Python Profile.setCalculationRange方法代码示例

# 需要导入模块: from diffpy.srfit.fitbase import Profile [as 别名]
# 或者: from diffpy.srfit.fitbase.Profile import setCalculationRange [as 别名]
def makeProfile(datafile):
    """Make an place data within a Profile."""
    profile = Profile()
    parser = PDFParser()
    parser.parseFile(datafile)
    profile.loadParsedData(parser)
    profile.setCalculationRange(xmax = 20)
    return profile

# 需要导入模块: from diffpy.srfit.fitbase import Profile [as 别名]
# 或者: from diffpy.srfit.fitbase.Profile import setCalculationRange [as 别名]
def makeRecipe(molecule, datname):
    """Create a recipe that uses the DebyePDFGenerator."""

    ## The Profile
    profile = Profile()

    # Load data and add it to the profile
    profile.loadtxt(datname)
    profile.setCalculationRange(xmin=1.2, xmax=8)

    ## The ProfileGenerator
    # Create a DebyePDFGenerator named "G".
    generator = DebyePDFGenerator("G")
    generator.setStructure(molecule)
    # These are metadata needed by the generator
    generator.setQmin(0.68)
    generator.setQmax(22)

    ## The FitContribution
    contribution = FitContribution("bucky")
    contribution.addProfileGenerator(generator)
    contribution.setProfile(profile, xname = "r")

    # Make a FitRecipe.
    recipe = FitRecipe()
    recipe.addContribution(contribution)

    # Specify which parameters we want to refine.
    c60 = generator.phase

    # We're not going to refine the ADPs. However, every atom must have a
    # small, but finite ADP for the PDF calculator to work properly.
    atoms = c60.getScatterers()
    for atom in atoms:
        atom.Uiso.value = 0.001

    # Scale factor. We cannot optimize this efficiently, so we take the value
    # from a previous refinement. In general, care must be taken to properly
    # determine the scale of the profile, or to make sure that the residual is
    # not affected by the scale.
    generator.scale.value = 1.24457360e+4

    # Allow every atom to move.  We define the bounds to be a window of radius
    # 0.1 centered on the current value of the position.
    win = 0.1
    for idx, atom in enumerate(atoms):
        xname, yname, zname = getXYZNames(idx)
        recipe.addVar(atom.x, name = xname).boundWindow(win)
        recipe.addVar(atom.y, name = yname).boundWindow(win)
        recipe.addVar(atom.z, name = zname).boundWindow(win)

    return recipe

# 需要导入模块: from diffpy.srfit.fitbase import Profile [as 别名]
# 或者: from diffpy.srfit.fitbase.Profile import setCalculationRange [as 别名]
def makeRecipe(ciffile, grdata):
    """Make a recipe to model a crystal-like nanoparticle PDF."""

    # Set up a PDF fit as has been done in other examples.
    pdfprofile = Profile()

    pdfparser = PDFParser()
    pdfparser.parseFile(grdata)
    pdfprofile.loadParsedData(pdfparser)
    pdfprofile.setCalculationRange(xmin = 0.1, xmax = 20)

    pdfcontribution = FitContribution("pdf")
    pdfcontribution.setProfile(pdfprofile, xname = "r")

    pdfgenerator = PDFGenerator("G")
    pdfgenerator.setQmax(30.0)
    stru = CreateCrystalFromCIF(file(ciffile))
    pdfgenerator.setStructure(stru)
    pdfcontribution.addProfileGenerator(pdfgenerator)

    # Register the nanoparticle shape factor.
    from diffpy.srfit.pdf.characteristicfunctions import sphericalCF
    pdfcontribution.registerFunction(sphericalCF, name = "f")

