def HCPoutputYAML(a0, c_a, z=1./8.):
"""
Generates YAML file corresponding to our HCP lattice with octahedral and tetrahedrals.
:param a0: lattice constant
:param c_a: c/a ratio
:param z: distance of tetrahedral from basal plane (unit cell coordinates)
:return: YAML string containing the *short* version, along with jump networks
"""
# Note: alternatively, we could construct our HCP crystal *then* generate Wyckoff positions
hexlatt = a0*np.array([[0.5, 0.5, 0],
[-np.sqrt(0.75), np.sqrt(0.75), 0],
[0, 0, c_a]])
hcpbasis = [[np.array([1./3.,2./3.,1./4.]),np.array([2./3.,1./3.,3./4.])],
[np.array([0.,0.,0.]), np.array([0.,0.,0.5]),
np.array([1./3.,2./3.,3./4.-z]), np.array([1./3.,2./3.,3./4.+z]),
np.array([2./3.,1./3.,1./4.-z]), np.array([2./3.,1./3.,1./4.+z])]]
HCP = crystal.Crystal(hexlatt, hcpbasis)
# these cutoffs are for: o->t, t->t, o->o along c
# (preferably all below a). The t->t should be shortest, and o->o the longest
cutoff = 1.01*a0*max(np.sqrt(1./3.+c_a**2/64), 2*z*c_a, 0.5*c_a)
if __debug__:
if cutoff > a0: raise AssertionError('Geometry such that we will include basal jumps')
if np.abs(z) > 0.25: raise AssertionError('Tetrahedral parameter out of range (>1/4)')
if np.abs(z) < 1e-2: raise AssertionError('Tetrahedral parameter out of range (approx. 0)')
return HeaderString + \
HCP.simpleYAML(a0) + \
OnsagerCalc.Interstitial.sitelistYAML(HCP.sitelist(1)) + \
OnsagerCalc.Interstitial.jumpnetworkYAML(HCP.jumpnetwork(1, cutoff))
def setUp(self):
latt = np.array([[0., 0.1, 0.5], [0.3, 0., 0.5], [0.5, 0.5, 0.]]) * 0.55
self.DC_Si = crystal.Crystal(latt, [[np.array([0., 0., 0.]), np.array([0.25, 0.25, 0.25])]], ["Si"])
# keep it simple with [1.,0.,0.] type orientations for now
o = np.array([1., 0., 0.]) / np.linalg.norm(np.array([1., 0., 0.])) * 0.126
famp0 = [o.copy()]
family = [famp0]
self.pdbcontainer_si = dbStates(self.DC_Si, 0, family)
self.mdbcontainer_si = mStates(self.DC_Si, 0, family)
self.jset0, self.jset2 = self.pdbcontainer_si.jumpnetwork(0.3, 0.01, 0.01), self.mdbcontainer_si.jumpnetwork(
0.3, 0.01, 0.01)
self.crys_stars = StarSet(self.pdbcontainer_si, self.mdbcontainer_si, self.jset0, self.jset2, Nshells=1)
self.vec_stars = vectorStars(self.crys_stars)
self.om2tags = self.vec_stars.starset.jtags2
# generate 1, 3 and 4 jumpnetworks
(self.jnet_1, self.jnet_1_indexed, self.om1tags), self.jtype = self.crys_stars.jumpnetwork_omega1()
(self.symjumplist_omega43_all, self.symjumplist_omega43_all_indexed), (
self.symjumplist_omega4, self.symjumplist_omega4_indexed, self.om4tags), (
self.symjumplist_omega3, self.symjumplist_omega3_indexed,
self.om3tags) = self.crys_stars.jumpnetwork_omega34(
0.3, 0.01, 0.01, 0.01)
self.W0list = np.random.rand(len(self.vec_stars.starset.jnet0))
self.W1list = np.random.rand(len(self.jnet_1))
self.W2list = np.random.rand(len(self.jset2[0]))
self.W3list = np.random.rand(len(self.symjumplist_omega3))
self.W4list = np.random.rand(len(self.symjumplist_omega4))
