def test_magres():
import numpy as np
from ase.io import read, write
from ase.build import bulk
from ase.calculators.singlepoint import SinglePointDFTCalculator
# Test with fictional data
si2 = bulk('Si')
ms = np.ones((2, 3, 3))
si2.set_array('ms', ms)
efg = np.repeat([[[1, 0, 0], [0, 1, 0], [0, 0, -2]]], 2, axis=0)
si2.set_array('efg', efg)
calc = SinglePointDFTCalculator(si2)
calc.results['sus'] = np.eye(3) * 2
si2.set_calculator(calc)
si2.info['magres_units'] = {
'ms': 'ppm',
'efg': 'au',
'sus': '10^-6.cm^3.mol^-1'
}
write('si2_test.magres', si2)
si2 = read('si2_test.magres')
assert (np.trace(si2.get_array('ms')[0]) == 3)
assert (np.all(np.isclose(si2.get_array('efg')[:, 2, 2], -2)))
assert (np.all(np.isclose(si2.calc.results['sus'], np.eye(3) * 2)))
def build(self, lines: _CHUNK) -> Atoms:
"""Apply outcar chunk parsers, and build an atoms object"""
self.update_parser_headers() # Ensure header is in sync
results = self.parse(lines)
symbols = self.header['symbols']
constraint = self.header.get('constraint', None)
atoms_kwargs = dict(symbols=symbols, constraint=constraint)
# Find some required properties in the parsed results.
# Raise ParseError if they are not present
for prop in ('positions', 'cell'):
try:
atoms_kwargs[prop] = results.pop(prop)
except KeyError:
raise ParseError(
'Did not find required property {} during parse.'.format(
prop))
atoms = Atoms(**atoms_kwargs)
kpts = results.pop('kpts', None)
calc = SinglePointDFTCalculator(atoms, **results)
if kpts is not None:
calc.kpts = kpts
calc.name = 'vasp'
atoms.calc = calc
return atoms
def parse_gto_chunk(chunk):
atoms = None
forces = None
energy = None
dipole = None
quadrupole = None
for theory in ['tce', 'ccsd', 'mp2', 'mf']:
matches = _e_gto[theory].findall(chunk)
if matches:
energy = float(matches[-1].replace('D', 'E')) * Hartree
break
gradblocks = _gto_grad.findall(chunk)
if gradblocks:
gradblock = gradblocks[-1].strip().split('\n')
natoms = len(gradblock)
symbols = []
pos = np.zeros((natoms, 3))
forces = np.zeros((natoms, 3))
for i, line in enumerate(gradblock):
line = line.strip().split()
symbols.append(line[1])
pos[i] = [float(x) for x in line[2:5]]
forces[i] = [-float(x) for x in line[5:8]]
pos *= Bohr
forces *= Hartree / Bohr
atoms = Atoms(symbols, positions=pos)
dipole, quadrupole = _get_multipole(chunk)
kpts = _get_gto_kpts(chunk)
atoms_new = _parse_geomblock(chunk)
if atoms_new is not None:
atoms = atoms_new
if atoms is None:
return
# SinglePointDFTCalculator doesn't support quadrupole moment currently
calc = SinglePointDFTCalculator(
atoms=atoms,
energy=energy,
forces=forces,
dipole=dipole,
# quadrupole=quadrupole,
)
calc.kpts = kpts
atoms.calc = calc
return atoms
def test_singlepoint_dft_calc():
import numpy as np
from ase.calculators.singlepoint import (SinglePointDFTCalculator,
arrays_to_kpoints)
from ase.build import bulk
rng = np.random.RandomState(17)
nspins, nkpts, nbands = shape = 2, 4, 5
eps = 2 * rng.rand(*shape)
occ = rng.rand(*shape)
weights = rng.rand(nkpts)
kpts = arrays_to_kpoints(eps, occ, weights)
atoms = bulk('Au')
calc = SinglePointDFTCalculator(atoms)
calc.kpts = kpts
assert calc.get_number_of_spins() == nspins
assert calc.get_spin_polarized()
assert np.allclose(calc.get_k_point_weights(), weights)
for s in range(nspins):
for k in range(nkpts):
eps1 = calc.get_eigenvalues(kpt=k, spin=s)
occ1 = calc.get_occupation_numbers(kpt=k, spin=s)
assert np.allclose(eps1, eps[s, k])
assert np.allclose(occ1, occ[s, k])
def parse_pw_chunk(chunk):
atoms = _parse_geomblock(chunk)
if atoms is None:
return
energy = None
efermi = None
forces = None
stress = None
matches = _nwpw_energy.findall(chunk)
if matches:
energy = float(matches[-1].replace('D', 'E')) * Hartree
matches = _fermi_energy.findall(chunk)
if matches:
efermi = float(matches[-1].replace('D', 'E')) * Hartree
gradblocks = _nwpw_grad.findall(chunk)
if not gradblocks:
gradblocks = _paw_grad.findall(chunk)
if gradblocks:
gradblock = gradblocks[-1].strip().split('\n')
natoms = len(gradblock)
symbols = []
forces = np.zeros((natoms, 3))
for i, line in enumerate(gradblock):
line = line.strip().split()
symbols.append(line[1])
forces[i] = [float(x) for x in line[3:6]]
forces *= Hartree / Bohr
if atoms.cell:
stress = _get_stress(chunk, atoms.cell)
ibz_kpts, kpts = _get_pw_kpts(chunk)
# NWChem does not calculate an energy extrapolated to the 0K limit,
# so right now, energy and free_energy will be the same.
calc = SinglePointDFTCalculator(atoms=atoms,
energy=energy,
efermi=efermi,
free_energy=energy,
forces=forces,
stress=stress,
ibzkpts=ibz_kpts)
calc.kpts = kpts
atoms.calc = calc
return atoms
def test_dos():
from ase.atoms import Atoms
from ase.calculators.singlepoint import SinglePointDFTCalculator
from ase.calculators.singlepoint import SinglePointKPoint
from ase.dft.dos import DOS
atoms = Atoms('H')
eFermi = [0, 1]
kpts = [SinglePointKPoint(1, 0, 0), SinglePointKPoint(1, 1, 0)]
kpts[0].eps_n = [-2, -1, 1]
kpts[0].f_n = [1, 0, 0]
kpts[1].eps_n = [-2.5, -1.5, 0.5]
kpts[1].f_n = [1, 0, 0]
calc = SinglePointDFTCalculator(atoms, efermi=eFermi)
calc.kpts = kpts
DOS(calc)
def read_wann2kc_out(fileobj):
"""Reads Wannier to KC output files.
Parameters
----------
fileobj : file|str
A file like object or filename
Yields
------
structure : Atoms
The next structure from the index slice. The Atoms has a
SinglePointCalculator attached with any results parsed from
the file.
"""
if isinstance(fileobj, basestring):
fileobj = open(fileobj, 'rU')
# work with a copy in memory for faster random access
flines = fileobj.readlines()
# For the moment, provide an empty atoms object
structure = Atoms()
# Extract calculation results
walltime = None
job_done = False
for line in flines:
if 'JOB DONE' in line:
job_done = True
if 'KC_WANN :' in line:
time_str = line.split()[-2]
walltime = time_to_float(time_str)
# Return an empty calculator object with ths solitary result 'job done'
calc = SinglePointDFTCalculator(structure)
calc.results['job_done'] = job_done
calc.results['walltime'] = walltime
structure.calc = calc
yield structure
def read_koopmans_screen_out(fileobj):
"""Reads Koopmans Screen output files.
Will probably raise errors for broken or incomplete files.
Parameters
----------
fileobj : file|str
A file like object or filename
Yields
------
structure : Atoms
The next structure from the index slice. The Atoms has a
SinglePointCalculator attached with any results parsed from
the file.
"""
if isinstance(fileobj, basestring):
fileobj = open(fileobj, 'rU')
# work with a copy in memory for faster random access
flines = fileobj.readlines()
# For the moment, provide an empty atoms object
structure = Atoms()
# Extract calculation results
job_done = False
walltime = None
alphas = [[]]
orbital_data = {'self-Hartree': []}
for i_line, line in enumerate(flines):
if 'relaxed' in line:
splitline = line.split()
alphas[-1].append(float(splitline[-5]))
orbital_data['self-Hartree'].append(
float(splitline[-1]) * units.Ry)
if 'JOB DONE' in line:
job_done = True
if 'KC_WANN :' in line:
time_str = line.split()[-2]
walltime = time_to_float(time_str)
# Put everything together
calc = SinglePointDFTCalculator(structure)
calc.results['job_done'] = job_done
calc.results['walltime'] = walltime
calc.results['alphas'] = alphas
calc.results['orbital_data'] = orbital_data
structure.calc = calc
yield structure
def read_gpw(filename):
try:
reader = ulm.open(filename)
except ulm.InvalidULMFileError:
return read_old_gpw(filename)
atoms = read_atoms(reader.atoms, _try_except=False)
wfs = reader.wave_functions
kpts = wfs.get('kpts')
if kpts is None:
ibzkpts = None
bzkpts = None
bz2ibz = None
else:
ibzkpts = kpts.ibzkpts
bzkpts = kpts.get('bzkpts')
bz2ibz = kpts.get('bz2ibz')
if reader.version >= 3:
efermi = reader.wave_functions.fermi_levels.mean()
else:
efermi = reader.occupations.fermilevel
atoms.calc = SinglePointDFTCalculator(atoms,
efermi=efermi,
ibzkpts=ibzkpts,
bzkpts=bzkpts,
bz2ibz=bz2ibz,
**reader.results.asdict())
if kpts is not None:
atoms.calc.kpts = []
spin = 0
for eps_kn, f_kn in zip(wfs.eigenvalues, wfs.occupations):
kpt = 0
for weight, eps_n, f_n in zip(kpts.weights, eps_kn, f_kn):
atoms.calc.kpts.append(
SinglePointKPoint(weight, spin, kpt, eps_n, f_n))
kpt += 1
spin += 1
return atoms
def read_old_gpw(filename):
from gpaw.io.tar import Reader
r = Reader(filename)
positions = r.get('CartesianPositions') * Bohr
numbers = r.get('AtomicNumbers')
cell = r.get('UnitCell') * Bohr
pbc = r.get('BoundaryConditions')
tags = r.get('Tags')
magmoms = r.get('MagneticMoments')
energy = r.get('PotentialEnergy') * Hartree
if r.has_array('CartesianForces'):
forces = r.get('CartesianForces') * Hartree / Bohr
else:
forces = None
atoms = Atoms(positions=positions, numbers=numbers, cell=cell, pbc=pbc)
if tags.any():
atoms.set_tags(tags)
if magmoms.any():
atoms.set_initial_magnetic_moments(magmoms)
magmom = magmoms.sum()
else:
magmoms = None
magmom = None
atoms.calc = SinglePointDFTCalculator(atoms,
energy=energy,
forces=forces,
magmoms=magmoms,
magmom=magmom)
kpts = []
if r.has_array('IBZKPoints'):
for w, kpt, eps_n, f_n in zip(r.get('IBZKPointWeights'),
r.get('IBZKPoints'),
r.get('Eigenvalues'),
r.get('OccupationNumbers')):
kpts.append(SinglePointKPoint(w, kpt[0], kpt[1], eps_n[0], f_n[0]))
atoms.calc.kpts = kpts
return atoms
from ase.build import bulk
rng = np.random.RandomState(17)
nspins, nkpts, nbands = shape = 2, 4, 5
eps = 2 * rng.rand(*shape)
occ = rng.rand(*shape)
weights = rng.rand(nkpts)
kpts = arrays_to_kpoints(eps, occ, weights)
atoms = bulk('Au')
calc = SinglePointDFTCalculator(atoms)
calc.kpts = kpts
assert calc.get_number_of_spins() == nspins
assert calc.get_spin_polarized()
assert np.allclose(calc.get_k_point_weights(), weights)
for s in range(nspins):
for k in range(nkpts):
eps1 = calc.get_eigenvalues(kpt=k, spin=s)
occ1 = calc.get_occupation_numbers(kpt=k, spin=s)
assert np.allclose(eps1, eps[s, k])
assert np.allclose(occ1, occ[s, k])
def read_magres(fd, include_unrecognised=False):
"""
Reader function for magres files.
"""
blocks_re = re.compile(r'[\[<](?P<block_name>.*?)[>\]](.*?)[<\[]/' +
r'(?P=block_name)[\]>]', re.M | re.S)
"""
Here are defined the various functions required to parse
different blocks.
"""
def tensor33(x):
return np.squeeze(np.reshape(x, (3, 3))).tolist()
def tensor31(x):
return np.squeeze(np.reshape(x, (3, 1))).tolist()
def get_version(file_contents):
"""
Look for and parse the magres file format version line
"""
lines = file_contents.split('\n')
match = re.match(r'\#\$magres-abinitio-v([0-9]+).([0-9]+)', lines[0])
if match:
version = match.groups()
version = tuple(vnum for vnum in version)
else:
version = None
return version
def parse_blocks(file_contents):
"""
Parse series of XML-like deliminated blocks into a list of
(block_name, contents) tuples
"""
blocks = blocks_re.findall(file_contents)
return blocks
def parse_block(block):
"""
Parse block contents into a series of (tag, data) records
"""
def clean_line(line):
# Remove comments and whitespace at start and ends of line
line = re.sub('#(.*?)\n', '', line)
line = line.strip()
return line
name, data = block
lines = [clean_line(line) for line in data.split('\n')]
records = []
for line in lines:
xs = line.split()
if len(xs) > 0:
tag = xs[0]
data = xs[1:]
records.append((tag, data))
return (name, records)
def check_units(d):
"""
Verify that given units for a particular tag are correct.
"""
allowed_units = {'lattice': 'Angstrom',
'atom': 'Angstrom',
'ms': 'ppm',
'efg': 'au',
'efg_local': 'au',
'efg_nonlocal': 'au',
'isc': '10^19.T^2.J^-1',
'isc_fc': '10^19.T^2.J^-1',
'isc_orbital_p': '10^19.T^2.J^-1',
'isc_orbital_d': '10^19.T^2.J^-1',
'isc_spin': '10^19.T^2.J^-1',
'isc': '10^19.T^2.J^-1',
'sus': '10^-6.cm^3.mol^-1',
'calc_cutoffenergy': 'Hartree', }
if d[0] in d and d[1] == allowed_units[d[0]]:
pass
else:
raise RuntimeError('Unrecognized units: %s %s' % (d[0], d[1]))
return d
def parse_magres_block(block):
"""
Parse magres block into data dictionary given list of record
tuples.
"""
name, records = block
# 3x3 tensor
def ntensor33(name):
return lambda d: {name: tensor33([float(x) for x in data])}
# Atom label, atom index and 3x3 tensor
def sitensor33(name):
return lambda d: {'atom': {'label': data[0],
'index': int(data[1])},
name: tensor33([float(x) for x in data[2:]])}
# 2x(Atom label, atom index) and 3x3 tensor
def sisitensor33(name):
return lambda d: {'atom1': {'label': data[0],
'index': int(data[1])},
'atom2': {'label': data[2],
'index': int(data[3])},
name: tensor33([float(x) for x in data[4:]])}
tags = {'ms': sitensor33('sigma'),
'sus': ntensor33('S'),
'efg': sitensor33('V'),
'efg_local': sitensor33('V'),
'efg_nonlocal': sitensor33('V'),
'isc': sisitensor33('K'),
'isc_fc': sisitensor33('K'),
'isc_spin': sisitensor33('K'),
'isc_orbital_p': sisitensor33('K'),
'isc_orbital_d': sisitensor33('K'),
'units': check_units}
data_dict = {}
for record in records:
tag, data = record
if tag not in data_dict:
data_dict[tag] = []
data_dict[tag].append(tags[tag](data))
return data_dict
def parse_atoms_block(block):
"""
Parse atoms block into data dictionary given list of record tuples.
