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Manual - University of Delaware Dept. of Physics & Astronomy

1. palk 1 2 D s i i Ye TOLAMP OU where tob and t are the double and single excitation amplitudes respectively Note that DE K is the relative correlation energy change The default values are TOLITER 107 and TOLAMP 107 DIIS convergence acceleration in the coupled cluster iterations can be turned off by the DIIS F directive DIIS is turned on by default recommended The variables RPA CCD CCSD and several others can be set to TRUE or FALSE to choose one of the possible forms of CC theory At this moment only CCSD T and CCD T are guaranteed to work and are needed for the SAPT corrections Since CCSD T and all other variables of this type are false by default these keywords can be omitted from the namelist The variables SITEA and SITEB allow to perform MBPT CC calculations for one of the monomers only for testing purposes The default values are TRUE and therefore these variables can be omitted from the list The variable WRTEACH allows writing of the cluster amplitudes from each iteration into separate disk files for future use It is FALSE by default and is not needed for the ordinary SAPT run however it must be set to TRUE 43 if one wants to calculate the dispersion energy at the CCD level see Sec 10 4 Finally the logical variable AOCC switches on off the atomic orbital AO based algorithm for calculating the most time consuming four virtual contribution to the CCSD amplitudes This slows down the CC cal
2. PL in E13PL are 22 d resulting from this terminology If tE ind iS requested its exchange counterpart will be estimated from the formula of Eq 7 The triple superscripts appearing for example in the correction REP denote the order with respect to the operators V W4 and Wp respectively The programs calculating the following corrections either have not been sufficiently tested or are known to contain errors Therefore calculations of the following corrections are not recom mended 45 1 E122 EP gas elst resp 9 E14PLR ECO elst resp without triples 3 TE14 Triples for BC elst resp 4 E1CC calculates the electrostatic energy from the formulas analogous to those appearing in BO using the converged CCSD amplitudes in place of the second order ones Instead elst use EU CCSD described in Sec 10 5 elst resp Six variables are provided to select groups of corrections SAPTO SAPT2 SAPTNOCC DELTASCF SAPTKS and SAPT and only one of them should be set to TRUE The settings SAPT2 T and SAPT T select the groups of corrections defined by Eqs 6 and 8 respectively The choice SAPTNOCC T is equivalent to SAPT T except that the intramonomer correlation contribution to E 0 exch is approximated as Eo EO instead of e CCSD The choice SAPT T is approximately equivalent in accuracy of predictions to using supermolecular MBPT through fourth order It has been
3. 70 executed under bash 14 4 1 Running psAPT2K2 on SGI We first consider a situation where there is no queuing system installed and a pSAPT2K2 job can be submitted interactively from the command line Before launching a pSAPT2K2 run the scratch directory should be created and all the input files should be copied to this directory The psaPT2K2 calculation is then launched in this scratch directory by typing pSAPT o02k with appropriate options If ksh is used as the login shell and an SGI machine is the platform one would type pSAPT o2k jobname opti nproc opt2 gt output file 2 gt amp 1 amp if psapt2K2 bin is not in your PATH then the full path to pSAPT o02k will have to be given The keyword jobname has to be the same as the beginning of the name of the input files for the system considered we use a naming scheme to reference the needed input files For example let the keyword be name Then as the script is running it will look for the nameP data file which contains the input data to the programs ptran pcc and psapt Similarly the pSAPT 02k script will look for GAMESS input files to the integral SCF parts of a calculation starting with name The number and full names of such files depend on the type of basis set used in calculations See Sec 10 for details on how to prepare GAMESS input files for different types of runs Using the string scfcp for opti will request in addition to the standard SAPT calculation also the CP corr
4. 9 4 GAMESS 9 4 1 Optional modification of GAMESS source In order to ensure that the SCF energies from GAMESS are printed with a sufficient number of decimals we recommend one FORMAT change in the rhfuhf src module prior to compilation of GAMESS In the subroutine RHFCL the statement 8000 FORMAT CLOSED SHELL ORBITALS GENERATED AT 3A8 10A8 EC A F20 10 ECNUC F16 10 15 ITERS should be replaced by 8000 FORMAT CLOSED SHELL ORBITALS GENERATED AT 3A8 10A8 EC A F24 16 E NUC F16 10 I5 ITERS 9 4 2 Required and recommended input options Please note that standard non direct SCF calculations must be performed and some options in the GAMESS input must have specific values e In the CONTRL input group NOSYM 1 option must be present i e no symmetry must be requested 27 e In the INTGRL input group NOPK 1 integrals must not be in supermatrix form and NINTMX 2048 options must be present Maximum number of integrals in a record block NINTMX must be the same as linrec variable in the SAPT2012 module trans f which is set in the IF isitgams THEN block The linrec is currently set to 2048 but can be changed to a different value e We recommend that the following thresholds for the two electron integrals linear dependence and SCF convergence are set instead of the GAMESS default values in the CONTRL input group I
5. Geometries of the monomers specified in nameA and nameB should correspond to whatever is considered to be the initial configuration of a given monomer i e the COM or other characteristic point around which rotations will be performed should coincide with the origin of the coordinate system and all Euler angles describing the orientation of the monomer will be assumed zero at this geometry 2 Prepare the file nameP data as for the regular MCBS SAPT calculation note that in the namelist TRN the variables basis and tags have to be specified for such a calculation as well as DIMER F In the namelist INPUTCOR the option CONVAMP TRUE must be requested and the namelist CCINP has to be set up so that the CCSD calculations for the monomers are 52 performed i e the variables CCSD and CCD should be either absent or set to CCSD TRUE CCD FALSE The corrections specified in INPUTCOR will be calculated and printed in the Summary Table for one dimer geometry obtained by shifting the position of monomer B by 10 bohr along the positive z axis with respect to the position specified in the nameB file The ECO else result from the Summary Table may be later compared to what comes out from the density algorithm 3 Prepare the file input edi specifying the dimer geometries for which the electrostatic en ergies are to be calculated by elstdenrot out of the precomputed monomer densities The file input edi consists of lines one fo
6. based on routines extracted from the GAMESS US code Currently only Gaussian basis functions with angular momenta up to f can be used The def2 SVP J auxiliary basis set requested in the ORCA input could be replaced by another basis set by using in the META section additional blocks with the keyword BAS replaced by AUX The order of these blocks is also arbitrary but no empty AUX blocks are allowed this is an ORCA restriction Note also that the RI J Coulomb fitting requested by the RI keyword in our example can only be used with pure density functionals For hybrid functionals ORCA has two other methods known as RIJCOSX and RI JK the latter requiring JK rather than J auxiliary basis sets All these DFT fitting basis sets must not be confused with auxiliary basis sets required by DF SAPT DFT and defined in the file name aux which are designed to fit the correlation effects and must be provided by the user as in the case of DALTON such basis sets are actually used in ORCA at the MP2 level and denoted by C The ORCA route in DF SAPT DFT requires a preparation of one input file not occuring in the DALTON route called kernel data This file contains just two lines of the form n_rad n_aug mem ksi where n_rad and n_aug are the numbers of radial and angular grid points around each atom in the quadrature of the CKS kernel integral In general much looser grids can be used here compared to the main DFT grids with
7. method is used with some other SCF program make sure that the value of SPHG matches the actual type of basis set for which the atomic integrals are generated Other examples of MC BS input files using the BASIS and TAGS options with GAMESS can be found in directories SAPT2012 examples GAMESS _MCBS For ATMOL1024 GAUSSIAN and MOLPRO the examples are in SAPT2012 examples ATMOL1024 ArHF_MCBS SAPT2012 examples GAUSSIAN CO2D_MCBS and SAPT2012 examples MOLPRO CO2D_MCBS respectively 10 2 Input for post Hartree Fock part The input for the transformation tran the MBPT CC code cc and the proper SAPT program sapt x is supplied in the file nameP data This input consists of a title line and three namelist sets The first line is reserved for the title of the run up to 80 characters The three namelists that follow are TRN which is for the input to the transformation program CCINP which passes 40 information to the MBPT CC program and INPUTCOR which informs the perturbation program which corrections are to be computed It should be noted that the exact syntax of a namelist statement depends on the platform For example on SGI and Linux platforms each namelist should start with the name preceded by amp e g amp TRN and end with amp END On the other hand IBM compilers require the forward slash as the namelist end marker Throughout this manual the former convention will be followed 10 2 1 Namelist TRN The maj
8. part of E Next to take into account the remaining S and T contributions to ES the expressions for these contributions Eqs 91 and 98 respectively of Ref 48 are evaluated with the converged CCD dispersion amplitudes replacing the first order ones hence the name CCD ST CCD The corrections listed above constitute the set typically used in SAPT calculations Recently it has become possible to calculate also the corrections of the third order in V and zeroth order in W 38 E E ee O a el 30 ge ind ind disp disp exc 30 h ind exch ind disp Pe fhe E 9 HF The first and fourth of these corrections constitute a part of the dF int resp quantity however for some systems it is advantageous to replace E resp by the sum ED Bon a 188 or by their response versions 35 Note that the third order polarization and exchange corrections tend to cancel each other to a large extent and one should not include any part of ENS without including the corresponding exchange correction A few other corrections have been developed by the authors of SAPT but these are either not working in the current version of the program or for some other reasons are not recommended to be computed These corrections include in particular various parts of E O 49 The theory presented above was restricted to SAPT MP CC for dimers The SAPT DFT approach is actually simpler since the intramonomer correlation effects a
9. 3 MAXMEM maximum memory in words to be used in the CKS calculation The program will allocate necessary memory not greater than MAXMEM If the required memory is greater than MAXMEM the program will exit If not set up to 100 megawords will be used IQUADTYP The type of quadrature scheme to be used in performing the w integral in the Casimir Polder dispersion formula e IQUADTYP 1 sets the Gauss Legendre quadrature with the transformation of the integral variable w wo e This is the default e IQUADTYP 2 sets the Gauss Legendre quadrature with the transformation w w tan t e IQUADTYP 3 sets the Gauss Laguerre quadrature scheme NQUAD The variable NQUAD sets the number of quadrature points to be used for the integra tion The default is 8 OMEGAO and ALPHA The transformation used in the Gauss Legendre quadrature schemes involves a constant wo The variable OMEGAO in the namelist SAPTDFT allows you to set this constant It is typically between 0 3 and 0 5 and the default is 0 5 The Gauss Laguerre quadrature scheme involves the constant a For the integrals encountered here one should set ALPHA 0 0 The DALTON patch enables some new options in DALTON which are required for SAPT DFT calculations All the new keywords belong to the DFT INPUT submodule The following new keywords are implemented 1 DFTAC the Fermi Amaldi asymptotic correction with the Tozer Handy splicing scheme 63 T
10. 5s3p2d H of HF 3s2p midbond 2s1p N 5s3p2d H1 of NH 3s2p H2 of NH 3s2p and H3 of NH 3s2p Now in this example the MC BS for monomer A HF is constructed by deleting the last two s the last p and the last d functions of N as well as the last s and p functions on each H of NH3 see the file HF_NH3MA inp The functions deleted here happen to be the most diffuse ones for each symmetry although in principle other choices could have been made as well Similarly the MC BS for monomer B NH3 is constructed from the whole DCTBS set by deleting the last two s the last p the last d functions of F and the last s and p functions of HF s hydrogen see the file HF _NH3MB inp Note that the sequence of basis functions in the input files is determined by the sequence of atomic centers and the sequence of functions within each center Thus simply deleting a contraction does not change the relative sequence in the remaining set as required The part of the TRN namelist corresponding to this setup is BLKMB F SPHG F BASIS ssssspppddsssppsspssssspppddsssppsssppssspp TAGS mmmaammamammamammmmmmbbmmbmbmmbmbmmbmbmmbmb Note that the variable SPHG has been set to FALSE since GAMESS always generates integrals in the Cartesian basis even if the SCF calculations are performed in variational space spanned by only pure spherical components as it is done with the option ISPHER 1 in GAMESS input files inp If the tags
11. Beowulf configurations differ so beware For other TARGETs ignore this option 4 GAMESS path containing the GAMESS exec you will be using 5 VERNO GAMESS version number compall assumes that the name of GAMESS executable is gamess VERNO x 6 TRGT_GMS if TARGET 02k specify how GAMESS should be run pick from sockets and sgi mpi consistently with your GAMESS installation For other TARGETs this will be set automatically 7 POE_COM if TARGET sp specify which poe command poe grd_poe or sge_mpirun will be used to run parallel codes Usually an MPI code on an SP machine is launched by the Load Leveler queuing system using the poe command At ARL a wrapper sge mpirun is used instead which works with the GRD queuing system or grid engine On IBM SP3 brainerd at ARL the command grd_poe also works For TARGETs other than SP ignore this variable 67 8 SCLPCK specify how the SCALAPACK and BLACS libraries are to be linked If this is set to NO then the sequential CHF procedure will be used will spoil scaling of psapt for large systems and the pcksdisp code for susceptibility functions will not be built at all 9 LPCKLIB specify how the LAPACK library is to be linked This library is needed to build the program tdenfit fitting the densities and propagators in terms of auxiliary bases If LPCKLIB is set to NO tdenfit will not be built On SP machines LAPACK is a part of ESSL libr
12. Complete set of sequential two body codes This file contains all the above modules On decompression it expands into SAPT2012 and asymp_SAPT 15 5 SAPT3B Contains the three body SAPT 17 and three body SAPT DFT 20 Requires SAPT2012 On decompression this file expands into sapt3b 6 pSAPT2K2 Contains the parallel version of the SAPT codes pSAPT2K2 To make the most of this version you will have to obtain and install parallel GAMESS US as the integral SCF package See Sec 14 and Ref 9 for a detailed description of psAPT2K2 7 SAPT os Contains SAPT DFT code for open shell high spin complexes 21 8 SAPT CC SAPT CC codes 24 31 This is actually not a separate package but a part of SAPT2012 point 1 above The codes are provided as a patch to MOLPRO in the directory misc patch ccsapt of the SAPT2012 package see Sec 15 The instructions on unpacking these files can be found on the SAPT web page in the Download Area 6 Structure of SAPT2012 directory After unpacking the SAPT2012 main directory will contain the following files and subdirectories e Cleandirs use this script to clean the entire SAPT2012 directory tree before recompiling from scratch e Compall script used to build the package see Sec 8 e Makefile a generic makefile used by Compal1 UPDATES log of the history of changes and updates atmo11024 present if ATMOL1024 has been downloaded this directory contains the
13. RI TightSCF bohrs method Grid 4 FinalGrid 5 gracLB true ip 12 62 end META 6 o 1 8 0 1088092367800 0 0000000000000 0 0607755435800 8 0 1 0 1616146814400 O 0000000000000 1 7553074350400 1 0 1 1 5793331071000 O 0000000000000 0 7828987377400 1 0 8 0 0964834851100 O 0000000000000 6 5351482873200 0 0 1 0 7718678809000 1 4536519623000 7 2451823417100 0 0 1 0 7718678809000 1 4536519623000 7 2451823417100 0 0 BAS 1 3 03 13 0107010000 0 0334854882 1 9622572000 0 2347218706 0 4445379600 0 8137702843 93 0 1219496200 1 0000000000 11 0 8000000000 1 0000000000 BAS 8 05 2266 1767785000 0 0053893504 340 8701019100 0 0402347214 77 3631351670 0 1800818421 21 4796449400 0 4682885766 6 6589433124 0 4469261716 01 0 8097597567 1 0000000000 o 1 0 2553077223 1 0000000000 13 17 7215043170 0 0626302488 3 8635505440 0 3333113849 1 0480920883 0 7414863830 11 0 2764154441 1 0000000000 21 1 2000000000 1 0000000000 The first line declares the use of the PBE functional def2 SVP as the main basis set and def2 SVP J as the Coulomb fitting auxiliary basis set as well as tight convergence criteria for the SCF procedure and the use of bohr units in the geometry section see the ORCA manual for details The gracLB true setting is essential for any SAPT DFT calculation as it turns on the GRAC asymptotic correction of the exchange correlation functional the other type of asymptotic correction Fermi Amaldi is curently not
14. Version 2 9 0 or later is required because earlier versions contain errors in the GRAC asymptotic correction code and lead to incorrect SAPT results The installation of ORCA can be done before or after the installation of SAPT as both are completely independent but in the latter case one has to edit the file vars cfg so that the variable ORCADIR is set to the directory with the ORCA executables 92 To use DF SAPT DFT with orca ISITORCA T must be set in the TRN namelist of the nameP data file The required monomer and or dimer ORCA input files follow the same naming pattern ending with data as in the case of GAUSSIAN see Sec 10 1 for the detailed description Each such file besides containing regular ORCA input in the first section must end with a special second section starting with a line containing the string META as its first four characters This section always defines the molecular geometry and basis set used in the DFT calculation even if a basis set is already defined in the first section it gets overridden here Additionally if one of the density fitting DFT algorithms implemented in ORCA is invoked the META section can be used to override the auxiliary density fitting basis set defined before or provided by ORCA as a default The example shown below can be used to performed the DFT calculation of the first monomer within the water dimer using the full dimer centered basis set file nameA data PBE def2 svp def2 svp J
15. bytes for index storage to give an upper bound in bytes for the file size In practice with usual integral thresholds this maximum size is often reduced by about 50 In the transformation step of the calculation the atomic integral file has to coexist with files produced by the transformation it is deleted after the tran program completes unless the AO based calculation of ES or BE disp has been requested During the most demanding four virtual transformations performed in the beginning the upper bound on the disk space becomes roughly 3n 8 v2n 4 v4 8 x 13 bytes Once the four virtual transformations are completed the files including raw integrals will take at most about n 8 v 4 x 13 bytes which will have to coexist with new incoming integrals being generated subsequently At the end of a typical transformation for a dimer consisting of identical monomers the disk space taken up by the raw and transformed integrals will scale approximately as 2 50 80 v 80 0 2 50v 0 25v which should be multiplied by 13 to give the maximum number of bytes Again due to nonzero thresholds this number has a good chance to be reduced by about 50 In the subsequent stages of the calculation the ccsdt and sapt x codes will generate addi tional scratch files of the order of 0 v ov and smaller which will have to share disk space with the transformed integrals Moreover unless the non default algorithm has been switched on at c
16. downloaded from this web site and mailed or faxed to us as described there We will then email to the interested party the password needed to complete the download The users who download the ASYMP_SAPT and ATMOL1024 modules will be also asked to notify the authors of the POLCOR and ATMOL suites of the intended use of their codes 5 Packages included in the distribution There are several options for downloading SAPT2012 and the accompanying programs so that users can download only the parts of interest to them 1 SAPT2012 This file contains only the sAPT2012 codes including SAPT DFT Users will have to obtain some integral SCF package like GAMESS MOLPRO GAUSSIAN etc or down load the ATMOL1024 code see below before running SAPT2012 On decompression this file expands into SAPT2012 2 ATMOL1024 This file contains the ATMOL1024 package This package is a subset of the ATMOL codes 23 modified by us to handle basis sets of up to 1023 orbitals On decompres sion this file expands into SAPT2012 atmo11024 so users should decompress it in the root directory that SAPT2012 is in 3 ASYMP_SAPT Contains the POLCOR suite 33 34 and the accompanying programs nec essary for computation of asymptotic coefficients Also included is the potential energy fitting program genfit_v1 developed in our group On decompression this file expands into asymp_SAPT Documentation for this package is located in asymp_SAPT doc 4
17. electron integral transfor mations MBPT CCSD calculations for monomers and finally the proper SAPT calculations All of this is performed automatically using the script pSAPT X from the psapt2K2 bin direc tory where X denoting a platform is one of 02k sp mpich mpich maui and mpich maui sep The last two cases pertain to the huinalu cluster at Maui center While pSAPT mpich maui con trols a calculation utilizing the common scratch file system scratch huinalu the other script pSAPT mpich maui sep makes use of local scratch disk scratch local on every node The pSAPT X script is executed on one master processor which in turn calls other executables and scripts also found in the psapt2K2 bin directory The MPI executables such as ptran pcc psapt are launched by the master using the mpirun command on SP systems poe grd_poe or sge_mpirun is used for this purpose The details of the calculation flowchart input files and the use of various types of basis sets are presented in Sec 10 Here we only expose the features characteristic of the parallel version of the code The executables invoked by the pSAPT X script communicate with one another through various usually large temporary files Most of these files are written and read by only one process and do not need to be accessed directly by other processes This means that such files can be stored locally in some scratch directory accessible only to one proces
18. example sam2 sam4 samb sam6 Make sure there are no blank lines in this file 3 Make sure that the appropriate scratch directory we will use tmp bukowski as an example is present on each of the compute nodes listed in the file calcnodes 4 Submit the job using a command submit JOB where JOB is the job name the core of the input file name and submit is a script similar to the following 4 bin bash HHHHHHHHHHE Customize scratch directory on compute nodes HHHHHHHHHH and the directory where the driver script resides SCRDIR tmp bukowski scratch directory SAPT_SCRIPT home bukowski psapt2K2 bin pSAPT mpich SAPT driver script HHHHHHH Paths to the SAPT executable directory SAPTDIR home bukowski psapt2K2 bin HHHHHHHHHHE End of customized part H HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHHHHHHHHHHHAHAHAEHEEHEHRHHR ERE HaHa HAH H HHH Create all the needed PROC files based on calcnodes PTRAN SAPTDIR ptran PCC SAPTDIR pcc PSAPT SAPTDIR psapt INT SAPTDIR int SORT SAPTDIR sort EVEN SAPTDIR even FRSTNODE head 1 calcnodes echo FRSTNODE O gt PROC echo FRSTNODE O gt PROCc echo FRSTNODE O gt PROCe echo FRSTNODE O gt PROCi echo FRSTNODE O gt PROCs echo FRSTNODE O gt PROCso for i in tail 2 calcnodes do echo i 1 PTRAN gt gt PROC 74 echo i 1 PCC gt gt PROCc echo i 1 EVEN gt gt PROCe echo i 1 INT gt gt PROCi echo i 1 PSAPT gt gt PROCs
19. gt full ccio F desym2 lt oo oo gt array symmetry unique elements gt full ccio F desym3 lt oolov gt array symmetry unique elements gt full ccio F getampa Add disk amplitudes to array obsolete replaced by newgeta ccml F izero Zero an INTEGER 4 array ccml F r8zero Zero a REAL 8 array indexed by an INTEGER 4 variable ccml F r8zero8 Zero a REAL 8 array indexed by an INTEGER 8 variable ccml F xdata Initialize some arrays ccml F 18zero Zero an INTEGER 8 array ccm2 F result Print final energies data F zdata Get user input data data F howmany Determine number of iterations data F params Initialize some parameters depending on o and v data F getinf Read the numbers of occupied and virtual orbitals o and v diis F diis_drv Driver for DIIS diis F diis Perform DIIS extrapolation after an iteration diis F writemat Write a matrix to disk diis F readmat Read a matrix from disk diis F closediis Cleanup of DIIS stuff close files double F d0a d2a Calculates t2 amplitude CCSD double F dlat2b Compute the most expensive ladder diagram of t2 amplitude obsolete replaced by dlprep and daxpys double F energy Calculate CC energy after each iteration double F vda Calculate single terms contributing to double amplitude double F ampcnv Convergence check for amplitudes int1 F iq0a Calculate 7 intermediate int1 F iqla iq6a Calculate two index x intermediates and x i 7 k l int1 F fi0a
20. of course requesting just one core 10 1 Calculations of integrals and SCF energies A saPT2012 run starts with calculations of atomic integrals i e integrals involving the basis functions and proceeds to calculations of the SCF orbitals and orbital energies for monomers Optionally if the opt1 keyword is set to scfcp a counterpoise CP corrected supermolecular calculation of the HF SCF interaction energy is also performed The number and type of SCF calculations depend on the chosen approach to the basis set construction and on the selection of the supermolecular calculation For a description of possible choices of basis sets see the following subsections and Ref 54 For information on the input to the integral SCF programs please refer to the original doc umentation for those codes Some remarks on this subject can also be found in Sec 9 For an ATMOL manual see http www theochem ru nl pwormer Please note that symmetry considerations are not built into the SAPT2012 codes so the SCF pack ages should be asked to output the integrals with no symmetry assumptions The SAPT2012 codes make an implicit assumption that for each monomer the number of occupied orbitals is smaller or equal to the number of virtual orbitals and a crash will occur if this condition is not met It is thus not recommended to run SAPT2012 calculations in minimal basis sets Regardless of the interface program SAPT2012 is limited to 65535 molecular orbi
21. part of P ns e3 F dspin2 Compute second part of Be disp e3 F eind3 Driver for EGY e3 F e3ind Actual calculation of BEO e3 F readbfsh2 Special version of elx F readbfshrink e3 F readbfsh3 e3 F readbfsh4 4 e3x F e30exi Driver routine for EC a e3x F e3x1 Prepare amplitudes for ES _ 10 and 01 e3x F e3x3a Calculate BG 20 e3x F e3x3b Calculate O 02 e3x F e30exdi Driver routine for BOO disp e3x F e3xidla Prepare amplitudes for Edo e3x F e3xidlb Prepare amplitudes for Eo m4 aisp 01 e3x F e3xid2a e3xid2b Prepare amplitudes for BOO _im4 disp 11 e3x F e3xidda e3xid6a Calculate Be img aisp 21 e3x F e3xid4b e3xid6b Calculate Be imq disp 12 e3x F e3x11 Calculate the 11 part of ESO e3x F ex2d3ind Version of e2ex F ex2d3 suitable for E 11 e3x F ex2d4ind Version of e2ex F ex2d4 suitable for E 11 e3x F prep11i Prepare amplitudes for BSI NA a 11 e3xd F e30exd Driver routine for PCO disp e3xd F e3xd2a e3xd2c Prepare amplitudes for BEI disp 11 e3xd F e3xd4a e3xd4c Calculate Ea 120 e3xd F e3xd4d e3xd4f Calculate B O _4isp 02 e3xd F e3xd5ab Calculate E oca 2D e3xd F e3xd5cd Calculate E 45 12 e3xd F e3xd6 Calculate EES isp 22 e3xd F preplid Prepare amplitudes for ES disp 11 direct F directe3d Driver for the semi AO based Be direct F directe3xd Driver for the semi AO based Be disp direct F eeo Calculat
22. programs In the case of ATMOL1024 the calculations of two electron integrals are omitted by simply including the BYPASS TWO statement in the proper intinp file and an SCF calculation is omitted by not executing the corresponding binary scf The two electron files from a previous ATMOL1024 run will be recognized by a subsequent SCF run due to the naming convention For DALTON the appropriate keyword is NOTWO and it can be used in the file nameB dal in MC BS calculations It appears that some integral SCF programs e g GAMESS do not have an input option to skip the calculation of two electron integrals There are two ways of arranging basis functions in an MCTBS or MCBS run The first way is known to work with ATMOL1024 and to fail with GAUSSIAN DALTON and MOLPRO It may work with other packages but it has not been tested This method is chosen by specifying the keyword BLKMB T in the TRN namelist read from the file nameP data this is also the default and therefore this keyword can be omitted If this path is used the basis functions in the DC BS type input 38 files specified above name nameA and nameB have to be ordered as follows pola isoa mid isog polg where sox is the isotropic part of the basis set of monomer X as defined above polx are the polarization functions on monomer X orbitals with symmetries p and higher for H and He and d and higher for the first and second row atoms and mid are midbond functions
23. resp i ind resp ind disp exch ind exch ind disp are fairly inexpensive the terms a Be aep and scale like o v4 and ovt respectively with the numbers 0 v of occupied and virtual orbitals for a given monomer Moreover these two corrections require the mixed monomer four virtual integrals over the molecular orbital basis that are expensive to produce Because of this SAPT has a built in mechanism to calculate these terms in a semi direct way utilizing the integrals over AOs and removing the need for a mixed monomer four virtual transformation Currently this mechanism just like the AO based algorithm for the 47 four virtual diagram in the monomer CCSD calculations controlled by the variable AOCC in the CCINP namelist works only when ATMOL1024 or MOLPRO are employed as integral and SCF front ends and when either the DCBS DC BS approach is used or in case of an MCTBS calcu lation the basis functions are properly grouped i e the variable BLKMB in the TRN namelist is equal to its default value of TRUE If this is the case the semi direct calculation is chosen by default the user can change this behavior by setting DIRECTE3 FALSE in the INPUTCOR namelist The 3y4 contribution to the EEO exch disp Correction can be omitted computation of the most expensive o by specifying E30XD FALSE and E30XDSDQ TRUE This contribution usually constitutes about gE 10 of B amp and converges fast
24. script runGAMESS is a slightly modified version of the standard script rungms distributed with GAMESS As already pointed out in Sec 8 the user must edit this script and supply the appropriate value of the TARGET variable The targets sockets and sgi mpi have been extensively tested while other targets may require some additional customization to make GAMESS run These additional changes are independent of the SAPT2012 related portions of runGAMESS and if needed can be introduced with the help of the standard GAMESS documentation 28 If you rather prefer your own GAMESS script instead of runGAMESS you can easily adapt it for use with SAPT2012 by following these steps e Copy your script into the SAPT2012 bin directory In the SAPT script change the name of runGAMESS to that of your own script e The SAPT script communicates with runGAMESS or your custom made script through the syntax of the type runGAMESS JOB VERNO NNODES SCR PUNCHDIR GMSPATH where JOB is the name of the input file like xxx inp give only the xxx part VERNO is the version number of the executable usually the name of the executable is something like gamess VERNO x NNODES is the number of compute processes to be run only 1 can be used with sequential SAPT2012 and that s what the SAPT script is requesting SCR is the scratch directory for GAMESS PUNCHDIR is the punch directory for GAMESS GMSPATH is the p
