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The PSI3 User's Manual

1. 3 4 Molecular QUIET cuoi koe koh e Sea dea X eS aa 3 5 Specifying Scratch Disk Usage in PSI3 lll 36 he peire 54 adda foe Se ehh Ee HGH GS POSSE Bae 3 1 Specifying Basis Sets hak ok zoo o o Ro EERE REE RE 3 4 1 Default Basis Sets 3 7 2 Custom Basis Sets 3 7 3 Automated Conversion of Basis Sets ln 3 8 Specification of Ghost Atoms lll 4 Theoretical Methods Available in PSI3 4 1 Hartree Fock SelEConsistent Field o ll 4 2 Second order Moller Plesset Theory MP2 and MP2 R12 methods 4 2 1 Basie Keywords 42 644 e ee eee eRe 3 Rex Re Y ES 4 2 2 Using the MP2 R12 method i 122 9 oS 4 2 3 Larger Calculationg 26 24 sou RR RERO a OUR Reb cn c CU gm A A A o ADO Oo OD 11 11 12 14 15 16 18 19 19 19 24 24 4 3 Coupled Cluster Methods 4 kan rte AL que ex 4 3 1 Basic Keyword 644 we d 4x wRdhRg dee he 43 EE ewe Ee s 4 3 2 Larger Calculations 2 6 4 26644 deb Ro p ORO ob a 4 3 3 Excited State Coupled Cluster Calculations 4 3 4 Linear Response CCLR Calculations 4 4 Configuration Interaction 2 14 ax OR dae G 379 b Re Re te REC ede Eo 44 1 Basic Keywords 4 4 2 Arb
2. G d p 6 311G 2d 2p H Ar 6 3114 4 G 2d 2p H Ar 6 311 G 3df3pd H Ar Table 4 Huzinaga Dunning basis sets available in PSI3 Basis Set Atoms 45 25 H 9S5P 482P B F 11S7P 6S4P Al Cl DZ H Li B F ALCI DZP H Li Be B F Na ALCI DZ DIF H B F ALCI DZP DIF H B F ALCI TZ2P H B F Al Cl TZ2PD H TZ2PF H B F Al Cl TZ DIF H B F Al Cl TZ2P DIF H B F Al Cl TZ2PD DIF H TZ2PF DIF H B F Al Cl 20 Table 5 Wachters basis sets available in PSI3 Basis Set Atoms WACHTERS K Sc Cu WACHTERS F Sc Cu Table 6 Correlation consistent basis sets available in PSI3 Basis Set Atoms Aliases N D T Q 5 6 cc pVNZ H Ar CC PVNZ cc pV N D Z ALAr CC PV N D Z cc pCVNZ B Ne CC PCVNZ aug cc pVNZ H He B Ne ALAr AUG CC PVNZ aug cc pV N D Z aug cc pCVNZ d aug cc pV NZ pV7Zi cc pV7Z2 aug pV7Z aug cc pV7Z Al Ar B F N 6 H H C NO F S H C NO F S H C NO F S H N O F AUG CC PCV N d Z AUG CC PCVNZ PV7Z CC PV7Z AUG PV7Z AUG CC PV7Z 21 where L l m n 2 is written as basis ATOM_NAME BASIS_SET_LABEL L C1 alphal C2 alpha2 C3 alpha3 CN alpha4 One must further specify whether Cartesian or spherical harmonics Gaussians are to be used One can specify that in two ways e It can be done on a basis by basis case such as basis BASIS SET LABEL1 puream true
3. ROHF for a restricted open shell calculation UHF for an unrestricted open shell calculation or TWOCON for a two configuration singlet The default is RHF MULTP integer Specifies the multiplicity of the molecule i e 25 1 Default is 1 singlet CHARGE integer Specifies the charge of the molecule Default is 0 DERTYPE string This specifies the order of the derivative that is to be obtained The default is NONE energy only DOCC integer vector This gives the number of doubly occupied orbitals in each irreducible representation There is no default If this is not given cscf will attempt to guess at the occupations SOCC integer vector This gives the number of singly occupied orbitals in each irreducible representation There is no default If this is not given cscf will attempt to guess at the occupations 13 FREEZE_CORE string PSI3 can automatically freeze core orbitals Core orbitals are defined as follows H Be no core B Ne 1s Na Ar small 1s2s large 1s2s2p YES or TRUE will freeze the core orbitals SMALL or LARGE are for elements Na Ar The default is NO or FALSE Always check to make sure that the occupations are correct 3 3 Geometry Specification The molecular geometry may be specified using either Cartesian a Z matrix coordinates Cartesian coordinates are specified via the keyword geometry geometry atomnamel x y1 zl atomname2 x2 y2 z2 atomname3 x3 y3 z3 atomnameN xN
4. J Aa Jensen J Chem Phys 89 2185 1988 3 B O Roos P R Taylor and P E M Siegbahn Chem Phys 48 157 1980 4 G Chaban M W Schmidt and M S Gordon Theor Chem Acc 97 88 1997 5 P Pulay Chem Phys Lett 73 393 1980 6 P A Malmqvist A Rendell and B O Roos J Phys Chem 94 5477 1990 7 K K Docken and J Hinze J Chem Phys 57 4928 1972 8 K Ruedenberg L M Cheung and S T Elbert Int J Quantum Chem 16 1069 1979 52
5. Turns the scaling off if set to zero otherwise the higher value the stronger the gradient field will be scaled Recommended value default is 5 This keyword is only useful when GRID 3 7 3 Grid specification mini tutorial Let s look at how to set up input for spin density evaluation on a two dimensional grid The relevant input section of PSI3 might look like this jobtype oeprop grid 2 spin_prop true grid_origin 0 0 5 0 5 0 grid_unit_x 0 0 1 0 0 0 grid_unit_y 0 0 0 0 1 0 grid_xy0 0 0 0 0 grid_xy1 10 0 10 0 nix 30 niy 30 grid specifies the type of a property and the type of a grid oeprop needs to compute Since spin prop is set and grid 2 the spin density will be evaluated on a grid Grid specification is a little bit tricky but very flexible grid origin specifies the ori gin of the rectangular coordinate system associated with the grid in the reference frame grid unit x specifies a reference frame vector which designates the direction of the x axis of the grid coordinate system grid unit y is analogously a reference frame vector which along with the grid unit x completely specifies the grid coordinate system grid unit x and grid unit y do not have to be normalized neither they need to be orthogonal to ei ther other orthogonalization is done automatically to ensure that unit vectors of the grid 47 coordinate system are normalized in the reference frame too grid_xy0 is a vector in
6. for MP2 R12 A There is no default REFERENCE string The only acceptable value are rhf uhf and rohf There is no default JOBTYPE string Acceptable values are sp and opt There is no default MEMORY real MB Specified the amount of core memory to be used in MB Defaults to 256 Other units e g KB or GB are also allowed DIRECT boolean Specifies whether to use the conventional false or integral direct true algorithm Default is false NUM_THREADS integer Specified the number of threads to be used in the integral direct computation only valid if DIRECT is set to true Default is 1 FREEZE_CORE boolean Specifies whether core orbitals which are determined automatically are to be excluded from the correlated calculations Default is false PRINT integer The desired print level for detailed output Setting this to 2 is a good idea for larger calculations so that the progress of the calculation may be easily followed Defaults to 0 OPDM boolean If true calculate the one particle density matrix The default is false OPDM_WRITE boolean If true write the one particle density matrix to disk OPDM PRINT boolean If true print the one particle density matrix to the output file 2f 4 2 2 Using the MP2 R12 method Although this manual is not a how to on running quantum chemistry applications the MP2 R12 method is a rather non standard tool hence a few comments on its use are appropriate
7. storage for integrals wave function ampltiudes etc By default PSI3 will write all such datafiles to tmp except for the checkpoint file which is written to by default However to allow for various customized arrangements of scratch disks the PSI3 files block gives the user considerable control over how temporary files are organized including file names scratch directories and the ability to stripe files over several disks much like RAIDO systems This section of keywords is normally placed within the psi section of input but may be used for specific PSI3 modules just like other keywords For example if the user is working with PSI3 on a computer system with only one scratch disk mounted at e g scr one could identify the disk in the input file as follows psi files 16 default nvolume 1 volumel scr The nvolume keyword indicates the number of scratch directories disks to be used to stripe files and each of these is specified by a corresponding volumen keyword NB the trailing slash is essential in the directoy name Thus in the above example all temporary storage files generated by the various PSI3 modules would automatically be placed in the scr directory By default the scratch files are given the prefix psi and named psi nnn where nnn is a number used by the PSI3 modules The user can select a different prefix by specifying it in the input file with the n
8. you can start any line with and the line will be a comment line This can make the input file easier to understand because you can provide explainations about each keyword Another way to make the input file more organized is to seperate it into sections that correspond to particular modules the calculation will use This can be particularly helpful for more complicated computations which can utilize many of keywords In the example below a CCSD T computation for the BH molecule is performed using a cc pVDZ basis set The keywords are divided into sections and several new keywords are introduced including ones to specify symmetry and orbital occupations Orbitial occupations are specified by a list of integers enclosed in parentheses These integers give the number of orbitials which belong to each irreducible representation in the point group The ordering of the irreps are those given by Cotton in Chemical Applications of Group Theory In this example comment lines will be included to explain the new keywords used psi wfn ccsd t reference rhf default label BH cc pVDZ CCSD T e Allocating memory for the calculation memory 600 0 MB charge and multiplicity 2S 1 default to values of 0 and 1 respectively charge 0 multp 1 The program will generally guess the symmetry of the molecule but it can be overridden Here we specify C2V because only D2H and its subgroups can be used by the program symmetry c
9. 1 The version of the MP2 R12 method implemented in PSI3 is a so called single basis MP2 R12 method in standard approximation A This means that a basis set rather complete in Hartree Fock or one particle sense is absolutely mandatory for mean ingful computations with the MP2 R12 method The user is strongly urged to read literature on linear R12 methods before using PSI3 to compute MP2 R12 energies 2 More robust two basis versions of the MP2 R12 method also known as the auxiliary basis MP2 R12 method have been implemented in a publicly available Massively Paral lel Quantum Chemistry MPQC package see http aros ca sandia gov cljanss mpqc The two basis version of the MP2 R12 method is a theoretically more sound approach and thus should be preferred to the single basis method In some situations however it may make sense to use the single basis method 4 2 3 Larger Calculations Here are a few recommendations for carrying out extended integral direct MP2 and MP2 R12 calculations with PSI3 1 While the integral direct MP2 algorithm doesn t need any significant disk storage the integral direct algorithm for the MP2 R12 energy stores the transformed integrals to disk hence very large computations will require a lot of disk space In general the storage requirement is 160 N bytes where o is the number of occupied orbitals and N is the size of the basis 2 If there is not enough memory to perform the computati