    # Now we set up the fitting equation.
    pdfcontribution.setEquation("f * G")

    # Now make the recipe. Make sure we fit the characteristic function shape
    # parameters, in this case 'psize', which is the diameter of the particle.
    recipe = FitRecipe()
    recipe.addContribution(pdfcontribution)

    phase = pdfgenerator.phase
    for par in phase.sgpars:
        recipe.addVar(par)

    recipe.addVar(pdfcontribution.psize, 20)
    recipe.addVar(pdfgenerator.scale, 1)
    recipe.addVar(pdfgenerator.delta2, 0)
    recipe.B11_0 = 0.1

    return recipe

# 需要导入模块: from diffpy.srfit.fitbase import Profile [as 别名]
# 或者: from diffpy.srfit.fitbase.Profile import setCalculationRange [as 别名]
def makeRecipe(niciffile, siciffile, datname):
    """Create a fitting recipe for crystalline PDF data."""

    ## The Profile
    profile = Profile()

    # Load data and add it to the profile
    parser = PDFParser()
    parser.parseFile(datname)
    profile.loadParsedData(parser)
    profile.setCalculationRange(xmax = 20)

    ## The ProfileGenerator
    # In order to fit two phases simultaneously, we must use two PDFGenerators.
    # PDFGenerator is designed to take care of as little information as it
    # must. (Don't do too much, and do it well.) A PDFGenerator can generate
    # the signal from only a single phase at a time. So, we will create one
    # PDFGenerator for each phase and compose them within the same
    # FitContribution. Note that both generators will be associated with the
    # same Profile within the FitContribution, so they will both be
    # automatically configured according to the metadata.
    #
    # The generator for the nickel phase. We call it "G_ni" and will use this
    # name later when we set the fitting equation in the FitContribution.
    generator_ni = PDFGenerator("G_ni")
    stru = CreateCrystalFromCIF(file(niciffile))
    generator_ni.setStructure(stru)
    # The generator for the silicon phase. We call it "G_si".
    generator_si = PDFGenerator("G_si")
    stru = CreateCrystalFromCIF(file(siciffile))
    generator_si.setStructure(stru)

    ## The FitContribution
    # Add both generators to the FitContribution. Add the Profile. This will
    # send the metadata to the generators.
    contribution = FitContribution("nisi")
    contribution.addProfileGenerator(generator_ni)
    contribution.addProfileGenerator(generator_si)
    contribution.setProfile(profile, xname = "r")

    # Write the fitting equation. We want to sum the PDFs from each phase and
    # multiply it by a scaling factor. We also want a certain phase scaling
    # relationship between the PDFs which we will enforce with constraints in
    # the FitRecipe.
    contribution.setEquation("scale * (G_ni +  G_si)")

    # Make the FitRecipe and add the FitContribution.
    recipe = FitRecipe()
    recipe.addContribution(contribution)

    ## Configure the fit variables
    # Start by configuring the scale factor and resolution factors.
    # We want the sum of the phase scale factors to be 1.
    recipe.newVar("scale_ni", 0.1)
    recipe.constrain(generator_ni.scale, "scale_ni")
    recipe.constrain(generator_si.scale, "1 - scale_ni")
    # We also want the resolution factor to be the same on each.
    recipe.newVar("qdamp", 0.03)
    recipe.constrain(generator_ni.qdamp, "qdamp")
    recipe.constrain(generator_si.qdamp, "qdamp")

    # Vary the gloabal scale as well.
    recipe.addVar(contribution.scale, 1)

    # Now we can configure the structural parameters. Since we're using
    # ObjCrystCrystalParSets, the space group constraints are automatically
    # applied to each phase. We must selectively vary the free parameters.
    #
    # First the nickel parameters
    phase_ni = generator_ni.phase
    for par in phase_ni.sgpars:
        recipe.addVar(par, name = par.name + "_ni")
    recipe.addVar(generator_ni.delta2, name = "delta2_ni")
    # Next the silicon parameters
    phase_si = generator_si.phase
    for par in phase_si.sgpars:
        recipe.addVar(par, name = par.name + "_si")
    recipe.addVar(generator_si.delta2, name = "delta2_si")

