CC2 eigenvalue problem Also disk space requirements are similar Running excitation energy calculations The calculat
460. s in the totally symmetric IRREP The optional real number e specifies the approximate second order energy change in a u default 0 1 velocity gauge Enables calculation of dipole polarizability rotatory dispersion in the velocity gauge Active only for pure DFT no HF exchange sum rules unit list of frequencies Enable calculation of oscillator and rotatory strength sum rules at frequencies specified by list of frequencies in unit unit see scfinstab dynpol Note that the sums will be taken only over the states specified in soes rpaconv n the vectors are considered as converged if the Euclidean residual norm is less than 107 Larger values of n lead to higher accuracy The default is a residual norm less than 1075 escfiterlimit n Sets the upper limit for the number of Davidson Iterations to n Default is n 25 18 2 12 Keywords for Module EGRAD egrad uses the same general keywords as escf and grad see Sections 18 2 9 and 18 2 11 The state to be optimized is by default the highest excited state specified in soes Note that only one IRREP can be treated at the same time in contrast to escf calculations When the desired excited state is nearly degenerate with another state of the same symmetry it may be necessary to include higher states in the initial calculation of the excitation energy and vector in order to avoid root flipping This is accomplished by means of the additional keyword exopt n whi
461. s the number of loops or passes over occupied orbitals n when doing an MP2 calculation the more passes the smaller file space requirements but CPU time will go up This flag will be set by the script mp2prep mointunit Scratch file settings for an MP2 calculation Please refer to Section 18 2 13 for a description of the syntax This flag will be set by the script mp2prep csconv real Sets the convergence threshold for the shielding constant of succeeding CPHF iterations The unit is ppm and the default value is 0 01 18 2 FORMAT OF KEYWORDS AND COMMENTS 361 csconvatom integer This selects the atom number for convergence check after each cphf iteration After this convergence is reached all other atoms are checked too default 1 thime thize scftol scfintunit scfmo have the save meaning as in dscf see Section 18 2 5 Since mpshift works semi direct it uses the same integral storage scratch files The scratch files allocated by mpshift can be placed anywhere in your file systems instead of the working directory by referencing their pathnames in this data group All possible scratch files are listed in the following example scratch files mpshift csssmat path1i filet mpshift cshsmat path2 file2 mpshift csdgsmat path3 file3 mpshift csusmat path4 file4 mpshift dens path5 file5d mpshift fock path6 file6 mpshift dfock path7 file7 mpshift idvds1 path8 file8 mpshift idvds2 path9 file9 mpshift
462. s usually break the molecular symmetry so even for symmetric cases the AO not the SAO basis is used for the output The localized orbitals are sorted with respect to the corresponding diagonal element of the Fock matrix in the LMO basis In order to characterize these orbitals dominant contributions of canonical MOs are written to standard output as well as results of a Mulliken PA for each LMO for plotting of LMOs see option pointval The keyword allows for following options to be written in the same line mo list of MOs Include only selected MOs e g valence MOs in localization procedure numbering as available from Eiger sweeps integer maximum number of orbital rotations to get LMOs default value is 10000 sometimes not enough in particular for highly delocalised sys tems thrcont real lower threshold for displaying MO and Mulliken contributions default 0 1 CAO LMOs are written to file in the CAO basis instead of AO 18 2 win FORMAT OF KEYWORDS AND COMMENTS 349 pipmez Pipek Mezey localization is used triggers the generations of a wfn file It can be used in dscf ridft single point calculations or in ricc2 egrad gradient calculations esp_fit fits point charges at the positions of nuclei to electrostatic potential arising from electric charge distribution also possible for two component calculations for UHF cases also for spin density For this purpose the real electrostatic p
463. se It resembles an electrostatic embedding with external point charges and or point dipoles but it is exact as it is based on the whole densities i e it considers all multipole moments of the density and the polarizabilies at all orders Equivalent command kin string fde input option kin string FDE charged subsystems FDE can perform calculations for charged closed shell systems whose charge is lo calized on one or both subsystems To localize the charge on a given subsystem chargeA integer must be used for the subsystem A and chargeB integer for the B one Here integer denotes the charge added to the neutral subsystem For example the command FDE p 3 chargeA 2 performs a FDE calculation for a negative charged closed shell system for example Zn H20 37 whose subsystem B has charge 2 Note that in this case the starting control file must have a charge 2 fde input option chargeA integer chargeB integer FDE with subsystem B taken frozen FDE can perform embedding calculations where the subsystem B is taken frozen i e without scf calculation on it using an embedding potential Therefore only one step will be performed if the flag frozen will be used FDE p 3 frozen The frozen embedding calculation is store in the subdirectory STEP1 SUBSYSTEM_A The control file is modified with the following keywords fde read fde input zj file fde_ZJ mat fde input kxc file fde_KXC mat The program ds
464. se use actual help aoforce2g98 usage aoforce2g98 aoforce out gt g98 out bend converts output from the aoforce program to Gaussian 98 style which can be interpreted by some molecular viewer e g jmol to animate the normal coordinates example bend 1 2 3 displays the bending angle of three atoms specified by their number from the control file Note that unlike in the TURBOMOLE definition of internal coordinates the apex atom is the second 26 cbasopt cgnce cosmoprep dist DRC eiger evalgrad FDE hcore jobex kdg lhfprep log2x log2egy mdprep CHAPTER 1 PREFACE AND GENERAL INFORMATION optimize auxiliary basis sets for RI MP2 and RI CC2 calculations Uses ricc2 to calculate the error functional and its gradient and relax as optimization module For further details call cbasopt h plots energies as a function of SCF iteration number gnuplot re quired sets up control file for a cosmo run see Chapter 17 example dist 1 2 calculates atomic distances from TURBOMOLE input files dist 1 4 gives all interatomic distances to 4 a u 5 a u is the default automates dynamic reaction coordinate calculations forward and back ward along the imaginary vibrational mode of a transition state struc ture A transition state optimization with a subsequent frequency calculation is prerequisite For further details call DRC h displays orbital eigenvalues obtained from data group sc
465. sed to distinguish different atoms of the same type For example if you have several carbon atoms in your molecule you could label some c ring and others c chain to distinguish them Whenever you want to enter an atomic identifier you have to put it in double quotation marks c ring You should take into account that define also creates from the atoms you entered all others according to symmetry If necessary you will therefore have to lower the formal symmetry before executing a command 4 0 5 control as Input and Output File define may be used to update an existing control file which is helpful if only the basis set has been changed In this case just keep all data i e reply with lt enter gt on 5l all questions and only specify new start MOs The more general usage is described now At the beginning of each define session you will be asked to enter the name of the file to be created As mentioned earlier all TURBOMOLE programs require their input to be on a file named control but it may be useful at this moment to choose another name for this file e g if you have an old input file control and you do not want to overwrite it Next you will be asked to enter the name of an old file which you want to use as input for this session This prevents you from creating the new input from scratch if you want to make only minor changes to an old control file It is possible to use the same file as input and output file during a defi
466. sequently to modified defintions of A 7 2 THEORETICAL BACKGROUND 149 and B 83 The vector X Y is determined as the solution of the TDHF TDDFT response problem A wA X Y P Q 7 4 If X Ya arises from an electric dipole perturbation Ha the electronic dipole polarizability at frequency w is Aoa w Xa Yo Ha 7 5 a 3 x y z Similarly if m_ is a component of the magnetic dipole moment operator the optical rotation is 84 dap w 351m Xa Yalma 7 6 where c is the light velocity Excitation energies Q are the poles of the frequency dependent density matrix response They are thus the zeros of the operator on the left hand side of Eq 7 4 NAO Ae Yn 0 7 7 The corresponding eigenvectors Xn Yn are the transition density matrices for a given excitation also called excitation vectors in the following They are required to be normalized according to Xn YnlA Xn Yn 1 7 8 Transition moments are evaluated by taking the trace with one particle operators e g N u Xn Yn b 7 9 for the electric and m Xn Yq m 7 10 for the magnetic transition dipole moments The full TDHF TDDFT formalism is gauge invariant i e the dipole length and dipole velocity gauges lead to the same transition dipole moments in the basis set limit This can be used as a check for basis set quality in excited state calculations The TDA can formally be derived
467. set of coordinates All coordinates which conflict with the molecular symmetry are set to ignore by iaut iman allows you to modify the values of internal coordinates If you specify a list of atoms a only those internal coordinates which refer to only these atoms will be handled You will get a list of all active and fixed internal coordinates and their current values and you will be able to enter a new value for each of them if you like Default lt enter gt keeps the value shown Be aware that all distances are given in atomic units La u 52 9 pm This option allows you to change the status of a coordinate e g from active to display or every other combination The syntax is ic 5 d if coordinate no 5 is to be set to display or ic k d if all active coordinates are to be set to display This option allows you to delete definitions of internal coordinates from your list The indices of the internal coordinates always refer to the full list of coordinates including display and ignore coordinates To make sure you delete the right ones use disi Also the indices will imme diately change if you delete coordinates If you want to delete several coordinates this is therefore done most easily if you delete them in order of descending indices because deletion of a coordinate has only an effect on the coordinates with higher indices After choosing the coordinates 60 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE to be deleted a l
