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The deMon-Nano User's Guide

1. 74 4 Keywords If the Berendsen thermostat 92 is used the scaling factor k is calculated using the Berend sen parameter 7 and the time step desired temperature and instantaneous temperature from the dynamics Because rescaling introduces a large perturbation in system s dynamics MDBATH SCALING should only be used for very rough initial equilibration of the system With BERENDSEN thermostat 92 the scaling coefficient is calculated as k 1 2 2 1 4 13 T Th where t is the MD time step That is the average temperature in this case will gradually approach the desired simulation temperature with a characteristic time constant T Finally MDBATH LOCAL invokes local version of the Berendsen thermostat In this case scaling coefficient k is still given by eq 13 However it is now calculated per atom from the individual atomic kinetic energies As a result local Berendsen thermostat will approach equilibrium faster that the global version at the cost of introducing additional dynamical aftefacts in the system Typically a molecular dynamics simulation would use SCALING thermostat for the initial equilibration then complete the equilibration with local Berendsen thermostat The pro duction runs used to collect statistical information on the system then will be done using either free running dynamics or global Berendsen thermostat with a large time constant T In a production run Berendsen 7 must be large compared to t
2. While doing all this please keep in mind that people you are asking for assistance are just as busy as you are Please try to help them to resolve your problem 2 6 How to Run deMon The use of deMon requires the preparation of the input file see Chapter 4 job execution and interpretation of the output see Chapter 5 To run the program three files are necessary 2 6 How to Run de Mon 17 deMon inp is the input file AUXIS contains the Gaussian auxiliary function BASIS contains the Gaussian orbital basis functions AUXIS and BASIS are ASCII files which are provided with the program It is possible to run deMon executable binaries found in deMon bin x directly In this case the above three files have to be present in the current directory The job can be executed by the command deMon bin x amp or without hangups by nohup deMon bin x amp in the background The current directory is used as working directory and all necessary scratch files are created here A second possibility less cumbersome is to use the standard deMon driver script provided in deMon bin deMon You may wish to add the deMon bin directory to your command search path to avoid repeatedly typing the complete path to the script The deMon driver script is invoked as follows deMon option job_name The driver script will attempt to determine the location of the deMon installation di rectory and will supply reasonable defaults for most optio
3. 4 2 Basis Set Input 39 Thus any ECPS definition for an atom can be overwritten by the explicit assignment of the ECP using the atomic symbol E g for Au3O the following ECPS definition ECPS ECP SD Au ECP19 SD Aui ECP1 SD assigns the one electron ECP denoted by ECP1 SD to the atom Aul the 19 electron ECP denoted by ECP19 SD to the gold atom and the global defined ECP SD ECP to the oxygen atom The file ECPS contains the ECPs from Stuttgart 26 in the deMon format Also the effective core potentials can be directly specified in the input file using the format ECPS SYMBOL Read ELECTRONS N L K EXPONENT COEFFICIENT EXPONENT COEFFICIENT where SYMBOL can be an element or atomic symbol ELECTRONS is an integer number specifying the number of valence electrons N denotes the radial power of the operator L the angular momentum of the effective potential and K the contraction degree The exponents and contraction coefficients are listed in free format under the ECP block definition line one line for each Gaussian EXPONENT and COEFFICIENT A user defined ECP input is shown in Example 5 7 Effective core potentials in deMon are defined according to the functional form ae UE UL 5 Ui r Ur r l m gt lt l m l 0 m l 5 Cyr e ur i 1 U r The radial power n must satisfy n gt 2 Positive coefficients Cu correspond to a repulsive contribution to the potential 40 4 Keywords 4 3 Electronic Stat
4. 66 4377 1977 31 C C J Roothaan Rev Mod Phys 23 69 1951 References 135 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 G G Hall Proc Roy Soc Ser A 205 541 1951 J A Pople R K Nesbet J Chem Phys 22 571 1954 C C J Roothaan Rev Mod Phys 32 179 1960 J S Binkley J A Pople P A Dobosh Mol Phys 28 1423 1974 T Amos L C Snyder J Chem Phys 41 1773 1964 A D Bacon M C Zerner Theor Chim Acta 53 21 1979 B I Dunlap J W D Connolly J R Sabin J Chem Phys 71 4993 1979 J W Mintmire B I Dunlap Phys Rev A 25 88 1982 A M Koster in preparation J Almlof K Faegri Jr K Korsell J Comput Chem 3 385 1982 A M Koster J Chem Phys 118 9943 2003 E Canc s J Chem Phys 114 10616 2001 D R Hartree The Calculation of Atomic Structures Wiley New York 1957 V R Saunders I H Hillier Int J Quantum Chem 8 699 1973 A M K ster P Calaminici Z G mez U Reveles in Reviews of Modern Quantum Chemistry A Celebration of the Contribution of Robert G Parr Ed K Sen World Scientific Publishing Co Singapore 2002 P Pulay J Comput Chem 3 556 1982 B Miehlich A Savin H Stoll H Preuss Chem Phys Lett 157 200 1989 P A M Dirac Proc Cambr Phil Soc 26 376 1930 J P Perdew Y Wang Phys Rev B 33 8800 198
5. More specific definition of the basis set overrides a less specific one so that QM MM CAP overrides atomic symbol overrides lt element symbol overrides global basis set Thus any basis set definition for an atom can be overriden by the explicit assignment of the basis set using the atomic symbol E g for CoH see input in 4 1 1 the following basis set definition Basis DZVP C TZVP C1 STO 3G assigns a STO 3G basis to atom Cl a TZVP to C2 and the DZVP basis to all other atoms Instead of using basis set strings the basis set of an atom may also be specified by the Huzinaga notation given in the BASIS file Using this notation the above basis set definition would read as Basis DZVP C 7111 411 1 Ct 33 3 The basis set file BASIS contains the basis sets listed in Table 6 Other basis sets can be obtained from the Extensible Computational Chemistry Environment Basis Set Database 12 at http www emsl pnl gov forms basisform html by choosing the deMon basis set 36 4 Keywords format Instead of reading the basis set from the BASIS file the user can also define it directly in the input file following the format Basis SYMBOL Read N L K EXPONENT COEFFICIENT EXPONENT COEFFICIENT where SYMBOL can be an element or atomic symbol N and L are the main and angular momentum quantum number of this shell and K is the contraction degree Here a shell collects all contracted orbitals of the same angular
6. The Cartesian coordinates of the embedding points refer to the input orientation of the molecule as defined in the input file If a Z Matrix input is used the embedding point coordinates are defined with respect to the Z Matrix input orientation see Figure 1 The point charge read from the read from the 108 4 Keywords coordinate unit Angstr m or atomic units correspond to the unit system selected for the input coordinates see keyword GEOMETRY in 4 1 1 Optional an element symbol or a radius real number may be specified after the point charge coordinates and the charge values This information will be used for the bond drawing in a Vu output of the embedding region see Section 8 The following input specifies an embedding in a distorted octahedron of positive point charges EMBED READ 5 0 0 0 0 0 1 0 H 5 0 0 0 0 0 1 0 H 0 0 5 0 0 0 1 0 H 0 0 5 0 0 0 1 0 H 0 0 0 0 2 0 1 0 1 5 0 0 0 0 2 0 1 0 1 5 The first line is only necessary if the embedding points are defined within the input file In this example a radius of the hydrogen atom is assigned to the first four embedding points For the two others the radius is explicitly defined to 1 5 ngstr m or atomic units depending on the unit system specification in the GEOMETRY keyword see Section 4 1 1 4 12 5 Keyword CHOLESKY With this keyword a Cholesky decomposition for the inversion of the auxiliary Coulomb matrix can be selected Options OFF Singular value
7. The default MEMORY method will choose between a CONVENTIONAL and DIRECT calculations based on the amount of the available memory see 4 12 1 This method will typicall lead to the lowest wall clock time for a calculations On computer systems with 4 4 SCF Control 49 an unusually high I O capacity or when CPU time rather than wall clock time is of interest CONVENTIONAL approach may be preferable If the calculated system has a large extension gt 10 A asymptotic expansions for long range ERIs 42 can be used This method is activated with the MULTIPOLE option Because asymptotic expansions are only implemented in the DIRECT method the MUL TIPOLE option also triggers the DIRECT option This is the method of choice for large extended systems Table 7 shows timings for the ERI calculation of small alkenes with the three methods The DZVP basis and A2 auxiliary function set was used The SCF convergence 107 was reached for all systems within 10 cycles Thus the ERIs hat to be calculated ten times in the DIRECT and MULTIPOLE method Table 7 shows the total time for these two methods and the time for the one ERI calculation with the CONVENTIONAL method In brackets the difference between the real and CPU time is given too All calculations were performed on a single SGI R14000 node with 2 Gbyte of RAM and a Ultra SCSI disk Table 7 Timing sec for the ERI calculation of alkenes with the CONVENTIONAL DI RECT and MULTIPOLE method
8. The new code which is named deMon 2003 8 was presented the first time at the third deMon developers meeting in Geneva The new deMon 2003 code is available for just about any computer made today including parallel architectures The versions for the different platforms are essentially the same The input file created according to this guide should give within the numerical accuracy of the used compile flags the same output The written word carries more legal complications than the spoken and the need to distinguish deMon 2003 from similarly spelled products restricts how you may write it The best way to refer to the program in the text is to use the unusual capitalization The new deMon code has to be cited as A M Koster R Flores Moreno G Geudtner A Goursot T Heine J U Reveles A Vela S Patchkovskii D R Salahub deMon 2004 NRC Canada There is another companion to this guide The deMon Programmer s Guide which cur 2 1 Getting Acquainted rently under development This companion is an in depth guide about the programming philosophy and style of the new deMon code Its the place to look if you want to extend or modify the program To learn more about other deMon utility programs and interfaces as well as activities of the deMon user community look at http www deMon software com 1 2 How to Avoid Reading this Manual If you are familiar with an older version of deMon or you rather prefer to learn by example
9. appear after the connectivity information in each Z Matrix line The possible substitution codes are listed in Table 5 Table 5 Substitution codes for the internal coordinate substitution in the Z Matrix Subst Code Internal Coordinates Description RAD RAB TABC PABCD Default distance angle dihedral RRD RAB RAC PABCD Angle ABC is substituted by length AC RAA RAB TABC TABD Torsion ABCD is substituted by ABD angle RRA RAB RAC TABD Combination of RRD and RAA RRR RAB RAC RAD Atom specified by three distances Similar to the CARTESIAN input the atomic mass and effective nuclear charge of an atom can be optionally specified at the end of each Z Matrix line The examples 5 2 and 28 4 Keywords 5 3 show some common applications of Z Matrix inputs If the geometry of the system is given in the MIXED format the first atoms are defined using their Cartesian coordinates At least the first three atoms some which may be dummy atoms have to be defined in this way The following atoms can then be specified in the Z Matrix format as described above The reference atoms can be defined using either Cartesian or internal coordinates The coordinate system is defined by the first three atoms The following example see Figure 3 shows a MIXED input of a CO molecule adsorbed on a MgO cluster GEOMETRY MIXED ANGSTROM Mgi 0 000 0 000 0 000 02 0 000 2 105 0 000 03 2 105 0 000 0 000 04 0 000 2 105 0 000 05 2 105 0 000 0 000 Mg6 2 105 2 10
10. of the atoms are frozen until the electronic system reaches a sta tionary point This option might be useful for very large system as it avoids diagonalisation DELMO Multiplier for MO energy gradient for the MO optimisation using the Car Parrinello approach in conjunction with the steepest de scent technique requires CARPAR BO The default is 0 1 MOMD Requests a molecular dynamics like optimisation of the molecular orbitals A Car Parrinello MD is carried out Whenever gradient and velocity of an orbital have opposite signs an additional friction term is added to the equations of motion MOMD Same as the MOMD keyword but specifying the friction parameter The default is 1072 Description deMon DF TB is able to perform Car Parrinello MD simulations The Car Parrinello technique see ref 121 is interesting for systems with band HOMO LUMO gap with protons and in particular if SCC DF TB is carried out In this case CPMD may significantly improve the performance The Car Parrinello approach does not require SCC cycles and avoids the diagonalisation of the secular equations By these means the scalability of the method is much supe rior compared to Born Oppenheimer molecular dynamics Note that this is still a young functionality of deMon nano 82 4 Keywords 4 9 Property Control 4 9 1 Keyword POPULATION This keyword requests population analysis In the absence of the POPULATION keyword the default is to skip popul
11. 118 Contents v 10 Quick Keyword Reference 119 11 Troubleshooting 120 A Automatic Generation of Auxiliary Functions 121 B Format of a platform description file 123 B 1 Philosophy of deMon configuration files 123 B 2 Structure of a platform configuration fles 123 C Working with the deMon Test Suite 129 D Global Counters Limits and Pointers 130 References 133 vi List of Tables List of Tables Oo o NN ALE Co N Ro Rh a eS eS ka Rw NRO Platform specific installation notes nn 7 Parameter Settings aaa a Se a ee Ge S 20 Logical and Physical Filenames lt 4 xoxo EORR E RU ee aK 21 Special Input Symbols Ze man as Baur UE ud S 21 Internal Coordinate Substitution 2 23 x xe oom X Rx X eR e OK 27 BADEN ESA a ES hen a o 37 ERI Calculation yenis Tenba ae cae acer tr Bae ls 49 Exchange and Correlation Functionals s 56 Molecular Fieldsi 2333 EA eg de ete tus a ae 96 Structure of a platform configuration De 124 Platform Specific Functions sa 2 2 2 2 a 128 COMICS yen de RSS O Be AKE Bend on Ha ES Bt Pe hee 130 a nc ho peraan E De Rs e emt ae co Soest enr ae 131 EIDEN Aria om barre ne ae eene eer Zeit eS Soe er CR See be Ge Der e 132 List of Figures vil List of Figures oF WwW N RE Z Matrix Input Orientation ooo 25 Dihedral Angle Definition 26 Mixed Input Definition ug Sy kha apa ek E 29 Set up of heatpipe zone masks a a ar ra ara a Sy 7
12. For PCM calculations the program will automatically check if the corresponding solvent is available in the database If the RMIN value is increased the number of the added spheres will be decreased RMIN 100 inhibits the creation of the added spheres which is recommended for large and complicated molecular systems The default value is RMIN 0 2 The increase of the number of tesserae for each sphere is not recommended for large molec ular system except if DIRECT procedure is selected The default value is TSNUM 60 4 10 Solvent Effects 91 Figure 5 Representation of the benzene cavity surface As an example in Figure 1 the cavity surface of the benzene using 1000 tesserae for each sphere is shown 4 10 2 Keyword PCM CARD In the keyword body PCM CARD the radius of each initial sphere RAD which initially is centered at the corresponding atom a scaling factor SCALRAD and an order number NORD can be read Each column of values is identified by the corresponding string So that under RAD for example the values of the radii must be tabulated As an example the PCM CARD of H20 could be PCM CARD RAD SCALRAD NORD 1 52 1 00 1 1 10 1 00 2 1 10 1 20 3 The numbers under NORD coincide with the position number of the atoms in the Z 92 4 Keywords MATRIX or CARTESIAN input If one of the columns is suppressed in the PCM CARD the corresponding values are set to be equal to the default ones 1 If the column ORD is suppr
13. Geometry Input 33 MIXED input this two syntax forms can be mixed see Figure 3 and the corresponding input example Constants H XYZ A 120 0 Here the first line freezes all hydrogen atoms to their positions In the second line the internal coordinate A is set to 120 and kept frozen Note that all parameters listed in CONSTANTS section are treated as VARIABLEs in a molecular dynamics simulation 4 1 3 Keyword VARIABLES This keyword assigns variable internal coordinates Options None Description The body of VARIABLES collects all symbolic coordinate strings of the Z Matrix with their values real number which should be optimized see 4 1 1 for examples 4 1 4 Keyword SYMMETRY This keyword controls the symmetry analysis of the molecular structure Options OFF ON OFF No symmetry analysis is performed ON A symmetry analysis is performed DETECT ON Symmetry detection is performed This is the default DETECT OFF No symmetry detection is performed Description If a symmetry analysis is performed the point group of the molecule is automatically detected and the molecular INPUT ORIENTATION is transformed into the STANDARD ORIENTATION defined by the center of mass and the main axes of the tensor of inertia All further calculations are done in this orientation If no symmetry analysis is performed the INPUT ORIENTATION is used for the SCF calculation However if a geometry optimization or a frequency analysis is r
14. Multiple instances of the BOND and NOBOND keywords are allowed Their effect is cumulative QM MM keywords are recognized but ignored by deMon in a QM only calculation QMMM QM see section 4 5 1 An example of a QM MM geometry input is GEOMETRY Z MATRIX C1 QMMM QM 01 1 RCO QMMM QM Q 1 0 BOND C1 1 0 H1 1 RH1 2 AH QMMM QM H2 1 RH2 2 AH2 3 DH2 QMMM QM O_Wi 1 RCW1 2 ACW1 3 DCW1 Q 0 834 H3 1 RH3 2 AH3 3 DH3 QMMM QM H W11 5 RH1W1 1 AH1W1 2 DH1W1 Q 0 417 BOND 01 0 03 0_W1 0 90 H W12 5 RH2W1 7 AH2W1 1 DH2W1 Q 0 417 0_W2 1 RCW2 2 ACW2 3 DCW2 QMMM QM Q 0 834 H W21 9 RH1W2 1 AH1W2 2 DH1W2 QMMM QM Q 0 417 amp BOND 01 0 03 0_W2 0 90 H_W22 9 RH2W2 10 AH2W2 1 DH2W2 QMMM QM Q 0 417 VARIABLES RCO 1 37257 RH1 1 11599 AH2W2 104 0 DH2W2 0 0 The full input for this caluclation is discussed in section 5 4 4 1 2 Keyword CONSTANTS This keyword assigns constant Cartesian and internal variables Options None Description In the body of CONSTANTS all atoms and internal coordinates which are kept frozen during the geometry optimization are listed The atomic or element symbol with the string XYZ is used to freeze the atom or group The string X will only freeze the x coordinate of the atom the string XY the x and y coordinates and so on For internal coordinate inputs the symbolic coordinate string of the Z Matrix and its value real number is given in order to freeze this degree of freedom In the case of a 4 1
15. Some examples and the test suite include Include files makefiles Make files see section 2 2 4 objects Scratch area for intermediate build objects 8 2 Getting Started source deMon source code timings Some representative timing data tools Additional deMon programs database Unsupported CREX configuration files unsupported Various unsupported tools and scripts Please keep in mind that many subdirectories contain specific README txt files You may find those useful 2 2 2 Installation Prereqisites You will need a computer system capable of running deMon At the absolute minimum you will need 1 Gbyte of free disk space to compile deMon and run the installation test set To run the full test set you will need at least 512 Mbytes of RAM installed in your computer Your computer must run a Unix like operating system to install deMon successfully We may be able to supply precompiled binaries for non Unix platforms You will also need a working Fortran 90 compiler Not all compilers claiming to be Fortran 90 actually are or are capable of producing correct machine code Unless deMon has already been tested with your compiler see 2 1 you very likely will see compilation problems ranging from compiler crashes to run time aborts to incorrect results On average we discover 2 5 compiler bugs and a few bugs in deMon itself every time deMon gets ported to a completely new Fortran compiler You
16. a new keyword line The keyword options have to be given directly after the keyword separated by space s If they are not present the default option setting for the keyword is used Numerical values are assigned by the sign to keyword options e g SCFTYPE Tol lt Real gt where Real indicates a real number For the combination of keyword options the sign is reserved e g VXCTYPE B88 LYP The keyword body starts in a new input line directly after the keyword line s and must have the appropriate structure given in Chapter 4 Keywords 4 Keywords 23 4 Keywords The description of the Keywords is grouped according to their functionality into geom etry input basis set input electronic state control self consistent field SCF control optimization control frequency control property control environmental control and in terface control keywords Keywords which don t fit into these groups are listed at the end of this chapter under miscellaneous keywords Keyword options which exclude each other are listed in one line separated by signs If these options are not specified in the input the underlined one is used by default If more than one of these options are given the last one will override the previous ones The boldface printed part first five letters of the keywords and options are mandatory for the input Therefore OPTIMIZATION OPTIMIZE and OPTIM are all allowed input forms for the keyword OPTIMIZATION 4 1 Ge
17. available in deMon The minimal abbrevi ations are given in bold Exchange DIRAC Local Dirac exchange 49 PW86 Perdew and Wang GGA exchange from 1986 50 B88 Becke GGA exchange from 1988 51 OPTX Handy and Cohen GGA exchange from 2001 52 PW91 Perdew and Wang GGA exchange from 1991 53 PBE96 Original Perdew Burke and Ernzerhof GGA exchange from 1996 54 PBE98 PBE GGA exchange modified by Y Zhang and W Yang 55 PBE99 PBE GGA exchange modified by B Hammer et al 56 Correlation VWN Local Vosko Wilk and Nusair correlation 57 PZ81 Local Perdew and Zunger correlation 58 PW92 Local Perdew and Wang correlation from 1992 59 PZ86 Perdew GGA correlation from 1986 60 P86 Perdew GGA correlation from 1986 with VWN local correlation 61 LYP Lee Yang and Parr GGA correlation from 1988 62 64 PW91 Perdew and Wang GGA correlation from 1991 53 PW9ISSSF PW91 with full spin scaling function PBE Perdew Burke and Ernzerhof GGA correlation form 1996 54 PBESSF PBE with full spin scaling function Note In the literature combinations of the PBE correlation functional and the PBE98 and PBE99 exchange functionals are often refered to as revPBE and RPBE functionals respectively 4 4 10 Keyword GRID This keyword specifies the grid for the numerical integration of the exchange correlation energy and potential Options 44 SCF Control 57 ADAPTIVE FIXED ADAPTIVE An adaptive grid is used for t
18. box is 0 3 Bohr In the case of the critical point search it is 0 5 Bohr This is the default COARSE The mesh spacing of the box is 0 9 Bohr In the case of the critical point search it is 1 0 Bohr FINE The mesh spacing of the box is 0 1 Bohr READ The box definition is read from the keyword body Description With the options STANDARD SMALL and LARGE the size of the box is specified The box will be every time created in STANDARD ORIENTATION see 4 1 4 and therefore is symmetry adapted to the system The options MEDIUM COARSE and FINE define 102 4 Keywords the mesh spacing within the box The FINE mesh spacing will generate huge data files and thus is only applicable for small systems With the READ option the box can be explicitly defined in the keyword body of BOX If only a part of the molecule should be considered the box can be defined simply by the atoms that should be included In this case the STANDARD SMALL and LARGE as well as the MEDIUM COARSE and FINE options remain active For a SMALL box with FINE resolution containing the H1 and O atom of the water molecule the input has the form BOX SMALL FINE READ O H1 Please note that the atoms are all defined in one input line Instead of the explicit definition of each atom elements can be used for the box definition too Therefore a SMALL box with MEDIUM resolution containing only the hydrogen atoms of water is defined as BOX SMALL MEDIUM READ H Alternatively the
19. convergence step is performed Each step yields a new set of reaction field factors to be used for the next SCF convergence step This iterative procedure is performed until energy convergence between two steps is achieved The tolerance value can be given by input By default TOL 10 SCFTOL By default CAVITATION and DISPERSION options are switched off and only elec trostatic energy contributions are calculated Formaly the bf COMP option is used to specify the charge compensation mode By option COMP 1 the virtual charge over each tessera is normalized as qy qr Qiu Qio Fes while by the option COMP 2 as ger a Si where q is the virtual charge over the surface of each tessera before of the compensation Q is the theoretical virtual charge Q is the total virtual charge over the cavity before of the compensation As is the area of each tessera and Aso is the area of the cavity surface The default option is COMP 1 For uncharged systems Qf 0 In this case if the option COMP 2 is selected for the Iterative and the Partial Closure procedures it will be automatically set equal to 1 The DIRECT option can be activated with the keywords ITPCM and CLSPCM The DIRECT procedure avoids the disk I O by calculating at each SCF cycle the PCM integral blocks This procedure is recommended for large molecular systems and should be carefully selected The solvent dielectric constant value can be given by input with the EPS keyword