"""
name, records = block
# Lattice record: a1, a2 a3, b1, b2, b3, c1, c2 c3
def lattice(d):
return tensor33([float(x) for x in data])
# Atom record: label, index, x, y, z
def atom(d):
return {'species': data[0],
'label': data[1],
'index': int(data[2]),
'position': tensor31([float(x) for x in data[3:]])}
def symmetry(d):
return ' '.join(data)
tags = {'lattice': lattice,
'atom': atom,
'units': check_units,
'symmetry': symmetry}
data_dict = {}
for record in records:
tag, data = record
if tag not in data_dict:
data_dict[tag] = []
data_dict[tag].append(tags[tag](data))
return data_dict
def parse_generic_block(block):
"""
Parse any other block into data dictionary given list of record
tuples.
"""
name, records = block
data_dict = {}
for record in records:
tag, data = record
if tag not in data_dict:
data_dict[tag] = []
data_dict[tag].append(data)
return data_dict
"""
Actual parser code.
"""
block_parsers = {'magres': parse_magres_block,
'atoms': parse_atoms_block,
'calculation': parse_generic_block, }
file_contents = fd.read()
# This works as a validity check
version = get_version(file_contents)
if version is None:
# This isn't even a .magres file!
raise RuntimeError('File is not in standard Magres format')
blocks = parse_blocks(file_contents)
data_dict = {}
for block_data in blocks:
block = parse_block(block_data)
if block[0] in block_parsers:
block_dict = block_parsers[block[0]](block)
data_dict[block[0]] = block_dict
else:
# Throw in the text content of blocks we don't recognise
if include_unrecognised:
data_dict[block[0]] = block_data[1]
# Now the loaded data must be turned into an ASE Atoms object
# First check if the file is even viable
if 'atoms' not in data_dict:
raise RuntimeError('Magres file does not contain structure data')
# Allowed units handling. This is redundant for now but
# could turn out useful in the future
magres_units = {'Angstrom': ase.units.Ang}
# Lattice parameters?
if 'lattice' in data_dict['atoms']:
try:
u = dict(data_dict['atoms']['units'])['lattice']
except KeyError:
raise RuntimeError('No units detected in file for lattice')
u = magres_units[u]
cell = np.array(data_dict['atoms']['lattice'][0]) * u
pbc = True
else:
cell = None
pbc = False
# Now the atoms
symbols = []
positions = []
indices = []
labels = []
if 'atom' in data_dict['atoms']:
try:
u = dict(data_dict['atoms']['units'])['atom']
except KeyError:
raise RuntimeError('No units detected in file for atom positions')
u = magres_units[u]
# Now we have to account for the possibility of there being CASTEP
# 'custom' species amongst the symbols
custom_species = None
for a in data_dict['atoms']['atom']:
spec_custom = a['species'].split(':', 1)
if len(spec_custom) > 1 and custom_species is None:
# Add it to the custom info!
custom_species = list(symbols)
symbols.append(spec_custom[0])
positions.append(a['position'])
indices.append(a['index'])
labels.append(a['label'])
if custom_species is not None:
custom_species.append(a['species'])
atoms = Atoms(cell=cell,
pbc=pbc,
symbols=symbols,
positions=positions)
# Add custom species if present
if custom_species is not None:
atoms.new_array('castep_custom_species', np.array(custom_species))
# Add the spacegroup, if present and recognizable
if 'symmetry' in data_dict['atoms']:
try:
spg = Spacegroup(data_dict['atoms']['symmetry'][0])
except:
# Not found
spg = Spacegroup(1) # Most generic one
atoms.info['spacegroup'] = spg
# Set up the rest of the properties as arrays
atoms.new_array('indices', np.array(indices))
atoms.new_array('labels', np.array(labels))
# Now for the magres specific stuff
li_list = list(zip(labels, indices))
def create_magres_array(name, order, block):
if order == 1:
u_arr = [None] * len(li_list)
elif order == 2:
u_arr = [[None] * (i + 1) for i in range(len(li_list))]
else:
raise ValueError(
'Invalid order value passed to create_magres_array')
for s in block:
# Find the atom index/indices
if order == 1:
# First find out which atom this is
at = (s['atom']['label'], s['atom']['index'])
try:
ai = li_list.index(at)
except ValueError:
raise RuntimeError('Invalid data in magres block')
# Then add the relevant quantity
u_arr[ai] = s[mn]
else:
at1 = (s['atom1']['label'], s['atom1']['index'])
at2 = (s['atom2']['label'], s['atom2']['index'])
ai1 = li_list.index(at1)
ai2 = li_list.index(at2)
# Sort them
ai1, ai2 = sorted((ai1, ai2), reverse=True)
u_arr[ai1][ai2] = s[mn]
return np.array(u_arr)
if 'magres' in data_dict:
if 'units' in data_dict['magres']:
atoms.info['magres_units'] = dict(data_dict['magres']['units'])
for u in atoms.info['magres_units']:
# This bit to keep track of tags
u0 = u.split('_')[0]
if u0 not in _mprops:
raise RuntimeError('Invalid data in magres block')
mn, order = _mprops[u0]
if order > 0:
u_arr = create_magres_array(mn, order,
data_dict['magres'][u])
atoms.new_array(u, u_arr)
else:
# atoms.info['magres_data'] = atoms.info.get('magres_data',
# {})
# # We only take element 0 because for this sort of data
# # there should be only that
# atoms.info['magres_data'][u] = data_dict['magres'][u][0][mn]
if atoms.calc is None:
calc = SinglePointDFTCalculator(atoms)
atoms.set_calculator(calc)
atoms.calc.results[u] = data_dict['magres'][u][0][mn]
if 'calculation' in data_dict:
atoms.info['magresblock_calculation'] = data_dict['calculation']
if include_unrecognised:
for b in data_dict:
if b not in block_parsers:
atoms.info['magresblock_' + b] = data_dict[b]
return atoms
from ase.atoms import Atoms
from ase.calculators.singlepoint import SinglePointDFTCalculator
from ase.calculators.singlepoint import SinglePointKPoint
from ase.dft.dos import DOS
atoms = Atoms('H')
eFermi = [0, 1]
kpts = [SinglePointKPoint(1, 0, 0), SinglePointKPoint(1, 1, 0)]
kpts[0].eps_n = [-2, -1, 1]
kpts[0].f_n = [1, 0, 0]
kpts[1].eps_n = [-2.5, -1.5, 0.5]
kpts[1].f_n = [1, 0, 0]
calc = SinglePointDFTCalculator(atoms, efermi=eFermi)
calc.kpts = kpts
dos = DOS(calc)
import numpy as np
from ase.io import read, write
from ase.build import bulk
from ase.calculators.singlepoint import SinglePointDFTCalculator
# Test with fictional data
si2 = bulk('Si')
ms = np.ones((2, 3, 3))
si2.set_array('ms', ms)
efg = np.repeat([[[1, 0, 0], [0, 1, 0], [0, 0, -2]]], 2, axis=0)
si2.set_array('efg', efg)
calc = SinglePointDFTCalculator(si2)
calc.results['sus'] = np.eye(3) * 2
si2.set_calculator(calc)
si2.info['magres_units'] = {
'ms': 'ppm',
'efg': 'au',
'sus': '10^-6.cm^3.mol^-1'
}
write('si2_test.magres', si2)
si2 = read('si2_test.magres')
assert (np.trace(si2.get_array('ms')[0]) == 3)
assert (np.all(np.isclose(si2.get_array('efg')[:, 2, 2], -2)))
assert (np.all(np.isclose(si2.calc.results['sus'], np.eye(3) * 2)))
def calc_fcs(
phono3py,
calc,
unitcell_f='Unknown',
cp_files=None,
sym_fc=True,
fc_calc=None,
r_cut=None,
):
"""
fc_calc: None or 'alm'
r_cut: None or float. Use hiPhive if provided.
"""
# Check if structure is lower triangular cell
for c in ((0, 1), (0, 2), (1, 2)):
if phono3py.primitive.get_cell()[c[0], c[1]] != 0. and calc == 'lmp':
raise ValueError('Please provide lower triangular cell.')
#
phono3py.generate_displacements()
fc2_snd = phono3py.get_phonon_supercells_with_displacements()
fc3_snd = phono3py.get_supercells_with_displacements()
fc2_job_name = '{}-x{}{}{}_d0.010_sym{}-fc2'.format(
calc,
*np.diag(phono3py.get_phonon_supercell_matrix()),
phono3py._is_symmetry,
)
fc3_job_name = '{}-x{}{}{}_d0.030_sym{}-fc3'.format(
calc,
*np.diag(phono3py.get_supercell_matrix()),
phono3py._is_symmetry,
)
fc2_npy_name = '{}-forces.npy'.format(fc2_job_name)
fc3_npy_name = '{}-forces.npy'.format(fc3_job_name)
calc_dir = 'calcs'
fc2_path = '{}/{}'.format(calc_dir, fc2_job_name)
fc3_path = '{}/{}'.format(calc_dir, fc3_job_name)
#
from phonopy.interface.vasp import write_vasp
call('mkdir -p {}/poscars'.format(fc2_path), shell=True)
write_vasp('{}/poscars/SPOSCAR'.format(fc2_path),
phono3py.get_phonon_supercell())
for i in range(len(fc2_snd)):
write_vasp('{}/poscars/POSCAR-{:03d}'.format(fc2_path, i + 1),
fc2_snd[i])
#
call('mkdir -p {}/poscars'.format(fc3_path), shell=True)
write_vasp('{}/poscars/SPOSCAR'.format(fc3_path), phono3py.get_supercell())
for i in range(len(fc3_snd)):
write_vasp('{}/poscars/POSCAR-{:05d}'.format(fc3_path, i + 1),
fc3_snd[i])
try:
fc2_forces = np.load(fc2_npy_name)
except:
calc_fc2 = True
print('\n*** NOTE) Failed to load {} file. ***\n'.format(fc2_npy_name))
else:
calc_fc2 = False
print('\n=== NOTE) Loaded: {} ===\n'.format(fc2_npy_name))
if calc_fc2:
print('=== NOTE) Starting fc2 calculations! ===\n')
fc2_forces = []
for i in range(len(fc2_snd)):
folder = 'disp-{:03d}'.format(i + 1)
wdir = '{}/{}'.format(fc2_path, folder)
budir = '{}/bu-{}'.format(fc2_path, folder)
call('rm -rf {}'.format(budir), shell=True)
call('mv {} {}'.format(wdir, budir), shell=True)
call('mkdir -p {}'.format(wdir), shell=True)
write_vasp('{}/POSCAR'.format(wdir), fc2_snd[i])
fc2_forces.append(_calc_forces(wdir, calc, cp_files))
print(' == Progress: {}/{}'.format(i + 1, len(fc2_snd)))
np.save(fc2_npy_name, fc2_forces)
try:
fc3_forces = np.load(fc3_npy_name)
except:
calc_fc3 = True
print('\n*** NOTE) Failed to load {} file. ***\n'.format(fc3_npy_name))
else:
calc_fc3 = False
print('\n=== NOTE) Loaded: {} ===\n'.format(fc3_npy_name))
if calc_fc3:
print('=== NOTE) Starting fc3 calculations! ===\n')
fc3_forces = []
for i in range(len(fc3_snd)):
folder = 'disp-{:05d}'.format(i + 1)
wdir = '{}/{}'.format(fc3_path, folder)
budir = '{}/bu-{}'.format(fc3_path, folder)
call('rm -rf {}'.format(budir), shell=True)
call('mv {} {}'.format(wdir, budir), shell=True)
call('mkdir -p {}'.format(wdir), shell=True)
write_vasp('{}/POSCAR'.format(wdir), fc3_snd[i])
fc3_forces.append(_calc_forces(wdir, calc, cp_files))
print(' == Progress: {}/{}'.format(i + 1, len(fc3_snd)))
np.save(fc3_npy_name, fc3_forces)
#
phono3py.phonon_forces = np.array(fc2_forces)
phono3py.forces = np.array(fc3_forces)
#
phono3py.produce_fc3(
symmetrize_fc3r=sym_fc,
fc_calculator=fc_calc,
)
phono3py.produce_fc2(
symmetrize_fc2=sym_fc,
fc_calculator=fc_calc,
)
if r_cut:
#
from ase.io import read
from ase.calculators.singlepoint import SinglePointDFTCalculator
fc2_disp_ds = phono3py.get_phonon_displacement_dataset()['first_atoms']
fc2_sposcar = read('{}/poscars/SPOSCAR'.format(fc2_path))
fc2_supers = []
for i in range(len(fc2_disp_ds)):
displacements = np.zeros(fc2_sposcar.get_positions().shape,
dtype=float)
displacements[fc2_disp_ds[i]
['number']] += fc2_disp_ds[i]['displacement']
fc2_supers.append(fc2_sposcar.copy())
fc2_supers[-1].new_array(
'displacements',
displacements,
)
fc2_supers[-1]._calc = SinglePointDFTCalculator(fc2_supers[-1])
fc2_supers[-1]._calc.results['forces'] = fc2_disp_ds[i]['forces']
# rotational sum rule
from hiphive import ForceConstants, ClusterSpace, StructureContainer
cs = ClusterSpace(fc2_sposcar, [r_cut])
sc = StructureContainer(cs)
for s in fc2_supers:
sc.add_structure(s)
from hiphive.fitting import Optimizer
opt = Optimizer(sc.get_fit_data(), train_size=1.0)
opt.train()
print(opt)
parameters = opt.parameters
from hiphive import ForceConstantPotential, enforce_rotational_sum_rules
parameters_rot = enforce_rotational_sum_rules(cs, parameters,
['Huang', 'Born-Huang'])
fcp_rot = ForceConstantPotential(cs, parameters_rot)
fcs = fcp_rot.get_force_constants(fc2_sposcar).get_fc_array(order=2)
phono3py.set_fc2(fcs)
# # Not implemented yet in hiPhive
# fc3_disp_ds = phono3py.get_displacement_dataset()['first_atoms']
# fc3_sposcar = read('{}/poscars/SPOSCAR'.format(fc3_path))
# fc3_supers = []
# for i in range(len(fc3_disp_ds)):
# displacements_1st = np.zeros(fc3_sposcar.get_positions().shape, dtype=float)
# displacements_1st[fc3_disp_ds[i]['number']] += fc3_disp_ds[i]['displacement']
# for j in range(len(fc3_disp_ds[i]['second_atoms'])):
# displacements_2nd = np.zeros(fc3_sposcar.get_positions().shape, dtype=float)
# displacements_2nd[fc3_disp_ds[i]['second_atoms'][j]['number']] += fc3_disp_ds[i]['second_atoms'][j]['displacement']
# displacements = displacements_1st + displacements_2nd
# fc3_supers.append(fc3_sposcar.copy())
# fc3_supers[-1].new_array(
# 'displacements',
# displacements,
# )
# fc3_supers[-1]._calc = SinglePointDFTCalculator(fc3_supers[-1])
# fc3_supers[-1]._calc.results['forces'] = fc3_disp_ds[i]['second_atoms'][j]['forces']
return phono3py
def read_gpaw_text(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj, "rU")
notfound = []
def index_startswith(lines, string):
if string in notfound:
raise ValueError
for i, line in enumerate(lines):
if line.startswith(string):
return i
notfound.append(string)
raise ValueError
lines = fileobj.readlines()
images = []
while True:
try:
i = lines.index("Unit Cell:\n")
except ValueError:
pass
else:
cell = []
pbc = []
for line in lines[i + 3 : i + 6]:
words = line.split()
if len(words) == 5: # old format
cell.append(float(words[2]))
pbc.append(words[1] == "yes")
else: # new format with GUC
cell.append([float(word) for word in words[3:6]])
pbc.append(words[2] == "yes")
try:
i = lines.index("Positions:\n")
except ValueError:
break
symbols = []
positions = []
for line in lines[i + 1 :]:
words = line.split()
if len(words) != 5:
break
n, symbol, x, y, z = words
