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()
def test_lammpslib_change_cell_bcs(factory, lattice_params, calc_params_NiH):
"""Test that a change in unit cell boundary conditions is
handled correctly by lammpslib"""
atoms = FaceCenteredCubic(**lattice_params)
calc = factory.calc(**calc_params_NiH)
atoms.calc = calc
energy_ppp_ref = -142.400000403
energy_ppp = atoms.get_potential_energy()
print("Computed energy with boundary ppp = {}".format(energy_ppp))
assert energy_ppp == pytest.approx(energy_ppp_ref, rel=1e-4)
atoms.set_pbc((False, False, True))
energy_ssp_ref = -114.524625705
energy_ssp = atoms.get_potential_energy()
print("Computed energy with boundary ssp = {}".format(energy_ssp))
assert energy_ssp == pytest.approx(energy_ssp_ref, rel=1e-4)
def test_lammpslib_change_cell_bcs():
# test that a change in unit cell boundary conditions is
# handled correctly by lammpslib
import numpy as np
from ase.calculators.lammpslib import LAMMPSlib
from ase.lattice.cubic import FaceCenteredCubic
cmds = ["pair_style eam/alloy", "pair_coeff * * NiAlH_jea.eam.alloy Ni H"]
lammps = LAMMPSlib(lmpcmds=cmds,
atom_types={
'Ni': 1,
'H': 2
},
log_file='test.log',
keep_alive=True)
atoms = FaceCenteredCubic(size=(2, 2, 2),
latticeconstant=3.52,
symbol="Ni",
pbc=True)
atoms.calc = lammps
energy_ppp_ref = -142.400000403
energy_ppp = atoms.get_potential_energy()
print("Computed energy with boundary ppp = {}".format(energy_ppp))
np.testing.assert_allclose(energy_ppp,
energy_ppp_ref,
atol=1e-4,
rtol=1e-4)
atoms.set_pbc((False, False, True))
energy_ssp_ref = -114.524625705
energy_ssp = atoms.get_potential_energy()
print("Computed energy with boundary ssp = {}".format(energy_ssp))
np.testing.assert_allclose(energy_ssp,
energy_ssp_ref,
atol=1e-4,
rtol=1e-4)
def get_structure(self, name, elements, a=None, c=None, l=None):
# Check number of elements
if name[:3] in ['fcc', 'hcp']:
if len(elements) != 1:
raise ValueError("Tuple of elements must be of length one")
if name[:3] in ['l12', 'l10'] or name[:2] == 'B2':
if len(elements) != 2:
raise ValueError("Tuple of elements must be of length two")
# Get lattice constants
if a is None:
if name[:2] == 'B2':
a = self.get_lattice_constant_a(name[:2], elements)
elif name[:3] in ['fcc', 'hcp', 'bcc', 'l12', 'l10']:
a = self.get_lattice_constant_a(name[:3], elements)
if c is None:
if name[:3] in ['hcp', 'l10']:
c = self.get_lattice_constant_c(name[:3], elements)
# Get size
if name in ['fcc', 'hcp', 'bcc', 'l12', 'l10', 'B2']:
size = self.properties[name + '_size']
elif name in ['fcc100', 'fcc111', 'hcp0001']:
size = self.properties[name + '_size'][:2] + (l, )
# Make structure
if name == 'fcc':
atoms = FaceCenteredCubic(symbol=elements[0],
size=size,
latticeconstant=a)
elif name == 'hcp':
atoms = HexagonalClosedPacked(symbol=elements[0],
size=size,
directions=[[2, -1, -1, 0],
[0, 1, -1, 0],
[0, 0, 0, 1]],
latticeconstant=(a, c))
elif name == 'bcc':
atoms = BodyCenteredCubic(symbol=elements[0],
size=size,
latticeconstant=a)
elif name == 'B2':
atoms = B2(symbol=elements, size=size, latticeconstant=a)
elif name == 'l12':
atoms = L1_2(symbol=elements, size=size, latticeconstant=a)
elif name == 'l10':
atoms = L1_0(symbol=elements, size=size, latticeconstant=(a, c))
elif name == 'fcc100':
atoms = fcc100(symbol=elements[0], size=size, a=a, vacuum=10.0)