20. coordinates is written in the output file deMon out TOL lt Real gt Tolerance for data reduction Description The options BINARY ASCII TABLE and TOL are identical to the corresponding op tions of the ISOSURFACE keyword The option SPHERE or ELLIPSOID is mandatory for the GEOSURFACE keyword The origin and radius or semi axes of the sphere or ellipsoid have to be defined in the keyword body of GEOSURFACE For a sphere with the origin at 7 1 3 4 and a radius of 7 the input has the form GEOSURFACE SPHERE 4 11 Visualization and Topology 101 1 0 3 0 4 0 7 0 The units are defined by the unit definition in the GEOMETRY keyword see Section 4 1 1 For an ellipsoid the following input form is used GEOSURFACE ELLIPSOID 1 0 3 0 4 0 7 0 1 0 0 5 The definition of all three semi axes is mandatory 4 11 6 Keyword BOX With this keyword the box around a molecule for plotting 4 11 2 critical point search 4 11 3 and iso and geosurface generation 4 11 4 and 4 11 5 is defined Options STANDARD SMALL LARGE STANDARD A box enclosing all defined atoms with an extension of two times there covalent radii This is the default SMALL A box enclosing all defined atoms with an extension of 1 2 times there covalent radii LARGE A box enclosing all defined atoms with an extension of four times there covalent radii This is the default for the critical point search MEDIUM COARSE FINE MEDIUM The mesh spacing of the
21. cycle The following example activates the printing of the density matrix in the first 10 SCF cycles PRINT MAX 10 P Printing of molecular orbitals can be limited with the MOS option The input MOS lt First gt lt Last gt specifies that only the MOs in the range from lt First gt to lt Last gt are printed Here lt First gt and lt Last gt refer to the integer numbers of the molecular orbitals With the MOE option the printing of the molecular orbital coefficients can be suppressed In order to print the orbital energies and occupation numbers of the orbitals 10 to 25 the following input can be used PRINT MOS 10 25 MOE Without MOE the MO coefficients would be printed too With the DEBUG option a complete printing of all matrices is activated Of course such a output is huge and should only be used for debugging The CAVITY option produces a deMon cav output that can be used as MOLDEN input to visualize the cavity surface Figure 1 For large systems the FULL option produces a very large deMon pcm output 4 12 4 Keyword EMBED This keyword specifies the embedding into point charges Options FILE The embedding point coordinates and charges are deMon cub file This is the default FILE READ READ The embedding point coordinates and charges are input file Description The coordinates and charges are given in free format as real numbers either in the em bedding file deMon cub see Table 3 or in the keyword body of EMBED
22. decomposition is used This is the default OFF ON ON Cholesky decomposition is used SVDTOL Tolerance for singular value decomposition Default is 10 SVDTO2 Description The Cholesky decomposition of the auxiliary function Coulomb matrix is considerably faster than the singular value decomposition SVD However it may introduce numerical instabilities for large auxiliary functions sets This may result in convergence failures of the SCF procedure The Cholesky and singular value decomposition results are identical if the SVD nullspace is empty By default the SVD procedure will eliminate eigenvalues of the auxiliary Coulomb matrix smaller than 10 This cut off is appropriate in the vast majority of cases However if necessary it can be modified with the SVDTOL parameter 4 12 Miscellaneous Keywords 109 Specifying SVDTO2 will activate gradual quenching of the eigenvalues see svdmat f 4 12 6 Keyword MATDIA This keyword chooses matrix diagonalization technique Options RS EISPACK Househol DSYEV LAPACK block Hot D amp C This is another nam DSYEVD LAPACK divide anc RS DSYEV D amp C DSYEVD DSYEVR JACOBI DSYEVR LAPACK Relatively JACOBI Jacobi diagonalizati SMALL Diagonalizer to use LARGE Diagonalizer to use THRESHOLD Maximum side dime Description The fastest diagonalizer available in deMon in the divide and conquer diagonalization from LAPACK 109 However it might fail in special situations Fa
23. describing the occupation of each real spherical harmonic orbital type is requested The occupation numbers can be given as real or integer values To access the excited triplet state of carbon 1s 2s 2p 3s the following keyword body of CONFIGURATION using the option OCCUPY is needed 0 0 k k HG k M GO oom ROBE 1 Here the 3 in the first configuration line indicates that the three lowest s type a orbitals have to be occupied according to the occupation scheme given in the third line 1 0 1 44 4 Keywords Based on this scheme the lowest o s orbital is occupied with 1 electron the next is empty and the following one is again occupied with 1 electron Therefore a hole in the a s orbital occupation is produced The next two occupation lines assign 1 electron to the p and to the p a orbital The two lowest 3 s orbitals are occupied with 1 electron each by the last occupation line Please also note that zero 0 entries in the configuration line s do not have corresponding occupation lines Example 5 13 describes the calculation of the excited 1s 2s 2p 3s carbon triplet state As already mentioned the OCCUPY option may also be used to generate fractional occupation e g for the calculation of spherical atoms In the case of the triplet carbon ground state the following CONFIGURATION keyword body produces a spherical atom 11 0 0 e NN FOR 0 6666 0 6666 0 6666 11 The first configuration line describes
24. file deMon inp Description With the option BINARY coordinates and connectivities are read from the file LAT bin Usually this file has been produced by a previous run calculating isosurfaces or geometrical surfaces see Sections 4 11 4 and 4 11 5 In this way molecular fields can plotted on isosurfaces Example 5 17 describes the plotting of the electrostatic potential on the isodensity surface of benzene The LAT bin file and the corresponding plot output can be visualized with VU see 8 With the ASCII option plot point coordinates and optional connectivities can be read from the external ascii file LAT asc The file format is 1814 312196E 00 729474E 00 105260E 01 243158E 00 765796E 00 105260E 01 243158E 00 729474E 00 917119E 00 1 2 3 4 5 6 6 7 8 The first integer number here 1814 denotes the number of points For each point one line with its coordinates x y and z is then given The integer triples after the coordinate specification are the connectivities This part of the input is optional The LAT asc file can be easily generated from the deMon lat file see 4 11 4 and can directly be used for the visualization with VU 104 4 Keywords With the POLYGON option starting points for the critical point search are automat ically generated In the case of the electronic density this algorithm usually generates a sufficient set of starting points to find all critical points This is not the case for the crit
25. in deMon Description Molecular orbitals By default the five highest occupied and lowest unoccupied orbitals are calculated Molecular orbitals and first derivatives By default the HOMO and LUMO are calculated Electron density By default the density of the occupied orbitals is calculated Electron density and first electronic derivatives By default the density and its derivatives of the occupied molecular orbitals are calculated Electron density first and second electronic derivatives By default the density and its derivatives of the occupied orbitals are calculated Spin density By default the spin density of the occupied molecular orbitals is calculated Spin density and first electronic derivatives By default the spin density and its derivatives of the occupied molecular orbitals are calculated Electron density Laplacian By default the Laplacian of the occupied molecular orbitals is calculated Molecular electrostatic potential By default the MEP of the occupied molecular orbitals is calculated A minus sign in front indicates that only the electronic part is calculated Molecular electrostatic potential and its first derivatives By default the MEP and its derivatives of the occupied orbitals are calculated Molecular electrostatic potential and its first and second derivatives By default the MEP and its derivatives of the occupied orbitals are calculated Molecular electric field By default the electric field of the o
26. look at the directory examples in the deMon tree you have obtained It contains sample inputs for the most common applications see Chapter 5 for the description of the examples In Chapter 10 you will find a quick reference guide of the input keywords Common problems and their solutions are described in Chapter 11 Troubleshooting If you prefer to learn more about the deMon input syntax before you use it read on Almost everything used in the sample inputs is explained in the next two chapters 1 3 How to Read this Manual While the example inputs cover the most common standard applications of an quantum chemistry program like deMon there is much more to learn about input possibilities Eventually you will want to control specific parts of a calculation or you will need more output information You will then have to look in this manual for the necessary infor mation You can read the information containing section without the preceding ones However all later chapters assume that you have read Chapters 2 and 3 For example suppose you want to print molecular orbitals MOs Looking up the table of contents will lead you to Section 4 12 3 which describes the PRINT Keyword The concept of keywords and options as well as their notation in this guide is described in Chapter 3 It will take you just a moment to construct the input line for printing molecular orbitals if you have already read chapter 3 it could be quite frustrating if you ha
27. momentum quantum number like Pr Py Pz Or daz dey dez dyy dyz and dzz The contracted orbitals u r are linear combination of atom centered normalized Gaussian type orbitals LCGTO Ansatz which are called the primitive orbitals g r u r 2 dy gi Y 4 1 gel z A y Ay z A e HEAP 4 2 The exponents C and contraction coefficients dp are listed in free format under the shell definition line one line for each primitive orbital EXPONENT and COEFFICIENT A user defined basis set input is shown in Example 5 6 4 2 2 Keyword AUXIS This keyword specifies the auxiliary function set Options lt Auxis gt The auxiliary function set string lt Auxis gt defines the global auxiliary function set If absent the A2 auxiliary function set is used by default Description Similar to the basis sets the auxiliary function sets can also be assigned to individual atoms according to the the atomic symbol or to atom groups based on the element symbol in the keyword block of AUXIS The syntax and hierarchy of these assignments are similar to the basis set assignments see 4 2 1 For C3H4 see input 4 1 1 the following auxiliary function definition 4 2 Basis Set Input Basis Set DZV DZVP DZVP2 TZVP TZVP FIP1 TZVP FIP2 SADLEJ FIP EPR III IGLO II IGLO III STO 3G SAD LIC WACHTERS DZ ANO Ahlrichs ECP SD EECP SD QECP SD 37 Table 6 Basis sets available in the deMon BASIS file El
28. periodic boundary conditions to be active see section 4 11 6 Be cause periodic boundary conditions are currently implemented only for MM and QM MM runs see section 4 5 1 constant pressure dynamics necessarily implies either MM or QM MM With MDPRESSURE on deMon will adjust the size of the periodic box to maintain the de sired pressure The periodic box parameters are controlled as described for the Berendsen thermostat see eq 13 in section 4 8 5 The corresponding time constant is defined by the TAU parameter Practical implementation of the Berendsen pressure bath also requires an estmation of the compressibility of the system which is specified with the COMP key word This value need not to be exact as it enters only the calculation of the coordinare scaling factor for coordinates Compressibilities of some representative systems are 4 8 MD Control 77 System Compressibility MPa gases at 0 1 Mpa amp 10 water 500 x 1076 solids 1 20 x 1078 Warning Constand pressure molecular dynamics only makes sense if the system is suf ficiently large thousands of particles and or time scales are reasonably long tens of picoseconds 4 8 9 Keyword HEATPIPE Activates calculation of heat conductivity using non equilibrium heatpipe molecular dy namics Options LENGTH MASKS GUESS FLUX AXIS BASE AREA If periodic boundary conditions are not used sets the length o
29. rather complex which matches the complex nature of the numerical experiment The essential parameter of the simulation is the direction of the heat transfer which is established by the AXIS keyword In a non periodic simulation any direction of the heat transfer is allowed although not every direction is sensible If periodic boundary conditions are used there exist only three heat transfer directions which do not break the periodicity of the system Namely directions which are perpen dicular to one of the sides of the simulation box AB AC or BC are allowed If you are interested in heat conductivity along a different crystallographic direction you will have to choose an appropriate supercell In the periodic case the unit cell and the direction of heat transfer also establish the length of the heat transfer axis and the crossection for the heat flow In the non periodic case these parameters have to be specified using LENGTH and AREA keywords Once the direction of heat transfer is chosen deMon will set up a set of overlapping temperature probes called zones The zones are infinite slabs in space oriented perpen dicular to the heat transfer direction The number of zones is specified using the MASKS 4 8 MD Control 79 keyword Each zone is associated with a masking function Fig 4 Masking functions are unit at the zone centre and decrease to zero at the zone edges Two of the zones also serve as heat source and s
30. requires additional input which must follow it in the input with no intervening comments or blank lines For the CUBIC box just one parameter is required the extent of the box edge in the same units as in the coordinate section For the RECTANGULAR box the extents along the X Y and Z spatial directions must be specified In either case the lattice vectors are taken to be parallel to the coordinate axes a X HIV and c Z For a GENERAL unit cell the Cartesian coordinates of the a b and c lattice vectors must be specified with one vector per line 64 4 Keywords If MINIMAL keyword is specified for each pair of atoms inside the unit cell only interactions with the closest image of the pair will be considered This is equivalent to the cyclic cluster periodic model Calculations using minimal image convention can be considerably faster than full periodic boundary conditions at the expense of the more approximate treatment of long range interactions Note that in a molecular dynamics run the unit cell parameters may be affected by the pressure bath see keyword MDPRESSURE in section 4 8 8 4 6 DFTB Control 65 4 6 DF TB Control 4 6 1 Keyword DFTB NOTE The usage of DFTB requires a little understanding of the method The predicitiv ity of this method is somewhat between MM and DFT therefore you should always know what you are doing At the moment both variants non self consistent DF TB 118 some times referred to as NSCC
31. that your calculation converged to the ground electronic state Conversely in approximate density functional theory it is also possible although extremely rate to have a non aufbau ground state Caveat user 4 4 7 Keyword DIIS This keyword activates the DIIS procedure Options ON OFF ON The DIIS procedure is switched on This is the default OFF The DIIS procedure is switched off TOL lt Real gt The DIIS procedure is switched on after the SCF energy error is smaller than lt Real gt CMAX lt Real gt Largest allowed expansion coefficient Default is 100 0 DMIN lt Real gt Smallest allowed determinant Default is 10714 Description By default the DIIS direct inversion in the iterative subspace procedure 47 is switched on if the energy error is less than 0 1 a u in a SCF step For most systems this result in a considerable speed up of the SCF convergence However for some systems this threshold is too large and a SCF convergence failure will occur In these cases the start of the DIIS procedure should be manipulated with the TOL option If the HOMO LUMO gap of a system is very small DIIS can be counter productive for the SCF convergence In these cases the DIIS procedure can be switched off with the OFF option It should be noted that in deMon different DIIS algorithms are used for the AUXIS and BASIS option of the VXCTYPE keyword see 4 4 9 Both are based on the energy gradient with respect to the charge density fitti
32. the suggested USED value and recompile the program Repeat this procedure until all PARAMETER EXCEEDED statements have disappeared It is recommended not to increase the MAXRAM value over the physical memory RAM available because otherwise it may result in large paging overheads during program execution This configuration is optimised for DFTB and MM calculations For large scale DFT calculations we encourage the interested user to obtain a recent version of deMon2K at http www demon software com The disk requirements are dominated by the size of the electron repulsion integral scratch file ioeri scr in the case of a conventional SCF calculation and by the files ioscf scr iocdf scr and iogrd scr in the case of direct SCF calculations see 4 4 1 3 2 Files All files in deMon are opened with explicit filenames rather than using operating system specific compiler defaults Throughout this guide the name used in the Fortran OPEN statement is referred to as the logical filename These logical filenames are read by the program or created in the working directory The logical files are connected to Fortran 1 0 units in the file fileio h Table 3 contains the logical and physical filenames used in the program Besides these files special plot files may be created for the visualization of molecular fields like the electronic density electrostatic potential etc with VU see Chapter 8 These files are named according to the molecular fie
33. used This implies a second SCF cycle for the initial energy calculation If the option GUESS is specified the adaptive grid is build using the start density for the calculation of the grid generating exchange correlation potential Molecular dynamics simulations where a good guess density is tipically available on each step typically run faster with GUESS grids due to smaller computational overhead due to grid generation 58 4 Keywords Fixed grids available in deMon can be selected by the option FIXED in combination with the options COARSE MEDIUM and FINE with MEDIUM being the default Options COARSE and MEDIUM select 50 194 p and 75 302 p pruned grids respectively In this notation the first value refer to the radial shells The second value is the size of the largest Lebdev grid 68 on each of these shells The p stands for pruned 67 indicating that smaller Lebedev grids have been used for some radial shells The FIXED FINE option requests the unpruned 200 1202 reference grid Due to its size its application is impractical for all but smallest systems 4 5 Molecular mechanics and QM MM Control 59 4 5 Molecular mechanics and QM MM Control 4 5 1 Keyword QMMM This keyword activates molecular mechanics or hybrid QM MM calculation Options QM MM QM MM QM MM QM MM COUPLING RUNTYPE QMPBC Description Treat the whole system using quantum mechanics parse but ignore all MM and QM MM related i
34. 00K 2000 in plane 6 across planes Note that the heatpipe approach implemented in deMon calculates only the lattice contribution to heat conductivity Once the the heatpipe simulation reached the steady state which may require 104 105 time steps heat conductivity A can be calculated by fitting the phenomenological heat 80 4 Keywords transfer equation dE S s AAT 4 15 to the observed temperature profile The resulting heat conductivity may be influenced by the errors in temperature measurement These errors decrease with increasing number of particles per slab and for longer simulation times Larger values of heat flux will also reduce the impact of the uncertainties in temperature measurements but see below Another potential source of errors is the finite width of the zones which introduces the uncertaintly in the length of heat transport This error decreases with increasing number of zones It is suggested that zones should contain at least 20 100 particles each using at least 6 8 zones Yet another potential source of errors is fractionation of the system and non linear heat conductivity effects induced by excessive heat flux To guard against this possibility one should perform several heat conductivity runs with thermal fluxes varying over 1 2 orders of magnitude Meaningful calculation of heat conductivities requires that the overall position and ori entation of the system remain constant over the simulation t
35. 112 5 Examples 5 Examples THIS SECTION NEEDS TO BE WRITTEN VOLUNTEERS 5 1 5 2 9 3 5 4 5 5 5 6 5 7 5 8 5 9 5 10 5 11 5 12 5 13 5 14 5 15 5 16 5 17 Example ps18 Examples amk5 amk6 amk7 and amk8 Examples amk29 amk30 and amk31 Example ps86 Example th6 Example amk17 Example ps84 Example amk19 Example amk20 Example ps15 Example ps6 Example amk24 Example amk26 Example amk33 Example amk35 Example ps88 Example ps90 6 Using QM MM in deMon 113 6 Using QM MM in deMon TO BE WRITTEN 114 7 Using MD in deMon 7 Using MD in deMon TO BE WRITTEN amp Vu 115 8 Vu This chapter contains an introduction to the basic operating instructions of the Vu graph ical interface which is part of the visualization program Vu It constitutes a subset of all the available options in the graphical interface of Vu This chapter shows only the most important features required to start using Vu Prior to its use it is highly recommended to read Chapter 4 11 of this guide For a complete description of the structure and operation of Vu please consult e The User Manual of the Configurable Scientific Visualization Program Vu Which contains full description of architecture capabilities and limitations of Vu e Description of the file format Describes the structure of pie files which are written by deMon and read by the Vu graphical interface e Frequently Asked Questions on the Ut
36. 2 9 Keyword ECPINTEGRATION This keyword chooses numerical integration scheme used in calculation of the effective core potentials Options COARSE MEDIUM FINE COARSE Use 67 radial shells 50 194 p fixed grid Nominal accuracy 10 MEDIUM Use 99 radial shells 75 302 p fixed grid Nominal accuracy 1078 FINE Use 131 radial shells 200 1202 fixed grid Nominal accuracy 1071 Description TO BE WRITTEN 4 12 10 Keyword GENAO Generate atomic orbitals This is an experimental keyword Do not use Options CUTOFF Cutoff energy in Hartree The default is 0 0 AO indices of atoms in a following list of integers whose basis will be transformed to AO s NOT indices of atoms in a following list of integers whose basis be ex cluded from the AO transformation Description 4 12 Miscellaneous Keywords 111 Default GENAO is switched off If GENAO is switched on the default is that all atoms are transformed CUTOFF 0 0 by default If GENAO is specified the GTO basis will be transformed to an atomic basis For the forthcoming SCF computation not all AO s need to be considered and hence the matrix size may be reduced The number of AO s which will be considered in the SCF depends on the cutoff energy Orbitals with higher atomic energy will be left out If the cutoff energy is higher than the highest atomic energy this is a unitary transformation and gives exactly the same result as the original GTO computation
37. 5 0 000 Mg7 2 105 2 105 0 000 Mg8 2 105 2 105 0 000 Mg9 2 105 2 105 0 000 010 0 000 0 000 2 105 Mgii 0 000 2 105 2 105 Mgi2 2 105 0 000 2 105 Mgi3 0 000 2 105 2 105 Mgi4 2 105 0 000 2 105 015 2 105 2 105 2 105 016 2 105 2 105 2 105 017 2 105 2 105 2 105 018 2 105 2 105 2 105 C19 Mgi RAD 02 AAD 03 DAD X20 019 1 0 Mgi 90 0 02 180 0 021 C19 RCO X20 90 0 Mgi 180 0 CONSTANTS Mg XYZ 02 XYZ 03 XYZ 04 XYZ 05 XYZ 010 XYZ 015 XYZ 016 XYZ 017 XYZ 018 XYZ VARIABLES 4 1 Geometry Input 29 RAD 2 0 AAD 90 0 DAD 90 0 RCO 1 4 In the example above geometry of the MgO cluster is fixed by freezing its Cartesian coordinates see 4 1 2 The carbon atom of the CO molecule is defined with respect to the Mg1 02 and 03 plane of the Cluster see Figure 3 by the internal coordinates RAD AAD and DAD These coordinates optimized because they are declared as variables see 4 1 3 The same holds for the CO bond length that is defined by the internal coordinate RCO The dummy atom X20 has to be used in order to avoid an ill defined dihedral angle if the 021 C Mg1 arrangement becomes linear Therefore the above example describes an input for the free optimization of an CO molecule including internal relaxation on a frozen MgO cluster surface Figure 3 Coordinate definition of the above MIXED input 30 For a hybrid QM MM calculation additional parameters can be added at the end of each geometry
38. 6 34 7406 E 1986 A D Becke Phys Rev A 38 3098 1988 N C Handy A J Cohen Mol Phys 99 403 2001 136 References 53 J P Perdew J A Chevary S H Vosko K A Jackson M R Pederson D J Singh 54 95 56 97 58 59 60 61 62 63 64 65 66 67 68 69 70 71 12 73 C Fiolhais Phys Rev B 46 6671 1992 J P Perdew K Burke M Ernzerhof Phys Rev Lett 77 3865 1996 Y Zhang W Yang Phys Rev Lett 80 890 1999 B Hammer L B Hansen J K Norskov Phys Rev B 59 7413 1999 S H Vosko L Wilk M Nusair Can J Phys 58 1200 1980 J P Perdew A Zunger Phys Rev B 23 5048 1981 J P Perdew Y Wang Phys Rev B 45 13244 1992 J P Perdew Phys Rev B 33 8822 1986 B Zimmermann Ph D Thesis Universit t Hannover 1999 C Lee W Yang R G Parr Phys Rev B 37 785 1988 R Colle D Salvetti Theor Chim Acta 37 329 1975 R Colle D Salvetti J Chem Phys 79 1404 1983 M Krack A M K ster J Chem Phys 108 3226 1998 A M Koster R Flores Moreno J U Reveles in preparation P M W Gill B G Johnson J A Pople Chem Phys Lett 209 506 1993 V I Lebedev Russian Acad Sci Dokl Math 50 283 1995 A K Rappe C J Casewit K S Colwell W A Goddard III W M Skiff J Am Chem Soc 114 10024 1992 A K Rappe W A Goddard III J Phys Chem 95 3358 1991 M
39. 72 Contents ili 4 9 4 10 4 11 4 12 4 8 4 Keyword TIMESTEP o sns 72 4 8 5 Keyword MDBATR os saas is WS ew ctm des 73 4 8 6 Keyword CONSERVE 4e EN a erbe veg A 74 4 8 7 Keyword MDCONSTRAINTS 2 222 2 0 0 75 4 8 8 Keyword MDPRESSURE care ad udo ge ELE 76 4 8 9 Keyword HEATPIPE ra 3 25 2 20 2 he he a IDEE Ue 77 4 8 10 Keyword CARPAR 2060000 wor aa e ew AT bide d 80 Property Control aa dera ae er A E eta tnr nez 82 4 9 1 Keyword POPULATION 22 XC SS 82 4 9 2 Keyword DIPOLE x 2 2 2 te to oe ele ee ran IO e 82 4 93 Keyword MAGOUP gert x Ed eR ed ad er de he 82 4 9 4 Keyword POLARIZABILITY 83 4 9 5 Keyword FREQUENCY wa er ee he 84 49 6 Keyword THERMO sa ke o a Gas ue nn 85 ADT Keyword EN MO nu Aaa Le AI RD MER hee RES 85 4 9 8 Keyword HARDNESS 2 eb au la ew hme die EP S 85 Solvent RSC dodo Xem A See oe ee he Eee ir se eng 87 4 10 1 Keyword et MEN 3u eee ra ara 87 4 10 2 Keyword PCM CARD 91 Visualization and Topology Le Zane zand ere eem e e s 93 4 11 1 Keyword VISUALIZATION 93 ML Keyword PLOT L2 n5 beken A m ELE Ee e 94 4 11 3 Keyword CPSEARCH 2a u died man near iP BE Eee cs 96 4 11 4 Keyword ISOSUREMOB 200 R1 Er 8 athe aa 3 97 4 11 5 Keyword GEOSURPAGE oo RO ER ea 100 4 116 Keyword BOX ra ec Sod E we Eie i i 101 AIEE Keyword POINTS 22 2 ae et e Eee ts 103 Miscellaneous Keywords nn 105 4 12 1 Keywo
