def testGenerator(self):
qmax = 27.0
gen = self.gen
gen.setScatteringType('N')
self.assertEqual('N', gen.getScatteringType())
gen.setQmax(qmax)
self.assertAlmostEqual(qmax, gen.getQmax())
from diffpy.Structure import PDFFitStructure
stru = PDFFitStructure()
ciffile = datafile("ni.cif")
stru.read(ciffile)
for i in range(4):
stru[i].Bisoequiv = 1
gen.setStructure(stru)
calc = gen._calc
# Test parameters
for par in gen.iterPars(recurse=False):
pname = par.name
defval = calc._getDoubleAttr(pname)
self.assertEquals(defval, par.getValue())
# Test setting values
par.setValue(1.0)
self.assertEquals(1.0, par.getValue())
par.setValue(defval)
self.assertEquals(defval, par.getValue())
r = numpy.arange(0, 10, 0.1)
y = gen(r)
# Now create a reference PDF. Since the calculator is testing its
# output, we just have to make sure we can calculate from the
# PDFGenerator interface.
from diffpy.srreal.pdfcalculator import PDFCalculator
calc = PDFCalculator()
calc.rstep = r[1] - r[0]
calc.rmin = r[0]
calc.rmax = r[-1] + 0.5 * calc.rstep
calc.qmax = qmax
calc.setScatteringFactorTableByType('N')
calc.eval(stru)
yref = calc.pdf
diff = y - yref
res = numpy.dot(diff, diff)
self.assertAlmostEquals(0, res)
return
def testGenerator(self):
qmax = 27.0
gen = PDFGenerator()
gen.setScatteringType('N')
self.assertEqual('N', gen.getScatteringType())
gen.setQmax(qmax)
self.assertAlmostEqual(qmax, gen.getQmax())
from diffpy.Structure import PDFFitStructure
stru = PDFFitStructure()
ciffile = datafile("ni.cif")
stru.read(ciffile)
for i in range(4):
stru[i].Bisoequiv = 1
gen.setStructure(stru)
calc = gen._calc
# Test parameters
for par in gen.iterPars(recurse = False):
pname = par.name
defval = calc._getDoubleAttr(pname)
self.assertEquals(defval, par.getValue())
# Test setting values
par.setValue(1.0)
self.assertEquals(1.0, par.getValue())
par.setValue(defval)
self.assertEquals(defval, par.getValue())
r = numpy.arange(0, 10, 0.1)
y = gen(r)
# Now create a reference PDF. Since the calculator is testing its
# output, we just have to make sure we can calculate from the
# PDFGenerator interface.
from diffpy.srreal.pdfcalculator import PDFCalculator
calc = PDFCalculator()
calc.rstep = r[1] - r[0]
calc.rmin = r[0]
calc.rmax = r[-1] + 0.5 * calc.rstep
calc.qmax = qmax
calc.setScatteringFactorTableByType('N')
calc.eval(stru)
yref = calc.pdf
diff = y - yref
res = numpy.dot(diff, diff)
self.assertAlmostEquals(0, res)
return
def read(self, filename, format='auto'):
"""Load structure from a file, raise ControlFileError for invalid
or unknown structure format.
filename -- file to be loaded
format -- structure format such as 'pdffit', 'pdb', 'xyz'. When
'auto' all available formats are tried in a row.
Return instance of StructureParser used to load the data.
See Structure.read() for more info.
"""
from diffpy.Structure import StructureFormatError
try:
p = PDFFitStructure.read(self, filename, format)
except StructureFormatError, err:
import os.path
emsg = "Unable to read file '%s'\n%s." % (
os.path.basename(filename), err)
raise ControlFileError(emsg)
def read(self, filename, format='auto'):
"""Load structure from a file, raise ControlFileError for invalid
or unknown structure format.
filename -- file to be loaded
format -- structure format such as 'pdffit', 'pdb', 'xyz'. When
'auto' all available formats are tried in a row.
Return instance of StructureParser used to load the data.
See Structure.read() for more info.
"""
from diffpy.Structure import StructureFormatError
try:
p = PDFFitStructure.read(self, filename, format)
except StructureFormatError, err:
import os.path
emsg = "Unable to read file '%s'\n%s." % (
os.path.basename(filename), err)
raise ControlFileError(emsg)