    # We have prior information from the earlier examples so we'll use it here
    # in the form of restraints.
    #
    # The nickel lattice parameter was measured to be 3.527. The uncertainty
    # values are invalid for that measurement, since the data from which it is
    # derived has no uncertainty. Thus, we will tell the recipe to scale the
    # residual, which means that it will be weighted as much as the average
    # data point during the fit.
    recipe.restrain("a_ni", lb = 3.527, ub = 3.527, scaled = True)
    # Now we do the same with the delta2 and Biso parameters (remember that
    # Biso = 8*pi**2*Uiso)
    recipe.restrain("delta2_ni", lb = 2.22, ub = 2.22, scaled = True)
    recipe.restrain("Biso_0_ni", lb = 0.454, ub = 0.454, scaled = True)
    #
    # We can do the same with the silicon values. We haven't done a thorough
    # job of measuring the uncertainties in the results, so we'll scale these
    # as well.
    recipe.restrain("a_si", lb = 5.430, ub = 5.430, scaled = True)
    recipe.restrain("delta2_si", lb = 3.54, ub = 3.54, scaled = True)
    recipe.restrain("Biso_0_si", lb = 0.645, ub = 0.645, scaled = True)

#.........这里部分代码省略.........

# 需要导入模块: from diffpy.srfit.fitbase import Profile [as 别名]
# 或者: from diffpy.srfit.fitbase.Profile import setCalculationRange [as 别名]
def makeRecipe(ciffile, datname):
    """Create a fitting recipe for crystalline PDF data."""

    ## The Profile
    # This will be used to store the observed and calculated PDF profile.
    profile = Profile()

    # Load data and add it to the Profile. As before we use a PDFParser. The
    # metadata is still passed to the PDFGenerator later on. The interaction
    # between the PDFGenerator and the metadata does not depend on type of
    # structure being refined.
    parser = PDFParser()
    parser.parseFile(datname)
    profile.loadParsedData(parser)
    profile.setCalculationRange(xmax = 20)

    ## The ProfileGenerator
    # This time we use the CreateCrystalFromCIF method of pyobjcryst.crystal to
    # create a Crystal object. That object is passed to the PDFGenerator as in
    # the previous example.
    generator = PDFGenerator("G")
    stru = CreateCrystalFromCIF(file(ciffile))
    generator.setStructure(stru)
    generator.setQmax(40.0)
    
    ## The FitContribution
    contribution = FitContribution("nickel")
    contribution.addProfileGenerator(generator)
    contribution.setProfile(profile, xname = "r")

    # Make the FitRecipe and add the FitContribution.
    recipe = FitRecipe()
    recipe.addContribution(contribution)

    ## Configure the fit variables

    # As before, we get a handle to the structure parameter set. In this case,
    # it is a ObjCrystCrystalParSet instance that was created when we called
    # 'setStructure' above. The ObjCrystCrystalParSet has different Parameters
    # and options than the DiffpyStructureParSet used in the last example. See
    # its documentation in diffpy.srfit.structure.objcrystparset.
    phase = generator.phase

    # Here is where we created space group constraints in the previous example.
    # The difference in this example is that the ObjCrystCrystalParSet is aware
    # of space groups, and the DiffpyStructureParSet is not. Constraints are
    # created internally when "sgpars" attribute is called for. These
    # constriants get enforced within the ObjCrystCrystalParSet. Free
    # Parameters are stored within the 'sgpars' member of the
    # ObjCrystCrystalParSet, which is the same as the object returned from
    # 'constrainAsSpaceGroup'.
    #
    # As before, we have one free lattice parameter ('a'). We can simplify
    # things by iterating through all the sgpars.
    for par in phase.sgpars: 
        recipe.addVar(par)
    # set the initial thermal factor to a non-zero value
    assert hasattr(recipe, 'B11_0')
    recipe.B11_0 = 0.1

