def setUp(self):
self.P = PdfFit()
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.alloc('N', 0.0, 0.05, 0.1, 10, 200)
return
def setUp(self):
self.P = PdfFit()
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.alloc('N', 0.0, 0.05, 0.1, 10, 200)
return
def test_getcrw(self):
"""check PdfFit.getcrw()
"""
import numpy
self.assertEqual(0, self.P.num_datasets())
# Setting qmax=0 so that partial crw are not disturbed by
# termination ripples.
self.P.read_data(datafile('Ni.dat'), 'X', 0.0, 0.0)
# crw is empty before data refinement
self.assertEqual([], self.P.getcrw())
self.P.read_struct(datafile('Ni.stru'))
self.P.pdfrange(1, 2, 19)
self.P.refine()
crw19 = numpy.array(self.P.getcrw())
self.assertTrue(numpy.all(crw19 >= 0.0))
# check that crw19 is non decreasing
self.assertTrue(numpy.all(numpy.diff(crw19) >= 0.0))
# check that crw19 and getrw give the same value
rw19 = crw19[-1]
self.assertAlmostEqual(self.P.getrw(), rw19, self.places)
# renormalize cumulative Rw and compare with Rw at r=15
Gobs19 = numpy.array(self.P.getpdf_obs())
Gnorm19 = numpy.sqrt(numpy.sum(Gobs19**2))
r = numpy.array(self.P.getR())
idx = numpy.nonzero(r <= 15)[0]
Gnorm15 = numpy.sqrt(numpy.sum(Gobs19[idx]**2))
i15 = idx[-1]
rw15 = crw19[i15] * Gnorm19 / Gnorm15
self.P.pdfrange(1, 2, r[i15] + 1e-5)
self.P.refine()
self.assertAlmostEqual(self.P.getrw(), rw15, self.places)
return
def test_getcrw(self):
"""check PdfFit.getcrw()
"""
import numpy
self.assertEqual(0, self.P.num_datasets())
# Setting qmax=0 so that partial crw are not disturbed by
# termination ripples.
self.P.read_data(datafile('Ni.dat'), 'X', 0.0, 0.0)
# crw is empty before data refinement
self.assertEqual([], self.P.getcrw())
self.P.read_struct(datafile('Ni.stru'))
self.P.pdfrange(1, 2, 19)
self.P.refine()
crw19 = numpy.array(self.P.getcrw())
self.failUnless(numpy.all(crw19 >= 0.0))
# check that crw19 is non decreasing
self.failUnless(numpy.all(numpy.diff(crw19) >= 0.0))
# check that crw19 and getrw give the same value
rw19 = crw19[-1]
self.assertAlmostEqual(self.P.getrw(), rw19, self.places)
# renormalize cumulative Rw and compare with Rw at r=15
Gobs19 = numpy.array(self.P.getpdf_obs())
Gnorm19 = numpy.sqrt(numpy.sum(Gobs19**2))
r = numpy.array(self.P.getR())
idx = numpy.nonzero(r <= 15)[0]
Gnorm15 = numpy.sqrt(numpy.sum(Gobs19[idx]**2))
i15 = idx[-1]
rw15 = crw19[i15] * Gnorm19 / Gnorm15
self.P.pdfrange(1, 2, r[i15] + 1e-5)
self.P.refine()
self.assertAlmostEqual(self.P.getrw(), rw15, self.places)
return
def test_twophase_calculation(self):
"""check PDF calculation for 2 phases with different spdiameters
"""
d1 = 6
d2 = 9
self.P.read_struct(datafile('Ni.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.setvar('spdiameter', d1)
self.P.calc()
G1 = numpy.array(self.P.getpdf_fit())
self.P.reset()
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.setvar('spdiameter', d2)
self.P.calc()
G2 = numpy.array(self.P.getpdf_fit())
self.P.reset()
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.setphase(1)
self.P.setvar('spdiameter', d1)
self.P.setphase(2)
self.P.setvar('spdiameter', d2)
self.P.calc()
Gtot = numpy.array(self.P.getpdf_fit())
dG = (G1 + G2 - Gtot)
r = numpy.array(self.P.getR())
msd = numpy.dot(dG, dG) / len(r)
self.assertAlmostEqual(0.0, numpy.sqrt(msd), self.places)
return
def test_twophase_calculation(self):
"""check PDF calculation for 2 phases with different spdiameters
"""
d1 = 6
d2 = 9
self.P.read_struct(datafile('Ni.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.setvar('spdiameter', d1)
self.P.calc()
G1 = numpy.array(self.P.getpdf_fit())
self.P.reset()
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.setvar('spdiameter', d2)
self.P.calc()
G2 = numpy.array(self.P.getpdf_fit())
self.P.reset()
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.setphase(1)
self.P.setvar('spdiameter', d1)
self.P.setphase(2)
self.P.setvar('spdiameter', d2)
self.P.calc()
Gtot = numpy.array(self.P.getpdf_fit())
dG = (G1 + G2 - Gtot)
r = numpy.array(self.P.getR())
msd = numpy.dot(dG, dG)/len(r)
self.assertAlmostEqual(0.0, numpy.sqrt(msd), self.places)
return
def test_alloc(self):
"""check PdfFit.alloc()
"""
