d = 1.1
 
from ase import Atoms
box = Atoms(pbc = True)
box.set_cell(cell = (4, 4, 4), scale_atoms = False)
 
from ase import Atom
box.append(Atom('C', (2, 2, 2), tag = 1))
box.append(Atom('O', (2 + d, 2, 2)))
 
from ase.constraints import FixAtoms
box.set_constraint(FixAtoms(mask=[atom.tag == 1 for atom in box]))
 
from ase.calculators.jacapo import Jacapo
solver = Jacapo('CO.nc', stay_alive = True, nbands = 10, atoms = box)
 
from ase.optimize import QuasiNewton
dyn = QuasiNewton(box)
dyn.run(fmax = 0.05)

$ python filter.py
BFGSLineSearch:   0[  0]  17:34:36     -591.604035       8.7218
BFGSLineSearch:   1[  2]  17:34:43     -591.849511       0.2591
BFGSLineSearch:   2[  3]  17:34:45     -591.849791       0.0507
BFGSLineSearch:   3[  4]  17:34:47     -591.849803       0.0018
$ 

$ grep Ion123 CO.txt 
 Ion123   1   1 1   0.50000000  0.50000000  0.50000000     1.0 1.0 1.0
 Ion123   2   1 2   0.82500000  0.50000000  0.50000000     1.0 1.0 1.0
 Ion123   1   1 1   0.50000000  0.50000000  0.50000000     1.0 1.0 1.0
 Ion123   2   1 2   0.79086707  0.50000000  0.50000000     1.0 1.0 1.0
 Ion123   1   1 1   0.50000000  0.50000000  0.50000000     1.0 1.0 1.0
 Ion123   2   1 2   0.79040935  0.50000000  0.50000000     1.0 1.0 1.0
 Ion123   1   1 1   0.50000000  0.50000000  0.50000000     1.0 1.0 1.0
 Ion123   2   1 2   0.79029789  0.50000000  0.50000000     1.0 1.0 1.0
 Ion123   1   1 1   0.50000000  0.50000000  0.50000000     1.0 1.0 1.0
 Ion123   2   1 2   0.79029789  0.50000000  0.50000000     1.0 1.0 1.0
$ 

目次へもどる