468. sets conventional direct SCF calcula tions are usually more efficient 8 3 HOW TO PREPARE AND PERFORM MP2 CALCULATIONS 163 8 With ricc2 spin component scaled SCS or SOS RI MP2 calculations can be carried out by adding in the ricc2 data group the line scs cos 1 2d0 css 0 3333d0 where the two parameters are the scaling factors for respectively the opposite and same spin contribution The specification of the scaling factors is optional the default values are cos 6 5 and css 1 3 as recommended by S Grimme in J Chem Phys 118 2003 9095 The abbreviation sos can be used for SOS MP2 calculations with cos 1 3 and css 0 0 Y Jung R C Lochan A D Dutoi and M Head Gordon J Chem Phys 121 2004 9793 SOS MP2 is in ricc2 implemented with O N scaling costs For such calculations the data group laplace has to be added 9 For technical recommendations and additional options for parallel RI MP2 calculations with the ricc2 program see Secs 3 2 and 9 6 MP2 calculations with a ROHF reference state With the program ricc2 it is possible to compute MP2 and spin component scaled MP2 energies with single determinant restricted open shell reference wavefunctions No additional input is required apart from the usual ROHF input for the dscf and ridft programs and a standard MPn or CC input for ricc2 TURBOMOLEs Hartree Fock codes can handle within the ROHF framework many cases which include beside common high and low spin confi
469. shift switched on the energies of virtual orbitals will be shifted if the HOMO LUMO gap drops below real such that a gap of real is sustained This is the default setting if the keyword is missing with real 0 1 closedshell real Option for open shell cases Closed shells are shifted to lower energies 288 CHAPTER 18 KEYWORDS IN THE CONTROL FILE by real The default shift value is closedshe11 0 4 Note Normally this will disable the automatic shift of energies of vir tual orbitals To override this you should append an exclamation mark to the automatic switch i e specify automatic real individual Set shifts for special occupied MOs To use this option start the line with the symmetry label and the list of MOs within this symmetry and append the desired shift in brackets as in the following example al 1 2 4 6 34 bi 8 3 scftol real Integral evaluation threshold Integrals smaller than real will not be evaluated Note that this threshold may affect accuracy and the convergence properties if it is chosen too large If scftol is absent a default value will be taken obtained from scfconv by real 107 scfconv 1 SHOT bf number of basis func tions scratch files The scratch files allocated by dscf can be placed anywhere in your file systems instead of the working directory by referencing their pathnames in this data group All possible scratch files are listed in the following example sc
470. should consider specifying them in a separate file This is most easily done using option file in the potential menu This option will create a file for your data groups points and will write a reference of this file to file control Option cowan griffin This option activates the computation of the first order relativistic correction to the energy as given by the expectation value of the Cowan Griffin operator Option localization Specifying option localization will switch on a Boys localization of molecular orbitals define by default chooses a set of MOs to be localized according to a certain threshold for the orbital energy Information about these are displayed like this BOYS localization will be performed with respect to x y z number of sweeps 10000 subset of molecular orbitals to be localized gt all occupied molecular orbitals with orbital energy above 2 00000 Hartree you are employing default options for localization do you want to modify them DEFAULT n If you want to change the MO selection or other options for the localization enter y at this point By default or when typing n you will reach the moloch options menu again You will then be asked whether to change the MO selection method If you want this you will enter a little submenu where you can choose one of three possible selection procedures all selects all occupied orbitals thr selects all occupied orbitals with orbital energy larger than a certain
471. sing ridft if jobex and NumForce are invoked with the rijk option How to quote If results obtained with the ricc2 program are used in publications the following citations should be included if you have used the methods program parts auxiliary basis sets or results reported in therein Methods for the approximate coupled cluster singles and doubles model CC2 O Christiansen H Koch P Jorgensen Chem Phys Lett 243 1995 409 418 for CI singles with a perturb correct for connected double excitations CIS D M Head Gordon R J Rico M Oumi and T J Lee Chem Phys Lett 219 1994 21 and for the iterative CIS D variant M Head Gordon M Oumi and D Maurice Mol Phys 96 1999 593 for the algebraic diagrammatic construction through second order ADC 2 J Schirmer Phys Rev A 26 1981 2395 A B Trofimov and J Schirmer J Phys B 28 1995 2299 for MP2 F12 W Klopper and C C M Samson J Chem Phys 116 2002 6397 6410 D P Tew and W Klopper J Chem Phys 123 2005 074101 for the SCS and SOS variants of MP2 S Grimme J Chem Phys 118 2003 9095 SCS or Y Jung R C Lochan A D Dutoi M Head Gordon J Chem Phys 121 2004 9793 SOS for the SCS and SOS variants of CC2 and ADC 2 A Hellweg S Gr n C Hattig Phys Chem Chem Phys 10 2008 4119 4127 Implementation please include always a reference to the publication reporting the imple mentation of
472. single points is needed quite often thus an example is given here pointval geo point 753 007 123 calculates densities at points 7 5 3 0 0 7 and 1 2 3 Output is x y z density output file suffix is xyz We note in passing that calculation of electrostatic potential at positions of nuclei may be used as an efficient tool to distinguish atoms of similiar atomic numbers thus providing a complement to X Ray Structure Analysis details see ref 145 Chapter 15 Frozen Density Embedding calculations 15 1 Background Theory In the subsystem formulation of the density functional theory a large system is de composed into several constituting fragments that are treated individually This approach offers the advantage of focusing the attention and computational cost on a limited portion of the whole system while including all the remaining enviromen tal effects through an effective embedding potential Here we refer in particular to the fully variational Frozen Density Embedding FDE 146 with the Kohn Sham Constrained Electron Density KSCED equations 147 148 In the FDE KSCED method the embedding potential required by an embedded subsystem with density p4 to account for the presence of another frozen subsystem with density pp is Ts pa pp _ Eze loa pal B Vemb r Vet r VU r 15 1 b JleB dpa r dpa r where v8 r and vj pg r are the electrostatic potentials generated by the n
473. sition moments In response theory transition strengths and moments for transitions from the ground to excited state are identified from the first residues of the response functions Due to the non variational structure of coupled cluster different expressions are obtained for the CCS and CC2 left and right transitions moments MY s and M feo The transition strengths ca w are obtained as a symmetrized combinations of both 115 of _ 1 V V V vi y Svv 5 My Mj T uy M 9 21 Note that only the transition strengths cue vy are a well defined observables but not the transition moments M _ and M _ For a review of the theory see refs 113 115 The transition strengths calculated by coupled cluster response theory according to Eq 9 21 have the same symmetry with respect to an interchange 194 CHAPTER 9 RI CC2 of the operators V and V2 and with respect to complex conjugation as the exact transition moments In difference to SCF RPA TD DFT or FCI transition strengths calculated by the coupled cluster response models CCS CC2 etc do not become gauge independent in the limit of a complete basis set i e for example the dipole oscillator strength calculated in the length velocity or acceleration gauge remain different until also the full coupled cluster equivalent to the full CI limit is reached For a description of the implementation in the ricc2 program see refs 111 13 The calculation of transiti
474. size and or memory are too small sh bash ksh users please do a ulimit a to get your actual limits The output should look like core file size blocks 0 data seg size kbytes unlimited file size blocks unlimited max locked memory kbytes unlimited max memory size kbytes unlimited open files 1024 pipe size 512 bytes 8 stack size kbytes unlimited cpu time seconds unlimited max user processes 8191 virtual memory kbytes unlimited The most important entries are data size stack size max memory size and virtual memory Those should be either unlimited or as big as your total RAM To set e g the stack size to the maximum allowed size on your system the so called hard limit do ulimit s hard csh tcsh users please do limit instead of ulimit and check the output Again like given above the limits should be at least as high as your memory avail able The syntax for changing the limits to unlimited using csh tcsh is 32 CHAPTER 2 INSTALLATION OF TURBOMOLE limit stacksize hard And please note that on 32bit machines unlimited can be the same as 4GB 4194303 kbytes If you are using a queuing system Note that if you are submitting jobs to a queue the user limits might be different from what you get when you log in on the machines To check your limits you have to add ulimit or limit in the script that is sent to the queue ulimit a gt mylimits out jobex ri c 200 statpt gt jobex out se
475. sks This can be done with the MPI version How to run the parallel TURBOMOLE MPI version on clusters Please see chapter DIVA The list of parallelized programs includes presently ridft parallel ground state Hartree Fock and DFT energies including RI J and the multipole accelerated RI MA RI J SMP and MPI rdgrad parallel ground state gradients from ridft calculations SMP and MPI dscf Hartree Fock and DFT ground state calculations for all available DFT functionals without the usage of RI J approximation SMP and MPI odft EXX or LHF ground state calculations SMP only grad parallel ground state gradients from dscf calculations SMP and MPI 3 2 PARALLEL RUNS USER INPUT coordinates input generator define ground state energy dscf ridft HF DFT TDDFT MP2 CC2 39 From TURBOMOLE library basis sets vib frequencies thermodynamics aoforce Freeh NumForce TDDFT excited states response properties escf egrad gradient energyt gradient grad ricc2 NMR shieldings rdgrad rimp2 i mpshift Raman spectrum geometry changes Raman molecular dynamics CC2 excited states and response properties ricc2 Figure 3 1 The modules of TURBOMOLE and the main data flow between them 40 CHAPTER 3 HOW TO RUN TURBOMOLE ricc2 parallel ground and excited state calculations of energies and gradi ents at MP2 and CC2 level using RI as we
476. spin cases work n f d a b 1 1 10 2D 0 0 2 1 5 3p Spit 5 8 5 4 IS 0 5 3 3 10 tp 4pit 5 6 5 3 4 2 5 5D oH 15 16 15 8 5 1 2 65 5A 1 2 6 3 5 5D H 35 36 25 18 7 7 10 IFP 95 98 55 49 8 4 5 3p 3pit 125 128 65 64 TS 15 16 5 8 9 9 10 D H 80 81 80 81 except cases e g Doq or D4n where e irreps which are not Roothaan cases t only p given the state for groups Ty etc follows from S A T O I P gt T T 0 I D gt H J E T T 0 This is not a CSF in T or O a b describes average of states resulting from E T 2 gives only one dimensional t a b describes weighted average of high spin states not a CSF Example The 4d 5s 2D state of Ag in symmetry I closed shells a 1 5 ti 1 3 h 1 open shells type 1 h 2 roothaan 1 a 80 81 b 80 81 C2 2 32 2 9 5 6 3 RESTRICTED OPEN SHELL HARTREE FOCK 131 6 3 3 More Than One Open Shell A Half filled shell and all spins parallel All open shells are collected in a single open shell and Example The 4d 5s 7S state of Mo treated in symmetry I roothaan 1 a i1 b 2 closed shells a 1 4 2 t1 1 3 2 h 1 2 open shells type 1 a 5 1 h 2 1 Two electron singlet coupling The two MOs must have different symmetries not required for triplet coupling see example 6 3 3 We have now two open shells and must specify three sets of a b i e one for each pair of shells following the keyword rohf Ex