25. second order induction energy may be expressed in terms of monomer charge densities and the static susceptibility functions The same holds also for the dispersion energy which is given by an integral of the product of two monomer dynamic susceptibility functions over imaginary frequency the so called Casimir Polder integral Thus with the exception of exchange energies all the components of the interaction are in fact determined exclusively by monomer properties These properties can be calculated only once for each monomer at a high level of intramonomer correlation and then used after rotating and translating to the new monomer positions to obtain the three interaction components for any dimer configuration The point is that the expensive parts of the calculation those of the correlated charge density and susceptibility functions have to be performed only once for each monomer and not at each and every dimer geometry In particular costly four index transformations usually needed in highly correlated methods such as the four virtual transformations are done only for a single point monomer calculation and avoided during the actual interaction energy calculations The electron density of a monomer can be expressed as a combination of n n 1 2 products of atomic orbitals AOs where n denotes the number of these orbitals in the basis set used Thus a calculation of the electrostatic energy from two precomputed monomer densit
26. shells in auxiliary basis sets SAPT DFT jobs Fixed crashing of DF SAPT DFT for calculations with large intermonomer distances Removed incorrect integral unsupported for DF TRAN in density fitting calculations for third order induction calculations that prevented such calculations with DF SAPT DFT Fixed a bug in the MOLPRO interface to prevent a crash when MOLPRO is compiled with ifort Fixed a compilation failure for TARGET gfortran and GAMSI8 YES Fixed a bug in the eldcbs program that resulted in a crash of ccsddSAPT when GAMSI8 YES Fixed SAPT script to correctly handle energies printed by MOLPRO Small fixes in the examples and scripts for running the examples Attached new DALTON patch with small compilation fixes and a fix to correctly handle ECP DALTON runs New in revision SAPT2008 1 Density fitting SAPT DFT 16 optionally with quadruple precision electrostatic compo nent Three body SAPT DFT with or without density fitting 20 SAPT DFT for open shell high spin complexes 21 Faster transformation algorithm for non four virtual integrals reusing partially transformed integrals whenever possible Optimal performance is achieved when twice as much memory as for the regular in core transformation is available When additional memory is not available the new implementation is still faster than the one from SAPT2006 1 especially in dimer centered basis sets The four virtual diagram i
27. single excitation contribution needs to be omitted from the calculation i e both CCD TRUE and CCSD FALSE need to be specified in the CCINP namelist Furthermore partial amplitudes from each coupled cluster iteration need to be saved for the further use in the e2disp program To save these amplitudes one needs to set the option WRTEACH to TRUE Finally a sufficiently tight convergence threshold for the CCD equations is required we recommend setting TOLITER 1 0d 9 in the CCINP namelist The computation of the CCD ST CCD dispersion energy proceeds as follows After the in tegral transformation the CC program is invoked to produce CCD amplitudes for both monomers Next the e2disp program is run which perturbatively calculates the converged intermolecular dispersion amplitudes and the CCD part of the dispersion energy Finally the amplitudes are used by the SAPT program with the option DCONVAMP TRUE specified in the INPUTCOR namelist to calculate the singles and triples contribution to the dispersion energy with converged doubles amplitudes i e the ST CCD term The final result for the CCD ST CCD dispersion energy is then listed in the SAPT summary table 10 5 Calculation of electrostatic energy from relaxed CCSD densities In order to compute the energy ED resp CCSD from the relaxed CCSD monomer densities it is necessary to use a special script ccsddSAPT from the bin subdirectory At present such a calculation can only be pe
28. sources of the ATMOL1024 integral and SCF code e tran program performing the one and two electron integral transformation e cc program performing the coupled cluster singles and doubles calculations for the monomers The first few iterations are performed perturbatively in this way producing MBPT order by order amplitudes needed in SAPT Both CCSD and MBPT amplitudes are later used by the sapt x module to compute intramonomer correlation contributions to various interaction energy components 16 e sapt x program computing the SAPT corrections e e2d program computing the dispersion energy with the intramonomer correlation effects included at the CCD level 39 e ccsdd programs computing the relaxed CCSD densities of the monomers and the integrals of Eq 2 in DCBS bases e elsden programs computing the electrostatic energy from monomer charge densities pre computed in MCBS bases translated and rotated to monomers positions in the dimer e cks program computing the coupled Kohn Sham CKS dispersion and induction energies used in SAPT DFT e df program computing the density version of the CKS dispersion and induction energies used in SAPT DFT e misc contains various interface and utility programs Most integral SCF packages need an interface program to extract one electron integrals and SCF orbital energies and coefficients from files created by these packages and transform them into a stan
29. than 2 GB The input file dal must include INTERFACE directive in WAVE FUNCTIONS and NOSUPSYM in ORBITAL If the job has more than 255 basis functions NOSUPMAT in AUXILLIARY INPUT is required see examples DALTON He2 The symmetry must be switched off For larger basis sets prone to linear dependencies AO DELETE and CMOMAX in ORBITAL INPUT should be set to a small and a large value e g 1 D 8 and 1 D 5 respectively to suppress removing of quasi linear dependencies from the basis set combinations since SAPT2012 would not work if such a removal is performed It is recommended to compile DALTON with the same compiler as SAPT 9 6 MOLPRO When using MOLPRO as an integral and SCF front end only one MOLPRO input file that takes care of the dimer and both monomers is required irregardless of whether the DCBS DC BS Sec 10 1 1 or MCBS MC BS Sec 10 1 2 approach is used The SAPT script assumes that this file is named name molpro where name is the name of the job Example name molpro files can be found in the examples MOLPRO subdirectory of SAPT2012 Several important things should be kept in mind when writing the name molpro file e The integral symmetry must be switched off using the SYMMETRY NOSYM keyword e After the SCF calculation for each monomer the records containing eigenvectors and other important quantities have to be saved so that these records are accessible to the interface routine Furthermore the number of elect
30. the so called monomer centered plus basis set MC BS 54 To understand this approach first notice that the conceptually simplest and most natural method is to use in SAPT the monomer centered basis set MCBS i e a basis that includes only functions that one would have used if 36 the calculations involved only the energies and properties of a given monomer calculations for monomer X involve only basis orbitals centered on this monomer In the limit of infinite orbital basis set the MCBS approach converges to the exact values for each SAPT correction However for several reasons this convergence is slow for some corrections 54 The simplest cure for this problem is to use the DCBS or even better the DC BS approach The advantage of such a method is a close relation to the supermolecular approach with the CP correction The disadvantage is that the basis set is increased by a factor of two between MCBS and DCBS methods for identical monomers Reference 54 has shown that many of the functions used in DCBS DCTBS are not needed for the SAPT convergence If a DCBS DC BS is reduced to some intermediate size it is called an MC BS It has been recommended in Ref 54 that MC BS s are constructed from an MCBS by adding all the midbond functions and only a part of the basis set on the interacting monomer so called farbond functions The simplest choice for the farbond part is the isotropic part of the basis set i e orb
31. the sequential SCF codes like ATMOL1024 although quite often the time cost of such a calculation would be dominated by the SCF step As stated above pSAPT2K2 is essentially the parallel version of SAPT2002 Thus the extensions introduced in later versions of SAPT codes are not available for parallel execution All modules of the pSAPT2K2 code have been parallelized using only the MPI library and thus the suite is very portable and should run on any parallel architecture It is also recommended that the program is linked with the SCALAPACK BLACS libraries as these are needed for the CHF routine to run in parallel In the case these libraries are not available the CHF routines will run in sequential mode which may have substantial impact on the timings especially for larger numbers of occupied orbitals The SCALAPACK BLACS libraries are also necessary to build the code generating the static and dynamic CHF propagators also referred to as susceptibility functions This code will not be built if the libraries are missing To date the program has been tested on the SGI Origin2000 and Origin3800 shared memory machines the IBM SP3 and SP4 platforms shared distributed memory as well as on Beowulf clusters running Linux From the standpoint of that latter machine it is important that pSAPT2K2 is able to distribute its temporary files over file systems local to the nodes so that the scratch file systems do not have to be NFS mounted across the whole
32. the virtual orbitals Therefore with a given basis set size calculations for larger systems will take longer At the present time 2012 the largest runs per formed at the full theory level included about 500 300 virtual orbitals for systems with monomers containing about 10 20 occupied orbitals whereas routine runs typically use basis sets of about 250 functions Larger systems can be tackled by using pSAPT2K2 and a few dozen of processors or by neglecting some effects of intramonomer correlation i e using the SAPT2 or SAPTO levels defined later on However the recommended option is to use SAPT DFT 14 see Sec 16 which gives interaction energies similarly accurate as those given by the full SAPT at the costs close to those of SAPTO Complete SAPT DFT calculations have been performed for dimers with nearly 100 atoms and the dispersion energies can be computed for dimers with about 300 atoms 32 In the asymptotic region i e for large intermonomer separations SAPT calculations may be significantly simplified by means of the multipole expansion which allows to express the interaction energy as a series of inverse powers of the intermonomer separation Coefficients of this series the so called van der Waals constants depend only on monomer multipole moments and polarizabilities static and dynamic and can be computed using the POLCOR suite of codes by Wormer and Hettema 33 34 The POLCOR suite as well as a fitting program develope
33. timt Architecture dependent function to read elapsed time m F omaoo Computes 2 A occ occ intermediate for A m F omavv vir vir for monomer A m F omboo occ occ for monomer B m F ombvv vir vir for monomer B m F rbfoo Read into core 1 el integrals and store occ occ m F rbfvv and store vir vir m F save Omit small values in a table m F nr2asc Integer gt string conversion for constructing filenames b F report Print a table with subroutine timings b F izero Zero an integer array b F r8zerobig Zero a REAL 8 array indexed by an INTEGER 8 variable b F r8zero Zero a REAL 8 array indexed by an INTEGER 4 variable b F saptbd Initialization block data for the program b F alarm0 Error exit with an INTEGER x8 message code b F alarm0a Error exit with an INTEGER 4 message code b F ienter Keep track of subroutines entered for timing purposes b F ndx0 Indexing function with entries ndxnn for various 2el integrals b F readin Read 2el integrals special version for ECO b F readon Read lel integrals store only occ occ b F readov Read lel integrals of a given type b F readbf Read 2el integrals most general version b F readvv Read lel integrals divided by number of electrons b F readen Read HF orbital energies from disk b F getbuf Get sorted 2el integral buffer from disk b F wrtbu Write sorted 2el buffer b F iexit Keep track of subroutines exited for timing purposes b F lrecl Adjust buffer sizes for sortin
34. to a string containing letters spdf one letter for each shell in the DCT BS type basis thus for a part of the basis with 3s2p1d the string should be sssppd Since the program expands each symbol into a number of orbitals one has to provide information on the type of basis set spherical or Cartesian which is done by setting the variable SPHG to TRUE or FALSE respectively Note that when running SAPT2012 with GAMESS as a front end SPHG must always be set to FALSE even if the ISPHER 1 option was applied during the SCF calculations to enforce removal of spurious spherical components from the Cartesian basis used by GAMESS The other string variable to be specified is TAGS It has to contain exactly the same number of characters as the BASIS variable The allowed characters are a b and m denoting basis functions appearing only in the MCTBS of monomer A which can be the same as in pola part of the basis discussed above only in the MC BS of B like polg and in the MC BS sets 39 of both monomers respectively Each of the variables BASIS and TAGS should end with a sign denoting the end of a string For an example of using tags with GAMESS see the files in the directory SAPT2012 examples GAMESS HF_NH3_MCBS This example does not use the iso pol splitting to show the more general character of the tags method Here in the files HF_NH3 inp HF_NH3A inp and HF_NH3B inp the DC BS basis functions are entered in the order F
35. to build all programs in this package The subdirectory doc contains the user s manual for these programs The asymptotics calculations are presently limited to 255 orbitals per monmer and the relevant codes are interfaced only with the older version of ATMOL included in the ASYMP_SAPT package Furthermore the POLCOR pro gram computing the dynamic polarizabilities works only under SGI s IRIX and IBM AIX operating systems 24 8 3 Testing SAPT2012 installation Once the compilation has been completed successfully if unsure just grep the compall 1og file for the word error we strongly recommend that you perform as many tests as possible before starting to use SAPT2012 for production runs A suite of test jobs of varying size and for various SCF front ends has been provided for this purpose in the subdirectory examples Sample outputs from different platforms can also be found there For more information on running the test jobs see Sec 13 9 Using SAPT2012 with different front end packages 9 1 ATMOL1024 A good place to look for the description of input to ATMOL1024 is Paul Wormer s web page http www theochem ru nl pwormer strictly speaking this is a description of the older ver sion of ATMOL but the input options are the same as for ATMOL1024 Below we discuss several options relevant for a SAPT2012 run It is convenient to reduce printouts from the integral integw module of ATMOL1024 by adding the directive NOPRIN
36. to the directory where the libraries or ex ecutables depending on the SCF package of a given package are located for example GAMESS home local gamess Otherwise set the variable to NO note the capitals In ad dition for GAMESS the so called version number environmental variable VERNO XX needs to be specified SAPT2012 assumes that the name of the GAMESS executable is gamess VERNO x The list of SCF codes in Compal11 does not include ATMOL1024 This latter option is activated automatically if ATMOL1024 has been downloaded and is present in the SAPT2012 atmo11024 directory Thus you may set all the integral SCF variables to NO provided that AT MOL1024 has been downloaded Otherwise at least one integral SCF variable must be set by specifying the path If ATMOL1024 is present and in addition one or more integral SCF packages are selected both ATMOL1024 and the explicitly selected interfaces should work with the created SAPT2012 executables In most cases the SAPT2012 codes use I O libraries of the integral SCF packages in order to read the data created by these packages Therefore a given SCF package has to be installed before SAPT2012 and its libraries must be accessible Three exceptions are CADPAC GAMESS and DALTON which generate data read by SAPT2012 using its own subroutines The SCF programs that can be used to generate atomic integrals and SCF vectors for SAPT2012 are 19 e ATMOL1024 This is the c
37. transformationless algo rithms for calculations of electrostatic induction and dispersion energies using the precom puted densities susceptibility functions and the Casimir Polder formula examples input and output files for a set of systems and platforms This is a good source of templates for your runs misc contains various interface and utility programs Most integral SCF packages need an interface program to extract one electron integrals and SCF orbital energies and coefficients from files created by these packages and transform them into a standard form readable by the transformation code two electron integrals are read by transformation directly without such preprocessing Other programs present in misc include int sort and even interfacing the transformation to coupled cluster code memory estimator memcalc and a utility program tmerge which can be used to merge the transformed integral files if these are to be used further by sequential codes pcc program performing the coupled cluster singles and doubles calculations for the monomers The first few iterations are performed perturbatively in this way producing MBPT order by order amplitudes needed in SAPT Both CCSD and MBPT amplitudes are later used by the psapt module to compute intramonomer correlation contributions to various interaction energy components as well as electron densities at various MBPT levels psapt program computing the SAPT corrections ptr
38. uncompressing the name prop tar gz file resulting from the modified pEDI X script and then run the caldisp fit executable by typing a command similar to mpirun np 8 caldisp_fit gt dimers out 2 gt amp 1 possibly modifying the number of processing nodes paths and output file name The output file dimers out in this case will contain for each dimer geometry the following corrections ESO BOD BOD a ES BOD oap E and ESO RPA Important note The number of processors to run caldisp_gms and caldisp_fit is indepen dent of the number of processors on which the pEDI X script was run It is however important that all the files used with an exception of input edi are obtained in a single pEDI X run For example using vecta data and vectb data obtained on a different number of processors or a dif ferent machine than that used to get denaMO data denbMO data or propa data propb data may result in nonsensical results if orbital degeneracies are present for one or both monomers as it is the case e g for atoms and linear molecules In such cases GAMESS can perform arbitrary rotations within the degenerate subspaces These rotations are dependent on the number of pro cessors and even on the platform where the calculation is run so it is imperative that all the files are obtained consistently It is therefore recommended that the monomer properties are always moved around in the form of the compressed files name prop tar gz rather th
39. util user f and src util user_sapt f The first two of these files must be placed in the src common subdirectory and the last two in the src util subdirectory of your parent MOLPRO directory before recompiling MOLPRO Note that the standard distributions of MOLPRO already contain a dummy version of the file src util user f It may safely be replaced by the file from SAPT2012 if as it is the case for a default MOLPRO installation no other user supplied subroutines have been placed there As a Fortran 90 compiler is required to build MOLPRO this interface has been tested only for such compilers Portland pgf90 and Intel ifort on a 64 bit AMD architecture running Linux so far e ACES This interface has not been tested recently but might work It is also possible to build the saPT2012 package for use with the older version of ATMOL such a version limited to 255 basis functions is included in the ASYMP_SAPT distribution This can be accomplished by setting the variable ATMOL in Compall equal to the path of the main ATMOL directory change the line ATMOL NO and removing or renaming the directory SAPT2012 atmo11024 if present The ATMOL package has to be compiled prior to the compilation of SAPT2012 SAPT2012 cannot be interfaced with ATMOL1024 and ATMOL simultaneously 3 PLATFORM Two variables need to be set e TARGET is the system on which SAPT2012 will be compiled This can be one of all lower case sgi ibm32 ibm64 alpha g
40. 012 with different front end packages OL APMOULO24 lt i Bellet E A a ah BS A ELE AAA Bec ee ia 9 2 CADPAC dd A oe yo da gd a aie eae oS 937 GAUSSIAN cf si fon ty Aenea wee seals sec Gel AD ge ro dence he de she et Pa Oy Bea to Mh a OA GAMES Saar fete belt he eR Ea ANA E AA A BM AA doth 2 9 4 1 Optional modification of GAMESS source 00 0 000 eee 9 4 2 Required and recommended input options 9 4 3 runGAMESS script Vota Pay Pe ee a ee ed 9 44 Intertace tot Gace a ae eyes BR wd Hod a ee A 930 DALTON a li ty Aes aie eka Se Ge ER we tos Be eee hed cl oe Pa Oy Naa i a 9 6 MOLPRO 4 4443 20 e A EE DS yA Eee EE ee ead 10 How to run SAPT2012 10 1 Calculations of integrals and SCF energies o o O AO NN 12 15 15 16 17 19 19 24 25 25 25 26 26 27 27 27 28 30 30 30 33 10 2 10 3 10 4 10 5 10 6 10 7 10 1 1 DCBS and DCTBS approaches 2 10 1 2 MCBS and MCTBS approaches Input for post Hartree Fock part e 10 2 1 Namelist TRN een a a a a e a a a E ee 10 2 2 Namelist CCINP 0 44 4 dick a rd a a risa 10 23 Namelist INPUTCOR c rece a e a a a a a How to read the output 2 ee Calculations of dispersion energy at CCD ST CCD level Calculation of electrostatic energy from relaxed CCSD densities 10 5 1 DCBS calculation 2 0 0 00 0000000000000 0000 10 5 2 MCBS calculation ici
41. 110 10345 2006 V Lotrich and K Szalewicz J Chem Phys 106 9668 1997 R Moszy ski P Wormer B Jeziorski and A van der Avoird J Chem Phys 103 8058 1995 erratum 107 672 1997 V F Lotrich and K Szalewicz J Chem Phys 112 112 2000 R Podeszwa and K Szalewicz J Chem Phys 126 194101 2007 P S Zuchowski R Podeszwa R Moszynski B Jeziorski and K Szalewicz J Chem Phys 129 084101 2008 M W Schmidt K K Baldridge J A Boatz S T Elbert M S Gordon J H Jensen S Koseki N Matsunaga K A Nguyen S Su et al J Comput Chem 14 1347 1993 V Saunders and M Guest ATMOL Program Package SERC Daresbury Laboratory Dares bury Great Britain T Korona R Moszyriski and B Jeziorski Mol Phys 100 1723 2002 T Korona and B Jeziorski J Chem Phys 125 184109 2006 T Korona M Przybytek and B Jeziorski Mol Phys 104 2303 2006 T Korona Phys Chem Chem Phys 9 6004 2007 T Korona and B Jeziorski J Chem Phys 128 144107 2008 T Korona J Chem Phys 128 224104 2008 T Korona Phys Chem Chem Phys 10 6509 2008 T Korona J Chem Theory Comput 5 2663 2009 R Podeszwa W Cencek and K Szalewicz J Chem Theory Comput 8 1963 2012 P E S Wormer and H Hettema POLCOR package University of Nijmegen 1992 P E S Wormer and H Hettema J Chem Phys 97 5592 1992 K Patkowski K Szalewicz and B Jezi
42. 14 The density fitting implementation of SAPT DFT 15 16 allowing calculations for dimers with nearly 100 atoms was the main addition appearing in SAPT2008 The current version of the programs became available in 2012 and is denoted as SAPT2012 The list of changes relative to SAPT2002 is given in Sec 2 A version of SAPT has also been developed 17 19 which allows calculations of the nonaddi tive portion of the interaction energy for an arbitrary trimer consisting of closed shell monomers Thus SAPT can now be used to calculate the two leading terms in the many body expansion of the interaction energy of a cluster The package SAPT3B containing the three body SAPT is distributed 1During work on SAPT2002 a small error was detected in the ccsdt module of SAPT96 which slightly affected the correction e CCSD especially in calculations for small systems in large basis sets In all tested cases the magnitude of this error was small enough not to change the published results optionally with saPT2012 The package also includes a set of codes for three body SAPT based on the Kohn Sham description of the monomers SAPT DFT with or without density fitting 20 Unfortunately no further description of the three body codes is available but users should be able to use these programs following the examples provided For details of the methods we refer to the original papers 17 19 20 The two body SAPT DFT can tackle high spin open shel
43. 252 62 e ATMOL1024 HE2 E2DISPCCD an example of the CCD ST CCD dispersion energy calculation Sec 10 4 for the helium dimer in the d aug cc pVQZ basis set This calculation will take about 15 minutes on an Opteron 252 A GAUSSIAN version of this example is also provided e MOLPRO ArHF_AVDZ a simple example for a MOLPRO SAPT2012 calculation Note that for MOLPRO a single input file ArHF molpro takes care of all integral and SCF calculations and only the usual ArHFP data post SCF input file is needed as well This example takes less than two minutes on an Opteron 252 A relativistic version of this example showing how to use SAPT with the MOLPRO front end and the second order Douglas Kroll Hess relativistic Hamiltonian can be found in the same directory files ArHFrel An ATMOL1024 equivalent of this example the nonrelativistic version is also provided e MOLPRO KR2_ECP an example of using SAPT2012 with an effective core potential An ECP basis set aug cc pVTZ PP 59 supplemented by a 3s3p2d2f1g midbond set is employed for the van der Waals minimum of the krypton dimer This example takes slightly more than two hours on an Opteron 250 e DALTON He2 helium dimer example with basis set larger than 255 basis functions The DALTON input files have dal and mol extensions e saptdft a few examples utilizing SAPT DFT with DALTON interface and DF SAPT DFT with ORCA interface ArHF is a quick example of basic SAPT DFT usage D
44. 4798432 0 88152506 308 3176 delta HF _ int 2 213324283 1 38888312 485 7685 delta HF _ int r 1 896340137 1 18997240 416 1985 CORRELATION E 12 _felst 0 616739822 0 38701041 135 3587 E 13 _felst 0 811463861 0 50920169 178 0957 eps 1 _ elst k 1 428203683 0 89621209 313 4545 E71 12 _felst resp 0 748858176 0 46991599 164 3554 E7 13 _felst resp 0 764997350 0 48004349 167 8975 eps 1 _felst r k 1 513855526 0 94995948 332 2529 E 11 _fexch 0 640864839 0 40214909 140 6536 E 12 _fexch 0 125792341 0 07893595 27 6082 eps 1 _ exch k 0 515072498 0 32321314 113 0453 eps 1 _ exch CCSD 0 784465905 0 49226020 172 1704 tE 22 _ ind 1 081861737 0 67887906 237 4412 tE 22 _ ex ind 0 945961754 0 59360046 207 6146 E 20 _ disp 1 195076004 0 74992214 262 2889 E 21 _ disp 0 203325820 0 12758899 44 6249 E 22 _ disp 0 473822197 0 29732817 103 9920 eps 2 _ disp k 0 270496376 0 16973918 59 3671 E 2 _ disp k 0 924579627 0 58018296 202 9218 E74 20 _fexch disp 0 069731391 0 04375715 15 3043 SAPT_ corr 0 075210475 0 04719533 16 5068 SAPT_ corr resp 0 010441367 0 00655206 2 2916 TOTAL hybrid 112 SCF SAPT_ corr 3 376349044 2 11869279 741 0230 SCF SAPT_ corr resp 3 290697201 2 06494540 722 2246 E Capabilities of pcksdisp program This Appendix contains a more detailed description of the program pcksdisp In the pEDI X
45. 76 1995 K A Peterson D Figgen E Goll H Stoll and M Dolg J Chem Phys 119 11113 2003 B I Dunlap Phys Chem Chem Phys 2 2113 2000 F Weigend A K hn and C H ttig J Chem Phys 116 3175 2002 A Hesselmann G Jansen and M Sch tz J Chem Phys 122 014103 2005 D J Tozer and N C Handy J Chem Phys 109 10180 1998 D J Tozer R D Amos N C Handy B O Roos and L Serrano Andr s Mol Phys 97 859 1999 65 F Weigend Phys Chem Chem Phys 4 4285 2002 66 A J Misquitta Ph D thesis University of Delaware 2004 99 A Porting saPT2012 to different platforms If one wants to port the SAPT codes to an architecture that is not supported in the official release there are three main fragments of the codes that are strongly architecture dependent and should be taken care of Note that the issues described below have to be resolved for each program e g tran cc and sapt x separately as the programs do not currently use any common library with the system dependent routines 1 The memory allocation routines Each of the programs in the SAPT suite uses a single REAL 8 array which is allocated when this program starts All matrices both real and integer used by the program are then defined within the allocated core array so that no further calls to any architecture dependent allocation routines are needed the programs assume that the integer variables are 4 byt
46. 77 pgf77 pgf90 ifort g77_32 g77_64 sunf90 or hpux sgi stands for the Silicon Graphics ORIGIN or POWER CHAL LENGE series computers with the MIPSPRO 7 3 or higher compiler ibm32 for the IBM RS6000 or SP machines on 64 bit IBM platforms ibm64 is also possible alpha for the formerly DEC ALPHA platform g77 and pgf77 are used for a 32 bit LINUX box with the compiler g77 or pgf77 Portland Group Fortran respectively If one needs to run SAPT on an old Linux machine which does not support files larger than 2 GB splitting of all potentially large temporary files into 2 GB chunks can be turned on at compile time by adding the DTWOGIGAMAX declaration to the variable EXTRADEFS at the beginning of the Compall file On a 64 bit AMD platform running Linux one may compile SAPT using the Portland Group Fortran 90 Portland Group Fortran 77 22 will not suffice in this case or the Intel Fortran Compiler versions 8 1 and above by setting TARGET pgf90 and TARGET ifort respectively For the compilation on 64 bit AMD using g77 the user needs to specify the g77_32 or g77_64 target flag for a 32 bit or a 64 bit binary respectively TARGET pgf90 and TARGET ifort work in the 64 bit mode by default note however that ATMOL1024 does not work with TARGET ifort in 64 bit mode GNU Fortran95 gfortran is supported starting with SAPT2008 2 except for ATMOL where some combinations of compiler versions systems do not work Since gfortran changed th
47. 84 5 geometry and basis set info of the monomers will be recorded in formatted files infoa data and infob data in the format readable by the subsequent transformationless codes After collecting these files and input edi in one scratch directory one can run the caldisp_gms program independently of the pEDI X script by typing or submitting through the queuing system a command similar to mpirun np 8 caldisp_gms gt dimers out 2 gt amp 1 modifying of course the number of processing nodes paths and output file name appropriately As usual the executable caldisp_gms can be found in psapt2K2 bin directory 14 7 2 Calculating electrostatic induction and dispersion energies from fitted monomer electron densities and susceptibility functions A promising alternative route of EDI calculations utilizes approximate representations of monomer properties in terms of the auxiliary basis sets The accuracy of this method strongly depends on the quality of these sets The auxiliary basis sets can be obtained using the utility program make_aux realizing the method described in Appendix F and the property fitting can be accomplished with the help of the program tdenfit the relevant lines in the compall script must be commented out if these two programs are to be built during installation Later in the work on SAPT DFT it was found 14 15 that the optimized auxiliary basis sets like those from Ref 61 perform better Thus we recommend t
48. CUT 24 ITOL 26 in the CONTRL input group QMTTOL 1 0E 30 this will prevent GAMESS from unex pectedly removing quasi linearly dependent combinations of basis functions from the variational space SAPT2012 does not work correctly if such a removal occurs in the SCF input group NCONV 9 e We recommend using the option ISPHER 1 in the CONTRL input group which forces GAMESS to do SCF calculations in the basis set of spherical Gaussian orbitals instead of the default Cartesian ones and thus reduces the risk of linear dependencies Unfortunately although using this option reduces the dimension of the variational space available to the system the atomic integral file produced by GAMESS remains Cartesian and thus its size is not reduced e In the MC BS type run see Sec 10 for explanations the variable SPHG in the namelist TRN in the P data file see Secs 10 and 10 2 for a detailed description of this file must be set to F or FALSE even if GAMESS was run with ISPHER 1 This is because of the Cartesian character of the integrals file as mentioned above The variable SPHG which defaults to TRUE i e spherical basis is assumed is only important for MC BS and MCBS runs and has no effect in the DCBS case 9 4 3 runGAMESS script Whereas most other integral SCF packages are invoked in the SAPT script by just executing a given program GAMESS needs its own script SAPT2012 bin runGAMESS called from the SAPT