10. 6 31Gx x zmat Hom Oo zvars a 104 5 In this example the psi identifier collects all the keywords of varying types together Every PSI3 module will have access to every keyword in the psi block by default One may use other identifiers e g ccenergy to separate certain keywords to be used only by selected modules For example consider the keyword convergence which is used by several PSI3 modules to determine the convergence criteria for constructing various types of wave functions If one wanted to use a high convergence cutoff for the PSI3 SCF module but a lower cutoff for the coupled cluster module one could modify the above input psi convergence 7 scf convergence 12 Note that since we have only one keyword associated with the scf block we do not need to enclose it parentheses Some additional aspects of the PSI3 grammar to keep in mind e The character denotes a comment line i e any information following the up to the next linebreak is ignored by the program e Anything in between double quotes i e strings is case sensitive e Multiple spaces are treated as a single space 3 2 Specifying the Type of Computation The most important keywords in a PSI3 input file are those which tell the program what type of computation are to be performed They jobtype keyword tells the psi3 program whether 12 this is a single point computation a geometry optimization a vibratio
11. BASIS SET LABEL2 puream false BASIS SET LABELS puream true By default if puream is not given for a basis then Cartesian Gaussians will be used e The choice between Cartesian or spherical harmonics Gaussian can be made globally by specifying puream keyword in the standard input section e g psi puream true Note that currently PSI3 cannot handle basis sets that consist of a mix of Cartesian and spherical harmonics Gaussians Note that the basis set must be given in a separate basis section of input outside all other sections including psi For example the PSI3 DZP basis set for carbon could be specified as 22 basis carbon DZP S 4232 6100 0 002029 634 8820 0 015535 146 0970 0 075411 42 4974 0 257121 14 1892 0 596555 1 9666 0 242517 S 5 1477 1 05 S X 0 4962 1 0 S 0 1533 1 0 P 18 1557 0 018534 3 9864 0 115442 1 1429 0 386206 0 3594 0 640089 P 0 1146 1 0 D 0 75 1 0 Here are a couple of additional points that may be useful when specifying customized basis sets e Normally the basis dat file is placed in the same directory as the main input file but it may also be placed in a global location specified by the keyword basisfile basisfile home users tool1 chem h20 mybasis in e To scale a basis set a scale factor may be added as the last item in the specification of each contracted Gaussian function For example to scale th
12. MAXNVECT Higher order energies 2n 1 and 2n 2 can be computed at no additional computational cost by using WIGNER TRUE By default the nth order energy is saved but 2n 1 or 2n 2 order energies can be saved using SAVE MPN2 1 or SAVE MPN2 2 respectively For open shell systems arbitary order ZAP Tn energies can be computed using WEN ZAPTN and REF ROHF All other options are the same as closed shell MPn 4 5 Complete Active Space Self Consistent Field CASSCF Multi configurational self consistent field MCSCF is a general method for obtaining qual itatively correct wavefunctions for highly strained molecules diradicals or bond breaking reactions The most commonly used MCSCF procedure is the complete active space self consistent field CASSCF approach 3 which includes all possible determinants with the proper symmetry that can be formed by distributing a set of active electrons among a set 36 of active orbitals The detcasman module performs CASSCF optimization of molecular or bitals via a two step procedure in which the CI wavefunction is computed using detci and the orbital rotation step is computed using detcas The detcas program is fairly simple and uses an approximate orbital Hessian 4 and a Newton Raphson update accelerated by Pulay s DIIS procedure 5 We have also implemented a prototype version of the RASSCF method 6 which is another kind of MCSCF which is typically less complete a
13. NB The A0 BASIS DIRECT option is not fully implemented and should only be used by experts Default is NONE Note The developers recommend use of this keyword only as a last resort because it significantly slows the calculation The current algorithms for handling the MO basis four virtual index integrals have been significantly improved and are preferable to the AO based approach FREEZE CORE boolean Specifies whether core orbitals which are determined automatically are to be excluded from the correlated calculations Default is FALSE RESTART boolean Determine whether previous amplitude vectors may be used as guesses in a given CC calculation Defaults to TRUE For geometry optimizations Brueckner calculations etc the iterative solution of the CC amplitude equations may benefit considerably by reusing old vectors as initial guesses Assuming that the MO phases remain the same 30 between updates the CC codes will by default re use old vectors unless the user sets RESTART false PRINT integer The desired print level for detailed output Setting this to 2 is a good idea for larger calculations so that the progress of the calculation may be easily followed Defaults to 0 CACHELEV integer Sets the level of automated cacheing of four index quantities in the CC modules These modules are capable of keeping in core as much as possible various four index quan tities categorized by the number of virtual unoccupied orbital i
14. PSI3 Installation Manual available as part of the package or at the PSI3 website above 1 3 Supported Architectures The majority of PSI3 was developed on IBM RS 6000 AIX and x86 GNU Linux worksta tions The complete list of tested architectures to which PSI3 has been ported is shown in Table 1 If you don t find your system in the Table there s a good chance that you will be able to install PSI3 on your system if you have the prerequisite tools and math and utility libraries described in the installation manual Table 1 Platforms on which PSI3 has been installed successfully Architecture Notes Compaq Alpha Tru64 UNIX 64 bit mode IBM AIX 4 3 3 5 x on PowerPC 64 bit mode Linux on Intel AMD x86 and x86 64 32 and 64 bit Apple OS X Darwin on PowerPC and Intel SGI IRIX64 gt 6 5 15 64 bit Table 2 Summary of theoretical methods available in PSI3 Method Energy Gradient Hessian RHF SCF Y Y Y ROHF SCF Y Y N UHF SCF Y N N HF DBOC Y N N CIS RPA TDHF Y N N TCSCF Y Y N CASSCF Y Y N RASSCF Y Y N RAS CI Y N N RAS CI DBOC Y N N RHF MP2 Y Y N UHF ROHF MP2 Y N N RHF MP2 R12 Y N N RHF UHF ROHF CCSD Y Y N RHF UHF ROHF CCSD T Y Y N RHF UHF ROHF EOM CCSD Y Y N CCSD T gradients implemented only via an experimental code A more efficient and robust implementa tion will appear in the next release 1 4 Capabilities PSI3 can perform ab initio computations employing basis sets of up
15. approaches which includes electron correlation directly Due to its simplicity the MP2 method is often the best level one can afford for a larger molecular system At the other end of the spectrum the MP2 R12 method of Kutzelnigg Klopper and co workers is a promising approach to computing MP2 energies in the complete basis set limit for smaller systems PSI3 is one of the very few publicly available programs to feature a robust implementation of the MP2 R12 method PSI3 is capable of computing closed shell MP2 and MP2 R12 A energies using integral direct techniques and a multithreaded algorithm which lends itself perfectly for execution on symmetric multiprocessor SMP machines PSI3 is also capable of computing RHF UHF and ROHF using semicanonical orbitals MP2 energies and one particle density matrices and RHF MP2 analytic gradients Occupied and virtual orbitals can be frozen during the energy calculation but not for the calculation of the one particle density matrix or the analytic gradient Table 7 summarizes these capabilities 4 2 1 Basic Keywords To compute a ground state MP2 or MP2 R12 energy at a fixed geometry the following keywords are common 26 Reference Method Energy conv Energy integral direct Gradient RHF MP2 Y Y Y UHF MP2 Y N N ROHF MP2 Y N N RHF MP2 R12 A N Y N Table 7 Current MP2 and MP2 R12 capabilities of PSI3 WEN string Acceptable values are mp2 for MP2 mp2r12
16. computation By default this information will be written to disk Transition dipole moments will be evaluated in detci Note only transition densities between roots of the same symmetry will be evaluated detci does not compute states of different irreps within the same computation to do this lower the symmetry using the subgroup keyword in psi O or default O see section 3 4 DIPMOM boolean If TRUE evaluate the dipole moment for each root using the expectation value formula orbital relaxation contributions are neglected This is an alternative to evaluation using the oeprop module which has more features REF_SYM integer This option allows the user to look for CI vectors of a different irrep than the reference This probably only makes sense for Full CI and it is not supported for unit vector guesses MPN boolean If TRUE compute MPn energies up to nth order where MAXNVECT n controls the maximum order energy computed For open shell systems REF ROHF WEN ZAPTN ZAPTn energies are computed For larger computations additional keywords may be required as described in the detci man pages 4 4 2 Arbitrary Order Perturbation Theory PSI3 is capable of computing arbitrary order Moller Plesset perturbation theory MPn closed shell systems and Z averaged perturbation theory ZAP Tn open shell systems en ergies invoked with MPN TRUE The maximum level of perturbation theory computed is controlled by
17. the grid coordinate system that specifies a vertex of the grid rectangle with the most negative coordinates Similarly grid xy1 specifies a vertex of the the grid rectangle diagonally op posite to grid xyO Finally nix and niy specify the number of intervals into which the x and y sides of the grid rectangle are subdivided To summarize the above input specifies a rectangular in fact square 30 by 30 grid of dimensions 10 0 by 10 0 lying in the yz plane and centered at origin of molecular frame Running PSI3 on such input will create a file called sdens dat for file names refer to man page on oeprop which can be fed directly to PlotMTV to plot the 2 D data Specification of a three dimensional grid for plotting MOs grid 5 or densities grid 6 is just slightly more complicated For example let s look at producing data for plotting a HOMO and a LUMO The indices of the MOs which needs to be plotted will be spec ified by keyword mo to plot The reference frame is specified by keywords grid origin grid unit x and grid origin y the third axis of the grid coordinate system is specified by by the vector product of grid unit x and grid unit y Since in this case we are dealing with the three dimensional grid coordinate system one needs to specify two diagonally op posite vertices of the grid box via grid xyzO and grid xyzi The number of intervals along z is specified via niz The relevant section of input file may look like this jobt