# alloc and read_struct can be called in any order.
self.P.alloc('X', 25, 0.0, 0.01, 10, 1000)
# without a structure calculated PDF is all zero
self.P.calc()
Gzero = self.P.getpdf_fit()
self.assertEqual(1000*[0.0], Gzero)
self.P.read_struct(datafile('Ni.stru'))
self.P.calc()
# check r-values
r = self.P.getR()
self.assertEqual(1000, len(r))
for i in range(1000):
self.assertAlmostEqual(0.01*(i + 1), r[i], self.places)
Gfit_alloc_read = self.P.getpdf_fit()
# now try the other order
self.P.reset()
self.P.read_struct(datafile('Ni.stru'))
self.P.alloc('X', 25, 0.0, 0.01, 10, 1000)
self.P.calc()
Gfit_read_alloc = self.P.getpdf_fit()
# and they should be the same
self.assertEqual(Gfit_read_alloc, Gfit_alloc_read)
return
def test_alloc(self):
"""check PdfFit.alloc()
"""
# alloc and read_struct can be called in any order.
self.P.alloc('X', 25, 0.0, 0.01, 10, 1000)
# without a structure calculated PDF is all zero
self.P.calc()
Gzero = self.P.getpdf_fit()
self.assertEqual(1000 * [0.0], Gzero)
self.P.read_struct(datafile('Ni.stru'))
self.P.calc()
# check r-values
r = self.P.getR()
self.assertEqual(1000, len(r))
for i in range(1000):
self.assertAlmostEqual(0.01 * (i + 1), r[i], self.places)
Gfit_alloc_read = self.P.getpdf_fit()
# now try the other order
self.P.reset()
self.P.read_struct(datafile('Ni.stru'))
self.P.alloc('X', 25, 0.0, 0.01, 10, 1000)
self.P.calc()
Gfit_read_alloc = self.P.getpdf_fit()
# and they should be the same
self.assertEqual(Gfit_read_alloc, Gfit_alloc_read)
return
def test_ijcharValueError(self):
"""raise ValueError when ijchar is neither 'i' nor 'j'"""
self.P.read_struct(datafile("Ni.stru"))
self.P.read_data(datafile("Ni.dat"), 'X', 25.0, 0.0)
self.P.selectAtomType(self.iset, 'i', 'Ni', True)
self.P.selectAtomType(self.iset, 'j', 'Ni', True)
self.assertRaises(ValueError, self.P.selectAtomType,
self.iset, 'k', 'Ni', True)
def test_IOError(self):
"""raise IOError when dif cannot be saved"""
self.P.read_struct(datafile("Ni.stru"))
self.P.alloc('X', 30.0, 0.05, 2, 10, 100)
self.P.calc()
self.P.read_data(datafile("Ni.dat"), 'X', 25.0, 0.5)
self.assertRaises(IOError, self.P.save_dif, 1,
"nodir183160/"+self.strufile)
def test_constraintError(self):
"""raise constraintError when constraint is bad"""
self.P.read_struct(datafile("Ni.stru"))
self.P.read_data(datafile("Ni.dat"), 'X', 25.0, 0.0)
self.P.constrain('x(1)', 'junk+@1')
self.P.setpar(1, 0.01)
self.assertRaises(pdffit2.constraintError, self.P.calc)
self.assertRaises(pdffit2.constraintError, self.P.refine)
return
def test_unassignedError2(self):
"""raise pdffit2.unassignedError when set does not exist"""
self.P.read_struct(datafile("Ni.stru"))
# pass for phase 1
self.P.read_data(datafile("Ni.dat"), 'X', 25.0, 0.0)
self.P.selectAtomIndex(self.iset, 'i', 1, True)
self.P.selectAtomIndex(self.iset, 'i', 2, False)
# fail for phase 2
self.assertRaises(pdffit2.unassignedError, self.P.selectAtomIndex,
2, 'i', 1, True)
def test_unassignedError2(self):
"""raise pdffit2.unassignedError when set does not exist"""
self.P.read_struct(datafile("Ni.stru"))
# selectAtomType should pass with one phase defined
self.P.read_data(datafile("Ni.dat"), 'X', 25.0, 0.0)
self.P.selectAtomType(self.iset, 'i', 'Ni', True)
self.P.selectAtomType(self.iset, 'j', 'Ni', False)
# but fail for phase 2 which is not present
self.assertRaises(pdffit2.unassignedError, self.P.selectAtomType,
2, 'i', 'Ca', True)
def test_IOError(self):
"""raise IOError when residual file cannot be saved"""
self.P.read_struct(datafile("Ni.stru"))
self.P.read_data(datafile("Ni.dat"), 'X', 30.0, 0.0)
self.P.constrain(self.P.lat(1), 1)
self.P.setpar(1, 3.0)
self.P.pdfrange(1,2.0,10.0)
self.P.refine_step()
self.assertRaises(IOError, self.P.save_res,
"nodir183160/"+self.resfile)
def test_bond_length_atoms(self):
"""check PdfFit.bond_length_atoms()
"""
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
dij, ddij = self.P.bond_length_atoms(1, 5)
self.assertAlmostEqual(4.03635, dij, self.places)
self.P.setphase(1)
self.assertRaises(ValueError, self.P.bond_length_atoms, 1, 5)
return
def test_bond_length_atoms(self):
"""check PdfFit.bond_length_atoms()
"""
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
dij, ddij = self.P.bond_length_atoms(1, 5)
self.assertAlmostEqual(4.03635, dij, self.places)
self.P.setphase(1)
