transition_sampling.colvar package

Submodules

transition_sampling.colvar.plumed_driver module

class transition_sampling.colvar.plumed_driver.PlumedDriver(plumed_cmd)

Bases: object

Interfaces with the Plumed Driver to calculate CVs.

Parameters

plumed_cmd (str) – Command to run plumed with from command line. E.g. “plumed” or “mpirun plumed”

run(plumed_file, xyz_file, csv_file, colvar_output, length_units='A')

Run the plumed driver with the given xyz file.

All CVs given a label in plumed_file will be printed to the output colvar_file. This print is added automatically, and any other user. defined prints will still occur.

Parameters

  • plumed_file (str) – Path to plumed input file containing the CVs to calculate

  • xyz_file (str) – Path to xyz file created by aimless shooting

  • csv_file (str) – Path to the csv file corresponding to xyz_file generated by aimless shooting

  • colvar_output (str) – Name of the file for calculated CVs to be printed to

  • length_units (str) – plumed string representation of the xyz units, passed directly to plumed.

Return type

None

Module contents