def test_average_atom_Fe_Cu_Ni(self):
"""Create A-atom potential for a Fe-Cu-Ni eam/alloy potential at equicomposition
The input potential is from Ref. [1]_ and was downloaded from
the NIST database [2]_. The generated The generated A-atom
potential is compared to a reference A-atom potential, which
was created with an independent implementation. This is not
a very strong test, but should capture some regressions.
References
----------
[1] G. Bonny, R.C. Pasianot, N. Castin, and L. Malerba (2009),
"Ternary Fe-Cu-Ni many-body potential to model reactor
pressure vessel steels: First validation by simulated
thermal annealing", Philosophical Magazine, 89(34-36),
3531-3546. DOI: 10.1080/14786430903299824.
[2] https://www.ctcms.nist.gov/potentials/Download/2009--Bonny-G-Pasianot-R-C-Castin-N-Malerba-L--Fe-Cu-Ni/1/FeCuNi.eam.alloy
"""
input_table = "FeCuNi.eam.alloy"
reference_table = "FeCuNi_reference_A-atom_Fe33Cu33Ni33.eam.alloy"
concentrations = np.array((1.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0))
source, parameters, F, f, rep = io.read_eam(input_table)
(new_parameters, new_F, new_f,
new_rep) = average_atom.average_potential(concentrations, parameters,
F, f, rep)
ref_source, ref_parameters, ref_F, ref_f, ref_rep = io.read_eam(
reference_table)
diff_F = np.linalg.norm(ref_F - new_F)
diff_f = np.linalg.norm(ref_f - new_f)
diff_rep = np.linalg.norm(ref_rep - new_rep)
print(diff_F, diff_f, diff_rep)
self.assertTrue(diff_F < self.tol)
self.assertTrue(diff_f < self.tol)
self.assertTrue(diff_rep < self.tol)
def test_eam_alloy_read_write(self):
source, parameters, F, f, rep = read_eam("CuAgNi_Zhou.eam.alloy",
kind="eam/alloy")
write_eam(source,
parameters,
F,
f,
rep,
"CuAgNi_Zhou.eam.alloy_copy",
kind="eam/alloy")
source1, parameters1, F1, f1, rep1 = read_eam(
"CuAgNi_Zhou.eam.alloy_copy", kind="eam/alloy")
os.remove("CuAgNi_Zhou.eam.alloy_copy")
fail = 0
for i, p in enumerate(parameters):
try:
for j, d in enumerate(p):
if d != parameters[i][j]:
fail += 1
except:
if p != parameters[i]:
fail += 1
self.assertTrue(fail == 0)
self.assertTrue((F == F1).all())
self.assertTrue((f == f1).all())
for i in range(len(rep)):
for j in range(len(rep)):
if j < i:
self.assertTrue((rep[i, j, :] == rep1[i, j, :]).all())
def test_average_atom_Ni_Al(self):
"""Create A-atom potential for a Ni-Al eam/alloy potential and 15% Al
The input potential is from Ref. [1]_ and was downloaded from
the NIST database [2]_. The generated The generated A-atom
potential is compared to a reference A-atom potential, which
was created with an independent implementation. This is not
a very strong test, but should capture some regressions.
References
----------
[1] G.P. Purja Pun, and Y. Mishin (2009), "Development of an
interatomic potential for the Ni-Al system", Philosophical
Magazine, 89(34-36), 3245-3267. DOI: 10.1080/14786430903258184.