49. D J Wales Springer 2005 vol 116 of Structure and Bonding pp 43 117 K Szalewicz R Bukowski and B Jeziorski in Theory and Applications of Computational Chemistry The First 40 Years A Volume of Technical and Historical Perspectives edited by C E Dykstra G Frenking K S Kim and G E Scuseria Elsevier Amsterdam 2005 chap 33 p 919 K Szalewicz Wiley Interdisc Rev Comp Mol Sci 2 254 2012 B Jeziorski R Moszy ski A Ratkiewicz S Rybak K Szalewicz and H L Williams in Methods and Techniques in Computational Chemistry METECC 94 edited by E Clementi STEF Cagliari 1993 vol B p 79 R Bukowski W Cencek K Patkowski P Jankowski M Jeziorska M Kolaski and K Sza lewicz Mol Phys 104 2241 2006 H L Williams and C F Chabalowski J Phys Chem A 105 646 2001 A J Misquitta and K Szalewicz Chem Phys Lett 357 301 2002 A J Misquitta B Jeziorski and K Szalewicz Phys Rev Lett 91 033201 2003 A J Misquitta and K Szalewicz J Chem Phys 122 214109 2005 A J Misquitta R Podeszwa B Jeziorski and K Szalewicz J Chem Phys 123 214103 2005 96 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 R Bukowski R Podeszwa and K Szalewicz Chem Phys Lett 414 111 2005 R Podeszwa R Bukowski and K Szalewicz J Phys Chem A
50. ESS where to run will have the form 76 hnfe01 hnfe01 hnfe02 hnfe02 hnfe03 hnfe03 The driver script to be called by submit is now pSAPT mpich maui which differs from samson s pSAPT mpich in the syntax of mpirun command as well as in some file management portions it is assumed here that the scratch directory is set to the common filesystem scratch huinalu In order to run GAMESS pSAPT mpich maui calls a custom script runGMS mpich maui which differs from runGMS mpich in details of how the DDI s HOSTLIST is constructed and in the use of ssh instead of rsh for internode communication Jobs on interactive nodes can only be run using the Ethernet network interface In the production stage psaPT2K2 jobs have to be run on compute nodes The legal way to accomplish this is to use the huinalu s queuing system called Maui Scheduler The scheduler requires the user to prepare two scripts The first is the scheduler command script which in turn calls the second script performing the file management tasks and invoking the pSAPT2K2 driver script The format of the scheduler commands script MAUI_script is as follows Initial working directory and wallclock time IWD u bukowski tests ArHF_Tc Job wall time limit in seconds WCLimit 1800 Task geometry Tasks 8 Nodes 8 TaskPerNode Feature requests Arch x86 OS Linux Account Account AFPRD 0102 001 MPI Ethernet job for Myrinet use gm inst
51. Euler angles and uses them along with the data of dimer cnf to produce a set of files geo d containing Cartesian coordinates of all atoms comprising the given dimer configuration with appropriately set charges A ghost i e zero charge site called Mb is also inserted halfway between the COMs of the monomers A copy of geoparm d is also produced fort 7 in which the just processed input line is given the label DONE The RunlotATMOL script then proceeds to overwrite the old geoparm d with this modified copy and create all the needed intinp files out of the previously prepared pieces head d end d iso d polA d polB d and the Cartesian geometry files geo d generated by getgeoATMOL Once all the intinp files are created the SAPT script is called the path pointing to this script is automatically set up during installation to do the proper SAPT2012 calculation for this geometry The output is written to the file name1 out After the SAPT script completes its task the whole cycle is repeated i e geoparm d is searched for the new geometry labeled DOIT the input files for this geometry are generated and the SAPT script invoked The process continues automatically until all the geometries in geoparm d are taken care of Consecutive output files are named name1 out name2 out name3 out in accordance with the position of geometries in geoparm d In this way using the Runlot utility the whole surface or a significant portion of i
52. Laguerre quadrature scheme The variable NQUAD sets the number of quadrature points to be used for the integration OMEGAO and ALPHA The transformation used in the Gauss Legendre quadrature schemes involves a constant wo The namelist variable OMEGAO allows one to set this constant It is typically between 0 3 and 0 5 The Gauss Laguerre quadrature scheme involves the constant a For the integrals encountered here one should set ALPHA 0 0 Debugging levels There are many debugging levels built into the code These can be activated by setting the relevant combination of debugging flags to T Nota bene large matrices may be printed out at certain levels Here is a list of current debugging levels DEBUG1 T F Test the quadrature grid DEBUG2 T F Use the un coupled propagator in the coupled propagator route This is very useful when testing the code as the dispersion energy obtained this way should be the same as the value of Eo obtained from the SOS formula DEBUG3 T F Print out all matrices in the construction of the coupled propagator DEBUG4 T F Print out all 2 electron integrals read in DEBUG5 T F Print out information in the N summation algorithm subroutine SUMN6 DEBUG6 T F Print out information in the PROPERTIES and C6DISP routines DEBUG T F Print out integrals etc Used in computing the H and HG matrices in the CHF approximation DEBUGS T F Print
53. MOL RunlotCADPAC and RunlotDALTON which allow automatic calculations for multiple points on a potential energy surface in a single submission of a computer task Some members of our group found it also convenient to utilize RunlotATMOL2 a more elaborate and flexible version of RunlotATMOL Currently available only for ATMOL1024 CADPAC and DALTON these scripts can be fairly easily extended to other integral SCF programs An example of using RunlotATMOL can be found in the directory SAPT2012 examples ATMOL1024 ArH20_MCBS The idea behind the Runlot scripts is to construct the input files appropriate for a given SCF front end by combining universal geometry independent templates containing basis set and all the necessary integral SCF options with Cartesian geometries calculated from a minimal set geometric data Once all the input files are generated the SAPT script is invoked to calculate the interaction energy for a given dimer geometry and the results are recorded in a file with a name unique for this geometry Then the input files are prepared and the calculation performed for the next geometry from the set and the process continues until the set of geometries is exhausted Below using the ArH20_MCBS example we describe steps needed to set up a RunlotATMOL job 1 Prepare the files containing the basis sets in ATMOL1024 format 54 e iso d isotropic part of the whole DCBS basis i e the functions which will be used i
54. N and that of SAPT DFT is O N in both cases significantly better than the O N scaling of the regular SAPT The scaling of SAPT DFT can be lowered to O N by using density fitting 12 14 15 57 62 Furthermore although the 87 density fitting transformation still scales as O N5 it has a greatly reduced prefactor 16 2 Installation and usage SAPT DFT requires DALTON 2 0 37 or ORCA 53 for monomer DFT calculations in the latter case only the density fitting version has been interfaced because ORCA does not provide two electron integrals needed for the standard version See Sec 16 4 2 for the detailed description The users of SAPT DFT need to obtain a separate license and download the package from http www kjemi uio no software dalton dalton html Consult the DALTON manual for in stallation requirements Some of the SAPT DFT functionality is available via a patch dalton diff distributed together with SAPT2012 First compile and install the standard DALTON 2 0 After testing the installation update the path to the DALTON directory in the patchdalton script lo cated in the main SAPT2012 directory and run the script If the patching is successful compile the patched DALTON The recompilation should last significantly shorter than the original compilation If you have not compiled SAPT2012 with DALTON support set the DALTON variable of the Compall script to the proper path to the DALTON executable make sure the variab
55. P code one should include QUADINV YES in the Compal1 script If the compiler does not support quadruple precision the compilation will fail Since QP calculations are more time consuming than double precision ones the QP inversion is not turned on by default To use it one needs to also specify quad option for SAPTdf or RunlotDALTONdf scripts With this option after the SAPT DFT calculation is complete an extra calculation of the electrostatic energy is 91 performed This result replaces the standard double precision results in the summary table By comparing the double and quadruple precision values one can estimate the severity of the quasi linear dependence Additionally slightly better accuracy of density fitting of the electrostatic energy is obtained by using basis sets of Ref 65 rather than those of Ref 61 One can include such basis set in name elst aux and it will be used instead of name aux in the quadruple precision calculation of the electrostatic energy If the file is missing the standard name aux will be used DF SAPT DFT is also partially parallelized All calculations performed by the patched DALTON program can be run in parallel Also the calculations of the CKS kernel integrals are parallelized The rest of the programs is not parallelized but can be used with parallel DALTON DF SAPT DFT is limited to up to g functions in the auxiliary basis set This restriction is due to the use of GAMESS integrals In additi
56. S2 FALSE in the INPUTCOR namelist 2 E2IND ECO in 3 E2INDR E ind resp 4 FEX21 ECO exch ind 5 EEX2IR EY exch ind resp 20 6 EEX2D Foch disp 7 EEX2 BE and B i e EEX2 TRUE implies EEX21 TRUE and EEX2D TRUE exch disp exch ind 8 EEX2R ECO a and Bee ind resp i EEX2R TRUE implies EEX2IR TRUE and EEX2D TRUE 9 E12 EG 10 E129R EU elst resp 44 11 E13PL EG 12 E13PLR EQ elst resp 13 E11 EGP exch 111 14 E111 Elo 15 E12x ELY y 202 16 CONVAMP E CCSD 17 E2DSP ECO disp 18 E21D EG 19 E22D EG 20 EMP2 E02 MBPT2 correction to monomer s correlation energy for tests only 21 E221 ge see Ref 2 30 22 E300D EG 23 ESIND ECO 30 24 DSPIND Erd disp 30 25 ESOXD ES disp 26 ESOXDSDQ EEY E 1 exch disp without the most time consuming triples term 97 E30XI EGO exch ind 30 28 DSPIX E ety indie 29 EZINDR EC and a scaled approximation to EEO ind resp exch ind resp 13 li Notice that the electrostatic energies E are sometimes denoted as Egg as these terms result els from the Rayleigh Schr dinger perturbation theory that in this context is often called polarization theory The acronym pol in several places in the program as well as the letters
57. SAPT KS where electrostatics first order exchange induction exchange induction dispersion and exchange dispersion are obtained by using SAPT terms of the zeroth order in W with SCF orbitals and orbital energies replaced by their KS equivalents For meaningful results SAPT KS requires asymptotically corrected AC Kohn Sham calculations SAPT KS does not reproduce dispersion correctly This problem was found to be due to the use of a formula asymptotically related to uncoupled dynamic polarizabilities Instead the dispersion and induction energies should be calculated from frequency dependent density susceptibility FDDS functions also referred to as propagators obtained from TD DFT i e at the coupled Kohn Sham CKS level The SAPT KS and CKS steps form the complete SAPT DFT The total SAPT DFT interaction energy up to second order in V can be defined as 14 EE pl Ks El KS EQ CKS BO ing CKS E CKS E EO disp CKS 14 where the terms with the CKS label result from the coupled Kohn Sham approach The E 2 CKS exch ind and E exch disp CKS are approximated by scaling their KS counterparts as described in Ref 14 The method can be shown to be potentially exact for all major components of the interaction energy asymptotically for exchange interactions in the sense that these components would be exact if the DFT description of the monomers were exact The nominal scaling of SAPT KS is O
58. SAPT2012 An Ab Initio Program for Symmetry Adapted Perturbation Theory Calculations of Intermolecular Interaction Energies Sequential and parallel versions User s Guide Revision SAPT2012 2 Robert Bukowski Wojciech Cencek Piotr Jankowski Matgorzata Jeziorska Bogumi Jeziorski Stanis aw A Kucharski Victor F Lotrich Alston J Misquitta Robert Moszy ski Konrad Patkowski Rafa Podeszwa Fazle Rob Stanis aw Rybak Krzysztof Szalewicz Hayes L Williams Richard J Wheatley Paul E S Wormer and Piotr S Zuchowski Department of Physics and Astronomy University of Delaware Newark Delaware 19716 Department of Chemistry University of Warsaw ul Pasteura 1 02 093 Warsaw Poland August 6 2013 Contents 1 Introduction 2 What s new since SAPT2002 2 1 New in revision SAPT2012 2 e 2 2 New in revision SAPT2012 1 e eee 2 3 New in revision SAPT2008 2 aoaaa aaa 2 4 New in revision SAPT2008 1 ee e 25 New it SAPT2O0 it A AA e E ae A h 3 Short overview of theory 4 Downloading saPT2012 5 Packages included in the distribution 6 Structure of SAPT2012 directory 7 SAPT installations at a glance 8 Installing SAPT2012 8 1 Compall installation SCTipt ee ee 8 2 Compall_asymp installation script 2 o o 000000000000 8 3 Testing SAPT2012 installation 2 ee 9 Using SAPT2
59. SCF runs for monomers A and B in an appropriate MCTBS Next the script will look for the file s name x to perform integral SCF calculations for the dimer in the DC BS equivalent of the MCTBS used In the next two steps the files nameA and nameB containing the same DC basis set will be used as in the calculations described in the previous paragraph However now neither the monomer A nor B calculation need to com pute the two electron integrals since these are already available from the dimer calculation Also in contrast to the case of the previous paragraph the SCF calculations are performed for each monomer since the total SCF energies are needed to compute the supermolecular HF SCF inter action energy The SCF orbital energies and coefficients from these runs are discarded Thus if for example ATMOL1024 is used as the integral SCF program the following input files are needed nameMA intinp nameMA scfinp nameMB intinp nameMB scfinp name intinp name scfinp nameA intinp nameA scfinp nameB intinp nameB scfinp and nameP data If GAUSSIAN is used as the integral SCF program the input files needed are nameMA data nameMB data name data nameA data nameB data and nameP data If DALTON is used the following input files are needed nameMA dal nameMA mol nameMB dal nameMB mol nameA dal nameA mol nameB dal nameB mol nameP data name dal and name mol The possibility of skipping parts of integral SCF calculations varies between
60. T GROU GTOS to the intinp files This will suppress printing of the groups or ordered Gaussian Type Orbitals GTOs Adding the word BASI to the list will also suppress the basis set printout To avoid computation of the multipole integrals not needed in a SAPT calculation include the directive BYPASS PROPERTY this may be important especially on SGI machines where the absence of such directive may cause a run time error Inclusion of a line FPRINT NVCT NEIG NFTE NITE NPOP in the scfinp input files will ask the scf program to skip the printout of the vectors eigenvalues Fock trial matrix iterations and populations for that run When the supermolecular SCF interaction energy is calculated during a SAPT run i e when the scfcp option is in effect most runs are like this the files nameA intinp and nameB intinp should contain the directive BYPASS TWO to avoid recalculation of two electron integrals This directive should not be present in the file name intinp or in the case of a MCTBS calculation in nameMA intinp and nameMB intinp name denotes here the name of the job If the supermolecular SCF calculations are not performed i e if the scfcp option is not in effect then the directive BYPASS TWO must be also removed from the file nameA intinp See Sec 10 for further explanation On old Linux platforms with the g77 compiler there is a 2 GB restriction on the size of any file In such a case if the two electron integral file gener
61. USSIAN GAMESS and DALTON see the tran unpack F file for details These routines are highly architecture dependent since the structure of the integral indices depends on the endianness big endian or little endian of the machine for GAUSSIAN and on the options selected when compiling GAUSSIAN Or GAMESS see Sec 8 1 GAUSSIAN and Sec 9 4 GAMESS for more on this sub ject When porting to a new architecture one must make sure that both the internal SAPT packing unpacking routines listed above and the routines used to unpack integral indices written by a particular front end program work correctly B Integral SCF interfacing The SAPT group of codes can be interfaced with virtually any integral SCF program A short description of the elements of the interfacing process is presented here The existing interfaces can be used as a template for the creation of new interfaces A short listing of what the tran program needs follows 101 e One electron integrals 1 Overlap 2 Hamiltonian 3 Kinetic 4 Potential Two electron integrals SCF eigenvalues SCF eigenvectors Information about the run 1 Basis set size 2 Number of occupied orbitals 3 Number of virtual orbitals 4 Charge on each atom 5 Geometry of the monomers Most of the information is read by a small interface program from the integral SCF program files and then rewritten into a simple form that the next stages of the process can easily under
62. a be en dee DA ee SE ee Pod dha Submitting a sequence of SAPT2012 jobs 2 2 o o ee Memory and disk requirements e 11 Description of some internal data sets 12 Performance of SAPT2012 13 Tests and example input and output files 13 1 13 2 The examples directory ci atro e ad RE et ey AA a Running test JOBS iss ed pe Heset A ee dd ge BIS Gane ae eo ele dnd 14 Parallel SAPT pSAPT2k2 14 1 14 2 14 3 14 4 14 5 14 6 14 7 Structure of psapt2K2 directory o o 0 000022 ee eee Installing psapt2k2 2 640 ee kk ee a a ee A 14 2 1 compall installation script o 000200000 14 2 2 Testing pSAPT2K2 installation lt o sa nnda o 0 0 2 0 000 Using pSAPT2K2 with GAMESS as a front end o o How to run pSAPP2K2 3 2 ga o Va be is E ae ee ee do ed 14 4 1 Running pSAPT2K2 on SGE o bucu Ehia aa p e a a o De a 14 4 2 Running pSAPT2K2 on an SP3 SP4 0 o o o o o 14 4 3 Running pSAPT2K2 on a Beowulf cluster o o Inp utyales 2 oca a it A e e Memory and disk requirements e Electrostatic dispersion and induction EDI energies from monomer properties 14 01 The PED LSCripts ds via os a a a oe D 58 59 61 61 63 64 65 67 67 68 68 70 71 73 73 79 79 80 14 7 2 Calculating electrostatic induction and dispersion energies from fitted monomer electron densities and susceptibility function
63. air unpack10 F joinindx Do the reverse of spltindx el F first ELN and E driver el F delta Special form of Kronecker delta function el F inv Calculate inverse matrix el F pmat Prepare the P matrix for inversion elxs2 F elxs2 Driver routine for ELO 62 elxs2 F els2k Actual calculation of ECO 62 e12 F srt12 Eo and EN A driver routine el2 F sort12 Presort of 2el integrals for E92 e12 F e120pl Compute Bo e12 F e102pl Compute B40 e13 F el3 A wrapper for the ES driver el3 F el3drv Actual driver for Ae and Boe el3 F el3pl11 e13p17 Compute components of ES e13 F komaov Compute occ vir electrostatic potential for A different version e13 F kombov As komaov but for monomer B el3 F komaoo As komaov but form occ occ matrix el3 F komavv As komaov but form vir vir matrix el3 F komboo As komaoo but for monomer B el3 F kombvv As komavv but for monomer B ellx F ellex Bo driver ellx F ellx Actual calculation of BOY ellx F transpov Transpose the overlap matrix ellx F ellxl ellx4 Compute components of EQD elx F ellle EO driver elx F elllexh Calculate BUD elx F mkg24 Construct g intermediate elx F readbfshrink Read two electron integrals omitting the core ones 108 Table 5 Comments on selected subroutines sapt x part 3 Module Subroutine Comments el2x F el2ex Main BO and B992 driver el2x F k2f1 Driver for the K part of pe el2x F k2fa Calcu
64. alu a Beowulf cluster at Maui supercomputer center runGMS mpich maui differs from runGMS mpich slightly in details of how the HOSTLIST is constructed and by the usage of ssh instead of rsh for interhost communication runGMS mpich maui will be called automatically from within the pSAPT mpich maui and pSAPT mpich maui sep driver scripts so the user does not have to worry about these details e Should you prefer to use your own script as a driver for GAMESS adapt it for pSAPT2K2 following the instructions of Sec 9 with one exception the integral file generated by process 0 JOB FO8 has to be renamed into inta 0 while the integral files from the other pro cesses JOB F08 X into inta X This can be accomplished in C shell using the following syntax mv JOB FO8 inta 0 set m 1 foreach fle ls 1 J0B F08 mv fle inta m m end e On some BEOWULF clusters such as huinalu at Maui center the communication between the nodes is furnished in terms of ssh rather than rsh In such cases GAMESS s parallel launcher ddikick x must be modified to use ssh instead of rsh and recompiled as suggested in the source ddikick c 69 14 4 How to run pSAPT2K2 To perform a pSAPT2K2 calculation for one dimer geometry one has to run a dozen or so pro grams integral SCF calculations for the monomers and possibly for the dimer interface programs in most cases rewriting integral SCF files into different forms 1 and 2
65. amplitudes for monomers A and B Finally the sapt x program is run to compute the interaction energy components Several short interface programs are also invoked between the calls to tran and ccsdt An alternative to that implemented in the sapt x module way of calculating the electrostatic component of the interaction energy computes the Coulomb interaction of the monomer charge densities obtained at the relaxed CCSD level If such a calculation is desired additional two codes are run after ccsdt These are ccsdm producing the relaxed CCSD densities and eldcbs performing the integration of these densities SAPT approach described above is a double perturbation expansion in powers of the oper ator V and in powers of the intramonomer correlation operator W Wa Wp the sum of the Moller Plesset fluctuation operators for monomers A and B The expansion in V is truncated at the third order terms The expansion in W is truncated at different orders depending on the particular component and the most important components the electrostatic first order exchange and dispersion energies are selectively summed to infinity in W Thus one may call this approach SAPT MP CC A complete SAPT CC approach at the CCSD CC with single and double exci tations level was developed by Korona et al 24 31 and is available in SAPT2012 The computational cost of the SAPT corrections scales as a product of some powers of the number of occupied orbitals and of
66. an parallel program performing the one and two electron integral transformation updates log log of the history of changes and updates 66 14 2 Installing psapt2k2 Installation of pSAPT2K2 is controlled by the ksh script compall a small portion of which has to be customized by the user The compal1 script sets the compilation options appropriate for a given hardware platform It is assumed that the integral SCF code used is GAMESS US No other SCF programs are currently supported by the compall script The use of other SCF packages is still possible although it would require some hand tuning of the compilation process After the compilation options have been set the compall script compiles and links all the pieces of the code Finally the scripts used to run pSAPT2K2 are updated by inserting the current paths to the executables 14 2 1 compall installation script The following environment variables must be adjusted by the user in the top section of the compall script 1 Execution shell Change the first line of the script to one of the following e bin bash The Bash shell on a LINUX box or e bin ksh The Korn shell on all other platforms 2 TARGET the machine the program is being compiled on Choose one from 02k will work for O3K also sp will work for SP3 and SP4 or mpich on Beowulf clusters 3 BLAS if TARGET mpich specify how you want the BLAS library to be linked usually this is just 1lblas but
67. an separately 15 SAPT CC A SAPT version of first and second order in V and of infinite order in W at the CCSD level devel oped by Korona et al 24 31 is avilable in SAPT2012 Such calculations require MOLPRO2010 1 since the code for these corrections has a form of a MOLPRO patch This patch is located in the misc patch ccsapt subdirectory of regular SAPT2012 In order to run these codes one must apply the patch by copying all the files from the misc patch ccsapt src eom subdirectory to the src eom subdirectory of an existing MOLPRO2010 1 installation and recompiling MOLPRO Exam 86 ple inputs for SAPT CC runs are provided in the misc patch ccsapt examples subdirectory One should note that the SAPT CC patch is independent from the patch required to run regular SAPT with MOLPRO as the integral and SCF front end Sec 8 1 and the two patches can but do not have to be applied simultaneously No further information is available on SAPT CC 16 SAPT DFT SAPT based on coupled Kohn Sham treat ment of monomers 16 1 Introduction SAPT DFT is an extension of the SAPT theory In SAPT DFT the monomers are described in terms of Kohn Sham KS orbitals and orbital energies as well as of TD DFT response functions A complete description of the theory together with references to the historical developments of the method as well as numerical examples can be found in Ref 14 SAPT DFT consists of two steps First is the so called
68. and dispersion can be found in directories psapt2K2 examples PLATFORM EDI where PLATFORM is one of 03K SP3 SP4 and BEOWULF 14 3 Using pSAPT2K2 with GAMESS as a front end GAMESS US is currently the only parallel SCF package pSAPT2K2 is interfaced with See Sec 9 for information about setting up the GAMESS input files for psAPT2K2 runs and about the structure of the GAMESS driver script runGAMESS and of the GAMESS ptran interface program gamsintf 68 There are a few minor differences between the runGAMESS script used with the sequential pro gram SAPT2012 described in Sec 9 and the one used with psAPT2K2 Although these differences are completely transparent to the user we list them here for the sake of completeness e Unlike in the sequential version of the code the variable TARGET in runGAMESS is set auto matically by the compall script so no additional action is needed here e A separate version of the runGAMESS script called runGMS mpich has been created for samson our Beowulf cluster here at UD The GAMESS submission instruction present in this script were causing syntax errors on other platforms hence the need to create a separate script for MPICH implementation of MPI runGMS mpich will be called automatically from within the pSAPT mpich driver script so the user does not have to worry about these details e A separate version of the runGAMESS script called runGMS mpich maui has been created for huin
69. ary and hence LPCKLIB does not have to be given at all just set it to YES Once all the variable mentioned above are set simply type e C Shell users compall gt amp compall log amp e K Shell users compall gt compall log 2 gt amp 1 amp and the compilation should begin Check compall 1log to see if all is well The compall script works by invoking the make command with platform specific makefiles Thus any subsequent invocation of compall will detect changes made to the sources and only those parts of the code will be rebuilt which were affected by these changes Running the script psapt2K2 cleandirs will restore the psapt2K2 directory to its distribution state i e all object files and executa bles except shell scripts will be deleted and a subsequent invocation of compall will start the compilation from the beginning 14 2 2 Testing pSAPT2K2 installation Once the compilation has been completed successfully if unsure just grep the compall 1og file for the word error we recommend that you perform as many tests as possible before starting to use pSAPT2K2 for production runs A suite of test jobs of varying size and for different parallel platforms has been provided for this purpose in the subdirectory examples Sample outputs from different machines out_ref and queuing system submission scripts can be also found there Examples of using the new monomer property based algorithms for electrostatics induction
70. ated by ATMOL1024 is likely to exceed this size it has to be split into several pieces each 2 GB or less For example if the integrals are anticipated to take 5 GB of disk space one should have them distributed over at least three files This can be done by specifying 25 MAINFILE MT3 MT4 MT5 MAXBLOCK 499999 in the intinp files somewhere below the basis set specification but before the ENTER directive The first of the lines above means that the files called MT3 MT4 MT5 will be used to store the integrals and that the size of each will not exceed MAXBLOCK 511 8 bytes which in this case amounts to somewhat less than 2 GB the number 511 comes from some internal data structures of ATMOL1024 Now we have to tell the transformation module of SAPT2012 how many files ATMOL1024 produced by including NMFILES 3 in the TRN namelist in the P data input file see Secs 10 and 10 2 for description of this file Of course the number 3 would have to be changed if some other number of MTx files were used ATMOL1024 and SAPT2012 support up to 18 such files MT3 through MT20 This option is left for compatibility but is not necessary on modern Linux distributions 9 2 CADPAC The CADPAC interface to SAPT2012 is not maintained anymore however it is likely to work Notice that CADPAC can use only Cartesian basis functions and only angular functions up to f are allowed The input file used for CADPAC runs must include the SAPT keyword This k
71. ath to the GAMESS executable All the parameters in the invocation of runGAMESS are set automatically in the SAPT script upon compilation of SAPT2012 or at run time Your custom made replacement of runGAMESS should recognize these command line parameters instead of having them hard coded as it is usually the case with the standard rungns e In your script after the SCF calculation is done but before file cleanup some GAMESS files should be saved with appropriate names SCR JOB FO5 as SCR JOB INP SCR JOB FOS as SCR inttw data and SCR JOB F10 as SCR JOB DAF where SCR denotes GAMESS scratch directory and JOB is a script variable which will be set by the SAPT script on each call to GAMESS 29 9 4 4 Interface The sources of GAMESS SAPT2012 interface are located in the SAPT2012 misc gamint subdi rectory The interface consists of the Fortran program gamsintf f which extracts one electron in tegrals and SCF vectors from the dictionary file of GAMESS and two simple awk scripts gms_awk1 and gms_awk2 which scan the GAMESS standard output for the number of basis functions occupied orbitals and system geometry 9 5 DALTON The DALTON 2 0 interface was tested on machines with 32 bit integers only but most of the 64 bit architectures including AMD64 and IBM64 have 32 bit integers DALTON must be compiled without DVAR_SPLITFILES option and the operating system must support files larger
72. ation ISITC6DISP T F Set if the Cg dispersion coefficient is to be computed At the moment the program outputs only the isotropic coefficient e USESUMN6 T F Sets the o v summation algorithm in a Casimir Polder dispersion calcu lation Set this to T unless you want to use the old o4v4 summation algorithm e MAKEH1H2 T F Set to enable construction of the Electric and Magnetic Hessians the HU and HG matrices in the CHF approximation Transformed integrals of certain types are required for this option If this option is set to F then the H and H matrices must be read in from a file in either the CHF or CKS approximation e NUMFREQ and FREQ1 FREQ2 FREQ8 NUMFREQ is the number of frequencies at which a frequency dependent polarization calculation is to be made This should be less than or 114 equal to 8 The variables FREQ1 FREQ2 FREQ8 contain the frequencies If complex frequencies are required set a negative frequency These variables override the quadrature scheme described below IQUADTYP and NQUAD The type of quadrature scheme to be used in performing the w integral in the Casimir Polder dispersion calculation and in the calculation of the Cg dispersion co efficient 1 t G IQUADTYP 2 sets the Gauss Legendre quadrature with the transformation w w tan t IQUADTYP 1 sets the Gauss Legendre quadrature with the transformation w w IQUADTYP 3 sets the Gauss
