def test_potcar_doenst_match_structure(self):
compat = MITCompatibility()
el_li = Element("Li")
el_o = Element("O")
el_h = Element("H")
latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
elts = [el_h, el_h, el_li, el_li, el_o, el_o]
coords = [[0.000000, 0.500000, 0.413969],
[0.500000, 0.000000, 0.586031],
[0.000000, 0.000000, 0.000000],
[0.500000, 0.500000, 0.000000],
[0.000000, 0.500000, 0.192672],
[0.500000, 0.000000, 0.807328]]
struct = Structure(latt, elts, coords)
lioh_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Fe 17Jan2003', 'PAW_PBE O 08Apr2002', 'PAW_PBE H 15Jun2001']})
self.assertIsNone(compat.process_entry(lioh_entry))
def cubic_supercell_info_wo_int(mocker, cubic_supercell):
mock = mocker.patch("pydefect.util.structure_tools.defaults")
mock.same_distance_criterion = defaults.same_distance_criterion
mock.cutoff_distance_factor = 1.7
sites = {
"H1":
Site(element="H",
wyckoff_letter="a",
site_symmetry="m-3m",
equivalent_atoms=[0, 1, 2, 3]),
"He1":
Site(element="He",
wyckoff_letter="b",
site_symmetry="m-3m",
equivalent_atoms=[4, 5, 6, 7])
}
unitcell = Structure(Lattice.rhombohedral(7.071068, 60),
species=["H", "He"],
coords=[[0.0] * 3, [0.5] * 3])
return SupercellInfo(cubic_supercell,
"Fm-3m", [[-2, 2, 2], [2, -2, 2], [2, 2, -2]],
sites,
unitcell_structure=unitcell)
def test_process_entry_superoxide(self):
el_li = Element("Li")
el_o = Element("O")
latt = Lattice([[3.985034, 0.0, 0.0],
[0.0, 4.881506, 0.0],
[0.0, 0.0, 2.959824]])
elts = [el_li, el_li, el_o, el_o, el_o, el_o]
coords = list()
coords.append([0.500000, 0.500000, 0.500000])
coords.append([0.0, 0.0, 0.0])
coords.append([0.632568, 0.085090, 0.500000])
coords.append([0.367432, 0.914910, 0.500000])
coords.append([0.132568, 0.414910, 0.000000])
coords.append([0.867432, 0.585090, 0.000000])
struct = Structure(latt, elts, coords)
lio2_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Fe 06Sep2000', 'PAW_PBE O 08Apr2002']})
lio2_entry_corrected = self.compat.process_entry(lio2_entry)
self.assertAlmostEqual(lio2_entry_corrected.energy, -3 -0.13893*4, 4)
def from_lines(lines_cell, lines_atom):
# ---------- lattice
unit = lines_cell[0].split()[1]
if unit[0] == '(' and unit[-1] == ')':
unit = unit[1:-1]
if unit.startswith('alat'):
scale = float(unit[unit.index('=') + 1:]) # in Bohr
scale = float(Length(scale, 'bohr').to('ang')) # in Ang
elif unit == 'bohr':
scale = float(Length(1.0, 'bohr').to('ang')) # in Ang
elif unit == 'angstrom':
scale = 1.0 # in Ang
else:
ValueError(
'unit "{0:s}" for CELL_PARAMETERS is not supported'.format(unit))
lattice = [[scale * float(x) for x in line.split()]
for line in lines_cell[1:4]]
# ---------- species & coordinates
unit = lines_atom[0].split()[1]
if unit[0] == '(' and unit[-1] == ')':
unit = unit[1:-1]
species = []
coords = []
for line in lines_atom[1:]:
fields = line.split()
species.append(fields[0])
coords.append([float(x) for x in fields[1:4]])
if unit == 'crystal':
pass # 'coords' are already internal coordinates
else:
ValueError(
'unit "{0:s}" for ATOMIC_POSITIONS is not supported yet'.
format(unit))
structure = Structure(lattice, species, coords)
return structure
def extract(entry):
struct = entry.structure
spacegroup = entry.spacegroup
pmg_s = Structure(struct.cell, struct.site_compositions,
struct.site_coords)
return OrderedDict([
('id', entry.id),
('label', entry.label),
('proto_label', entry.proto_label),
('formula', entry.name),
('composition', entry.spec_comp),
('reduced_comp', entry.red_comp),
('unit_comp', entry.unit_comp),
('total_energy_pa', entry.total_energy),
('formation_energy_pa', entry.energy),
('experiment', entry.composition.experiment),
('mass', entry.mass),
('stable', entry.stable),
('e_above_hull', entry.formationenergy_set.first().stability),
('is_ordered', pmg_s.is_ordered),
('band_gap', entry.band_gap),
('spacegroup', spacegroup.hm),
('spacegroup_hall', spacegroup.hall),
('spacegroup_id', spacegroup.number),
('spacegroup_schoenflies', spacegroup.schoenflies),
('is_centro_symmetric', spacegroup.centrosymmetric),
('natoms', struct.natoms),
('ntypes', struct.ntypes),
('nsites', struct.nsites),
# ('stresses', struct.stresses),
# ('forces', struct.forces),
('volume', struct.volume),
('volume_pa', struct.volume_pa),
# ('magmon', struct.magmom),
# ('magmon_pa', struct.magmom_pa),
]), OrderedDict([('id', entry.id), ('structure', pmg_s.as_dict())])
def run_displacement(file_primitive, prefix, scaling_matrix,
disp_magnitude_angstrom):
qeobj = QEParser()
qeobj.load_initial_structure(file_primitive)
structure = Structure(qeobj.lattice_vector.transpose(), qeobj.kd_in_str,
qeobj.x_fractional)
Structure.make_supercell(structure, scaling_matrix)
print("Supercell generated. # Atoms: %i" % structure.num_sites)
print("")
prefix0 = 'supercell'
disp = np.zeros((structure.num_sites, 3))
