atomate.lammps.firetasks package¶
Submodules¶
atomate.lammps.firetasks.parse_outputs module¶
-
class
atomate.lammps.firetasks.parse_outputs.
LammpsToDBTask
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Enter a LAMMPS run into the database.
- Require params:
- lammps_input (DictLammpsInput)
- Optional params:
- calc_dir (str): path to dir (on current filesystem) that contains LAMMPS
- output files. Default: use current working directory.
- calc_loc (str OR bool): if True will set most recent calc_loc. If str
- search for the most recent calc_loc with the matching name
- diffusion_params (dict): parameters to the diffusion_analyzer. If specified a summary
- of diffusion statistics will be added.
- db_file (str): path to file containing the database credentials.
- Supports env_chk. Default: write data to JSON file.
-
optional_params
= ['calc_dir', 'calc_loc', 'diffusion_params', 'db_file']¶
-
required_params
= ['lammps_input']¶
-
run_task
(fw_spec)¶
atomate.lammps.firetasks.run_calc module¶
-
class
atomate.lammps.firetasks.run_calc.
RunLammpsDirect
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Run LAMMPS directly (no custodian).
- Required params:
- lammsps_cmd (str): full command string
-
required_params
= ['lammps_cmd']¶
-
run_task
(fw_spec)¶
-
class
atomate.lammps.firetasks.run_calc.
RunPackmol
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Run packmol.
- Required params:
molecules (list): list of constituent molecules(Molecule objects) packing_config (list): list of dict config settings for each molecule in the
molecules list. eg: config settings for a single moelcule [{“number”: 1, “inside box”:[0,0,0,100,100,100]}]- Optional params:
tolerance (float): packmol tolerance filetype (string): input/output structure file type control_params: packmol control parameters dictionary. Basically all parameters other
than structure/atomsoutput_file: output file name. The extension will be adjusted according to the filetype
-
optional_params
= ['tolerance', 'filetype', 'control_params', 'output_file']¶
-
required_params
= ['molecules', 'packing_config']¶
-
run_task
(fw_spec)¶
atomate.lammps.firetasks.write_inputs module¶
-
class
atomate.lammps.firetasks.write_inputs.
WriteLammpsFromIOSet
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Writes LAMMPS Input files(data file and the control parameters file) from DictLammpsInput.
- required_params:
- lammps_input_set (DictLammpsInput) input_file (string): name of the file to which the input params will be written
- optional_params:
- data_file (string): if specified the data file will be renamed
-
optional_params
= ['data_file']¶
-
required_params
= ['lammps_input_set', 'input_file']¶
-
run_task
(fw_spec)¶