def test_main():
# create calculator
#modelname = 'ex_model_Ar_P_MLJ_C'
modelname = 'ex_model_Ar_P_Morse_07C'
calc = KIMCalculator(modelname, debug=True)
# create an FCC crystal
argon = 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 coords of the first atoms
argon.positions[0,0] += 0.01
# attach the calculator to the atoms object
argon.set_calculator(calc)
for i in range(4):
print ('step', i)
# get energy and forces
energy = argon.get_potential_energy()
forces = argon.get_forces()
# rigidly move the atoms
argon.positions[:,0] += 1.629/2. # the cutoff skin is 1.63
# create an FCC crystal with no periodic BC
argon = FaceCenteredCubic(directions=[[1,0,0], [0,1,0], [0,0,1]], size=(2,1,1),
symbol='Ar', pbc=(0,0,0), latticeconstant=3.0)
# attach the SAME calculator to the new atoms object
argon.set_calculator(calc)
for i in range(4):
print('step', i)
# get energy and forces
energy = argon.get_potential_energy()
forces = argon.get_forces()
# rigidly move the atoms
argon.positions[:,0] += 1.631/2. # the cutoff skin is 1.63
def test_forces_random_structure(self):
atoms = FaceCenteredCubic('H', size=[2,2,2], latticeconstant=2.37126)
calc = Polydisperse(InversePowerLawPotential(1.0, 1.4, 0.1, 3, 1, 2.22))
atoms.set_masses(masses=np.repeat(1.0, len(atoms)))
atoms.set_array("size", np.random.uniform(1.0, 2.22, size=len(atoms)), dtype=float)
atoms.set_calculator(calc)
f = atoms.get_forces()
fn = calc.calculate_numerical_forces(atoms, d=0.0001)
self.assertArrayAlmostEqual(f, fn, tol=self.tol)
def test_direct_evaluation(self):
a = FaceCenteredCubic('Au', size=[2,2,2])
a.rattle(0.1)
calc = EAM('Au-Grochola-JCP05.eam.alloy')
a.set_calculator(calc)
f = a.get_forces()
calc2 = EAM('Au-Grochola-JCP05.eam.alloy')
i_n, j_n, dr_nc, abs_dr_n = neighbour_list('ijDd', a, cutoff=calc2.cutoff)
epot, virial, f2 = calc2.energy_virial_and_forces(a.numbers, i_n, j_n, dr_nc, abs_dr_n)
self.assertArrayAlmostEqual(f, f2)
a = FaceCenteredCubic('Cu', size=[2,2,2])
calc = EAM('CuAg.eam.alloy')
a.set_calculator(calc)
FIRE(StrainFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e_Cu = a.get_potential_energy()/len(a)
a = FaceCenteredCubic('Ag', size=[2,2,2])
a.set_calculator(calc)
FIRE(StrainFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e_Ag = a.get_potential_energy()/len(a)
self.assertTrue(abs(e_Ag+2.85)<1e-6)
a = L1_2(['Ag', 'Cu'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(abs((e-(syms=='Cu').sum()*e_Cu-
(syms=='Ag').sum()*e_Ag)/len(a)-0.096)<0.0005)
a = B1(['Ag', 'Cu'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(abs((e-(syms=='Cu').sum()*e_Cu-
(syms=='Ag').sum()*e_Ag)/len(a)-0.516)<0.0005)
a = B2(['Ag', 'Cu'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(abs((e-(syms=='Cu').sum()*e_Cu-
(syms=='Ag').sum()*e_Ag)/len(a)-0.177)<0.0003)
a = L1_2(['Cu', 'Ag'], size=[2,2,2], latticeconstant=4.0)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
e = a.get_potential_energy()
syms = np.array(a.get_chemical_symbols())
self.assertTrue(abs((e-(syms=='Cu').sum()*e_Cu-
(syms=='Ag').sum()*e_Ag)/len(a)-0.083)<0.0005)
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()
norbs = []
sccs = ['non-SCC', 'SCC'][SCC]
for nx in [1, 2, 3, 4, 5]:
for ny in [1, 2, 3, 4, 5]:
print('nx', nx, ny)
atoms = FaceCenteredCubic(directions=[[1,-1,0], [1,1,-2], [1,1,1]],\
size=(nx,ny,1), symbol='Au', pbc=(0,0,0))
calc = Hotbit(verbose=True,
SCC=SCC,
gamma_cut=3,
txt='size2.cal',
**default_param)
atoms.set_calculator(calc)
try:
atoms.get_forces()
except:
continue
calc.timer.summary()
timings.append(calc.timer.get_timings())
norbs.append(calc.el.get_nr_orbitals())
calc.__del__()
order = argsort(norbs)
norbs = sort(norbs)
timings2 = []
for i in order:
timings2.append(timings[i])
times = {}
maxtime = 0.0
from asap3 import *
from asap3.Timing import report_timing
from ase.lattice.cubic import FaceCenteredCubic
import time
nsteps = 10
start = time.time()
if len(sys.argv) >= 2 and sys.argv[1] == '-t':
AsapThreads()
if len(sys.argv) >= 2 and sys.argv[1] == '-T':
AsapThreads(6)
atoms = FaceCenteredCubic(size=(100,100,50), symbol='Cu')
atoms.set_calculator(EMT())
print "Number of atoms:", len(atoms)
d = 0.1
pos = atoms.arrays['positions'] # Nasty!
for i in range(nsteps):
pos[50][0] += d
d = -d
f = atoms.get_forces()
report_timing()
print "Wall time elapsed:", time.time() - start
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()
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()
"""Check that energy is correct even after wrapping through periodic boundary conditions.