[2] https://www.ctcms.nist.gov/potentials/Download/2009--Purja-Pun-G-P-Mishin-Y--Ni-Al/2/Mishin-Ni-Al-2009.eam.alloy
"""
input_table = "Mishin-Ni-Al-2009.eam.alloy"
reference_table = "Mishin-Ni-Al-2009_reference_A-atom_Ni85Al15.eam.alloy"
concentrations = np.array((0.85, 0.15))
source, parameters, F, f, rep = io.read_eam(input_table)
(new_parameters, new_F, new_f,
new_rep) = average_atom.average_potential(concentrations, parameters,
F, f, rep)
ref_source, ref_parameters, ref_F, ref_f, ref_rep = io.read_eam(
reference_table)
diff_F = np.linalg.norm(ref_F - new_F)
diff_f = np.linalg.norm(ref_f - new_f)
diff_rep = np.linalg.norm(ref_rep - new_rep)
print(diff_F, diff_f, diff_rep)
self.assertTrue(diff_F < self.tol)
self.assertTrue(diff_f < self.tol)
self.assertTrue(diff_rep < self.tol)
def __init__(self, fn=None, atomic_numbers=None, F=None, f=None, rep=None,
cutoff=None, kind='eam/alloy'):
Calculator.__init__(self)
if fn is not None:
source, parameters, F, f, rep = read_eam(fn, kind=kind)
self.atnums = parameters.atomic_numbers
self.cutoff = parameters.cutoff
dr = parameters.distance_grid_spacing
dF = parameters.density_grid_spacing
# Create spline interpolation
self.F = _make_splines(dF, F)
self.f = _make_splines(dr, f)
self.rep = _make_splines(dr, rep)
else:
self.atnums = atomic_numbers
self.F = F
self.f = f
self.rep = rep
self.cutoff = cutoff
self.atnum_to_index = -np.ones(np.max(self.atnums)+1, dtype=int)
self.atnum_to_index[self.atnums] = \
np.arange(len(self.atnums))
# Derivative of spline interpolation
self.dF = _make_derivative(self.F)
self.df = _make_derivative(self.f)
self.drep = _make_derivative(self.rep)
def average(input_table, output_table, concentrations):
"""Create Average-atom potential for an Embedded Atom Method potential
Read an EAM potential from INPUT_TABLE, create the Average-atom
potential for the random alloy with composition specified
by CONCENTRATIONS and write a new table with both the original
and the A-atom potential functions to OUTPUT_TABLE.
CONCENTRATIONS is a whitespace-separated list of the concentration of
the elements, in the order in which the appear in the input table.
"""
source, parameters, F, f, rep = io.read_eam(input_table)
(new_parameters, new_F, new_f, new_rep) = average_atom.average_potential(
np.array(concentrations, dtype=float), parameters, F, f, rep
)
composition = " ".join(
[str(c * 100.0) + f"% {e}," for c, e in zip(np.array(concentrations, dtype=float), parameters.symbols)]
)
composition = composition.rstrip(",")
source += f", averaged for composition {composition}"
io.write_eam(
source,
new_parameters,
new_F,
new_f,
new_rep,
output_table,
kind="eam/alloy",
)
def test_mix_eam_alloy(self):
if False:
source,parameters,F,f,rep = read_eam("CuAu_Zhou.eam.alloy",kind="eam/alloy")
source1,parameters1,F1,f1,rep1 = mix_eam(["Cu_Zhou.eam.alloy","Au_Zhou.eam.alloy"],"eam/alloy","weight")
write_eam(source1,parameters1,F1,f1,rep1,"CuAu_mixed.eam.alloy",kind="eam/alloy")
calc0 = EAM('CuAu_Zhou.eam.alloy')
calc1 = EAM('CuAu_mixed.eam.alloy')
a = FaceCenteredCubic('Cu', size=[2,2,2])
a.set_calculator(calc0)
FIRE(StrainFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy()/len(a)
a = FaceCenteredCubic('Cu', size=[2,2,2])
a.set_calculator(calc1)
FIRE(StrainFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy()/len(a)
self.assertTrue(e0-e1 < 0.0005)
a = FaceCenteredCubic('Au', size=[2,2,2])
a.set_calculator(calc0)
FIRE(StrainFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy()/len(a)
a = FaceCenteredCubic('Au', size=[2,2,2])
a.set_calculator(calc1)
FIRE(StrainFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy()/len(a)
self.assertTrue(e0-e1 < 0.0005)
a = L1_2(['Au', 'Cu'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc0)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy()/len(a)
a = L1_2(['Au', 'Cu'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc1)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy()/len(a)
self.assertTrue(e0-e1 < 0.0005)
a = L1_2(['Cu', 'Au'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc0)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy()/len(a)
a = L1_2(['Cu', 'Au'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc1)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy()/len(a)
