def test_direct_evaluation(self):
a = FaceCenteredCubic('Au', size=[2,2,2])
a.rattle(0.1)
calc = EAM('Au-Grochola-JCP05.eam.alloy')
a.set_calculator(calc)
f = a.get_forces()
calc2 = EAM('Au-Grochola-JCP05.eam.alloy')
i_n, j_n, dr_nc, abs_dr_n = neighbour_list('ijDd', a, cutoff=calc2.cutoff)
epot, virial, f2 = calc2.energy_virial_and_forces(a.numbers, i_n, j_n, dr_nc, abs_dr_n)
self.assertArrayAlmostEqual(f, f2)
a = FaceCenteredCubic('Cu', size=[2,2,2])
calc = EAM('CuAg.eam.alloy')
a.set_calculator(calc)
FIRE(StrainFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e_Cu = a.get_potential_energy()/len(a)
a = FaceCenteredCubic('Ag', size=[2,2,2])
a.set_calculator(calc)
FIRE(StrainFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e_Ag = a.get_potential_energy()/len(a)
self.assertTrue(abs(e_Ag+2.85)<1e-6)
a = L1_2(['Ag', 'Cu'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(abs((e-(syms=='Cu').sum()*e_Cu-
(syms=='Ag').sum()*e_Ag)/len(a)-0.096)<0.0005)
a = B1(['Ag', 'Cu'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(abs((e-(syms=='Cu').sum()*e_Cu-
(syms=='Ag').sum()*e_Ag)/len(a)-0.516)<0.0005)
a = B2(['Ag', 'Cu'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(abs((e-(syms=='Cu').sum()*e_Cu-
(syms=='Ag').sum()*e_Ag)/len(a)-0.177)<0.0003)
a = L1_2(['Cu', 'Ag'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(abs((e-(syms=='Cu').sum()*e_Cu-
(syms=='Ag').sum()*e_Ag)/len(a)-0.083)<0.0005)
def test_CuAg(self):
a = FaceCenteredCubic('Cu', size=[2, 2, 2])
calc = EAM('CuAg.eam.alloy')
a.set_calculator(calc)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e_Cu = a.get_potential_energy() / len(a)
a = FaceCenteredCubic('Ag', size=[2, 2, 2])
a.set_calculator(calc)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e_Ag = a.get_potential_energy() / len(a)
self.assertTrue(abs(e_Ag + 2.85) < 1e-6)
a = L1_2(['Ag', 'Cu'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(
abs((e - (syms == 'Cu').sum() * e_Cu -
(syms == 'Ag').sum() * e_Ag) / len(a) - 0.096) < 0.0005)
a = B1(['Ag', 'Cu'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(
abs((e - (syms == 'Cu').sum() * e_Cu -
(syms == 'Ag').sum() * e_Ag) / len(a) - 0.516) < 0.0005)
a = B2(['Ag', 'Cu'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(
abs((e - (syms == 'Cu').sum() * e_Cu -
(syms == 'Ag').sum() * e_Ag) / len(a) - 0.177) < 0.0003)
a = L1_2(['Cu', 'Ag'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(
abs((e - (syms == 'Cu').sum() * e_Cu -
(syms == 'Ag').sum() * e_Ag) / len(a) - 0.083) < 0.0005)
def test_CuAg(self):
a = FaceCenteredCubic('Cu', size=[2,2,2])
calc = EAM('CuAg.eam.alloy')
a.set_calculator(calc)
FIRE(StrainFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e_Cu = a.get_potential_energy()/len(a)
a = FaceCenteredCubic('Ag', size=[2,2,2])
a.set_calculator(calc)
FIRE(StrainFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e_Ag = a.get_potential_energy()/len(a)
self.assertTrue(abs(e_Ag+2.85)<1e-6)
a = L1_2(['Ag', 'Cu'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(abs((e-(syms=='Cu').sum()*e_Cu-
(syms=='Ag').sum()*e_Ag)/len(a)-0.096)<0.0005)
a = B1(['Ag', 'Cu'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(abs((e-(syms=='Cu').sum()*e_Cu-
(syms=='Ag').sum()*e_Ag)/len(a)-0.516)<0.0005)
a = B2(['Ag', 'Cu'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(abs((e-(syms=='Cu').sum()*e_Cu-
(syms=='Ag').sum()*e_Ag)/len(a)-0.177)<0.0003)
a = L1_2(['Cu', 'Ag'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(abs((e-(syms=='Cu').sum()*e_Cu-
(syms=='Ag').sum()*e_Ag)/len(a)-0.083)<0.0005)
def phonon_unfold():
atoms = FaceCenteredCubic(size=(1, 1, 1), symbol="Cu", pbc=True)
symbols = atoms.get_chemical_symbols()
#symbols[-1] = 'Ag'
atoms.set_chemical_symbols(symbols)
calc = EMT()
atoms.set_calculator(calc)
phonon = calculate_phonon(atoms,
calc,
ndim=np.eye(3) * 2,
primitive_matrix=np.eye(3) / 1.0)
kpts, x, X, names = kpath()
kpts = [
np.dot(
k,
np.linalg.inv((np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]]) / 2.0)))
for k in kpts
]
phonon.set_qpoints_phonon(kpts, is_eigenvectors=True)
freqs, eigvecs = phonon.get_qpoints_phonon()
sc = atoms
sc_mat = np.linalg.inv((np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]]) / 2.0))
spos = sc.get_scaled_positions()
uf = phonon_unfolder(atoms, sc_mat, eigvecs, kpts)
weights = uf.get_weights()
ax = None
ax = plot_band_weight([list(x)] * freqs.shape[1],
freqs.T * 33.356,
weights[:, :].T * 0.98 + 0.01,
xticks=[names, X],
axis=ax)
# print freqs
# for i in range(freqs.shape[1]):
# plt.plot(x, freqs[:, i], color='blue', alpha=0.2, linewidth=2.5)
plt.xticks(X, names)
plt.ylabel('Frequency (cm$^{-1}$)')
plt.ylim([0, 350])
plt.title('with defect (1/4) (method: reciprocal)')
get_phonon_prim(ax)
plt.savefig('defrec4.png')
plt.show()
from ase.lattice.cubic import FaceCenteredCubic
from ase.io import *
from ase.visualize import view
import math
a = float(input("Ingrese parametro de red : "))
arc = open("fcc_108000.txt","w")
atomos = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
size=(30,30,30),symbol='Cu',pbc=(1,1,1),latticeconstant=a)
posi = atomos.get_positions()
simbol = atomos.get_chemical_symbols()
arc.write(str(len(simbol))+"\n")
for i in range(len(simbol)):
arc.write(str(posi[i,0])+" ")
arc.write(str(posi[i,1])+" ")
arc.write(str(posi[i,2])+"\n")
#----Luego borrar----#
#write('fcc_108000.txt',atomos,format='xyz')
pos = atomos.get_positions()
c_m = atomos.get_center_of_mass()
coor_x = pos[:,0]
coor_y = pos[:,1]
coor_z = pos[:,2]
print "posicion de cero",pos[0]
print "centro de masa", c_m
print "x_max y x_min:",coor_x.max(),coor_x.min()