    # We now select non-structural parameters to refine.
    # This controls the scaling of the PDF.
    recipe.addVar(generator.scale, 1)
    # This is a peak-damping resolution term.
    recipe.addVar(generator.qdamp, 0.01)
    # This is a vibrational correlation term that sharpens peaks at low-r.
    recipe.addVar(generator.delta2, 5)

    # Give the recipe away so it can be used!
    return recipe

# 需要导入模块: from diffpy.srfit.fitbase import Profile [as 别名]
# 或者: from diffpy.srfit.fitbase.Profile import setCalculationRange [as 别名]
def makeRecipe(stru1, stru2, datname):
    """Create a fitting recipe for crystalline PDF data."""

    ## The Profile
    profile = Profile()

    # Load data and add it to the profile
    parser = PDFParser()
    parser.parseFile(datname)
    profile.loadParsedData(parser)
    profile.setCalculationRange(xmin=1.5, xmax = 45, dx = 0.1)

    ## The ProfileGenerator
    # In order to fit the core and shell phases simultaneously, we must use two
    # PDFGenerators.
    #
    # The generator for the CdS core. We call it "G_CdS" and will use this name
    # later when we set the fitting equation in the FitContribution.
    generator_cds = PDFGenerator("G_CdS")
    generator_cds.setStructure(stru1)
    generator_cds.setQmax(26)
    generator_cds.qdamp.value = 0.0396
    # The generator for the ZnS shell. We call it "G_ZnS".
    generator_zns = PDFGenerator("G_ZnS")
    generator_zns.setStructure(stru2)
    generator_zns.setQmax(26)
    generator_zns.qdamp.value = 0.0396

    ## The FitContribution
    # Add both generators and the profile to the FitContribution.
    contribution = FitContribution("cdszns")
    contribution.addProfileGenerator(generator_cds)
    contribution.addProfileGenerator(generator_zns)
    contribution.setProfile(profile, xname = "r")

    # Set up the characteristic functions. We use a spherical CF for the core
    # and a spherical shell CF for the shell. Since this is set up as two
    # phases, we implicitly assume that the core-shell correlations contribute
    # very little to the PDF.
    from diffpy.srfit.pdf.characteristicfunctions import sphericalCF, shellCF
    contribution.registerFunction(sphericalCF, name = "f_CdS")
    contribution.registerFunction(shellCF, name = "f_ZnS")

    # Write the fitting equation. We want to sum the PDFs from each phase and
    # multiply it by a scaling factor.
    contribution.setEquation("scale * (f_CdS * G_CdS +  f_ZnS * G_ZnS)")

    # Make the FitRecipe and add the FitContribution.
    recipe = FitRecipe()
    recipe.addContribution(contribution)

    # Vary the inner radius and thickness of the shell. Constrain the core
    # diameter to twice the shell radius.
    recipe.addVar(contribution.radius, 15)
    recipe.addVar(contribution.thickness, 11)
    recipe.constrain(contribution.psize, "2 * radius")

    ## Configure the fit variables
    # Start by configuring the scale factor and resolution factors.
    # We want the sum of the phase scale factors to be 1.
    recipe.newVar("scale_CdS", 0.7)
    recipe.constrain(generator_cds.scale, "scale_CdS")
    recipe.constrain(generator_zns.scale, "1 - scale_CdS")
    # We also want the resolution factor to be the same on each.

    # Vary the gloabal scale as well.
    recipe.addVar(contribution.scale, 0.3)

    # Now we can configure the structural parameters. We tag the different
    # structural variables so we can easily turn them on and off in the
    # subsequent refinement.
    phase_cds = generator_cds.phase
    for par in phase_cds.sgpars.latpars:
        recipe.addVar(par, name = par.name + "_cds", tag = "lat")
    for par in phase_cds.sgpars.adppars:
        recipe.addVar(par, 1, name = par.name + "_cds", tag = "adp")
    recipe.addVar(phase_cds.sgpars.xyzpars.z_1, name = "z_1_cds", tag = "xyz")
    # Since we know these have stacking disorder, constrain the B33 adps for
    # each atom type.
    recipe.constrain("B33_1_cds", "B33_0_cds")
    recipe.addVar(generator_cds.delta2, name = "delta2_cds", value = 5)