symbols.append(symbol.split(".")[0])
positions.append([float(x), float(y), float(z)])
if len(symbols):
atoms = Atoms(symbols=symbols, positions=positions, cell=cell, pbc=pbc)
else:
atoms = Atoms(cell=cell, pbc=pbc)
lines = lines[i + 5 :]
try:
ii = index_startswith(lines, "Reference Energy:")
Eref = float(lines[ii].split()[-1])
except ValueError:
Eref = None
ene = {
# key position
"Kinetic:": 1,
"Potential:": 2,
"XC:": 4,
}
try:
i = lines.index("-------------------------\n")
except ValueError:
e = None
else:
for key in ene:
pos = ene[key]
ene[key] = None
line = lines[i + pos]
try:
assert line.startswith(key)
ene[key] = float(line.split()[-1])
except ValueError:
pass
line = lines[i + 9]
assert line.startswith("Zero Kelvin:")
e = float(line.split()[-1])
try:
ii = index_startswith(lines, "Fermi Level")
except ValueError:
eFermi = None
else:
try:
eFermi = float(lines[ii].split()[2])
except ValueError: # we have two Fermi levels
fields = lines[ii].split()
def strip(string):
for rubbish in "[],":
string = string.replace(rubbish, "")
return string
eFermi = [float(strip(fields[2])), float(strip(fields[3]))]
# read Eigenvalues and occupations
ii1 = ii2 = 1e32
try:
ii1 = index_startswith(lines, " Band Eigenvalues Occupancy")
except ValueError:
pass
try:
ii2 = index_startswith(lines, " Band Eigenvalues Occupancy")
except ValueError:
pass
ii = min(ii1, ii2)
if ii == 1e32:
kpts = None
else:
ii += 1
words = lines[ii].split()
vals = []
while len(words) > 2:
vals.append([float(word) for word in words])
ii += 1
words = lines[ii].split()
vals = np.array(vals).transpose()
kpts = [SinglePointKPoint(1, 0, 0)]
kpts[0].eps_n = vals[1]
kpts[0].f_n = vals[2]
if vals.shape[0] > 3:
kpts.append(SinglePointKPoint(1, 1, 0))
kpts[1].eps_n = vals[3]
kpts[1].f_n = vals[4]
# read charge
try:
ii = index_startswith(lines, "Total Charge:")
except ValueError:
q = None
else:
q = float(lines[ii].split()[2])
# read dipole moment
try:
ii = index_startswith(lines, "Dipole Moment:")
except ValueError:
dipole = None
else:
line = lines[ii].replace("]", "").replace("[", "")
dipole = np.array([float(c) for c in line.split()[-3:]])
try:
ii = index_startswith(lines, "Local Magnetic Moments")
except ValueError:
magmoms = None
else:
magmoms = []
for i in range(ii + 1, ii + 1 + len(atoms)):
iii, magmom = lines[i].split()[:2]
magmoms.append(float(magmom))
try:
ii = lines.index("Forces in eV/Ang:\n")
except ValueError:
f = None
else:
f = []
for i in range(ii + 1, ii + 1 + len(atoms)):
try:
x, y, z = lines[i].split()[-3:]
f.append((float(x), float(y), float(z)))
except (ValueError, IndexError), m:
raise IOError("Malformed GPAW log file: %s" % m)
if len(images) > 0 and e is None:
break
if q is not None and len(atoms) > 0:
n = len(atoms)
atoms.set_initial_charges([q / n] * n)
if e is not None or f is not None:
calc = SinglePointDFTCalculator(
atoms, energy=e, forces=f, dipole=dipole, magmoms=magmoms, eFermi=eFermi, Eref=Eref
)
if kpts is not None:
calc.kpts = kpts
atoms.set_calculator(calc)
images.append(atoms)
lines = lines[i:]
def read_gpaw_text(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj)
def index_startswith(lines, string):
for i, line in enumerate(lines):
if line.startswith(string):
return i
raise ValueError
lines = fileobj.readlines()
images = []
while True:
try:
i = lines.index('Unit Cell:\n')
except ValueError:
pass
else:
cell = []
pbc = []
for line in lines[i + 3:i + 6]:
words = line.split()
if len(words) == 5: # old format
cell.append(float(words[2]))
pbc.append(words[1] == 'yes')
else: # new format with GUC
cell.append([float(word) for word in words[3:6]])
pbc.append(words[2] == 'yes')
try:
i = lines.index('Positions:\n')
except ValueError:
break
atoms = Atoms(cell=cell, pbc=pbc)
for line in lines[i + 1:]:
words = line.split()
if len(words) != 5:
break
n, symbol, x, y, z = words
symbol = symbol.split('.')[0]
atoms.append(Atom(symbol, [float(x), float(y), float(z)]))
lines = lines[i + 5:]
try:
i = lines.index('-------------------------\n')
except ValueError:
e = None
else:
line = lines[i + 9]
assert line.startswith('Zero Kelvin:')
e = float(line.split()[-1])
try:
ii = index_startswith(lines, 'Fermi Level:')
except ValueError:
eFermi = None
else:
try:
eFermi = float(lines[ii].split()[2])
except ValueError: # we have two Fermi levels
fields = lines[ii].split()
def strip(string):
for rubbish in '[],':
string = string.replace(rubbish, '')
return string
eFermi = [float(strip(fields[2])), float(strip(fields[3]))]
try:
ii = index_startswith(lines, 'Total Charge:')
except ValueError:
q = None
else:
q = float(lines[ii].split()[2])
try:
ii = index_startswith(lines, 'Local Magnetic Moments')
except ValueError:
magmoms = None
else:
magmoms = []
for i in range(ii + 1, ii + 1 + len(atoms)):
iii, magmom = lines[i].split()[:2]
magmoms.append(float(magmom))
try:
ii = lines.index('Forces in eV/Ang:\n')
except ValueError:
f = None
else:
f = []
for i in range(ii + 1, ii + 1 + len(atoms)):
try:
x, y, z = lines[i].split()[-3:]
f.append((float(x), float(y), float(z)))
except (ValueError, IndexError), m:
raise IOError('Malformed GPAW log file: %s' % m)
if len(images) > 0 and e is None:
break
if e is not None or f is not None:
calc = SinglePointDFTCalculator(e, f, None, magmoms, atoms, eFermi)
atoms.set_calculator(calc)
if q is not None:
n = len(atoms)
atoms.set_charges([q / n] * n)
images.append(atoms)
lines = lines[i:]
def read_gpaw_out(fileobj, index):
if isinstance(fileobj, str):
fileobj = open(fileobj, 'rU')
notfound = []
def index_startswith(lines, string):
if string in notfound:
raise ValueError
for i, line in enumerate(lines):
if line.startswith(string):
return i
notfound.append(string)
raise ValueError
def index_pattern(lines, pattern):
repat = re.compile(pattern)
if pattern in notfound:
raise ValueError
for i, line in enumerate(lines):
if repat.match(line):
return i
notfound.append(pattern)
raise ValueError
def read_forces(lines, ii):
f = []
for i in range(ii + 1, ii + 1 + len(atoms)):
try:
x, y, z = lines[i].split()[-3:]
f.append((float(x), float(y), float(z)))
except (ValueError, IndexError) as m:
raise IOError('Malformed GPAW log file: %s' % m)
return f, i
lines = fileobj.readlines()
images = []
while True:
try:
i = lines.index('Unit Cell:\n')
except ValueError:
pass
else:
cell = []
pbc = []
for line in lines[i + 3:i + 6]:
words = line.split()
if len(words) == 5: # old format
cell.append(float(words[2]))
pbc.append(words[1] == 'yes')
else: # new format with GUC
cell.append([float(word) for word in words[3:6]])
pbc.append(words[2] == 'yes')
try:
i = lines.index('Positions:\n')
except ValueError:
break
symbols = []
positions = []
for line in lines[i + 1:]:
words = line.split()
if len(words) != 5:
break
n, symbol, x, y, z = words
symbols.append(symbol.split('.')[0])
positions.append([float(x), float(y), float(z)])
if len(symbols):
atoms = Atoms(symbols=symbols, positions=positions,
cell=cell, pbc=pbc)
else:
atoms = Atoms(cell=cell, pbc=pbc)
lines = lines[i + 5:]
try:
ii = index_startswith(lines, 'Reference Energy:')
Eref = float(lines[ii].split()[-1])
except ValueError:
Eref = None
try:
ii = index_pattern(lines, '\d+ k-point')
word = lines[ii].split()
kx = int(word[2])
ky = int(word[4])
kz = int(word[6])
bz_kpts = (kx, ky, kz)
ibz_kpts = int(lines[ii + 1].split()[0])
except (ValueError, TypeError):
bz_kpts = None
ibz_kpts = None
ene = {
# key position
'Kinetic:': 1,
'Potential:': 2,
'XC:': 4}
try:
i = lines.index('-------------------------\n')
except ValueError:
e = None
else:
for key in ene:
pos = ene[key]
ene[key] = None
line = lines[i + pos]
try:
assert line.startswith(key)
ene[key] = float(line.split()[-1])
except ValueError:
pass
line = lines[i + 9]
assert line.startswith('Zero Kelvin:')
e = float(line.split()[-1])
try:
ii = index_startswith(lines, 'Fermi Level')
except ValueError:
eFermi = None
else:
try:
eFermi = float(lines[ii].split()[2])
except ValueError: # we have two Fermi levels
fields = lines[ii].split()
def strip(string):
for rubbish in '[],':
string = string.replace(rubbish, '')
return string
eFermi = [float(strip(fields[2])),
float(strip(fields[3]))]
# read Eigenvalues and occupations
ii1 = ii2 = 1e32
try:
ii1 = index_startswith(lines, ' Band Eigenvalues Occupancy')
except ValueError:
pass
try:
ii2 = index_startswith(lines, ' Band Eigenvalues Occupancy')
except ValueError:
pass
ii = min(ii1, ii2)
if ii == 1e32:
kpts = None
else:
ii += 1
words = lines[ii].split()
vals = []
while(len(words) > 2):
vals.append([float(w) for w in words])
ii += 1
words = lines[ii].split()
vals = np.array(vals).transpose()
kpts = [SinglePointKPoint(1, 0, 0)]
kpts[0].eps_n = vals[1]
kpts[0].f_n = vals[2]
if vals.shape[0] > 3:
kpts.append(SinglePointKPoint(1, 1, 0))
kpts[1].eps_n = vals[3]
kpts[1].f_n = vals[4]
# read charge
try:
ii = index_startswith(lines, 'Total Charge:')
except ValueError:
q = None
else:
q = float(lines[ii].split()[2])
# read dipole moment
try:
ii = index_startswith(lines, 'Dipole Moment:')
except ValueError:
dipole = None
else:
line = lines[ii].replace(']', '').replace('[', '')
dipole = np.array([float(c) for c in line.split()[-3:]])
try:
ii = index_startswith(lines, 'Local Magnetic Moments')
except ValueError:
magmoms = None
else:
magmoms = []
for i in range(ii + 1, ii + 1 + len(atoms)):
iii, magmom = lines[i].split()[:2]
magmoms.append(float(magmom))
try:
ii = lines.index('Forces in eV/Ang:\n')
except ValueError:
f = None
else:
f, i = read_forces(lines, ii)
try:
ii = index_startswith(lines, 'vdW correction:')
except ValueError:
pass
else:
line = lines[ii + 1]
assert line.startswith('Energy:')
e = float(line.split()[-1])
f, i = read_forces(lines, ii + 3)
if len(images) > 0 and e is None:
break
if q is not None and len(atoms) > 0:
n = len(atoms)
atoms.set_initial_charges([q / n] * n)
if e is not None or f is not None:
calc = SinglePointDFTCalculator(atoms, energy=e, forces=f,
dipole=dipole, magmoms=magmoms,
eFermi=eFermi, Eref=Eref,
bz_kpts=bz_kpts, ibz_kpts=ibz_kpts)
calc.name = 'gpaw'
if kpts is not None:
calc.kpts = kpts
atoms.set_calculator(calc)
if magmoms is not None:
atoms.set_initial_magnetic_moments(magmoms)
images.append(atoms)
lines = lines[i:]
if len(images) == 0:
raise IOError('Corrupted GPAW-text file!')
return images[index]
def get_atoms(structure, **kwargs):
"""
Returns ASE Atoms object from pymatgen structure or molecule.
Args:
structure: pymatgen.core.structure.Structure or pymatgen.core.structure.Molecule
**kwargs: other keyword args to pass into the ASE Atoms constructor
Returns:
ASE Atoms object
"""
if not structure.is_ordered:
raise ValueError("ASE Atoms only supports ordered structures")
if not ase_loaded:
raise ImportError(
"AseAtomsAdaptor requires the ASE package.\nUse `pip install ase` or `conda install ase -c conda-forge`"
)
# Construct the base ASE Atoms object
symbols = [str(site.specie.symbol) for site in structure]
positions = [site.coords for site in structure]
if hasattr(structure, "lattice"):
cell = structure.lattice.matrix
pbc = True
else:
cell = None
pbc = None
atoms = Atoms(symbols=symbols,
positions=positions,
pbc=pbc,
cell=cell,
**kwargs)
# Set the site magmoms in the ASE Atoms object
# Note: ASE distinguishes between initial and converged
# magnetic moment site properties, whereas pymatgen does not. Therefore, we
# have to distinguish between these two when constructing the Structure/Molecule.
# The mapping selected here is:
# ASE initial magmom <--> Pymatgen "magmom"
# ASE final magmom <--> Pymatgen "final_magmom"
# ASE initial charge <--> Pymatgen "charge"
# ASE final charge <--> Pymatgen "final_charge"
if "magmom" in structure.site_properties:
initial_magmoms = structure.site_properties["magmom"]
atoms.set_initial_magnetic_moments(initial_magmoms)
if "charge" in structure.site_properties:
initial_charges = structure.site_properties["charge"]
atoms.set_initial_charges(initial_charges)
if "final_magmom" in structure.site_properties:
magmoms = structure.site_properties["final_magmom"]
else:
magmoms = None
if "final_charge" in structure.site_properties:
charges = structure.site_properties["final_charge"]
else:
charges = None
if magmoms or charges:
if magmoms and charges:
calc = SinglePointDFTCalculator(
atoms, **{
"magmoms": magmoms,
"charges": charges
})
elif magmoms:
calc = SinglePointDFTCalculator(atoms, **{"magmoms": magmoms})
elif charges:
calc = SinglePointDFTCalculator(atoms, **{"charges": charges})
atoms.calc = calc
# Get the oxidation states from the structure
oxi_states = [
getattr(site.specie, "oxi_state", None) for site in structure
]
# Read in selective dynamics if present. Note that the ASE FixAtoms class fixes (x,y,z), so
# here we make sure that [False, False, False] or [True, True, True] is set for the site selective
# dynamics property. As a consequence, if only a subset of dimensions are fixed, this won't get passed to ASE.
if "selective_dynamics" in structure.site_properties:
fix_atoms = []
for site in structure:
site_prop = site.properties["selective_dynamics"]
if site_prop not in [[True, True, True], [False, False,
False]]:
raise ValueError(
"ASE FixAtoms constraint does not support selective dynamics in only some dimensions."
