def setUp(self):
self.gnd_real = pmg.Structure.from_file(TEST_FILES / 'POSCAR.C0.gz')
self.exd_real = pmg.Structure.from_file(TEST_FILES / 'POSCAR.C-.gz')
self.gnd_test = pmg.Structure(pmg.Lattice.cubic(1.), ['H'],
[[0., 0., 0.]])
self.exd_test = pmg.Structure(pmg.Lattice.cubic(1.), ['H'],
[[0.5, 0.5, 0.5]])
self.sct_test = pmg.Structure(pmg.Lattice.cubic(1.), ['H'],
[[0.25, 0.25, 0.25]])
self.vrs = [TEST_FILES / 'vasprun.xml.0.gz'] + \
glob.glob(str(TEST_FILES / 'lower' / '*' / 'vasprun.xml.gz'))
def MAST2Structure(lattice=None,
coordinates=None,
atom_list=None,
coord_type='fractional'):
"""Helper function for converting input options into a pymatgen Structure object"""
if (coord_type.lower() == 'fractional'):
return pmg.Structure(lattice, atom_list, coordinates)
elif (coord_type.lower() == 'cartesian'):
return pmg.Structure(lattice,
atom_list,
coordinates,
coords_are_cartesian=True)
def _parse_structure(self, xml_structure, xml_lattice):
coordinates = []
symbols = []
for atom in xml_structure:
symbols.append(atom.attrib["elementType"])
coordinates.append(
[atom.attrib["x3"], atom.attrib["y3"], atom.attrib["z3"]])
coordinates = np.array(coordinates).reshape(-1, 3).astype(float)
namespaces = {'xml': 'http://www.xml-cml.org/schema'}
XML_LATTICE_LENGTHS = './xml:cellParameter[@parameterType="length"]'
XML_LATTICE_ANGLES = './xml:cellParameter[@parameterType="angle"]'
lattice_lengths = [
float(_)
for _ in xml_lattice.find(XML_LATTICE_LENGTHS,
namespaces=namespaces).text.split()
]
lattice_angles = [
float(_)
for _ in xml_lattice.find(XML_LATTICE_ANGLES,
namespaces=namespaces).text.split()
]
lattice = pmg.Lattice.from_parameters(*lattice_lengths,
*lattice_angles)
return pmg.Structure(lattice,
symbols,
coordinates,
coords_are_cartesian=True)
def test_show_pymatgen():
import pymatgen as mg
lattice = mg.Lattice.cubic(4.2)
structure = mg.Structure(lattice, ["Cs", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
view = nv.show_pymatgen(structure)
view
def Structure_start(sn, fn, coords):
'Write lattice, elements, coords to pymatgen structure; returns pymatgen structure.'
if sn.Lattice.size == 6: #tests for lattice vectors or parameters
lattice = mg.Lattice.from_parameters(sn.Lattice[0][0],sn.Lattice[0][1],sn.Lattice[0][2],\
sn.Lattice[1][0],sn.Lattice[1][1],sn.Lattice[1][2])
else:
lattice = sn.Lattice
wn = 6 #the (max) number of water molecules. This part handles missing waters.
for i in [sn.L1, sn.L2, sn.L3]:
for j in [i.W1, i.W2]:
if True in np.isnan(j):
wn -= 1
else:
pass
#Writes the list of atoms by element, which must be in the same order as the list of coordinates.
On = wn + 45
Hn = (wn * 2) + 36
atoms = []
for i in range(On):
atoms.append('O')
for i in range(Hn):
atoms.append('H')
for i in range(6):
atoms.append('Li')
for i in range(12):
atoms.append('Al')
for i in range(3):
atoms.append('C')
s = mg.Structure(lattice, atoms, coords) #makes the pymatgen structure
return s
def Layer_transform(s, sn):
'This takes the previous M+ layer and transforms it according to the symmetry genes.'
