def test_stress(self):
a = FaceCenteredCubic('Au', size=[2,2,2])
calc = EAM('Au-Grochola-JCP05.eam.alloy')
a.set_calculator(calc)
self.assertArrayAlmostEqual(a.get_stress(), calc.calculate_numerical_stress(a), tol=self.tol)
sx, sy, sz = a.cell.diagonal()
a.set_cell([sx, 0.9*sy, 1.2*sz], scale_atoms=True)
self.assertArrayAlmostEqual(a.get_stress(), calc.calculate_numerical_stress(a), tol=self.tol)
a.set_cell([[sx, 0.1*sx, 0], [0, 0.9*sy, 0], [0, -0.1*sy, 1.2*sz]], scale_atoms=True)
self.assertArrayAlmostEqual(a.get_stress(), calc.calculate_numerical_stress(a), tol=self.tol)
def test_stress(self):
a = FaceCenteredCubic('Au', size=[2,2,2])
calc = EAM('Au-Grochola-JCP05.eam.alloy')
a.set_calculator(calc)
self.assertArrayAlmostEqual(a.get_stress(), calc.calculate_numerical_stress(a), tol=self.tol)
sx, sy, sz = a.cell.diagonal()
a.set_cell([sx, 0.9*sy, 1.2*sz], scale_atoms=True)
self.assertArrayAlmostEqual(a.get_stress(), calc.calculate_numerical_stress(a), tol=self.tol)
a.set_cell([[sx, 0.1*sx, 0], [0, 0.9*sy, 0], [0, -0.1*sy, 1.2*sz]], scale_atoms=True)
self.assertArrayAlmostEqual(a.get_stress(), calc.calculate_numerical_stress(a), tol=self.tol)
def test_energy_forces_stress():
"""
To test that the calculator can produce correct energy and forces. This
is done by comparing the energy for an FCC argon lattice with an example
model to the known value; the forces/stress returned by the model are
compared to numerical estimates via finite difference.
"""
import numpy as np
from pytest import importorskip
importorskip('kimpy')
from ase.calculators.kim import KIM
from ase.lattice.cubic import FaceCenteredCubic
# Create an FCC atoms crystal
atoms = FaceCenteredCubic(
directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=(1, 1, 1),
symbol="Ar",
pbc=(1, 0, 0),
latticeconstant=3.0,
)
# Perturb the x coordinate of the first atom by less than the cutoff distance
atoms.positions[0, 0] += 0.01
calc = KIM("ex_model_Ar_P_Morse_07C")
atoms.set_calculator(calc)
# Get energy and analytical forces/stress from KIM model
energy = atoms.get_potential_energy()
forces = atoms.get_forces()
stress = atoms.get_stress()
# Previously computed energy for this configuration for this model
energy_ref = 19.7196709065 # eV
# Compute forces and virial stress numerically
forces_numer = calc.calculate_numerical_forces(atoms, d=0.0001)
stress_numer = calc.calculate_numerical_stress(atoms, d=0.0001, voigt=True)
tol = 1e-6
assert np.isclose(energy, energy_ref, tol)
assert np.allclose(forces, forces_numer, tol)
assert np.allclose(stress, stress_numer, tol)
# This has been known to segfault
atoms.set_pbc(True)
atoms.get_potential_energy()
for j in range(3):
if i != j and np.abs(uc[i, j]) > 1e-15:
diagonal = False
if not (self.allow_mi_opbc and atoms.get_pbc().all() and diagonal):
# Minimum Image Orthogonal Periodic Boundary Conditions
# are not allowed
remove.extend(["MI_OPBC_H", "MI_OPBC_F"])
if atoms.get_pbc().any():
# Cluster method is not allowed
remove.append("CLUSTER")
for rem in remove:
if rem in allowed:
allowed.remove(rem)
if self.verbose:
print "Allowed PBC:", allowed
return allowed
if __name__ == '__main__':
from ase.lattice.cubic import FaceCenteredCubic
