def collect_errors(self, dens, ham, wfs):
"""Check convergence of eigenstates, energy and density."""
errors = {'eigenstates': wfs.eigensolver.error,
'density': dens.error,
'force': np.inf,
'energy': np.inf}
if dens.fixed:
errors['density'] = 0.0
if len(self.old_energies) >= 3:
errors['energy'] = np.ptp(self.old_energies[-3:])
if self.max_errors['force'] < np.inf:
F_av = calculate_forces(wfs, dens, ham)
if self.old_F_av is not None:
errors['force'] = ((F_av - self.old_F_av)**2).sum(1).max()**0.5
self.old_F_av = F_av
return errors
def calculate(self,
atoms=None,
properties=['energy'],
system_changes=['cell']):
"""Calculate things."""
Calculator.calculate(self, atoms)
atoms = self.atoms
if system_changes:
self.log('System changes:', ', '.join(system_changes), '\n')
if system_changes == ['positions']:
# Only positions have changed:
self.density.reset()
else:
# Drastic changes:
self.wfs = None
self.occupations = None
self.density = None
self.hamiltonian = None
self.scf = None
self.initialize(atoms)
self.set_positions(atoms)
if not self.initialized:
self.initialize(atoms)
self.set_positions(atoms)
if not (self.wfs.positions_set and self.hamiltonian.positions_set):
self.set_positions(atoms)
if not self.scf.converged:
print_cell(self.wfs.gd, self.atoms.pbc, self.log)
with self.timer('SCF-cycle'):
self.scf.run(self.wfs, self.hamiltonian, self.density,
self.occupations, self.log, self.call_observers)
self.log('\nConverged after {0} iterations.\n'.format(
self.scf.niter))
e_free = self.hamiltonian.e_total_free
e_extrapolated = self.hamiltonian.e_total_extrapolated
self.results['energy'] = e_extrapolated * Ha
self.results['free_energy'] = e_free * Ha
if not self.atoms.pbc.all():
dipole_v = self.density.calculate_dipole_moment() * Bohr
self.log(
'Dipole moment: ({0:.6f}, {1:.6f}, {2:.6f}) |e|*Ang\n'.
format(*dipole_v))
self.results['dipole'] = dipole_v
if self.wfs.nspins == 2:
magmom = self.occupations.magmom
magmom_a = self.density.estimate_magnetic_moments(total=magmom)
self.log('Total magnetic moment: %f' % magmom)
self.log('Local magnetic moments:')
symbols = self.atoms.get_chemical_symbols()
for a, mom in enumerate(magmom_a):
self.log('{0:4} {1:2} {2:.6f}'.format(a, symbols[a], mom))
self.log()
self.results['magmom'] = self.occupations.magmom
self.results['magmoms'] = magmom_a
self.summary()
self.call_observers(self.scf.niter, final=True)
if 'forces' in properties:
with self.timer('Forces'):
F_av = calculate_forces(self.wfs, self.density,
self.hamiltonian, self.log)
self.results['forces'] = F_av * (Ha / Bohr)
if 'stress' in properties:
with self.timer('Stress'):
try:
stress = calculate_stress(self).flat[[0, 4, 8, 5, 2, 1]]
except NotImplementedError:
# Our ASE Calculator base class will raise
# PropertyNotImplementedError for us.
pass
else:
self.results['stress'] = stress * (Ha / Bohr**3)
def run(formula='H2O', vacuum=1.5, cell=None, pbc=1, **morekwargs):
print(formula, parallel)
system = molecule(formula)
kwargs = dict(basekwargs)
kwargs.update(morekwargs)
calc = GPAW(**kwargs)
system.set_calculator(calc)
system.center(vacuum)
if cell is None:
system.center(vacuum)
else:
system.set_cell(cell)
system.set_pbc(pbc)
try:
system.get_potential_energy()
except KohnShamConvergenceError:
pass
E = calc.hamiltonian.e_total_free
F_av = calculate_forces(calc.wfs, calc.density,
calc.hamiltonian)
global Eref, Fref_av
if Eref is None:
Eref = E
Fref_av = F_av
eerr = abs(E - Eref)
ferr = abs(F_av - Fref_av).max()
if calc.wfs.world.rank == 0:
print('Energy', E)
print()
print('Forces')
print(F_av)
print()
print('Errs', eerr, ferr)
if eerr > tolerance or ferr > tolerance:
if calc.wfs.world.rank == 0:
stderr = sys.stderr
else:
stderr = devnull
if eerr > tolerance:
print('Failed!', file=stderr)
print('E = %f, Eref = %f' % (E, Eref), file=stderr)
msg = 'Energy err larger than tolerance: %f' % eerr
if ferr > tolerance:
print('Failed!', file=stderr)
print('Forces:', file=stderr)
print(F_av, file=stderr)
print(file=stderr)
print('Ref forces:', file=stderr)
print(Fref_av, file=stderr)
print(file=stderr)
msg = 'Force err larger than tolerance: %f' % ferr
print(file=stderr)
print('Args:', file=stderr)
print(formula, vacuum, cell, pbc, morekwargs, file=stderr)
print(parallel, file=stderr)
raise AssertionError(msg)
def get_forces(self):
return calculate_forces(self.calc.wfs,
self.calc.td_density.get_density(),
self.calc.td_hamiltonian.hamiltonian,
self.calc.log)