self.assertRaises(ValueError, self.P.bond_length_atoms, 1, 5)
return
def test_get_atoms(self):
"""check PdfFit.get_atoms()
"""
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.setphase(1)
a1 = self.P.get_atoms()
a2 = self.P.get_atoms(2)
self.assertEqual(4*['NI'], a1)
self.assertEqual(8*['PB']+24*['O']+8*['SC']+8*['W']+8*['TI'], a2)
return
def test_get_atom_types(self):
"""check PdfFit.get_atom_types()
"""
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.setphase(1)
atp1 = self.P.get_atom_types()
atp2 = self.P.get_atom_types(2)
self.assertEqual(['NI'], atp1)
self.assertEqual(['PB', 'O', 'SC', 'W', 'TI'], atp2)
return
def test_num_phases(self):
"""check PdfFit.num_phases()
"""
self.assertEqual(0, self.P.num_phases())
self.P.read_struct(datafile('Ni.stru'))
self.assertEqual(1, self.P.num_phases())
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.assertEqual(2, self.P.num_phases())
self.P.reset()
self.assertEqual(0, self.P.num_phases())
return
def test_constrainNonRefVar(self):
"raise constraintError when attempting to constrain non-refinables"
self.P.read_struct(datafile("Ni.stru"))
self.P.read_data(datafile("Ni.dat"), 'X', 25.0, 0.0)
self.assertRaises(pdffit2.constraintError,
self.P.constrain, 'rcut', '@7')
self.assertRaises(pdffit2.constraintError,
self.P.constrain, 'rcut', 13)
self.assertRaises(pdffit2.constraintError,
self.P.constrain, 'stepcut', '@17')
return
def test_num_phases(self):
"""check PdfFit.num_phases()
"""
self.assertEqual(0, self.P.num_phases())
self.P.read_struct(datafile('Ni.stru'))
self.assertEqual(1, self.P.num_phases())
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.assertEqual(2, self.P.num_phases())
self.P.reset()
self.assertEqual(0, self.P.num_phases())
return
def test_get_atom_types(self):
"""check PdfFit.get_atom_types()
"""
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.setphase(1)
atp1 = self.P.get_atom_types()
atp2 = self.P.get_atom_types(2)
self.assertEqual(['NI'], atp1)
self.assertEqual(['PB', 'O', 'SC', 'W', 'TI'], atp2)
return
def test_get_structure(self):
"""check PdfFit.get_structure()
"""
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
stru1 = self.P.get_structure(1)
self.assertEqual(4, len(stru1))
self.assertEqual('Ni', stru1[0].element)
stru2 = self.P.get_structure(2)
self.assertEqual(56, len(stru2))
self.assertEqual('Ti', stru2[-1].element)
return
def test_get_structure(self):
"""check PdfFit.get_structure()
"""
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
stru1 = self.P.get_structure(1)
self.assertEqual(4, len(stru1))
self.assertEqual('Ni', stru1[0].element)
stru2 = self.P.get_structure(2)
self.assertEqual(56, len(stru2))
self.assertEqual('Ti', stru2[-1].element)
return
def test_num_atoms(self):
"""check PdfFit.num_atoms()
"""
self.P.read_struct(datafile('Ni.stru'))
self.assertEqual(4, self.P.num_atoms())
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.assertEqual(56, self.P.num_atoms())
self.P.setphase(1)
self.assertEqual(4, self.P.num_atoms())
self.P.setphase(2)
self.assertEqual(56, self.P.num_atoms())
return
def test_get_atoms(self):
"""check PdfFit.get_atoms()
"""
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.setphase(1)
a1 = self.P.get_atoms()
a2 = self.P.get_atoms(2)
self.assertEqual(4 * ['NI'], a1)
self.assertEqual(
8 * ['PB'] + 24 * ['O'] + 8 * ['SC'] + 8 * ['W'] + 8 * ['TI'], a2)
return
def test_num_atoms(self):
"""check PdfFit.num_atoms()
"""
self.P.read_struct(datafile('Ni.stru'))
self.assertEqual(4, self.P.num_atoms())
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.assertEqual(56, self.P.num_atoms())
self.P.setphase(1)
self.assertEqual(4, self.P.num_atoms())
self.P.setphase(2)
self.assertEqual(56, self.P.num_atoms())
return
def test_unassignedError2(self):
"""raise pdffit2.unassignedError when set does not exist"""
self.P.read_struct(datafile("Ni.stru"))
# fail when there is no dataset
self.assertRaises(pdffit2.unassignedError, self.P.selectNone,
self.iset, 'i')
# pass with dataset
self.P.read_data(datafile("Ni.dat"), 'X', 25.0, 0.0)
self.P.selectNone(self.iset, 'i')
self.P.selectNone(self.iset, 'j')
# fail for phase 2
self.assertRaises(pdffit2.unassignedError, self.P.selectNone, 2, 'i')
self.assertRaises(pdffit2.unassignedError, self.P.selectNone, 2, 'j')
def test_stepcut_io(self):
"""Check reading and writing of stepcut from structure file.