477. split into an analytical and a numerical part The latter is evaluated on a dft type integration grid The seminumerical calculation scales better with system size than RIK and is suitable for large molecules and large basis sets 6 1 BACKGROUND THEORY 123 Prerequisites Both dscf and ridft require the control file and starting orbitals obtained from the extended Hiickel guess using define Energy calculations using dscf can be performed in a direct or semi direct mode In the direct mode all four center ERI s are recalculated at each SCF iteration The semi direct mode uses a selective storage of the most time consuming and frequently used integrals The amount of integrals stored is controlled by the keywords thize and thime related to integral size and computational cost The semi direct mode requires a separate dscf statistics run to estimate the disk space needed for integral storage The statistics run requires the keyword statistics dscf to be present in the control file It can be set either manually or using the tool Stati For ridft and rdgrad following additional prerequisites are required 1 An auxiliary basis defined in the data group jbas This group is created automatically when using ri menu of define 2 The maximum core memory the program is allowed to allocate should be defined in the data group ricore the recommended value is 75 85 of the available physical core memory 3 Calculations using MARI J method r
478. st excited state of those included in the excitation energy calculation but else of arbitrary multiplicity and symmetry the short cut s1 can be used x is treated as synonym for the ground state the opposite spin scaling factor cos and the same spin scaling factor css can be chosen If scs is set without further input the SCS parameters cos 6 5 and css 1 3 are applied This keyword can presently only be used in connection with MP2 the SOS parameters cos 1 3 and css 0 0 are applied This keyword can presently only be used in connection with MP2 didiag request the calculation of the D diagnostic for the ground state wave function Only needed for MP2 see above for the alternative input option mp2 didiag For all other correlated methods the D diagnos tic is evaluated by default without significant extra costs intcorr riri2 calculates the second order corrections to the CCSD T energy from the interference corrected MP2 F12 INT MP2 F12 if rir12 is switched on It can be combined either with the mp2 or the ccsd t meth ods In the latter case the CCSD T INT F12 energy is printed The intcorr all keyword writes on the output all pair energies ansatz ri2model comaprox 320 CHAPTER 18 KEYWORDS IN THE CONTROL FILE cabs examp ri2orb pairenergy corrfac cabsingles ansatz char char 1 2 or 2 The ansatz flag determines which ansatz is used to calculate the RI MP2 F12 ground state energy
479. st include the keyword hotfcht in the control file The option is also active in analysis mode that is as long as you still have the data group hessian in the control file or in a file refer enced in the control file you can always use aoforce in analysis mode to quickly generate the hotFCHT input The program will write three files The first one hotfcht_header inp contains a collection of the most important keywords of hot FCHT set to some default values please adapt to your needs and list of all atomic masses either TURBOMOLE s default masses or the ones given in the atoms data group The other two hotfcht_data_i inp and hotfcht_data_f inp contain the vibrational frequencies normal modes and the names of the irreducible representa tions of the normal modes In the former file these data are associated with the hotFCHT keywords for the initial state while the latter file contains the same data but associated with the keywords for the final state In order to run a hotFCHT calculation you need to optimize the structures of two electronic states usually the electronic ground state and an excited or ionized state and obtain the harmonic force fields for both using either aoforce or NumForce In order to generate the hotFCHT input just concatenate the hotfcht_header inp file from any of the two calculations and the hotfcht_data_i inp file from the calculation that refers 12 4 INTERFACE TO HOTFCHT 223 to the initial state e
480. st of the correlation consistent basis set series 4 2 1 Description of the commands b With b you can specify basis sets for all atoms in your molecule After entering b you will be asked to specify the atoms to which you want to assign basis sets You can do this in the usual ways refer to Sec tion 4 0 4 including all and none Then you will be asked to enter the nickname of the basis set to be assigned There are two principal ways to do this 1 If you are in the append mode the nickname you entered will be appended to the atomic symbol of the element under consideration This is especially useful if you want to assign basis sets to different atoms with one command For example if you want to assign basis sets to hydrogen and oxygen atoms and you enter only DZ the basis sets h DZ and o DZ will be read from the basis set library bb bl bm bp ecp ecpb ecpi ecpl CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE 2 If you are in the non append mode no atomic symbol will be in serted in front of the nickname entered Therefore you have to enter the full basis set nickname e g h DZ This mode is advantageous if you want to assign basis sets to dummy centers i e points without nuclear charge but with basis functions e g for counterpoise cal culations or if you want to use the basis set nickname none which means no basis functions at this atom You can switch between the two modes with switches to
481. step 050 min 100 scfdump scfintunit unit 30 size 0 file twoint scfdiis start 0 5 drvopt cartesian on basis off global off 19 4 TACLs INPUT FOR AN REDFT CALCULATION WITH ECPS 375 hessian on dipole on nuclear polarizability interconversion off qconv 1 d 10 maxiter 25 optimize internal on cartesian off global off basis off logarithm coordinateupdate dqmax 0 3 interpolate on statistics 5 forceupdate ahlrichs numgeo 0 mingeo 3 maxgeo 4 modus lt g dq gt dynamic fail 0 1 threig 0 005 reseig 0 005 thrbig 3 0 scale 1 00 damping 0 0 forceinit on diag default energy file energy grad file grad forceapprox file force lock off dft functional b p gridsize m3 last step define ricore 20 ridft jbas file auxbasis closed shells al 1 11 22 gt a2 1 2 2 e 1 10 2 a2 1 8 2 e 1 4 2 end File coord coord 00000000000000 00000000000000 00000000000000 ta CHAPTER 19 SAMPLE CONTROL FILES 376 2 19392179448315 3 79998401587749 2 19392179448315 3 79998401587749 4 38784358896629 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 intdef definitions of internal coordinates 1 k 1 0000000000000 stre 1 2 2 k 1 0000000000000 stre 1 5 end File basis basis ta def SVP ta 2 s 14 400000000 12 000000000 1 s 5 0701477302 1 s 86033356487 1 s 37158938894 1 s 10745336254 1 s 39142776556E 01
482. t 1 9 for switching off option lt i gt specify lt i gt 1 trace off 2 moments off 3 potential off 4 cowan griffin off 5 localization off 6 population analyses off 7 plot off 8 firstorder off selecting an already active option indicates that suboptions shall be modified or q uit quit for help type help lt integer gt All options in this menu are selected by entering their number as indicated in the first column For example to switch on option trace enter 1 The flag off will then change to active To switch off an option enter its negative number e g 1 for trace Most of the options require additional input and will therefore lead you to further submenus These are briefly described below Option trace trace will calculate the trace of density times overlap matrix N tr DS If the orbitals are orthonormal N should yield the total number of electrons in your molecule If this is not true your MO vector will most probably be erroneous For example the vector might belong to another geometry or basis set As this is a very sensitive test for errors like these and the calculation requires almost no time you should always switch on this option Option moments This option leads you to the following submenu add change options for data group moments option status description ESE sar jhe res 2 Uta ne ae ae en E ee eee ae point lt x gt lt y gt lt z gt T reference point
483. t charges It is implemented within HF and DFT energy and gradient TURBOMOLE modules dscf grad ridft rdgrad and escf Unlike embed ding within a finite set of point charges the PEEC method always yields the correct electrostatic Madelung potential independent of the electrostatic moments of the point charges field It is also significantly faster than the traditional finite point charges embedding 6 6 2 Theoretical Background Generally the PEEC method divides the entire periodic and infinite system into two parts the inner I part or so called cluster and the outer O part which describes its environment Thus unlike true periodic quantum mechanical meth ods PEECM primarily aims at calculations of structure and properties of localized defects in dominantly ionic crystals The innermost part of the cluster is treated quantum mechanically QM whereas in the remaining cluster part cations are re placed by effective core potentials ECPs and anions by ECPs or by simply point charges Such an isolating outer ECP shell surrounding the actual QM part is necessary in order to prevent artificial polarization of the electron density by cations which would otherwise be in a direct contact with the QM boundary The outer part or the environment of the cluster is described by a periodic array of point charges representing cationic and anionic sites of a perfect ionic crystal The electronic Coulomb energy term arising from the
484. t implies the calculation of the same variational den sities as needed for relaxed one electron properties and the solution of the same equations The construction of the gradient contributions from the densities and derivative integrals takes about the same CPU time as 3 4 SCF iterations and only minor extra disk space For details of the implementation of CC2 relaxed first order properties and gradients and a discussion of applicability and trends of CC2 ground state equilibrium geometries see ref 13 The following is in example input for a MP2 and CC2 single point calculation of first order properties and gradients ricc2 mp2 cc2 response static relaxed operators diplen qudlen gradient A different input is required for geometry optimizations in this case the model for which the geometry should be optimized must be specified in the data group ricc2 by the keyword geoopt ricc2 mp2 cc2 geoopt model cc2 For CC2 calculations the single substitution part of the Lagrangian multipliers t are saved in the file CCLO 1 1 0 and can be kept for a restart for MP2 and CCS the single substitution part vanishes For MP2 only relaxed first order properties and gradients are implemented unre laxed MP2 properties are defined differently than in CC response theory and are not implemented For MP2 only the CPHF like Z vector equations for Kuo need to be solved no equations have to be solved for the Lagrangian multipliers t
485. t is as sumed that only excitation energies are requested This switches on some shortcuts to avoid the computation of intermediates needed e g for the generation of improved start vectors for CC2 no restart If the restart flag is set the program will try to restart the CC2 cal culations from previous solution vectors on file If the norestart flag is 318 CHAPTER 18 KEYWORDS IN THE CONTROL FILE set no restart will be done Default is to do a restart for CC2 if and only if the file CCRO 1 1 0 exists Note There is no restart possibility for CCS CIS or MP2 CIS D no hard_restart If the hard_restart flag is set the program will try to reuse integrals and intermediates from a previous calculation This requires that the restart cc file has been kept which contains check sums and some other informations needed The hard_restart flag is switched on by default if the restart cc file is present conv The conv parameter gives the convergence threshold for the CC2 ground state energy as 10 The default value is taken from the data group deneps oconv The oconv parameter gives an additional threshold for the residual of the cluster equations vector function If this parameter is given the iterations for the cluster equations are not stopped before the norm of the residual is lt 107 By default the threshold is set to oconv conv 1 or 10x deneps if no input for conv is given lindep If the norm of