18. to 32768 contracted Gaussian type functions of virtually arbitrary orbital quantum number PSI3 can recognize and exploit the largest Abelian subgroup of the point group describing the full symmetry of the molecule Table 2 displays the range of theoretical methods available in PSI3 Geometry optimization currently restricted to true minima on the potential energy sur face can be performed using either analytic gradients or energy points Likewise vibrational frequencies can be computed using analytic second derivatives by finite differences of ana lytic gradients or finite differences of energies PSI3 can also compute an extensive list of one electron properties 1 5 Technical Support The PSI3 package is distributed for free and without any guarantee of reliability accuracy suitability for any particular purpose No obligation to provide technical support is expressed or implied As time allows the developers will attempt to answer inquiries directed to crawdad vt edu For bug reports specific and detailed information with example inputs would be appreciated Questions or comments regarding this user s manual may be sent to SherrillO0gatech edu 2 A PSI3 Tutorial 2 1 Before Getting Started A Warning about Scratch Files Generally electronic structure programs like PSI3 make significant use of disk drives There fore it is very important to ensure that PSI3 is writing its temporary files to
19. to be executed to STDOUT The default is false EXEC string vector The EXEC vector contains a list of commands to be executed by psi3 Explicit com mands can be entered in double quotes or preset variables can be entered using the convention variable e g psi or exec psi ints exec ints ints ints 8 4 Loop Control Loop control is handled with the repeat and end commands The syntax is repeat n commands to be executed end where n is the number of times to repeat the loop An inspection of the psi dat file will show that this is how geometry optimizations and finite displacements are performed 9 Additional Documentation Additional information and the most recent version of this manual may be found at the PSI3 website www psicode org age is available in the PSI3 Installation Manual For programmers the is available online along with complete library documentation 51 More complete information on the installation of the PSI3 pack PSI3 Programmer s Manual A PSI3 Reference T Daniel Crawford C David Sherrill Edward F Valeev Justin T Fermann Rollin A King Matthew L Leininger Shawn T Brown Curtis L Janssen Edward T Seidl Joseph P Kenny and Wesley D Allen J Comput Chem 28 1610 1616 2007 References 1 N C Handy Chem Phys Lett 74 280 1980 N J Olsen B O Roos P J rgensen and H
20. 2v sk x x Number of doubly occupied orbitals per irrep can be specified manually if desired docc 3 0 0 0 Freeze the 1A1 orbital Boron 1s like in the CCSD T computation frozen_docc 1 0 0 0 The input section contains information about the molecule and the basis set The geometry here is specified by cartesian coordinates input basis cc pVDZ units angstroms geometry b 0 0000 0 0000 0 0000 Ch 0 0000 0 0000 0 8000 origin 0 0 0 0 0 0 The modular input structure lets you specify convergence criteria for each part of the computation separately scf maxiter 100 convergence 11 The final example of this tutorial demonstrates an example of a complete active space self consistent field CASSCF computation CAS computations require specification of sev eral additional keywords because you must specify which orbitals you wish to be in the active space The notation and ordering for specifying CAS orbitals is the same as for occupied orbitals 6 31G H20 Test CASSCF Energy Point psi label 6 31G CASSCF H20 jobtype sp wfn casscf reference rhf The restricted docc orbitals are those which are optimized but are not in the active space restricted docc 1 0 0 0 The active space orbitals here the valence orbitals are chosen active 3 0 1 2 basis 6 31Gx x zmat O h 1 1 00 h 1 1 00 2 103 1 10 3 PSI3 Input Files 3 1 Sy
21. ASSCF computations has been added This is accomplished using the average states keyword See the casscf sp and casscf sa sp examples in the tests directory and the example below 4 5 1 Basic Keywords WEN string This may be casscf or rasscf REFERENCE string Any of the references allowed by detci should work i e not uhf but there should be no reason not to use rhf DERTYPE string At present only energies none are supported future releases will implement gradients first CONVERGENCE integer Convergence desired on the orbital gradient Convergence is achieved when the RMS of the error in the orbital gradient is less than 10 n The default is 4 for energy 37 calculations and 7 for gradients Note that this is a different convergence criterion than for the detci program itself These can be differentiated if changed by the user by placing the CONVERGENCE keywords within separate sections of input such as detcas convergence x ENERGY CONVERGENCE integer Convergence desired on the total MCSCF energy The default is 7 RESTRICTED DOCC integer array Should be in psi O or default sections of input The number of lowest energy doubly occupied orbitals in each irreducible representation from which there will be no excitations These orbitals are optimized in the MCSCF The Cotton ordering of the irredicible representations is used The default is the zero vector RESTRICTED
22. Acceptable values are ccsd ccsd_t for CCSD T beca for Brueckner orbital based CCD or bccd t for Brueckner orbital based CCSD T There is no default REFERENCE string Acceptable values are reference rhf rohf or uhf There is no default JOBTYPE string Acceptable values are sp opt freq oeprop or response There is no default CONVERGENCE integer Sets the order of magnitude on the convergence of the CC wave function perturbed wave function and or lambda parameters The root mean square of the difference in amplitude vectors from consecutive iterations is used to determine the convergence The default is 7 MAXITER integer The maximum number of iterations allowed for solving the CC amplitude or lambda amplitude equations Defaults to 50 MEMORY real MB Specified the amount of core memory to be used in MB Defaults to 256 Other units e g KB or GB are also allowed BRUECKNER CONV integer Specifies the order of magnitude convergence required for the Brueckner orbitals The convergence is determined based on the largest T1 amplitude AO BASIS string Specifies the algorithm to be used in computing the contribution of the four virtual index integrals ab cd to the CC amplitude equations If AO BASIS NONE the MO basis integrals will be used if A0 BASIS DISK the AO basis integrals stored on disk will be used if A0 BASIS DIRECT the AO basis integrals will be computed on the fly as necessary
23. However it cannot utilize distributed memory machines such as commodity PC clusters and massively parallel machines to their full potential since one computation can only take advantage of one node of such machine at a time In such environments the aformentioned MPQC implementation of the MP2 R12 method should be preferred see http aros ca sandia gov cljanss mpqc 4 3 Coupled Cluster Methods The coupled cluster approach is one of the most accurate and reliable quantum chemical techniques for including the effects of electron correlation PSI3 is capable of computing energies analytic gradients and linear response properties using a number of coupled cluster models Table 8 summarizes these capabilities This section describes how to carry out coupled cluster calculations within PSI3 Table 8 Current coupled cluster capabilities of PSI3 Reference Method Energy Gradient Exc Energies LR Props RHF CC2 Y N X Y UHF CC2 Y N Y N ROHF CC2 Y N Y N RHF CCSD Y Y Y Y RHF CCSD T Y N ROHF CCSD Y Y Y N ROHF CCSD T N N UHF CCSD Y Y Y N UHF CCSD T Y am Brueckner CCD Y N N N Brueckner CCD T X N CCSD T gradients implemented via an experimental code A more efficient and robust implementation will appear in the next release 4 3 1 Basic Keywords To compute a ground state CCSD or CCSD T energy at a fixed geometry the following keywords are common 29 WEN string
24. NIT XY1 real vector A vector of 2 real numbers this keyword specifies the coordinates of the upper right corner of a 2 D grid in the 2 D coordinate system defined by GRID ORIGIN GRID UNIT X and GRID UNIT Y This keyword is only used to specify a 2 D grid There is no default GRID UNIT XYZO real vector A vector of 3 real numbers this keyword specifies the coordinates of the far lower left corner of a 3 D grid in the 3 D coordinate system defined by GRID ORIGIN GRID UNIT X and GRID_UNIT_Y This keyword is only used to specify a 3 D grid There is no default GRID_UNIT_XYZ1 real vector A vector of 3 real numbers this keyword specifies the coordinates of the near up per right corner of a 3 D grid in the 3 D coordinate system defined by GRID_ORIGIN GRID UNIT X and GRID UNIT Y This keyword is only used to specify a 3 D grid There is no default 46 In addition the following keywords are useful for evaluation of certain properties on 2 D grids GRID ZMIN real This keyword specifies the lower limit on displayed z values for contour plots of electron density and its Laplacian Only useful when GRID 2 or GRID 4 Default is 0 0 GRID ZMAX real This keyword specifies the upper limit on displayed z values for contour plots of electron density and its Laplacian Only useful when GRID 2 or GRID 4 Default is 3 0 EDGRAD_LOGSCALE integer This keyword controls the logarithmic scaling of the produced electron density gradient plot
25. PRINT CARTESIANS DISPLACEMENTS integer float A user may specify displacments along internal coordinates using this keyword For example displacements 2 0 01 3 0 01 will compute a new cartesian geometry with the second and third internal coordinates increased by 0 01 6 Vibrational Frequency Computations PSI3 is also capable of computing harmonic vibrational frequencies for a number of different methods using energy points or analytic energy first or second derivatives At present only RHF SCF analytic second derivatives are available If analytic energy second derivatives are not available PSI3 will generate displaced geometries along symmetry adapted cartesian coordinates compute the appropriate energies or first derivatives and use finite difference methods to compute the Hessian The following keywords are pertinent for vibrational frequency analyses JOBTYPE string This keyword must be set to FREQ for frequency analyses DERTYPE string This keyword may be set to NONE if only energies are available for the chosen method or FIRST if analytic gradients are available 42 POINTS 3or 5 Specifies whether frequencies are determined by a 3 point or a 5 point formula of gradient differences If only energy points are used more displacements are required but the effect of this keyword in terms of accuracy is the same Note In some situations vibrational frequency analysis via finite differences may f
26. Sets PSI3 default basis sets are located in pbasis dat which may be found by default in psipath share Tables 3 4 5 and 6 list basis sets pre defined in pbasis dat The predefined basis sets use either spherical harmonics or Cartesian Gaussians which is determined by the authors of the basis Currently PSI3 cannot handle basis sets that consist of a mix of Cartesian and spherical harmonics Gaussians Therefore there may be combinations of basis sets that are forbidden e g cc pVTZ and 6 31G In such case one can override the predetermined choice of the type of the Gaussians by specifying the puream keyword It takes two values true or false for spherical harmonics and Cartesian Gaussians respectively 3 7 2 Custom Basis Sets If the basis set you desire is not already defined in PSI3 a custom set may be used by specifying its exponents and contraction coefficients either in the input file or another file named basis dat A contracted Cartesian Gaussian type orbital N caro Y y 2 Y C exp as x y z 1 19 Table 3 Pople type basis sets available in PSI3 Basis Set Atoms Aliases STO 3G H Ar 3 21G H Ar 6 31G H Ar K Ca Cu 6 31G H Ar K Ca Cu 6 31G d 6 314 G H Ar 6 31 G d 6 31G H Ar K Ca Cu 6 31G d p 6 311G H Ar 6 311G H Ar 6 311G d 6 311 G H Ne 6 311 G d 6 311G H Ar 6 311G d p 6 311G 2df 2pd H Ne 6 311 G H B Ar 6 311
