CamCASP 5.5 - Stone, Anthony

100 Pages·2016·0.97 MB·English

am
C CASP 6.0
AlstonJ.Misquitta†andAnthonyJ.Stone††
†DepartmentofPhysicsandAstronomy,
andtheThomasYoungCentreforTheoryandSimulationofMaterials,
QueenMaryUniversityofLondon,327MileEndRoad,LondonE14NS
††UniversityChemicalLaboratory,LensfieldRoad,CambridgeCB21EW
February28,2020
Abstract
CamCASP is a suite of programs designed to calculate molecular properties (multipoles and frequency-
dependentpolarizabilities)insingle-siteanddistributedform,andinteractionenergiesbetweenpairsofmolecules,
and thence to construct atom–atom potentials. The CamCASP distribution also includes the programs PFIT,
Casimir,GDMA2.3,Cluster,andProcess.
Copyright(cid:13)c 2007–2018AlstonJ.MisquittaandAnthonyJ.Stone
Contents
1 Introduction 1
1.1 Authors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Citations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
2 What’snew? 2
3 OutlineofthecapabilitiesofCamCASP andotherprograms 3
3.1 CamCASP limits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
4 Installation 5
4.1 BuildingCamCASP fromsource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
5 UsingCamCASP 9
5.1 Workflows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
5.2 High-levelscripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
5.3 Theruncamcasp.pyandsubmit_camcasp.pyscripts . . . . . . . . . . . . . . . . . . . . . . . . 10
5.4 Low-levelscripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
6 Dataconventions 12
7 CLUSTER:Detailedspecification 13
7.1 Prologue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
7.2 Moleculedefinitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
7.3 Geometrymanipulationsandothertransformations . . . . . . . . . . . . . . . . . . . . . . . . 15
7.4 Jobspecification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
7.5 Energy&Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
7.6 Crystal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
7.7 ORIENT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
7.8 Finally,... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
8 Examples 35
8.1 ASAPT(DFT)calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
8.2 Anexamplepropertiescalculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
8.3 Dispersioncoefficients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
8.4 UsingCLUSTERtoobtainthedimergeometry . . . . . . . . . . . . . . . . . . . . . . . . . . 43
9 CamCASPprogramspecification 45
9.1 Globaldata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
9.2 Moleculedefinition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
9.3 TheEDITmodule:Modifyingamolecularspecification . . . . . . . . . . . . . . . . . . . . . . 48
9.4 Density-fitting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
9.5 Propagatorsettings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
9.6 Quadraturesettings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
9.7 TheISAmodule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
9.8 Multipolemoments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
9.9 Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
9.10 Polarizabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
9.11 Lattice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
9.12 Numericalintegrationgrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
9.13 Electrostaticinteraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
9.14 First-orderexchange(exchange-repulsion) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
9.15 Second-orderinductionenergy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
9.16 Second-orderdispersionenergy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
9.17 Distributeddensity-overlap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
9.18 Energyscan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
9.19 Overlapmodel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
9.20 Integrals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
10 PROCESS:Syntax 82
11 CASIMIR 86
A Basissets 88
B Dispersioncoefficients:indetail 89
C Changehistory 91
D OlderScripts 94
D.1 High-levelscripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
D.2 Low-levelscripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
3
1 Introduction
CamCASP is a suite of programs for the calculation of interaction energies between pairs of molecules, and
molecularproperties(multipolesandfrequency-dependentpolarizabilities)insingle-siteanddistributedform.The
CamCASP distributionalsoincludestheprogramsPFIT,Casimir,GDMA2.3,Cluster,andProcess,andtogether
theseformapackagefortheabinitiogenerationofsite–siteforcefieldsbetweenorganicmoleculescontainingup
toabout60atoms.
1.1 Authors
The CamCASP suite of programs, which includes PFIT, Casimir, GDMA 2.3, Process, and Cluster, has been
writtenbyAlstonJ.MisquittaandAnthonyJ.StonewithimportantcontributionsfromRobertBukowski,Wojciech
Cencek,theGAMESS(US)teamandtheGAUSSINTteam.
