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 test_DiffPy_constrainAsSpaceGroup(self):
"""Test the constrainAsSpaceGroup function."""
from diffpy.srfit.structure.diffpyparset import DiffpyStructureParSet
from diffpy.srfit.structure.sgconstraints import constrainAsSpaceGroup
stru = makeLaMnO3_P1()
parset = DiffpyStructureParSet("LaMnO3", stru)
sgpars = constrainAsSpaceGroup(parset, "P b n m",
scatterers = parset.getScatterers()[::2],
constrainadps = True)
# Make sure that the new parameters were created
for par in sgpars:
self.assertNotEqual(None, par)
self.assertNotEqual(None, par.getValue() )
# Test the unconstrained atoms
for scatterer in parset.getScatterers()[1::2]:
self.assertFalse(scatterer.x.const)
self.assertFalse(scatterer.y.const)
self.assertFalse(scatterer.z.const)
self.assertFalse(scatterer.U11.const)
self.assertFalse(scatterer.U22.const)
self.assertFalse(scatterer.U33.const)
self.assertFalse(scatterer.U12.const)
self.assertFalse(scatterer.U13.const)
self.assertFalse(scatterer.U23.const)
self.assertEqual(0, len(scatterer._constraints))
proxied = [p.par for p in sgpars]
def _consttest(par):
return par.const
def _constrainedtest(par):
return par.constrained
def _proxytest(par):
return par in proxied
def _alltests(par):
return _consttest(par) or _constrainedtest(par) or _proxytest(par)
for idx, scatterer in enumerate(parset.getScatterers()[::2]):
# Under this scheme, atom 6 is free to vary
test = False
for par in [scatterer.x, scatterer.y, scatterer.z]:
test |= _alltests(par)
self.assertTrue(test)
test = False
for par in [scatterer.U11, scatterer.U22, scatterer.U33,
scatterer.U12, scatterer.U13, scatterer.U23]:
test |= _alltests(par)
self.assertTrue(test)
return
def testConstrainAsSpaceGroup(self):
"""Test the constrainAsSpaceGroup function."""
from diffpy.srfit.structure.sgconstraints import constrainAsSpaceGroup
stru = makeLaMnO3_P1()
parset = DiffpyStructureParSet("LaMnO3", stru)
sgpars = constrainAsSpaceGroup(parset, "P b n m",
scatterers = parset.getScatterers()[::2],
constrainadps = True)
# Make sure that the new parameters were created
for par in sgpars:
self.assertNotEquals(None, par)
self.assertNotEquals(None, par.getValue() )
# Test the unconstrained atoms
for scatterer in parset.getScatterers()[1::2]:
self.assertFalse(scatterer.x.const)
self.assertFalse(scatterer.y.const)
self.assertFalse(scatterer.z.const)
self.assertFalse(scatterer.U11.const)
self.assertFalse(scatterer.U22.const)
self.assertFalse(scatterer.U33.const)
self.assertFalse(scatterer.U12.const)
self.assertFalse(scatterer.U13.const)
self.assertFalse(scatterer.U23.const)
self.assertEquals(0, len(scatterer._constraints))
proxied = [p.par for p in sgpars]
def _consttest(par):
return par.const
def _constrainedtest(par):
return par.constrained
def _proxytest(par):
return par in proxied
def _alltests(par):
return _consttest(par) or _constrainedtest(par) or _proxytest(par)
for idx, scatterer in enumerate(parset.getScatterers()[::2]):
# Under this scheme, atom 6 is free to vary
test = False
for par in [scatterer.x, scatterer.y, scatterer.z]:
test |= _alltests(par)
self.assertTrue(test)
test = False
for par in [scatterer.U11, scatterer.U22, scatterer.U33,
scatterer.U12, scatterer.U13, scatterer.U23]:
test |= _alltests(par)
self.assertTrue(test)
return
def test_ConstrainAsSpaceGroup_args(self):
"""Test the arguments processing of constrainAsSpaceGroup function.
"""
from diffpy.srfit.structure.sgconstraints import constrainAsSpaceGroup
from diffpy.Structure.SpaceGroups import GetSpaceGroup
stru = makeLaMnO3_P1()
parset = DiffpyStructureParSet("LaMnO3", stru)
sgpars = constrainAsSpaceGroup(parset, "P b n m")
sg = GetSpaceGroup('P b n m')
parset2 = DiffpyStructureParSet("LMO", makeLaMnO3_P1())
sgpars2 = constrainAsSpaceGroup(parset2, sg)
list(sgpars)
list(sgpars2)
self.assertEqual(sgpars.names, sgpars2.names)
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 test_pickling(self):
"""Test pickling of DiffpyStructureParSet.
"""
stru = Structure([Atom("C", [0, 0.2, 0.5])])
dsps = DiffpyStructureParSet("dsps", stru)
data = pickle.dumps(dsps)
dsps2 = pickle.loads(data)
self.assertEqual(1, len(dsps2.atoms))
self.assertEqual(0.2, dsps2.atoms[0].y.value)
return
def test___repr__(self):
"""Test representation of DiffpyStructureParSet objects.
