import os
import numpy as np
from copy import deepcopy
from ase.calculators.calculator import KPoints, kpts2kpts
_special_kws = ['center', 'autosym', 'autoz', 'theory', 'basis', 'xc', 'task',
'set', 'symmetry', 'label', 'geompar', 'basispar', 'kpts',
'bandpath', 'restart_kw']
_system_type = {1: 'polymer', 2: 'surface', 3: 'crystal'}
def _get_geom(atoms, **params):
geom_header = ['geometry units angstrom']
for geomkw in ['center', 'autosym', 'autoz']:
geom_header.append(geomkw if params.get(geomkw) else 'no' + geomkw)
if 'geompar' in params:
geom_header.append(params['geompar'])
geom = [' '.join(geom_header)]
outpos = atoms.get_positions()
pbc = atoms.pbc
if np.any(pbc):
scpos = atoms.get_scaled_positions()
for i, pbci in enumerate(pbc):
if pbci:
outpos[:, i] = scpos[:, i]
npbc = pbc.sum()
cellpars = atoms.cell.cellpar()
geom.append(' system {} units angstrom'.format(_system_type[npbc]))
if npbc == 3:
geom.append(' lattice_vectors')
for row in atoms.cell:
geom.append(' {:20.16e} {:20.16e} {:20.16e}'.format(*row))
else:
if pbc[0]:
geom.append(' lat_a {:20.16e}'.format(cellpars[0]))
if pbc[1]:
geom.append(' lat_b {:20.16e}'.format(cellpars[1]))
if pbc[2]:
geom.append(' lat_c {:20.16e}'.format(cellpars[2]))
if pbc[1] and pbc[2]:
geom.append(' alpha {:20.16e}'.format(cellpars[3]))
if pbc[0] and pbc[2]:
geom.append(' beta {:20.16e}'.format(cellpars[4]))
if pbc[1] and pbc[0]:
geom.append(' gamma {:20.16e}'.format(cellpars[5]))
geom.append(' end')
for i, atom in enumerate(atoms):
geom.append(' {:<2} {:20.16e} {:20.16e} {:20.16e}'
''.format(atom.symbol, *outpos[i]))
symm = params.get('symmetry')
if symm is not None:
geom.append(' symmetry {}'.format(symm))
geom.append('end')
return geom
def _get_basis(theory, **params):
if 'basis' not in params:
if theory in ['pspw', 'band', 'paw']:
return []
basis_in = params.get('basis', '3-21G')
if 'basispar' in params:
header = 'basis {} noprint'.format(params['basispar'])
else:
header = 'basis noprint'
basis_out = [header]
if isinstance(basis_in, str):
basis_out.append(' * library {}'.format(basis_in))
else:
for symbol, ibasis in basis_in.items():
basis_out.append('{:>4} library {}'.format(symbol, ibasis))
basis_out.append('end')
return basis_out
_special_keypairs = [('nwpw', 'simulation_cell'),
('nwpw', 'carr-parinello'),
('nwpw', 'brillouin_zone'),
('tddft', 'grad'),
]
def _format_brillouin_zone(array, name=None):
out = [' brillouin_zone']
if name is not None:
out += [' zone_name {}'.format(name)]
template = ' kvector' + ' {:20.16e}' * array.shape[1]
for row in array:
out.append(template.format(*row))
out.append(' end')
return out
def _get_bandpath(bp):
if bp is None:
return []
out = ['nwpw']
out += _format_brillouin_zone(bp.kpts, name=bp.path)
out += [' zone_structure_name {}'.format(bp.path),
'end',
'task band structure']
return out
def _format_line(key, val):
if val is None:
return key
if isinstance(val, bool):
return '{} .{}.'.format(key, str(val).lower())
else:
return ' '.join([key, str(val)])
def _format_block(key, val, nindent=0):
prefix = ' ' * nindent
prefix2 = ' ' * (nindent + 1)
if val is None:
return [prefix + key]
if not isinstance(val, dict):
return [prefix + _format_line(key, val)]
out = [prefix + key]
for subkey, subval in val.items():
if (key, subkey) in _special_keypairs:
if (key, subkey) == ('nwpw', 'brillouin_zone'):
out += _format_brillouin_zone(subval)
else:
out += _format_block(subkey, subval, nindent + 1)
else:
if isinstance(subval, dict):
subval = ' '.join([_format_line(a, b)
for a, b in subval.items()])
out.append(prefix2 + ' '.join([_format_line(subkey, subval)]))
out.append(prefix + 'end')
return out
def _get_other(**params):
out = []
for kw, block in params.items():
if kw in _special_kws:
continue
out += _format_block(kw, block)
return out
def _get_set(**params):
return ['set ' + _format_line(key, val) for key, val in params.items()]
_gto_theories = ['tce', 'ccsd', 'mp2', 'tddft', 'scf', 'dft']
_pw_theories = ['band', 'pspw', 'paw']
_all_theories = _gto_theories + _pw_theories
def _get_theory(**params):
# Default: user-provided theory
theory = params.get('theory')
if theory is not None:
return theory
# Check if the user passed a theory to xc
xc = params.get('xc')
if xc in _all_theories:
