def _initialize(self):
"""Updates PWBase to reflect self.parameters and atoms to be ready for a run
"""
self._pw = PWBase()
# Setup Unit Cell
cell = self.atoms.cell
self._pw.system.add_keypair(('ibrav', 0))
self._pw.cell_parameters.add_lattice_vec(cell[0], cell[1], cell[2], option='angstrom')
# Setup Atom Positions
self._pw.system.add_keypair(('nat', len(self.atoms)))
for atom in self.atoms:
self._pw.atomic_positions.add_atom_position(atom.symbol, atom.position, option='angstrom')
# Setup Atom Psuedo Potentials
from itertools import groupby
for symbol, atoms in groupby(self.atoms, lambda atom: atom.symbol):
pseudo_file = self.parameters['pseudo'].get(symbol)
if pseudo_file:
self._pw.atomic_species.add_atom_type(symbol, list(atoms)[0].mass, pseudo_file)
else:
error_str = "Must provide pseudo potential for all atom types {0}"
raise Exception(error_str.format(symbol))
self._pw.system.add_keypair(('ntyp', len(self._pw.atomic_species.atoms)))
# Set User Input Parameters [easy ones first, hard last]
if self.parameters.get('calculation'):
self._pw.control.add_keypair(('calculation', self.parameters.get('calculation')))
if self.parameters.get('ecutwfc'):
self._pw.system.add_keypair(('ecutwfc', self.parameters['ecutwfc'] / Ry))
if self.parameters.get('nbands'):
self._pw.system.add_keypair(('nbnd', self.parameters['nbands']))
if self.parameters.get('usesymm'):
self._pw.system.add_keypair(('nosym', not self.parameters['usesymm']))
if self.parameters.get('maxiter'):
self._pw.electrons.add_keypair(('electron_maxstep', self.parameters['maxiter']))
if self.parameters.get('prefix'):
self._pw.control.add_keypair(('prefix', self.parameters['prefix']))
if self.parameters.get('outdir'):
self._pw.control.add_keypair(('outdir', self.parameters['outdir']))
if self.parameters.get('pseudo_dir'):
self._pw.control.add_keypair(('pseudo_dir', self.parameters['pseudo_dir']))
if self.parameters.get('occupations'):
self._pw.system.add_keypair(('occupations', self.parameters['occupations']))
if self.parameters.get('input_dft'):
self._pw.system.add_keypair(('input_dft', self.parameters['input_dft']))
if self.parameters.get('fft_mesh'):
fft_mesh = self.parameters['fft_mesh']
if len(fft_mesh) == 3 and isinstance(fft_mesh[0], int):
self._pw.system.add_keypairs({'nr1': fft_mesh[0],
'nr2': fft_mesh[1],
'nr3': fft_mesh[2]})
else:
error_str = 'FFT MESH = [nr1, nr2, nr3] each is integer'
raise Exception(error_str)
if self.parameters.get('convergence'):
conv = self.parameters['convergence']
if isinstance(conv, dict):
if conv.get('energy'):
self._pw.electrons.add_keypair(('conv_thr', conv['energy']))
else:
raise Exception('Only energy convergence implemented currently')
else:
raise Exception("Unknown convergence format declared (dict required)")
if self.parameters.get('kpts') is not None:
kpts = self.parameters['kpts']
if isinstance(kpts, dict):
if kpts.get('density'):
from ase.calculator.calculator import kptdensity2monkhorstpack
self._pw.k_points.from_list(kptdensity2monkhorstpack(
kpts['density'], kpts.get('even', False)))
elif kpts.get('size'):
self._pw.k_points.from_monkhorst_pack(
kpts['size'], kpts.get('offset', [0, 0, 0]))
else:
raise Exception("Unknown kpts format declared")
elif hasattr(kpts, "__iter__"):
self._pw.k_points.from_list(kpts)
else:
raise Exception("Unknown kpts format declared")
# Add all PWBase initializer keypairs [READ VALUES TO NOT SET]
if self.parameters.get('keypairs'):
self._pw.add_keypairs_to_namelist(self.parameters['keypairs'])
# Always calculate stress and strain
self._pw.control.add_keypairs({
'tstress': True,
'tprnfor': True})
self._pw.validate()
class QE(Calculator):
"""Quantum Espresso ASE Calculator
"""
implemented_properties = ['energy', 'forces', 'stress',
'ibz_kpoint_eigenvalues', 'ibz_kpoints_position', 'ibz_kpoints_weight',
'nspins', 'nbands', 'xc_functional', 'fermi_energy', 'dos']
default_parameters = {
'calculation': 'scf',
'convergence': {'energy': 1E-6}
}
def __init__(self, restart=None, ignore_bad_restart_file=False, label=None,
atoms=None, **kwargs):
"""Accepted Keypairs
calculation:
str - only scf[default] supported at the moment
ecutwfc:
plane wave cuttoff [eV] notice not in Ry!