1.2 Citations
Thiscodeisprovidedasaservicetothescientificcommunityandouronlyrecompense,suchasitis,isincitations.
Therefore,ifyouuseanyresultsfromCamCASP inyourpublicationswerequestthatyoucitethefollowingpapers.
Thechoiceofcitationswoulddependonthepartsofthecodeyouhaveusedforthepublishedresults.
• SAPT(DFT)energies
◦ A.J.MisquittaandK.Szalewicz. Intermolecularforcesfromasymptoticallycorrecteddensityfunc-
tionaldescriptionofmonomers. Chem.Phys.Lett.,357:301–306,2002
◦ A. J. Misquitta, B. Jeziorski, and K. Szalewicz. Dispersion energy from density-functional theory
descriptionofmonomers. Phys.Rev.Lett.,91:33201,2003
◦ A.J.MisquittaandK.Szalewicz. Symmetry-adaptedperturbation-theorycalculationsofintermolecu-
larforcesemployingdensity-functionaldescriptionofmonomers. J.Chem.Phys.,122:214109,2005
◦ A. J. Misquitta, R. Podeszwa, B. Jeziorski, and K. Szalewicz. Intermolecular potentials based on
symmetry-adaptedperturbationtheorywithdispersionenergiesfromtime-dependentdensity-functional
theory. J.Chem.Phys.,123:214103,2005
◦ R.Bukowski,R.Podeszwa,andK.Szalewicz.EfficientgenerationofthecoupledKohn–Shamdynamic
susceptibility functions and dispersion energy with density fitting. Chem. Phys. Lett., 414:111–116,
2005
• WSMpolarizabilities
◦ A.J.MisquittaandA.J.Stone. Distributedpolarizabilitiesobtainedusingaconstraineddensity-fitting
algorithm. J.Chem.Phys.,124:024111,2006
◦ A.J.MisquittaandA.J.Stone. Accurateinductionenergiesforsmallorganicmolecules:I.Theory.
J.Chem.TheoryComput.,4:7–18,2008a
◦ A.J.Misquitta,A.J.Stone,andS.L.Price. Accurateinductionenergiesforsmallorganicmolecules.
2.DevelopmentandtestingofdistributedpolarizabilitymodelsagainstSAPT(DFT)energies.J.Chem.
TheoryComput.,4:19–32,2008a. doi:10.1021/ct700105f
• WSMDispersionmodels
◦ A. J. Misquitta and A. J. Stone. Dispersion energies for small organic molecules: first row atoms.
Molec.Phys.,106:1631–1643,2008b
• SRLOpolarizabilities
◦ A.J.MisquittaandA.J.Stone. Distributedpolarizabilitiesobtainedusingaconstraineddensity-fitting
algorithm. J.Chem.Phys.,124:024111,2006
◦ FazleRobandKrzysztofSzalewicz. Asymptoticdispersionenergiesfromdistributedpolarizabilities.
Chem.Phys.Lett.,572:146–149,2013
1
• GDMAmultipolemoments
◦ A.J.Stone. Distributedmultipoleanalysis:Stabilityforlargebasissets. J.Chem.TheoryComput.,1:
1128–1132,2005
• Potentials&Overlapmodels
◦ A. J. Stone and A. J. Misquitta. Atom–atom potentials from ab initio calculations. Int. Rev. Phys.
Chem.,26:193–222,2007
◦ A.J.Misquitta,G.W.A.Welch,A.J.Stone,andS.L.Price. Afirstprinciplespredictionofthecrystal
structureofC Br ClFH . Chem.Phys.Lett.,456:105–109,2008b
6 2 2
◦ AlstonJ.MisquittaandAnthonyJ.Stone. Abinitioatom-atompotentialsusingcamcasp:Theoryand
applicationtomany-bodymodelsforthepyridinedimer. J.Chem.TheoryComput.,12(9):4184–4208,
2016.doi:10.1021/acs.jctc.5b01241.URLhttps://doi.org/10.1021/acs.jctc.5b01241.PMID:
27467814
• Charge-tranferviaregularisation
◦ A. J. Misquitta. Charge-transfer from regularized symmetry-adapted perturbation theory. J. Chem.
