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/atomsoutput_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)¶