def test_springcalc():
# setup
k = 3.0
atoms_ideal = bulk('Al').repeat(3)
calc = SpringCalculator(atoms_ideal.get_positions(), k)
displacements = np.array([(d, 2 * d, 3 * d)
for d in np.linspace(0, 1, len(atoms_ideal))])
# calc forces and energy
atoms = atoms_ideal.copy()
atoms.positions += displacements
atoms.calc = calc
forces = atoms.get_forces()
Epot = atoms.get_potential_energy()
# reference forces and energy
Epot_target = np.sum(k / 2.0 * displacements**2)
forces_target = -k * displacements
assert np.allclose(forces, forces_target)
assert np.isclose(Epot, Epot_target)
# numeric forces test
atoms_ideal.calc = calc
f, fn = gradient_test(atoms_ideal)
assert abs(f - fn).max() < 1e-10
def test_unitcellfilterpressure():
a0 = bulk('Cu', cubic=True)
# perturb the atoms
s = a0.get_scaled_positions()
s[:, 0] *= 0.995
a0.set_scaled_positions(s)
# perturb the cell
a0.cell[...] += np.random.uniform(-1e-2, 1e-2, size=9).reshape((3, 3))
atoms = a0.copy()
atoms.calc = LennardJones()
ucf = UnitCellFilter(atoms, scalar_pressure=10.0 * GPa)
# test all derivatives
f, fn = gradient_test(ucf)
assert abs(f - fn).max() < 1e-6
opt = FIRE(ucf)
opt.run(1e-3)
# check pressure is within 0.1 GPa of target
sigma = atoms.get_stress() / GPa
pressure = -(sigma[0] + sigma[1] + sigma[2]) / 3.0
assert abs(pressure - 10.0) < 0.1
atoms = a0.copy()
atoms.calc = LennardJones()
ecf = ExpCellFilter(atoms, scalar_pressure=10.0 * GPa)
# test all deritatives
f, fn = gradient_test(ecf)
assert abs(f - fn).max() < 1e-6
opt = LBFGSLineSearch(ecf)
opt.run(1e-3)
# check pressure is within 0.1 GPa of target
sigma = atoms.get_stress() / GPa
pressure = -(sigma[0] + sigma[1] + sigma[2]) / 3.0
assert abs(pressure - 10.0) < 0.1
def test_pressure(atoms, cellfilter):
xcellfilter = cellfilter(atoms, scalar_pressure=10.0 * GPa)
# test all derivatives
f, fn = gradient_test(xcellfilter)
assert abs(f - fn).max() < 5e-6
opt = LBFGS(xcellfilter)
opt.run(1e-3)
# check pressure is within 0.1 GPa of target
sigma = atoms.get_stress() / GPa
pressure = -(sigma[0] + sigma[1] + sigma[2]) / 3.0
assert abs(pressure - 10.0) < 0.1
def test_cellfilter(atoms, cellfilter):
xcellfilter = cellfilter(atoms)
f, fn = gradient_test(xcellfilter)
assert abs(f - fn).max() < 3e-6
import numpy as np
from ase.build import bulk
from ase.calculators.test import gradient_test
from ase.calculators.lj import LennardJones
from ase.constraints import UnitCellFilter
a0 = bulk('Cu', cubic=True)
# perturb the atoms
s = a0.get_scaled_positions()
s[:, 0] *= 0.995
a0.set_scaled_positions(s)
# perturb the cell
a0.cell[...] += np.random.uniform(-1e-2, 1e-2, size=9).reshape((3, 3))
atoms = a0.copy()
atoms.set_calculator(LennardJones())
ucf = UnitCellFilter(atoms)
# test all deritatives
f, fn = gradient_test(ucf)
assert abs(f - fn).max() < 1e-6
def test_expcellfilter(setup_atoms):
ecf = ExpCellFilter(setup_atoms)
# test all derivatives
f, fn = gradient_test(ecf)
assert abs(f - fn).max() < 3e-6
def test_unitcellfilter(setup_atoms):
ucf = UnitCellFilter(setup_atoms)
f, fn = gradient_test(ucf)
assert abs(f - fn).max() < 3e-6
import numpy as np
from ase.build import bulk
from ase.calculators.harmonic import SpringCalculator
from ase.calculators.test import gradient_test
# setup
k = 3.0
atoms_ideal = bulk('Al').repeat(3)
calc = SpringCalculator(atoms_ideal.get_positions(), k)
displacements = np.array([(d, 2 * d, 3 * d)
for d in np.linspace(0, 1, len(atoms_ideal))])
# calc forces and energy
atoms = atoms_ideal.copy()
atoms.positions += displacements
atoms.set_calculator(calc)
forces = atoms.get_forces()
Epot = atoms.get_potential_energy()
# reference forces and energy
Epot_target = np.sum(k / 2.0 * displacements**2)
forces_target = -k * displacements
assert np.allclose(forces, forces_target)
assert np.isclose(Epot, Epot_target)
# numeric forces test
atoms_ideal.set_calculator(calc)
f, fn = gradient_test(atoms_ideal)
assert abs(f - fn).max() < 1e-10
import numpy as np
from ase.build import bulk
from ase.calculators.test import gradient_test
from ase.calculators.lj import LennardJones
from ase.constraints import UnitCellFilter
a0 = bulk('Cu', cubic=True)
# perturb the atoms
s = a0.get_scaled_positions()
s[:, 0] *= 0.995
a0.set_scaled_positions(s)
# perturb the cell
a0.cell[...] += np.random.uniform(-1e-2, 1e-2,
size=9).reshape((3,3))
atoms = a0.copy()
atoms.set_calculator(LennardJones())
ucf = UnitCellFilter(atoms)
# test all deritatives
f, fn = gradient_test(ucf)
assert abs(f - fn).max() < 1e-6
