def test_ff_from_etree_iterable(self):
ff_etrees = [
lxml.etree.parse(get_path('opls_charmm_buck.xml')),
lxml.etree.parse(get_path('trimmed_charmm.xml'))
]
ff = ForceField(ff_etrees)
assert ff
def test_spce_xml(self):
spce = ForceField(get_path('spce.xml'))
assert len(spce.atom_types) == 2
assert len(spce.bond_types) == 1
assert len(spce.angle_types) == 1
assert len(spce.dihedral_types) == 0
# Store expected expressions in list
ref_exprs = [sympy.sympify(expr) for expr in [
"4*epsilon*((sigma/r)**12 - (sigma/r)**6)",
"0.5 * k * (r-r_eq)**2",
"0.5 * k * (theta-theta_eq)**2",
]
]
assert allclose(spce.atom_types['opls_116'].charge, -0.8476 * u.elementary_charge)
assert allclose(spce.atom_types['opls_117'].charge, 0.4238 * u.elementary_charge)
assert sympy.simplify(spce.atom_types['opls_116'].expression - ref_exprs[0]) == 0
assert sympy.simplify(spce.atom_types['opls_117'].expression - ref_exprs[0]) == 0
assert sympy.simplify(spce.bond_types['opls_116~opls_117'].expression - ref_exprs[1]) == 0
assert sympy.simplify(spce.angle_types['opls_117~opls_116~opls_117'].expression - ref_exprs[2]) == 0
assert allclose(spce.atom_types['opls_116'].parameters['sigma'], 0.316557 * u.nm)
assert allclose(spce.atom_types['opls_116'].parameters['epsilon'], 0.650194 * u.Unit('kJ/mol'))
assert allclose(spce.atom_types['opls_117'].parameters['sigma'], 0.1 * u.nm)
assert allclose(spce.atom_types['opls_117'].parameters['epsilon'], 0.0 * u.Unit('kJ/mol'))
assert allclose(spce.bond_types['opls_116~opls_117'].parameters['r_eq'], 0.1 * u.nm)
assert allclose(spce.bond_types['opls_116~opls_117'].parameters['k'], 345000.0 * u.Unit('kJ/(mol*nm**2)'))
assert allclose(spce.angle_types['opls_117~opls_116~opls_117'].parameters['theta_eq'], 109.47 * u.degree)
assert allclose(spce.angle_types['opls_117~opls_116~opls_117'].parameters['k'], 383.0 * u.Unit('kJ/mol/rad**2'))
def test_ff_periodic_dihedrals_from_alphanumeric_symbols(self):
ff = ForceField(get_path("opls_charmm_buck.xml"))
assert "A" in ff.atom_types["buck_O"].parameters
with pytest.raises(TypeError):
assert len(
ff.dihedral_types["opls_140~*~*~opls_140"].parameters["c0"])
assert len(ff.dihedral_types["NH2~CT1~C~O"].parameters["delta"]) == 1
def test_tip3p_force_field(self):
water = ForceField(get_path('tip3p.xml'))
assert len(water.atom_types) == 2
assert len(water.bond_types) == 1
assert len(water.angle_types) == 1
assert len(water.dihedral_types) == 0
# Store expected expressions in list
ref_exprs = [sympy.sympify(expr) for expr in [
"4*epsilon*((sigma/r)**12 - (sigma/r)**6)",
"0.5 * k * (r-r_eq)**2",
"0.5 * k * (theta-theta_eq)**2",
]
]
assert water.atom_types['opls_111'].charge.value == -0.834
assert water.atom_types['opls_112'].charge.value == 0.417
assert sympy.simplify(water.atom_types['opls_111'].expression - ref_exprs[0]) == 0
assert sympy.simplify(water.atom_types['opls_112'].expression - ref_exprs[0]) == 0
assert sympy.simplify(water.bond_types['opls_111~opls_112'].expression - ref_exprs[1]) == 0
assert sympy.simplify(water.angle_types['opls_112~opls_111~opls_112'].expression - ref_exprs[2]) == 0
assert allclose(water.atom_types['opls_111'].parameters['sigma'], 0.315061 * u.nm)
assert allclose(water.atom_types['opls_111'].parameters['epsilon'], 0.636386 * u.Unit('kJ/mol'))
assert allclose(water.atom_types['opls_112'].parameters['sigma'], 1.0 * u.nm)