40. 8 Representation of the benzene cavity surface 22 222 2m 91 1 Getting Acquainted 1 1 Getting Acquainted 1 1 The Game of the Name deMon is a system of programs for density functional theory DFT calculations of atoms molecules and solids 1 3 Its first widely available version 4 appeared in 1992 Shortly after its appearance the original deMon code was substantially modified for commercial ization by BIOSYM Technologies The beta release of this version appeared 1993 It was the basis of the deMon KS1 5 series of programs developed in Montreal until 1997 Meanwhile the original deMon version was further developed in Montpellier and Stock holm These developments were first independent from each other In 1997 they merged to the deMon KS3 6 series of programs Independently from the deMon development the ALLCHEM project started 7 in Han nover in 1995 The aim of this project was to write a well structured DFT code from scratch The first ALLCHEM version appeared in 1997 The structured programming of ALLCHEM proved very useful for the development and testing of new DFT approaches and algorithms In March 2000 the first deMon developers meeting was hold in Ottawa At this meeting the deMon and ALLCHEM developers agreed to merge their codes in order to keep a Tower of Babel from rising As a result the new code couples the deMon functionality with the stable and efficient integral and self consistent field SCF part from ALLCHEM
41. A NOSPLA SCC The self consistent charge variant of DFTB The default is non SCC DISP London dispersion energy and gradients are included By default this option is switched off DIAG User specified diagonalisation routine for the generalised Eigen value systems The method is specified after the Legal options are DSYGVD DSYGV DSYGVR SOM The default is DSYGVD DSYGV DSYGVD and DSYGVR are standard LAPACK subroutines for documen tation see http www netlib org SOM uses the built in mecha nism to orthogonalise the secular equations and makes use of the global variable MATDIA 4 6 DFTB Control BS SIMPLE MIX MAX TOL L DEP FERMI FERMI ETOL SPLA NOSPLA 67 All Eigen values and vectors are computed This option is useful when using the subspace diagonaliser and per default it is switched off The option makes only sense for DSYGVR Simple mixing instead of Broyden convergence acceleration is per formed for SCC This is per default switched off Mixing value for simple and Broyden mixing The default is 0 2 This value is independent from the DFT mixing value Maximum number of SCC cycles The default is 100 The SCC convergence criterion in electron charges The default is 1 0E 8 Angular momentum resolved SCC Here the self consistent charge procedure is applied to Mulliken shell charges rather than to Mul liken atomic charges Otherwise the formalism remains as in stan dard SC
42. C DFTB This option might be important when treating transition metals where d and s p shells have significantly differ ent hardness parameters By default this option is deactivated The electron occupation follows a Fermi distribution as described in Ref 123 The Fermi temperature is 5 K so in practise de generate orbitals are occupied fractionally Note that no spin polarised calculation is carried out The FERMI keyword overwrites the MULTIPLICITY of the system As FERMI but with used specified Fermi temperature in K follow ing the keyword Requested energy tolerance for iterative solvers of the total energy so far only used for CPBO see CARPAR section Use Sparse Linear Algebra for overlap and Hamiltonian matrix as well as for density and energy weighted density matrices This op tion is faster for large problems and requires only a small amount of memory By default the program selects this mode if the overlap matrix has less than 5 occupation Contrary to SPLA this mode uses full matrices and allows the usage of BLAS throughout the program Requires significantly more memory than SPLA Might be a good option for computers with very high BLAS efficiency 68 4 Keywords Some remarks on the diagonalisation The default diagonaliser is a self written DSYGVR This is LAPACK s DSYGV routine which is solving the generalised Eigen value system of a symmetric positively defined problem using Cholesky decomposition and a s
43. Can J Phys 70 560 1992 134 References 14 A M K ster Habilitation Thesis Universit t Hannover 1998 15 J Guan P Duffy J T Carter D P Chong K C Casida M E Casida M Wrinn 16 17 18 19 20 21 22 23 24 25 26 24 28 J Chem Phys 98 4753 1993 D P Chong private communication N Rega M Cossi V Barone J Chem Phys 105 11060 1996 S Huzinaga J Chem Phys 42 1293 1965 W J Hehre R F Stewart J A Pople J Chem Phys 51 2657 1969 W J Hehre R Ditchfield R F Stewart J A Pople J Chem Phys 52 2769 1970 A J Sadlej Collection Czech Chem Commun 53 1995 1988 G C Lie E Clementi J Chem Phys 60 1275 1974 A J H Wachters J Chem Phys 52 1033 1970 P O Widmark B J Persson B O Roos Theor Chim Acta 79 419 1991 R Pou Am rigo M Merch n I Nebot Gil P O Widmark B O Roos Theor Chim Acta 92 149 1995 J Andzelm E Radzio D R Salahub J Comput Chem 6 520 1985 J Andzelm N Russo D R Salahub J Chem Phys 87 6562 1987 http www theochem uni stuttgart de H B Schlegel M J Frisch Int J Quantum Chem 54 83 1995 H J Glaeske J Reinhold P Volkmer Quantenchemie Band 5 Eds W Hab erditzl M Scholz L Z licke Dr Alfred H htig Verlag Heidelberg 1987 29 C Daul Int J Quantum Chem 52 867 1994 30 P J Hay J Chem Phys
44. DFTB and self consistent charge DFTB SCC DFTB 119 are used For systems where London dispersion forces are relevant a UFF based 69 dis persion correction can be used 120 Recently a Car Parrinello version has been devel oped and can be used 121 Note that this method is still in an early stage and use it with particular caution An Open Access review of DFTB has been published recently 122 The default method for electron structure calculations is DFT The DFTB keyword activates the alternative the Density Functional Tight binding DFTB method This method runs similarly as molecular mechanics principally independent from the SCF core of the deMon code In future a hybrid run DFT DFTB is planned but not realised yet In the present installation the DFTB keyword disables all DFT features and a DFTB computation is performed DFTB is running as single point with optimisation and molec ular dynamics QM MM is available with DF TB UFF You can run it for finite molecules as well as for periodic boundary conditions Various features of DFTB are still missing the most important list is e Frequency analysis e LSDA extension e TD DFTB For the moment the following features are working and tested e standard DFTB and self consistent charge SCC DFTB in molecular and periodic representation e London dispersion correction for DFTB and SCC DFTB e geometry optimisation for molecules e geometry optimisation for solids with fixed un
45. IATOM Number of the first orbital of shell ISHL Number of the last orbital of shell ISHL 132 D Global Counters Limits and Pointers Table 14 Pointers Pointer Description AUXPTR IAUX I Auxiliary function pointer I 1 Origin of auxiliary function LAUX number of atom I 2 Auxiliary function shell I 3 AX of auxiliary function AUX I 4 AY of auxiliary function IAUX I 5 AZ of auxiliary function AUX AUXSETPTR IAUXSET I Auxiliary function set pointer I 1 Origin of auxiliary function set IAUXSET number of atom I 2 Maximum angular quantum number L in the set IAUXSET AUXSHLPTR IAUXSHL I Auxiliary function shell pointer I 1 Origin of auxiliary function shell IAUXSHL number of atom I 2 Auxiliary function set of auxiliary function shell IAUXSHL I 3 Angular quantum number L of auxiliary function shell IAUXSHL SHLPTR ISHL I Shell pointer I 1 Origin of shell ISHL number of atom I 2 Main quantum number N of shell ISHL I 3 Angular quantum number L of shell ISHL I 4 Contraction of shell ISHL STOPTR ISTO I Orbital pointer STO pointer I 1 Origin of orbital number of atom I 2 Shell of orbital ISTO I9 AX of orbital ISTO I 4 AY of orbital ISTO I 5 AZ of orbital ISTO References 133 References H 2 3 10 11 12 13 P Hohenberg W Kohn Phys Rev 136 B864 1964 W Kohn L J Sham Phys Rev 140 A1133 1965
46. IPOLE method becomes more favorable with increasing size of the alkenes This is due to the reduced scaling N57 of this method even for such small systems as the alkenes in Table 7 The TOL option controls screening of the ERIs The screening threshold 7 is calculated as TOL 7 Number of Electrons ven ERIs with an orbital overlap smaller than 7 are not calculated screened The thresh old r also enters into the asymptotic expansion radii for the MULTIPOLE method The density screening threshold for the numerical integration of the exchange correlation potential is given by 7 too The default settings for TOL are 10714 and 10 for the CONVENTIONAL and DIRECT MULTIPOLE method respectively Please note that the screening of the ERIs can deteriorate the SCF convergence particularly for systems with extensive electron delocalization 4 4 4 Keyword GUESS This keyword specifies the SCF start density Options TB CORE FERMI RESTART TB A tight binding SCF start density is calculated This is the default FTB Use Free tight binding guess This is a synonym for TB HTB Use Harmonic tight binding guess CORE The SCF start density is obtained from the diagonalization of the core Hamiltonian FERMI The start density is obtained by quenching a fractional occupied SCF solution to integer occupation numbers 4 4 SCF Control 51 RESTART The start density is read from the restart file deMon rst ONLY The program st
47. In the directory deMon makefiles sys choose a platform definition file which is already compatible with your system If you do not remember which plat forms are compatible you can execute command make makesys in the directory deMon makefiles 2 5 What to do when things go wrong 13 Hint If you would like the platform file to apply to a single computer the appropriate test in the checkplatform rule is hostname whatever the name is Don t forget to start this line with a tab or make will refuse to accept your configuration file Hint You can choose the location to search for the optimized libraries by setting the LIBPATH environment variable either in your shell initialization file or in the platform configuration file itself 2 5 What to do when things go wrong First of all DON T PANIC Installation of any complex software package is rarely entirely problem free and deMon consists of more than 1 200 source files and almost 200 000 lines of code There several ways of getting assistance However there are a few things you can do yourself before asking for help First of all please make sure that you are using the most up to date version of deMon the problem you see may have already been resolved Please also check that your Fortran compiler and numerical libraries are up to date If this does not resolve your problem here are a few more things you may want to try deMon build scripts rely on ha
48. Keywords MECHANICAL Use simple mechanical embedding The total energy of the system in this case is given by Eto Em QM MM Euu QM Eo QM Apart from bond termination the molecular mechanics subsystem does not directly influence the electronic structure of the QM part ELECTROSTATIC Also include cross system electrostatic polarization terms This op tion is not yet implemented Regardless of the coupling scheme used bond termination at the partition boundary is handled using capping effective potential approach using either pseudo halogen 10 or pseudo hydrogen 11 pseudopotentials The dynamical relationship between the QM and MM partitions can be controlled with the RUNTYPE keyword The recognized options are SYNCHRONOUS Time steps are identical across the partitions This is the default RELAX_MM The MM partition is completely relaxed for every time step in the QM partition This option is not yet implemented FREE_ENERGY Time runs faster in the MM partition the QM partition moves on the free energy surface of the MM partition This option is not yet implemented If your application requires a currently unimplemented coupling scheme or RUNTYPE you are encouraged to contact Serguei Patchkovskii nrc ca Note Currently the RESTART option is not supported for calculations where a change in the system Hamiltonian occurs Molecular dynamics simulations can be restarted see 4 8 1 from a simulation using d
49. MP has no effect unless one of the thermostat options is activated see MDBATH section 4 8 5 4 8 4 Keyword TIMESTEP This keyword specifies the time step of the molecular dynamic MD simulation Options lt Real gt MD time step in femtoseconds fs The default is 1 Description The default MD time step is determined by the most light weighted atom and the sim ulation temperature and rounded down to 1 4 fs units The determination is done using the following formula dt 0 25 4 Mmin My 1 300K MAX To 5K This assumes a time step of 0 25 fs for a system containing protons at 300K In systems where hard wall like parts of the potential energy surfaces are probed e g gases at high pressures time steps smaller than the default may be required to maintain total energy constant An excessively large time step will manifest itself in poor energy conservation during an MD simulation 4 8 MD Control 73 Negative time steps allow reverse time dynamics However note that this option is ex tremely sensitive to numerical errors which include time steps SCF convergence and alike If Car Parrinello molecular dynamics is requested the default time step is 0 05 fs 4 8 5 Keyword MDBATH This keyword specifies the temperature bath used in the molecular dynamic MD sim ulation Options NONE SCALING BERENDSEN LOCAL NONE No temperature bath This is the default SCALING The velocities are scaled in order to control t
50. O Keeffe and N E Brese J Am Chem Soc 113 3226 1991 S L Mayo B D Olafson W A Goddard III J Phys Chem 94 8897 1990 C J Casewit K S Colwell A K Rappe J Am Chem Soc 114 10046 1992 References 137 74 75 76 TT 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 C J Casewit K S Colwell A K Rappe J Am Chem Soc 114 10035 1992 G te Velde E J Baerends Phys Rev B 44 7888 1991 J Baker A Kessi B Delley J Chem Phys 105 192 1996 A Banerjee N Adams J Simons R Shepard J Phys Chem 89 52 1985 J Baker J Comput Chem 7 385 1986 M J D Powell Math Prog 1 26 1971 T H Fisher J Alml f J Phys Chem 96 9768 1992 R Lindh A Bernhardsson G Karlstr m P Malmqvist Chem Phys Lett 241 423 1995 J Nichols H Taylor P Schmidt J Simons J Chem Phys 92 340 1990 R Fletcher Practical Methods of Optimization Second Edition Wiley New York 1987 C G Broyden J Inst Maths Applns 6 76 1970 ibid 6 222 1970 R Fletcher Computer J 13 317 1970 D Goldfarb Maths Comp 24 23 1970 D F Shanno Maths Comp 24 647 1970 H B Schlegel J Comput Chem 3 214 1982 W C Davidon AEC Res amp Dev Report ANL 5990 1959 R Fletcher M J D Powell Computer J 6 163 1963 J M Bofill J Comp Chem 15 1 1994 H J C Berendsen J P M P
51. R M Dreizler E K U Gross Density Functional Theory Springer Verlag Berlin 1990 A St Amant Ph D Thesis Universit de Montr al 1992 M E Casida C Daul A Goursot A M K ster L G M Pettersson E Proynov A St Amant D R Salahub H Duarte N Godbout J Guan C Jamorski M Leboeuf V Malkin O Malkina F Sim A Vela deMon KS Version 3 4 deMon Software Montr al 1996 M E Casida C Daul A Goursot A M K ster L G M Pettersson E Proynov A St Amant D R Salahub H Duarte N Godbout J Guan K Hermann C Jamorski M Leboeuf V Malkin O Malkina M Nyberg L Pedocchi F Sim L Triguero A Vela deMon Software 2001 A M K ster M Krack M Leboeuf B Zimmermann ALLCHEM Universit t Han nover 1998 A M K ster R Flores Moreno G Geudtner A Goursot 16292 T Heine J U Reveles A Vela D R Salahub deMon NRC Canada 2003 R G Parr W Yang Density Functional Theory of Atoms and Molecules Oxford University Press New York 1989 Y Zhang T S Lee W Yang J Chem Phys 110 46 1999 G A DiLabio M M Hurley P A Christiansen J Chem Phys 116 9578 2002 Extensible Computational Chemistry Environment Basis Set Database Version 4 05 02 Molecular Science Computing Facility Environmental and Molecular Sci ences Laboratory Pacific Northwest Laboratory P O Box 999 Richland Washing ton 99352 USA N Godbout D R Salahub J Andzelm E Wimmer
52. RINT keyword Section 4 12 3 Other relevant keywords to alter or enforce SCF convergence are MOEXCHANGE Section 4 3 3 FIXMOS Section 4 3 4 and SMEAR Section 4 12 3 For atomic calculation the CONFIGURATION keyword Section 4 3 6 should be used in order to ensure SCF convergence By default the electron repulsion integrals ERIs are calculated at the beginning of the SCF and kept in main memory RAM For larger systems the ERIs may not fit into the RAM In this case deMon will automatically switch to a direct SCF procedure which may also be activated manually by using option DIRECT of the ERIS keyword see 6 1 Getting Acquainted 4 4 3 It is also possible to store ERIs on disk by using ERIS CONVENTIONAL input keyword However this results in an I O bottleneck which will slow down the calculation on most computer architectures For very large systems the option MULTIPOLE of the ERIS keyword is recommended It activates an asymptotic expansion of the ERIs which results in a considerable time saving It should also be noted that for very large systems the linear algebra steps in deMon may become a bottleneck The keyword PRINT RAM may be useful in resolving such issues The amount of memory required in the matrix diagonalization step which dominates memory requirements for large systems can be adjusted with the keyword MATDIA see 4 12 6 If the calculation has to be restarted the new input file produced in each deMon run may be usef
53. S EXCLUDE Source code files including the f extension but without the path mentioned in this list will not be compiled Instead you are supposed to provide optimized versions of these rou tines see LINKLIB above If you supply an optimized BLAS library such as Atlas or a vendor provided library please list the following source files in FILES EXCLUDE blas1 f blas2 f dgemm f dsyrk f lsame f xerbla f If you link with an op timized LAPACK library such as MKL complib sgimath or LAPACK with Atlas also list these files dpptrf f dpptri f dtptri f dsyev f dsyevd f dsyevr f dgelss f Finally if you link with a vendor optimized EISPACK library also exclude pythag f rs f All these files are located in subdirectories of deMon source math 126 FILES_PLATFORM FILES_LOW FILES_HIGH FILES_SPECIAL ARCMD RANLIBCMD B Format of a platform description file This entry gives the list of platform specific source code files These source code files implement functionality which is impos sible or difficult to provide in a platform independent man ner The corresponding source code files are found in the deMon source platform directory and its subdirectories You need to specify the implementation for the functions DEFLUSH and DETIME see below The complete list of the platform dependent implementations included with deMon is given in Table 11 The list of files with the f or 90 extension but without paths whic
54. TIME Linux HP UX OSF1 SunOS IRIX and many others DETIME platform AIX detime F Use system library function MCLOCK IBM AIX and many others DETIME platform Generic detime f90 F Portable Fortran 90 routine using SYS TEM_CLOCK intrinsic This routine re turns real time rather than the CPU time and should only be used as the last resort DEFLUSH platform Generic qflush POSIX F Use POSIX function PXFFFLUSH IEEE 003 9 1992 ISO IEC 9945 1 1990 DEFLUSH platform Linux deflush F Use one argument FLUSH library routine Linux HP UX OSF1 SunOS many others DEFLUSH platform IRIX deflush F Use two argument FLUSH library routine IRIX DEFLUSH platform AIX deflush F Use FLUSH subroutine IBM AIX C Working with the deMon Test Suite C Working with the deMon Test Suite 129 130 D Global Counters Limits and Pointers D Global Counters Limits and Pointers The following tables list the most important global counter limit and pointer variables in deMon Counters NATOM NAUX NAUXSET NAUXSHL NCN NELEC NGTO NSEC NSES NSHL NSIG NSN NSTO Table 12 Counters Description Number of atoms Number of auxiliary functions Number of auxiliary function sets Number of auxiliary function shells Degree of C axis of highest degree Number of electrons Number of primitive Gaussian functions Number of n fold C axes Number of n fold S axes Number of shells Number reflection planes Degree o
55. TTEN VOLUNTEERS A Automatic Generation of Auxiliary Functions 121 A Automatic Generation of Auxiliary Functions With the auxiliary function definition GEN An and GEN An n 1 2 and 3 automati cally generated auxiliary function sets are selected in deMon The GEN An sets consist of s p and d Hermite Gaussian functions The GEN An sets possess also f and g Hermite Gaussians Because the auxiliary functions are used to fit the electronic density they are grouped in s spd and spdfg sets The exponents are shared within each of these sets 24 25 Therefore the auxiliary function notation 3 2 2 describes 3 s sets with together 3 functions 2 spd sets with together 20 functions and 2 spdfg sets with together 42 func tions see also 4 2 2 The range of exponents of all auxiliary functions is determined by the smallest min and largest max primitive Gaussian exponent of the chosen basis set Therefore the GEN An and GEN An automatically generated auxiliary function sets are different for different basis sets The number of exponents N auxiliary function sets is given by In 6 n Here n is 2 3 or 4 according to the chosen GEN An or GEN An set The exponents are N Int A 1 generated almost as it is explained below even tempered and splitted into s spd and if a GEN An set is requested spdfg sets The tightest largest exponents are assigned to the s sets followed by the spd and if exist spdfg sets The basic
56. The deMon Nano User s Guide Installation Guide and Reference Manual The deMon Nano User s Guide Installation Guide and Reference Manual Version deMon Nano 2009 Experiment September 2009 Reference The deMon User s Guide Version deMon Nano Experiment 2009 Authors T Heine M Rapacioli S Patchkovskii J Frenzel A M Koster P Calaminici H A Duarte S Escalante R Flores Moreno A Goursot J U Reveles D R Salahub A Vela Title Picture A CNT Imogolite multiwalled nanocable The procedures and applications presented in this guide have been included for their instructional value They have been tested with care but are not guaranteed for any particular purpose The authors do not offer any warranties or representations nor do they accept any liabilities with respect to the programs or applications The software described in this guide is furnished under a license and may be used or copied only in accordance with the terms of such license Copyright 2003 2009 by the authors All rights reserved No part of this publication may be reproduced stored in a retrieval system or transmitted in any form or by any means electronic mechanical photocopy ing recording or otherwise without prior written permission of one of the authors Contents Contents 1 Getting Acquainted 1 1 1 2 1 3 1 4 The Game of the Name aa E 48 93 4 23 sh aes How to Avoid Reading this Manual lll How to Read thi
57. The number of basis and auxiliary functions is given by Npasis and Nais The difference of real and CPU time is given in brackets Alkene Npasis Nausis CONVENTIONAL DIRECT MULTIPOLE CuHso 610 1016 1924 345 266 CasHz 910 1520 CysHos 1210 2024 CepHizg 1510 2528 CrH s 1810 3032 Disk I O is performed As Table 7 shows the CONVENTIONAL method is most economic for the two smallest alkenes In these cases in core calculations can be performed and the disk I O is reduced to a minimum The ERI calculation with the DIRECT method takes almost three times more Remarkable is also the relative large overhead of the DIRECT method 434 sec for C3gH74 The reason is the incremental build of the Kohn Sham matrix which involves I O operations reading and writing of the Kohn Sham matrix not present in the in core calculation However the Kohn Sham matrix is only a N2 object and therefore the 50 4 Keywords I O overhead of the DIRECT method becomes less important for large systems In the case of the C4ygHog and larger alkenes the ERIs do not fit any longer in the RAM Now I O ERI operations are necessary with the CONVENTIONAL method This im mediately increases the overhead of the calculations Altogether the real time for the CONVENTIONAL calculation in CygHog 2946 sec is larger than for the DIRECT cal culation 2015 sec A further reduction is obtained with the MULTIPOLE method 1162 sec As can be seen from Table 7 the MULT
58. Z 312196E 00 729474E 00 105260E 01 243158E 00 765796E 00 105260E 01 243158E 00 729474E 00 917119E 00 CONNECTIVITY 1 2 3 4 5 6 6 7 8 The first line is the file header including the field information RHO the isovalue 0 1 a u and the units ANGSTROM used for the coordinates area and volume data The NUMBER OF VERTICES correspond to the number of interpolation points for the iso surface The NUMBER OF FACETS is the number of surface elements of the isosurface The volume here in A and the surface area here in A are then given It should be noted that the volume includes all volume elements with field values under the given threshold Therefore the volume of an 0 1 a u isosurface of a field with positive and negative values includes all volume elements with positive field values less than 0 1 a u and all volume elements with negative field values The next block represents the coordi nates of the interpolation points here in A The last block entitled CONNECTIVITY describes the triangulation of the interpolation points With the option TABLE the same data as with the ASCII option are written into the file deMon out The options LINEAR and LOGARITHMIC specify the interpolation scheme for the construction of the isosurface using the marching tetrahedron algorithm 107 The value of the isosurface is specified with the ISO option A value in vertical delimiters e g 0 1 indicates an absolute isosurface value It
