def test_modified_potentials(self, n_typed_ar_system):
top = n_typed_ar_system(n_sites=1)
top.atom_types[0].set_expression("sigma + epsilon")
with pytest.raises(EngineIncompatibilityError):
write_mcf(top, "out.mcf")
alternate_lj = "4*epsilon*sigma**12/r**12 - 4*epsilon*sigma**6/r**6"
top.atom_types[0].set_expression(alternate_lj)
write_mcf(top, "ar.mcf")
def test_write_mie_full(self, n_typed_xe_mie):
top = n_typed_xe_mie()
write_mcf(top, "xe.mcf")
mcf_data = []
with open("xe.mcf") as f:
for line in f:
mcf_data.append(line.strip().split())
for idx, line in enumerate(mcf_data):
if len(line) > 1:
if line[1] == "Atom_Info":
atom_section_start = idx
# Check a some atom info
assert mcf_data[atom_section_start + 1][0] == "1"
assert mcf_data[atom_section_start + 2][1] == "Xe"
assert mcf_data[atom_section_start + 2][2] == "Xe"
assert mcf_data[atom_section_start + 2][5] == "Mie"
assert np.isclose(
float(mcf_data[atom_section_start + 2][3]),
top.sites[0].mass.in_units(u.amu).value,
)
assert np.isclose(
float(mcf_data[atom_section_start + 2][4]),
top.sites[0].charge.in_units(u.elementary_charge).value,
)
assert np.isclose(
float(mcf_data[atom_section_start + 2][6]),
(top.sites[0].atom_type.parameters["epsilon"] / u.kb).in_units(
u.K).value,
)
assert np.isclose(
float(mcf_data[atom_section_start + 2][7]),
top.sites[0].atom_type.parameters["sigma"].in_units(
u.Angstrom).value,
)
assert np.isclose(
float(mcf_data[atom_section_start + 2][8]),
top.sites[0].atom_type.parameters["n"],
)
assert np.isclose(
float(mcf_data[atom_section_start + 2][9]),
top.sites[0].atom_type.parameters["m"],
)
def test_scaling_factors(self, n_typed_ar_system):
top = n_typed_ar_system()
write_mcf(top, "ar.mcf")
mcf_data = []
with open("ar.mcf") as f:
for line in f:
mcf_data.append(line.strip().split())
assert np.allclose(float(mcf_data[-5][0]), 0.0)
assert np.allclose(float(mcf_data[-5][1]), 0.0)
assert np.allclose(float(mcf_data[-5][2]), 0.5)
assert np.allclose(float(mcf_data[-5][3]), 1.0)
assert np.allclose(float(mcf_data[-4][0]), 0.0)
assert np.allclose(float(mcf_data[-4][1]), 0.0)
assert np.allclose(float(mcf_data[-4][2]), 0.5)
assert np.allclose(float(mcf_data[-4][3]), 1.0)
top.scaling_factors = {
"vdw_12": 0.1,
"vdw_13": 0.2,
"vdw_14": 0.5,
"coul_12": 0.2,
"coul_13": 0.4,
"coul_14": 0.6,
}
write_mcf(top, "ar.mcf")
mcf_data = []
with open("ar.mcf") as f:
for line in f:
mcf_data.append(line.strip().split())
assert np.allclose(float(mcf_data[-5][0]), 0.1)
assert np.allclose(float(mcf_data[-5][1]), 0.2)
assert np.allclose(float(mcf_data[-5][2]), 0.5)
assert np.allclose(float(mcf_data[-5][3]), 1.0)
assert np.allclose(float(mcf_data[-4][0]), 0.2)
assert np.allclose(float(mcf_data[-4][1]), 0.4)
assert np.allclose(float(mcf_data[-4][2]), 0.6)
assert np.allclose(float(mcf_data[-4][3]), 1.0)
def test_write_lj_full(self, n_typed_ar_system):
top = n_typed_ar_system(n_sites=1)
write_mcf(top, "ar.mcf")
mcf_data = []
with open("ar.mcf") as f:
for line in f:
mcf_data.append(line.strip().split())
for idx, line in enumerate(mcf_data):
if len(line) > 1:
if line[1] == "Atom_Info":
atom_section_start = idx
assert mcf_data[atom_section_start + 1][0] == "1"
assert mcf_data[atom_section_start + 2][1] == "Ar"
assert mcf_data[atom_section_start + 2][2] == "Ar"
assert mcf_data[atom_section_start + 2][5] == "LJ"
assert np.isclose(
float(mcf_data[atom_section_start + 2][3]),
top.sites[0].mass.in_units(u.amu).value,
)
assert np.isclose(
float(mcf_data[atom_section_start + 2][4]),
top.sites[0].charge.in_units(u.elementary_charge).value,
)
assert np.isclose(
float(mcf_data[atom_section_start + 2][6]),
(top.sites[0].atom_type.parameters["epsilon"] / u.kb).in_units(
u.K).value,
)
assert np.isclose(
float(mcf_data[atom_section_start + 2][7]),
top.sites[0].atom_type.parameters["sigma"].in_units(
u.Angstrom).value,
)
def test_write_mie_simple(self, n_typed_xe_mie):
top = n_typed_xe_mie()
write_mcf(top, "xe.mcf")
def test_write_lj_simple(self, n_typed_ar_system):
top = n_typed_ar_system(n_sites=1)
write_mcf(top, "ar.mcf")
