def test_pass_box(self, mb_ethane):
mb_box = Box(lengths=[3, 3, 3])
top = from_mbuild(mb_ethane, box=mb_box)
assert_allclose_units(top.box.lengths, [3, 3, 3] * u.nm,
rtol=1e-5,
atol=1e-8)
def test_power():
"""
Take units to some power.
"""
from sympy import nsimplify
from unyt import dimensionless
pc_mks = m_per_pc
mK_mks = 1e-3
u1_dims = mass * length**2 * time**-3 * temperature**4
u1 = Unit("kg * pc**2 * s**-3 * mK**4")
u2 = u1**2
assert u2.dimensions == u1_dims**2
assert_allclose_units(u2.base_value, (pc_mks**2 * mK_mks**4)**2, 1e-12)
u3 = u1**(-1.0 / 3)
assert u3.dimensions == nsimplify(u1_dims**(-1.0 / 3))
assert_allclose_units(u3.base_value, (pc_mks**2 * mK_mks**4)**(-1.0 / 3),
1e-12)
assert u1**0.0 == dimensionless
def test_double_conversion(self, templates):
# Pick some OPLS parameters at random
params = {
'k0': 1.38 * u.Unit('kJ/mol'),
'k1': -0.51 * u.Unit('kJ/mol'),
'k2': 2.2 * u.Unit('kJ/mol'),
'k3': -0.25 * u.Unit('kJ/mol'),
'k4': 1.44 * u.Unit('kJ/mol')
}
opls_torsion_potential = templates['OPLSTorsionPotential']
name = opls_torsion_potential.name
expression = opls_torsion_potential.expression
variables = opls_torsion_potential.independent_variables
opls_connection_type = DihedralType(name=name,
expression=expression,
independent_variables=variables,
parameters=params)
# Convert connection to RB
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
# Convert connection back to OPLS
final_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
assert_allclose_units([*opls_connection_type.parameters.values()],
[*final_connection_type.parameters.values()],
rtol=1e-5,
atol=1e-8)
def test_box_dims(self, typed_ar_system):
n_topology_sites = len(typed_ar_system.sites)
omm_top = to_openmm(typed_ar_system)
topology_lengths = typed_ar_system.box.lengths
omm_lengths = omm_top.getUnitCellDimensions()
assert_allclose_units(topology_lengths.value, omm_lengths._value, rtol=1e-5, atol=1e-8)
def test_multiplication():
"""
Multiply two units.
"""
msun_mks = mass_sun_kg
pc_mks = m_per_pc
# Create symbols
msun_sym = Symbol("Msun", positive=True)
pc_sym = Symbol("pc", positive=True)
s_sym = Symbol("s", positive=True)
# Create units
u1 = Unit("Msun")
u2 = Unit("pc")
# Mul operation
u3 = u1 * u2
assert u3.expr == msun_sym * pc_sym
assert_allclose_units(u3.base_value, msun_mks * pc_mks, 1e-12)
assert u3.dimensions == mass * length
# Pow and Mul operations
u4 = Unit("pc**2")
u5 = Unit("Msun * s")
u6 = u4 * u5
assert u6.expr == pc_sym**2 * msun_sym * s_sym
assert_allclose_units(u6.base_value, pc_mks**2 * msun_mks, 1e-12)
assert u6.dimensions == length**2 * mass * time
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_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 test_pass_box_bounding(self, mb_ethane):
mb_ethane.periodicity = [0, 0, 0]
top = from_mbuild(mb_ethane)
assert_allclose_units(
top.box.lengths,
(mb_ethane.boundingbox.lengths + [0.5, 0.5, 0.5]) * u.nm,
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_scaled_vectors(self):
box = Box(lengths=u.unyt_array((2, 2, 2), u.nm), angles=u.degree*[40.0, 50.0, 60.0])
