def relaxGPAW(structure, label, forcemax=0.1, niter_max=1, steps=10):
# Set calculator
# loop a number of times to capture if minimization stops with high force
# due to the VariansBreak calls
niter = 0
# If the structure is already fully relaxed just return it
traj = Trajectory(label + '_lcao.traj', 'w', structure)
while (structure.get_forces()**
2).sum(axis=1).max()**0.5 > forcemax and niter < niter_max:
dyn = BFGS(structure, logfile=label + '.log')
vb = VariansBreak(structure, dyn, min_stdev=0.01, N=15)
dyn.attach(traj)
dyn.attach(vb)
dyn.run(fmax=forcemax, steps=steps)
niter += 1
#print('relaxgpaw over',flush=True)
return structure
def relax_VarianceBreak(structure,
calc,
label='',
slab=None,
niter_max=3,
forcemax=0.1,
zlim=None):
# Set calculator
structure.set_calculator(calc)
if slab is not None:
# Make temporary constraint
Natoms_slab = slab.get_number_of_atoms()
c_temp = FixAtoms(indices=[i for i in range(Natoms_slab)])
# Save old constraint
c0 = structure.constraints
# Apply temporary constraint
structure.set_constraint(c_temp)
# loop a number of times to capture if minimization stops with high force
# due to the VariansBreak calls
niter = 0
# If the structure is already fully relaxed just return it
if (structure.get_forces()**2).sum(axis=1).max()**0.5 < forcemax:
return structure
while (structure.get_forces()**
2).sum(axis=1).max()**0.5 > forcemax and niter < niter_max:
dyn = BFGSLineSearch_zlim(structure, zlim=zlim, logfile=label + '.log')
vb = VariansBreak(structure, dyn, min_stdev=0.01, N=15)
dyn.attach(vb)
dyn.run(fmax=forcemax, steps=200)
niter += 1
if slab is not None:
# set constraint back to old one
structure.set_constraint(c0)
# relax a little with old constraints
dyn = BFGSLineSearch_zlim(structure, zlim=zlim, logfile=label + '.log')
dyn.run(fmax=forcemax, steps=20)
return structure
else:
return structure
def relaxGPAW(structure, label, calc=None, forcemax=0.1, niter_max=1, steps=10):
# Create calculator
if calc is None:
calc=GPAW(poissonsolver = PoissonSolver(relax = 'GS',eps = 1.0e-7), # C
mode = 'lcao',
basis = 'dzp',
xc='PBE',
gpts = h2gpts(0.2, structure.get_cell(), idiv = 8), # C
occupations=FermiDirac(0.1),
maxiter=99, # C
#maxiter=49, # Sn3O3
mixer=Mixer(nmaxold=5, beta=0.05, weight=75),
nbands=-50,
#kpts=(1,1,1), # C
kpts=(2,2,1), # Sn3O3
txt = label+ '_lcao.txt')
else:
calc.set(txt=label+'_true.txt')
# Set calculator
structure.set_calculator(calc)
# loop a number of times to capture if minimization stops with high force
# due to the VariansBreak calls
niter = 0
# If the structure is already fully relaxed just return it
if (structure.get_forces()**2).sum(axis = 1).max()**0.5 < forcemax:
return structure
traj = Trajectory(label+'_lcao.traj','w', structure)
while (structure.get_forces()**2).sum(axis = 1).max()**0.5 > forcemax and niter < niter_max:
dyn = BFGS(structure,
logfile=label+'.log')
vb = VariansBreak(structure, dyn, min_stdev = 0.01, N = 15)
dyn.attach(traj)
dyn.attach(vb)
dyn.run(fmax = forcemax, steps = steps)
niter += 1
return structure
from ase.optimize import BFGS
from ase.io import read, write
from ase.calculators.emt import EMT
from ase.ga.relax_attaches import VariansBreak
import sys
fname = sys.argv[1]
print('Now relaxing {0}'.format(fname))
a = read(fname)
a.calc = EMT()
dyn = BFGS(a, trajectory=None, logfile=None)
vb = VariansBreak(a, dyn)
dyn.attach(vb.write)
dyn.run(fmax=0.05)
a.info['key_value_pairs']['raw_score'] = -a.get_potential_energy()
write(fname[:-5] + '_done.traj', a)
print('Done relaxing {0}'.format(fname))
