def test_structure(self):
quartz = self.quartz.structure
np.testing.assert_array_almost_equal(
quartz.lattice.matrix,
[[4.913400, 0, 0], [-2.456700, 4.255129, 0], [0, 0, 5.405200]])
self.assertEqual(quartz.formula, "Si3 O6")
self.assertNotIn("molecule-ID", self.quartz.atoms.columns)
ethane = self.ethane.structure
np.testing.assert_array_almost_equal(ethane.lattice.matrix,
np.diag([10.0] * 3))
lbounds = np.array(self.ethane.box.bounds)[:, 0]
coords = self.ethane.atoms[["x", "y", "z"]].values - lbounds
np.testing.assert_array_almost_equal(ethane.cart_coords, coords)
np.testing.assert_array_almost_equal(ethane.site_properties["charge"],
self.ethane.atoms["q"])
tatb = self.tatb.structure
frac_coords = tatb.frac_coords[381]
real_frac_coords = frac_coords - np.floor(frac_coords)
np.testing.assert_array_almost_equal(
real_frac_coords, [0.01553397, 0.71487872, 0.14134139])
co = Structure.from_spacegroup(194,
Lattice.hexagonal(2.50078, 4.03333),
["Co"], [[1 / 3, 2 / 3, 1 / 4]])
ld_co = LammpsData.from_structure(co)
self.assertEqual(ld_co.structure.composition.reduced_formula, "Co")
ni = Structure.from_spacegroup(225, Lattice.cubic(3.50804), ["Ni"],
[[0, 0, 0]])
ld_ni = LammpsData.from_structure(ni)
self.assertEqual(ld_ni.structure.composition.reduced_formula, "Ni")
def get_unit_cell(self, specie, lattice, alat):
"""
Get the unit cell from specie, lattice type and lattice constant.
Args
specie (str): Name of specie.
lattice (str): The lattice type of structure. e.g. bcc or diamond.
alat (float): The lattice constant of specific lattice and specie.
"""
if lattice == 'fcc':
unit_cell = Structure.from_spacegroup(sg='Fm-3m',
lattice=Lattice.cubic(alat),
species=[specie],
coords=[[0, 0, 0]])
elif lattice == 'bcc':
unit_cell = Structure.from_spacegroup(sg='Im-3m',
lattice=Lattice.cubic(alat),
species=[specie],
coords=[[0, 0, 0]])
elif lattice == 'diamond':
unit_cell = Structure.from_spacegroup(sg='Fd-3m',
lattice=Lattice.cubic(alat),
species=[specie],
coords=[[0, 0, 0]])
else:
raise ValueError("Lattice type is invalid.")
return unit_cell
def test_structure(self):
quartz = self.quartz.structure
np.testing.assert_array_equal(quartz.lattice.matrix,
[[4.913400, 0, 0],
[-2.456700, 4.255129, 0],
[0, 0, 5.405200]])
self.assertEqual(quartz.formula, "Si3 O6")
self.assertNotIn("molecule-ID", self.quartz.atoms.columns)
ethane = self.ethane.structure
np.testing.assert_array_equal(ethane.lattice.matrix,
np.diag([10.0] * 3))
lbounds = np.array(self.ethane.box.bounds)[:, 0]
coords = self.ethane.atoms[["x", "y", "z"]].values - lbounds
np.testing.assert_array_equal(ethane.cart_coords, coords)
np.testing.assert_array_equal(ethane.site_properties["charge"],
self.ethane.atoms["q"])
tatb = self.tatb.structure
frac_coords = tatb.frac_coords[381]
real_frac_coords = frac_coords - np.floor(frac_coords)
np.testing.assert_array_almost_equal(real_frac_coords,
[0.01553397,
0.71487872,
0.14134139])
co = Structure.from_spacegroup(194,
Lattice.hexagonal(2.50078, 4.03333),
["Co"], [[1/3, 2/3, 1/4]])
ld_co = LammpsData.from_structure(co)
self.assertEqual(ld_co.structure.composition.reduced_formula, "Co")
ni = Structure.from_spacegroup(225, Lattice.cubic(3.50804),
["Ni"], [[0, 0, 0]])
ld_ni = LammpsData.from_structure(ni)
self.assertEqual(ld_ni.structure.composition.reduced_formula, "Ni")
def test_sulfide_type(self):
# NaS2 -> polysulfide
latt = Lattice.tetragonal(9.59650, 11.78850)
species = ["Na"] * 2 + ["S"] * 2
coords = [[0.00000, 0.00000, 0.17000], [0.27600, 0.25000, 0.12500],
[0.03400, 0.25000, 0.29600], [0.14700, 0.11600, 0.40000]]
struct = Structure.from_spacegroup(122, latt, species, coords)
self.assertEqual(sulfide_type(struct), "polysulfide")
# NaCl type NaS -> sulfide
latt = Lattice.cubic(5.75)
species = ["Na", "S"]
coords = [[0.00000, 0.00000, 0.00000], [0.50000, 0.50000, 0.50000]]
struct = Structure.from_spacegroup(225, latt, species, coords)
self.assertEqual(sulfide_type(struct), "sulfide")
# Na2S2O3 -> None (sulfate)
latt = Lattice.monoclinic(6.40100, 8.10000, 8.47400, 96.8800)
species = ["Na"] * 2 + ["S"] * 2 + ["O"] * 3
coords = [[0.29706, 0.62396, 0.08575], [0.37673, 0.30411, 0.45416],
[0.52324, 0.10651, 0.21126], [0.29660, -0.04671, 0.26607],
[0.17577, 0.03720, 0.38049], [0.38604, -0.20144, 0.33624],
[0.16248, -0.08546, 0.11608]]
struct = Structure.from_spacegroup(14, latt, species, coords)
self.assertEqual(sulfide_type(struct), None)
# Na3PS3O -> sulfide
latt = Lattice.orthorhombic(9.51050, 11.54630, 5.93230)
species = ["Na"] * 2 + ["S"] * 2 + ["P", "O"]