vectors = box.get_vectors()
test_vectors = np.array([[1, 0, 0],
[0.5, 0.86603, 0],
[0.64278, 0.51344, 0.56852]])
test_vectors = (test_vectors.T * box.lengths).T
assert_allclose_units(vectors, test_vectors, rtol=1e-5, atol=u.nm*1e-3)
assert vectors.units == u.nm
def test_scaling_unit_vectors(self):
box = Box(lengths=u.unyt_array((2, 2, 2), u.nm), angles=u.degree*[40.0, 50.0, 60.0])
u_vectors = box.get_unit_vectors()
scaled_u_vectors = (u_vectors.T * box.lengths).T
scaled_vectors = box.get_vectors()
assert_allclose_units(scaled_vectors, scaled_u_vectors, rtol=1e-5, atol=u.nm*1e-3)
assert scaled_u_vectors.units == u.nm
def test_pass_box_bounding(self, mb_ethane):
mb_ethane.periodicity = [False, False, False]
top = from_mbuild(mb_ethane)
assert_allclose_units(
top.box.lengths,
(mb_ethane.get_boundingbox().lengths) * u.nm,
rtol=1e-5,
atol=1e-8,
)
def test_add_box(self):
top = Topology()
box = Box(2 * u.nm * np.ones(3))
assert top.box is None
top.box = box
assert top.box is not None
assert_allclose_units(
top.box.lengths, u.nm * 2 * np.ones(3), rtol=1e-5, atol=1e-8
)
def test_read_water(self, typed_water_system):
write_lammpsdata(typed_water_system, filename='data.water')
water = read_lammpsdata('data.water')
assert_allclose_units(water.sites[0].charge,
u.unyt_array(-0.834, u.elementary_charge),
rtol=1e-5,
atol=1e-8)
assert water.n_sites == 6
assert water.n_connections == 6
def test_particle_positions(self, typed_ar_system):
typed_ar_system.sites[0].position = (1, 1, 1) * u.nanometer
omm_top = to_openmm(typed_ar_system, openmm_object="modeller")
assert_allclose_units(
omm_top.positions._value,
typed_ar_system.positions.value,
rtol=1e-5,
atol=1e-8,
)
def test_bel_neper():
assert Unit("B").dimensions == Unit("Np").dimensions
a = 1 * Unit("B") / (np.log(10) / 2)
assert_allclose_units(a.to("Np"), 1 * Unit("Np"))
a = 2 * Unit("B")
b = 20 * Unit("decibel")
assert (a == b).all()
c = 2 * Unit("Np")
d = 20 * Unit("decineper")
assert (c == d).all()
assert Unit("dB")**1 == Unit("dB")
def test_full_io(self):
original_top = read_xyz(get_fn("ethane.xyz"))
write_xyz(original_top, "full_conversion.xyz")
new_top = read_xyz("full_conversion.xyz")
assert original_top.n_sites == new_top.n_sites
assert original_top.n_connections == new_top.n_connections
assert_allclose_units(original_top.positions,
new_top.positions,
rtol=1e-5,
atol=1e-8)
def test_read_gro(self):
top = read_gro(get_fn('acn.gro'))
assert top.name == 'ACN'
assert top.n_sites == 6
assert_allclose_units(top.box.lengths, 4*np.ones(3)*u.nm, rtol=1e-5, atol=1e-8)
top = read_gro(get_fn('350-waters.gro'))
assert top.name == 'Generic title'
assert top.n_sites == 1050
assert_allclose_units(top.box.lengths, 2.20866*np.ones(3)*u.nm, rtol=1e-5, atol=1e-8)
def test_read_lammps_triclinic(self, typed_ar_system):
typed_ar_system.box = Box(lengths=[1, 1, 1], angles=[60, 90, 120])
write_lammpsdata(typed_ar_system, filename='data.triclinic')
read = read_lammpsdata('data.triclinic')
assert_allclose_units(read.box.lengths,
u.unyt_array([1, 1, 1], u.nm),
