def write_eam_setfl_file(self,parameters,potential,setfl_fn):
from pypospack.potential import EamPotential
is_debug = False
assert isinstance(parameters,OrderedDict)
assert isinstance(potential,OrderedDict)
assert isinstance(setfl_fn,str)
if is_debug:
print(parameters)
print(potential)
print(setfl_fn)
p = EamPotential(
symbols=potential['symbols'],
func_pair=potential['pair_type'],
func_density=potential['density_type'],
func_embedding=potential['embedding_type']
)
p.write_setfl_file(
filename=setfl_fn,
symbols=potential['symbols'],
Nr=potential['N_r'],
rmax=potential['r_max'],
rcut=potential['r_cut'],
Nrho=potential['N_rho'],
rhomax=potential['rho_max'],
parameters=parameters
)
for name in datafile.parameter_names:
parameters[name] = subselect_df[name].values[0]
# plotting portion copied from pypospack.tests.tests_integration.eamtools.EamSetflFile.dev_EamSetflFile
setfl_fn = "Ni__eam__born_exp_fs.eam.alloy"
n_r = 2000
r_max = 10.0
r_cut = 10.0
n_rho = 2000
rho_max = 10.0
eam_potential.write_setfl_file(filename=setfl_fn,
symbols=symbols,
Nr=n_r,
rmax=r_max,
rcut=r_cut,
Nrho=n_rho,
rhomax=rho_max,
parameters=parameters)
setfl_file = EamSetflFile()
setfl_file.read(setfl_fn)
r = setfl_file.r
rho = setfl_file.rho
pair = setfl_file.func_pairpotential['Ni.Ni']
embed = setfl_file.func_embedding['Ni']
dens = setfl_file.func_density['Ni']
fig, axes = plt.subplots(3, 1)
r_low = 1
_pair = [p for p in rho]
for p in _pair:
for s in sites:
print("{s:^10}{N_s:^10}{da:^10.4f}{rho:^15.4e}{ttl_rho:^15.4e}".format(
s=s,
N_s=N[s],
da=da[s],
rho=rho[p][s],
ttl_rho=N[s]*rho[p][s]))
sites_lte_1NN = ['1NN']
rho_lte_1NN = 0.
filename = "Ni.eam.alloy"
Nr = configuration['potential']['N_r']
rmax = configuration['potential']['r_max']
rcut = configuration['potential']['r_cut']
Nrho = configuration['potential']['N_rho']
rhomax = configuration['potential']['rho_max']
eam.write_setfl_file(
filename=filename,
symbols=symbols,
Nr=Nr,
rmax=rmax,
rcut=rcut,
Nrho=Nrho,
rhomax=rhomax,
parameters=parameters)
assert os.path.isfile(filename)