coords = [[0.19920, 0.11580, 0.24950], [0.00000, 0.36840, 0.29380],
[0.32210, 0.36730, 0.22530], [0.50000, 0.11910, 0.27210],
[0.50000, 0.29400, 0.35500], [0.50000, 0.30300, 0.61140]]
struct = Structure.from_spacegroup(36, latt, species, coords)
self.assertEqual(sulfide_type(struct), "sulfide")
def setUp(self):
self.structure1 = Structure.from_spacegroup("Fd-3m", Lattice.cubic(5.46873),
["Si"], [[0, 0, 0]])
self.structure2 = Structure.from_spacegroup("Fm-3m", Lattice.cubic(5.69169),
['Na', 'Cl'], [[0, 0, 0], [0, 0, 0.5]])
self.structure3 = Structure.from_spacegroup("Pm-3m", Lattice.cubic(3.88947),
['Ca', 'Ti', 'O'], [[0.5, 0.5, 0.5], [0, 0, 0], [0, 0, 0.5]])
def setUp(self):
self.unary_struct = Structure.from_spacegroup("Im-3m",
Lattice.cubic(3.4268),
["Li"], [[0, 0, 0]])
self.binary_struct = Structure.from_spacegroup(
"Fm-3m", Lattice.cubic(5.69169), ['Na', 'Cl'],
[[0, 0, 0], [0, 0, 0.5]])
self.describer = SmoothOverlapAtomicPosition(cutoff=4.8,
l_max=8,
n_max=8)
def setUp(self):
self.unary_struct = Structure.from_spacegroup('Im-3m',
Lattice.cubic(3.4268),
[{
"Li": 1
}], [[0, 0, 0]])
self.binary_struct = Structure.from_spacegroup(
225, Lattice.cubic(5.69169), ['Na', 'Cl'],
[[0, 0, 0], [0, 0, 0.5]])
self.describer = SOAPDescriptor(cutoff=4.8, l_max=8, n_max=8)
def setUp(self):
self.structure1 = Structure.from_spacegroup("Fd-3m",
Lattice.cubic(5.46873),
["Si"], [[0, 0, 0]])
self.structure2 = Structure.from_spacegroup("Fm-3m",
Lattice.cubic(5.69169),
["Na", "Cl"],
[[0, 0, 0], [0, 0, 0.5]])
self.structure3 = Structure.from_spacegroup(
"Pm-3m", Lattice.cubic(3.88947), ["Ca", "Ti", "O"],
[[0.5, 0.5, 0.5], [0, 0, 0], [0, 0, 0.5]])
def setUp(self):
element_profile = {'Ni': {'r': 0.5, 'w': 1}}
describer1 = BispectrumCoefficients(rcutfac=4.1,
twojmax=8,
element_profile=element_profile,
quadratic=False,
pot_fit=True)
model1 = LinearModel(describer=describer1)
model1.model.coef_ = coeff
model1.model.intercept_ = intercept
snap1 = SNAPotential(model=model1)
snap1.specie = Element('Ni')
self.ff_settings1 = snap1
describer2 = BispectrumCoefficients(rcutfac=4.1,
twojmax=8,
element_profile=element_profile,
quadratic=True,
pot_fit=True)
model2 = LinearModel(describer=describer2)
model2.model.coef_ = coeff
model2.model.intercept_ = intercept
snap2 = SNAPotential(model=model2)
snap2.specie = Element('Ni')
self.ff_settings2 = snap2
self.struct = Structure.from_spacegroup('Fm-3m', Lattice.cubic(3.506),
['Ni'], [[0, 0, 0]])
def setUp(self):
latt = Lattice.cubic(4.17)
species = ["Ni", "O"]
coords = [[0, 0, 0], [0.5, 0.5, 0.5]]
self.NiO = Structure.from_spacegroup(225, latt, species, coords)
latt = Lattice([[2.085, 2.085, 0.0], [0.0, -2.085, -2.085],
[-2.085, 2.085, -4.17]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0, 0.5], [0, 0, 0], [0.25, 0.5, 0.25],
[0.75, 0.5, 0.75]]
self.NiO_AFM_111 = Structure(latt, species, coords)
self.NiO_AFM_111.add_spin_by_site([-5, 5, 0, 0])
latt = Lattice([[2.085, 2.085, 0], [0, 0, -4.17], [-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5], [0, 0, 0], [0, 0.5, 0], [0.5, 0, 0.5]]
self.NiO_AFM_001 = Structure(latt, species, coords)
self.NiO_AFM_001.add_spin_by_site([-5, 5, 0, 0])
parser = CifParser(os.path.join(test_dir, 'Fe3O4.cif'))
self.Fe3O4 = parser.get_structures()[0]
trans = AutoOxiStateDecorationTransformation()
self.Fe3O4_oxi = trans.apply_transformation(self.Fe3O4)
parser = CifParser(os.path.join(test_dir, 'Li8Fe2NiCoO8.cif'))
self.Li8Fe2NiCoO8 = parser.get_structures()[0]
self.Li8Fe2NiCoO8.remove_oxidation_states()
warnings.simplefilter("ignore")
def setUp(self):
element_profile = {"Ni": {"r": 0.5, "w": 1}}
describer1 = BispectrumCoefficients(rcutfac=4.1,
twojmax=8,
element_profile=element_profile,
quadratic=False,
pot_fit=True)
model1 = SKLModel(describer=describer1, model=LinearRegression())
model1.model.coef_ = coeff
model1.model.intercept_ = intercept
snap1 = SNAPotential(model=model1)
self.ff_settings1 = snap1
describer2 = BispectrumCoefficients(rcutfac=4.1,
twojmax=8,
element_profile=element_profile,
quadratic=True,
pot_fit=True)
model2 = SKLModel(describer=describer2, model=LinearRegression())
model2.model.coef_ = coeff
model2.model.intercept_ = intercept
snap2 = SNAPotential(model=model2)
self.ff_settings2 = snap2
self.struct = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.506),
["Ni"], [[0, 0, 0]])
def setUp(self):
self.structure = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.5),
["Ni"], [[0, 0, 0]])
lattice = Lattice.cubic(3.010)
frac_coords = [[0.00000, 0.00000, 0.00000],
[0.00000, 0.50000, 0.50000],
[0.50000, 0.00000, 0.50000],