atoms = FaceCenteredCubic(size=(10, 10, 10), symbol='Cu')
print "Creating calculator"
pot = OpenKIMcalculator(
'EMT_Asap_Standard_AlAgAuCuNiPdPt__MO_118428466217_000')
print "Setting atoms"
atoms.set_calculator(pot)
print "Calculating energy"
print atoms.get_potential_energy()
print atoms.get_forces()[10:]
print atoms.get_stress()
1, 0)
ReportTest("Forces required", pot.calculation_required(atoms, ["forces"]),
1, 0)
ReportTest("Stress required", pot.calculation_required(atoms, ["stress"]),
1, 0)
ReportTest("Magmom required", pot.calculation_required(atoms, ["magmoms"]),
1, 0)
e = atoms.get_potential_energy()
ReportTest("Energy not required",
pot.calculation_required(atoms, ["energy"]), 0, 0)
ReportTest("Forces required (II)",
pot.calculation_required(atoms, ["forces"]), 1, 0)
f = atoms.get_forces()
ReportTest("Energy not required (II)",
pot.calculation_required(atoms, ["energy"]), 0, 0)
ReportTest("Forces not required",
pot.calculation_required(atoms, ["forces"]), 0, 0)
ReportTest("Energy or forces not required",
pot.calculation_required(atoms, ["energy", "forces"]), 0, 0)
ReportTest("Energy or stress required",
pot.calculation_required(atoms, ["energy", "stress"]), 1, 0)
s = atoms.get_stress()
ReportTest("Stress not required",
pot.calculation_required(atoms, ["stress"]), 0, 0)
r = atoms.get_positions()
r[0, 0] += 0.1
atoms.set_positions(r)
ReportTest.Summary()
print "Number of atoms:", atoms.get_number_of_atoms()
print "Heating to %d K using Langevin" % T_goal
lgv = Langevin(atoms, 5 * units.fs, temperature=2*T_goal*units.kB, friction=0.05)
while atoms.get_kinetic_energy() < 1.5 * atoms.get_number_of_atoms() * T_goal * units.kB:
lgv.run(5)
T = atoms.get_kinetic_energy() / (1.5 * atoms.get_number_of_atoms() * units.kB)
print "Temperature is now %.2f K" % (T,)
print "Desired temperature reached!"
lgv.set_temperature(T_goal*units.kB)
for i in range(2):
lgv.run(20)
s = atoms.get_stress()
p = -(s[0] + s[1] + s[2])/3.0 / units.GPa
T = atoms.get_kinetic_energy() / (1.5 * atoms.get_number_of_atoms() * units.kB)
print "Pressure is %f GPa, desired pressure is %f GPa (T = %.2f K)" % (p, p_goal, T)
dv = (p - p_goal) / bulk
print "Adjusting volume by", dv
cell = atoms.get_cell()
atoms.set_cell(cell * (1.0 + dv/3.0))
T = atoms.get_kinetic_energy() / (1.5 * atoms.get_number_of_atoms() * units.kB)
print "Temperature is now %.2f K" % (T,)
stressstate = array([-2, -1, 0, 0, 0, 0])*p_goal*units.GPa
dyn = NPT(atoms, 5 * units.fs, T_goal*units.kB, stressstate,
ttime*units.fs, (ptime*units.fs)**2 * bulk * units.GPa)
traj = PickleTrajectory("NPT-atoms.traj", "w", atoms)
#!/usr/bin/env python
from jasp import *
from ase.lattice.cubic import FaceCenteredCubic
atoms = FaceCenteredCubic(symbol='Al')
with jasp('bulk/Al-bulk',
xc='PBE',
kpts=(12, 12, 12),
encut=350,
prec='High',
isif=3,
nsw=30,
ibrion=1,
atoms=atoms) as calc:
print atoms.get_potential_energy()
print atoms.get_stress()
temperature=2 * T_goal * units.kB,
friction=0.05)
while atoms.get_kinetic_energy(
) < 1.5 * atoms.get_number_of_atoms() * T_goal * units.kB:
lgv.run(5)
T = atoms.get_kinetic_energy() / (1.5 * atoms.get_number_of_atoms() *
units.kB)
print "Temperature is now %.2f K" % (T, )
print "Desired temperature reached!"
