def parse_log_file(self, compute_stress=False):
"""Parse the log file."""
output_filename = self.node.get_option("output_filename")
output_txt = self.retrieved.get_object_content(output_filename)
try:
output_data = read_log_file(output_txt, compute_stress=compute_stress)
except Exception:
traceback.print_exc()
return None, self.exit_codes.ERROR_LOG_PARSING
return output_data, None
def parse_with_retrieved(self, retrieved):
"""
Parses the datafolder, stores results.
"""
# suppose at the start that the job is successful
successful = True
# select the folder object
# Check that the retrieved folder is there
try:
out_folder = retrieved[self._calc._get_linkname_retrieved()]
except KeyError:
self.logger.error("No retrieved folder found")
return False, ()
# check what is inside the folder
list_of_files = out_folder.get_folder_list()
# OUTPUT file should exist
if not self._calc._OUTPUT_FILE_NAME in list_of_files:
successful = False
self.logger.error("Output file not found")
return successful, ()
# Get file and do the parsing
outfile = out_folder.get_abs_path(self._calc._OUTPUT_FILE_NAME)
ouput_trajectory = out_folder.get_abs_path(
self._calc._OUTPUT_TRAJECTORY_FILE_NAME)
outputa_data = read_log_file(outfile)
forces = read_lammps_forces(ouput_trajectory)
# look at warnings
warnings = []
with open(out_folder.get_abs_path(self._calc._SCHED_ERROR_FILE)) as f:
errors = f.read()
if errors:
warnings = [errors]
# ====================== prepare the output node ======================
# save the outputs
new_nodes_list = []
# save trajectory into node
array_data = ArrayData()
array_data.set_array('forces', forces)
new_nodes_list.append(('output_array', array_data))
# add the dictionary with warnings
outputa_data.update({'warnings': warnings})
parameters_data = ParameterData(dict=outputa_data)
new_nodes_list.append((self.get_linkname_outparams(), parameters_data))
# add the dictionary with warnings
# new_nodes_list.append((self.get_linkname_outparams(), ParameterData(dict={'warnings': warnings})))
return successful, new_nodes_list