"""
import re
self.P.read_struct(datafile('Ni.stru'))
self.assertEqual(0.0, self.P.getvar('stepcut'))
# engine should not write shape factor when not defined
sscnone = self.P.save_struct_string(1)
self.assertTrue(not re.search('(?m)^shape +stepcut,', sscnone))
self.P.setvar('stepcut', 7)
ssc7 = self.P.save_struct_string(1)
# ssc7 should contain shape factor data
self.assertTrue(re.search('(?m)^shape +stepcut,', ssc7))
self.P.reset()
self.P.read_struct_string(ssc7)
self.assertEqual(7.0, self.P.getvar('stepcut'))
# try to read without comma
ssc14 = re.sub('(?m)^shape +stepcut.*$', 'shape stepcut 14.00', ssc7)
self.P.read_struct_string(ssc14)
self.assertEqual(14.0, self.P.getvar('stepcut'))
# try to read invalid shape data
sinvalid = re.sub('(?m)^shape .*', 'shape invalid, 1', ssc7)
self.assertRaises(pdffit2.structureError, self.P.read_struct_string,
sinvalid)
return
def test_stepcut_io(self):
"""Check reading and writing of stepcut from structure file.
"""
import re
self.P.read_struct(datafile('Ni.stru'))
self.assertEqual(0.0, self.P.getvar('stepcut'))
# engine should not write shape factor when not defined
sscnone = self.P.save_struct_string(1)
self.failUnless(not re.search('(?m)^shape +stepcut,', sscnone))
self.P.setvar('stepcut', 7)
ssc7 = self.P.save_struct_string(1)
# ssc7 should contain shape factor data
self.failUnless(re.search('(?m)^shape +stepcut,', ssc7))
self.P.reset()
self.P.read_struct_string(ssc7)
self.assertEqual(7.0, self.P.getvar('stepcut'))
# try to read without comma
ssc14 = re.sub('(?m)^shape +stepcut.*$', 'shape stepcut 14.00', ssc7)
self.P.read_struct_string(ssc14)
self.assertEqual(14.0, self.P.getvar('stepcut'))
# try to read invalid shape data
sinvalid = re.sub('(?m)^shape .*', 'shape invalid, 1', ssc7)
self.assertRaises(pdffit2.structureError,
self.P.read_struct_string, sinvalid)
return
def test_add_structure(self):
"""check PdfFit.add_structure()
"""
from diffpy.structure import Structure
ni = Structure(filename=datafile('Ni.stru'))
self.P.add_structure(ni)
self.assertEqual(4, self.P.num_atoms())
return
def test_get_structure(self):
"""check PdfFit.get_structure()
"""
# skip test when diffpy.Structure is not installed
try:
from diffpy.Structure import Structure
except ImportError:
return
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
stru1 = self.P.get_structure(1)
self.assertEqual(4, len(stru1))
self.assertEqual('Ni', stru1[0].element)
stru2 = self.P.get_structure(2)
self.assertEqual(56, len(stru2))
self.assertEqual('Ti', stru2[-1].element)
return
def test_bond_angle(self):
"""check PdfFit.bond_angle()
"""
self.P.read_struct(datafile('Ni.stru'))
a, e = self.P.bond_angle(1, 2, 3)
self.assertAlmostEqual(60.0, a, self.places)
self.assertRaises(ValueError, self.P.bond_angle, 0, 1, 2)
self.assertRaises(ValueError, self.P.bond_angle, 1, 2, 7)
return
def test_bond_angle(self):
"""check PdfFit.bond_angle()
"""
self.P.read_struct(datafile('Ni.stru'))
a, e = self.P.bond_angle(1, 2, 3)
self.assertAlmostEqual(60.0, a, self.places)
self.assertRaises(ValueError, self.P.bond_angle, 0, 1, 2)
self.assertRaises(ValueError, self.P.bond_angle, 1, 2, 7)
return
def test_bond_length_types(self):
"""check PdfFit.bond_length_types()
"""
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
dPbO = self.P.bond_length_types('Pb', 'O', 0.1, 3.0)
# check if keys are present
self.assertTrue('dij' in dPbO)
self.assertTrue('ddij' in dPbO)
self.assertTrue('ij0' in dPbO)
self.assertTrue('ij1' in dPbO)
# check if they have the same length
npts = len(dPbO['dij'])
self.assertEqual(npts, len(dPbO['ddij']))
self.assertEqual(npts, len(dPbO['ij0']))
self.assertEqual(npts, len(dPbO['ij1']))
# 8 Pb atoms have coordination 12 in perovskite structure
self.assertEqual(8 * 12, len(dPbO['dij']))
