Description of MolMod package

by Andriy Zhugayevych

MolMod is a molecular modelling package.

If you have comments, suggestions, or have found a bug, please email me.

Tested for Maple 17 on Windows 7 and 10.

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.

Installation

• Download source files MolMod.zip, unzip to any location, open install.mw and follow the instructions.
• Windows users: If failed to install or you don't need the source, download MolMod_lib.zip and unzip to Maple library folder MapleXX/lib.
• Experienced users: the package can be initialized by reading MolMod.ini with Maple "read" command.
• If not exist, create MolMod_Setup.ini in UserConfigurationFolder (see its definition here). Use MolMod_Setup.ini as a template.
• The documentation is built into the Maple Help system. Individual help pages are also available as individual mw-files.

Credits

• Sergey Matveev
• 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.