def optimize_lammpslib(struc,
lmp,
parameters=None,
path='tmp',
calc_type=None,
lmp_file=None,
molecule=False,
strain=np.ones([3, 3]),
method='FIRE',
fmax=0.01):
if lmp_file is not None:
lammps = LAMMPSlib(lmp=lmp, lmp_file=lmp_file, log_file='lammps.log', \
molecule=molecule, path=path)
elif calc_type is not None:
lammps = LAMMPSlib(lmp=lmp, lmpcmds=parameters, calc_type=calc_type, \
log_file='lammps.log', molecule=molecule, path=path)
else:
lammps = LAMMPSlib(lmp=lmp, lmpcmds=parameters, log_file='lammps.log', \
molecule=molecule, path=path)
struc.set_calculator(lammps)
box = mushybox(struc, fixstrain=strain)
if method == 'FIRE':
dyn = FIRE(box)
else:
dyn = LBFGS(box)
dyn.run(fmax=fmax, steps=500)
return struc
def optimize_lammpslib(pbcgb, lmp, parameters, path, method='FIRE', fmax=0.1):
lammps = LAMMPSlib(lmp=lmp,
lmpcmds=parameters,
log_file='lammps.log',
path=path)
pbcgb.set_calculator(lammps)
cell0 = pbcgb.cell
fixstrain = np.zeros((3, 3))
fixstrain[2][2] = 1
box = mushybox(pbcgb, fixstrain=fixstrain)
if method == 'FIRE':
dyn = FIRE(box)
else:
dyn = BFGS(box)
dyn.run(fmax=fmax, steps=500)
return pbcgb
for i in range(1):
while True:
sg = randint(2, 230)
crystal = molecular_crystal(sg, ['H2O'], [randint(1, 4)],
1.0) #, lattice=para)
if crystal.valid:
struc = Atoms(
crystal.spg_struct[2],
cell=crystal.spg_struct[0],
scaled_positions=crystal.spg_struct[1],
)
break
#struc = struc.repeat((2,2,2))
lammps = LAMMPSlib(lmp=lmp, lmpcmds=parameters, mol=True)
struc.set_calculator(lammps)
box = mushybox(struc)
dyn = FIRE(box)
dyn.run(fmax=0.00, steps=1100)
#dyn = BFGS(box)
#dyn.run(fmax=0.01, steps=200)
#dyn = BFGS(box)
#dyn.run(fmax=0.01, steps=200)
Eng = struc.get_potential_energy() * 96 / len(struc) * 3
Vol = struc.get_volume() / len(struc) * 3
stress = np.max(struc.get_stress())
struc = sort(struc)
try:
spg = get_symmetry_dataset(struc, symprec=1e-1)['number']