elif name == 'fcc111':
atoms = fcc111(symbol=elements[0],
size=size,
a=a,
vacuum=10.0,
orthogonal=True)
elif name == 'hcp0001':
atoms = hcp0001(symbol=elements[0],
size=size,
a=a,
c=c,
vacuum=10.0,
orthogonal=True)
elif name == 'hcp1010A':
raise ValueError("Structure '%s' not supported" % (name, ))
atoms = None
elif name == 'hcp1010B':
raise ValueError("Structure '%s' not supported" % (name, ))
atoms = None
elif name == 'l12100':
n = (l + 1) / 2
atoms = L1_2(symbol=elements, size=(8, 8, n), latticeconstant=a)
atoms.set_pbc([True, True, False])
# Remove layers
atoms = atoms[atoms.get_positions()[:, 2] > 0.1 * a]
# Set vacuum
atoms.center(axis=2, vacuum=10.0)
elif name == 'l12111':
if l % 3 == 0:
n = l / 3
c = 0
else:
n = l / 3 + 1
c = 3 - l % 3
atoms = L1_2(
symbol=elements,
size=(8, 4, n),
#directions=[[1,-1,0],[1,0,-1],[1,1,1]], latticeconstant=a)
directions=[[1, -1, 0], [1, 1, -2], [1, 1, 1]],
latticeconstant=a)
atoms.set_pbc([True, True, False])
# Wrap positions
scpos = atoms.get_scaled_positions()
scpos[scpos > (1.0 - 1e-12)] = 0.0
atoms.set_scaled_positions(scpos)
# Remove layers
if c > 0:
atoms = atoms[atoms.get_positions()[:, 2] > (c - 0.5) * a /
np.sqrt(3.0)]
# Set vacuum
atoms.center(axis=2, vacuum=10.0)
else:
raise ValueError("Structure '%s' not supported" % (name, ))
return atoms
from numpy import *
symbol = 'Ar'
cells = 15
ar = FaceCenteredCubic(symbol,
pbc=[(1, 1, 1)],
directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=[cells, cells, 1])
for m in listmodels():
if symbol in m:
try:
print "Try model: ", m
calc1 = KIMCalculator(m)
ar.set_calculator(calc1)
N = ar.get_number_of_atoms()
ar.set_pbc([(1, 1, 1)])
bulk_energy = ar.get_potential_energy() / N
ar.set_pbc([(1, 1, 0)])
surf_energy = ar.get_potential_energy() / N
print "\tsurface = ", surf_energy - bulk_energy
#virial = ar.get_stresses()
#print "\tvirial = ", virial
print
except SupportError, e:
print "\tskipping ", m, "\n\t", e, " ...\n"
continue
from asap3 import *
from ase.lattice.cubic import FaceCenteredCubic
from numpy import *
from asap3.testtools import ReportTest
print_version(1)
#set_verbose(1)
atoms = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]], size=(6,6,6),
symbol="Cu", pbc=(1,1,0))
atoms.set_calculator(EMT())
ecorrect = atoms.get_potential_energy()
atoms2 = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]], size=(6,6,6),
symbol="Cu", pbc=(0,0,0))
atoms2.set_pbc((1,1,0))
atoms2.set_calculator(EMT())
e1= atoms2.get_potential_energy()
ReportTest("e1 correct", e1, ecorrect, 0.001)
atoms.set_pbc((0,1,0))
atoms.set_pbc((1,1,0))
e2 = atoms.get_potential_energy()
ReportTest("e2 correct", e2, ecorrect, 0.001)
print "Setting pbc"
atoms.set_pbc((0,1,0))
print "Calculating energy"
dummy = atoms.get_potential_energy()
assert(fabs(dummy - ecorrect) > 1.0)
atoms.set_pbc((1,1,0))
radius = 15
size = [14, 10, 100]
# radius = 30
# size = [28, 20, 100] # 51500 atoms
a = FaceCenteredCubic('Au',
directions=[[1, 0, -1], [0, 1, 0], [1, 0, 1]],
size=size)
c = a.cell.diagonal() / 2
dir1 = [sqrt(2), 1, 0]
dir2 = [sqrt(2), -1, 0]
dir3 = [0, 1, 0]
dir1 = np.array(dir1) / np.linalg.norm(dir1)
dir2 = np.array(dir2) / np.linalg.norm(dir2)
dir3 = np.array(dir3) / np.linalg.norm(dir3)
r = a.get_positions() - c
m = np.abs(r.dot(dir1)) > radius
m = np.logical_or(m, np.abs(r.dot(dir2)) > radius)