self.P.setphase(1)
dfcc = self.P.bond_length_types('ALL', 'ALL', 0.1, 2.6)
# 4 Ni atoms with coordination 12
self.assertEqual(4 * 12, len(dfcc['dij']))
# invalid element
self.assertRaises(ValueError, self.P.bond_length_types, 'Ni', 'Nix',
0.1, 5.0)
# check indices ij0
allij0 = sum(dfcc['ij0'], tuple())
self.assertEqual(0, min(allij0))
self.assertEqual(3, max(allij0))
# check indices ij1
allij1 = sum(dfcc['ij1'], tuple())
self.assertEqual(1, min(allij1))
self.assertEqual(4, max(allij1))
# check index values
ij0check = [(i1 - 1, j1 - 1) for i1, j1 in dfcc['ij1']]
self.assertEqual(ij0check, dfcc['ij0'])
# test valid element which is not present in the structure
dnone = self.P.bond_length_types('Ni', 'Au', 0.1, 5.0)
self.assertEqual(0, len(dnone['dij']))
self.assertEqual(0, len(dnone['ddij']))
self.assertEqual(0, len(dnone['ij0']))
self.assertEqual(0, len(dnone['ij1']))
return
def test_bond_length_types(self):
"""check PdfFit.bond_length_types()
"""
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
dPbO = self.P.bond_length_types('Pb', 'O', 0.1, 3.0)
# check if keys are present
self.failUnless('dij' in dPbO)
self.failUnless('ddij' in dPbO)
self.failUnless('ij0' in dPbO)
self.failUnless('ij1' in dPbO)
# check if they have the same length
npts = len(dPbO['dij'])
self.assertEqual(npts, len(dPbO['ddij']))
self.assertEqual(npts, len(dPbO['ij0']))
self.assertEqual(npts, len(dPbO['ij1']))
# 8 Pb atoms have coordination 12 in perovskite structure
self.assertEqual(8*12, len(dPbO['dij']))
self.P.setphase(1)
dfcc = self.P.bond_length_types('ALL', 'ALL', 0.1, 2.6)
# 4 Ni atoms with coordination 12
self.assertEqual(4*12, len(dfcc['dij']))
# invalid element
self.assertRaises(ValueError, self.P.bond_length_types, 'Ni', 'Nix', 0.1, 5.0)
# check indices ij0
allij0 = sum(dfcc['ij0'], tuple())
self.assertEqual(0, min(allij0))
self.assertEqual(3, max(allij0))
# check indices ij1
allij1 = sum(dfcc['ij1'], tuple())
self.assertEqual(1, min(allij1))
self.assertEqual(4, max(allij1))
# check index values
ij0check = [(i1 - 1, j1 - 1) for i1, j1 in dfcc['ij1']]
self.assertEqual(ij0check, dfcc['ij0'])
# test valid element which is not present in the structure
dnone = self.P.bond_length_types('Ni', 'Au', 0.1, 5.0)
self.assertEqual(0, len(dnone['dij']))
self.assertEqual(0, len(dnone['ddij']))
self.assertEqual(0, len(dnone['ij0']))
self.assertEqual(0, len(dnone['ij1']))
return
def test_num_datasets(self):
"""check PdfFit.num_datasets()
"""
self.assertEqual(0, self.P.num_datasets())
self.P.read_data(datafile('Ni.dat'), 'X', 25.0, 0.5)
self.assertEqual(1, self.P.num_datasets())
# failed data should not increase num_datasets
try:
self.P.read_data(datafile('badNi.dat'))
except:
pass
self.assertEqual(1, self.P.num_datasets())
# alloc should increase number of datasets
# alloc requires a loaded structure
self.P.read_struct(datafile('Ni.stru'))
self.P.alloc('X', 30.0, 0.05, 2, 10, 100)
self.assertEqual(2, self.P.num_datasets())
self.P.reset()
self.assertEqual(0, self.P.num_datasets())
return
def test_num_datasets(self):
"""check PdfFit.num_datasets()
"""
self.assertEqual(0, self.P.num_datasets())
self.P.read_data(datafile('Ni.dat'), 'X', 25.0, 0.5)
self.assertEqual(1, self.P.num_datasets())
# failed data should not increase num_datasets
try:
self.P.read_data(datafile('badNi.dat'))
except:
pass
self.assertEqual(1, self.P.num_datasets())
# alloc should increase number of datasets
# alloc requires a loaded structure
self.P.read_struct(datafile('Ni.stru'))
self.P.alloc('X', 30.0, 0.05, 2, 10, 100)
self.assertEqual(2, self.P.num_datasets())
self.P.reset()
self.assertEqual(0, self.P.num_datasets())
return
def test_getcrw_two_datasets(self):
"""check that getcrw() and getrw() are consistent for two datasets.