27. The PSI3 User s Manual C David Sherrill T Daniel Crawford Edward F Valeev Micah L Abrams Rollin A King and Ashley Ringer Center for Computational Molecular Science and Technology Georgia Institute of Technology Atlanta Georgia 30332 0400 Department of Chemistry Virginia Tech Blacksburg Virginia 24061 0001 Department of Chemistry Bethel College St Paul Minnesota 55112 6999 PSI3 Version 3 4 0 Created on February 16 2009 Report bugs to psicodeQusers sourceforge net Contents 1 Introduction 1 1 Overview e 1 2 Obtaining and Installing PSUS 42 2 uox eo od oe RO ox o9 REOR ox 1 3 Supported Architectureg 0 4 ORO RCRUM Ue e NR ge e lp OMS bardas ed m4 Bees Ge dor ee de edo p Irsa eed 1 5 Technical S ppatt s s s c s seresa noa segta om eh Ru Keo Be 2 A PSI3 Tutorial 2 1 Before Getting Started A Warning about Scratch Files 22 Basic Input File Structure 54 47x ora ia AAA 2 3 Running a basic SCF calculation lt 4 21569 o Roe RES 2 4 Geometry Optimization and Vibrational Frequency Analysis 2 5 More Advanced Input Options 43k ok a Rn Ox NOx we eS 3 PSIS3 Input Files 3 1 Syntax 2 ss 3 2 Specifying the Type of Computation len 3 3 Geometry Specification ee
28. UOCC integer array Should be in psi O or default sections of input The number of highest en ergy unoccupied orbitals in each irreducible representation into which there will be no excitations These orbitals are optimized in the MCSCF The default is the zero vector FROZEN DOCC integer array Should be in psi O or default sections of input The number of lowest energy doubly occupied orbitals in each irreducible representation from which there will be no excitations These orbitals are literally frozen and are not optimized in the MCSCF usually one wishes to use RESTRICTED DOCC instead The current version of the pro gram does not allow both RESTRICTED DOCC and FROZEN DOCC Should be in psi O or default sections of input The Cotton ordering of the irredicible representations is used The default is the zero vector FROZEN UOCC integer array Should be in psi O or default sections of input The number of highest energy unoccupied orbitals in each irreducible representation into which there will be no ex citations These orbitals are literally frozen and are not optimized in the MCSCF usually one wishes to use RESTRICTED UOCC instead The current version of the pro gram does not allow both RESTRICTED UOCC and FROZEN UOCC Should be in psi O or default sections of input The default is the zero vector NCASITER integer Maximum number of iterations to optimize the orbitals This option should be specified
29. a disk drive phsyically attached to the computer running the computation If it is not it will signifi cantly slow down the program and the network By default PSI3 will write temporary files to tmp but you will want to set up a default scratch path as described in sections 3 5 and 3 6 because the tmp directory is usually not large enough except for small test cases In any event you want to be very careful that you are not writing scratch files to an NFS mounted directory that is physically attached to a fileserver elsewhere on the network 2 2 Basic Input File Structure PSI3 reads input from a text file which can be prepared in any standard text editor The default input file name is input dat and the default output file name is output dat So that you can give your files meaningful names these defaults can be changed by specifying the input file name and output file name on the the command line The syntax is psi3 input name output name PSI3 is a modular program with each module performing specific tasks and computa tions Which modules are run for a particular computation depends on the type of com putation and the particular keywords specified in the input file All keywords in PSI3 use the structure keyword value where values may be strings booleans integers or real numbers If the value is a string which contains a special character such as a space or a dash you must enclose the string in dou
30. ail if the full point group symmetry is specified via the symmetry keyword This happens because the user given symmetry value can become incompatible with the actual symmetry of the molecule when energies or gradients are evaluated for symmetry lowering displacements In such situations the user is advised to let the program determine the symmetry automatically rather than specifying symmetry manually Otherwise an error such as the following may result error problem assigning number of operations per class stopping execution The manual pages for the normco and intder95 modules contain information on addi tional tools useful in vibrational frequency analysis and coordinate transformation 7 Evaluation of one electron properties PSI3 is capable of computing a number of one electron properties Table 9 summarizes these capabilities This section describes details of how to have PSI3 compute desired one electron properties 7 1 Basic Keywords To compute one electron properties at a fixed geometry the following keywords are common JOBTYPE string This keyword should be set to oeprop for PSI3 to compute electron properties There is no default For CI wavefunctions limited properties such as dipole and transition moments may be evaluated directly in detci without having to specify JOBTYPE oeprop WEN string Acceptable values are scf for HF mp2 for MP2 detci for CI detcas for CASSCF and ccsd for CCSD The
31. ame keyword psi files default name H20 nvolume 1 volumel scr The name keyword allows the user to store data associated with multiple calculations in the same scratch area Alternatively one may specify the filename prefix on the command line of the psi3 driver program or any PSI3 module with the p argument psi3 p H20 If the user has multiple scratch areas available PSI3 files may be automatically split evenly across them psi files default nvolume 3 volumel scr1 volume2 scr2 volume3 scr3 17 In this case each PSI3 datafile will be written in chunks 65 kB each to three separate files e g scr1 psi 72 scr2 psi 72 and scr3 psi 72 The maximum number of volumes allowed for striping files is eight 8 though this may be easily extended in the PSI3 I O code if necessary The format of the files section of input also allows the user to place selected files in alter native directories such as the current working directory This feature is especially important if some of the data need to be retained between calculations For example the following files section will put file32 the PSI3 checkpoint file into the working directory but all scratch files into the temporary areas psi files default nvolume 3 volumel scr1 volume2 scr2 volume3 scr3 file32 nvolume 1 volumel 3 6 The psirc Fil
32. ar 3 D grid that covers the entire molecular system However there s no default way to construct a useful 2 D grid in general Even in the 3 D case you may want to zoom in on a particular part of the molecule Hence one needs to be able to specify general 2 D and 3 D grids In the absence of graphical user interface PSI3 has a very flexible system for specifying arbitrary rectalinear grids The following keywords may be used in construction of the grid GRID ORIGIN real vector A vector of 3 real numbers this keyword specifies the origin of the grid coordinate system A rectangular grid box which envelops the entire molecule will be computed automatically if GRID ORIGIN is missing however there is no default for 2 D grids GRID UNIT X real vector A vector of 3 real numbers this keyword specifies the direction of the first x side of the grid It doesn t have have to be of unit length There is no default for 2 D grids GRID UNIT Y real vector A vector of 3 real numbers this keyword specifies the direction of the second y side It doesn t have to be of unit length or even orthogonal to GRID_UNIT_X There is no default for 2 D grids GRID UNIT XYO real vector A vector of 2 real numbers this keyword specifies the coordinates of the lower left corner of a 2 D grid in the 2 D coordinate system defined by GRID ORIGIN GRID UNIT X and GRID UNIT Y This keyword is only used to specify a 2 D grid There is no default GRID U
33. ariables in the z matrix which end in a dollar sign will be taken as simple internals to be optimized and all other variables will be taken as simple internals to keep frozen To aid optimizations force constants may be computed using jobtype symm_fc The determined force constants will be saved in a binary file PSIF OPTKING currently file 1 Subsequent optimizations will read and use these force constants In general PSI3 looks for force constants in the following order in this binary file in the FCONST section of the input and in the fconst dat file If no force constants are found in any of these then an empirical diagonal force constant matrix is generated For methods for which only energies are available PSI3 will use non redundant symmetry adapted delocalized internal coordinates to generate geometrical displacements for comput ing finite difference gradients The simple coordinates can be linearly combined by hand or automatically The goal is to form 3N 6 5 symmetry adapted internal coordinates The automated delocalized coordinates may work for low symmetry molecules without linear an gles but have not been extensively tested For both analytic and finite difference gradient optimization methods Hessian updates are performed using the BFGS method The list below shows which coordinates are used by default for different types of jobs jobtype freq dertype first symmetry adapted cartesians jobtype freq dertype none s
34. ble quotation marks You can give keywords in the input file for specific modules however in the first few examples we will place all our keywords in one section of our input file called psi Generally every module you run during your computation will read the keywords in psi so you can place all your keywords in this section if you choose to do so 2 3 Running a basic SCF calculation In our first example we will consider a Hartree Fock SCF computation for the water molecule using a cc pVDZ basis set We will specify the geometry of our water molecule using a standard z matrix psi label cc pVDZ SCF H20 jobtype sp win scf reference rhf basis cc pVDZ zmat o h 1 0 957 h 1 0 957 2 104 5 In each computation you can specify the type of wavefunction keyword wfn the refer ence wavefunction for post Hartree Fock computations keyword reference and the type of computation you want to perform keyword jobtype In the example above we used a restricted Hartree Fock RHF reference in an SCF computation of a single point energy To change the level of electron correlation one would specify a different wavefunction type using the keyword wfn In the example above to perform an MP2 computation simply set wfn mp2 2 4 Geometry Optimization and Vibrational Frequency Analysis The above example was a simple single point energy computation To perform a different type of computation change the keywo
