def write_xsf(cell, filename=None):
if filename == None: filename = 'mcu'
comment = misc.date()
lattice = np.asarray(cell[0])
positions = np.asarray(cell[1])
abs_positions = positions.dot(lattice)
atoms = np.asarray(cell[2])
natom = len(atoms)
symbol = cell_utils.convert_atomtype(atoms)
with open(filename + '.xsf', 'w') as f:
f.write('Generated by mcu on ' + comment + '\n')
f.write('CRYSTAL\n')
f.write('PRIMVEC\n')
for i in range(3):
f.write(' %15.10f %15.10f %15.10f\n' %
(lattice[i, 0], lattice[i, 1], lattice[i, 2]))
f.write('CONVVEC\n')
for i in range(3):
f.write(' %15.10f %15.10f %15.10f\n' %
(lattice[i, 0], lattice[i, 1], lattice[i, 2]))
f.write('PRIMCOORD\n')
f.write('%3d %3d\n' % (natom, 1))
for atom in range(natom):
f.write(' %s %15.10f %15.10f %15.10f\n' %
(symbol[atom], abs_positions[atom][0],
abs_positions[atom][1], abs_positions[atom][2]))
def cell_to_spgcell(cell, atoms):
'''Providing the cell attribute from vasprun.xml, return the cell for spglib'''
lattice = np.ndarray.tolist(cell[0])
positions = np.ndarray.tolist(cell[2])
numbers = utils.convert_atomtype(atoms)
return (lattice, positions, numbers)
def write_poscar(cell, filename=None):
if filename == None: filename = 'POSCAR_mcu'
comment = misc.date()
lattice = np.asarray(cell[0])
positions = np.asarray(cell[1])
atoms = np.asarray(cell[2])
idx = np.argsort(atoms)
atoms = atoms[idx]
symbol = cell_utils.convert_atomtype(atoms)
irred_symbol, count = misc.unique(symbol)
positions = positions[idx]
with open(filename, 'w') as f:
f.write('Generated by mcu on ' + comment + '\n')
f.write('1.0\n')
for i in range(3):
f.write(' %15.10f %15.10f %15.10f\n' %
(lattice[i, 0], lattice[i, 1], lattice[i, 2]))
for symb in irred_symbol:
f.write(' %s ' % (symb))
f.write('\n')
for num_atom in count:
f.write(' %d ' % (num_atom))
f.write('\n')
f.write('Direct\n')
for atom in positions:
f.write(' %15.10f %15.10f %15.10f\n' %
(atom[0], atom[1], atom[2]))
def get_sym(cell, symprec=1e-5, print_atom=False, export_operator=False):
#Space group info
intl_label, number = spglib.get_spacegroup(cell, symprec).split(' ')
number = number.split("(")[1].split(")")[0]
Schoenflies_label = spglib.get_spacegroup(cell, symprec,
symbol_type=1).split(' ')[0]
sym = spglib.get_symmetry(cell, symprec)
rotations = sym['rotations']
translations = sym['translations']
equi_atoms = sym['equivalent_atoms']
is_std = is_prim = False
std_cell = spglib.refine_cell(cell, symprec)
prim_cell = spglib.find_primitive(cell, symprec)
if compare_cells(cell, std_cell): is_std = True
if compare_cells(cell, prim_cell): is_prim = True
atoms = utils.convert_atomtype(cell[2])
if export_operator == False:
#Cell info
std_cell = spglib.refine_cell(cell, symprec)
prim_cell = spglib.find_primitive(cell, symprec)
#Print
misc.print_msg("Spacegroup number : %s" % (number))
misc.print_msg("Short International symbol : %s" % (intl_label))
misc.print_msg("Schoenflies symbol : %s" %
(Schoenflies_label))
if print_atom == True:
misc.print_msg("Atoms list (No. - Sym - Symbol):")
for i, atom in enumerate(atoms):
misc.print_msg("%3d %3d %s" %
