def si(cmd=None):
cwd = os.getcwd()
if cmd == None:
cmd = os.path.join(cwd, 'lmp_serial')
os.environ['LAMMPS_COMMAND'] = cmd
os.chdir(os.path.dirname(os.path.abspath(__file__)))
parameters = {
'pair_style': 'meam',
'pair_coeff': ['* * library.meam Si Si.meam Si']
}
files = ['library.meam', 'Si.meam']
calc = LAMMPS(parameters=parameters, files=files)
os.chdir(cwd)
return calc
print "struct: ", struct
print "lp: ", lp
if struct == 'hcp':
print "catoi: ", catoi
print "ecoh: ", esub
print "surf: ", surf
print "size: ", mysize
print "vacuum: ", vac
import model
from model import pick_elements
species = [el1]
pick_elements(model, species)
from ase.calculators.lammps import LAMMPS
calc = LAMMPS(parameters=model.parameters, files=model.files)
from ase.lattice.surface import *
if surf == "10m10":
myorth = True
else:
myorth = False
if el1 != 'Mg':
atoms = surface(el1,
struct,
surf,
size=mysize,
a=lp,
c=None,
while Sigma % 2 == 0:
Sigma = Sigma / 2
DSC = (GB_cor_up[1, 0] ** 2 + GB_cor_up[1, 1] ** 2 + GB_cor_up[1, 2] ** 2)
xinc = 1. / grid_x / DSC
zinc = 1. / grid_z
overlapdist = np.arange(0.275, 0.705, 0.005) * a0
lable = 'S%d_%d%d%d_' % (Sigma, GB_plane[0], GB_plane[1], GB_plane[2])
traj_name = 'Fe_GB_' + lable
el1 = "Fe"
el2 = "H"
species = [el1, el2]
import potpara
print potpara.parameters
#, keep_tmp_files=False)
lammps_cal = LAMMPS(
parameters=potpara.parameters, specorder=species, tmp_dir=tmp_dir)
mm_pot = Potential(calculator=lammps_cal)
f = open('GB_result_S%d_%d%d%d_.txt' %
(Sigma, GB_plane[0], GB_plane[1], GB_plane[2]), 'w')
f.write('%s %s %s %s %s %s %s %s %s %s\n' %
('Angle', 'Count', 'del_cri', 'RBT_X', 'RBT_Z', 'Bulk_pe_GB', 'N_atoms', 'Surface_e', 'GB_e', 'GB_coh_e'))
f.close()
# create unit cell for GB#################
unit_GB_up = create_unit_GB(GB_cor_up, a0)
unit_GB_down = create_unit_GB(GB_cor_down, a0)
# view(unit_GB)
unit_GB_up = Atoms(unit_GB_up, fortran_indexing=False)
unit_GB_up.set_calculator(mm_pot)
print('Minimising GB_up unit cell...')
potpara.parameters["fix"] = "relax all box/relax y 0 vmax 0.001"
potpara.parameters["minimize"] = "%s %s 10000 10000" % (eng_tol, force_tol)
if argc < 4:
print 'usage:', sys.argv[0], 'Mg hcp octa/tetr/dump lp catoi'
sys.exit(1)
else:
catoi = float(sys.argv[4])
species = [el1]
import model
from model import pick_elements
pick_elements(model, species)
from ase.calculators.lammps import LAMMPS
calc = LAMMPS(parameters=model.parameters,
files=model.files,
specorder=species)
if str == "fcc":
from ase.lattice.cubic import FaceCenteredCubic
atoms = FaceCenteredCubic(symbol=el1, latticeconstant=lp, size=(5, 5, 5))
elif str == "bcc":
from ase.lattice.cubic import BodyCenteredCubic
atoms = BodyCenteredCubic(symbol=el1, latticeconstant=lp, size=(5, 5, 5))
elif str == "dia":
from ase.lattice.cubic import Diamond
atoms = Diamond(symbol=el1, latticeconstant=lp, size=(3, 3, 3))
elif str == "hcp":
from math import sqrt
a = lp
b = sqrt(3.) * lp