def test_from_file(self):
self.lammps_ff_data.write_data_file(
os.path.join(test_dir, "lammps_ff_data.dat"))
lammps_ff_data = LammpsForceFieldData.from_file(
os.path.join(test_dir, "lammps_ff_data.dat"))
np.testing.assert_almost_equal(lammps_ff_data.atomic_masses,
self.lammps_ff_data.atomic_masses,
decimal=10)
np.testing.assert_almost_equal(lammps_ff_data.pair_coeffs,
self.lammps_ff_data.pair_coeffs,
decimal=10)
np.testing.assert_almost_equal(lammps_ff_data.bond_coeffs,
self.lammps_ff_data.bond_coeffs,
decimal=10)
np.testing.assert_almost_equal(lammps_ff_data.angle_coeffs,
self.lammps_ff_data.angle_coeffs,
decimal=10)
np.testing.assert_almost_equal(lammps_ff_data.atoms_data,
self.lammps_ff_data.atoms_data,
decimal=10)
np.testing.assert_almost_equal(lammps_ff_data.bonds_data,
self.lammps_ff_data.bonds_data,
decimal=10)
np.testing.assert_almost_equal(lammps_ff_data.angles_data,
self.lammps_ff_data.angles_data,
decimal=10)
self.assertEqual(str(lammps_ff_data), str(self.lammps_ff_data))
def from_file(name, filename, data_filename=None, is_forcefield=False):
"""
Read in the input settings from json file as ordereddict. Also
reads in the datafile if provided.
Note: with monty.serialization.loadfn the order of paramters in the
json file is not preserved
Args:
filename (string): name of the file with the lamps control
paramters
data_filename (string): path to the data file
is_forcefield (bool): whether the data file has forcefield and
topology info in it.
Returns:
DictLammpsInput
"""
with open(filename) as f:
config_dict = json.load(f, object_pairs_hook=OrderedDict)
lammps_data = None
if data_filename:
if is_forcefield:
lammps_data = LammpsForceFieldData.from_file(data_filename)
else:
lammps_data = LammpsData.from_file(data_filename)
return DictLammpsInput(name, config_dict, lammps_data)
def from_file(cls,
name,
input_template,
user_settings,
lammps_data=None,
data_filename="in.data",
is_forcefield=False):
"""
Returns LammpsInputSet from input file template and input data.
Args:
input_template (string): path to the input template file.
user_settings (dict): User lammps settings, the keys must
correspond to the keys in the template.
lammps_data (string/LammpsData/LammpsForceFieldData): path to the
data file or an appropriate object
data_filename (string): name of the the lammps data file.
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.
Returns:
LammpsInputSet
"""
lammps_input = LammpsInput.from_file(input_template, user_settings)
if isinstance(lammps_data, six.string_types):
if is_forcefield:
lammps_data = LammpsForceFieldData.from_file(lammps_data)
else:
lammps_data = LammpsData.from_file(lammps_data)
return cls(name,
lammps_input,
lammps_data=lammps_data,
data_filename=data_filename)
def test_from_file(self):
self.lammps_ff_data.write_data_file(
os.path.join(test_dir, "lammps_ff_data.dat"))
lammps_ff_data = LammpsForceFieldData.from_file(
os.path.join(test_dir, "lammps_ff_data.dat"))
np.testing.assert_almost_equal(lammps_ff_data.atomic_masses,
self.lammps_ff_data.atomic_masses,
decimal=10)
np.testing.assert_almost_equal(lammps_ff_data.pair_coeffs,
self.lammps_ff_data.pair_coeffs,
decimal=10)
np.testing.assert_almost_equal(lammps_ff_data.bond_coeffs,
self.lammps_ff_data.bond_coeffs,
decimal=10)
np.testing.assert_almost_equal(lammps_ff_data.angle_coeffs,
self.lammps_ff_data.angle_coeffs,
decimal=10)
np.testing.assert_almost_equal(lammps_ff_data.atoms_data,
self.lammps_ff_data.atoms_data,
decimal=10)
np.testing.assert_almost_equal(lammps_ff_data.bonds_data,
self.lammps_ff_data.bonds_data,
decimal=10)
np.testing.assert_almost_equal(lammps_ff_data.angles_data,
self.lammps_ff_data.angles_data,
decimal=10)
self.assertEqual(str(lammps_ff_data), str(self.lammps_ff_data))
def from_file(name,
filename,
data_obj=None,
data_file=None,
is_forcefield=False):
"""
Read in the input settings from json file as ordereddict. Also
reads in the datafile if provided.
