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"""Reads quantum espresso files. Tested for output on PWSCF v.5.0.2, only
for typical output of input files made with ASE -- that is, ibrav=0."""
import numpy as np
from ase.atoms import Atoms, Atom
from ase import units
from ase.calculators.singlepoint import SinglePointCalculator
def read_espresso_out(fileobj, index):
"""Reads quantum espresso output text files."""
if isinstance(fileobj, str):
fileobj = open(fileobj, 'rU')
lines = fileobj.readlines()
images = []
# Get unit cell info.
bl_line = [line for line in lines if 'bravais-lattice index' in line]
if len(bl_line) != 1:
raise NotImplementedError('Unsupported: unit cell changing.')
bl_line = bl_line[0].strip()
brav_latt_index = bl_line.split('=')[1].strip()
if brav_latt_index != '0':
raise NotImplementedError('Supported only for Bravais-lattice '
'index of 0 (free).')
lp_line = [line for line in lines if 'lattice parameter (alat)' in
line]
if len(lp_line) != 1:
raise NotImplementedError('Unsupported: unit cell changing.')
lp_line = lp_line[0].strip().split('=')[1].strip().split()[0]
lattice_parameter = float(lp_line) * units.Bohr
ca_line_no = [number for (number, line) in enumerate(lines) if
'crystal axes: (cart. coord. in units of alat)' in line]
if len(ca_line_no) != 1:
raise NotImplementedError('Unsupported: unit cell changing.')
ca_line_no = int(ca_line_no[0])
cell = np.zeros((3, 3))
for number, line in enumerate(lines[ca_line_no + 1: ca_line_no + 4]):
line = line.split('=')[1].strip()[1:-1]
values = [float(value) for value in line.split()]
cell[number, 0] = values[0]
cell[number, 1] = values[1]
cell[number, 2] = values[2]
cell *= lattice_parameter
# Find atomic positions and add to images.
for number, line in enumerate(lines):
key = 'Begin final coordinates' # these just reprint last posn.
if key in line:
break
key = 'Cartesian axes'
if key in line:
atoms = make_atoms(number, lines, key, cell)
images.append(atoms)
key = 'ATOMIC_POSITIONS (crystal)'
if key in line:
atoms = make_atoms(number, lines, key, cell)
images.append(atoms)
return images[index]
def make_atoms(index, lines, key, cell):
"""Scan through lines to get the atomic positions."""
atoms = Atoms()
if key == 'Cartesian axes':
for line in lines[index + 3:]:
entries = line.split()
if len(entries) == 0:
break
symbol = entries[1][:-1]
x = float(entries[6])
y = float(entries[7])
z = float(entries[8])
atoms.append(Atom(symbol, (x, y, z)))
atoms.set_cell(cell)
elif key == 'ATOMIC_POSITIONS (crystal)':
for line in lines[index + 1:]:
entries = line.split()
if len(entries) == 0 or (entries[0] == 'End'):
break
symbol = entries[0][:-1]
x = float(entries[1])
y = float(entries[2])
z = float(entries[3])
atoms.append(Atom(symbol, (x, y, z)))
atoms.set_cell(cell, scale_atoms=True)
# Energy is located after positions.
energylines = [number for number, line in enumerate(lines) if
('!' in line and 'total energy' in line)]
energyline = min([n for n in energylines if n > index])
energy = float(lines[energyline].split()[-2]) * units.Ry
# Forces are located after positions.
forces = np.zeros((len(atoms), 3))
forcelines = [number for number, line in enumerate(lines) if
'Forces acting on atoms (Ry/au):' in line]
forceline = min([n for n in forcelines if n > index])
for line in lines[forceline + 4:]:
words = line.split()
if len(words) == 0:
break
fx = float(words[-3])
fy = float(words[-2])
fz = float(words[-1])
atom_number = int(words[1]) - 1
forces[atom_number] = (fx, fy, fz)
forces *= units.Ry / units.Bohr
calc = SinglePointCalculator(atoms, energy=energy, forces=forces)
atoms.set_calculator(calc)
return atoms
def read_espresso_in(fileobj):
"""Reads espresso input files."""
if isinstance(fileobj, str):
fileobj = open(fileobj, 'rU')
data, extralines = read_fortran_namelist(fileobj)
positions, method = get_atomic_positions(extralines,
n_atoms=data['system']['nat'])
cell = get_cell_parameters(extralines)
if data['system']['ibrav'] == 0:
atoms = build_atoms(positions, method, cell,
data['system']['celldm(1)'])
else:
raise NotImplementedError('ibrav=%i not implemented.' %
data['system']['ibrav'])
return atoms
def build_atoms(positions, method, cell, alat):
"""Creates the atoms for a quantum espresso in file."""
if method != 'crystal':
raise NotImplementedError('Only supported for crystal method of '
'ATOMIC_POSITIONS, not %s.' % method)
atoms = Atoms()
for el, (x, y, z) in positions:
atoms.append(Atom(el, (x, y, z)))
cell *= alat * units.Bohr
atoms.set_cell(cell, scale_atoms=True)
return atoms
def get_atomic_positions(lines, n_atoms):
"""Returns the atomic positions of the atoms as an (ordered) list from
the lines of text of the espresso input file."""
atomic_positions = []
line = [n for (n, l) in enumerate(lines) if 'ATOMIC_POSITIONS' in l]
if len(line) == 0:
return None
if len(line) > 1:
raise RuntimeError('More than one ATOMIC_POSITIONS section?')
line_no = line[0]
for line in lines[line_no + 1:line_no + n_atoms + 1]:
el, x, y, z = line.split()
atomic_positions.append([el, (f2f(x), f2f(y), f2f(z))])
line = lines[line_no]
if '{' in line:
method = line[line.find('{') + 1:line.find('}')]
elif '(' in line:
method = line[line.find('(') + 1:line.find(')')]
else:
method = None
return atomic_positions, method
def get_cell_parameters(lines):
"""Returns the cell parameters as a matrix."""
cell_parameters = np.zeros((3, 3))
line = [n for (n, l) in enumerate(lines) if 'CELL_PARAMETERS' in l]
if len(line) == 0:
return None
if len(line) > 1:
raise RuntimeError('More than one CELL_PARAMETERS section?')
line_no = line[0]
for vector, line in enumerate(lines[line_no + 1:line_no + 4]):
x, y, z = line.split()
cell_parameters[vector] = (f2f(x), f2f(y), f2f(z))
return cell_parameters
def str2value(string):
"""Convert string into int, float, or bool, if possible, else return it."""
for datatype in [int, float]:
try:
return datatype(string)
except ValueError:
pass
return {'.true.': True, '.false.': False}.get(string, string)
def read_fortran_namelist(fileobj):
"""Takes a fortran-namelist formatted file and returns appropriate
dictionaries, followed by lines of text that do not fit this pattern.
"""
data = {}
extralines = []
indict = False
fileobj.seek(0)
for line in fileobj.readlines():
if indict and line.strip().startswith('/'):
indict = False
elif line.strip().startswith('&'):
indict = True
dictname = line.strip()[1:].lower()
data[dictname] = {}
elif (not indict) and (len(line.strip()) > 0):
extralines.append(line)
elif indict:
key, value = line.strip().split('=')
if value.endswith(','):
value = value[:-1]
value = str2value(value.strip())
data[dictname][key.strip()] = value
return data, extralines
def f2f(value):
"""Converts a fortran-formatted double precision number (e.g., 2.323d2)
to a python float. value should be a string."""
value = value.replace('d', 'e')
value = value.replace('D', 'e')
return float(value)
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