# generate all the bias expansions - will separate out later
self.biases = self.vec_stars.biasexpansion(self.jnet_1, self.jset2[0], self.jtype, self.symjumplist_omega43_all)
self.rateExps = self.vec_stars.rateexpansion(self.jnet_1, self.jtype, self.symjumplist_omega43_all)
def setUp(self):
self.crys2d = crystal.Crystal(np.array([[1., 0.], [0., 1.5]]), [[np.array([0, 0]), np.array([0.5, 0.5])]], ["A"])
print("Crystal dimension: {}".format(self.crys2d.dim))
o = np.array([0., 0.1])
famp02d = [o.copy()]
family2d = [famp02d]
self.pdbcontainer_si = dbStates(self.crys2d, 0, family2d)
self.mdbcontainer_si = mStates(self.crys2d, 0, family2d)
jset02d, jset22d = self.pdbcontainer_si.jumpnetwork(1.51, 0.01, 0.01), self.mdbcontainer_si.jumpnetwork(1.51, 0.01, 0.01)
self.crys_stars = StarSet(self.pdbcontainer_si, self.mdbcontainer_si, jset02d, jset22d, Nshells=1)
self.vec_stars = vectorStars(self.crys_stars)
self.om2tags = self.vec_stars.starset.jtags2
# generate 1, 3 and 4 jumpnetworks
(self.jnet_1, self.jnet_1_indexed, self.om1tags), self.jtype = self.crys_stars.jumpnetwork_omega1()
(self.symjumplist_omega43_all, self.symjumplist_omega43_all_indexed), (
self.symjumplist_omega4, self.symjumplist_omega4_indexed, self.om4tags), (
self.symjumplist_omega3, self.symjumplist_omega3_indexed,
self.om3tags) = self.crys_stars.jumpnetwork_omega34(1.51, 0.01, 0.01, 0.01)
self.jset2 = jset22d
self.W0list = np.random.rand(len(self.vec_stars.starset.jnet0))
self.W1list = np.random.rand(len(self.jnet_1))
self.W2list = np.random.rand(len(self.jset2[0]))
self.W3list = np.random.rand(len(self.symjumplist_omega3))
self.W4list = np.random.rand(len(self.symjumplist_omega4))
# generate all the bias expansions - will separate out later
self.biases = self.vec_stars.biasexpansion(self.jnet_1, self.jset2[0], self.jtype, self.symjumplist_omega43_all)
self.rateExps = self.vec_stars.rateexpansion(self.jnet_1, self.jtype, self.symjumplist_omega43_all)
print("Instantiated")
def setUp(self):
o = np.array([0.1, 0.])
famp0 = [o.copy()]
self.family = [famp0]
latt = np.array([[1., 0.], [0., 1.]])
self.crys = crystal.Crystal(latt, [np.array([0, 0])], ["A"])
def testBCC_B2(self):
"""Test that BCC and B2 produce the same GF"""
a0 = 1.
chem = 0
BCC = crystal.Crystal.BCC(a0)
BCC_sitelist = BCC.sitelist(chem)
BCC_jumpnetwork = BCC.jumpnetwork(chem, 0.87 * a0)
BCC_GF = GFcalc.GFCrystalcalc(BCC,
chem,
BCC_sitelist,
BCC_jumpnetwork,
Nmax=6)
BCC_GF.SetRates(np.ones(len(BCC_sitelist)),
np.zeros(len(BCC_sitelist)),
2. * np.ones(len(BCC_jumpnetwork)),
np.zeros(len(BCC_jumpnetwork)))
B2 = crystal.Crystal(
a0 * np.eye(3),
[np.zeros(3), np.array([0.45, 0.45, 0.45])])
B2_sitelist = B2.sitelist(chem)
B2_jumpnetwork = B2.jumpnetwork(chem, 0.99 * a0)
B2_GF = GFcalc.GFCrystalcalc(B2,
chem,
B2_sitelist,
B2_jumpnetwork,
Nmax=6)
B2_GF.SetRates(np.ones(len(B2_sitelist)), np.zeros(len(B2_sitelist)),
2. * np.ones(len(B2_jumpnetwork)),
