def test_mishin():
from ase.calculators.eam import EAM
sys_setting ={'elements':['Al', 'Fe'], 'pot':'zhou', \
'pca':[10], 'nAtoms':250,\
#'structure':'bcc',\
#'positions':'rnd','a':3.0, 'period':[5,5,5]}
'structure':'fcc',\
'positions':'rnd','a':4.6, 'period':[2,2,2]}
sys1 = sys.System(sys_setting)
potDir = './'
fileName = potDir + 'Zhou_AlFe.alloy'
#potDir = '../../lammps/potentials/'
#fileName = potDir + 'Ni.adp'
mishin = EAM(potential=fileName)
mishin.write_potential('new.eam.alloy')
sys1.bulk.set_calculator(mishin)
nAtoms = sys1.bulk.get_number_of_atoms()
ep = sys1.bulk.get_potential_energy() / nAtoms
forces = sys1.bulk.get_forces()
print ep
print mishin.Z
print mishin.mass
print mishin.a
print mishin.lattice
print mishin.nrho
print mishin.drho
print mishin.nr
print mishin.dr
#print mishin.d_d
mishin.set_splines()
print mishin.embedded_energy[0](30)
mishin.plot()
m_densityf = spline(rs, m_density)
m_embeddedf = spline(rhos, m_embedded)
m_phif = spline(rs, m_phi)
a = 4.05 # Angstrom lattice spacing
al = bulk('Al', 'fcc', a=a)
mishin_approx = EAM(elements=['Al'], embedded_energy=np.array([m_embeddedf]),
electron_density=np.array([m_densityf]),
phi=np.array([[m_phif]]), cutoff=cutoff, form='alloy',
# the following terms are only required to write out a file
Z=[13], nr=n, nrho=n, dr=cutoff / n, drho=2. / n,
lattice=['fcc'], mass=[26.982], a=[a])
al.set_calculator(mishin_approx)
mishin_approx_energy = al.get_potential_energy()
mishin_approx.write_potential('Al99-test.eam.alloy')
mishin_check = EAM(potential='Al99-test.eam.alloy')
al.set_calculator(mishin_check)
mishin_check_energy = al.get_potential_energy()
print('Cohesive Energy for Al = ', mishin_approx_energy, ' eV')
error = (mishin_approx_energy - mishin_check_energy) / mishin_approx_energy
print('read/write check error = ', error)
assert abs(error) < 1e-4
def test_eam():
# test to generate an EAM potential file using a simplified
# approximation to the Mishin potential Al99.eam.alloy data
from scipy.interpolate import InterpolatedUnivariateSpline as spline
cutoff = 6.28721
n = 21
rs = np.arange(0, n) * (cutoff / n)
rhos = np.arange(0, 2, 2. / n)
# generated from
# mishin = EAM(potential='../potentials/Al99.eam.alloy')
# m_density = mishin.electron_density[0](rs)
# m_embedded = mishin.embedded_energy[0](rhos)
# m_phi = mishin.phi[0,0](rs)
m_density = np.array([
2.78589606e-01, 2.02694937e-01, 1.45334053e-01, 1.06069912e-01,
8.42517168e-02, 7.65140344e-02, 7.76263116e-02, 8.23214224e-02,
8.53322309e-02, 8.13915861e-02, 6.59095390e-02, 4.28915711e-02,
2.27910928e-02, 1.13713167e-02, 6.05020311e-03, 3.65836583e-03,
2.60587564e-03, 2.06750708e-03, 1.48749693e-03, 7.40019174e-04,
6.21225205e-05
])
m_embedded = np.array([
1.04222211e-10, -1.04142633e+00, -1.60359806e+00, -1.89287637e+00,
-2.09490167e+00, -2.26456628e+00, -2.40590322e+00, -2.52245359e+00,
-2.61385603e+00, -2.67744693e+00, -2.71053295e+00, -2.71110418e+00,
-2.69287013e+00, -2.68464527e+00, -2.69204083e+00, -2.68976209e+00,
-2.66001244e+00, -2.60122024e+00, -2.51338548e+00, -2.39650817e+00,
-2.25058831e+00
])
m_phi = np.array([
6.27032242e+01, 3.49638589e+01, 1.79007014e+01, 8.69001383e+00,
4.51545250e+00, 2.83260884e+00, 1.93216616e+00, 1.06795515e+00,
3.37740836e-01, 1.61087890e-02, -6.20816372e-02, -6.51314297e-02,
-5.35210341e-02, -5.20950200e-02, -5.51709524e-02, -4.89093894e-02,
-3.28051688e-02, -1.13738785e-02, 2.33833655e-03, 4.19132033e-03,
1.68600692e-04
])
m_densityf = spline(rs, m_density)
m_embeddedf = spline(rhos, m_embedded)
m_phif = spline(rs, m_phi)
a = 4.05 # Angstrom lattice spacing
al = bulk('Al', 'fcc', a=a)
mishin_approx = EAM(
elements=['Al'],
embedded_energy=np.array([m_embeddedf]),
electron_density=np.array([m_densityf]),
phi=np.array([[m_phif]]),
cutoff=cutoff,
form='alloy',
# the following terms are only required to write out a file
Z=[13],
nr=n,
nrho=n,
dr=cutoff / n,
drho=2. / n,
lattice=['fcc'],
mass=[26.982],
a=[a])
al.calc = mishin_approx
mishin_approx_energy = al.get_potential_energy()
mishin_approx.write_potential('Al99-test.eam.alloy')
mishin_check = EAM(potential='Al99-test.eam.alloy')
al.calc = mishin_check
mishin_check_energy = al.get_potential_energy()
print('Cohesive Energy for Al = ', mishin_approx_energy, ' eV')
error = (mishin_approx_energy - mishin_check_energy) / mishin_approx_energy
print('read/write check error = ', error)
assert abs(error) < 1e-4