rtol=1e-5,
atol=1e-8)
assert_allclose_units(read.box.angles,
u.unyt_array([60, 90, 120], u.degree),
rtol=1e-5,
atol=1e-8)
def test_new_potential(self):
new_potential = ParametricPotential(
name='mypotential',
expression='a*x+b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
assert new_potential.name == 'mypotential'
assert new_potential.expression == sympy.sympify('a*x+b')
assert_allclose_units(new_potential.parameters['a'], 1.0 * u.g, rtol=1e-5, atol=1e-8)
assert_allclose_units(new_potential.parameters['b'], 1.0 * u.m, rtol=1e-5, atol=1e-8)
assert new_potential.independent_variables == {sympy.symbols('x')}
def test_from_parmed_basic(self, angles):
struc = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top = from_parmed(struc, refer_type=False)
for site in top.sites:
assert site.atom_type is None
for connection in top.connections:
assert connection.connection_type is None
assert top.n_sites == 8
assert top.n_bonds == 7
assert top.box is not None
lengths = u.nm * [0.714, 0.7938, 0.6646]
assert_allclose_units(top.box.lengths, lengths, rtol=1e-5, atol=1e-8)
assert_allclose_units(top.box.angles, angles, rtol=1e-5, atol=1e-8)
def test_create_from_expr():
"""
Create units from sympy Exprs and check attributes.
"""
pc_mks = m_per_pc
yr_mks = sec_per_year
# Symbol expr
s1 = Symbol("pc", positive=True)
s2 = Symbol("yr", positive=True)
# Mul expr
s3 = s1 * s2
# Pow expr
s4 = s1**2 * s2**(-1)
u1 = Unit(s1)
u2 = Unit(s2)
u3 = Unit(s3)
u4 = Unit(s4)
assert u1.expr == s1
assert u2.expr == s2
assert u3.expr == s3
assert u4.expr == s4
assert_allclose_units(u1.base_value, pc_mks, 1e-12)
assert_allclose_units(u2.base_value, yr_mks, 1e-12)
assert_allclose_units(u3.base_value, pc_mks * yr_mks, 1e-12)
assert_allclose_units(u4.base_value, pc_mks**2 / yr_mks, 1e-12)
assert u1.dimensions == length
assert u2.dimensions == time
assert u3.dimensions == length * time
assert u4.dimensions == length**2 / time
def test_create_with_duplicate_dimensions():
"""
Create units with overlapping dimensions. Ex: km/Mpc.
"""
u1 = Unit("J * s**-1")
u2 = Unit("km/s/Mpc")
km_mks = m_per_km
Mpc_mks = m_per_mpc
assert u1.base_value == 1
assert u1.dimensions == power
assert_allclose_units(u2.base_value, km_mks / Mpc_mks, 1e-12)
assert u2.dimensions == rate
def test_setters(self, charge, mass):
new_type = AtomType()
new_type.name = "SettingName"
new_type.charge = -1.0 * charge
new_type.mass = 1 * mass
new_type.independent_variables = 'r'
new_type.parameters = {'sigma': 1 * u.nm,
'epsilon': 10 * u.Unit('kcal / mol')}
new_type.expression = 'r * sigma * epsilon'
assert new_type.name == "SettingName"
assert_allclose_units(new_type.charge, -1.0 * charge, rtol=1e-5, atol=1e-8)
assert_allclose_units(new_type.mass, 1 * mass, rtol=1e-5, atol=1e-8)
assert new_type.independent_variables == {sympy.symbols('r')}
assert new_type.parameters == {'sigma': 1 * u.nm,
'epsilon': 10 * u.Unit('kcal / mol')}
assert new_type.expression == sympy.sympify('r * sigma * epsilon')
def test_base_equivalent():
"""
Check base equivalent of a unit.