73. ation should begin Check compall 1log to see if all is well The Compal1 script will create a file SAPT2012 stamp intf containing a summary of the settings you have used in the compilation A subsequent invocation of Compall will detect any changes made to these settings since stamp intf was last created and only those parts of the code which were affected by these changes will be rebuilt Running the script SAPT2012 Cleandirs will restore the SAPT2012 directory to its distribution state i e all object files and executables except shell scripts will be deleted and a subsequent invocation of Compall will start the compilation from scratch One more customization step may be required before SAPT2012 is run with GAMESS as the SCF front end the SAPT2012 bin runGAMESS script must be modified by setting the TARGET variable which depends on the platform and on the way GAMESS has been compiled In most cases the default TARGET sockets will be appropriate although on SGI machines TARGET sgi mpi is also popular Consult your local GAMESS installation Further customization of runGAMESS will be needed for other targets if you need to do such a customization see examples given in both runGAMESS and the standard rungms script for the GAMESS distribution 8 2 Compall_asymp installation script If you have downloaded the ASYMP_SAPT package it will expand into asymp_SAPT directory Change to this directory and use Compall_asymp script
74. cd SCRDIR SAPT_SCRIPT JOB nocp NPROC SCRDIR gt OUTFILE 2 gt amp 1 for i in awk print 1 calcnodes do echo Cleaning up on i ssh i rm SCRDIR done 78 The script sub_s_sep launches the pSAPT2K2 calculation using the local scratch file systems scratch local where all the necessary data files including input are copied using the scp com mand The number and the list of nodes are retrieved from the environment variables MAUI_TASK_COUNT and MAUI_JOB_NODES supplied from within the scheduler environment Due to some file manage ment issues which could not be resolved it is necessary that only one process is launched on each compute node i e the parameter TaskPerNode in MAUI_script must be set to 1 The actual pSAPT2K2 run is started using the driver pSAPT mpich maui sep adapted to make use of the local scratch environment Replacing this driver with pSAPT mpich maui changing the scratch directory to the global one say scratch huinalu bukowski and replacing the loop structure with scp by a set of simple cp commands would result in a pSAPT2K2 calculation utilizing the common scratch directory instead of the local ones Since psaPT2K2 jobs are crucially dependent on the efficiency of I O opera tions the local scratch option should be preferred as it allows to avoid competition for bandwidth between the processes 14 5 Input files The input files for GAMESS and the SAPT suite of codes are constructed in e
75. chosen in this case despite the fact that for this platform GAUSSIAN itself is compiled with pgf77 The TARGET pgf77 setting is restricted to the 32 bit i386 architecture and will not produce a valid code on an AMD64 machine GAMESS 22 SAPT2008 1 works with the most recent release of GAMESS dated 11 Apr 2008 If you want to use an older version of GAMESS you may need to edit the file misc gamint gamsintf F subroutine OPENDA changing the value of the variable IRECLN from 4090 to whatever is returned by the GAMESS function NRASIZ 10 see GAMESS source code file iolib src If the GAMESS interface is used set the variable GAMESS to the path where the GAMESS executable is located Also set the variable VERNO which is the middle part of the name of this executable e g for gamess 01 x VERNO 01 The sole purpose of the variable GAMESS in Compall is to pass the path and name of the GAMESS executable to the SAPT execution script No access is needed to any GAMESS files at the compilation time Thus compilation will proceed even if GAMESS is not installed beforehand 64 bit GAMESS if you intend to use GAMESS compiled with a 64 bit integer this happens by default on the ALPHA platform but may also happen on SGI when sgi64 is specified during compilation of GAMESS replace the line GAMSI8 NO with GAMSI8 YES CADPAC 52 This package does not need any interface programs since the files created by it can be read directly by SAPT2012 c
76. cluster Novel algorithms have also been developed for efficient calculation of the electrostatic induc tion and dispersion energies see Sec 14 7 The idea behind these algorithms is that all these interaction components are expressible through monomer charge densities and dynamic suscepti bility functions These monomer properties can be calculated just once for each monomer at a high level of correlation then simplified stored and reused many times for different dimer ge ometries Scalable beta versions of these new algorithms are also included in this distribution As mentioned before the induction dispersion module requires the SCALAPACK BLACS libraries to be installed 14 1 Structure of psapt2K2 directory After unpacking the psapt2K2 main directory will contain the following files and subdirectories 65 bin utility scripts for running SAPT After compilation this directory will also contain the executables used in a SAPT run pcksdisp contains sources and detailed documentation for the code generating the static and dynamic susceptibility functions currently at the CHF level cleandirs use this script to clean the entire psapt2k2 directory tree before recompiling from scratch compall script used to build the package see Sec 14 2 doc documentation for SAPT2002 contains this document and the METECC paper 8 in the postscript form edi_notran contains sources of the code implementing the new
77. corrected supermolecular SCF interaction energy in the dimer centered basis set If such a calculation is not required leave opti blank or better yet use noscfcp instead Using the keyword gototran as opt1 will result in restarting a SAPT run from the transformation step i e from the program tran Both parameters opti and opt2 are required when GAMESS is used as the SCF program opti can assume one of the values listed above but noscfcp must now be used instead of a blank while opt2 must be the full path of the scratch directory in which the whole calculation is taking place opt2 has the same meaning when DALTON is used However for DALTON opt2 is optional and the place where SAPT is launched will be assumed as the scratch directory if this parameter is omitted The output from all programs executed by SAPT is written to a file output file this name can be set by the user to an arbitrary string usually connected with the system being computed and its geometry The last two elements in the command line given above are Unix ksh constructs 34 which indicate that standard error messages will be written to the same file as the standard output and that the process will be run in the background Most modern computer clusters do not allow command line submission of jobs Instead one has to use a queuing system batch processor In this case the sequential SAPT should be submitted in a way analogous to that described in Sec 14 on pSAPT2K2
78. cular approach The SAPT methodology and its applications are discussed in several review papers 1 7 where complete references to the original developments can be found Most of the formulas programmed in SAPT2012 are given in the paper published in the book accompanying the METECC collection of computer codes 8 The METECC paper is available on the SAPT web page http www physics udel edu szalewic SAPT SAPT html and can be also found in the SAPT2012 distribution SAPT2012 doc METECC ps Note that the formulas for the SAPT corrections in the METECC paper contain several misprints for an errata see Ref 9 The METECC project 8 was the first distribution of the SAPT codes The next version of SAPT called sapT96 was available since 1996 Compared to SAPT96 the next version SAPT2002 was about a factor of two faster in medium size about 200 functions bases It also allowed calculations with up to 1023 basis functions SAPT96 was restricted to 255 was interfaced with a larger number of front end SCF packages and ran on a larger number of platforms A parallel version of the SAPT suite 9 referred to as pSAPT2K2 became available in SAPT2002 This version runs on SGI Origin IBM SP and on Linux clusters and scales well up to about 32 processors See Sec 14 for a detailed description of this version The SAPT2006 edition added a new powerful version of SAPT based on the density functional description of monomers and called SAPT DFT 10
79. culations slightly but the tran program requires much less time since no four virtual transformation is needed At present AOCC TRUE works only when ATMOL1024 or MOLPRO has been used as the integral SCF interface and when either the DCBS DCTBS approach is used or in case of an MC BS calculation the basis functions are properly grouped i e the variable BLKMB in the TRN namelist is equal to its default value of TRUE Note that this implies that the AOCC TRUE algorithm with the MOLPRO interface works only for the DCBS DCTBS approach The default value of AOCC is TRUE if the above conditions are satisfied and FALSE otherwise so an explicit specification of this variable is not needed unless one wants to turn off the AO based pathway for ATMOL1024 or MOLPRO interfaces The defaults should be sufficient for this namelist so all that is absolutely necessary to specify would be a statement of the form amp CCINP amp END i e no input 10 2 3 Namelist INPUTCOR This namelist tells the SAPT program which of the perturbation theory corrections are to be computed All the variables are by default set to FALSE so only those corrections that one wants to be computed have to be mentioned in the namelist The list of variables and of the associated currently available corrections is as follows 1 E1TOT ELN and BOY By default the so called approximation to Elo is also computed This computation can be turned off by setting E1
80. d in newer versions of this code the default method of SCF calculations is direct two electron integrals calculated in core and not written to disk Since SAPT2012 always needs the two electron integrals the command SCF CONV which stands for do conventional SCF must be used to force the two electron integrals to be written to disk Note that in the conventional non direct mode GAUSSIAN is limited to s p d f basis functions and one must use a different integral and SCF front end when g or higher functions are present in the basis set We recommend the SCF TIGHT CONV keyword to be used to tighten the SCF iterations convergence criteria Moreover the keywords SYMM NOINT and NORAFF must be present in all inputs to GAUSSIAN since SAPT does not use the point group symmetry of integrals and accepts integrals in the regular non Raffenetti format only For unknown reasons these settings do not always work in GAUSSIANO3 if the default method of selecting the initial guess for the SCF iterations is used In case of such problems the user should specify GUESS INDO so that the initial guess is obtained using the method which was the default in GAUSSIAN98 and previous releases note that the GUESS INDO keyword is not understood by GAUSSIAN98 and older versions Finally we remind the user that the MASSAGE keyword should be used in GAUSSIAN when setting the charges to zero e g to perform an SCF run for a monomer in a dimer centered basis set
81. d in our group and utilizing the ab initio asymptotic information comprise the independent package ASYMP_SAPT distributed optionally with SAPT2012 This document is intended to provide a basic introduction to the SAPT method and the instructions on how to download compile and run the SAPT2012 and pSAPT2K2 codes Also included are some details on the types of computers compilers and integral plus Hartree Fock self consistent field SCF packages that SAPT has been tested with Whereas extensive tests of SAPT have been performed there may appear unforeseen difficulties with the installation and running of the codes As SAPT2012 and pSAPT2K2 are products of a research project no resources are available to provide support for users The authors of the code will try to provide limited help within the restrictions of their schedules 2 What s new since SAPT2002 2 1 New in revision SAPT2012 2 e This is a bugfix release No new features were added e Fixed gfortran compilation problem caused by the use of entry statements in integer 8 functions 2 2 Fixed several gfortran runtime errors Restored compatibility with Fortran 77 compilers such as g77 New in revision SAPT2012 1 SAPT CC interaction energy contributions from relaxed monomer CCSD density matrices and their cumulants 24 31 This functionality requires MOLPRO and the patch supplied here Relaxed third order induction correction E4 35 ind resp Removed lim
82. dard form readable by the transformation code two electron integrals are read by the transformation program directly without such preprocessing Other programs present in misc include int and sort interfacing the transformation to the coupled cluster code the memory estimator memcalc a set of geometry converters which can be used with the bin Runlot scripts for automatic generation of potential energy surfaces see Sec 10 for details and a few scripts helpful in creating DALTON input files e bin utility scripts for running SAPT After compilation this directory will also contain the executables used in a SAPT run e doc documentation for SAPT2012 contains this document and the METECC paper 8 in the postscript form Documentation for ASYMP_SAPT can be found in the directory asymp_SAPT doc e examples input and output files for a set of systems and a variety of integral SCF packages This is a good source of templates for users runs 7 SAPT installations at a glance Table 1 presents a summary of hardware configurations compilers and integral SCF packages with which SAPT has been tested This list is meant to be used as a guide only In case one needs to port SAPT to a new architecture some important hints are provided in Appendix A 17 Table 1 Grid of operating systems OS and front end programs with which saPT2012 has been tested Symbols used tested and working 4 E tested
83. e by default Note that whereas the CC program automatically determines the core size needed and allocates that much memory all other programs need to have the requested core size declared in an appropriate namelist unless the default value of 40000 000 words is sufficient see Sec 10 2 for details Currently the SAPT codes use the following mechanisms to allocate the core arrays e The Fortran 90 ALLOCATE routine for SUN HPUX and Linux with the PGF90 or Intel compilers e The Fortran malloc intrinsic for SGI and Linux with the PGF77 compiler e AC function memget supplied by SAPT for the G77 compiler under Linux and for IBM AIX For a new platform a proper way of handling memory allocation must be chosen The Fortran 90 ALLOCATE is recommended where available 2 The timing routines The routines timit in tran main F second in cc whole F timing in e2d ccbits F and timt in sapt m F return time in seconds elapsed since some fixed moment and are called throughout the program These routines call system timing routines which are architecture dependent e the etime routine for SUN and HPUX e the mclock routine for SGI IBM and Linux with Portland or Intel compilers note that this one returns time in hundredths of seconds e the second routine for Linux and the G77 compiler Again a proper system timing routine needs to be chosen for a new architecture 100 3 The packing unpacking routines which manipulate the inte
84. e computed in a separate run see Sec 10 4 The six leading components of the third order SAPT energy Eq 9 are calculated when the variables E3IND DSPIND E300D E30XI DSPIX and E30XD respectively are set to TRUE It 30 is also possible to calculate the relaxed third order induction correction Ea Se 35 by setting gE E3INDR TRUE In this case the corresponding relaxed exchange induction energy each indre has to be estimated by a scaling of the nonrelaxed quantity 80 30 E Er eh marep Pexch ind D cO 11 ind Note that the polarization corrections especially EEO or E tend to cancel to a large extent with the corresponding exchange corrections so calculating also the latter is highly rec ommended The effects described by E and O together with the higher order ind resp exch ind resp induction and exchange induction contributions are approximately included in the as term resulting from the supermolecular Hartree Fock interaction energy For the interactions of po lar molecules where the induction component of the interaction energy plays an important role essa tends to provide a more accurate description of the high order induction interactions than the third order approximation For nonpolar and nearly nonpolar systems the inclusion of ES and ESO a or of Eos and ES gies usually gives more accurate results than the addi tion of EHF Whereas the corrections BEO Ee Ben gE and BEO int
85. e end of each output file should be compared to the reference ones provided in each test directory for at least one platform One can notice slight differences between the results obtained with different front ends and or on different platforms In any case reproducibility of at least 5 significant digits should be expected The main differences come in the corrections using the converged CCSD amplitudes The CC convergence threshold has sometimes to be adjusted to obtain several digit agreement Notice also that in different versions of SAPT the threshold was changing between relative and absolute which of course makes a significant difference 14 Parallel SAPT pSAPT2K2 The parallel implementation of SAPT has been described in detail in Ref 9 The parallel psAPT2K2 codes have essentially the same functionality as their sequential counterpart SAPT2002 Slight 64 differences exist in user interface related areas such as compilation more libraries are needed in pSAPT2K2 input options SAPT2002 is more user friendly when it comes to input defaults or output presentation Since pSAPT2K2 parallel runs are more prone to various types of problems the output of pSAPT2K2 contains a lot of debugging and profiling information SAPT2012 has been tested with a large number of sequential SCF front end programs while in the case of psAPT2K2 the parallel GAMESS US is effectively the only SCF code which can be used pSAPT2K2 should also work with
86. e file binary format between versions 4 1 and 4 2 it is strongly recommended that all programs including SCF DFT interface programs are compiled with the same version of the compiler TARGET sunf90 is for the Sun SPARC machines equipped with the FORTRAN90 compiler Finally TARGET hpux corresponds to the 64 bit Itanium architecture running HPUX and equipped with the HP Fortran90 com piler Note that for this platform several necessary system calls used e g in the timing routines are contained in the 1ibU77 a library whose location may vary on different machines 1ib hpux64 or other To compile SAPT for TARGET hpux the user must make sure that the correct 64 bit version of the 1ibU77 a library is present in one of the directories in which the linker searches for libraries e BLAS points to the Basic Linear Algebra Subprograms BLAS and the Linear Alge bra PACKage LAPACK libraries On SGIset BLAS llapack lblas On an ALPHA set BLAS ldxml on IBM AIX RS6000 or SP4 BLAS lessl and on SPARC BLAS xlic_lib sunperf On Linux machines one may set BLAS llapack lblas however other options usually lead to substantially bet ter performance For example if you have compiled yourself a self optimizing BLAS li brary like ATLAS http math atlas sourceforge net set BLAS L lt Full Path to Library gt llapack lcblas 1f77blas latlas However a simpler option which usually leads to onl
87. e option DI64 64 bit integers default on several architectures and or DPACK64 64 bit packing of integral indices also default on a few platforms the same set of options DI64 and or DPACK64 must be given to the variable EXTRADEFS so that the GAUSSIAN interface and the transformation program are compiled to work with this particular configuration of GAUSSIAN These options do not affect running SAPT with any other integral and SCF front ends One should note that as the SAPT codes are linked to the GAUSSIAN s util a library the user must make sure that this library and the whole GAUSSIAN code has been compiled for exactly the same architecture as SAPT For example the Sun SPARC architecture TARGET sunf90 supports generation of codes for several different flavors of SPARC via the compilation option xarch PLATFORM If GAUSSIAN was compiled for an architecture other than the default xarch generic the user needs to edit all occurrences of xarch generic in both Compall and atmol1024 Makefile sunf90 replacing generic by the architecture for which GAUSSIAN was compiled It is not a problem if Fortran 77 rather than Fortran 90 as in the case of SAPT was used to compile GAUSSIAN for TARGET sunf90 as the compatibility library 1 77compat is automatically linked in where necessary 20 SAPT does work with the latest releases of GAUSSIANO3 that support the AMD64 architecture Note however that the TARGET pgf90 architecture has to be
88. e sorted integrals to disk tpdrvn F getbufv4mod Read sorted integrals from disk tpdrvn F getbufseq Read re sorted integrals from disk triple F totsamp totamp Sum single and double amplitudes unpack F unpack10 Unpack an INTEGER 4 INTEGERx1 pair into four indices whole F errorx errorx8 Error exit from program whole F get2el Get integrals from disk obsolete replaced by newget whole F timing Gather and print timing info from subroutines whole F nmfind Locate a subroutine in a list whole F indxsm Calculate an index in a triangular matrix whole F bdaxpy bdnrm2 Wrappers to BLAS routines DAXPY and DNRM2 whole F other Auxiliary routines for get2el obsolete A good reference for this program is the paper by M Urban I Cernus k V Kell and J Noga in Methods in Computational Chemistry edited by S Wilson ene 1987 page 117 Table 5 Comments on selected subroutines sapt x part 1 Module Subroutine Comments m F driver Main SAPT driver m F theta Calculate O intermediate for monomer A m F thetb Same as theta for monomer B m F veta Calculate v intermediate for monomer A m F vetb Same as veta for monomer B m F omaov Calculate Q occ vir intermediate for monomer A m F ombov Same as omaov for monomer B m F tsa Evaluate singles amplitudes for monomer A m F tsb As tsa for monomer B m F copy Copy vector A to vector B m F rbfov Read into core lel integrals of occ vir type m F
89. e the four virtual diagram in AO basis direct F de3dsp Actual semi AO based calculation of rae direct F de30exd Actual semi AO based calculation of ESY disp direct F de3xd2a Version of e3xd F e3xd2a with amplitudes computed in AOs direct F namemain Get the name of the ATMOL1024 integral file direct F search Manipulate the ATMOL1024 integral file direct F find direct F rdsam pe 111 Summary table from output for the example BER Bez Mono A 2 occupied 8 virtual 10 total Mono B 2 occupied 8 virtual 10 total To Molecule A 4 Electron s ATOM XX YY ZZ Charge 1 0 000000000 0 000000000 0 000000000 4 0 2223225 Molecule B 4 Electron s 2 0 000000000 7 000000000 0 000000000 4 0 E HF _ AB 21 5579794623086016 hartrees E HF _ A 10 7773391618701009 hartrees E HF _ B 10 7773391618701009 hartrees Correction mHartree Kcal mol 1 cm SCF SAPT_super E HF _ int 3 301138568 2 07149746 724 5162 E 10 _ elst 3 687513408 2 31395154 809 3156 E 10 _fexch 3 149525953 1 97635903 691 2410 E 10 _ exch S 2 3 135991881 1 96786627 688 2707 E 10 _ exch S 2 0 013534072 0 00849277 2 9704 E 20 _ ind 4 659057533 2 92360519 1022 5449 E 20 _ ind resp 6 900439657 4 33009489 1514 4714 E 20 _ ex ind 4 109230703 2 57858336 901 8719 E 20 _ ex ind r 6 033628681 3 78616233 1324 2284 SAPT SCF a 1 087814286 0 68261434 238 7476 SAPT SCF_ resp b 1 40
90. ead of p4 JobType mpi ch_p4 Execute a script file managing files and submitting the SAPT job Exec u bukowski tests ArHF_Tc sub_s_sep Optional arguments to the Exec script Args un Where scheduler output will end up TT Output u bukowski LOGS MAUI_JOB_1D out Error u bukowski LOGS MAUI_JOB_ID err Log u bukowski LOGS MAUI_JOB_ID log Input Input dev null The launch script sub_s_sep should be similar to bin sh JOB ArHF job name CURDIR u bukowski tests ArHF_Tc SCRDIR scratch local bukowski local scratch directory SAPT_SCRIPT u bukowski psapt2K2 bin pSAPT mpich maui sep SAPT driver script Set the number of nodes as assigned by the scheduler NPROC MAUI_TASK_COUNT OUTFILE scratch huinalu bukowski JOB out_tst NPROC copy all SAPT input files onto the scratch dir on every node assigned by scheduler With common file system use just a simple copy cd CURDIR Create the list of nodes rm f calcnodes for node in echo MAUI_JOB_NODES sed e s g do echo node gt gt calcnodes done cp calcnodes PROC Copy input files and lists of nodes to each local scratch directory for i in awk print 1 calcnodes do echo Copying input to i ssh i mkdir SCRDIR scp inp i SCRDIR scp JOB P data i SCRDIR scp PROC i SCRDIR scp calcnodes i SCRDIR done Submit the job in scratch directory
91. echo i 1 SORT gt gt PROCso done HHHHHHHHHHHE PROCs file ready run the job now HHHHHHHHHHHHHHHHHAEHH JOB 1 tt job name copy all SAPT input files and the PROC file onto the scratch dir on every node specified in PROC file for i in awk print 1 PROC do echo Copying input to i rcp inp i SCRDIR rcp JOB P data i SCRDIR rcp PROC i SCRDIR rcp PROCs i SCRDIR rcp PROCi i SCRDIR rcp PROCc i SCRDIR rcp PROCso i SCRDIR rcp PROCe i SCRDIR done Set the number of nodes NPROC wc PROC awk print 1 lt Determine the master node the first one in PROC MASTER head 1 PROC awk print 1 echo Submitting job on MASTER Submit the job on master node Make sure that master knows what LOGNAME is needed for psapt rsh MASTER LOGNAME bukowski export LOGNAME echo LOGNAME cd SCRDIR SAPT_SCRIPT JOB scfcp NPROC SCRDIR gt OUT 2 gt 1 amp exit The variables SCRDIR the scratch directory its name assumed to be the same on each node SAPT_SCRIPT full path to the driver script and SAPTDIR location of psAPT2K2 executables have to be customized by the user Using the node information from calcnodes the script first creates the files PROC PROCc PROCe PROCi PROCs and PROCso which will be used by MPICH to run the consecutive modules of pSAPT2K2 The input files and the PROC files are then copied from the home subdirectory to the scratc
92. ected supermolecular SCF interaction energy in the dimer centered basis set If such a calculation is not required use noscfcp instead Using the keyword gototran as opti will result in restarting a pSAPT o02k run from the transformation step i e from the program ptran The parameter nproc is the number of processors to launch the job on The parameter opt2 must be the full path of the scratch directory in which the whole calculation is taking place The output from all programs executed by pSAPT 02k is written to a file output file located in the scratch directory this name can be set by the user to an arbitrary string usually connected with the system being considered and its geometry The last two elements in the command line given above are Unix ksh constructs which indicate that standard error messages will be written to the same file as standard output and that the processes will be run in the background A more common situation occurs when jobs have to be submitted through some sort of a queuing system such as GRD or more recently the grid engine In this case all the opera tions described above should be performed by a script submitted to the queue A sample script ARL_script could look like 4 bin ksh S bin ksh 71 N ArHF_Tc 1 03k pe pe_4hr 8 HHHHHHHHEAHHAAHHAR HHA EHRAR HAAR RA EH ER HRA R ARH Set the these parameters HHHHHHHHEAHHARHHERHHARHAAR HARE AA THAR ERR ARH NODT 8 number of process
93. ed typically by the SAPT2012 programs requires on some systems the use of the ulimit command to change the default user resources This command built into the SAPT script is currently commented out but it may be reactivated and adjusted as needed The SAPT script is written in ksh although on Linux platforms some of which are not equipped in ksh it is actually executed under bash A SAPT2012 calculation is launched by typing SAPT with appropriate options Typing SAPT without any options will produce a brief description of the necessary input A typical run statement might be something like in Unix ksh SAPT jobname opti opt2 gt output file 2 gt 1 amp The keyword jobname has to be the same as the beginning of the name of the input files for the system considered we use a naming scheme to reference the needed input files For example let the keyword be name Then as the script is running it will look for the nameP data file which contains the input data to the programs tran ccsdt and sapt x Similarly the SAPT script will look for input files to the integral SCF parts of a calculation starting with name The number and full names of such files depend on the type of basis set used in calculations and on the choice of the integral SCF code For all SCF front ends except GAMESS the keyword opt2 can be skipped and opt1 is optional Using the string scfcp for opt1 will request in addition to the standard SAPT calculation also the CP
94. entation of this correction in SAPT2002 was valid in DCBS only and for MCBS a wrong result was printed This correction does not enter the final SAPT interaction energy as the formula of infinite order in S is used geo New much faster algorithm for the calculation of Exch disp the most demanding correction at the SAPTO or SAPT DFT level An out of core algorithm utilizing much less memory is also available for this correction New faster and more memory efficient CHF routines Frozen core implemented for all standard SAPT corrections 40 New interfaces DALTON 2 0 MOLPRO 41 and GAUSSIANO3 42 New architectures AMD64 Opteron Athlon64 and Intel EMT64 with g77 32 and 64 bit and pgf compilers 32 and 64 bit as well as HPUX Itanium DIIS 43 in coupled cluster calculations Turned on by default if compiled in More efficient algorithms for the four virtual diagram in CC calculations Both energy based and amplitude based convergence criteria for CC available Smarter scripts for running SAPT Fixed a memory allocation bug on x86 Linux machines with kernel 2 6 x using g77 Several small bug fixes and enhancements Note that turning DIIS on off as well as changing the CC convergence criterion from energy based CCSD exch SAPT correction if CC convergence thresholds are not very tight as it is in the default case This CCSD between SAPT2006 and older versions exch 11 3 Short overview of
95. ersion energies for specified dimer geometries The detailed instructions for running pEDI X are as follows 1 Assuming that the name of your job is name prepare the files nameA and nameB containing the specifications of the geometries and basis sets of monomers A and B in GAMESS US format Remember to put blank lines after basis set of each atom including the blank at the end of the file Out of these files the pEDI X script will construct GAMESS input files needed to calculate the SCF vectors and generate integrals A spherical basis set will be assumed i e ISPHER 1 and the name of the job will be used as the comment line Geometries of the monomers specified in nameA and nameB should correspond to whatever you consider to be the initial configuration of the given monomer i e the COM or other characteristic point around which rotations will be performed should coincide with the origin of the coordinate system and all Euler angles describing the orientation of the monomer will be assumed zero at this geometry 2 Prepare the file nameP data as for the regular pure MCBS SAPT calculation note that in namelist TRN the variables BASIS and TAGS have to be specified for such a calculation In the namelist INPUTCOR the variables CHFDISP T CHFIND T E12 T E12R T E13PL T E13PLR T have to be specified in order for the MBPT2 and MBPTS3 densities to be dumped on disk Failure to specify any of these corrections will result in the corres
96. es RPA MPENER CCD and CCSD in the E2DINP namelist control the level of theory employed in the e2disp program Currently only the CCD TRUE version works so this variable should be set to TRUE and all others to FALSE Note that the default values are CCD TRUE and RPA MPENER CCSD FALSE so that no explicit specification of these variables in the E2DINP namelist is necessary The logical variable PT governs the perturbative nonperturbative methodology of the iterations currently only the first one works so this variable should be always set to TRUE The logical variables PMEM PNRM PKL PSEP and PCOMP control the printing of various intermediate quantities Finally the variable TOLITER states the relative convergence threshold for the dispersion iterations the recommended default is TOLITER 1 0d 5 The CCD ST CCD path of the calculation is turned on by specifying DCONVAMP TRUE 50 in the namelist INPUTCOR Note that this turns off all SAPT corrections other than the second order dispersion energy since the values of some of these corrections would be incorrect when CCD rather than CCSD amplitudes for monomers are calculated Note also that the frozen core FROZEN TRUE option has not been implemented for the CCD ST CCD dispersion energy The namelist CCINP controlling the behavior of the CC program also needs to be adjusted when one performs the calculation of the dispersion energy at the CCD ST CCD level First of all the
