def struToParameterSet(name, stru):
"""Creates a ParameterSet from an structure.
This returns a ParameterSet adapted for the structure depending on its
type.
stru -- a structure object known by this module
name -- A name to give the structure.
Raises TypeError if stru cannot be adapted
"""
from diffpy.srfit.structure.diffpyparset import DiffpyStructureParSet
if DiffpyStructureParSet.canAdapt(stru):
return DiffpyStructureParSet(name, stru)
from diffpy.srfit.structure.objcrystparset import ObjCrystCrystalParSet
if ObjCrystCrystalParSet.canAdapt(stru):
return ObjCrystCrystalParSet(name, stru)
from diffpy.srfit.structure.objcrystparset import ObjCrystMoleculeParSet
if ObjCrystMoleculeParSet.canAdapt(stru):
return ObjCrystMoleculeParSet(name, stru)
from diffpy.srfit.structure.cctbxparset import CCTBXCrystalParSet
if CCTBXCrystalParSet.canAdapt(stru):
return CCTBXCrystalParSet(name, stru)
raise TypeError("Unadaptable structure format")
def testExplicitDihedralAngleRestraints(self):
"""Test the structure with explicit dihedral angles."""
occryst = self.occryst
ocmol = self.ocmol
# make our crystal
cryst = ObjCrystCrystalParSet("bucky", occryst)
m = cryst.c60
# Restrain some dihedral angles.
res0 = m.restrainDihedralAngle(m.atoms[0], m.atoms[5], m.atoms[8],
m.atoms[41], 1.1, 0.1, 0.1)
res1 = m.restrainDihedralAngle(m.atoms[0], m.atoms[7], m.atoms[44],
m.atoms[2], 1.1, 0.1, 0.1)
# make sure that we have some restraints in the molecule
self.assertTrue(2, len(m._restraints))
# make sure these evaluate to whatver we get from objcryst
p0 = set([res0.penalty(), res1.penalty()])
angles = ocmol.GetDihedralAngleList()
p1 = set([angles[0].GetLogLikelihood(), angles[1].GetLogLikelihood()])
self.assertEqual(p0, p1)
return
def testExplicitBondAngleRestraints(self):
"""Test the structure with explicit bond angles.
Note that this cannot work with co-linear points as the direction of
rotation cannot be defined in this case.
"""
occryst = self.occryst
ocmol = self.ocmol
# make our crystal
cryst = ObjCrystCrystalParSet("bucky", occryst)
m = cryst.c60
# restrain some bond angles
res0 = m.restrainBondAngle(m.atoms[0], m.atoms[5], m.atoms[8], 3.3,
0.1, 0.1)
res1 = m.restrainBondAngle(m.atoms[0], m.atoms[7], m.atoms[44], 3.3,
0.1, 0.1)
# make sure that we have some restraints in the molecule
self.assertTrue(2, len(m._restraints))
# make sure these evaluate to whatver we get from objcryst
p0 = set([res0.penalty(), res1.penalty()])
angles = ocmol.GetBondAngleList()
p1 = set([angles[0].GetLogLikelihood(), angles[1].GetLogLikelihood()])
self.assertEqual(p0, p1)
return
def testImplicitDihedralAngleRestraints(self):
"""Test the structure with implicit dihedral angles."""
occryst = self.occryst
ocmol = self.ocmol
# Add some bond angles to the molecule
ocmol.AddDihedralAngle(ocmol[0], ocmol[5], ocmol[8], ocmol[41], 1.1,
0.1, 0.1)
ocmol.AddDihedralAngle(ocmol[0], ocmol[7], ocmol[44], ocmol[2], 1.3,
0.1, 0.1)
# make our crystal
cryst = ObjCrystCrystalParSet("bucky", occryst)
m = cryst.c60
m.wrapRestraints()
# make sure that we have some restraints in the molecule
self.assertTrue(2, len(m._restraints))
# make sure these evaluate to whatver we get from objcryst
res0, res1 = m._restraints
p0 = set([res0.penalty(), res1.penalty()])
angles = ocmol.GetDihedralAngleList()
p1 = set([angles[0].GetLogLikelihood(), angles[1].GetLogLikelihood()])
self.assertEqual(p0, p1)
return
def testImplicitBondLengthRestraints(self):
"""Test the structure with implicit bond lengths."""