TheoryComput.,9:5313–5326,2013. doi:10.1021/ct400704a
• Iteratedstockholderatom(ISA)
◦ AlstonJ.Misquitta,AnthonyJ.Stone,andFarhangFazeli. Distributedmultipolesfromarobustbasis-
space implementation of the iterated stockholder atoms procedure. J. Chem. Theory Comput., 2014.
doi:10.1021/ct5008444
◦ A. J. Misquitta and A. J. Stone. Isa-pol: Distributed polarizabilities and dispersion models from a
basis-spaceimplementationoftheiteratedstockholderatomsprocedure. Theor.Chim.Acta,137:153
(20),2018
• ISA-Poldistributedpolarizabilitiesanddispersionmodels
◦ A. J. Misquitta and A. J. Stone. Isa-pol: Distributed polarizabilities and dispersion models from a
basis-spaceimplementationoftheiteratedstockholderatomsprocedure. Theor.Chim.Acta,137:153
(20),2018
Furthermore,ifyoumakeanychangesoradditionstothecodeandwouldliketosharethemforinclusioninfuture
releases,pleasesubmitthemodificationstouswithsuitabledocumentationandexamples.
2 What’s new?
Thecurrentversionis6.0.xx.Enhancementstothecodesinceversion5.9:
• E(2) withouttheS2approximation.Implementationofaclosed-shellversionoftheformulaefromSchäf-
ind,exch
ferandJansen[SchäfferandJansen,2012].
• NewversionoftheBS-ISAalgorithm.Moreflexibilityinthebasissetsandconsequenthigheraccuracies.
DetailsofthisalgorithmaredescribedbyMisquittaandStone[MisquittaandStone,2018].
• ISA-Pol: ISA-based distributed polarization code that computes frequency-dependent distributed polariz-
abilitiesanddispersionmodels.SeeA.J.MisquittaandA.J.Stone. Isa-pol:Distributedpolarizabilitiesand
dispersion models from a basis-space implementation of the iterated stockholder atoms procedure. Theor.
Chim.Acta,137:153(20),2018foradescription.
• Distributeddensity-overlapwiththeISA.SeeAlstonJ.MisquittaandAnthonyJ.Stone.Abinitioatom-atom
potentials using camcasp: Theory and application to many-body models for the pyridine dimer. J. Chem.
Theory Comput., 12(9):4184–4208, 2016. doi: 10.1021/acs.jctc.5b01241. URL https://doi.org/10.
1021/acs.jctc.5b01241. PMID:27467814fordetails.
2
• Advances in the fitting strategy for the development of atom–atom interaction models. See Alston J. Mis-
quitta and Anthony J. Stone. Ab initio atom-atom potentials using camcasp: Theory and application to
many-bodymodelsforthepyridinedimer. J.Chem.TheoryComput.,12(9):4184–4208,2016. doi:10.1021/
acs.jctc.5b01241. URLhttps://doi.org/10.1021/acs.jctc.5b01241. PMID:27467814fordetails.
• Interface with Psi4 1.1 and the unreleased github versions. Both SAPT(DFT) and δHF energies can be
int
computedusingPsi4 asthefront-endcode.
• The introduction of methods for important types of calculations with CamCASP . These methods allow
complexcalculationsinaneasywayandalsoallowtheusertodevelopandmaintaintheirownvariationson
theprovidedmethods.
• IntegrationwithOrient4.9.
• ManymorekindsofoperationspossiblewiththeClustercode.