97. executed adjust the for statement in runtstGAMESS and runtstATMOL The names of output files from the tests are given an ending see the variable MACHINE which can be used e g to distinguish between the runs performed on different platforms Under Unix the output file can be viewed while the program is run This allows to check how far the program has advanced Note however that Unix first writes the data to fairly large buffers and only when the buffers are filled to the output file It is important to remember about it when debugging the program some info may not appear in the output after a crash although it may come from a successful part of the run SAPT uses instructions flushing buffers in several places but more such statements may have to be added for debugging Also for larger runs one should monitor the disk use by just doing 1s 1t or du k in the working directory The memory actually used by the program can be checked by using the top command called prstat or monitor on some systems When the program crashes our practice shows that in most cases it is due to errors in the integral SCF parts of the code Thus make first sure that these stages have finished successfully When there is an error there consecutive stages of the code do start and immediately fail creating an impression that the code crashed in a later stage than it was the case Once the test runs are completed the results especially the Summary Table at th
98. eyword makes CADPAC write out to a file the SCF vectors and other information in the format required by the SAPT2012 transformation code tran Thus there is no interface program required for CADPAC CADPAC was the first front end for SAPT DFT and the use of this package may be still be of some interest despite the slowness of this interface due to the large number of DFT eX change Correlation XC functionals implemented in CADPAC Notice however that the complete SAPT DFT 14 with coupled Kohn Sham dispersion and induction energies does not work any more with CADPAC it works with DALTON 2 0 and ORCA only To run SAPT2012 with CADPAC as the front end a special script SAPT2012 bin SAPT_CADPAC should be used instead of SAPT used for all other SCF programs 9 3 GAUSSIAN When using GAUSSIAN with saPT2012 a symbolic link in the compilation script Compall is made to point to the util a file in the GAUSSIAN directory structure The transformation module tran of SAPT2012 links to this library to be able to read the rwf and two electron integral files In the input to the post Hartree Fock stage of the calculation the file nameP data in the TRN namelist the user must specify either ISITG94 T for GAUSSIAN94 or ISITGO3 T for GAUSSIAN98 GAUSSIANO3 or GAUSSIANO9 In the latter case the variable GAUEXE set up during the compilation of SAPT is passed to the script so that it knows whether to execute g98 g03 or g09 26 In GAUSSIAN94 an
99. fi2a fi3a Calculate f intermediates int2 F iq7a iq9a Calculate four index x intermediates mem F ccmem Memory partitioning mpi F mpion mpioff Initialize and close MPI environment mpi F mpiarl mpiar Wrappers to MPI_ALL_REDUCE routine mpi F dist Assign task numbers to all processes mpi F sy2124 u i j k l 2z i j k l z i l k j mpi F de2124 Do the reverse of sy2124 mpi F nr2asc Integer gt string conversion for constructing filenames mpi F wcread wewrit Simplified versions of newget and newput mpi F newput Write amplitudes to disk mpi F newget Read amplitudes from disk mpi F newgeta Add amplitudes from disk to array mpi F inwc14 x i j k l E z l j k 1 105 Table 4 List of subroutines cc continued Module Subroutine Comments mpi F iveccp Copy an integer vector mpi F ioset Establish I O channel numbers mpi F opens Open integral amplitude and intermediate files mpi F estim Calculate core size needed for CC newr F symtr x i a j b x t a 7 b x 5 b i a newr F vecmul Multiply vector by a constant newr F matmulsk Wrapper to DGEMM matrix multiplier newr F matmula Perform C A B for one column of C newr F symt21 i j k l 2z i j k l x 0 7 k U two indices switched newr F desm21 Do the reverse of symt21 newr F insil2 x 0 j k x 3 1 k newr F insil3 x t j k x k j i newr F insi23 x t j k x t k j newr F in
100. fort version 8 1 and above on i386 and AMD64 Linux systems k ATMOL does not work in 64 bit mode on AMD64 64 bit mode not tested Tested on AMD64 only Tested with GAUSSIAN98 but should work with newer versions just as well 18 8 Installing SAPT2012 Installation of SAPT2012 is controlled by a universal script Compa11 a small portion of which has to be customized by the user The Compal1 script sets the compilation options appropriate for a given hardware platform and for the integral SCF interfaces chosen It then compiles and links all the pieces of the code which sometimes requires access to the I O libraries of the integral SCF pack ages If ATMOL1024 has been downloaded and the SAPT2012 atmo11024 directory is present this package is also built Finally Compall updates the scripts used to run SAPT2012 SAPT Runlot by inserting updated paths to executables The ASYMP_SAPT package is installed by a separate script 8 1 Compall installation script The following adjustments must be made by the user to the Compal1 script 1 Execution shell Change the first line of the script to one of the following e bin bash The Bash shell on a Linux box or e bin ksh The Korn shell on all other platforms 2 Integral SCF program Declare the SCF packages you wish SAPT2012 to be inter faced with An integral SCF package is activated by simply setting the corresponding variable in the script to the complete path
101. g 2el integrals b F rbfab Read first order dispersion amplitudes b F getamprll Reads amplitudes written by the e2disp program b F getr11 Opens an appropriate file and calls getampr11 chf F setchf Coupled Hartree Fock routine driver chf F solvea Linear eq solver for monomer A chf F solvea_ooc Out of core version of the above chf F solveb Linear eq solver for monomer B chf F solveb_ooc Out of core version of the above chf F quit Exit routine if no convergence chf F putchf Write computed CHF coefficients onto disk chf F getchf Get computed CHF coefficients back 107 Table 5 Comments on selected subroutines sapt x part 2 Module Subroutine Comments getamp F getamp Retrieve monomer CC amplitudes from disk getamp F gampoovv Like getamp but with permuted indices getamp F gampvovo y getamp F gampvvoo getamp F newget Actual reading of amplitudes getamp F newoovv Like newget but with permuted indices getamp F newvovo l getamp F newvvoo ds getamp F ampopen Open files with monomer CC amplitudes memreq F memreq Calculate memory needed for different corrections unpack10 F unpack10 Unpack an INTEGER 4 INTEGERx1 pair into four indices unpack10 F pack10 Do the reverse of unpack10 unpack10 F unpack10a Unpack an INTEGER 4 INTEGERx1 pair into two indices unpack10 F pack10a Do the reverse of unpack10a unpack10 F spltindx Split an index into an INTEGER 4 INTEGERx1 p
102. gral indices As the current basis set size limit for SAPT is 1023 functions 40 bits are needed to store the four orbital in dices for a transformed two electron integral These indices are stored on disk packed into one 4 byte integer and one 1 byte integer and the routines that take care of the integral packing and unpacking are located in tran unpack F cc unpack F e2d ccbits F and sapt unpack10 F These routines have the following functions e unpack10 INTEGERx4 INTEGERx1 gt 4 orbital indices pack10 4 orbital indices gt INTEGER 4 INTEGER 1 unpack10a INTEGER 4 INTEGER x1 gt 2 pair indices pack10a 2 pair indices gt INTEGER 4 INTEGERx1 e spltindx INTEGER 8 gt INTEGER x4 INTEGERx1 e joinindx INTEGER 4 INTEGER x1 gt INTEGERx8 The packing unpacking routines are implemented using the intrinsic functions for bitwise operations ishft ibits and iand The efficiency of packing and unpacking influences the total calculation time quite notably and the implementation through bitwise opera tions has been found to be optimal for several architectures Note however that subtle differences in the syntax of these intrinsics exist for different architectures and some of the packing unpacking routines are platform dependent Apart from the set of routines described above the tran program needs another set of unpacking procedures to access two electron integral indices written by various integral and SCF front ends including GA
103. h directory on each node Based on analyzing the PROC file the script detects the number of processors and the master node on which pSAPT mpich will be submitted this is the first node listed in calcnodes Finally having set up some environment 75 parameters it launches pSAPT mpich on the master node The temporary files produced by GAMESS and pSAPT2K2 will be created and stored in local directories tmp bukowski The output from the run will be written to the file OUT in the scratch directory tmp bukowski of the master node in this case sam2 only It will have to be copied by rcp for example back to the home subdirectory huinalu cluster The machine consists of 256 batch nodes and 4 interactive or login nodes each equipped with two 933 MHz Pentium III processors and 1 GB of memory The nodes are connected via a 200 MB s Myrinet Switch and also via 100 Mbit s Ethernet Each node is equipped with a local scratch file system not accessible from other nodes On each node this filesystem is mounted as scratch local In addition to the local scratch all nodes have access to a shared scratch area mounted as scratch huinalu with the capacity of 239 GB All nodes have also access to users home directories and other shared resources The machine features the MPICH implementation of MPI and a variety of Fortran compilers g77 Intel and Portland all capable of using both the Myrinet and the Ethernet co
104. h interfaces Then the MBPT CC program is run It uses the files generated by int and sort as well as 72 000 xxx 73 000 xxx infoa data infob data vecta data vectb data and nfiles The generated cluster amplitudes are stored in sequential files locx_y_m where x is s for singles and d for doubles m is a or b depending on the monomer and y can be 1 2 3 or i amplitudes from the first 3 iterations or from the last one The last step of the process is the calculation of the SAPT corrections The needed input files are vecta data vectb data infoa data infob data loc and f2e 000 xxx These files contain the output from each of the previous steps The perturbation program uses some temporary files and prints to output file the values of the corrections as well as time needed to compute them Near the end of the output file there is a table collecting all the corrections expressed in various energy units 12 Performance of SAPT2012 The computational cost of SAPT2012 calculations depends on the system size in the following way The integral SCF calculation time scales at most as o v with a somewhat lower power expected 59 for large systems When the AO based algorithm for the four virtual diagram in CC is used which is the default in SAPT2012 2 when ATMOL1024 or MOLPRO are used as the integral SCF program the transformation step scales as o 0 v and the CCSD step as 0 0 v Otherwise the scalings of the transformati
105. he other monomer Similarly the third order polarization corrections are decomposed as 3j 3j 3j 3j E B as Dees E 4 and the same holds for the corresponding exchange corrections A detailed discussion of the physical interpretation of various parts of the third order polarization energy can be found in Refs 1 and 38 The SAPT interaction energy can be computed at different levels of intramonomer correlation and an approximate correspondence can be made between these levels and the correlation levels of the supermolecular methods It can be shown 47 for example that an appropriate sum of the polarization and exchange corrections of the zeroth order in W provides a good approximation to the supermolecular Hartree Fock interaction energy EPF int elst xch ind resp exch ind resp int resp gt where OE tepi defined by the equation above collects all third and higher order induction and exchange induction terms The subscript resp means that the coupled Hartree Fock type response of a perturbed system is incorporated in the calculation of this correction Including the intramonomer correlation up to a level roughly equivalent to the supermolecular second order MBPT calculation we obtain the interaction energy referred to as SAPT2 ESAPT2_ PHF pO 0D 2 ga tp Elio ECD 6 int int elst resp exch exch ind exch disp where the notation e k eae E3 has been used tp is the part of Ee no
106. he subsequent line should contain 4 numbers DFTIPT DFTBR1 DFTBR2 DELTAIPT The first parameter DFTIPT is the ionization potential of the monomer in atomic units It is recom mended to use an experimental value The parameters DFTBR1 and DFTBR2 are related to the Tozer Handy switching function and are distances in Bragg radii where the switching takes place Tozer et al recommend values of 3 and 4 64 The last parameter DELTATPT is reserved for the open shell program and should be set to zero for all closed shell systems For open shell calculation it is equal to IPg IPa where IPg are IP are ionization potentials for 8 and a electrons respectively CKS Calculates TD DFT integrals for the CKS program Mandatory if the CKS code is used By default the LDA kernel is used in TD DFT see point 3 below GGAKER Use generalized gradient approximation GGA instead of LDA in the TD DFT kernel It is significantly slower and is not recommended for large systems More details and a discussion of accuracy of the LDA kernel is given in Ref 14 89 4 GRAC Gradient regulated asymptotic correction GRAC of Ref 36 The subsequent line should contain 4 numbers The first and last one are identical to the Fermi Amaldi asymptotic correction see above and describe the ionization potential The second and third numbers describe switching function parameters Recomended values are 0 5 and 40 respectively For the DFT calc
107. hese three bases have exactly the same ordering of functions apart from some DC BS functions being omitted in the MCTBS sets Special care should be taken when specifying different basis sets for different atoms of the same type as under some circumstances MOLPRO changes the ordering of atoms compared to the ordering given in the geometry specification The user is strongly advised to check in the MOLPRO output if the ordering of atoms is consistent with the basis set specification The post SCF input file nameP data must in this case contain the BLKMB F directive so that the assignment of the basis functions to monomer A monomer B dimer sets is specified using the tags mechanism cf Sec 10 1 2 One should note that the geometry section of the final SAPT summary table looks a little different than usual when MOLPRO is used as the integral and SCF front end The charges on the 32 nuclei are not given and all atoms those of monomer A those of monomer B and dummy atoms are listed together Nevertheless all energies calculated by SAPT should be correct 10 How to run SAPT2012 To perform a SAPT2012 calculation for one dimer geometry one has to run a dozen or so programs integral SCF calculations for the monomers and possibly for the dimer interface programs in most cases rewriting integral SCF files into different forms one and two electron integral transforma tions MBPT CCSD calculations for monomers and finally the
108. iate matrix from disk e2xdooc F writechunk Write a chunk of the intermediate matrix e2xdooc F readchunk Read a chunk of the intermediate matrix e2xdooc F wrooo Special version of wrseq e2xdooc F exd200c Actual out of core calculation of ECO disp e2xdooc F exd2semiooc Actual semi out of core calculation of Be disp e2xdooc F oex2dla oex2d1c Out of core versions of e2ex F ex2dla ex2d1c e2xdooc F preoex2d2 Prepare matrices for oex2d2 e2xdooc F oex2d2 Out of core version of e2ex F ex2d2 e2xdooc F preoex2d3 Prepare matrices for oex2d3 e2xdooc F oex2d3 oex2d4 Out of core versions of e2ex F ex2d3 ex2d4 e2xdooc F preoex2d5 Prepare matrices for oex2d5 e2xdooc F oex2d5 Out of core version of e2ex F ex2d5 e2xdooc F preoex2d6 Prepare matrices for oex2d6 e2xdooc F oex2d6 oex2d8 Out of core versions of e2ex F ex2d6 ex2d8 e2xdooc F srte2xd Sort integrals for out of core BOO disp e2xdooc F getbufshrink Like b F getbuf but omit core integrals e2xdooc F readbfs14 Read integrals for a fixed index e2xdooc F readbfs15 j e2xdooc F readbfs48 g 110 Table 5 Comments on selected subroutines sapt x part 5 Module Subroutine Comments e3 F srt3d0 Driver routine for a e3 F sort3d Sorting routine for above e3 F e3dsp Calculate above e3 F dspin0 Driver routine for ER disp e3 F srtind Sorting routine for above e3 F dspinla dspinlb Compute first
109. ies requires 80 of the order of n 2 electron integrals for similar size monomers so that n is approximately the same for both of them The monomer susceptibility functions both static and dynamic are given as combinations of ov x ov 1 2 terms products of four molecular orbitals two depending on coordinates of electron 1 and the other two on coordinates of electron 2 The time cost of obtaining induction and dispersion components is again dominated by the need to compute nt 2 electron integrals This unfavorable scaling can be greatly reduced if both the electron densities and the susceptibility functions are fitted in terms of a suitably chosen auxiliary basis In most cases the size of this basis m can be assumed to be proportional to the size of the original AO basis but several times larger The electron density can now be expressed as a combination of m terms while the susceptibility functions consist of m m 1 2 terms products of the auxiliary basis functions The cost of the calculation of electrostatics induction and dispersion dominated by 2 electron integrals between the auxiliary functions is now proportional to just m instead of n The electron densities and susceptibility functions are fitted by minimizing functionals of the type A fim p r1 10 r12 lp r2 p r2 dr drz 12 J penar N or zero 13 The quantity p denotes here either one of the MBPT contributions to electron density which is normali
110. implemented in ORCA The correction requires the ionization potential of the molecule which must be given in electron volt units as opposed to the hartree units used in DALTON The META section starts with a line containing three integers number of atoms including ghosts total charge and multiplicity For each atom there is a line containing atomic number x y and z Cartesian coordinates and atomic charge zero for ghost atoms The main basis set for each element is defined in a block separated by exactly one 94 empty line from previous blocks starting with a line containing the string BAS as the first three characters and the atomic number The next line of the BAS block gives the total number of contracted orbitals For each such orbital there is a sub block starting with two integers angular momentum and number of primitive functions and then containing in separates lines pairs of exponential Gaussian parameters and contraction coefficients The order of elements BAS blocks is arbitrary but all elements contained in the geometry specification must have an explicitly defined basis set in particular it can be specified as empty by setting the number of contracted orbitals to zero even if this definition is redundant with respect to the basis set keyword in the general ORCA input This requirement stems from the fact that the META section information is used not only by ORCA but also by a separate one electron integral module
111. in degrees for monomer A a is assumed as zero followed by the a 8 and y Euler angles of monomer B It is assumed that the COM of monomer A coincides with the origin of the coordinate system and that monomer B is shifted in the positive direction of the z axis For example 5 29177249 0 O O O O 2 38521611 86 80692336 90 00000000 180 00000000 93 37890335 360 00000000 2 63658901 87 13779711 90 00000000 180 00000000 81 94039222 360 00000000 2 89422970 87 42491802 90 00000000 180 00000000 75 80434134 359 99999915 would be a valid input edi file containing 4 geometries The first of these geometries is exactly the same as the one for which the interaction energies are computed during the pEDI X run 83 4 Run the EDI job the same way a regular pSAPT2K2 job would be run For example on 02K 03K platform without a queuing system to run in scratch mydir on 8 processors one would type pEDI o2k name noscfcp 8 scratch mydir gt name out 2 gt amp 1 amp Note that the noscfcp keyword has been used since the supermolecular SCF interaction energy is of no interest here A result of running the pEDI X script will be the file name out containing standard output from the whole run In this file the SAPT corrections requested in the nameP data file will be reported in the Summary Table section together with the dispersion and induction energies calculated by the propagator code pcksdisp for one specific dimer configuratio
112. information for monomer B Then run the program by typing memcalc lt nameP data gt memcalc out The file memcalc out will contain detailed information about memory requirements of different parts of the code The variables MEMTRAN from namelist TRN and MEMSAPT from namelist INPUTCOR should then be adjusted accordingly The memory needed to run the cc program is calculated there explicitly so that no separate namelist variable is needed The memory requirements of the SCF programs are much smaller than those of SAPT2012 For specific information consult the manuals distributed with these programs Disk space requirements of SAPT2012 are more difficult to estimate as these depend not only on the size of the monomers and basis set dimensions but also on the assumed integral thresholds and the dimer configuration For larger intermonomer separations more two electron integrals will be neglected and the integral files will be smaller than for close configurations While providing an accurate estimate of the required disk space is not possible some guidance can be obtained by 97 considering the upper limits on sizes of different scratch files involved and their scaling with the system and basis sizes With the dimension of the atomic basis DCTBS equal to n the size of the raw integral file produced by an SCF run scales as n 8 This should be multiplied by 12 to 16 bytes each integral is represented by an 8 byte real number plus 4 to 8
113. ion can be found in examples GAMESS HF2_MCBS Finally the last set of entries in the Summary Table gives the hybrid interaction energies i e the sums of the supermolecular SCF and the correlation parts represented by SAPT_ corr resp or SAPT_ corr If all the relevant corrections have been computed such as when one of the SAPTx variables is set to true in INPUTCOR the quantity SCF SAPT_ corr resp should be considered the recommended SAPT interaction energy If the third order induction and exchange induction energies have been computed the sums SAPT SCF 3 SAPT_ corr and SAPT SCF 3 _ resp SAPT_ corr resp with the terms delta HF _ int and delta HF _f int r respec tively replaced by their third order component E 30 _ ind E 30 _ exch ind are also displayed 10 4 Calculations of dispersion energy at CCD ST CCD level An algorithm for calculating the second order dispersion energy with the inter and intramonomer correlation effects included at the CCD level has been developed in Ref 39 This energy cannot be calculated along with the other SAPT corrections instead a separate run of the SAPT script must be performed For this run the user needs to supply a set of integral and SCF inputs just like for the ordinary SAPT calculation and the file nameP data must contain apart from the TRN CCINP and INPUTCOR namelists a namelist E2DINP which contains the necessary input for the e2disp program The logical variabl
114. iorski and J Cizek Int J Quantum Chem 32 149 1987 S Rybak B Jeziorski and K Szalewicz J Chem Phys 95 6579 1991 R Moszy ski B Jeziorski A Ratkiewicz and S Rybak J Chem Phys 99 8856 1993 E M Mas K Szalewicz R Bukowski and B Jeziorski J Chem Phys 107 4207 1997 R Bukowski J Sadlej B Jeziorski P Jankowski K Szalewicz S A Kucharski H L Williams and B S Rice J Chem Phys 110 3785 1999 CADPAC The Cambridge Analytic Derivatives Package Issue 6 Cambridge 1995 A suite of quantum chemistry programs developed by R D Amos with contributions from I L Alberts et al F Neese ORCA An Ab Initio DFT and Semiempirical electronic structure package with contributions from U Becker D Ganyushin A Hansen D Liakos C Kollmar S Kossmann T Petrenko C Reimann C Riplinger K Sivalingam B Wezisla and F Wennmohs 98 54 55 56 57 58 59 60 61 62 63 64 H L Williams E M Mas K Szalewicz and B Jeziorski J Chem Phys 103 7374 1995 A J Stone The Theory of Intermolecular Forces Clarendon Press Oxford 1996 p 8 O Akin Ojo R Bukowski and K Szalewicz J Chem Phys 119 8379 2003 R Podeszwa R Bukowski and K Szalewicz J Chem Theory Comput 2 400 2006 V F Lotrich H L Williams K Szalewicz B Jeziorski R Moszynski P E S Wormer and A van der Avoird J Chem Phys 103 60
115. irectories Ne2 aTZ GGAKER and Ne2 aTZ LDAKER contain neon dimer with GGA kernel or LDA kernel default respectively see Sec 16 2 H202_MCBS contains water dimer example with calcula tion of E resp Finally C6H6 contains a large calculation for benzene dimer All examples except ArHF utilize RunlotDALTON described in Sec 10 6 e dfsaptdft examples utilizing DF SAPT DFT with DALTON interface e ORCA water dimer examples utilizing DF SAPT DFT with ORCA interface compared with analogous jobs with DALTON interface 13 2 Running test jobs The simplest way to run an example is to copy all files from the corresponding directory e g SAPT2012 examples ATMOL1024 BER to a scratch directory then cd to this scratch directory and submit the job using the submit line described in Sec 10 for example in ksh SAPT BER scfcp gt BER out 2 gt 1 amp 63 Recall that the string BER is the same as the initial part of the name of all input files If the SAPT2012 bin directory is not in your PATH you may need to supply the full path to the SAPT script To simplify the process of running multiple tests two simple ksh scripts runtstGAMESS and runtstATMOL are provided in the directories examples GAMESS and examples ATMOL1024 respectively The scripts execute loops over the subdirectories selected in the for statement running the SAPT script inside these directories and cleaning up after each such run To select the jobs to be
116. itals with symmetries appearing in the occupied orbitals of constituent atoms i e s part of the basis for H and He and sp part of the basis centered on the first and second row atoms In practice MCT basis sets match the accuracies of DCT bases and at the same time reduce several times the costs of SAPT calculations An MC BS approach requires a little more work with setting up the basis sets than a DC BS calculation The reason is that in the former approach the basis functions appear in three different roles a given basis function can belong only to monomer A only to monomer B or to both monomers A calculation of the integrals in a set with repeated functions would be unnecessarily time and disk space consuming but a method has been developed to avoid this problem Below the individual files needed for an MC tBS calculation are listed first and then the dependence between the structure of these files and the control parameters in the file nameP data is described If MCTBS calculations are performed and the supermolecular SCF interaction energy is not requested scfcp keyword not present the SAPT script will look for input files nameMA nameMB to perform integral SCF calculations for monomers A and B respectively The input files for these runs should contain the basis of a given monomer plus the midbond and farbond functions on the shost centers Since the basis sets are different for A and B the two electron integrals from A cann
117. itation of 1024 orbitals current limitation is 65535 The option has to be compiled in not enabled by default Added code for calculating CKS exchange dispersion both non DF and DF versions with amplitudes obtained from CKS propagators in addition to version scaled from uncoupled versions This correction together with analogous exchange induction corrections is en abled by default when SAPT DFT calculations are requested Old versions are retained for compatibility ORCA interface for DF SAPT DFT Gaussian09 interface Gradient regulated asymptotic correction GRAC 36 for the DALTON program Optional support for dimer cnf in Angstroms Lowered memory requirements in DF SAPT DFT transformation Added automatic auto matic calculation of required memory in DF tran Added trailing zeroes to the name of output of Runlot Helps with sorting Fixed timing routines with Intel Fortran Renamed sapt program to sapt x enabling correct use of SAPT2012 on filesystems that are not case sensitive e g Mac OS X Fix for DF SAPT DFT going into infinite loop in some cases when compiled with gfortran Fixed DF SAPT DFT code in some calculations with large intermonomer distances Fixed SAPT DFT geometry code with some versions of awk Fixed integer overflows for large scale SAPT DFT calculations 2 3 2 4 New in revision SAPT2008 2 This is a bugfix release No new features were added Fixed crashing of very large over 1000
118. l systems 21 This option is avail able since the SAPT2008 edition However density fitting has not been implemented in open shell SAPT DFT No manual is available for open shell SAPT DFT but it is quite similar from a user point of view to closed shell SAPT DFT and therefore with the examples provided in the distribution package the use of these codes should not be problematic The calculation of the interaction energy of a dimer using SAPT2012 involves four steps In the first step one and two electron integrals are computed in a chosen orbital basis set and then SCF calculations are performed on both monomers The SCF calculation for the dimer can also be performed at this stage Several integral SCF packages are interfaced to SAPT2012 and can be used including free packages such as GAMESS 22 see http www msg ameslab gov GAMESS GAMESS html and ATMOL 23 a modified version of the latter package ATMOL1024 is included in the saPT2012 distribution and can be downloaded from the SAPT web page After the SCF calculations are completed the atomic integrals i e integrals between the functions of the basis set used are transformed into molecular integrals using the 4 index transformation program tran In the third step the Coupled Cluster CC program ccsdt is invoked to calculate the many body perturbation theory MBPT known also as the MP method since it is based on the Moller Plesset partition of the Hamiltonian and or CC
119. l to the main basis set used The quality of the auxiliary basis set is critical for the accuracy of the DF approach and using auxiliary basis set optimized for a different main basis would result in poor accuracy In the TRN namelist of the nameP data one should specify T2EL F to suppress the stan dard two electron transformation There is also an additional DF namelist The only parametr used in this memlist is MEMTRAN x keyword where x is equal to either the number of requested memory words or zero In the latter case the memory is allocated automatically to the lowest reasonable level Finally for running DF SAPT DFT one uses SAPTdf and RunlotDALTONdf scripts instead of SAPT and RunlotDALTON respectively Example inputs and scripts for running DF SAPT DFT analogous to non DF SAPT DFT counterparts in examples saptdft are lo cated in examples dfsaptdft along with the pertinent outputs Notice small DF errors when comparing the results of DF and non DF calculations For larger auxiliary basis sets where the linear dependencies start to emerge the numerical errors start to amplify and the accuracy of the electrostatic energy is diminished The problem has been described in Ref 57 An effective solution is to perform the inversion of the auxiliary J matrix with quadruple precision QP For compilers supporting QP one should use this option to improve the accuracy The QP code has been tested with ifort and ibm64 platforms To compile the Q
120. late the K part of BO el2x F k2f2 Driver for the K2 part of EQ02 el2x F k2fb Calculate the K part of EC el2x F addla Prepare the one electron component for k2fa el2x F add2a Prepare the one electron component for k2fb kllu F kilu Driver for the K1 part of qu kllu F k1lul k11u32 Calculate components of K kllu F writemat Write a matrix to a temporary file kllu F getmat Read a matrix from a temporary file kllu F getmat2 Another version of getmat e2 F e02 piro i monomer energies calculation e2 F e200d E driver e2 F e200disp Calculate BON e2 F eind BEO driver e2 F eindab o ECD e2 F e21 E driver e2 F prep210 Prepare matrices for He e2 F prep201 Prepare matrices for Po 2 e2 F e21d Actual calculation of Elo 0 r EY e2 F e21d1 e21d3 Compute components of E e4iF e22i0 EC driver e4i F e22its Compute triple excitation part of ES e4i F e22is Compute single excitation part of BO e4i F e22irl Compute the ring ladder diagram of oe e4i F e22ib Compute the remainder of Ee 2 e4 F e22d0 ES driver e4 F srt220 Sort three virtual integrals for ra e4 F srt202 As above but for 1a e4 F e2lla Calculate the first part of E e4 F e211b Calculate the remaining terms in Es e4 F e22ds Compute Ea 8 or E Sl e4 F e22dr The ring contribution to ES D ME D e4 F e22rl The ring ladder contribution to E DE D e4 F e22da First part of EY Q EXS Q e4 F e22db Sec