occryst = self.occryst
ocmol = self.ocmol
# Add some bonds to the molecule
ocmol.AddBond(ocmol[0], ocmol[5], 3.3, 0.1, 0.1)
ocmol.AddBond(ocmol[0], ocmol[7], 3.3, 0.1, 0.1)
# make our crystal
cryst = ObjCrystCrystalParSet("bucky", occryst)
m = cryst.c60
m.wrapRestraints()
# make sure that we have some restraints in the molecule
self.assertTrue(2, len(m._restraints))
# make sure these evaluate to whatver we get from objcryst
res0, res1 = m._restraints
p0 = set([res0.penalty(), res1.penalty()])
bonds = ocmol.GetBondList()
p1 = set([bonds[0].GetLogLikelihood(), bonds[1].GetLogLikelihood()])
self.assertEqual(p0, p1)
return
def struToParameterSet(name, stru):
"""Creates a ParameterSet from an structure.
This returns a ParameterSet adapted for the structure depending on its
type.
stru -- a structure object known by this module
name -- A name to give the structure.
Raises TypeError if stru cannot be adapted
"""
from diffpy.srfit.structure.diffpyparset import DiffpyStructureParSet
if DiffpyStructureParSet.canAdapt(stru):
return DiffpyStructureParSet(name, stru)
from diffpy.srfit.structure.objcrystparset import ObjCrystCrystalParSet
if ObjCrystCrystalParSet.canAdapt(stru):
return ObjCrystCrystalParSet(name, stru)
from diffpy.srfit.structure.objcrystparset import ObjCrystMoleculeParSet
if ObjCrystMoleculeParSet.canAdapt(stru):
return ObjCrystMoleculeParSet(name, stru)
from diffpy.srfit.structure.cctbxparset import CCTBXCrystalParSet
if CCTBXCrystalParSet.canAdapt(stru):
return CCTBXCrystalParSet(name, stru)
raise TypeError("Unadaptable structure format")
def testExplicitBondLengthParameter(self):
"""Test adding bond length parameters to the molecule."""
occryst = self.occryst
# make our crystal
cryst = ObjCrystCrystalParSet("bucky", occryst)
m = cryst.c60
a0 = m.atoms[0]
a7 = m.atoms[7]
a20 = m.atoms[20]
# Add a parameter
p1 = m.addBondLengthParameter("C07", a0, a7)
# Have another atom tag along for the ride
p1.addAtoms([a20])
xyz0 = numpy.array([a0.x.getValue(), a0.y.getValue(), a0.z.getValue()])
xyz7 = numpy.array([a7.x.getValue(), a7.y.getValue(), a7.z.getValue()])
xyz20 = numpy.array([a20.x.getValue(), a20.y.getValue(),
a20.z.getValue()])
dd = xyz0 - xyz7
d0 = numpy.dot(dd, dd)**0.5
self.assertAlmostEquals(d0, p1.getValue(), 6)
# Record the unit direction of change for later
u = dd/d0
# Change the value
scale = 1.05
p1.setValue(scale*d0)
# Verify that it has changed.
self.assertAlmostEquals(scale*d0, p1.getValue())
xyz0a = numpy.array([a0.x.getValue(), a0.y.getValue(), a0.z.getValue()])
xyz7a = numpy.array([a7.x.getValue(), a7.y.getValue(), a7.z.getValue()])
xyz20a = numpy.array([a20.x.getValue(), a20.y.getValue(),
a20.z.getValue()])
dda = xyz0a - xyz7a
d1 = numpy.dot(dda, dda)**0.5
self.assertAlmostEquals(scale*d0, d1)
# Verify that only the second and third atoms have moved.
self.assertTrue(numpy.array_equal(xyz0, xyz0a))
xyz7calc = xyz7 + (1-scale)*d0*u
for i in range(3):
self.assertAlmostEqual(xyz7a[i], xyz7calc[i], 6)
xyz20calc = xyz20 + (1-scale)*d0*u
for i in range(3):
self.assertAlmostEqual(xyz20a[i], xyz20calc[i], 6)
return
def testExplicitBondLengthRestraints(self):
"""Test the structure with explicit bond lengths."""