    phase_zns = generator_zns.phase
    for par in phase_zns.sgpars.latpars:
        recipe.addVar(par, name = par.name + "_zns", tag = "lat")
    for par in phase_zns.sgpars.adppars:
        recipe.addVar(par, 1, name = par.name + "_zns", tag = "adp")
    recipe.addVar(phase_zns.sgpars.xyzpars.z_1, name = "z_1_zns", tag = "xyz")
    recipe.constrain("B33_1_zns", "B33_0_zns")
    recipe.addVar(generator_zns.delta2, name = "delta2_zns", value = 2.5)

    # Give the recipe away so it can be used!
    return recipe

# 需要导入模块: from diffpy.srfit.fitbase import Profile [as 别名]
# 或者: from diffpy.srfit.fitbase.Profile import setCalculationRange [as 别名]
def makeRecipe(molecule, datname):
    """Create a recipe that uses the DebyePDFGenerator."""

    ## The Profile
    profile = Profile()

    # Load data and add it to the profile
    profile.loadtxt(datname)
    profile.setCalculationRange(xmin=1.2, xmax=8)

    ## The ProfileGenerator
    # Create a DebyePDFGenerator named "G".
    generator = DebyePDFGenerator("G")
    generator.setStructure(molecule)
    # These are metadata needed by the generator
    generator.setQmin(0.68)
    generator.setQmax(22)

    ## The FitContribution
    contribution = FitContribution("bucky")
    contribution.addProfileGenerator(generator)
    contribution.setProfile(profile, xname = "r")

    # Make a FitRecipe.
    recipe = FitRecipe()
    recipe.addContribution(contribution)

    # Specify which parameters we want to refine. We'll be using the
    # MoleculeParSet within the generator, so let's get a handle to it. See the
    # diffpy.srfit.structure.objcryststructure module for more information
    # about the MoleculeParSet hierarchy.
    c60 = generator.phase

    # First, the isotropic thermal displacement factor.
    Biso = recipe.newVar("Biso")
    for atom in c60.getScatterers():

        # We have defined a 'center' atom that is a dummy, which means that it
        # has no scattering power. It is only used as a reference point for
        # our bond length. We don't want to constrain it.
        if not atom.isDummy():
            recipe.constrain(atom.Biso, Biso)

    # We need to let the molecule expand. If we were modeling it as a crystal,
    # we could let the unit cell expand. For instruction purposes, we use a
    # Molecule to model C60, and molecules have different modeling options than
    # crystals. To make the molecule expand from a central point, we will
    # constrain the distance from each atom to a dummy center atom that was
    # created with the molecule, and allow that distance to vary. (We could
    # also let the nearest-neighbor bond lengths vary, but that would be much
    # more difficult to set up.)
    center = c60.center
    # Create a new Parameter that represents the radius of the molecule. Note
    # that we don't give it an initial value. Since the variable is being
    # directly constrained to further below, its initial value will be inferred
    # from the constraint.
    radius = recipe.newVar("radius")
    for i, atom in enumerate(c60.getScatterers()):

        if atom.isDummy():
            continue

        # This creates a Parameter that moves the second atom according to the
        # bond length. Note that each Parameter needs a unique name.
        par = c60.addBondLengthParameter("rad%i"%i, center, atom)
        recipe.constrain(par, radius)

    # Add the correlation term, scale. The scale is too short to effectively
    # determine qdamp.
    recipe.addVar(generator.delta2, 2)
    recipe.addVar(generator.scale, 1.3e4)

    # Give the recipe away so it can be used!
    return recipe

# 需要导入模块: from diffpy.srfit.fitbase import Profile [as 别名]
# 或者: from diffpy.srfit.fitbase.Profile import setCalculationRange [as 别名]
def makeRecipe(ciffile, datname):
    """Create a fitting recipe for crystalline PDF data."""

