atomate.lammps package¶
Subpackages¶
Submodules¶
atomate.lammps.database module¶
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class
atomate.lammps.database.
LammpsCalcDb
(host='localhost', port=27017, database='lammps', collection='tasks', user=None, password=None)¶ Bases:
atomate.utils.database.CalcDb
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__init__
(host='localhost', port=27017, database='lammps', collection='tasks', user=None, password=None)¶
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build_indexes
(indexes=None, background=True)¶
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reset
()¶
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atomate.lammps.drones module¶
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class
atomate.lammps.drones.
LammpsDrone
(additional_fields=None, use_full_uri=True, diffusion_params=None)¶ Bases:
pymatgen.apps.borg.hive.AbstractDrone
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__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.
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as_dict
()¶
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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
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classmethod
from_dict
(d)¶
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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
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get_valid_paths
(path)¶
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post_process
(d, lmps_run)¶ Simple post processing.
- Args:
- d (dict) lmps_run (LammpsRun)
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schema
= {'root': {'input', 'completed_at', 'schema', 'output', 'dir_name', 'state', 'last_updated'}}¶
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