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_CuAg(self):
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_utilities():
eps = 1e-5
atoms = Icosahedron('Cu', 3)
atoms.numbers[[0, 13, 15, 16, 18, 19, 21, 22, 24, 25, 27, 28, 30]] = 79
atoms.center(vacuum=0.0)
atoms.calc = EMT()
with FIRE(atoms, logfile=None) as opt:
opt.run(fmax=0.05)
rmax = 8.
nbins = 5
rdf, dists = get_rdf(atoms, rmax, nbins)
calc_dists = np.arange(rmax / (2 * nbins), rmax, rmax / nbins)
assert all(abs(dists - calc_dists) < eps)
calc_rdf = [0., 0.84408157, 0.398689, 0.23748934, 0.15398546]
assert all(abs(rdf - calc_rdf) < eps)
dm = atoms.get_all_distances()
s = np.zeros(5)
for c in [(29, 29), (29, 79), (79, 29), (79, 79)]:
inv_norm = len(np.where(atoms.numbers == c[0])[0]) / len(atoms)
s += get_rdf(atoms, rmax, nbins, elements=c,
distance_matrix=dm, no_dists=True) * inv_norm
assert all(abs(s - calc_rdf) < eps)
AuAu = get_rdf(atoms, rmax, nbins, elements=(79, 79),
distance_matrix=dm, no_dists=True)
assert all(abs(AuAu[-2:] - [0.12126445, 0.]) < eps)
bulk = L1_2(['Au', 'Cu'], size=(3, 3, 3), latticeconstant=2 * np.sqrt(2))
rdf = get_rdf(bulk, 4.2, 5)[0]
calc_rdf = [0., 0., 1.43905094, 0.36948605, 1.34468694]
assert all(abs(rdf - calc_rdf) < eps)
def makeatoms(causetrouble):
atoms = L1_2(size=(10,10,10), symbol=('Au', 'Cu'), latticeconstant=4.0)
r = atoms.get_positions()
r += np.random.normal(0.0, 0.0001, r.shape)
if causetrouble:
r[100] = r[110]
atoms.set_positions(r)
return atoms
def test_hessian_crystalline_alloy(self):
"""Calculate Hessian matrix of crystalline alloy
Reference: finite difference approximation of
Hessian from ASE
"""
calculator = EAM('ZrCu.onecolumn.eam.alloy')
lattice_size = [4, 4, 4]
# The lattice parameters are not correct, but that should be irrelevant
# CuZr3
atoms = L1_2(['Cu', 'Zr'], size=lattice_size, latticeconstant=4.0)
self._test_hessian(atoms, calculator)
# Cu3Zr
atoms = L1_2(['Zr', 'Cu'], size=lattice_size, latticeconstant=4.0)
self._test_hessian(atoms, calculator)
# CuZr
atoms = B2(['Zr', 'Cu'], size=lattice_size, latticeconstant=3.3)
self._test_hessian(atoms, calculator)
def test_CuZr(self):
# This is a test for the potential published in:
# Mendelev, Sordelet, Kramer, J. Appl. Phys. 102, 043501 (2007)
a = FaceCenteredCubic('Cu', size=[2, 2, 2])
calc = EAM('CuZr_mm.eam.fs', kind='eam/fs')
a.set_calculator(calc)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
a_Cu = a.cell.diagonal().mean() / 2
#print('a_Cu (3.639) = ', a_Cu)
self.assertAlmostEqual(a_Cu, 3.639, 3)
a = HexagonalClosedPacked('Zr', size=[2, 2, 2])
a.set_calculator(calc)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
a, b, c = a.cell / 2
#print('a_Zr (3.220) = ', norm(a), norm(b))
#print('c_Zr (5.215) = ', norm(c))
self.assertAlmostEqual(norm(a), 3.220, 3)
self.assertAlmostEqual(norm(b), 3.220, 3)
self.assertAlmostEqual(norm(c), 5.215, 3)
# CuZr3
a = L1_2(['Cu', 'Zr'], 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)
self.assertAlmostEqual(a.cell.diagonal().mean() / 2, 4.324, 3)
# Cu3Zr
a = L1_2(['Zr', '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)
self.assertAlmostEqual(a.cell.diagonal().mean() / 2, 3.936, 3)
# CuZr
a = B2(['Zr', 'Cu'], size=[2, 2, 2], latticeconstant=3.3)
a.set_calculator(calc)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
self.assertAlmostEqual(a.cell.diagonal().mean() / 2, 3.237, 3)
def MakeCu3Ni(T=300):
print "Preparing", T, "K NiCu3 system."
