pysimm.apps.polymatic module

pysimm.apps.polymatic.lmps_cycle_npt_md(s, bonds, settings)

Runs LAMMPS npt cycle md for the Polymatic algorithm.

Parameters:

• s – System to minimize
• bonds – number of bond to be made
• settings – object containing Polymatic settings

Returns:

result from lmps.md

pysimm.apps.polymatic.lmps_cycle_nvt_md(s, bonds, settings)

Runs LAMMPS nvt cycle md for the Polymatic algorithm.

Parameters:

• s – System to minimize
• bonds – number of bond to be made
• settings – object containing Polymatic settings

Returns:

result from md()

pysimm.apps.polymatic.lmps_min(s, name, settings)

Runs LAMMPS minimization for the Polymatic algorithm.

Parameters:

• s – System to minimize
• name – name of simulation
• settings – object containing Polymatic settings

Returns:

result from minimize()

pysimm.apps.polymatic.lmps_step_md(s, bonds, attempt, settings)

Runs LAMMPS step md for the Polymatic algorithm.

Parameters:

• s – System to minimize
• bonds – number of bond to be made
• attempt – number of bonding attempt
• settings – object containing Polymatic settings

Returns:

result from md()

pysimm.apps.polymatic.pack(script, file_in, nrep, boxl, file_out)

Calls Polymatic random packing code

Parameters:

• script – name of packing script
• file_in – list of file names of reference molecules to pack
• nrep – list of number of monomers for each reference molecule
• boxl – length of one dimension of simulation box for random packing
• file_out – name of output file (packed system)

Returns:

output from perl code

pysimm.apps.polymatic.polymatic(script, file_in, file_out)

Calls Polymatic code. polym.in and types.txt are assumed to exist.

Parameters:

• script – name of Polymatic script
• file_in – initial system file name
• file_out – final system file name

Returns:

output from perl code

pysimm.apps.polymatic.run(settings)

Runs Polymatic algorithm.

Parameters:settings – object containing Polymatic settings Returns:(True/False, System)