assert allclose(water.atom_types['opls_112'].parameters['epsilon'], 0.0 * u.Unit('kJ/mol'))
assert allclose(water.bond_types['opls_111~opls_112'].parameters['r_eq'], 0.09572 * u.nm)
assert allclose(water.bond_types['opls_111~opls_112'].parameters['k'], 502416.0 * u.Unit('kJ/(mol*nm**2)'))
assert allclose(water.angle_types['opls_112~opls_111~opls_112'].parameters['theta_eq'], 1.824218134 * u.radian)
assert allclose(water.angle_types['opls_112~opls_111~opls_112'].parameters['k'], 682.02 * u.Unit('kJ/(mol*rad**2)'))
def test_ff_periodic_dihedrals_from_alphanumeric_symbols(self):
ff = ForceField(get_path('opls_charmm_buck.xml'))
assert 'A' in ff.atom_types['buck_O'].parameters
with pytest.raises(TypeError):
assert len(
ff.dihedral_types['opls_140~*~*~opls_140'].parameters['c0'])
assert len(ff.dihedral_types['NH2~CT1~C~O'].parameters['delta']) == 1
def test_water_top(self, water_system):
top = water_system
ff = gmso.ForceField(get_path('tip3p.xml'))
for site in top.sites:
site.atom_type = ff.atom_types[site.name]
top.update_sites()
top.update_atom_types()
for bond in top.bonds:
bond.bond_type = bond.connection_type = ff.bond_types[
'opls_111~opls_112']
top.update_bonds()
top.update_bond_types()
for subtop in top.subtops:
angle = gmso.core.angle.Angle(
connection_members=[site for site in subtop.sites],
name="opls_112~opls_111~opls_112",
connection_type=ff.angle_types["opls_112~opls_111~opls_112"])
top.add_connection(angle)
top.update_angles()
top.update_angle_types()
write_top(top, 'water.top')
def test_read_epsilon(self, filename=get_path('data.lammps')):
read = read_lammpsdata(filename)
lj = [i.parameters for i in read.atom_types][0]
assert_allclose_units(lj['epsilon'],
u.unyt_array(0.0717, (u.kcal / u.mol)),
rtol=1e-5,
atol=1e-8)
def test_read_sigma(self, filename=get_path('data.lammps')):
read = read_lammpsdata(filename)
lj = [i.parameters for i in read.atom_types][0]
assert_allclose_units(lj['sigma'],
u.unyt_array(3, u.angstrom),
rtol=1e-5,
atol=1e-8)
def test_read_charge(self, filename=get_path('data.lammps')):
read = read_lammpsdata(filename)
charge = [i.charge for i in read.atom_types]
assert_allclose_units(charge,
u.unyt_array(0, u.C),
rtol=1e-5,
atol=1e-8)
def test_read_mass(self, filename=get_path('data.lammps')):
read = read_lammpsdata(filename)
masses = [i.mass for i in read.atom_types]
assert_allclose_units(masses,
u.unyt_array(1.0079, u.g),
rtol=1e-5,
atol=1e-8)
def water_system(self):
water = mb.load(get_path('tip3p.mol2'))
water.name = 'water'
water[0].name = 'opls_111'
water[1].name = water[2].name = 'opls_112'
packed_system = mb.fill_box(compound=water,
n_compounds=2,
box=mb.Box([2, 2, 2]))
return from_mbuild(packed_system)
def test_noble_mie_xml(self):
ff = ForceField(get_path('noble_mie.xml'))
templates = PotentialTemplateLibrary()
ref_expr = templates['MiePotential'].expression
assert len(ff.atom_types) == 4
assert len(ff.bond_types) == 0
assert len(ff.angle_types) == 0
assert len(ff.dihedral_types) == 0
for (name, atom_type) in ff.atom_types.items():
assert sympy.simplify(atom_type.expression - ref_expr) == 0
assert allclose(ff.atom_types['Ne'].parameters['epsilon'],
0.26855713 * u.Unit('kJ/mol'))
assert allclose(ff.atom_types['Ne'].parameters['sigma'],
2.794 * u.Angstrom)
assert allclose(ff.atom_types['Ne'].parameters['n'],
11 * u.dimensionless)
assert allclose(ff.atom_types['Ne'].parameters['m'],