"""
Msun_mks = mass_sun_kg
Mpc_mks = m_per_mpc
u1 = Unit("Msun * Mpc**-3")
u2 = Unit("kg * m**-3")
u3 = u1.get_base_equivalent()
assert u2.expr == u3.expr
assert u2 == u3
assert_allclose_units(u1.base_value, Msun_mks / Mpc_mks ** 3, 1e-12)
assert u2.base_value == 1
assert u3.base_value == 1
mass_density = mass / length ** 3
assert u1.dimensions == mass_density
assert u2.dimensions == mass_density
assert u3.dimensions == mass_density
assert_allclose_units(
u1.get_conversion_factor(u3)[0], Msun_mks / Mpc_mks ** 3, 1e-12
)
with pytest.raises(UnitConversionError):
u1.get_conversion_factor(Unit("m"))
with pytest.raises(UnitConversionError):
u1.get_conversion_factor(Unit("degF"))
reg = UnitRegistry(unit_system=cgs_unit_system)
u = Unit("kg", registry=reg)
assert u.get_base_equivalent() == Unit("g")
u = Unit("kg")
assert u.get_base_equivalent() == Unit("kg")
u = Unit("A")
assert u.get_base_equivalent(unit_system="mks") == Unit("A")
def test_new_atom_type(self, charge, mass):
new_type = AtomType(name='mytype', charge=charge, mass=mass,
parameters={'sigma': 1 * u.nm,
'epsilon': 10 * u.Unit('kcal / mol')},
independent_variables={'r'})
assert new_type.name == 'mytype'
assert_allclose_units(new_type.charge, charge, rtol=1e-5, atol=1e-8)
assert_allclose_units(new_type.parameters['sigma'], 1 * u.nm, rtol=1e-5, atol=1e-8)
assert_allclose_units(new_type.parameters['epsilon'], 10 * u.Unit('kcal / mol'), rtol=1e-5, atol=1e-8)
assert_allclose_units(new_type.mass, mass, rtol=1e-5, atol=1e-8)
def test_from_parmed_parametrized_structure(self, angles):
struc = pmd.load_file(get_fn('ethane.top'), xyz=get_fn('ethane.gro'))
top = from_parmed(struc)
assert top.n_sites == 8
assert top.n_bonds == 7
assert top.n_angles == 12
assert top.n_dihedrals == 9
assert top.n_connections == 28
for site in top.sites:
assert site.atom_type is not None
assert site.charge is not None
for connection in top.connections:
assert connection.connection_type is not None
assert top.box is not None
lengths = u.nm * [0.714, 0.7938, 0.6646]
assert_allclose_units(top.box.lengths, lengths, rtol=1e-5, atol=1e-8)
assert_allclose_units(top.box.angles, angles, rtol=1e-5, atol=1e-8)
def test_new_potential(self):
new_potential = ParametricPotential(
name="mypotential",
expression="a*x+b",
parameters={
"a": 1.0 * u.g,
"b": 1.0 * u.m
},
independent_variables={"x"},
)
assert new_potential.name == "mypotential"
assert new_potential.expression == sympy.sympify("a*x+b")
assert_allclose_units(new_potential.parameters["a"],
1.0 * u.g,
rtol=1e-5,
atol=1e-8)
assert_allclose_units(new_potential.parameters["b"],
1.0 * u.m,
rtol=1e-5,
atol=1e-8)
assert new_potential.independent_variables == {sympy.symbols("x")}
def test_division():
"""
Divide two units.
"""
pc_mks = m_per_pc
km_mks = m_per_km
# Create symbols
pc_sym = Symbol("pc", positive=True)
km_sym = Symbol("km", positive=True)
s_sym = Symbol("s", positive=True)
# Create units
u1 = Unit("pc")
u2 = Unit("km * s")
u3 = u1 / u2
assert u3.expr == pc_sym / (km_sym * s_sym)
assert_allclose_units(u3.base_value, pc_mks / km_mks, 1e-12)
assert u3.dimensions == 1 / time