lgv.set_temperature(T_goal * units.kB)
for i in range(2):
lgv.run(20)
s = atoms.get_stress()
p = -(s[0] + s[1] + s[2]) / 3.0 / units.GPa
T = atoms.get_kinetic_energy() / (1.5 * atoms.get_number_of_atoms() *
units.kB)
print "Pressure is %f GPa, desired pressure is %f GPa (T = %.2f K)" % (
p, p_goal, T)
dv = (p - p_goal) / bulk
print "Adjusting volume by", dv
cell = atoms.get_cell()
atoms.set_cell(cell * (1.0 + dv / 3.0))
T = atoms.get_kinetic_energy() / (1.5 * atoms.get_number_of_atoms() *
units.kB)
print "Temperature is now %.2f K" % (T, )
stressstate = array([-2, -1, 0, 0, 0, 0]) * p_goal * units.GPa
#set_verbose(1)
atoms = FaceCenteredCubic(directions=((1,0,0), (0,1,0), (0,0,1)),
size=(15,15,15), symbol="Cu", pbc=True)
atoms.set_calculator(EMT())
atoms.get_forces()
atoms.get_forces()
MaxwellBoltzmannDistribution(atoms, 300 * units.kB)
atoms.get_forces()
atoms.get_forces()
atoms = FaceCenteredCubic(directions=((1,0,0), (0,1,0), (0,0,1)),
size=(15,15,15), symbol="Cu", pbc=True)
atoms.set_calculator(EMT())
s = atoms.get_stress()
print
print "Stress:", s
s = atoms.get_stress()
print
print "Stress:", s
MaxwellBoltzmannDistribution(atoms, 300 * units.kB)
s = atoms.get_stress()
print
print "Stress:", s
s = atoms.get_stress()
print
print "Stress:", s
MaxwellBoltzmannDistribution(atoms, 300 * units.kB)
s = atoms.get_stress()
print
emt.set_subtractE0(False)
atoms_kim.set_calculator(kim)
atoms_emt.set_calculator(emt)
ek = atoms_kim.get_potential_energy()
ee = atoms_emt.get_potential_energy()
ReportTest(txt + "Total energy", ek, ee, 1e-8)
ek = atoms_kim.get_potential_energies()
ee = atoms_emt.get_potential_energies()
for i in range(0, natoms, step):
ReportTest(txt + "Energy of atom %i" % (i, ), ek[i], ee[i], 1e-8)
fk = atoms_kim.get_forces()
fe = atoms_emt.get_forces()
n = 0
for i in range(0, natoms, step):
n = (n + 1) % 3
ReportTest(txt + "Force(%i) of atom %i" % (n, i), fk[i, n],
fe[i, n], 1e-8)
sk = atoms_kim.get_stress()
se = atoms_emt.get_stress()
for i in range(6):
ReportTest(txt + "Stress(%i)" % (i, ), sk[i], se[i], 1e-8)
sk = atoms_kim.get_stresses()
se = atoms_emt.get_stresses()
for i in range(0, natoms, step):
n = (n + 1) % 6
# Volume per atom is not defined the same way: greater tolerance needed
ReportTest(txt + "Stress(%i) of atom %i" % (n, i), sk[i, n],
se[i, n], 1e-3)
ReportTest.Summary()
emt = EMT()
emt.set_subtractE0(False)
atoms_kim.set_calculator(kim)
atoms_emt.set_calculator(emt)
ek = atoms_kim.get_potential_energy()
ee = atoms_emt.get_potential_energy()
ReportTest(txt+"Total energy", ek, ee, 1e-8)
ek = atoms_kim.get_potential_energies()
ee = atoms_emt.get_potential_energies()
for i in range(0, natoms, step):
ReportTest(txt+"Energy of atom %i" % (i,), ek[i], ee[i], 1e-8)
fk = atoms_kim.get_forces()
fe = atoms_emt.get_forces()
n = 0
for i in range(0, natoms, step):
n = (n + 1) % 3
ReportTest(txt+"Force(%i) of atom %i" % (n, i), fk[i, n], fe[i, n], 1e-8)
sk = atoms_kim.get_stress()
se = atoms_emt.get_stress()
for i in range(6):
ReportTest(txt+"Stress(%i)" % (i,), sk[i], se[i], 1e-8)
sk = atoms_kim.get_stresses()
se = atoms_emt.get_stresses()
for i in range(0, natoms, step):
n = (n + 1) % 6
# Volume per atom is not defined the same way: greater tolerance needed
ReportTest(txt+"Stress(%i) of atom %i" % (n, i), sk[i, n], se[i, n], 1e-3)
ReportTest.Summary()