• Basissets:ThebasissetlibraryincludedwithCamCASP hasbeensignificantlyexpanded.Whenusedwith
Psi4 themainbasissetsaretakenfromthePsi4 basislibrary.WehavealsoincludedtheaugA-Sadlejbasis
which is a modified version of the Sadlej-pVTZ basis that results in interaction energies of much higher
quality(i.e.,closertotheCBSlimit),particularlywhenusedwiththelargerofthemid-bondsets.Thisbasis
ishighlyrecommended.
Formoredetails,seetheChangeLogfile.
EarlierchangesarelistedinAppendixC.
3 Outline of the capabilities of CamCASP and other programs
ThefollowingtypesofcalculationarepossiblewithCamCASP:
• Dimerenergies:
Thefirst-orderelectrostaticandexchangeenergies,E(1) andE(1) ,andthesecond-ordertotaldispersionand
elst exch
totalinductionenergies,E(2) andE(2) (includingtheirexchangeterms).Allarecalculatedusingdensity-
IND DISP
fitting,andthesecond-orderdispersioncaninprinciplebecalculatedwithoutdensity-fitting,thoughthispart
ofthecodehasnotbeentestedinalongtime.TheδHFcorrectioncanalsobecalculated.
int
• Molecularproperties:
◦ Multipole moments: Total and distributed multipole moments can be calculated using a constrained
density-fittingalgorithmandtheGDMA2.3code,whichhasbeeninterfacedtoCamCASP.
◦ Frequency-dependent polarizabilities: Total and distributed frequency-dependent polarizabilities are
calculatedusingaconstraineddensity-fittingalgorithm.TheWilliams–Stone–Misquitta(WSM)method
canbeusedtoobtainthemostaccuratepolarizabilitymodelwithinconstraintsimposedbytheuser.
◦ Point-to-pointpolarizabilities:Responsestoafrequency-dependentpoint-chargeperturbation—called
point-to-pointpolarizabilities—canbecalculated.TheseareneededbythePFITprogramwhenopti-
mizingthedistributedpolarizabilities.
TheOrientprogramisneededforsomeaspectsofthepropertycalculations.Itisdistributedseparatelybut
accesstoitisprovidedusingthesamecredentialsasforCamCASP.
• Energyscans:
Surfaces around a molecule can be defined (or supplied as a grid of points) and all dimer energies can be
calculatedonthissurface,usingapointcharge(fortheinductionandelectrostaticsonly)oraprobemolecule.
Thetotalanddistributedcharge-densityoverlapisalsoscanned.
• Atom–atompotentials:
Usingtheresultsoftheenergyscansandmolecularproperties,atom–atompotentialscanbeobtainedusing
thedensityoverlapmodeltomodeltheshort-rangeenergies.TheOrientprogramisusedforsomepartsof
thiscalculation.
3
• Theorylevels:
Inallcases,calculationscanbeperformedusingeitherthecoupled/uncoupledKohn–Sham(CKS/UCKS)or
coupled/uncoupledHartree–Fockpropagators.Inpractice,theCKSpropagatorwillbeused.
• Density-fittedIntegralPackage:
The density-fitted (DF) integral package allows the calculation of 2-electron 4-index integrals in very effi-
ciently, both in computation time and memory usage. With this package, the intermediate TRAN step is no
longerneededfortheHessiancalculation,therebysavingalotoftime.Inprinciple,theSapt2008program
canalsoberunusingintegralsobtainedfromthispackage,butthiswouldinvolvesomemoreeffort.
Atpresent,theDF-integralpackagecomputesmorethan30kindsofintegral.
ThefunctionalityofCamCASP isgreatlyenhancedwhenusedwiththePFITandOrientprograms.Onlysome
ofthemanyfeaturesofOrient—thosemostusefulforthecalculationandanalysisofintermolecularforces—are
listedhere.
• PFIT
◦ Fitting of polarizability models: At present, polarizability models are not fitted from scratch, but po-
larizability models from the CamCASP code can be optimised using PFIT and the point-to-point
polarizabilitiesfromCamCASP.
