transition_sampling package

Subpackages

• transition_sampling.algo package
  • Submodules
  • transition_sampling.algo.acceptors module
  • transition_sampling.algo.aimless_shooting module
  • Module contents
• transition_sampling.colvar package
  • Submodules
  • transition_sampling.colvar.plumed_driver module
  • Module contents
• transition_sampling.engines package
  • Subpackages
    • transition_sampling.engines.cp2k package
      • Submodules
      • transition_sampling.engines.cp2k.CP2K_engine module
      • transition_sampling.engines.cp2k.CP2K_inputs module
      • transition_sampling.engines.cp2k.CP2K_outputs module
      • Module contents
    • transition_sampling.engines.gromacs package
      • Submodules
      • transition_sampling.engines.gromacs.mdp module
      • Module contents
  • Submodules
  • transition_sampling.engines.abstract_engine module
  • transition_sampling.engines.plumed module
  • Module contents
• transition_sampling.likelihood package
  • Submodules
  • transition_sampling.likelihood.likelihood_max module
  • transition_sampling.likelihood.optimization module
  • Module contents
• transition_sampling.util package
  • Subpackages
    • transition_sampling.util.atomic_masses package
      • Module contents
  • Submodules
  • transition_sampling.util.periodic_table module
  • transition_sampling.util.xyz module
  • Module contents

Submodules

transition_sampling.driver module

transition_sampling.driver.execute(inputs)

Run from the yml input parsed as a dictionary

Parameters

inputs (dict) – yml file in dictionary format

transition_sampling.driver.main()

transition_sampling.driver.parse_aimless(aimless_inputs, engine)

Validate aimless_inputs section of input file and create the Driver.

Defines global variables for xyz and csv to be used in later sections if not explicitly set.

Parameters

• aimless_inputs (dict) – The “aimless_inputs” dictionary of the input file

• engine (AbstractEngine) – The corresponding AbstractEngine created from the “engine_inputs” section

Return type

AimlessShootingDriver

Returns

The AimlessShootingDriver that is ready to be run.

transition_sampling.driver.parse_colvar(colvar_inputs)

Validate colvar_inputs section of input file.

If xyz and csv files are not explicitly in the inputs, checks the globals set above, then errors if those are not set.

Parameters

colvar_inputs (dict) – The “engine_inputs” dictionary of the input file

Return type

None

transition_sampling.driver.parse_engine(engine_inputs)

Validate engine_inputs section of input file and create the engine.

Parameters

engine_inputs (dict) – The “engine_inputs” dictionary of the input file

Return type

AbstractEngine

Returns

The AbstractEngine representation of this input section

transition_sampling.driver.parse_likelihood(likelihood_inputs)

Validate likelihood_inputs section of input file.

If colvar and csv files are not explicitly in the inputs, checks the globals set above, then errors if those are not set.

Parameters

likelihood_inputs (dict) – The “likelihood_inputs” dictionary of the input file

Return type

None

transition_sampling.driver.read_and_run(input_yml)

Parse the yml input and run

Parameters

input_yml (str) – Path to the yml file to parse

transition_sampling.driver.run_aimless(md_inputs)

Validate and run the aimless shooting section

Parameters

md_inputs (dict) – The “md_inputs” dictionary of the input file

Return type

None

transition_sampling.driver.run_colvar(colvar_inputs)

Validate and run the colvar section

Parameters

colvar_inputs (dict) – The “colvar_inputs” dictionary of the input file

Return type

None

transition_sampling.driver.run_likelihood(likelihood_inputs)

Validate and run the likelihood section

Parameters

likelihood_inputs (dict) – The “likelihood_inputs” dictionary of the input file

Return type

None

Module contents