486. t mul tiplications where O and V are respectively the number occupied and virtual orbitals and Ny is the number of auxiliary functions for the RI approximation For the LT SOS RI MP2 implementation the most expensive step involves nLOV N2 floating point multiplications where nz is the number of grid points for the numerical integration Thus the ratio of the computational costs is approximately 30 V7N OV LT amp O 6 oe ntOVN2 2nzNy L where for the last step Nz 3V has been assumed Thus the Laplace transformed implementation will be faster than the conventional implementa tion if O gt 6nz The number of grid points nz depends on the requested accuracy and the spread of the orbital energy denominators in Eq 8 8 The efficiency of Laplace transformed SOS RI MP2 calculations can therefore in difference to conventional RI MP2 cal culations be enhanced significantly by a carefull choice of the thresholds the basis set and the orbitals included in the correlation treatment e The threshold conv for the numerical integration is by default set to the value of conv specified for the ground state energy in the data group ricc2 see Sec 18 2 14 which is initialized using the threshold denconv which by default is set conservatively to the tight value of 107 For single point energy calculations conv in laplace can savely be set to 4 which gives SOS MP2 energies converged within 10 4 a u with com put
487. t the values for scfdamp and scforbit alshift if you encounter convergence problems In UHF runs this option can be used to automatically locate the lowest spin state In order to obtain integer occupation numbers tmend should be set to relatively low value e g 50K 18 2 FORMAT OF KEYWORDS AND COMMENTS 281 Calculation of fractional occupation numbers should be used only for single point calculations When used during structure optimizations it may lead to energy oscillations The optional nue value number of unpaired electrons can be used to force a certain multiplicity in case of an unrestricted calculation nue 0 is for singlet nue 1 for doublet etc In addition there is an option addTS which adds the entropic contribution to the total energy This term stems from partly occupied orbitals and is only necessary for very high temperatures to make the total energy consistent with the gradient firstorder Perform first order SCF calculation i e perform only one SCF iteration with the start MOs which should be the orthogonalized MOs of two independent subsystems as is explained in detail in Chapter 14 fldopt options Specification of options related with external electrostatic fields The following options are available 1st derivative on off Calculate numerical 1st derivative of SCF energy with respect to elec trostatic field default off increment for numerical differentiation is edelt see below 2nd derivative
488. t they are for all methods guaranteed to be postive and can be evaluated with the same insignificantly low costs as T and To They are invariant with respect to unitary transformations of the occupied or the virtual orbitals and give by construction identical results in spin orbital and spin free calculations For CC2 and CIS D the diagnostics 7 and Tz agree for left and right eigenvectors usually with a few 0 01 for CIS D and 9 3 FIRST ORDER PROPERTIES AND GRADIENTS 185 ADC 2 they are exactly identical For singlet excitations in spin free calculations T2 is typically by a factors of 1 5 2 larger than T gt The second order methods CC2 ADC 2 CIS D and CIS D can usually be trusted for 73 lt 15 For compatibility the program can be switched to use of the old 7 and 72 diag nostics printed with the headers T1 and T2 by setting the flag oldnorm in the data group excitations Note that the choice of the norm effects the individ ual results left and right one and two photon transition moments while transition strengths and all other observable properties independent of the individual normal ization of the right and left eigenvectors The T2 and T diagnostics can not be monitored in the output of the quasi linear solver But it is possible to do in advance a CIS D calculation The CIS D results for the 72 and T gt correlate usually well with the results for this diagnos tic from the iterativ second order
489. ted state esd plt differential spin density for excited state lt myname gt plt general density passed e g by the ricc2 program The plt files may directly be visualized by gOpenMol the file coord xyz which is also necessary for gOpenMol is generated by the above programs if pointval is set in the contro1 file Two component wave functions only module ridft and only if soghf is set Total density is on file td plt like for one component wave functions this is also true for all other quantities depending only on the density matrix electrostatic potential etc sd plt contains the absolute value of the spin vector density which is the absolute value of the following vector y sir Y4 waf g t 2 Y z pointval fmt txt leads to a file containing the spin vector density vectors which can be used by gOpenMol It is advisable to choose ca one Bohr as the distance between two eridpoints 232 CHAPTER 14 PROPERTIES AND ANALYSIS AND GRAPHICS Electrostatic potentials In an analogous way electrostatic potentials can be calculated on grids pointval pot leads to calculation of the electrostatic potential of electrons and nuclei and external constant electric fields and point charges Q if present Vip Marrs D4 RrB Dg a4 rT A Q In order to prevent the calculation of singularities at the positions of nuclei for gridpoints that are closer to a nucleus than 10 a u the charge of the respective nucl
490. ter 9 for further details 8 1 1 How to quote e For calculations with mpgrad Semi direct MP2 Gradient Evaluation on Workstation Computers The MP GRAD Program F Haase and R Ahlrichs J Comp Chem 14 907 1993 e For calculations with rimp2 RI MP2 first derivatives and global consistency F Weigend and M Haser Theor Chem Acc 97 331 1997 160 CHAPTER 8 2ND ORDER MOLLER PLESSET PERTURB THEORY e For calculations with ricc2 CC2 excitation energy calculations on large molecules using the resolution of the identity approximation C Hattig and F Weigend e for MPI parallel calculations with ricc2 in addition Distributed memory parallel implementation of energies and gradients for second order Mgller Plesset perturbation theory with the resolution of the identity approximation Christof Hattig Arnim Hellweg Andreas K hn Phys Chem Chem Phys 8 1159 1169 2006 e for MP2 F12 calculations in addition The MP2 F12 Method in the TURBOMOLE Programm Package Rafal A Ba chorz Florian A Bischoff Andreas Gl Christof Hattig Sebastian Hofener Wim Klopper David P Tew J Comput Chem 32 2492 2513 2011 e for O N scaling LT SOS MP2 calculations Scaled opposite spin CC2 for ground and excited states with fourth order scal ing computational costs Nina O C Winter Christof Hattig J Chem Phys 134 184101 2011 and Scaled opposite spin second order Moller Plesset cor relation energy An ec
491. teration so the HXX energy must be computed after the RIRPA correlation energy Comments on the Output e The most important output for rirpa are the Hatre Fock HXX energy and the RIRPA correlation energy which are written to the standard output e The optimal scaling parameter for the quadrature grid is printed together with a sensitivity parameter The sensitivity parameter provides a numerical estimate for the error in the numerical integration used to evaluate EC RIRPA Experience demonstrates that the sensitivity parameter correlates well with the condition number of the matrix Q Small gap systems have large condition numbers and therefore require large grids An estimate of the number of eigenvalues smaller than 0 05 H is given and if necessary a warning to increase the grid size is printed to standard output e Enabling the option rpaprof will output additional timings information Chapter 12 Calculation of Vibrational Frequencies and Vibrational Spectra Calculation of second derivatives of total energies leads to the molecular Hessian which enables prediction of vibrational frequencies and infrared spectra within the harmonic approximation as well as the application of improved algorithms for ge ometry optimization and transition state search The aoforce module calculates analytically harmonic vibrational frequencies with in the HF or RI DFT methods for closed shell and spin unrestricted open shell systems Broke
492. test script works recursively executing all test examples underneath its starting directory This requires that the test examples be arranged in a TURBOTEST like directory structure progname short long example e g dscf short H20 SCF E1 and the TURBOTEST directory contain a DEFCRIT file with general test suite settings If TTEST is started in the central TURBOTEST without any options all available test examples are executed By giving the list of module names for full list check TTEST help as argument to the script the test can be restricted to these modules The 20 3 TAKING THE TIMINGS AND BENCHMARKING 389 short and long options allow the user to select only the short or long test examples respectively Some examples of usage are given in the following table TTEST dscf called in the TURBOTEST directory performs only the tests for DSCF module TTEST called in the TURBOTEST dscf directory does the same TTEST long executes long examples for all modules TTEST ridft short performs all short examples from the ridft directory Recursive testing creates some additional files in the central TURBOTEST directory The global protocol file TESTPROTOKOLL sysname contains short result messages for all test and a list of errors occurred The list of failed tests is also written to the PROBLEMS sysname file and can be rerun by calling the test script with the r option TTEST r PROBLEMS i786 pc linux gnu The r ma
493. this it calculates an analytical Hessian Cartesian which will be used as a start Hessian for an ab initio geometry optimization for semi direct SCF HF and DFT calculations see keywords for func tionals supported dscf supports restricted closed shell RHF spin restricted ROHF as well as UHF runs dscf includes an in core version for small molecules for Orbital dependent Kohn Sham DFT calculations namely Exact Exchange EXX and the Localized Hartree Fock LHF method odft supports spin restricted as well as spin unrestricted runs requires a successful dscf run and calculates the gradient of the energy with respect to nuclear coordinates for all cases treated by dscf perform direct SCF HF and DFT calculations as dscf and grad within the very efficient RI J approximation for the interelectronic Coulomb term These programs also permit to approximate HF ex change within the RI K approximation The exchange correlation func tionals supported are specified in define requires a well converged SCF run by dscf see keywords and per forms closed shell RHF or UHF calculations yielding single point MP2 energies and if desired the corresponding gradient calculates MP2 energies and gradients for RHF and UHF wavefunctions significantly more efficient than mpgrad by using the RI technique 8 9 This module is deprecated please use ricc2instead calculates electronic excitation energies transition moments and pro