np.zeros(len(B2_jumpnetwork)))
veclist = [
np.array([a0, 0, 0]),
np.array([0, a0, 0]),
np.array([0, 0, a0]),
np.array([-a0, 0, 0]),
np.array([0, -a0, 0]),
np.array([0, 0, -a0])
]
for v1 in veclist:
for v2 in veclist:
# print('{}: '.format(v1+v2) + '{} vs {} vs {}'.format(B2_GF(0,0,v1+v2),B2_GF(1,1,v1+v2),BCC_GF(0,0,v1+v2)))
self.assertAlmostEqual(BCC_GF(0, 0, v1 + v2),
B2_GF(0, 0, v1 + v2),
places=5)
self.assertAlmostEqual(BCC_GF(0, 0, v1 + v2),
B2_GF(1, 1, v1 + v2),
places=5)
for jlist in B2_jumpnetwork:
for (i, j), dx in jlist:
# convert our B2 dx into a corresponding BCC dx:
BCCdx = (0.5 * a0) * np.round(dx / (0.5 * a0))
# print('({},{}), {} / {}: '.format(i,j,dx,BCCdx) + '{} vs {}'.format(B2_GF(i,j,dx), BCC_GF(0,0,BCCdx)))
self.assertAlmostEqual(BCC_GF(0, 0, BCCdx),
B2_GF(i, j, dx),
places=5)
def testtria(self):
"""Test on triagonal"""
tria = crystal.Crystal(
np.array([[1 / 2, 1 / 2], [-np.sqrt(3 / 4),
np.sqrt(3 / 4)]]), [np.zeros(2)])
tria_sitelist = tria.sitelist(0)
tria_jumpnetwork = tria.jumpnetwork(0, 1.01)
tria_GF = GFcalc.GFCrystalcalc(tria,
0,
tria_sitelist,
tria_jumpnetwork,
Nmax=4)
tria_GF.SetRates([1], [0], [1], [0])
tria_zero = np.zeros(2)
tria_1nn = np.array([1., 0.])
g0 = tria_GF(0, 0, tria_zero)
g1 = tria_GF(0, 0, tria_1nn)
self.assertAlmostEqual(-6 * g0 + 6 * g1, 1, places=6)
def testhoneycomb(self):
"""Test on honeycomb"""
honey = crystal.Crystal(
np.array([[1 / 2, 1 / 2], [-np.sqrt(3 / 4),
np.sqrt(3 / 4)]]),
[np.array([2 / 3, 1 / 3]),
np.array([1 / 3, 2 / 3])])
honey_sitelist = honey.sitelist(0)
honey_jumpnetwork = honey.jumpnetwork(0, 0.6)
honey_GF = GFcalc.GFCrystalcalc(honey,
0,
honey_sitelist,
honey_jumpnetwork,
Nmax=4)
honey_GF.SetRates([1], [0], [1], [0])
honey_zero = np.zeros(2)
honey_1nn = honey.pos2cart(np.zeros(2), (0, 1)) - honey.pos2cart(
np.zeros(2), (0, 0))
g0 = honey_GF(0, 0, honey_zero)
g1 = honey_GF(0, 1, honey_1nn)
self.assertAlmostEqual(-3 * g0 + 3 * g1, 1, places=6)
def testsquare(self):
"""Test on square"""
square = crystal.Crystal(np.eye(2), [np.zeros(2)])
square_sitelist = square.sitelist(0)
square_jumpnetwork = square.jumpnetwork(0, 1.01)
square_GF = GFcalc.GFCrystalcalc(square,
0,
square_sitelist,
square_jumpnetwork,
Nmax=4)
square_GF.SetRates([1], [0], [1], [0])
square_zero = np.zeros(2)
square_1nn = np.array([1., 0.])
square_2nn = np.array([1., 1.])
square_3nn = np.array([2., 0.])
g0 = square_GF(0, 0, square_zero)
g1 = square_GF(0, 0, square_1nn)
g2 = square_GF(0, 0, square_2nn)
g3 = square_GF(0, 0, square_3nn)
self.assertAlmostEqual(-4 * g0 + 4 * g1, 1, places=6)
self.assertAlmostEqual(-4 * g1 + g0 + 2 * g2 + g3, 0, places=6)
import numpy as np
import onsager.crystal as crystal
#This will be used to store crystal structures needed to create tests
#omega_Ti crystal structure
a0 = 4.576855
c_a = 2.828683 / a0
alatt = np.array([[0.5, 0.5, 0.], [-np.sqrt(0.75),
np.sqrt(0.75), 0.], [0., 0., c_a]]) * a0
u1 = np.array([0., 0., 0.])