59. Z Matrix defines the origin of the input see Figure 1 No connectivity information should be given for this atom Figure 1 Orientation of the first three atoms defined in the Z Matrix Z lt V The second atom B lies on the z axis of the input coordinate system and is found at the distance RBC from atom C The third atom A lies in the xz plane at a distance RAB from atom B The two atoms A and B form angle TABC with the first atom C All the remaining atoms are defined by input line s in the free format containing the information LABEL NB RAB NC TABC ND PABCD Here LABEL is the atomic label of atom A NB NC and ND are the Z Matrix line numbers or the atomic labels of the atoms B C and D over which atom A is defined by a length RAB angle TABC and dihedral angle PABCD These are the so called internal coordinates of the system There values are given by RAB in ngstr m or Bohr TABC and PABCD in degrees respectively The dihedral angle is defined by the angle between the planes spanned by the atoms A B C and B C D respectively The sign of 26 4 Keywords the dihedral angle is defined according to the Newman projection shown in Figure 2 If the projection angle is oriented clockwise the dihedral angle is taken to be positive Figure 2 Definition of positive top and negative bottom dihedral angles in deMon Structure Newman Projection 9 A o a M Instead of giving
60. a aged BAE due de Els 40 4 3 3 Keyword MOEXCHANGE 2 40 4 3 4 Keyword INOS a 2 2 tad a de Dom IE REX CAE ie a 41 4 3 9 Wey words SMEAR etn oles eR ted A aa 41 4 3 6 Keyword CONFIGURE 4 a2 82 matte dk wee ged 42 SE Control bot rde pen deny PED IN EUR DE SR rer ea ar eo 46 4 4 1 Keyword SGEVYPE 224d ar re Fan 46 4 4 2 Keyword ORBITALS 4 4 o ns 4T 4 4 3 Keyword ERIS oe mu qus 8 2er are E 48 4 4 4 Keyword GUESS 22 028 22 4 Ex ER Ee Bekele ee 50 4 4 5 Keyword MIXING oe 4 22 bP Ee en 2 denk ceu 51 4 4 6 Keyword SHIFT 2 datada ten ae 52 AAC Keyword DLS wate d i aa eona a ei AOL els 53 LAS Keyword BROY DEN acosa geet vee an E Rt derne 54 4 4 9 Keyword VXCTYPE es eeh ee ee 54 4 4 10 Keyword GRID Zu ig ic A A EUR Reg 56 Molecular mechanics and QM MM Control 59 45 0 Keyword QMMM ua A at Sie ee 59 4 5 2 Keyword FORCEFIELD ee 60 15 3 Keyword MMOP TIONS 3 2er Aant an el en Ween E Ce 61 4 5 4 Keyword VDWAALS cone 0 a 84 0 AE 6 e 62 4 5 5 Keyword MADELUNG o o o nn 62 4 5 6 Keyword PERIOIQ sux er RUE e a 63 DETBD1COM OL ei ai ere EE e BER e 65 4 6 1 Keyword DETB o ou u a aha A A 65 Optimization Control Ei Be Be ek ech Ra ERE 69 4 7 1 Keyword OPTIMIZATION rg Go Rk Geta Sees 69 NUE e 4 6 bos Hak la EADE d BBE BEB EE dus dows 70 4 8 1 Keyword MDYNAMICS vera tes benen der Dar a Ce 70 4 8 2 Keyword MDSTEPS emana y de Be aaa 71 4 8 3 Keyword MIUDTEMP ens
61. agnetic field and then writes out information atomic coor dinates basis set grid MO coefficients orbital energies to different files The MASTER program in a second step calculates the magnetic properties The NMR calculation is valid for closed shell and EPR for open shell systems Recall that if a ROKS calculation has been performed there will be no spin polarization possible and the Fermi term will then be zero except if the unpaired electron is in an s type orbital The interface routine prepares 4 output files leMon nmr11 deMon nmr70 deMon nmr71 deMon nmr72 for NMR and 3 output files deMon nmr70 deMon nmr71 deMon nmr72 for EPR The MASTER program has been successfully used for various applications NMR screen ing constants for all magnetic nuclei for closed shell systems and hyperfine structure cal culations for open shells The IGLO bases are recommended to obtain good NMR results 117 The README files available in the MASTER program provide useful information to the users NMR calculations are only possible within DFT It might be possible to recompile the code with much larger values for specifying the maximum number of basis functions and auxiliary basis functions and depending variables For this purpose inspect the file parameter h in the deMon include folder 10 Quick Keyword Reference 119 10 Quick Keyword Reference TO BE WRITTEN VOLUNTEERS 120 11 Troubleshooting 11 Troubleshooting NEED TO BE WRI
62. and LAPACK libraries such as ESSL or SCS which are not supplied with deMon Often such vendor supplied libraries increase computational efficiency by sacrificing numerical accuracy Because The deMon Developers don t have any control over the trade off made by the library s vendor the opt version may either fail altogether or produce wrong answers Additionally the location of the vendor optimized libraries on different computers may vary For this reason you may have to adjust the opt makefile to reflect these location Although we make an effort to test the opt settings this configuration is very sensitive to minor changes in compiler optimizations and vendor s libraries If the opt version fails please try repeating the same calculation with the std version before submitting a bug report The std for standard version does not use any external numerical libraries and employs conservative optimization setting These settings are expected to result in good but not the best possible performance Usually compiling the std version does not require anything beyond the deMon distribution and Fortran compiler to get it running Finally the dbg for debug version allows meaningful symbolic debugging of the exe cutable In order to achieve high performance the compiler will rearrange the execution order of the Fortran statements in the opt and std versions The dbg version requests the compiler to generate machine code which is as clo
63. and molec ular dynamics with an additional friction term 70 4 Keywords 4 8 MD Control 4 8 1 Keyword MDYNAMICS This keyword activates the Born Oppenheimer molecular dynamic BOMD simulation Options ZERO RANDOM RESTART READ RESET RESTART Restart previous molecular dynamics simulation using information of deMon qmd file ZERO Start a trajectory with initial velocities of the nuclei set to zero This is the default RANDOM Start a tajectory using random initial velocities which have no net momentum or angular momentum and give the requested temperature READ Start a new MD trajectory Velocities of the nuclei are given in Cartesian form in the input file immediately following the MDYNAMICS keyword RESET This option resets all averages and the MD step of the trajectory It only makes only sense with the RESTART option otherwise it has no effect Description During an MD restart the following processing occurs Atom types and masses are taken from the input file All other information including coordinates velocities last gradients unit cell parameters and information for computing averages are taken from the MD restart file which has a qmd extension Running averages of the temperature total and potential energy pressure etc are taken from the MD restart file as well All other computational parameters SCF MD QM MM etc are taken from the input file If the molecular dynamics time step or QM MM partit
64. and y coordinates and so on In the following example the oxygen atom is kept frozen and the movements of all hydrogen atoms are restricted to the xz plane y coordinate frozen during the optimization GEOMETRY CARTESIAN ANGSTROM 0 0 00 0 00 0 00 H 0 76 0 00 0 52 H 0 76 0 00 0 52 CONSTANTS O XYZ H Y As usual the comment line is only given for clarity The effective nuclear charge in atomic units which is identical to the number of electrons counted for the atom and the nuclear mass in atomic mass units amu can be specified by an integer and real number after the coordinates respectively Therefore the following input for water consists of a frozen oxygen atom a hydrogen atom H1 fixed in the xz plane with the effective nuclear charge 0 no electrons are counted for this hydrogen and another hydrogen atom H2 with the effective nuclear charge 2 and the nuclear mass 2 014 Deuterium GEOMETRY CARTESIAN ANGSTROM 0 0 00 0 00 0 00 H1 0 76 0 00 0 52 0 H2 0 76 0 00 0 52 2 2 014 CONSTANTS 0 XYZ Hi Y If quantities are not specified the default values are used e g the O atom in the above example has a nuclear charge from 8 and a mass of 15 999 amu If the geometry of the system is given by a Z Matrix using the option ZMATRIX each line in the keyword body of GEOMETRY describes the connectivity of the atom which 4 1 Geometry Input 25 again is defined over its atomic symbol The first atom C of the
65. ar momentum of a diatomic molecule Additionally in many cases we are interested in the time evolution of a system which is at rest with respect to the laboratory frame However constructing an initial guess with zero initial momenta may be cumbersome Therefore the CONSERVE keyword provides a band aid for both problems deMon keeps track of the total energy loss due to these constraints 4 8 7 Keyword MDCONSTRAINTS This keyword imposes atomic constraints during a molecular dynamics simulation Description Atomic positions or separate X Y Z Cartesian coordinates of atoms can be constrained using the following syntax 76 or or or or POSITION atom1 POSITION atoml atom3 POSITION atoml atom3 I atoml atom3 DI atoml atom3 The default is no constraints 4 Keywords XYZ coordinates of atom1 are fixed XYZ coordinates of atoml and atom3 are fixed XYZ coordinates of atoml through atom3 are fixed I ie X or Y or Z coordinate of atoml and atoms fixed D ie X or Y or Z coordinate of atoml through atoms are fixed Other constraint types will be added in the future 4 8 8 Keyword MDPRESSURE Activates constant pressure molecular dynamics Options P TAU COMP External pressure in MPa The default is 0 1 Berendsen Coupling constant in ps The default is 1 0 Compressibility of the system in 1 MPa The default is set to be reasonable for water Description This keyword requires
66. arizability tensor a is calculated This is the default BETA The first hyperpolarizability 8 is calculated GAMMA The second hyperpolarizability y is calculated FFS lt Real gt Finite field strength used in the polarizability calculation EFISH Activate the EFISH orientation Description The polarizabilities are calculated by the finite field method 98 using field strengths of 0 003 a u for o and 9 and 0 01 a u for y The field value can be modified by the option FFS The hyperpolarizabilities 6 and y are always calculated in the so called EFISH Electric Field Induced Second Harmonic generation orientation In this orientation the 84 4 Keywords z axis of the molecule is oriented along the permanent dipole moment of the system The mean first and second hyperpolarizabilities are defined in EFISH orientation as 3 D 1 EE 4 17 5j For the calculation of the polarizability tensor no special orientation is used With the option EFISH the EFISH orientation can be enforced The mean polarizability and polarizability anisotropy Aa are calculate as 1 a a Qs Qyy Azz 4 18 Jsa 2 Aa 3tr a ure 4 19 Requesting 3 or higher polarizabilities changes default for the grid generating function to GUESS See section 4 4 10 4 9 5 Keyword FREQUENCY This keyword activates frequency analysis Options RAMAN The Raman intensities are calculated RESTART The frequency analysis is restarted from the deMo
67. asc bin lat mkl mol new pie rst nmr11 nmr70 nmr71 and nmr72 may be gen erated The driver script takes care not to delete any previously existing output files If any of the output files with these extensions exist at the time execution begins the driver will create backup copies These copies will have an additional extension bak appended to their full name if any of the files with these extensions exist they will be removed Note that most of the deMon output files are originally created in the scratch area and are only copied to the job starting directory after the job completes The only exception is the system information file with the err extension If you need to examine the output of a running deMon job you will find the exact location of the scratch directory in the system information file 8 Carrying On 19 3 Carrying On 3 1 Parameters Table 2 summarizes the limits of the shipped deMon version for memory and disk space requirements number of atoms as well as basis and auxiliary functions These limits are specified in the section user defined parameters of the parameter h file This file is found in the directory deMon include If a calculation violates these limits the pro gram stops and prints PARAMETER EXCEEDED statement s for the parameters that have to be changed In this case please change only the first exceeded parameter the fol lowing ones may be corrupted by array bound violations to
68. ation analysis Options MULLIKEN LOEWDIN BADER MULLIKEN A Mulliken population analysis is performed This is the default LOEWDIN A Lowdin population analysis is performed BADER A Bader population analysis is performed unimplemented Description In all three cases deMon calculates atomic charges and in the case of open shell systems atomic spin charges For the Mulliken 93 and L wdin 94 population analysis the bond order 95 or valence matrix 96 are calculated as well closed shell systems only In the case of the population analysis of Bader 97 critical points of the electronic density and the molecular graph are calculated These quantities can be visualized with Vu see 8 using the deMon pie file 4 9 2 Keyword DIPOLE This keyword activates the calculation of molecular electrostatic moments Description With the DIPOLE keyword the calculation of the electrostatic dipole quadrupole and octupole moment is activated If higher moments are required the parameter MAXMOM in the parameter h file has to be adjusted The electrostatic moments are calculated from the orbital density see Section 1 4 independent from the chosen energy approximation If the electrostatic moments should be calculated in STANDARD ORIENTATION see Section 4 1 4 for the definition a single point calculation with the symmetry keyword activated SYMMETRY ON has to be performed 4 9 3 Keyword MAGOUT This keyword requests writing of th
69. can be omitted In contrast to many examples in the literature the PW86 exchange functional in deMon is implemented with a cutoff The local contribution of the P86 correlation functional is calculated using the VWN functional All other functionals are implemented according to the cited references Where possible second derivatives with respecy to density were eliminated by integration by parts 48 The AUXIS and BASIS options specify the density that is used for the calculation of the exchange correlation energy and potential By default the auxiliary function density is used for the calculation of the exchange correlation energy and potential Using the option BASIS results in a significant slow down of the SCF calculation However for sensitive property calculation the BASIS option is recommended For more details and recommendations see Section 1 4 How to Use deMon For the PW91 and PBE functional two different spin scaling functions are implemented in deMon By default a numerical more stable cutoff function is used The suffix SSF options PW91SSF and PBESSF selects the original form of the spin scaling function 56 4 Keywords This may change the orbital energies considerably For the total energies the effect is usually negligible For other functionals the default choice of the spin scaling function can be overriden by specifying SSF FULL or SSF G98 options of the VXTYPE keyword Table 8 Exchange and correlation functionals
70. can be used to generated simultaneously two isosurfaces with the same positive and negative threshold e g for molecular orbitals If the threshold of the two isosurfaces should be different e g for molecular electrostatic potentials the two values can be specified as ISO 0 1 0 05 The ISO option has no default setting and therefore is mandatory With the TOL 100 4 Keywords option the amount of data reduction is specified Allowed values range from 10 to 0 5 specifying the severity of the data reduction A value of 107 indicates no data reduction at all This is the default With increasing TOL values the data reduction increases thus decreasing the memory request and at the same time the resolution 4 11 5 Keyword GEOSURFACE This keyword controls the calculation and plotting of geometrical surfaces like spheres or ellipsoids See the keyword BOX 4 11 6 for the definition of the geosurface boundary Options SPHERE ELLIPSOID SPHERE A sphere with the radius a around the origin f is constructed ELLIPSOID An ellipsoid with the semi axes a b and c around the origin 7 is constructed BINARY ASCII TABLE BINARY A binary output of the geometrical surface is written in the file LAT bin using the VU file format The VU control file deMon pie is written too This is the default ASCII An ascii output of the geometrical surface is written in the file deMon lat TABLE A function table of the geometrical surface
71. ccupied molecular orbitals is calculated Molecular electric field and its first derivatives By default the electric field and its derivatives of the occupied orbitals are calculated Molecular electric field gradients Identical to DIEFI Anion surface generation 104 Electron localization function 105 106 4 11 3 Keyword CPSEARCH This keyword activates the critical point search of scalar molecular fields For the defini tion of the search area see the keywords BOX 4 11 6 and POINTS 4 11 7 Options 4 11 Visualization and Topology 97 FIELD Scalar molecular field specification The available field acronyms are RHO and ESP See Table 9 for the acronym meanings This option is mandatory BASIS AUXIS BASIS The orbital density is used for the calculation of the scalar molecular field This is the default AUXIS The auxiliary function density is used for the calculation of the scalar molecular field Description The critical points of the density RHO and molecular electrostatic potential ESP can be searched with this option By default the critical point search is performed in a marching cube like style 107 embedding the molecule in a rectangular box BOX LARGE see Section 4 11 6 which is in turn divided into subboxes Each subbox is then searched for a critical point 108 The box size and shape can be manipulated by the BOX keyword As an alternative start points for the critical point search can be sup
72. ch is shared 24 25 by all functions in the set Thus an auxiliary function set with LMAX 2 contains ten functions namely one s three p and six Cartesian d functions In deMon these functions are primitive Hermite Gaussians of the form without normalization a r L l 22 i e c A 4 3 The input of an user defined auxiliary function set is described in Example 5 6 4 2 3 Keyword ECPS This keyword specifies the effective core potentials ECPS Options lt ECP gt The ECP string lt ECP gt defines the global effective core potentials If absent an all electron calculation is assumed by default The keyword ECPS is very similar to the keyword BASIS Section 4 2 1 Different ECPs can be assigned to individual atoms according to the atomic symbol e g Aul or to atom groups based on the element symbol e g Au The global ECP is used for all atoms which are not explicitly defined Requesting a QM MM capping potential see section 6 overrides ECP section in the ECPS keyword If ECPS is not specified for an atom but the substring ECP is present in the basis set definition then an ECP with the same name will be automatically assigned to the atom The assignment of the ECP based on atomic symbols element symbols and global ECPS definition possesses the hierarchy QM MM CAP overrides atomic symbol overrides lt element symbol overrides lt global ECPS gt overrides lt basis set name gt
73. ding your questions to one of the mailing lists The addresses of the lists can be found on the same web site 16 2 Getting Started Finally if everything else fails you can ask deMon developers for assistance Important Please do not bother telling to the gatekeeper or to any of the developers Your stuff does not work and it is just a piece of junk This kind of approach will only pi off people who put a lot of effort into making sure that everything works as smoothly as it possibly could Instead please provide answers to these questions e Which version of deMon are you using Check deMon source deMon f e Which hardware platform are you using The processor and system model are important e Which operating system are you using Try uname a shell command e Which compiler are you using Please give both the name and the version e Which numerical libraries if any are you using Both name and version are im portant e Which options for the build platforms are you offered by the install sh script e Which build platform did do you choose e If your build fails while running install sh what are the contents of the the build log file it produced in the makefiles subdirectory e If you experience failures in the test set which test cases fail e If you experience failures in a specific test case please include both the out and err files from the corresponding subdirectory of examples directory
74. e Argonne National Lab and Rice University 1999 A D Becke J Chem Phys 88 2547 1987 R E Stratmann G E Scuseria M J Frisch Chem Phys Lett 257 213 1996 H B Jansen P Ross Chem Phys Lett 3 140 1969 P Fuentealba Y Sim n Manson Chem Phys Lett 314 108 1999 References 139 114 K Jug B Zimmermann P Calaminici A M K ster J Chem Phys 116 4497 2002 115 V G Malkin O L Malkina M E Casida D R Salahub J Am Chem Soc 116 5898 1994 116 V G Malkin O L Malkina L A Eriksson D R Salahub in Theoretical and Com putational Chemistry Eds P Politzer and J M Seminario Elsevier Amsterdam 1995 117 W Kutzelnigg U Fleischer M Schindler in NMR Basic Principles and Progress Vol 23 Springer Verlag Heidelberg 1990 118 G Seifert D Porezag T Frauenheim Int J Quantum Chem 58 185 1996 119 M Elstner D Porezag G Jungnickel J Elsner M Haugk T Frauenheim S Suhai G Seifert Phys Rev B 58 7260 1998 120 L Zhechkov T Heine S Patchkovskii G Seifert H A Duarte J Chem Theor Comput 1 841 2005 121 M Rapacioli R Barthel T Heine G Seifert J Chem Phys 126 124103 2007 122 O F Oliveira G Seifert T Heine H A Duarte J Braz Chem Soc 20 1193 2009 123 M Springborg R C Albers K Schmidt Phys Rev B 57 1427 1998
75. e Control 4 3 1 Keyword MULTIPLICITY This keyword specifies the multiplicity of the system Options lt Integer gt Multiplicity of the system Description The default multiplicities are 1 for closed and 2 for open shell systems The program will check automatically if the defined multiplicity is allowed for a given molecular system and its charge 4 3 2 Keyword CHARGE This keyword specifies the charge of the system Options lt Integer gt Charge of the system Description The default charge is 0 4 3 3 Keyword MOEXCHANGE This keyword alters the molecular orbital ordering in the start or restart density Options lt Integerl gt Number of spin a molecular orbital exchanges lt Integer2 gt Number of spin 3 molecular orbital exchanges Description The numbers of the molecular orbitals to be exchanged are read in pairs of integers in the keyword body of MOEXCHANGE one line for each pair First all spin a exchanges are read and then in the case of an unrestricted calculation see UKS in 4 4 1 spin exchanges are read The application of MOEXCHANGE is shown in Example 5 8 4 9 Electronic State Control 41 4 3 4 Keyword FIXMOS This keyword fixes a molecular orbital occupations during the SCF by projection Options FIXED ITERATIVE FIXED The molecular orbital configuration at the beginning of the projection is used as reference configuration ITERATIVE The molecular orbital configuration of the previou
76. e interface files for the NMR EPR program MAG Options 4 9 Property Control 83 MASTER MAG MASTER Produce output for MASTER NMR programs see section 22 MAG Produce output for MAG NMR program see section 9 Description If MAGOUT MASTER is given four interface files deMon nmr11 deMon nmr70 deMon nmr71 and deMon nmr72 are written These are data files for the MASTER program see Sec tion The file deMon nmr11 contains the grid information points and weights The other files deMon nmr70 deMon nmr71 and deMon nmr72 contain dimension pointer and molecular coordinates basis etc informations respectively In the case of an EPR cal culation the file deMon nmr11 is not produced It should be noted that for NMR and EPR calculations the angular momentum for the auxiliary functions is limited to l 2 If MAGOUT MAG is given deMon will create two interface files deMon nmr11 and deMon nmr50 in the format expected by the MAG program see Section 9 Note that the version of the MAG program included in this distribution lacks some of the key features due to li censing restrictions on it s redistribution An up to date version of the MAG code should be requested directly from Vladimir Malkin The use of the MASTER and MAG programs is described in Sections and 9 4 9 4 Keyword POLARIZABILITY This keyword activates calculation of the polarizabilities and hyperpolarizabilities Options ALPHA BETA GAMMA ALPHA The pol
77. eMon environment variable to point to the installation directory for example export deMon HOME deMon For bash setenv deMon HOME deMon For csh 3 Run install sh script cd deMon install sh 4 Follow instructions on your screen If no errors are reported you have a working deMon installation Otherwise proceed to the advanced installation instructions in section 2 2 4 2 2 4 Advanced Installation The procedure outlined in this section is functionally identical to the express installation 2 2 3 However you will have an opportunity to take immediate corrective action if any problems arise 1 Set deMon environment variable to point to the installation directory for example export deMon HOME deMon for bash setenv deMon HOME deMon for csh The rest of this section will assume what deMon is installed in the directory de Mon 2 Getting Started 2 If you intend to study very large systems with more than 5000 atoms or more than 10000 contracted basis functions you will need to modify some of the settings in file SdeMon include parameter h See section 3 1 for the instructions 3 Go to the deMon makefiles subdirectory and issue the command make makesys The installation script will attempt to find combinations of options which are compatible with your platform Please sevect the most specific set of parameters which applies to your configuration If the only platform choice you are
78. ements H C H Xe De H Al Ar Sc Zn H Li C F Si Cl H C F S Cl H C F S Cl H C N O F H F H F Si Cr Fe H F i Cr Fe H I H C F H Ne Sc Cu H Zn H Kr Modified for Li and Na 14 AUXIS A2 C GEN A2 C1 GEN A2 assigns a GEN A2 auxiliary function set to atom C1 a GEN A2 to atom C2 and the A2 auxiliary function set to all other atoms The AUXIS file of deMon contains only the Description Double basis set for saturation only LDA double polarization basis set 13 Modified DZVP basis set LDA optimized triple polarization basis set TZVP with field induced polarization 15 16 for a 8 FIP1 and y FIP2 calculations EPR basis set 17 NMR basis set 18 NMR basis set 18 STO 3G basis set for testing only 19 Sadlej FIP basis set 20 Lie Clementi basis set 21 Wachters basis set without f functions 22 Double G ANO basis set from Roos 23 Ahlrichs basis sets A VDZ A PVDZ A VTZ A PVTZ A2 auxiliary functions set The other auxiliary function sets used above GEN A2 and GEN A2 are automatically generated according to the procedure described in Appendix A Additionally the auxiliary function sets can be directly specified in the input file using 38 4 Keywords the format Auxis SYMBOL Read LMAX EXPONENT LMAX EXPONENT where LMAX denotes the maximum angular momentum quantum number of the auxiliary function set and EXPONENT the exponent whi