494. threshold man enables you to select the MOs manually later in this section If the selection method thr is specified you then will be asked for the threshold to be applied for the selection Afterwards you have the possibility to change some other topics concerning the localization 94 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE e specify other localization directions e switch on utilization of localized orbitals for population analysis and or prepa ration of plot data within the same moloch run e set the maximum number of sweeps in the localization procedure e specify a file where localized orbitals shall be written to Option population analyses When activating this option you first have to specify whether the population analy sis PA should be performed in the CAO default or AO basis Afterwards define will ask you whether you want to perform a Mulliken population analysis In this case the following submenu will be displayed add or delete one or more special options for a mulliken population analysis option status description spdf F compute MO contributions to atomic brutto populations molap F compute MO contributions to atomic overlap populations netto F compute atomic netto populations l l l l l irpspd F compute IRREP contributions to atomic brutto populations l l l l irpmol F compute IRREP contributions to atomic overlap populations mommul F print electrostatic
495. tinuum is split into a fast contribution described by the electronic polarization and a slow term related to the orientational relaxation As can be shown 171 the dielectric energy for the disturbed state can be written as Eta ZFP 5 f n a P B P F a P B P4 where P denotes the density difference between the distorted state and the initial state with density P The interaction is composed of three contributions the initial state dielectric energy the interaction of the potential difference with the initial state charges and the electronic screening energy that results from the density difference The energy expression can be used to derive the correspondent gradients which can be applied in a numerical frequency calculation Because the COSMO cavity changes for every distorted geometry the initial state potential has to be mapped onto the new cavity in every step The mapped potential of a segment of the new cavity is calculated from the distance weighted potentials of all segments of the old cavity that fulfill a certain distance criterion The mapped initial state screening charges are re calculated from the new potential Iterative MP2 Cosmo For ab initio MP2 calculations within the CSM frame work three alternatives can be found in the literature 172 The first approach often 262 CHAPTER 17 TREATMENT OF SOLVATION EFFECTS WITH COSMO referred to as PTE performs a normal MP2 energy calculation on the solvated HF wave f
496. to a practical post kohn sham correlation model J Chem Phys 129 114105 2008 P Deglmann F Furche R Ahlrichs An efficient implementation of sec ond analytical derivatives for density functional methods Chem Phys Lett 362 5 6 511 518 2002 P Deglmann F Furche Efficient characterization of stationary points on potential energy surfaces J Chem Phys 117 21 9535 9538 2002 M H ser R Ahlrichs H P Baron P Weis H Horn Direct computation of second order SCF properties of large molecules on workstation computers with an application to large carbon clusters Theor Chim Acta 83 5 6 455 470 1992 T Ziegler G Schreckenbach Calculation of NMR shielding tensors using gauge including atomic orbitals and modern density functional theory J Phys Chem 99 2 606 611 1995 A E Reed R B Weinstock F Weinhold Natural population analysis J Chem Phys 83 2 735 746 1985 C Ehrhardt R Ahlrichs Population Analysis Based on Occupation Numbers II Relationship between Shared Electron Numbers and Bond Energies and Characterization of Hypervalent Contributions Theor Chim Acta 68 3 231 245 1985 A V Luzanov A A Sukhorukov V E Umanskii Theor Exp Chem 10 354 1976 R L Martin J Chem Phys 118 4775 2003 F Weigend C Schrodt Atom type assignment in molecule and clusters by pertubation theory A complement to X ray structure analysis Chem
497. to run on a cluster we highly recommed the usage of a queuing system like PBS The parallel version of TURBOMOLE will automatically recognise that it is started from within the PBS environment and the binaries will run on the machines PBS provides for each job Other supported queuing systems besides PBS and PBS derivatives are LSF Sun Grid Engine SGE and IBMs LoadLeveler Important Make sure that the input files are located on a network directory like an NFS disk which can be accessed on all nodes that participate at the calculation A file that contains a list of machines has to be created each line containing one machine name nodei nodei node2 node3 node4 node4 And the environment variable HOSTS_FILE has to be set to that file export HOSTS_FILE nfshome username hostsfile Note Do not forget to set PARNODES to the number of lines in HOSTS_FILE Note In general the stack size limit has to be raised to a reasonable amount of the memory or to ulimited In the serial version the user can set this by ulimit s unlimited on bash sh ksh shells or limit stacksize unlimited on csh tesh shells However for the parallel version that is not sufficient if several nodes are used and the etc security limits conf files on all nodes might have to be changed See chapter 2 2 3 2 PARALLEL RUNS 47 Testing the parallel binaries The binaries ridft rdgrad dscf grad and ricc2 can be tested by the usual test suite go to TURBODI
498. tor the spin vector is no longer an observable In case of DFT for open shell systems rotational invariance of the exchange correlation energy was ensured by the non collinear approach In this approach the exchange correlation energy is a functional of the particle density and the absolute value of the spin vector density m r are the Pauli matrices mle X v ovl This quantity replaces the spin density difference between density of alpha and beta electrons of non or scalar relativistic treatments For closed shell species the Kramers restricted scheme a generalization of the RHF scheme of one component treatments is applicable 6 4 2 How to use The keyword soghf enforces the two component calculations Keywords for specifi cation of the method of calculation are the same as for the one component case dft and rij for pure density functional calculations within the RI J approximation rij and rik for Hartree Fock with the RI approximation for Coulomb and ex change operators and all three keywords for Hybrid DFT The DIIS scheme for 136 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS complex Fock operators can be activated by inserting gdiis in the control file For closed shell species a Kramers invariant density functional formalism only pure den sity functionals can be switched on with the keyword kramers These keywords have to be inserted into the control file manually As start wavefunctions Hiickel U
499. treatment have to be specified in data group freeze e the calculation of MP2 gradients is omitted by adding the flag mp2energy to the control file in this case only MP2 energy is calculated Calculations with rimp2 and ricc2 moreover require e an auxiliary basis defined in the data group cbas This is not needed for mpgrad but here one needs e a specification for scratch files and their size in data group mointunit see Section 18 2 13 e and the number of passes for integral evaluations and transformations in data group traloop 162 CHAPTER 8 2ND ORDER MOLLER PLESSET PERTURB THEORY For explicitly correlated MP2 F12 calculations one needs depending the details of the applied approximations additionally a so called complementary auxiliary basis set CABS defined in cabs and a RI SCF auxiliary basis set defined in jkbas Calculations with rimp2 and ricc2 1 RI MP2 calculations require the specification of auxiliary basis sets cbas and a converged SCF calculation with the one electron density convergence threshold set to denconv 1 d 7 or less In addition the options freeze frozen core approximation and maxcor maximum core memory usage should be set All these settings can be done during the input generation with the program define under the entry mp2 cc2 of last main menu 2 Alternatively the interactive program Rimp2prep can be used This program sets default values for auxiliary basis sets data group cbas
500. ts as well as com binations of them relax carries out e update of general coordinates e update of approximate hessians if needed e conversion of coordinates internal cartesian The mode of operation is chosen by the keywords optimize and interconversion and the corresponding options which will be described in the following sections 5 3 PROGRAM RELAX 105 5 3 2 Optimization of General Coordinates After gradients G have been calculated for coordinates g in optimization cycle k new coordinates or basis set exponents g can be obtained from the quasi Newton update ght gt FRG where F is the inverse of an approximate force constant matrix H This method would immediately converge to the equilibrium geometry if F would be the inverse of the exact force constant matrix and the force field would be quadratic In real applications usually none of these requirements is fulfilled Often only a crude approximation to the force constant matrix H is known Sometimes a unit matrix is employed which means coordinate update along the negative gradient with all coordinates treated on an equal footing The optimization of nuclear coordinates in the space of internal coordinates is the default task performed by relax and does not need to be enabled Any other optimization task requires explicit specifications in data group optimize which takes several possible options optimize options internal on off Structu
501. ts and Demonstration of Efficiency F Weigend M Haser H Patzelt and R Ahlrichs Chem Phys Letters 294 143 1998 g Contracted all electron Gaussian basis sets for Rb to Xe R Ahlrichs and K May Phys Chem Chem Phys 2 943 2000 h Efficient use of the correlation consistent basis sets in resolution of the identity MP2 calculations F Weigend A K hn and C Hattig J Chem Phys 116 3175 2002 i Gaussian basis sets of quadruple zeta valence quality for atoms H Kr F Weigend F Furche and R Ahlrichs J Chem Phys 119 12753 2003 j Balanced basis sets of split valence triple zeta valence and quadruple zeta va lence quality for H to Rn Design an assessment of accuracy F Weigend and R Ahlrichs Phys Chem Chem Phys 7 3297 2005 k Optimization of auxiliary basis sets for RI MP2 and RI CC2 calculation Core valence and quintuple basis sets for H to Ar and QZVPP basis sets for Li to Kr C Hattig Phys Chem Chem Phys 7 59 2005 l Accurate Coulomb fitting basis sets for H to Rn F Weigend Phys Chem Chem Phys 8 1057 2006 m Optimized accurate auxiliary basis sets for RI MP2 and RI CC2 calculations for the atoms Rb to Rn A Hellweg C Hattig S Hofener and W Klopper Theor Chem Acc 117 587 2007 n Property optimized Gaussian basis sets for molecular response calculations D Rappoport and F Furche J Chem Phys 133 134105 2010 o Segmented contracted bas
502. ty and charge for the two states can be set For further details call MECPprep h driver for geometry optimizations of minimum energy crossing points The electronic structure calculations are carried out in the subdirec tories state1 and state2 and the optimizer step is performed in the starting directory For further details call MECPopt h prepares MP2 calculations interactively by adjusting parameters of the control file according to your system resources calculates numerically force constants vibrational frequencies and IR intensities Note that the name of the shell script is NumForce with capital F example outp 1 2 3 4 displays the out of plan angle between atom1 and the plane that is defined by the last three atoms atom1 is fixed at atom4 calculates vibrational frequencies and Raman intensities See Sec tion 12 2 for explanation distorts a molecule along a vibrational mode distorts a molecule along a vibrational mode or generates a plot of an IR spectrum gnuplot required shows data group from control file for example sdg energy shows the list of calculated energies returns the name of your system used in almost all TURBOMOLE scripts prepares the control file for a statistics run converts TURBOMOLE coordinates to xyz format creates an input file for the AOMix program AOMix a software the analysis of molecular orbitals For more information see http www sg chem net aomix creates a mold