u2 = np.array([1. / 3., 2. / 3., 1. / 2.])
u3 = np.array([2. / 3., 1. / 3., 1. / 2.])
omega_Ti = crystal.Crystal(alatt, [[u1, u2, u3]], ["Ti"])
#simple tetragonal crystal structure
# tet = crystal.Crystal(np.array([[1.2,0.,0.],[0.,1.2,0.],[0.,0.,1.5]]),[[np.zeros(3)]])
# tet2 = crystal.Crystal(np.array([[0.32,0.,0.],[0.,0.32,0.],[0.,0.,0.45]]),[[np.zeros(3),np.array([0.5,0.,0.]),np.array([0.,0.5,0.])]])
# tet3 = crystal.Crystal(np.array([[0.32,0.,0.],[0.,0.32,0.],[0.,0.,0.45]]),[[np.zeros(3),np.array([0.0,0.5,0.])],[np.array([0.5,0.,0.])]],["A","B"])
# print (tet3)
tet = crystal.Crystal(
np.array([[0.28, 0., 0.], [0., 0.28, 0.], [0., 0., 0.32]]),
[[np.zeros(3)]])
tet2 = crystal.Crystal(
np.array([[0.28, 0., 0.], [0., 0.28, 0.], [0., 0., 0.32]]),
[[np.zeros(3),
np.array([0.5, 0., 0.]),
np.array([0., 0.5, 0.])]])
tet3 = crystal.Crystal(
np.array([[0.32, 0., 0.], [0., 0.32, 0.], [0., 0., 0.45]]),
[[np.zeros(3), np.array([0.0, 0.5, 0.])], [np.array([0.5, 0., 0.])]],
["A", "B"])
tet4 = crystal.Crystal(
np.array([[0.28, 0., 0.], [0., 0.28, 0.], [0., 0., 0.32]]),
def test_jnet0(self):
# cube
famp0 = [
np.array([1., 0., 0.]) / np.linalg.norm(np.array([1., 0., 0.])) *
0.126
]
family = [famp0]
pdbcontainer_cube = dbStates(cube, 0, family)
jset_cube, jind_cube = pdbcontainer_cube.jumpnetwork(0.3, 0.01, 0.01)
test_dbi = dumbbell(
pdbcontainer_cube.getIndex((0, np.array([0.126, 0., 0.]))),
np.array([0, 0, 0]))
test_dbf = dumbbell(
pdbcontainer_cube.getIndex((0, np.array([0.126, 0., 0.]))),
np.array([0, 1, 0]))
count = 0
indices = []
for i, jlist in enumerate(jset_cube):
for q, j in enumerate(jlist):
if j.state1 == test_dbi:
if j.state2 == test_dbf:
if j.c1 == j.c2 == -1:
count += 1
indices.append((i, q))
jtest = jlist
# print (indices)
self.assertEqual(
count,
1) # see that this jump has been taken only once into account
self.assertEqual(len(jtest), 24)
# Next FCC
# test this out with FCC
fcc = crystal.Crystal.FCC(0.55)
famp0 = [np.array([1., 1., 0.]) / np.sqrt(2) * 0.2]
family = [famp0]
pdbcontainer_fcc = dbStates(fcc, 0, family)
jset_fcc, jind_fcc = pdbcontainer_fcc.jumpnetwork(0.4, 0.01, 0.01)
o1 = np.array([1., -1., 0.]) * 0.2 / np.sqrt(2)
if any(np.allclose(-o1, o) for i, o in pdbcontainer_fcc.iorlist):
o1 = -o1.copy()
db1 = dumbbell(pdbcontainer_fcc.getIndex((0, o1)), np.array([0, 0, 0]))
db2 = dumbbell(pdbcontainer_fcc.getIndex((0, o1)), np.array([0, 0, 1]))
jmp = jump(db1, db2, 1, 1)
jtest = []
for jl in jset_fcc:
for j in jl:
if j == jmp:
jtest.append(jl)
# see that the jump has been accounted just once.
self.assertEqual(len(jtest), 1)
# See that there 24 jumps. 24 0->0.
self.assertEqual(len(jtest[0]), 24)
# DC_Si - same symmetry as FCC, except twice the number of jumps, since we have two basis
# atoms belonging to the same Wyckoff site, in a crystal with the same lattice vectors.
latt = np.array([[0., 0.5, 0.5], [0.5, 0., 0.5], [0.5, 0.5, 0.]
