def mix_poscars(s1,s2, roll=True):
""" Crossover operations where atoms are from one and cell from other.
Mating operation on two parent structures s1 and s2.
Done on scaled atomic positions (cubic systems) by
interchanging their cells and scaled positions.
Returns two offspring structures each with the same
number of atoms as the parent from which the atoms
are inhereted.
"""
from random import choice
from numpy import dot
from numpy.linalg import det
from ..crystal import Structure
# swap structures randomly.
if choice([True, False]): s1, s2 = s2, s1
# chem. symbols and scaled positions of the two parents
sc_pos2 = zip([atom.type for atom in s2],fractional_pos(s2, roll))
# cell from s1
result = Structure(s1.cell, scal=s1.scale)
# atoms from s2
for type, pos in sc_pos2:
result.add_atom(*dot(result.cell, pos), type=type)
result.scale = s1.scale * (float(len(result)) / float(len(s1)))**(1./3.)
return result
def mix_atoms(s1, s2, roll=True):
""" Randomly mix cell and atoms from parents.
Mating operation on two parent structures s1 and s2.
Done by mixing randomly atoms from s1 and s2 into the
cell coming from one of them. Returns two offspring
structures.
"""
from random import choice
from itertools import chain
from numpy.linalg import det
from numpy import dot, abs
from ..crystal import Structure
# swap structures randomly.
if choice([True, False]): s1, s2 = s2, s1
# chem. symbols and scaled positions of the two parents
sc_pos1 = zip([atom.type for atom in s1], fractional_pos(s1, roll))
sc_pos2 = zip([atom.type for atom in s2], fractional_pos(s2, roll))
result = Structure(s1.cell)
for pos, type in chain(sc_pos1, sc_pos2):
if choice([True, False]):
result.add_atom(*dot(result.cell, pot), type=type)
result.scale = s1.scale * (float(len(result)) / float(len(s1)))**(1./3.)
return result
def icsd_cif_b(filename):
from os.path import basename
from numpy import dot, transpose
from pylada.crystal import Structure, primitive
from . import readCif
rdr = readCif.CifReader(0, filename) # buglevel = 0
vaspMap = rdr.getVaspMap()
cellBasis = vaspMap['cellBasis']
structure = Structure(
transpose(cellBasis),
scale=1,
name=basename(filename))
usyms = vaspMap['uniqueSyms']
posVecs = vaspMap['posVecs']
# multiplicities = num atoms of each type.
mults = [len(x) for x in posVecs]
# For each unique type of atom ...
for ii in range(len(usyms)):
# For each atom of that type ...
for jj in range(mults[ii]):
atpos = dot(transpose(cellBasis), posVecs[ii][jj])
structure.add_atom(atpos[0], atpos[1], atpos[2], usyms[ii])
prim = primitive(structure)
logger.info(" crystal/read: icsd_cif_b: structure: %s" % structure)
return prim
def get_madelungenergy(latt_vec_array, charge, epsilon, cutoff):
""" Function returns leading first order correction term, i.e.,
screened Madelung-like lattice energy of point charge
Reference: M. Leslie and M. J. Gillan, J. Phys. C: Solid State Phys. 18 (1985) 973
Parameters
defect = pylada.vasp.Extract object
charge = charge of point defect. Default 1e0 elementary charge
epsilon = dimensionless relative permittivity, SKW: isotropic average of dielectric constant
cutoff = Ewald cutoff parameter
Returns
Madelung (electrostatic) energy in eV
Note:
1. Units in this function are either handled by the module Quantities, or\
defaults to Angstrom and elementary charges
2. Function is adopted from Haowei Peng's version in pylada.defects modules
"""
ewald_cutoff = cutoff * Ry
cell_scale = 1.0 # SKW: In notebook workflow cell parameters are converted to Cartesians and units of Angstroms
# SKW: Create point charge in pylada.crystal.structure class (used for charge model)
# http://pylada.github.io/pylada/userguide/crystal.html
struc = Structure()
struc.cell = latt_vec_array
struc.scale = cell_scale
struc.add_atom(0., 0., 0., "P", charge=charge)
#Anuj_05/22/18: added "cutoff" in ewald syntax
result = ewald(struc, cutoff=ewald_cutoff).energy / epsilon
return -1 * result.rescale(eV)
def from_spglib(strc):
"""
converting the pylada structure object
from the spglib format to pylada
"""
import numpy as np
from pylada import periodic_table
from pylada.crystal import Structure
out_s = Structure()
out_s.scale = 1.
cell = strc[0]
positions = strc[1]
symbols = strc[2]
out_s.cell = np.transpose(cell)
for ii in range(len(positions)):
pp=np.dot(np.transpose(cell),positions[ii])
ss=periodic_table.symbols[symbols[ii]-1]
out_s.add_atom(pp[0],pp[1],pp[2],ss)
return out_s
def icsd_cif_b(filename):
from os.path import basename
from numpy import dot, transpose
from pylada.crystal import Structure, primitive
from . import readCif
rdr = readCif.CifReader(0, filename) # buglevel = 0
vaspMap = rdr.getVaspMap()
cellBasis = vaspMap['cellBasis']
structure = Structure(
transpose(cellBasis),
scale=1,
name=basename(filename))
usyms = vaspMap['uniqueSyms']
posVecs = vaspMap['posVecs']
# multiplicities = num atoms of each type.
mults = [len(x) for x in posVecs]
# For each unique type of atom ...
for ii in range(len(usyms)):
# For each atom of that type ...
for jj in range(mults[ii]):
atpos = dot(transpose(cellBasis), posVecs[ii][jj])
structure.add_atom(atpos[0], atpos[1], atpos[2], usyms[ii])
prim = primitive(structure)
logger.info(" crystal/read: icsd_cif_b: structure: %s" % structure)
return prim
def crystal(file='fort.34'):
""" Reads CRYSTAL's external format. """
from numpy import array, abs, zeros, any, dot
from numpy.linalg import inv
from ..crystal import which_site
from ..misc import RelativePath
from ..error import IOError
from ..periodic_table import find as find_specie
from . import Structure
if isinstance(file, str):
if file.find('\n') == -1:
with open(RelativePath(file).path, 'r') as file: return crystal(file)
else: file = file.splitlines().__iter__()
# read first line
try: line = file.next()
except StopIteration: raise IOError('Premature end of stream.')
else: dimensionality, centering, type = [int(u) for u in line.split()[:3]]
# read cell
try: cell = array( [file.next().split()[:3] for i in xrange(3)],
dtype='float64' ).T
except StopIteration: raise IOError('Premature end of stream.')
result = Structure( cell=cell, centering=centering,
dimensionality=dimensionality, type=type, scale=1e0 )
# read symmetry operators
result.spacegroup = []
try: N = int(file.next())
except StopIteration: raise IOError('Premature end of stream.')
for i in xrange(N):
try: op = array( [file.next().split()[:3] for j in xrange(4)],
dtype='float64' )
except StopIteration: raise IOError('Premature end of stream.')
else: op[:3] = op[:3].copy().T
result.spacegroup.append(op)
result.spacegroup = array(result.spacegroup)
# read atoms.
try: N = int(file.next())
except StopIteration: raise IOError('Premature end of stream.')
for i in xrange(N):
try: line = file.next().split()
except StopIteration: raise IOError('Premature end of stream.')
else: type, pos = int(line[0]), array(line[1:4], dtype='float64')
if type < 100: type = find_specie(atomic_number=type).symbol
result.add_atom(pos=pos, type=type, asymmetric=True)
# Adds symmetrically equivalent structures.
identity = zeros((4, 3), dtype='float64')
for i in xrange(3): identity[i, i] == 1
symops = [u for u in result.spacegroup if any(abs(u - identity) > 1e-8)]
invcell = inv(result.cell)
for atom in [u for u in result]:
for op in symops:
pos = dot(op[:3], atom.pos) + op[3]
if which_site(pos, result, invcell=invcell) == -1:
result.add_atom(pos=pos, type=atom.type, asymmetric=False)
return result
def icsd_cif_b( filename):
from os.path import basename
from numpy import dot, transpose
from pylada.crystal import Structure, primitive
from pylada.misc import bugLev
from . import readCif
rdr = readCif.CifReader( 0, filename) # buglevel = 0
vaspMap = rdr.getVaspMap()
cellBasis = vaspMap['cellBasis']
structure = Structure(
transpose( cellBasis),
scale = 1,
name = basename( filename))
usyms = vaspMap['uniqueSyms']
posVecs = vaspMap['posVecs']
# multiplicities = num atoms of each type.
mults = [len(x) for x in posVecs]
if bugLev >= 5:
print " crystal/read: len(usyms): %d usyms: %s" \
% (len( usyms), usyms,)
print " crystal/read: len(posVecs): %d" % (len(posVecs),)
print " crystal/read: len(mults): %d mults: %s" \
% (len( mults), mults,)
# For each unique type of atom ...
for ii in range( len( usyms)):
if bugLev >= 5:
print " crystal/read: icsd_cif_b: ii: ", ii, \
" usym: ", usyms[ii], \
" mult: ", mults[ii], \
" posVecs: ", posVecs[ii]
# crystal/read: i: 0 symbol: Mo len position: 2
# For each atom of that type ...
for jj in range( mults[ii]):
atpos = dot( transpose( cellBasis), posVecs[ii][jj])
if bugLev >= 5:
print " jj: ", jj, " pos: ", posVecs[ii][jj]
print " atpos: ", atpos
# j: 0 pos: [0.3333, 0.6666000000000001, 0.25]
# atpos: [ 6.32378655e-16 1.81847148e+00 3.07500000e+00]
structure.add_atom( atpos[0], atpos[1], atpos[2], usyms[ii])
if bugLev >= 2:
print " crystal/read: icsd_cif_b: structure:\n", structure
prim = primitive( structure)
if bugLev >= 2:
print " crystal/read: icsd_cif_b: primitive structure:\n", prim
return prim
def to_pylada(self):
A = Structure(self.cell)
if self.unit == "alat":
for elem in self.atomic_pos:
for pos in self.atomic_pos[elem]:
A.add_atom(pos[0], pos[1], pos[2], elem)
elif self.unit == "crystal":
for elem in self.atomic_pos:
for pos in self.atomic_pos[elem]:
pos.dot(self.cell)
A.add_atom(pos[0], pos[1], pos[2], elem)
else:
raise RuntimeError("Wrong unit must be alat or crystal")
return A
def pmg_to_pyl(pmg : Structure):
from pylada.crystal import Structure as Pyl_Structure
from pylada.crystal import Atom
pyl = Pyl_Structure(np.transpose(pmg.lattice.matrix))
for i in range(len(pmg)):
if pmg.site_properties:
kwargs = {x: pmg.site_properties[x][i] for x in pmg.site_properties}
else:
kwargs = {}
coords = pmg[i].coords
specie = str(pmg[i].specie)
pyl_atom = Atom(coords[0], coords[1], coords[2], specie, **kwargs)
pyl.add_atom(pyl_atom)
return pyl
def first_order_charge_correction(structure,
charge=None,
epsilon=1e0,
cutoff=20.0,
**kwargs):
""" First order charge correction of +1 charge in given supercell.
