Source code for ase.calculators.nwchem

"""This module defines an ASE interface to NWchem

http://www.nwchem-sw.org/
"""
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


[docs]class NWChem(FileIOCalculator): implemented_properties = ['energy', 'forces', 'stress', 'dipole'] command = 'nwchem PREFIX.nwi > PREFIX.nwo' accepts_bandpath_keyword = True def __init__(self, restart=None, ignore_bad_restart_file=False, 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 set(self, **kwargs): changed_parameters = FileIOCalculator.set(self, **kwargs) if changed_parameters: self.reset() 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)