]) * 0.55
DC_Si = crystal.Crystal(
latt, [[np.array([0., 0., 0.]),
np.array([0.25, 0.25, 0.25])]], ["Si"])
famp0 = [np.array([1., 1., 0.]) / np.sqrt(2) * 0.2]
family = [famp0]
pdbcontainer_si = dbStates(DC_Si, 0, family)
jset_si, jind_si = pdbcontainer_si.jumpnetwork(0.4, 0.01, 0.01)
o1 = np.array([1., -1., 0.]) * 0.2 / np.sqrt(2)
if any(np.allclose(-o1, o) for i, o in pdbcontainer_si.iorlist):
o1 = -o1.copy()
db1 = dumbbell(pdbcontainer_si.getIndex((0, o1)), np.array([0, 0, 0]))
db2 = dumbbell(pdbcontainer_si.getIndex((0, o1)), np.array([0, 0, 1]))
jmp = jump(db1, db2, 1, 1)
jtest = []
for jl in jset_si:
for j in jl:
if j == jmp:
jtest.append(jl)
# see that the jump has been accounted just once.
self.assertEqual(len(jtest), 1)
# See that there 48 jumps. 24 0->0 and 24 1->1.
self.assertEqual(len(jtest[0]), 48)
# HCP
Mg = crystal.Crystal.HCP(0.3294, chemistry=["Mg"])
famp0 = [np.array([1., 0., 0.]) * 0.145]
family = [famp0]
pdbcontainer_hcp = dbStates(Mg, 0, family)
jset_hcp, jind_hcp = pdbcontainer_hcp.jumpnetwork(0.45, 0.01, 0.01)
o = np.array([0.145, 0., 0.])
if any(np.allclose(-o, o1) for i, o1 in pdbcontainer_hcp.iorlist):
o = -o + 0.
db1 = dumbbell(pdbcontainer_hcp.getIndex((0, o)),
np.array([0, 0, 0], dtype=int))
db2 = dumbbell(pdbcontainer_hcp.getIndex((1, o)),
np.array([0, 0, 0], dtype=int))
testjump = jump(db1, db2, 1, 1)
count = 0
testlist = []
for jl in jset_hcp:
for j in jl:
if j == testjump:
count += 1
testlist = jl
self.assertEqual(len(testlist), 24)
self.assertEqual(count, 1)
# test_indices
# First check if they have the same number of lists and elements
jindlist = [jind_cube, jind_fcc, jind_si, jind_hcp]
jsetlist = [jset_cube, jset_fcc, jset_si, jset_hcp]
pdbcontainerlist = [
pdbcontainer_cube, pdbcontainer_fcc, pdbcontainer_si,
pdbcontainer_hcp
]
for pdbcontainer, jset, jind in zip(pdbcontainerlist, jsetlist,
jindlist):
self.assertEqual(len(jind), len(jset))
# now check if all the elements are correctly correspondent
for lindex in range(len(jind)):
self.assertEqual(len(jind[lindex]), len(jset[lindex]))
for jindex in range(len(jind[lindex])):
(i1, o1) = pdbcontainer.iorlist[jind[lindex][jindex][0][0]]
(i2, o2) = pdbcontainer.iorlist[jind[lindex][jindex][0][1]]
self.assertEqual(
pdbcontainer.iorlist[jset[lindex]
[jindex].state1.iorind][0], i1)
self.assertEqual(
pdbcontainer.iorlist[jset[lindex]
[jindex].state2.iorind][0], i2)
self.assertTrue(
np.allclose(
pdbcontainer.iorlist[
jset[lindex][jindex].state1.iorind][1], o1))
self.assertTrue(
np.allclose(
pdbcontainer.iorlist[
jset[lindex][jindex].state2.iorind][1], o2))
dx = disp(pdbcontainer, jset[lindex][jindex].state1,
jset[lindex][jindex].state2)
self.assertTrue(np.allclose(dx, jind[lindex][jindex][1]))
def test_mixedjumps(self):
latt = np.array([[0., 0.5, 0.5], [0.5, 0., 0.5], [0.5, 0.5, 0.]