35. e Users of PSI3 often find that they wish to use certain keywords or input sections in every calculation they run especially those keywords associated with the files section The psirc file which is kept in the user s HOME directory helps to avoid repetition of keywords whose defaults are essentially user or system specific A typical psirc file would look like psi files default nvolume 3 volumel tmp1 mylogin volume2 tmp2 mylogin volume3 tmp3 mylogin file32 nvolume 1 volumel 18 3 7 Specifying Basis Sets PSI3 uses basis sets comprised of Cartesian or spherical harmonic Gaussian functions A basis set is identified by a string enclosed in double quotes Currently there exist three ways to specify which basis sets to use for which atoms e basis string all atoms use basis set type e basis stringl string2 string3 stringN string 4 specifies the basis set for atom 7 Thus the number of strings in the basis vector has to be the same as the number of atoms including ghost atoms but excluding dummy atoms Another restriction is that symmetry equivalent atoms should have same basis sets otherwise input will use the string provided for the so called unique atom out of the set of symmetry equivalent ones e basis elementi string1 element2 string2 elementN stringN string 1 specifies the basis set for chemical element element 2 3 7 1 Default Basis
36. e S functions in a 6 31G basis for hydrogen one would use the following hydrogen 6 31G C S 18 73113696 0 03349460 2 82539437 0 23472695 0 64012169 0 81375733 1 2 S 0 16127776 1 00000000 1 2 P 1 10000000 1 00000000 In this example both contracted S functions have their exponents scaled by a factor of 1 2 1 44 The output file should show the exponents after scaling 23 3 7 3 Automated Conversion of Basis Sets The PSI3 package is distributed with a Perl based utility named g94_2_PSI3 which will convert basis sets from the Gaussian 794 or later format to PSI3 format automatically This utility is especially useful for basis sets downloaded from the EMSL database at http www emsl pnl gov forms basisform html To use this utility save the desired basis set to a file e g g94 basis dat in the Gaussian format Then execute g94 2 PSIS3 lt g94 basis dat gt basis dat You may either incorporate the results from the basis dat file into your input file as de scribed above or place the results into a global basis dat file Be sure to surround the basis set definition with the basis keyword as shown in the above examples or input parsing errors will result 3 8 Specification of Ghost Atoms To specify ghost atoms use atom symbol G in zmat or geometry keywords zmat he gir basis aug cc pVTZ Basis sets for ghost atoms must be defined explicitly us
37. eger This integer specifies the highest order electric multipole moment to be computed Valid values are 1 dipole 2 up to quadrupole or 3 up to octupole Default is 1 MP_REF integer This integer specifies the reference point for the evaluation of electric multipole mo ments Valid values are 1 center of mass 2 origin 3 center of electronic change and 4 center of the nuclear charge For charge neutral systems the choice of MP_REF is irrelevant Default is 1 GRID integer This integer specifies the type of one electron property and the type of grid on which to evaluate it The valid choices are e 0 compute nothing e 1 electrostatic potential on a 2 D grid e 2 electron density on a 2 D grid spin density if SPIN PROP true 44 e 3 projection of electron density gradient on a 2 D grid spin density gradient if SPIN PROP true e 4 Laplacian of electron density on a 2 D grid Laplacian of spin density if SPIN_PROP true e 5 values of molecular orbitals on a 3 D grid e 6 electron density on a 3 D grid spin density if SPIN_PROP true Default is O NIX integer The number of grid points along the x direction This parameter has be greater than 1 Default is 20 NIY integer The number of grid points along the y direction This parameter has be greater than 1 Default is 20 NIZ integer The number of grid points along the z direction if a 3 D grid is chosen This
38. eger Excitation level for excitations into virtual orbitals default 2 i e CISD In a RAS CI this is the number of electrons allowed in RAS III VAL EX LVL integer In a RAS CI this is the additional excitation level for allowing electrons out of RAS I into RAS II The maximum number of holes in RAS I is therefore EX_LVL VAL EX LVL Defaults to zero 34 FROZEN DOCC integer array Core may be frozen by setting FREEZE_CORE To manually select how many orbitals per irrep to freeze use the FROZEN DOCC keyword Should be in psi or default O sections of input The number of lowest energy doubly occupied orbitals in each irre ducible representation from which there will be no excitations The Cotton ordering of the irredicible representations is used The default is the zero vector FROZEN UOCC integer array Should be in psi O or default sections of input The number of highest en ergy unoccupied orbitals in each irreducible representation into which there will be no excitations The default is the zero vector RASI integer array Should be in psi or default O sections of input The number of orbitals for each irrep making up the RAS I space from which a maximum of EX_LVL VAL EX LVL excitations are allowed This does not include frozen core orbitals For a normal CI truncated at an excitation level such as CISD CISDT etc it is not necessary to specify this or RAS2 or RAS3 Note this keyword must be visible t
39. ficient program to handle more general CI wavefunctions which may be helpful in more challenging cases such as highly strained molecules or bond breaking reactions The detci program is a fast determinant based CI program based upon the string formalism of Handy 1 It can solve for restricted active space configuration interaction RAS CI wavefunctions as described by Olsen Roos Jorgensen and Aa Jensen 2 Excitation class selected multi reference CI wavefunctions such as second order CI can be formulated as RAS CTs A RAS CI selects determinants for the model space as those which have no more than n holes in the lowest set of orbitals called RAS I and no more than m electrons in the highest set of orbitals called RAS III An intermediate set of orbitals if present RAS II has no restrictions placed upon it All determinants satisfying these rules are included in the CI The detci program is also very efficient at full configuration interaction wavefunctions 33 and is used in this capacity in the complete active space self consistent field CASSCF code Use of detci for CASSCF wavefunctions is described in the following section of this manual As just mentioned the PSI3 program is designed for challenging chemical systems for which simple CISD is not suitable Because CI wavefunctions which go beyond CISD such as RAS CI are fairly complex typically the detci program will be used in cases where the tradeoffs between comp
40. final molecular orbitals are those which minimize the energy subject to the electron configuration specified by the user or guessed by the program The process is continued until the largest change in an element of the density matrix drops below 10 where n is an integer specified by the convergence keyword Of course the efficiency of the iterative procedure depends on the choice of initial guess The cscf module will attempt to use previously obtained orbitals as a guess if they are available This can be particularly advantageous when diffuse functions are present in that case it may be easiest to run the computation with a smaller basis and project those orbitals onto the larger basis by specifying the chkptmos command line argument or the chkpt_mos true keyword in input when running the input program for the larger basis If old MO s are not available cscf uses a core Hamiltonian guess by default The convergence of the SCF procedure is accelerated by Pulay s direct inversion of the iterative subspace DIIS approach and it is possible to modify the behavior of the DIIS through various keywords although this is seldom necessary It is important to point out that the SCF approach does not rigorously guarantee that the final orbitals actually correspond to a minimum in orbital space at convergence the only guarantee is that the gradient of the energy with respect to orbital rotations is zero this could be a global minimum a local mini
41. in the DEFAULT section of input because it needs to be visible to the control program PSI Defaults to 20 AVERAGE STATES integer array This gives a list of what states to average for the orbital optimization States are numbered starting from 1 PRINT integer This option determines the verbosity of the output A value of 1 or 2 specifies minimal 38 printing a value of 3 specifies verbose printing Values of 4 or 5 are used for debugging Do not use level 5 unless the test case is very small e g STO HO CISD 4 5 2 Examples 6 31G H20 Test CASSCF Energy Point psi label 6 31G CASSCF H20 jobtype sp wfn casscf reference rhf restricted_docc 1 0 0 0 active 301 2 basis 6 31Gx x zmat o h 1 1 00 h 1 1 00 2 103 1 Figure 1 Example of a CASSCF single point calculation for H20 using a valence active space 3a 1b 2b 5 Geometry Optimization PSI3 is capable of carrying out geometry optimizations minimization only at present for a variety of molecular structures using either analytic and numerical energy gradients When present internal coordinates provided in the INTCO section of the input will be read and used by PSI3 If these are missing PSI3 will automatically generate and use redundant simple internal coordinates for carrying out the optimization These simple stretch bend torsion and linear bend coordinates are determined by distance criteria using the input geometr
42. ing GHOST as the element name basis GHOST aug cc pVTZ This method leads to replication of existing basis set definitions It is usually more convenient to specify ghost atoms as regular atoms with zero charge zmat he he 1 r charges 2 0 0 0 basis aug cc pVTZ In this example the second helium atom is a ghost atom which carries helium s aug cc pVTZ basis set 24 4 Theoretical Methods Available in PSI3 Several electronic structure methods are available in the PSI3 package from Hartree Fock molecular orbital theory to coupled cluster theory to full configuration interaction This section introduces the methods available and some of their most common input parameters Less commonly used keywords are described in the man pages for each module 4 1 Hartree Fock Self Consistent Field Hartree Fock molecular orbital theory forms the cornerstone of ab initio quantum chemistry Until the advances in the accuracy of Kohn Sham density functional theory in the 1990 s Hartree Fock theory was the method of choice for obtaining results for large molecules with out resorting to standard empirical or semiempirical approaches Molecular properties ob tained by Hatree Fock theory are generally at least qualitatively correct although they can be quantitatively poor in many instances PSI3 solves the Hatree Fock equations in a basis of Gaussian functions using an iterative self consistent field SCF procedure The
