def setUpClass(cls):
cls.json_input = DictLammpsInput.from_file(
"NVT",
os.path.join(test_dir, "NVT.json"),
data_filename=os.path.join(test_dir, "nvt.data"),
is_forcefield=True)
cls.lammps_input = DictLammpsInput.from_file(
"peptide",
os.path.join(test_dir, "in.peptide"),
lammps_data=os.path.join(test_dir, "data.peptide"),
data_filename="data.peptide",
is_forcefield=True)
def wf_from_input_template(input_template_file, lammps_data, data_filename, user_settings,
is_forcefield=False, input_filename="lammps.inp", lammps_bin="lammps",
db_file=None, dry_run=False):
"""
Returns workflow where the input file parameters are set from the give json template file.
Args:
input_template_file: json template input file
lammps_data (string/LammpsData/LammpsForceFieldData): path to the data file or
an appropriate object
data_filename (string): name of the the lammps data file
user_settings (dict): User lammps settings
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
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
"""
wf_name = "LAMMPS Wflow from input template {}".format(input_template_file)
lammps_dict_input = DictLammpsInput.from_file(wf_name, input_template_file, lammps_data=lammps_data,
data_filename=data_filename,
user_lammps_settings=user_settings,
is_forcefield=is_forcefield)
return get_wf(wf_name, lammps_dict_input, input_filename=input_filename, lammps_bin=lammps_bin,
db_file=db_file, dry_run=dry_run)
def wf_from_input_template(input_template_file,
lammps_data,
data_filename,
user_settings,
is_forcefield=False,
input_filename="lammps.inp",
lammps_bin="lammps",
db_file=None,
dry_run=False):
"""
Returns workflow where the input file parameters are set from the give json template file.
Args:
input_template_file: json template input file
lammps_data (string/LammpsData/LammpsForceFieldData): path to the data file or
an appropriate object
data_filename (string): name of the the lammps data file
user_settings (dict): User lammps settings
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
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
"""
wf_name = "LAMMPS Wflow from input template {}".format(input_template_file)
lammps_dict_input = DictLammpsInput.from_file(
wf_name,
input_template_file,
lammps_data=lammps_data,
data_filename=data_filename,
user_lammps_settings=user_settings,
is_forcefield=is_forcefield)
return get_wf(wf_name,
lammps_dict_input,
input_filename=input_filename,
lammps_bin=lammps_bin,
db_file=db_file,
dry_run=dry_run)
def setUpClass(cls):
cls.lammps_input = DictLammpsInput.from_file(
"NVT",
os.path.join(test_dir, "NVT.json"),
data_file=os.path.join(test_dir, "nvt.data"),
is_forcefield=True)
def setUpClass(cls):
cls.lammps_input = DictLammpsInput.from_file(
"NVT", os.path.join(test_dir, "NVT.json"),
data_filename=os.path.join(test_dir, "nvt.data"),
is_forcefield=True)