# update structural information of qeobj
qeobj_mod = update_qeobj(qeobj, structure)
# create the supercell structure
qeobj_mod.generate_structures(prefix0, ['original'], [disp])
# rename the file
command = ("mv %s1.pw.in %s0.scf.in" % (prefix0, prefix0))
os.system(command)
# Generate displacement files
gen_alm_input('ALM0.in', prefix0, 'suggest', structure, 1, "*-* None")
command = ("%s/alm/alm ALM0.in > ALM0.log" % ALAMODE_root)
os.system(command)
dispobj = AlamodeDisplace("fd", qeobj_mod, verbosity=0)
header_list, disp_list \
= dispobj.generate(file_pattern=["%s.pattern_HARMONIC" % prefix0],
magnitude=disp_magnitude_angstrom)
qeobj_mod.generate_structures(prefix, header_list, disp_list)
def from_file(name):
# ---------- last structure
with open(name, 'r') as f:
lines = f.readlines()
for i, line in enumerate(lines):
if 'ITEM: TIMESTEP' in line:
tmp_lines = lines[i:i+rin.natot+9]
lines = tmp_lines
# ---------- lattice
xlo_bound, xhi_bound, xy = [float(x) for x in lines[5].split()]
ylo_bound, yhi_bound, xz = [float(x) for x in lines[6].split()]
zlo_bound, zhi_bound, yz = [float(x) for x in lines[7].split()]
xlo = xlo_bound - min(0.0, xy, xz, xy+xz)
xhi = xhi_bound - max(0.0, xy, xz, xy+xz)
ylo = ylo_bound - min(0.0, yz)
yhi = yhi_bound - max(0.0, yz)
zlo = zlo_bound
zhi = zhi_bound
a = [xhi-xlo, 0, 0]
b = [xy, yhi-ylo, 0]
c = [xz, yz, zhi-zlo]
lattice = np.array([a, b, c]) # in Ang, each row is a lattice vector
# ---------- non replica coordinates
coords = [[float(x) for x in line.split()][2:] for line in lines[9:]]
# ---------- species
species = [itertools.repeat(typ, times=num) for typ, num in zip(rin.atype, rin.nat)]
species = list(itertools.chain.from_iterable(species))
structure = Structure(lattice, species, coords)
return structure
def test_interstice_distribution_of_glass(self):
cuzr_glass = Structure(Lattice([[25, 0, 0], [0, 25, 0], [0, 0, 25]]),
["Cu", "Cu", "Cu", "Cu", "Cu", "Zr", "Cu", "Zr",
"Cu", "Zr", "Cu", "Zr", "Cu", "Cu"],
[[11.81159679, 16.49480537, 21.69139442],
[11.16777208, 17.87850033, 18.57877144],
[12.22394796, 15.83218325, 19.37763412],
[13.07053548, 14.34025424, 21.77557646],
[10.78147725, 19.61647494, 20.77595531],
[10.87541011, 14.65986432, 23.61517624],
[12.76631002, 18.41479521, 20.46717947],
[14.63911675, 16.47487037, 20.52671362],
[14.2470256, 18.44215167, 22.56257566],
[9.38050168, 16.87974592, 20.51885879],
[10.66332986, 14.43900833, 20.545186],
[11.57096832, 18.79848982, 23.26073408],
[13.27048138, 16.38613795, 23.59697472],
[9.55774984, 17.09220537, 23.1856528]],
coords_are_cartesian=True)
df_glass= pd.DataFrame({'struct': [cuzr_glass], 'site': [0]})
interstice_distribution = IntersticeDistribution()
intersticefp = interstice_distribution.featurize_dataframe(
df_glass, ['struct', 'site'])
self.assertAlmostEqual(intersticefp['Interstice_vol_mean'][0], 0.28905, 5)
self.assertAlmostEqual(intersticefp['Interstice_vol_std_dev'][0], 0.04037, 5)
self.assertAlmostEqual(intersticefp['Interstice_vol_minimum'][0], 0.21672, 5)
self.assertAlmostEqual(intersticefp['Interstice_vol_maximum'][0], 0.39084, 5)
self.assertAlmostEqual(intersticefp['Interstice_area_mean'][0], 0.16070, 5)
self.assertAlmostEqual(intersticefp['Interstice_area_std_dev'][0], 0.05245, 5)
self.assertAlmostEqual(intersticefp['Interstice_area_minimum'][0], 0.07132, 5)
self.assertAlmostEqual(intersticefp['Interstice_area_maximum'][0], 0.26953, 5)
self.assertAlmostEqual(intersticefp['Interstice_dist_mean'][0], 0.08154, 5)
self.assertAlmostEqual(intersticefp['Interstice_dist_std_dev'][0], 0.14778, 5)
self.assertAlmostEqual(intersticefp['Interstice_dist_minimum'][0], -0.04668, 5)
self.assertAlmostEqual(intersticefp['Interstice_dist_maximum'][0], 0.37565, 5)
def __init__(self,
structure: PymatgenStructure,
aos: List[str],
pbc: List[bool],
ns: int = 1,
na: int = 1,
cutoff: float = 6.00):
"""
Parameters
----------
structure: : PymatgenStructure
Pymatgen Structure object of the primitive cell used for calculating
neighbors from lattice transformations.It also requires site_properties
attribute with "Sitetypes"(Active or spectator site).
aos: List[str]
A list of all the active site species. For the Pt, N, NO configuration
set it as ['0', '1', '2']
pbc: List[bool]
Periodic Boundary Condition
ns: int (default 1)
The number of spectator types elements. For "S1" its 1.
na: int (default 1)
the number of active types elements. For "A1" its 1.
cutoff: float (default 6.00)
Cutoff of radius for getting local environment.Only
used down to 2 digits.
"""
try:
from pymatgen import Structure
except:
raise ImportError("This class requires pymatgen to be installed.")
if type(structure) is not Structure:
structure = Structure(**structure)
self.aos = aos
self.cutoff = np.around(cutoff, 2)
self.setup_env = _load_primitive_cell(structure, aos, pbc, ns, na, cutoff)
def test_velocities(self):