79. equested the STANDARD ORIENTATION is 34 4 Keywords used in any case see 5 1 For atoms the use of the SYMMETRY keyword enforces the zeroing of the off diagonal elements of the Kohn Sham matrix for different angular momenta Currently deMon symmetry analyser supports Ch Cry Cnh Dn Dna and Dn point groups with n lt 6 The rotation inversion groups Sn are supported for n lt 8 If a higher group is present in a molecule deMon will abort the calculation even when SYMMETRY OFF is specified Symmetry analysis can be suppressed altogether by including DETECT OFF on the symmetry line See example 5 5 If you are uncertain about a symmetry assignment made by deMon or are wondering whether your system is approximately symmetric you may find an unsupported program deMon unsupported symmetry c useful 4 2 Basis Set Input 35 4 2 Basis Set Input 4 2 1 Keyword BASIS This keyword specifies the basis set Options lt Basis gt The basis set string lt Basis gt defines the global basis set If absent the DZVP basis set is used by default Description In the BASIS keyword body basis sets can be assigned to individual atoms according to the atomic symbol e g H4 or to atom groups over based on the element symbol e g H The global basis set is used for all atoms which are not defined by either of these mechanisms Specifying QM MM capping potential will override basis set selection made with the BASIS keyword see section 6
80. eral builds at the same time as long as the deMonPlatform settings of the builds are different 2 8 Porting deMon to a new platform 11 6 Build addional tools MASTER and MAG by issuing the command make tools You can combine the last two steps by using the command make clean build tools 7 Go to the deMon examples directory and run deMon test suite cd deMon examples make clean remove old test results make cheap execute minimal test set make all execute the complete test set You can also say make clean all which is equivalent The test suite Appendix C can take a while to run If all goes right you should see the message de Mon installation tests completed successfully after each of the test phases Otherwise do not use the deMon executable you have compiled Currently the minimal test set requires about ten minutes on a mid range PC 2 4GHz P4 The complete test set requires about two CPU days If you have a queuing system such as PBS SGE or LSF installed you can run the test set in parallel To activate parallel execution set the environment variable QSUB_COMMAND to qsub or whatever the name of your job submission command it export QSUB_COMMAND qsub for bash setenv QSUB_COMMAND qsub for csh before starting the test set Please consult deMon examples README txt for more information on running deMon test set with batch queuing systems If the test set comp
81. erties like frequencies polarizabilities etc are intended to be calculated the use of VXCTYPE BASIS is recommended The differences between VXCTYPE AUXIS and VXCTYPE BASIS for geometries and bond energies are in the range of the accuracy of the methodology An exception should be made for very weak bonds where the geometry may be significantly affected by the use of fitted density It should be noted that the default setting for the auxiliary functions is A2 independent which energy expression is used see Section 4 2 2 For all theoretical models available in deMon VXCTYPE AUXIS results can be used as a restart guess GUESS RESTART see Section 4 4 4 for VXCTYPE BASIS calculations The most often encountered problem in DFT calculations is the failure of the SCF conver gence This is usually due to the small gap between the highest occupied HOMO and lowest unoccupied LUMO molecular orbital In deMon the DIIS procedure Section 4 4 7 is activated by default For a small HOMO LUMO gap DIIS may be counter productive and should be switched off Several alternative methods are available in de Mon to enforce SCF convergence Most important are modification in the choice of the starting GUESS Section 4 4 4 and the MIXING Section 4 4 5 procedure of the old and new densities and the enlarging of the HOMO LUMO gap by the level SHIFT Section 4 4 6 procedure In all cases it is recommended to check the orbital energies and occu pations using the P
82. essed the order numbers are determined by the Z MATRIX or CARTESIAN input coordinates If the RAD column is suppressed the radii of the spheres are determined by the option BONDI or MERZKOLLMAN 3 If the SCALRAD column is suppressed the scaling factors are set equal to 1 0 In this way only the parameters of the desired spheres can be modified NORD RAD SCALRAD 2 1 10 1 20 4 11 Visualization and Topology 93 4 11 Visualization and Topology The keywords PLOT ISOSURFACE and GEOSURFACE of this section are exclusive and cannot be combined The same holds for the keywords BOX and POINTS 4 11 1 Keyword VISUALIZATION This keyword activates the interface to the visualization programs MOLDEN 102 and MOLEKEL 103 Options MOLDEN MOLEKEL MOLDEN The MOLDEN interface is activated The MOLDEN input is written to the file deMon mol This is the default MOLEKEL The MOLEKEL interface is activated The MOLEKEL input is written to the file deMon mkl XYZ OPT FULL XYZ Only the molecular structures and energies of each optimization step are written to the deMon mol file This is the default if the option MOLDEN or MOLEKEL is missing OPT The molecular structures as well as the forces and step sizes of each optimization step are written to the deMon mol file This option triggers the MOLDEN interface FULL A full MOLDEN or MOLEKEL input is written This is the default if the option MOLDEN or MOLEKEL is set Description For
83. exponent from which the generation starts is defined as Co 2 Gnin 6 n 79 A 2 From this exponent the two tightest s set exponents and gt are generated according to the formulas n 1 _ G A 3 a 57 lt A3 Go A 4 Q 2 A4 The other s set exponents are generated according to the even tempered progression Gi irl Ah Gu ge A5 The Co exponent of the following spd sets is also generated according to the progression A 5 Based on this exponent the exponents of the first two spd sets are calculated 122 A Automatic Generation of Auxiliary Functions with the formulas A 3 and A 4 The following spd set exponents are then calculated again according to the even tempered progression A 5 In the same way the spdfg set exponents are calculated In the case of 3d elements an extra diffuse s auxiliary function set is added B Format of a platform description file 123 B Format of a platform description file B 1 Philosophy of deMon configuration files On most of the supported platforms deMon comes with three sets of compilation flags these are designated by stars in the table above These sets are dbg std and opt The idea behind these options is as follows The opt for optimized version is intended to give maximum performance To achieve this this set of compilation options uses aggressive optimization flags Compiling an opt version may also require vendor optimized BLAS
84. f S axis of highest degree Number of orbitals gt IATOM JATOM IAUX JAUX IAUXSET JAUXSET gt IAUXSHL JAUXSHL ICN JCN IELEC JELEC ICTO IO TO 31850 JSEC ISES JSES ISHL JSHL cadet JIE i ISN JSN 23 ISTO JSTO D Global Counters Limits and Pointers 131 Table 13 Limits Limit Description LL IATOM UL IATOM LLAUX IAUXSHL ULAUX IAUXSHL LLAUXSET IATOM ULAUXSET IATOM LLAUXSHL IAUXSET ULAUXSHL IAUXSET LLGP IATOM ULGP IATOM LLGTO ISHL ULGTO ISHL LLSHL IATOM ULSHL IATOM LLSTO ISHL ULSTO ISHL Number of the first orbital STO of atom IATOM Number of the last orbital STO of atom IATOM Number of the first auxiliary function of auxiliary function shell IAUXSHL Number of the last auxiliary function of auxiliary function shell IAUXSHL Number of the first auxiliary function set of atom IATOM Number of the last auxiliary function set of atom IATOM Number of the first auxiliary function shell of auxiliary function set IAUXSET Number of the last auxiliary function shell of auxiliary function set IAUXSET Number of the first grid point of atom IATOM Number of the last grid point of atom IATOM Number of the first primitive Gaussian function of shell ISHL Number of the last primitive Gaussian function of shell ISHL Number of the first shell of atom IATOM Number of the last shell of atom
85. f the heat transfer axis in Angstrom Not allowed in PBC simulations Number of temperature probes in the simulation Must be at least four see below Expected order of magnitude of heat conductivity in Watts meter Kelvin The default 0 1 W m K is appropriate for amorthous solids and liquids Desired heat flux between the cold and the hot zones in Hartree per time step It is usually safer to use GUESS instead Orientation of the heat transfer axis Only three choices are al lowed for periodic calculations AB AC and BC choosing a direction normal to one of the sides of the periodic box For non periodic calculations Cartesian direction must be provided in the form dx dy dz Position of the heat transfer axis origin which corresponds to the centre of zone 1 Can be specified as an integer giving the atom located at the origin or as Cartesian coordinates in the format x y z If PBCs are not used area of the section through which heat flows ngstrom squared Not allowed in PBC simulations 78 4 Keywords n 1 2 3 n 2 n i n 1 Base Length periodic Length non periodic Figure 4 Set up of heatpipe zone masks COLD Index of the cold zone of the heatpipe Must be between 1 and number of masks HOT Index of the hot zone of the heatpipe Must be between 1 and number of masks Hot and cold zones must not overlap OFF Turn the heatpipe off Description The structure of this keyword is
86. fects 87 4 10 Solvent Effects WARNING THE IMPLEMENTATION OF SOLVENT EFFECTS IS NOT FINAL AND MAY BE SIGNIFICANTLY MODIFIED OR EVEN REMOVED IN A FUTURE RELEASE 4 10 1 Keyword SOLVENT This keyword activates calculation of the solvent effects Options ONSAGER IT PCM CLS PCM BEM PCM ONSAGER The calculations are performed using the Onsager Model IT PCM The calculations are performed using the Polarizable Continuum Model PCM Iterative Procedure CLS PCM The calculations are performed using the PCM Partial Closure Approximation BEM PCM The calculations are performed using the PCM Bound ary Element Method BONDI Bondi s atomic van der Waals radii MERZ Merz Kollman s atomic van der Waals radii RAD Value of the spherical cavity radius in ngstr ms only for the Onsager Model SCALR The radius of each sphere is determined by multiplying the van der Waals radius by a scaling factor DIPOLE Dipolar perturbative reaction field QUADRUPOLE Dipolar and Quadrupolar perturbative reaction field OCTUPOLE Dipolar Quadrupolar and Octupolar perturbative reac tion field CLS 1 First level of truncation in CLSPCM procedure 2 Second level of truncation in CLSPCM procedure ITER Self Consistent Reaction Field SCRF iterative procedure 88 4 Keywords TOL Tolerance for SCRF iterative procedure only for On sager Model CAVITATION The cavitation energy contribution is calculated DISPERSION The dispe
87. flags in the GEOMETRY section This is the default Finally PROG chooses the name of the external executable or a shell script which will be called to evaluate MM energies and forces if an external force field is activated This must be a absolute path name paths relative to the current directory will not work There is no default for this option 4 5 3 Keyword MMOPTIONS This keyword sets various technical parameters for the MM simulation part Not all of those parameters have a meaning for all run types Options TSTEP MM MD time step in atomic time units STEPS Number of MM MD time steps or maximum number of MM ge ometry optimization steps TOLE Energy convergence criterion for MM optimizations in Hartree TOLG Gradient convergence criterion for MM optimizations in Hartree Bohr TOLX Displacement convergence criterion for MM optimizations in Bohr TOL Set TOLE TOLG and TOLX to values suitable for energy con vergence specified here in Hartree TAU Berendsen tau parameter in atomic time units TS MM simulation temperature in Kelvin 62 4 Keywords 4 5 4 Keyword VDWAALS This keyword sets defaults for van der Waals non bonded interaction summation cutoffs used in DFTB MM and QM MM Options ECUT Energy cutoff in Hartree The default is 10 SMOOTH The van der Waals energy is shifted for long range interactions by a value AE as specified by the X keyword and repulsive contri bution
88. ft value is sub tracted from the orbital energies once SCF procedure has converged Because of the small HOMO LUMO gap in DFT calculations this procedure is very valuable to improve SCF convergence However with a fixed level shift calculation may converge to an excited state Therefore the converged orbital occupation should be examined using the MOS option of the PRINT keyword see 4 12 3 This problem can be reduced if the dynamical level shift procedure 14 is used Here the shift value is adapted to the Minmax SCF er ror While the error is large usually at the beginning of the SCF procedure the full shift value is used When the error decreases the shift value is decreased too see Example 5 15 Usually a small shift value remains at the end of the SCF procedure The dynam ical level shift procedure has proven very valuable for the SCF convergence of transition metal clusters and systems 46 If the SHIFT keyword is used the level shift procedure is applied in all calculation steps optimization frequencies properties etc If this is not desirable a single point SCF can to be performed with the SHIFT keyword The converged density can then to be 44 SCF Control 53 used as the restart density see 4 4 4 in the following calculations without the SHIFT keyword See example 5 16 A cautionary note Neither having the aufbau orbital occupations at the end of the SCF nor using dynamis level shifting procedure provide a guarantee
89. g e Try increasing process limits such as the stack size limit data segment size limit or memory size limit If you use Bourne shell or derivative sh ksh bash the appropriate command is ulimit For C shell or its ilk csh tesh the right command is limit On some operating systems tuning kernel parameters may be required to adjust the limits e Try building deMon without using any external libraries the libraries may be in compatible with the compilation options in the deMon makefile or may not support functions needed by deMon properly Debugging and generic versions typically do not require external libraries e Try decreasing optimization level see section 2 2 4 and appendix B for the in structions on modifying platform configuration files If your compiled binary runs but fails some of the tests you can try some of the following e Try decreasing optimization level see section 2 2 4 and appendix B for the in structions on modifying platform configuration files The following routines are particularly numerically sensitive and may be affected by aggessive compiler opti mizations 2 5 What to do when things go wrong 15 tensor f rs f jacobi f pythag f dsyev f dsyevd f dsyevr f dgelss f dpptrf f dpptri f dtptri f blas1 f blas2 f dgemm f dsyrk f Calculation of the molecular inertia tensor EISPACK diagonalization routine Jacobi diagonalization routine auxiliary routine f
90. gence criterion is increased to 107 It may be overwritten by a smaller value with the TOL option if desired Note that tight SCF convergence criteria are largerly meaningless unless tight numerical cri teria a used for the the numerical integration of the exchange correlation potential and ECPs In addition to the standard orbital based convergence criterion deMon also monitors the convergence of the fit density The default convergence criterion is adequate for an overwhelming majority of applications and should not be modified In a few rare cases for example when very accurate values are needed for the multipole moments of the molecular charge distribution the fit convergence threshold can be modified using the CDF option 44 2 Keyword ORBITALS This keyword controls the atomic orbital choice Options SPHERICAL CARTESIAN SPHERICAL Spherical atomic orbitals 5d 7f are used This is the default CARTESIAN Cartesian atomic orbitals 6d 10f are used Description In deMon the spherical see 4 3 6 for the definition of real spherical harmonic Gaussians and Cartesian atomic orbitals have the general form omitting the normalization diat e oP 4 8 bijk r a yl hert 4 9 48 4 Keywords Because spherical orbitals do not include contaminants with lower angular momenta V 1 2 1 4 they are the recommended choice for most applications 4 4 3 Keyword ERIS This keyword controls the calculation meth
91. ges deMon must evaluated the electrostatic potential of the infinite periodic charge 4 5 Molecular mechanics and QM MM Control 63 distribution Madelung potential This can be done using the Ewald technique or alter natively employing real space summation with a screened interaction potential 75 In this technique the usual Coulomb interaction potential is replaced with A EE r 1 exp r ro d The screening parameters rg and d must be selected such that vr 4 11 e The screening function is not distinguishable from 1 within the unit cell surrounding the origin e The fall off region of the screening function is wider than the typical extent of non neutral charge distrubutions in the system The defaults are appropriate for simulation of liquids of small polar molecules Simulations of systems with long range charge correlations may require large values of d and ro 4 5 6 Keyword PERIOIC This keyword activates periodic boundary conditions in MM and QM MM calculations and specifies the initial extent of the unit cell Options CUBIC RECTANGULAR GENERAL CUBIC Cubic simulation box is used RECTANGULAR Rectangular simulation box is used GENERAL General simulation box is used This is the default FULL Use true periodic boundary conditions This is the default MINIMAL Use minimal image cyclic cluster periodic boundary condi tions in the molecular mechanics part Description The PERIODIC keyword
92. given is Generic settings deMon does not have a pre defined set of compilation options for your system In this case consult section 2 3 below Please set the environment variable s suggested by the platform detection script Usually the only required variable is deMonPlatform To make these settings permanent please add them to your shell initialization file usually cshrc or profile found in your home directory The deMonPlatform setting will also affect the default choice of the deMon executable selected by the deMon driver script see Section 2 6 4 It is usually a good idea to review the default compilation settings particularly the library locations and optimization flags The file sys deMonPlatform mak which is located in the directory deMon makefiles sys contains this information If you change any of the compilation options in the platform specific makefile sys deMonPlatform mak please execute the command make clean before rebuilding your program Otherwise your build may be inconsistent 5 Build main deMon binary by executing the command make clean make build The first command make clean removes all old makefiles objects and binaries for this platform The second command make build builds the main deMon ex ecutable which is placed in the directory deMon bin The build script takes care to keep all platform specific data in unique files It is therefore safe to perform sev
93. h require low optimization settings see F900PTLOW above The list of files which require extra high optimization settings see also FOOOPTHIGH above The list of files which require special treatment such as using a different compiler or special preprocessing Any files men tioned on this line will be excluded from the standard compila tion process Instead you should provide complete compilation instructions using Makefile rules The command required to add or replace an object file to in an archive library The command will be invoked as ARCMD library name object file name On most UNIX systems you can leave the default ar r unchanged The command required to make an archive library usable by the system linker This command will be invoked as RANLIBCMD library name Usually this is not required and can be set to RANLIBCMD true However on some UNIX systems this should be set to RANLIBCMD ranlib B 2 Structure of a platform configuration files 127 TOOLOBJ checkplatform describeplatform commentplatform deMon object files which must be included while build ing auxiliary tools The usual set is OBJ deflush o 0BJ detime o However if you intend to build the MAG tool you may also need to include some of the files from the generic BLAS library This make target should succeed if this platform definition file is appropriate for the current system The actual command line used b
94. have been warned Additionally for best performance you will need optimized BLAS libraries If your vendor does not provide such you will have to obtain and install one of the publicly available BLAS libraries yourself A good place to start is http www netlib org atlas Having an optimized LAPACK is also helpful but less important If your BLAS and LAPACK are installed in non standard directories you can specify their location by setting the LIBPATH environment variable For example if your BLAS libraries are in the directory usr local lib64 you should say export LIBPATH L usr local lib64 for bash setenv LIBPATH L usr local lib64 for csh Many people insist on spelling this language name as FORTRAN In fact the correct spelling is simply Fortran It is specified by an international standard ISO IEC 1539 2 2 How to Install deMon 9 If you require an unusual command line option or a linker parameter to make your BLAS work it can be included in LIBPATH as well This command has to be executed each time you build deMon so you may find it useful to put it in your shell profile 2 2 3 Express Installation If deMon has been previously ported to the operating system and compiler you are using and all needed libraries are installed in standard locations you can use the express installation procedure namely 1 Unpack deMon distribution files in subdirectory deMon of your home directory 2 Set d
95. he characteristic time of the process of interest For MD runs where the initial configuration is already well equilibrated eg taken from a previous MD run using an empirical forcefield the equilibration should start with the LOCAL thermostat and omit SCALING altogether 4 8 6 Keyword CONSERVE The keywords requests imposition of constraints on some or all mechanical constants of the overall motion of the system Options NONE POSITION MOMENTUM ANGULAR ALL 4 8 MD Control 75 NONE Do not impose constraints This is the default except for MDYNAMICS RANDOM POSITION Reset position of the centre of mass of the system to 0 0 0 on each MD step MOMENTUM Reset overall momentum of motiom of the system to zero on each MD step ANGULAR Reset overall angular momentum of the system to zero on each MD step This constraint makes no sense and is ignored for periodic calculations ALL Equivalent to POSITION MOMENTUM ANGULAR This is the default for MDYNAMICS RANDOM Description For infinitely accurate arithmetics and an infinitely small time step overall constants of motion must be conserved automatically Unfortunately in the presence of numerical noise and residual errors in the time evolution algorithms mechanical constants of motion are no longer conserved in practice For example it is easy to show that the residual error of the velocity Verlet algorithm used in deMon with lead to an unbound amplification of the angul
96. he integration This is the default FIXED A fixed grid is used for the integration MEDIUM COARSE FINE MEDIUM A medium grid accuracy is requested This is the default COARSE A coarse grid accuracy is requested FINE A fine grid accuracy is requested TOL lt Real gt Adaptive grid tolerance SCF GUESS SCF The converged SCF density is used for the adaptive grid generation This is the default GUESS The start density is used for the adaptive grid generation Description By default deMon uses an adaptive grid 65 with a tolerance of 107 MEDIUM for the numerical integration of the exchange correlation energy and potential This tolerance corresponds to the accuracy of the numerical integration of the diagonal elements of the exchange correlation potential matrix For the converged SCF energy an accuracy better than 100 uHartree is usually obtained with this setting 66 The COARSE and FINE option for the adaptive grid refer to grid tolerances of 1074 and 10 respectively Thus the stability of the numerical integration can be easily checked by choosing different grid tolerances The COARSE adaptive grid should not be used for final energy or property calculations User defined grid tolerances can be specified using TOL option This option is only applicable for an adaptive grid The same holds for the SCF and GUESS options which specify the trial density used for the grid generation By default the converged SCF density is
97. he temperature This option is only meaningful for very large systems of for the first equilibration steps of a trajectory BERENDSEN Berendsen thermostat is applied to the system as a whole LOCAL Berendsen thermostat is applied individually to each atom VAL lt Integer gt SCALING number of steps between velocity resets VAL lt Real gt BERENDSEN or LOCAL Thermostat time constant 7 in picoseconds ps Default is 7 0 5 ps Description Free running MD equations generate trajectories with constant energy to within the numerical error of the time evolution algorithm velocity Verlet in deMon and of the energy gradients In other words molecular dynamics simulation is performed for the mi crocanonical N V E ensemble However it is often of interest to perform simulations at constant temperature which requires modifications to the standard equations of motion There are a number of different approaches for performing constant temperature MD In deMon the temperature can be controlled by scaling the velocities i e at each time step the velocities are scaled according to v kv The three temperature control meth ods implemented in deMon differ in how this constant k is calculated With the SCALING thermostat the velocities of all atoms are scaled by the same factor so that the instantaneous temperature Tkin matches desired temperature T set by the MDTEMP keyword see Section 4 8 3 In this case k is simply To 12