Units in this function are either handled by the module Quantities, or
defaults to Angstroems and elementary charges.
:Parameters:
structure : `pylada.crystal.Structure`
Defect supercell, with cartesian positions in angstrom.
charge
Charge of the point-defect. Defaults to 1e0 elementary charge. If no
units are attached, expects units of elementary charges.
epsilon
dimensionless relative permittivity.
cutoff
Ewald cutoff parameter.
:return: Electrostatic energy in eV.
"""
from quantities import elementary_charge, eV
from pylada.crystal import Structure
from pylada.physics import Ry
from pylada.ewald import ewald
if charge is None:
charge = 1
elif charge == 0:
return 0e0 * eV
if hasattr(charge, "units"):
charge = float(charge.rescale(elementary_charge))
ewald_cutoff = cutoff * Ry
struc = Structure()
struc.cell = structure.cell
struc.scale = structure.scale
struc.add_atom(0e0, 0, 0, "A", charge=charge)
result = ewald(struc, ewald_cutoff).energy / epsilon
return -result.rescale(eV)
def get_madelungenergy(defect, charge=None, epsilon=1e0, cutoff=100.0):
""" Function returns leading first order correction term, i.e.,
screened Madelung-like lattice energy of point charge
Reference: M. Leslie and M. J. Gillan, J. Phys. C: Solid State Phys. 18 (1985) 973
Parameters
defect = pylada.vasp.Extract object
charge = charge of point defect. Default 1e0 elementary charge
epsilon = dimensionless relative permittivity
cutoff = Ewald cutoff parameter
Returns
Madelung (electrostatic) energy in eV
Note:
1. Units in this function are either handled by the module Quantities, or\
defaults to Angstrom and elementary charges
2. Function is adopted from Haowei Peng's version in pylada.defects modules
"""
from quantities import elementary_charge, eV
from pylada.crystal import Structure
from pylada.physics import Ry
from pylada.ewald import ewald
if charge is None: charge = 1
elif charge == 0: return 0e0 * eV
if hasattr(charge, "units"):
charge = float(charge.rescale(elementary_charge))
ewald_cutoff = cutoff * Ry
structure = defect.structure
struc = Structure()
struc.cell = structure.cell
struc.scale = structure.scale
struc.add_atom(0., 0., 0., "P", charge=charge)
#Anuj_05/22/18: added "cutoff" in ewald syntax
result = ewald(struc, cutoff=ewald_cutoff).energy / epsilon
return -1 * result.rescale(eV)
def first_order_charge_correction(structure, charge=None, epsilon=1e0, cutoff=20.0, **kwargs):
""" First order charge correction of +1 charge in given supercell.
Units in this function are either handled by the module Quantities, or
defaults to Angstroems and elementary charges.
:Parameters:
structure : `pylada.crystal.Structure`
Defect supercell, with cartesian positions in angstrom.
charge
Charge of the point-defect. Defaults to 1e0 elementary charge. If no
units are attached, expects units of elementary charges.
epsilon
dimensionless relative permittivity.
cutoff
Ewald cutoff parameter.
:return: Electrostatic energy in eV.
"""
from quantities import elementary_charge, eV
from pylada.crystal import Structure
from pylada.physics import Ry
from pylada.ewald import ewald
if charge is None:
charge = 1
elif charge == 0:
return 0e0 * eV
if hasattr(charge, "units"):
charge = float(charge.rescale(elementary_charge))
ewald_cutoff = cutoff * Ry
struc = Structure()
struc.cell = structure.cell
struc.scale = structure.scale
struc.add_atom(0e0, 0, 0, "A", charge=charge)
result = ewald(struc, ewald_cutoff).energy / epsilon
return -result.rescale(eV)
def cut_and_splice(s1, s2, roll=True):
""" Cut-n-splice GSGO crossover operation
Mating operation on two parent structures s1 and s2.
Done on scaled atomic positions (cubic systems) by
cutting them in half and mixing their upper and
lower parts.
"""
from random import choice, random
from numpy import dot, abs
from numpy.linalg import det
from pylada.crystal import Structure
# swap structures randomly.
if choice([True, False]): s1, s2 = s2, s1
# chem. symbols and scaled positions of the two parents
sc_pos1 = zip([atom.type for atom in s1],fractional_pos(s1, roll=True))
sc_pos2 = zip([atom.type for atom in s2],fractional_pos(s2, roll=True))
result = Structure(s1.cell, scale=s1.scale)
# choose random positions of split-plane
xsep = 0.5 - (random() * 0.45 + 0.15)
# choose direction of split-plane randomly from cell-vectors.
direction = choice(range(3))
for type, pos in sc_pos1:
if pos[direction] >= xsep: result.add_atom(*dot(result.cell, pos), type=type)
for type, pos in sc_pos2:
if pos[direction] < xsep: result.add_atom(*dot(result.cell, pos), type=type)
result.scale = s1.scale * (float(len(result)) / float(len(s1)))**(1./3.)
return result
from pylada.physics import a0, Ry
from quantities import angstrom, eV, hartree
clj = Clj()
""" Point charge + r^12 + r^6 model. """
clj.ewald_cutoff = 80 * Ry
clj.charges["A"] = -1.0
clj.charges["B"] = 1.0
structure = Structure()
structure.set_cell = (1,0,0),\
(0,1,0),\
(0,0,1)
structure.scale = 50
structure.add_atom = (0,0,0), "A"
structure.add_atom = (a0.rescale(angstrom)/structure.scale,0,0), "B"
print clj.ewald(structure).energy, hartree.rescale(eV)
from pylada.crystal.A2BX4 import b5
from pylada.crystal import fill_structure
from numpy import array
clj.ewald_cutoff = 20 * Ry
lattice = b5()
lattice.sites[4].type='A'
structure = fill_structure(lattice.cell, lattice)
structure.scale = 8.0
clj.charges["A"] = 3.0
def test_istruc():
from collections import namedtuple
from pickle import loads, dumps
from os import remove
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import POSCAR, CONTCAR
from pylada.vasp import Vasp
from pylada.crystal import Structure, read, specieset, write
from pylada.error import ValueError
structure = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.43, name='has a name')\
.add_atom(0,0,0, "Si")\
.add_atom(0.25,0.25,0.25, "Si")
Extract = namedtuple("Extract", ['directory', 'success', 'structure'])
a = Vasp()
o = a._input['istruc']
d = {'IStruc': o.__class__}
directory = mkdtemp()
try:
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory, structure=structure) is None
assert eval(repr(o), d).value == 'auto'
assert loads(dumps(o)).value == 'auto'
assert exists(join(directory, POSCAR))
remove(join(directory, POSCAR))
# check reading from outcar but only on success.
a.restart = Extract(directory, False, structure.copy())
a.restart.structure[1].pos[0] += 0.02
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory, structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR), types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) < 1e-8
assert abs(other[1].pos[0] - 0.27) > 1e-8
# check reading from outcar but only on success.
a.restart = Extract(directory, True, structure.copy())
a.restart.structure[1].pos[0] += 0.02
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory, structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR), types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) > 1e-8
assert abs(other[1].pos[0] - 0.27) < 1e-8
# Now check CONTCAR
write.poscar(structure, join(directory, CONTCAR))
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory, structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR), types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) < 1e-8
assert abs(other[1].pos[0] - 0.27) > 1e-8
# Check some failure modes.
write.poscar(structure, join(directory, CONTCAR))
structure[0].type = 'Ge'
a.restart = None
try: o.output_map(vasp=a, outdir=directory, structure=structure)
except ValueError: pass
else: raise Exception()
structure[0].type = 'Si'
structure.add_atom(0.25,0,0, 'Si')
try: o.output_map(vasp=a, outdir=directory, structure=structure)
except ValueError: pass
else: raise Exception()
finally: rmtree(directory)
def test_istruc():
from collections import namedtuple
from pickle import loads, dumps
from os import remove
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import POSCAR, CONTCAR
from pylada.vasp import Vasp
from pylada.crystal import Structure, read, specieset, write
from pylada.error import ValueError
structure = Structure([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.43, name='has a name')\
.add_atom(0, 0, 0, "Si")\
.add_atom(0.25, 0.25, 0.25, "Si")
Extract = namedtuple("Extract", ['directory', 'success', 'structure'])
a = Vasp()
o = a._input['istruc']
d = {'IStruc': o.__class__}
directory = mkdtemp()
try:
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory,
structure=structure) is None
assert eval(repr(o), d).value == 'auto'
assert loads(dumps(o)).value == 'auto'
assert exists(join(directory, POSCAR))
remove(join(directory, POSCAR))
# check reading from outcar but only on success.
a.restart = Extract(directory, False, structure.copy())
a.restart.structure[1].pos[0] += 0.02
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory,
structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR),
types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) < 1e-8
assert abs(other[1].pos[0] - 0.27) > 1e-8
# check reading from outcar but only on success.
a.restart = Extract(directory, True, structure.copy())
a.restart.structure[1].pos[0] += 0.02
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory,
structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR),
types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) > 1e-8
assert abs(other[1].pos[0] - 0.27) < 1e-8
# Now check CONTCAR
write.poscar(structure, join(directory, CONTCAR))
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory,
structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR),
types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) < 1e-8
assert abs(other[1].pos[0] - 0.27) > 1e-8
# Check some failure modes.
write.poscar(structure, join(directory, CONTCAR))
structure[0].type = 'Ge'
a.restart = None
try:
o.output_map(vasp=a, outdir=directory, structure=structure)
except ValueError:
pass
else:
raise Exception()
structure[0].type = 'Si'
structure.add_atom(0.25, 0, 0, 'Si')
try:
o.output_map(vasp=a, outdir=directory, structure=structure)
except ValueError:
pass
else:
raise Exception()
finally:
rmtree(directory)
def icsd_cif_a(filename):
""" Reads lattice from the ICSD \*cif files.