◦ Dispersioncoefficients:ThesecanbecalculatedbyPFITusingfrequency-dependentdistributedpolar-
izabilitiesfromCamCASP.ThisfunctionisbetterperformedbytheCasimirprogram.
• Casimir
◦ Dispersioncoefficients:C ,C ,etc.toC .Dispersioncoefficientsbetweenpairsofidenticalordissim-
6 7 12
ilarmoleculescanbecalculatedbyCasimirusingfrequency-dependentdistributedpolarizabilitiesfrom
CamCASP thathavebeenlocalizedusingOrientandpossiblyrefinedusingPFIT.Theinputfilefor
CasimircanbecreatedwiththeProcessprogramfromlocalizedfrequency-dependentpolarizabilities.
Minorchangestotheinputfilesallowthecalculationofmixed-moleculedispersioncoefficients.
• Dispersion
◦ Dispersionenergiesusingnon-localpolarizabilities:Thisprogramallowstwoandthree-bodydisper-
sionenergycalculationsusingfrequency-dependentnon-localpolarizabilitiessuchasthosecalculated
using the distributed polarizability module in CamCASP . These calculations include contributions
fromthecharge-flowpolarizabilities.
• Orient
◦ Local polarizabilities: The distributed polarizabilities from CamCASP include non-local contribu-
tions.ThesecanbetransformedawayusingthelocalizationmoduleinOrient.
◦ Simplificationofmodels:ThepolarizabilitymodelscanbemodifiedorsimplifiedusingOrient.
◦ Displayingenergies:Energiescanbedisplayedin3-DusingtheOpenGLdisplaymoduleinOrient.
◦ Calculationsofasymptoticenergies:Usingthedistributedmultipolesandpolarizabilities,interaction
energiescanbecomputedinthelong-range(asymptotic)approximation.
Miscellaneousprograms:
• Process:ThiscodeisaninterfacecodetoprocesspolarizabilitiesfromCamCASP or(localized/modified)
polarizabilitiesfromOrientintoaformPFITcanuse.Italsoperformstransformationsofthepolarizabilities
andisabletowriteoutpolarizabilitiesinLATEXformatforpublications.
• Cluster:Thisistheprogramthathandlestheuser’sinputdataandgeneratesthesubsidiarydatafilesneeded
byotherpartsofthepackageandbytheauxiliaryabinitiocodes.Italsoenablestheusertoconductelemen-
tarymanipulationsofthemoleculegeometry,buildclusters,determinerotationalandtranslationaxes,and
writeoutputinaformsuitableforCamCASP,Orient,andanyprogramthatcanreadPDBfilesforimaging.
An important function of Cluster is to create the input files for CamCASP , DALTON (versions 2.0 and
2013orlater),NWChem6.x,Psi4 andSapt2008programs.Alltheuserneeddoisdefinethedimerwithin
4
Cluster,performanymanipulationsthatmightbeneeded,andthenusetheRUN-TYPEcommandtogenerate
the files for the calculation. This greatly simplifies the file generation process and removes the chance of
errors in the rather complicated input file structure of Sapt2008, DALTON and (to a lesser extent) Psi4 ,
NWChem6.xandCamCASP.
3.1 CamCASP limits
CamCASP isaresearchcodeandwhileitisefficientlycoded,itisnotasyetparallelised,socalculationsonlarge
systemscanbechallenging.Neverthelesscalculationsonmoderatelylargedimersarepossible:fortheRDXdimer
(30 heavy atoms and 6 hydrogen atoms) using PBE0 with the ALDA kernel and the 6.0 version of CamCASP ,
theSAPT(DFT)calculationtakes17honasinglecoreandtheDFTcalculationsneededforthistake1h20musing
thePsi4 coderunningon4cores.IfthemoreaccuratebutmorecomputationallydemandingALDA+CHFkernel
is used, then the SAPT(DFT) calculation takes 22h on 1 core. The differences in memory used are larger: the
ALDA calculation used 30GB while the ALDA+CHF calculation used 41GB. These timings and memory sizes
werefortheaugA-Sadlejmainbasisandaug-cc-pVTZ-RIdensity-fittingbasiswiththe3s3p2d2fmid-bondsetand
correspondingRIbasis.Thisgivesamainbasissizeof803functions,andauxiliarybasissizeof4805functions.