#define symmop as mg.symmop, then apply using s.apply(symop)
lat = s.lattice; atoms = s.species; coords = s.frac_coords
s1 = mg.Structure(lat, atoms, coords)
i = sn.Polytope.Symmetry #rotate by Cn, translate by (x,y) vector
if i.Cn == 0: Cn = 0
else: Cn = 360/i.Cn
so = mg.SymmOp.from_axis_angle_and_translation(axis=[0,0,1], angle=Cn,\
translation_vec=(i.Tx,i.Ty,0))
s1.apply_operation(so, fractional=True)
#reflect across xy plane
if i.Sz == 1:
so = mg.SymmOp.reflection([0,0,1], origin=(0.5,0.5,0.5))
s1.apply_operation(so, fractional=True)
else: pass
#reflect across xz or yz plane
if i.Sxy == 0: pass
else:
if i.Sxy < 0: #zx plane
nd = (0,1)
elif i.Sxy > 0: #zy plane
nd = (1,0)
so = mg.SymmOp.reflection([nd[0],nd[1],0],origin=(0.5,0.5,0.5))
s1.apply_operation(so, fractional=True)
lat = s1.lattice; atoms = s1.species; coords = s1.frac_coords
snew = mg.IStructure(lat, atoms, coords, to_unit_cell=True)
return snew
def get_supercell(self, sc, vac=[0, 0, 0]):
'''
Input-
sc:super cell lattice 3x3
vaccume: 1x3
returns: pymatgen structure
usefull for making use of pymatgen's codes for making finite complex slabs and defects
'''
try:
import pymatgen as p
except:
print("Needs pymatgen please install using pip install pymatgen")
new_s = p.Structure(lattice=self.get_lattice(),
species=[i.element for i in self.atoms],
coords=[list(i.pos) for i in self.atoms])
new_s.make_supercell(sc)
def get_vaccume(s, vac):
abc = np.add([new_s.lattice.a, new_s.lattice.b, new_s.lattice.c],
vac)
ang = new_s.lattice.angles
l = p.core.lattice.Lattice.from_parameters(a=abc[0],
b=abc[1],
c=abc[2],
alpha=ang[0],
beta=ang[1],
gamma=ang[2])
return p.Structure(lattice=l,
species=new_s.species,
coords=new_s.frac_coords)
final = get_vaccume(new_s, vac)
return final
def create_pure_structure(self,
oxidation_states,
basic_atoms,
noCells,
lattice_system='cubic',
lattice_lengths=None,
lattice_angles=None,
supercell=False):
"""Creates pure structure given input parameters.
"""
oxidationA = oxidation_states[0]
oxidationB = oxidation_states[1]
oxidationC = oxidation_states[2]
dopantAtoms = []
noDopants = []
noVacancies = []
noInterstitials = []
vacancyAtoms = []
interstitialAtoms = []
siteA = basic_atoms[0]
siteB = basic_atoms[1]
siteC = basic_atoms[2]
atomA = mg.Element(siteA)
atomB = mg.Element(siteB)
atomC = mg.Element(siteC)
if not lattice_lengths:
ionic_radiiA = atomA.ionic_radii[oxidationA]
ionic_radiiB = atomB.ionic_radii[oxidationB]
ionic_radiiC = atomC.ionic_radii[oxidationC]
latticeVal1 = 2 * (ionic_radiiA + ionic_radiiB) / math.pow(
3, 1 / 2)
latticeVal2 = 2 * (ionic_radiiA + ionic_radiiC) / math.pow(
2, 1 / 2)
latticeConst = max(latticeVal1, latticeVal2)
latticeLength = [latticeConst, latticeConst, latticeConst]
latticeAngles = [90, 90, 90] # WARNING: HARD-CODE ALERT
else:
latticeLength = lattice_lengths
latticeAngles = lattice_angles
lattice = mg.Lattice.from_lengths_and_angles(latticeLength,
latticeAngles)
structure = mg.Structure(lattice, [siteA, siteB, siteC, siteC, siteC],
[[0, 0, 0], [0.5, 0.5, 0.5], [0.5, 0.5, 0],
[0.5, 0, 0.5], [0, 0.5, 0.5]])
if supercell:
structure.make_supercell(noCells)
keyVal = self.structureKey(lattice_system, basic_atoms, dopantAtoms,
noDopants, vacancyAtoms, noVacancies,
noCells, interstitialAtoms, noInterstitials)
return structure, keyVal
def CreateTemplateStructure(strutype, size, specie):
if strutype == 'bcc':
lattice = [[size, 0, 0], [0, size, 0], [0, 0, size]]
species = [specie, specie]
coords = [[0, 0, 0], [1.0 / 2.0, 1.0 / 2.0, 1.0 / 2.0]]
return pmg.Structure(lattice, species, coords)
elif strutype == 'fcc':
lattice = [[size, 0, 0], [0, size, 0], [0, 0, size]]
species = [specie] * 4
