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/atoms

output_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)

Module contents