"""
self.P.read_data(datafile('Ni.dat'), 'X', 25.0, 0.0)
self.P.pdfrange(1, 2, 8)
self.P.read_data(datafile('300K.gr'), 'N', 32.0, 0.0)
self.P.pdfrange(2, 1, 11)
self.P.read_struct(datafile('Ni.stru'))
# mess lattice parameters to have comparable Rw contributions
self.P.setvar('lat(1)', 3)
self.P.setvar('lat(2)', 3)
self.P.setvar('lat(3)', 3)
self.P.refine()
rwtot = self.P.getrw()
self.failUnless(rwtot > 0.0)
self.P.setdata(1)
rw1 = self.P.getcrw()[-1]
self.P.setdata(2)
rw2 = self.P.getcrw()[-1]
self.assertAlmostEqual(rwtot**2, rw1**2 + rw2**2, self.places)
return
def test_add_structure(self):
"""check PdfFit.add_structure()
"""
# skip test when diffpy.Structure is not installed
try:
from diffpy.Structure import Structure
except ImportError:
return
ni = Structure(filename=datafile('Ni.stru'))
self.P.add_structure(ni)
self.assertEqual(4, self.P.num_atoms())
return
def test_getcrw_two_datasets(self):
"""check that getcrw() and getrw() are consistent for two datasets.
"""
self.P.read_data(datafile('Ni.dat'), 'X', 25.0, 0.0)
self.P.pdfrange(1, 2, 8)
self.P.read_data(datafile('300K.gr'), 'N', 32.0, 0.0)
self.P.pdfrange(2, 1, 11)
self.P.read_struct(datafile('Ni.stru'))
# mess lattice parameters to have comparable Rw contributions
self.P.setvar('lat(1)', 3)
self.P.setvar('lat(2)', 3)
self.P.setvar('lat(3)', 3)
self.P.refine()
rwtot = self.P.getrw()
self.assertTrue(rwtot > 0.0)
self.P.setdata(1)
rw1 = self.P.getcrw()[-1]
self.P.setdata(2)
rw2 = self.P.getcrw()[-1]
self.assertAlmostEqual(rwtot**2, rw1**2 + rw2**2, self.places)
return
def test_psel(self):
"""check PdfFit.psel()
"""
def doalloc():
self.P.alloc('X', 30.0, 0.05, 2, 10, 100)
return
self.assertRaises(pdffit2.unassignedError, self.P.psel, 0)
self.assertRaises(pdffit2.unassignedError, self.P.psel, 1)
self.P.read_struct(datafile('Ni.stru'))
doalloc()
self.P.calc()
G1 = self.P.getpdf_fit()
self.P.reset()
self.P.read_struct(datafile('PbScW25TiO3.stru'))
doalloc()
self.P.calc()
G2 = self.P.getpdf_fit()
self.P.reset()
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
doalloc()
self.P.pdesel('ALL')
self.P.psel(1)
self.P.calc()
self.assertEqual(G1, self.P.getpdf_fit())
self.P.pdesel('ALL')
self.P.psel(2)
self.P.calc()
self.assertEqual(G2, self.P.getpdf_fit())
self.P.psel('ALL')
self.P.calc()
Gall = self.P.getpdf_fit()
dGmax = max(
[abs(g1 + g2 - gall) for g1, g2, gall in zip(G1, G2, Gall)])
self.assertAlmostEqual(0, dGmax, self.places)
self.assertRaises(pdffit2.unassignedError, self.P.psel, 10)
self.assertRaises(pdffit2.unassignedError, self.P.psel, 0)
self.assertRaises(pdffit2.unassignedError, self.P.psel, -100)
return
def test_twophase_refinement(self):
"""check PDF refinement of 2 phases that have different spdiameter.
