pysimm.apps.polymatic

Module Contents

Functions

pack(script, file_in, nrep, boxl, file_out)

pysimm.apps.polymatic.pack

polymatic(script, file_in, file_out)

pysimm.apps.polymatic.polymatic

run(settings)

pysimm.apps.polymatic.run

lmps_min(s, name, settings)

pysimm.apps.polymatic.lmps_min

lmps_step_md(s, bonds, attempt, settings)

pysimm.apps.polymatic.lmps_step_md

lmps_cycle_nvt_md(s, bonds, settings)

pysimm.apps.polymatic.lmps_cycle_nvt_md

lmps_cycle_npt_md(s, bonds, settings)

pysimm.apps.polymatic.lmps_cycle_npt_md

Attributes

rappture

rappture

pysimm.apps.polymatic.rappture = True[source]
pysimm.apps.polymatic.rappture = False[source]
pysimm.apps.polymatic.pack(script, file_in, nrep, boxl, file_out)[source]

pysimm.apps.polymatic.pack

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)[source]

pysimm.apps.polymatic.polymatic

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)[source]

pysimm.apps.polymatic.run

Runs Polymatic algorithm.

Parameters

settings – object containing Polymatic settings

Returns

(True/False, System)

pysimm.apps.polymatic.lmps_min(s, name, settings)[source]

pysimm.apps.polymatic.lmps_min

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)[source]

pysimm.apps.polymatic.lmps_step_md

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.lmps_cycle_nvt_md(s, bonds, settings)[source]

pysimm.apps.polymatic.lmps_cycle_nvt_md

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_cycle_npt_md(s, bonds, settings)[source]

pysimm.apps.polymatic.lmps_cycle_npt_md

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