def testOrientub(self):
with pytest.raises(TypeError):
self.ub.orientub(1) # wrong input
# no ubcalc started:
with pytest.raises(DiffcalcException):
self.ub.orientub()
self.ub.newub('testorientub')
# not enough orientations:
with pytest.raises(DiffcalcException):
self.ub.orientub()
self.ub.newub('testorientub')
s = scenarios.sessions(settings.Pos)[1]
self.ub.setlat(s.name, *s.lattice)
r1 = s.ref1
orient1 = self.t_matrix * matrix('1; 0; 0')
self.ub.addorient((r1.h, r1.k, r1.l), orient1.T.tolist()[0], r1.tag)
r2 = s.ref2
orient2 = self.t_matrix * matrix('0; -1; 0')
self.ub.addorient((r2.h, r2.k, r2.l), orient2.T.tolist()[0], r2.tag)
self.ub.orientub()
mneq_(self.ub.ubcalc.UB,
matrix(s.umatrix) * matrix(s.bmatrix),
4,
note="wrong UB matrix after calculating U")
def testCalculateU(self):
for sess in scenarios.sessions():
self.setup_method()
self.ubcalc.start_new('testcalc')
# Skip this test case unless it contains a umatrix
if sess.umatrix is None:
continue
self.ubcalc.set_lattice(sess.name, *sess.lattice)
ref1 = sess.ref1
ref2 = sess.ref2
t = sess.time
self.ubcalc.add_reflection(
ref1.h, ref1.k, ref1.l, ref1.pos, ref1.energy, ref1.tag, t)
self.ubcalc.add_reflection(
ref2.h, ref2.k, ref2.l, ref2.pos, ref2.energy, ref2.tag, t)
self.ubcalc.calculate_UB()
returned = self.ubcalc.U.tolist()
print "*Required:"
print sess.umatrix
print "*Returned:"
print returned
mneq_(self.ubcalc.U, matrix(sess.umatrix), 4,
note="wrong U calulated for sess.name=" + sess.name)
def test__str__(self):
sess = scenarios.sessions()[0]
print "***"
print self.ubcalc.__str__()
print "***"
self.ubcalc.start_new('test')
print self.ubcalc.__str__()
print "***"
self.ubcalc.set_lattice(sess.name, *sess.lattice)
print self.ubcalc.__str__()
print "***"
ref1 = sess.ref1
ref2 = sess.ref2
t = sess.time
self.ubcalc.add_reflection(
ref1.h, ref1.k, ref1.l, ref1.pos, ref1.energy, ref1.tag, t)
self.ubcalc.add_reflection(
ref2.h, ref2.k, ref2.l, ref2.pos, ref2.energy, ref2.tag, t)
print self.ubcalc.__str__()
print "***"
self.ubcalc.calculate_UB()
print self.ubcalc.__str__()
def testset_U_manually(self):
# Test the calculations with U=I
U = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
for sess in scenarios.sessions():
self.setup_method()
self.ubcalc.start_new('testcalc')
self.ubcalc.set_lattice(sess.name, *sess.lattice)
self.ubcalc.set_U_manually(U)
# Check the U matrix
mneq_(self.ubcalc.U,
matrix(U),
4,
note="wrong U after manually setting U")
# Check the UB matrix
if sess.bmatrix is None:
continue
print "U: ", U
print "actual ub: ", self.ubcalc.UB.tolist()
print " desired b: ", sess.bmatrix
mneq_(self.ubcalc.UB,
matrix(sess.bmatrix),
4,
note="wrong UB after manually setting U")
def testGetBMatrix(self):
# Check the calculated B Matrix
for sess in scenarios.sessions():
if sess.bmatrix is None:
continue
cut = CrystalUnderTest('tc', *sess.lattice)
desired = matrix(sess.bmatrix)
print desired.tolist()
answer = cut.B
print answer.tolist()
note = "Incorrect B matrix calculation for scenario " + sess.name
mneq_(answer, desired, 4, note=note)
def testGetBMatrix(self):
# Check the calculated B Matrix
for sess in scenarios.sessions():
if sess.bmatrix is None:
continue
cut = CrystalUnderTest('tc', *sess.lattice)
desired = matrix(sess.bmatrix)
print desired.tolist()
answer = cut.B
print answer.tolist()
note = "Incorrect B matrix calculation for scenario " + sess.name
mneq_(answer, desired, 4, note=note)
def testset_U_manually(self):
# Test the calculations with U=I
U = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
for sess in scenarios.sessions():
self.setUp()
self.ubcalc.start_new("testcalc")
self.ubcalc.set_lattice(sess.name, *sess.lattice)
self.ubcalc.set_U_manually(U)
# Check the U matrix
mneq_(self.ubcalc.U, matrix(U), 4, note="wrong U after manually setting U")
# Check the UB matrix
if sess.bmatrix is None:
continue
print "U: ", U
print "actual ub: ", self.ubcalc.UB.tolist()