"Remove the selective dynamics and try again if you do not need them."
)
is_fixed = bool(~np.all(site.properties["selective_dynamics"]))
fix_atoms.append(is_fixed)
else:
fix_atoms = None
# Set the selective dynamics with the FixAtoms class.
if fix_atoms is not None:
atoms.set_constraint(FixAtoms(mask=fix_atoms))
# Add any remaining site properties to the ASE Atoms object
for prop in structure.site_properties:
if prop not in [
"magmom", "charge", "final_magmom", "final_charge",
"selective_dynamics"
]:
atoms.set_array(prop,
np.array(structure.site_properties[prop]))
if np.any(oxi_states):
atoms.set_array("oxi_states", np.array(oxi_states))
return atoms
def read_pw_out(fileobj, index=-1, results_required=True):
"""Reads Quantum ESPRESSO output files.
The atomistic configurations as well as results (energy, force, stress,
magnetic moments) of the calculation are read for all configurations
within the output file.
Will probably raise errors for broken or incomplete files.
Parameters
----------
fileobj : file|str
A file like object or filename
index : slice
The index of configurations to extract.
results_required : bool
If True, atomistic configurations that do not have any
associated results will not be included. This prevents double
printed configurations and incomplete calculations from being
returned as the final configuration with no results data.
Yields
------
structure : Atoms
The next structure from the index slice. The Atoms has a
SinglePointCalculator attached with any results parsed from
the file.
"""
if isinstance(fileobj, str):
fileobj = open(fileobj, 'rU')
# work with a copy in memory for faster random access
pwo_lines = fileobj.readlines()
# TODO: index -1 special case?
# Index all the interesting points
indexes = {
_PW_START: [],
_PW_END: [],
_PW_CELL: [],
_PW_POS: [],
_PW_MAGMOM: [],
_PW_FORCE: [],
_PW_TOTEN: [],
_PW_STRESS: [],
_PW_FERMI: [],
_PW_HIGHEST_OCCUPIED: [],
_PW_HIGHEST_OCCUPIED_LOWEST_FREE: [],
_PW_KPTS: [],
_PW_BANDS: [],
_PW_BANDSTRUCTURE: [],
_PW_ELECTROSTATIC_EMBEDDING: [],
_PW_NITER: [],
_PW_DONE: [],
_PW_WALLTIME: []
}
for idx, line in enumerate(pwo_lines):
for identifier in indexes:
if identifier in line:
indexes[identifier].append(idx)
# Configurations are either at the start, or defined in ATOMIC_POSITIONS
# in a subsequent step. Can deal with concatenated output files.
all_config_indexes = sorted(indexes[_PW_START] + indexes[_PW_POS])
# Slice only requested indexes
# setting results_required argument stops configuration-only
# structures from being returned. This ensures the [-1] structure
# is one that has results. Two cases:
# - SCF of last configuration is not converged, job terminated
# abnormally.
# - 'relax' and 'vc-relax' re-prints the final configuration but
# only 'vc-relax' recalculates.
if results_required:
results_indexes = sorted(indexes[_PW_TOTEN] + indexes[_PW_FORCE] +
indexes[_PW_STRESS] + indexes[_PW_MAGMOM] +
indexes[_PW_BANDS] +
indexes[_PW_ELECTROSTATIC_EMBEDDING] +
indexes[_PW_BANDSTRUCTURE])
# Prune to only configurations with results data before the next
# configuration
results_config_indexes = []
for config_index, config_index_next in zip(
all_config_indexes, all_config_indexes[1:] + [len(pwo_lines)]):
if any([
config_index < results_index < config_index_next
for results_index in results_indexes
]):
results_config_indexes.append(config_index)
# slice from the subset
image_indexes = results_config_indexes[index]
else:
image_indexes = all_config_indexes[index]
# Extract initialisation information each time PWSCF starts
# to add to subsequent configurations. Use None so slices know
# when to fill in the blanks.
pwscf_start_info = dict((idx, None) for idx in indexes[_PW_START])
if isinstance(image_indexes, int):
image_indexes = [image_indexes]
for image_index in image_indexes:
# Find the nearest calculation start to parse info. Needed in,
# for example, relaxation where cell is only printed at the
# start.
if image_index in indexes[_PW_START]:
prev_start_index = image_index
else:
# The greatest start index before this structure
prev_start_index = [
idx for idx in indexes[_PW_START] if idx < image_index
][-1]
# add structure to reference if not there
if pwscf_start_info[prev_start_index] is None:
pwscf_start_info[prev_start_index] = parse_pwo_start(
pwo_lines, prev_start_index)
# Get the bounds for information for this structure. Any associated
# values will be between the image_index and the following one,
# EXCEPT for cell, which will be 4 lines before if it exists.
for next_index in all_config_indexes:
if next_index > image_index:
break
else:
# right to the end of the file
next_index = len(pwo_lines)
# Get the structure
# Use this for any missing data
prev_structure = pwscf_start_info[prev_start_index]['atoms']
if image_index in indexes[_PW_START]:
structure = prev_structure.copy() # parsed from start info
else:
if _PW_CELL in pwo_lines[image_index - 5]:
# CELL_PARAMETERS would be just before positions if present
cell, cell_alat = get_cell_parameters(pwo_lines[image_index -
5:image_index])
else:
cell = prev_structure.cell
cell_alat = pwscf_start_info[prev_start_index]['alat']
# give at least enough lines to parse the positions
# should be same format as input card
n_atoms = len(prev_structure)
positions_card = get_atomic_positions(
pwo_lines[image_index:image_index + n_atoms + 1],
n_atoms=n_atoms,
cell=cell,
alat=cell_alat)
# convert to Atoms object
symbols = [
label_to_symbol(position[0]) for position in positions_card
]
tags = [label_to_tag(position[0]) for position in positions_card]
positions = [position[1] for position in positions_card]
constraint_idx = [position[2] for position in positions_card]
constraint = get_constraint(constraint_idx)
structure = Atoms(symbols=symbols,
positions=positions,
cell=cell,
constraint=constraint,
pbc=True,
tags=tags)
# Extract calculation results
# Energy
energy = None
for energy_index in indexes[_PW_TOTEN]:
if image_index < energy_index < next_index:
energy = float(
pwo_lines[energy_index].split()[-2]) * units['Ry']
# Electrostatic enbedding energy
elec_embedding_energy = None
for eee_index in indexes[_PW_ELECTROSTATIC_EMBEDDING]:
if image_index < eee_index < next_index:
elec_embedding_energy = float(
pwo_lines[eee_index].split()[-2]) * units['Ry']
# Number of iterations
n_iterations = None
for niter_index in indexes[_PW_NITER]:
if image_index < niter_index < next_index:
n_iterations = int(
pwo_lines[niter_index].split('#')[1].split()[0])
# Forces
forces = None
for force_index in indexes[_PW_FORCE]:
if image_index < force_index < next_index:
# Before QE 5.3 'negative rho' added 2 lines before forces
# Use exact lines to stop before 'non-local' forces
# in high verbosity
if not pwo_lines[force_index + 2].strip():
force_index += 4
else:
force_index += 2
# assume contiguous
forces = [[float(x) for x in force_line.split()[-3:]]
for force_line in pwo_lines[force_index:force_index +
len(structure)]]
forces = np.array(forces) * units['Ry'] / units['Bohr']
# Stress
stress = None
for stress_index in indexes[_PW_STRESS]:
if image_index < stress_index < next_index:
sxx, sxy, sxz = pwo_lines[stress_index + 1].split()[:3]
_, syy, syz = pwo_lines[stress_index + 2].split()[:3]
_, _, szz = pwo_lines[stress_index + 3].split()[:3]
stress = np.array([sxx, syy, szz, syz, sxz, sxy], dtype=float)
# sign convention is opposite of ase
stress *= -1 * units['Ry'] / (units['Bohr']**3)
# Magmoms
magmoms = None
for magmoms_index in indexes[_PW_MAGMOM]:
if image_index < magmoms_index < next_index:
magmoms = [
float(mag_line.split('=')[-1])
for mag_line in pwo_lines[magmoms_index + 1:magmoms_index +
1 + len(structure)]
]
# Fermi level / highest occupied level and lowest unoccupied level
efermi = None
lumo_ene = None
for fermi_index in indexes[_PW_FERMI]:
if image_index < fermi_index < next_index:
efermi = float(pwo_lines[fermi_index].split()[-2])
if efermi is None:
for ho_index in indexes[_PW_HIGHEST_OCCUPIED]:
if image_index < ho_index < next_index:
efermi = float(pwo_lines[ho_index].split()[-1])
if efermi is None:
for holf_index in indexes[_PW_HIGHEST_OCCUPIED_LOWEST_FREE]:
if image_index < holf_index < next_index:
efermi = float(pwo_lines[holf_index].split()[-2])
lumo_ene = float(pwo_lines[holf_index].split()[-1])
# K-points
ibzkpts = None
weights = None
kpoints_warning = "Number of k-points >= 100: " + \
"set verbosity='high' to print them."
for kpts_index in indexes[_PW_KPTS]:
nkpts = int(pwo_lines[kpts_index].split()[4])
kpts_index += 2
if pwo_lines[kpts_index].strip() == kpoints_warning:
continue
# QE prints the k-points in units of 2*pi/alat
# with alat defined as the length of the first
# cell vector
cell = structure.get_cell()
alat = np.linalg.norm(cell[0])
ibzkpts = []
weights = []
for i in range(nkpts):
L = pwo_lines[kpts_index + i].split()
weights.append(float(L[-1]))
coord = np.array([L[-6], L[-5], L[-4].strip('),')],
dtype=float)
coord *= 2 * np.pi / alat
coord = kpoint_convert(cell, ckpts_kv=coord)
ibzkpts.append(coord)
ibzkpts = np.array(ibzkpts)
weights = np.array(weights)
# Bands
kpts = None
kpoints_warning = "Number of k-points >= 100: " + \
"set verbosity='high' to print the bands."
for bands_index in indexes[_PW_BANDS] + indexes[_PW_BANDSTRUCTURE]:
if image_index < bands_index < next_index:
bands_index += 2
if pwo_lines[bands_index].strip() == kpoints_warning:
continue
assert ibzkpts is not None
spin, bands, eigenvalues = 0, [], [[], []]
while True:
L = pwo_lines[bands_index].replace('-', ' -').split()
if len(L) == 0:
if len(bands) > 0:
eigenvalues[spin].append(bands)
bands = []
elif L == ['occupation', 'numbers']:
# Skip the lines with the occupation numbers
bands_index += len(eigenvalues[spin][0]) // 8 + 1
elif L[0] == 'k' and L[1].startswith('='):
pass
elif 'SPIN' in L:
if 'DOWN' in L:
spin += 1
else:
try:
bands.extend(map(float, L))
except ValueError:
break
bands_index += 1
if spin == 1:
assert len(eigenvalues[0]) == len(eigenvalues[1])
# assert len(eigenvalues[0]) == len(ibzkpts), \
# (np.shape(eigenvalues), len(ibzkpts))
kpts = []
for s in range(spin + 1):
for w, k, e in zip(weights, ibzkpts, eigenvalues[s]):
kpt = SinglePointKPoint(w, s, k, eps_n=e)
kpts.append(kpt)
# Convergence
job_done = False
for done_index in indexes[_PW_DONE]:
if image_index < done_index < next_index:
job_done = True
# Walltime
walltime = None
for wt_index in indexes[_PW_WALLTIME]:
if image_index < wt_index < next_index:
walltime = time_to_float(pwo_lines[wt_index].split()[-2])
# Put everything together
calc = SinglePointDFTCalculator(structure,
energy=energy,
forces=forces,
stress=stress,
magmoms=magmoms,
efermi=efermi,
ibzkpts=ibzkpts)
calc.results['homo_energy'] = efermi
calc.results['lumo_energy'] = lumo_ene
calc.results['electrostatic embedding'] = elec_embedding_energy
calc.results['iterations'] = n_iterations
calc.results['job done'] = job_done
calc.results['walltime'] = walltime
calc.kpts = kpts
structure.calc = calc
yield structure
def read_gpaw_out(fileobj, index):
notfound = []
def index_startswith(lines, string):
if not isinstance(string, str):
# assume it's a list
for entry in string:
try:
return index_startswith(lines, entry)
except ValueError:
pass
raise ValueError
if string in notfound:
raise ValueError
for i, line in enumerate(lines):
if line.startswith(string):
return i
notfound.append(string)
raise ValueError
def index_pattern(lines, pattern):
repat = re.compile(pattern)
if pattern in notfound:
raise ValueError
for i, line in enumerate(lines):
if repat.match(line):
return i
notfound.append(pattern)
raise ValueError
def read_forces(lines, ii):
f = []
for i in range(ii + 1, ii + 1 + len(atoms)):
try:
x, y, z = lines[i].split()[-3:]
f.append((float(x), float(y), float(z)))
except (ValueError, IndexError) as m:
raise IOError('Malformed GPAW log file: %s' % m)
return f, i
lines = [line.lower() for line in fileobj.readlines()]
images = []
while True:
try:
i = index_startswith(lines, 'reference energy:')
Eref = float(lines[i].split()[-1])
except ValueError:
Eref = None
try:
i = lines.index('unit cell:\n')
except ValueError:
pass
else:
if lines[i + 2].startswith(' -'):
del lines[i + 2] # old format
cell = []
pbc = []
for line in lines[i + 2:i + 5]:
words = line.split()
if len(words) == 5: # old format
cell.append(float(words[2]))
pbc.append(words[1] == 'yes')
else: # new format with GUC
cell.append([float(word) for word in words[3:6]])
pbc.append(words[2] == 'yes')
try:
i = lines.index('positions:\n')
except ValueError:
break
symbols = []
positions = []
for line in lines[i + 1:]:
words = line.split()
if len(words) < 5:
break
n, symbol, x, y, z = words[:5]
symbols.append(symbol.split('.')[0].title())
positions.append([float(x), float(y), float(z)])
if len(symbols):
atoms = Atoms(symbols=symbols,
positions=positions,
cell=cell,
pbc=pbc)
else:
atoms = Atoms(cell=cell, pbc=pbc)
lines = lines[i + 5:]
try:
ii = index_pattern(lines, '\\d+ k-point')
word = lines[ii].split()
kx = int(word[2])
ky = int(word[4])
kz = int(word[6])
bz_kpts = (kx, ky, kz)
ibz_kpts = int(lines[ii + 1].split()[0])
except (ValueError, TypeError, IndexError):
bz_kpts = None
ibz_kpts = None
try:
i = index_startswith(lines, 'energy contributions relative to')
except ValueError:
e = energy_contributions = None
else:
energy_contributions = {}
for line in lines[i + 2:i + 8]:
fields = line.split(':')
energy_contributions[fields[0]] = float(fields[1])
line = lines[i + 10]
assert (line.startswith('zero kelvin:')
or line.startswith('extrapolated:'))
e = float(line.split()[-1])
try:
ii = index_pattern(lines, '(fixed )?fermi level(s)?:')
except ValueError:
eFermi = None
else:
fields = lines[ii].split()
try:
def strip(string):
for rubbish in '[],':
string = string.replace(rubbish, '')
return string
eFermi = [float(strip(fields[-2])), float(strip(fields[-1]))]
except ValueError:
eFermi = float(fields[-1])
# read Eigenvalues and occupations
ii1 = ii2 = 1e32
try:
ii1 = index_startswith(lines, ' band eigenvalues occupancy')
except ValueError:
pass
try:
ii2 = index_startswith(lines, ' band eigenvalues occupancy')
except ValueError:
pass
ii = min(ii1, ii2)
if ii == 1e32:
kpts = None
else:
ii += 1
words = lines[ii].split()
vals = []
while (len(words) > 2):
vals.append([float(w) for w in words])
ii += 1
words = lines[ii].split()
vals = np.array(vals).transpose()
kpts = [SinglePointKPoint(1, 0, 0)]
kpts[0].eps_n = vals[1]
kpts[0].f_n = vals[2]
if vals.shape[0] > 3:
kpts.append(SinglePointKPoint(1, 1, 0))
kpts[1].eps_n = vals[3]
kpts[1].f_n = vals[4]
# read charge
try:
ii = index_startswith(lines, 'total charge:')
except ValueError:
q = None
else:
q = float(lines[ii].split()[2])
# read dipole moment
try:
ii = index_startswith(lines, 'dipole moment:')
except ValueError:
dipole = None
else:
line = lines[ii]
for x in '()[],':
line = line.replace(x, '')
dipole = np.array([float(c) for c in line.split()[2:5]])
try:
ii = index_startswith(lines, 'local magnetic moments')
except ValueError:
magmoms = None
else:
magmoms = []
for j in range(ii + 1, ii + 1 + len(atoms)):
magmom = lines[j].split()[-1].rstrip(')')
magmoms.append(float(magmom))
try:
ii = lines.index('forces in ev/ang:\n')
except ValueError:
f = None
else:
f, i = read_forces(lines, ii)
try:
ii = index_startswith(lines, 'vdw correction:')
except ValueError:
pass
else:
line = lines[ii + 1]
assert line.startswith('energy:')
e = float(line.split()[-1])
f, i = read_forces(lines, ii + 3)
if len(images) > 0 and e is None:
break
if q is not None and len(atoms) > 0:
n = len(atoms)
atoms.set_initial_charges([q / n] * n)
if magmoms is not None:
atoms.set_initial_magnetic_moments(magmoms)
if e is not None or f is not None:
calc = SinglePointDFTCalculator(atoms,
energy=e,
forces=f,
dipole=dipole,
magmoms=magmoms,
efermi=eFermi,
bzkpts=bz_kpts,
ibzkpts=ibz_kpts)
calc.eref = Eref
calc.name = 'gpaw'
if energy_contributions is not None:
calc.energy_contributions = energy_contributions
if kpts is not None:
calc.kpts = kpts
atoms.calc = calc
images.append(atoms)
lines = lines[i:]
if len(images) == 0:
raise IOError('Corrupted GPAW-text file!')
