def test__fit_potential_pair(symbols, setfl_fn, pair_definition):
o = EamPotentialFitter(symbols)
o.read_setfl_file(filename=setfl_fn)
o.fit_potential_pair(func_pair_potential=pair_definition['formalism'],
symbol_pair=pair_definition['pair'],
param0=pair_definition['param'])
def test__fit_potential_pair(symbols, setfl_fn, func_pair_potential,
symbol_pair, param0):
o = EamPotentialFitter(symbols)
o.read_setfl_file(filename=setfl_fn)
o.fit_potential_pair(func_pair_potential=func_pair_potential,
symbol_pair=symbol_pair,
param0=param0,
rlow=1.5)
def test__EamPotentialFitter__init__(symbols):
o = EamPotentialFitter(symbols)
assert isinstance(o.pair_potentials, OrderedDict)
assert isinstance(o.density_functions, OrderedDict)
assert isinstance(o.embedding_functions, OrderedDict)
assert list(o.pair_potentials.keys()) \
== list(["".join(k) for k in determine_eam_setfl_pairs(symbols)])
assert list(o.density_functions.keys()) == symbols
assert list(o.embedding_functions.keys()) == symbols
for k1 in ['p0', 'popt']:
assert k1 in o.parameters
for k2 in ['pair', 'embedding', 'density']:
assert k2 in o.parameters[k1]
for pair in determine_eam_setfl_pairs(symbols):
assert "".join(pair) in o.parameters[k1]['pair']
assert o.parameters[k1]['pair']["".join(pair)] is None
for s in symbols:
assert s in o.parameters[k1]['embedding']
assert o.parameters[k1]['embedding'][s] is None
for s in symbols:
assert s in o.parameters[k1]['density']
assert o.parameters[k1]['embedding'][s] is None
for k in ['pair', 'embedding', 'density']:
assert isinstance(o.formalisms[k], OrderedDict)
for pair in determine_eam_setfl_pairs(symbols):
pair_name = "".join(pair)
assert o.formalisms['pair'][pair_name] is None
for s in symbols:
assert o.formalisms['density'][s] is None
for s in symbols:
assert o.formalisms['embedding'][s] is None
assert all([v is None for v in o.pair_potentials.values()])
assert all([v is None for v in o.density_functions.values()])
assert all([v is None for v in o.embedding_functions.values()])
assert o.setfl_reader is None
def test__read_setfl_file(symbols, setfl_fn):
o = EamPotentialFitter(symbols)
o.read_setfl_file(filename=setfl_fn)
def test____init__(symbols):
o = EamPotentialFitter(symbols)
ax[1].set_xlim([1.5, 5.168])
#ax[0].set_ylim([-1,5])
#
ax[2].plot(rho, o.setfl_reader.embedding_function('Ni'), label='from_file')
ax[2].plot(rho,
o.formalisms['embedding']['Ni'](
r, **o.parameters['popt']['embedding']['Ni']),
label='fitted')
plt.show()
setfl_fn = os.path.join(pypospack.utils.get_pypospack_root_directory(), 'data',
'potentials', 'Ni__eam', 'Mishin-Ni-Al-2009.eam.alloy')
symbols = ['Ni']
o = EamPotentialFitter(symbols)
o.read_setfl_file(filename=setfl_fn)
print('fitting the pair potential')
o.fit_potential_pair(
func_pair_potential=potentials['pair']['NiNi']['formalism'],
symbol_pair=['Ni', 'Ni'],
param0=potentials['pair']['NiNi']['param'],
bounds=potentials['pair']['NiNi']['bounds'],
rlow=1.5,
rhigh=5.168)
assert o.formalisms['pair']['NiNi'] == potentials['pair']['NiNi']['formalism']
print(o.parameters['p0']['pair']['NiNi'])
print(o.parameters['popt']['pair']['NiNi'])
print('fitting the density function')
o.fit_density_function(func_density=potentials['density']['Ni']['formalism'],
potentials['pair']['NiNi']['param']['rc'] = 5.168 # angs
potentials['pair']['NiNi']['param']['h'] = 3.3228 # angs
potentials['embedding'] = OrderedDict()
potentials['embedding']['Ni'] = OrderedDict()