"""
dcheck1 = 8.0
dstart1 = 8.2
dcheck2 = 6.0
dstart2 = 5.5
self.P.read_struct(datafile('Ni.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.setvar('spdiameter', dcheck1)
self.P.calc()
G1 = numpy.array(self.P.getpdf_fit())
self.P.reset()
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.setvar('spdiameter', dcheck2)
self.P.calc()
G2 = numpy.array(self.P.getpdf_fit())
r = numpy.array(self.P.getR())
Gnoise = G1 + G2
Gnoise[::2] += 0.01
Gnoise[1::2] -= 0.01
self.P.reset()
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.read_data_lists('X', 0.0, 0.05, list(r), list(Gnoise))
self.P.setphase(1)
self.P.constrain('spdiameter', '@11')
self.P.setphase(2)
self.P.constrain('spdiameter', '@12')
self.P.setpar(11, dstart1)
self.P.setpar(12, dstart2)
self.P.refine()
dfinal2 = self.P.getvar('spdiameter')
self.P.setphase(1)
dfinal1 = self.P.getvar('spdiameter')
self.assertAlmostEqual(dcheck1, dfinal1, 3)
self.assertAlmostEqual(dcheck2, dfinal2, 3)
return
def test_psel(self):
"""check PdfFit.psel()
"""
def doalloc():
self.P.alloc('X', 30.0, 0.05, 2, 10, 100)
return
self.assertRaises(pdffit2.unassignedError, self.P.psel, 0)
self.assertRaises(pdffit2.unassignedError, self.P.psel, 1)
self.P.read_struct(datafile('Ni.stru'))
doalloc()
self.P.calc()
G1 = self.P.getpdf_fit()
self.P.reset()
self.P.read_struct(datafile('PbScW25TiO3.stru'))
doalloc()
self.P.calc()
G2 = self.P.getpdf_fit()
self.P.reset()
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
doalloc()
self.P.pdesel('ALL')
self.P.psel(1)
self.P.calc()
self.assertEqual(G1, self.P.getpdf_fit())
self.P.pdesel('ALL')
self.P.psel(2)
self.P.calc()
self.assertEqual(G2, self.P.getpdf_fit())
self.P.psel('ALL')
self.P.calc()
Gall = self.P.getpdf_fit()
dGmax = max([abs(g1 + g2 - gall)
for g1, g2, gall in zip(G1, G2, Gall)])
self.assertAlmostEqual(0, dGmax, self.places)
self.assertRaises(pdffit2.unassignedError, self.P.psel, 10)
self.assertRaises(pdffit2.unassignedError, self.P.psel, 0)
self.assertRaises(pdffit2.unassignedError, self.P.psel, -100)
return
def test_twophase_refinement(self):
"""check PDF refinement of 2 phases that have different spdiameter.
"""
dcheck1 = 8.0
dstart1 = 8.2
dcheck2 = 6.0
dstart2 = 5.5
self.P.read_struct(datafile('Ni.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.setvar('spdiameter', dcheck1)
self.P.calc()
G1 = numpy.array(self.P.getpdf_fit())
self.P.reset()
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.setvar('spdiameter', dcheck2)
self.P.calc()
G2 = numpy.array(self.P.getpdf_fit())
r = numpy.array(self.P.getR())
Gnoise = G1 + G2
Gnoise[::2] += 0.01
Gnoise[1::2] -= 0.01
self.P.reset()
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.read_data_lists('X', 0.0, 0.05, list(r), list(Gnoise))
self.P.setphase(1)
self.P.constrain('spdiameter', '@11')
self.P.setphase(2)
self.P.constrain('spdiameter', '@12')
self.P.setpar(11, dstart1)
self.P.setpar(12, dstart2)
self.P.refine()
dfinal2 = self.P.getvar('spdiameter')
self.P.setphase(1)
dfinal1 = self.P.getvar('spdiameter')
self.assertAlmostEqual(dcheck1, dfinal1, 3)
self.assertAlmostEqual(dcheck2, dfinal2, 3)
return
def test_pdesel(self):
"""check PdfFit.pdesel()
"""
def doalloc():
self.P.alloc('X', 30.0, 0.05, 2, 10, 100)
return
self.assertRaises(pdffit2.unassignedError, self.P.pdesel, 0)
self.assertRaises(pdffit2.unassignedError, self.P.pdesel, 1)
self.P.read_struct(datafile('Ni.stru'))
doalloc()
self.P.calc()
G1 = self.P.getpdf_fit()
self.P.reset()
self.P.read_struct(datafile('PbScW25TiO3.stru'))
doalloc()
self.P.calc()
G2 = self.P.getpdf_fit()
self.P.reset()
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
doalloc()
self.P.psel('ALL')
self.P.pdesel(2)
self.P.calc()
self.assertEqual(G1, self.P.getpdf_fit())
self.P.psel('ALL')
self.P.pdesel(1)
self.P.calc()
self.assertEqual(G2, self.P.getpdf_fit())
self.P.pdesel('ALL')
self.P.calc()
G0 = self.P.getpdf_fit()
self.assertEqual([0.0] * len(G0), G0)
self.assertRaises(pdffit2.unassignedError, self.P.pdesel, 10)
self.assertRaises(pdffit2.unassignedError, self.P.pdesel, 0)
self.assertRaises(pdffit2.unassignedError, self.P.pdesel, -100)
return
def test_reset_scat(self):
"""check PdfFit.reset_scat()
"""
# raises exception when no phase exists
self.assertRaises(pdffit2.unassignedError, self.P.reset_scat, 'Ti')