121. lation of the electrostatic energy from the CCSD densities can be found in examples GAMESS CO_E1DEN_DCBS 10 5 2 MCBS calculation In the pure MCBS basis set i e without midbond or farbond functions it is possible to pre compute the electron densities for both monomers and then reuse them after suitable translations and rotations for a whole set of dimer geometries In this way the expensive calculation of CCSD densities has to be done only once per monomer A calculation of this type can be accomplished using the ccsddSAPT script described above and a separate program elstdenrot which computes the electrostatic energies using the AO density files produced by ccsdm and basis set information extracted for this purpose from GAMESS output files The script ccsddSAPT follows the appropriate path once the option DIMER F is detected in the TRN namelist The steps involved in the calculation are the following 1 Assuming that the name of the job is name prepare the files nameA and nameB containing the specifications of the geometries and basis sets of monomers A and B in GAMESS US format Remember to put blank lines after the basis set of each atom including the blank line at the end of the file From these files the ccsddSAPT script will construct the GAMESS input files needed to calculate the SCF vectors and generate integrals A spherical basis set will be assumed i e ISPHER 1 and the name of the job will be used as the comment line
122. le SAPTDFT YES and recompile SAPT2012 If the compilation is error free the SAPT DFT code is ready to use both the regular and density fitted versions are created Before performing calculations for systems of interest to you check the examples from examples saptdft directory The SAPT DFT run consists of the monomers calculation transformation the SAPT KS step and the CKS step Notice that some of the errors printed by Dalton are harmless in the SAPT DFT calculations In particular SEVERE ERROR PROGRAM WILL BE ABORTED SIRIUS NORMAL STOP AFTER ORBITAL ORTHONORMALIZATION is a normal stop after calculating the necessary one electron integrals Warning Patched DALTON should not be used for any ather purpose except for SCF DFT calculations The effect of the patch on other parts of the DALTON code has not been tested The keywords discussed below are for both the regular and density fitted versions of SAPT DFT Some additional keywords for the latter case are described in Sec 16 4 SAPT DFT requires SAPTKS T keyword in the INPUTCOR namelist of the nameP data file and proper keywords in the TRN namelist prepared like for the regular runs see also Sec 9 5 For CKS calculations that are a part of SAPT DFT a separate SAPTDFT namelist with keywords CKSDISP T and CKSIND T should also be present at the minimum The complete set of SAPTDFT namelist keywords is 1 CKSDISP E disp CKS 2 CKSIND E CKS 88
123. m level and no special input or options are needed for SAPT In particular the variable FROZEN in the INPUTCOR namelist should be set to its default value of FALSE unless freezing of a larger core on top of a small core ECP is requested The frozen core and ECP SAPT approaches are described in Ref 40 Note that when using SAPT with ECPs the inclusion of the bE resp term Eq 5 is strongly recommended 40 this requires the scfcp keyword as a command line parameter to the SAPT script The relativistic contributions to the SAPT interaction energy can be estimated by using rela tivistic ECPs Alternatively one can calculate a relativistic SAPT interaction energy by employing the second order Douglas Kroll Hess relativistic one electron Hamiltonian as implemented in MOL PRO This requires a special syntax of the MOLPRO integral and SCF input please see the example in the directory MOLPRO ArHF_AVDZ for details 48 The variable PRINT is used to print more information about intermediate results and memory partitioning The variable MEMSAPT can be used to dynamically allocate memory for the perturba tion theory stage sapt x of SAPT2012 As a default the memory for the sapt x program is set to 20 Mwords The amount of memory required by the sapt x program may be computed using the memcalc utility as described in Sec 10 7 10 3 How to read the output The values of all the calculated SAPT corrections are summarized at the end of the out
124. mall memory although it may then choose the out of core path which significantly increases the time of this step To allow the transformation to work entirely in core the amount of available memory should be slightly more than on 2 8 byte words where n is the dimension of the basis set and o is the number of occupied orbitals of the larger monomer For DCBS or DC BS calculations it is advantageous to set memory if possible to about twice as much i e slightly more than on words as a somewhat faster algorithm is chosen when additional memory is available For the cc part memory requirements can be roughly estimated as 207v 207n or o u 207n n words whichever is greater v is the number of virtual orbitals for the larger monomer The sapt x code will ask for about 507v or v 307u words whichever is greater and max 20 v v ov 6000000 words will be needed to generate the relaxed CCSD densities using the ccsdm code More precise calculation of the memory required for an efficient run can be done using the program memcalc built automatically during installation In order to use this program prepare the regular nameP data file with the first title line containing five numbers in the following order the total number of DC BS basis functions the total number of functions for monomer A will be different than the previous number in a MC BS type run the number of occupied orbitals for monomer A and then the same
125. minute to complete In the GAMESS input files the option ISPHER 1 is used so that the results of this test performed with GAMESS should agree with those from an ATMOL1024 run e HF2_MCBS the MC BS version of the above monomer basis set files HF2MA and HF2MB are obtained by removing the d and p orbitals of F and H respectively of the ghost 61 molecule In the GAMESS version of this test the tags technique is used to enforce MC BS whereas in the ATMOL1024 version the basis functions are arranged in blocks polA isoA mid isoB polB as described in Sec 10 1 2 As in the DCTBS variant the space spanned by the basis functions is always restricted to spherical Gaussian functions even in the GAMESS version e ArHF_DCBS the basis set 8s5p2d1f 6s3p2d1f 352p1d has been taken from Ref 58 No midbond functions are present here This run will need about 6 Mwords of memory and about 4 minutes to complete on an Opteron 252 machine e ArHF_MCBS an MC BS version of the above Monomer basis sets in files ArHFMA and ArHFMB are obtained by deleting the polarization functions d and f on F and Ar and p and d on H of the ghost molecule The tags technique is used for MCTBS for both the GAMESS and ATMOL1024 examples e CO2D_MCBS an MCTBS run for the CO dimer in the basis of Ref 51 DCBS size 200 MC BS size 149 This example is larger than the previous ones it requires about 40 Mwords of memo
126. mtr F sort2 Second sort for the four virtual transformation atmtr F calc2 Transform last two indices for four virtual integrals atmtr F peswrec Write final transformed integrals to file atmtr F writem Print matrix for debugging atmtr F chksuml Check control sum for debugging atmtr F get_cadp Manipulate CADPAC integral buffer atmtr F find_ cadp Read CADPAC integral buffer io F daopen Open direct access files io F dawrit Write to direct access files io F daread Read from direct access files io F daclos Close direct access files io F r8zero Zero a REAL 8 array indexed by an INTEGER 4 variable io F r8zero8 Zero a REALx8 array indexed by an INTEGER 8 variable io F i4zero Zero an INTEGER 4 array io F putrec Put a record on disk io F ropen Open input file io F seopen Open other sequential files io F closeall Close all files io F seqopn Open GAMESS integral file io F nr2asc Integer gt string conversion for constructing filenames io F inittwoeldalt Initialize DALTON integral file io F readtwoel Read integrals from DALTON io F findlab Find DALTON labels io F readmolpro Read integrals from MOLPRO main F timit Read elapsed time main F prsq Print square matrix main F rdvc Read eigenvectors main F ifa Initialize table lookup values main F flagl Choose either eigenvectors main F flag2 of monomer A or B main F alarmx Abnormal ending 103 Table 3 List of subrou
127. n MPICH The home and shared directories are NFS mounted on all compute nodes Commands and programs can be executed on compute nodes from the login node through the rsh utility It is also possible to rlogin to the compute nodes although it is not necessary for running pSAPT2K2 The consecutive modules of psAPT2K2 are launched from within the script pSAPT mpich using the mpirun command while GAMESS is started using the ddikick x utility of the DDI package It is a good rule on samson that jobs are to be run on compute nodes only and not on the login node For any MPI application this may be accomplished by executing the mpirun command on the login node with the option nolocal supported by MPICH Unfortunately this option or a similar one is not available in the DDI package which is the GAMESS parallelization tool This creates a problem if an MPI application depends on files generated by GAMESS and both are to be run from the same driver script such as pSAPT mpich This means that pSAPT mpich has to be submitted directly on one of the compute nodes rather than on the login node and that the MPI programs should be launched without the nonlocal option The process of submitting a pSAPT2K2 run on samson consists of the following steps 1 In your HOME create a subdirectory for the job and copy the input files job inp and jobP data to this subdirectory 73 2 Create file calcnodes listing the nodes about to be used in the calculation for
128. n described earlier The last part of name out will be the output from the caldisp_gms code i e the electrostatic induction and dispersion energies for all geometries specified in input edi Specifically the fol pCO 7702 ga pas pO pO pe p lowing corrections will be calculated elst gt elst gt elst resp elst gt elst resp ind ind resp disp and Ea RPA The last of the corrections mentioned above is calculated from the dynamic susceptibility functions at the CHF level equivalent to RPA and currently does not have its counterpart among the corrections calculated in a regular pSAPT2K2 run It is more accurate in terms of theory level than ppal The calculated monomer properties will be packed for further use e g for a standalone invocation of caldisp_gms into a file name prop tar gz which after running gzip d name prop tar gz tar xvf name prop tar will decompress info the following files 1 vecta data and vectb data unformatted sequential files with orbital energies and SCF vectors 2 unformatted sequential files denaMO data and denbMO data containing MBPT2 and MBPT3 densities relaxed and non relaxed 3 propa data and propb data dynamic susceptibility functions currently at the CHF level unformatted sequential files 4 prop0a data prop0b data static susceptibility functions currently at the CHF level un formatted sequential files
129. n SCF calculations for both monomers the sequence should be A midbond if present and B e polA d and polB d polarization functions for A and B respectively functions for polA d will not be used in expansion of molecular orbitals of B and vice versa e head d a simple file containing a header common to all intinp files e end d endA d endB d endMA d and endMB d end parts of intinp files specific for a given system e g end d corresponds to the dimer endMA d to monomer A in its MC BS endA d to monomer A in DCTBS and so on note that in this example the files endA d and endB d contain the ATMOL1024 directive BYPASS TWO which allows to avoid recalculation of two electron integrals generated during the dimer SCF run e scfinp files needed for SCF calculations on all subsystems 2 Prepare the file dimer cnf which specifies the Cartesian geometry in bohr of monomers A and B in their initial configurations i e for all Euler angles equal to zero The charge atomic mass and an up to two character symbol are also given for each atom 3 Prepare the file geoparm d which contains dimer geometries for which the SAPT calculations are to be performed Each such geometry is specified by a single line containing the separation in A between the centers of mass as defined by the masses and geometries supplied in dimer cnf of the monomers the z y z Euler angles 55 84 and y4 of monomer A and the
130. n cc can now be evaluated in atomic orbitals eliminating the need for a four virtual transformation The AO algorithm currently works only with ATMOL1024 and MOLPRO interfaces 22 243 not ov implementation of the E 4 correction backported from parallel Faster o SAPT Support for monomer centered basis sets in the MOLPRO interface The C6H6_H20_DCBS example replaced by a similar C6H6_H20_ADZM one In the old example the basis set was nearly linearly dependent which caused problems with the coupled cluster convergence A new example showing how to run SAPT with effective core potentials ECPs using the MOLPRO interface A new example showing how to calculate a relativistic SAPT interaction energy utilizing the second order Douglas Kroll Hess Hamiltonian with the relevant integrals generated by MOLPRO CKS program can now allocate more than 2 Gwords of memory Fixed a bug resulting in a crash of the sapt x program in an extremely unlikely situation when no transformed integrals of a given type were larger than the threshold so that no integrals of this type were written to disk Fixed a bug causing the ccsdm program to allocate too little memory in some cases Fixed a bug in misc atmolstuff F resulting in a compile error under HPUX Fixed a bug in cc tpdrvn F resulting in a compile error when setting EXTRADEFS DTWOGIGAMAX Fixed a bug in the MOLPRO interface which caused SAPT to produce nonsen
131. ne again To calculate only E resp One should prepare inputs as for the regular SAPT runs any interface can be used as long as the geometry and basis sets are the same as in the SAPT DFT run set DELTASCF T in the INPUTCOR namelist cf Sec 10 2 3 and use scfcp option for the SAPT script The ss value should then be added to the SAPT DFT interaction energy An example of such a calculation is in the directory examples saptdft H20 aTZ MC 16 4 Density fitting version of SAPT DFT Density fitting DF method also known as resolution of identity has been implemented in SAPT DFT 15 57 The resulting approach has the scaling reduced from O N to O N Substantial savings are also achieved for O N5 terms The code with density fitting is also more memory and disk efficient Running DF SAPT DFT requires some modifications of the input files and the creation 90 of a file with an auxiliary basis set The latter file should be named name aux and contains coefficients of the auxiliary basis function for each atom The format is the following see also examples dfsaptdft 0 z charge 0 0 0 0 0 0 coefficients oz charge 0 0 0 0 0 0 coefficients where charge is the charge of an atom and the coefficients are in the TURBOMOLE format We recommend basis sets from Ref 61 These basis sets are available in turbomole format at ftp ftp chemie uni karlsruhe de pub cbasen The number and ordering of the atoms must be identica
132. nnectivity Special care must be taken at the time of compilation and execution so that the PATH variable points to the proper libraries and the mpirun command ap propriate for a given connection compiler combination Commands and programs can be executed on compute nodes from the login node through the ssh utility It is also possible to ssh login to the compute nodes although it is not necessary for running pSAPT2K2 The consecutive modules of pSAPT2K2 are launched from within the script pSAPT mpich maui or pSAPT mpich maui sep described in the following using the appropriate mpirun command while GAMESS is started using the ddikick x utility of the DDI package The default source of ddikick x ddikick c has to be modified to use ssh instead of rsh In the debugging stage pSAPT2K2 jobs may be submitted on the four interactive nodes hnfe01 hnfe04 i e on up to 8 processors using a technique similar to that described above for samson The only practical difference is that the invocation of the mpirun command utilizes the machinefile option which for some reason is not working on samson Consequently the PROC file is only needed by GAMESS while the psaPT2K2 modules use a file called calcnodes in a format similar to hnfe01 2 hnfe02 2 hnfe03 2 where 2 means that two processes will be run on each of the three interactive 2 processor nodes a total of 6 processes In this case a PROC file consistent with calcnodes needed to inform GAM
133. ns necessary for computing the 6 EHF int resp term i e BOO pO gen and E This setting should be selected when only elst gt exch ind resp exch ind resp a is required since it skips calculations of the dispersion and exchange dispersion correc tions Such separate calculations of E resp May be required for certain SAPT DFT jobs see 46 Sec 16 3 Since E resp 18 Calculated automatically also for SAPTO SAPT2 SAPTNOCC and SAPT as long as the keyword scfcp has been specified upon the submission of the SAPT script it is not necessary to select DELTASCF T when the former options are used For additional keywords required for SAPT DFT see Sec 16 2 The SAPTx variable takes precedence over the settings of individual corrections in the sense that a correction included in a given level will be computed even if it is explicitly set to FALSE However a correction not included will be computed if it is explicitly set to TRUE The variable CONVAMP selects the use of the converged CCSD amplitudes in the expressions analogous to those appearing in the corrections EUD 7020 and een Setting this variable exch exch gt to TRUE results in the calculation of the e CCSD correction regardless of whether HOD BLO and gE terms are calculated or not The logical variable DCONVAMP selects the calculation of the dispersion energy with the inter and intramonomer correlation treated at the CCD level However this energy must b
134. nts of the subroutine mkoffset of the module trans F in subdirectory SAPT2012 tran Setting the OUT variable to TRUE will give more extensive printing from tran showing mainly memory partitioning and the input vectors The variable TOLER sets the threshold for writing the transformed integrals to disk The input is an integer n which is then used to discard all integrals which are less than 107 in absolute value An input of 1 gives a threshold of identically 0 We recommend values slightly tighter than normally used for similar purposes in isolated molecules calculations of about 1071 around the van der Waals minimum and progressively smaller as one proceeds farther away from the minimum Note that the usual default thresholds in most integral SCF programs will be larger than this value and must therefore be lowered so that the atomic integral files which are the input to the transformation contain sufficiently small integrals It is also advisable to tighten the threshold for the convergence on the density matrices in order to increase the accuracy of the SCF eigenvectors If the SCF program used is ATMOL1024 and if the two electron integrals produced by this program are stored in more than one file the number of such files has to be given in TRN as the variable NMFILES For example NMFILES 3 will tell the transformation to look for ATMOL1024 integrals in the files MT3 MT4 and MT5 The most likely use of this option is on old Linux pla
135. o release unnecessary disk space after finishing calculations in a given working directory The actual running of the program when using the SAPT script is very simple On most installations runs are performed in a working or scratch directory designed to hold large temporary files We find it simplest to make a subdirectory there copy the input files created by the user or taken from the SAPT2012 examples to this subdirectory and either execute the SAPT script in this directory using the full path e g home local SAPT2012 bin SAPT or simply copy the SAPT script to the working directory several other possibilities exist for example users can add the SAPT2012 bin directory to their PATH environment variable However the SAPT script requires the vars cfg file present in the same directory so this file must be copied accordingly if the script is not run from the SAPT2012 bin directory During the compilation the script Compall updates vars cfg file with proper paths to ex 33 ecutables and the scripts should run properly on any installation without changes if vars cfg is present in the same directory If the paths need to be changed for some reasons the file vars cfg should be edited and the variable MAIN_SAPT_DIR and the SCF_HOME_DIRECTORIES changed to re flect user s directory structure if GAMESS is used it concerns also additional directories relevant for this program Also note that the large core memory request
136. o use these sets in EDI calculations The driver scripts pEDI X can be easily adapted to perform the property fitting by uncomment ing the Generate auxiliary basis and Fit propagators and densities using auxiliary basis sections The invocation of the tar command should also be changed so that the fitted representations of monomer properties are included in the name prop tar file The pEDI X script modified in this way will ask for two additional input files input aux A and input aux B spec ifying parameters needed for the construction of auxiliary bases These involve the number of pruning cycles and the e parameter for each of these cycles for each atom For example in the case of molecule A consisting of 2 atoms and with 3 pruning cycles required for each of them the file input aux A could look like 0 8 0 9 1 0 0 8 85 0 9 1 0 After the run finishes the auxiliary bases generated by make_aux will be placed in files auxa data and auxb data similar to infoa data and infob data whereas the fitted properties will be placed in unformatted sequential files auxdena data auxdenb data auxprop0a data auxprop0b data auxpropa data and auxpropb data The automatic generation of auxiliary basis sets results in rather large sets if high accuracy of the fits is required To perform the interaction energy calculation using density fitted monomer properties col lect all these files along with input edi in a scratch directory e g by
137. odes Also SAPT2012 does not need access to any CADPAC libraries so that the compilation will proceed even if CADPAC is not installed on your system DALTON 37 If used set the path to wherever the DALTON executable script is located The sole purpose of the variable DALTON in Compall is to pass the path and name of DALTON executable to the SAPT execution script No access is needed to any DALTON files at the compilation time Thus compilation will proceed even if DALTON is not installed on your system beforehand ORCA 53 If used set the path with the ORCA executable files Similarly as for DALTON the only use of the variable ORCA during the compilation is to pass the path to ORCA executable files to the SAPT execution script MOLPRO 41 If the MOLPRO interface is used set the variable MOLPRO to the full name of the MOLPRO executable including the path All versions of MOLPRO start ing from MOLPRO2002 1 up to and including MOLPRO2010 1 are supported During the compilation of SAPT2012 no access to any MOLPRO libraries is needed so the 21 compilation will proceed even if MOLPRO is not installed on your system beforehand However the MOLPRO program itself must be modified and recompiled before using it with SAPT2012 as the SAPT interface to this front end has the form of a MOL PRO patch This interface is located in the misc patch molpro2sapt subdirectory and consists of four files src common sapt1 src common sapt2 src
138. ompile time by adding the DTPDRVN definition to the EXTRADEFS variable one more file of the order v 4 will be temporarily created by the ccsdt program However the original file of raw atomic integrals n 8 will be removed beforehand unless the corrections E 30 gE disp and or exch disp employing the AO integrals are to be calculated 11 Description of some internal data sets We present here a short schematic of the program run sequence with emphasis on the description of various files used First the integral SCF program performs the appropriate calculations for the dimer monomer A and monomer B depending on the type of basis set used and on the choice whether to calculate the supermolecular SCF interaction energy The output of the integral SCF calculations is included in the file output file with the name selected on the command submitting the SAPT script In the later stages output from other programs as well as output of some system commands will be added to this file Next with the aid of an interface program written specifically for that integral SCF package several new files are created by extracting information from the 58 data sets of the integral SCF program just run The vecta data and vectb data files contain the eigenvalues orbital energies and eigenvectors molecular orbital coefficients produced by the SCF step The onela data and onelb data files contain the one electron integrals of site A and B res
139. on when using the ORCA interface the main basis set is currently limited to up to f functions in practice both these restrictions are equivalent because the auxiliary basis set should contain functions with the highest angular momentum L at least by one larger than the main basis set The density fitting code contains some atomic integrals code from GAMESS The GAMESS authors requested that the users of density fitting SAPT DFT should cite GAMESs 22 along with SAPT 16 4 1 Using DALTON for monomer DFT calculations The DALTON input files required in a DF SAPT DFT run are almost identical with those in regular SAPT DFT However in name dal files CKS keyword should be replaced by CKSAUX This keyword works only with the LDA kernel therefore GGAKER keyword cannot be used It it recommended to include NOTWO keyword in INTEGRALS of nameA dal and nameB dal when monomer basis sets are used 16 4 2 Using ORCA for monomer DFT calculations ORCA is a quantum chemistry package developed by Neese and coworkers 53 Its DFT module has very efficient density fitting techniques and we recommend this front end for DF SAPT DFT calculations especially in the case of monomers larger than about a dozen of atoms The Linux Windows and Mac OS X binaries are available at http www thch uni bonn de tc orca free of charge for academic users a registration and acquiring a license is necessary The ORCA source files are not needed by DF SAPT DFT
140. on and CCSD steps are proportional to v o v and 0 v respectively Finally the scaling of the perturbation theory code strongly depends on the required level of theory 0 for SAPT 0 0 v for SAPT2 and ovt for the full SAPT For a general orientation Table 2 contains timings from an Opteron 252 Linux system obtained with the SAPT2012 suite compiled in the 64 bit mode with Portland pgf90 compiler The examples chosen are described in Sec 13 under the labels ArHF_DCBS CO2D MCBS and C6H6_H20_DCBS For the sake of completeness the amounts of memory and disk space required in each calculation are also reported see Sec 10 7 for a general discussion of these two issues The memory requirements of the integral SCF calculations are omitted because they are negligible compared to the other steps Table 2 is restricted to regular SAPT calculations on a single core See Ref 57 for a detailed analysis of the SAPT DFT performance and Ref 9 for a discussion of the parallel SAPT scaling Table 2 Wall clock execution times and memory disk requirements of different parts of the SAPT2012 suite on the Opteron 252 Linux system The integral SCF package used is ATMOL1024 system Ar HF CO C Hs H20 occupied orbitals A B 9 5 11 11 21 5 DCBS size 86 200 262 MC BS size 149 integral SCF time 21s 13 min 53 min transformation time 15s 21 min 53 min CC time 128 s 32 min 16 h 25 min sapt x time 84 s 41 min 8 h 9 min transforma
141. ond part of EOQ YE Q e4 F e220dso Compute singles term for Eip CCD ST CCD e4 F e202dso Compute singles term for T A CCD ST CCD e4 F prntimel Print extended timings for ES disp 109 Table 5 Comments on selected subroutines sapt x part 4 Module Subroutine Comments e22t94 F e22t94 EM 1 Elisp T driver e22t94 F eq98 Outer loops for EY T e22t94 F eq99 Inner loops for EGA T e22t94 F invndx Calculate orbital indices from the amplitude index e22t94 F srt22t94 Sort three virtual integrals for EG T e22t94 F getvvb Special version of b F getbuf e22t94 F getvva 4 e22t94 F rbfabx Special version of b F rbfab e22t94 F pack2 Pack two integers into one INTEGER 4 word e22t94 F unpack2 Undo pack2 e22t94 F getrllx Special version of b F getr11 e22t94 F getampx Special version of b F getampr11 e2ex F e2ex Main driver for ECO e2ex F exia Driver for EC AB e2ex F e2iba Calculate BCO O E B e2ex F exib Driver for E BA e2ex F e2iab Calculate ES BB A e2ex F ex2d Driver for the in core version of BCO disp e2ex F exd2 Actual in core calculation of EO disp e2ex F ex2dla ex2d1c Calculate components of BCO disp e2ex F ex2d2 ex2d8 n e2ex F transp13 Transpose an intermediate matrix e2xdooc F ex2dsemiooc Driver for the out of core version of po disp e2xdooc F wrseq Write an intermediate matrix to disk e2xdooc F rdseq Read an intermed
142. optional In the calculations producing the orbital energies and coefficients for monomers A and B files nameMA and nameMB the basis set should be ordered as pola isoa mid isop and iso mid isog polp respectively The method is in fact more general than the names isox and polx indicate As it should be clear from the above the basis set for each monomer can be divided into two arbitrary subsets Examples of MCTBS input files set up using this strategy can be found in the directo ries SAPT2012 examples ATMOL1024 HF2 MCBS SAPT2012 examples ATMOL1024 C02D_MCBS and also SAPT2012 examples ATMOL1024 ArH20_MCBS A more general method that works for all integral SCF front ends is the tags method In this method chosen by BLKMB F the ordering of functions is arbitrary except that it has to be the same in all input files Of course the MCBS files nameMA and nameMB will contain only subsets of the whole basis It is however required that the basis specifications in these files differ from the specification in the files name nameA and nameB by only the deletion of functions which belong exclusively to the other monomer i e the sequence of functions in the subset remaining after such deletion is not altered with respect to the whole DCTBS set The role of a given function is specified by tagging it in the TRN namelist read from the file nameP data This is achieved by first setting the variable BASIS
143. or function of this namelist is to tell the tran program which integral SCF package is in use Currently supported codes are listed in Table 1 In addition a number of legacy codes should still work although several of them have not been used for years Out of the 10 possible integral SCF selections the user should select only one by setting the corresponding variable equal to TRUE and all the other variables equal to FALSE The selection variables are given by e ISITANEW selects ATMOL1024 e ISITGAMS selects GAMESS e ISITGO3 selects GAUSSIAN98 GAUSSIANO3 or GAUSSIANO9 e ISITDALT selects DALTON 2 0 e ISITMOLP selects MOLPRO e ISITG94 selects GAUSSIAN94 e ISITCADP selects CADPAC e ISITACES selects ACES e ISITATM selects the older version of ATMOL e ISITORCA selects ORCA only works in SAPT DFT Of course selecting a given SCF package in the TRN namelist will work only if SAPT2012 has been compiled for use with this package see Sec 8 The variable DIMER is used to determine whether the transformation type is dimer default or monomer DIMER FALSE The dimer type transformation is chosen for DCBS DC BS cal culations and the monomer type one for MCTBS calculations If monomer type of transformation is set several other options become available These are BLKMB BASIS TAGS and SPHG variables connected with the tags system The use of these 41 variables was described in Sec 10 1 2 Also a description is provided in comme
144. ors to run everything CURDIR home bukowski ArHF_Tc Starting directory WRKROOT usr var tmp bukowski root of the scratch directory SAPTSCRIPT home bukowski psapt2K2 bin pSAPT o2k driver script JOB ArHF Core of the job name HEREHHRREHREARHHEA RHEE R RAH RRR RRR REAPER RRR No need to modify anything below this line HEHEHHRHEHHEARHHEARHER HERE R RRR RRR R RRR R RRR WRKDIR WRKROOT JOB scratch directory where the calculation will take place cd CURDIR Create the job specific scratch directory if d WRKDIR then mkdir WRKDIR fi Copy the input files from HOME to scratch cp JOB inp WRKDIR cp JOB A inp WRKDIR cp JOB B inp WRKDIR cp JOB P data WRKDIR Run the job in scratch cd WRKDIR SAPTSCRIPT JOB scfcp NODT WRKDIR gt gt JOB out_test NODT 2 gt amp 1 Copy output file back to HOME cp JOB out_test NODT CURDIR The first few lines starting with are options passed on to the queuing system in this case GRD specifying the name of the job what machine it should be run on in what queue and on how many processors The syntax of these options depends of the queuing system at hand and so these few lines must be adjusted accordingly The script is submitted typically using the command qsub ARL_script After the script enters execution it first creates a scratch directory named after the name of the job then copies the input files from the home s
