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"""
This module contains functionality for reading an ASE
Atoms object in ABINIT input format.
"""
def read_abinit(filename='abinit.in'):
"""Import ABINIT input file.
Reads cell, atom positions, etc. from abinit input file
"""
from ase import Atoms, units
if isinstance(filename, str):
f = open(filename)
else: # Assume it's a file-like object
f = filename
lines = []
for line in f.readlines():
meat = line.split('#', 1)[0]
lines.append(meat)
tokens = ' '.join(lines).lower().split()
if isinstance(filename, str):
f.close()
# note that the file can not be scanned sequentially
index = tokens.index("acell")
unit = 1.0
if(tokens[index + 4].lower()[:3] != 'ang'):
unit = units.Bohr
acell = [unit * float(tokens[index + 1]),
unit * float(tokens[index + 2]),
unit * float(tokens[index + 3])]
index = tokens.index("natom")
natom = int(tokens[index+1])
index = tokens.index("ntypat")
ntypat = int(tokens[index+1])
index = tokens.index("typat")
typat = []
for i in range(natom):
t = tokens[index+1+i]
if '*' in t: # e.g. typat 4*1 3*2 ...
typat.extend([int(t) for t in ((t.split('*')[1] + ' ') * int(t.split('*')[0])).split()])
else:
typat.append(int(t))
if len(typat) == natom: break
index = tokens.index("znucl")
znucl = []
for i in range(ntypat):
znucl.append(int(tokens[index+1+i]))
index = tokens.index("rprim")
rprim = []
for i in range(3):
rprim.append([acell[i]*float(tokens[index+3*i+1]),
acell[i]*float(tokens[index+3*i+2]),
acell[i]*float(tokens[index+3*i+3])])
# create a list with the atomic numbers
numbers = []
for i in range(natom):
ii = typat[i] - 1
numbers.append(znucl[ii])
# now the positions of the atoms
if "xred" in tokens:
index = tokens.index("xred")
xred = []
for i in range(natom):
xred.append([float(tokens[index+3*i+1]),
float(tokens[index+3*i+2]),
float(tokens[index+3*i+3])])
atoms = Atoms(cell=rprim, scaled_positions=xred, numbers=numbers,
pbc=True)
else:
if "xcart" in tokens:
index = tokens.index("xcart")
unit = units.Bohr
elif "xangst" in tokens:
unit = 1.0
index = tokens.index("xangst")
else:
raise IOError(
"No xred, xcart, or xangs keyword in abinit input file")
xangs = []
for i in range(natom):
xangs.append([unit*float(tokens[index+3*i+1]),
unit*float(tokens[index+3*i+2]),
unit*float(tokens[index+3*i+3])])
atoms = Atoms(cell=rprim, positions=xangs, numbers=numbers, pbc=True)
try:
ii = tokens.index('nsppol')
except ValueError:
nsppol = None
else:
nsppol = int(tokens[ii + 1])
if nsppol == 2:
index = tokens.index('spinat')
magmoms = [float(tokens[index + 3 * i + 3]) for i in range(natom)]
atoms.set_initial_magnetic_moments(magmoms)
return atoms
def write_abinit(filename, atoms, cartesian=False, long_format=True):
"""Method to write abinit input files."""
import numpy as np
from ase import data
if isinstance(filename, str):
f = open(filename, 'w')
else: # Assume it's a 'file-like object'
f = filename
if isinstance(atoms, (list, tuple)):
if len(atoms) > 1:
raise RuntimeError("Don't know how to save more than "+
"one image to input")
else:
atoms = atoms[0]
# Write atom positions in scaled or cartesian coordinates
if cartesian:
coord = atoms.get_positions()
else:
coord = atoms.get_scaled_positions()
# let us order the atoms according to chemical symbol
ind = np.argsort(atoms.get_chemical_symbols())
symbols = np.array(atoms.get_chemical_symbols())[ind]
coord = coord[ind]
# and now we count how many atoms of which type we have
sc = []
psym = symbols[0]
count = 0
for sym in symbols:
if sym != psym:
sc.append((psym, count))
psym = sym
count = 1
else:
count += 1
sc.append((psym, count))
f.write('\n# Definition of the atom types\n')
f.write("ntypat " + str(len(sc)) + "\n")
f.write("znucl ")
for specie in sc:
f.write(str(data.atomic_numbers[specie[0]]) + " ")
f.write('\n')
f.write('\n# Definition of the atoms\n')
f.write('natom ' + str(len(symbols)) + '\n')
f.write('typat ')
typat = 1
for specie in sc:
for natom in range(specie[1]):
f.write(str(typat) + ' ')
typat = typat + 1
f.write('\n')
f.write('\n# Definition of the unit cell\n')
f.write('acell\n')
f.write('%.14f %.14f %.14f Angstrom\n' % (1.0, 1.0, 1.0))
f.write('\n')
f.write('rprim\n')
if long_format:
latt_form = ' %21.16f'
else:
latt_form = ' %11.6f'
for vec in atoms.get_cell():
f.write(' ')
for el in vec:
f.write(latt_form % el)
f.write('\n')
f.write('\n')
# Write atom positions in scaled or cartesian coordinates
if cartesian:
f.write('xangst\n')
else:
f.write('xred\n')
if long_format:
cform = ' %19.16f'
else:
cform = ' %9.6f'
for iatom, atom in enumerate(coord):
f.write(' ')
for dcoord in atom:
f.write(cform % dcoord)
f.write('\n')
if isinstance(filename, str):
f.close()
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