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"""This module defines an ASE interface to NWchem
https://nwchemgit.github.io
"""
import os
import numpy as np
from ase import io
from ase.units import Hartree
from ase.calculators.calculator import FileIOCalculator
from ase.spectrum.band_structure import BandStructure
class NWChem(FileIOCalculator):
implemented_properties = ['energy', 'forces', 'stress', 'dipole']
command = 'nwchem PREFIX.nwi > PREFIX.nwo'
accepts_bandpath_keyword = True
discard_results_on_any_change = True
def __init__(self, restart=None,
ignore_bad_restart_file=FileIOCalculator._deprecated,
label='nwchem', atoms=None, command=None, **kwargs):
"""
NWChem keywords are specified using (potentially nested)
dictionaries. Consider the following input file block:
>>> dft
>>> odft
>>> mult 2
>>> convergence energy 1e-9 density 1e-7 gradient 5e-6
>>> end
This can be generated by the NWChem calculator by using the
following settings:
>>> calc = NWChem(dft={'odft': None,
>>> 'mult': 2,
>>> 'convergence': {'energy': 1e-9,
>>> 'density': 1e-7,
>>> 'gradient': 5e-6,
>>> },
>>> },
>>> )
In addition, the calculator supports several special keywords:
theory: str
Which NWChem module should be used to calculate the
energies and forces. Supported values are ``'dft'``,
``'scf'``, ``'mp2'``, ``'ccsd'``, ``'tce'``, ``'tddft'``,
``'pspw'``, ``'band'``, and ``'paw'``. If not provided, the
calculator will attempt to guess which theory to use based
on the keywords provided by the user.
xc: str
The exchange-correlation functional to use. Only relevant
for DFT calculations.
task: str
What type of calculation is to be performed, e.g.
``'energy'``, ``'gradient'``, ``'optimize'``, etc. When
using ``'SocketIOCalculator'``, ``task`` should be set
to ``'optimize'``. In most other circumstances, ``task``
should not be set manually.
basis: str or dict
Which basis set to use for gaussian-type orbital
calculations. Set to a string to use the same basis for all
elements. To use a different basis for different elements,
provide a dict of the form:
>>> calc = NWChem(...,
>>> basis={'O': '3-21G',
>>> 'Si': '6-31g'})
basispar: str
Additional keywords to put in the NWChem ``basis`` block,
e.g. ``'rel'`` for relativistic bases.
symmetry: int or str
The point group (for gaussian-type orbital calculations) or
space group (for plane-wave calculations) of the system.
Supports both group names (e.g. ``'c2v'``, ``'Fm3m'``) and
numbers (e.g. ``225``).
autosym: bool
Whether NWChem should automatically determine the symmetry
of the structure (defaults to ``False``).
center: bool
Whether NWChem should automatically center the structure
(defaults to ``False``). Enable at your own risk.
autoz: bool
Whether NWChem should automatically construct a Z-matrix
for your molecular system (defaults to ``False``).
geompar: str
Additional keywords to put in the NWChem `geometry` block,
e.g. ``'nucleus finite'`` for gaussian-shaped nuclear
charges. Do not set ``'autosym'``, ``'center'``, or
``'autoz'`` in this way; instead, use the appropriate
keyword described above for these settings.
set: dict
Used to manually create or modify entries in the NWChem
rtdb. For example, the following settings enable
pseudopotential filtering for plane-wave calculations:
>>> set nwpw:kbpp_ray .true.
>>> set nwpw:kbpp_filter .true.
These settings are generated by the NWChem calculator by
passing the arguments:
>>> calc = NWChem(...,
>>> set={'nwpw:kbpp_ray': True,
>>> 'nwpw:kbpp_filter': True})
kpts: (int, int, int), or dict
Indicates which k-point mesh to use. Supported syntax is
similar to that of GPAW. Implies ``theory='band'``.
bandpath: BandPath object
The band path to use for a band structure calculation.
Implies ``theory='band'``.
"""
FileIOCalculator.__init__(self, restart, ignore_bad_restart_file,
label, atoms, command, **kwargs)
self.calc = None
def write_input(self, atoms, properties=None, system_changes=None):
FileIOCalculator.write_input(self, atoms, properties, system_changes)
# Prepare perm and scratch directories
perm = os.path.abspath(self.parameters.get('perm', self.label))
scratch = os.path.abspath(self.parameters.get('scratch', self.label))
os.makedirs(perm, exist_ok=True)
os.makedirs(scratch, exist_ok=True)
io.write(self.label + '.nwi', atoms, properties=properties,
label=self.label, **self.parameters)
def read_results(self):
output = io.read(self.label + '.nwo')
self.calc = output.calc
self.results = output.calc.results
def band_structure(self):
self.calculate()
perm = self.parameters.get('perm', self.label)
if self.calc.get_spin_polarized():
alpha = np.loadtxt(os.path.join(perm, self.label + '.alpha_band'))
beta = np.loadtxt(os.path.join(perm, self.label + '.beta_band'))
energies = np.array([alpha[:, 1:], beta[:, 1:]]) * Hartree
else:
data = np.loadtxt(os.path.join(perm,
self.label + '.restricted_band'))
energies = data[np.newaxis, :, 1:] * Hartree
eref = self.calc.get_fermi_level()
if eref is None:
eref = 0.
return BandStructure(self.parameters.bandpath, energies, eref)
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