1. PAMoC
  2. User's Manual, Click here to get a list of volumes,
    and eventually click an item to change the current volume.
  3. List of Keywords,Click here to get a list of chapters,
    and eventually click an item to change the current chapter.
  4. None.All sections are embedded in this page.

List of Keywords

Control of a PAMoC run is realized through keywords and options which are entered in the form of single-line data-input sections:

keyword   <option1 option2 … >

Keywords and options can be entered also as environment variables or on the command line. In the latter case the keyword must be prepended by the minus sign (-).

The following notations will be used to represent keywords and options. The “Lucida Sans Typewriter” monospaced font family denotes keywords recognized by PAMoC. These have to be typed as shown, but may be in upper or lower case. Keywords which have the same meaning and produce the same action are enclosed in parentheses "()" with a vertical bar "|" as the delimiter, i.e. ( keyword1 | keyword2 | | keywordN ). A double vertical bar "||" is used to delimite two mutually exclusive options. Parentheses "( )" can be omitted if no ambiguity occurs. Keywords may require one or more parameters: italic text embedded in brackets "< >" is used for parameters and options which should be replaced with actual values. Brackets "< >" usually indicate a set of parameters and options and can be omitted if no ambiguity occurs. Square brackets "[ ]" denote optional keywords and options.

A complete list of keywords is given below, both alphabetically ordered, and grouped according to the topics or categories to which they refer.

