GALAMOSTTopology(eps, inpMagiC=None, system=None, outfile="topology.xml", pyfile='tables.inc.py', **kwargs)

Creates GALAMOST topology files (.xml, and .py) for the system

The system can be directly provided as a parameter, read from magic.inp file, or initiated from list of molecular types and number of corresponding molecules. For two latter cases *.mcm-files shall be present in the same directory.

The resulting topology is made of two files: XML-file, with system's geometry, atom types, atoms, bonds, angles. This file has same format as HOOMD-blue topology, so it can be directly opened by VMD. The second file is a python-script, which is assigning tabulated potential files to every particular interactions in the system. These files are shall be independently created using [PotsExport]PotsExport.

*eps (float)

: Dielectric permittivity, required for charge conversion into GALAMOST internal units

inpMagiC (str)

: Input file for MagiC.Core, used to define system's composition, i.e. list of moleculartypes and number of molecules of each type

system (system)

: the system topology to export

geometry (str)

: File with the starting geometry of the system in xmol format. If provided a corresponding .gro-file will be generated

outfile (str)

: file to write the topology. Default: 'topology.xml'

pyfile (str)

: File for writing python records for tabulated potentials. Default 'tables.inc.py'

dfset (DFset)

: Set of potentials/RDFs having SameAsBond-records. If provided, the topology will take into account SameAsBond records from the DFset

These two parameters only required if the system to be directly composed from mcm-files

mcmfile

: List of mcm-files defining molecular types

NMolMType

: List of number of molecules of each type

Example:
MT.GALAMOSTTopology(inpMagiC='01.magic.inp', geometry='start.xmol', eps=78.0)