coords = [[0, 0, 0], [0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]]
return pmg.Structure(lattice, species, coords)
elif strutype == 'hcp':
lattice = [[size, 0, 0], [0, size, 0],
[0, 0, size * math.sqrt(6) * (2 / 3)]]
species = [specie] * 2
coords = [[0, 0, 0], [2.0 / 3.0, 1.0 / 3.0, 1.0 / 2.0]]
return pmg.Structure(lattice, species, coords)
def get_distortion_dec_struct(wycks, struct_to_match, high_sym_wyckoff,
struct_hs):
coords = []
species = []
proj_vecs = []
wycks_done = [] # dirty maybe wrong fix
for wyck in wycks: # CURRENTLY ONLY ONE WYCKOFF IS PASSED AT A TIME, SO THIS IS FINE, BUT UNNECESSARY
w = wyck["Wyckoff"]
# PEROVSKITE SPECIFIC, AND I DON'T KNOW IF IT'S THE RIGHT THING TO DO!!!!
if w in wycks_done:
# print("SKIPPING duplicate instance of wyckoff {} in irrep {}, this is a perovskite specific thing, and may be wrong even here".format(w, irrep))
# print("I believe the two sets isotropy returns are equivalent choices, but I'm not certain")
continue
wycks_done.append(w) # dirty maybe wrong fix
for i, ss in enumerate(high_sym_wyckoff):
if ss == w:
sp = struct_hs[i].specie
break
for coord, pv in zip(wyck["Point"], wyck["Projected Vectors"]):
species.append(sp)
coords.append(coord)
proj_vecs.append(pv)
logger.debug("get_distortion_dec_struct:")
logger.debug("coords:\n{}".format(coords))
logger.debug("species:\n{}".format(species))
logger.debug("proj_vecs:\n{}".format(proj_vecs))
lat = struct_to_match.lattice
dist_struct = pmg.Structure(lat,
species,
coords,
site_properties={"projvecs": proj_vecs})
logger.debug("dist_struct:\n{}".format(dist_struct))
# sm_dist = StructureMatcher(ltol = 0.02, primitive_cell=False, allow_subset=True)
sm_dist = ModifiedSM_I(ltol=0.02, primitive_cell=False, allow_subset=True)
try:
sc_d, trans_d, mapping = sm_dist.get_transformation(
struct_to_match, dist_struct)
except TypeError:
logger.warning(
"couldn't map dist decorated structure to actual structure")
logger.warning("dist dec struct:\n{}".format(dist_struct))
logger.warning("struct to match:\n{}".format(struct_to_match))
logger.debug("matching dist def to struct")
dist_struct_matched = dist_struct * sc_d
dist_struct_matched.translate_sites(list(range(len(dist_struct_matched))),
trans_d)
logger.debug(struct_to_match)
logger.debug(dist_struct)
logger.debug(sc_d)
logger.debug(trans_d)
logger.debug(mapping)
logger.debug(dist_struct_matched)
logger.debug("\n")
return dist_struct_matched, mapping
def main(self, filename='crystal.cif'):
a, b, c = self.configure.lattice_length[:3]
a, b, c = [self.bohr2ang(x) for x in [a, b, c]]
alpha, beta, gamma = self.configure.lattice_angle[:3]
lattice = mg.Lattice.from_parameters(a, b, c, alpha, beta, gamma)
atoms = self.configure.atom_list
atomic_position = self.configure.atomic_position
structure = mg.Structure(lattice, atoms, atomic_position)
structure.to(filename=filename)
print('generated:{}'.format(filename))
def set_structure(self):
#
# ======= ATOMIC POSITIONS =======
#
a, b, c = self.config_obj.lattice_length[:3]
alpha, beta, gamma = self.config_obj.lattice_angle[:3]
lattice = mg.Lattice.from_parameters(a, b, c, alpha, beta, gamma)
self.atoms = self.config_obj.atom_list
atomic_positions = self.config_obj.atomic_position
self.structure = mg.Structure(lattice, self.atoms, atomic_positions)
def calculate_standard_path(structure):
lattice = mg.Lattice(structure.lattice_vectors)
atoms = structure.atoms
structure_mg = mg.Structure(lattice, atoms[:, 3], atoms[:, :3])
hs_path = HighSymmKpath(structure_mg, symprec=0.1)
if not hs_path.kpath: # fix for bug in pymatgen that for certain structures no path is returned
raise Exception('High symmetry path generation failed.')