Ordered Alphabetically
2dg2D grid data file 3dgCUBE file (nD grid data file) adp aliasAtomic Parameters for Dispersion Energy apde aliasAtomic Parameters for Dispersion Energy apre aliasAtomic Parameters for Repulsion Energy arc aliasArchive file for QTAIM volume properties arp aliasAtomic Parameters for Repulsion Energy atmSelect atoms to be integrated (QTAIM) AtmParDspAtomic Parameters for Dispersion Energy AtmParRepAtomic Parameters for Repulsion Energy atoms aliasSelect atoms to be integrated (QTAIM) BaderRequire QTAIM partitioning of the electron density bckArchive file for Becke atomic properties bdf aliasInterface Data-File bnkXD Data Bank file cf aliasConfiguration file cfgConfiguration file ChargeNorm aliasNormalize charges of individual molecules so that each molecule is neutral Chkt2f aliasChkTopo2F ChkTopo2f aliasChkTopo2F CluDim aliasDimension of the cluster of unit cells CluTypDimension of the cluster of unit cells CovRad aliasDefine Covalent Radii cryCrystal (cell, lattice, symmetry operations) data-file crys aliasCrystal calculation crystalCrystal calculation csizeLengths of crystal edges cub aliasCUBE file (nD grid data file) damp aliasDamping function for Dispersion energy DampDispDamping function for Dispersion energy DbgMomCalculation of Stewart's pseudoatom multipole moments by numerical volume integration (for debugging purpose) DbgNuMom aliasCalculation of Stewart's pseudoatom multipole moments by numerical volume integration (for debugging purpose) debugDebug print output dfde aliasDamping function for Dispersion energy dftEvaluate exchange and correlation energy density functionals DiagVarUse diagonal variance/covariance matrix DiagVarCov aliasUse diagonal variance/covariance matrix dimSpecify the second monomer of a dimer dimer aliasSpecify the second monomer of a dimer ecdElectrostatic interaction energy data-file ecm aliasInteraction Energy Model, E-Cryst model ecprt aliasRequire E_Cryst extended Printing ECrystPrtRequire E_Cryst extended Printing eemElectronegativity Equalization Method epmmExact Potential and Multipole Moment hybrid method for electrostatic interaction energy evaluation export_dmaSave a DMA on disk file extExternal DMA data-file ExtDbgExtended Debug print output ExtPrt aliasSpecify the amount of printing fra aliasMolecular fragment specification data-file frgMolecular fragment specification data-file g2d alias2D grid data file g3d aliasCUBE file (nD grid data file) GetTop aliasRead Topological data from disk file (.top) grid aliasUse a grid of points as guesses for topological analysis HandyOrder of Handy Quadrature Grid hrfArchive file for Hirshfeld atomic properties iamModify density basis set idfInterface Data-File iemInteraction Energy Model, E-Cryst model igt aliasSelect an Integration Grid ilhb aliasInclude Loose Hydrogen Bonds in ECryst model indDMA of unpolarized monomers data-file inpAuxiliary input file IntGridSelect an Integration Grid Knowles aliasOrder of Knowles Quadrature Grid lhb aliasInclude Loose Hydrogen Bonds in ECryst model lmx aliasMaximum multipole order used in the E-Cryst model logkOrder of Knowles Quadrature Grid LooseHBInclude Loose Hydrogen Bonds in ECryst model lsqData input file for least-squares multipole analysis of the electron density lsqLeast-squares Input Data File LsqFitLeast-squares Multipole Analysis of the Electron Density MaxErr aliasThreshold for laplacian energy, 10**(-N) MaxLapThreshold for laplacian energy, 10**(-N) MaxMulOrdMaximum multipole order used in the E-Cryst model MomentOrOrigin of moments nct aliasSkip topological analysis of crystal nim aliasSkip calculation of Inner Moments NoECryst aliasSkip ECryst calculation NoESD aliasDo not use/calculate variance/covariance metrix NoMolRecAvoid Recognition of individual Molecules normalize aliasNormalize charges of individual molecules so that each molecule is neutral NormChgNormalize charges of individual molecules so that each molecule is neutral NoVarDo not use/calculate variance/covariance metrix NoVariance aliasDo not use/calculate variance/covariance metrix NumAcc aliasSelect an Integration Grid or aliasOrigin of moments origin aliasOrigin of moments outAuxiliary output file PenT aliasEPMM Penetration Threshold (J/mol) PenThreshEPMM Penetration Threshold (J/mol) PeT aliasEPMM Penetration Threshold (J/mol) PrintDMAPrinting Options for nuclear centred Distributed Multipole Analysis PrintMomPrinting Options for Molecular Electric Moments pro aliasModify density basis set ProMol aliasModify density basis set PrtDMA aliasPrinting Options for nuclear centred Distributed Multipole Analysis PrtMom aliasPrinting Options for Molecular Electric Moments qtaim aliasRequire QTAIM partitioning of the electron density RadRuleSelect the Radial Integration Rule rc aliasConfiguration file rcovDefine Covalent Radii RdTop aliasRead Topological data from disk file (.top) ReadTopRead Topological data from disk file (.top) rir aliasSelect the Radial Integration Rule SaveTopSave Topological data on disk file (.top) ScaPopScale VALRAY-1994 populations shift aliasMoment shift procedure (0|1|2|3) ShiftMomMoment shift procedure (0|1|2|3) SkipCrysTopSkip topological analysis of crystal SkipECrystSkip ECryst calculation SkipInnerMomSkip calculation of Inner Moments sm aliasMoment shift procedure (0|1|2|3) StdQuad aliasStandardization of Radial Quadrature Grid StdRadStandardization of Radial Quadrature Grid stkArchive file for stockholder atomic properties StopAfterIdf aliasStop after reading the IDF StopAfterMom aliasStop after calculation of Moments StopAfterTop aliasStop after Topological Analysis StopECrystStop after ECryst calculation StopIdfStop after reading the IDF StopMomStop after calculation of Moments StopTopStop after Topological Analysis stwArchive file for Stewart atomic properties surArchive file for QTAIM surfaces sym aliasUse Symmetry T2 aliasUse Topological Algorithm 2 t2errChkTopo2F topArchive file for topological data Topo2 aliasUse Topological Algorithm 2 UseDMASpecify which DMA to use UseGrid aliasUse a grid of points as guesses for topological analysis UseGridTopUse a grid of points as guesses for topological analysis UseSym aliasUse Symmetry UseSymmetryUse Symmetry UseTopo2Use Topological Algorithm 2 vVerbose print output valray1994 aliasScale VALRAY-1994 populations verbose aliasVerbose print output volArchive file for QTAIM volume properties vprt aliasVerbose print output vr1994 aliasScale VALRAY-1994 populations vvSpecify the amount of printing wfn aliasInterface Data-File xdb aliasXD Data Bank file xderrCheck XD calculation of moments xderror aliasCheck XD calculation of moments xdmXD Master file xdpXD Parameter file
Ordered by Topics and Categories

I/O files:

(2dg | g2d)2D grid data file (3dg | g3d | cub)CUBE file (nD grid data file) bckArchive file for Becke atomic properties (bnk | xdb)XD Data Bank file (cfg | cf | rc)Configuration file cryCrystal (cell, lattice, symmetry operations) data-file ecdElectrostatic interaction energy data-file extExternal DMA data-file (frg | fra)Molecular fragment specification data-file hrfArchive file for Hirshfeld atomic properties (idf | bdf | wfn)Interface Data-File indDMA of unpolarized monomers data-file inpAuxiliary input file lsqLeast-squares Input Data File outAuxiliary output file stkArchive file for stockholder atomic properties stwArchive file for Stewart atomic properties surArchive file for QTAIM surfaces topArchive file for topological data (vol | arc)Archive file for QTAIM volume properties xdmXD Master file xdpXD Parameter file

Charge Distributions:

eemElectronegativity Equalization Method export_dmaSave a DMA on disk file extExternal DMA data-file (PrintDMA | PrtDMA)Printing Options for nuclear centred Distributed Multipole Analysis (PrintMom | PrtMom)Printing Options for Molecular Electric Moments