return images[index]
def read_vasp_xml(filename='vasprun.xml', index=-1):
"""Parse vasprun.xml file.
Reads unit cell, atom positions, energies, forces, and constraints
from vasprun.xml file
"""
import numpy as np
import xml.etree.ElementTree as ET
from ase import Atoms
from ase.constraints import FixAtoms, FixScaled
from ase.calculators.singlepoint import (SinglePointDFTCalculator,
SinglePointKPoint)
from ase.units import GPa
from collections import OrderedDict
tree = ET.iterparse(filename, events=['start', 'end'])
atoms_init = None
calculation = []
ibz_kpts = None
kpt_weights = None
parameters = OrderedDict()
try:
for event, elem in tree:
if event == 'end':
if elem.tag == 'kpoints':
for subelem in elem.iter(tag='generation'):
kpts_params = OrderedDict()
parameters['kpoints_generation'] = kpts_params
for par in subelem.iter():
if par.tag in ['v', 'i']:
parname = par.attrib['name'].lower()
kpts_params[parname] = __get_xml_parameter(par)
kpts = elem.findall("varray[@name='kpointlist']/v")
ibz_kpts = np.zeros((len(kpts), 3))
for i, kpt in enumerate(kpts):
ibz_kpts[i] = [float(val) for val in kpt.text.split()]
kpt_weights = elem.findall('varray[@name="weights"]/v')
kpt_weights = [float(val.text) for val in kpt_weights]
elif elem.tag == 'parameters':
for par in elem.iter():
if par.tag in ['v', 'i']:
parname = par.attrib['name'].lower()
parameters[parname] = __get_xml_parameter(par)
elif elem.tag == 'atominfo':
species = []
for entry in elem.find("array[@name='atoms']/set"):
species.append(entry[0].text.strip())
natoms = len(species)
elif (elem.tag == 'structure'
and elem.attrib.get('name') == 'initialpos'):
cell_init = np.zeros((3, 3), dtype=float)
for i, v in enumerate(
elem.find("crystal/varray[@name='basis']")):
cell_init[i] = np.array(
[float(val) for val in v.text.split()])
scpos_init = np.zeros((natoms, 3), dtype=float)
for i, v in enumerate(
elem.find("varray[@name='positions']")):
scpos_init[i] = np.array(
[float(val) for val in v.text.split()])
constraints = []
fixed_indices = []
for i, entry in enumerate(
elem.findall("varray[@name='selective']/v")):
flags = (np.array(
entry.text.split() == np.array(['F', 'F', 'F'])))
if flags.all():
fixed_indices.append(i)
elif flags.any():
constraints.append(FixScaled(cell_init, i, flags))
if fixed_indices:
constraints.append(FixAtoms(fixed_indices))
atoms_init = Atoms(species,
cell=cell_init,
scaled_positions=scpos_init,
constraint=constraints,
pbc=True)
elif elem.tag == 'dipole':
dblock = elem.find('v[@name="dipole"]')
if dblock is not None:
dipole = np.array(
[float(val) for val in dblock.text.split()])
elif event == 'start' and elem.tag == 'calculation':
calculation.append(elem)
except ET.ParseError as parse_error:
if atoms_init is None:
raise parse_error
if calculation[-1].find('energy') is None:
calculation = calculation[:-1]
if not calculation:
yield atoms_init
if calculation:
if isinstance(index, int):
steps = [calculation[index]]
else:
steps = calculation[index]
else:
steps = []
for step in steps:
# Workaround for VASP bug, e_0_energy contains the wrong value
# in calculation/energy, but calculation/scstep/energy does not
# include classical VDW corrections. So, first calculate
# e_0_energy - e_fr_energy from calculation/scstep/energy, then
# apply that correction to e_fr_energy from calculation/energy.
lastscf = step.findall('scstep/energy')[-1]
try:
lastdipole = step.findall('scstep/dipole')[-1]
except:
lastdipole = None
de = (float(lastscf.find('i[@name="e_0_energy"]').text) -
float(lastscf.find('i[@name="e_fr_energy"]').text))
free_energy = float(step.find('energy/i[@name="e_fr_energy"]').text)
energy = free_energy + de
cell = np.zeros((3, 3), dtype=float)
for i, vector in enumerate(
step.find('structure/crystal/varray[@name="basis"]')):
cell[i] = np.array([float(val) for val in vector.text.split()])
scpos = np.zeros((natoms, 3), dtype=float)
for i, vector in enumerate(
step.find('structure/varray[@name="positions"]')):
scpos[i] = np.array([float(val) for val in vector.text.split()])
forces = None
fblocks = step.find('varray[@name="forces"]')
if fblocks is not None:
forces = np.zeros((natoms, 3), dtype=float)
for i, vector in enumerate(fblocks):
forces[i] = np.array(
[float(val) for val in vector.text.split()])
stress = None
sblocks = step.find('varray[@name="stress"]')
if sblocks is not None:
stress = np.zeros((3, 3), dtype=float)
for i, vector in enumerate(sblocks):
stress[i] = np.array(
[float(val) for val in vector.text.split()])
stress *= -0.1 * GPa
stress = stress.reshape(9)[[0, 4, 8, 5, 2, 1]]
dipole = None
if lastdipole is not None:
dblock = lastdipole.find('v[@name="dipole"]')
if dblock is not None:
dipole = np.zeros((1, 3), dtype=float)
dipole = np.array([float(val) for val in dblock.text.split()])
dblock = step.find('dipole/v[@name="dipole"]')
if dblock is not None:
dipole = np.zeros((1, 3), dtype=float)
dipole = np.array([float(val) for val in dblock.text.split()])
efermi = step.find('dos/i[@name="efermi"]')
if efermi is not None:
efermi = float(efermi.text)
kpoints = []
for ikpt in range(1, len(ibz_kpts) + 1):
kblocks = step.findall(
'eigenvalues/array/set/set/set[@comment="kpoint %d"]' % ikpt)
if kblocks is not None:
for spin, kpoint in enumerate(kblocks):
eigenvals = kpoint.findall('r')
eps_n = np.zeros(len(eigenvals))
f_n = np.zeros(len(eigenvals))
for j, val in enumerate(eigenvals):
val = val.text.split()
eps_n[j] = float(val[0])
f_n[j] = float(val[1])
if len(kblocks) == 1:
f_n *= 2
kpoints.append(
SinglePointKPoint(kpt_weights[ikpt - 1], spin, ikpt,
eps_n, f_n))
if len(kpoints) == 0:
kpoints = None
atoms = atoms_init.copy()
atoms.set_cell(cell)
atoms.set_scaled_positions(scpos)
atoms.set_calculator(
SinglePointDFTCalculator(atoms,
energy=energy,
forces=forces,
stress=stress,
free_energy=free_energy,
ibzkpts=ibz_kpts,
efermi=efermi,
dipole=dipole))
atoms.calc.name = 'vasp'
atoms.calc.kpts = kpoints
atoms.calc.parameters = parameters
yield atoms
def _read_outcar_frame(lines, header_data):
from ase.calculators.singlepoint import (SinglePointDFTCalculator,
SinglePointKPoint)
mag_x = None
mag_y = None
mag_z = None
magmoms = None
magmom = None
stress = None
efermi = None
symbols = header_data['symbols']
constraints = header_data['constraints']
natoms = header_data['natoms']
# nkpts = header_data['nkpts']
nbands = header_data['nbands']
kpt_weights = header_data['kpt_weights']
ibzkpts = header_data['ibzkpts']
atoms = Atoms(symbols=symbols, pbc=True, constraint=constraints)
cl = _outcar_check_line # Aliasing
spinc = 0 # Spin component
kpts = []
forces = np.zeros((natoms, 3))
positions = np.zeros((natoms, 3))
f_n = np.zeros(nbands) # kpt occupations
eps_n = np.zeros(nbands) # kpt eigenvalues
# Parse each atoms object
for n, line in enumerate(lines):
line = line.strip()
if 'direct lattice vectors' in line:
cell = []
for i in range(3):
parts = cl(lines[n + i + 1]).split()
cell += [list(map(float, parts[0:3]))]
atoms.set_cell(cell)
elif 'magnetization (x)' in line:
# Magnetization in both collinear and non-collinear
nskip = 4 # Skip some lines
mag_x = [float(cl(lines[n + i + nskip]).split()[-1])
for i in range(natoms)]
# XXX: !!!Uncomment these lines when non-collinear spin is supported!!!
# Remember to check that format fits!
# elif 'magnetization (y)' in line:
# # Non-collinear spin
# nskip = 4 # Skip some lines
# mag_y = [float(cl(lines[n + i + nskip]).split()[-1])
# for i in range(natoms)]
# elif 'magnetization (z)' in line:
# # Non-collinear spin
# nskip = 4 # Skip some lines
# mag_z = [float(cl(lines[n + i + nskip]).split()[-1])
# for i in range(natoms)]
elif 'number of electron' in line:
parts = cl(line).split()
if len(parts) > 5 and parts[0].strip() != "NELECT":
i = parts.index('magnetization') + 1
magmom = parts[i:]
if len(magmom) == 1:
# Collinear spin
magmom = float(magmom[0])
# !Uncomment these lines when non-collinear spin is supported!
# Remember to check that format fits!
# else:
# # Non-collinear spin
# # Make a (3,) dim array
# magmom = np.array(list(map(float, magmom)))
elif 'in kB ' in line:
stress = -np.asarray([float(a) for a in cl(line).split()[2:]])
stress = stress[[0, 1, 2, 4, 5, 3]] * 1e-1 * ase.units.GPa
elif 'POSITION ' in line:
nskip = 2
for i in range(natoms):
parts = list(map(float, cl(lines[n + i + nskip]).split()))
positions[i] = parts[0:3]
forces[i] = parts[3:6]
atoms.set_positions(positions, apply_constraint=False)
elif 'E-fermi :' in line:
parts = line.split()
efermi = float(parts[2])
elif 'spin component' in line:
# Update spin component for kpts
# Make spin be in [0, 1], VASP writes 1 or 2
tmp = int(line.split()[-1]) - 1
if tmp < spinc:
# if NWRITE=3, we write KPTS after every electronic step,
# so we just reset it, since we went from spin=2 to spin=1
# in the same ionic step.
# XXX: Only read it at last electronic step
kpts = []
spinc = tmp
elif 'k-point ' in line:
if 'plane waves' in line:
# Can happen if we still have part of header
continue
# Parse all kpts and bands
parts = line.split()
ikpt = int(parts[1]) - 1 # Make kpt idx start from 0
w = kpt_weights[ikpt]
nskip = 2
for i in range(nbands):
parts = lines[n + i + nskip].split()
eps_n[i] = float(parts[1])
f_n[i] = float(parts[2])
kpts.append(SinglePointKPoint(w, spinc, ikpt,
eps_n=eps_n, f_n=f_n))
elif _OUTCAR_SCF_DELIM in line:
# Last section before next ionic step
nskip = 2
parts = cl(lines[n + nskip]).strip().split()
energy_free = float(parts[4]) # Force consistent
nskip = 4
parts = cl(lines[n + nskip]).strip().split()
energy_zero = float(parts[6]) # Extrapolated to 0 K
# For debugging
# assert len(kpts) == 0 or len(kpts) == (spinc + 1) * nkpts
if mag_x is not None:
if mag_y is not None:
# Non-collinear
assert len(mag_x) == len(mag_y) == len(mag_z)
magmoms = np.zeros((len(atoms), 3))
magmoms[:, 0] = mag_x
magmoms[:, 1] = mag_y
magmoms[:, 2] = mag_z
else:
# Collinear
magmoms = np.array(mag_x)
atoms.set_calculator(
SinglePointDFTCalculator(atoms,
energy=energy_zero,
free_energy=energy_free,
ibzkpts=ibzkpts,
forces=forces,
efermi=efermi,
magmom=magmom,
magmoms=magmoms,
stress=stress))
atoms.calc.name = 'vasp'
atoms.calc.kpts = kpts
return atoms
def read_koopmans_cp_out(fileobj, index=-1, results_required=True):
"""Reads Quantum ESPRESSO output files.
The atomistic configurations as well as results (energy, force, stress,
magnetic moments) of the calculation are read for all configurations
within the output file.
Will probably raise errors for broken or incomplete files.