conv_path = convert_hs_path_to_own(hs_path)
return conv_path
def read_structure(filename, lattice, charges):
# Lattice was not specified in file
# Charges supplied as dict { specie : charge }
with open(filename) as f:
species = []
positions = []
for line in f:
specie, x, y, z = line.split()
species.append(specie)
positions.append([float(_) for _ in [x, y, z]])
structure = pmg.Structure(lattice, species, positions, coords_are_cartesian=True)
structure.add_oxidation_state_by_element(charges)
return structure
def get_vaccume(s, vac):
abc = np.add([new_s.lattice.a, new_s.lattice.b, new_s.lattice.c],
vac)
ang = new_s.lattice.angles
l = p.core.lattice.Lattice.from_parameters(a=abc[0],
b=abc[1],
c=abc[2],
alpha=ang[0],
beta=ang[1],
gamma=ang[2])
return p.Structure(lattice=l,
species=new_s.species,
coords=new_s.frac_coords)
def lattice_information(self):
lattice = mg.Lattice(self.lattice_vectors)
atoms = self.atoms
if len(atoms) == 0:
return {'space group': '', 'point group': '', 'crystal system': ''}
structure_mg = mg.Structure(lattice, atoms[:, 3], atoms[:, :3])
analyzer = SpacegroupAnalyzer(structure_mg)
res = {
'space group': analyzer.get_space_group_symbol(),
'point group': analyzer.get_point_group_symbol(),
'crystal system': analyzer.get_crystal_system()
}
return res
def test_get_Q_from_struct(self):
q = get_Q_from_struct(self.gnd_test, self.exd_test, self.sct_test)
self.assertAlmostEqual(q, 0.5 * 0.86945, places=4)
q = get_Q_from_struct(self.gnd_real, self.exd_real,
str(TEST_FILES / 'POSCAR.C0.gz'))
self.assertAlmostEqual(q, 0., places=4)
gs, es = get_cc_structures(self.gnd_real, self.exd_real,
np.linspace(-0.5, 0.5, 100),
remove_zero=False)
Q = 1.68587 * np.linspace(-0.5, 0.5, 100)
for s, q in zip(gs, Q):
tq = get_Q_from_struct(self.gnd_real, self.exd_real, s)
self.assertAlmostEqual(tq, q, places=4)
for s, q in zip(es, Q + 1.68587):
tq = get_Q_from_struct(self.gnd_real, self.exd_real, s)
self.assertAlmostEqual(tq, q, places=4)
# test when one of the coordinates stays the same
sg = pmg.Structure(np.eye(3), ['H'], [[0.0, 0.0, 0.0]])
sq = pmg.Structure(np.eye(3), ['H'], [[0.1, 0.0, 0.1]])
se = pmg.Structure(np.eye(3), ['H'], [[0.2, 0.0, 0.2]])
dQ = get_dQ(sg, se)
self.assertAlmostEqual(get_Q_from_struct(sg, se, sq)/dQ, 0.5)
def get_structure(filename):
if filename.lower().endswith('.cif'):
structure = CifParser(filename).get_structures()[0]
lattice = pmg.Lattice.from_parameters(*structure.lattice.abc,
*structure.lattice.angles)
return pmg.Structure(lattice,
structure.species,
structure.frac_coords,
coords_are_cartesian=False)
elif filename.lower().endswith('poscar'):
return Poscar.from_file(filename).structure
else:
raise ValueError(
'Cannot determine file type from filename [.cif, poscar]')
def _parse_structure(self, structure_schema):
data = structure_schema['data']
format = structure_schema['format']
if format == 'cif':
# cif lattice can be weird non standard shape
structure = (CifParser.from_string(data)).get_structures()[0]
lattice = pmg.Lattice.from_parameters(*structure.lattice.abc,
*structure.lattice.angles)
structure = pmg.Structure(lattice,
structure.species,
structure.frac_coords,
coords_are_cartesian=False)
elif format == 'POSCAR':
structure = (Poscar.from_string(data)).structure
return structure
def dump(system, symbols=None):
"""
Convert an atomman.System into a pymatgen.Structure.