It will not work in the case of other \*cif.
It is likely to produce wrong output if the site occupations are fractional.
If the occupation is > 0.5 it will treat it as 1 and
in the case occupation < 0.5 it will treat it as 0 and
it will accept all occupation = 0.5 as 1 and create a mess!
"""
from pylada import logger
import re
from os.path import basename
from numpy.linalg import norm
from numpy import array, transpose
from numpy import pi, sin, cos, sqrt, dot
lines = open(filename, 'r').readlines()
logger.info("crystal/read: icsd_cif_a: %s" % filename)
sym_big = 0
sym_end = 0
pos_big = 0
pos_end = 0
for l in lines:
x = l.split()
if len(x) > 0:
# CELL
if x[0] == '_cell_length_a':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
a = float(x[-1][:index])
if x[0] == '_cell_length_b':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
b = float(x[-1][:index])
if x[0] == '_cell_length_c':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
c = float(x[-1][:index])
if x[0] == '_cell_angle_alpha':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
alpha = float(x[-1][:index])
if x[0] == '_cell_angle_beta':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
beta = float(x[-1][:index])
if x[0] == '_cell_angle_gamma':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
gamma = float(x[-1][:index])
# SYMMETRY OPERATIONS
if len(x) > 0 and x[0] == '_symmetry_equiv_pos_as_xyz':
sym_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_type_symbol':
sym_end = lines.index(l)
# WYCKOFF POSITIONS
if len(x) > 0 and x[0] == '_atom_site_attached_hydrogens':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_B_iso_or_equiv':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_U_iso_or_equiv':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_0_iso_or_equiv':
pos_big = lines.index(l)
# if pos_end == 0 and l in ['\n', '\r\n'] and lines.index(l) > pos_big:
if pos_end == 0 and pos_big > 0 \
and (l in ['\n', '\r\n'] or l.startswith('#')) \
and lines.index(l) > pos_big:
pos_end = lines.index(l)
# _symmetry_equiv_pos_* lines are like:
# 1 'x, x-y, -z+1/2'
logger.debug("crystal/read: icsd_cif_a: sym_big: %s" % sym_big)
logger.debug("crystal/read: icsd_cif_a: sym_end: %s" % sym_end)
symm_ops = ['(' + x.split()[1][1:] + x.split()[2] + x.split()[3][:-1] + ')'
for x in lines[sym_big + 1:sym_end - 1]]
logger.debug("crystal/read: icsd_cif_a: symm_ops a: %s" % symm_ops)
# ['(x,x-y,-z+1/2)', '(-x+y,y,-z+1/2)', ...]
# Insert decimal points after integers
symm_ops = [re.sub(r'(\d+)', r'\1.', x) for x in symm_ops]
logger.debug("crystal/read: icsd_cif_a: symm_ops b: %s" % symm_ops)
# ['(x,x-y,-z+1./2.)', '(-x+y,y,-z+1./2.)', ...]
# _atom_site_* lines are like:
# Mo1 Mo4+ 2 c 0.3333 0.6667 0.25 1. 0
logger.debug("crystal/read: icsd_cif_a: pos_big: %s" % pos_big)
logger.debug("crystal/read: icsd_cif_a: pos_end: %s" % pos_end)
wyckoff = [[x.split()[0], [x.split()[4], x.split()[5], x.split()[6]], x.split()[7]]
for x in lines[pos_big + 1:pos_end]]
logger.debug("crystal/read: icsd_cif_a: wyckoff a: %s" % wyckoff)
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
wyckoff = [w for w in wyckoff if int(float(w[-1][:4]) + 0.5) != 0]
logger.debug("crystal/read: icsd_cif_a: wyckoff b: %s" % wyckoff)
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
# Setting up a good wyckoff list
for w in wyckoff:
# Strip trailing numerals from w[0] == 'Mo1'
pom = 0
for i in range(len(w[0])):
try:
int(w[0][i])
if pom == 0:
pom = i
except:
pass
w[0] = w[0][:pom]
# Strip trailing standard uncertainty, if any, from w[1], ..., w[3]
for i in range(3):
if '(' in w[1][i]:
index = w[1][i].index('(')
else:
index = len(w[1][i])
w[1][i] = float(w[1][i][:index])
# Delete w[4]
del w[-1]
##########################################
# List of unique symbols ["Mo", "S"]
symbols = list({w[0] for w in wyckoff})
logger.debug("crystal/read: icsd_cif_a: symbols: %s" % symbols)
# List of position vectors for each symbol
positions = [[] for i in range(len(symbols))]
for w in wyckoff:
symbol = w[0]
x, y, z = w[1][0], w[1][1], w[1][2]
logger.debug("symbol: %s x: %s y: %s z: %s" % (symbol, x, y, z))
for i in range(len(symm_ops)):
# Set pom = new position based on symmetry transform
pom = list(eval(symm_ops[i]))
logger.debug("i: %s pom a: %s" % (i, pom))
# [0.3333, -0.3334, 0.25]
# Move positions to range [0,1]:
for j in range(len(pom)):
if pom[j] < 0.:
pom[j] = pom[j] + 1.
if pom[j] >= 0.999:
pom[j] = pom[j] - 1.
logger.debug("i: %s pom b: %s" % (i, pom))
# [0.3333, 0.6666, 0.25]
# If pom is not in positions[symbol], append pom
if not any(norm(array(u) - array(pom)) < 0.01 for u in positions[symbols.index(symbol)]):
ix = symbols.index(symbol)
positions[ix].append(pom)
logger.debug("new positions for %s: %s" % (symbol, repr(positions[ix])))
################ CELL ####################
a1 = a * array([1., 0., 0.])
a2 = b * array([cos(gamma * pi / 180.), sin(gamma * pi / 180.), 0.])
c1 = c * cos(beta * pi / 180.)
c2 = c / sin(gamma * pi / 180.) * (-cos(beta * pi / 180.) *
cos(gamma * pi / 180.) + cos(alpha * pi / 180.))
a3 = array([c1, c2, sqrt(c**2 - (c1**2 + c2**2))])
cell = array([a1, a2, a3])
logger.debug("crystal/read: icsd_cif_a: a1: %s" % a1)
logger.debug("crystal/read: icsd_cif_a: a2: %s" % a2)
logger.debug("crystal/read: icsd_cif_a: a3: %s" % a3)
##########################################
from pylada.crystal import Structure, primitive
logger.debug("crystal/read: icsd_cif_a: cell: %s" % cell)
structure = Structure(
transpose(cell),
scale=1,
name=basename(filename))
for i in range(len(symbols)):
logger.debug("crystal/read: icsd_cif_a: i: %s symbol: %s len(position): %i" % (
i, symbols[i], len(positions[i])
))
# crystal/read: i: 0 symbol: Mo len position: 2
for j in range(len(positions[i])):
atpos = dot(transpose(cell), positions[i][j])
logger.debug("j: %s pos: %s" % (j, positions[i][j]))
logger.debug("atpos: " % atpos)
# j: 0 pos: [0.3333, 0.6666000000000001, 0.25]
# atpos: [ 6.32378655e-16 1.81847148e+00 3.07500000e+00]
structure.add_atom(atpos[0], atpos[1], atpos[2], symbols[i])
logger.info("crystal/read: icsd_cif_a: structure: %s" % structure)
prim = primitive(structure)
logger.info("crystal/read: icsd_cif_a: primitive structure: %s" % prim)
return prim
def crystal(file='fort.34'):
""" Reads CRYSTAL's external format. """
from six import next
from numpy import array, abs, zeros, any, dot
from numpy.linalg import inv
from ..crystal import which_site
from ..misc import RelativePath
from .. import error
from ..periodic_table import find as find_specie
from . import Structure
if isinstance(file, str):
if file.find('\n') == -1:
with open(RelativePath(file).path, 'r') as file:
return crystal(file)
else:
file = file.splitlines().__iter__()
# read first line
try:
line = next(file)
except StopIteration:
raise error.IOError('Premature end of stream.')
else:
dimensionality, centering, type = [int(u) for u in line.split()[:3]]
# read cell
try:
cell = array([next(file).split()[:3] for i in range(3)],
dtype='float64').T
except StopIteration:
raise error.IOError('Premature end of stream.')
result = Structure(cell=cell, centering=centering,
dimensionality=dimensionality, type=type, scale=1e0)
# read symmetry operators
result.spacegroup = []
try:
N = int(next(file))
except StopIteration:
raise error.IOError('Premature end of stream.')
for i in range(N):
try:
op = array([next(file).split()[:3] for j in range(4)],
dtype='float64')
except StopIteration:
raise error.IOError('Premature end of stream.')
else:
op[:3] = op[:3].copy().T
result.spacegroup.append(op)
result.spacegroup = array(result.spacegroup)
# read atoms.
try:
N = int(next(file))
except StopIteration:
raise error.IOError('Premature end of stream.')
for i in range(N):
try:
line = next(file).split()
except StopIteration:
raise error.IOError('Premature end of stream.')
else:
type, pos = int(line[0]), array(line[1:4], dtype='float64')
if type < 100:
type = find_specie(atomic_number=type).symbol
result.add_atom(pos=pos, type=type, asymmetric=True)
# Adds symmetrically equivalent structures.
identity = zeros((4, 3), dtype='float64')
for i in range(3):
identity[i, i] == 1
symops = [u for u in result.spacegroup if any(abs(u - identity) > 1e-8)]
invcell = inv(result.cell)
for atom in [u for u in result]:
for op in symops:
pos = dot(op[:3], atom.pos) + op[3]
if which_site(pos, result, invcell=invcell) == -1:
result.add_atom(pos=pos, type=atom.type, asymmetric=False)
return result
def poscar(path="POSCAR", types=None):
""" Tries to read a VASP POSCAR file.