145. orski Theor Chem Acc 127 211 2010 M Griining O V Gritsenko S J A van Gisbergen and E J Baerends J Chem Phys 114 652 2001 97 87 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 DALTON a molecular electronic structure program Release 2 0 2005 see http www kjemi uio no software dalton dalton html K Patkowski K Szalewicz and B Jeziorski J Chem Phys 125 154107 2006 H L Williams K Szalewicz R Moszy ski and B Jeziorski J Chem Phys 103 4586 1995 K Patkowski and K Szalewicz J Chem Phys 127 164103 2007 MOLPRO a package of ab initio programs designed by H J Werner and P J Knowles version 2002 6 R D Amos A Bernhardsson A Berning P Celani D L Cooper M J O Deegan A J Dobbyn F Eckert C Hampel G Hetzer P J Knowles T Korona R Lindh A W Lloyd S J McNicholas F R Manby W Meyer M E Mura A Nicklass P Palmieri R Pitzer G Rauhut M Schiitz U Schumann H Stoll A J Stone R Tarroni T Thorsteins son and H J Werner M J Frisch et al Gaussian 09 Revision A 1 Gaussian Inc Wallingford CT 2009 P Pulay J Comp Chem 3 556 1982 J O Hirschfelder Chem Phys Lett 1 325 1967 R J Wheatley unpublished R Moszynski B Jeziorski S Rybak K Szalewicz and H L Williams J Chem Phys 100 5080 1994 M Jeziorska B Jez
146. ost SCF part of the calculation tran cc and sapt x stages In a DC BS run the variable DIMER in the namelist TRN in this file must be set to T or TRUE If DCBS or DCTBS is used and a supermolecular SCF interaction energy calculation is re quested the scfcp option is set the script will additionally look for a dimer input file or files name notice the convention nameA nameB and name for the monomers A B and for the dimer respectively Thus for example for ATMOL1024 the complete set of input files necessary for this type of run are name intinp name scfinp nameA intinp nameA scfinp nameB intinp nameB scfinp and nameP data In the DCBS or DC BS approach the basis set specifications for all integral SCF calculations are identical except for different charges set to zero in different files and for different numbers of electrons in each run If the scfcp option is used the file of two electron integrals can be computed only once during the dimer run and the subsequent SCF calculations for monomers A and B can then use this file most integral SCF programs are flexible enough to allow such a route Note however that the one electron integrals must be computed separately for monomers A and B If the scfcp option is not used only the monomer A calculation needs to compute the two electron integrals 10 1 2 MCBS and MC BS approaches An alternative and strongly recommended way of performing SAPT calculations is to use
147. ot be reused for B The eigenvalues and eigenvectors from these two runs are saved whereas both one and two electron integrals are discarded The script will next look for an input file nameA to calculate one and two electron integrals for monomer A in the DCTBS equivalent of the MC BS used this basis is identical to the one described in the previous subsection but in some cases the functions have to be ordered in a special way or the proper tag parameters have to be specified in the file nameP data as discussed below No SCF calculations are needed if performed the results will be discarded This step is needed to produce the integrals for the SAPT calculations Next the script will look for a file nameB to calculate one electron integrals only for 37 the monomer B in the DC basis set the two electron integrals need not be calculated since these are identical as for monomer A Again no SCF step is needed Thus if for example ATMOL1024 is used as the integral SCF program the needed input files are nameMA intinp nameMA scfinp nameMB intinp nameMB scfinp nameA intinp nameB intinp and nameP data In the last of these files the variable DIMER in namelist TRN should be set to F or FALSE If MCTBS calculations are performed and the supermolecular HF SCF interaction energy is requested the scfcp option is used the script will as in the previous case first look for input files nameMA and nameMB to perform integral
148. ould contain the directives CHFDISP T CHFIND T The actual control parameters for pcksdisp are collected in the namelist INPUT which should be appended to nameP data the scripts pEDI X do this automatically and look similar to amp INPUT ISITCASPOL T ISITINDUCT T ISITSOSDISP T ISITPROP F ISITCKS F ISITUCKS T ISITPOL F ISITC6DISP F USESUMN6 T MAKEH1H2 T 113 IQUADTYP 1 NQUAD 10 OMEGAO 0 5 DEBUG1 T DEBUG2 F DEBUG3 F DEBUG4 F DEBUG5 F DEBUG6 F DEBUG7 F DEBUG8 F amp END The meaning of the options is as follows e Main Control flags ISITCASPOL T F Set if this is a Casimir Polder dispersion calculation ISITINDUCT T F Set if this is an induction calculation ISITPROP T F Set if a properties calculation needs to be performed ISITSOSDISP T F Set to perform the regular sum over states SOS ee calculation e Propagator Type only one can be selected ISITCKS T F Set to T if the propagator is to be computed in the CHF approximation otherwise set to F ISITUCKS T F Set to T if the UCHF approximation is to be used otherwise set to F e Properties calculation options ISITPOL T F Set if the frequency dependent dipole polarizability tensor a w is to be computed The frequencies at which the computation will be made are set by the input keywords NUMFREQ and FREQ lt gt see below The dipole integrals are needed for this calcul
149. out any significant loss of accuracy Typically the values of n rad 50 and n_ang 50 lead to completely negligible errors while values of n rad 30 and n_ang 26 introduce errors in the dispersion energy of just a few tenths of one percent Parameter mem specifies the maximum amount of memory in 8 byte words to be used in the kernel generation For larger systems limiting memory use requires slower multipass calculations The parameter ksi is the fraction of exact exchange of the employed functional for instance 0 25 for PBEO As the last difference compared to the DALTON route the script dfSAPT orca rather than dfSAPT is 95 used References 1 B Jeziorski R Moszy ski and K Szalewicz Chem Rev 94 1887 1994 2 K Szalewicz and B Jeziorski in Molecular Interactions from van der Waals to strongly 10 11 12 13 14 bound complexes edited by S Scheiner Wiley New York 1997 p 3 B Jeziorski and K Szalewicz in Encyclopedia of Computational Chemistry edited by P von Ragu Schleyer N L Allinger T Clark J Gasteiger P A Kollman H F Schaefer III and P R Schreiner Wiley Chichester UK 1998 vol 2 pp 1376 1398 B Jeziorski and K Szalewicz in Handbook of Molecular Physics and Quantum Chemistry edited by S Wilson Wiley 2003 vol 3 part 2 chap 9 pp 232 279 K Szalewicz K Patkowski and B Jeziorski in Intermolecular Forces and Clusters edited by
150. out information in the induction module Integrals and interme diates are printed This can generate a very large output 115 F Generation of auxiliary basis This Appendix is adopted from the Ph D Thesis by Alston Misquitta 66 The following procedure can be applied to construct an auxiliary basis set for each atom in the dimer under consideration Denoted by M is the decontracted basis set used in calculations for given dimer The auxiliary basis denoted by Y is developed as follows 1 Construct an auxiliary basis as the tensor product of M with itself That is Xx M8M 15 If G 1 a and GM l 0 are two basis functions of M centered at the same point where l and J are the angular quantum numbers and a and a are the exponents then the product is a basis function belonging to Y centered at the same point and given by G lk ax where I l lj and a a aj The resulting basis Y is a large basis including high symmetry functions compared to the original basis All the products involving basis functions from different centers are rejected 2 Within each angular symmetry of Y a reduction is performed in the number of basis functions as follows Given an e if there are n basis functions for which log ax log ax log Qk are in an e neighborhood then these n functions are replaced by one function with the exponent B Ap Oky Op Perform this reduction for the whole basis set 3 If necessar
151. p gms and the other working with the density fitted monomer properties called caldisp_fit 81 14 7 1 The pEDI scripts Most of the the tasks mentioned above are accomplished with the help of the script pEDI X where X stands for the platform at hand This script works very much like the script pSAPT X used in regular psAPT2K2 calculations Thus the SCF runs for the two monomers are performed first followed by the integral transformation the CCSD MBPT and psapt runs A new element is that the psapt module now calculates the MBPT2 and MBPT3 densities and stores them on disk and the pcksdisp program is called to produce the susceptibility functions currently at the CHF or RPA level In addition to generating the monomer properties the regular psAPT2K2 calculation is also performed for one dimer geometry obtained by shifting the position of monomer B by 10 bohr along the positive z axis with respect to the position specified in the nameB file The CHF dispersion energy is also computed for this geometry by the program pcksdisp the same one that generates the susceptibility functions The results for this one geometry reported in the output from the pEDI X run may then be compared to their counterparts obtained using the transforma tionless codes to assess the correctness and accuracy of the latter The transformationless code itself caldisp_gms is invoked at the end of pEDI X to compute the electrostatics induction and disp
152. pectively The file inta data contains the two electron integrals in some cases the original two electron file from a given package is used The infoa data and infob data files contain some general information about the system being investigated like the number of occupied orbitals the geometry and charges of each of the monomers These files vecta data vectb data onela data onelb data infoa data infob data and inta data serve as input files to the four index transformation program This program transforms the one and two electron atomic integrals into molecular integrals and produces the files 2e 000 xxx direct access integrals other than four virtual 72 000 xxx sequential vvvv integrals for monomer A and 73 000 xxx vvvv for monomer B as output xxx is normally always 001 but on legacy systems with file size limitations a series of files with consecutive labels is produced instead The numbers of these chunks for different file types are stored in the file nfiles which is used by the other programs Next two interfacing programs int and sort are called to extract different types of integrals from 2e 000 xxx and to put them in ccsorta 000 xxx ccsortb 000 xxx ov integrals direct access files and in a number of sequential files named 0 __a and 0 __b Additionally small formatted files ccloca 000 and cclocb 000 with indexing information are created The infoa data infob data and nfiles files are required by bot
153. persion and induction dispersion energies as defined in Sec 3 Two partial sums are also provided SAPT_ corr resp and SAPT_ corr The first of these quantities is the sum of eps 1 _felst r k eps 1 _ exch k or if available eps 1 _ exch CCSD tE 22 _ ind tE 22 _ ex ind E 2 _ disp k E 20 _ exch disp E 30 _ disp E 30 _ ind disp E 30 _fexch disp and E 30 _fexch ind disp The defini tion of the second partial sum is completely analogous except that eps 1 _felst k is used Note that if any of the corrections appearing in the definition of a partial sum is not com puted for example because it has not been requested in the namelist INPUTCOR this partial sum will not contain this correction For example if only SAPT T is requested in the INPUTCOR namelist the non response electrostatic corrections as well as the components of E will not be computed 49 and the quantity SAPT_ corr will not contain any correlation contribution to electrostatics and neither SAPT_ corr nor SAPT_ corr resp will include any contribution of the third order in the intermolecular interaction operator If the E CCSD energy is requested by setting E1CC T in the namelist INPUTCOR the quantity e CC EW A aa CCSD ECO will be reported in the correlation section of Summary elst Table but it will not be counted as a part of SAPT_ corr resp An example of using the E1CC opt
154. ponding density missing in the dump files denaMO data and denbMO data it does not hurt the subsequent calculations except that the quantities requiring the missing densities will be reported as 82 zero Also some other corrections may be specified so that the results from the Summary Table may be later compared to what comes out of the transformationless algorithms for the geometry considered in the pEDI X run These may include E1TOT T E2IND T E2INDR T and E2DSP T The namelist INPUT controlling the behavior of the propagator code pcksdisp is generated automatically by the pEDI X script and appended to file5 dat so the user does not have to worry about it For the sake of completeness we state here that this namelist currently contains the following ISITCASPOL T ISITINDUCI T ISITSOSDISP F ISITPROP F ISITCKS T ISITUCKS F ISITPOL F ISITC6DISP F USESUMN6 T MAKEH1H2 T IQUADTYP 1 NQUAD 16 OMEGAO 0 5 The meaning of these parameters is described in Appendix E In particular the user may want to alter the length NQUAD of the quadrature employed in the calculation of the Casimir Polder integral Prepare the file input edi specifying the dimer geometries for which the interaction energies are to be calculated by caldisp_gms out of the precomputed monomer properties input edi consists of lines one for each dimer geometry containing in this order the COM COM separation in A the 8 and y Euler angles
155. proper SAPT calculations All of this is performed automatically using the script SAPT from SAPT2012 bin directory note however that a special script doSAPT_CADPAC has to be used if CADPAC is the front end SCF program This script calls other executables and scripts which can be found in the same place Calculation of the interaction potential energy surface of a dimer involves multiple invocations of the SAPT script for different dimer geometries This process can be simplified and automated with the help of the Runlot utility scripts described in Sec 10 6 One of the scripts called by SAPT is the script bin Clean that cleans up unnecessary files after a SAPT run it will erase the SAPT related files from the directory in which it is run The files are not automatically erased at the end of of each run in order to enable restarts which has to be done on a case by case basis by modifying the SAPT script except when starting from the transformation step Therefore bin Clean is called at the beginning of the SAPT script so that a consecutive calculation can be performed in the same directory do not forget to change the name of the output file This is necessary since several temporary files are named with no reference to the job name Thus two simultaneous calculations cannot be done in the same directory but can be run of course in separate directories It is also prudent to run bin Clean itself just by executing SAPT2012 bin Clean t
156. put file in the section entitled Summary Table An example of the Summary Table can be found in Ap pendix D The first part of the table lists the numbers of orbitals the Cartesian geometry of the dimer and the SCF energies of the monomers and the dimer if computed obtained in the full DC BS What follows is a set of low order SAPT corrections which when summed up ap proximate the supermolecular SCF interaction energy also printed as E HF _ int if the key word scfcp was used on job submission The quantity SAPT SCF_ resp is equal to the sum of E 10 _felst E 10 _fexch E 20 _ ind resp and E 20 _fex ind r i e the first 4 terms on the rhs of Eq 5 The quantity delta HF _ int r represents the last term in this equation If the third order induction and exchange induction corrections have been calcu lated the quantity SAPT SCF 3 _f resp equal to a sum of SAPT SCF_ resp E 30 _ ind and E 30 _ fexch ind is displayed and the appropriate third order effects are subtracted from delta HF _ int r to form the delta3 HF _ int r quantity If the non response corrections E 20 _find and E 20 _ ex ind have been computed the corresponding non response approximation to the SCF interaction energy SAPT SCF and delta HF _ int are also given The CORRELATION part of the Summary Table contains all the computed SAPT corrections of order higher than zero in the intramonomer correlation operator and the dis
157. quired The simplest way to get nucdimer is to request a zero iteration SCF calculation for the dimer in some minimal basis set like STO 3G basis sto 3g hf maxit 0 nucdimer enuc e At the very end of the MOLPRO input the interface routine has to be called using the keyword user Starting from the SAPT2008 1 release the MOLPRO interface supports the use of a monomer centered basis set as well as of a dimer centered one An example of an MC BS saPT2012 run em ploying the MOLPRO interface can be found in the directory SAPT2012 examples MOLPRO CO2D_MCBS Several changes in the MOLPRO input file name molpro are needed to perform an MCTBS run e Before not after the regular set of dimer and monomer integral SCF calculations in the full DC BS basis is done separate monomer SCF calculations have to be performed in restricted MC BS parts of the full dimer basis The only data that is needed from these calculations are the SCF orbitals and orbital energies and these quantities must be saved using the keywords orbital 2110 3 for monomer A and orbital 2111 3 for monomer B e The same orbital keywords must be removed for the subsequent monomer SCF calculations employing full DCTBS set to avoid overwriting the MC BS orbitals e One should note that a name molpro input file for an MC BS run contains three basis specifications the MC BS set for monomer A the MCTBS set for monomer B and the full DC BS set The user must make sure that t
158. r Furthermore the calculated monomer densities will be packed for a further use into a file name den tar gz which after running gzip d name den tar gz tar xvf name den tar 53 will decompress info the following files 1 unformatted sequential files ccsd_dena out A and ccsd dena out B containing the SCF and relaxed CCSD densities of monomer A and B respectively 2 formatted files infoa_m data and infob_m data in the format readable by the code elstdenrot run subsequently containing geometry and basis set info for the monomers After collecting the files listed above and input edi in one scratch directory one can run the elstdenrot program by issuing a command similar to elstdenrot gt dimers out 2 gt amp 1 modifying of course the paths and the output file name appropriately As usual the executable pD elst and elstdenrot can be found in SAPT2012 bin directory The electrostatic energies at the CCSD levels calculated from the monomer densities translated and rotated into appropriate posi tions will be reported in the standard output from elstdenrot is this example in dimers out An example of MCBS CCSD densities calculation using the ccsddSAPT script followed by a batch of electrostatic energy calculations with the elstdenrot program can be found in examples GAMESS CO_E1DEN_MCBS 10 6 Submitting a sequence of SAPT2012 jobs The directory SAPT2012 bin contains three utility scripts RunlotAT
159. r each dimer geometry containing in this order the COM COM separation in A the 8 and y Euler angles in degrees for monomer A a is assumed as zero followed by the a and y Euler angles of monomer B It is assumed that the COM of monomer A coincides with the origin of the coordinate system and that monomer B is shifted in the positive direction of the z axis For example 5 29177249 0 O O O O 2 38521611 86 80692336 90 00000000 180 00000000 93 37890335 360 00000000 2 63658901 87 13779711 90 00000000 180 00000000 81 94039222 360 00000000 2 89422970 87 42491802 90 00000000 180 00000000 75 80434134 359 99999915 would be a valid input edi file containing 4 geometries The first of these geometries is exactly the same as the one for which the interaction energies are computed by the sapt x module during the ccsddSAPT run 4 Run the ccsddSAPT job the same way a regular job would be run For example to run in scratch mydir from ksh one would type ccsddSAPT name noscfcp scratch mydir gt name out 2 gt amp 1 Note that the noscfcp keyword has been used since the supermolecular SCF interaction energy is of no interest here The result of running the ccsddSAPT script in MCBS will be the file name out containing the standard output from the whole run In this file the SAPT corrections requested in the nameP data file will be reported in the Summary Table section for one specific dimer configuration described earlie
160. re accounted for by DFT and the only operator is V The SAPT approach is quite similar for trimers except that there is a total of six perturbation operators Vag Vac Vgc Wa We Wo in SAPT MP CC and the three former operators in SAPT DFT At intermonomer separations R large enough for the exchange effects to be negligible the SAPT results become identical to those of the regular Rayleigh Schr dinger perturbation theory The calculation of the interaction energies in this region can be substantially simplified by ne glecting the overlap effects and expanding V in the multipole series The long range part of the interaction energy becomes then expressed as a power series in Rt with coefficients that can be obtained using only monomer properties viz multipole moments and polarizabilities These monomer properties can be calculated ab initio at the correlation level consistent with finite R 14 SAPT calculations 50 51 using the monomer parts of the basis set and the POLCOR suite of codes developed by Wormer and Hettema 33 34 and distributed as a part of the package ASYMP_SAPT 4 Downloading saPT2012 The SAPT2012 distribution the parallel version psaPT2K2 the ASYMP_SAPT asymptotic package and the ATMOL1024 integral and SCF code can be obtained from the web page http www physics udel edu szalewic SAPT SAPT html All these codes are distributed free of charge but we require users to sign a license agreement which can be
161. rformed using GAMESS as the SCF program 10 5 1 DCBS calculation In the DCBS or DC BS approach the user needs to supply a set of GAMESS SCF input files just like for the ordinary SAPT calculation in DCBS or DCTBS basis The namelist TRN in the file nameP data has to set ISITGAMS T and DIMER T In the namelist INPUTCOR the option CONVAMP TRUE must be requested and the namelist CCINP has to be set up so that the CCSD calculations for the monomers are performed i e the variables CCSD and CCD should be either omitted or set to CCSD TRUE and CCD FALSE The computation of the ES respl CCSD elec trostatic energy using the ccsddSAPT script proceeds as follows After the integral transformation the ccsdt program is invoked to produce the CCSD amplitudes for both monomers Next the 5l ccsdm program is run twice for each monomer to calculate the relaxed CCSD densities The latter are stored in the AO representation in the unformatted sequential files ccsd_dena out A and ccsd_dena out B The obtained densities are then used by the program eldcbs together with the atomic one and two electron integrals to compute E 1 CCSD reported in the out elst resp put as CCSD electrostatics The correction EO is computed here as well and reported as SCF electrostatics The script ccsddSAPT then proceeds to invoke the sapt x module which calculates the other SAPT corrections as specified by namelist INPUTCOR An example of a DCBS calcu
162. rons the spin multiplicity the nuclear repulsion energy and the total SCF energy must be saved to appropriate variables This is accom plished in case of the DCBS DC BS approach by a series of keywords in the MOLPRO input file orbital 2110 3 30 NelecA nelec NspinA spin nucmonoA enuc emonoA energy data copy 1200 1 1202 1 data copy 1410 1 1412 1 data copy 700 1 702 1 for monomer A and orbital 2111 3 NelecB nelec NspinB spin nucmonoB enuc emonoB energy data copy 1200 1 1201 1 data copy 1410 1 1411 1 data copy 700 1 701 1 for monomer B Note that the order of some of these keywords is important as MOLPRO2006 appears to forget the SCF energy after the data copy command The interface also needs the variable nucrep containing the nuclear repulsion term between monomers nucrep nucdimer nucmonoA nucmonoB If the CP corrected supermolecular SCF interaction energy is requested apart from the SAPT corrections the SCF energy for the dimer must be calculated and saved hf edim energy Later in the script all three SCF energies should be listed with sufficient precision show 1 d25 15 edim show 1 d25 15 emonoA show 1 d25 15 emonoB as the SAPT programs extract these values from the output of the MOLPRO part of calcula tion If the supermolecular SCF interaction energy is not requested the dimer SCF energy 31 edim is not needed however the nuclear repulsion energy for the dimer nucdimer is still re
163. ry and takes slightly less than two hours to complete on an Opteron 252 machine The GAUSSIAN and MOLPRO versions of this example are also provided note that these two require the specification of monomer A monomer B dimer sets using the tags mechanism presented in Sec 10 1 2 e C6H6_H20_ADZM the benzene water dimer in a 262 term basis This is the largest example included and will take about 27 hours on an Opteron 252 to complete Some additional examples are also included namely e GAMESS HF_NH3_MCBS an example illustrating the use of the MCTBS technique in GAMESS with the tags and basis options as described in Sec 10 1 2 About 7 minutes on a 2 80 GHz processor e ATMOL1024 ArH20_MCBS an example of using the RunlotATMOL script as described in Sec 10 6 Consists of two jobs each taking about 6 minutes on an Opteron 252 e ATMOL1024 Ar2 FROZENCORE_30RDER an example of calculating the third order SAPT correc tions in Eq 9 and of performing a frozen core calculation The files Ar2P data allelectron and Ar2P data frozencore present in this example s subdirectory correspond to an ordi nary all electron calculation and a frozen core calculation respectively Rename either one to Ar2P data and invoke the SAPT script The basis set employed is aug cc pVQZ 3s3p2d2f1g midbond and the MCTBS approach is used The calculation requires about 1 5 hours all electron or half an hour frozen core on an Opteron
164. s 85 15 SAPT CC 86 16 SAPT DFT SAPT based on coupled Kohn Sham treatment of monomers 87 16 4 Introduction 2246 Gb ne he eae lh ie hide GS boa are oh OS 87 16 2 Installation and usage s s sa aoo n e 88 16 3 Terms beyond second order in the interaction operator 90 16 4 Density fitting version of SAPT DFT o o 90 16 4 1 Using DALTON for monomer DFT calculations 92 16 4 2 Using ORCA for monomer DFT calculations 92 References 99 A Porting saPT2012 to different platforms 100 B Integral SCF interfacing 101 C List of subroutines 102 D Summary table from output for the example BER Bez 112 E Capabilities of pcksdisp program 113 F Generation of auxiliary basis 116 1 Introduction SAPT2012 is a computer code implementing Symmetry Adapted Perturbation Theory SAPT SAPT is designed to calculate the interaction energy of a dimer i e a system consisting of two arbitrary closed shell or high spin open shell monomers Calculations can also be performed for trimers Each monomer can be an atom or a molecule In SAPT the interaction energy is expressed as a sum of perturbative corrections in the intermolecular interaction operator V each correction resulting from a different physical effect This decomposition of the interaction energy into distinct physical components is a unique feature of SAPT which distinguishes this method from the popular supermole
165. s This is indeed the case on a Beowulf cluster where scratch file systems are usually local to the nodes Another class of smaller temporary and input files have to be accessed from all processes On a Beowulf cluster such files have to be replicated in each processes local scratch area This problem does not exist on most other multiprocessor platforms like the SGIs and SPs in the DoD centers where all temporary files are stored in a common large file system accessible to all processes All the details of how the files are handled are taken care of by the pSAPT X scripts and the MPI executables themselves and are completely transparent to the user with the exception of the input files vide infra During the compilation the script compall adapts the appropriate pSAPT X script by insert ing the proper global paths to executables and should run properly on any installation without changes Currently this feature is not functional in the case of scripts used on huinalu namely pSAPT mpich maui and pSAPT mpich maui sep The paths in these scripts need to be changed manually so that the variables MAIN_SAPT_DIR and SCF_HOME_DIRECTORIES reflect user s directory structure if GAMESS is used it concerns also additional directories relevant for this program These variables are set about 500 lines down in the pSAPT X script The pSAPT X script is written in ksh although on Linux platforms some of which are not equipped with ksh it is actually
166. scripts this program is used to calculate the CHF static and dynamic susceptibility functions of the monomers In addition both these objects can also be calculated at the UCHF level The CHF and UCHF induction and dispersion energies are also reported The uncoupled UCHF dispersion and induction energies are equivalent to Ee and Be CHF level the induction energy is equal to ECO ind resp SAPT corrections respectively At the The CHF dispersion is equivalent to the so called RPA dispersion see Ref 39 for examples The RPA dispersion energy is currently not computed by the regular non parallel SAPT algorithms Two other quantities that can be obtained using pcksdisp are the static dynamic dipole dipole polarizability tensor and the isotropic Cg dispersion asymptotic coefficient for the interaction of identical monomers both at the UCHF and CHF levels The pcksdisp program uses the transformed intra and intermonomer integrals i e the MO representation as generated by the ptran module Therefore within a script like pEDI X it should be run after the SCF and transformation programs Note that currently pcksdisp assumes all integrals to be located in a single file 2e 000 001 Thus all such files have to be properly merged after a parallel ptran run This task is accomplished with the help of the program tmerge To ensure that ptran generates all the integrals necessary for pcksdisp the namelist INPUTCOR in the nameP data file sh
167. sical results when used with MOLPRO2006 1 Updated example input files for use with MOLPRO2006 1 and MOLPRO2008 1 Updated the GAMESS interface for use with the 2008 release of GAMESS Corrected a POSIX noncompliant use of the tail command in the Compall script that resulted in compile errors on some of the platforms Replaced an advanced regular expression in the SAPT script by a simpler one which is compatible with mawk The previous version was problematic for systems for which mawk was the default awk program Added a preliminary version of the library with common utilities saptlib New in SAPT2006 SAPT DFT 14 calculations available with DFT quantities extracted from DALTON 2 0 37 Third order SAPT corrections EO BOO par Bee disp Eso i apt Elio and BEY jip 38 10 to energy and amplitude based affects the converged CC amplitudes as well as the E 1 may lead to slight differences in the value of E o of SAPT Optional computation of EU from relaxed monomer CCSD densities If a pure monomer elst basis set is used the densities may be precomputed and reused after translation and rotation to compute the whole surface of E CCSD using direct integrals Optional calculation of the second order dispersion energy using converged CCD ampli tudes 39 The ELO 52 correction reimplemented using a formula valid in both dimer centered basis set DCBS and monomer centered basis set MCBS The implem
168. sionally appear later on in this manual The RS corrections of the first order in V Eli describe the classical electrostatic interaction and are denoted by Eo An alternative to expanding the electrostatic energy in powers of the intramonomer correlation operator is to calculate monomer electron charge densities p4 and pg at a certain level of correlation and then use these densities in the formula Eo fra pnlea deidre patrvanar onto vatejar Vo 2 where V4 and Vg denote the electrostatic potential of the nuclei of monomer A and B respectively and Vo is the nuclear repulsion term In SAPT2012 the densities in Eq 2 can be computed at the relaxed CCSD level The quantity El elst resp CCSD obtained in this way contains all the second and third order intramonomer correlation corrections as well as some other classes of diagrams diagrams resulting from single and double coupled cluster excitations summed up to infinite order 45 Similarly the E CCSD correction sums up the respective exchange contributions 46 The second order corrections can be decomposed into the induction and dispersion parts ERS Ema Egisy and ESS Ehina Eoxeh disp 3 12 The induction component is the energy of interaction of the permanent multipole moments of one monomer and the induced multipole moments on the other whereas the dispersion part comes from the correlation of electron motions on one monomer with those on t