98. ical points of other molecular fields The READ option can be used to read point coordinates from the input file deMon inp The coordinates are given in free format in the keyword body of POINTS one input line for each point 4 12 Miscellaneous Keywords 105 4 12 Miscellaneous Keywords 4 12 1 Keyword MAXMEM This keyword specifies the amount of memory available to the job Options lt integer gt Amount of memory available The default is 256 Mbytes KBYTE Units Kilobytes MBYTE Units Megabytes This is the default GBYTE Units Gigabytes Description deMon can use the MAXMEM value for choosing the appropriate handling of ERIS MEMORY see 4 4 3 and the value of MATDIA THRESHOLD see 4 12 6 The amount of memory specified in MAXMEM cannot exceed the MAXRAM compilation time parameter 4 12 2 Keyword TITLE This keyword specifies the job title Options None The job title is limited to 60 characters and the title line cannot be continued over more than one line 4 12 3 Keyword PRINT This keyword controls optional printing Options 106 ALWAYS ATOMMAP AUXIS BASIS CGTO COORD DE2 DEBUG ECP EMBED ERIS FLUX G GRID GTO KS 4 Keywords Print requested output for all calculation phases Print atom ordering maps Print auxiliary function table Print molecular orbitals in long format Print GTO contraction table Print primitive internal coordinates Print Hessian matrix Generate debug ou
99. ifferent system partitioning 4 5 2 Keyword FORCEFIELD This keyword is used to specify molecular mechanics forcefield and to set forcefield related computational options Options TYPE Chooses molecular mechanics forcefield This can be either UFF or EXTERNAL Only UFF which is the default is currently implemented BONDS Chooses the bond matrix definition This can be either EXPLICIT or AUTO AUTO is the default PROG Name of an external molecular mechanics program There is no default Description 4 5 Molecular mechanics and QM MM Control 61 The default molecular mechanics forcefield used in molecular mechanics and QM MM calculations is the Universal Force Field UFF by Rappe et al 69 74 see also section 6 While this force field is not particularly accurate for any specific system it covers the entire periodic table and often produces reasonable structures This forcefield implemen tation is integrated in deMon and carries minimal overhead in applications The option BONDS selects handling of the connection matrix which is needed in most MM force fields The two options are EXPLICIT All bonds and bond orders must be specified explicitly in the ge ometry input see keywords BOND and NOBOND in section 4 1 1 AUTO deMon will try to guess the connection matrix suitable for the specified starting geometry It is still possible to override the guess partially or completely by supplying BOND and NOBOND
100. il safe diagonalizers in deMon are based on the Householder algorithm For large systems the DSYEV diago nalizer is considerably faster than the RS diagonalizer However it is also more memory demanding Therefore it should only be used if enough RAM space is available The JACOBI diagonalizer is much slower but produces very pure eigenvectors It is used by default for atomic calculations Normally deMon will make the optimal diagonalizer choice based on the amount of memory available see MAXMEM section 4 12 1 4 12 7 Keyword WEIGHTING This keyword specifies the weight function used for the grid partitioning Options SCREENED A screened weight function is used This is the default SCREENED BECKE BECKE The original Becke weight function is used Description The BECKE weight function 110 introduces a cubic scaling in the grid generation step 111 By introducing a new piece wise defined weight function 66 near linear scaling for the grid generation can be obtained This weight function is specified by the option 110 4 Keywords SCREENED 4 12 8 Keyword QUADRATURE Numerical quadrature scheme can be modified using this keyword Options GAUSS A Gauss Chebyshev radial quadrature is selected This is the GAUSS EULER default EULER A Euler MacLaurin radial quadrature is selected RANDOM Random rotation of the Lebedev grids is activated REFERENCE A reference grid is generated Description TO BE WRITTEN 4 1
101. ile deMon out READ Specifies that an orbital list is read in the keyword body of PLOT This keyword is incompatible with the EFIDS field Description The definition of the molecular field is mandatory for the PLOT keyword The available molecular fields are listed in Table 9 If the BOX and POINTS keywords are missing the default BOX setting is used for the plot Only one molecular field at a time can be calculated If several fields have to be calculated restart calculations with SCFTYPE MAX 0 and GUESS RESTART see 4 4 1 and 4 4 4 may be performed In any case no more than 20 molecular field entries at a time can be calculated A field with its first and second derivatives counts for 10 entries 1 3 6 4 11 Visualization and Topology 95 The AUXIS and BASIS option specify the density auxiliary function or orbital density respectively used for the calculation of the molecular field The AUXIS option is incom patible with the READ option If the auxiliary function density is used for the calculation of the molecular field a considerable speed up will be achieved However the field values may show deviations with up to 10 compared to the orbital density Nevertheless the field topology is in most cases qualitatively correct By default the PLOT keyword produces two additional output files the binary file FIELD bin and the VU control file deMon pie With these files a VU session can be started see Section 8 With the ASCII opt
102. ilization of Vu Contains answers to many of the doubts involved with the use of Vu e http www3 sympatico ca chantal pic vu eng index html This is a temporarily ad dress 8 1 What is Vu Vu is a configurable visualization software tool for the display and analysis of numerical solutions It is used for exploring and interpreting results from simulation programs or experimental measurements Based on a dictionary and a grammar common to researchers of various domains it finds applications in fluid mechanics civil engineering applied mathematics manufacturing injection molding combustion structures computational chemistry etc Vu is available on computers of various sizes from laptops using Linux to virtual reality immersion environments CAVE ImmersaDesk Reality Center etc on all Unix platforms Vu uses three ingredients to construct an image a support an entity and a mode The support is the place where the image resides a plane sphere cylinder geometric etc The entity is what it is represented graphically a set of vectors like velocity a scalar field like electron density etc There are eight types of entities mesh graph iso vector tensor among others The mode is the way the user wants to see the image static dynamic injection or animation 116 amp Vu 8 2 Vu and deMon As a part of deMon there are a set of routines that build the required files for visualization with Vu This allows the users
103. ime Overall momentum of the system must be zero to eliminate the mass flow contribution These constraints can be enforced by using the CONSERVE keyword see section 4 8 6 Heatpipe dynamics is not compatible with constant pressure dynamics MDPRESSURE section 4 8 8 The only allowed thermostat is global Berendsen MDBATH section 4 8 5 If possible heatpipe dynamics should be performed with the thermostat off MDBATH NONE 4 8 10 Keyword CARPAR Activates a Car Parrinello Molecular Dynamics simulation This option is only available for DF TB By default this option is off Options FOM Ficticious orbital mass for Car Parrinello DFTB in atomic units The default is 25 At in atomic units The higher the value the stronger are the deviations from the Born Oppenheimer surface and also the electronic vibrations get larger periods so large values allow larger time steps 4 8 MD Control 81 LGTOL The requested tolerance to ensure orthonormality of the orbitals using a Lagrange multiplier The default is 107 in atomic units LGPROP Requests propagation of the Lagrange multiplier matrix This com putational step might be time demanding so extrapolating the mul tiplier matrix might be of advantage The performance of this op tion needs to be tested for each individual system The default is false BO The Car Parrinello approach is used to reach the Born Oppenheimer surface at each point For this purpose the positions
104. ink for the heatpipe These zones are specifies by HOT and COLD keywords In the absence of the source and sink specification deMon will place the cold zone in position 1 The hot zone will then be placed as far away as possible taking periodicity of the system into account On each time step the heat pipe transfers a constant amount of kinetic energy from the cold zone to the hot zone by scaling velocities of particles v 1 afe Fi on fn Fi 0 acfe fi on fn Fi Vo 4 14 where f 7 and fr 7 are masking functions of the hot and cold zones Parameters ae ap and vg are chosen such that the total energy and total momentum of the system are conserved The amount of energy in Hartrees transfered per time step can be specified using the FLUX keyword Usually it is more convenient to let deMon to choose the flux which will lead to the difference of 10K between the hot and the cold zones In addition to the heat transfer length and cross section estimation of the necessary heat flux requires a guess of the heat conductivity of the system It can be specified in Watts per meter Kelvin using GUESS keyword The default is 0 1 W m K Heat conductivities of some representative system are System Heat conductivity W m K Argon gas 300K 0 1MPa 0 02 Argon liquid 85K 0 IMPa 0 13 Argon solid 8K 6 NaCl 373K x5 NaCl 20K 300 Asbestos 273K 0 09 Copper solid 400 Diamond 300K 900 2300 Graphite 3
105. ion energy and potential calculation Options VWN PZ81 PW92 PW86 BLYP PW91 PW91SSF PBE PBESSF OLYP XALPHA NONE VWN Dirac exchange with local VWN correlation PZ81 Dirac exchange with local PZ81 correlation PW92 Dirac exchange with local PW92 correlation PW86 PW86 GGA exchange with P86 GGA correlation BLYP B88 GGA exchange with LYP GGA correlation OLYP OPTX GGA exchange with LYP GGA correlation 4 4 SCF Control 55 PW91 PW91 GGA exchange and correlation PW91SSF PW91 with full spin scaling function PBE PBE GGA exchange and correlation PBESSF PBE with full spin scaling function XALPHA Xa calculation The default o value is 0 75 A user defined a value can be selected with the X lt Real gt option NONE No exchange correlation functional is used ie Hartree calculation is done AUXIS BASIS AUXIS The auxiliary function density is used for the calculation of the exchange correlation energy and potential This is the default BASIS The orbital density is used for the calculation of the exchange correlation energy and potential Description The above options represent the most common combinations of exchange and correlation functionals Besides these combinations the exchange and correlation functionals listed in Table 8 can be combined by the user The syntax for the user defined potentials is lt Exchange gt lt Correlation gt e g B88 P86 With NONE the exchange or correlation part
106. ion file BINARY deMon nmr71 NMR71 NMR pointer file BINARY deMon nmr72 NMR72 NMR orbital file BINARY deMon mag MAGTAPE 17 Alternative NMR file BINARY The I O unit 8 is connected either to the MOLDEN or MOLEKEL input file depending on the VISUALIZATION 4 11 1 keyword For the XYZ output the MOLDEN file deMon mol is used in any case DE WN rR k OO Co N 7 1 1 1 1 w E ST NT NT SS SN IL I O R S NZZ Beer NEIN A N Na Bee E al E c Table 4 Special symbols of the deMon input Symbol Description Continuation of a keyword line First character of a comment line Assignment of numerical values to options Combination of keyword options Separation of keyword and options Separation of different options optional End of a keyword data block is not case sensitive A keyword line can be continued by the amp symbol at the very end of the line At most five continuation lines are permitted The TITLE line cannot be 22 3 Carrying On continued and the length of the title string is restricted to 60 characters The symbol indicates a comment line Comment lines can only occur between complete keyword data blocks including the keyword body if existing Comments inside a keyword line or body result in unpredictable read operations The end of a keyword block can be indicated by an END statement or comment symbol in a new input line or simply by
107. ion only the file FIELD asc is created The coordinates and molecular field values are listed in this file With the TABLE option a function table is created in the output file With the READ option a set of molecular orbitals for the calculation of the molecular field can be selected This option cannot be used for the EFIDS field In the case of the PSI and D1PSI field the READ option specifies directly the calculated molecular orbitals Again not more than 20 orbitals at a time can be calculated in the case of D1PSI not more than 5 If for the other fields orbitals are selected than the field is constructed from the sum of the selected orbitals E g the following input specifies the calculation of the density using the molecular orbitals 1 2 and 4 PLOT RHO READ 124 Virtual orbitals can be included They will be occupied by one electron In the case of an unrestricted calculations UKS option of keyword SCFTYPE see 4 4 1 o and orbitals can be selected each set in a separate input line In the following example the a orbitals 1 2 3 4 5 6 7 and the orbitals 1 2 3 4 5 6 are selected for the calculation of the molecular electrostatic potential PLOT ESP READ 1234567 123456 If only the P orbitals should be selected the first line in the above example must have a 0 entry PLOT ESP READ 0 123456 96 Acronym PSI D1PSI RHO D1RHO D2RHO SPIN D1SPIN LAP ESP 4 Keywords Table 9 Molecular fields available
108. ioning scheme are different in the restart file and the input file all running averages will be reset and simulation will start at time t 0 WARNING You should always use the same atom ordering in the input file used to produce the MD restart file and in the file used to contue the simulation In particular you should never use the new file generated by deMon for performing an MD restart there is no guarantee that atom ordering is identical in the original input file and the new file When MDYNAMICS RANDOM is specified the initial velocity components of an atom i are 4 8 MD Control 71 calculated as 4 k sin 2m rand 0 2 S 8 rn gt Mm v i TE sin 2m rand 0 2 mi 4 DAR E sin 2m rand 0 2 where rand is a random number uniformly distributed on the interval 1 1 and m is mass of atom i Scaling coefficient k is calculated such that the initial kinetic energy matches the desired temperature T Important this initial velocity distribution is non physical and must be equilibrated before any production sampling runs MDYNAMICS READ expects velocity specification in the format I VX VY VZ where I is the sequential atom number in the input order and VX VY and VZ are initial velocity components Velocities must be specified in Bohr au time or in A femtosecond depending on the units used to specify the geometry Atoms not mentioned in MDYNAMICS READ input section are give
109. it cells 66 4 Keywords e molecular dynamics DFTB uses parameters which are stored in Slater Koster SlaKo integral tables For the moment there are two independent sets of these tables given and their location is specified in deMon basis SLAKO for standard DFTB and in deMon basis SCC SLAKO for self consistent charge DFTB The parameter tables differ slightly from those which are available at http www dftb org so before you use your own tables please contact one of the deMon Nano authors Moreover deMon Nano comes with two sets of SCC DFTB parameters The default parameters have been developed for materials and should be cited as follows J Frenzel A F Oliveira N Jardillier T Heine and G Seifert Semi relativistic self consistent charge Slater Koster tables for density functional based tight binding DF TB for materials science simulations TU Dresden 2004 2009 The content of the default SCC DFTB parameter file deMon basis SCC SLAKO file is identical to deMon basis MAT SCC SLAKO If you study organic or biological systems we recommend to use a parameter set which has been optimised for these applications An excellent choice is the set of Marcus Elstner to be cited as in ref 119 which is available in BIO SCC SLAKO In order to activate this you may want to copy BIO SCC SLAKO to SCC SLAKO Options DFTB SCC DISP DIAG nethod BS SIMPLE MIX value MAX value TOL value L DEP FERMI FERMI ETOL SPL
110. ith the ones in the deMon pie file These entries can also be modified manually in order to use the same VU control file for different molecular fields 3 3 Input Syntax The input of deMon is easy and mnemonic and at the same time offers high flexibility The input file contains keywords options and keyword bodies A keyword forms together with its options and the keyword body a keyword block The ordering of these blocks is free All keywords with exception of GEOMETRY have associated default values which are used if the keyword is not explicitly specified in the input Table 4 summarizes the special symbols allowed in the job input file deMon inp The input lines in the job input file deMon inp are restricted to 160 characters The input 3 3 Input Syntax 21 Table 3 Logical and physical filenames in deMon The I 0 units are given in parentheses Logical Physical Filename Filename Description AUXIS AUX Auxiliary function file ASCII BASIS BAS Basis set file ASCII ECPS ECP ECP file ASCII deMon cub CUB Embedding file ASCII deMon inp INP Input file ASCII deMon out OUT Output file ASCII deMon new NEW New input file for restart ASCII deMon mol MOL MOLDEN input file ASCII deMon mkl MOL MOLEKEL input file ASCII deMon pie PIE VU control file ASCII deMon rst RST RESTART file BINARY deMon lat LAT Plot lattice file ASCII BINARY deMon qmd MDRST MD restart file ASCII deMon nmrll NMR11 NMR grid file BINARY deMon nmr70 NMR70 NMR dimens
111. izations To print guess molecular orbitals use a combination of the keywords SCFTYP MAX 1 and PRINT MOS 4 4 5 Keyword MIXING This keyword controls the charge density mixing Options lt Real gt Fixed charge density mixing parameter between 0 and 1 lt Real gt Dynamic charge density mixing parameter The default is 0 3 OMA The optimal mixing algorithm is activated Description 52 4 Keywords Hartree damping 44 of the charge density fitting coefficients is performed using the specified the charge density mixing parameter Smaller mixing parameters correspond to stronger damping For some systems mixing parameter smaller than default e g 0 1 may be necessary to achieve convergence If a dynamic mixing parameter is chosen the mixing ratio is reduced during the SCF iterations if the Minmax SCF error increases The OMA option activates the optimal mixing algorithm of Canc s 43 This option is recommended if the dynamical mixing fails or is converging slowly It should be noted that OMA possesses a considerable overhead and exhibits bad convergence for small HOMO LUMO gaps 4 4 6 Keyword SHIFT This keyword activates the level shift procedure Options lt Real gt Fixed level shift value in a u lt Real gt Dynamic level shift value in a u Description The level shift procedure allows artificially expanding the HOMO LUMO gap during SCF iterations 45 This stabilizes the initial SCF configuration The shi
112. large systems the FULL option of the VISUALIZATION keyword produces very large MOLDEN and MOLEKEL input files Therefore it is recommended to use the VU interface for the plotting of molecular fields of large systems see the keyword PLOT and ISOSURFACE below In the case of a frequency analysis the FULL option is activated by default in order to animate the vibrations For molecular dynamics runs only VISUALIZATION MOLDEN XYZ is supported This option will be used regardless of the parameters supplied here 94 4 Keywords 4 11 2 Keyword PLOT This keyword controls the calculation and plotting of molecular fields See the keywords BOX 4 11 6 and POINTS 4 11 7 for the definition of the plot support Options FIELD Molecular field specification The available field acronyms are given in Table 9 This option is mandatory BASIS AUXIS BASIS The orbital density is used for the construction of the plot function This is the default AUXIS The auxiliary function density is used for the construction of the plot function This option is incompatible with the READ option BINARY ASCII TABLE BINARY A binary file FIELD bin is written containing the coordinates and plot function values The VU file format is used The VU control file deMon pie is written too This is the default ASCII An ascii file FIELD asc is written containing the coordinates and plot function values TABLE A function table is written in the output f
113. ld to be visualized For example a file RHO bin is created for the visualization of the electronic density The deMon pie file is the VU control file and refers in this case to the RHO bin file If the job is executed 20 3 Carrying On Table 2 Parameter settings in the shipped deMon version Parameter Setting Description MAXDISK 8192 Maximum disk size for scratch files in Mbytes MAXRAM 32768 Maximum RAM size for program kernel in Mbytes MAXATOM 20000 Maximum number of atoms MAXAUX 5000 Maximum number of auxiliary functions MAXAUXSET 2000 Maximum number of auxiliary function sets MAXAUXSHL 2000 Maximum number of auxiliary function shells MAXCON 21 Maximum degree of contraction MAXCUBE 100000 Maximum number of cube embedding points MAXGTO 5000 Maximum number of primitive Gaussian functions MAXECPGTO 2500 Maximum number of ECP Gaussian functions MAXECPSHL 500 Maximum number of ECP shells MAXLAUX 6 Maximum L quantum number for auxiliary functions MAXLBAS 5 Maximum L quantum number for basis functions MAXLECP 5 Maximum L quantum number for ECP functions MAXSHL 3000 Maximum number of orbital basis shells MAXSTO 3000 Maximum number of contracted STO orbitals MAXTBSTO 3000 Maximum number of tight binding STO orbitals MAXADJ 25 Maximum number of close bond line contacts per atom by a script care has to be taken that these files are copied from the working directory to the output path and that the filenames are consistent w
114. letes successfully you are now ready to use deMon 2 3 Porting deMon to a new platform Compiling deMon on a previously upsupported platform involves a bit more work 1 Examine the existing platform definition files in the deMon makefiles sys directory Select a platform definition file which is most similar to your system If none of the platforms appear similar choose sys generic mak 12 2 Getting Started 2 Create a copy of the prototype platform definition file using a short descriptive name corresponding to your platform 3 Edit the new platform definiton file following the instruction within the file itself Also see the appendix B 4 Set the environment variable deMonPlatform to reflect the name of your configura tion file For example if your new platform configuration file is called sys babayaga mak the appropriate shell command is export deMonPlatform babayaga for bash setenv deMonPlatform babayaga for csh 5 Execute the commands cd deMon makefiles make clean build tools 6 Run the test suite see sections 2 2 4 and C 7 If any of the tests fail iterate to 3 above 2 4 Tuning deMon for a specific host You can almost always improve the preformance of deMon by using higher optimization levels and or supplying vendor optimized mathematical libraries The tuning procedure is very similar to the porting procedure outlined section 2 3 above The only difference is 1
115. mic gas 100 and harmonic vibrational approximation For diatomic molecules a ro vibronic correction term is included see code The electronic contributions are neglected apart from the trivial contribution due to the multiplicity of the ground electronic state The options MAX and MIN allow specification of the temperature range The step size of the temperature interval is defined by the option INT The output contains the heat capacities Cp the entropy S the enthalpy H and the inner energy U for each temperature Also the natural logarithm of the partition function z zyransZrotZvibZel 18 given Imaginary normal modes are not included in the summation 4 9 7 Keyword FNMC Requests finite nuclear mass correction Options OFF ON Description With this keyword the finite nuclear mass correction to the self atomic elements of the kinetic energy matrix are switched on Before you use this you should read the literature e g ref 101 4 9 8 Keyword HARDNESS Compute orbital dependent reactivity indices hardness softness and Fukui function Options 86 4 Keywords DELN Energy perturbation in electrons The defalt is 0 01 FPMO First perturbed molecular orbital The default is 1 TOL Tolerance for degeneracy detection in Hartree The default is 107 Description Compute orbital dependent reactivity indices hardness softness and Fukui function as given in a supplied preprint by Mineva and Heine 4 10 Solvent Ef
116. n auxiliary function expansion for the electron density This approximated density p r is expanded in primitive Hermite Gaussians k r which are centered at the atoms Pe Dar Kr 1 5 With the LCGTO expansion for p r and p r we obtain the following approximate SCF energy Escr i S Paty ED dk Y Pw py k HA k KV 1 2 3 ty i k 1 Exc p 1 6 k l Therefore only three center electron repulsion integrals ERIs are necessary for the SCF and energy calculation in deMon This represents the most accurate energy model available in deMon It is activated by the keyword VXCTYPE BASIS see Section 4 4 9 for more details about the VXCTYPE keyword By default VXCTYPE AUXIS the approximated energy is also used for the calculation of the exchange correlation energy Escr S Pw Hy tr Y Pw pw k HH k HH 1 4 How to Use deMon 5 Den lk SR 1 7 Dol This approximation has proven very accurate c1 kcal mol in combination with GEN A auxiliary functions sets see Section 4 2 2 and Appendix A for the selection and auto matic generation of GEN A auxiliary function sets Because it represents a considerable saving in computational time we suggest to use this approximation at the beginning of each study If high accuracy is requested the systems optimized with VXCTYPE AUXIS 1 7 should be further optimized with VXCTYPE BASIS 1 6 Usually convergence will be achieved within a few cycles If sensitive prop
