def get_wf(job_name,
lammps_input_set,
input_filename="lammps.inp",
lammps_bin="lammps",
db_file=None,
dry_run=False):
"""
Returns workflow that writes lammps input/data files, runs lammps and inserts to DB.
Args:
job_name: job name
lammps_input_set (DictLammpsInput): lammps input
input_filename (string): input file name
lammps_bin (string): path to the lammps binary
db_file (string): path to the db file
dry_run (bool): for test purposes, decides whether or not to run the lammps binary
with the input file.
Returns:
Workflow
"""
task1 = WriteLammpsFromIOSet(lammps_input_set=lammps_input_set,
input_file=input_filename)
if dry_run:
lammps_cmd = lammps_bin
else:
lammps_cmd = lammps_bin + " -in " + input_filename
task2 = RunLammpsDirect(lammps_cmd=lammps_cmd)
task3 = LammpsToDBTask(lammps_input=lammps_input_set, db_file=db_file)
fw1 = Firework([task1, task2, task3], name=job_name)
return Workflow([fw1], name=job_name)
def __init__(self, lammps_input_set, input_filename="lammps.in", data_filename="lammps.data",
lammps_cmd="lammps", db_file=None, parents=None, name="LammpsFW",
log_filename="log.lammps", dump_filename=None, **kwargs):
"""
write lammps inputset, run, and store the output.
Args:
lammps_input_set (DictLammpsInput): lammps input set
input_filename (str): input file name
data_filename (str): data file name
lammps_cmd (str): command to run lammps (skip the input file).
e.g. 'mpirun -n 8 lmp_mpi'
db_file (str): path to file specifying db credentials to place output parsing.
parents ([Fireworks)]: parents of this particular Firework.
name (str): descriptive name for lammps simulation
log_filename (str)
dump_filename (str)
\*\*kwargs: other kwargs that are passed to Firework.__init__.
"""
tasks = [
WriteInputFromIOSet(lammps_input_set=lammps_input_set, input_filename=input_filename,
data_filename=data_filename),
RunLammpsDirect(lammps_cmd=lammps_cmd, input_filename=input_filename),
LammpsToDB(input_filename=input_filename, data_filename=data_filename,
log_filename=log_filename, dump_filename=dump_filename,
db_file=db_file, additional_fields={"task_label": name})
]
super(LammpsFW, self).__init__(tasks, parents=parents, name=name, **kwargs)
def __init__(self, input_file, final_molecule, forcefield, box_size, topologies=None,
constituent_molecules=None, mols_number=None, user_settings=None,
ff_site_property=None, input_filename="lammps.in", data_filename="lammps.data",
lammps_cmd="lammps", db_file=None, parents=None, log_filename="log.lammps",
dump_filenames=None, name="LammpsFFFW", **kwargs):
"""
Write lammps input from forcefield and topology, run lammps, store results. Can be used
with RunPackmol firework.
Args:
input_file (str): path to lammps input(or template) file.
final_molecule (str/Molecule): either path to the moelcule of Molecule object.
forcefield (ForceField): pymatgen.io.lammps.force_field.ForceField object
box_size (list): list of list of low and high values for each dimension [[xlow, xhigh], ...]
topologies ([Topology]): list of pymatgen.io.lammps.topology.Topology objects, one for
each constituent molecule.
constituent_molecules ([Molecule]): list of Molecule objects that make up the final_molecule
mols_number (list): list of number of each constituent moelcule.
user_settings (dict):
ff_site_property (str): the site property used for forcefiled mapping
input_filename (str): name of the input file to be written
data_filename (str):name of the data file to be written
lammps_cmd (str): lammps command run (without the input file)
db_file (str): path to the db settings
parents (list): list of Fireworks
log_filename (str): lammps log file name
dump_filenames (str): list of dump files
name (str): firework name
**kwargs:
"""
user_settings = user_settings or {}
constituent_molecules = constituent_molecules or [final_molecule]
mols_number = mols_number or [1]
topologies = topologies or Topology.from_molecule(final_molecule, ff_map=ff_site_property)
tasks = [
WriteInputFromForceFieldAndTopology(input_file=input_file, final_molecule=final_molecule,
constituent_molecules=constituent_molecules,
mols_number=mols_number, forcefield=forcefield,
topologies=topologies, input_filename=input_filename,
user_settings=user_settings, data_filename=data_filename,
ff_site_property=ff_site_property, box_size=box_size),
RunLammpsDirect(lammps_cmd=lammps_cmd, input_filename=input_filename),
LammpsToDB(input_filename=input_filename, data_filename=data_filename,
log_filename=log_filename, dump_filenames=dump_filenames,
db_file=db_file, additional_fields={"task_label": name})
]
super(LammpsForceFieldFW, self).__init__(tasks, parents=parents, name=name, **kwargs)