nbands:
number of bands for calculation (see pw.x -> nbnd)
usesymm:
whether or not to use symmetry in calculation (True/False)
maxiter:
maximum number of iterations in an scf step
convergence:
{'energy', <value>} - only one implemented
kpts:
(1, 1, 1) - gamma point
(n1, n2, n3) - Morstead Packing
[[k1, k2, k3] ... ] - List of kpoints
prefix: (self.label is meaningless at moment)
str - string to append to output files
pseudo:
{'atom symbol': 'name of pseudo potential', ...} - dictionary of pseudo per atom
outdir:
str - relative or absolute path to output directory.
Will create it if it does not exist.
pseudo_dir:
str - relative or absolute path to pseudo directory.
occupations:
str - 'smearing', 'tetrahedra', 'fixed', 'from_input'
input_dft:
str - functional to use
fft_mesh:
[nr1, nr2, nr3] - fft mesh to use for calculation
keypairs:
way to initialize via the base class PWBase.
(DO NOT SET CELL OR ATOM POSITIONS via PWBase this is done
automagically via ASE Atoms)
debug:
if True will print input and output QE files
AUTOMATICALLY SET KEYPAIRS:
Set so we can always extract stress and forces:
control.tstress=True
control.tprnfor=True
From atoms object:
CARD 'CELL PARAMETERS (angstroms)' from atoms.cell
CARD 'ATOMIC POSITIONS (angstroms)' from atoms[i]
system.nat from number of unique atoms in atoms[i]
system.ntyp from len(atoms)
Thus DO NOT SET:
A, B, C, cosAB, cosBC, cosAC, celldm(1-6)
or any of these previously mentioned. Be smart
"""
Calculator.__init__(self, restart, ignore_bad_restart_file, label, atoms, **kwargs)
self._pw = None
def set(self, **kwargs):
"""Sets parameters list and determines if calculation needs to be reset
*for now it is reset if any parameters change*
"""
# Read parameters from file
if 'parameters' in kwargs:
filename = kwargs.pop('parameters')
parameters = Parameters.read(filename)
parameters.update(kwargs)
kwargs = parameters
changed_parameters = {}
for key, value in kwargs.items():
oldvalue = self.parameters.get(key)
if key not in self.parameters or not equal(value, oldvalue):
changed_parameters[key] = value
self.parameters[key] = value
if changed_parameters:
self.reset()
return changed_parameters
def reset(self):
"""Clear all information from old calculation."""