117. n rst file VIB lt Real gt Scaling factor for the numerical step size Description By default only the infra red adsorption intensities of the harmonic normal modes are calculated using the dipolar approximation With the option RAMAN the Raman in tensities in atomic units and the depolarization ratio 99 are calculated too This is considerably more time consuming conpared to the standard frequency analysis The RESTART option permits the restart of a frequency analysis The Hessian matrix el ements already calculated are read from the restart file deMon rst and the analysis is continued The VIB option allows adjustments to the numerical step size used for dif ferentiation of the ananytical gradients By default step size of 0 001 Bohr is used for VXCTYP BASIS see section 4 4 9 If VXCTYP AUXIS is used the default displacement is changed to 0 025 Bohr For examples with VIB 2 and VXCTYP BASIS the step size becomes 0 01 Bohr 4 9 Property Control 85 4 9 6 Keyword THERMO This keyword activates the calculation of thermodynamic functions The THERMO key word can only be used in combination with the FREQUENCY keyword see Section 4 9 5 Options MAX lt Real gt Maximum temperature The default is 2000 K MIN lt Real gt Minimum temperature The default is 100 K INT lt Real gt Temperature interval The default is 100K Description The thermodynamic functions are calculated in the approximation of the ideal polyato
118. n zero initial velocities 4 8 2 Keyword MDSTEPS This keyword controls the steps of the molecular dynamic MD simulation Options MAX OUT SOUT MDRST TSIM MAX lt Integer gt Maximum number of MD steps The default is 1 TSIM lt Real gt Maximum MD run time in ps OUT lt Integer gt Step interval to update the deMon mol file The default is 10 SOUT lt Integer gt Step interval to update the deMon out file The default is 1 MDRST lt Integer gt Step interval to update the deMon qmd file The default is 1 Description MDSTEPS controls the total runtime of the MD simulation either by the number of MD steps or by specifying a requested runtime 12 4 Keywords In addition parameters which control the I O load of the calculation can be specified The output to deMon mol and to deMon qmd trajectory and restart might be time consuming in particular when running in parallel Therefore it makes sense to select larger intervals for saving restart information and to write the trajectory only at intervals where they are meaningful 4 8 3 Keyword MDTEMP This keyword specifies the desired temperature of the molecular dynamic MD simula tion Options lt Real gt Desired MD temperature in Kelvin The default is 300 Description This keyword may affect a molecular dynamics run in two ways For MDYNAMICS RANDOM the desired temperature is used to rescale initial velocities Otherwise in a normal MD run MDTE
119. ng coefficients In the case of the AUXIS option only charge density fitting coefficients are used in the DHS step Therefore no extra I O is necessary In the case of the BASIS option also density matrices are used in the DIIS step leading to an increase in the I O overhead 54 4 Keywords DIIS procedure will be restarted if any of the extrapolation coefficients exceeds CMAX in absolute magnitude or if the determinant of the DIIS linear problem drops below DMIN The defaults for these values are adequate in an overwhelming majority of cases and should not be tinkered with 4 4 8 Keyword BROYDEN This keyword activates the BROYDEN convergence procedure Options TOL lt Real gt The BROYDEN procedure is switched on after the SCF energy error is smaller than lt Real gt MAX lt Integer gt Number of iterations stored in BROYDEN procedure The default is 10 Description The BROYDEN procedure is a special form of mixing which tries to minimize the error ie the difference between a guess vector and a returned vector of the SCF procedure by inversion of an error matrix The error matrix is defined in the standard way as for example in DIIS The new guess depends on the former iterations as well as on the MIXING coefficient The method is applied only on charge density coefficients 4 4 9 Keyword VXCTYPE With this keyword the exchange correlation potential is selected It also controls the density used for the exchange correlat
120. nput keywords This is the default Treat the whole system using molecular mechanics Partition system into QM and MM parts as specified by the QM MM keywords in the geometry section This keyword can also be given as simply ON Specifies coupling Hamiltonian used to describe interactions be tween the QM and MM parts The default is MECHANICAL Specifies time synchronization between the partitions The default is SYNCHRONOUS Both QM part and MM part are treated within periodic boundary conditions This option is only available for DFTB as QM part As default the QM region is treated as a cluster molecule and PBC are applied only to the embedding MM part With the default QMMM QM setting all keywords and flags related to molecular mechanics and hybrid calculations are recognized but ignored in the input file The whole system is therefore treated using DFT Hamiltonian The opposite setting QMMM MM will use molec ular mechanics forcefield specified by the FORCEFIELD keyword see 4 5 2 to treat the entire system If this option is specified deMon will behaive as if QMMM MM has been given for each atom in the GEOMETRY section see 4 1 1 This option is particularly useful for the initial geometry optimization or for the initial part of a molecular dynamics equilibration run Finally the QMMM QM MM will honour all QM MM related input options The two options supported for the QM MM coupling Hamiltonian COUPLING are 60 4
121. ns Additionally the following options can be specified a auxis Specify alternate basis set file The default fiting basis set file is looked up in the current directory then in deMon installation directory b basis Specify alternate basis set file The default is looked up exactly as for the auxis d debugger Specify an alternative debugger the default is gdb e ecp Specify alternate ECP file The default is looked up as described for auxis 8 Start deMon interactively in a debugger p Print the name of deMon binary to be used and exit h Print summary of the available options r directory Use directory to store restart files and other large files pro duced by the simulation By default it is the current directory s directory Use directory for scratch files V Be verbose q Be quiet 18 2 Getting Started x program Use an alternative deMon binary The deMon driver expects to find the job input using the syntax described in Section 3 3 in the file specified on the command line with the extension inp attached Depending on the job type additional data have to be provided in files with the same base name and extensions cub lat rst and qmd The main deMon output is stored in a file with the extension out Additionally some system information is provided in a file with the same base name and extension err Depending on the nature of the job additional output files with extensions
122. ns to lower energy or bitals and will give identical occupations to degenerate MOs An application of SMEAR is shown in Example 5 10 4 3 6 Keyword CONFIGURE This keyword controls the atomic configuration and is therefore only applicable for atoms Options MAX lt Integer gt Maximum number of SCF cycles for which the configuration is used By default it is used for all SCF cycles OCCUPY The fractional occupation of the specified atomic configuration will be given explicitly Description The orbital configuration is defined in the first line of the keyword body of CONFIGURE In the case of OKS and ROKS calculations see 4 4 1 two lines the first for the a orbital configuration and the second for the P orbital configuration are requested If spherical orbitals see 4 4 2 are used one integer number for s three for p five for d etc have to be specified Empty shells see 4 2 1 for the definition of a shell can be omitted In deMon spherical orbitals are defined over real spherical harmonic Gaussians 27 as omitting normalization de sm 4 5 Here 57 are real spherical harmonics which have been constructed from complex spherical harmonics by 28 n ttr 4 6 i v2 It should be noted that the 57 are not eigenfunction of the lm operator and therefore SC es ron Yr7 4 7 m is no longer a good quantum number for these orbitals The ordering of the integer numbers in the configuration line f
123. od for the three center electron repulsion integrals ERIs Options CONVENTIONAL DIRECT MULTIPOLE MEMORY CONVENTIONAL All ERIs are calculated at the beginning of the SCF procedure and stored DIRECT All ERIs are recalculated at each SCF iteration MEMORY Chooses between CONVENTIONAL and DIRECT based on the available memory This is the default MULTIPOLE An asymptotic multipole expansion for long range ERIs is performed The DIRECT option is activated too TOL lt Real gt Threshold for ERI screening The default is 10 for CONVENTIONAL and 10 otherwise Description Calculation of the three center ERIs is one of the most time critical steps in a deMon calculation Therefore the calculation method should be carefully selected The CON VENTIONAL method calculates ERIs before of the SCF procedure and if possible stores them in memory RAM This so called in core method is extremely fast as long as all integrals fit into the RAM The RAM size is controlled with the MAXMEM keyword see Section 4 12 1 If the RAM space is not sufficient deMon will write ERIs to the scratch file ioeri scr Thus the ERIs have to be read from the disk in each SCF step For larger systems this disk I O becomes the bottleneck of the calculation The DIRECT method 41 avoids the disk I O by recalculating the ERIs in each SCF step This is therefore the method of choice for larger systems where the ERIs do not fit in the available RAM space
124. of atomic Gaussian type orbitals LCGTO are used for representing Kohn Sham orbitals In this ansatz the Kohn Sham orbitals v r are given by bir Liu 1 1 Here u r represents an atomic orbital build from contracted Gaussians and c the corresponding molecular orbital coefficient With this expansion we find for the electronic density p r Y Pw ur vr 1 2 4 1 Getting Acquainted Pv represents an element of the closed shell density matrix defined as occ Py 2 DONO Cyi 1 3 Using the LCGTO expansions for the Kohn Sham orbitals 1 1 and the electronic density 1 2 the Kohn Sham self consistent field SCF energy expression 9 can be calculated as Esce Y Pao Hw 5 IL Paw Por uu lor End 14 m iv oT The total energy is the sum of Escr and the nuclear repulsion energy which can be calculated analytically In 1 4 H represents matrix elements of the core Hamiltonian They are built from the kinetic and nuclear attraction energy of the electrons and de scribe the movement of an electron in the nuclear framework The second term in 1 4 represents the Coulomb repulsion energy of the electrons In contrast to Hartree Fock theory the calculation of the Coulomb and exchange energies are separated in DFT For the calculation of the exchange correlation energy E pl a numerical integration has to be performed In deMon the calculation of the N scaling Coulomb repulsion energy is avoided by introducing a
125. ollows the shell and m index of the real spherical harmonics 4 3 Electronic State Control 43 Shell S p d l 0 1 2 m 0 1 0 1 2 1 0 1 2 Orbital E Py Pz Pz dry due d dez die As an example the open shell OKS or ROKS triplet ground state configuration of the carbon atom 1s 2s 2p can be defined in the keyword block of CONFIGURE as 211 200 The first line defines the a orbital configuration with 2 electrons in the most stable s 0 0 orbital 1s and 2s and 1 electron each in the most stable p m 1 and p m 0 a orbital The second line assigns 2 electrons to the two most stable 3 s orbitals Not specified shells here d and higher are not considered If Cartesian orbitals are used only the number of electrons in the s p d etc shells have to be specified Thus the above configuration changes for Cartesian orbitals to 22 20 Because of the p orbital degeneracy the chosen Cartesian configuration has to be stabi lized during the SCF procedure see 4 3 4 or 4 4 6 The calculation of the triplet carbon ground state with spherical and Cartesian orbitals using CONFIGURE is described in the examples 5 11 and 5 12 respectively In order to access excited atomic states or to use fractional occupation numbers the option OCCUPY has to be selected In this case an explicit definition of the orbital occupation is expected after the orbital configuration line s In the case of spherical atomic orbitals an input line
126. ometry Input 4 1 1 Keyword GEOMETRY This keyword is mandatory It specifies the molecular geometry Options CARTESIAN ZMATRIX MIXED CARTESIAN The molecular structure is given in Cartesian coordinates ZMATRIX The molecular structure is defined by a Z Matrix MIXED The first atoms of the molecular structure are defined by Cartesian coordinates and the following ones are defined by a Z Matrix ANGSTROM BOHR ANGSTROM Coordinates or bond distances are given in Angstr m BOHR Coordinates or bond distances are given in atomic units Description The geometry is read in the keyword body of GEOMETRY in free format one line for each atom In the case of a CARTESIAN input the atomic symbol e g H which may carry an identification number e g H1 and the x y and z coordinates of each atom of the system have to be specified As an example the geometry of H2O may be specified as 24 4 Keywords GEOMETRY CARTESIAN ANGSTROM 0 0 00 0 00 0 00 H 0 76 0 00 0 52 H 0 76 0 00 0 52 The Cartesian coordinates of an individual atom defined by the atomic symbol e g H2 or an atom group defined by the element symbol e g H can be frozen during the geometry optimization In order to keep all three degrees of freedom of an atom fixed the corresponding atomic symbol or element symbol has to be specified with the string XYZ in the keyword body of CONSTANTS The string X will only freeze the x coordinate of the atom the string XY the x
127. ops after the generation of the start density HARM Radius of the harmonic restraining potential in units of covalent atomic radius The default is 2 0 FREE Radius of the restraining potential for a free atom The default is 100 0 SCC Perform self consistent charge DFTB computation Description The choice of the start density can be crucial for the SCF convergence In most cases the tight binding start density is the recommended choice For metal clusters the core start density may be sometimes advantageous If the molecular orbitals of the start density for the printing of the MOs see Section 4 12 3 show only a very small HOMO LUMO gap the FERMI option may be used to obtain a better start density It should be noted that this option implies a SCF calculation and therefore is much more time consuming than the other start density options If a FERMI start density is used the OMA option of the keyword MIXING see 4 4 5 should not be applied The start density can also be read from the restart file deMon rst of a previous run With the keyword MOEXCHANGE see 4 3 3 the molecular orbital ordering of the start density can be altered The option ONLY stops the program after the start density is generated and written to the restart file This option is recommended if a FERMI start density was requested or the start density should be altered after inspection see example 5 14 Note that GUESS RESTART is currently not supported for geometry optim
128. or jacobi f LAPACK diagonalization routine LAPACK diagonalization routine divide and conquer LAPACK diagonalization routine relatively robust representations LAPACK least squares fit routine LAPACK routine for Cholesky factorization LAPACK routine for matrix inversion using Cholesky factorization LAPACK routine for triangular matrix inversion BLAS Level 1 routines BLAS Level 2 routines BLAS Level 3 DGEMM routine BLAS Level 3 symmetric rank k update e Try enforcing strict conformance to the IEEE 754 floating point standard Your compiler documentation should provide the instructions for enforcing the confor Mance e If you are building deMon with an external BLAS or LAPACK libraries try build ing using Fortran routines supplied with deMon itself Sometimes vendor supplied libraries are trading off accuracy for extra speed e If you are building deMon using Fortran BLAS or LAPACK included with the deMon distribution try building with vendor supplied numerical libraries Some times vendor compilers have issues with generating numerically accurate code for these routines but hand optimized numerical libraries work around these issues If none of these suggestions help try searching the archives of the deMon users mailing list and deMon developers mailing list Both archives are found at http www deMon software com If you cannot find the solution to your problem in the archives you can try sen
129. ostma W F van Gunsteren D DiNola J R Haak J Chem Phys 81 3684 1984 R S Mulliken J Chem Phys 23 1833 1955 138 References 94 P O Lowdin J Chem Phys 18 365 1950 95 I Mayer Chem Phys Lett 97 270 1983 Gonvalves Mohallem Chem Phys 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 Lett 280 378 2003 M S Gopinathan K Jug Theor Chim Acta 63 497 1983 R F W Bader Atoms in Molecules A Quantum Theory Clarendon Oxford 1990 P Calaminici K Jug A M K ster J Chem Phys 109 7756 1998 W F Murphy W Holzer H J Bernstein Appl Spectrosc 23 211 1969 K Jug F Janetzko A M K ster J Chem Phys 114 5472 2001 J R Mohallem T de O Coura L G Diniz G de Castro D Assafrao T Heine J Phys Chem A 112 2008 8896 8901 G Schaftenaar Molden3 2 CAOS CAMM Center University of Nijmegen 1997 S Portmann P F Fluekiger CSCS ETHZ and CSCS UNI Geneva 2002 R K Pathak S R Gadre J Chem Phys 93 1770 1990 A D Becke K Edgecomb J Chem Phys 92 5397 1990 B Silvi A Savin Nature 371 683 1994 W E Lorensen H E Cline Comp Graph 21 163 1987 M Leboeuf A M K ster K Jug D R Salahub J Chem Phys 111 4893 1999 LAPACK driver routine version 3 0 Univ of Tennessee Univ of California Berkeley NAG Ltd Courant Institut
130. plied by the POINTS keyword see Section 4 11 7 With the POINTS option POLYGON start points between atom pairs and triples are automatically generated This option is recommended for the critical point search of the density In addition to the critical point search the molecular connectivity over 3 1 critical points is generated 97 EFFECT OF AUXIS ON THE CPS gt SIGFRIDO 4 11 4 Keyword ISOSURFACE This keyword controls the calculation and plotting of molecular field isosurfaces Only one isosurface at a time can be generated For the generation of multiple isosurfaces the restart description of the keyword PLOT Section 4 11 2 can be applied See the keyword BOX 4 11 6 for the definition of the isosurface boundary Options FIELD Molecular field specification The available field acronyms are PSI RHO SPIN LAP ESP EFIDS and ELF See Table 9 for the acronym meanings This option is mandatory BASIS AUXIS 98 4 Keywords BASIS The orbital density is used for the construction of the isosurface This is the default AUXIS The auxiliary function density is used for the construction of the isosurface This option is incompatible with the READ option LINEAR BILINEAR LOGARITHMIC LINEAR Linear interpolation scheme for the isosurface construction This is the default LOGARITHMIC Logarithmic interpolation scheme for the isosurface construction BINARY ASCII TABLE BINARY A binary output of the isosurface is writ
131. plot box can be defined by vectors in the keyword body of BOX In this case the options STANDARD SMALL and LARGE as well as MEDIUM COARSE and FINE loose their meaning The following format is used for the box definition with vectors BOX READ i NI NJ NK XO YO ZO e XI YI ZI u XJ YJ ZJ Ti XK YK ZK To O where NI NJ and NK specify the number of points in the corresponding T J and k direc tions The 7 Zo Yo zo position vector defines the origin of the box The other three orthogonal vectors 7 i Yi zi T rj yj Zj and Fh Tk Yk Zk span the box as sketched above In the case of a plane two dimensional box the definition of NK XK YK and ZK are obsolete For a line one dimensional box only NI 7 and 7 have to be defined The explicit definition of a plot box is described in Example 5 17 4 11 Visualization and Topology 103 4 11 7 Keyword POINTS With this keyword points for the plotting of molecular fields 4 11 2 and start points for the critical point search 4 11 3 can be specified Options BINARY ASCII POLYGON READ BINARY The plot point coordinates and connectivities are read from the external binary file LAT bin This is the default ASCII The plot point coordinates and connectivities are read from the external ascii file LAT asc POLYGON Starting points for the critical point search are generated by the polygon algorithm READ The plot point coordinates are read from the input
132. r Due to the variational fitting of the Coulomb potential 38 39 a Minmax SCF procedure is implemented in deMon 40 In the variational Minmax procedure strict convergence from above is not guaranteed Therefore it is possible to obtain energies below the con verged energy during the SCF iterations in deMon Fitting can also lead to small scale noise on the order of the SCF convergence criterion in the energy during the geometry optimization The maximum number of SCF iterations is specified with the MAX option With MAX 0 an energy only calculation with the molecular orbital coefficients from the restart file is 44 SCF Control 47 performed No SCF iteration is done The MAX 0 option automatically triggers GUESS RESTART see 4 4 4 and therefore fails if no adequate restart file deMon rst exists The ordering and thus the occupation of the molecular orbitals in the restart file can be altered with the MOEXCHANGE keyword see Section 4 3 3 The SCF convergence criterion can be modified using the TOL option During geometry optimization user defined SCF convergence criterion is applied to the first single point SCF calculation In the course of optimization the convergence criterion is automati cally tightened according to the residual forces However if the user defined convergence criterion is smaller than the actual requested value it is used instead If self consistent perturbation calculation is performed the default SCF conver
133. r the ASCF method or time dependent density functional theory are preferable and usually lead to more accurate results 46 4 Keywords 4 4 SCF Control 4 4 1 Keyword SCFTYPE This keyword selects SCF method and convergence thresholds Options RKS UKS ROKS RKS The restricted Kohn Sham method will be used This is the default for closed shell systems UKS The unrestricted Kohn Sham method will be used This is the default for open shell systems ROKS The spin restricted open shell Kohn Sham method will be used MAX lt Integer gt Maximum number of SCF iterations Default is 100 TOL lt Real gt Minmax SCF convergence criterion Default is 1075 CDF lt Real gt Fit convergence criterion Default is max 107 10 TOL Description The Kohn Sham SCF methods are in their implementation similar to the corresponding Hartree Fock methods 31 35 Therefore they have similar advantages and disadvan tages Importantly in the case of UKS calculations spin contamination may appear In deMon the approximated spin contamination 36 37 is calculated and printed before of the converged UKS SCF energy This value has proven to be a good guide to judge the spin contamination of UKS calculations Please keep in mind however that this value is calculated for the Kohn Sham reference wavefunction and not for the true wavefunction of the system The physical significance of this spin contamination parameter is therefore not entirely clea
134. rd MT AXMEM 5 2 4 amp wedn a 5 eom Kap a BU a 105 412 2 Keyword TITLE s ee craba Bt Ba AAA 105 4 12 3 Keyword PRINT men 2 2 Wte Bae Se e 105 1124 Keyword EMBED y toorn ese ee O Gee ee 107 4 12 5 Keyword CHOLESkY llle 108 iv 5 Contents 4 12 6 Keyword MATDIA 4 12 7 Keyword WEIGHTING 4 12 8 Keyword QUADRATURE 2 nn 4 12 9 Keyword ECPINTEGRATION 4 12 10 Keyword GENAO EENEG Examples Bolt Example psig d e soe oe ERE ets ee ie BR GS ES Re ICR 5 2 Examples amk5 amk6 amk7 and amk8 5 3 Examples amk29 amk30 and amksl wise xw Eu a bdo Example ps0 2 utu Ae Mee E SOS m S esce ut AAA nu Example Thon uds u a E AE A dE Ee dmi os Gib Example ali o uos gts ab xor Ae deese ee HUE de ae dede te 3 7 Example psg4 s x Ae 2 dee dede adde E Woex A th 5 8 Example amk IB a opem eun ck E ego e e dE S 5 9 Example EE EE 5 10 Example pelo 4 css 2 22 E A EM e EE haw E BUD Example DSO Lent ume e tk koe ub Erbe es ee Seok de c PERROS S Ek 5 DA B sample dk A dw gical NL ad ably ae MOM IN ads are E Sc las eelere dta sos teu ea eu EE OE ENS 9 14 Example anmik3 gns aan Rav A ee a ero adc Loy os 5 15 Example rale vo aise 2 02 RC RA ber Aq nen dE Usado geh 5210 Example SOO xe de EA E ee GIVE DS Eon a E Robe be Siete Et 517 Example SOO a e eg fe P n EE Using QM MM in deMon Using MD in deMon Vu MAG 113 114 115 115 116 116
135. ropriate force field type see below This is the default 4 1 Geometry Input 31 BOND NOBOND charge This option can be used to specify partical charge on the MM atom in proton charge units It is up to the forcefield to use or not to use this charge GUESS A special charge GUESS which is the defalt will instruct deMon to guess the appropriate value list Specifies the list of explicit bonds for this atom Bond speci fication contains a list of colon separated atom ranges each followed by optional slash sign and the bond order Both atom numbers in the input order and atom labels are rec ognized atom labels must refer to a previously defined atom There are no restrictions on atom numbers A few examples 3 Bond to atom 3 the bond order will be guessed automatically C_PHEN 1 5 Bond of the order 1 5 to a previously defined atom with the label C_PHEN 15 17 Bonds to atoms 15 through 17 with automatically defined orders 1 2 2 3 1 0 Double bond to atom 1 single bonds to atoms 2 and 3 It is OK to specify a bond for only one of the connected atoms If FORCEFIELD BONDS AUTO is in effect explicit bonds take precedence over the guessed bonds list Specifies that no bond should be formed to these atoms The syntax of the atom ranges is identical to the BOND option NOBOND overrides automatically guessed bonds 32 4 Keywords Keywords QMMM CAP MMTYPE and Q can only appear once for each atom
136. rsion and repulsion energy contributions are calculated COMP O No charge compensation 1 The difference between calculated and theoretical polar ized total charge is distributed on each tessera propor tionally to its area 2 The calculated charge on each tessera is scaled by a costant factor SOLV Solvent one of WATER H20 DMSO DIMETHYL SUL FOXIDE NITROMETHANE METHANOL CH30H ETHANOL CH3CH20H ACETONE CH3COCH3 DICHLOROETHANE CH2CH2CL2 DICHLOROMETHANE CH2CL2 THF TETRAHY DROFURAN ANILINE CHLOROBENZENE CHLO ROFORM CHCL3 DIETHYLETHER ETHER TOLUENE BENZENE C6H6 CARBONTETRACHLORIDE CCL4 CYCLO HEXANE HEPTANE ACETONITRILE 4 10 Solvent Effects 89 EPS Value of dielectric constant DIRECT The PCM integral blocks are calculated at each SCF cycle RMIN Sets the minimum radius in Angstr ms of the added spheres to build the cavity TSNUM Number of tesserae on each sphere Description For the generation of the cavity the PCM and the Onsager Model require the definition of the atomic radii For the PCM the van der Waals radii can be used to build up the cavity putting a sphere around each atom The cavity is constructed by overlapping spheres with radii equal to the van der Waals radii For the Onsager Model the solute is enclosed in a spherical cavity whose radius by default is calculated as maximum distance between atoms of the solute plus the respective BONDI van der Waals radii The value of the