atoms = L1_2(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol=('Ni', 'Cu'),
latticeconstant=3.61,
size=(29, 29, 30))
atoms.set_calculator(EMT())
MaxwellBoltzmannDistribution(atoms, 2 * T * units.kB)
#dyn = VelocityVerlet(atoms, 5*units.fs)
dyn = Langevin(atoms, 5 * units.fs, T * units.kB, 0.05)
dyn.run(50)
print "Done. Temperature =", temperature(atoms), \
"K. Number of atoms: ", len(atoms)
return atoms
kpts = (2, 2, 2)
QNA = {
'alpha': 2.0,
'name': 'QNA',
'stencil': 1,
'orbital_dependent': False,
'parameters': {
'Au': (0.125, 0.1),
'Cu': (0.0795, 0.005)
},
'setup_name': 'PBE',
'type': 'qna-gga'
}
atoms = L1_2(['Au', 'Cu'], latticeconstant=3.74)
# Displace atoms to have non-zero forces in the first place
atoms[0].position[0] += 0.1
dx_array = [-0.005, 0.000, 0.005]
E = []
for i, dx in enumerate(dx_array):
calc = GPAW(mode=PW(ecut),
experimental={'niter_fixdensity': 2},
xc=QNA,
kpts=kpts,
parallel={'domain': 1},
txt=name + '%.0f.txt' % ecut)
atoms[0].position[0] += dx
rmax = 8.
nbins = 5
rdf, dists = get_rdf(atoms, rmax, nbins)
calc_dists = np.arange(rmax / (2 * nbins), rmax, rmax / nbins)
assert all(abs(dists - calc_dists) < eps)
calc_rdf = [0., 0.84408157, 0.398689, 0.23748934, 0.15398546]
assert all(abs(rdf - calc_rdf) < eps)
dm = atoms.get_all_distances()
s = np.zeros(5)
for c in [(29, 29), (29, 79), (79, 29), (79, 79)]:
inv_norm = len(np.where(atoms.numbers == c[0])[0]) / len(atoms)
s += get_rdf(
atoms, rmax, nbins, elements=c, distance_matrix=dm,
no_dists=True) * inv_norm
assert all(abs(s - calc_rdf) < eps)
AuAu = get_rdf(atoms,
rmax,
nbins,
elements=(79, 79),
distance_matrix=dm,
no_dists=True)
assert all(abs(AuAu[-2:] - [0.12126445, 0.]) < eps)
bulk = L1_2(['Au', 'Cu'], size=(3, 3, 3), latticeconstant=2 * np.sqrt(2))
rdf = get_rdf(bulk, 4.2, 5)[0]
calc_rdf = [0., 0., 1.43905094, 0.36948605, 1.34468694]
assert all(abs(rdf - calc_rdf) < eps)
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
def test_mix_eam_alloy(self):
if False:
source, parameters, F, f, rep = read_eam("CuAu_Zhou.eam.alloy",
kind="eam/alloy")
source1, parameters1, F1, f1, rep1 = mix_eam(
["Cu_Zhou.eam.alloy", "Au_Zhou.eam.alloy"], "eam/alloy",
"weight")
write_eam(source1,
parameters1,
F1,
f1,
rep1,
"CuAu_mixed.eam.alloy",
kind="eam/alloy")
calc0 = EAM('CuAu_Zhou.eam.alloy')
calc1 = EAM('CuAu_mixed.eam.alloy')
a = FaceCenteredCubic('Cu', size=[2, 2, 2])
a.set_calculator(calc0)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy() / len(a)
a = FaceCenteredCubic('Cu', size=[2, 2, 2])
a.set_calculator(calc1)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy() / len(a)
self.assertTrue(e0 - e1 < 0.0005)
a = FaceCenteredCubic('Au', size=[2, 2, 2])
a.set_calculator(calc0)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy() / len(a)
a = FaceCenteredCubic('Au', size=[2, 2, 2])
a.set_calculator(calc1)
FIRE(StrainFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy() / len(a)
self.assertTrue(e0 - e1 < 0.0005)
a = L1_2(['Au', 'Cu'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc0)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy() / len(a)
a = L1_2(['Au', 'Cu'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc1)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy() / len(a)
self.assertTrue(e0 - e1 < 0.0005)
a = L1_2(['Cu', 'Au'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc0)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy() / len(a)
a = L1_2(['Cu', 'Au'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc1)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy() / len(a)
self.assertTrue(e0 - e1 < 0.0005)
a = B1(['Au', 'Cu'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc0)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e0 = a.get_potential_energy() / len(a)