:param path: Path to the POSCAR file. Can also be an object with
file-like behavior.
:type path: str or file object
:param types: Species in the POSCAR.
:type types: None or sequence of str
:return: `pylada.crystal.Structure` instance.
"""
import re
from os.path import join, exists, isdir
from copy import deepcopy
from numpy import array, dot, transpose
from numpy.linalg import det
from quantities import angstrom
from . import Structure
from .. import error
# if types is not none, converts to a list of strings.
if types is not None:
if isinstance(types, str):
types = [types] # can't see another way of doing this...
elif not hasattr(types, "__iter__"):
types = [str(types)] # single lone vasp.specie.Specie
else:
types = [str(s) for s in types]
if path is None:
path = "POSCAR"
if not hasattr(path, 'read'):
assert exists(path), IOError("Could not find path %s." % (path))
if isdir(path):
assert exists(join(path, "POSCAR")), IOError("Could not find POSCAR in %s." % (path))
path = join(path, "POSCAR")
result = Structure()
poscar = path if hasattr(path, "read") else open(path, 'r')
try:
# gets name of structure
result.name = poscar.readline().strip()
if len(result.name) > 0 and result.name[0] == "#":
result.name = result.name[1:].strip()
# reads scale
scale = float(poscar.readline().split()[0])
# gets cell vectors.
cell = []
for i in range(3):
line = poscar.readline()
assert len(line.split()) >= 3,\
RuntimeError("Could not read column vector from poscar: %s." % (line))
cell.append([float(f) for f in line.split()[:3]])
result.cell = transpose(array(cell))
vol = det(cell)
if scale < 1.E-8:
scale = abs(scale / vol) ** (1.0 / 3)
print(result)
print(scale)
result.scale = scale * angstrom
# checks for vasp 5 input.
is_vasp_5 = True
line = poscar.readline().split()
for i in line:
if not re.match(r"[A-Z][a-z]?", i):
is_vasp_5 = False
break
if is_vasp_5:
text_types = deepcopy(line)
if types is not None and not set(text_types).issubset(set(types)):
raise error.ValueError("Unknown species in poscar: {0} not in {1}."
.format(text_types, types))
types = text_types
line = poscar.readline().split()
if types is None:
raise RuntimeError("No atomic species given in POSCAR or input.")
# checks/reads for number of each specie
if len(types) < len(line):
raise RuntimeError("Too many atomic species in POSCAR.")
nb_atoms = [int(u) for u in line]
# Check whether selective dynamics, cartesian, or direct.
first_char = poscar.readline().strip().lower()[0]
selective_dynamics = False
if first_char == 's':
selective_dynamics = True
first_char = poscar.readline().strip().lower()[0]
# Checks whether cartesian or direct.
is_direct = first_char not in ['c', 'k']
# reads atoms.
for n, specie in zip(nb_atoms, types):
for i in range(n):
line = poscar.readline().split()
pos = array([float(u) for u in line[:3]], dtype="float64")
if is_direct:
pos = dot(result.cell, pos)
result.add_atom(pos=pos, type=specie)
if selective_dynamics:
for which, freeze in zip(line[3:], ['x', 'y', 'z']):
if which.lower()[0] == 't':
result[-1].freeze = getattr(result[-1], 'freeze', '') + freeze
finally:
poscar.close()
return result
def castep(file):
""" Tries to read a castep structure file. """
from numpy import array, dot
from ..periodic_table import find as find_specie
from ..misc import RelativePath
from . import Structure
from .. import error
if isinstance(file, str):
if file.find('\n') == -1:
with open(RelativePath(file).path, 'r') as file:
return castep(file)
else:
file = file.splitlines()
file = [l for l in file]
def parse_input(input):
""" Retrieves blocks from CASTEP input file. """
current_block = None
result = {}
for line in file:
if '#' in line:
line = line[:line.find('#')]
if current_block is not None:
if line.split()[0].lower() == '%endblock':
current_block = None
continue
result[current_block] += line
elif len(line.split()) == 0:
continue
elif len(line.split()[0]) == 0:
continue
elif line.split()[0].lower() == '%block':
name = line.split()[1].lower().replace('.', '').replace('_', '')
if name in result:
raise error.ValueError('Found two {0} blocks in input.'.format(name))
result[name] = ""
current_block = name
else:
name = line.split()[0].lower().replace('.', '').replace('_', '')
if name[-1] in ['=' or ':']:
name = name[:-1]
if name in result:
raise error.ValueError('Found two {0} tags in input.'.format(name))
data = line.split()[1:]
if len(data) == 0:
result[name] = None
continue
if data[0] in [':', '=']:
data = data[1:]
result[name] = ' '.join(data)
return result
def parse_units(line):
from quantities import a0, meter, centimeter, millimeter, angstrom, emass, \
amu, second, millisecond, microsecond, nanosecond, \
picosecond, femtosecond, elementary_charge, coulomb,\
hartree, eV, meV, Ry, joule, cal, erg, hertz, \
megahertz, gigahertz, tera, kelvin, newton, dyne, \
h_bar, UnitQuantity, pascal, megapascal, gigapascal,\
bar, atm, milli, mol
auv = UnitQuantity('auv', a0 * Ry / h_bar) # velocity
units = {'a0': a0, 'bohr': a0, 'm': meter, 'cm': centimeter,
'mm': millimeter, 'ang': angstrom, 'me': emass, 'amu': amu,
's': second, 'ms': millisecond, 'mus': microsecond,
'ns': nanosecond, 'ps': picosecond, 'fs': femtosecond,
'e': elementary_charge, 'c': coulomb, 'hartree': hartree,
'ha': hartree, 'mha': 1e-3 * hartree, 'ev': eV, 'mev': meV,
'ry': Ry, 'mry': 1e-3 * Ry, 'kj': 1e3 * joule, 'mol': mol,
'kcal': 1e3 * cal, 'j': joule, 'erg': erg, 'hz': hertz,
'mhz': megahertz, 'ghz': gigahertz, 'thz': tera * hertz,
'k': kelvin, 'n': newton, 'dyne': dyne, 'auv': auv, 'pa': pascal,
'mpa': megapascal, 'gpa': gigapascal, 'atm': atm, 'bar': bar,
'atm': atm, 'mbar': milli * bar}
line = line.replace('cm-1', '1/cm')
return eval(line, units)
input = parse_input(file)
if 'latticecart' in input:
data = input['latticecart'].splitlines()
if len(data) == 4:
units = parse_units(data[0])
data = data[1:]
else:
units = 1
cell = array([l.split() for l in data], dtype='float64')
elif 'latticeabc' in input:
raise error.NotImplementedError('Cannot read lattice in ABC format yet.')
else:
raise error.ValueError('Could not find lattice block in input.')
# create structure
result = Structure(cell, scale=units)
# now look for position block.
units = None
if 'positionsfrac' in input:
posdata, isfrac = input['positionsfrac'].splitlines(), True
elif 'positionsabs' in input:
posdata, isfrac = input['positionsabs'].splitlines(), False
try:
units = parse_units(posdata[0])
except:
units = None
else:
posdata = posdata[1:]
else:
raise error.ValueError('Could not find position block in input.')
# and parse it
for line in posdata:
line = line.split()
if len(line) < 2:
raise error.IOError(
'Wrong file format: line with less than two items in positions block.')
pos = array(line[1:4], dtype='float64')
if isfrac:
pos = dot(result.cell, pos)
try:
dummy = int(line[0])
except:
type = line[0]
else:
type = find_specie(atomic_number=dummy).symbol
result.add_atom(pos=pos, type=type)
if len(line) == 5:
result[-1].magmom = float(line[4])
return result
def icsd_cif_a( filename):
""" Reads lattice from the ICSD \*cif files.
It will not work in the case of other \*cif.
It is likely to produce wrong output if the site occupations are fractional.
If the occupation is > 0.5 it will treat it as 1 and
in the case occupation < 0.5 it will treat it as 0 and
it will accept all occupation = 0.5 as 1 and create a mess!