"""
from ase.lattice.cubic import FaceCenteredCubic
from asap3 import *
from asap3.testtools import *
import random
ref_atoms = FaceCenteredCubic(size=(7, 7, 7),
symbol="Cu",
pbc=(True, False, True))
ref_atoms.set_calculator(EMT())
ref_energy = ref_atoms.get_potential_energy()
ref_energies = ref_atoms.get_potential_energies()
ref_forces = ref_atoms.get_forces()
passes = 5
for ps in range(passes):
print "Pass", ps, "of", passes
atoms = ref_atoms.copy()
atoms.set_calculator(EMT())
nat = random.randint(0, len(atoms))
assert nat < len(atoms)
pos0 = atoms[nat].position
cell = atoms.get_cell()
for d in range(1, 4):
for dx in (-d, 0, d):
#for dy in (-d, 0, d):
for dy in (0, ):
from asap3 import *
from ase.lattice.cubic import FaceCenteredCubic
from asap3.testtools import ReportTest
atoms = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
size=(6,6,6), symbol="Cu")
atoms.set_calculator(EMT())
f1 = atoms.get_forces()
atoms.set_calculator(EMT())
f2 = atoms.get_forces()
maxdev = abs(f2 - f1).max()
print maxdev
ReportTest("Max error 1:", maxdev, 0.0, 1e-6)
atoms2 = Atoms(atoms)
if atoms2.get_calculator() is None:
# Slightly old ase
atoms2.set_calculator(atoms.get_calculator())
f2 = atoms2.get_forces()
maxdev = abs(f2 - f1).max()
print maxdev
ReportTest("Max error 2:", maxdev, 0.0, 1e-6)
f2 = atoms.get_forces()
maxdev = abs(f2 - f1).max()
print maxdev
ReportTest("Max error 1:", maxdev, 0.0, 1e-6)
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
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):
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
#set_verbose(1)
master = world.rank == 0
if master:
atoms0 = FaceCenteredCubic(symbol='Pt', size=(15, 15, 30))
else:
atoms0 = None
atoms0 = MakeParallelAtoms(atoms0, (1, 1, 2))
atoms0.set_calculator(pot())
print >> sys.stderr, "*********** FIRST FORCE CALCULATION ************"
print >> sys.stderr, "len(atoms) =", len(
atoms0), " no. atoms =", atoms0.get_number_of_atoms()
f0 = atoms0.get_forces()
perturbation = 0.01 * np.random.standard_normal(atoms0.get_positions().shape)
r = atoms0.get_positions() + perturbation
atoms0.set_positions(r)
print >> sys.stderr, "*********** SECOND FORCE CALCULATION ************"
f1 = atoms0.get_forces()
print >> sys.stderr, "*********** COPYING ATOMS **************"
atoms2 = ParallelAtoms((1, 1, 2), atoms0.comm, atoms0, distribute=False)
atoms2.set_calculator(pot())
print >> sys.stderr, "*********** THIRD FORCE CALCULATION ************"
f2 = atoms2.get_forces()
#maxdev = abs(f2 - f1).max()
#print maxdev
"""Check that energy is correct even after wrapping through periodic boundary conditions.
"""
from ase.lattice.cubic import FaceCenteredCubic
from asap3 import *
from asap3.testtools import *
import random
ref_atoms = FaceCenteredCubic(size=(7,7,7), symbol="Cu", pbc=(True, False, True))
ref_atoms.set_calculator(EMT())
ref_energy = ref_atoms.get_potential_energy()
ref_energies = ref_atoms.get_potential_energies()
ref_forces = ref_atoms.get_forces()
passes = 5
for ps in range(passes):
print "Pass", ps, "of", passes
atoms = ref_atoms.copy()
atoms.set_calculator(EMT())
nat = random.randint(0, len(atoms))
assert nat < len(atoms)
pos0 = atoms[nat].position
cell = atoms.get_cell()
for d in range(1,4):
for dx in (-d, 0, d):
#for dy in (-d, 0, d):
for dy in (0,):
for dz in (-d, 0 ,d):
deltar = dx * cell[0] + dy * cell[1] + dz * cell[2]
def MakeEMT2013():
"EMT2013 potential."
return EMT2013(PtY_parameters)
for pot in (EMT, MakeLJ, MakeEMT2013):
print "Testing:", pot.__doc__.split("\n")[0]
atoms1 = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=(6, 6, 6),
symbol="Pt")
emt = pot()
atoms1.set_calculator(emt)
f1 = atoms1.get_forces()
atoms2 = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=(5, 5, 5),
symbol="Pt")
atoms2.set_calculator(emt)
f3 = atoms1.get_forces()
maxdev = abs(f3 - f1).max()
print maxdev
ReportTest("Max error 1:", maxdev, 0.0, 1e-6)
atoms1 = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=(6, 6, 6),
symbol="Pt")
emt = pot()
atoms1.set_calculator(emt)
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):
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)