503. ty matrices larger than 0 1 will be 342 CHAPTER 18 KEYWORDS IN THE CONTROL FILE taken into account This is a reasonable minimal basis set for most molecules If modified atomic orbitals shall not be selected according to this criterion the data group mao selection has to be specified mao selection threshold real The default criterion for the selection of MAOs is the occupation number for which a global threshold can be specified within the same line as the keyword maoselection If the global criterion or threshold is not desirable for some atoms lines of the following syntax have to be added for each atom type of these atom symb list nmao 2 method meth threshold r The parameters in this definition have the following meaning symb atom symbol list list of all atoms for which this definition should apply The syntax for this list is as usual in TURBOMOLE e g 2 3 8 10 12 nmao means number of MAOs to be included method meth means selection criterion for MAOs meth can be occ default eig or man string where occ denotes selection of MAOs by occupation num bers eig selection by eigenvalues and man allows manual selection In the latter case the string max 8 characters appended to man serves as nickname for the definition of the MAOs to be chosen This nick name is expected to appear as the leftmost word in a line somewhere within data group mao selection and is followed by the indices of the modified atomi
504. uclei and electron density of the subsystem B respectively and T3 p4 pB Ts pa pB Tslpa Tsloal 15 2 joa ee pB Exclpa pB Exclpa EzcleB 15 3 are the non additive non interacting kinetic energy and exchange correlation en ergy functionals respectively In the expressions above T p is the unknown non interacting kinetic energy density functional and F p is the exchange correlation energy functional Note that while the first two terms in Eq 15 1 refer to classical electrostatics and could be described by e g external point charges the last two terms are related to quantum mechanical effects 235 236 CHAPTER 15 FROZEN DENSITY EMBEDDING CALCULATIONS Using freeze and thaw 149 cycles the role of the frozen and the embedded subsys tem is iteratively exchanged till convergence If expressions 15 2 and 15 3 are computed exactly then the density p4 pg will coincide with the exact density of the total system Because the FDE KSCED was originally developed in the Kohn Sham framework using standard GGA approximations for E p the non additive exchange correlation potential 522244 dp 4 r can be computed exactly as a functional of the density leaving the expression of the non additive kinetic energy term as the only approxima tion with respect the corresponding GGA calculation of the total system because the exact explicit density dependence of T from the density is not kn
505. uesting relaxed one electron properties or as a by product of a gradient calculation you will end up with two files named like cc1td cc2 gs 1a1 001 cc1td cc2 xs 3a2 001 In case of open shell molecules additional files with names cc1isd for one electron spin densities will be generated These files are currently in a binary format similar as the files dens mdens and edens Therefore be aware that a transfer between different computer architectures may result in trouble The densities on these files can be analysed with the tools and interfaces provided by Moloch see Section 14 2 This can be done by calling ricc2 with the option fanal which bypasses the usual wavefunction calculation and triggers the program into an analysis mode for densities In this mode the program interpretes anadens and the keywords described in Section 14 2 To plot for example the difference density of the two above mentioned total densities you have to add the following lines in your control file anadens calc my_favourite_diffden from 1d0 ccltd cc2 xs 3a2 001 1d0 cc1itd cc2 gs 1a1 001 pointval and invoke ricc2 fanal This will generate the files my favourite diffden and my favourite _diffden map The latter can be converted into gOpenMol format as described in Section 14 2 9 4 TRANSITION MOMENTS 193 9 3 4 Fast geometry optimizations with RI SCF based gradients If geometry optimizations on MP2 or CC2 level are performed with large
506. uisites ground state energy calculations with the ricc2 module require only the data group ricc2 180 CHAPTER 9 RI CC2 see Section 18 2 14 which defines the methods convergence thresholds and limits for the number of iterations etc If this data group is not set the program will carry out a CC2 calculation With the input ricc2 mp2 cc2 conv 6 the ricc2 program will calculate the MP2 and CC2 ground state energies the latter converged to approximately 10 6 a u The solution for the single substitution cluster amplitudes is saved in the file CCRO 1 1 0 which can be kept for a later restart Ground State calculations for other methods than CC2 The MP2 equa tions and the energy are obtained by restricting in the CC2 equations the single substitution amplitudes tg to zero In this sense MP2 can be derived as a simplifi cation of CC2 But it should be noted that CC2 energies and geometries are usually not more accurate than MP2 For CCS and CIS the double substitution amplitudes are excluded from the cluster expansion and the single substitution amplitudes for the ground state wavefunction are zero for closed shell RHF and open shell UHF reference wavefunctions and thus energy is identical to the SCF energy For the Methods CIS D CIS D and ADC 2 the ground state is identified with the MP2 ground state to define is total energy of the excited state which is needed for the definition of gradients and relaxed first orde
507. ulk CaF In this example a QM cluster with the composition Ca4F19 surrounded by 212 ECPs and 370 explicit point charges representing Ca cations and F anions is embedded in a periodic field of point charges 2 for Ca and 1 for F corresponding to the CaF fluorite lattice First the program has to know that this is a three dimensional periodic system This is specified by the keyword periodic 3 meaning periodicity in three dimensions The dimensions of the unit cell for bulk CaF are given in the subsection cell of the embed keyword By default the unit cell dimensions are specified in atomic units and can be changed to A using cell ang The positions of the point charges in the unit cell are specified in the subsection content In this example positions are given in fractional crystal coordinates content frac You can change this by specifying content for Cartesian coordinates in atomic units or content ang for 140 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS Cartesian coordinates in A The values of point charges for Ca and F are given in the subsection charges embed periodic 3 cell 10 47977 10 47977 10 47977 90 0 90 0 90 0 content frac F 0 00 0 00 0 00 Ca 0 25 0 75 0 75 F 0 50 0 50 0 00 F 0 50 0 00 0 50 F 0 00 0 50 0 50 F 0 50 0 50 0 50 F 0 00 0 00 0 50 F 0 50 0 00 0 00 F 0 00 0 50 0 00 Ca 0 25 0 25 0 25 Ca 0 25 0 75 0 25 Ca 0 25 0 25 0 75 end charges F 1 0 Ca 2 0 end The above input
508. unction The response of the solvent also called reaction field is still on the HF level It is the only of the three approaches that is formally consistent in the sense of second order perturbation theory 173 174 In the so called PTD approach the vacuum MP2 density is used to calculate the reaction field The third approach often called PTED is iterative so that the reaction field reflects the density of the first order wave function In contrast to the PTE approach the reaction field i e the screening charges change during the iterations until self consistency is reached Gradients are available on the formally consistent PTE level only 175 Vertical excitations and Polarizabilities for TDDFT TDA and RPA The escf program accounts for the COSMO contribution to the excitation energies and polarizabilities The Cosmo settings have to be defined for the underlying Cosmo dscf or ridft calculation In case of the excitation energies the solvent response will be divided into the so called slow and fast term 171 176 The screening function of the fast term depends on the refractive index of the solvent which can be defined in the input If only the COSMO influence on the ground state should be taken into account we recommend to perform a normal Cosmo calculation dscf or ridft and to switch off Cosmo i e deactivate cosmo before the escf calculation The Direct COSMO RS method DCOSMO RS In order to go beyond the pure electrostatic model
509. use the TURBOMOLE tool x2t to convert it into a TURBOMOLE coord file see Section 1 5 Internal Coordinates Structure optimizations see jobex are most efficient if carried out in internal coor dinates and TURBOMOLE offers the following choices internals based on bond distances and angles see Section 4 1 2 52 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE redundant internals defined as linearly independent combinations of internals see ref 23 provided automatically by the command ired in the geometry main menw in Section 4 1 below This works in almost all cases and is efficient The disadvantage is that this is a black box procedure the coordinates employed have no direct meaning and cannot be modified easily by the user cartesians should always work but are inefficient more cycles needed for conver gence Cartesians are the last resort if other options fail they are assigned as default if one leaves the main geometry menu and no other internals have been defined 4 1 The Geometry Main Menu After some preliminaries providing the title etc you reach the geometry main menu SPECIFICATION OF MOLECULAR GEOMETRY ATOMS 0 SYMMETRY c1 YOU MAY USE ONE OF THE FOLLOWING COMMANDS sy lt group gt lt eps gt DEFINE MOLECULAR SYMMETRY default for eps 3d 1 desy lt eps gt DETERMINE MOLECULAR SYMMETRY AND ADJUST COORDINATES default for eps id 6 susy ADJUST COORDINATES FOR SUBGROUPS ai ADD ATOM
510. using soes For example to calculate the 17 lowest excitations in IRREP blg the 23 lowest excitations in IRREP eu and all excitations in IRREP t2g use soes big 17 eu 23 t2g all and run escf Note that soes specifies the IRREP of the excitation vector which is not necessarily identical to the IRREP of the excited state s involved In general the IRREP s of the excitation s from the ground to an excited state is given by the direct product of the IRREPs of the tow states For example to calculate the first Ag state in a Cy symmetric molecule with a By open shell ground state it is necessary to specify soes bi 1 The number of excitations that have to be calculated in order to cover a certain spectral range is often difficult to determine in advance The total number of exci tations within each IRREP as provided by the define ex menu may give some hint A good strategy is to start with a smaller number of excitations and if necessary perform a second escf run on a larger number of states using the already converged excitation vectors as input To compute absorption and CD spectra it is often sufficient to include optically allowed transitions only This leads to substantial reduction of computational effort for molecules with higher symmetry For example in the UV VIS spectrum of an Op symmetric molecule only ti excitations are optically allowed The IRREPs of the electric and magnetic dipole moments as well as of the e
