atomate.lammps package

Submodules

atomate.lammps.database module

class atomate.lammps.database.LammpsCalcDb(host='localhost', port=27017, database='lammps', collection='tasks', user=None, password=None)

Bases: atomate.utils.database.CalcDb

__init__(host='localhost', port=27017, database='lammps', collection='tasks', user=None, password=None)
build_indexes(indexes=None, background=True)
reset()

atomate.lammps.drones module

class atomate.lammps.drones.LammpsDrone(additional_fields=None, use_full_uri=True, diffusion_params=None)

Bases: pymatgen.apps.borg.hive.AbstractDrone

__init__(additional_fields=None, use_full_uri=True, diffusion_params=None)
Args:

additional_fields (dict): use_full_uri (bool): diffusion_params (dict): parameters to the diffusion_analyzer. If specified a summary

of diffusion statistics will be added.
as_dict()
assimilate(path, input_filename, log_filename='log.lammps', is_forcefield=False, data_filename=None, dump_files=None)

Parses lammps input, data and log files and insert the result into the db.

Args:
path (str): path to the run folder input_filename (str): just the name of the input file log_filename (str): lammps log file name is_forcefield (bool): whether or not ot parse forcefield info data_filename (str): name of the data file dump_files ([str]): list of dump file names
Returns:
dict
classmethod from_dict(d)
generate_doc(dir_name, lmps_input, log, dumps)
Args:
dir_name (str): path to the run dir. lmps_input (LammpsInput/LammpsInputSet): log (LammpsLog): dumps ([(filename, LammpsDump)]): list of (dump filename, dump) tuples
Returns:
dict
get_valid_paths(path)
post_process(d, lmps_run)

Simple post processing.

Args:
d (dict) lmps_run (LammpsRun)
schema = {'root': {'state', 'output', 'last_updated', 'schema', 'dir_name', 'input', 'completed_at'}}

atomate.lammps.utils module

atomate.lammps.utils.use_fake_lammps(original_wf, ref_dir)

Module contents