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 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 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"