matmethods.lammps.firetasks package

Submodules

matmethods.lammps.firetasks.parse_outputs module

class matmethods.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 = [u'calc_dir', u'calc_loc', u'diffusion_params', u'db_file']

required_params = [u'lammps_input']

run_task(fw_spec)

matmethods.lammps.firetasks.run_calc module

class matmethods.lammps.firetasks.run_calc.RunLammpsCustodian(*args, **kwargs)

Bases: fireworks.core.firework.FireTaskBase

class matmethods.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 = [u'lammps_cmd']

run_task(fw_spec)

class matmethods.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 = [u'tolerance', u'filetype', u'control_params', u'output_file']

required_params = [u'molecules', u'packing_config']

run_task(fw_spec)

matmethods.lammps.firetasks.write_inputs module

class matmethods.lammps.firetasks.write_inputs.WritelammpsInputFromDictInput(*args, **kwargs)

Bases: fireworks.core.firework.FireTaskBase

Writes LAMMPS Input files(data file and the control parameters file) from DictLammpsInput.

required_params:

lammps_dict_input (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 = [u'data_file']

required_params = [u'lammps_dict_input', u'input_file']

run_task(fw_spec)

Module contents