def test_run_failure(self):
custom_args = {"vdw_cutoff": 17.0 * u.angstrom}
with temporary_directory() as tmp_dir:
with temporary_cd(tmp_dir):
with pytest.raises(CassandraRuntimeError,
match=r"Cassandra exited with"):
ex.run_nvt(**custom_args)
def test_run_nvt_custom_mixing(self):
mixing_dict = {"opls_138_s1 opls_140_s1": "1.0 1.0"}
custom_args = {
"mixing_rule": "custom",
"custom_mixing_dict": mixing_dict,
}
with temporary_directory() as tmp_dir:
with temporary_cd(tmp_dir):
ex.run_nvt(**custom_args)
log_files = sorted(glob.glob("./mosdef_cassandra*.log"),
key=os.path.getmtime)
log_file = log_files[-1]
log_data = []
save_data = False
with open(log_file) as log:
for line in log:
if "CASSANDRA STANDARD" in line:
save_data = True
if save_data:
log_data.append(line)
completed = False
for line in log_data:
if "Cassandra simulation complete" in line:
completed = True
assert completed
def test_run_nvt(self):
with temporary_directory() as tmp_dir:
with temporary_cd(tmp_dir):
ex.run_nvt()
log_files = sorted(glob.glob("./mosdef_cassandra*.log"),
key=os.path.getmtime)
log_file = log_files[-1]
log_data = []
save_data = False
with open(log_file) as log:
for line in log:
if "CASSANDRA STANDARD" in line:
save_data = True
if save_data == True:
log_data.append(line)
completed = False
for line in log_data:
if "Cassandra simulation complete" in line:
completed = True
assert completed