m = np.logical_or(m, np.abs(r.dot(dir3)) > radius)
del a[m]
a.center()
a.set_pbc([False, False, True])
io.write('whisker.xyz', a)
io.write('whisker.data', a, format='lammps-data')
from kimcalculator import *
from numpy import *
symbol = 'Ar'
cells = 15
ar = FaceCenteredCubic(symbol, pbc=[(1,1,1)], directions=[[1,0,0],[0,1,0],[0,0,1]], size=[cells,cells,1])
for m in listmodels():
if symbol in m:
try:
print "Try model: ", m
calc1 = KIMCalculator(m)
ar.set_calculator(calc1)
N = ar.get_number_of_atoms()
ar.set_pbc([(1,1,1)])
bulk_energy = ar.get_potential_energy() / N
ar.set_pbc([(1,1,0)])
surf_energy = ar.get_potential_energy() / N
print "\tsurface = ", surf_energy - bulk_energy
#virial = ar.get_stresses()
#print "\tvirial = ", virial
print
except SupportError, e:
print "\tskipping ", m, "\n\t", e, " ...\n"
continue
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()
# test that a change in unit cell boundary conditions is
# handled correctly by lammpslib
import numpy as np
from ase.calculators.lammpslib import LAMMPSlib
from ase.lattice.cubic import FaceCenteredCubic
cmds = ["pair_style eam/alloy", "pair_coeff * * NiAlH_jea.eam.alloy Ni H"]
lammps = LAMMPSlib(lmpcmds=cmds,
atom_types={
'Ni': 1,
'H': 2
},
log_file='test.log',
keep_alive=True)
atoms = FaceCenteredCubic(size=(2, 2, 2),
latticeconstant=3.52,
symbol="Ni",
pbc=True)
atoms.set_calculator(lammps)
energy_ppp_ref = -142.400000403
energy_ppp = atoms.get_potential_energy()
print("Computed energy with boundary ppp = {}".format(energy_ppp))
np.testing.assert_allclose(energy_ppp, energy_ppp_ref, atol=1e-4, rtol=1e-4)
atoms.set_pbc((False, False, True))
energy_ssp_ref = -114.524625705
energy_ssp = atoms.get_potential_energy()
print("Computed energy with boundary ssp = {}".format(energy_ssp))
np.testing.assert_allclose(energy_ssp, energy_ssp_ref, atol=1e-4, rtol=1e-4)
if nbltype.startswith("MI_OPBC"):
boundaries = ((1, 1, 1), )
elif nbltype == "CLUSTER":
boundaries = ((0, 0, 0), )
else:
boundaries = ((1, 1, 1), (0, 0, 0), (0, 0, 1))
for pbc in boundaries:
txt = nbltype + (" PBC=%1i%1i%1i " % pbc)
# Test that EMT reimported through OpenKIM gives the right results.
atoms_kim = FaceCenteredCubic(size=(10, 10, 10), symbol='Cu')
#atoms_kim = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
# size=(30, 30, 30),
# symbol="Cu")
natoms = len(atoms_kim)
atoms_kim.set_pbc(pbc)
r = atoms_kim.get_positions()
r.flat[:] += 0.1 * np.sin(np.arange(3 * natoms))
atoms_kim.set_positions(r)
atoms_emt = atoms_kim.copy()
kim = OpenKIMcalculator(openkimmodel, allowed=nbltype)
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):
if nbltype.startswith("MI_OPBC"):
boundaries = ((1,1,1),)
elif nbltype == "CLUSTER":
boundaries = ((0,0,0),)
else:
boundaries = ((1,1,1), (0,0,0), (0,0,1))
for pbc in boundaries:
txt = nbltype + (" PBC=%1i%1i%1i " % pbc)
# Test that EMT reimported through OpenKIM gives the right results.
atoms_kim = FaceCenteredCubic(size=(10,10,10), symbol='Cu')
#atoms_kim = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
# size=(30, 30, 30),
# symbol="Cu")
natoms = len(atoms_kim)
atoms_kim.set_pbc(pbc)
r = atoms_kim.get_positions()
r.flat[:] += 0.1 * np.sin(np.arange(3*natoms))
atoms_kim.set_positions(r)
atoms_emt = atoms_kim.copy()
kim = OpenKIMcalculator(openkimmodel, allowed=nbltype)
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):