169. situ Permute two indices of a 4 dimensional array newr F transq Transpose a square array newr F veccop vecadd Copy add one vector to another newr F tranmd permute two indices same size of a 4 dimensional array newr F trtl Transpose a rectangular array newr F vadd21 x i a j b E 2x 1 a j b y i j a b newr F trnspl x a t b 7 lt y t a 7 b newr F trnsp2 x i a j k E x k 5 1 a newr F filli Fill an INTEGER 4 array with natural numbers newr F wt2 Calculate second order energy newr F vminus Multiply a vector by 1 rpamono F RPA stuff currently not functional single F sda Calculate single amplitude terms depending on 7 intermediates single F vsta Calculate single amplitude terms depending on x intermediates single F ssa Calculate single amplitude terms depending on 7 intermediates single F t1ft2 Calculate single ampl terms depending on integrals and singles tpdrvn F tpdrvn Loop over vvvv integrals in the ladder diagram tpdrvn F dlprep Store indices involved in the ladder diagram tpdrvn F daxpys Perform the ladder diagram for one vvvv integral batch tpdrvn F fort_daxpy Explicitly calculate DAXPY usually faster than BLAS1 tpdrvn F sort2 Sort indices from dlprep to optimize cache use tpdrvn F resort Re sort four virtual integrals for faster access tpdrvn F vvvvsort4 Evaluate four virtual diagram tpdrvn F sort4v Sort four virtual integrals with 2 fold desymmetrization tpdrvn F wrtbu Writ
170. some problems not working 0 not tested This table is only for SAPT MP CC SAPT DFT is interfaced only with DALTON 2 0 and ORCA OS processor compiler ATMOL1024 GAMESS US GAUSSIANO3 09 DALTON 2 0 MOLPRO Linux amd64 gfortran 0 0 0 Linux i386 g77 pe _d Linux amd64 g77 af pe ale _d Linux i386 pgf779 ah ale 0 _d Linux amd64 pgf90 f db Linux ifort k 0 0 0 ym SUN OS 2 a 4 0 0 IBM AIX 4 0 a 0 HPUX Itanium 0 qn 0 0 The systems presented in the table were tested with SAPT2012 Some obsolete systems such as SGI OnK Alpha and IBM RS 6000 were tested at the time of the SAPT2002 version and may still work with saPT2012 gt Tested on various i386 Linux systems with g77 versions 3 3 x and 3 4 x gfortran 4 x should work with SAPT2008 2 and above GAUSSIAN does not support compilation with g77 d MOLPRO requires a Fortran 90 compiler e AMD Opteron AMD Athlon64 and Intel EM64T Both 32 bit and 64 bit mode available Compilation requires use of proper target flags g77_32 or g77_64 f The SCF package does not work in 64 bit mode Integral files calculated with 32 bit g77 GAMESS can be processed with 32 bit g77 or 32 and 64 bit pgf90 SAPT 9 Portland Fortran Compiler pgf77 on i386 Linux systems h GAMESS does not work it Portland Fortran Compiler pgf90 on AMD64 Linux systems J Intel Fortran Compiler i
171. ssentially the same way as in the case of the sequential version of the program SAPT2012 as described in detail in Sec 10 The only difference is that the options SAPTO SAPT2 SAPT and others of this kind introduced in later editions of SAPT codes are currently not supported in the namelist INPUTCOR The theory levels corresponding to these options may of course be recovered by requesting the appropriate SAPT corrections individually Note also that no SAPT corrections beyond the standard level like e g the components of PED Eq 9 are available in pSAPT2K2 and frozen core is not implemented in the parallel SAPT program 14 6 Memory and disk requirements Memory requirements of psAPT2K2 can be estimated based on the total number of basis functions the numbers of occupied and virtual orbitals and the number of processors involved The trans formation code ptran requires slightly more than on P 8 byte words on each of the P processors where n is the dimension of the basis set and o is the number of occupied orbitals of the bigger monomer For the pcc and psapt parts memory requirements can be roughly estimated as 30 words on each processor where v is the number of virtual orbitals for the larger monomer More precise calculation of the memory required for a psAPT2K2 run can be done using the program memcalc built automatically during installation In order to use this program prepare the regular nameP data file with the first
172. stand Modifications to the transformation program must be made to read in the two electron integrals in trans f atmtr f and trnn f modules Notice also the common block SCFPACK which contains logical variables indicating which integral SCF program is used This common block must be changed throughout the program to include a logical variable for any new integral SCF program Finally in the driver subroutine trans F make sure that there is a correct setting of the logical input record length for the new integral SCF program C List of subroutines This appendix contains the list of saPT2012 subroutines with a short description of their functions 102 Table 3 List of subroutines tran Module Subroutine Comments trans F metatrans Allocate memory and call main driver trans F trans Main driver routine trans F mkoffset Prepare auxiliary arrays for MC BS trans F lvalue Number of orbitals for a given shell trans F cpve Copy eigenvectors for a MCTBS transformation trans F whichint Flag integral types needed trans F pread Read GAMESS integral file trans F preadl pread2 Variants of pread atmtr F atmtr Driver for the four virtual transformation atmtr F index4 Perform four virtual transformation atmtr F sortl First sort for the four virtual transformation atmtr F wrda Write intermediates to a direct access file atmtr F calcl Transform first two indices for four virtual integrals at
173. t can be filled up with data points with a minimum interference on the user s part For larger systems placing of the midbond ghost atom halfway between monomer COMs can result in significant linear dependencies since the location chosen in this way can be close or overlapping with the monomers In such cases the DOR6 directive can be used instead of DOIT With the DOR6 directive getgeoATMOL places the midbond according to the 1 r weights based on distances from all atoms With this scheme the midbond is placed in a more balanced way 56 The rest of the atoms and the behavior of the getgeoATMOL program is identical to the DOIT directive The DOR6 scheme is recommended for all non trivial monomers The philosophy behind the scripts RunlotCADPAC and RunlotDALTON and the related getgeoCADPAC geometry conversion program is very similar consult the scripts themselves for details The struc ture of both scripts is simple enough to allow relatively easy modifications 56 10 7 Memory and disk requirements When setting up a SAPT2012 computational project it is imperative to know how much computa tional resources this project will consume and whether or not it will fit into the memory and disk of the machine at hand Memory requirements of SAPT2012 can be estimated based on the total number of basis func tions and the numbers of occupied and virtual orbitals The transformation code tran should work even with s
174. t included in ECY p and ER 22 iid resp oxch ina 18 the estimated exchange counterpart of El 2 tp 22 tpe p20 Eina 7 exch ind exch ind resp 20 ind resp The highest routinely used level of SAPT approximately equivalent to the supermolecular MBPT theory through fourth order is defined by ESAPT _ pSAPT2 p13 7 E int int elst resp exch 2 2 2 8 CCSD e a exch a exch where e CCSD El CCSD ELO exch exch at the CCSD level only The SAPT2 level of theory takes much less time than the full SAPT calculation and therefore is the part of ebkcn 00 with intramonomer excitations it is recommended for large systems If still faster calculations are required the correction pe can be omitted as it is usually fairly small 13 A 20 20 12 13 The corrections FE drepi Pee a O che aes and Eoist resp COM also be computed in non response versions but these forms are not recommended and are not calculated unless explicitly requested In case the sum EO diso T 2 2 is not converged well enough the CCD ST CCD approach disp developed in Ref 39 is also available in SAPT2012 In this method first the dispersion energy 2 CCD is approximated at a level corresponding to the dimer CCD calculation The energy Be obtained in this way can be shown 39 to contain the full corrections oY and EY and the so called DQ
175. t loop limits for tr3w unpack F packg Pack four 8 bit numbers into a 32 bit integer unpack F unpackg Do the reverse of packg unpack F packg64 Pack four 16 bit numbers into two 32 bit integers unpack F unpackg64 Do the reverse of packg64 unpack F unpack64to32 Unpack a 64 bit integer into two 32 bit ones unpack F unpack10 Unpack an INTEGER 4 INTEGER 1 pair into four indices unpack F unpack10a Unpack an INTEGER 4 INTEGER 1 pair into two indices unpack F pack10 Do the reverse of unpack10 unpack F packl0a Do the reverse of unpack10a unpack F spltindx Split an index into an INTEGER 4 INTEGER 1 pair unpack F itobyte Integer byte conversion unpack F unpckgms Unpack GAMESS integral labels unpack F unpckdlt Unpack DALTON integral labels 104 Table 4 List of subroutines cc Module Subroutine Comments mcc F mecsd Main driver mcc F mono Perform CC for a given monomer ccio F getamp getampn Get amplitudes from disk obsolete replaced by newget ccio F putamp Write amplitudes to disk obsolete replaced by newput ccio F ampinf mapda Auxiliary routines for getamp and putamp obsolete ccio F getbuf Read one packet of the size ov of ovvv integrals ccio F readen Read orbital energies ccio F lrecl Adjust buffer sizes for sorting 2el integrals ccio F save Omit small values in an array ccio F desyml lt oo vv gt array symmetry unique elements
176. tal indices or 1024 if the setting BEYOND1024 YES was not used in the Compall script 10 1 1 DCBS and DC BS approaches If a dimer centered basis set DCBS possibly including bond functions denoted then by DC BS is used and the supermolecular SCF interaction energy is not needed then only two inte gral SCF calculations for monomer A and for monomer B will be performed The DCBS DC BS approach means that the calculations for monomer X are performed using the orbital basis set con sisting of all functions those belonging to monomer X i e centered on the nuclei of monomer X those of the interacting partner i e centered at the positions where the partner s nuclei are 35 in the dimer and the bond functions in DC BS case In the inputs the bond functions and the functions of the interacting partner are typically connected with zero charge centers and are sometimes called ghost orbitals The script will then look for files nameA and nameB for the respective monomers The number and full names of the files depend on the integral SCF code used Here is a list of files needed for some of the front end codes ATMOL1024 nameA intinp nameA scfinp nameB intinp and nameB scfinp GAMESS nameA inp and nameB inp GAUSSIAN nameA data and nameB data DALTON nameA dal nameA mol nameB dal and nameB mol MOLPRO name molpro In each case the file nameP data will also be needed containing input for the p
177. tforms which do not support files larger than 2 Gbytes so that the integrals have to distributed over several smaller files Finally the MEMTRAN variable can be used to dynamically allocate memory for the transfor mation section tran of SAPT2012 As a default the memory for the tran program is set to 40 Mwords 320 Mbytes If possible the memory should be set large enough so that the transfor mation program uses the faster in core path When DIMER TRUE an even faster algorithm is switched on if twice as much memory as for the ordinary in core algorithm is available The amount of memory needed for the available transformation paths can be calculated beforehand using the program memcalc in SAPT2012 bin see Sec 10 7 Declaring more than the amount needed for the fast in core algorithm when DIMER TRUE or more than needed for the standard in core approach for DIMER FALSE makes no difference for the performance of transformation and may increase the probability of crashing due to requesting more memory than available on a system at a given time The transformation will work in smaller memory except that the slower out of core pathway will be chosen see the source module memory F for more details One can read from the transformation output of a test run whether the out of core or in core faster pathway has been chosen and what was the largest size of memory used This method can also be used
178. theory In SAPT the total Hamiltonian for the dimer is partitioned as H F V W where F F4 FB is the sum of the Fock operators for monomers A and B V is the intermolecular interaction operator and W Wa Wg is the sum of the Mgller Plesset fluctuation operators The latter operators are defined as Wx Hx Fx where Hx is the total Hamiltonian of monomer X The interaction energy Fint is expanded as a perturbative series o Ein DI Y EP FERA 1 n 1 0 with the indices n and j denoting the orders in the operators V and W respectively The energies Ea are the corrections defined by the regular Rayleigh Schrodinger perturbation theory These terms were named polarization energies by Hirschfelder 44 and this terminology was used in earlier editions of SAPT but was dropped later due to the confusion with the induction interactions Ens often called polarization interactions The exchange corrections Eich arise from the use of a global antisymmetrizer to force the correct permutational symmetry of the dimer wave function in each order hence the name symmetry adaptation Whereas the double perturbation theory expansion of Eq 1 is very convenient for analyzing the results SAPT is actually a triple perturbation theory as the Wa and Wp operators appear individually in SAPT expressions The resulting triple index corrections E with the consecutive indices referring to V Wa and Wa respectively will occa
179. tines tran part 2 Module Subroutine Comments memory F memory Partition core memory mono F chkitype Analyze indices for a MC BS transformation mono F permut Perform index permutation mono F sameinds Compare index quadruplets tonel F onel One electron transformation driver tonel F trle Actual transformation of one electron integrals tran F tran Driver for in core two electron transformation tran F igetlda Get dimension of the eigenvector matrix tranw F tranw Driver for out of core two electron transformation trnn F intowp Calculate space for an integer array trnn F inread Read integrals from GAUSSIAN trnn F labscf90 Unpack record label for GAUSSIAN90 and later trnn F unpacka Unpack ACES indices trnn F seeka Search for ACES labels trnn F namemain Get names of ATMOL1024 mainfile parts trnn F atmini Initialize ATMOL two electron integral file trnn F atmininew Initialize ATMOL1024 two electron integral file trnn F trl First step of in core and out of core transformation trnn F canon Return indices in canonical order trnn F tr2 Second step of in core transformation trnn F loop2lims Set loop limits for tr2 and tr2w trnn F tr3 Third step of in core transformation trnn F loop3lims Set loop limits for tr3 and tr4w trnnw F tr2w Second step of out of core transformation trnnw F tr3w Third step of out of core transformation trnnw F tr4w Fourth step of out of core transformation trnnw F looptr3w Se
180. tion memory 5 8 Mwords 40 Mwords 380 Mwords CC memory 2 3 Mwords 11 Mwords 112 Mwords sapt x memory 3 0 Mwords 12 Mwords 128 Mwords integral SCF disk 42 MB 11GB 7 8 GB transformation disk 138 MB 1 9 GB 17 GB CC disk 300 MB 4 8 GB 38 GB sapt x disk 268 MB 2 0 GB 23 GB Memory amount required for the fastest in core algorithm is given tran can also run is significantly smaller memory at the expense of execution time 60 13 Tests and example input and output files A set of test and example runs is provided in the distribution of saPT2012 These include several very small cases which should finish in seconds or minutes and which can be used to check the correctness of the SAPT2012 installation In each case both the complete set of input files and the output files at least from one platform are provided With the large number of front end SCF programs interfaced with saPT2012 and with the large number of hardware platforms on which it can be run it is not practical to provide examples for all possible cases The mix of combination of various factors chosen should be sufficient to establish the correctness of installation and help in preparation of user s production runs In some cases the test files compute all currently available SAPT corrections This is not needed for calculations of interaction potentials In such calculations use one of the SAPTn control variables to select the minimal needed set of corrections This
181. title line containing in this order the total number of 79 DC BS basis functions the total number of functions for monomer A will be different than the previous one in a MC BS type run the number of occupied orbitals for monomer A and then the same information for monomer B followed by the number of processors Then run the program by typing memcalc lt nameP data gt memcalc out The file memcalc out will contain detailed information about memory requirements of different parts of the code The variables MEMTRAN from namelist TRN and MEMSAPT from namelist INPUTCOR should then be adjusted accordingly The memory needed to run the pcc program is calculated there explicitly so that no separate namelist variable is needed An estimate of the total disk space requirement can be obtained as presented in Sec 10 7 for a sequential program It should be noted here that most of the large scratch files are distributed between the processes The amount of disk space needed on a single processor is thus only a fraction 1 P of the total disk requirement This feature becomes important on Beowulf clusters where typically only a relatively small scratch area is available on each node 14 7 Electrostatic dispersion and induction EDI energies from monomer properties It is well known that the electrostatic component of the interaction energy can be calculated from monomer charge densities which are purely monomer properties Similarly the
182. to adjust the MEMTRAN variable appropriately look for lines containing phrases similar to Mem 8182228 CPU 463 7 or 42 AABBOVVV Integrals Out of core 2 passes Mem 29848693 The minimal information absolutely necessary for the namelist TRN is given by amp TRN ISITx T amp END where x is one of the symbols denoting the integral SCF program listed above 10 2 2 Namelist CCINP The purpose of this namelist is to pass information to the MBPT CC program which generates the required cluster amplitudes for the intermolecular perturbation theory program sapt x The namelist variable CCPRINT tells the program whether or not to do extra printing This printing involves information about the memory partitioning and the integral class which is currently being read in The namelist variable VCRIT gives the tolerance for retaining cluster amplitudes Here we recommend a tolerance of 1 x 10719 The variables TOLITER and TOLAMP determine the convergence criteria of the CC iterations if the converged amplitudes are required i e if the variable CONVAMP see namelist INPUTCOR is set to TRUE In such a calculation the CC program continues the iterations until one of the following two conditions is fulfilled 1 The iteration number k exceeds 39 no convergence 2 All of the conditions listed below are met k _ p k 1 DEW a lt TOLITER Esc p Escr a k ab k 1 pub pal 2 D DJW jem Io lt TOLAMP OU pal
183. ubdirectory CURDIR to the scratch directory and runs the pSAPT o2k script SAPTSCRIPT Upon completion of the psaPT2K2 calculation the 72 output file is copied back to the home subdirectory CURDIR Note that after the job is finished the scratch directory will contain all kinds of temporary files which are kept there in case a restart is needed These files should be manually cleaned up 14 4 2 Running pSAPT2K2 on an SP3 SP4 The job submission technique here is very similar to the one used on an SGI platform except that interactive submissions are generally not possible and everything must be handled by a queuing system Consult the ARL_script and NAVO_script in the psapt2K2 examples SP directories for examples of the GRD and Load Leveler submission scripts 14 4 3 Running pSAPT2K2 on a Beowulf cluster Configurations of Linux based Beowulf clusters may vary between installations Presented below are techniques of running pSAPT2K2 on our local cluster samson at University of Delaware and on the huinalu cluster at Maui supercomputer center samson cluster The machine consists of 132 compute nodes equipped with 1 GHz AMD Athlon processors and connected by Ethernet Each node is equipped with a local scratch file system not accessible from other nodes On each node this file system is mounted as tmp In addition there is a login node which hosts home directories of the users and some shared resources like the MPI implementatio
184. ulations we recommend the standard Dalton grid or one of the denser grids For the THRESH parameter in HF INPUT we recommend values of about 107 Since SAPT DFT currently works with DALTON interface only and with ORCA in the density fitted version a few scripts are located in misc daltutil to help in creating DALTON input files Script atmol2dalton converts ATMOL name intinp input files into name mol required by DAL TON altergeo awk updates the name mol geometry and with createinputs one can construct name mol files using basis sets included in the DALTON distribution The usage of the scripts is explained in the sources The name dal files can be taken from the examples 16 3 Terms beyond second order in the interaction operator The SAPT DFT formalism presented above has been implemented up to second order in the operator V For systems with a significant induction component e g the water dimer some higher order terms constitute a large fraction of the total interaction energy Those terms can be estimated from the supermolecular HF SCF approach with Ea rosp defined in Eq 5 Since no such term can be computed from a pure DFT calculation this term has to be extracted from a separate SAPT HF SCF run For the calculation of ERE resp NO expensive SAPT terms are needed and the scaling is O N Nevertheless the time of this calculation would be similar to that of the SAPT DFT step since the costly transformation step must be do
185. urrent and maintained by us version of ATMOL 23 extended to handle up to 1023 basis functions ATMOL1024 is the default integral SCF package The Compal1 script checks if the ATMOL1024 source is present in SAPT2012 atmo11024 subdirectory and compiles it automatically If for some reasons ATMOL1024 has to be kept in another location and compiled separately it can still be used by SAPT2012 if the line ATMOL1024 NO in Compall is changed to reflect the current location of the ATMOL1024 main directory ATMOL1024 code has been tested with SAPT2012 more extensively than any other package and is the recommended choice e GAUSSIAN GAUSSIAN94 G94 and GAUSSIAN98 GAUSSIANO3 or GAUSSIANO9 42 G03 A full GAUSSIAN installation including the source code must be present at the location specified by the G94 G03 variable A binary only GAUSSIAN in stallation will not suffice Set at least one of the variables G94 GO3 to NO as these packages are mutually exclusive The path specified here should contain the GAUSSIAN s library util a usually it is the main directory of the GAUSSIAN distribution Addi tionally the variable GAUEXE holds the name of the GAUSSIAN executable no path is necessary so that the SAPT scripts know which executable to call The default value GAUEXE g09 must be changed if a different version is used Finally the Compall script declares a variable EXTRADEFS which is an empty string by default If GAUSSIAN was compiled with th
186. used for most published recent SAPT calculations for small and medium size systems The choice SAPT2 T equivalent to MBPT2 requires significantly less computer time and can be recommended for larger dimers if time of calculations at the SAPT T level becomes an issue In most cases we recommend that the OL resp term defined by Eq 5 is included as implied by Eq 6 this requires the scfcp keyword as a command line parameter to the SAPT script Only for nonpolar or nearly nonpolar monomers this term should be omitted see Ref 38 and the text below for a discussion of this issue The choice SAPTO T selects all available SAPT corrections of the first and second order in V and of zeroth order in W i e Be pO ee R Ds EOD ECY 10 elst exc ind resp exch ind resp disp exch disp This level is recommended for calculations for very large systems when a higher level of theory would be too time consuming however note that SAPT DFT described in Sec 16 would offer much better accuracy at similar computational costs One can expect that this level of theory may introduce about 20 30 errors with respect to the exact interaction energies but such an accuracy can be acceptable for large systems Also the errors due to the basis set truncation will most likely be of the same order of magnitude for systems that large For increased accuracy we recommend the addition of the S EHF resp berm The choice DELTASCF T selects all SAPT correctio
187. will reduce the time of calculations 13 1 The examples directory The directory SAPT2012 examples is divided into subdirectories corresponding to different SCF front end programs e g GAMESS or ATMOL1024 Each of those subdirectories contains the fol lowing test job directories named the same for all SCF programs e BER a very small test calculation for the beryllium dimer in a DCBS consisting of a 2s1p set on each atom The run will complete in a few seconds using 0 1 Mwords of memory and should be tried first We note again the naming convention for clarity for ATMOL1024 the dimer files are called BER intinp and BER scfinp the monomer A files are called BERA intinp and BERA scfinp the monomer B files are called BERB intinp and BERB scfinp and the perturbation file input is given by BERP data The input files needed when using GAMESS are called BER inp BERA inp and BERB inp integral SCF input files and BERP data pertur bation input file Monomer A and monomer B input files are created by setting the charge to zero on the proper site For example in the case of monomer A the charges on site B should be set to zero The perturbation program should produce the results given below in Appendix D These results can be found in the Summary Table at the end of an output e HF2_DCBS the HF basis set 4s2p1d 2s1p is taken from Ref 48 and a 2s1p set of midbond functions is added Needs about 1 Mword of memory and takes less than a
188. with the basis set size 38 The remaining part of Exch disp exch disp scales like o v with the number of orbitals The variables FROZEN NFOA NFOB NFVA and NFVB control the range of orbitals used for electron excitations 40 If FROZEN is set to FALSE an all electron calculation is performed and the values of NFOA NFOB NFVA and NFVB are irrelevant this is the default setting If FROZEN is set to TRUE NFOA lowest orbitals on A and NFOB lowest orbitals on B are treated as core and no excitations out of these orbitals are taken into account Additionally NFVA highest virtual orbitals on A and NFVB highest virtual orbitals on B are also excluded from the excitation space One may set NFVA NFVB 0 to perform a conventional frozen core calculation with excitations onto all virtual orbitals allowed Setting NFVA NFOB and NFVB NFOA is another reasonable choice Note that setting FROZEN TRUE affects not only the SAPT program but also the integral transformation and the calculation of monomer CC amplitudes However the parameters FROZEN NFOA NFOB NFVA and NFVB need and can be set only in the INPUTCOR namelist SAPT2012 can be used with effective core potentials ECPs So far this option has only been tested with the MOLPRO front end however using other ECP enabled integral front ends interfaced with SAPT2012 should be pretty straightforward Contrary to a frozen core SAPT run the ECP effects are taken care of at the integral progra
189. y the resulting basis can be reduced even further with the previous step repeated on the reduced basis with a different value of e 4 Further pruning of the reduced basis Y can be done as follows a Reject all functions of g symmetry and higher This is necessary if CADPAC is used to obtain integrals b The large exponents particularly the ones of high symmetries can generally be re moved The criterion for this removal is best found by trial and error and by monitoring the constraint conditions We have found the optimal values of e used in the pruning process to be between 0 3 and 0 5 This procedure typically results in an auxiliary basis Y that is 2 to 3 times larger than the basis used to obtain molecular orbitals and eigenvalues While in general the auxiliary basis for a molecule should be centered also on sites between pairs of atoms in addition to atomic sites it is our experience that the use of only atomic centers is adequate This is also true for the optimized auxiliary basis sets 14 116
190. y slightly lower performance may be to download the pre built ATLAS library for your architecture from e g www netlib org The efficiency of the BLAS library is important for the performance of SAPT and users are encour aged to use the fastest BLAS library on their machines The performance of LAPACK however is of minor importance and if optimized LAPACK is unavailable one can set BUILDLAPACK YES in the Compal11 script and the subset of LAPACK required for SAPT will be compiled 4 Several additional preprocessor definitions may be specified during the compilation by listing them in the variable EXTRADEFS in the Compall script This variable equal to an empty string by default may contain the options DI64 and or DPACK64 defining the format of 23 files imported from GAUSSIAN the option DTWOGIGAMAX which requests splitting of all large temporary files into chunks smaller than 2 GB and or the definition DTPDRVN used to switch on the old algorithm of calculating the four virtual contribution to the monomer CC amplitudes using unsorted integrals The default algorithm uses sorted integrals and is faster especially when a well optimized BLAS library is available but it requires more disk space during the CC stage of the calculation Once all the variables mentioned above are set simply type e C Shell users Compall gt amp compall log amp e K Shell or Bash users Compall gt compall log 2 gt amp 1 amp and the compil
191. z y z Euler angles ag Pg and yg of monomer B These angles to be supplied in degrees are measured with respect to the coordinate system in which the z axis points from A to B The Euler angle a is not needed since the intermolecular potential depends only on the difference ag aa so that a4 may be assumed zero without loss of generality At the end of each line of geoparm d there is also a string DOIT including the apostrophes If for some reason you do not need the calculation for a given geometry but still want to keep it in the geoparm d file put DONE instead The file geoparm d may contain any number of lines Once all these files are prepared copy them along with the RunlotATMOL script itself to your scratch directory where the whole calculation is to take place Then start the job with the command nohup time RunlotATMOL name gt name con 2 gt 1 amp in ksh or bash or time RunlotATMOL name gt amp name con amp 55 in csh where as usual name is how the job is called and how the names of all input files start The calculation will then proceed as follows First the program getgeoATMOL is invoked by RunlotATMOL this program is automatically compiled during the installation of SAPT2012 and the path to it is inserted into RunlotATMOL which analyzes the geoparm d file looking for the first line containing the DOIT directive When such a line is found getgeoATMOL reads the COM separation and
192. zed to the number of electrons N or a transition density a product of an occupied and a virtual orbital which is normalized to zero The quantity p is an approximation to p in the form of a linear expansion in terms of auxiliary basis functions The choice of 1 r 2 as the weight in the functional A has been suggested by Dunlap 60 Minimization of the functional A reduces then to solving a system of linear equations for the expansion coefficients Only one such equation system needs to be solved for each of the MBPT components of density whereas fitting of the susceptibility function for each imaginary frequency requires solving ov such systems one for each pair of the occupied and virtual orbitals Presented here is the beta version of the suite of codes implementing the ideas discussed above The codes allow the generation of monomer charge densities currently at the SCF MBPT2 and MBPT3 levels with and without orbital relaxation and susceptibility functions currently at the CHF level generation of an auxiliary basis and the fitting of the monomer properties in terms of this basis The charge densities susceptibility functions and SCF vectors are then used as input to a program which calculates the electrostatic induction and dispersion energies for an arbitrary set of dimer geometries Two versions of this code exist one utilizing the exact representation of monomer properties i e in terms of the original AO basis called caldis

Manual - University of Delaware Dept. of Physics & Astronomy

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Manual - University of Delaware Dept. of Physics &amp; Astronomy

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Manual - University of Delaware Dept. of Physics & Astronomy