pysimm.apps.polymatic
¶
Module Contents¶
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pysimm.apps.polymatic.
rappture
= False[source]
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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
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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
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pysimm.apps.polymatic.
run
(settings)[source]¶ pysimm.apps.polymatic.run
Runs Polymatic algorithm.
Parameters: settings – object containing Polymatic settings Returns: (True/False, System
)
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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()
- s –
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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()
- s –
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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()
- s –
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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
- s –