Parameters
----------
fileobj : file|str
A file like object or filename
index : slice
The index of configurations to extract.
results_required : bool
If True, atomistic configurations that do not have any
associated results will not be included. This prevents double
printed configurations and incomplete calculations from being
returned as the final configuration with no results data.
Yields
------
structure : Atoms
The next structure from the index slice. The Atoms has a
SinglePointCalculator attached with any results parsed from
the file.
"""
if isinstance(fileobj, basestring):
fileobj = open(fileobj, 'rU')
# work with a copy in memory for faster random access
cpo_lines = fileobj.readlines()
# For the moment, provide an empty atoms object
structure = Atoms()
# Extract calculation results
energy = None
odd_energy = None
lumo_energy = None
homo_energy = None
mp1_energy = None
mp2_energy = None
lambda_ii = None
eigenvalues = []
job_done = False
orbital_data = {
'charge': [],
'centres': [],
'spreads': [],
'self-Hartree': []
}
walltime = None
convergence = {'filled': [], 'empty': []}
convergence_key = 'filled'
i_spin_orbital_data = None
for i_line, line in enumerate(cpo_lines):
# Energy
if _CP_TOTEN in line:
energy = float(line.split()[-3]) * units.Hartree
if _CP_LAMBDA in line and lambda_ii is None:
lambda_ii = float(line.split()[-1]) * units.Hartree
# Bands
if _CP_BANDS in line:
if 'Empty' not in line:
eigenvalues.append([])
j_line = i_line + 2
while len(cpo_lines[j_line].strip()) > 0:
eigenvalues[-1] += safe_string_to_list_of_floats(
cpo_lines[j_line])
j_line += 1
if 'odd energy' in line:
odd_energy = float(line.split()[3]) * units.Hartree
if 'H**O Eigenvalue (eV)' in line and '*' not in cpo_lines[i_line + 2]:
homo_energy = float(cpo_lines[i_line + 2])
if 'LUMO Eigenvalue (eV)' in line and '*' not in cpo_lines[i_line + 2]:
lumo_energy = float(cpo_lines[i_line + 2])
if 'Makov-Payne 1-order energy' in line:
mp1_energy = float(line.split()[4]) * units.Hartree
if 'Makov-Payne 2-order energy' in line:
mp2_energy = float(line.split()[4]) * units.Hartree
if 'JOB DONE' in line:
job_done = True
# Start of block of orbitals for a given spin channel
if 'Orb -- Charge ---' in line or 'Orb -- Empty Charge' in line:
i_spin_orbital_data = int(line.split()[-1]) - 1
for key in orbital_data:
if len(orbital_data[key]) < i_spin_orbital_data + 1:
orbital_data[key].append([])
# Orbital information
if line.startswith(('OCC', 'EMP')):
if 'NaN' in line:
continue
line = line.replace('********', ' 0.000')
values = [
float(line[i - 4:i + 4]) for i, c in enumerate(line)
if c == '.'
]
orbital_data['charge'][i_spin_orbital_data].append(values[0])
orbital_data['centres'][i_spin_orbital_data].append(
[x * units.Bohr for x in values[1:4]])
orbital_data['spreads'][i_spin_orbital_data].append(values[4] *
units.Bohr**2)
orbital_data['self-Hartree'][i_spin_orbital_data].append(values[5])
# Tracking convergence
if 'PERFORMING CONJUGATE GRADIENT MINIMIZATION OF EMPTY STATES' in line:
convergence_key = 'empty'
if 'iteration = ' in line and 'eff iteration = ' in line:
values = [l.split()[0] for l in line.split('=')[1:]]
[it, eff_it, etot] = values[:3]
entry = {
'iteration': int(it),
'eff iteration': int(eff_it),
'Etot': float(etot) * units.Hartree
}
if len(values) == 4:
entry['delta_E'] = float(values[3]) * units.Hartree
convergence[convergence_key].append(entry)
if 'wall time' in line:
time_str = line.split(',')[1].strip().rstrip('wall time')
walltime = time_to_float(time_str)
# Put everything together
calc = SinglePointDFTCalculator(structure, energy=energy) # ,
# forces=forces, stress=stress,
# magmoms=magmoms, efermi=efermi,
# ibzkpts=ibzkpts)
calc.results['energy'] = energy
calc.results['odd_energy'] = odd_energy
calc.results['homo_energy'] = homo_energy
calc.results['lumo_energy'] = lumo_energy
calc.results['mp1_energy'] = mp1_energy
calc.results['mp2_energy'] = mp2_energy
calc.results['eigenvalues'] = eigenvalues
calc.results['lambda_ii'] = lambda_ii
calc.results['orbital_data'] = orbital_data
calc.results['convergence'] = convergence
calc.results['job_done'] = job_done
calc.results['walltime'] = walltime
structure.calc = calc
yield structure
def read_gpaw_text(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj)
def index_startswith(lines, string):
for i, line in enumerate(lines):
if line.startswith(string):
return i
raise ValueError
lines = fileobj.readlines()
images = []
while True:
try:
i = lines.index('Unit Cell:\n')
except ValueError:
pass
else:
cell = []
pbc = []
for line in lines[i + 3:i + 6]:
words = line.split()
if len(words) == 5: # old format
cell.append(float(words[2]))
pbc.append(words[1] == 'yes')
else: # new format with GUC
cell.append([float(word) for word in words[3:6]])
pbc.append(words[2] == 'yes')
try:
i = lines.index('Positions:\n')
except ValueError:
break
atoms = Atoms(cell=cell, pbc=pbc)
for line in lines[i + 1:]:
words = line.split()
if len(words) != 5:
break
n, symbol, x, y, z = words
symbol = symbol.split('.')[0]
atoms.append(Atom(symbol, [float(x), float(y), float(z)]))
lines = lines[i + 5:]
try:
i = lines.index('-------------------------\n')
except ValueError:
e = None
else:
line = lines[i + 9]
assert line.startswith('Zero Kelvin:')
e = float(line.split()[-1])
try:
ii = index_startswith(lines, 'Fermi Level:')
except ValueError:
eFermi = None
else:
try:
eFermi = float(lines[ii].split()[2])
except ValueError: # we have two Fermi levels
fields = lines[ii].split()
def strip(string):
for rubbish in '[],':
string = string.replace(rubbish, '')
return string
eFermi = [float(strip(fields[2])),
float(strip(fields[3])) ]
# read Eigenvalues and occupations
ii1 = ii2 = 1e32
try:
ii1 = index_startswith(lines, ' Band Eigenvalues Occupancy')
except ValueError:
pass
try:
ii2 = index_startswith(lines, ' Band Eigenvalues Occupancy')
except ValueError:
pass
ii = min(ii1, ii2)
if ii == 1e32:
kpts = None
else:
ii += 1
words = lines[ii].split()
vals = []
while(len(words) > 2):
vals.append([float(word) for word in words])
ii += 1
words = lines[ii].split()
vals = np.array(vals).transpose()
kpts = [SinglePointKPoint(0, 0)]
kpts[0].eps_n = vals[1]
kpts[0].f_n = vals[2]
if vals.shape[0] > 3:
kpts.append(SinglePointKPoint(0, 1))
kpts[1].eps_n = vals[3]
kpts[1].f_n = vals[4]
# read charge
try:
ii = index_startswith(lines, 'Total Charge:')
except ValueError:
q = None
else:
q = float(lines[ii].split()[2])
try:
ii = index_startswith(lines, 'Local Magnetic Moments')
except ValueError:
magmoms = None
else:
magmoms = []
for i in range(ii + 1, ii + 1 + len(atoms)):
iii, magmom = lines[i].split()[:2]
magmoms.append(float(magmom))
try:
ii = lines.index('Forces in eV/Ang:\n')
except ValueError:
f = None
else:
f = []
for i in range(ii + 1, ii + 1 + len(atoms)):
try:
x, y, z = lines[i].split()[-3:]
f.append((float(x), float(y), float(z)))
except (ValueError, IndexError), m:
raise IOError('Malformed GPAW log file: %s' % m)
if len(images) > 0 and e is None:
break
if e is not None or f is not None:
calc = SinglePointDFTCalculator(e, f, None, magmoms, atoms, eFermi)
if kpts is not None:
calc.kpts = kpts
atoms.set_calculator(calc)
if q is not None and len(atoms) > 0:
n = len(atoms)
atoms.set_charges([q / n] * n)
images.append(atoms)
lines = lines[i:]
def read_gpaw_text(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj, 'rU')
notfound = []
def index_startswith(lines, string):
if string in notfound:
raise ValueError
for i, line in enumerate(lines):
if line.startswith(string):
return i
notfound.append(string)
raise ValueError
lines = fileobj.readlines()
images = []
while True:
try:
i = lines.index('Unit Cell:\n')
except ValueError:
pass
else:
cell = []
pbc = []
for line in lines[i + 3:i + 6]:
words = line.split()
if len(words) == 5: # old format
cell.append(float(words[2]))
pbc.append(words[1] == 'yes')
else: # new format with GUC
cell.append([float(word) for word in words[3:6]])
pbc.append(words[2] == 'yes')
try:
i = lines.index('Positions:\n')
except ValueError:
break
symbols = []
positions = []
for line in lines[i + 1:]:
words = line.split()
if len(words) != 5:
break
n, symbol, x, y, z = words
symbols.append(symbol.split('.')[0])
positions.append([float(x), float(y), float(z)])
if len(symbols):
atoms = Atoms(symbols=symbols,
positions=positions,
cell=cell,
pbc=pbc)
else:
atoms = Atoms(cell=cell, pbc=pbc)
lines = lines[i + 5:]
ene = {
# key position
'Kinetic:': 1,
'Potential:': 2,
'XC:': 4
}
try:
i = lines.index('-------------------------\n')
except ValueError:
e = None
else:
for key in ene:
pos = ene[key]
ene[key] = None
line = lines[i + pos]
try:
assert line.startswith(key)
ene[key] = float(line.split()[-1])
except ValueError:
pass
line = lines[i + 9]
assert line.startswith('Zero Kelvin:')
e = float(line.split()[-1])
try:
ii = index_startswith(lines, 'Fermi Level')
except ValueError:
eFermi = None
else:
try:
eFermi = float(lines[ii].split()[2])
except ValueError: # we have two Fermi levels
fields = lines[ii].split()
def strip(string):
for rubbish in '[],':
string = string.replace(rubbish, '')
return string
eFermi = [float(strip(fields[2])), float(strip(fields[3]))]
# read Eigenvalues and occupations
ii1 = ii2 = 1e32
try:
ii1 = index_startswith(lines, ' Band Eigenvalues Occupancy')
except ValueError:
pass
try:
ii2 = index_startswith(lines, ' Band Eigenvalues Occupancy')
except ValueError:
pass
ii = min(ii1, ii2)
if ii == 1e32:
kpts = None
else:
ii += 1
words = lines[ii].split()
vals = []
while (len(words) > 2):
vals.append([float(word) for word in words])
ii += 1
words = lines[ii].split()
vals = np.array(vals).transpose()
kpts = [SinglePointKPoint(1, 0, 0)]
kpts[0].eps_n = vals[1]
kpts[0].f_n = vals[2]
if vals.shape[0] > 3:
kpts.append(SinglePointKPoint(1, 1, 0))
kpts[1].eps_n = vals[3]
kpts[1].f_n = vals[4]
# read charge
try:
ii = index_startswith(lines, 'Total Charge:')
except ValueError:
q = None
else:
q = float(lines[ii].split()[2])
# read dipole moment
try:
ii = index_startswith(lines, 'Dipole Moment:')
except ValueError:
dipole = None
else:
line = lines[ii].replace(']', '').replace('[', '')
dipole = np.array([float(c) for c in line.split()[-3:]])
try:
ii = index_startswith(lines, 'Local Magnetic Moments')
except ValueError:
magmoms = None
else:
magmoms = []
for i in range(ii + 1, ii + 1 + len(atoms)):
iii, magmom = lines[i].split()[:2]
magmoms.append(float(magmom))
try:
ii = lines.index('Forces in eV/Ang:\n')
except ValueError:
f = None
else:
f = []
for i in range(ii + 1, ii + 1 + len(atoms)):
try:
x, y, z = lines[i].split()[-3:]
f.append((float(x), float(y), float(z)))
except (ValueError, IndexError), m:
raise IOError('Malformed GPAW log file: %s' % m)
if len(images) > 0 and e is None:
break
if q is not None and len(atoms) > 0:
n = len(atoms)
atoms.set_initial_charges([q / n] * n)
if e is not None or f is not None:
calc = SinglePointDFTCalculator(atoms,
energy=e,
forces=f,
dipole=dipole,
magmoms=magmoms,
eFermi=eFermi)
if kpts is not None:
calc.kpts = kpts
atoms.set_calculator(calc)
images.append(atoms)
lines = lines[i:]
syms = ''
y = s.readline().split()
while len(y) > 0:
nf = len(y)
pos.append([float(x) for x in y[nf - 4:nf - 1]])
syms += y[1].strip('0123456789')
y = s.readline().split()
pos = np.array(pos) * alat
natoms = len(pos)
# create atoms object with coordinates and unit cell
# as specified in the initial ionic step in log
atoms = Atoms(syms, pos, cell=cell * alat, pbc=(1, 1, 1))
# Attach calculator object to atoms.
calc = SinglePointDFTCalculator(atoms)
atoms.set_calculator(calc)
# Get total energy at first ionic step and store it in the calculator.
en = get_total_energy(s)
if en is not None:
calc.results['energy'] = en
else:
print('no total energy found', file=stderr)
exit(3)
# Write to .traj file
traj = Trajectory(argv[2], 'w')
traj.write(atoms)
# Append the following images.
a = s.readline()
def read_gpaw_out(fileobj, index): # -> Union[Atoms, List[Atoms]]:
"""Read text output from GPAW calculation."""