137. s Manual od ud ane ern RISE are How Use delVIOH ae cs aus doque cue OE Rae A See E cs 2 Getting Started 2 1 2 2 2 3 2 4 2 5 2 6 3 1 3 2 3 3 4 1 4 2 Before von BEB secet uw E EE How to Install deMon 2 3 2 2 gies E ER WEN We ae Eeke 2 2 1 Contents of the Distribution Package 2 2 2 Installation Preregisites ts A eg ae 2 2 3 Express Installation 25 te ta dw ate hed pex x RS 2 2 4 Advanced Installation ciar ea Il Porting deMon to a new Ee EE EE Tuning deMom for a specific host fuel ee wi den eten a a S What to do when things go wrong How to Run deMon os ea teen ad ee ee AE M RO Carrying On Parameters na ia Eet EL nd ae Se aeons Se ee Eust Lus lee Ar le ite E Ee e Ee dg E ce em ete Jnp t ADE sae ee E e ded Keywords Geometry pts dps In a er QR ee ee eat 4 1 1 Keyword GEOMETRY vz se gee Ya 8 22 2a eres es 4 1 2 Keyword CONSTANTS toernee meteen 2 ra SE 4 13 Keyword VARIABLES o 4 1 4 Keyword SYMMETRY nerd asten a ia Basis Set Input q sert te ui Rob he ao She a EE Ber delen ey 421 Keyword BASIS 22 pa 2 wee tette 422 Keyword AURIS curiose Ratbone oe ee Yk ee Se eae a ADs Keyword BOPS Luca wle Heden eae haten eS wW N N e E 0 A AA A 11 12 13 16 19 19 19 20 il 4 3 4 4 4 5 4 6 4 7 4 8 Contents Electronic State Control 22 e a 40 43 1 Keyword MULTIPLICITY occ 3 22822 re 40 4 3 2 Keyword CHARGE 2 2 2 5 d arn oale 2 und
138. s SCF cycle is used as reference configuration SCF lt Integer gt SCF cycle at which the projection procedure is turned on By default the projection starts with the first SCF cycle TOL lt Real gt SCF convergence tolerance after which the projection procedure is turned on Description The projection of the molecular orbital configuration is based on the maximum overlap criterion Qa in the form Once ese 4 4 LV where cha are the new molecular orbital coefficients and Le are MO coefficients of the reference configuration Occupations of a new MOs a is choosen to match the occupation of the most similar MO j of the reference cycle which occurs when Q is at maximum Note that FIXMOS and SMEAR keywords are mutually exclusive An application of FIXMOS is shown in 5 9 4 3 5 Keyword SMEAR This keyword allows fractional orbital occupations close to the Fermi level Options lt Real gt Energy range AE in a u around the Fermi level in which orbitals are fractionally occupied Description The SMEAR keyword effects only the molecular orbitals within the specified energy inter val Eyomo AE 2 Enowo AE 2 Therefore the AE value should be selected based 42 4 Keywords on the orbital energy spectrum see MOS option of PRINT in 4 12 3 The converged fractional orbital occupation is used in any further step of the calculation optimization frequencies properties etc SMEAR will assign higher occupatio
139. s are set to zero This allows tighter cutoffs and hence faster calculations but shifts the potential energy upwards X Specifies the energy shift which is X dij di specifying the depth of the van der Waals minimum of the interaction potential between centres and j The default is X 0 01 Description All van der Waals type non bonded pair interactions smaller than ECUT will be neglected This parameter affects both periodic and non periodic calculation Although this cut off looks extremely tight it is necessary to guarantee total energy conservation to within 0 1 kcal mol in a typical periodic MD simulation 4 5 5 Keyword MADELUNG This keyword sets defaults for the summation of the Madelung contribution to the elec trostatic potential used in DFTB MM and QM MM Options EWALD The Ewald summation technique is used for the Madelung poten tial This is the default SCREEN The real space summation described below is applied KAPPA The amp parameter for the Ewald summation If amp is negative deMon chooses it such that the real space part can be calculated within the minimum image convention This is the default D d parameter of the screening function in Bohr The default is 6 0 RO To parameter of the screening function in Bohr The default is 70 0 ECUT Energy cutoff in Hartee The default is 10 Description In periodic MM QM MM and DF TB calculation on systems with non negligible atomic char
140. se as possible to the original Fortran source B 2 Structure of a platform configuration files Platform configuration files in deMon are processes by the standard Unix make utility To be accepted by make these files have to follow a few simple syntactic rules 124 B Format of a platform description file e Lines beginning with the hash mark are treated as comments e A backslash character V in the last column of a line indicates that a line is to be continued on the following line e An alphanumeric sequence followed by the equals sign and a value indicates a variable assignment e As alphanumeric sequence followed by a colon introduces a rule A rule may be followed by zero or more actions Each action must consist of a tabulation character followed by a shell command Variables and rules which deMon build scripts expect to find in a platform configuration files are summarized in Table 10 Table 10 Structure of a platform configuration file SHELL Name of a POSIX compliant version of Bourne shell F90 Command used to invoke Fortran 90 compiler FTN_FIXED Command line option which selects the fixed Fortran 77 style source form FTN_FREE Command line option which selects the free source form F90COMMON Common compilation flags which will be applied to all Fortran source files In order to compile the deMon source code correctly you should instruct the compiler to treat REAL
141. sed for large systems deMon nano only uses robust opti misers with low memory consumption and with moderate numerical effort Options MAX Maximum number of optimisation steps The default is 100 TOL lt Real gt Optimization convergence criterion for the energy Default is 3 x 107 Hartree GRADTOL lt Re p imization convergence criterion for the gradients Default is 3 x 1075 Hartree STEP lt Real gt Maximum step size in optimization Default is 0 3 Bohr CGRAD Uses the conjugate gradient method This is the default SDC Uses the steepest descent method for geometry optimisation SDC lt Real gt Uses the steepest descent method for geometry optimisation with specified multiplied for the gradient The default is 0 1 OUT lt Integer gt Interval to output structure during optmimisation NUCFRIC Perform geometry optimisation via MD with additional friction term for degrees of freedom where velocity and gradient have op posite sign The multiplier of the dissipative term is by default 0 6 NUCFRIC lt ReaPe form optimisation via MD with additional friction term with a user defined mulitplier to the dissipative term INTQMO Interval when MOs are quenched during simultaneous optmimisa tion procedure of MOs and coordinates The default is 0 all steps Description deMon nano uses simple robust optimisation techniques which are scalable to large sys tems They include the steepest descent method a conjugate gradient scheme
142. specification line These parameters are in the keyword form parame ter value and do not need to appear in any particular order QM MM keywords are recognized and behave identically in all three input formats The QM MM related ge ometry keywords are Keyword Value QMMM MM QM LINK CAP ZLY1 ZLY2 DHC1 DHC2 DHC3 DHC4 ecp MMTYPE type GUESS 4 Keywords Description Specifies handling of this atom when QM MM is activated This atom is a part of the molecular mechanical subsystem This atom is a part of the quantum mechanical subsystem This a bond terminating atom at the QM MM boundary The default is MM if QM MM is activated and QM if it is not Specifies choice of the capping potential for a link atom 3 21G pseudohalogene capping potential of Ref 10 6 31G pseudohalogene capping potential of Ref 10 QCP1 pseudohydrogen capping potential of Ref 11 11 QCP4 pseudohydrogen capping potential of Ref 11 11 QCP2 pseudohydrogen capping potential of Ref 11 QCP3 pseudohydrogen capping potential of Ref 11 11 Use specified potential from the ECP library Specifies forcefield atom type Atom types are forcefield specific The list of the known atom types for the built in UFF force field is given in section 6 MMTYPE is relevant for all types of atoms including QM and LINK atoms A special atom type GUESS will instruct deMon to try to guess the app
143. spherical cavity radius can be modified by the option RAD value The options DIPOLE QUADRUPOLE and OCTUPOLE are valid only for Onsager Model and define the level of the expansion of the potential Basically only the core Hamiltonian is modified as 3 3 3 Aw He F gt fi bute bv 22 fin Oy Tk Tn Ov Ss gt 2 Trap Py TkTnTp by n np Where H is the core Hamiltonian matrix fj fj and eh are the dipolar quadrupolar and octupolar reaction field factors and bt dv Ou TrTn Ov and Lu tu Fal are the dipolar quadrupolar and octupolar integral blocks respectively The Partial Closure procedure CLS keyword permits to avoid the iterative self polarization internal cycles to calculate the virtual charge over the surface of each tessera One of the two levels of truncation can be selected by the option CLS 1 or CLS 2 By default the first level of truncation approach is switched on An iterative SCRF procedure can be performed by specifying the IT keyword For the Polarizable Continuum Model the electronic component of the electric field and the ap parent surface charge el I Ep E Pr CM ren t ES EN x ol DI E Ez EF are calculated at each I Self Consistent Field SCF cycle by the p density matrix If 90 4 Keywords this option is not active the electronic component of the electric field and the apparent surface charge are calculated once by the gas phase density matrix Pp For the Onsager Model more than one SCF
144. tandard diagonalisation tool DSYEV The computa tionally inefficient DSYEV routine is replaced by DSYEVR which is LAPACK s most perfor mant diagonaliser and which uses only a small work field This allows Born Oppenheimer DFTB computations with only 2 matrices in memory plus a little work field which is Or der N DFTB parameter files The DFTB method requires interaction parameters These are stored in so called Slater Koster tables With this distribution we provide three sets of tables which can be used for different types of applications If you have your own parameter files or if you obtained them through the www dftb org website you need to make them compatible to deMon In the deMon basis directory are two files which the program uses to identify the necessary parameter files These files are called SLAKO and SCC SLAKO These files has the following structure First it gives the atomic numbers of the pair of interaction so for exampe for H H 1 1 Then it gives the full string to the location of the parameter file At your installation it uses variables which are resolved in the deMon script If you want to use your own parameter tables you will have to adopt these files All parameter files are in the deMon basis skf directory 4 7 Optimization Control 69 4 7 Optimization Control 4 7 1 Keyword OPTIMIZATION This keyword controls the geometry optimization It differs considerably from the de Mon2K version as it is optimi
145. ten in the file LAT bin using the VU file format The VU control file deMon pie is written too This is the default ASCII An ascii output of the isosurface is written in the file deMon lat TABLE A function table of isosurface coordinates is written in the output file deMon out READ Specifies that an orbital list is read in the body of ISOSURFACE ISO lt Real gt Isosurface value This value is mandatory TOL lt Real gt Tolerance for data reduction Description The options AUXIS BASIS and READ of the ISOSURFACE keyword are identical to the corresponding options of the PLOT keyword 4 11 2 The BINARY option specifies that the isosurface coordinates and connectivities are written into the binary file LAT bin With the VU control file deMon pie that is also generated the isosurface grid can be visualized in VU see 8 It is important to note that the LAT bin file can be used as an input file for the plotting of a molecular field on the isosurface For this purpose this file has to be in the same directory as the deMon inp file and the POINTS keyword see Section 4 11 7 has to be used to define the isosurface in LAT bin as plot support With the ASCII option the ascii file deMon lat is generated This file contains the following data RHO 100000E 00 A U ISOSURFACE COORDINATES IN ANGSTROM 4 11 Visualization and Topology 99 NUMBER OF VERTICES 1814 NUMBER OF FACETS 3624 VOLUME 163076E 04 AREA 176664E 03 X Y
146. the occupation of 2 s orbitals and of all three p orbitals According to the defined occupation third line the two s orbitals are occupied each by 1 electron The three a p orbitals are homogeneously occupied by 2 3 of an electron 0 6666 in line 4 5 and 6 Finally the s orbital occupation is given by the last line see Example 5 14 Because the Kohn Sham method is a one determinant approach atomic states have to be approximated by one configuration see however 29 for a multi determinant approach This can be done as in spatially unrestricted Hartree Fock calculations 30 For s and p occupations all possible configurations yield the correct spatial symmetry However for d occupation this is not the case and care has to be taken to the occupation scheme The following d configuration have to be used d 4D dez PR dz Le el d P dey ds Ek CD dia lf ENK dz dy PES dez deez dev dee dye APD da da2 y2 dey dex dyz d F di Le el day dee dy 4 3 Electronic State Control 45 d C P dez da2 y2 dey daz AED dez dez day dee N N ZN HE a A Ed e D N Nef N N For the d d d and d configurations the orbital occupancies are purely arbitrary but for the d d d and d configurations the orbital occupancies must be as given above to yield the correct spatial symmetry Note however that for truly multiconfigurational cases eithe
147. the values for RAB TABC and PABCD directly in the Z Matrix they may also be represented by symbolic strings up to eight characters long These labels have to be defined in the CONSTANT and VARIABLE input sections see 4 1 2 and 4 1 3 As an example ethene C2H4 can be defined as GEOMETRY ZMATRIX ANGSTROM C1 C2 H1 H2 H3 H4 C1 Cl C1 C2 C2 rCC rCH rCH rCH rCH VARIABLES rCC 1 3390 C2 C2 C1 C1 aCCH aCCH aCCH aCCH Hi dHCCH H2 dHCCH Hi dHCCH 4 1 Geometry Input 27 rCH 1 0850 aCCH 121 09 CONSTANT dHCCH 180 0 The internal coordinates listed under VARIABLES may change during geometry opti mization whereas the coordinates given under CONSTANTS are kept frozen If one uses internal coordinates dummy atoms are often useful The atomic symbol X has been reserved for them The following example shows the use of a dummy atom in the definition of HCN GEOMETRY ZMATRIX ANGSTROM H C 1 R1 X 2 1 0 1 90 0 N 2 R2 3 A 1 180 0 VARIABLES R1 1 089 R3 1 166 A1 90 00 Here the dummy atom is used to avoid a 180 angle which may cause problems in a geometry optimization Example 5 1 shows the use of a dummy atom for the definition of a ring system In order to facilitate the input of the internal coordinates for some special cases alternative geometrical parameters can be given instead of angles and dihedral angles in the Z Matrix input The substitutions are indicated by string codes which may
148. to display many scalar fields critical points etc and select the way of visualize it Before using Vu the user has to run deMon with the proper visualization keywords in order to generate the two required files for the graphical interface deMon pie The control file for Vu It contains all the definitions for construct the images FIELD bin This file is referred by the deMon pie file Contains the values of the scalar field selected for plotting Most supporting definitions for chemistry used by deMon reside in the deMonMacros vu file which is included automatically at run time So deMonMacros vu file should reside in the location where Vu stands 8 3 Running Vu To start Vu first export the display to your current window then on the command line type Vu and press Enter key The program starts without any file and then you can get your own deMon pie file from the menu or type Vu deMon pie The program starts with the structure associated to the pie file that you typed There are other ways to read files See Vu reference manual When Vu starts three windows appear on the screen 1 Menu Window Used to build images 2 Visualization Window Empty at startup or displaying the molecular structure if a pie file was selected Used to visualize and modify images 3 Message Window Used by Vu to show information extracted of the files and error messages The user can adjust the size and position of these windows with the mo
149. tput Print ECP table Print embedding charges Print three center electron repulsion integrals Prints the program flux for debugging purpose Print auxiliary function Coulomb matrix Generate full grid output Print primitive GTO table Print Kohn Sham and core Hamiltonian matrix MAX lt Integer gt Maximum number of SCF cycles with print output MD MDEXTRA MM MOE MOS OPT ORTHO P POPAN PBC QMMM RAM S SYMMETRY T TB XCE XCV PC MC AVTTY Print detailed MD output Print insanely detailed MD output Print additional MM output Print molecular orbital energies and occupations Print molecular orbital energies occupations and coefficients Generate full optimization output Print orthogonalization matrix S Print density matrix Generate full population analysis output Print periodic bondary conditions information Print additional QM MM information Print RAM allocation table Print overlap matrix Generate full symmetry output Print kinetic energy matrix Print tight binding matrices Generate full exchange correlation energy output Generate full exchange correlation potential output Print cavity information in deM on cav and deVM on nem oantnnte 4 12 Miscellaneous Keywords 107 Description With the MAX option the number of SCF cycles with active print output can be specified All matrices that are changing during the SCF e g P KS MOS etc can be printed for each
150. ul The input may be modified and extended However the molecular geometry specified in this file should not be changed if the restart file will be used However the new input file may change the ordering of the atoms in the molecule As a result it should not be used for continuing molecular dynamics simulations 2 Getting Started 7 2 Getting Started 2 1 Before you Begin Before you begin the installation process please make sure to consult operating system specific instructions which came with the distribution They are found in the subdirectory doc os of the deMon distribution The list of system specific notes available at the time this manual was prepared is given in tablel Table 1 Platform specific installation notes in doc os README forcheck Forchek http www forcheck nl README ifc Intel Fortran compiler on Linux x86 README pathscale PathScale Fortran 90 compiler on Linux x86 64 AMD64 README pgi Portland Group Fortran 90 compiler on Linux x86 and Linux x86 64 README SunOS SUN OS and Solaris hosts README Tru64 OSF 1 Digital Unix and Tru64 hosts README windows MicroSoft Windows These notes summarise many days of porting and debugging and may save you countless hours of frustration 2 2 How to Install deMon 2 2 1 Contents of the Distribution Package deMon distribution package contains the following basis deMon basis sets bin Executable directory doc Documentation examples
151. use Menu window This window is composed of 1 a menu bar File Zones Info Options Stereo Help 2 a list of images proposed by Vu 8 3 Running Vu 117 3 the lists of Supports Entities and Windows components of the image See figure Through the File option of the menu bar the user can open a pie file among others Or can import files in other formats Gaussian PDB etc or save profiles data and images The Images part of this Menu window lets the user select the image to be displayed in the visualization window By default the Geometry image is active at startup To select other image just click with the mouse on the box at the left of the image desired An unlimited number of images can be displayed simultaneously on the Visualization window Each time the user selects an image on the Image section the corresponding Support Entity and Window associated with is shaded in the bottom section of this window By clicking with the mouse these shaded Supports Entities and Windows the user open new windows where their attributes can be changed to modify the way the image is displayed See chapter 8 of the Vu Reference Manual 118 9 MAG 9 MAG The deMon program prepares the data needed to run the MASTER program 115 116 for NMR shielding tensor and EPR Fermi term and anisotropic hyperfine tensor proper ties The deMon program provides the ground state electronic structure of a system in the absence of an external m
152. variables and con stants as well as all untyped floating point literals in at least 64 bit precision On many Unix systems the r8 compilation option will do this You should also instruct the compiler to look in the deMon include directory On many systems I INCL is the right option Please do NOT add optimization options to this line B 2 Structure of a platform configuration files 125 F900PT Normal optimization flags which should apply to most source files On many UNIX systems the 0 compilation option will correspond to safe optimization setting please consult your com piler s documentation F900PTLOW Low optimization settings which may be required to compile a few of the source code files which are not treated correctly at the default level You ll be able to specify the affected files later in FILES_LOW F900PTHIGH Extra high optimization settings not suitable for most files but required for a few of them You l be able to specify the affected files later in FILES HIGH LIBPATH Use this entry to specify non standard locations of the object libraries required to link the code On most UNIX systems the correct syntax is Lpath Several locations may be specified if necessary LINKLIB Specify any additional libraries here usually BLAS If you in clude an optimized BLAS or LAPACK libraries please make sure to exclude generic versions of these routines supplied with deMon in FILES EXCLUDE FILE
153. ven t So it s best to read the three first chapters now Here is a brief sketch of what s in the remaining chapters Chapter 2 gives an overview about how to install and run the program using the make files and scripts which come with deMon Chapter 3 explains how to customize the program parameters and input output files It also explains the input syntax 1 4 How to Use deMon 3 Chapter 4 gives a detailed description of all input keywords and their options Chapter 5 discusses the input and output of the examples Chapter 8 describes the interface between deMon and Vu a configurable visualization tool It also explains basic operations within Vu Chapter 9 describes the interface between deMon and MAG a program for the calcu lation of NMR properties It also describes the use of MAG Chapter 10 is a quick reference guide to all input keywords Chapter 6 is a more in depth introduction to QM MM features implemented in deMon Chapter 7 gives additional hints on running molecular dynamics simulations Chapter 4 6 gives all DFTB and CP DFTB related commands Chapter 11 describes troubleshooting of common problems Appendix A describes the automatic generation of auxiliary function sets Appendix B describes the format of the platform configuration files used by the deMon build system Appendix C describes the structure test suite for deMon and how to expand it 1 4 How to Use deMon In deMon linear combinations
154. ving a large subset of tools specified by the POSIX Unix standard IEEE Std 1003 1 2001 If you need to build deMon on a platform lacking full POSIX support such as Microsoft Windows or some exotic variants of Unix you can do the following 1 Find a POSIX compliant Unix system Linux or SGI Irix will work very well Most recent Unix systems should also work 2 Unpack deMon distribution and follow advanced installation instructions in section 2 2 4 The platform you will need to build for is called flatsource It cannot be invoked through the express installation script The build script will populate the deMon flatsource directory with symbolic links to all relevant source code files 3 In the directory deMon flatsource execute shell script deMon unsupported flat makedepen It will create a rudimentary Makefile for building deMon 14 2 Getting Started 4 Transfer all files collected in the flatsource dirctory to your target system You may find this command tar chf deMon source tar useful for following symbolic links 5 Build deMon on your target system using the minimum necessary force If you experience errors while running deMon shell scripts check your operating system documentantion for instructions on enabling POSIX conformance Some hints for the Tru64 and Solaris operating systems are found in deMon doc os If you experience mysterious crashes running compiled binary try some of the followin
155. y the driver script is make s f platform_makefile checkplatform This target will typically check the operating system name CPU model compiler name and version Please keep in mind that all platform specific makefiles get invoked in this way by make makesys on every platform this is how make makesys determines which makefiles are appropriate This target should produce a one line description of the platform specific makefile on standard output You should always put something here This target should produce any platform specific installation in structions or warnings on standard output If there are no spe cific instructions leave this empty For a successful compilation you need to provide platform specific implementations of the following two functions DETIME This REAL function must return CPU time in seconds used by the program since it started DEFLUSH This subroutine taking one integer argument the Fortran LUN num ber must ensure that all outstanding write operations on that LUN have completed deMon comes with several pre defined implementations for these routines which are listed in Table 11 128 B Format of a platform description file Table 11 Platform specific functions in the shipped deMon version Function Path Description DETIME platform Generic detime f95 F Portable Fortran 95 routine using CPU_TIME intrinsic DETIME platform Linux detime F Use system library subroutine E

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