[0.50000, 0.50000, 0.00000],
[0.50000, 0.00000, 0.00000],
[0.50000, 0.50000, 0.50000],
[0.00000, 0.00000, 0.50000],
[0.00000, 0.50000, 0.00000]]
species = ['Mg', 'Mg', 'Mg', 'Mg', 'O', 'O', 'O', 'O']
self.MgO = Structure(lattice, species, frac_coords)
slabs = generate_all_slabs(self.structure, max_index=2,
min_slab_size=6.0, min_vacuum_size=15.0,
max_normal_search=1, center_slab=True)
self.slab_dict = {''.join([str(i) for i in slab.miller_index]):
slab for slab in slabs}
self.asf_211 = AdsorbateSiteFinder(self.slab_dict["211"])
self.asf_100 = AdsorbateSiteFinder(self.slab_dict["100"])
self.asf_111 = AdsorbateSiteFinder(self.slab_dict["111"])
self.asf_110 = AdsorbateSiteFinder(self.slab_dict["110"])
self.asf_struct = AdsorbateSiteFinder(
Structure.from_sites(self.slab_dict["111"].sites))
def setUp(self):
with open(os.path.join(test_dir, 'test_toec_data.json')) as f:
self.data_dict = json.load(f)
self.strains = [Strain(sm) for sm in self.data_dict['strains']]
self.pk_stresses = [Stress(d) for d in self.data_dict['pk_stresses']]
self.c2 = self.data_dict["C2_raw"]
self.c3 = self.data_dict["C3_raw"]
self.exp = ElasticTensorExpansion.from_voigt([self.c2, self.c3])
self.cu = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.623),
["Cu"], [[0] * 3])
indices = [(0, 0), (0, 1), (3, 3)]
values = [167.8, 113.5, 74.5]
cu_c2 = ElasticTensor.from_values_indices(values,
indices,
structure=self.cu,
populate=True)
indices = [(0, 0, 0), (0, 0, 1), (0, 1, 2), (0, 3, 3), (0, 5, 5),
(3, 4, 5)]
values = [-1507., -965., -71., -7., -901., 45.]
cu_c3 = Tensor.from_values_indices(values,
indices,
structure=self.cu,
populate=True)
self.exp_cu = ElasticTensorExpansion([cu_c2, cu_c3])
cu_c4 = Tensor.from_voigt(self.data_dict["Cu_fourth_order"])
self.exp_cu_4 = ElasticTensorExpansion([cu_c2, cu_c3, cu_c4])
warnings.simplefilter("ignore")
def setUp(self):
self.structure = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.5),
["Ni"], [[0, 0, 0]])
lattice = Lattice.cubic(3.010)
frac_coords = [
[0.00000, 0.00000, 0.00000],
[0.00000, 0.50000, 0.50000],
[0.50000, 0.00000, 0.50000],
[0.50000, 0.50000, 0.00000],
[0.50000, 0.00000, 0.00000],
[0.50000, 0.50000, 0.50000],
[0.00000, 0.00000, 0.50000],
[0.00000, 0.50000, 0.00000],
]
species = ["Mg", "Mg", "Mg", "Mg", "O", "O", "O", "O"]
self.MgO = Structure(lattice, species, frac_coords)
slabs = generate_all_slabs(
self.structure,
max_index=2,
min_slab_size=6.0,
min_vacuum_size=15.0,
max_normal_search=1,
center_slab=True,
)
self.slab_dict = {
"".join([str(i) for i in slab.miller_index]): slab
for slab in slabs
}
self.asf_211 = AdsorbateSiteFinder(self.slab_dict["211"])
self.asf_100 = AdsorbateSiteFinder(self.slab_dict["100"])
self.asf_111 = AdsorbateSiteFinder(self.slab_dict["111"])
self.asf_110 = AdsorbateSiteFinder(self.slab_dict["110"])
self.asf_struct = AdsorbateSiteFinder(
Structure.from_sites(self.slab_dict["111"].sites))
def disorder(self,apecies,spacegroup="C2"):
from pymatgen import Structure, Lattice
from pymatgen.io.vasp.sets import MPRelaxSet
import numpy as np
import os
cod=[]
for i in apecies:
cod.append(np.random.rand(3).tolist())
# print(cod)
custom_settings = {"NELMIN": 5}
specie = apecies
cuau = Structure.from_spacegroup(sg=spacegroup, lattice=Lattice.cubic(10), species=apecies, coords=cod)
relax = MPRelaxSet(cuau, user_incar_settings=custom_settings)
os.chdir(self.dire)
print (os.getcwd())
gge=[]
for n in specie:
for key,value in n.items():
gge.append(key)
jji=[]
for j in gge:
jji.append(str(j)[:-2])
str1 = "-".join(jji)
print (str1)
relax.write_input(str(str1))
def test_from_structure(self):
latt = Lattice.monoclinic(9.78746, 4.75058, 8.95892, 115.9693)
structure = Structure.from_spacegroup(
15,
latt,
["Os", "O", "O"],
[
[0, 0.25583, 0.75],
[0.11146, 0.46611, 0.91631],
[0.11445, 0.04564, 0.69518],
],
)
velocities = np.random.randn(20, 3) * 0.1
structure.add_site_property("velocities", velocities)
ld = LammpsData.from_structure(structure=structure,
ff_elements=["O", "Os", "Na"])
i = random.randint(0, 19)
a = latt.matrix[0]
va = velocities[i].dot(a) / np.linalg.norm(a)
self.assertAlmostEqual(va, ld.velocities.loc[i + 1, "vx"])
self.assertAlmostEqual(velocities[i, 1], ld.velocities.loc[i + 1,
"vy"])
np.testing.assert_array_almost_equal(ld.masses["mass"],
[22.989769, 190.23, 15.9994])
np.testing.assert_array_equal(ld.atoms["type"], [2] * 4 + [3] * 16)
def test_sulfide_type(self):
# NaS2 -> polysulfide
latt = Lattice.tetragonal(9.59650, 11.78850)
species = ["Na"] * 2 + ["S"] * 2
coords = [[0.00000, 0.00000, 0.17000],
