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 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_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_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_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_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_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_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_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_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_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_add_structure(self): """check PdfFit.add_structure() """ ni = loadStructure(datafile('Ni.stru')) self.P.add_structure(ni) self.assertEqual(4, self.P.num_atoms()) 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.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_bang(self): "check PdfFit.bang() function" self.P.read_struct(datafile('Ni.stru')) out = capture_output(self.P.bang, 1, 2, 3).strip() self.assertTrue(out.endswith('60 degrees')) self.assertTrue(out.startswith('NI (#1) - NI (#2) - NI (#3)')) return
def test_occ(self): """check PdfFit.occ() """ pf = self.P pf.read_struct(datafile('Ni.stru')) for i in range(1, 5): self.assertEqual(1, pf.getvar(pf.occ(i))) 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_xyz(self): """check PdfFit.x() PdfFit.y(), PdfFit.z() """ pf = self.P pf.read_struct(datafile('Ni.stru')) self.assertEqual(0.5, pf.getvar(pf.x(3))) self.assertEqual(0, pf.getvar(pf.y(3))) self.assertEqual(0.5, pf.getvar(pf.z(3))) return
def test_setvar(self): """check PdfFit.setvar() """ pf = self.P pf.read_struct(datafile('Ni.stru')) pf.setvar(pf.delta1, 1.2) self.assertEqual(1.2, pf.getvar(pf.delta1)) pf.setvar('delta1', 1.7) self.assertEqual(1.7, pf.getvar('delta1')) return
def test_lat(self): """check PdfFit.lat() """ pf = self.P pf.read_struct(datafile('Ni.stru')) for i in ('a', 'b', 'c', 1, 2, 3): self.assertEqual(3.52, pf.getvar(pf.lat(i))) for i in ('alpha', 'beta', 'gamma', 4, 5, 6): self.assertEqual(90, pf.getvar(pf.lat(i))) 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_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_setpar(self): """check PdfFit.setpar() """ pf = self.P pf.read_struct(datafile('Ni.stru')) pf.setpar(1, 'lat(1)') self.assertEqual(3.52, pf.getpar(1)) pf.setpar(1, 4.0) self.assertEqual(4, pf.getpar(1)) pf.setpar(1, pf.lat('a')) self.assertEqual(3.52, pf.getpar(1)) 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