si = 14
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
# Silicon structure for testing.
latt = [
[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603],
]
struct = Structure(latt, [si, si], coords)
poscar = Poscar(struct)
poscar.set_temperature(900)
v = np.array(poscar.velocities)
for x in np.sum(v, axis=0):
self.assertAlmostEqual(x, 0, 7)
temperature = (struct[0].specie.atomic_mass.to("kg") * np.sum(v**2) /
(3 * const.k) * 1e10)
self.assertAlmostEqual(temperature, 900, 4,
"Temperature instantiated incorrectly")
poscar.set_temperature(700)
v = np.array(poscar.velocities)
for x in np.sum(v, axis=0):
self.assertAlmostEqual(
x, 0, 7, "Velocities initialized with a net momentum")
temperature = (struct[0].specie.atomic_mass.to("kg") * np.sum(v**2) /
(3 * const.k) * 1e10)
self.assertAlmostEqual(temperature, 700, 4,
"Temperature instantiated incorrectly")
def run_optimize(file_primitive, file_dfset, scaling_matrix):
qeobj = QEParser()
qeobj.load_initial_structure(file_primitive)
structure = Structure(qeobj.lattice_vector.transpose(), qeobj.kd_in_str,
qeobj.x_fractional)
Structure.make_supercell(structure, scaling_matrix)
print("Supercell generated. # Atoms: %i" % structure.num_sites)
print("")
prefix0 = 'supercell'
# Generate displacement files
gen_alm_input('ALM1.in',
prefix0,
'optimize',
structure,
1,
"*-* None",
dfset=file_dfset)
command = ("%s/alm/alm ALM1.in > ALM1.log" % ALAMODE_root)
os.system(command)
def test_from_seed(self):
from pymatgen import Lattice, Structure
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
lattice = Lattice.from_parameters(a=3.84,
b=3.84,
c=3.84,
alpha=120,
beta=90,
gamma=60)
struct = Structure(lattice, ["Si", "C"], coords)
s1 = pyxtal()
s1.from_seed(struct)
s2 = s1.subgroup_once(eps=0)
pmg_s1 = s1.to_pymatgen()
pmg_s2 = s2.to_pymatgen()
self.assertTrue(sm.StructureMatcher().fit(pmg_s1, pmg_s2))
pmg_s1 = Structure.from_file(cif_path + "B28.vasp")
struc = pyxtal()
struc.from_seed(seed=cif_path + "B28.vasp")
pmg_s2 = struc.to_pymatgen()
self.assertTrue(sm.StructureMatcher().fit(pmg_s1, pmg_s2))
permutation = {"B": "C"}
struc.subgroup_once(0.01, None, permutation, max_cell=2)
def test_aqueous_compat(self):
el_li = Element("Li")
el_o = Element("O")
el_h = Element("H")
latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
elts = [el_h, el_h, el_li, el_li, el_o, el_o]
coords = [[0.000000, 0.500000, 0.413969],
[0.500000, 0.000000, 0.586031],
[0.000000, 0.000000, 0.000000],
[0.500000, 0.500000, 0.000000],
[0.000000, 0.500000, 0.192672],
[0.500000, 0.000000, 0.807328]]
struct = Structure(latt, elts, coords)
lioh_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Fe 17Jan2003', 'PAW_PBE O 08Apr2002', 'PAW_PBE H 15Jun2001']})
lioh_entry_compat = self.compat.process_entry(lioh_entry)
lioh_entry_compat_aqcorr = self.aqcorr.correct_entry(lioh_entry_compat)
lioh_entry_aqcompat = self.aqcompat.process_entry(lioh_entry)
self.assertAlmostEqual(lioh_entry_compat_aqcorr.energy, lioh_entry_aqcompat.energy, 4)
def from_structure(cls, structure, ff_elements=None, atom_style="charge"):
"""
Simple constructor building LammpsData from a structure without
force field parameters and topologies.
Args:
structure (Structure): Input structure.
ff_elements ([str]): List of strings of elements that must
be present due to force field settings but not
necessarily in the structure. Default to None.
atom_style (str): Choose between "atomic" (neutral) and
"charge" (charged). Default to "charge".
"""
s = structure.get_sorted_structure()
box, symmop = lattice_2_lmpbox(s.lattice)
coords = symmop.operate_multi(s.cart_coords)
site_properties = s.site_properties
if "velocities" in site_properties:
velos = np.array(s.site_properties["velocities"])
rot = SymmOp.from_rotation_and_translation(symmop.rotation_matrix)
rot_velos = rot.operate_multi(velos)
site_properties.update({"velocities": rot_velos})
boxed_s = Structure(box.to_lattice(), s.species, coords,
site_properties=site_properties,
coords_are_cartesian=True)
symbols = list(s.symbol_set)
if ff_elements:
symbols.extend(ff_elements)
elements = sorted(Element(el) for el in set(symbols))
mass_info = [tuple([i.symbol] * 2) for i in elements]
ff = ForceField(mass_info)
topo = Topology(boxed_s)
return cls.from_ff_and_topologies(box=box, ff=ff, topologies=[topo],
atom_style=atom_style)
def get_recp_symmetry_operation(
self, symprec: float = 0.01) -> List:
"""
Find the symmetric operations of the reciprocal lattice,
to be used for hkl transformations
Args:
symprec: default is 0.001
"""
recp_lattice = self.reciprocal_lattice_crystallographic
# get symmetry operations from input conventional unit cell
# Need to make sure recp lattice is big enough, otherwise symmetry
# determination will fail. We set the overall volume to 1.
recp_lattice = recp_lattice.scale(1)
# need a localized import of structure to build a
# pseudo empty lattice for SpacegroupAnalyzer
from pymatgen import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
recp = Structure(recp_lattice, ["H"], [[0, 0, 0]])
# Creates a function that uses the symmetry operations in the
# structure to find Miller indices that might give repetitive slabs
analyzer = SpacegroupAnalyzer(recp, symprec=symprec)
recp_symmops = analyzer.get_symmetry_operations()
return recp_symmops
def test_peroxide_energy_corr(self):
latt = Lattice.from_parameters(3.159597, 3.159572, 7.685205, 89.999884, 89.999674, 60.000510)
el_li = Element("Li")
el_o = Element("O")
elts = [el_li, el_li, el_li, el_li, el_o, el_o, el_o, el_o]
coords = [[0.666656, 0.666705, 0.750001],
[0.333342, 0.333378, 0.250001],
[0.000001, 0.000041, 0.500001],
[0.000001, 0.000021, 0.000001],
[0.333347, 0.333332, 0.649191],
[0.333322, 0.333353, 0.850803],
[0.666666, 0.666686, 0.350813],
[0.666665, 0.666684, 0.149189]]
struct = Structure(latt, elts, coords)
li2o2_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Fe 06Sep2000', 'PAW_PBE O 08Apr2002']})
li2o2_entry_corrected = self.compat.process_entry(li2o2_entry)
self.assertRaises(AssertionError, self.assertAlmostEqual,
*(li2o2_entry_corrected.energy, -3 - 0.44317 * 4, 4))
self.assertAlmostEqual(li2o2_entry_corrected.energy, -3 - 0.66975 * 4, 4)
def test_subset(self):
sm = StructureMatcher(ltol=0.2,
stol=0.3,
angle_tol=5,
primitive_cell=False,
scale=True,
attempt_supercell=False,
allow_subset=True)
l = Lattice.orthorhombic(10, 20, 30)
s1 = Structure(l, ['Si', 'Si', 'Ag'],
[[0, 0, 0.1], [0, 0, 0.2], [.7, .4, .5]])
