MolMod package

MolMod is a molecular and crystal modeling package.

Download source or library or ini-file, and sample configuration file. Tested for Maple 17.

Prerequisite packages: BasicTools, FiniteGroups, SSH

Highlighted features

• Use the same commands to process input/output of various programs (Gaussian, VASP, MOPAC, LAMMPS etc).
• Read/write of commonly used formats for geometry and wave-function.
• Comprehensive support of symmetry: e.g. you can find all symmetry inequivalent elements of tight binding Hamiltonian.
• Computational geometry: matching/morphing two systems of atoms, coordination polyhedra, fragmentation, atom type classification etc.
• Quantum chemistry: vibrationally resolved electronic spectra, coarse graining of electronic Hamiltonian.
• Ready-to-use notebooks for most common tasks in computational materials science including batch calculations.

Documentation

• Notations and notes
• Setup
• Auxiliary routines
BestProgram,TypeMethod,
NormalizeCharges,LabelAtoms,SaveTempData
• Decorders
DecodeFormula,EncodeFormula,
DecodeTranslation,DecodeTranslation1,EncodeTranslation,EncodeTranslation1,
DecodeState,DecodeFilename,DecodeMethod,DecodeBS,DecodeKgrid
• Atomic data
AtomicNumber,ElementSymbol,ElementName,AtomicType,pg2Z,AtomMass,
tb_rcov,tb_rion,tb_rvdw,
GetASD
• Molecular data
tb_solvents
• Geometry: Coordinates
len,angle,dihedral,len2,angle2,dihedral2,
Get4th,GetInternals,Int2Cart,Cart2Int
• Geometry: Lattices
ReduceLattice2D, ReduceLattice3D, CVP, CVP2, CVPfcc
• Geometry: Unit cells
Atoms2Cell,SuperCell,FoldCells,
cryst2M,M2cryst,ReshapeCell,DecodeAxes,DecodeAxes2
• Geometry: Connectivity
ConnectAtoms,RemoveAtoms,MolGraph,ChemDistance,
Clusterize,ContactDistance,FragmentMolecule,FragmentPlot,
CooPolyhedra,CooPolyhedron,SelectAtoms,
ClassifyAtoms,atype_mm3,atype_opls,GetTopology,HasTopology
• Geometry: Orient
ODR,Centroid,OrientBy2Vectors,CanonicOrientation
• Geometry: Match
Superimpose,GuessPermutation,MatchMol
• Geometry: Modify
ChangeDihedral,JoinMol,AttachPoints,
AliphaticDihedrals,Alkane,SortAlkane
• Geometry: Symmetry
SymmetrizeCell,SymmetrizeAtoms,UnfoldBySymmetry
• Wave-function: Atomic orbitals
AOangular,AOl,AOt,AOr,AOxyz,AOnormalize
• Wave-function: GTO
GTOreduce,GTOadd,GTOexpand1,GTOexpand3,GTOexpand,
GTOint1,GTOint2,GTOint3,GTOint4,GTOint42,GTOoverlap,GTOoverlap2
• Wave-function: Basis sets
shell2LtN,LtN2shell,UnfoldBS,FoldBS,ReadBS,RewriteBasis
• Wave-function: Transform
Hybrid,RotationM4AO,TransformMO
• Wave-function: Match
MatchMO
• Wave-function: Localize
LocalizeMO,MultimerH
• Wave-function: Visualize
WriteMGF,CompressMGF
• File tools: Geometry
ReadXYZ,WriteXYZ,CombineXYZ,
ReadCIF,WriteCIF,cif2xyz,xyz2cif,
ReadPOSCAR,WritePOSCAR,ReadPDB,WritePDB,
ReadAtomsCube
• File tools: GROMACS geometry
ReadGRO
• File tools: Force field parameters
IndexPRM,ReadPRM,WritePRM,MergePRM
• File tools: Structural models
ReadPAR,WritePAR
• File tools: Hamiltonians
ReadTBH
• Chemistry
ChemBalance,EnergyBalance
• Quantum chemistry: Wave-function
showkgrids,DetermineBandGap,AFMorder
• Quantum chemistry: Vibrations
VibrationalModes,MatchVibrations
• Quantum chemistry: Vibronic couplings
VibronicCouplings,TransSp,CoarsegrainSp,fTransSp,
GenerateES,SingleQMode,SingleQModeFit
• Materials science
EOSfit
• Output
PrintSpherPolynom,pqrlabel,SPindex,SPDindex,printAO,
plotE,plot3Dgrid,plotMol,acolor_azh,acolor_azh2,asize_azh,
simplifySVG,CompressEigenvectors,DomainMO,printMO
• External programs input
WriteAtom,WriteMethod,WriteBS,WriteEBS,
WriteInput,WriteScript,Run,CleanUp,
SubmitJob,DownloadJob
• External programs output
WhatProgram,IsNormalTermination,GetTiming,
ReadOutput,LoadMO,
ReadAtoms,ReadExcStates,ReadVibrations,
ReadDOS,ReadNBO,ReadRawMatrixElement,
CorrectSymmetryOrientation,OptimCurve,
ReadDump,WriteDump,ReadAUX,CompressAUX,
getv,getvlbl
• MOPAC output
ReadFockM
• Materials data
MaterialsData,MaterialsTable,MaterialsIndex,
IdentifyMolecule,MolFingerprint,MolSearchInit

Notebooks of examples and gray-box solutions

• exam_{gau,lam,mop,tin,vas}.mw – routine calculations in the corresponding programs.
• exam_Geometry.mw – routine geometrical calculations.
• exam_Statistic.mw – statistical analysis of MD trajectories.
• exam_VibCoup.mw – calculation and analysis of vibronic couplings.
• exam_cif2xyz.mw – clean up CIF for molecular crystal.
• exam_xyz2cif.mw – convert XYZ to CIF.
• exam_pdb2xyzcif.mw – convert PDB-file to XYZ or CIF.
• exam_prm.mw – force field explorer.
• exam_fitESPmodel.mw – fit electrostatic model.
• exam_BinFileFormats.mw – binary file formats used in MolMod.

Acknowledgements

• Sergey Matveev – translation to Python of some commands.
• Artem Naumov – force fields.
• Sergei Tretiak – vibronic couplings.

Requires implementation

• Read/write/manipulate wave-function (for VASP see Fortran code here)
• WritePAR command
• WriteMGF for Slater orbitals
• Canonic fundamental domain (similar to CanonicOrientation command)
• SymmetrizeCell for subperiodic groups
• Convert point group symmetry to MOPAC input format
• A program (f90 or any C) which takes a LAMMPS binary dump file and creates md-file in this binary format. This program should run autonomously locally or remotely. See also ReadDump/WriteDump commands, lammps/.../tools/binary2txt.cpp, Gaussian readdump for examples.