[0.27600, 0.25000, 0.12500],
[0.03400, 0.25000, 0.29600],
[0.14700, 0.11600, 0.40000]]
struct = Structure.from_spacegroup(122, latt, species, coords)
self.assertEqual(sulfide_type(struct), "polysulfide")
# NaCl type NaS -> sulfide
latt = Lattice.cubic(5.75)
species = ["Na", "S"]
coords = [[0.00000, 0.00000, 0.00000],
[0.50000, 0.50000, 0.50000]]
struct = Structure.from_spacegroup(225, latt, species, coords)
self.assertEqual(sulfide_type(struct), "sulfide")
# Na2S2O3 -> None (sulfate)
latt = Lattice.monoclinic(6.40100, 8.10000, 8.47400, 96.8800)
species = ["Na"] * 2 + ["S"] * 2 + ["O"] * 3
coords = [[0.29706, 0.62396, 0.08575],
[0.37673, 0.30411, 0.45416],
[0.52324, 0.10651, 0.21126],
[0.29660, -0.04671, 0.26607],
[0.17577, 0.03720, 0.38049],
[0.38604, -0.20144, 0.33624],
[0.16248, -0.08546, 0.11608]]
struct = Structure.from_spacegroup(14, latt, species, coords)
self.assertEqual(sulfide_type(struct), None)
# Na3PS3O -> sulfide
latt = Lattice.orthorhombic(9.51050, 11.54630, 5.93230)
species = ["Na"] * 2 + ["S"] * 2 + ["P", "O"]
coords = [[0.19920, 0.11580, 0.24950],
[0.00000, 0.36840, 0.29380],
[0.32210, 0.36730, 0.22530],
[0.50000, 0.11910, 0.27210],
[0.50000, 0.29400, 0.35500],
[0.50000, 0.30300, 0.61140]]
struct = Structure.from_spacegroup(36, latt, species, coords)
self.assertEqual(sulfide_type(struct), "sulfide")
# test for unphysical cells
struct.scale_lattice(struct.volume*10)
self.assertEqual(sulfide_type(struct), "sulfide")
def bi(self):
"""Return BCC Bi structure."""
bcc_bi = Structure.from_spacegroup(
"Im-3m", Lattice.cubic(3.453), ["Bi"], [[0, 0, 0]]
)
bcc_bi = bcc_bi.get_reduced_structure("niggli")
return bcc_bi
def setUp(self):
self.unary_struct = Structure.from_spacegroup("Im-3m",
Lattice.cubic(3.4268),
["Li"], [[0, 0, 0]])
self.binary_struct = Structure.from_spacegroup(
"Fm-3m", Lattice.cubic(5.69169), ['Na', 'Cl'],
[[0, 0, 0], [0, 0, 0.5]])
self.r_etas = [0.01, 0.02, 0.05]
self.r_shift = [0]
self.zetas = [1.0, 4.0]
self.a_etas = [0.01, 0.05]
self.lambdas = [-1, 1]
self.describer = BPSymmetryFunctions(cutoff=4.8,
r_etas=self.r_etas,
r_shift=self.r_shift,
lambdas=self.lambdas,
a_etas=self.a_etas,
zetas=self.zetas)
def setUp(self):
super(TestAdsorptionWorkflow, self).setUp()
self.struct_ir = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.875728), ["Ir"], [[0, 0, 0]])
sgp = {"max_index": 1, "min_slab_size": 7.0, "min_vacuum_size": 20.0}
slabs = generate_all_slabs(self.struct_ir, **sgp)
slabs = [slab for slab in slabs if slab.miller_index==(1, 0, 0)]
sgp.pop("max_index")
self.wf_1 = get_wf_surface(slabs, [Molecule("H", [[0, 0, 0]])], self.struct_ir, sgp,
db_file=os.path.join(db_dir, "db.json"))
def setUpClass(cls):
cls.s = Structure.from_spacegroup('Fm-3m', Lattice.cubic(5.69169),
['Na', 'Cl'],
[[0, 0, 0], [0, 0, 0.5]])
cls.dummy_model = MEGNetModel(100,
2,
nblocks=1,
n1=4,
n2=2,
n3=2,
npass=1)
def setUp(self):
self.structure = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.5),
["Ni"], [[0, 0, 0]])
slabs = generate_all_slabs(self.structure, max_index=2,
min_slab_size=6.0, min_vacuum_size=15.0,
max_normal_search=1, center_slab=True)
self.slab_dict = {''.join([str(i) for i in slab.miller_index]):
slab for slab in slabs}
self.asf_211 = AdsorbateSiteFinder(self.slab_dict["211"])
self.asf_100 = AdsorbateSiteFinder(self.slab_dict["100"])
self.asf_111 = AdsorbateSiteFinder(self.slab_dict["111"])
self.asf_110 = AdsorbateSiteFinder(self.slab_dict["110"])
def setUp(self):
element_profile = {'Ni': {'r': 0.5, 'w': 1}}
describer = BispectrumCoefficients(cutoff=4.1, twojmax=8,
element_profile=element_profile,
pot_fit=True)
model = SKLModel(describer=describer, model=LinearRegression())
model.model.coef_ = coeff
model.model.intercept_ = intercept
snap = SNAPotential(model=model)
self.struct = Structure.from_spacegroup('Fm-3m', Lattice.cubic(3.506),
['Ni'], [[0, 0, 0]])
self.ff_settings = snap
def setUp(self):
super(TestAdsorptionWorkflow, self).setUp()
self.struct_ir = Structure.from_spacegroup(
"Fm-3m", Lattice.cubic(3.875728), ["Ir"], [[0, 0, 0]])
sgp = {"max_index": 1, "min_slab_size": 7.0, "min_vacuum_size": 20.0}
self.slabs = generate_all_slabs(self.struct_ir, **sgp)
self.slab_100 = [slab for slab in self.slabs
if slab.miller_index==(1, 0, 0)][0]
self.wf_1 = get_wf_slab(self.slab_100, True,
[Molecule("H", [[0, 0, 0]])],
db_file=os.path.join(db_dir, "db.json"))
def setUp(self):
self.unary_struct = Structure.from_spacegroup('Im-3m',
Lattice.cubic(3.4268),
[{
"Li": 1
}], [[0, 0, 0]])
self.num_symm2 = 3
self.a_etas = [0.01, 0.05]
self.describer = BPSymmetryFunctions(dmin=2.0,