s2 = Structure(l, ['Si', 'Ag'], [[0, 0.1, 0], [-.7, .5, .4]])
result = sm.get_s2_like_s1(s1, s2)
self.assertEqual(
len(find_in_coord_list_pbc(result.frac_coords, [0, 0, 0.1])), 1)
self.assertEqual(
len(find_in_coord_list_pbc(result.frac_coords, [0.7, 0.4, 0.5])),
1)
#test with fewer species in s2
s1 = Structure(l, ['Si', 'Ag', 'Si'],
[[0, 0, 0.1], [0, 0, 0.2], [.7, .4, .5]])
s2 = Structure(l, ['Si', 'Si'], [[0, 0.1, 0], [-.7, .5, .4]])
result = sm.get_s2_like_s1(s1, s2)
mindists = np.min(s1.lattice.get_all_distances(s1.frac_coords,
result.frac_coords),
axis=0)
self.assertLess(np.max(mindists), 1e-6)
self.assertEqual(
len(find_in_coord_list_pbc(result.frac_coords, [0, 0, 0.1])), 1)
self.assertEqual(
len(find_in_coord_list_pbc(result.frac_coords, [0.7, 0.4, 0.5])),
1)
#test with not enough sites in s1
#test with fewer species in s2
s1 = Structure(l, ['Si', 'Ag', 'Cl'],
[[0, 0, 0.1], [0, 0, 0.2], [.7, .4, .5]])
s2 = Structure(l, ['Si', 'Si'], [[0, 0.1, 0], [-.7, .5, .4]])
self.assertEqual(sm.get_s2_like_s1(s1, s2), None)
def setUp(self):
self.diamond = Structure(
Lattice([[2.189, 0, 1.264], [0.73, 2.064, 1.264],
[0, 0, 2.528]]), ["C0+", "C0+"], [[2.554, 1.806, 4.423],
[0.365, 0.258, 0.632]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.diamond_no_oxi = Structure(
Lattice([[2.189, 0, 1.264], [0.73, 2.064, 1.264],
[0, 0, 2.528]]), ["C", "C"], [[2.554, 1.806, 4.423],
[0.365, 0.258, 0.632]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.nacl = Structure(
Lattice([[3.485, 0, 2.012], [1.162, 3.286, 2.012],
[0, 0, 4.025]]), ["Na1+", "Cl1-"], [[0, 0, 0],
[2.324, 1.643, 4.025]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.cscl = Structure(
Lattice([[4.209, 0, 0], [0, 4.209, 0], [0, 0, 4.209]]),
["Cl1-", "Cs1+"], [[2.105, 2.1045, 2.1045], [0, 0, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.ni3al = Structure(
Lattice([[3.52, 0, 0], [0, 3.52, 0], [0, 0, 3.52]]),
["Al", ] + ["Ni"] * 3,
[[0, 0, 0], [0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.sc = Structure(Lattice([[3.52, 0, 0], [0, 3.52, 0], [0, 0, 3.52]]),
["Al"], [[0, 0, 0]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False)
self.bond_angles = range(5, 180, 5)
def get_spg(data):
atomNames = data["name_array"]
latt = data["finalpos"]["basis"]
pos = data["finalpos"]["positions"]
crystal = Structure(latt, atomNames, pos)
return SpacegroupAnalyzer(crystal,symprec=0.02).get_space_group_symbol()
from pymatgen import Lattice, Structure
from pymatgen.analysis.diffraction.xrd import XRDCalculator
from IPython.display import Image, display
from matplotlib import pyplot
# Create CsCl structure
a = 4.209 #Angstrom(埃:一个长度单位，用来表示原子尺寸、键长和电磁波波长。)
latt = Lattice.cubic(a)
#latt:点阵一个长度为a的立方体
#species：物质，这里是["Cs", "Cl"]
#坐标：三位数组的列表，表示物质的坐标
structure = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
c = XRDCalculator()
#get_plot返回的结果就是一个pyplot类型的图片
image = c.get_plot(structure, two_theta_range=(0, 90), annotate_peaks=True, ax=None, with_labels=True, fontsize=16)
#image.show()
image.savefig("alpha CsCl.jpg")
#display(Image(filename=('./PDF - alpha CsCl.png')))
a = 6.923 #Angstrom
latt = Lattice.cubic(a)
structure = Structure(latt, ["Cs", "Cs", "Cs", "Cs", "Cl", "Cl", "Cl", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0], [0, 0.5, 0.5], [0.5, 0, 0.5],
[0.5, 0.5, 0.5], [0, 0, 0.5], [0, 0.5, 0], [0.5, 0, 0]])
image = c.get_plot(structure, two_theta_range=(0, 90), annotate_peaks=True, ax=None, with_labels=True, fontsize=16)
#display(Image(filename=('./PDF - beta CsCl.png')))这段代码display我还没有弄明白，帮我看看哪里出问题了
def test_write(self):
cw_ref_string = """# generated using pymatgen
data_GdB4
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 7.13160000
_cell_length_b 7.13160000
_cell_length_c 4.05050000
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural GdB4
_chemical_formula_sum 'Gd4 B16'
_cell_volume 206.00729003
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Gd Gd0 1 0.31746000 0.81746000 0.00000000 1.0
Gd Gd1 1 0.18254000 0.31746000 0.00000000 1.0
Gd Gd2 1 0.81746000 0.68254000 0.00000000 1.0
Gd Gd3 1 0.68254000 0.18254000 0.00000000 1.0
B B4 1 0.00000000 0.00000000 0.20290000 1.0
B B5 1 0.50000000 0.50000000 0.79710000 1.0
B B6 1 0.00000000 0.00000000 0.79710000 1.0
B B7 1 0.50000000 0.50000000 0.20290000 1.0
B B8 1 0.17590000 0.03800000 0.50000000 1.0
B B9 1 0.96200000 0.17590000 0.50000000 1.0
B B10 1 0.03800000 0.82410000 0.50000000 1.0
B B11 1 0.67590000 0.46200000 0.50000000 1.0
B B12 1 0.32410000 0.53800000 0.50000000 1.0
B B13 1 0.82410000 0.96200000 0.50000000 1.0
B B14 1 0.53800000 0.67590000 0.50000000 1.0
B B15 1 0.46200000 0.32410000 0.50000000 1.0
B B16 1 0.08670000 0.58670000 0.50000000 1.0
B B17 1 0.41330000 0.08670000 0.50000000 1.0
B B18 1 0.58670000 0.91330000 0.50000000 1.0
B B19 1 0.91330000 0.41330000 0.50000000 1.0
loop_
_atom_site_moment_label
_atom_site_moment_crystalaxis_x
_atom_site_moment_crystalaxis_y
_atom_site_moment_crystalaxis_z
Gd0 5.05000000 5.05000000 0.00000000
Gd1 -5.05000000 5.05000000 0.00000000
Gd2 5.05000000 -5.05000000 0.00000000
Gd3 -5.05000000 -5.05000000 0.00000000
"""
s_ncl = self.mcif_ncl.get_structures(primitive=False)[0]
cw = CifWriter(s_ncl, write_magmoms=True)
self.assertEqual(cw.__str__(), cw_ref_string)
# from list-type magmoms
list_magmoms = [list(m) for m in s_ncl.site_properties['magmom']]
# float magmoms (magnitude only)
float_magmoms = [float(m) for m in s_ncl.site_properties['magmom']]
s_ncl.add_site_property('magmom', list_magmoms)
cw = CifWriter(s_ncl, write_magmoms=True)
self.assertEqual(cw.__str__(), cw_ref_string)
s_ncl.add_site_property('magmom', float_magmoms)
cw = CifWriter(s_ncl, write_magmoms=True)
cw_ref_string_magnitudes = """# generated using pymatgen
data_GdB4
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 7.13160000
_cell_length_b 7.13160000
_cell_length_c 4.05050000
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural GdB4
_chemical_formula_sum 'Gd4 B16'
_cell_volume 206.00729003
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Gd Gd0 1 0.31746000 0.81746000 0.00000000 1.0
Gd Gd1 1 0.18254000 0.31746000 0.00000000 1.0
Gd Gd2 1 0.81746000 0.68254000 0.00000000 1.0
Gd Gd3 1 0.68254000 0.18254000 0.00000000 1.0
B B4 1 0.00000000 0.00000000 0.20290000 1.0
B B5 1 0.50000000 0.50000000 0.79710000 1.0
B B6 1 0.00000000 0.00000000 0.79710000 1.0
B B7 1 0.50000000 0.50000000 0.20290000 1.0
B B8 1 0.17590000 0.03800000 0.50000000 1.0
B B9 1 0.96200000 0.17590000 0.50000000 1.0
