def update(self, atoms):
from Dacapo import Dacapo
if self.calc is None:
if 'nbands' not in self.kwargs:
n = sum([valence[atom.symbol] for atom in atoms])
self.kwargs['nbands'] = int(n * 0.65) + 4
magmoms = atoms.get_initial_magnetic_moments()
if magmoms.any():
self.kwargs['spinpol'] = True
self.calc = Dacapo(**self.kwargs)
if self.stay_alive:
self.calc.StayAliveOn()
else:
self.calc.StayAliveOff()
if self.stress:
self.calc.CalculateStress()
for Z, path in self.pps:
self.calc.SetPseudoPotential(Z, path)
if self.loa is None:
from ASE import Atom, ListOfAtoms
numbers = atoms.get_atomic_numbers()
positions = atoms.get_positions()
magmoms = atoms.get_initial_magnetic_moments()
self.loa = ListOfAtoms([
Atom(Z=numbers[a], position=positions[a], magmom=magmoms[a])
for a in range(len(atoms))
],
cell=np2num(atoms.get_cell()),
periodic=tuple(atoms.get_pbc()))
self.loa.SetCalculator(self.calc)
else:
self.loa.SetCartesianPositions(np2num(atoms.get_positions()))
self.loa.SetUnitCell(np2num(atoms.get_cell()), fix=True)
def __init__(self, filename=None, stay_alive=False, stress=False,
**kwargs):
self.kwargs = kwargs
self.stay_alive = stay_alive
self.stress = stress
if filename is not None:
from Dacapo import Dacapo
self.loa = Dacapo.ReadAtoms(filename, **kwargs)
self.calc = self.loa.GetCalculator()
else:
self.loa = None
self.calc = None
self.pps = []
def restart(filename, **kwargs):
calc = Dacapo(filename, **kwargs)
atoms = calc.get_atoms()
return atoms, calc
class Dacapo:
def __init__(self,
filename=None,
stay_alive=False,
stress=False,
**kwargs):
self.kwargs = kwargs
self.stay_alive = stay_alive
self.stress = stress
if filename is not None:
from Dacapo import Dacapo
self.loa = Dacapo.ReadAtoms(filename, **kwargs)
self.calc = self.loa.GetCalculator()
else:
self.loa = None
self.calc = None
self.pps = []
def set_pp(self, Z, path):
self.pps.append((Z, path))
def set_txt(self, txt):
if self.calc is None:
self.kwargs['txtout'] = txt
else:
self.calc.SetTxtFile(txt)
def set_nc(self, nc):
if self.calc is None:
self.kwargs['out'] = nc
else:
self.calc.SetNetCDFFile(nc)
def update(self, atoms):
from Dacapo import Dacapo
if self.calc is None:
if 'nbands' not in self.kwargs:
n = sum([valence[atom.symbol] for atom in atoms])
self.kwargs['nbands'] = int(n * 0.65) + 4
magmoms = atoms.get_initial_magnetic_moments()
if magmoms.any():
self.kwargs['spinpol'] = True
self.calc = Dacapo(**self.kwargs)
if self.stay_alive:
self.calc.StayAliveOn()
else:
self.calc.StayAliveOff()
if self.stress:
self.calc.CalculateStress()
for Z, path in self.pps:
self.calc.SetPseudoPotential(Z, path)
if self.loa is None:
from ASE import Atom, ListOfAtoms
numbers = atoms.get_atomic_numbers()
positions = atoms.get_positions()
magmoms = atoms.get_initial_magnetic_moments()
self.loa = ListOfAtoms([
Atom(Z=numbers[a], position=positions[a], magmom=magmoms[a])
for a in range(len(atoms))
],
cell=np2num(atoms.get_cell()),
periodic=tuple(atoms.get_pbc()))
self.loa.SetCalculator(self.calc)
else:
self.loa.SetCartesianPositions(np2num(atoms.get_positions()))
self.loa.SetUnitCell(np2num(atoms.get_cell()), fix=True)
def get_atoms(self):
atoms = OldASEListOfAtomsWrapper(self.loa).copy()
atoms.set_calculator(self)
return atoms
def get_potential_energy(self, atoms):
self.update(atoms)
return self.calc.GetPotentialEnergy()
def get_forces(self, atoms):
self.update(atoms)
return np.array(self.calc.GetCartesianForces())
def get_stress(self, atoms):
self.update(atoms)
stress = np.array(self.calc.GetStress())
if stress.ndim == 2:
return stress.ravel()[[0, 4, 8, 5, 2, 1]]
else:
return stress
def calculation_required(self, atoms, quantities):
if self.calc is None:
return True
if atoms != self.get_atoms():
return True
return False
def get_number_of_bands(self):
return self.calc.GetNumberOfBands()
def get_k_point_weights(self):
return np.array(self.calc.GetIBZKPointWeights())
def get_number_of_spins(self):
return 1 + int(self.calc.GetSpinPolarized())
def get_eigenvalues(self, kpt=0, spin=0):
return np.array(self.calc.GetEigenvalues(kpt, spin))
def get_fermi_level(self):
return self.calc.GetFermiLevel()
def get_number_of_grid_points(self):
return np.array(self.get_pseudo_wave_function(0, 0, 0).shape)
def get_pseudo_density(self, spin=0):
return np.array(self.calc.GetDensityArray(s))
def get_pseudo_wave_function(self, band=0, kpt=0, spin=0, pad=True):
kpt_c = self.get_bz_k_points()[kpt]
state = self.calc.GetElectronicStates().GetState(band=band,
spin=spin,
kptindex=kpt)
# Get wf, without bloch phase (Phase = True doesn't do anything!)
wave = state.GetWavefunctionOnGrid(phase=False)
# Add bloch phase if this is not the Gamma point
if np.all(kpt_c == 0):
return wave
coord = state.GetCoordinates()
phase = coord[0] * kpt_c[0] + coord[1] * kpt_c[1] + coord[2] * kpt_c[2]
return np.array(wave) * np.exp(-2.j * np.pi * phase) # sign! XXX
#return np.array(self.calc.GetWaveFunctionArray(n, k, s)) # No phase!
def get_bz_k_points(self):
return np.array(self.calc.GetBZKPoints())
def get_ibz_k_points(self):
return np.array(self.calc.GetIBZKPoints())
def get_wannier_localization_matrix(self, nbands, dirG, kpoint, nextkpoint,
G_I, spin):
return np.array(
self.calc.GetWannierLocalizationMatrix(G_I=G_I.tolist(),
nbands=nbands,
dirG=dirG.tolist(),
kpoint=kpoint,
nextkpoint=nextkpoint,
spin=spin))
def initial_wannier(self, initialwannier, kpointgrid, fixedstates, edf,
spin):
# Use initial guess to determine U and C
init = self.calc.InitialWannier(initialwannier, self.atoms,
np2num(kpointgrid, num.Int))
states = self.calc.GetElectronicStates()
waves = [[
state.GetWaveFunction()
for state in states.GetStatesKPoint(k, spin)
] for k in self.calc.GetIBZKPoints()]
init.SetupMMatrix(waves, self.calc.GetBZKPoints())
c, U = init.GetListOfCoefficientsAndRotationMatrices(
(self.calc.GetNumberOfBands(), fixedstates, edf))
U = np.array(U)
for k in range(len(c)):
c[k] = np.array(c[k])
return c, U
def restart(filename, **kwargs):
calc = Dacapo(filename, **kwargs)
atoms = calc.get_atoms()
return atoms, calc