43. ing out large basis set coupled cluster calculations with PSI3 1 Set the MEMORY keyword to 90 of the available physical memory at most There is a small amount of overhead associated with the coupled cluster modules that is not accounted for by the internal CC memory handling routines Thus the user should not sepcify the entire physical memory of the system or swapping is likely 31 2 Set the CACHELEV keyword to 0 This will turn off cacheing which for very large calculations can lead to heap fragmentation and memory faults even when sufficient physical memory exists 3 Set the PRINT keyword to 2 This will help narrow where memory bottlenecks or other errors exist in the event of a crash 4 3 3 Excited State Coupled Cluster Calculations The most important keywords associated with EOM CC calculations are STATES PER IRREP integer array Specifies the desired number of excited states per irreducible representation for both EOM CC and CC LR calculations Note that the irreps in this keyword denote the final state symmetry not the symmetry of the transition PRINT SINGLES boolean Specifies whether information regarding the iterative solution to the single excitation EOM CC problem normally used to obtain guesses for a ful EOM CCSD calculation will be printed RESIDUAL TOL integer Specifies the order of magnitude cutoff used to determine the convergence of the David son algorithm residuals in the EOM CC iterative p
44. itrary Order Perturbation Theory 4 5 Complete Active Space Self Consistent Field CASSCF 4 5 1 Basic Keywords 4 5 2 Examples Evaluation of properties on rectalinear grids Grid specification mini tutorial Visualizing Molecular Obitals with gOpenMol Environment Variables 00 eee ee a ee Command Line Optiong uo o ee ds ee ew ee et we a 5 Geometry Optimization 6 Vibrational Frequency Computations 7 Evaluation of one electron properties 7 1 Basic Keywords 7 2 7 3 7 4 Plotting grid data 7 5 8 PSI3 Driver 8 1 8 2 8 8 Input Format 8 4 Loop Control 9 Additional Documentation A PSI3 Reference 39 42 43 43 46 47 48 49 49 50 50 50 51 51 52 1 Introduction 1 1 Overview This manual explains how to use the PSI3 suite of ab initio quantum chemical programs In this section we provide an overview of some of the features of PSI3 along with the prerequisite steps for running calculations Section 2 provides a brief tutorial to help new users get started Section 3 offers further details into the structure of PSI3 input files and a discussion of some of the most important options Later sections deal with the different t
45. mum or a saddle point in orbital rotation space While this is not usually an issue typically the lowest minimum consistent with the electron configuration is found it can be a problem sometimes for radicals diradicals bond breaking or unusual bonding situations The stable module can be used to test for the stability of Hartree Fock wave functions The most commonly used keywords are found below More specialized keywords are available in the man pages MAXITER integer This gives the maximum number of iterations The default is 40 25 CONVERGENCE integer This specifies how tightly the wavefunction will be converged Convergence is deter mined by comparing the RMS change in the density matrix delta P to the given value The convergence criterion is 10 integer The default is 7 if both DERTYPE NONE and WFN SCF are given and 10 otherwise LEVELSHIFT real This specifies the level shift The default is 1 DIRECT boolean Specifies whether to do the SCF calculation with an integral direct technique The default is false NUM THREADS integer Specified the number of threads to be used in the integral direct computation only valid if DIRECT is set to true Default is 1 PRINT MOS boolean Specifies whether to print the molecular orbitals or not The default is false 4 2 Second order Mgller Plesset Theory MP2 and MP2 R12 meth ods Second order Moller Plesset theory is one of the most basic wave function
46. nal frequency calcu lation etc The reference keyword specifies whether an RHF ROHF UHF etc reference is to be used for the SCF wavefunction The wfn specifies what theoretical method is to be used either SCF determinant based CI coupled cluster etc Also of critical importance are the charge and multiplicity of the molecule the molecular geometry and the basis set to be used The latter two topics are discussed below in sections 3 3 and 3 7 General keywords determining the general type of computation to be performed are described below LABEL string This is character string to be included in the output to help keep track of what computation has been run It is not otherwise used by the program There is no default JOBTYPE string This tells the program whether to run a single point energy calculation SP a ge ometry optimization OPT a series of calculations at different displaced geometries DISP a frequency calculation FREQ frequencies only for symmetric vibrational modes SYMM FREQ a Diagonal Born Oppenheimer Correction DBOC energy computation or certain response properties RESPONSE The default is SP WEN string This specifies the wavefunction type Possible values are SCF MP2 MP2R12 CIS DETCI CASSCF RASSCF CCSD CCSD_T BCCD BCCD_T EOM_CCSD ZAPTN REFERENCE string This specifies the type of SCF calculation one wants to do It can be one of RHF for a closed shell singlet
47. nce installed the first step to viewing molecular orbitals is to convert the mo cube into a format that gOpenMol recognizes Under the Run menu select gCube2p1t g94cub2p1 cube this will bring up window with the heading Run gCube2plt g94cub2pl In the input file name field select the mo cube file you want to convert Likewise in the output file name field type the name of the output file you want Click the Apply button to perform the conversion This procedure will create a plt and a crd file Once converted click Dismiss to close the window The Gaussian Cube file is now converted and in a form that gOpenMol can recognize In order to view the molecular orbital the first step is to import the coordinate file crd This is done under the File menu Import Coords Again a window will pop up In the Import file name field chose the crd you just created from the conversion procedure Click apply then Dismiss to close the window Now we have to import the plt file to view the molecular orbital Under the the Plot menu selct Contour this will bring up a window In the File name field either type the full path of the file name or use browse to select the plt file you just created in the conversion then click Import In the Define contour levels we have to define the contour cutoffs for the positive and negative parts of the wave function seperately I recommend trying 0 1 in the first box and 0 1 in the second Click Appl
48. nd less ex pensive than CASSCF However orbital convergence for RASSCF can be difficult in our current implementation Inactive orbitals in the MCSCF may be specified by the RESTRICTED DOCC and RESTRICTED UOCC keywords These orbitals will remain doubly occupied or doubly unoccupied respectively in the MCSCF wavefunction However the form of these orbitals will be optimized in the MCSCF procedure It is also possible to literally freeze inactive orbitals in their original SCF form using the FROZEN DOCC and FROZEN UOCC keywords This is not normally what one wishes to do in an MCSCF computation e g it complicates the computation of gradi ents but it can make the computations faster and is helpful in some circumstances where unphysical mixing of inactive and active occupied orbitals might occur Presently it is not possible to mix the use of restricted and frozen orbitals in PSI3 The division of the molecular orbitals into various subspaces such as RAS spaces or frozen vs active orbitals etc needs to be clear not only to the detci program but also at least to the transformation program and in the case of MCSCF to other programs as well Thus orbital subspace keywords such as RAS1 RAS2 RAS3 frozen docc frozen uocc active etc need to be in the psi or default sections of input so they may also be read by other modules The ability to perform state averaged 7 8 CASSCF or R
49. ndices they contain Setting CACHELEV 0 will cache nothing wise and sometimes necessary for very large CC calculations CACHELEV 1 will keep quantities with up to one virtual index in core e g integrals of the form 4j ka CACHELEV 2 will keep quantities with up two two virtual indices in core e g integrals of the form ij ab or T amplitudes CACHELEV 3 will keep three virtual index quantities in core and CACHELEV 4 will keep everything in core Note that the cache behavior is tempered by the MEMORY keyword and items will be deleted from the cache in an order determined based on the CACHETYEP keyword as additional memory is required in a given calculation CACHETYPE string Specifies the type of cache to be used either LOW or LRU If CACHETYPE LOW then ele ments are deleted from the cache based on a predefined order of priority If CACHETYPE LRU then elements are deleted from the cache based on a least recently used criterion the least recently used item is the first to be deleted The LOW criterion has been developed only ccenergy codes The default is LRU for all CC modules except ccenergy NUM_AMPS integer Specifies the number of wave function amplitudes to print at the end of the energy calculation Defaults to 10 PRINT_MP2_AMPS boolean Specifies if the initial guess MP2 amplitudes should be printed in the output file Defaults to FALSE 4 3 2 Larger Calculations Here are a few recommendations for carry
50. nt set ZMAT_SIMPLES boolean If set to true the simple internal coordinates are taken from the zmat entry in the input file The default is false POINTS 3 or 5 Specifies a 3 point or a 5 point formula for optimization by energy points EDISP float The default displacment size in au for finite difference computations The default is 0 005 FRAGMENT DISTANCE INVERSE boolean For interfragment coordinates If true then 1 R AB is used if false then R AB is used The default is true FIX INTRAFRAGMENT boolean If true all intrafragment coordinates are constrained A FIX INTERFRAGMENT boolean If true all interfragment coordinates are constrained DUMMY_AXIS_1 1 or 2 or 3 Specifies the axis for the location of a dummy atom for the definition of a linear bending coordinate The default is 2 DUMMY_AXIS_2 1 or 2 or 3 Specifies the axis for the location of a dummy atom for the definition of a linear bending coordinate The default is 3 TEST_B boolean If set to true a numerical test of the B matrix is performed PRINT_FCONST boolean If set to true and jobtype symm_fc then the force constants will be written to the fconst dat file This allows force constants to be reused even if the binary PSIF OPTKING file is no longer present Print options The following when set to true print additional information to the output file PRINT SIMPLES PRINT PARAMS PRINT DELOCALIZE PRINT SYMMETRY PRINT HESSIAN
51. ntax PSI3 input files are case insensitive and free format with a grammar designed for maximum flexibility and relative simplicity Input values are assigned using the structure keyword value where keyword is the parameter chosen e g convergence and value has one of the fol lowing data types e string A character sequence surrounded by double quotes Example basis cc pVDZ e integer Any positive or negative number or zero with no decimal point Example maxiter 100 e real Any floating point number Example omega 0 077357 e boolean true false yes no 1 0 e array a parenthetical list of values of the above data types Example docc 3 0 1 1 Note that the input parsing system is general enough to allow multidimensional arrays with elements of more than one data type A good example is the z matrix keyword zmat 0 H 1r H1r2a For z matrices z matrix variables and Cartesian coordinates it is also possible to discard the inner parentheses The following is equivalent in this case zmat 0 Heder Hir2a Keywords must grouped together in blocks based on the module or modules that require them The default block is labelled psi and most users will require only a psi block when using PSI3 For example the following is a simple input file for a single point CCSD energy calculation on H20 11 psi label 6 31G CCSD H20 wfn ccsd reference rhf jobtype sp basis