The followinglimits applyonly tothose partsof the calculationthat requireintegrals ofthe type OVOV or OOVV.
Theseoccurinthehybridkernelsandinthesecond-orderexchange-dispersionandexchange-inductionenergies.
Ifonlythenon-exchangeenergiesarerequired(E(1),E(2) andE(2) )andtheALDAXkernelisused,thelimits
elst ind,pol disp,pol
aresignificantlyhigher.
For example, if we impose a 16GB limit to the sizes of individual arrays that need to be stored completely in
memory,thenthefollowinglimitsapply:
• Mainbasissize:N =n +n wheren n ≤131072
o v o v
Examples:
◦ N-methylpropanamide:n =24,thereforeN ≤5461.
o
◦ Carbamazepine:n =62,thereforeN ≤2114.
o
◦ C :n =180,soN ≤728.
60 o
• Auxiliarybasissize:M ≤131072.Inpracticethelimitwillbelowerforcomputationalreasons.
• Computationalbottlenecks:
◦ Hessians:CalculationofthehybridHessians(ALDA+CHF)isanO(n3n3)process.Thiscanbereduced
o v
using the methods recently developed by Bukowski et al. [2005]. This has been done for the ALDAX
andALDAkernelswhichcanbecalculatedinO(M2n n )effortandwithO(M2)memoryrequirements.
o v
◦ 2-electron 4-index integrals: These are required for the exchange energies. In particular the second-
orderexchangeenergies.
• Otherlimitations
◦ Notparallelised.
◦ Whilereasonablylargecalculationsarepossiblewiththisversionofthecode(seetheexamplesgiven
above),bearinmindthatthisstillisaserialcodeandthatcalculationsofthesecond-orderexchange
energies for large systems will be difficult as they will typically require more resources and a re-
programmingoftherelevantCamCASP modulestomakebetteruseofmemoryanddiskresources.
4 Installation
The CamCASP package comprises several different programs, and also uses a number of third-party programs
— specifically, an ab initio package for the DFT or wavefunction calculations and the Orient program. While
we have interfaced CamCASP to the DALTON, NWChem 6.x, GAMESS(US) and Psi4 programs, the scripts
suppliedwithCamCASP supportPsi4,DALTONandNWChem6.xmorefullythantheothers.Consequently,we
recommendthatthePsi4,DALTON(2.0,or2015orlater)orNWChem6.xabinitiopackagesareused,andthis
5
isassumedbelow.SeveralPythonscriptsareprovidedtosimplifythetaskofsettingupthevariousfilesthatare
neededforthecalculation,andfeedingthemtotheprogramsthatdothework.ThescriptsrequirePython3.6or
later.Inorderforthistoworksuccessfully,afewconventionsneedtobefollowedinthewaythatyourcomputeris
organised,andbecauseoftheuseofthird-partyprogramstheinstallationprocedurecannotbeasfullyautomated
asyoumightwish.ThefollowinginstructionsapplytoUnixandLinuxsystems;theycanbefollowedwithlittle
changeforMacOSXandWindowssystemsbyworkingfromaterminalwindowontheMacorbyusingaUnix
emulatorsuchasCygwinunderWindows.
1. TherecommendedprocedureistoclonethepackagefromtheCamCASP repository,byusing
git clone https://gitlab.com/anthonyjs/camcasp.git directory
Thiswilldownloadallthefilesintothedirectoryyouspecified.ItincludesprogrambinariesforLinux.Fora
MacOSversion,usethesamecommandwiththeadditionaloption--branch CamCASP-6.0-macos
2. Next,youneedtoaddtheCamCASP /bindirectorytoyourpath;forexample:
export PATH=/home/<user>/camcasp/bin:$PATH
Thiscanbeincludedinyourinitializationfile.Thiswouldprobablybeyour.bashrcfileifyouusetheBash
shell.