Parameters
----------
system : atomman.System
A atomman representation of a system.
symbols : tuple, optional
List of the element symbols that correspond to the atom types. If not
given, will use system.symbols if set, otherwise no element content
will be included.
Returns
-------
structure : pymatgen.Structure
A pymatgen representation of a structure.
"""
assert has_pmg, 'pymatgen not imported'
# Get box/lattice information
lattice = pmg.Lattice(system.box.vects)
# Get symbols information
if symbols is None:
symbols = system.symbols
symbols = np.asarray(symbols)
if None in symbols:
raise ValueError('Symbols needed for all atypes')
# Convert short symbols list to full species list
atype = system.atoms.atype
species = symbols[atype - 1]
# Get atomic information
sites = system.atoms_prop(key='pos', scale=True)
prop = {}
for p in system.atoms_prop():
if p != 'atype' and p != 'pos':
prop[p] = system.atoms_prop(key=p)
# Build structure
structure = pmg.Structure(lattice, species, sites, site_properties=prop)
return structure
def to_pymatgen(mol):
"""
Creates a pymatgen structure object from a mol object
:Parameters:
- mol: mol object
"""
try:
import pymatgen as mg
except ImportError:
logger.error("Pymatgen not available!")
exit()
latt = mg.Lattice.from_parameters(*mol.get_cellparams())
elems = mol.get_elems()
nelems = []
for e in elems:
nelems.append(e.title())
structure = mg.Structure(latt, nelems, mol.get_frac_xyz())
return structure
def Layer_A(sn, layer):
'Generates A- layers.'
atoms = ['C', 'O', 'O', 'O']
lat, g = setlat(sn)
coords = C_positions(sn, layer) #start the carbonate with C, then with O.