]) * 0.55
DC_Si = crystal.Crystal(
latt, [[np.array([0., 0., 0.]),
np.array([0.25, 0.25, 0.25])]], ["Si"])
famp0 = [np.array([1., 1., 0.]) / np.sqrt(2) * 0.2]
family = [famp0]
mdbcontainer = mStates(DC_Si, 0, family)
jset, jind = mdbcontainer.jumpnetwork(0.4, 0.01, 0.01)
o1 = np.array([1., 1., 0.]) * 0.2 / np.sqrt(2)
# if any(np.allclose(-o1, o) for i, o in pdbcontainer.iorlist):
# o1 = -o1.copy()
# db1 = dumbbell(pdbcontainer_si.getIndex((0, o1)), np.array([0, 0, 0]))
# db2 = dumbbell(pdbcontainer_si.getIndex((0, o1)), np.array([0, 0, 1]))
test_dbi = dumbbell(mdbcontainer.getIndex((0, o1)), np.array([0, 0,
0]))
test_dbf = dumbbell(mdbcontainer.getIndex((1, o1)), np.array([0, 0,
0]))
count = 0
jtest = None
for i, jlist in enumerate(jset):
for q, j in enumerate(jlist):
if j.state1.db == test_dbi:
if j.state2.db == test_dbf:
if j.c1 == j.c2 == 1:
count += 1
jtest = jlist
self.assertEqual(
count,
1) # see that this jump has been taken only once into account
self.assertEqual(len(jtest), 48)
# check if conditions for mixed dumbbell transitions are satisfied
count = 0
for jl in jset:
for j in jl:
if j.c1 == -1 or j.c2 == -1:
count += 1
break
if not (j.state1.i_s
== mdbcontainer.iorlist[j.state1.db.iorind][0]
and j.state2.i_s
== mdbcontainer.iorlist[j.state2.db.iorind][0]
and np.allclose(j.state1.R_s, j.state1.db.R)
and np.allclose(j.state2.R_s, j.state2.db.R)):
count += 1
break
if count == 1:
break
self.assertEqual(count, 0)
# test_indices
# First check if they have the same number of lists and elements
self.assertEqual(len(jind), len(jset))
# now check if all the elements are correctly correspondent
for lindex in range(len(jind)):
self.assertEqual(len(jind[lindex]), len(jset[lindex]))
for jindex in range(len(jind[lindex])):
(i1, o1) = mdbcontainer.iorlist[jind[lindex][jindex][0][0]]
(i2, o2) = mdbcontainer.iorlist[jind[lindex][jindex][0][1]]
self.assertEqual(
mdbcontainer.iorlist[jset[lindex][jindex].state1.db.iorind]
[0], i1)
self.assertEqual(
mdbcontainer.iorlist[jset[lindex][jindex].state2.db.iorind]
[0], i2)
self.assertTrue(
np.allclose(
mdbcontainer.iorlist[
jset[lindex][jindex].state1.db.iorind][1], o1))
self.assertTrue(
np.allclose(
mdbcontainer.iorlist[
jset[lindex][jindex].state2.db.iorind][1], o2))
def testPyrope(self):
"""Test using the pyrope structure: two disconnected symmetry-related networks"""
a0 = 1.