3. InstallOrient,mosteasilyusing
git clone [email protected]:anthonyjs/orient.git directory
TheOrientpackageincludesthesourcefiles,soyoucancompileityourself,butthereareexecutablebinaries
includedforLinuxandOSX.
4. Install an ab initio wavefunction code – DALTON, NWChem 6.x or Psi4 – if you don’t already have one or
more of them already installed. DALTON 2.0 and DALTON-2015 (and later) require slightly different input,
butCamCASP canhandleeither.TheCamCASP interfacetoPsi4 isnewinversion6.0andshouldbetreated
asexperimental.ThisinterfacehasbeentestedonthePsi4 versions1.1,1.2and1.3;thelattertwoversionsare
availableontheGitHubpageofPsi4 andmustbebuiltbytheUser.
5. YoucouldalsoinstalltheGAMESS(US) program,butbearinmindthatforthepresent,wedonotincludeany
examplesofscriptstoperformcalculationswithGAMESS(US) andCamCASP.
6. Dalton-specific:IfyouwishtousetheSapt2008programwiththeDALTON2.0program,itisnecessarytoap-
plythepatchtoDALTON2.0includedinthedistribution.ThisallowscalculationsusingtheALDA/ALDA+CHF
kernelswithxc-kernelintegralsdirectlyfromDALTONandallowstheFermi–Amaldi(FA)asymptoticcorrec-
tion with the Tozer & Handy splicing scheme [Tozer and Handy, 1998]. The patch for DALTON needs to be
applied,andDALTONrecompiledifnecessary.Forsourcesfortheseprogramssee
http://www.kjemi.uio.no/software/dalton/dalton.html
http://www-stone.ch.cam.ac.uk/programs.html#Orient4
http://www.physics.udel.edu/~szalewic/SAPT/SAPT.html
DALTON2015doesn’trequirethepatch,asithastheasymptoticcorrectionalreadyincluded,andCamCASP
cannowhandletheALDAandALDA+CHFkernelitself.
7. NWChem6.x-specific:TheCS00asymptoticcorrection[CasidaandSalahub,2000]willbeusedwithNWChem
6.x.Ideallyanenergyshiftshouldbeprovidedforthismethod;itisthesumofthe(positive)ionizationenergy
and the (negative) HOMO eigenvalue. If this is not provided an empirical relationship between the HOMO
eigenvalueandtheIPisusedinstead.Neitherisasgoodanapproximationastheasymptoticcorrectionscheme
usedwithDALTON(above).TheCS00schemeissimilartotheGRACschemeofGruningetal.[2001].
8. Psi4 -specific: CamCASP uses the main basis sets from the Psi4 basis library, so many more basis sets are
possible. However you need to ensure that the relevant auxiliary basis is available in the CamCASP basis
library.Psi4 usestheGRACasymptoticcorrection.
9. Windows specific: the interface codes that convert the results of the wavefunction calculation into a suitable
form for CamCASP are provided as Linux or Mac OS binaries, and may need to be recompiled. To do this,
changetotheCamCASPdirectoryandrun
make interfaces
Youwillneedagfortrancompiler.
CamCASPhasbeentestedbutnotextensivelyusedbyusunderMacOSandnotusedatallunderWindows,so
wecannotguaranteethatitwillrunsmoothlyundertheseoperatingsystems.
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10. Nowyouneedtodefinesomeenvironmentvariables.
• CAMCASP shouldbesettothefullpathnameofthebasedirectoryfortheCamCASP package.
• SCRATCH shouldbesettothefullpathnameofascratchdirectorythatcanbeusedfortemporaryfiles.