"""
lat = Lattice(3, 3, 2, 90, 90, 90)
atom = Atom("C", [0, 0.2, 0.5])
stru = Structure([atom], lattice=lat)
dsps = DiffpyStructureParSet("dsps", stru)
self.assertEqual(repr(stru), repr(dsps))
self.assertEqual(repr(lat), repr(dsps.lattice))
self.assertEqual(repr(atom), repr(dsps.atoms[0]))
return
def setStructure(self, strufile):
"""Set the structure used in the calculation.
strufile -- The name of a structure file. A
diffpy.Structure.Structure object will be created from
the file, and that object will be passed to the 'iofq'
function whenever it is called.
This will create the refinement Parameters using the
DiffpyStructureParSet adapter from diffpy.srfit.structure.diffpyparset.
DiffpyStructureParSet is a ParameterSet object that organizes and gives
attribute access to Parameters and ParameterSets adapted from a diffpy
Structure object. The Parameters embedded in the DiffpyStructureParSet
are proxies for attributes of the diffpy.Structure.Structure object
that is needed by the 'iofq' function. The Parameters will be
accessible by name under the 'phase' attribute of this generator, and
are organized hierarchically:
phase
- lattice (retrieved with 'getLattice')
- a
- b
- c
- alpha
- beta
- gamma
- scatterers (retrieved with 'getScatterers')
- atom1 (the name depends on the element)
- x
- y
- z
- occ
- U11
- U22
- U33
- U12
- U13
- U23
- Uiso
- etc.
The diffpy.Structure.Structure instance is held within the
DiffpyStructureParSet as the 'stru' attribute.
"""
# Load the structure from file
from diffpy.Structure import Structure
stru = Structure()
stru.read(strufile)
# Create a ParameterSet designed to interface with
# diffpy.Structure.Structure objects that organizes the Parameter
# hierarchy. Note that the DiffpyStructureParSet holds a handle to the
# loaded structure that we use in the __call__ method below.
#
# We pass the diffpy.Structure.Structure instance, and give the
# DiffpyStructureParSet the name "phase".
parset = DiffpyStructureParSet("phase", stru)
# Put this ParameterSet in the ProfileGenerator.
self.addParameterSet(parset)
return
def testDiffpyStructureParSet(self):
"""Test the structure conversion."""
a1 = Atom("Cu", xyz = numpy.array([.0, .1, .2]), Uisoequiv = 0.003)
a2 = Atom("Ag", xyz = numpy.array([.3, .4, .5]), Uisoequiv = 0.002)
l = Lattice(2.5, 2.5, 2.5, 90, 90, 90)
dsstru = Structure([a1,a2], l)
# Structure makes copies
a1 = dsstru[0]
a2 = dsstru[1]
s = DiffpyStructureParSet("CuAg", dsstru)
self.assertEquals(s.name, "CuAg")
def _testAtoms():
# Check the atoms thoroughly
self.assertEquals(a1.element, s.Cu0.element)
self.assertEquals(a2.element, s.Ag0.element)
self.assertEquals(a1.Uisoequiv, s.Cu0.Uiso.getValue())
self.assertEquals(a2.Uisoequiv, s.Ag0.Uiso.getValue())
self.assertEquals(a1.Bisoequiv, s.Cu0.Biso.getValue())
self.assertEquals(a2.Bisoequiv, s.Ag0.Biso.getValue())
for i in xrange(1,4):
for j in xrange(i,4):
uijstru = getattr(a1, "U%i%i"%(i,j))
uij = getattr(s.Cu0, "U%i%i"%(i,j)).getValue()
uji = getattr(s.Cu0, "U%i%i"%(j,i)).getValue()
self.assertEquals(uijstru, uij)
self.assertEquals(uijstru, uji)
bijstru = getattr(a1, "B%i%i"%(i,j))
bij = getattr(s.Cu0, "B%i%i"%(i,j)).getValue()
bji = getattr(s.Cu0, "B%i%i"%(j,i)).getValue()
self.assertEquals(bijstru, bij)
self.assertEquals(bijstru, bji)
self.assertEquals(a1.xyz[0], s.Cu0.x.getValue())
self.assertEquals(a1.xyz[1], s.Cu0.y.getValue())
self.assertEquals(a1.xyz[2], s.Cu0.z.getValue())
return
def _testLattice():
# Test the lattice
self.assertEquals(dsstru.lattice.a, s.lattice.a.getValue())
self.assertEquals(dsstru.lattice.b, s.lattice.b.getValue())
self.assertEquals(dsstru.lattice.c, s.lattice.c.getValue())
self.assertEquals(dsstru.lattice.alpha, s.lattice.alpha.getValue())
self.assertEquals(dsstru.lattice.beta, s.lattice.beta.getValue())
self.assertEquals(dsstru.lattice.gamma, s.lattice.gamma.getValue())
_testAtoms()
_testLattice()
# Now change some values from the diffpy Structure
a1.xyz[1] = 0.123
a1.U11 = 0.321
a1.B32 = 0.111
dsstru.lattice.setLatPar(a=3.0, gamma=121)
_testAtoms()
_testLattice()
# Now change values from the srfit DiffpyStructureParSet
s.Cu0.x.setValue(0.456)
s.Cu0.U22.setValue(0.441)
s.Cu0.B13.setValue(0.550)
d = dsstru.lattice.dist(a1.xyz, a2.xyz)
s.lattice.b.setValue(4.6)
s.lattice.alpha.setValue(91.3)
_testAtoms()
_testLattice()
# Make sure the distance changed
self.assertNotEquals(d, dsstru.lattice.dist(a1.xyz, a2.xyz))
return