B B10 1 0.03800000 0.82410000 0.50000000 1.0
B B11 1 0.67590000 0.46200000 0.50000000 1.0
B B12 1 0.32410000 0.53800000 0.50000000 1.0
B B13 1 0.82410000 0.96200000 0.50000000 1.0
B B14 1 0.53800000 0.67590000 0.50000000 1.0
B B15 1 0.46200000 0.32410000 0.50000000 1.0
B B16 1 0.08670000 0.58670000 0.50000000 1.0
B B17 1 0.41330000 0.08670000 0.50000000 1.0
B B18 1 0.58670000 0.91330000 0.50000000 1.0
B B19 1 0.91330000 0.41330000 0.50000000 1.0
loop_
_atom_site_moment_label
_atom_site_moment_crystalaxis_x
_atom_site_moment_crystalaxis_y
_atom_site_moment_crystalaxis_z
Gd0 0.00000000 0.00000000 7.14177849
Gd1 0.00000000 0.00000000 7.14177849
Gd2 0.00000000 0.00000000 -7.14177849
Gd3 0.00000000 0.00000000 -7.14177849
"""
self.assertEqual(cw.__str__().strip(),
cw_ref_string_magnitudes.strip())
# test we're getting correct magmoms in ncl case
s_ncl2 = self.mcif_ncl2.get_structures()[0]
list_magmoms = [list(m) for m in s_ncl2.site_properties['magmom']]
self.assertEqual(list_magmoms[0][0], 0.0)
self.assertAlmostEqual(list_magmoms[0][1], 5.9160793408726366)
self.assertAlmostEqual(list_magmoms[1][0], -5.1234749999999991)
self.assertAlmostEqual(list_magmoms[1][1], 2.9580396704363183)
# test creating an structure without oxidation state doesn't raise errors
s_manual = Structure(Lattice.cubic(4.2), ["Cs", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
s_manual.add_spin_by_site([1, -1])
cw = CifWriter(s_manual, write_magmoms=True)
# check oxidation state
cw_manual_oxi_string = """# generated using pymatgen
data_CsCl
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 4.20000000
_cell_length_b 4.20000000
_cell_length_c 4.20000000
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural CsCl
_chemical_formula_sum 'Cs1 Cl1'
_cell_volume 74.08800000
_cell_formula_units_Z 1
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Cs+ 1.0
Cl+ 1.0
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Cs+ Cs0 1 0.00000000 0.00000000 0.00000000 1
Cl+ Cl1 1 0.50000000 0.50000000 0.50000000 1
loop_
_atom_site_moment_label
_atom_site_moment_crystalaxis_x
_atom_site_moment_crystalaxis_y
_atom_site_moment_crystalaxis_z
"""
s_manual.add_oxidation_state_by_site([1, 1])
cw = CifWriter(s_manual, write_magmoms=True)
self.assertEqual(cw.__str__(), cw_manual_oxi_string)
def setUp(self):
self.single_bond = Structure(Lattice.from_lengths_and_angles(
[10, 10, 10], [90, 90, 90]), ["H", "H", "H"],
[[1, 0, 0], [0, 0, 0], [6, 0, 0]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=True,
site_properties=None)
self.linear = Structure(Lattice.from_lengths_and_angles([10, 10, 10],
[90, 90, 90]),
["H", "H", "H"],
[[1, 0, 0], [0, 0, 0], [2, 0, 0]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=True,
site_properties=None)
self.bent45 = Structure(Lattice.from_lengths_and_angles([10, 10, 10],
[90, 90, 90]),
["H", "H", "H"],
[[0, 0, 0], [0.707, 0.707, 0], [0.707, 0, 0]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=True,
site_properties=None)
self.cubic = Structure(Lattice.from_lengths_and_angles([1, 1, 1],
[90, 90, 90]),
["H"], [[0, 0, 0]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=False,
site_properties=None)
self.bcc = Structure(Lattice.from_lengths_and_angles([1, 1, 1],
[90, 90, 90]),
["H", "H"], [[0, 0, 0], [0.5, 0.5, 0.5]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=False,
site_properties=None)
self.fcc = Structure(
Lattice.from_lengths_and_angles([1, 1, 1], [90, 90, 90]),
["H", "H", "H", "H"],
[[0, 0, 0], [0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=False,
site_properties=None)
self.hcp = Structure(Lattice.from_lengths_and_angles([1, 1, 1.633],
[90, 90, 120]),
["H", "H"],
[[0.3333, 0.6667, 0.25], [0.6667, 0.3333, 0.75]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=False,
site_properties=None)
self.diamond = Structure(
Lattice.from_lengths_and_angles([1, 1, 1], [90, 90, 90]),
["H", "H", "H", "H", "H", "H", "H", "H"],
[[0, 0, 0.5], [0.75, 0.75, 0.75], [0, 0.5, 0], [0.75, 0.25, 0.25],
[0.5, 0, 0], [0.25, 0.75, 0.25], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.75]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=False,
site_properties=None)
self.trigonal_off_plane = Structure(
Lattice.from_lengths_and_angles(
[100, 100, 100], [90, 90, 90]),
["H", "H", "H", "H"],
[[0.50, 0.50, 0.50], [0.25, 0.75, 0.25], \
[0.25, 0.25, 0.75], [0.75, 0.25, 0.25]], \
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.regular_triangle = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["H", "H", "H", "H"],
[[15, 15.28867, 15.65], [14.5, 15, 15], [15.5, 15, 15], \
[15, 15.866, 15]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.trigonal_planar = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["H", "H", "H", "H"],
[[15, 15.28867, 15], [14.5, 15, 15], [15.5, 15, 15], \
[15, 15.866, 15]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.square_planar = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["H", "H", "H", "H", "H"],
[[15, 15, 15], [14.75, 14.75, 15], [14.75, 15.25, 15], \
[15.25, 14.75, 15], [15.25, 15.25, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.square = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["H", "H", "H", "H", "H"],
[[15, 15, 15.707], [14.75, 14.75, 15], [14.75, 15.25, 15], \
[15.25, 14.75, 15], [15.25, 15.25, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.T_shape = Structure(
Lattice.from_lengths_and_angles([30, 30, 30], [90, 90, 90]),
["H", "H", "H", "H"],
[[15, 15, 15], [15, 15, 15.5], [15, 15.5, 15], [15, 14.5, 15]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=True,
site_properties=None)
self.square_pyramid = Structure(
Lattice.from_lengths_and_angles([30, 30, 30], [90, 90, 90]),
["H", "H", "H", "H", "H", "H"],
[[15, 15, 15], [15, 15, 15.3535], [14.75, 14.75, 15],
[14.75, 15.25, 15], [15.25, 14.75, 15], [15.25, 15.25, 15]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=True,
site_properties=None)
self.pentagonal_planar = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["Xe", "F", "F", "F", "F", "F"],
[[0, -1.6237, 0], [1.17969, 0, 0], [-1.17969, 0, 0], \
[1.90877, -2.24389, 0], [-1.90877, -2.24389, 0], [0, -3.6307, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.pentagonal_pyramid = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["Xe", "F", "F", "F", "F", "F", "F"],
[[0, -1.6237, 0], [0, -1.6237, 1.17969], [1.17969, 0, 0], \
[-1.17969, 0, 0], [1.90877, -2.24389, 0], \