(i + 1, equi_atoms[i] + 1, atom))
misc.print_msg("Irreducible atoms:")
for i, index in enumerate(np.unique(equi_atoms)):
misc.print_msg("%3d %3s %7f5 %7f5 %7f5" %
(i + 1, atoms[index], cell[1][index][0],
cell[1][index][1], cell[1][index][2]))
misc.print_msg("Number of irreducible atoms : %d" %
(np.unique(equi_atoms).shape[0]))
misc.print_msg("Standard cell : %r" % (is_std))
misc.print_msg("Primitive cell : %r" % (is_prim))
return is_std, is_prim
else:
return (number, intl_label), equi_atoms, rotations, translations
def write_cif(cell, spacegroup, equi_atoms, symopt, filename=None):
if filename == None: filename = 'mcu'
comment = misc.date()
lattice = np.asarray(cell[0])
lattice = cell_utils.convert_lattice(lattice)
positions = np.asarray(cell[1])
atoms = np.asarray(cell[2])
new_atm = [atoms[atm] for atm in np.unique(equi_atoms)]
new_pos = [positions[atm] for atm in np.unique(equi_atoms)]
natom = len(new_atm)
symbol = cell_utils.convert_atomtype(new_atm)
nsymopt = len(symopt)
with open(filename + '.cif', 'w') as f:
f.write('data_New_Crystal\n')
f.write("_audit_creation_method '%s'\n" %
('Generated by mcu on ' + comment))
f.write('_cell_length_a %15.10f\n' % (lattice[0]))
f.write('_cell_length_b %15.10f\n' % (lattice[1]))
f.write('_cell_length_c %15.10f\n' % (lattice[2]))
f.write('_cell_angle_alpha %15.10f\n' % (lattice[3]))
f.write('_cell_angle_beta %15.10f\n' % (lattice[4]))
f.write('_cell_angle_gamma %15.10f\n' % (lattice[5]))
f.write('\n')
f.write("_symmetry_space_group_name_H-M '%s'\n" % (spacegroup[1]))
f.write('_symmetry_Int_Tables_number %s\n' % (spacegroup[0]))
f.write('loop_\n')
f.write('_symmetry_equiv_pos_as_xyz\n')
for i in range(nsymopt):
f.write('%s\n' % (symopt[i]))
f.write('\n')
f.write('loop_\n')
f.write('_atom_site_label\n')
f.write('_atom_site_type_symbol\n')
f.write('_atom_site_fract_x\n')
f.write('_atom_site_fract_y\n')
f.write('_atom_site_fract_z\n')
for atom in range(natom):
f.write(' %s %s %15.10f %15.10f %15.10f\n' %
(symbol[atom], symbol[atom], new_pos[atom][0],
new_pos[atom][1], new_pos[atom][2]))
def read_win(self, seedname=None):
'''Read the seedname.win file'''
if seedname is None: seedname = self.seedname
if check_exist(seedname + '.win'):
with open(seedname + '.win', "r") as file:
win = file.read().splitlines()
# Cell information
lattice = copy_block(win, 'Unit_Cell_Cart', convert_to_float=True)
atom_block = copy_block(win, 'atoms_cart')
atom_sym = []
atom_position = []
for atm in atom_block:
temp = atm.split()
atom_sym.append(temp[0])
atom_position.append(np.float64(temp[1:]))
self.atom = atom_sym
atom_number = utils.convert_atomtype(self.atom )
self.cell = (lattice, atom_position, atom_number)
# kmesh info
self.kpts = np.asarray(copy_block(win, 'kpoints', convert_to_float=True))
self.klabel = None
kpoint_path = copy_block(win, 'kpoint_path')
if kpoint_path is not []:
num_kpoint = len(kpoint_path)
high_sym_kpoints = []
for i, kpoint in enumerate(kpoint_path):
if i == (num_kpoint - 1):
temp = kpoint.split()
high_sym_kpoints.append([temp[0], np.float64(temp[1:4])])