511. ut there is no general rule check those internal coordinates for consistency which contribute to the correspond ing eigenvector s 5 3 6 Structure Optimization in Cartesian Coordinates For this task you have to specify optimize cartesian on internal off These lines switch on the non default optimization in cartesian coordinates and switch off the optimization in internal coordinates this has to be done explicitly As input data groups you need only grad as provided by on of the gradient pro grams For the first coordinate update an approximate force constant matrix is needed in data group forceapprox Output will be the updated coordinates on coord and the updated force constant matrix on forceapprox The coordinates for any single atom can be fixed by placing an f in the third to eighth column of the chemical symbol flag group As an example the following coordinates specify acetone with a fixed carbonyl group coord 2 02693271108611 2 03672551266230 O 00000000000000 1 08247228252865 0 68857387733323 O 00000000000000 2 53154870318830 2 48171472134488 O 00000000000000 o f 110 CHAPTER 5 STRUCTURE OPTIMIZATIONS 1 78063790034738 1 04586399389434 O 00000000000000 2 64348282517094 0 13141435997713 1 68855816889786 2 23779643042546 3 09026673535431 O 00000000000000 2 64348282517094 0 13141435997713 1 68855816889786 1 31008893646566 3 07002878668872 1 68840815751978 1 31008893646566 3 07002
512. v 10 format 4d20 14 SCF energy is 54 3329250250 a u virial theorem 2 000000001 1 alg eigenvalue 15623888057347D 02 nsaos 3 99166890864040D 00 28420294406651D 010 91519592317893D 02 2 alg eigenvalue 92524548524703D 00 nsaos 3 0 30506869715453D 00 65051761026701D 00 44610487551870D 00 3 alg eigenvalue 0 74881229854801D 00 nsaos 3 0 30759302935434D 00 16295969601691D 010 16126161147521D 01 1 tiu eigenvalue 56865046629517D 00 nsaos 2 0 67926397018841D 000 46005039868410D 00 2 tiu eigenvalue 0 96169069264790D 00 nsaos 2 95675659621171D 000 10794148212163D 01 end 384 CHAPTER 19 SAMPLE CONTROL FILES 19 6 ROHF of Two Open Shells Extracts from control for O2 in D3 Symmetry HF SCF SVP Reference triplet sigma in D3d This is a Roothaan case as is D infinity h coord 0 0 0 0 1 08597397921317 o 0 0 0 0 1 08597397921317 o symmetry d3d closed shells alg 1 3 2 a2u 1 2 2 eu 1 2 open shells type 1 eg 1 1 roothaan 1 a i1 b 2 energy SCF SCFKIN SCFPOT 1 149 4774402753 149 4799190239 298 9573592992 Reference singlet delta in D3d This is a Roothaan case as is D infinity h coord 0 0 0 0 1 08597397921317 o 0 0 0 0 1 08597397921317 o symmetry d3d closed shells alg 1 3 2 a2u 1 2 2 eu 1 2 open shells type 1 eg 1 1 roothaan al a 1 2 b 0 energy SCF SCFKIN SCFPOT 1 149 4297623470 149 4298692899 298 8596316369
513. value The default value is 200 debug Print further information about the OEP calculation especially matrices and vectors used during the OEP calculation Use this option carefully since a lot of data is written The default value is false eigenvalue difference integer plot Two molecular orbitals are considered as degenerated due to symmetry or incidentally if the difference between them is smaller then 1074er The variable integer must have an integer value The default value is 6 coefficient string The expansion coefficients for the auxiliary basis functions which build the local exact exchange potential are written to the file oepcVx dat or in case of a spin unrestricted calculation to the files oepcVxa dat and oepcVxb dat If string is cartesian the expansion coefficients are given for a cartesian atomic orbital auxiliary basis if string equals spherical the expansion coefficients are given for a spherical atomic orbital auxiliary basis In any case the expansion coefficients are given for the single atomic orbital auxiliary basis function and contain no information about the symmetry of the system cl case The default value is cartesian reference potential Use the reference potential constructed by the applied conditions to the OEP calculation as exchange potential The solution of the OEP equation is skipped The default value is false To run a LHF calculations select dft functional lhf gridsize 3
514. vatives and gridordering together Example for switching off gridordering dft gridordering 0 electrostatic field Specification of external electrostatic field s The specification may take place either by Ex Ey Ez orby x y z E See also fldopt Example electrostatic field 0 1000E 03 0 000 0 000 fermi tmstrt lt 300 0 gt tmend lt 100 0 gt tmfac lt 0 9 gt hlcrt lt 1 0E 01 gt stop lt 1 0E 03 gt nue lt N gt Requests calculation of occupation numbers at a finite temperature T For an orbital with the energy c the occupation number n 0 1 is calculated as La ei pb er ON ie ol where u is the Fermi level The factor f 4k z is chosen to yield the same slope at the Fermi level as the Fermi distribution Calculation of the fractional occupation numbers starts when the current HOMO LUMO gap drops below the value given by hlcrit default 0 1 The initial temperature given by tmstrt default 300 K is reduced at each SCF cycle by the factor tmfac default 1 0 until it reaches the value tmend default 300K Note that the default values lead to occupation numbers calculated at a constant T 300K Current occupation numbers are frozen if the energy change drops below the value given by stop default 1 1073 This prevents oscillations at the end of the SCF procedure Calculation of fractional occupation numbers often requires much higher damp ing and orbital shifting Please adjus
515. vel can be carried out in two ways dscf and grad perform conventional calculations based on four center two electron repulsion integrals ERI s ridft and rdgrad employ the RI J approximation as detailed below dscf and grad are modules for energy and gradient calculations at the HF and DFT level which use an efficient semi direct SCF algorithm Calculation of the Coulomb and HF exchange terms is based on the conventional method employing four center two electron repulsion integrals ERI s These modules should be used for HF and DFT calculations with exchange correlation functionals including HF exchange contribution e g B3 LYP if further approximations RI J are to be avoided All functionalities are implemented for closed shell RHF and open shell UHF reference wavefunctions Restricted open shell treatments ROHF are supported on the HF level only i e not for DFT The most important special features of the dscf and grad modules are e Selective storage of the most time consuming and frequently used integrals The integral storage is controlled by two threshold parameters thize and thime related to integral size and computational cost e Efficient convergence acceleration techniques for energy calculations They in clude standard methods for convergence acceleration DIIS which reduce the number of SCF iterations needed as well as methods to reduce the effort within each iteration when the calculation is almost converge
516. vernelli U Rothlisberger Trajectory surface hopping within linear response time dependent density functional theory Phys Rev Lett 98 023001 2007 E Tapavicza A M Meyer F Furche Unravelling the details of vitamin d photosynthesis by non adiabatic molecular dynamics simulations Phys Chem Chem Phys 13 20986 2011 B G Levine C Ko J Quenneville T J Martinez Conical intersections and double excitations in density functional theory Mol Phys 104 1039 2006 E Tapavicza I Tavernelli U Rothlisberger C Filippi M E Casida Mixed time dependent density functional theory classical trajectory surface hopping study of oxirane photochemistry J Chem Phys 129 12 124108 2008 Index non append mode 66 49 central 222 fanal 192 frznuclei 221 222 relax 99 119 map 192 352 sys data 56 2e ints _shell statistics 363 364 2e ints_shell statistics 363 D2 diagnostic 328 Laplace 175 195 TURBODIR uff parms in 272 actual step 226 alpha shells 136 154 269 290 anadens 191 192 atoms 67 142 145 267 268 292 307 314 barrier 356 basis 67 106 110 266 336 beta shells 136 154 269 290 boys 340 clalgorithm 314 cabs 162 176 cbas 161 162 175 176 205 216 314 315 328 cbasopt 314 cc2_natocc 328 cdspectrum 156 310 316 cgrad 328 closed shells 69 70 136 268 282 289 290 constraints
517. w starting with the number of the non bonded terms In each line is one nonbond term I J d Here J and J are the atom numbers d the distance in a u Then the partial charges follow If the determination of the molecule connectivity failed you can specify the block nxtneil2 in the file ufftopology Then the program calculates the other blocks Based on the numbers of the next neighbours block nxtneil2 in the file ufftopology the program tries to determine the UFF type of an atom The following rules are implemented If the atom has three next neighbours and it is in the nitrogen group then it has a hybridization three If it is not in the nitrogen group it has hybridiza tion two If the atom has four next neighbours and it is in the carbon group it has hybridization three If it is not in the carbon group it becomes hybridization four If the number of next neighbours is six then it gets the hybridization six Since the smallest eigenvalues A of the Hessian has the greatest influence on the convergence of the geometry optimization one can shift these values with Ni Ai a Be and calculates a new Hessian with these modified eigenvalues 18 2 5 Keywords for Modules Dscr and RIDFT denconv real Convergency criterion for the root mean square of the density matrix If you want to calculate an analytical MP2 gradient program mpgrad real should be 1 d 7 or less dft options Listing of all possible sub keywords for d
518. where they are located path name and file halfint file moint 0 file moint 1 file moint j file moint k file moint a file gamma 1i file gamma 2 file moint u file moint v file gamma iu 314 CHAPTER 18 KEYWORDS IN THE CONTROL FILE e after a statistics run see below an estimated file size statistics mpgrad statistics run estimation of disc space needed for the adjustment of the file sizes will be performed MPGRAD Optional Keywords mp2pair calculation of MP2 pair correlation energies RiImMpP2 Essential Keywords Apart from keywords maxcor mp2energy and freeze see above rimp2 also needs cbas file auxbasis cross reference for the file specifying the auxiliary basis as referenced in atoms We strongly recommend using auxbasis sets optimized for the corresponding MO basis sets Reasonable settings for these keywords may be generated by the tool Rimp2prep Moreover you may specify by hand tmpdir work thisjob specification of directory for scratch files by default files are written to the working directory works also with capital letters for consistency with ricc2 clalgorithm avoids symmetry gymnastics in case of Cy symmetry rather for debugging cbasopt enforces calculation of lt ij ab gt exact lt ij ab gt RI eli elj ela e b i necessary for characterization of auxiliary basis set quality and for auxiliary basis optimizations works o
519. which reduces computational cost The numerical calculation of force constants is also possible see tool Numforce in Section 1 5 requires a well converged SCF or DFT run and calculates time de pendent and dielectric properties spin restricted closed shell or spin unrestricted open shell reference static and frequency dependent polarizabilities within the SCF ap proximation static and frequency dependent polarizabilities within the time dependent Kohn Sham formalism including hybrid functionals such as B3 LYP electronic excitations within the RHF and UHF CI S restricted CI method electronic excitations within the so called SCF RPA approxima tion poles of the frequency dependent polarizability electronic excitations within the time dependent Kohn Sham for malism adiabatic approximation It can be very efficient to use the RI approximation here provided that the functional is of non hybrid type we recommend B P86 but slightly better results are obtained for the hybrid functional B3 LYP 18 stability analysis of single determinant closed shell wave functions second derivative of energy with respect to orbital rotations 19 1 5 TOOLS 25 egrad mpshift freeh intense computes gradients and first order properties of excited states Well converged orbitals are required The following methods are available for spin restricted closed shell or spin unrestricted open shell reference