self.assertTrue(e0-e1 < 0.0005)
a = B1(['Au', 'Cu'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc0)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy()/len(a)
a = B1(['Au', 'Cu'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc1)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy()/len(a)
self.assertTrue(e0-e1 < 0.0005)
os.remove("CuAu_mixed.eam.alloy")
def test_eam_read_write(self):
source,parameters,F,f,rep = read_eam("Au_u3.eam",kind="eam")
write_eam(source,parameters,F,f,rep,"Au_u3_copy.eam",kind="eam")
source1,parameters1,F1,f1,rep1 = read_eam("Au_u3_copy.eam",kind="eam")
os.remove("Au_u3_copy.eam")
for i,p in enumerate(parameters):
try:
diff = p - parameters1[i]
except:
diff = None
if diff is None:
self.assertTrue(p == parameters1[i])
else:
print(i, p, parameters1[i], diff, self.tol, diff < self.tol)
self.assertTrue(diff < self.tol)
self.assertTrue((F == F1).all())
self.assertTrue((f == f1).all())
self.assertTrue((rep == rep1).all())
def test_eam_read_write(self):
source, parameters, F, f, rep = read_eam("Au_u3.eam", kind="eam")
write_eam(source, parameters, F, f, rep, "Au_u3_copy.eam", kind="eam")
source1, parameters1, F1, f1, rep1 = read_eam("Au_u3_copy.eam",
kind="eam")
os.remove("Au_u3_copy.eam")
for i, p in enumerate(parameters):
try:
diff = p - parameters1[i]
except:
diff = None
if diff is None:
self.assertTrue(p == parameters1[i])
else:
print(i, p, parameters1[i], diff, self.tol, diff < self.tol)
self.assertTrue(diff < self.tol)
self.assertTrue((F == F1).all())
self.assertTrue((f == f1).all())
self.assertArrayAlmostEqual(rep, rep1)
def test_eam_alloy_read_write(self):
source,parameters,F,f,rep = read_eam("CuAgNi_Zhou.eam.alloy",kind="eam/alloy")
write_eam(source,parameters,F,f,rep,"CuAgNi_Zhou.eam.alloy_copy",kind="eam/alloy")
source1,parameters1,F1,f1,rep1 = read_eam("CuAgNi_Zhou.eam.alloy_copy",kind="eam/alloy")
os.remove("CuAgNi_Zhou.eam.alloy_copy")
fail = 0
for i,p in enumerate(parameters):
try:
for j,d in enumerate(p):
if d != parameters[i][j]:
fail+=1
except:
if p != parameters[i]:
fail +=1
self.assertTrue(fail == 0)
self.assertTrue((F == F1).all())
self.assertTrue((f == f1).all())
for i in range(len(rep)):
for j in range(len(rep)):
if j < i :
self.assertTrue((rep[i,j,:] == rep1[i,j,:]).all())
def test_mix_eam_alloy(self):
if False:
source, parameters, F, f, rep = read_eam("CuAu_Zhou.eam.alloy",
kind="eam/alloy")
source1, parameters1, F1, f1, rep1 = mix_eam(
["Cu_Zhou.eam.alloy", "Au_Zhou.eam.alloy"], "eam/alloy",
"weight")
write_eam(source1,
parameters1,
F1,
f1,
rep1,
"CuAu_mixed.eam.alloy",
kind="eam/alloy")
calc0 = EAM('CuAu_Zhou.eam.alloy')
calc1 = EAM('CuAu_mixed.eam.alloy')
a = FaceCenteredCubic('Cu', size=[2, 2, 2])
a.set_calculator(calc0)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy() / len(a)
a = FaceCenteredCubic('Cu', size=[2, 2, 2])
a.set_calculator(calc1)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy() / len(a)
self.assertTrue(e0 - e1 < 0.0005)
a = FaceCenteredCubic('Au', size=[2, 2, 2])
a.set_calculator(calc0)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy() / len(a)
a = FaceCenteredCubic('Au', size=[2, 2, 2])
a.set_calculator(calc1)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy() / len(a)
self.assertTrue(e0 - e1 < 0.0005)
a = L1_2(['Au', 'Cu'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc0)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy() / len(a)
a = L1_2(['Au', 'Cu'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc1)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy() / len(a)
self.assertTrue(e0 - e1 < 0.0005)
a = L1_2(['Cu', 'Au'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc0)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy() / len(a)
a = L1_2(['Cu', 'Au'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc1)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy() / len(a)
self.assertTrue(e0 - e1 < 0.0005)
a = B1(['Au', 'Cu'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc0)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy() / len(a)
a = B1(['Au', 'Cu'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc1)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy() / len(a)
self.assertTrue(e0 - e1 < 0.0005)
os.remove("CuAu_mixed.eam.alloy")