cutoff=4.8,
num_symm2=self.num_symm2,
a_etas=self.a_etas)
def test_md(self):
s = Structure.from_spacegroup(225, Lattice.cubic(3.62126), ["Cu"],
[[0, 0, 0]])
ld = LammpsData.from_structure(s, atom_style="atomic")
ff = "\n".join(["pair_style eam", "pair_coeff * * Cu_u3.eam"])
md = LammpsRun.md(data=ld,
force_field=ff,
temperature=1600.0,
nsteps=10000)
md.write_inputs(output_dir="md")
with open(os.path.join("md", "in.md")) as f:
md_script = f.read()
script_string = """# Sample input script template for MD
# Initialization
units metal
atom_style atomic
# Atom definition
read_data md.data
#read_restart md.restart
# Force field settings (consult official document for detailed formats)
pair_style eam
pair_coeff * * Cu_u3.eam
# Create velocities
velocity all create 1600.0 142857 mom yes rot yes dist gaussian
# Ensemble constraints
#fix 1 all nve
fix 1 all nvt temp 1600.0 1600.0 0.1
#fix 1 all npt temp 1600.0 1600.0 0.1 iso $pressure $pressure 1.0
# Various operations within timestepping
#fix ...
#compute ...
# Output settings
#thermo_style custom ... # control the thermo data type to output
thermo 100 # output thermo data every N steps
#dump 1 all atom 100 traj.*.gz # dump a snapshot every 100 steps
# Actions
run 10000
"""
self.assertEqual(md_script, script_string)
self.assertTrue(os.path.exists(os.path.join("md", "md.data")))
def setUp(self):
# trivial example, simple square lattice for testing
structure = Structure(Lattice.tetragonal(5.0, 50.0), ['H'], [[0, 0, 0]])
self.square_sg = StructureGraph.with_empty_graph(structure, edge_weight_name="", edge_weight_units="")
self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(1, 0, 0))
self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, 1, 0))
self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
# body-centered square lattice for testing
structure = Structure(Lattice.tetragonal(5.0, 50.0), ['H', 'He'], [[0, 0, 0], [0.5, 0.5, 0.5]])
self.bc_square_sg = StructureGraph.with_empty_graph(structure, edge_weight_name="", edge_weight_units="")
self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(1, 0, 0))
self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, 1, 0))
self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(0, 0, 0))
self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(-1, -1, 0))
self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
# body-centered square lattice for testing
# directions reversed, should be equivalent to as bc_square
structure = Structure(Lattice.tetragonal(5.0, 50.0), ['H', 'He'], [[0, 0, 0], [0.5, 0.5, 0.5]])
self.bc_square_sg_r = StructureGraph.with_empty_graph(structure, edge_weight_name="", edge_weight_units="")
self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(1, 0, 0))
self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, 1, 0))
self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
self.bc_square_sg_r.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(0, 0, 0))
self.bc_square_sg_r.add_edge(1, 0, from_jimage=(-1, 0, 0), to_jimage=(0, 0, 0))
self.bc_square_sg_r.add_edge(1, 0, from_jimage=(-1, -1, 0), to_jimage=(0, 0, 0))
self.bc_square_sg_r.add_edge(1, 0, from_jimage=(0, -1, 0), to_jimage=(0, 0, 0))
# MoS2 example, structure graph obtained from critic2
# (not ground state, from mp-1023924, single layer)
stdout_file = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files/critic2/MoS2_critic2_stdout.txt')
with open(stdout_file, 'r') as f:
reference_stdout = f.read()
self.structure = Structure.from_file(os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files/critic2/MoS2.cif'))
c2o = Critic2Output(self.structure, reference_stdout)
self.mos2_sg = c2o.structure_graph(edge_weight="bond_length", edge_weight_units="Å")
latt = Lattice.cubic(4.17)
species = ["Ni", "O"]
coords = [[0, 0, 0],
[0.5, 0.5, 0.5]]
self.NiO = Structure.from_spacegroup(225, latt, species, coords).get_primitive_structure()
def test_apply_transformation(self):
Li_bulk = Structure.from_spacegroup("Im-3m", Lattice.cubic(2.96771),
["Li"], [[0, 0, 0]])
gb_gen_params_s3 = {"rotation_axis": [1, 1, 1], "rotation_angle": 60.0,
"expand_times": 2, "vacuum_thickness": 0.0, "normal": True,
"ratio": None, "plane": None}
gbg = GBGenerator(Li_bulk)
gb_from_generator = gbg.gb_from_parameters(**gb_gen_params_s3)
gbt_s3 = GrainBoundaryTransformation(**gb_gen_params_s3)
gb_from_trans = gbt_s3.apply_transformation(Li_bulk)
self.assertArrayAlmostEqual(gb_from_generator.lattice.matrix,
gb_from_trans.lattice.matrix)
self.assertArrayAlmostEqual(gb_from_generator.cart_coords,