return xc
# Check for input blocks that correspond to a particular level of
# theory. Correlated theories (e.g. CCSD) are checked first.
for kw in _gto_theories:
if kw in params:
return kw
# If the user passed an 'nwpw' block, then they want a plane-wave
# calculation, but what kind? If they request k-points, then
# they want 'band', otherwise assume 'pspw' (if the user wants
# to use 'paw', they will have to ask for it specifically).
nwpw = params.get('nwpw')
if nwpw is not None:
if 'monkhorst-pack' in nwpw or 'brillouin_zone' in nwpw:
return 'band'
return 'pspw'
# When all else fails, default to dft.
return 'dft'
_xc_conv = dict(lda='slater pw91lda',
pbe='xpbe96 cpbe96',
revpbe='revpbe cpbe96',
rpbe='rpbe cpbe96',
pw91='xperdew91 perdew91',
)
def _update_mult(magmom_tot, **params):
theory = params['theory']
if magmom_tot == 0:
magmom_mult = 1
else:
magmom_mult = np.sign(magmom_tot) * (abs(magmom_tot) + 1)
if 'scf' in params:
for kw in ['nopen', 'singlet', 'doublet', 'triplet', 'quartet',
'quintet', 'sextet', 'septet', 'octet']:
if kw in params['scf']:
break
else:
params['scf']['nopen'] = magmom_tot
elif theory in ['scf', 'mp2', 'ccsd', 'tce']:
params['scf'] = dict(nopen=magmom_tot)
if 'dft' in params:
if 'mult' not in params['dft']:
params['dft']['mult'] = magmom_mult
elif theory in ['dft', 'tddft']:
params['dft'] = dict(mult=magmom_mult)
if 'nwpw' in params:
if 'mult' not in params['nwpw']:
params['nwpw']['mult'] = magmom_mult
elif theory in ['pspw', 'band', 'paw']:
params['nwpw'] = dict(mult=magmom_mult)
return params
def _get_kpts(atoms, **params):
"""Converts top-level 'kpts' argument to native keywords"""
kpts = params.get('kpts')
if kpts is None:
return params
nwpw = params.get('nwpw', dict())
if 'monkhorst-pack' in nwpw or 'brillouin_zone' in nwpw:
raise ValueError("Redundant k-points specified!")
if isinstance(kpts, KPoints):
nwpw['brillouin_zone'] = kpts.kpts
elif isinstance(kpts, dict):
if kpts.get('gamma', False) or 'size' not in kpts:
nwpw['brillouin_zone'] = kpts2kpts(kpts, atoms).kpts
else:
nwpw['monkhorst-pack'] = ' '.join(map(str, kpts['size']))
elif isinstance(kpts, np.ndarray):
nwpw['brillouin_zone'] = kpts
else:
nwpw['monkhorst-pack'] = ' '.join(map(str, kpts))
params['nwpw'] = nwpw
return params
[docs]def write_nwchem_in(fd, atoms, properties=None, echo=False, **params):
"""Writes NWChem input file.
Parameters
----------
fd
file descriptor
atoms
atomic configuration
properties
list of properties to compute; by default only the
calculation of the energy is requested
echo
if True include the `echo` keyword at the top of the file,
which causes the content of the input file to be included
in the output file
params
dict of instructions blocks to be included
"""
params = deepcopy(params)
if properties is None:
properties = ['energy']
if 'stress' in properties:
if 'set' not in params:
params['set'] = dict()
params['set']['includestress'] = True
task = params.get('task')
if task is None:
if 'stress' in properties or 'forces' in properties:
task = 'gradient'
else:
task = 'energy'
params = _get_kpts(atoms, **params)
theory = _get_theory(**params)
params['theory'] = theory
xc = params.get('xc')
if 'xc' in params:
xc = _xc_conv.get(params['xc'].lower(), params['xc'])
if theory in ['dft', 'tddft']:
if 'dft' not in params:
params['dft'] = dict()
params['dft']['xc'] = xc
elif theory in ['pspw', 'band', 'paw']:
if 'nwpw' not in params:
params['nwpw'] = dict()
params['nwpw']['xc'] = xc
magmom_tot = int(atoms.get_initial_magnetic_moments().sum())
params = _update_mult(magmom_tot, **params)
label = params.get('label', 'nwchem')
perm = os.path.abspath(params.pop('perm', label))
scratch = os.path.abspath(params.pop('scratch', label))
restart_kw = params.get('restart_kw', 'start')
if restart_kw not in ('start', 'restart'):
raise ValueError("Unrecognised restart keyword: {}!"
.format(restart_kw))
short_label = label.rsplit('/', 1)[-1]
if echo:
out = ['echo']
else:
out = []
out.extend(['title "{}"'.format(short_label),
'permanent_dir {}'.format(perm),
'scratch_dir {}'.format(scratch),
'{} {}'.format(restart_kw, short_label),
'\n'.join(_get_geom(atoms, **params)),
'\n'.join(_get_basis(**params)),
'\n'.join(_get_other(**params)),
'\n'.join(_get_set(**params.get('set', dict()))),
'task {} {}'.format(theory, task),
'\n'.join(_get_bandpath(params.get('bandpath', None)))])
fd.write('\n\n'.join(out))