"""
import re
from os.path import basename
from numpy.linalg import norm
from numpy import array, transpose
from numpy import pi, sin, cos, sqrt, dot
from pylada.misc import bugLev
lines = open(filename,'r').readlines()
if bugLev >= 2:
print " crystal/read: icsd_cif_a: filename: ", filename
sym_big = 0
sym_end = 0
pos_big = 0
pos_end = 0
for l in lines:
x = l.split()
if len(x)>0:
# CELL
if x[0] == '_cell_length_a':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
a = float(x[-1][:index])
if x[0] == '_cell_length_b':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
b = float(x[-1][:index])
if x[0] == '_cell_length_c':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
c = float(x[-1][:index])
if x[0] == '_cell_angle_alpha':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
alpha = float(x[-1][:index])
if x[0] == '_cell_angle_beta':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
beta = float(x[-1][:index])
if x[0] == '_cell_angle_gamma':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
gamma = float(x[-1][:index])
# SYMMETRY OPERATIONS
if len(x)>0 and x[0] == '_symmetry_equiv_pos_as_xyz':
sym_big = lines.index(l)
if len(x)>0 and x[0] == '_atom_type_symbol':
sym_end = lines.index(l)
# WYCKOFF POSITIONS
if len(x)>0 and x[0] == '_atom_site_attached_hydrogens':
pos_big = lines.index(l)
if len(x)>0 and x[0] == '_atom_site_B_iso_or_equiv':
pos_big = lines.index(l)
if len(x)>0 and x[0] == '_atom_site_U_iso_or_equiv':
pos_big = lines.index(l)
if len(x)>0 and x[0] == '_atom_site_0_iso_or_equiv':
pos_big = lines.index(l)
#if pos_end == 0 and l in ['\n', '\r\n'] and lines.index(l) > pos_big:
if pos_end == 0 and pos_big > 0 \
and (l in ['\n', '\r\n'] or l.startswith('#')) \
and lines.index(l) > pos_big:
pos_end = lines.index(l)
# _symmetry_equiv_pos_* lines are like:
# 1 'x, x-y, -z+1/2'
if bugLev >= 5:
print " crystal/read: icsd_cif_a: sym_big: ", sym_big
print " crystal/read: icsd_cif_a: sym_end: ", sym_end
symm_ops = [ '(' + x.split()[1][1:] + x.split()[2] + x.split()[3][:-1] + ')'\
for x in lines[sym_big+1:sym_end-1] ]
if bugLev >= 5:
print " crystal/read: icsd_cif_a: symm_ops a: ", symm_ops
# ['(x,x-y,-z+1/2)', '(-x+y,y,-z+1/2)', ...]
# Insert decimal points after integers
symm_ops = [re.sub(r'(\d+)', r'\1.', x) for x in symm_ops]
if bugLev >= 5:
print " crystal/read: icsd_cif_a: symm_ops b: ", symm_ops
# ['(x,x-y,-z+1./2.)', '(-x+y,y,-z+1./2.)', ...]
# _atom_site_* lines are like:
# Mo1 Mo4+ 2 c 0.3333 0.6667 0.25 1. 0
if bugLev >= 5:
print " crystal/read: icsd_cif_a: pos_big: ", pos_big
print " crystal/read: icsd_cif_a: pos_end: ", pos_end
wyckoff = [ [x.split()[0],[x.split()[4],x.split()[5],x.split()[6]],x.split()[7]]\
for x in lines[pos_big+1:pos_end] ]
if bugLev >= 5:
print " crystal/read: icsd_cif_a: wyckoff a: ", wyckoff
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
wyckoff = [w for w in wyckoff if int(float(w[-1][:4])+0.5) != 0]
if bugLev >= 5:
print " crystal/read: icsd_cif_a: wyckoff b: ", wyckoff
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
############## Setting up a good wyckoff list
for w in wyckoff:
# Strip trailing numerals from w[0] == 'Mo1'
pom = 0
for i in range(len(w[0])):
try:
int(w[0][i])
if pom ==0: pom=i
except:
pass
w[0] = w[0][:pom]
# Strip trailing standard uncertainty, if any, from w[1], ..., w[3]
for i in range(3):
if '(' in w[1][i]:
index = w[1][i].index('(')
else:
index = len(w[1][i])
w[1][i] = float(w[1][i][:index])
# Delete w[4]
del w[-1]
##########################################
# List of unique symbols ["Mo", "S"]
symbols = list(set([w[0] for w in wyckoff]))
if bugLev >= 5:
print " crystal/read: icsd_cif_a: symbols: ", symbols
# List of position vectors for each symbol
positions = [[] for i in range(len(symbols))]
for w in wyckoff:
symbol = w[0]
x,y,z = w[1][0],w[1][1],w[1][2]
if bugLev >= 5:
print " symbol: ", symbol, " x: ", x, " y: ", y, " z: ", z
for i in range(len(symm_ops)):
# Set pom = new position based on symmetry transform
pom = list(eval(symm_ops[i]))
if bugLev >= 5:
print " i: ", i, " pom a: ", pom
# [0.3333, -0.3334, 0.25]
# Move positions to range [0,1]:
for j in range(len(pom)):
if pom[j] < 0.: pom[j] = pom[j]+1.
if pom[j] >= 0.999: pom[j] = pom[j]-1.
if bugLev >= 5:
print " i: ", i, " pom b: ", pom
# [0.3333, 0.6666, 0.25]
# If pom is not in positions[symbol], append pom
if not any(norm(array(u)-array(pom)) < 0.01 for u in positions[symbols.index(symbol)]):
ix = symbols.index(symbol)
positions[ix].append(pom)
if bugLev >= 5:
print " new positions for ", symbol, ": ", positions[ix]
################ CELL ####################
a1 = a*array([1.,0.,0.])
a2 = b*array([cos(gamma*pi/180.),sin(gamma*pi/180.),0.])
c1 = c*cos(beta*pi/180.)
c2 = c/sin(gamma*pi/180.)*(-cos(beta*pi/180.)*cos(gamma*pi/180.) + cos(alpha*pi/180.))
a3 = array([c1, c2, sqrt(c**2-(c1**2+c2**2))])
cell = array([a1,a2,a3])
if bugLev >= 2:
print " crystal/read: icsd_cif_a: a1: ", a1
print " crystal/read: icsd_cif_a: a2: ", a2
print " crystal/read: icsd_cif_a: a3: ", a3
# a1: [ 3.15 0. 0. ]
# a2: [-1.575 2.72798002 0. ]
# a3: [ 7.53157781e-16 1.30450754e-15 1.23000000e+01]
##########################################
from pylada.crystal import Structure, primitive
if bugLev >= 2:
print " crystal/read: icsd_cif_a: cell: ", cell
# [[ 3.15000000e+00 0.00000000e+00 0.00000000e+00]
# [ -1.57500000e+00 2.72798002e+00 0.00000000e+00]
# [ 7.53157781e-16 1.30450754e-15 1.23000000e+01]]
structure = Structure(
transpose( cell),
scale = 1,
name = basename( filename))
for i in range(len(symbols)):
if bugLev >= 5:
print " crystal/read: icsd_cif_a: i: ", i, \
" symbol: ", symbols[i], \
" len position: ", len(positions[i])
# crystal/read: i: 0 symbol: Mo len position: 2
for j in range(len(positions[i])):
atpos = dot( transpose(cell), positions[i][j])
if bugLev >= 5:
print " j: ", j, " pos: ", positions[i][j]
print " atpos: ", atpos
# j: 0 pos: [0.3333, 0.6666000000000001, 0.25]
# atpos: [ 6.32378655e-16 1.81847148e+00 3.07500000e+00]
structure.add_atom( atpos[0], atpos[1], atpos[2], symbols[i])
if bugLev >= 2:
print " crystal/read: icsd_cif_a: structure:\n", structure
prim = primitive( structure)
if bugLev >= 2:
print " crystal/read: icsd_cif_a: primitive structure:\n", prim
return prim
def poscar(path="POSCAR", types=None):
""" Tries to read a VASP POSCAR file.
:param path: Path to the POSCAR file. Can also be an object with
file-like behavior.
:type path: str or file object
:param types: Species in the POSCAR.
:type types: None or sequence of str
:return: `pylada.crystal.Structure` instance.
"""
import re
from os.path import join, exists, isdir
from copy import deepcopy
from numpy import array, dot, transpose
from numpy.linalg import det
from quantities import angstrom
from . import Structure
# if types is not none, converts to a list of strings.
if types is not None:
if isinstance(types, str): types = [types] # can't see another way of doing this...
elif not hasattr(types, "__iter__"): types = [str(types)] # single lone vasp.specie.Specie
else: types = [str(s) for s in types]
if path is None: path = "POSCAR"
if not hasattr(path, 'read'):
assert exists(path), IOError("Could not find path %s." % (path))
if isdir(path):
assert exists(join(path, "POSCAR")), IOError("Could not find POSCAR in %s." % (path))
path = join(path, "POSCAR")
result = Structure()
poscar = path if hasattr(path, "read") else open(path, 'r')
try:
# gets name of structure
result.name = poscar.readline().strip()
if len(result.name) > 0:
if result.name[0] == "#": result.name = result.name[1:].strip()
# reads scale
scale = float(poscar.readline().split()[0])
# gets cell vectors.
cell = []
for i in range(3):
line = poscar.readline()
assert len(line.split()) >= 3,\
RuntimeError("Could not read column vector from poscar: %s." % (line))
cell.append( [float(f) for f in line.split()[:3]] )
result.cell = transpose(array(cell))
vol = det(cell)
if scale < 1.E-8 : scale = abs(scale/vol) **(1.0/3)
result.scale = scale * angstrom
# checks for vasp 5 input.
is_vasp_5 = True
line = poscar.readline().split()
for i in line:
if not re.match(r"[A-Z][a-z]?", i):
is_vasp_5 = False
break
if is_vasp_5:
text_types = deepcopy(line)
if types is not None and not set(text_types).issubset(set(types)):
raise RuntimeError( "Unknown species in poscar: {0} not in {1}."\
.format(text_types, types) )
types = text_types
line = poscar.readline().split()
assert types is not None, RuntimeError("No atomic species given in POSCAR or input.")
