atomate.lammps.workflows package

Submodules

atomate.lammps.workflows.core module

atomate.lammps.workflows.core.get_packmol_wf(input_file, user_settings, constituent_molecules, packing_config, forcefield, final_box_size, topologies=None, ff_site_property=None, tolerance=2.0, filetype='xyz', control_params=None, lammps_cmd='lmp_serial', packmol_cmd='packmol', dump_filenames=None, db_file=None, name='Packmol Lammps Wflow')

Returns workflow that uses Packmol to pack the constituent molecules into the given configuration and then run lammps on the final packed molecule for the given list of user_settings.

Args:

input_file (str): path to lammps input(or template) file. user_settings ([dict] or dict): list of settings dict. if the input_file is a tempalte file

then each dict contains the key value pairs for the template file.

constituent_molecules ([Molecules]): list of pymatgen Molecule objects packing_config ([dict]): list of configuration dictionaries, one for each constituent molecule. forcefield (ForceField): pymatgen.io.lammps.forcefield.ForceField object final_box_size ([list]): list of list of low and high values for each dimension [[xlow, xhigh], …] topologies ([Topology]): list of Topology objects. If not given, will be set from the

topology of the constituent molecules.

ff_site_property (str): the name of the site property used for forcefield mapping tolerance (float): packmol tolerance filetype (str): packmol i/o file type. control_params (dict): packmol control params lammps_cmd (string): lammps command to run (skip the input file). packmol_cmd (string): path to packmol bin dump_filenames ([str]): list of dump file names db_file (string): path to the db file. name (str): workflow name

Returns:
Workflow
atomate.lammps.workflows.core.get_wf_basic(input_file, user_settings, lammps_data=None, input_filename='lammps.in', is_forcefield=False, lammps_cmd='lmp_serial', dump_filenames=None, db_file=None, name='LAMMPS Wflow')

Returns basic lammps workflow. This is more useful if the input_file is template file with the corresponding settings defined in user_settings

Args:
input_file (str): path to lammps input file.
Note: It could be a template file too, then the user_settings must be set.
user_settings ([dict] or dict): list of settings dict. if the input_file is a tempalte file
then each dict contains the key value pairs for the template file.
lammps_data (string/LammpsData/LammpsForceFieldData): path to the data file or
an appropriate object.
input_filename (string): input file name. This is the name of the input file passed to the
lammps binary.
is_forcefield (bool): whether the data file has forcefield and topology info in it.
This is required only if lammps_data is a path to the data file instead of a data object.

lammps_cmd (string): lammps command to run (skip the input file). dump_filenames ([str]): list of dump file names db_file (string): path to the db file. name (str): workflow name

Returns:
Workflow

Module contents