[-1.90877, -2.24389, 0], [0, -3.6307, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.pentagonal_bipyramid = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]),
["Xe", "F", "F", "F", "F", "F", "F", "F"],
[[0, -1.6237, 0], [0, -1.6237, -1.17969], \
[0, -1.6237, 1.17969], [1.17969, 0, 0], \
[-1.17969, 0, 0], [1.90877, -2.24389, 0], \
[-1.90877, -2.24389, 0], [0, -3.6307, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.hexagonal_planar = Structure(
Lattice.from_lengths_and_angles([30, 30, 30], [90, 90, 90]),
["H", "C", "C", "C", "C", "C", "C"],
[[0, 0, 0], [0.71, 1.2298, 0], [-0.71, 1.2298, 0],
[0.71, -1.2298, 0], [-0.71, -1.2298, 0], [1.4199, 0, 0],
[-1.4199, 0, 0]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=True,
site_properties=None)
self.hexagonal_pyramid = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), \
["H", "Li", "C", "C", "C", "C", "C", "C"],
[[0, 0, 0], [0, 0, 1.675], [0.71, 1.2298, 0], \
[-0.71, 1.2298, 0], [0.71, -1.2298, 0], [-0.71, -1.2298, 0], \
[1.4199, 0, 0], [-1.4199, 0, 0]], \
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.hexagonal_bipyramid = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), \
["H", "Li", "Li", "C", "C", "C", "C", "C", "C"],
[[0, 0, 0], [0, 0, 1.675], [0, 0, -1.675], \
[0.71, 1.2298, 0], [-0.71, 1.2298, 0], \
[0.71, -1.2298, 0], [-0.71, -1.2298, 0], \
[1.4199, 0, 0], [-1.4199, 0, 0]], \
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.trigonal_pyramid = Structure(
Lattice.from_lengths_and_angles([30, 30, 30], [90, 90, 90]),
["P", "Cl", "Cl", "Cl", "Cl"],
[[0, 0, 0], [0, 0, 2.14], [0, 2.02, 0], [1.74937, -1.01, 0],
[-1.74937, -1.01, 0]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=True,
site_properties=None)
self.trigonal_bipyramidal = Structure(
Lattice.from_lengths_and_angles([30, 30, 30], [90, 90, 90]),
["P", "Cl", "Cl", "Cl", "Cl", "Cl"],
[[0, 0, 0], [0, 0, 2.14], [0, 2.02, 0], [1.74937, -1.01, 0],
[-1.74937, -1.01, 0], [0, 0, -2.14]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=True,
site_properties=None)
self.cuboctahedron = Structure(
Lattice.from_lengths_and_angles([30, 30, 30], [90, 90, 90]),
["H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H"],
[[15, 15, 15], [15, 14.5, 14.5], [15, 14.5, 15.5], [
15, 15.5, 14.5
], [15, 15.5, 15.5], [14.5, 15, 14.5], [14.5, 15, 15.5],
[15.5, 15, 14.5], [15.5, 15, 15.5], [14.5, 14.5, 15],
[14.5, 15.5, 15], [15.5, 14.5, 15], [15.5, 15.5, 15]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=True,
site_properties=None)
self.see_saw_rect = Structure(
Lattice.from_lengths_and_angles([30, 30, 30], [90, 90, 90]),
["H", "H", "H", "H", "H"],
[[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, -1.0, 0.0],
[0.0, 0.0, -1.0], [-1.0, 0.0, 0.0]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=True,
site_properties=None)
def test_supercell_subsets(self):
sm = StructureMatcher(ltol=0.2,
stol=0.3,
angle_tol=5,
primitive_cell=False,
scale=True,
attempt_supercell=True,
allow_subset=True,
supercell_size='volume')
sm_no_s = StructureMatcher(ltol=0.2,
stol=0.3,
angle_tol=5,
primitive_cell=False,
scale=True,
attempt_supercell=True,
allow_subset=False,
supercell_size='volume')
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ['Ag', 'Si', 'Si'],
[[.7, .4, .5], [0, 0, 0.1], [0, 0, 0.2]])
s1.make_supercell([2, 1, 1])
s2 = Structure(l, ['Si', 'Si', 'Ag'],
[[0, 0.1, -0.95], [0, 0.1, 0], [-.7, .5, .375]])
shuffle = [0, 2, 1, 3, 4, 5]
s1 = Structure.from_sites([s1[i] for i in shuffle])
#test when s1 is exact supercell of s2
result = sm.get_s2_like_s1(s1, s2)
for a, b in zip(s1, result):
self.assertTrue(a.distance(b) < 0.08)
self.assertEqual(a.species_and_occu, b.species_and_occu)
self.assertTrue(sm.fit(s1, s2))
self.assertTrue(sm.fit(s2, s1))
self.assertTrue(sm_no_s.fit(s1, s2))
self.assertTrue(sm_no_s.fit(s2, s1))
rms = (0.048604032430991401, 0.059527539448807391)
self.assertTrue(np.allclose(sm.get_rms_dist(s1, s2), rms))
self.assertTrue(np.allclose(sm.get_rms_dist(s2, s1), rms))
#test when the supercell is a subset of s2
subset_supercell = s1.copy()
del subset_supercell[0]
result = sm.get_s2_like_s1(subset_supercell, s2)
self.assertEqual(len(result), 6)
for a, b in zip(subset_supercell, result):
self.assertTrue(a.distance(b) < 0.08)
self.assertEqual(a.species_and_occu, b.species_and_occu)
self.assertTrue(sm.fit(subset_supercell, s2))
self.assertTrue(sm.fit(s2, subset_supercell))
self.assertFalse(sm_no_s.fit(subset_supercell, s2))
self.assertFalse(sm_no_s.fit(s2, subset_supercell))
rms = (0.053243049896333279, 0.059527539448807336)
self.assertTrue(np.allclose(sm.get_rms_dist(subset_supercell, s2),
rms))
self.assertTrue(np.allclose(sm.get_rms_dist(s2, subset_supercell),
rms))
#test when s2 (once made a supercell) is a subset of s1
s2_missing_site = s2.copy()
del s2_missing_site[1]
result = sm.get_s2_like_s1(s1, s2_missing_site)
for a, b in zip((s1[i] for i in (0, 2, 4, 5)), result):
self.assertTrue(a.distance(b) < 0.08)
self.assertEqual(a.species_and_occu, b.species_and_occu)
self.assertTrue(sm.fit(s1, s2_missing_site))
self.assertTrue(sm.fit(s2_missing_site, s1))
self.assertFalse(sm_no_s.fit(s1, s2_missing_site))
self.assertFalse(sm_no_s.fit(s2_missing_site, s1))
rms = (0.029763769724403633, 0.029763769724403987)
self.assertTrue(np.allclose(sm.get_rms_dist(s1, s2_missing_site), rms))
self.assertTrue(np.allclose(sm.get_rms_dist(s2_missing_site, s1), rms))
def test_fit(self):
"""
Take two known matched structures
1) Ensure match
2) Ensure match after translation and rotations
3) Ensure no-match after large site translation
4) Ensure match after site shuffling
"""
sm = StructureMatcher()
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
# Test rotational/translational invariance
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False,
np.array([0.4, 0.7, 0.9]))
self.struct_list[1].apply_operation(op)
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
#Test failure under large atomic translation
self.struct_list[1].translate_sites([0], [.4, .4, .2],
frac_coords=True)
self.assertFalse(sm.fit(self.struct_list[0], self.struct_list[1]))
self.struct_list[1].translate_sites([0], [-.4, -.4, -.2],
frac_coords=True)
# random.shuffle(editor._sites)
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
#Test FrameworkComporator
sm2 = StructureMatcher(comparator=FrameworkComparator())
lfp = self.get_structure("LiFePO4")
nfp = self.get_structure("NaFePO4")
self.assertTrue(sm2.fit(lfp, nfp))
self.assertFalse(sm.fit(lfp, nfp))
#Test anonymous fit.