occryst = self.occryst
ocmol = self.ocmol
# make our crystal
cryst = ObjCrystCrystalParSet("bucky", occryst)
return
m = cryst.c60
# make some bond angle restraints
res0 = m.restrainBondLength(m.atoms[0], m.atoms[5], 3.3, 0.1, 0.1)
res1 = m.restrainBondLength(m.atoms[0], m.atoms[7], 3.3, 0.1, 0.1)
# make sure that we have some restraints in the molecule
self.assertTrue(2, len(m._restraints))
# make sure these evaluate to whatver we get from objcryst
p0 = set([res0.penalty(), res1.penalty()])
bonds = ocmol.GetBondList()
p1 = set([bonds[0].GetLogLikelihood(), bonds[1].GetLogLikelihood()])
self.assertEqual(p0, p1)
return
def getObjCrystParSetSpaceGroup(sg):
"""Make an ObjCrystCrystalParSet with the proper space group."""
from pyobjcryst.spacegroup import SpaceGroup
sgobjcryst = SpaceGroup(sg.short_name)
sgnew = ObjCrystCrystalParSet._createSpaceGroup(sgobjcryst)
return sgnew
def testExplicitDihedralAngleParameter(self):
"""Test adding dihedral angle parameters to the molecule."""
occryst = self.occryst
# make our crystal
cryst = ObjCrystCrystalParSet("bucky", occryst)
m = cryst.c60
a0 = m.atoms[0]
a7 = m.atoms[7]
a20 = m.atoms[20]
a25 = m.atoms[25]
a33 = m.atoms[33]
xyz0 = numpy.array([a0.x.getValue(), a0.y.getValue(), a0.z.getValue()])
xyz7 = numpy.array([a7.x.getValue(), a7.y.getValue(), a7.z.getValue()])
xyz20 = numpy.array([a20.x.getValue(), a20.y.getValue(),
a20.z.getValue()])
xyz25 = numpy.array([a25.x.getValue(), a25.y.getValue(),
a25.z.getValue()])
xyz33 = numpy.array([a33.x.getValue(), a33.y.getValue(),
a33.z.getValue()])
v12 = xyz0 - xyz7
v23 = xyz7 - xyz20
v34 = xyz20 - xyz25
v123 = numpy.cross(v12, v23)
v234 = numpy.cross(v23, v34)
d123 = numpy.dot(v123, v123)**0.5
d234 = numpy.dot(v234, v234)**0.5
angle0 = -numpy.arccos(numpy.dot(v123, v234)/(d123*d234))
# Add a parameter
p1 = m.addDihedralAngleParameter("C072025", a0, a7, a20, a25)
# Have another atom tag along for the ride
p1.addAtoms([a33])
self.assertAlmostEqual(angle0, p1.getValue(), 6)
# Change the value
scale = 1.05
p1.setValue(scale*angle0)
# Verify that it has changed.
self.assertAlmostEqual(scale*angle0, p1.getValue(), 6)
xyz0a = numpy.array([a0.x.getValue(), a0.y.getValue(), a0.z.getValue()])
xyz7a = numpy.array([a7.x.getValue(), a7.y.getValue(), a7.z.getValue()])
xyz20a = numpy.array([a20.x.getValue(), a20.y.getValue(),
a20.z.getValue()])
xyz25a = numpy.array([a25.x.getValue(), a25.y.getValue(),
a25.z.getValue()])
xyz33a = numpy.array([a33.x.getValue(), a33.y.getValue(),
a33.z.getValue()])
v12a = xyz0a - xyz7a
v23a = xyz7a - xyz20a
v34a = xyz20a - xyz25a
v123a = numpy.cross(v12a, v23a)
v234a = numpy.cross(v23a, v34a)
d123a = numpy.dot(v123a, v123a)**0.5
d234a = numpy.dot(v234a, v234a)**0.5
angle1 = -numpy.arccos(numpy.dot(v123a, v234a)/(d123a*d234a))
self.assertAlmostEquals(scale*angle0, angle1)
# Verify that only the last two atoms have moved.
self.assertTrue(numpy.array_equal(xyz0, xyz0a))
self.assertTrue(numpy.array_equal(xyz7, xyz7a))
self.assertTrue(numpy.array_equal(xyz20, xyz20a))
self.assertFalse(numpy.array_equal(xyz25, xyz25a))
self.assertFalse(numpy.array_equal(xyz33, xyz33a))
return
def testExplicitBondAngleParameter(self):
"""Test adding bond angle parameters to the molecule."""