high_sym_kpoints.append([temp[4], np.float64(temp[5:])])
else:
temp = kpoint.split()
high_sym_kpoints.append([temp[0], np.float64(temp[1:4])])
self.klabel = high_sym_kpoints
else:
print('Cannot find the *.win file. Check the path:', seedname + '.win')
def read_ouput(self, filename=None):
'''Read the cp2k output file'''
if filename is None: filename = self.output
assert check_exist(
filename), "Cannot find the output. Check the path: " + filename
with open(filename, "r") as file:
outfile = file.read().splitlines()
# Cell information
cell_block = copy_block(outfile, "CELL_TOP")
a_vec = cell_block[1].split()[4:7]
b_vec = cell_block[2].split()[4:7]
c_vec = cell_block[3].split()[4:7]
lattice = np.float64([a_vec, b_vec, c_vec])
atom_type, atom_position = get_atoms(outfile)
self.atom = atom_type
atom_number = utils.convert_atomtype(atom_type)
self.cell = (lattice, atom_position, atom_number)
self.efermi = get_value(outfile, keyword="Fermi energy")
self.kpts = 0 # kmesh info: TODO: will test the Gamma point case first
def __init__(self,
mp_grid,
num_wann,
wavecar='WAVECAR',
poscar='POSCAR',
gamma=False,
spinors=False,
spin_up=True,
other_keywords=None):
self.pos = mcu.POSCAR(poscar)
self.wave = mcu.WAVECAR(wavecar)
self.num_wann = num_wann
self.keywords = other_keywords
# Collect the pyscf calculation info
self.num_bands_tot = self.wave.band.shape[-1]
self.num_kpts_loc = self.wave.band.shape[-2]
self.mp_grid_loc = mp_grid
assert self.num_kpts_loc == np.asarray(self.mp_grid_loc).prod()
self.real_lattice_loc = self.wave.cell[0]
self.recip_lattice_loc = self.wave.cell[1]
self.kpt_latt_loc = self.wave.kpts
self.kpts_abs = self.kpt_latt_loc.dot(self.recip_lattice_loc)
self.abs_kpts = self.wave.kpts.dot(self.recip_lattice_loc)
self.num_atoms_loc = len(self.pos.cell[2])
self.atom_symbols_loc = cell_utils.convert_atomtype(self.pos.cell[2])
self.atom_atomic_loc = self.pos.cell[2]
self.atoms_cart_loc = np.asarray(self.pos.cell[1]).dot(
self.real_lattice_loc)
self.gamma_only, self.spinors = (0, 0)
if gamma == True: self.gamma_only = 1
if spinors == True:
self.spinors = 1
self.spin = 0
# Wannier90_setup outputs
self.num_bands_loc = None
self.num_wann_loc = None
self.nntot_loc = None
self.nn_list = None
self.proj_site = None
self.proj_l = None
proj_m = None
self.proj_radial = None
self.proj_z = None
self.proj_x = None
self.proj_zona = None
self.exclude_bands = None
self.proj_s = None
self.proj_s_qaxis = None
# Input for Wannier90_run
self.band_included_list = None
self.A_matrix_loc = None
self.M_matrix_loc = None
self.eigenvalues_loc = None
# Wannier90_run outputs
self.U_matrix = None
self.U_matrix_opt = None
self.lwindow = None
self.wann_centres = None
self.wann_spreads = None
self.spread = None
# Others
self.use_bloch_phases = False
self.check_complex = False
self.spin_up = spin_up
if spin_up == True:
self.spin = 0
self.mo_energy_kpts = self.wave.band[self.spin]
else:
self.spin = 1
assert self.wave.band.shape[
0] == 2, 'WAVECAR is from a non spin-polarized calculation: spin_up == True'
self.mo_energy_kpts = self.wave.band[self.spin]