atomate.lammps.firetasks package¶
Submodules¶
atomate.lammps.firetasks.glue_tasks module¶
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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.
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optional_params
= [u'calc_loc', u'calc_dir', u'filesystem', u'exclude_files']¶
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run_task
(fw_spec)¶
atomate.lammps.firetasks.parse_outputs module¶
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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:
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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']¶
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run_task
(fw_spec)¶
atomate.lammps.firetasks.run_calc module¶
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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’
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required_params
= [u'lammps_cmd', u'input_filename']¶
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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
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required_params
= [u'ref_dir']¶
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run_task
(fw_spec)¶
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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.
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optional_params
= [u'tolerance', u'filetype', u'control_params', u'output_file', u'copy_to_current_on_exit', u'site_property']¶
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required_params
= [u'molecules', u'packing_config', u'packmol_cmd']¶
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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']¶
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required_params
= [u'input_file', u'final_molecule', u'constituent_molecules', u'mols_number', u'box_size', u'forcefield', u'topologies', u'input_filename']¶
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run_task
(fw_spec)¶
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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
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optional_params
= [u'data_filename']¶
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required_params
= [u'lammps_input_set', u'input_filename']¶
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run_task
(fw_spec)¶