occryst = self.occryst
# make our crystal
cryst = ObjCrystCrystalParSet("bucky", occryst)
m = cryst.c60
a0 = m.atoms[0]
a7 = m.atoms[7]
a20 = m.atoms[20]
a25 = m.atoms[25]
xyz0 = numpy.array([a0.x.getValue(), a0.y.getValue(), a0.z.getValue()])
xyz7 = numpy.array([a7.x.getValue(), a7.y.getValue(), a7.z.getValue()])
xyz20 = numpy.array([a20.x.getValue(), a20.y.getValue(),
a20.z.getValue()])
xyz25 = numpy.array([a25.x.getValue(), a25.y.getValue(),
a25.z.getValue()])
v1 = xyz7 - xyz0
d1 = numpy.dot(v1, v1)**0.5
v2 = xyz7 - xyz20
d2 = numpy.dot(v2, v2)**0.5
angle0 = numpy.arccos(numpy.dot(v1, v2)/(d1*d2))
# Add a parameter
p1 = m.addBondAngleParameter("C0720", a0, a7, a20)
# Have another atom tag along for the ride
p1.addAtoms([a25])
self.assertAlmostEqual(angle0, p1.getValue(), 6)
# Change the value
scale = 1.05
p1.setValue(scale*angle0)
# Verify that it has changed.
self.assertAlmostEqual(scale*angle0, p1.getValue(), 6)
xyz0a = numpy.array([a0.x.getValue(), a0.y.getValue(), a0.z.getValue()])
xyz7a = numpy.array([a7.x.getValue(), a7.y.getValue(), a7.z.getValue()])
xyz20a = numpy.array([a20.x.getValue(), a20.y.getValue(),
a20.z.getValue()])
xyz25a = numpy.array([a25.x.getValue(), a25.y.getValue(),
a25.z.getValue()])
v1a = xyz7a - xyz0a
d1a = numpy.dot(v1a, v1a)**0.5
v2a = xyz7a - xyz20a
d2a = numpy.dot(v2a, v2a)**0.5
angle1 = numpy.arccos(numpy.dot(v1a, v2a)/(d1a*d2a))
self.assertAlmostEquals(scale*angle0, angle1)
# Verify that only the last two atoms have moved.
self.assertTrue(numpy.array_equal(xyz0, xyz0a))
self.assertTrue(numpy.array_equal(xyz7, xyz7a))
self.assertFalse(numpy.array_equal(xyz20, xyz20a))
self.assertFalse(numpy.array_equal(xyz25, xyz25a))
return
def testObjCrystParSet(self):
"""Test the structure conversion."""