oc, oa = O_positions(sn, layer, lat, g)
for i in oc:
coords.append(i)
if len(oa): #only add water atoms if O_pos found water in layer
for i in oa:
atoms.append(i)
hc, ha = H_positions(sn, layer, lat, g)
for i in hc:
coords.append(i)
for i in ha:
atoms.append(i)
else: pass
s = mg.Structure(lat, atoms, coords)
return s
def readCaesarEquilibriumStructure(equilibrium_dat,
lattice_dat,
get_spins=True):
"""
Helper method for reading structures written by caesar
Args:
equilibrium_dat:
dat file containing atomic positions
lattice_dat:
dat file containing lattice
get_spins:
whether or not to read spins from equilibrium_dat (default is True)
Returns:
if get_spins==True:
returns a tuple (structure, masses, spins) where structure is a pymatgen structure and masses, spins are numpy arrays
if get_spins==False:
returns a tuple (structure, masses) where structure is a pymatgen structure and masses is a numpy array
"""
latdat = np.genfromtxt(lattice_dat)
lattice = pmg.Lattice(BOHR_TO_ANG * latdat)
with open(equilibrium_dat) as f:
num_sites = int(f.readline())
species = []
coords = []
spins = []
masses = []
for i in range(num_sites):
line = f.readline().strip('\n').split()
species.append(line[0])
coords.append(line[2:5])
if get_spins:
spins.append(float(line[-1]))
masses.append(float(line[1]))
coords = np.array(coords, dtype=float) * BOHR_TO_ANG
structure = pmg.Structure(lattice,
species,
coords,
coords_are_cartesian=True)
if get_spins:
return (structure, masses, spins)
else:
return (structure, masses)
def match_structures(s1, s2, scale_lattice=False, rh_only=True):
"""
Args
s1: high sym structure
s2: low sym structure
scale_lattice (optional): high_sym_superlcell has same lattice vectors as s2 (no strain)
Returns
basis: should be the basis that when applied to s1 makes a supercell of the size and orentation of s2
origin: any additional translation to best match (applied before applying the basis change to match what isotropy does)
displacements
high_sym_supercell
"""
sm = StructureMatcher(ltol=0.3,
stol=0.3,
angle_tol=15,
scale=True,
attempt_supercell=True,
primitive_cell=False)
basis, origin, mapping = sm.get_transformation(s1, s2, rh_only=rh_only)
struct_hs_supercell = sm.get_s2_like_s1(s1, s2, rh_only=rh_only)
# change origin from the supercell basis to the high sym basis
origin = np.round_(frac_vec_convert(origin, struct_hs_supercell.lattice,
s2.lattice),
decimals=5)
if scale_lattice:
hs_lat = struct_hs_supercell.lattice
hs_std = pmg.Lattice.from_lengths_and_angles(hs_lat.abc, hs_lat.angles)
ls_lat = s2.lattice
ls_std = pmg.Lattice.from_lengths_and_angles(ls_lat.abc, ls_lat.angles)
for aligned, rot, scale in hs_lat.find_all_mappings(hs_std):
if (abs(aligned.matrix - hs_lat.matrix) < 1.e-3).all():
strained_hs_lattice = pmg.Lattice(np.inner(ls_std.matrix, rot))
struct_hs_supercell = pmg.Structure(
strained_hs_lattice, struct_hs_supercell.species,
[site.frac_coords for site in struct_hs_supercell])
displacements = []
for s_hs, s_ls in zip(struct_hs_supercell, s1):
disp = np.round_(smallest_disp(s_hs.frac_coords, s_ls.frac_coords),
decimals=5)
displacements.append(disp)
return basis, origin, displacements, struct_hs_supercell
def poscar(self,
perturb_dist=0.0,
comment='Automatically generated POSCAR'):
structure = mg.Structure(
self._lattice,
self._site_species_list(),
self._site_position_list(),
)
poscar = mg.io.vaspio.Poscar(
structure,
comment,
selective_dynamics=self._site_dynamics_list(),
velocities=self._site_velocity_list()
if self.has_velocity() else None,
)
poscar.structure.perturb(perturb_dist)
return poscar
def to_pymatgen_structure(lattice_params, coords, alpha=90, beta=90, gamma=90):
""" Convert lattice params and coords to pymatgen """
species = [c[0] for c in coords]
positions = np.array([c[1:] for c in coords])
# Create a lattice to place the sites
lattice = mg.Lattice.from_parameters(*lattice_params,
alpha=90,
beta=90,
gamma=90)
# Create the structure
structure = mg.Structure(lattice,
species,
positions,
coords_are_cartesian=True)
new_lattice = mg.Lattice.from_parameters(*lattice_params,
alpha=alpha,
beta=beta,
gamma=gamma)
structure.lattice = new_lattice
return structure
def read_lammps_dump_file(filename=''):
''' Attributes: path of a LAMMPS dump file
Returns: pymatgen structure of final relaxed structure.