Cartesian Multipole Moment Tensors and Polytensors:

export_dmaSave a DMA on disk file (MomentOr | origin | or)Origin of moments (PrintDMA | PrtDMA)Printing Options for nuclear centred Distributed Multipole Analysis (PrintMom | PrtMom)Printing Options for Molecular Electric Moments (ShiftMom | sm | shift)Moment shift procedure (0|1|2|3) (StopMom | StopAfterMom)Stop after calculation of Moments

Spherical Harmonic Tensors:

export_dmaSave a DMA on disk file lsqData input file for least-squares multipole analysis of the electron density (PrintDMA | PrtDMA)Printing Options for nuclear centred Distributed Multipole Analysis (PrintMom | PrtMom)Printing Options for Molecular Electric Moments (ShiftMom | sm | shift)Moment shift procedure (0|1|2|3) (StopMom | StopAfterMom)Stop after calculation of Moments

Methods of Electron Density Partitioning (MEDPAC):

(atm | atoms)Select atoms to be integrated (QTAIM) (Bader | qtaim)Require QTAIM partitioning of the electron density bckArchive file for Becke atomic properties (DbgMom | DbgNuMom)Calculation of Stewart's pseudoatom multipole moments by numerical volume integration (for debugging purpose) hrfArchive file for Hirshfeld atomic properties lsqData input file for least-squares multipole analysis of the electron density (MaxLap | MaxErr)Threshold for laplacian energy, 10**(-N) stkArchive file for stockholder atomic properties stwArchive file for Stewart atomic properties surArchive file for QTAIM surfaces UseDMASpecify which DMA to use (vol | arc)Archive file for QTAIM volume properties

Methods of Numerical Integration:

HandyOrder of Handy Quadrature Grid (IntGrid | igt | NumAcc)Select an Integration Grid (logk | Knowles)Order of Knowles Quadrature Grid (RadRule | rir)Select the Radial Integration Rule (rcov | CovRad)Define Covalent Radii (StdRad | StdQuad)Standardization of Radial Quadrature Grid

Energies of nonbonded interactions:

(AtmParDsp | apde | adp)Atomic Parameters for Dispersion Energy (AtmParRep | apre | arp)Atomic Parameters for Repulsion Energy csizeLengths of crystal edges (DampDisp | dfde | damp)Damping function for Dispersion energy (dim | dimer)Specify the second monomer of a dimer ecdElectrostatic interaction energy data-file (ECrystPrt | ecprt)Require E_Cryst extended Printing epmmExact Potential and Multipole Moment hybrid method for electrostatic interaction energy evaluation (iem | ecm)Interaction Energy Model, E-Cryst model indDMA of unpolarized monomers data-file (LooseHB | lhb | ilhb)Include Loose Hydrogen Bonds in ECryst model (MaxMulOrd | lmx)Maximum multipole order used in the E-Cryst model (PenThresh | PenT | PeT)EPMM Penetration Threshold (J/mol) (SkipECryst | NoECryst)Skip ECryst calculation StopECrystStop after ECryst calculation

Electrostatic energy:

csizeLengths of crystal edges (dim | dimer)Specify the second monomer of a dimer ecdElectrostatic interaction energy data-file (ECrystPrt | ecprt)Require E_Cryst extended Printing epmmExact Potential and Multipole Moment hybrid method for electrostatic interaction energy evaluation (iem | ecm)Interaction Energy Model, E-Cryst model indDMA of unpolarized monomers data-file (LooseHB | lhb | ilhb)Include Loose Hydrogen Bonds in ECryst model (MaxMulOrd | lmx)Maximum multipole order used in the E-Cryst model (PenThresh | PenT | PeT)EPMM Penetration Threshold (J/mol) (SkipECryst | NoECryst)Skip ECryst calculation StopECrystStop after ECryst calculation

Exchange-repulsion energy:

(AtmParRep | apre | arp)Atomic Parameters for Repulsion Energy

Dispersion energy:

(AtmParDsp | apde | adp)Atomic Parameters for Dispersion Energy (DampDisp | dfde | damp)Damping function for Dispersion energy

Induction or polarization energy:

Printing options:

debugDebug print output ExtDbgExtended Debug print output (PrintDMA | PrtDMA)Printing Options for nuclear centred Distributed Multipole Analysis (PrintMom | PrtMom)Printing Options for Molecular Electric Moments (v | verbose | vprt)Verbose print output (vv | ExtPrt)Specify the amount of printing

Miscellanea:

(CluTyp | CluDim)Dimension of the cluster of unit cells (crystal | crys)Crystal calculation dftEvaluate exchange and correlation energy density functionals (DiagVar | DiagVarCov)Use diagonal variance/covariance matrix (dim | dimer)Specify the second monomer of a dimer (ECrystPrt | ecprt)Require E_Cryst extended Printing (iam | pro | ProMol)Modify density basis set (LooseHB | lhb | ilhb)Include Loose Hydrogen Bonds in ECryst model LsqFitLeast-squares Multipole Analysis of the Electron Density NoMolRecAvoid Recognition of individual Molecules (NormChg | normalize | ChargeNorm)Normalize charges of individual molecules so that each molecule is neutral (NoVar | NoESD | NoVariance)Do not use/calculate variance/covariance metrix (ReadTop | RdTop | GetTop)Read Topological data from disk file (.top) SaveTopSave Topological data on disk file (.top) (ScaPop | vr1994 | valray1994)Scale VALRAY-1994 populations (SkipCrysTop | nct)Skip topological analysis of crystal (SkipECryst | NoECryst)Skip ECryst calculation (SkipInnerMom | nim)Skip calculation of Inner Moments StopECrystStop after ECryst calculation (StopIdf | StopAfterIdf)Stop after reading the IDF (StopMom | StopAfterMom)Stop after calculation of Moments (StopTop | StopAfterTop)Stop after Topological Analysis (t2err | Chkt2f | ChkTopo2f)ChkTopo2F (UseGridTop | UseGrid | grid)Use a grid of points as guesses for topological analysis (UseSymmetry | UseSym | sym)Use Symmetry (UseTopo2 | Topo2 | T2)Use Topological Algorithm 2 (xderr | xderror)Check XD calculation of moments
Ordered by type and internal number (programmer reference)

Logical Options (no arguments, default value: false)

numbernamesdescription
1(stopidf | interface | stopafteridf)Stop after reading the IDF
2(stopmom | moments | stopaftermom)Stop after moment calculation
3(ecryst | stopecryst)Stop after ECryst calculation
4(noecryst | skipecryst)Skip ECryst calculation
5(stoptop | toponly | stopaftertop)Stop after Topological Analysis
6(topo2 | usetopo2 | t2)g
7(grid | usegrid | usegridtop)g
8(t2err | chkt2f | chktopo2f)g
9(sym | usesym | usesymmetry)g
10(crys | crystal)g
11(normchg | normalize | chargenorm)g
12lsqfitLeast-squares Multipole Analysis
13(novar | noesd | novariance )g
14(diagvar | diagvarcov)g
15(dbgmom | -dbgnumom)g
16dftg
17export_dmag
18nomolrecg
19(scapop | vr1994 | valray1994)g
20(nim | noelprop | skipinnermom)g
21(nct | nocrytop | skipcrystop )g
22 not used
23 not used
24 not used
25(lhb | ilhb | loosehb)Include Loose Hydrogen Bonds
26 not used
27(readtop | rdtop | gettop)READ TOPology from disk file
28savetopSAVE TOPology on disk file
29(bader | qtaim)QTAIM partitioning
30epmmEP/MM
31(ecprt | ecrystprt)E-Cryst extended Printing
32(xderr | xderror)g

Options with integer argument(s)

numbernamesdescriptiondefault value
     $    '    ' , '-lmx    ', '-maxmulord',         !  1)
     $    '-igs' , '-intgrid', '-numacc'   ,         !  2)
     $    '-or ' , '-origin ', '-momentor' ,         !  3)
     $    '    ' , '        ', '-usedma'   ,         !  4)
     $    '    ' , '-clutyp ', '-cludim'   ,         !  5)
     $    '    ' , '-maxerr ', '-maxlap'   ,         !  6)
     $    '    ' , '-atm'    , '-atoms'    ,         !  7)
     $    '    ' , '-dim'    , '-dimer'    ,         !  8)
     $    '-iem' , '-ecm'    , '         ' ,         !  9)
     $    '-arp' , '-apre'   , '-AtmParRep',         ! 10)
     $    '-adp' , '-apde'   , '-AtmParDsp',         ! 11)
     $    '-damp', '-dfde'   , '-DampDisp' ,         ! 12)
     $    '-iam' , '-pro'    , '-promol'   ,         ! 13)
     $    '-pet' , '-pent'   , '-penthresh',         ! 14)
     $    '-sm ' , '-shift'  , '-shiftmom' ,         ! 15)
     $    '    ' , '-prtmom ', '-printmom' ,         ! 16)
     $    '    ' , '-rir'    , '-radrule'  ,         ! 17)
     $    '    ' , '-stdrad' , '-stdquad'  ,         ! 18)
     $    '    ' , '-logk'   , '-knowles'  ,         ! 19)
     $    '    ' , '-handy'  , '        '  ,         ! 20)
     $    '    ' , '-rcov'   , '-covrad'   ,         ! 21)
     $    '    ' , '-prtdma' , '-printdma' ,         ! 22)
     $    '-svc' , '-sclvcm' , '-scalevcm' ,         ! 23)