potentials['embedding']['Ni']['formalism'] = func_zopemishin_eos
potentials['embedding']['Ni']['param'] = OrderedDict()
potentials['embedding']['Ni']['param']['a0'] = 0.3138 * 10
potentials['embedding']['Ni']['param']['B0'] = 1.1914e4 * 10
potentials['embedding']['Ni']['param']['E0'] = -4.45
potentials['embedding']['Ni']['param']['beta'] = 0.4890e-2
setfl_fn = os.path.join(pypospack.utils.get_pypospack_root_directory(), 'data',
'potentials', 'Ni__eam', 'Mishin-Ni-Al-2009.eam.alloy')
symbols = ['Ni']
o = EamPotentialFitter(symbols)
o.read_setfl_file(filename=setfl_fn)
print('fitting the pair potential')
GGo.fit_potential_pair(
func_pair_potential=potentials['pair']['NiNi']['formalism'],
symbol_pair=['Ni', 'Ni'],
param0=potentials['pair']['NiNi']['param'],
rlow=1.5)
assert o.formalisms['pair']['NiNi'] == potentials['pair']['NiNi']['formalism']
print(o.parameters['p0']['pair']['NiNi'])
print(o.parameters['popt']['pair']['NiNi'])
print('fitting the density function')
o.fit_density_function(func_density=potentials['density']['Ni']['formalism'],
symbol='Ni',
def test__read_setfl_filename(symbols, setfl_filename):
o = EamPotentialFitter(symbols)
o.read_setfl_file(filename=setfl_filename)
assert isinstance(o.setfl_reader, SeatonSetflReader)
'symbols,setfl_fn,func_pair_potential,symbol_pair,param0', [(
['Ni', 'Al'],
potentials['setfl_fn'],
potentials['pair']['NiNi']['formalism'],
['Ni', 'Ni'],
potentials['pair']['NiNi']['param'],
)])
def test__fit_potential_pair(symbols, setfl_fn, func_pair_potential,
symbol_pair, param0):
o = EamPotentialFitter(symbols)
o.read_setfl_file(filename=setfl_fn)
o.fit_potential_pair(func_pair_potential=func_pair_potential,
symbol_pair=symbol_pair,
param0=param0,
rlow=1.5)
if __name__ == "__main__":
setfl_fn = os.path.join(pypospack.utils.get_pypospack_root_directory(),
'data', 'potentials', 'Ni__eam',
'Mishin-Ni-Al-2009.eam.alloy')
symbols = ['Ni']
o = EamPotentialFitter(symbols)
o.read_setfl_file(filename=setfl_fn)
o.fit_potential_pair(
func_pair_potential=potentials['pair']['NiNi']['formalism'],
symbol_pair=['Ni', 'Ni'],
param0=potentials['pair']['NiNi']['param'],
rlow=2.)
potentials['pair']['NiNi']['param']['hc'] = 3.3228 # angs
potentials['pair']['NiNi']['param']['h0'] = 3.3228 # angs
potentials['embedding'] = OrderedDict()
potentials['embedding']['Ni'] = OrderedDict()
potentials['embedding']['Ni']['formalism'] = func_zopemishin_eos
potentials['embedding']['Ni']['param'] = OrderedDict()
potentials['embedding']['Ni']['param']['a0'] = 0.3138 * 10
potentials['embedding']['Ni']['param']['B'] = 1.1914e4 * 10
potentials['embedding']['Ni']['param']['E0'] = -4.45
potentials['embedding']['Ni']['param']['beta'] = 0.4890e-2
setfl_fn = os.path.join(pypospack.utils.get_pypospack_root_directory(), 'data',
'potentials', 'Ni__eam', 'Mishin-Ni-Al-2009.eam.alloy')
symbols = ['Ni']
o = EamPotentialFitter(symbols)
o.read_setfl_file(filename=setfl_fn)
print('fitting the pair potential')
o.fit_potential_pair(
func_pair_potential=potentials['pair']['NiNi']['formalism'],
symbol_pair=['Ni', 'Ni'],
param0=potentials['pair']['NiNi']['param'],
rlow=1.5)
assert o.formalisms['pair']['NiNi'] == potentials['pair']['NiNi']['formalism']
print(o.parameters['p0']['pair']['NiNi'])
print(o.parameters['popt']['pair']['NiNi'])
print('fitting the density function')
o.fit_density_function(func_density=potentials['density']['Ni']['formalism'],
symbol='Ni',