    ## The Profile
    # This will be used to store the observed and calculated PDF profile.
    profile = Profile()

    # Load data and add it to the Profile. Unlike in other examples, we use a
    # class (PDFParser) to help us load the data. This class will read the data
    # and relevant metadata from a two- to four-column data file generated
    # with PDFGetX2 or PDFGetN. The metadata will be passed to the PDFGenerator
    # when they are associated in the FitContribution, which saves some
    # configuration steps.
    parser = PDFParser()
    parser.parseFile(datname)
    profile.loadParsedData(parser)
    profile.setCalculationRange(xmax = 20)

    ## The ProfileGenerator
    # The PDFGenerator is for configuring and calculating a PDF profile. Here,
    # we want to refine a Structure object from diffpy.structure. We tell the
    # PDFGenerator that with the 'setStructure' method. All other configuration
    # options will be inferred from the metadata that is read by the PDFParser.
    # In particular, this will set the scattering type (x-ray or neutron), the
    # Qmax value, as well as initial values for the non-structural Parameters.
    generator = PDFGenerator("G")
    stru = Structure()
    stru.read(ciffile)
    generator.setStructure(stru)

    ## The FitContribution
    # Here we associate the Profile and ProfileGenerator, as has been done
    # before.
    contribution = FitContribution("nickel")
    contribution.addProfileGenerator(generator)
    contribution.setProfile(profile, xname = "r")

    ## Make the FitRecipe and add the FitContribution.
    recipe = FitRecipe()
    recipe.addContribution(contribution)

    ## Configure the fit variables

    # The PDFGenerator class holds the ParameterSet associated with the
    # Structure passed above in a data member named "phase". (We could have
    # given the ParameterSet a name other than "phase" when we added it to the
    # PDFGenerator.) The ParameterSet in this case is a StructureParameterSet,
    # the documentation for which is found in the
    # diffpy.srfit.structure.diffpystructure module.
    phase = generator.phase

    # We start by constraining the phase to the known space group. We could do
    # this by hand, but there is a method in diffpy.srfit.structure named
    # 'constrainAsSpaceGroup' for this purpose. The constraints will by default
    # be applied to the sites, the lattice and to the ADPs. See the method
    # documentation for more details. The 'constrainAsSpaceGroup' method may
    # create new Parameters, which it returns in a SpaceGroupParameters object.
    from diffpy.srfit.structure import constrainAsSpaceGroup
    sgpars = constrainAsSpaceGroup(phase, "Fm-3m")

    # The SpaceGroupParameters object returned by 'constrainAsSpaceGroup' holds
    # the free Parameters allowed by the space group constraints. Once a
    # structure is constrained, we need (should) only use the Parameters
    # provided in the SpaceGroupParameters, as the relevant structure
    # Parameters are constrained to these.
    #
    # We know that the space group does not allow for any free sites because
    # each atom is on a special position. There is one free (cubic) lattice
    # parameter and one free (isotropic) ADP. We can access these Parameters in
    # the xyzpars, latpars, and adppars members of the SpaceGroupParameters
    # object.
    for par in sgpars.latpars:
        recipe.addVar(par)
    for par in sgpars.adppars:
        recipe.addVar(par, 0.005)

    # We now select non-structural parameters to refine.
    # This controls the scaling of the PDF.
    recipe.addVar(generator.scale, 1)
    # This is a peak-damping resolution term.
    recipe.addVar(generator.qdamp, 0.01)
    # This is a vibrational correlation term that sharpens peaks at low-r.
    recipe.addVar(generator.delta2, 5)

    # Give the recipe away so it can be used!
    return recipe

# 需要导入模块: from diffpy.srfit.fitbase import Profile [as 别名]
# 或者: from diffpy.srfit.fitbase.Profile import setCalculationRange [as 别名]
def makeRecipe(ciffile, grdata, iqdata):
    """Make complex-modeling recipe where I(q) and G(r) are fit
    simultaneously.

