Computational materials science capabilities

Routine calculations

• Gaussian - MolMod/exam_gau
• VASP - MolMod/exam_vas
• LAMMPS - MolMod/exam_lam
• TINKER - MolMod/exam_tin
• MOPAC - MolMod/exam_mop
• Force fields - MolMod/exam_prm

Geometry

• Routine geometry calculations - MolMod/exam_Geometry
  • Partition molecule and identify fragments
  • Check and correct atom ordering for multiple files
  • Morph two molecules (e.g. to substitute a fragment)
• Refine CIF of molecular crystals - MolMod/exam_cif2xyz
• Convert XYZ to CIF - MolMod/exam_xyz2cif
• Convert PDB to XYZ or CIF - MolMod/exam_pdb2xyzcif

Complex calculations

• Statistical analysis of MD trajectories - MolMod/exam_Statistic
• Calculation and analysis of vibronic couplings - MolMod/exam_VibCoup
• Calculation of effective Hamiltonian for charge carriers and Frenkel excitons - MolMod/exam_Heff

Selected subroutines of MolMod package

• Filename encoding: DecodeFilename, DecodeMethod (DecodeBS, DecodeKgrid), DecodeState, DecodeTranslation (EncodeTranslation)
• Atomic data: AtomicData (tb_rcov, tb_rion, tb_rvdw), AtomicType (pg2Z)
• Molecular data: MolecularData (tb_solvents)
• Geometry:
  • Basics: Int2Cart (Cart2Int), ODR, ReduceLattice2D (ReduceLattice3D), CVP (CVP2, CVPfcc), ChangeDihedral, AliphaticDihedrals, SelectAtoms
  • Conversions: Atoms2Cell, SuperCell (FoldCells), cif2xyz (xyz2cif), cryst2M (M2cryst, ReshapeCell, DecodeAxes)
  • Connectivity: ConnectAtoms, RemoveAtoms, MolGraph, ChemDistance, Centroid, CooPolyhedra, ClassifyAtoms, GetTopology, Clusterize, ContactDistance, FragmentMolecule, JoinMol, AttachPoints
  • Symmetry: SymmetrizeCell, SymmetrizeAtoms, UnfoldBySymmetry
  • Matching: OrientBy2Vectors, CanonicOrientation, Superimpose, MatchMol (GuessPermutation)
  • Generators: Alkane
• Molecular file tools (ReadXXX/WriteXXX): XYZ, PDB, CIF, POSCAR, ReadAtomsCube, CombineXYZ
• Other file tools:
  • Parameterized geometry: ReadPAR (WritePAR)
  • Force fields: ReadPRM (WritePRM, IndexPRM, MergePRM)
• Wave-function:
  • Atomic orbitals and integrals: AO (AOangular, AOl, AOr, AOxyz, AOnormalize), GTOint, GTOreduce (GTOadd), GTOexpand, Hybrid, RotationM4AO
  • Molecular orbitals: LocalizeMO, MatchOrbitals
  • Basis sets: InitBS (ReadBS, CheckBSnorm), UnfoldBS
  • File tools: WriteMGF, CompressMGF
• Quantum chemistry:
  • Vibrations: VibrationalModes, MatchVibrations
  • Vibronic effects: VibronicCouplings, TransSp, SingleQMode
  • Electronic couplings: MultimerH
  • Other chemistry: ChemBalance (EnergyBalance)
• Output: printAO, plotE, plot3Dgrid, plotMol, simplifySVG, CompressEigenvectors
• External programs input and run: WriteAtom, WriteMethod (WriteBS, WriteEBS), WriteInput, WriteScript, Run, CleanUp, SubmitJob (DownloadJob), AFMorder, showkgrids
• External programs output: ReadAtoms, ReadOutput, ReadExcStates, ReadVibrations, ReadNBO, OptimCurve, GetTiming, ReadDump, ReadAUX, CompressAUX, ReadRawMatrixElement, ReadDOS, getv (getvlbl)
• Materials science: MaterialsData, IdentifyMolecule (MolFingerprint), EOSfit