'''
dump = parse_lammps_dumps(filename)
for i in dump:
a = i
lattice = a.box.to_lattice()
df = a.data.sort_values(by=['id'])
element_array = []
for i in df['type'].tolist():
if i == 1:
element_array.append('Al')
if i == 2:
element_array.append('N')
if i == 3:
element_array.append('Ti')
cord_np = df[['xs', 'ys', 'zs']].values
pymatgen_struct = mg.Structure(lattice, element_array, cord_np)
return pymatgen_struct
def inner(projections_dict={'kind_name': 'As', 'ang_mtm_name': 'sp3'}):
from aiida.orm import DataFactory, CalculationFactory
from aiida_wannier90.orbitals import generate_projections
res = dict()
a = 5.367 * pymatgen.core.units.bohr_to_ang
structure_pmg = pymatgen.Structure(lattice=[[-a, 0, a], [0, a, a],
[-a, a, 0]],
species=['Ga', 'As'],
coords=[[0] * 3, [0.25] * 3])
structure = DataFactory('structure')()
structure.set_pymatgen_structure(structure_pmg)
res['structure'] = structure
res['projections'] = generate_projections(projections_dict,
structure=structure)
KpointsData = DataFactory('array.kpoints')
kpoints = KpointsData()
kpoints.set_kpoints_mesh([2, 2, 2])
res['kpoints'] = kpoints
kpoint_path_tmp = KpointsData()
kpoint_path_tmp.set_cell_from_structure(structure)
kpoint_path_tmp.set_kpoints_path()
point_coords, path = kpoint_path_tmp.get_special_points()
kpoint_path = DataFactory('parameter')(dict={
'path': path,
'point_coords': point_coords,
})
res['kpoint_path'] = kpoint_path
res['parameters'] = DataFactory('parameter')(
dict=dict(num_wann=4, num_iter=12, wvfn_formatted=True))
return res
BGWpy relies on pymatgen.Structure objects to construct
the primitive cells for all calculations.
See http://pymatgen.org/ for more information.
"""
import os
import numpy as np
import pymatgen
# Construct the structure object.
acell_angstrom = 5.6535
rprim = np.array([[.0, .5, .5], [.5, .0, .5], [.5, .5, .0]]) * acell_angstrom
structure = pymatgen.Structure(
lattice=pymatgen.core.lattice.Lattice(rprim),
species=['Ga', 'As'],
coords=[3 * [.0], 3 * [.25]],
)
# Create a directory to store the structure.
dirname = '01-GaAs'
if not os.path.exists(dirname):
os.mkdir(dirname)
# Write file in Crystallographic Information Framework.
# This the format defined by the International Union of Crystallography.
structure.to(filename=os.path.join(dirname, 'GaAs.cif'))
# Write in json format. This is the prefered format
# since it preserves the above definition of the unit cell.
structure.to(filename=os.path.join(dirname, 'GaAs.json'))
model_nosym = tb.Model.from_hdf5_file('data/model_nosym.hdf5')
reference_model = tb.Model.from_hdf5_file('data/reference_model.hdf5')
# change the order of the orbitals from (In: s, py, pz, px; As: py, pz, px) * 2
# to (In: s, px, py, pz; As: s, px, py, pz) * 2
model_nosym = model_nosym.slice_orbitals(
[0, 2, 3, 1, 5, 6, 4, 7, 9, 10, 8, 12, 13, 11])
# set up symmetry operations
time_reversal = SymmetryOperation(rotation_matrix=np.eye(3),
repr_matrix=np.kron([[0, -1j], [1j, 0]],
np.eye(7)),
repr_has_cc=True)
structure = mg.Structure(lattice=model_nosym.uc,
species=['In', 'As'],
coords=np.array([[0, 0, 0], [0.25, 0.25, 0.25]]))
# get real-space representations
analyzer = mg.symmetry.analyzer.SpacegroupAnalyzer(structure)
symops = analyzer.get_symmetry_operations(cartesian=False)
symops_cart = analyzer.get_symmetry_operations(cartesian=True)
rots = [x.rotation_matrix for x in symops]
taus = [x.translation_vector for x in symops]
# get corresponding represesentations in the Hamiltonian basis
reps = []
for n, (rot, tau) in enumerate(zip(rots, taus)):
C = symops_cart[n].rotation_matrix
tauc = symops_cart[n].translation_vector
prep = C