self.assertEqual(sm.fit_anonymous(lfp, nfp), True)
self.assertAlmostEqual(
sm.get_rms_anonymous(lfp, nfp)[0], 0.060895871160262717)
#Test partial occupancies.
s1 = Structure(Lattice.cubic(3), [{
"Fe": 0.5
}, {
"Fe": 0.5
}, {
"Fe": 0.5
}, {
"Fe": 0.5
}], [[0, 0, 0], [0.25, 0.25, 0.25], [0.5, 0.5, 0.5],
[0.75, 0.75, 0.75]])
s2 = Structure(Lattice.cubic(3), [{
"Fe": 0.25
}, {
"Fe": 0.5
}, {
"Fe": 0.5
}, {
"Fe": 0.75
}], [[0, 0, 0], [0.25, 0.25, 0.25], [0.5, 0.5, 0.5],
[0.75, 0.75, 0.75]])
self.assertFalse(sm.fit(s1, s2))
self.assertFalse(sm.fit(s2, s1))
s2 = Structure(Lattice.cubic(3), [{
"Mn": 0.5
}, {
"Mn": 0.5
}, {
"Mn": 0.5
}, {
"Mn": 0.5
}], [[0, 0, 0], [0.25, 0.25, 0.25], [0.5, 0.5, 0.5],
[0.75, 0.75, 0.75]])
self.assertEqual(sm.fit_anonymous(s1, s2), True)
self.assertAlmostEqual(sm.get_rms_anonymous(s1, s2)[0], 0)
import dash_core_components as dcc
from dash.dependencies import Input, Output, State
from dash.exceptions import PreventUpdate
# standard Crystal Toolkit import
import crystal_toolkit.components as ctc
from dash_mp_components import JsonView
# import for this example
from pymatgen import Structure, Lattice
# create Dash app as normal
app = dash.Dash()
# create the Structure object
structure = Structure(Lattice.cubic(4.2), ["Na", "K"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
from pymatgen import MPRester
# create an input structure as an example
structure_component = ctc.StructureMoleculeComponent(
MPRester().get_structure_by_material_id("mp-804"), id="structure_in")
# and a way to view the transformed structure
structure_component_transformed = ctc.StructureMoleculeComponent(
MPRester().get_structure_by_material_id("mp-804"), id="structure_out")
# and the transformation component itself
transformation_component = ctc.AllTransformationsComponent(
input_structure_component=structure_component, )
# example layout to demonstrate capabilities of component
def test_oxide_type(self):
el_li = Element("Li")
el_o = Element("O")
latt = Lattice([[3.985034, 0.0, 0.0],
[0.0, 4.881506, 0.0],
[0.0, 0.0, 2.959824]])
elts = [el_li, el_li, el_o, el_o, el_o, el_o]
coords = list()
coords.append([0.500000, 0.500000, 0.500000])
coords.append([0.0, 0.0, 0.0])
coords.append([0.632568, 0.085090, 0.500000])
coords.append([0.367432, 0.914910, 0.500000])
coords.append([0.132568, 0.414910, 0.000000])
coords.append([0.867432, 0.585090, 0.000000])
struct = Structure(latt, elts, coords)
self.assertEqual(oxide_type(struct, 1.1), "superoxide")
el_li = Element("Li")
el_o = Element("O")
elts = [el_li, el_o, el_o, el_o]
latt = Lattice.from_parameters(3.999911, 3.999911, 3.999911, 133.847504,
102.228244, 95.477342)
coords = [[0.513004, 0.513004, 1.000000],
[0.017616, 0.017616, 0.000000],
[0.649993, 0.874790, 0.775203],
[0.099587, 0.874790, 0.224797]]
struct = Structure(latt, elts, coords)
self.assertEqual(oxide_type(struct, 1.1), "ozonide")
latt = Lattice.from_parameters(3.159597, 3.159572, 7.685205, 89.999884,
89.999674, 60.000510)
el_li = Element("Li")
el_o = Element("O")
elts = [el_li, el_li, el_li, el_li, el_o, el_o, el_o, el_o]
coords = [[0.666656, 0.666705, 0.750001],
[0.333342, 0.333378, 0.250001],
[0.000001, 0.000041, 0.500001],
[0.000001, 0.000021, 0.000001],
[0.333347, 0.333332, 0.649191],
[0.333322, 0.333353, 0.850803],
[0.666666, 0.666686, 0.350813],
[0.666665, 0.666684, 0.149189]]
struct = Structure(latt, elts, coords)
self.assertEqual(oxide_type(struct, 1.1), "peroxide")
el_li = Element("Li")
el_o = Element("O")
el_h = Element("H")
latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000,
90.000000, 90.000000)
elts = [el_h, el_h, el_li, el_li, el_o, el_o]
coords = [[0.000000, 0.500000, 0.413969],
[0.500000, 0.000000, 0.586031],
[0.000000, 0.000000, 0.000000],
[0.500000, 0.500000, 0.000000],
[0.000000, 0.500000, 0.192672],
[0.500000, 0.000000, 0.807328]]
struct = Structure(latt, elts, coords)
self.assertEqual(oxide_type(struct, 1.1), "hydroxide")
el_li = Element("Li")
el_n = Element("N")
el_h = Element("H")
latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000,
90.000000, 90.000000)
elts = [el_h, el_h, el_li, el_li, el_n, el_n]
coords = [[0.000000, 0.500000, 0.413969],
[0.500000, 0.000000, 0.586031],
[0.000000, 0.000000, 0.000000],
[0.500000, 0.500000, 0.000000],
[0.000000, 0.500000, 0.192672],
[0.500000, 0.000000, 0.807328]]
struct = Structure(latt, elts, coords)
self.assertEqual(oxide_type(struct, 1.1), "None")
el_o = Element("O")
latt = Lattice.from_parameters(4.389828, 5.369789, 5.369789, 70.786622,
69.244828, 69.244828)
elts = [el_o, el_o, el_o, el_o, el_o, el_o, el_o, el_o]
coords = [[0.844609, 0.273459, 0.786089],
[0.155391, 0.213911, 0.726541],
[0.155391, 0.726541, 0.213911],
[0.844609, 0.786089, 0.273459],
[0.821680, 0.207748, 0.207748],
[0.178320, 0.792252, 0.792252],
[0.132641, 0.148222, 0.148222],
[0.867359, 0.851778, 0.851778]]
struct = Structure(latt, elts, coords)
self.assertEqual(oxide_type(struct, 1.1), "None")
def structure_from_string(data):
"""
Parses a rndstr.in or lat.in file into pymatgen's
Structure format.