a = B1(['Au', 'Cu'], size=[2, 2, 2], latticeconstant=4.0)
a.set_calculator(calc1)
FIRE(UnitCellFilter(a, mask=[1, 1, 1, 0, 0, 0]),
logfile=None).run(fmax=0.001)
e1 = a.get_potential_energy() / len(a)
self.assertTrue(e0 - e1 < 0.0005)
os.remove("CuAu_mixed.eam.alloy")
def L12_BM_LC_Calculator(self, EMT, PARAMETERS):
# Return 0 is used when the method is not desired to be used
# return 0
""" The method L12_BM_LC_Calculator uses the EMT calculator to find the lattice constant which gives
the lowest possible energy for an alloy of two elements and from a polynomial fit of the energy as a
function of the lattice constant it calculates and returns the Bulk modulus, the volume of the system at
the lowest possible energy and this energy """
# Three values for the lattice constant, a0, are chosen. The highest and lowest value is chosen so that it
# is certain that these are to high/low respectively compared to the "correct" value. This is done by using the
# experimental value of the lattice constant, a0_exp, as the middle value and to high/low values are then:
# a0_exp +- a0_mod, a0_mod = a0_exp/10
a0_exp = ((PARAMETERS[self.Element[0]][1] +
3 * PARAMETERS[self.Element[1]][1]) * numpy.sqrt(2) * beta *
Bohr / 4)
a0_mod = a0_exp * 0.20
a0_guesses = numpy.array([a0_exp - a0_mod, a0_exp, a0_exp + a0_mod])
# An atoms object consisting of atoms of the chosen element is initialized
atoms = L1_2(size=(self.Size, self.Size, self.Size),
symbol=self.Element,
latticeconstant=a0_exp)
atoms.set_calculator(EMT)
# An identity matrix for the system is saved to a variable
IdentityMatrix = numpy.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
# An array for the energy for the chosen guesses for a0 is initialized:
E_guesses = numpy.zeros(5)
# The energies are calculated
for i in range(3):
# Changes the lattice constant for the atoms object
atoms.set_cell(a0_guesses[i] * self.Size * IdentityMatrix,
scale_atoms=True)
# Calculates the energy of the system for the new lattice constant
E_guesses[i] = atoms.get_potential_energy()
# Bisection is used in order to find a small interval of the lattice constant for the minimum of the energy (an
# abitrary interval length is chosen), This is possible because we are certian from theory that there is only
# one minimum of the energy function in the interval of interest and thus we wont "fall" into a local minimum
# and stay there by accident.
while (a0_guesses[2] - a0_guesses[0]) >= self.Tol:
if min([E_guesses[0], E_guesses[2]]) == E_guesses[0]:
# A new guess for the lattice constant is introduced
a0_new_guess = 0.67 * a0_guesses[1] + 0.33 * a0_guesses[2]
# The energy for this new guess is calculated
atoms.set_cell(a0_new_guess * self.Size * IdentityMatrix,
scale_atoms=True)
E_new_guess = atoms.get_potential_energy()
# A check for changes in the energy minimum is made and the guesses for a0 and their corrosponding
# energies are ajusted.
if min(E_new_guess, min(E_guesses[0:3])) != E_new_guess:
a0_guesses[2] = a0_new_guess
E_guesses[2] = E_new_guess
else:
a0_guesses[0] = a0_guesses[1]
a0_guesses[1] = a0_new_guess
E_guesses[0] = E_guesses[1]
E_guesses[1] = E_new_guess
elif min([E_guesses[0], E_guesses[2]]) == E_guesses[2]:
# A new guess for the lattice constant is introduced
a0_new_guess = 0.33 * a0_guesses[0] + 0.67 * a0_guesses[1]
# The energy for this new guess is calculated
atoms.set_cell(a0_new_guess * self.Size * IdentityMatrix,
scale_atoms=True)
E_new_guess = atoms.get_potential_energy()
# A check for changes in the energy minimum is made and the guesses for a0 and their corrosponding
# energies are ajusted.
if min(E_new_guess, min(E_guesses[0:3])) != E_new_guess:
a0_guesses[0] = a0_new_guess
E_guesses[0] = E_new_guess
else:
a0_guesses[2] = a0_guesses[1]
a0_guesses[1] = a0_new_guess
E_guesses[2] = E_guesses[1]