# checks/reads for number of each specie
assert len(types) >= len(line), RuntimeError("Too many atomic species in POSCAR.")
nb_atoms = [int(u) for u in line]
# Check whether selective dynamics, cartesian, or direct.
first_char = poscar.readline().strip().lower()[0]
selective_dynamics = False
if first_char == 's':
selective_dynamics = True
first_char = poscar.readline().strip().lower()[0]
# Checks whether cartesian or direct.
is_direct = first_char not in ['c', 'k']
# reads atoms.
for n, specie in zip(nb_atoms, types):
for i in range(n):
line = poscar.readline().split()
pos = array([float(u) for u in line[:3]], dtype="float64")
if is_direct: pos = dot(result.cell, pos)
result.add_atom(pos=pos, type=specie)
if selective_dynamics:
for which, freeze in zip(line[3:], ['x', 'y', 'z']):
if which.lower()[0] == 't':
result[-1].freeze = getattr(result[-1], 'freeze', '') + freeze
finally: poscar.close()
return result
def castep(file):
""" Tries to read a castep structure file. """
from numpy import array, dot
from ..periodic_table import find as find_specie
from ..error import IOError, NotImplementedError, input as InputError
from ..misc import RelativePath
from . import Structure
if isinstance(file, str):
if file.find('\n') == -1:
with open(RelativePath(file).path, 'r') as file: return castep(file)
else: file = file.splitlines()
file = [l for l in file]
def parse_input(input):
""" Retrieves blocks from CASTEP input file. """
current_block = None
result = {}
for line in file:
if '#' in line: line = line[:line.find('#')]
if current_block is not None:
if line.split()[0].lower() == '%endblock':
current_block = None
continue
result[current_block] += line
elif len(line.split()) == 0: continue
elif len(line.split()[0]) == 0: continue
elif line.split()[0].lower() == '%block':
name = line.split()[1].lower().replace('.', '').replace('_', '')
if name in result:
raise InputError('Found two {0} blocks in input.'.format(name))
result[name] = ""
current_block = name
else:
name = line.split()[0].lower().replace('.', '').replace('_', '')
if name[-1] in ['=' or ':']: name = name[:-1]
if name in result:
raise InputError('Found two {0} tags in input.'.format(name))
data = line.split()[1:]
if len(data) == 0: result[name] = None; continue
if data[0] in [':', '=']: data = data[1:]
result[name] = ' '.join(data)
return result
def parse_units(line):
from quantities import a0, meter, centimeter, millimeter, angstrom, emass, \
amu, second, millisecond, microsecond, nanosecond, \
picosecond, femtosecond, elementary_charge, coulomb,\
hartree, eV, meV, Ry, joule, cal, erg, hertz, \
megahertz, gigahertz, tera, kelvin, newton, dyne, \
h_bar, UnitQuantity, pascal, megapascal, gigapascal,\
bar, atm, milli, mol
auv = UnitQuantity('auv', a0*Ry/h_bar) # velocity
units = { 'a0': a0, 'bohr': a0, 'm': meter, 'cm': centimeter,
'mm': millimeter, 'ang': angstrom, 'me': emass, 'amu': amu,
's': second, 'ms': millisecond, 'mus': microsecond,
'ns': nanosecond, 'ps': picosecond, 'fs': femtosecond,
'e': elementary_charge, 'c': coulomb, 'hartree': hartree,
'ha': hartree, 'mha': 1e-3*hartree, 'ev': eV, 'mev': meV,
'ry': Ry, 'mry': 1e-3*Ry, 'kj': 1e3*joule, 'mol': mol,
'kcal': 1e3*cal, 'j': joule, 'erg': erg, 'hz': hertz,
'mhz': megahertz, 'ghz': gigahertz, 'thz': tera*hertz,
'k': kelvin, 'n': newton, 'dyne': dyne, 'auv': auv, 'pa': pascal,
'mpa': megapascal, 'gpa': gigapascal, 'atm': atm, 'bar': bar,
'atm': atm, 'mbar': milli*bar }
line = line.replace('cm-1', '1/cm')
return eval(line, units)
input = parse_input(file)
if 'latticecart' in input:
data = input['latticecart'].splitlines()
if len(data) == 4:
units = parse_units(data[0])
data = data[1:]
else: units = 1
cell = array([l.split() for l in data], dtype='float64')
elif 'latticeabc' in input:
raise NotImplementedError('Cannot read lattice in ABC format yet.')
else:
raise InputError('Could not find lattice block in input.')
# create structure
result = Structure(cell, scale=units)
# now look for position block.
units = None
if 'positionsfrac' in input:
posdata, isfrac = input['positionsfrac'].splitlines(), True
elif 'positionsabs' in input:
posdata, isfrac = input['positionsabs'].splitlines(), False
try: units = parse_units(posdata[0])
except: units = None
else: posdata = posdata[1:]
else: raise InputError('Could not find position block in input.')
# and parse it
for line in posdata:
line = line.split()
if len(line) < 2:
raise IOError( 'Wrong file format: line with less ' \
'than two items in positions block.')
pos = array(line[1:4], dtype='float64')
if isfrac: pos = dot(result.cell, pos)
try: dummy = int(line[0])
except: type = line[0]
else: type = find_specie(atomic_number=dummy).symbol
result.add_atom(pos=pos, type=type)
if len(line) == 5: result[-1].magmom = float(line[4])
return result
def icsd_cif_a(filename, make_primitive=True):
""" Reads lattice from the ICSD \*cif files.
It will not work in the case of other \*cif.
It is likely to produce wrong output if the site occupations are fractional.
If the occupation is > 0.5 it will treat it as 1 and
in the case occupation < 0.5 it will treat it as 0 and
it will accept all occupation = 0.5 as 1 and create a mess!
"""
from pylada import logger
import re
from copy import deepcopy
from os.path import basename
from numpy.linalg import norm
from numpy import array, transpose
from numpy import pi, sin, cos, sqrt, dot
lines = open(filename, 'r').readlines()
logger.info("crystal/read: icsd_cif_a: %s" % filename)
sym_big = 0
sym_end = 0
pos_big = 0
pos_end = 0
for l in lines:
x = l.split()
if len(x) > 0:
# CELL
if x[0] == '_cell_length_a':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
a = float(x[-1][:index])
if x[0] == '_cell_length_b':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
b = float(x[-1][:index])
if x[0] == '_cell_length_c':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
c = float(x[-1][:index])
if x[0] == '_cell_angle_alpha':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
alpha = float(x[-1][:index])
if x[0] == '_cell_angle_beta':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
beta = float(x[-1][:index])
if x[0] == '_cell_angle_gamma':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
gamma = float(x[-1][:index])
# SYMMETRY OPERATIONS
if len(x) > 0 and x[0] == '_symmetry_equiv_pos_as_xyz':
sym_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_type_symbol':
sym_end = lines.index(l)
# WYCKOFF POSITIONS
if len(x) > 0 and x[0] == '_atom_site_attached_hydrogens':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_B_iso_or_equiv':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_U_iso_or_equiv':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_0_iso_or_equiv':
pos_big = lines.index(l)
# if pos_end == 0 and l in ['\n', '\r\n'] and lines.index(l) > pos_big:
if pos_end == 0 and pos_big > 0 \
and (l in ['\n', '\r\n'] or l.startswith('#')) \
and lines.index(l) > pos_big:
pos_end = lines.index(l)
# _symmetry_equiv_pos_* lines are like:
# 1 'x, x-y, -z+1/2'
logger.debug("crystal/read: icsd_cif_a: sym_big: %s" % sym_big)
logger.debug("crystal/read: icsd_cif_a: sym_end: %s" % sym_end)
symm_ops = ['(' + x.split()[1][1:] + x.split()[2] + x.split()[3][:-1] + ')'
for x in lines[sym_big + 1:sym_end - 1]]
logger.debug("crystal/read: icsd_cif_a: symm_ops a: %s" % symm_ops)
# ['(x,x-y,-z+1/2)', '(-x+y,y,-z+1/2)', ...]
# Insert decimal points after integers
symm_ops = [re.sub(r'(\d+)', r'\1.', x) for x in symm_ops]
logger.debug("crystal/read: icsd_cif_a: symm_ops b: %s" % symm_ops)
# ['(x,x-y,-z+1./2.)', '(-x+y,y,-z+1./2.)', ...]
# _atom_site_* lines are like:
# Mo1 Mo4+ 2 c 0.3333 0.6667 0.25 1. 0
logger.debug("crystal/read: icsd_cif_a: pos_big: %s" % pos_big)
logger.debug("crystal/read: icsd_cif_a: pos_end: %s" % pos_end)
wyckoff = [[x.split()[0], [x.split()[4], x.split()[5], x.split()[6]], x.split()[7]]
for x in lines[pos_big + 1:pos_end]]
logger.debug("crystal/read: icsd_cif_a: wyckoff a: %s" % wyckoff)
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
wyckoff = [w for w in wyckoff if int(float(w[-1][:4]) + 0.5) != 0]
logger.debug("crystal/read: icsd_cif_a: wyckoff b: %s" % wyckoff)
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
# Setting up a good wyckoff list
for w in wyckoff:
# Strip trailing numerals from w[0] == 'Mo1'
pom = 0
for i in range(len(w[0])):
try:
int(w[0][i])
if pom == 0:
pom = i
except:
pass
w[0] = w[0][:pom]
# Strip trailing standard uncertainty, if any, from w[1], ..., w[3]
for i in range(3):
if '(' in w[1][i]:
index = w[1][i].index('(')
else:
index = len(w[1][i])
w[1][i] = float(w[1][i][:index])
# Delete w[4]
del w[-1]
##########################################
# List of unique symbols ["Mo", "S"]
symbols = list({w[0] for w in wyckoff})
logger.debug("crystal/read: icsd_cif_a: symbols: %s" % symbols)
# List of position vectors for each symbol
positions = [[] for i in range(len(symbols))]
for w in wyckoff:
symbol = w[0]
x, y, z = w[1][0], w[1][1], w[1][2]
logger.debug("symbol: %s x: %s y: %s z: %s" % (symbol, x, y, z))
for i in range(len(symm_ops)):
# Set pom = new position based on symmetry transform
pom = list(eval(symm_ops[i]))
logger.debug("i: %s pom a: %s" % (i, pom))
# [0.3333, -0.3334, 0.25]
# Move positions to range [0,1]:
for j in range(len(pom)):
if pom[j] < 0.:
pom[j] = pom[j] + 1.