lines = [line.lower() for line in fileobj.readlines()]
blocks = []
i1 = 0
for i2, line in enumerate(lines):
if line == 'positions:\n':
if i1 > 0:
blocks.append(lines[i1:i2])
i1 = i2
blocks.append(lines[i1:])
images: List[Atoms] = []
for lines in blocks:
try:
i = lines.index('unit cell:\n')
except ValueError:
pass
else:
if lines[i + 2].startswith(' -'):
del lines[i + 2] # old format
cell: List[Union[float, List[float]]] = []
pbc = []
for line in lines[i + 2:i + 5]:
words = line.split()
if len(words) == 5: # old format
cell.append(float(words[2]))
pbc.append(words[1] == 'yes')
else: # new format with GUC
cell.append([float(word) for word in words[3:6]])
pbc.append(words[2] == 'yes')
symbols = []
positions = []
magmoms = []
for line in lines[1:]:
words = line.split()
if len(words) < 5:
break
n, symbol, x, y, z = words[:5]
symbols.append(symbol.split('.')[0].title())
positions.append([float(x), float(y), float(z)])
if len(words) > 5:
mom = float(words[-1].rstrip(')'))
magmoms.append(mom)
if len(symbols):
atoms = Atoms(symbols=symbols, positions=positions,
cell=cell, pbc=pbc)
else:
atoms = Atoms(cell=cell, pbc=pbc)
try:
ii = index_pattern(lines, '\\d+ k-point')
word = lines[ii].split()
kx = int(word[2])
ky = int(word[4])
kz = int(word[6])
bz_kpts = (kx, ky, kz)
ibz_kpts = int(lines[ii + 1].split()[0])
except (ValueError, TypeError, IndexError):
bz_kpts = None
ibz_kpts = None
try:
i = index_startswith(lines, 'energy contributions relative to')
except ValueError:
e = energy_contributions = None
else:
energy_contributions = {}
for line in lines[i + 2:i + 8]:
fields = line.split(':')
energy_contributions[fields[0]] = float(fields[1])
line = lines[i + 10]
assert (line.startswith('zero kelvin:') or
line.startswith('extrapolated:'))
e = float(line.split()[-1])
try:
ii = index_pattern(lines, '(fixed )?fermi level(s)?:')
except ValueError:
eFermi = None
else:
fields = lines[ii].split()
try:
def strip(string):
for rubbish in '[],':
string = string.replace(rubbish, '')
return string
eFermi = [float(strip(fields[-2])),
float(strip(fields[-1]))]
except ValueError:
eFermi = float(fields[-1])
# read Eigenvalues and occupations
ii1 = ii2 = 1e32
try:
ii1 = index_startswith(lines, ' band eigenvalues occupancy')
except ValueError:
pass
try:
ii2 = index_startswith(lines, ' band eigenvalues occupancy')
except ValueError:
pass
ii = min(ii1, ii2)
if ii == 1e32:
kpts = None
else:
ii += 1
words = lines[ii].split()
vals = []
while(len(words) > 2):
vals.append([float(w) for w in words])
ii += 1
words = lines[ii].split()
vals = np.array(vals).transpose()
kpts = [SinglePointKPoint(1, 0, 0)]
kpts[0].eps_n = vals[1]
kpts[0].f_n = vals[2]
if vals.shape[0] > 3:
kpts.append(SinglePointKPoint(1, 1, 0))
kpts[1].eps_n = vals[3]
kpts[1].f_n = vals[4]
# read charge
try:
ii = index_startswith(lines, 'total charge:')
except ValueError:
q = None
else:
q = float(lines[ii].split()[2])
# read dipole moment
try:
ii = index_startswith(lines, 'dipole moment:')
except ValueError:
dipole = None
else:
line = lines[ii]
for x in '()[],':
line = line.replace(x, '')
dipole = np.array([float(c) for c in line.split()[2:5]])
try:
ii = index_startswith(lines, 'local magnetic moments')
except ValueError:
pass
else:
magmoms = []
for j in range(ii + 1, ii + 1 + len(atoms)):
magmom = lines[j].split()[-1].rstrip(')')
magmoms.append(float(magmom))
try:
ii = lines.index('forces in ev/ang:\n')
except ValueError:
f = None
else:
f, i = read_forces(lines, ii, atoms)
try:
parameters = {}
ii = index_startswith(lines, 'vdw correction:')
except ValueError:
name = 'gpaw'
else:
name = lines[ii - 1].strip()
# save uncorrected values
parameters.update({
'calculator': 'gpaw',
'uncorrected_energy': e,
})
line = lines[ii + 1]
assert line.startswith('energy:')
e = float(line.split()[-1])
f, i = read_forces(lines, ii + 3, atoms)
if len(images) > 0 and e is None:
break
if q is not None and len(atoms) > 0:
n = len(atoms)
atoms.set_initial_charges([q / n] * n)
if magmoms:
atoms.set_initial_magnetic_moments(magmoms)
else:
magmoms = None
if e is not None or f is not None:
calc = SinglePointDFTCalculator(atoms, energy=e, forces=f,
dipole=dipole, magmoms=magmoms,
efermi=eFermi,
bzkpts=bz_kpts, ibzkpts=ibz_kpts)
calc.name = name
calc.parameters = parameters
if energy_contributions is not None:
calc.energy_contributions = energy_contributions
if kpts is not None:
calc.kpts = kpts
atoms.calc = calc
images.append(atoms)
if len(images) == 0:
raise IOError('Corrupted GPAW-text file!')
return images[index]
def read_koopmans_ham_out(fileobj):
"""Reads Koopmans Ham output files.
Will probably raise errors for broken or incomplete files.
Parameters
----------
fileobj : file|str
A file like object or filename
Yields
------
structure : Atoms
The next structure. The Atoms has a SinglePointCalculator attached with any results parsed from the file.
"""
if isinstance(fileobj, basestring):
fileobj = open(fileobj, 'rU')
# work with a copy in memory for faster random access
flines = fileobj.readlines()
# For the moment, provide an empty atoms object
structure = Atoms()
# Extract calculation results
job_done = False
walltime = None
kpts = []
eigenvalues = []
ks_eigenvalues_on_grid = []
ki_eigenvalues_on_grid = []
for i_line, line in enumerate(flines):
if 'KC interpolated eigenvalues at k=' in line:
kpts.append([float(x) for x in line.split()[-3:]])
eigenvalues.append([])
j_line = i_line + 2
while True:
line2 = flines[j_line].strip()
if len(line2) == 0:
break
eigenvalues[-1] += [float(x) for x in line2.split()]
j_line += 1
if 'INFO: KI[2nd] HAMILTONIAN CALCULATION ik=' in line:
ks_eigenvalues_on_grid.append([])
ki_eigenvalues_on_grid.append([])
if line.startswith(' KS '):
ks_eigenvalues_on_grid[-1] += safe_string_to_list_of_floats(
line.replace('KS', ''))
if line.startswith(' KI '):
ki_eigenvalues_on_grid[-1] += safe_string_to_list_of_floats(
line.replace('KI', ''))
if 'JOB DONE' in line:
job_done = True
if 'KC_WANN :' in line:
time_str = line.split()[-2]
walltime = time_to_float(time_str)
# Put everything together
calc = SinglePointDFTCalculator(structure)
calc.results['job_done'] = job_done
calc.results['walltime'] = walltime
calc.results['eigenvalues'] = eigenvalues
calc.results['ks_eigenvalues_on_grid'] = ks_eigenvalues_on_grid
calc.results['ki_eigenvalues_on_grid'] = ki_eigenvalues_on_grid
structure.calc = calc
yield structure
def xml2atoms(xml_elem):
# symbols = [el.items()[0][1] for el in xml_elem.find('atomic_species').findall('species')]
#
# nat = int(xml_elem.find('atomic_structure').items()[0][1])
# alat = float(xml_elem.find('atomic_structure').items()[1][1])
atoms = []
for item in xml_elem.find('atomic_structure').find(
'atomic_positions').findall('atom'):
coords = np.array(item.text.split(), dtype=np.float) * units['Bohr']
atom = Atom(symbol=item.items()[0][1], position=coords)
atoms.append(atom)
a1 = np.array(
xml_elem.find('atomic_structure').find('cell').find('a1').text.split(),
dtype=np.float)
a2 = np.array(
xml_elem.find('atomic_structure').find('cell').find('a2').text.split(),
dtype=np.float)
a3 = np.array(
xml_elem.find('atomic_structure').find('cell').find('a3').text.split(),
dtype=np.float)
cell = np.array([a1, a2, a3]) * units['Bohr']
atoms = Atoms(atoms, cell=cell, pbc=True)
# ------------------------------------------------------------------------------------------
# Extract calculation results
# Energy
energy = 2 * float(
xml_elem.find('total_energy').find('etot').text) * units['Ry']
# Forces
forces = []
if xml_elem.find('forces') is not None:
for item in xml_elem.find('forces').text.strip().split('\n'):
forces.append(np.fromstring(item.strip(), sep=' ', dtype=np.float))
forces = np.array(forces) * units['Ry'] / units['Bohr']
# Stress
stress = None
# Magmoms
magmoms = None
# Fermi level / highest occupied level
efermi = None
if xml_elem.find('band_structure') is not None:
efermi = 2 * float(
xml_elem.find('band_structure').find(
'fermi_energy').text) * units['Ry']
# # K-points
ibzkpts = None
# weights = None
# kpoints_warning = "Number of k-points >= 100: " + \
# "set verbosity='high' to print them."
#
# for kpts_index in indexes[_PW_KPTS]:
# nkpts = int(pwo_lines[kpts_index].split()[4])
# kpts_index += 2
#
# if pwo_lines[kpts_index].strip() == kpoints_warning:
# continue
#
# # QE prints the k-points in units of 2*pi/alat
# # with alat defined as the length of the first
# # cell vector
# cell = structure.get_cell()
# alat = np.linalg.norm(cell[0])
# ibzkpts = []
# weights = []
# for i in range(nkpts):
# L = pwo_lines[kpts_index + i].split()
# weights.append(float(L[-1]))
# coord = np.array([L[-6], L[-5], L[-4].strip('),')],
# dtype=float)
# coord *= 2 * np.pi / alat
# coord = kpoint_convert(cell, ckpts_kv=coord)
# ibzkpts.append(coord)
# ibzkpts = np.array(ibzkpts)
# weights = np.array(weights)
#
# # Bands
# kpts = None
# kpoints_warning = "Number of k-points >= 100: " + \
# "set verbosity='high' to print the bands."
#
# for bands_index in indexes[_PW_BANDS] + indexes[_PW_BANDSTRUCTURE]:
# if image_index < bands_index < next_index:
# bands_index += 2
#
# if pwo_lines[bands_index].strip() == kpoints_warning:
# continue
#
# assert ibzkpts is not None
# spin, bands, eigenvalues = 0, [], [[], []]
#
# while True:
# L = pwo_lines[bands_index].replace('-', ' -').split()
# if len(L) == 0:
# if len(bands) > 0:
# eigenvalues[spin].append(bands)
# bands = []
# elif L == ['occupation', 'numbers']:
# # Skip the lines with the occupation numbers
# bands_index += len(eigenvalues[spin][0]) // 8 + 1
# elif L[0] == 'k' and L[1].startswith('='):
# pass
# elif 'SPIN' in L:
# if 'DOWN' in L:
# spin += 1
# else:
# try:
# bands.extend(map(float, L))
# except ValueError:
# break
# bands_index += 1
#
# if spin == 1:
# assert len(eigenvalues[0]) == len(eigenvalues[1])
# assert len(eigenvalues[0]) == len(ibzkpts), \
# (np.shape(eigenvalues), len(ibzkpts))
#
# kpts = []
# for s in range(spin + 1):
# for w, k, e in zip(weights, ibzkpts, eigenvalues[s]):
# kpt = SinglePointKPoint(w, s, k, eps_n=e)
# kpts.append(kpt)
# ------------------------------------------------------------------------------------------
calc = SinglePointDFTCalculator(atoms,
energy=energy,
forces=forces,
stress=stress,
magmoms=magmoms,
efermi=efermi,
ibzkpts=ibzkpts)
# calc.kpts = kpts
atoms.calc = calc
input_parameters = {}
input_parameters['ecut'] = None
if xml_elem.find('basis_set') is not None:
input_parameters['ecut'] = 2 * float(
xml_elem.find('basis_set').find('ecutwfc').text)
input_parameters['input_dft'] = None
if xml_elem.find('dft') is not None:
input_parameters['input_dft'] = xml_elem.find('dft').find(
'functional').text.lower()
input_parameters['k_points'] = None
if xml_elem.find('band_structure') is not None:
k_points = xml_elem.find('band_structure').find(
'starting_k_points').find('monkhorst_pack').items()
k_points = [int(item[1]) for item in k_points]
input_parameters['k_points'] = k_points
input_parameters['fft_grid'] = None
if xml_elem.find('basis_set') is not None:
fft_points = xml_elem.find('basis_set').find('fft_grid').items()
fft_points = [int(item[1]) for item in fft_points]
input_parameters['fft_grid'] = fft_points
return atoms, input_parameters
def read_gpaw_out(fileobj, index):
notfound = []
def index_startswith(lines, string):
if not isinstance(string, basestring):
# assume it's a list
for entry in string:
try:
return index_startswith(lines, entry)
except ValueError:
pass
raise ValueError
if string in notfound:
raise ValueError
for i, line in enumerate(lines):
if line.startswith(string):
return i
notfound.append(string)
raise ValueError
def index_pattern(lines, pattern):
repat = re.compile(pattern)
if pattern in notfound:
raise ValueError
for i, line in enumerate(lines):
if repat.match(line):
return i
notfound.append(pattern)
raise ValueError
def read_forces(lines, ii):
f = []
for i in range(ii + 1, ii + 1 + len(atoms)):
try:
x, y, z = lines[i].split()[-3:]
f.append((float(x), float(y), float(z)))
except (ValueError, IndexError) as m:
raise IOError('Malformed GPAW log file: %s' % m)
return f, i
lines = [line.lower() for line in fileobj.readlines()]
images = []
while True:
try:
i = lines.index('unit cell:\n')
except ValueError:
pass
else:
if lines[i + 2].startswith(' -'):
del lines[i + 2] # old format
cell = []
pbc = []
for line in lines[i + 2:i + 5]:
words = line.split()
if len(words) == 5: # old format
cell.append(float(words[2]))
pbc.append(words[1] == 'yes')
else: # new format with GUC
cell.append([float(word) for word in words[3:6]])
pbc.append(words[2] == 'yes')
try:
i = lines.index('positions:\n')
except ValueError:
break
symbols = []
positions = []
for line in lines[i + 1:]:
words = line.split()
if len(words) != 5:
break
n, symbol, x, y, z = words
symbols.append(symbol.split('.')[0].title())
positions.append([float(x), float(y), float(z)])
if len(symbols):
atoms = Atoms(symbols=symbols, positions=positions,
cell=cell, pbc=pbc)
else:
atoms = Atoms(cell=cell, pbc=pbc)
lines = lines[i + 5:]
try:
ii = index_startswith(lines, 'reference energy:')
Eref = float(lines[ii].split()[-1])
except ValueError:
Eref = None
try:
ii = index_pattern(lines, '\d+ k-point')
word = lines[ii].split()
kx = int(word[2])
ky = int(word[4])
kz = int(word[6])
bz_kpts = (kx, ky, kz)
ibz_kpts = int(lines[ii + 1].split()[0])
except (ValueError, TypeError, IndexError):
bz_kpts = None
ibz_kpts = None
try:
i = index_startswith(lines, 'energy contributions relative to')
except ValueError:
e = None
else:
line = lines[i + 10]
assert (line.startswith('zero kelvin:') or
line.startswith('extrapolated:'))
e = float(line.split()[-1])
try:
ii = index_pattern(lines, '(fixed )?fermi level(s)?:')
except ValueError:
eFermi = None
else:
fields = lines[ii].split()
try:
def strip(string):
for rubbish in '[],':
string = string.replace(rubbish, '')
return string
eFermi = [float(strip(fields[-2])),
float(strip(fields[-1]))]
except ValueError:
eFermi = float(fields[-1])
# read Eigenvalues and occupations
ii1 = ii2 = 1e32
try:
ii1 = index_startswith(lines, ' band eigenvalues occupancy')
except ValueError:
pass
try:
ii2 = index_startswith(lines, ' band eigenvalues occupancy')
except ValueError:
pass
ii = min(ii1, ii2)
if ii == 1e32:
kpts = None
else:
ii += 1
words = lines[ii].split()
vals = []
while(len(words) > 2):
vals.append([float(w) for w in words])
ii += 1
words = lines[ii].split()
vals = np.array(vals).transpose()
kpts = [SinglePointKPoint(1, 0, 0)]
kpts[0].eps_n = vals[1]
kpts[0].f_n = vals[2]
if vals.shape[0] > 3:
kpts.append(SinglePointKPoint(1, 1, 0))
kpts[1].eps_n = vals[3]
kpts[1].f_n = vals[4]
# read charge
try:
ii = index_startswith(lines, 'total charge:')
except ValueError:
q = None
else:
q = float(lines[ii].split()[2])
# read dipole moment
try:
ii = index_startswith(lines, 'dipole moment:')
except ValueError:
dipole = None
else:
line = lines[ii]
for x in '()[],':
line = line.replace(x, '')
dipole = np.array([float(c) for c in line.split()[2:5]])
try:
ii = index_startswith(lines, 'local magnetic moments')
except ValueError:
magmoms = None
else:
magmoms = []
for j in range(ii + 1, ii + 1 + len(atoms)):
magmom = lines[j].split()[-1]
magmoms.append(float(magmom))
try:
ii = lines.index('forces in ev/ang:\n')
except ValueError:
f = None
else:
f, i = read_forces(lines, ii)
try:
ii = index_startswith(lines, 'vdw correction:')
except ValueError:
pass
else:
line = lines[ii + 1]
assert line.startswith('energy:')
e = float(line.split()[-1])
f, i = read_forces(lines, ii + 3)
if len(images) > 0 and e is None:
break
if q is not None and len(atoms) > 0:
n = len(atoms)
atoms.set_initial_charges([q / n] * n)
if magmoms is not None:
atoms.set_initial_magnetic_moments(magmoms)
if e is not None or f is not None:
calc = SinglePointDFTCalculator(atoms, energy=e, forces=f,
dipole=dipole, magmoms=magmoms,
efermi=eFermi,
bzkpts=bz_kpts, ibzkpts=ibz_kpts)
calc.eref = Eref
calc.name = 'gpaw'
if kpts is not None:
calc.kpts = kpts
atoms.set_calculator(calc)
images.append(atoms)
lines = lines[i:]
if len(images) == 0:
raise IOError('Corrupted GPAW-text file!')
return images[index]
def read(filename, index=None, format=None):
"""Read Atoms object(s) from file.
filename: str
Name of the file to read from.
index: int or slice
If the file contains several configurations, the last configuration
will be returned by default. Use index=n to get configuration
number n (counting from zero).
format: str
Used to specify the file-format. If not given, the
file-format will be guessed by the *filetype* function.