Note: with monty.serialization.loadfn the order of paramters in the
json file is not preserved
Args:
filename (string): name of the file with the lamps control
paramters
data_obj (LammpsData): LammpsData object
data_file (string): name of the data file name
is_forcefield (bool): whether the data file has forcefield and
topology info in it.
Returns:
DictLammpsInput
"""
with open(filename) as f:
config_dict = json.load(f, object_pairs_hook=OrderedDict)
lammps_data = None
if data_file:
if is_forcefield:
lammps_data = LammpsForceFieldData.from_file(data_file)
else:
lammps_data = LammpsData.from_file(data_file)
if data_obj and isinstance(data_obj, LammpsData):
lammps_data = data_obj
return DictLammpsInput(name, config_dict, lammps_data)
def from_file(name, filename, lammps_data=None, data_filename="in.data",
user_lammps_settings={}, is_forcefield=False):
"""
Read in the input settings from json file as ordereddict.
Note: with monty.serialization.loadfn the order of paramters in the
json file is not preserved
Args:
filename (string): name of the file with the lamps control
paramters
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_lammps_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
Returns:
DictLammpsInput
"""
with open(filename) as f:
config_dict = json.load(f, object_pairs_hook=OrderedDict)
lammps_data = lammps_data
if isinstance(lammps_data, six.string_types):
if is_forcefield:
lammps_data = LammpsForceFieldData.from_file(lammps_data)
else:
lammps_data = LammpsData.from_file(lammps_data)
return DictLammpsInput(name, config_dict, lammps_data=lammps_data,
data_filename=data_filename,
user_lammps_settings=user_lammps_settings)
def from_file(cls, name, input_template, user_settings,
lammps_data=None, data_filename="in.data",
is_forcefield=False):
"""
Returns LammpsInputSet from input file template and input data.
Args:
name (str)
input_template (string): path to the input template file.
user_settings (dict): User lammps settings, the keys must
correspond to the keys in the template.
lammps_data (string/LammpsData/LammpsForceFieldData): path to the
data file or an appropriate object
data_filename (string): name of the the lammps data file.
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.
Returns:
LammpsInputSet
"""
user_settings["data_file"] = data_filename
lammps_input = LammpsInput.from_file(input_template, user_settings)
if isinstance(lammps_data, six.string_types):
if is_forcefield:
lammps_data = LammpsForceFieldData.from_file(lammps_data)
else:
lammps_data = LammpsData.from_file(lammps_data)
return cls(name, lammps_input, lammps_data=lammps_data,
data_filename=data_filename)
def __init__(self, data_file, trajectory_file, log_file="log.lammps",
is_forcefield=False):
self.data_file = data_file
self.trajectory_file = trajectory_file
self.log_file = log_file
self.lammps_log = LammpsLog(log_file)
if is_forcefield:
self.lammps_data = LammpsForceFieldData.from_file(data_file)
else:
self.lammps_data = LammpsData.from_file(data_file)
self._set_mol_masses_and_charges()
self._parse_trajectory()
def from_file(cls, name, filename, lammps_data=None, data_filename="in.data",
user_lammps_settings={}, is_forcefield=False):
"""
Reads lammps style and JSON style input files putting the settings in an ordered dict (config_dict).
