atomate.lammps.firetasks package

Submodules

atomate.lammps.firetasks.glue_tasks module

class atomate.lammps.firetasks.glue_tasks.CopyPackmolOutputs(*args, **kwargs)

Bases: atomate.common.firetasks.glue_tasks.CopyFiles

Copy files from a previous run directory to the current directory. Note: must specify either “calc_loc” or “calc_dir” to indicate the directory

containing the files to copy.

Optional params:

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.

calc_dir (str): path to dir that contains VASP output files. filesystem (str): remote filesystem. e.g. username@host exclude_files (list): list fo filenames to be excluded when copying.

NOte: by default nothing is excluded.

optional_params = [u'calc_loc', u'calc_dir', u'filesystem', u'exclude_files']

run_task(fw_spec)

atomate.lammps.firetasks.parse_outputs module

class atomate.lammps.firetasks.parse_outputs.LammpsToDB(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Enter a LAMMPS calculation into the database.

required_params:

input_filename (str)

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

db_file (str): path to file containing the database credentials.

Supports env_chk. Default: write data to JSON file.

fw_spec_field: data_filename: log_filename: dump_filenames: diffusion_params additional_fields:

optional_params = [u'calc_dir', u'calc_loc', u'db_file', u'fw_spec_field', u'data_filename', u'log_filename', u'dump_filenames', u'diffusion_params', u'additional_fields']

required_params = [u'input_filename']

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): lammps command to run sans the input file name.

e.g. ‘mpirun -n 4 lmp_mpi’

required_params = [u'lammps_cmd', u'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 = [u'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 = [u'tolerance', u'filetype', u'control_params', u'output_file', u'copy_to_current_on_exit', u'site_property']

required_params = [u'molecules', u'packing_config', u'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 = [u'data_filename', u'user_settings', u'ff_site_property']

required_params = [u'input_file', u'final_molecule', u'constituent_molecules', u'mols_number', u'box_size', u'forcefield', u'topologies', u'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 = [u'data_filename']

required_params = [u'lammps_input_set', u'input_filename']

run_task(fw_spec)

Module contents