# check if it is local to phase
fPb = self.P.get_scat('X', 'Pb')
bPb = self.P.get_scat('N', 'Pb')
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.set_scat('X', 'Pb', 142)
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.set_scat('N', 'Pb', -17)
self.P.setphase(1)
self.assertNotEqual(fPb, self.P.get_scat('X', 'Pb'))
self.P.reset_scat('Pb')
self.assertEqual(fPb, self.P.get_scat('X', 'Pb'))
self.P.setphase(2)
self.assertNotEqual(bPb, self.P.get_scat('N', 'Pb'))
self.P.reset_scat('Pb')
self.assertEqual(bPb, self.P.get_scat('N', 'Pb'))
# check exception for invalid inputs
self.assertRaises(ValueError, self.P.reset_scat, 'Zz')
return
def test_reset_scat(self):
"""check PdfFit.reset_scat()
"""
# raises exception when no phase exists
self.assertRaises(pdffit2.unassignedError, self.P.reset_scat, 'Ti')
# check if it is local to phase
fPb = self.P.get_scat('X', 'Pb')
bPb = self.P.get_scat('N', 'Pb')
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.set_scat('X', 'Pb', 142)
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.set_scat('N', 'Pb', -17)
self.P.setphase(1)
self.assertNotEqual(fPb, self.P.get_scat('X', 'Pb'))
self.P.reset_scat('Pb')
self.assertEqual(fPb, self.P.get_scat('X', 'Pb'))
self.P.setphase(2)
self.assertNotEqual(bPb, self.P.get_scat('N', 'Pb'))
self.P.reset_scat('Pb')
self.assertEqual(bPb, self.P.get_scat('N', 'Pb'))
# check exception for invalid inputs
self.assertRaises(ValueError, self.P.reset_scat, 'Zz')
return
def test_refinement(self):
"""check refinement of sphere envelope factor
"""
dcheck = 8.0
dstart = 12.0
self.P.read_struct(datafile('Ni.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.setvar('spdiameter', dcheck)
self.P.calc()
r = numpy.array(self.P.getR())
Gd8 = numpy.array(self.P.getpdf_fit())
Gd8noise = Gd8
Gd8noise[::2] += 0.01
Gd8noise[1::2] -= 0.01
self.P.reset()
self.P.read_struct(datafile('Ni.stru'))
self.P.read_data_lists('X', 0.0, 0.05, list(r), list(Gd8noise))
self.P.constrain('spdiameter', '@8')
self.P.setpar(8, dstart)
self.P.refine()
dfinal = self.P.getvar('spdiameter')
self.assertAlmostEqual(dcheck, dfinal, 3)
return
def test_refinement(self):
"""check refinement of sphere envelope factor
"""
dcheck = 8.0
dstart = 12.0
self.P.read_struct(datafile('Ni.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.setvar('spdiameter', dcheck)
self.P.calc()
r = numpy.array(self.P.getR())
Gd8 = numpy.array(self.P.getpdf_fit())
Gd8noise = Gd8
Gd8noise[::2] += 0.01
Gd8noise[1::2] -= 0.01
self.P.reset()
self.P.read_struct(datafile('Ni.stru'))
self.P.read_data_lists('X', 0.0, 0.05, list(r), list(Gd8noise))
self.P.constrain('spdiameter', '@8')
self.P.setpar(8, dstart)
self.P.refine()
dfinal = self.P.getvar('spdiameter')
self.assertAlmostEqual(dcheck, dfinal, 3)
return
def test_pdesel(self):
"""check PdfFit.pdesel()
"""
def doalloc():
self.P.alloc('X', 30.0, 0.05, 2, 10, 100)
return
self.assertRaises(pdffit2.unassignedError, self.P.pdesel, 0)
self.assertRaises(pdffit2.unassignedError, self.P.pdesel, 1)
self.P.read_struct(datafile('Ni.stru'))
doalloc()
self.P.calc()
G1 = self.P.getpdf_fit()
self.P.reset()
self.P.read_struct(datafile('PbScW25TiO3.stru'))
doalloc()
self.P.calc()
G2 = self.P.getpdf_fit()
self.P.reset()
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
doalloc()
self.P.psel('ALL')
self.P.pdesel(2)
self.P.calc()
self.assertEqual(G1, self.P.getpdf_fit())
self.P.psel('ALL')
self.P.pdesel(1)
self.P.calc()
self.assertEqual(G2, self.P.getpdf_fit())
self.P.pdesel('ALL')
self.P.calc()
G0 = self.P.getpdf_fit()
self.assertEqual([0.0]*len(G0), G0)
self.assertRaises(pdffit2.unassignedError, self.P.pdesel, 10)
self.assertRaises(pdffit2.unassignedError, self.P.pdesel, 0)
self.assertRaises(pdffit2.unassignedError, self.P.pdesel, -100)
return
def test_calculation(self):
"""check calculation of sphere envelope factor
"""
self.P.read_struct(datafile('Ni.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.calc()
d = 8.0
r = numpy.array(self.P.getR())
G0 = numpy.array(self.P.getpdf_fit())
self.P.setvar('spdiameter', d)
self.P.calc()
G1 = numpy.array(self.P.getpdf_fit())
dG = (G0 * spherefactor(r, d) - G1)
msd = numpy.dot(dG, dG) / len(r)
self.assertAlmostEqual(0.0, numpy.sqrt(msd), self.places)
return