def test_lammpstraj_get_step_struct(db_test_app, data_regression):
path = os.path.join(TEST_DIR, "input_files", "trajectory.lammpstrj")
data = LammpsTrajectory(path)
data_regression.check(
recursive_round(data.get_step_structure(-1).attributes,
2,
apply_lists=True))
def test_lammpstraj_get_step_struct(db_test_app, data_regression): # pylint: disable=unused-argument
"""Get the structure data for a given trajectory step"""
path = os.path.join(TEST_DIR, 'input_files', 'trajectory.lammpstrj')
data = LammpsTrajectory(path)
data_regression.check(
recursive_round(data.get_step_structure(-1).attributes,
2,
apply_lists=True))
def parse(self, **kwargs):
"""Parses the datafolder, stores results."""
resources = self.get_parsing_resources(kwargs, traj_in_temp=True)
if resources.exit_code is not None:
return resources.exit_code
log_data, exit_code = self.parse_log_file()
if exit_code is not None:
return exit_code
traj_error = None
if not resources.traj_paths:
traj_error = self.exit_codes.ERROR_TRAJ_FILE_MISSING
else:
try:
trajectory_data = LammpsTrajectory(
resources.traj_paths[0],
aliases={
'stresses': [f'c_stpa[{i+1}]' for i in range(6)],
'forces': ['fx', 'fy', 'fz'],
},
)
self.out('trajectory_data', trajectory_data)
self.out(
'structure',
trajectory_data.get_step_structure(
-1, original_structure=self.node.inputs.structure),
)
except Exception as err: # pylint: disable=broad-except
traceback.print_exc()
self.logger.error(str(err))
traj_error = self.exit_codes.ERROR_TRAJ_PARSING
# save results into node
output_data = log_data['data']
if 'units_style' in output_data:
output_data.update(
get_units_dict(
output_data['units_style'],
['energy', 'force', 'distance', 'pressure'],
))
output_data['stress_units'] = output_data.pop('pressure_units')
else:
self.logger.warning('units missing in log')
self.add_warnings_and_errors(output_data)
self.add_standard_info(output_data)
parameters_data = Dict(dict=output_data)
self.out('results', parameters_data)
if output_data['errors']:
return self.exit_codes.ERROR_LAMMPS_RUN
if traj_error:
return traj_error
if not log_data.get('found_end', False):
return self.exit_codes.ERROR_RUN_INCOMPLETE
return None
def parse(self, **kwargs):
"""Parses the datafolder, stores results."""
resources = self.get_parsing_resources(kwargs, traj_in_temp=True)
if resources.exit_code is not None:
return resources.exit_code
log_data, exit_code = self.parse_log_file()
if exit_code is not None:
return exit_code
traj_error = None
if not resources.traj_paths:
traj_error = self.exit_codes.ERROR_TRAJ_FILE_MISSING
else:
try:
trajectory_data = LammpsTrajectory(
resources.traj_paths[0],
aliases={
"stresses":
["c_stpa[{}]".format(i + 1) for i in range(6)],
"forces": ["fx", "fy", "fz"],
},
)
self.out("trajectory_data", trajectory_data)
self.out(
"structure",
trajectory_data.get_step_structure(
-1, original_structure=self.node.inputs.structure),
)
except Exception as err:
traceback.print_exc()
self.logger.error(str(err))
traj_error = self.exit_codes.ERROR_TRAJ_PARSING
# save results into node
output_data = log_data["data"]
if "units_style" in output_data:
output_data.update(
get_units_dict(
output_data["units_style"],
["energy", "force", "distance", "pressure"],
))
output_data["stress_units"] = output_data.pop("pressure_units")
else:
self.logger.warning("units missing in log")
self.add_warnings_and_errors(output_data)
self.add_standard_info(output_data)
parameters_data = Dict(dict=output_data)
self.out("results", parameters_data)
if output_data["errors"]:
return self.exit_codes.ERROR_LAMMPS_RUN
if traj_error:
return traj_error
if not log_data.get("found_end", False):
return self.exit_codes.ERROR_RUN_INCOMPLETE
def parse(self, **kwargs):
"""
Parse the files produced by lammps.
It takes care of parsing the log.lammps file, the trajectory file and the
yaml file with the final value of the variables printed in the
``thermo_style``.
"""
# pylint: disable=too-many-return-statements
try:
out_folder = self.retrieved
except exceptions.NotExistent:
return self.exit_codes.ERROR_NO_RETRIEVED_FOLDER
list_of_files = out_folder.list_object_names()
# check log file
if self.node.get_option('logfile_filename') not in list_of_files:
return self.exit_codes.ERROR_LOG_FILE_MISSING
filename = self.node.get_option('logfile_filename')
parsed_data = parse_logfile(file_contents=self.node.outputs.retrieved.
get_object_content(filename))
if parsed_data is None:
return self.exit_codes.ERROR_PARSING_LOGFILE
global_data = parsed_data['global']
arrays = parsed_data['time_dependent']
# check final variable file
if self.node.get_option('variables_filename') not in list_of_files:
return self.exit_codes.ERROR_FINAL_VARIABLE_FILE_MISSING
filename = self.node.get_option('variables_filename')
final_variables = parse_final_data(
file_contents=self.node.outputs.retrieved.get_object_content(
filename))
if final_variables is None:
return self.exit_codes.ERROR_PARSING_FINAL_VARIABLES
results = orm.Dict(dict={
**final_variables, 'compute_variables': global_data
})
# Expose the results from the log.lammps outputs
self.out('results', results)
# Get the time-dependent outputs exposed as a dictionary
time_dependent_computes = orm.Dict(dict=arrays)
self.out('time_dependent_computes', time_dependent_computes)
# check trajectory file
if self.node.get_option('trajectory_filename') not in list_of_files:
return self.exit_codes.ERROR_TRAJECTORY_FILE_MISSING
# Gather the lammps trajectory data
filename = self.node.get_option('trajectory_filename')
with self.node.outputs.retrieved.open(filename) as handle:
lammps_trajectory = LammpsTrajectory(handle)
self.out('trajectories', lammps_trajectory)
self.out('structure', lammps_trajectory.get_step_structure(-1))
# check stdout
if self.node.get_option('scheduler_stdout') not in list_of_files:
return self.exit_codes.ERROR_STDOUT_FILE_MISSING
# check stderr
if self.node.get_option('scheduler_stderr') not in list_of_files:
return self.exit_codes.ERROR_STDERR_FILE_MISSING
return None