print " desired b: ", sess.bmatrix
mneq_(self.ubcalc.UB, matrix(sess.bmatrix), 4, note="wrong UB after manually setting U")
def testCalcub(self):
self.assertRaises(TypeError, self.ubcommands.calcub, 1) # wrong input
# no ubcalc started:
self.assertRaises(DiffcalcException, self.ubcommands.calcub)
self.ubcommands.newub('testcalcub')
# not enougth reflections:
self.assertRaises(DiffcalcException, self.ubcommands.calcub)
s = scenarios.sessions()[0]
self.ubcommands.setlat(s.name, *s.lattice)
r = s.ref1
self.ubcommands.addref(
[r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
r = s.ref2
self.ubcommands.addref(
[r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
self.ubcommands.calcub()
mneq_(self.ubcalc.UB, matrix(s.umatrix) * matrix(s.bmatrix),
4, note="wrong UB matrix after calculating U")
def testCalcub(self):
with pytest.raises(TypeError):
self.ub.calcub(1) # wrong input
# no ubcalc started:
with pytest.raises(DiffcalcException):
self.ub.calcub()
self.ub.newub('testcalcub')
# not enough reflections:
with pytest.raises(DiffcalcException):
self.ub.calcub()
s = scenarios.sessions(settings.Pos)[0]
self.ub.setlat(s.name, *s.lattice)
r = s.ref1
self.ub.addref([r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
r = s.ref2
self.ub.addref([r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
self.ub.calcub()
mneq_(self.ub.ubcalc.UB,
matrix(s.umatrix) * matrix(s.bmatrix),
4,
note="wrong UB matrix after calculating U")
def testOrientub(self):
with pytest.raises(DiffcalcException):
self.ub.orientub(1) # wrong input
# no ubcalc started:
with pytest.raises(DiffcalcException):
self.ub.orientub()
self.ub.newub('testorientub')
# not enough orientations:
with pytest.raises(DiffcalcException):
self.ub.orientub()
s = scenarios.sessions(settings.Pos)[1]
self.ub.setlat(s.name, *s.lattice)
r1 = s.ref1
orient1 = self.conv.transform(matrix('1; 0; 0'), True)
tag1 = 'or'+r1.tag
self.ub.addorient(
(r1.h, r1.k, r1.l), orient1.T.tolist()[0], tag1)
r2 = s.ref2
orient2 = self.conv.transform(matrix('0; -1; 0'), True)
tag2 = 'or'+r2.tag
self.ub.addorient(
(r2.h, r2.k, r2.l), orient2.T.tolist()[0], tag2)
self.ub.orientub()
mneq_(self.ub.ubcalc.UB, matrix(s.umatrix) * matrix(s.bmatrix),
4, note="wrong UB matrix after calculating U")
self.ub.orientub(tag1, tag2)
mneq_(self.ub.ubcalc.UB, matrix(s.umatrix) * matrix(s.bmatrix),
4, note="wrong UB matrix after calculating U")
self.ub.addref(
[r1.h, r1.k, r1.l], r1.pos.totuple(), r1.energy, r1.tag)
self.ub.orientub(r1.tag, tag2)
mneq_(self.ub.ubcalc.UB, matrix(s.umatrix) * matrix(s.bmatrix),
4, note="wrong UB matrix after calculating U")
self.ub.addref(
[r2.h, r2.k, r2.l], r2.pos.totuple(), r2.energy, r2.tag)
self.ub.orientub(tag1, r2.tag)
mneq_(self.ub.ubcalc.UB, matrix(s.umatrix) * matrix(s.bmatrix),
4, note="wrong UB matrix after calculating U")
def testFitub(self):
self.ub.newub('testfitub')
for s in scenarios.sessions(settings.Pos)[-3:]:
a, b, c, alpha, beta, gamma = s.lattice
self.ub.clearref()
for r in s.reflist:
self.ub.addref(
[r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
self.ub.setlat(s.name, s.system, *s.lattice)
self.ub.calcub(s.ref1.tag, s.ref2.tag)
init_latt = (1.06 * a, 1.07 * b, 0.94 * c,
1.05 * alpha, 1.06 * beta, 0.95 * gamma)
self.ub.setlat(s.name, s.system, *init_latt)
self.ub.addmiscut(3., [0.2, 0.8, 0.1])
prepareRawInput(['y', 'y'])
self.ub.fitub(*tuple(r.tag for r in s.reflist))
assert self.ub.ubcalc._state.crystal._system == s.system
mneq_(matrix((self.ub.ubcalc._state.crystal.getLattice()[1:])), matrix(s.lattice),
2, note="wrong lattice after fitting UB")
mneq_(self.ub.ubcalc.U, matrix(s.umatrix),
3, note="wrong U matrix after fitting UB")
def setSessionAndCalculation(self):
self.sess = scenarios.sessions()[2]
self.calc = self.sess.calculations[0]
def setSessionAndCalculation(self):
self.sess = scenarios.sessions()[0]
self.calc = None