Note: with monty.serialization.loadfn the order of paramters in the
json file is not preserved
Args:
filename (string): name of the file with the lamps control
paramters
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_lammps_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
Returns:
DictLammpsInput
"""
try:
with open(filename) as f:
config_dict = json.load(f, object_pairs_hook=OrderedDict)
except ValueError:
with open(filename, 'r') as f:
data = f.read().splitlines()
config_dict = OrderedDict()
for line in data:
if line and not line.startswith("#"):
spt_line = (line.split(None, 1))
if spt_line[0] in config_dict:
if isinstance(config_dict[spt_line[0]], list):
config_dict[spt_line[0]].append(spt_line[1])
else:
config_dict[spt_line[0]] = [config_dict[spt_line[0]], spt_line[1]]
else:
config_dict[spt_line[0]] = spt_line[1]
lammps_data = lammps_data
if isinstance(lammps_data, six.string_types):
if is_forcefield:
lammps_data = LammpsForceFieldData.from_file(lammps_data)
else:
lammps_data = LammpsData.from_file(lammps_data)
return cls(name, config_dict, lammps_data=lammps_data,
data_filename=data_filename,
user_lammps_settings=user_lammps_settings)
def test_lammps_wflow(self):
lammps_data = LammpsForceFieldData.from_file(self.data_file)
log_filename = "peo.log"
dump_filename = "peo.dump"
dcd_traj_filename = "peo.dcd"
timestep = 1 # in fmsec for 'real' units
n_timesteps = 1000
dump_freq = 50
T = [300, 300, 100.0] # start, end, damp
P = [0, 0, 100.0]
# override default settings read from the json file with these
user_settings = {"log": log_filename,
"timestep": timestep,
"run": n_timesteps,
"pair_style": "buck/coul/cut 15.0",
"pair_coeff": ["1 1 2649.6 0.2674 27.22",
"1 2 4320.0 0.2928 137.6",
"1 3 14176.0 0.2563 104.0",
"2 2 14976.0 0.3236 637.6",
"2 3 33702.4 0.2796 503.0",
"3 3 75844.8 0.2461 396.9"],
"thermo_style": "custom step time temp press pe ke etotal enthalpy fmax fnorm",
"fix": "NPT all npt temp {T[0]} {T[1]} {T[2]} iso {P[0]} {P[1]} {P[2]}".format(T=T, P=P),
"dump": [
"peodump all custom {} {} id type x y z ix iy iz mol".format(dump_freq, dump_filename),
"traj all dcd {} {}".format(dump_freq, dcd_traj_filename)]}
if not LAMMPS_CMD:
# fake run
lammps_bin = "cp ../../reference_files/peo.* ."
dry_run = True
else:
lammps_bin = LAMMPS_CMD
dry_run = False
wf = wf_from_input_template(self.input_template, lammps_data, "npt.data", user_settings,
is_forcefield=True, input_filename="lammps.inp", lammps_bin=lammps_bin,
db_file=">>db_file<<", dry_run=dry_run)
self.lp.add_wf(wf)
# run
rapidfire(self.lp, fworker=FWorker(env={"db_file": os.path.join(db_dir, "db.json")}))
d = self._get_task_collection().find_one()
self._check_run(d)
def test_to_and_from_file(self):
self.lammps_ff_data_1.write_data_file(
os.path.join(test_dir,"lammps_ff_data.dat"))
lammps_ff_data_2 = LammpsForceFieldData.from_file(
os.path.join(test_dir,"lammps_ff_data.dat"))
np.testing.assert_almost_equal(self.lammps_ff_data_1.bond_coeffs,
lammps_ff_data_2.bond_coeffs)
np.testing.assert_almost_equal(self.lammps_ff_data_1.pair_coeffs,
lammps_ff_data_2.pair_coeffs)
np.testing.assert_almost_equal(self.lammps_ff_data_1.angle_coeffs,
lammps_ff_data_2.angle_coeffs)
np.testing.assert_almost_equal(self.lammps_ff_data_1.dihedral_coeffs,
lammps_ff_data_2.dihedral_coeffs)
np.testing.assert_almost_equal(self.lammps_ff_data_1.atoms_data,
lammps_ff_data_2.atoms_data, decimal=10)
self.assertEqual(self.lammps_ff_data_1.bonds_data,
lammps_ff_data_2.bonds_data)
self.assertEqual(self.lammps_ff_data_1.angles_data,
lammps_ff_data_2.angles_data)
self.assertEqual(self.lammps_ff_data_1.dihedrals_data,
lammps_ff_data_2.dihedrals_data)
def from_file(name,
filename,
lammps_data=None,
data_filename="in.data",
user_lammps_settings={},
is_forcefield=False):
"""
Read in the input settings from json file as ordereddict.
Note: with monty.serialization.loadfn the order of paramters in the
json file is not preserved
Args:
filename (string): name of the file with the lamps control
paramters
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_lammps_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
Returns:
DictLammpsInput
"""
with open(filename) as f:
config_dict = json.load(f, object_pairs_hook=OrderedDict)
lammps_data = lammps_data
if isinstance(lammps_data, six.string_types):
if is_forcefield:
lammps_data = LammpsForceFieldData.from_file(lammps_data)
else:
lammps_data = LammpsData.from_file(lammps_data)
return DictLammpsInput(name,
config_dict,
lammps_data=lammps_data,
data_filename=data_filename,
user_lammps_settings=user_lammps_settings)