self.results = {}
def set_atoms(self, atoms):
self.atoms = atoms.copy()
def _initialize(self):
"""Updates PWBase to reflect self.parameters and atoms to be ready for a run
"""
self._pw = PWBase()
# Setup Unit Cell
cell = self.atoms.cell
self._pw.system.add_keypair(('ibrav', 0))
self._pw.cell_parameters.add_lattice_vec(cell[0], cell[1], cell[2], option='angstrom')
# Setup Atom Positions
self._pw.system.add_keypair(('nat', len(self.atoms)))
for atom in self.atoms:
self._pw.atomic_positions.add_atom_position(atom.symbol, atom.position, option='angstrom')
# Setup Atom Psuedo Potentials
from itertools import groupby
for symbol, atoms in groupby(self.atoms, lambda atom: atom.symbol):
pseudo_file = self.parameters['pseudo'].get(symbol)
if pseudo_file:
self._pw.atomic_species.add_atom_type(symbol, list(atoms)[0].mass, pseudo_file)
else:
error_str = "Must provide pseudo potential for all atom types {0}"
raise Exception(error_str.format(symbol))
self._pw.system.add_keypair(('ntyp', len(self._pw.atomic_species.atoms)))
# Set User Input Parameters [easy ones first, hard last]
if self.parameters.get('calculation'):
self._pw.control.add_keypair(('calculation', self.parameters.get('calculation')))
if self.parameters.get('ecutwfc'):
self._pw.system.add_keypair(('ecutwfc', self.parameters['ecutwfc'] / Ry))
if self.parameters.get('nbands'):
self._pw.system.add_keypair(('nbnd', self.parameters['nbands']))
if self.parameters.get('usesymm'):
self._pw.system.add_keypair(('nosym', not self.parameters['usesymm']))
if self.parameters.get('maxiter'):
self._pw.electrons.add_keypair(('electron_maxstep', self.parameters['maxiter']))
if self.parameters.get('prefix'):
self._pw.control.add_keypair(('prefix', self.parameters['prefix']))
if self.parameters.get('outdir'):
self._pw.control.add_keypair(('outdir', self.parameters['outdir']))
if self.parameters.get('pseudo_dir'):
self._pw.control.add_keypair(('pseudo_dir', self.parameters['pseudo_dir']))
if self.parameters.get('occupations'):
self._pw.system.add_keypair(('occupations', self.parameters['occupations']))
if self.parameters.get('input_dft'):
self._pw.system.add_keypair(('input_dft', self.parameters['input_dft']))
if self.parameters.get('fft_mesh'):
fft_mesh = self.parameters['fft_mesh']
if len(fft_mesh) == 3 and isinstance(fft_mesh[0], int):
self._pw.system.add_keypairs({'nr1': fft_mesh[0],
'nr2': fft_mesh[1],
'nr3': fft_mesh[2]})
else:
error_str = 'FFT MESH = [nr1, nr2, nr3] each is integer'
raise Exception(error_str)
if self.parameters.get('convergence'):
conv = self.parameters['convergence']
if isinstance(conv, dict):
if conv.get('energy'):
self._pw.electrons.add_keypair(('conv_thr', conv['energy']))
else:
raise Exception('Only energy convergence implemented currently')
else:
raise Exception("Unknown convergence format declared (dict required)")
if self.parameters.get('kpts') is not None:
kpts = self.parameters['kpts']
if isinstance(kpts, dict):
if kpts.get('density'):
from ase.calculator.calculator import kptdensity2monkhorstpack
self._pw.k_points.from_list(kptdensity2monkhorstpack(
kpts['density'], kpts.get('even', False)))
elif kpts.get('size'):
self._pw.k_points.from_monkhorst_pack(
kpts['size'], kpts.get('offset', [0, 0, 0]))
else:
raise Exception("Unknown kpts format declared")
elif hasattr(kpts, "__iter__"):
self._pw.k_points.from_list(kpts)
else:
raise Exception("Unknown kpts format declared")
# Add all PWBase initializer keypairs [READ VALUES TO NOT SET]
if self.parameters.get('keypairs'):
self._pw.add_keypairs_to_namelist(self.parameters['keypairs'])
# Always calculate stress and strain
self._pw.control.add_keypairs({
'tstress': True,
'tprnfor': True})
self._pw.validate()
def _calculate(self, property_name):
"""Preforms calculation.