if pom[j] >= 0.999:
pom[j] = pom[j] - 1.
logger.debug("i: %s pom b: %s" % (i, pom))
# [0.3333, 0.6666, 0.25]
# If pom is not in positions[symbol], append pom
if not any(norm(array(u) - array(pom)) < 0.01 for u in positions[symbols.index(symbol)]):
ix = symbols.index(symbol)
positions[ix].append(pom)
logger.debug("new positions for %s: %s" % (symbol, repr(positions[ix])))
################ CELL ####################
a1 = a * array([1., 0., 0.])
a2 = b * array([cos(gamma * pi / 180.), sin(gamma * pi / 180.), 0.])
c1 = c * cos(beta * pi / 180.)
c2 = c / sin(gamma * pi / 180.) * (-cos(beta * pi / 180.) *
cos(gamma * pi / 180.) + cos(alpha * pi / 180.))
a3 = array([c1, c2, sqrt(c**2 - (c1**2 + c2**2))])
cell = array([a1, a2, a3])
logger.debug("crystal/read: icsd_cif_a: a1: %s" % a1)
logger.debug("crystal/read: icsd_cif_a: a2: %s" % a2)
logger.debug("crystal/read: icsd_cif_a: a3: %s" % a3)
##########################################
from pylada.crystal import Structure, primitive
logger.debug("crystal/read: icsd_cif_a: cell: %s" % cell)
structure = Structure(
transpose(cell),
scale=1,
name=basename(filename))
for i in range(len(symbols)):
logger.debug("crystal/read: icsd_cif_a: i: %s symbol: %s len(position): %i" % (
i, symbols[i], len(positions[i])
))
# crystal/read: i: 0 symbol: Mo len position: 2
for j in range(len(positions[i])):
atpos = dot(transpose(cell), positions[i][j])
logger.debug("j: %s pos: %s" % (j, positions[i][j]))
logger.debug("atpos: " % atpos)
# j: 0 pos: [0.3333, 0.6666000000000001, 0.25]
# atpos: [ 6.32378655e-16 1.81847148e+00 3.07500000e+00]
structure.add_atom(atpos[0], atpos[1], atpos[2], symbols[i])
logger.info("crystal/read: icsd_cif_a: structure: %s" % structure)
if make_primitive:
prim = primitive(structure)
else:
prim = deepcopy(structure)
logger.info("crystal/read: icsd_cif_a: primitive structure: %s" % prim)
return prim
def make_surface(structure=None, miller=None, nlayers=5, vacuum=15, acc=5):
"""Returns a slab from the 3D structure
Takes a structure and makes a slab defined by the miller indices
with nlayers number of layers and vacuum defining the size
of the vacuum thickness. Variable acc determines the number of
loops used to get the direct lattice vectors perpendicular
and parallel to miller. For high index surfaces use larger acc value
.. warning: (1) cell is always set such that miller is alogn z-axes
(2) nlayers and vacuum are always along z-axes.
:param structure: LaDa structure
:param miller: 3x1 float64 array
Miller indices defining the slab
:param nlayers: integer
Number of layers in the slab
:param vacuum: real
Vacuum thicness in angstroms
:param acc: integer
number of loops for finding the cell vectors of the slab structure
"""
direct_cell = transpose(structure.cell)
reciprocal_cell = 2 * pi * transpose(inv(direct_cell))
orthogonal = [] # lattice vectors orthogonal to miller
for n1 in arange(-acc, acc + 1):
for n2 in arange(-acc, acc + 1):
for n3 in arange(-acc, acc + 1):
pom = array([n1, n2, n3])
if dot(pom, miller) == 0 and dot(pom, pom) != 0:
orthogonal.append(array([n1, n2, n3]))
# chose the shortest parallel and set it to be a3 lattice vector
norm_orthogonal = [sqrt(dot(dot(x, direct_cell), dot(x, direct_cell))) for x in orthogonal]
a1 = orthogonal[norm_orthogonal.index(min(norm_orthogonal))]
# chose the shortest orthogonal to miller and not colinear with a1 and set it as a2
in_plane = []
for x in orthogonal:
if dot(x, x) > 1e-3:
v = cross(dot(x, direct_cell), dot(a1, direct_cell))
v = sqrt(dot(v, v))
if v > 1e-3:
in_plane.append(x)
norm_in_plane = [sqrt(dot(dot(x, direct_cell), dot(x, direct_cell))) for x in in_plane]
a2 = in_plane[norm_in_plane.index(min(norm_in_plane))]
a1 = dot(a1, direct_cell)
a2 = dot(a2, direct_cell)
# new cartesian axes z-along miller, x-along a1, and y-to define the right-hand orientation
e1 = a1 / sqrt(dot(a1, a1))
e2 = a2 - dot(e1, a2) * e1
e2 = e2 / sqrt(dot(e2, e2))
e3 = cross(e1, e2)
# find vectors parallel to miller and set the shortest to be a3
parallel = []
for n1 in arange(-acc, acc + 1):
for n2 in arange(-acc, acc + 1):
for n3 in arange(-acc, acc + 1):
pom = dot(array([n1, n2, n3]), direct_cell)
if sqrt(dot(pom, pom)) - dot(e3, pom) < 1e-8 and sqrt(dot(pom, pom)) > 1e-3:
parallel.append(pom)
# if there are no lattice vectors parallel to miller
if len(parallel) == 0:
for n1 in arange(-acc, acc + 1):
for n2 in arange(-acc, acc + 1):
for n3 in arange(-acc, acc + 1):
pom = dot(array([n1, n2, n3]), direct_cell)
if dot(e3, pom) > 1e-3:
parallel.append(pom)
parallel = [x for x in parallel if sqrt(
dot(x - dot(e1, x) * e1 - dot(e2, x) * e2, x - dot(e1, x) * e1 - dot(e2, x) * e2)) > 1e-3]
norm_parallel = [sqrt(dot(x, x)) for x in parallel]
assert len(norm_parallel) != 0, "Increase acc, found no lattice vectors parallel to (hkl)"
a3 = parallel[norm_parallel.index(min(norm_parallel))]
# making a structure in the new unit cell - defined by the a1,a2,a3
new_direct_cell = array([a1, a2, a3])
assert abs(det(new_direct_cell)) > 1e-5, "Something is wrong your volume is equal to zero"
# make sure determinant is positive
if det(new_direct_cell) < 0.:
new_direct_cell = array([-a1, a2, a3])
#structure = fill_structure(transpose(new_direct_cell),structure.to_lattice())
structure = supercell(lattice=structure, supercell=transpose(new_direct_cell))
# transformation matrix to new coordinates x' = dot(m,x)
m = array([e1, e2, e3])
# seting output structure
out_structure = Structure()
out_structure.scale = structure.scale
out_structure.cell = transpose(dot(new_direct_cell, transpose(m)))
for atom in structure:
p = dot(m, atom.pos)
out_structure.add_atom(p[0], p[1], p[2], atom.type)
# repaeting to get nlayers and vacuum
repeat_cell = dot(out_structure.cell, array([[1., 0., 0.], [0., 1., 0.], [0., 0., nlayers]]))
out_structure = supercell(lattice=out_structure, supercell=repeat_cell)
# checking whether there are atoms close to the cell faces and putting them back to zero
for i in range(len(out_structure)):
scaled_pos = dot(out_structure[i].pos, inv(transpose(out_structure.cell)))
for j in range(3):
if abs(scaled_pos[j] - 1.) < 1e-5:
scaled_pos[j] = 0.
out_structure[i].pos = dot(scaled_pos, transpose(out_structure.cell))
# adding vaccum to the cell
out_structure.cell = out_structure.cell + \
array([[0., 0., 0.], [0., 0., 0.], [0., 0., float(vacuum) / float(out_structure.scale)]])
# translating atoms so that center of the slab and the center of the cell along z-axes coincide
max_z = max([x.pos[2] for x in out_structure])
min_z = min([x.pos[2] for x in out_structure])
center_atoms = 0.5 * (max_z + min_z)
center_cell = 0.5 * out_structure.cell[2][2]
for i in range(len(out_structure)):
out_structure[i].pos = out_structure[i].pos + array([0., 0., center_cell - center_atoms])
# exporting the final structure
return out_structure
def icsd_cif_a(filename, make_primitive=True):
""" Reads lattice from the ICSD \*cif files.
It will not work in the case of other \*cif.
It is likely to produce wrong output if the site occupations are fractional.
If the occupation is > 0.5 it will treat it as 1 and
in the case occupation < 0.5 it will treat it as 0 and
it will accept all occupation = 0.5 as 1 and create a mess!