6 * u.dimensionless)
assert ff.atom_types['Ne'].charge.value == 0
assert allclose(ff.atom_types['Ar'].parameters['epsilon'],
1.01519583 * u.Unit('kJ/mol'))
assert allclose(ff.atom_types['Ar'].parameters['sigma'],
3.405 * u.Angstrom)
assert allclose(ff.atom_types['Ar'].parameters['n'],
13 * u.dimensionless)
assert allclose(ff.atom_types['Ar'].parameters['m'],
6 * u.dimensionless)
assert ff.atom_types['Ar'].charge.value == 0
assert allclose(ff.atom_types['Kr'].parameters['epsilon'],
1.46417678 * u.Unit('kJ/mol'))
assert allclose(ff.atom_types['Kr'].parameters['sigma'],
3.645 * u.Angstrom)
assert allclose(ff.atom_types['Kr'].parameters['n'],
14 * u.dimensionless)
assert allclose(ff.atom_types['Kr'].parameters['m'],
6 * u.dimensionless)
assert ff.atom_types['Kr'].charge.value == 0
assert allclose(ff.atom_types['Xe'].parameters['epsilon'],
2.02706587 * u.Unit('kJ/mol'))
assert allclose(ff.atom_types['Xe'].parameters['sigma'],
3.964 * u.Angstrom)
assert allclose(ff.atom_types['Xe'].parameters['n'],
14 * u.dimensionless)
assert allclose(ff.atom_types['Xe'].parameters['m'],
6 * u.dimensionless)
assert ff.atom_types['Xe'].charge.value == 0
def test_carbon_force_field(self):
carbon = ForceField(get_path('carbon.xml'))
assert len(carbon.atom_types) == 1
assert len(carbon.bond_types) == 1
assert len(carbon.angle_types) == 1
assert len(carbon.dihedral_types) == 1
# Store expected expressions in list
ref_exprs = [
sympy.sympify(expr) for expr in [
"4*epsilon*((sigma/r)**12 - (sigma/r)**6)",
"0.5 * k * (r-r_eq)**2",
"0.5 * k * (theta-theta_eq)**2",
"k * (1 + cos(n * theta - theta_0))",
]
]
assert carbon.atom_types['C'].charge.value == 0
assert sympy.simplify(carbon.atom_types['C'].expression -
ref_exprs[0]) == 0
assert sympy.simplify(carbon.bond_types['C~C'].expression -
ref_exprs[1]) == 0
assert sympy.simplify(carbon.angle_types['C~C~C'].expression -
ref_exprs[2]) == 0
assert sympy.simplify(carbon.dihedral_types['*~C~C~*'].expression -
ref_exprs[3]) == 0
assert allclose(carbon.atom_types['C'].parameters['sigma'],
0.339966950842 * u.nm)
assert allclose(carbon.atom_types['C'].parameters['epsilon'],
0.359824 * u.Unit('kJ/mol'))
assert allclose(carbon.bond_types['C~C'].parameters['r_eq'],
0.1324 * u.nm)
assert allclose(carbon.bond_types['C~C'].parameters['k'],
493460.96 * u.Unit('kJ/(mol*nm**2)'))
assert allclose(carbon.angle_types['C~C~C'].parameters['theta_eq'],
2.12598556185 * u.radian)
assert allclose(carbon.angle_types['C~C~C'].parameters['k'],
584.42112 * u.Unit('kJ/(mol*rad**2)'))
assert allclose(carbon.dihedral_types['*~C~C~*'].parameters['k'],
27.8236 * u.Unit('kJ/mol'))
assert allclose(carbon.dihedral_types['*~C~C~*'].parameters['n'],
2 * u.dimensionless)
assert allclose(carbon.dihedral_types['*~C~C~*'].parameters['theta_0'],
np.pi * u.radian)
def test_ff_charmm_xml(self):
charm_ff = ForceField(get_path('trimmed_charmm.xml'))
assert charm_ff.name == 'topologyCharmm'
assert "*~CS~SS~*" in charm_ff.dihedral_types
# Test list of parameters
assert isinstance(
charm_ff.dihedral_types["*~CE1~CE1~*"].parameters['k'], list)
# This ensures that even though the parameters is a list, they can be hashed (by equality checks)
assert charm_ff.dihedral_types[
"*~CE1~CE1~*"] == charm_ff.dihedral_types["*~CE1~CE1~*"]
assert len(charm_ff.dihedral_types["*~CE1~CE1~*"].parameters['k']) == 2