:param data: contents of a rndstr.in or lat.in file
:return: Structure object
"""
data = data.splitlines()
data = [x.split() for x in data if x] # remove empty lines
# following specification/terminology given in manual
if len(data[0]) == 6: # lattice parameters
a, b, c, alpha, beta, gamma = map(float, data[0])
coord_system = Lattice.from_parameters(a, b, c,
alpha, beta, gamma).matrix
lattice_vecs = np.array([
[data[1][0], data[1][1], data[1][2]],
[data[2][0], data[2][1], data[2][2]],
[data[3][0], data[3][1], data[3][2]]
], dtype=float)
first_species_line = 4
else:
coord_system = np.array([
[data[0][0], data[0][1], data[0][2]],
[data[1][0], data[1][1], data[1][2]],
[data[2][0], data[2][1], data[2][2]]
], dtype=float)
lattice_vecs = np.array([
[data[3][0], data[3][1], data[3][2]],
[data[4][0], data[4][1], data[4][2]],
[data[5][0], data[5][1], data[5][2]]
], dtype=float)
first_species_line = 6
scaled_matrix = np.matmul(coord_system, lattice_vecs)
lattice = Lattice(scaled_matrix)
all_coords = []
all_species = []
for l in data[first_species_line:]:
all_coords.append(np.array([l[0], l[1], l[2]], dtype=float))
species_strs = "".join(l[3:]) # join multiple strings back together
species_strs = species_strs.replace(" ", "") # trim any white space
species_strs = species_strs.split(",") # comma-delimited
species = {}
for species_str in species_strs:
species_str = species_str.split('=')
if len(species_str) == 1:
# assume occupancy is 1.0
species_str = [species_str[0], 1.0]
try:
species[Specie(species_str[0])] = float(species_str[1])
except Exception:
species[DummySpecie(species_str[0])] = float(species_str[1])
all_species.append(species)
return Structure(lattice, all_species, all_coords)
def setUp(self):
self.diamond = Structure(
Lattice([[2.189, 0, 1.264], [0.73, 2.064, 1.264], [0, 0, 2.528]]),
["C", "C"], [[2.554, 1.806, 4.423], [0.365, 0.258, 0.632]],
coords_are_cartesian=True)
def read_cfgs(self, filename, predict=False):
"""
Args:
filename (str): The configuration file to be read.
"""
type_convert = {'R': np.float32, 'I': np.int, 'S': np.str}
data_pool = []
with zopen(filename, 'rt') as f:
lines = f.read()
repl = re.compile('AT ')
lines = repl.sub('', string=lines)
block_pattern = re.compile(
'(\n[0-9]+\n|^[0-9]+\n)(.+?)(?=\n[0-9]+\n|$)', re.S)
lattice_pattern = re.compile('Lattice="(.+)"')
# energy_pattern = re.compile('dft_energy=(-?[0-9]+.[0-9]+)', re.I)
energy_pattern = re.compile(
r'(?<=\S{3}\s|dft_)energy=(-?[0-9]+.[0-9]+)')
# stress_pattern = re.compile('dft_virial={(.+)}')
stress_pattern = re.compile('dft_virial=({|)(.+?)(}|) \S.*')
properties_pattern = re.compile('properties=(\S+)', re.I)
# position_pattern = re.compile('\n(.+)', re.S)
position_pattern = re.compile('\n(.+?)(?=\nE.*|\n\n.*|$)', re.S)
# formatify = lambda string: [float(s) for s in string.split()]
for (size, block) in block_pattern.findall(lines):
d = {'outputs': {}}
size = int(size)
lattice_str = lattice_pattern.findall(block)[0]
lattice = Lattice(
list(map(lambda s: float(s), lattice_str.split())))
# energy_str = energy_pattern.findall(block)[0]
energy_str = energy_pattern.findall(block)[-1]
energy = float(energy_str)
# stress_str = stress_pattern.findall(block)[0]
stress_str = stress_pattern.findall(block)[0][1]
virial_stress = np.array(
list(map(lambda s: float(s), stress_str.split())))
virial_stress = [virial_stress[i] for i in [0, 4, 8, 1, 5, 6]]
properties = properties_pattern.findall(block)[0].split(":")
labels_columns = OrderedDict()
labels = defaultdict()
for i in range(0, len(properties), 3):
labels_columns[properties[i]] = [
int(properties[i + 2]), properties[i + 1]
]
position_str = position_pattern.findall(block)[0].split('\n')
position = np.array([p.split() for p in position_str])
column_index = 0
for key in labels_columns:
num_columns, dtype = labels_columns[key]
labels[key] = position[:, column_index:column_index +
num_columns].astype(type_convert[dtype])
column_index += num_columns
struct = Structure(lattice=lattice,
species=labels['species'].ravel(),
coords=labels['pos'],
coords_are_cartesian=True)
if predict:
forces = labels['force']
else:
forces = labels['dft_force']
d['structure'] = struct.as_dict()
d['outputs']['energy'] = energy
assert size == struct.num_sites
d['num_atoms'] = size
d['outputs']['forces'] = forces
d['outputs']['virial_stress'] = virial_stress
data_pool.append(d)
_, df = convert_docs(docs=data_pool)
return data_pool, df
def test_two_targets(self):
s = Structure(Lattice.cubic(3), ['Si'], [[0, 0, 0]])
# initialize the model
self.model2.train([s, s], [[0.1, 0.2], [0.1, 0.2]], epochs=1)
pred = self.model2.predict_structure(s)
self.assertEqual(len(pred.ravel()), 2)
