def process_log(log_file):
"""
Gather key info from log file
@param log_file: name of log file
@return: lists of dicts of key data extracted; 1 dict per timestep and/or summary
"""
result_list = []
file_root = get_fname_root(log_file)
with open(log_file) as l_file:
reading_data = False
result_dict = {}
for line in l_file:
line = line.strip()
if RUN_PAT.match(line):
reading_data = True
result_dict[FILE_NAME] = file_root
elif reading_data:
if ENERGY_PAT.match(line):
s_line = line.split()
result_dict[TIMESTEP] = int(s_line[1])
result_dict[E_DIHED] = float(s_line[4])
result_list.append(dict(result_dict))
return result_list
def testGetRootName(self):
"""
Check for prefix addition.
"""
root_name = get_fname_root(ORIG_WHAM_PATH)
self.assertEqual(root_name, ORIG_WHAM_ROOT)
self.assertNotEqual(root_name, ORIG_WHAM_FNAME)
self.assertNotEqual(root_name, ORIG_WHAM_PATH)
def process_log(log_file):
"""
Gather key info from lammps log file
@param log_file: name of log file
@return: lists of dicts of key data extracted; 1 dict per timestep
"""
result_list = []
file_root = get_fname_root(log_file)
with open(log_file) as l_file:
reading_steps = False
result_dict = {}
for line in l_file:
line = line.strip()
if STEP_PAT.match(line):
reading_steps = True
result_dict[FILE_NAME] = file_root
result_dict[TIMESTEP] = int(line.split()[2])
elif reading_steps:
if len(line) == 0:
break
s_line = line.split()
if s_line[0] == TOTENG:
for key_id, key in enumerate([TOTENG, KINENG, TEMP]):
result_dict[key] = float(s_line[2 + key_id * 3])
elif s_line[0] == POTENG:
for key_id, key in enumerate([POTENG, E_BOND, E_ANGL]):
result_dict[key] = float(s_line[2 + key_id * 3])
elif s_line[0] == E_DIHED:
for key_id, key in enumerate([E_DIHED, E_IMPRO, E_VDWL]):
result_dict[key] = float(s_line[2 + key_id * 3])
elif s_line[0] == E_COUL:
for key_id, key in enumerate([E_COUL, E_LONG, PRESS]):
result_dict[key] = float(s_line[2 + key_id * 3])
result_list.append(dict(result_dict))
else:
# when stop matching, done reading file (either by normal or abnormal termination)
break
return result_list