occryst = self.occryst
ocmol = self.ocmol
cryst = ObjCrystCrystalParSet("bucky", occryst)
m = cryst.c60
self.assertEquals(cryst.name, "bucky")
def _testCrystal():
# Test the lattice
self.assertAlmostEquals(occryst.a, cryst.a.value)
self.assertAlmostEquals(occryst.b, cryst.b.getValue())
self.assertAlmostEquals(occryst.c, cryst.c.getValue())
self.assertAlmostEquals(occryst.alpha, cryst.alpha.getValue())
self.assertAlmostEquals(occryst.beta, cryst.beta.getValue())
self.assertAlmostEquals(occryst.gamma, cryst.gamma.getValue())
return
def _testMolecule():
# Test position / occupancy
self.assertAlmostEquals(ocmol.X, m.x.getValue())
self.assertAlmostEquals(ocmol.Y, m.y.getValue())
self.assertAlmostEquals(ocmol.Z, m.z.getValue())
self.assertAlmostEquals(ocmol.Occupancy, m.occ.getValue())
# Test orientation
self.assertAlmostEquals(ocmol.Q0, m.q0.getValue())
self.assertAlmostEquals(ocmol.Q1, m.q1.getValue())
self.assertAlmostEquals(ocmol.Q2, m.q2.getValue())
self.assertAlmostEquals(ocmol.Q3, m.q3.getValue())
# Check the atoms thoroughly
for i in range(len(ocmol)):
oca = ocmol[i]
ocsp = oca.GetScatteringPower()
a = m.atoms[i]
self.assertEquals(ocsp.GetSymbol(), a.element)
self.assertAlmostEquals(oca.X, a.x.getValue())
self.assertAlmostEquals(oca.Y, a.y.getValue())
self.assertAlmostEquals(oca.Z, a.z.getValue())
self.assertAlmostEquals(oca.Occupancy, a.occ.getValue())
self.assertAlmostEquals(ocsp.Biso, a.Biso.getValue())
return
_testCrystal()
_testMolecule()
## Now change some values from ObjCryst
ocmol[0].X *= 1.1
ocmol[0].Occupancy *= 1.1
ocmol[0].GetScatteringPower().Biso *= 1.1
ocmol.Q0 *= 1.1
occryst.a *= 1.1
_testCrystal()
_testMolecule()
## Now change values from the srfit StructureParSet
cryst.c60.C44.x.setValue( 1.1 )
cryst.c60.C44.occ.setValue( 1.1 )
cryst.c60.C44.Biso.setValue( 1.1 )
cryst.c60.q3.setValue( 1.1 )
cryst.a.setValue(1.1)
_testCrystal()
_testMolecule()
return
def testConstrainSpaceGroup(self):
"""Make sure that all Parameters are constrained properly.
This tests constrainSpaceGroup from
diffpy.srfit.structure.sgconstraints, which is performed automatically
when an ObjCrystCrystalParSet is created.
"""
pi = numpy.pi
occryst = makeLaMnO3()
stru = ObjCrystCrystalParSet(occryst.GetName(), occryst)
# Make sure we actually create the constraints
stru._constrainSpaceGroup()
# Make the space group parameters individually
stru.sgpars.latpars
stru.sgpars.xyzpars
stru.sgpars.adppars
# Check the orthorhombic lattice
l = stru.getLattice()
self.assertTrue( l.alpha.const )
self.assertTrue( l.beta.const )
self.assertTrue( l.gamma.const )
self.assertEquals(pi/2, l.alpha.getValue())
self.assertEquals(pi/2, l.beta.getValue())
self.assertEquals(pi/2, l.gamma.getValue())
self.assertFalse( l.a.const )
self.assertFalse( l.b.const )
self.assertFalse( l.c.const )
self.assertEquals(0, len(l._constraints))
# Now make sure the scatterers are constrained properly
scatterers = stru.getScatterers()
la = scatterers[0]
self.assertFalse(la.x.const)
self.assertFalse(la.y.const)
self.assertTrue(la.z.const)
self.assertEquals(0, len(la._constraints))
mn = scatterers[1]
self.assertTrue(mn.x.const)
self.assertTrue(mn.y.const)
self.assertTrue(mn.z.const)
self.assertEquals(0, len(mn._constraints))
o1 = scatterers[2]
self.assertFalse(o1.x.const)
self.assertFalse(o1.y.const)
self.assertTrue(o1.z.const)
self.assertEquals(0, len(o1._constraints))
o2 = scatterers[3]
self.assertFalse(o2.x.const)
self.assertFalse(o2.y.const)
self.assertFalse(o2.z.const)
self.assertEquals(0, len(o2._constraints))
# Make sure we can't constrain these
self.assertRaises(ValueError, mn.constrain, mn.x, "y")
self.assertRaises(ValueError, mn.constrain, mn.y, "z")
self.assertRaises(ValueError, mn.constrain, mn.z, "x")
# Nor can we make them into variables
from diffpy.srfit.fitbase.fitrecipe import FitRecipe
f = FitRecipe()
self.assertRaises(ValueError, f.addVar, mn.x)
return