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()
for clust in allClust:
# General info
atoms = clust.toatoms()
N = len(atoms.positions)
# Define calculator
mishin = EAM(
potential='../CourseGitRepo/HA5_al_potential.alloy') # Set up EAM
atoms.set_calculator(mishin)
# Relax structure
dyn = BFGS(atoms, trajectory=f'traj/Al{N}.traj')
dyn.run(fmax=0.05)
# Calculate cohesive energy
ECoh = np.abs(atoms.get_potential_energy() /
N) # Cohesive energy is the positive potential energy
# Print results
str1 = f'| N={N}'
str2 = 'Cohesive energy/atom:'
str3 = f' {ECoh:.4f} eV |'
out(str1 + str2.rjust(30 - len(str1)) + str3.rjust(35 - len(str2)),
f=Efile)
out('---------------------------------------------', f=Efile)
# Plot and save a picture of the potential
mishin.plot()
plt.tight_layout()
plt.savefig('al_potential.png')
# plt.show()
# The potential may not be perfectly suited for the smaller nanoparticles, since they don't exhibit the same symmetries as the bulk Al.
# Bulk Al is crystalline fcc.
