def handle_batch_file_task(f_record, sid, model):
# 只添加成功的任务，对失败的输入直接过滤掉
path = join(settings.SETTINGS_ROOT, f_record.file_obj.path)
with open(path, 'r') as f:
for line in f.readlines():
line = line.strip().strip('\n')
try:
# TODO: 需要检测是否符合格式
if f_record.file_type.lower() == 'cas':
smile = get_smile_by_cas(line)
else:
smile = line
handle_smile_task(smile, model, sid)
except:
chemistry_logger.error('failed to submit %s' % line)
def fetch_polarizability(name, model):
path = os.path.join(config.GAUSSIAN_PATH, model, name, '%s.log' % name)
if not os.path.exists(path):
chemistry_logger.error('Cannot fetch Polarizability %s' % path)
return path
with open(path, 'r') as f:
for line in f.readlines():
if P_RE.search(line):
try:
v = float(line.split()[-2])
except:
chemistry_logger.error('Cannot get Polarizability value %s' % line)
v = 0
else:
break
return v
def fetch_ehomo_by_mopac(name, model):
path = os.path.join(config.MOPAC_PATH, model, name, '%s.out' % name)
if not os.path.exists(path):
chemistry_logger.error('Cannot fetch H**O %s by mopac' % path)
return 0.0
with open(path, 'r') as f:
for line in f.readlines():
if EHOMO_MOPAC_RE.search(line):
try:
v = line.split('=')[1].strip().strip('\t').split()[0]
v = float(v)
except:
chemistry_logger.exception('Cannot get EHOMO value %s ' % line)
v = 0.0
finally:
return v
chemistry_logger.error('%s no H**O' % path)
return 0.0
def fetch_polarizability(name, model):
path = os.path.join(config.GAUSSIAN_PATH, model, name, '%s.log' % name)
if not os.path.exists(path):
chemistry_logger.error('Cannot fetch Polarizability %s' % path)
return path
with open(path, 'r') as f:
for line in f.readlines():
if P_RE.search(line):
try:
v = float(line.split()[-2])
except:
chemistry_logger.error(
'Cannot get Polarizability value %s' % line)
v = 0
else:
break
return v
def cnt_batch_file_task(f_record):
# 只添加成功的任务，对失败的输入直接过滤掉
#TODO: 计算需要优化
cnt = 0
path = join(settings.SETTINGS_ROOT, f_record.file_obj.path)
with open(path, 'r') as f:
for line in f.readlines():
line = line.strip().strip('\n')
try:
# TODO: 需要检测是否符合格式
if f_record.file_type.lower() == 'cas':
smile = get_smile_by_cas(line)
else:
smile = line
except:
chemistry_logger.error('failed to submit %s' % line)
else:
cnt += 1
return cnt - 1
def fetch_ehomo(name, model):
path = os.path.join(config.GAUSSIAN_PATH, model, name, '%s.log' % name)
if not os.path.exists(path):
chemistry_logger.error('Cannot fetch H**O %s' % path)
return 0.0
ret = []
with open(path, 'r') as f:
for line in f.readlines():
if EHOMO_RE.search(line):
chemistry_logger.info(line)
ret.append(line)
try:
v = float(ret[-1].split()[-1])
except Exception as e:
chemistry_logger.exception('Cannot get EHOMO value %s ' % line)
v = 0
return v
def fetch_ehomo_by_mopac(name, model):
path = os.path.join(config.MOPAC_PATH, model, name, '%s.out' % name)
if not os.path.exists(path):
chemistry_logger.error('Cannot fetch H**O %s by mopac' % path)
return 0.0
with open(path, 'r') as f:
for line in f.readlines():
if EHOMO_MOPAC_RE.search(line):
try:
v = line.split('=')[1].strip().strip('\t').split()[0]
v = float(v)
except:
chemistry_logger.exception('Cannot get EHOMO value %s ' %
line)
v = 0.0
finally:
return v
chemistry_logger.error('%s no H**O' % path)
return 0.0
def fetch_ehomo(name, model):
path = os.path.join(config.GAUSSIAN_PATH, model, name, '%s.log' % name)
if not os.path.exists(path):
chemistry_logger.error('Cannot fetch H**O %s' % path)
return 0.0
ret = []
with open(path, 'r') as f:
for line in f.readlines():
if EHOMO_RE.search(line):
chemistry_logger.info(line)
ret.append(line)
try:
v = float(ret[-1].split()[-1])
except Exception as e:
chemistry_logger.exception('Cannot get EHOMO value %s ' % line)
v = 0
return v