Known formats:
========================= =============
format short name
========================= =============
GPAW restart-file gpw
Dacapo netCDF output file dacapo
Old ASE netCDF trajectory nc
Virtual Nano Lab file vnl
ASE pickle trajectory traj
ASE bundle trajectory bundle
GPAW text output gpaw-text
CUBE file cube
XCrySDen Structure File xsf
Dacapo text output dacapo-text
XYZ-file xyz
VASP POSCAR/CONTCAR file vasp
VASP OUTCAR file vasp_out
SIESTA STRUCT file struct_out
ABINIT input file abinit
V_Sim ascii file v_sim
Protein Data Bank pdb
CIF-file cif
FHI-aims geometry file aims
FHI-aims output file aims_out
VTK XML Image Data vti
VTK XML Structured Grid vts
VTK XML Unstructured Grid vtu
TURBOMOLE coord file tmol
TURBOMOLE gradient file tmol-gradient
exciting input exi
AtomEye configuration cfg
WIEN2k structure file struct
DftbPlus input file dftb
CASTEP geom file cell
CASTEP output file castep
CASTEP trajectory file geom
ETSF format etsf.nc
DFTBPlus GEN format gen
CMR db/cmr-file db
CMR db/cmr-file cmr
LAMMPS dump file lammps
EON reactant.con file eon
Gromacs coordinates gro
Gaussian com (input) file gaussian
Gaussian output file gaussian_out
Quantum espresso in file esp_in
Quantum espresso out file esp_out
Extended XYZ file extxyz
NWChem input file nw
========================= =============
"""
if isinstance(filename,
str) and ('.json@' in filename or '.db@' in filename or
filename.startswith('pg://') and '@' in filename):
filename, index = filename.rsplit('@', 1)
if index.isdigit():
index = int(index)
else:
if isinstance(filename, str):
p = filename.rfind('@')
if p != -1:
try:
index = string2index(filename[p + 1:])
except ValueError:
pass
else:
filename = filename[:p]
if isinstance(index, str):
index = string2index(index)
if format is None:
format = filetype(filename)
if format.startswith('gpw'):
import gpaw
r = gpaw.io.open(filename, 'r')
positions = r.get('CartesianPositions') * Bohr
numbers = r.get('AtomicNumbers')
cell = r.get('UnitCell') * Bohr
pbc = r.get('BoundaryConditions')
tags = r.get('Tags')
magmoms = r.get('MagneticMoments')
energy = r.get('PotentialEnergy') * Hartree
if r.has_array('CartesianForces'):
forces = r.get('CartesianForces') * Hartree / Bohr
else:
forces = None
atoms = Atoms(positions=positions, numbers=numbers, cell=cell, pbc=pbc)
if tags.any():
atoms.set_tags(tags)
if magmoms.any():
atoms.set_initial_magnetic_moments(magmoms)
else:
magmoms = None
atoms.calc = SinglePointDFTCalculator(atoms,
energy=energy,
forces=forces,
magmoms=magmoms)
kpts = []
if r.has_array('IBZKPoints'):
for w, kpt, eps_n, f_n in zip(r.get('IBZKPointWeights'),
r.get('IBZKPoints'),
r.get('Eigenvalues'),
r.get('OccupationNumbers')):
kpts.append(
SinglePointKPoint(w, kpt[0], kpt[1], eps_n[0], f_n[0]))
atoms.calc.kpts = kpts
return atoms
if format in ['json', 'db', 'postgresql']:
from ase.db.core import connect, dict2atoms
if index == slice(None, None):
index = None
images = [
dict2atoms(d) for d in connect(filename, format).select(index)
]
if len(images) == 1:
return images[0]
else:
return images
if index is None:
index = -1
if format == 'castep':
from ase.io.castep import read_castep
return read_castep(filename, index)
if format == 'castep_cell':
import ase.io.castep
return ase.io.castep.read_cell(filename, index)
if format == 'castep_geom':
import ase.io.castep
return ase.io.castep.read_geom(filename, index)
if format == 'exi':
from ase.io.exciting import read_exciting
return read_exciting(filename, index)
if format in ['xyz', 'extxyz']:
from ase.io.extxyz import read_xyz
return read_xyz(filename, index)
if format == 'traj':
from ase.io.trajectory import read_trajectory
return read_trajectory(filename, index)
if format == 'bundle':
from ase.io.bundletrajectory import read_bundletrajectory
return read_bundletrajectory(filename, index)
if format == 'cube':
from ase.io.cube import read_cube
return read_cube(filename, index)
if format == 'nc':
from ase.io.netcdf import read_netcdf
return read_netcdf(filename, index)
if format == 'gpaw-text':
from ase.io.gpawtext import read_gpaw_text
return read_gpaw_text(filename, index)
if format == 'dacapo-text':
from ase.io.dacapo import read_dacapo_text
return read_dacapo_text(filename)
if format == 'dacapo':
from ase.io.dacapo import read_dacapo
return read_dacapo(filename)
if format == 'xsf':
from ase.io.xsf import read_xsf
return read_xsf(filename, index)
if format == 'vasp':
from ase.io.vasp import read_vasp
return read_vasp(filename)
if format == 'vasp_out':
from ase.io.vasp import read_vasp_out
return read_vasp_out(filename, index)
if format == 'abinit':
from ase.io.abinit import read_abinit
return read_abinit(filename)
if format == 'v_sim':
from ase.io.v_sim import read_v_sim
return read_v_sim(filename)
if format == 'mol':
from ase.io.mol import read_mol
return read_mol(filename)
if format == 'pdb':
from ase.io.pdb import read_pdb
return read_pdb(filename, index)
if format == 'cif':
from ase.io.cif import read_cif
return read_cif(filename, index)
if format == 'struct':
from ase.io.wien2k import read_struct
return read_struct(filename)
if format == 'struct_out':
from ase.io.siesta import read_struct
return read_struct(filename)
if format == 'vti':
from ase.io.vtkxml import read_vti
return read_vti(filename)
if format == 'vts':
from ase.io.vtkxml import read_vts
return read_vts(filename)
if format == 'vtu':
from ase.io.vtkxml import read_vtu
return read_vtu(filename)
if format == 'aims':
from ase.io.aims import read_aims
return read_aims(filename)
if format == 'aims_out':
from ase.io.aims import read_aims_output
return read_aims_output(filename, index)
if format == 'iwm':
from ase.io.iwm import read_iwm
return read_iwm(filename)
if format == 'Cmdft':
from ase.io.cmdft import read_I_info
return read_I_info(filename)
if format == 'tmol':
from ase.io.turbomole import read_turbomole
return read_turbomole(filename)
if format == 'tmol-gradient':
from ase.io.turbomole import read_turbomole_gradient
return read_turbomole_gradient(filename)
if format == 'cfg':
from ase.io.cfg import read_cfg
return read_cfg(filename)
if format == 'dftb':
from ase.io.dftb import read_dftb
return read_dftb(filename)
if format == 'sdf':
from ase.io.sdf import read_sdf
return read_sdf(filename)
if format == 'etsf':
from ase.io.etsf import ETSFReader
return ETSFReader(filename).read_atoms()
if format == 'gen':
from ase.io.gen import read_gen
return read_gen(filename)
if format == 'cmr':
from ase.io.cmr_io import read_db
return read_db(filename, index)
if format == 'lammps':
from ase.io.lammpsrun import read_lammps_dump
return read_lammps_dump(filename, index)
if format == 'eon':
from ase.io.eon import read_reactant_con
return read_reactant_con(filename)
if format == 'gromacs':
from ase.io.gromacs import read_gromacs
return read_gromacs(filename)
if format == 'gaussian':
from ase.io.gaussian import read_gaussian
return read_gaussian(filename)
if format == 'gaussian_out':
from ase.io.gaussian import read_gaussian_out
return read_gaussian_out(filename, index)
if format == 'esp_in':
from ase.io.espresso import read_espresso_in
return read_espresso_in(filename)
if format == 'esp_out':
from ase.io.espresso import read_espresso_out
return read_espresso_out(filename, index)
if format == 'nw':
from ase.io.nwchem import read_nwchem_input
return read_nwchem_input(filename)
raise RuntimeError('File format descriptor ' + format + ' not recognized!')
def calc_phonon(
calculator,
phonon,
acoustic_sum_rule=True,
rot_sum_rule=False,
r_cut=None,
F_0_correction=False,
verbose=False,
ase_calc=None,
cp_files=None,
subscript=None,
fc_calc=None,
):
"""
calc -- Specify calculator. One of these. [vasp, lmp, amp, amp_tf, amp_tf_bunch]
phonon -- Phonopy phonon object.
"""
# Check if structure is lower triangular cell
# for c in ((0,1), (0,2), (1,2)):
# if phonon._primitive.get_cell()[c[0],c[1]] != 0. and calculator == 'lmp':
# raise ValueError('Please provide lower triangular cell.')
import sys
if verbose:
np.set_printoptions(threshold=sys.maxsize)
if fc_calc == 'alm':
disp = phonon.get_displacements()
delta = np.linalg.norm(disp[0][0])
disp = np.concatenate([[np.zeros(disp.shape[1:])], disp], axis=0)
else:
delta = np.linalg.norm(phonon.get_displacements()[0][1:4])
disp = [[0, 0, 0, 0]] + phonon.get_displacements()
job_name = '{}-x{}{}{}_d{:5.3f}_sym{}'.format(
calculator,
*np.diag(phonon.get_supercell_matrix()),
delta,
phonon._is_symmetry,
)
if subscript is not None:
job_name += '_s' + str(subscript)
# Define names
npy_name = '{}-fc2-forces.npy'.format(job_name)
if phonon._nac_params is not None:
nac = True
else:
nac = False
pckl_name = '{}-RSR{}-rcut{}-NAC{}-fc2.bin'.format(job_name, rot_sum_rule,
r_cut, nac)
calc_dir = './calcs/{}'.format(job_name)
# Environment preset
call(['rm -rf ' + calc_dir + '/poscars'], shell=True)
call(['mkdir -p ' + calc_dir + '/poscars'], shell=True)
call(['cp SPOSCAR POSCAR-000'], shell=True)
call(['mv POSCAR-* SPOSCAR ' + calc_dir + '/poscars/'], shell=True)
# Load saved pickle file
print('')
try:
forces = np.load(npy_name)
if forces is None:
raise ValueError(' Error:: npy file is not containing forces info')
except:
print(
'<< CAUTION >> Fail to load npy file. << CAUTION >>'
.center(120))
print(('<< CAUTION >>' + ':: Expected file name ::'.center(43) +
'<< CAUTION >>').center(120))
print(('<< CAUTION >>' + npy_name.center(43) +
'<< CAUTION >>').center(120))
do_calc = True
else:
print('>>>>>>> Pickle file "{}" has been loaded. <<<<<<<<'.format(
npy_name).center(120))
do_calc = False
print('')
if do_calc:
if calculator == 'vasp':
calc = calc_vasp
elif calculator == 'lmp':
calc = calc_lmp
elif calculator == 'ase_calc':
calc = calc_ase_calc
elif calculator == 'amp_tf':
calc = calc_amp_tf
elif calculator == 'amp_tf_bunch':
calc = calc_amp_tf_bunch
else:
raise ValueError(
'Unknown calculator ({}) has been provided.'.format(
calculator))
print(">>>>>>> {} calculation will be carried out. <<<<<<<<".format(
calculator).center(120))
forces = calc(phonon, disp, calc_dir, F_0_correction, ase_calc,
cp_files)
np.save(npy_name, forces)
if verbose:
print('\n\n' + 'forces' + '\n' + str(forces))
phonon.set_forces(forces)
# Produce fc
phonon.produce_force_constants(fc_calculator=fc_calc)
if acoustic_sum_rule:
phonon.symmetrize_force_constants()
if r_cut:
if rot_sum_rule:
#
from ase.io import read
from ase.calculators.singlepoint import SinglePointDFTCalculator
sposcar = read(calc_dir + '/poscars/SPOSCAR')
supers = []
for i in range(len(forces)):
supers.append(sposcar.copy())
displacements = np.zeros(sposcar.get_positions().shape,
dtype=float)
displacements[disp[i + 1][0]] += disp[i + 1][1:]
supers[-1].new_array(
'displacements',
displacements,
)
supers[-1]._calc = SinglePointDFTCalculator(supers[-1])
supers[-1]._calc.results['forces'] = forces[i]
# rotational sum rule
from hiphive import ForceConstants, ClusterSpace, StructureContainer
cs = ClusterSpace(sposcar, [r_cut])
sc = StructureContainer(cs)
for s in supers:
sc.add_structure(s)
from hiphive.fitting import Optimizer
opt = Optimizer(sc.get_fit_data(), train_size=1.0)
opt.train()
print(opt)
parameters = opt.parameters
from hiphive import ForceConstantPotential, enforce_rotational_sum_rules
parameters_rot = enforce_rotational_sum_rules(
cs, parameters, ['Huang', 'Born-Huang'])
fcp_rot = ForceConstantPotential(cs, parameters_rot)
fcs = fcp_rot.get_force_constants(sposcar).get_fc_array(order=2)
phonon.set_force_constants(fcs)
else:
phonon.set_force_constants_zero_with_radius(r_cut)
if verbose:
print('\n\ndisplacement_dataset =>\n\n')
print(phonon.get_displacement_dataset())
print('\n\nforce_constants =>\n\n')
print(phonon.get_force_constants())
import pickle as pckl
pckl.dump(phonon, open(pckl_name, 'wb'), protocol=2)
return phonon