gb_from_trans.cart_coords)
def setUp(self):
self.s1 = Structure.from_spacegroup(225,
Lattice.cubic(5.69169),
["Na", "Cl"],
[[0, 0, 0], [0, 0, 0.5]])
self.s2 = Structure.from_dict({'@class': 'Structure',
'@module': 'pymatgen.core.structure',
'charge': None,
'lattice': {'a': 5.488739045730133,
'alpha': 60.0000000484055,
'b': 5.488739048031658,
'beta': 60.00000003453459,
'c': 5.48873905,
'gamma': 60.000000071689925,
'matrix': [[4.75338745, 0.0, 2.74436952],
[1.58446248, 4.48153667, 2.74436952],
[0.0, 0.0, 5.48873905]],
'volume': 116.92375473740876},
'sites': [{'abc': [0.5, 0.5, 0.5],
'label': 'Al',
'properties': {'coordination_no': 10, 'forces': [0.0, 0.0, 0.0]},
'species': [{'element': 'Al', 'occu': 1}],
'xyz': [3.168924965, 2.240768335, 5.488739045]},
{'abc': [0.5, 0.5, 0.0],
'label': 'Al',
'properties': {'coordination_no': 10, 'forces': [0.0, 0.0, 0.0]},
'species': [{'element': 'Al', 'occu': 1}],
'xyz': [3.168924965, 2.240768335, 2.74436952]},
{'abc': [0.0, 0.5, 0.5],
'label': 'Al',
'properties': {'coordination_no': 10, 'forces': [0.0, 0.0, 0.0]},
'species': [{'element': 'Al', 'occu': 1}],
'xyz': [0.79223124, 2.240768335, 4.116554285]},
{'abc': [0.5, 0.0, 0.5],
'label': 'Al',
'properties': {'coordination_no': 10, 'forces': [0.0, 0.0, 0.0]},
'species': [{'element': 'Al', 'occu': 1}],
'xyz': [2.376693725, 0.0, 4.116554285]},
{'abc': [0.875, 0.875, 0.875],
'label': 'Lu',
'properties': {'coordination_no': 16, 'forces': [0.0, 0.0, 0.0]},
'species': [{'element': 'Lu', 'occu': 1}],
'xyz': [5.54561868875, 3.9213445862499996, 9.60529332875]},
{'abc': [0.125, 0.125, 0.125],
'label': 'Lu',
'properties': {'coordination_no': 16, 'forces': [0.0, 0.0, 0.0]},
'species': [{'element': 'Lu', 'occu': 1}],
'xyz': [0.79223124125, 0.56019208375, 1.37218476125]}]})
def test_md(self):
s = Structure.from_spacegroup(225, Lattice.cubic(3.62126),
["Cu"], [[0, 0, 0]])
ld = LammpsData.from_structure(s, atom_style="atomic")
ff = "\n".join(["pair_style eam", "pair_coeff * * Cu_u3.eam"])
md = LammpsRun.md(data=ld, force_field=ff, temperature=1600.0,
nsteps=10000)
md.write_inputs(output_dir="md")
with open(os.path.join("md", "in.md")) as f:
md_script = f.read()
script_string = """# Sample input script template for MD
# Initialization
units metal
atom_style atomic
# Atom definition
read_data md.data
#read_restart md.restart
# Force field settings (consult official document for detailed formats)
pair_style eam
pair_coeff * * Cu_u3.eam
# Create velocities
velocity all create 1600.0 142857 mom yes rot yes dist gaussian
# Ensemble constraints
#fix 1 all nve
fix 1 all nvt temp 1600.0 1600.0 0.1
#fix 1 all npt temp 1600.0 1600.0 0.1 iso $pressure $pressure 1.0
# Various operations within timestepping
#fix ...
#compute ...
# Output settings
#thermo_style custom ... # control the thermo data type to output
thermo 100 # output thermo data every N steps
#dump 1 all atom 100 traj.*.gz # dump a snapshot every 100 steps
# Actions
run 10000
"""
self.assertEqual(md_script, script_string)
self.assertTrue(os.path.exists(os.path.join("md", "md.data")))
def test_apply_transformation(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
Al_bulk = Structure.from_spacegroup("Fm-3m", Lattice.cubic(2.8575585),
["Al"], [[0, 0, 0]])
gb_gen_params_s5 = {"rotation_axis": [1, 0, 0], "rotation_angle": 53.13010235415599,
"expand_times": 3, "vacuum_thickness": 0.0, "normal": True,
"plane": [0, -1, -3], 'rm_ratio': 0.6}
gbg = GrainBoundaryGenerator(Al_bulk)
gb_from_generator = gbg.gb_from_parameters(**gb_gen_params_s5)
gbt_s5 = GrainBoundaryTransformation(**gb_gen_params_s5)
gb_from_trans = gbt_s5.apply_transformation(Al_bulk)
self.assertArrayAlmostEqual(gb_from_generator.lattice.matrix,
gb_from_trans.lattice.matrix)
self.assertArrayAlmostEqual(gb_from_generator.cart_coords,
gb_from_trans.cart_coords)
def setUp(self):
self.structure = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.5),
["Ni"], [[0, 0, 0]])
slabs = generate_all_slabs(self.structure,
max_index=2,
min_slab_size=6.0,
min_vacuum_size=15.0,
max_normal_search=1,
center_slab=True)
self.slab_dict = {
''.join([str(i) for i in slab.miller_index]): slab
for slab in slabs
}
self.asf_211 = AdsorbateSiteFinder(self.slab_dict["211"])
self.asf_100 = AdsorbateSiteFinder(self.slab_dict["100"])
self.asf_111 = AdsorbateSiteFinder(self.slab_dict["111"])
self.asf_110 = AdsorbateSiteFinder(self.slab_dict["110"])
def from_parameters(structure_parameters: StructureParameters) -> Structure:
"""Generates a pymatgen ``Structure`` object using a material's structural
parameters.