• ARCH shouldbeset,forhistoricalreasons,to’x86-64’ifyouarerunningunderLinuxandto’osx’if
runningunderDarwin(MacOS).
Thesevariablescanallbesetinyourinitializationscript,sothatyoudon’tneedtosetthemeverysession.For
example:
export CAMCASP=/usr/local/camcasp-6.0
YoumayalsoalsoneedtoaddtheSapt2008\bindirectorytoyourpathifyouplantousethisprogram:
export PATH=$SAPT/bin:$PATH
11. If you wish to use NWChem 6.x or Psi4 on a multi-processor or multi-threaded machine, you may need to
provide shell scripts nwchem.sh or psi4.sh in the CamCASP bin directory. They should deal with any
initial setup and execute the command required to launch NWChem 6.x or Psi4 with the required number of
processors. The procedure for doing this will vary from one computer to another, and we cannot provide a
generalsolution,butthefilesnwchem.sh.exampleandpsi4.sh.exampleareprovidedasaguide.
12. Finally you need to ensure that CamCASP can access the SCF codes and other programs that it uses. These
include at least one of the SCF codes Dalton (2013 or later), Dalton2006 (Dalton 2.0), NWChem and Psi4,
andalsotheOrientprogramandpossiblytheSAPTprogram(i.e.theHartree-FockbasedSAPT–CamCASP
providesSAPT(DFT)itself).ThisjustrequiresthattheexecutablefilescanbefoundinyourPATH.Sincethe
CamCASP /bin directory must be in your path anyway, one way to achieve this is to set up symbolic links
(aliases) in the CamCASP bin directory to these programs. This only needs to be done once. Alternatively
it may be necessary, or just more convenient, to install a little shell script, e.g. psi4.sh, in the CamCASP /bin
directorytoinvoketheprogram,asexplainedabove.
TocheckthattheprogramsareallaccessibletoCamCASP,runthecommand
setup.py
(afterchangingthePATHandsettingtheenvironmentvariablesasexplainedabove).
13. Testingtheinstallation
Onceeverythingissetup,youcanrunsometeststhatwillexercisetheprograms.GototheCamCASP subdi-
rectorytestsandfollowtheinstructionsintheREADMEfile.Therearetestsforsingle-configurationdimer
energycalculationsandforproperties.andforenergyscansoverasetofdimerconfigurations.
4.1 BuildingCamCASP fromsource
ExecutablebinariesoftheCamCASP,Process,Casimir,PFITandClusterprogramsareprovidedforPCsrunning
LinuxandforMacOSX.Wherepossiblethesearestaticbinariesanddon’trequireadditionallibraries.Ifyouneed
tocompilethepackageyourself,youwillneedtoobtainaccesstothesource.Thisisnotnormallyavailable,but
may be permitted on request. The Makefile supplied with the CamCASP source files will build the CamCASP ,
Process,Casimir,PFITandClusterprograms.Herearesomebriefinstructions.
Thebuildwillhappeninadirectory$CAMCASP/arch/compilerwherearchisthemachinearchitectureandcompiler
isthenameofthecompilerchosen.Thearchitectureandcompilermustbespecified,eitheronthemakecommand
line:
make all ARCH=archCOMPILER=compiler
bychangingthebeginningoftheMakefiletosetthedefaultvalues,orbysettingenvironmentvariablesARCHand
COMPILER.
Thecompilerflagsusedaresetinthefile$CAMCASP/arch/compiler/exe/Flags.Youwillhavetosetmachine-
specificflagshere.TheMACHINEvariableprovidesanalternativewaytoselectflagsfordifferentplatforms,using
the same Flags file — see the examples provided. On a Linux machine the name of the machine should be de-
terminedautomatically,butifthisdoesn’tworkyoucanspecifyitonthemakecommandline.Probablytheonly
thingthatwillneedchangingistheLIBSflagthatsetsthelibrariestobelinkedto.
Architectureoptionsarex86-64andosx.
Compileroptionsare:pgf90,gfortran,andifort.
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