E_guesses[1] = E_new_guess
# An estimate of the minimum energy can now be found from a second degree polynomial fit through the three
# current guesses for a0 and the corresponding values of the energy.
Poly = numpyfit.polyfit(a0_guesses, E_guesses[0:3], 2)
# The lattice constant corresponding to the lowest energy from the Polynomiel fit is found
a0 = -Poly[1] / (2 * Poly[0])
# Now five guesses for a0 and the corresponding energy are evaluated from and around the current a0.
a0_guesses = a0 * numpy.array([
1 - 2 * self.Tol / 5, 1 - self.Tol / 5, 1, 1 + self.Tol / 5,
1 + 2 * self.Tol / 5
])
for i in range(5):
# Changes the lattice constant for the atoms object
atoms.set_cell(a0_guesses[i] * self.Size * IdentityMatrix,
scale_atoms=True)
# Calculates the energy of the system for the new lattice constant
E_guesses[i] = atoms.get_potential_energy()
# The method EquationOfState is now used to find the Bulk modulus and the minimum energy for the system.
# The volume of the sample for the given a0_guesses
Vol = (self.Size * a0_guesses)**3
# The equilibrium volume, energy and bulk modulus are calculated
(Vol0, E0, B) = EquationOfState(Vol.tolist(), E_guesses.tolist()).fit()
return (Vol0, E0, B, Vol0**(1. / 3) / self.Size)
rmax = 8.
nbins = 5
rdf, dists = get_rdf(atoms, rmax, nbins)
calc_dists = np.arange(rmax / (2 * nbins), rmax, rmax / nbins)
assert all(abs(dists - calc_dists) < eps)
calc_rdf = [0., 0.84408157, 0.398689, 0.23748934, 0.15398546]
assert all(abs(rdf - calc_rdf) < eps)
dm = atoms.get_all_distances()
s = np.zeros(5)
for c in [(29, 29), (29, 79), (79, 29), (79, 79)]:
inv_norm = len(np.where(atoms.numbers == c[0])[0]) / len(atoms)
s += get_rdf(
atoms, rmax, nbins, elements=c, distance_matrix=dm,
no_dists=True) * inv_norm
assert all(abs(s - calc_rdf) < eps)
AuAu = get_rdf(atoms,
rmax,
nbins,
elements=(79, 79),
distance_matrix=dm,
no_dists=True)
assert all(abs(AuAu[-2:] - [0.12126445, 0.]) < eps)
bulk = L1_2(['Au', 'Cu'], size=(2, 2, 2), latticeconstant=np.sqrt(2))
dm = bulk.get_all_distances(mic=True)
rdf = get_rdf(bulk, 5., 3, distance_matrix=dm)[0]
calc_rdf = [0.54694216, 0.08334357, 0.]
assert all(abs(rdf - calc_rdf) < eps)
latticeconstant=3.61,
size=(29, 29, 30))
atoms.set_calculator(EMT())
MaxwellBoltzmannDistribution(atoms, 2 * T * units.kB)
#dyn = VelocityVerlet(atoms, 5*units.fs)
dyn = Langevin(atoms, 5 * units.fs, T * units.kB, 0.05)
dyn.run(50)
print "Done. Temperature =", temperature(atoms), \
"K. Number of atoms: ", len(atoms)
return atoms
# Make sure that CPU speed is revved up.
dummy = L1_2(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol=('Au', 'Cu'),
latticeconstant=4.08,
size=(10, 10, 10),
debug=0)
dummy.set_calculator(EMT())
dyn = Langevin(dummy, 5 * units.fs, 300 * units.kB, 0.05)
dyn.run(10)
del dummy
logger.write("\n\nRunning on %s %s\n" % (host, when))
modelname = "Unknown CPU model name"
cpumhz = "Unknown CPU speed"
try:
lines = open("/proc/cpuinfo").readlines()
for line in lines:
if line[:10] == "model name":
modelname = line