chem = 0
cutoff = 0.31 * a0
alatt = a0 * np.array([[-0.5, 0.5, 0.5], [0.5, -0.5, 0.5],
[0.5, 0.5, -0.5]])
invlatt = np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]])
uMg = ((1 / 8, 0, 1 / 4), (3 / 8, 0, 3 / 4), (1 / 4, 1 / 8, 0),
(3 / 4, 3 / 8, 0), (0, 1 / 4, 1 / 8), (0, 3 / 4, 3 / 8),
(7 / 8, 0, 3 / 4), (5 / 8, 0, 1 / 4), (3 / 4, 7 / 8, 0),
(1 / 4, 5 / 8, 0), (0, 3 / 4, 7 / 8), (0, 1 / 4, 5 / 8))
tovec = lambda x: np.dot(invlatt, x)
# this is a reduced version of pyrope: just the Mg (24c sites in 230)
# pyrope2 = half of the sites; makes for a single, connected network
pyropeMg = crystal.Crystal(alatt,
[[vec(w) for w in uMg
for vec in (tovec, )]], ['Mg'])
pyropeMg2 = crystal.Crystal(
alatt, [[vec(w) for w in uMg[:6] for vec in (tovec, )]], ['Mg'])
sitelist = pyropeMg.sitelist(chem)
sitelist2 = pyropeMg2.sitelist(chem)
jumpnetwork = pyropeMg.jumpnetwork(chem, cutoff)
jumpnetwork2 = pyropeMg2.jumpnetwork(chem, cutoff)
self.assertEqual(len(jumpnetwork), 1)
self.assertEqual(len(jumpnetwork2), 1)
GF = GFcalc.GFCrystalcalc(pyropeMg, chem, sitelist, jumpnetwork)
GF2 = GFcalc.GFCrystalcalc(pyropeMg2, chem, sitelist2, jumpnetwork2)
GF.SetRates(np.ones(1), np.zeros(1), 0.25 * np.ones(1),
np.zeros(1)) # simple tracer
GF2.SetRates(np.ones(1), np.zeros(1), 0.25 * np.ones(1),
np.zeros(1)) # simple tracer
D0 = np.eye(3) * (1 / 64)
for D in (GF.D, GF2.D):
self.assertTrue(
np.allclose(D0, D),
msg='Diffusivity does not match?\n{}\n!=\n{}'.format(D0, D))
basis = pyropeMg.basis[chem]
# order of testing: 000, 211
ijlist = ((0, 0), (0, 2))
dxlist = [np.dot(alatt, basis[j] - basis[i]) for (i, j) in ijlist]
glist = np.array([GF(i, j, dx) for (i, j), dx in zip(ijlist, dxlist)])
g2list = np.array(
[GF2(i, j, dx) for (i, j), dx in zip(ijlist, dxlist)])
Gref = np.array([2.30796022, 1.30807261])
self.assertTrue(
np.allclose(glist, -Gref, rtol=1e-4),
msg='Does not match Carlson and Wilson values?\n{} !=\n{}'.format(
glist, Gref))
# with the nearly disconnected, the rate anisotropy makes comparison of differences
# much more stable
self.assertTrue(
np.allclose(glist, g2list, rtol=1e-12),
msg='Does not match single network GF values?\n{} !=\n{}'.format(
glist, g2list))
for i in range(12):
for j in range(12):
dx = np.dot(alatt, basis[j] - basis[i])
if i // 6 != j // 6:
self.assertAlmostEqual(
GF(i, j, dx),
0,
msg='Does not give disconnected networks? {},{}'.