# Test Correct Parameter Values
assert charm_ff.dihedral_types["*~CE1~CE1~*"].parameters['k'] == \
[u.unyt_quantity(0.6276, u.kJ), u.unyt_quantity(35.564, u.kJ)]
def _typed_topology(n_sites=1):
xe = mb.Compound(name="Xe")
packed_system = mb.fill_box(
compound=xe,
n_compounds=n_sites,
box=mb.Box([3, 3, 3]),
)
top = from_mbuild(packed_system)
ff = ForceField(get_path("noble_mie.xml"))
for site in top.sites:
site.atom_type = ff.atom_types["Xe"]
top.update_topology()
return top
def typed_water_system(self, water_system):
top = water_system
ff = ForceField(get_path('tip3p.xml'))
element_map = {"O": "opls_111", "H": "opls_112"}
for atom in top.sites:
atom.atom_type = ff.atom_types[atom.name]
for bond in top.bonds:
bond.connection_type = ff.bond_types["opls_111~opls_112"]
for subtop in top.subtops:
angle = Angle(
connection_members=[site for site in subtop.sites],
name="opls_112~opls_111~opls_112",
connection_type=ff.angle_types["opls_112~opls_111~opls_112"])
top.add_connection(angle)
top.update_topology()
return top
def test_ethylene_forcefield(self):
ethylene = ForceField(get_path('ethylene.xml'))
assert len(ethylene.atom_types) == 2
assert len(ethylene.bond_types) == 2
assert len(ethylene.angle_types) == 2
assert len(ethylene.dihedral_types) == 1
# Store expected expressions in list
ref_exprs = [sympy.sympify(expr) for expr in [
"4*epsilon*((sigma/r)**12 - (sigma/r)**6)",
"0.5 * k * (r-r_eq)**2",
"0.5 * k * (theta-theta_eq)**2",
"c_0 + c_1 * cos(psi) + c_2 * cos(psi)**2 + c_3 * cos(psi)**3 + c_4 * cos(psi)**4 + c_5 * cos(psi)**5"
]
]
assert allclose(ethylene.atom_types['opls_143'].charge, -0.23 * u.elementary_charge)
assert allclose(ethylene.atom_types['opls_144'].charge, 0.115 * u.elementary_charge)
assert sympy.simplify(ethylene.atom_types['opls_143'].expression - ref_exprs[0]) == 0
assert sympy.simplify(ethylene.atom_types['opls_144'].expression - ref_exprs[0]) == 0
assert sympy.simplify(ethylene.bond_types['opls_143~opls_144'].expression - ref_exprs[1]) == 0
assert sympy.simplify(ethylene.angle_types['opls_144~opls_143~opls_144'].expression - ref_exprs[2]) == 0
assert sympy.simplify(ethylene.dihedral_types['opls_144~opls_143~opls_143~opls_144'].expression - ref_exprs[3]) == 0
assert allclose(ethylene.atom_types['opls_143'].parameters['sigma'], 0.317984 * u.nm)
assert allclose(ethylene.atom_types['opls_143'].parameters['epsilon'], 0.355 * u.Unit('kJ/mol'))
assert allclose(ethylene.atom_types['opls_144'].parameters['sigma'], 0.12552 * u.nm)
assert allclose(ethylene.atom_types['opls_144'].parameters['epsilon'], 0.242 * u.Unit('kJ/mol'))
assert allclose(ethylene.bond_types['opls_143~opls_143'].parameters['r_eq'], 0.134 * u.nm)
assert allclose(ethylene.bond_types['opls_143~opls_144'].parameters['k'], 284512.0 * u.Unit('kJ/(mol*nm**2)'))
assert allclose(ethylene.angle_types['opls_143~opls_143~opls_144'].parameters['theta_eq'], 2.0943951 * u.rad)
assert allclose(ethylene.angle_types['opls_144~opls_143~opls_144'].parameters['k'], 292.88 * u.Unit('kJ/mol/rad**2'))
assert allclose(ethylene.dihedral_types['opls_144~opls_143~opls_143~opls_144'].parameters['c_0'], 58.576 * u.Unit('kJ/mol'))
assert allclose(ethylene.dihedral_types['opls_144~opls_143~opls_143~opls_144'].parameters['c_2'], -58.576 * u.Unit('kJ/mol'))
assert allclose(ethylene.dihedral_types['opls_144~opls_143~opls_143~opls_144'].parameters['c_5'], 0.0 * u.Unit('kJ/mol'))
