def writeNEB(
self,
runfile,
neb,
kpts,
):
dictionary = self.__ase_calculator.parameters.copy()
dictionary.pop('pseudo_qualifier')
dictionary.pop('pseudo_path')
dictionary.pop('ignore_bad_restart_file')
dictionary.pop('label')
dictionary.pop('atoms')
dictionary['kpts'] = kpts
c_string = 'calculator = '
c_string += makeScript('Siesta', dictionary, detail_level=ALL) + '\n'
path = os.path.dirname(runfile)
n_images = len(neb.images)
filename = join(path, 'neb.traj')
write_traj(filename, neb.images)
script = """from CalcTroll.Programs.ASE.Trajectory import myread_traj, write_traj, Trajectory
from ase import io
from ase.neb import NEB
from ase.optimize import FIRE
from CalcTroll.Programs.ASESIESTA import SiestaCalculator as Siesta
"""
script += """calculator = %s""" % c_string + """
kwargs = calculator.parameters.copy()
images = []
for i in range(%d):""" % n_images + """
kwargs['label'] = 'siesta_%d' % i
calculator = Siesta(**kwargs)
image = myread_traj('neb.traj', i)
image.set_calculator(calculator)
image.get_total_energy()
images.append(image)
""" + """
k=0.5
neb = NEB(images, k=k, climb=False)
qn = FIRE(neb, trajectory='neb.traj')
qn.run(fmax=%.3f)
""" % self['force_tolerance']
with open(runfile, 'w') as f:
f.write(script)
def calculatorScript(
self,
atoms,
kpts,
min_iterations=True,
save_behaviour=None,
):
net_charge = 0
for doping in atoms.dopings():
net_charge += doping.charge()
c_string = 'calculator = '
dictionary = self.__ase_calculator.parameters.copy()
dictionary['fdf_arguments']['NetCharge'] = net_charge
dictionary.pop('pseudo_qualifier')
dictionary.pop('pseudo_path')
dictionary.pop('ignore_bad_restart_file')
dictionary.pop('label')
dictionary.pop('atoms')
if not min_iterations:
dictionary['fdf_arguments']['MinSCFIterations'] = 1
dictionary['kpts'] = kpts
c_string += makeScript('Siesta', dictionary, detail_level=API.ALL) + '\n'
return c_string
def writeRelaxation(self,
runfile,
atoms,
kpts,
relax_cell,
save_behaviour,
):
atoms = atoms.copy()
net_charge = 0
for doping in atoms.dopings():
net_charge += doping.charge()
# Remove electrodes to avoid transiesta relacation (for now).
atoms.purgeTags()
c_string = 'calculator = '
dictionary = self.__ase_calculator.parameters.copy()
dictionary['fdf_arguments']['NetCharge'] = net_charge
dictionary.pop('pseudo_qualifier')
dictionary.pop('pseudo_path')
dictionary.pop('ignore_bad_restart_file')
dictionary.pop('label')
dictionary.pop('atoms')
dictionary['kpts'] = kpts
c_string += makeScript('Siesta', dictionary, detail_level=API.ALL) + '\n'
path = os.path.dirname(runfile)
filename = join(path, 'input.traj')
if relax_cell:
eff_force_tolerance = np.min([self['force_tolerance'], self['stress_tolerance']])
else:
eff_force_tolerance = self['force_tolerance']
write_traj(filename, atoms)
script = """from CalcTrollASE.Trajectory import myread_traj, write_traj, Trajectory
from ase.constraints import UnitCellFilter
from ase.optimize import FIRE, BFGS
from CalcTroll.Plugins.Programs.Siesta.Siesta import SiestaCalculator as Siesta
from ase.calculators.siesta.parameters import Specie
from CalcTroll.Plugins.Programs.Siesta.SiestaIO import convertXVtoASE
"""
script += c_string
script += """
atoms = myread_traj('input.traj', -1)
try:
restart_atoms = myread_traj('relax.traj', -1)
except:
print 'initializing from input.traj...'
else:
print 'restarting from previous geometry...'
atoms.positions = restart_atoms.positions
atoms.cell = restart_atoms.cell
atoms.set_calculator(calculator)
"""
if relax_cell:
pbc = tuple(atoms.get_pbc())
if pbc == (False, False, True):
mask = (False, False, True, False, False, False)
elif pbc == (True, True, True):
mask = None
script += """
relax = UnitCellFilter(atoms, mask=%s)
""" % str(mask)
else:
script += "relax = atoms\n"
script += """
opt = BFGS(relax)
traj = Trajectory('relax.traj', 'w', atoms)
opt.attach(traj)
opt.run(fmax=%.5f)
"""%eff_force_tolerance
with open(runfile, 'w') as f:
f.write(script)