format(i, j))
else:
if i >= 6: dxmap = -dx # inversion
else: dxmap = dx
self.assertAlmostEqual(
GF(i, j, dx),
GF2(i % 6, j % 6, dxmap),
msg='Does not match single network? {},{}'.format(
i, j))
def testOnsagerVacancyMediated(self):
"""Test whether we can write and read an HDF5 group containing a VacancyMediated Onsager Calculator"""
HCP = crystal.Crystal.HCP(1., np.sqrt(8 / 3))
HCP_sitelist = HCP.sitelist(0)
HCP_jumpnetwork = HCP.jumpnetwork(0, 1.01)
HCP_diffuser = OnsagerCalc.VacancyMediated(HCP, 0, HCP_sitelist,
HCP_jumpnetwork, 1)
HCP_diffuser.addhdf5(self.f) # we'll usually dump it in main
HCP_diffuser_copy = OnsagerCalc.VacancyMediated.loadhdf5(
self.f) # should be fully self-contained
thermaldef = {
'preV': np.array([1.]),
'eneV': np.array([0.]),
'preT0': np.array([1., 1.5]),
'eneT0': np.array([0.25, 0.35])
}
thermaldef.update(HCP_diffuser.maketracerpreene(**thermaldef))
for L0, Lcopy in zip(
HCP_diffuser.Lij(
*HCP_diffuser.preene2betafree(1.0, **thermaldef)),
HCP_diffuser_copy.Lij(
*HCP_diffuser_copy.preene2betafree(1.0, **thermaldef))):
self.assertTrue(np.allclose(L0, Lcopy),
msg='{}\n!=\n{}'.format(L0, Lcopy))
# compare tags
for k in HCP_diffuser.tags.keys():
self.assertEqual(HCP_diffuser.tags[k], HCP_diffuser_copy.tags[k])
# do a dictionary check (dictionaries are only added *after* a minimum of one call
HCP_diffuser.addhdf5(self.f.create_group('new'))
HCP_diffuser_copy = OnsagerCalc.VacancyMediated.loadhdf5(
self.f['new']) # should be fully self-contained
for L0, Lcopy in zip(
HCP_diffuser.Lij(
*HCP_diffuser.preene2betafree(1.0, **thermaldef)),
HCP_diffuser_copy.Lij(
*HCP_diffuser_copy.preene2betafree(1.0, **thermaldef))):
self.assertTrue(np.allclose(L0, Lcopy),
msg='{}\n!=\n{}'.format(L0, Lcopy))
# Test with B2 (there are additional terms that get used when we have origin states)
B2 = crystal.Crystal(
np.eye(3), [np.zeros(3), np.array([0.45, 0.45, 0.45])])
B2diffuser = OnsagerCalc.VacancyMediated(B2, 0, B2.sitelist(0),
B2.jumpnetwork(0, 0.99), 1)
B2diffuser.addhdf5(self.f.create_group('B2'))
B2diffuser_copy = OnsagerCalc.VacancyMediated.loadhdf5(self.f['B2'])
Nsites, Njumps = len(B2diffuser.sitelist), len(B2diffuser.om0_jn)
tdef = {
'preV': np.ones(Nsites),
'eneV': np.zeros(Njumps),
'preT0': np.ones(Njumps),
'eneT0': np.zeros(Njumps)
}
tdef.update(B2diffuser.maketracerpreene(**tdef))
for L0, Lcopy in zip(
B2diffuser.Lij(*B2diffuser.preene2betafree(1.0, **tdef)),
B2diffuser_copy.Lij(
*B2diffuser_copy.preene2betafree(1.0, **tdef))):
self.assertTrue(np.allclose(L0, Lcopy),
msg='{}\n!=\n{}'.format(L0, Lcopy))
# Test with displaced triangle (2D "B2" example):
tria2 = crystal.Crystal(
np.array([[1., 0.], [0., np.sqrt(3.)]]),
[np.zeros(2), np.array([0.5, 0.4])])
tria2diffuser = OnsagerCalc.VacancyMediated(tria2, 0,
tria2.sitelist(0),
tria2.jumpnetwork(0,
1.2), 1)
tria2diffuser.addhdf5(self.f.create_group('tria'))
tria2diffuser_copy = OnsagerCalc.VacancyMediated.loadhdf5(
self.f['tria'])
Nsites, Njumps = len(tria2diffuser.sitelist), len(tria2diffuser.om0_jn)
tdef2 = {
'preV': np.ones(Nsites),
'eneV': np.zeros(Njumps),
'preT0': np.ones(Njumps),
'eneT0': np.zeros(Njumps)
}
tdef2.update(tria2diffuser.maketracerpreene(**tdef2))
for L0, Lcopy in zip(
tria2diffuser.Lij(
*tria2diffuser.preene2betafree(1.0, **tdef2)),
tria2diffuser_copy.Lij(
*tria2diffuser_copy.preene2betafree(1.0, **tdef2))):
self.assertTrue(np.allclose(L0, Lcopy),
msg='{}\n!=\n{}'.format(L0, Lcopy))
# compare tags
for k in tria2diffuser.tags.keys():
self.assertEqual(tria2diffuser.tags[k], tria2diffuser_copy.tags[k])