def test_missing_params(self):
with pytest.raises(ForceFieldParseError):
ForceField(get_path('ff-example-missing-parameter.xml'))
def test_empty_foyer_atomtype(self):
with pytest.raises(ForceFieldParseError):
from_foyer_xml(get_path("empty_foyer.xml"))
def test_read_sites(self, filename=get_path('data.lammps')):
read = read_lammpsdata(filename)
assert read.box == Box(lengths=[1, 1, 1])
def test_read_lammps(self, filename=get_path('data.lammps')):
read_lammpsdata(filename)
def opls_ethane_foyer(self):
return ForceField(
get_path(filename=get_path("oplsaa-ethane_foyer.xml")))
def test_forcefield_missing_atom_types_non_strict(self):
ff = ForceField(
get_path(filename=get_path('ff_missing_atom_types.xml')),
strict=False)
def ff(self):
return ForceField(get_path('ff-example0.xml'))
def test_forcefield_missing_atom_types(self):
with pytest.raises(MissingAtomTypesError):
ff = ForceField(
get_path(filename=get_path('ff_missing_atom_types.xml')))
def test_ff_from_etree(self):
ff_etree = lxml.etree.parse(get_path('opls_charmm_buck.xml'))
ff = ForceField(ff_etree)
assert ff
def named_groups_ff(self):
return ForceField(get_path('ff-example1.xml'))
def test_non_unique_params(self):
with pytest.raises(DocumentInvalid):
ForceField(get_path('ff-example-nonunique-params.xml'))
def test_atomclass_groups_charm_buck_ff(self):
ff = ForceField(get_path('opls_charmm_buck.xml'))
assert len(ff.atom_class_groups['CT']) == 2
def test_tip3p_force_field(self):
water = ForceField(get_path("tip3p.xml"))
assert len(water.atom_types) == 2
assert len(water.bond_types) == 1
assert len(water.angle_types) == 1
assert len(water.dihedral_types) == 0
# Store expected expressions in list
ref_exprs = [
sympy.sympify(expr) for expr in [
"4*epsilon*((sigma/r)**12 - (sigma/r)**6)",
"0.5 * k * (r-r_eq)**2",
"0.5 * k * (theta-theta_eq)**2",
]
]
assert water.atom_types["opls_111"].charge.value == -0.834
assert water.atom_types["opls_112"].charge.value == 0.417
assert (sympy.simplify(water.atom_types["opls_111"].expression -
ref_exprs[0]) == 0)
assert (sympy.simplify(water.atom_types["opls_112"].expression -
ref_exprs[0]) == 0)
assert (
sympy.simplify(water.bond_types["opls_111~opls_112"].expression -
ref_exprs[1]) == 0)
assert (sympy.simplify(
water.angle_types["opls_112~opls_111~opls_112"].expression -
ref_exprs[2]) == 0)
assert_allclose_units(
water.atom_types["opls_111"].parameters["sigma"],
0.315061 * u.nm,
rtol=1e-5,
atol=1e-8,
)
assert_allclose_units(
water.atom_types["opls_111"].parameters["epsilon"],
0.636386 * u.Unit("kJ/mol"),
rtol=1e-5,
atol=1e-8,
)
assert_allclose_units(
water.atom_types["opls_112"].parameters["sigma"],
1.0 * u.nm,
rtol=1e-5,
atol=1e-8,
)
assert_allclose_units(
water.atom_types["opls_112"].parameters["epsilon"],
0.0 * u.Unit("kJ/mol"),
rtol=1e-5,
atol=1e-8,
)
assert_allclose_units(
water.bond_types["opls_111~opls_112"].parameters["r_eq"],
0.09572 * u.nm,
rtol=1e-5,
atol=1e-8,
)
assert_allclose_units(
water.bond_types["opls_111~opls_112"].parameters["k"],
502416.0 * u.Unit("kJ/(mol*nm**2)"),
rtol=1e-5,
atol=1e-8,
)
assert_allclose_units(
water.angle_types["opls_112~opls_111~opls_112"].
parameters["theta_eq"],
1.824218134 * u.radian,
rtol=1e-5,
atol=1e-8,
)
assert_allclose_units(
water.angle_types["opls_112~opls_111~opls_112"].parameters["k"],
682.02 * u.Unit("kJ/(mol*rad**2)"),
rtol=1e-5,
atol=1e-8,
)