:param structure_parameters: A ``StructureParameters`` tuple that specifies a
material's crystal structure.
:return: A pymatgen ``Structure`` object.
"""
cell_lattice: Lattice = Lattice.from_lengths_and_angles(
abc=structure_parameters.abc, ang=structure_parameters.ang)
cell_structure: Structure = Structure.from_spacegroup(
sg=structure_parameters.spacegroup,
lattice=cell_lattice,
species=structure_parameters.species,
coords=structure_parameters.coordinates,
)
return cell_structure
def test_from_structure(self):
latt = Lattice.monoclinic(9.78746, 4.75058, 8.95892, 115.9693)
structure = Structure.from_spacegroup(15, latt, ["Os", "O", "O"],
[[0, 0.25583, 0.75],
[0.11146, 0.46611, 0.91631],
[0.11445, 0.04564, 0.69518]])
velocities = np.random.randn(20, 3) * 0.1
structure.add_site_property("velocities", velocities)
ld = LammpsData.from_structure(structure=structure,
ff_elements=["O", "Os", "Na"])
i = random.randint(0, 19)
a = latt.matrix[0]
va = velocities[i].dot(a) / np.linalg.norm(a)
self.assertAlmostEqual(va, ld.velocities.loc[i + 1, "vx"])
self.assertAlmostEqual(velocities[i, 1],
ld.velocities.loc[i + 1, "vy"])
np.testing.assert_array_almost_equal(ld.masses["mass"],
[22.989769, 190.23, 15.9994])
np.testing.assert_array_equal(ld.atoms["type"], [2] * 4 + [3] * 16)
def test_describe(self):
s = Structure.from_spacegroup(225, Lattice.cubic(5.69169),
['Na', 'Cl'], [[0, 0, 0], [0, 0, 0.5]])
profile = dict(Na=dict(r=0.3, w=0.9), Cl=dict(r=0.7, w=3.0))
s *= [2, 2, 2]
structures = [s] * 10
for s in structures:
n = np.random.randint(4)
inds = np.random.randint(16, size=n)
s.remove_sites(inds)
bc_atom = BispectrumCoefficients(5,
3,
profile,
diagonalstyle=2,
quadratic=False,
pot_fit=False)
df_atom = bc_atom.describe_all(structures)
for i, s in enumerate(structures):
df_s = df_atom.xs(i, level='input_index')
self.assertEqual(df_s.shape, (len(s), 4))
self.assertTrue(df_s.equals(bc_atom.describe(s)))
bc_pot = BispectrumCoefficients(5,
3,
profile,
diagonalstyle=2,
quadratic=False,
pot_fit=True)
df_pot = bc_pot.describe_all(structures, include_stress=True)
for i, s in enumerate(structures):
df_s = df_pot.xs(i, level='input_index')
self.assertEqual(df_s.shape, ((1 + len(s) * 3 + 6, 10)))
self.assertTrue(
df_s.equals(bc_pot.describe(s, include_stress=True)))
sna = df_s.iloc[0]
for specie in ['Na', 'Cl']:
self.assertAlmostEqual(
sna[specie, 'n'],
s.composition.fractional_composition[specie])
np.testing.assert_array_equal(df_s[specie, 'n'][1:],
np.zeros(len(s) * 3 + 6))
def test_apply_transformation(self):
s = self.get_structure("LiFePO4")
trans = SlabTransformation([0, 0, 1], 10, 10, shift=0.25)
gen = SlabGenerator(s, [0, 0, 1], 10, 10)
slab_from_gen = gen.get_slab(0.25)
slab_from_trans = trans.apply_transformation(s)
self.assertArrayAlmostEqual(slab_from_gen.lattice.matrix,
slab_from_trans.lattice.matrix)
self.assertArrayAlmostEqual(slab_from_gen.cart_coords,
slab_from_trans.cart_coords)
fcc = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"],
[[0, 0, 0]])
trans = SlabTransformation([1, 1, 1], 10, 10)
slab_from_trans = trans.apply_transformation(fcc)
gen = SlabGenerator(fcc, [1, 1, 1], 10, 10)
slab_from_gen = gen.get_slab()
self.assertArrayAlmostEqual(slab_from_gen.lattice.matrix,
slab_from_trans.lattice.matrix)
self.assertArrayAlmostEqual(slab_from_gen.cart_coords,
slab_from_trans.cart_coords)
def test_apply_transformation(self):
s = self.get_structure("LiFePO4")
trans = SlabTransformation([0, 0, 1], 10, 10, shift = 0.25)
gen = SlabGenerator(s, [0, 0, 1], 10, 10)
slab_from_gen = gen.get_slab(0.25)
slab_from_trans = trans.apply_transformation(s)
self.assertArrayAlmostEqual(slab_from_gen.lattice.matrix,
slab_from_trans.lattice.matrix)
self.assertArrayAlmostEqual(slab_from_gen.cart_coords,
slab_from_trans.cart_coords)
fcc = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"],
[[0, 0, 0]])
trans = SlabTransformation([1, 1, 1], 10, 10)
slab_from_trans = trans.apply_transformation(fcc)
gen = SlabGenerator(fcc, [1, 1, 1], 10, 10)
slab_from_gen = gen.get_slab()
self.assertArrayAlmostEqual(slab_from_gen.lattice.matrix,
slab_from_trans.lattice.matrix)
self.assertArrayAlmostEqual(slab_from_gen.cart_coords,
