def test_packmol_with_str(self):
"""
Test coords input as strings
"""
with tempfile.TemporaryDirectory() as scratch_dir:
pw = PackmolBoxGen().get_input_set(molecules=[
{
"name":
"EMC",
"number":
10,
"coords":
os.path.join(test_dir, "subdir with spaces", "EMC.xyz")
},
{
"name": "LiTFSi",
"number": 20,
"coords": os.path.join(test_dir, "LiTFSi.xyz")
},
], )
pw.write_input(scratch_dir)
pw.run(scratch_dir)
assert os.path.exists(os.path.join(scratch_dir, "packmol_out.xyz"))
out = Molecule.from_file(
os.path.join(scratch_dir, "packmol_out.xyz"))
assert out.composition.num_atoms == 10 * 15 + 20 * 16
def test_no_return_and_box(self, water, ethanol):
"""
Make sure the code raises an error if packmol doesn't
exit cleanly. Also verify the box arg works properly.
"""
with tempfile.TemporaryDirectory() as scratch_dir:
pw = PackmolBoxGen().get_input_set(
molecules=[
{
"name": "water",
"number": 1000,
"coords": water
},
{
"name": "ethanol",
"number": 2000,
"coords": ethanol
},
],
box=[0, 0, 0, 2, 2, 2],
)
pw.write_input(scratch_dir)
with open(os.path.join(scratch_dir, "packmol.inp")) as f:
input_string = f.read()
assert "inside box 0 0 0 2 2 2" in input_string
with pytest.raises(ValueError):
pw.run(scratch_dir)
def test_control_params(self, water, ethanol):
"""
Check that custom control_params work and that ValueError
is raised when 'ERROR' appears in stdout (even if return code is 0)
"""
with tempfile.TemporaryDirectory() as scratch_dir:
pw = PackmolBoxGen(control_params={
"maxit": 0,
"nloop": 0
}, ).get_input_set(molecules=[
{
"name": "water",
"number": 1000,
"coords": water
},
{
"name": "ethanol",
"number": 2000,
"coords": ethanol
},
], )
pw.write_input(scratch_dir)
with open(os.path.join(scratch_dir, "packmol.inp")) as f:
input_string = f.read()
assert "maxit 0" in input_string
assert "nloop 0" in input_string
with pytest.raises(ValueError):
pw.run(scratch_dir)
def test_timeout(self, water, ethanol):
"""
Check that the timeout works
"""
with tempfile.TemporaryDirectory() as scratch_dir:
pw = PackmolBoxGen().get_input_set(molecules=[
{
"name": "water",
"number": 1000,
"coords": water
},
{
"name": "ethanol",
"number": 2000,
"coords": ethanol
},
], )
pw.write_input(scratch_dir)
with pytest.raises(TimeoutExpired):
pw.run(scratch_dir, 1)
def test_arbitrary_filenames(self, water, ethanol):
"""
Make sure custom input and output filenames work.
Use a subdirectory with spaces.
"""
with tempfile.TemporaryDirectory() as scratch_dir:
os.mkdir(os.path.join(scratch_dir, "subdirectory with spaces"))
pw = PackmolBoxGen(inputfile="input.in",
outputfile=Path("output.xyz"),
stdoutfile=Path("stdout.txt")).get_input_set(
molecules=[
{
"name": "water",
"number": 10,
"coords": water
},
{
"name": "ethanol",
"number": 20,
"coords": ethanol
},
], )
pw.write_input(
os.path.join(scratch_dir, "subdirectory with spaces"), )
assert os.path.exists(
os.path.join(scratch_dir, "subdirectory with spaces",
"input.in"))
pw.run(os.path.join(scratch_dir, "subdirectory with spaces"), )
assert os.path.exists(
os.path.join(scratch_dir, "subdirectory with spaces",
"output.xyz"))
assert os.path.exists(
os.path.join(scratch_dir, "subdirectory with spaces",
"stdout.txt"))
out = Molecule.from_file(
os.path.join(scratch_dir, "subdirectory with spaces",
"output.xyz"))
assert out.composition.num_atoms == 10 * 3 + 20 * 9
def test_packmol_with_molecule(self, water, ethanol):
"""
Test coords input as Molecule
"""
with tempfile.TemporaryDirectory() as scratch_dir:
pw = PackmolBoxGen().get_input_set(molecules=[
{
"name": "water",
"number": 10,
"coords": water
},
{
"name": "ethanol",
"number": 20,
"coords": ethanol
},
], )
pw.write_input(scratch_dir)
pw.run(scratch_dir)
assert os.path.exists(os.path.join(scratch_dir, "packmol_out.xyz"))
out = Molecule.from_file(
os.path.join(scratch_dir, "packmol_out.xyz"))
assert out.composition.num_atoms == 10 * 3 + 20 * 9
def test_random_seed(self, water, ethanol):
"""
Confirm that seed = -1 generates random structures
while seed = 1 is deterministic
"""
mm = MoleculeMatcher()
# deterministic output
with tempfile.TemporaryDirectory() as scratch_dir:
pw = PackmolBoxGen(
seed=1,
inputfile="input.in",
outputfile="output.xyz",
).get_input_set(
# scratch_dir,
molecules=[
{
"name": "water",
"number": 10,
"coords": water
},
{
"name": "ethanol",
"number": 20,
"coords": ethanol
},
], )
pw.write_input(scratch_dir)
pw.run(scratch_dir)
out1 = Molecule.from_file(os.path.join(scratch_dir, "output.xyz"))
pw.run(scratch_dir)
out2 = Molecule.from_file(os.path.join(scratch_dir, "output.xyz"))
assert mm.fit(out1, out2)
# randomly generated structures
with tempfile.TemporaryDirectory() as scratch_dir:
pw = PackmolBoxGen(
seed=-1,
inputfile="input.in",
outputfile="output.xyz",
).get_input_set(molecules=[
{
"name": "water",
"number": 10,
"coords": water
},
{
"name": "ethanol",
"number": 20,
"coords": ethanol
},
], )
pw.write_input(scratch_dir)
pw.run(scratch_dir)
out1 = Molecule.from_file(os.path.join(scratch_dir, "output.xyz"))
pw.run(scratch_dir)
out2 = Molecule.from_file(os.path.join(scratch_dir, "output.xyz"))
assert not mm.fit(out1, out2)
def test_chdir_behavior(self, water, ethanol):
"""
Make sure the code returns to the starting directory whether
or not packmol exits cleanly.
"""
startdir = str(Path.cwd())
with tempfile.TemporaryDirectory() as scratch_dir:
# this one will not exit cleanly b/c the box is too small
pw = PackmolBoxGen().get_input_set(
molecules=[
{
"name": "water",
"number": 1000,
"coords": water
},
{
"name": "ethanol",
"number": 2000,
"coords": ethanol
},
],
box=[0, 0, 0, 2, 2, 2],
)
pw.write_input(scratch_dir)
with pytest.raises(ValueError):
pw.run(scratch_dir)
assert str(Path.cwd()) == startdir
with tempfile.TemporaryDirectory() as scratch_dir:
# this one will exit cleanly
pw = PackmolBoxGen().get_input_set(molecules=[
{
"name": "water",
"number": 1000,
"coords": water
},
{
"name": "ethanol",
"number": 2000,
"coords": ethanol
},
], )
pw.write_input(scratch_dir)
pw.run(scratch_dir)
assert str(Path.cwd()) == startdir