520. while D is a diagnostic for strong interactions with singly excited determinants 8 5 RI MP2 F12 Calculations To obtain the F12 correction to the MP2 energy the data group rir12 must be added to the control file A typical run will include the input ricc2 8 5 RI MP2 F12 CALCULATIONS 167 mp2 energy only rir12 The MP2 F12 ground state energy is Eyp2ri2 EMP2 Eri 8 3 where Fyyp2 is the conventional MP2 energy and Ep12 the correction from explicitly correlated theory The second term contains contributions from explicitly correlated geminal basis functions of the form Qia fizlij 8 4 where i7 is a two electron determinant of occupied semi canonical Hartree Fock spin orbitals f 2 is a correlation factor which can be either linear r12 in this case the approach is denoted MP2 R12 instead of MP2 F12 or a function of r12 and 2 defines the doubles excitation space covered by the geminals it also ensures strong orthogonality to the occupied orbitals Usually Qi is chosen to be ane 1 O1 1 O2 Vi V2 where p gt pr u ve H is the projection operator onto the space spanned by the occupied spin orbitals px and V Yalu Pal is the projector onto the virtual spin orbitals The F12 correction is obtained by minimizing the functional Friz gt c Bijciz 2c Viz 8 5 i lt j with respect to the amplitudes collected in the vector cij The vectors vij and the matrices B
521. with scaling factors of cos 1 3 and css 0 0 Y Jung R C Lochan A D Dutoi and M Head Gordon J Chem Phys 121 2004 9793 which are also recommended for SOS variants of CC2 CIS D CIS D and ADC 2 The Laplace transformed algorithm for the SOS variants are activated by the additional data group laplace laplace conv 4 For further details on the Laplace transformed implementation see Sec 8 6 Restrictions e the spin S expectation value for open shell calculation can not be evaluated in the SCS or SOS approaches e for LT SOS CC2 and the related CIS D and ADC 2 versions the following further limitations apply restricted to ground state and excitation energies only parallelized with MPI no OpenMP parallelization incompatible with the calculation of the D and D diagnostics 9 8 Polarizable embedding calculations Polarizable embedding PE calculations are a based on a hybrid model of quan tum mechanics and molecular mechanics QM MM in which the classical region is 9 8 POLARIZABLE EMBEDDING CALCULATIONS 199 represented by an electrostatic potential with up to octupole moments and induced point dipole moments The main improvement over the more common QM MM ap proaches without polarizable MM sites can be found for the description of electronic excitations but also for any other process which causes a significant change in the QM density and which is accompanied by a fast response of the
522. written either in ASCII or in binary format This command switches from one option to the other and it is highly recommended to read which setting is currently active ASCII format is portable and allows the usage of TURBOMOLEinput files on different systems with incompatible binary format Binary format is faster and smaller files will be written The external program atbandbta can be used to transform existing mos alpha and beta files from ASCII to binary format and vice versa eht eht performs an extended Hiickel calculation for your molecule The orbital energies available from this calculation are then used to provide occupation numbers for your calculation and the H ckel MOs will be projected onto the space that is spanned by your basis set This start vectors are not as good as the ones which may be obtained by projection of an old SCF vector but they are still better than the core Hamilto nian guess that is used if no start vectors are available When using this command you will be asked if you want to accept the standard Htickel parameters and to enter the molecular charge Afterwards you will normally get a list of the few highest occupied and lowest unoccu 4 3 GENERATING MO START VECTORS 69 use file man hcore pied MOs their energies and their default occupation If you don t want to accept the default occupation you will enter the occupation number assignment menu which is described in Section 4 3 2 Note that the
523. y to obtain a good guess is to built an approximate TS and to perform a constrained minimization by freezing internal coordinates that change most during the reaction Alternatively you can generate several structures intermediate to reactants and products and compute the energy at each point The maximum energy structure is usually a good guess for the true TS After obtaining a reasonable initial guess for the TS structure you have to perform a vibrational analysis or LES calculation for a large molecule and to identify the index of the transition vector to follow during the optimization Ideally this is a vector with a negative eigenvalue or imaginary frequency The best way to find the right vector is to use some graphical interface to visualize vibrations For a reasonable guess structure there should be one vibration that resembles the reaction under study Remember that statpt uses a different ordering of eigenvalues as compared to the aoforce output six five zero eigenvalues are shifted to the end 104 CHAPTER 5 STRUCTURE OPTIMIZATIONS There is an important thing to remember at this point Even such sophisticated optimization methods like TRIM will not replace your own chemical intuition about where transition states may be located If you need to restart your run do so with the coordinates which have the smallest RMS gradient Note that the energy does not have necessarily to decrease in a transition state search as oppose
524. y a Without symmetry this is just 3N 6 where N is the number of atoms but if there is symmetry some of these degrees of freedom will violate symmetry and therefore are not valid For geometry optimizations only the symmetry allowed degrees of freedom are needed because the symmetry requirements are imposed anyway In connection with the optional atomic set a this com mand can help you to find out in which part of a complicated molecule internal coordinates are missing if you fail to get the full number of ideg which equals the result of ideg all for the molecule as a whole iaut tries an automatic definition of internal coordinates This com mand relies on an recursive procedure which tries to simplify the molecule as far as possible and then starts the definition of internal coordinates At present not all molecular topologies are supported therefore it may happen that no internal coordinates can be assigned to your molecule or at least a part of it However for all cases in which an automatic assign ment of coordinates is possible iaut has up to now proved to provide very good internal coordinates If iaut works for your molecule and in most non pathological cases it will we recommend strongly to use these coordinates as they may help you to save several cycles in the geometry optimization procedure After creating internal coordinates with iaut you should always use imet see above because iaut may provide an overcomplete
525. y also be useful to create any user defined selection of test examples The full list of available examples is obtained by the TTEST list command Once you are done with testing you may wish to clean up afterwards To do it use the clean and realclean options of the TTEST script The difference between these two is that TTEST clean deletes only the test directories and protocols that were created for the current computer architecture as returned by Sysname In contrast the TTEST realclean wipes out all test directories and protocols that get in its way 20 3 Taking the timings and benchmarking Benchmarking differs from testing only in that program timings are computed and compared with reference timings Calling the script as TTEST timings performs the test calculates the CPU and wall clock timings and writes the raw results to the TESTTIMINGS sysname nodename file Auxiliary scripts Tbtim and Tblist help to convert this data to a more readable form and produce summaries as TFX tables The Tbtim script creates a summary of benchmark results for a given computer platform from the original timings file Tblist produces benchmark 390 CHAPTER 20 PERL BASED TEST SUITE comparisons of different platforms The corresponding timings files must be provided as arguments to the Tblist script For more details and options see TBTIM help and TBLIST help 20 4 Modes and options of the TTEST script run check
526. ystem d Vemb iy b Vemb i ee 15 11 for the j th iteration Here Gre iy is the matrix element effectively used in the j th iteration after the damping In FDE the starting value of 7 can be changed using start damp real default value is 0 45 where real is a decimal number The damping parameter can also dynamically change at each iterative step according to the convergence process of a quantity set by step damp real default value is 0 10 The minimum value set by max damp real default value is 0 90 fde input options epsilon real max iter integer start damp real max damp real step damp real Embedding energy error The embedding error in the total energy is computed as AE EFPE 5 4 pp EET 15 12 where EP is the DFT total energy of total system with density p r In order to compute AF as well as its components the flag err energy must be used This flag will required also the DFT calculation on the total system In this case the converged SCF output file must be named output dscf An example of session output for the computation of embedding energy and energy error decomposition 155 when err energy flag is present is the following FDE ENERGY TOTAL SYSTEM 200 99720391651 Ha FDE BINDING ENERGY 4 960885 mHa 3 113002 kcal mol FDE ENERGY ERROR 2 003352 mHa ERROR ENERGY DECOMPOSITION 15 2 FROZEN DENSITY EMBEDDING CALCULATIONS USING THE FDE SCRIPT245 Table 15 1 Other opt
527. ystems The keywords themselves are explained in Chapter 18 365 366 CHAPTER 19 SAMPLE CONTROL FILES 19 2 NH Input for a RHF Calculation Main File control title NH3 c3v SVP operating system unix symmetry c3v coord file coord intdef atoms file coord n 1 basis n def SVP h 2 4 basis h def SVP pople AO basis file basis rundimensions dim fock dens 495 natoms 4 nshell 15 nbf CAQ 30 nbf AQ 29 dim trafo SA0 lt gt AO CAO 69 rhfshells 1 scfmo file mos closed shells al 1 3 e 1 scfiterlimit 30 scfconv 7 thize LOOOOO00E 04 thime 5 scfdamp start 500 step 050 min 100 scfdump scfintunit unit 30 size 0 file twoint scfdiis start 0 5 drvopt cartesian on basis off global off hessian on 2 2 19 2 NH INPUT FOR A RHF CALCULATION 367 dipole on nuclear polarizability interconversion off qconv 1 d 10 maxiter 25 optimize internal on cartesian off global off basis off logarithm coordinateupdate dqmax 0 3 interpolate on statistics 5 forceupdate ahlrichs numgeo 0 mingeo 3 maxgeo 4 modus lt g dq gt dynamic fail 0 1 threig 0 005 reseig 0 005 thrbig 3 0 scale 1 00 damping 0 0 forceinit on diag default energy file energy grad file grad forceapprox file force lock off last step define end File coord coord 00000000000000 00000000000000 54561506935122 n 87806233111566 1 52084856970468 18187168978374 h 8780623311156

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