"""
import re
from copy import deepcopy
from os.path import basename
from numpy.linalg import norm
from numpy import array, transpose
from numpy import pi, sin, cos, sqrt, dot
from sys import version_info
if version_info[0] >= 3:
lines = open(filename, 'r', encoding='latin1').readlines()
else:
lines = open(filename, 'r').readlines()
sym_big = 0
sym_end = 0
pos_big = 0
pos_end = 0
for l in lines:
x = l.split()
if len(x) > 0:
# CELL
if x[0] == '_cell_length_a':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
a = float(x[-1][:index])
if x[0] == '_cell_length_b':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
b = float(x[-1][:index])
if x[0] == '_cell_length_c':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
c = float(x[-1][:index])
if x[0] == '_cell_angle_alpha':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
alpha = float(x[-1][:index])
if x[0] == '_cell_angle_beta':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
beta = float(x[-1][:index])
if x[0] == '_cell_angle_gamma':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
gamma = float(x[-1][:index])
if len(x) > 0 and x[0] == '_symmetry_Int_Tables_number':
spg = int(x[1])
# SYMMETRY OPERATIONS
if len(x) > 0 and x[0] == '_symmetry_equiv_pos_as_xyz':
sym_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_type_symbol':
sym_end = lines.index(l)
## FT: reads oxydation states
# OXYDATION STATE
if len(x) > 0 and x[0] == '_atom_site_label':
ox_end = lines.index(l)
# WYCKOFF POSITIONS
if len(x) > 0 and x[0] == '_atom_site_attached_hydrogens':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_B_iso_or_equiv':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_U_iso_or_equiv':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_0_iso_or_equiv':
pos_big = lines.index(l)
# if pos_end == 0 and l in ['\n', '\r\n'] and lines.index(l) > pos_big:
if pos_end == 0 and pos_big > 0 \
and (l in ['\n', '\r\n'] or l.startswith('#')) \
and lines.index(l) > pos_big:
pos_end = lines.index(l)
# _symmetry_equiv_pos_* lines are like:
# 1 'x, x-y, -z+1/2'
symm_ops = [
'(' + x.split()[1][1:] + x.split()[2] + x.split()[3][:-1] + ')'
for x in lines[sym_big + 1:sym_end - 1]
]
# ['(x,x-y,-z+1/2)', '(-x+y,y,-z+1/2)', ...]
# Insert decimal points after integers
symm_ops = [re.sub(r'(\d+)', r'\1.', x) for x in symm_ops]
# ['(x,x-y,-z+1./2.)', '(-x+y,y,-z+1./2.)', ...]
# _atom_site_* lines are like:
# Mo1 Mo4+ 2 c 0.3333 0.6667 0.25 1. 0
## FT: replaced [0] by [1] to take the ion name instead (ex: Mo4+ instead of Mo1)
wyckoff = [[
x.split()[1], [x.split()[4], x.split()[5],
x.split()[6]],
x.split()[7]
] for x in lines[pos_big + 1:pos_end]]
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
wyckoff = [w for w in wyckoff if int(float(w[-1][:4]) + 0.5) != 0]
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
##FT: reading the proper oxidation states
oxidation = [[x.split()[0],
int(round(float(x.split()[1]), 0))]
for x in lines[sym_end + 2:ox_end - 1]]
# Setting up a good wyckoff list
for w in wyckoff:
## FT: Not stripping anymore to keep different oxydation states different
# Strip trailing numerals from w[0] == 'Mo1'
# pom = 0
# for i in range(len(w[0])):
# try:
# int(w[0][i])
# if pom == 0:
# pom = i
# except:
# pass
# w[0] = w[0][:pom]
# Strip trailing standard uncertainty, if any, from w[1], ..., w[3]
for i in range(3):
if '(' in w[1][i]:
index = w[1][i].index('(')
else:
index = len(w[1][i])
w[1][i] = float(w[1][i][:index])
# Delete w[4]
del w[-1]
##########################################
# List of unique symbols ["Mo", "S"]
symbols = list({w[0] for w in wyckoff})
# List of position vectors for each symbol
positions = [[] for i in range(len(symbols))]
for w in wyckoff:
symbol = w[0]
x, y, z = w[1][0], w[1][1], w[1][2]
for i in range(len(symm_ops)):
# Set pom = new position based on symmetry transform
pom = list(eval(symm_ops[i]))
# [0.3333, -0.3334, 0.25]
# Move positions to range [0,1]:
for j in range(len(pom)):
if pom[j] < 0.:
pom[j] = pom[j] + 1.
if pom[j] >= 0.999:
pom[j] = pom[j] - 1.
# [0.3333, 0.6666, 0.25]
# If pom is not in positions[symbol], append pom
if not any(
norm(array(u) - array(pom)) < 0.01
for u in positions[symbols.index(symbol)]):
ix = symbols.index(symbol)
positions[ix].append(pom)
################ CELL ####################
a1 = a * array([1., 0., 0.])
a2 = b * array([cos(gamma * pi / 180.), sin(gamma * pi / 180.), 0.])
c1 = c * cos(beta * pi / 180.)
c2 = c / sin(
gamma * pi / 180.) * (-cos(beta * pi / 180.) * cos(gamma * pi / 180.) +
cos(alpha * pi / 180.))
a3 = array([c1, c2, sqrt(c**2 - (c1**2 + c2**2))])
cell = array([a1, a2, a3])
##########################################
from pylada.crystal import Structure, primitive
structure = Structure(transpose(cell),
scale=1,
name=basename(filename),
group=spg)
for i in range(len(symbols)):
# crystal/read: i: 0 symbol: Mo len position: 2
for j in range(len(positions[i])):
atpos = dot(transpose(cell), positions[i][j])
# j: 0 pos: [0.3333, 0.6666000000000001, 0.25]
# atpos: [ 6.32378655e-16 1.81847148e+00 3.07500000e+00]
## FT: Finds the corresponding oxidation
for o in oxidation:
if o[0] == symbols[i]:
ox = o[1]
break
structure.add_atom(atpos[0], atpos[1], atpos[2], symbols[i], ox=ox)
if make_primitive:
prim = primitive(structure)
else:
prim = deepcopy(structure)
return prim
import numpy as np
from pylada.crystal import supercell, Structure
from prepare import reciprocal
from mpl_toolkits.mplot3d import Axes3D
import matplotlib
matplotlib.use('TkAgg')
import matplotlib.pyplot as plt
tol = 1e-12
# Primittive structure
A = Structure([[0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]])
A.add_atom(0, 0, 0, 'Si')
A.add_atom(0.25, 0.25, 0.25, 'Si')
# Building the (perfect) supercell
Asc = supercell(A, [[3, 0, 0], [0, 3, 0], [0, 0, 3]])
rpc = reciprocal(A.cell) #reciprocal lattice of PC
irpc = np.linalg.inv(rpc) #inverse of reciprocal lattice of PC
rsc = reciprocal(Asc.cell) #reciprocal lattice of SC
irsc = np.linalg.inv(rsc) #inverse of reciprocal lattice of SC
# big square
# Finds the furthest corner
corner = np.array([[0, 0, 0]])
for i in range(2):
for j in range(2):
for k in range(2):
corner = np.reshape(
(0, 1, 0),\
(0, 0, 0.5)
structure = fill_structure(structure.cell)
for i, atom in enumerate(structure.atoms):
atom.type = "Si" if i < len(structure.atoms)/2 else "Ge"
result_str = Structure()
result_str.scale = 5.450000e+00
result_str.set_cell = (4.068890e+00, -4.235770e-18, 5.083297e-01),\
(-1.694308e-17, 1.016103e+00, 2.238072e-18),\
(-2.252168e-03, 8.711913e-18, 5.083297e-01)
result_str.weight = 1.000000e+00
result_str.name = ""
result_str.energy = 0.0938967086716
result_str.add_atom = (0.000000e+00, 0.000000e+00, 0.000000e+00), "Si", 0, 0
result_str.add_atom = (2.541649e-01, 2.473273e-01, 2.541649e-01), "Si", 1, 0
result_str.add_atom = (3.567265e+00, 5.062000e-01, -8.956567e-03), "Si", 0, 0
result_str.add_atom = (3.821430e+00, 7.572301e-01, 2.452083e-01), "Si", 1, 0
result_str.add_atom = (3.065136e+00, -1.851371e-03, -1.515736e-02), "Si", 0, 0
result_str.add_atom = (3.319301e+00, 2.491787e-01, 2.390075e-01), "Si", 1, 0
result_str.add_atom = (2.563510e+00, 5.080514e-01, -2.186176e-02), "Si", 0, 0
result_str.add_atom = (2.817675e+00, 7.553787e-01, 2.323031e-01), "Si", 1, 0
result_str.add_atom = (2.055673e+00, -6.642716e-03, -2.235452e-02), "Ge", 0, 0
result_str.add_atom = (2.309838e+00, 2.539701e-01, 2.318104e-01), "Ge", 1, 0
result_str.add_atom = (1.539450e+00, 5.026981e-01, -1.446032e-02), "Ge", 0, 0
result_str.add_atom = (1.793614e+00, 7.607320e-01, 2.397046e-01), "Ge", 1, 0
result_str.add_atom = (1.024061e+00, -5.353269e-03, -7.401445e-03), "Ge", 0, 0
result_str.add_atom = (1.278226e+00, 2.526806e-01, 2.467634e-01), "Ge", 1, 0
result_str.add_atom = (5.078370e-01, 5.014086e-01, 4.927555e-04), "Ge", 0, 0
result_str.add_atom = (7.620018e-01, 7.620214e-01, 2.546576e-01), "Ge", 1, 0
from pythonQE import *
from copy import deepcopy
import os
from pylada.crystal import supercell, Structure
import pylada.periodic_table as pt
import pickle
import numpy as np
nproc = 96
# Primittive structure
perfectStruc = Structure([[0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]])
perfectStruc.add_atom(0, 0, 0, 'Si')
perfectStruc.add_atom(0.25, 0.25, 0.25, 'Si')
# Building the (perfect) supercell
perfectStrucsc = supercell(perfectStruc, 4 * perfectStruc.cell)
# Primitive Cell Calculations ########################################################
# Relaxation
pwrelax = pwcalc()
pwrelax.name = "pcPara"
pwrelax.calc_type = "vc-relax"
pwrelax.restart_mode = "from_scratch"
pwrelax.pseudo_dir = os.path.expanduser("~/scratch/pseudo_pz-bhs/")
pwrelax.celldm = 10.7
pwrelax.ecutwfc = 45.0
pwrelax.ecutrho = 400.0
pwrelax.nbnd = len(perfectStruc) * 4
pwrelax.occupations = "fixed"