atomate.lammps.firetasks package

Submodules

atomate.lammps.firetasks.glue_tasks module

atomate.lammps.firetasks.parse_outputs module

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): lammps command to run sans the input file name.
e.g. ‘mpirun -n 4 lmp_mpi’
required_params = ['lammps_cmd', 'input_filename']
run_task(fw_spec)
class atomate.lammps.firetasks.run_calc.RunLammpsFake(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Pretend run i.e just copy files from existing run dir.

Required params:
ref_dir (str): path to the reference dir
required_params = ['ref_dir']
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 (dict): packmol control parameters dictionary. Basically all parameters other

than structure/atoms

output_file (str): output file name. The extension will be adjusted according to the filetype copy_to_current_on_exit (bool): whether or not to copy the packed molecule output file to

the current directory.

site_property (str): the specified site property will be restored for the final Molecule object.

optional_params = ['tolerance', 'filetype', 'control_params', 'output_file', 'copy_to_current_on_exit', 'site_property']
required_params = ['molecules', 'packing_config', 'packmol_cmd']
run_task(fw_spec)

atomate.lammps.firetasks.write_inputs module

class atomate.lammps.firetasks.write_inputs.WriteInputFromForceFieldAndTopology(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

optional_params = ['data_filename', 'user_settings', 'ff_site_property']
required_params = ['input_file', 'final_molecule', 'constituent_molecules', 'mols_number', 'box_size', 'forcefield', 'topologies', 'input_filename']
run_task(fw_spec)
class atomate.lammps.firetasks.write_inputs.WriteInputFromIOSet(*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 (LammpsInputSet) input_file (string): name of the file to which the input params will be written
optional_params:
data_filename (string): if specified the data file will be renamed
optional_params = ['data_filename']
required_params = ['lammps_input_set', 'input_filename']
run_task(fw_spec)

Module contents