52. o the transqt program also so that orbitals are ordered correctly placing it in default or psi should be adequate RAS2 integer array Should be in psi O or default sections of input As above for RAS1 but for the RAS II subspace No restrictions are placed on the occupancy of RAS II orbitals Typically this will correspond to the conventional idea of an active space in multi reference CI RAS3 integer array Should be in psi O or default O sections of input As above for RAS3 but for the RAS III subspace A maximum of EX_LVL electrons are allowed in RAS III MAXITER integer Maximum number of iterations to diagonalize the Hamiltonian Defaults to 12 NUM ROOTS integer This value gives the number of roots which are to be obtained from the secular equa tions The default is one If more than one root is required set DIAG METHOD to SEM or for very small cases RSP or SEMTEST Note that only roots of the same irrep as the reference will be computed To compute roots of a different irrep one can use the REF_SYM keyword for full CI only OPDM boolean If TRUE compute the one particle density matrix for each root By default it will be written to disk Except for MCSCF computations e g CASSCF RASSCF this will also turn on computation of dipole moments by default TRANSITION DENSITY boolean If TRUE compute the transition density matrix from the ground state to each other 35 state obtained in the
53. on in one pass the program will do multiple passes through the entire set of integrals hence your computation will run that many times longer In such case find the machine with the most memory and processors available 3 On SMP machines set the NUM THREADS to the number of processors available for the job or if all processors are allocated for your job set NUM THREADS to twice the number of processors you have Modern operating systems schedulers are usually very efficient at handling multithreaded programs so the overhead of thread context switching is not significant but using more threads may lead to better load balancing and lower execution times For example on a 32 processor IBM eServer p690 we found that the optimal number of threads was 128 For the optimal performance do a few runs with different number of threads and see which number works best Avoid excessively large number of threads as this descreases the net amount of memory available to the computation and thus may increase the number of passes 28 4 Set the MEMORY keyword to the 90 of the available physical memory at most There is a small amount of overhead associated with the integral direct algorithms that is not accounted for by the internal memory handling routines 5 The implementation of the integral direct MP2 R12 and MP2 method in PSI3 can run efficiently on SMP or shared memory machines by utilizing multiple processors via multithreaded approach
54. ormed by nuclei refi1 and ref12 e tors anglei is the torsion angle formed by nuclei 7 refi1 refi2 and ref13 3 4 Molecular Symmetry PSI3 can determine automatically the largest Abelian point group for a valid framework of centers including ghost atoms but dummy atoms are ignored It will then use the symmetry properties of the system in computing the energy forces and other properties However in certain instances it is desirable to use less than the full symmetry of the molecule The keyword subgroup is used to specify a subgroup of the full molecular point group The allowed values are c2v c2h d2 c2 cs ci and c1 For certain combinations of a group and its subgroup there is no unique way to determine which subgroup is implied 15 For example D has 3 non equivalent C subgroups e g Cay X consists of symmetry operations Cs a 6 and ozz To specify such subgroups precisely one has to use the keyword unique axis For example the following input will specify the Co X subgroup of D n to be the computational point group psi geometry units angstrom subgroup c2v unique axis x Point Group Cotton Ordering of Irreps C A o ASA Ca AB Cs A A on A B Ay Bu C Ay A B B2 D A B By B3 Don Ag Big Bay Ba Ay Biu B Ba 3 5 Specifying Scratch Disk Usage in PSI3 Depending on the calculation the PSI3 package often requires substantial temporary disk
55. parameter has be greater than 1 Default is 20 GRID FORMAT string This keyword specifies in which format to produce grid data The only valid choice for 2 D grids is plotmtv format of plotting software program PlotMTV For 3 D grids valid choices are gausscube Gaussian 94 cube format and megapovplus format of 3D rendering software MegaPOV The defaults are plotmtv and gausscube for 2 d and 3 d grids respectively MO TO PLOT vector Specifies indices of the molecular orbitals to be computed on the 3 d grid Indices can be specified as e unsigned integer index in Pitzer ordering ordered accoring to irreps not eigen values Ranges from 1 to the number of MOs e signed integer index with respect to Fermi level 1 means LUMO 2 means second lowest virtual orbital 1 means HOMO etc All indices have to be either unsigned or signed you can t mix and match or you will get unpredictable results Default is to compute HOMO and LUMO SPIN PROP boolean Whether to compute spin dependent properties Default is false WRTNOS boolean If set to true natural orbitals will be written to the checkpoint file Default is false 45 7 2 Evaluation of properties on rectalinear grids PSI3 can evaluate a number of one electron properties on rectalinear 2 D and 3 D grids In most cases 3 D grids are utilized In such cases you only need to specify the appropriate value for GRID and PSI3 will automatically construct a rectaline
56. psi3 o h20 out where h20 out is the name of the output file By default psi3 and the other PSI3 modules look for output dat P This flag is used to specify the PSI3 file prefix e g psi3 p h20 dzp where h20 dzp is the prefix that will be used for all PSI3 files By default psi3 and the other PSI3 modules use psi for the file prefix Hence the checkpoint file is by default called psi 32 n This flag tells psi3 not to run the input module This flag is useful for scripting and debugging C This flag tells psi3 to check the input and print out the list of programs which would be executed to STDOUT Equivalent to check true in the input file m This flag tells psi3 not to run the cleanup module psiclean Usually psiclean is invoked by the done macro in psi dat This flag is useful for scripting and debugging 8 3 Input Format The psi3 module searches through the default keyword path first PSI then DEFAULT for the following keywords JOBTYPE string This keyword specifies what kind of calculation to run 50 WEN string This keyword specifies the type of wave function REFERENCE string This keyword specifies the spin reference DERTYPE string This keyword specifies the order of the derivative to be used The default is none OPT boolean Set equal to true if performing a geometry optimization The default is false CHECK boolean If true psi3 will parse your input file and print the sequence of programs
57. rd jobtype In the example below we will set up a CCSD geometry optimization To illustrate a more flexible z matrix input we will now define variables for the bond length and bond angle in the zvars section 6 31G H20 Test optimization calculation psi label 6 31G SCF H20 jobtype opt wfn ccsd reference rhf dertype first basis 6 31Gx x zmat o h 1 roh h 1 roh 2 ahoh zvars roh 0 96031231 ahoh 104 09437511 Once you have optimized the geometry of a molecule you might wish to perform a frequency analysis to determine the nature of the stationary point To do this change the value of jobtype to freq For an SCF frequeny calculation you would also set dertype second to compute the second derivatives analytically Unfortunately analytical second derivitives are not available in PSI3 for wavefunctions beyond SCF so instead use the highest order analytical derivitives that are available for the type of wavefunction you have chosen This information is given in Table 2 For our CCSD example the highest order derivitives available are first so dertype first 6 31G H20 Test computation of frequencies psi label 6 31G SCF H20 jobtype freq wfn ccsd reference rhf dertype first basis 6 31Gx x zmat O h 1 roh h 1 roh 2 ahoh zvars roh 0 96031231 ahoh 104 09437511 2 5 More Advanced Input Options If you wish to add comments to your input file
58. re is no default REFERENCE string Acceptable value are rhf and rohf There is no default FREEZE_CORE boolean Specifies whether core orbitals which are determined automatically are to be excluded from the correlated calculations Default is false 43 Feature On by default Notes Electric dipole moment Electric quadrupole moment Electric octupole moment Electrostatic potential Electric field Electric field gradient Hyperfine coupling constant Relativistic MVD corrections Electron density Spin density Electron density gradient Spin density gradient Electron density Laplacian Spin density Laplacian Molecular Orbitals MO Natural Orbitals NO MO NO spatial extents KZZKKKZZK zZ ZZZZZZ Z Set MPMAX to 2 or 3 Set MPMAX to 3 At the nuclei on 2 D grid set GRID 2 At the nuclei At the nuclei Set SPIN_PROP true Set MPMAX to 2 At the nuclei on 2 D grid set GRID 2 on 3 D grid set GRID 6 Set SPIN_PROP true at the nuclei on 3 D grid set GRID 6 on 2 D grid set GRID 3 on 2 D grid set GRID 3 and SPIN PROP true on 2 D grid set GRID 4 on 2 D grid set GRID 4 and SPIN PROP true on 3 D grid set GRID 5 Set WRTNOS to true written to file32 Set MPMAX to 2 or 3 MOs are used if WFN SCF otherwise NOs Table 9 Current one electron property capabilities of PSI3 PRINT integer The desired print level for detailed output Defaults to 1 MPMAX int
59. rees are assumed MU_IRREPS integer array Specifies the irreducible representations associated with the z y and z axes This may be determined from the standard Cotton tables Eventually this will be deter mined automatically by the program so this keyword will go away 4 4 Configuration Interaction Configuration interaction CI is one of the most general ways to improve upon Hartree Fock theory by adding a description of the correlations between electron motions Simply put a CI wavefunction is a linear combination of Slater determinants or spin adapted configuration state functions with the linear coefficients being determined variationally via diagonaliza tion of the Hamiltonian in the given subspace of determinants The simplest standard CI method which improves upon Hartree Fock is a CI which adds all singly and doubly substi tuted determinants CISD The CISD wavefunction has fallen out of favor because truncated CI wavefunctions short of full configuration interaction are not size extensive meaning that their quality degrades for larger molecules MP2 offers a less expensive alternative whose quality does not degrade for larger molecules and which gives similar results to CISD for well behaved molecules CCSD is usually a more accurate alternative at only slightly higher cost For the reasons stated above the CI code in PSI3 is not optimized for CISD computations Instead emphasis has been placed on developing a very ef