slab_from_trans.cart_coords)
def test_transform(self):
s = Structure.from_spacegroup("Fm-3m", Lattice.cubic(5.69169),
["Na", "Cl"], [[0, 0, 0], [0, 0, 0.5]])
profile = dict(Na=dict(r=0.3, w=0.9), Cl=dict(r=0.7, w=3.0))
s *= [2, 2, 2]
structures = [s] * 10
for s in structures:
n = np.random.randint(4)
inds = np.random.randint(16, size=n)
s.remove_sites(inds)
bc_atom = BispectrumCoefficients(rcutfac=5,
twojmax=3,
element_profile=profile,
quadratic=False,
pot_fit=False)
df_atom = bc_atom.transform(structures)
for i, s in enumerate(structures):
df_s = df_atom.xs(i, level="input_index")
self.assertEqual(df_s.shape, (len(s), 8))
self.assertTrue(df_s.equals(bc_atom.transform_one(s)))
bc_pot = BispectrumCoefficients(rcutfac=5,
twojmax=3,
element_profile=profile,
quadratic=False,
pot_fit=True,
include_stress=True)
df_pot = bc_pot.transform(structures)
for i, s in enumerate(structures):
df_s = df_pot.xs(i, level="input_index")
self.assertEqual(df_s.shape, (1 + len(s) * 3 + 6, 18))
self.assertTrue(df_s.equals(bc_pot.transform_one(s)))
sna = df_s.iloc[0]
for specie in ["Na", "Cl"]:
self.assertAlmostEqual(
sna[specie, "n"],
s.composition.fractional_composition[specie])
np.testing.assert_array_equal(df_s[specie, "n"][1:],
np.zeros(len(s) * 3 + 6))
def setUp(self):
latt = Lattice.cubic(4.17)
species = ["Ni", "O"]
coords = [[0, 0, 0],
[0.5, 0.5, 0.5]]
self.NiO = Structure.from_spacegroup(225, latt, species, coords)
latt = Lattice([[2.085, 2.085, 0.0],
[0.0, -2.085, -2.085],
[-2.085, 2.085, -4.17]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0, 0.5],
[0, 0, 0],
[0.25, 0.5, 0.25],
[0.75, 0.5, 0.75]]
self.NiO_AFM_111 = Structure(latt, species, coords)
self.NiO_AFM_111.add_spin_by_site([-5, 5, 0, 0])
latt = Lattice([[2.085, 2.085, 0],
[0, 0, -4.17],
[-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5],
[0, 0, 0],
[0, 0.5, 0],
[0.5, 0, 0.5]]
self.NiO_AFM_001 = Structure(latt, species, coords)
self.NiO_AFM_001.add_spin_by_site([-5, 5, 0, 0])
parser = CifParser(os.path.join(test_dir, 'Fe3O4.cif'))
self.Fe3O4 = parser.get_structures()[0]
trans = AutoOxiStateDecorationTransformation()
self.Fe3O4_oxi = trans.apply_transformation(self.Fe3O4)
parser = CifParser(os.path.join(test_dir, 'Li8Fe2NiCoO8.cif'))
self.Li8Fe2NiCoO8 = parser.get_structures()[0]
self.Li8Fe2NiCoO8.remove_oxidation_states()
warnings.simplefilter("ignore")
def setUp(self):
with open(os.path.join(test_dir, 'test_toec_data.json')) as f:
self.data_dict = json.load(f)
self.strains = [Strain(sm) for sm in self.data_dict['strains']]
self.pk_stresses = [Stress(d) for d in self.data_dict['pk_stresses']]
self.c2 = self.data_dict["C2_raw"]
self.c3 = self.data_dict["C3_raw"]
self.exp = ElasticTensorExpansion.from_voigt([self.c2, self.c3])
self.cu = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.623),
["Cu"], [[0]*3])
indices = [(0, 0), (0, 1), (3, 3)]
values = [167.8, 113.5, 74.5]
cu_c2 = ElasticTensor.from_values_indices(values, indices, structure=self.cu,
populate=True)
indices = [(0, 0, 0), (0, 0, 1), (0, 1, 2),
(0, 3, 3), (0, 5, 5), (3, 4, 5)]
values = [-1507., -965., -71., -7., -901., 45.]
cu_c3 = Tensor.from_values_indices(values, indices, structure=self.cu,
populate=True)
self.exp_cu = ElasticTensorExpansion([cu_c2, cu_c3])
cu_c4 = Tensor.from_voigt(self.data_dict["Cu_fourth_order"])
self.exp_cu_4 = ElasticTensorExpansion([cu_c2, cu_c3, cu_c4])
def test_describe(self):
s = Structure.from_spacegroup(225, Lattice.cubic(5.69169),
["Na", "Cl"], [[0, 0, 0], [0, 0, 0.5]])
profile = dict(Na=dict(r=0.5, w=1.0), Cl=dict(r=0.5, w=0.8))
bc = BispectrumCoefficients(rcutfac=5,
twojmax=4,
element_profile=profile,
diagonalstyle=3)
df = bc.describe(s)
self.assertAlmostEqual(df.loc[0, "0-0-0"], 62.9328)
self.assertTupleEqual(df.shape, (len(s), len(bc.subscripts)))
s *= [2, 2, 2]
structures = [s] * 10
for s in structures:
n = np.random.randint(4)
inds = np.random.randint(16, size=n)
s.remove_sites(inds)
df_all = bc.describe_all(structures)
i = random.randint(0, 9)
df_s = df_all.xs(i, level="input_index")
self.assertEqual(df_s.shape[0], len(structures[i]))
self.assertTrue(df_s.equals(bc.describe(structures[i])))