"""
if self.parameters.get('debug'):
return self._pw.run(infile="in", outfile="out", errfile="err")
return self._pw.run()
def _calculation_required(self, atoms, property_name):
# TODO need to do better check on results (using cached idea)
if self.results == {}:
return True
if self.atoms and atoms:
system_changes = self.check_state(atoms)
if system_changes:
return True
return False
def _set_results(self, results):
# Extract Results from outfile and convert to appropriate units
# Updates from output file (some values may not be output!!)
if self.parameters.get('calculation') != "bands":
energy = results['calculation']['total energy'] * Ry
forces = np.array([_[2] for _ in results['calculation']['forces']]) * Ry / Bohr
stress = np.array(results['calculation']['stress']) * Ry / (Bohr**3)
# xx, yy, zz, yz, xz, xy
stress = np.array([stress[0, 0], stress[1, 1], stress[2, 2],
stress[1, 2], stress[0, 2], stress[0, 1]])
self.results.update(
{'energy': energy,
'forces': forces,
'stress': stress})
# Update from data file (guarenteed to be in output)
fermi_energy = results['data-file']['band-structure-info']['fermi-energy'] * Hartree
for kpt in results['data-file']['kpoints']:
kpt['eigenvalues'] = np.array(kpt['eigenvalues']) * Hartree
self.results.update(
{'fermi-energy': fermi_energy,
'xc-functional': results['data-file']['exchange-correlation'],
'nspins': results['data-file']['band-structure-info']['number spin-components'],
'nbands': results['data-file']['band-structure-info']['number bands'],
'charge-density': results['data-file']['charge-density'],
'ibz-kpoints': results['data-file']['kpoints']})
@calculation("energy")
def get_potential_energy(self, atoms=None):
return self.results['energy']
@calculation("forces")
def get_forces(self, atoms=None):
return self.results['forces']
@calculation("stress")
def get_stress(self, atoms=None):
return self.results['stress']
@calculation("ibz_kpoint_eigenvalues")
def get_eigenvalues(self, atoms=None, kpt=0, spin=0):
if spin == 1:
raise Exception("Spin systems not implemented yet!")
return self.results['ibz-kpoints'][kpt]['eigenvalues']
@calculation("ibz_kpoints_position")
def get_ibz_k_points(self, atoms=None):
return np.array([kpoint['coordinate'] for kpoint in self.results['ibz-kpoints']])
@calculation("ibz_kpoints_weight")
def get_k_point_weights(self, atoms=None):
return np.array([kpoint['weight'] for kpoint in self.results['ibz-kpoints']])
@calculation("nspins")
def get_number_of_spins(self, atoms=None):
return self.results['nspins']
@calculation("nbands")
def get_number_of_bands(self, atoms=None):
return self.results['nbands']
@calculation("xc_functional")
def get_xc_functional(self, atoms=None):
return self.results['xc_functional']
@calculation("fermi_energy")
def get_fermi_level(self, atoms=None):
return self.results['fermi-energy']
@calculation("pseudo_density")
def get_pseudo_density(self, atoms=None, spin=None, pad=True):
if spin != None:
raise Exception("Spin systems not implemented yet!")
return self.results['charge-density']
@calculation("dos")
def get_dos(self, atoms=None, spin=None, width=0.1, npts=201):
from ase.dft import DOS
dos = DOS(self, width=width, npts=npts)
return dos.get_energies(), dos.get_dos(spin)
'conv_thr': 1E-8,
}
}
atom_types = [
['Si', 28.086, 'Si.pz-vbc.UPF']
]
atom_positions = [
['Si', [0.0, 0.0, 0.0]],
['Si', [0.25, 0.25, 0.25]]
]
kpoints = (4, 4, 4)
# Create QE Run
qe = PWBase()
qe.add_keypairs_to_namelist(qe_namelist)
for symbol, mass, pseudo in atom_types:
qe.atomic_species.add_atom_type(symbol, mass, pseudo)
for symbol, position in atom_positions:
qe.atomic_positions.add_atom_position(symbol, position)
qe.k_points.from_monkhorst_pack([8, 8, 8], [0, 0, 0])
# Validate and Run quantum espresso
qe.validate()
results = qe.run()