60. rocedure EVAL TOL integer Specifies the order of magnitude cutoff used to determine the convergence of the final eigenvalues in the EOM CC iterative procedure EOM GUESS mixed array Specifies a set of single excitation guess vectors for the EOM CC procedure This is especially useful for converging to difficult states The EOM GUESS keyword is an array each element of which includes an occupied orbital index in coupled cluster ordering a virtual orbital index a weighting factor and a spin 0 for o and 1 for 5 The guess vector will be normalized after it is read so only the relative magnitudes of the weight factors are important JOBTYPE string A value of oeprop will result in the calculation of oscillator strengths rotational strengths and dipole moments for an RHF reference and all but the rotational strengths for an ROHF or UHF reference 4 3 4 Linear Response CCLR Calculations The most important keywords associated with CC LR calculations are 32 JOBTYPE string A value of RESPONSE will invoke the linear response programs PROPERTY string This leyword specifies the type or response property desired Acceptable values are POLARIZABILITY default for dipole polarizabilities and ROTATION for specific rota tions OMEGA real or real UNITS Specifies the desired frequency of the incident radia tion field in CCLR calculations Acceptable units are HZ NM and EV If given without units atomic units Hart
61. utational expense and completeness of the model space are nontrivial Hence the user is advised to develop a good working knowledge of multi reference and RAS CI methods before attempting to use the program for a production level project This user s manual will provide only an elementary introduction to the most important keywords Additional information is available in the man pages for detci The division of the molecular orbitals into various subspaces such as RAS spaces or frozen vs active orbitals etc needs to be clear not only to the detci program but also at least to the transformation program and in the case of MCSCF to other programs as well Thus orbital subspace keywords such as RAS1 RAS2 RAS3 frozen docc frozen uocc active etc need to be in the psi or default sections of input so they may also be read by other modules 4 4 1 Basic Keywords WEN string Acceptable values for determinant based CI computations in PSI3 are detci and for CASSCF detcas REFERENCE string Most reference types allowed by PSI3 are allowed by detci except that uhf is not supported DERTYPE string Only single point calculations are allowed for wfn detci For wfn detcas first derivatives are also available CONVERGENCE integer Convergence desired on the CI vector Convergence is achieved when the RMS of the error in the CI vector is less than 10 n The default is 4 for energies and 7 for gradients EX LVL int
62. y By default optimization is performed in redundant internal coordinates regardless of how the geometry was provided in the input Alternatively the user may specify zmat_simples true in which case the simple internal coordinates will be taken from the ZMAT given in the input file Also the user may specify optimization in non redundant delocalized internal coordi nates with delocalize true In this case the automatically generated simple coordinates are delocalized and redandancies are removed Advanced users may wish to specify the simple internal coordinates in the intco dat file and then allow PSI3 to delocalize them 39 Only those coordinates or combinations of coordinates that are specified by the symm keyword in the INTCO section are optimized Coordinates can be approximately frozen by commenting them out within the symm section Geometrical constraints may be precisely imposed by the addition of a section with nearly the same format as in INTCO For example to fix the distance between atoms 1 and 2 as well as the angle between atoms 2 1 and 3 in an optimization add the following to your input file fixed intco stre 12 bend 2 1 3 The constrained simple internals must be ones present either manually or automatically among the simple internals in the INTCO section Alternatively the z matrix input format may be used to specify constrained optimizations If zmat_simples true then v
63. y to view the molecular orbital You can change the colors of the positive and negative sections independently by clicking on the Colour button next to the respective cutoffs Also in the Details section you can fine tune the properties of the molecular orbital such as the opacity solid vs mesh smoothness and cullface state You can play around with various settings to get the surface to look exactly how you want it to There is more information in the Help Tutorials menu on this subject as well as many other abilities of gOpenMol 8 PSI3 Driver The PSI3 suite of programs is built around a modular design Any module can be run independently or the driver module psi3 can parse the input file recognize the calculation desired and run all the necessary modules in the correct order psi3 reads the file psi dat by default psi dat contains macros for several standard calculations however anything in psi dat can be overriden by the user 49 8 1 Environment Variables PSIDATADIR This flag is used to specify an alternate location for platform independent read only files such as psi dat and pbasis dat By default PSI3 will look for these files under psipath share 8 2 Command Line Options i or f This flag is used to specify the input file name e g psi3 i h20 in where h2o in is the name of the input file By default psi3 and the other PSI3 modules look for input dat 0 This flag is used to specify the output file name e g
64. yN zN where atomname can take the following values e The element symbol H He Li Be B etc e The full element name hydrogen helium lithium etc e Asa ghost atom with the symbol G or name ghost A ghost atom has a formal charge 0 0 and can be useful to specify the location of the off nucleus basis functions e As a dummy atom with the symbol X Dummy atoms can be useful only to specify Z matrix coordinates of proper symmetry or which contain linear fragments Hence the following two examples are equivalent to one another geometry H 0 0 0 0 0 0 f 1 0 0 0 0 0 Li 3 0 0 0 0 0 BE 6 0 0 0 0 0 14 geometry hydrogen 0 FLUORINE 1 Lithium 3 beryllium 6 It is also possible to include an inner set of parentheses around each line containing atomname1 x1 yl z1 The keyword units specifies the units for the coordinates e units angstrom angstroms A default e units bohr atomic units Bohr Z matrix coordinates are specified using the keyword zmat zmat atomnamel atomname2 ref21 bond_dist2 atomname3 ref31 bond_dist3 ref32 bond angle3 atomname4 ref41 bond dist4 ref42 bond angle4 ref43 tors angle4 atomnameb ref51 bond dist5 ref52 bond angleb ref53 tors angle5 atomnameN refN1 bond distN refN2 bond angleN refN3 tors angleN where e bond disti is the distance in units specified by keyword units from nucleus number i to nucleus number ref7z1 The units e bond anglei is the angle f
65. ymmetry adapted cartesians jobtype fc dertype first delocalized internals or user defined SALCs jobtype symm fc dertype first delocalized internals or user defined SALCs jobtype opt dertype first redundant internals jobtype opt dertype none delocalized internals or user defined SALCS The following keywords are pertinent for geometry optimizations 40 JOBTYPE string This keyword must be set to OPT for geometry optimizations and SYMM_FC to compute force constants DERTYPE string This keyword must be set to NONE if only energies are available for the chosen method and FIRST if analytic gradients are available CONV integer The maximum force criteria for optimization is 1070 BFGS boolean If true the default a BFGS Hessian update is performed BFGS_USE_LAST integer This keyword is used to specify the number of gradient step for the BFGS update of the Hessian The default is six SCALE_CONNECTIVITY float Determines how close atoms must be to be considered bonded in the automatic gener ation of the bonded list The default is 1 3 DELOCALIZE integer Whether to delocalize simple internal coordinates to attempt to produce a symmetry adapted non redundant set MIX_TYPES boolean If set to false different types of internal coordinates are not allowed to mix in the formation of the delocalized coordinates Although this produces cleaner coordinates often the resulting delocalized coordinates form a redunda
66. ype oeprop grid 5 mo_to_plot 1 1 grid_origin 5 0 5 0 5 0 grid_unit_x 1 0 0 0 0 0 grid_unit_y 0 0 1 0 0 0 grid_xyz0 0 0 0 0 0 0 grid_xyz1 10 0 10 0 10 0 nix 30 niy 30 niz 30 Running PSI3 on input like this will produce a Gaussian Cube file called mo cube which can be used to render images of HOMO and LUMO using an external visualization software 7 4 Plotting grid data 2 D grids should be plotted by an interactive visualization code PlotMTV PlotMTV is a freeware code developed by Kenny Toh It can be downloaded off many web sites in source or binary form 3 D grids can be produced in two formats megapovplus and gausscube see GRID FORMAT First is used to render high quality images with a program MegaPov version 0 5 MegaPov is 48 an unofficial patch for a ray tracing code POV Ray Information on MegaPov can be found at http nathan kopp com patched htm Gaussian Cube files can be processed by a number of programs We cannot recommend any particular program for that purpose here 7 5 Visualizing Molecular Obitals with gOpenMol The Gaussian Cube files generated by oeprop can be converted and viewed with gOpenMol gOpenMol offers good looking plots in a graphical user interface Information on downloading gOpenMol and samples of gOpenMol output may be found at http www csc fi gopenmol Installation instructions are included with the gOpenMol download O
67. ypes of computations which can be done using PSI3 e g Hartree Fock MP2 coupled cluster and general procedures such as geometry optimization and vibrational frequency analysis The appendix will eventually include a description of the input keywords and command line options for each module as well as numerous examples of PSI3 input and basis set files For the latest PSI3 documentation check www psicode org The PSI3 package was developed to perform high accuracy quantum mechanical compu tations on challenging chemical species and to provide an infrastructure for the development of new theoretical techniques Hence it has a very flexible input scheme which allows non standard computations and it is easily adapted to enable new capabilities The following citation should be used in any publication utilizing the PSI3 program package T Daniel Crawford C David Sherrill Edward F Valeev Justin T Fermann Rollin A King Matthew L Leininger Shawn T Brown Curtis L Janssen Edward T Seidl Joseph P Kenny and Wesley D Allen J Comput Chem 28 1610 1616 2007 1 2 Obtaining and Installing PSI3 The latest version of the PSI3 program package may be obtained at www psicode org The source code is available as a gzipped tar archive named for example psi3 X tar gz and binaries may be available for certain architectures For detailed installation and testing instructions please refer to the the

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