LAMMPSTopology(inpMagiC=None, system=None, outfile="LAMMPS.data", hybrid=False, **kwargs)

Creates LAMMPS's topology file (LAMMPS.data) 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.

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 LAMMPS topology. Default: LAMMPS.data

dfset (DFset)

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

hybrid (bool)

: Add explicit bond-types to the topology file. Needed if few bond types are used, e.g. *table* and *zero*.

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

Examples:

MT.LAMMPSTopology('01.magic.inp', geometry='start.xmol')
MT.LAMMPSTopology(geometry='start.xmol', outfile='LAMMPS.data', 
                   mcmfile=['DMPC.CG', 'Chol.CG'],  NMolMType=[30, 30])