    The fit I(q) is fed into the calculation of G(r), which provides feedback
    for the fit parameters of both.
    
    """

    # Create a PDF contribution as before
    pdfprofile = Profile()
    pdfparser = PDFParser()
    pdfparser.parseFile(grdata)
    pdfprofile.loadParsedData(pdfparser)
    pdfprofile.setCalculationRange(xmin = 0.1, xmax = 20)

    pdfcontribution = FitContribution("pdf")
    pdfcontribution.setProfile(pdfprofile, xname = "r")

    pdfgenerator = PDFGenerator("G")
    pdfgenerator.setQmax(30.0)
    stru = CreateCrystalFromCIF(file(ciffile))
    pdfgenerator.setStructure(stru)
    pdfcontribution.addProfileGenerator(pdfgenerator)
    pdfcontribution.setResidualEquation("resv")

    # Create a SAS contribution as well. We assume the nanoparticle is roughly
    # elliptical.
    sasprofile = Profile()
    sasparser = SASParser()
    sasparser.parseFile(iqdata)
    sasprofile.loadParsedData(sasparser)

    sascontribution = FitContribution("sas")
    sascontribution.setProfile(sasprofile)

    from sans.models.EllipsoidModel import EllipsoidModel
    model = EllipsoidModel()
    sasgenerator = SASGenerator("generator", model)
    sascontribution.addProfileGenerator(sasgenerator)
    sascontribution.setResidualEquation("resv")

    # Now we set up a characteristic function calculator that depends on the
    # sas model.
    cfcalculator = SASCF("f", model)

    # Register the calculator with the pdf contribution and define the fitting
    # equation.
    pdfcontribution.registerCalculator(cfcalculator)
    # The PDF for a nanoscale crystalline is approximated by
    # Gnano = f * Gcryst
    pdfcontribution.setEquation("f * G")

    # Moving on
    recipe = FitRecipe()
    recipe.addContribution(pdfcontribution)
    recipe.addContribution(sascontribution)

    # PDF
    phase = pdfgenerator.phase
    for par in phase.sgpars:
        recipe.addVar(par)

    recipe.addVar(pdfgenerator.scale, 1)
    recipe.addVar(pdfgenerator.delta2, 0)

    # SAS
    recipe.addVar(sasgenerator.scale, 1, name = "iqscale")
    recipe.addVar(sasgenerator.radius_a, 10)
    recipe.addVar(sasgenerator.radius_b, 10)

    # Even though the cfcalculator and sasgenerator depend on the same sas
    # model, we must still constrain the cfcalculator Parameters so that it is
    # informed of changes in the refined parameters.
    recipe.constrain(cfcalculator.radius_a, "radius_a")
    recipe.constrain(cfcalculator.radius_b, "radius_b")

    return recipe

# 需要导入模块: from diffpy.srfit.fitbase import Profile [as 别名]
# 或者: from diffpy.srfit.fitbase.Profile import setCalculationRange [as 别名]
pcif = getParser('cif')
mno = pcif.parseFile(structureFile)

# prepare profile object with experimental data
profile = Profile()
parser = PDFParser()
parser.parseFile(dataFile)
profile.loadParsedData(parser)

# define range for pdf calculation
rmin = 0.01
rmax = 20
rstep = 0.01

# setup calculation range for the PDF simulation
profile.setCalculationRange(xmin=rmin, xmax=rmax, dx=rstep)

# prepare nucpdf function that simulates the nuclear PDF
nucpdf = PDFGenerator("nucpdf")
nucpdf.setStructure(mno)
nucpdf.setProfile(profile)

# prepare magpdf function that simulates the magnetic PDF

# Create the Mn2+ magnetic species
mn2p = magSpecies(struc=mno, label='Mn2+', magIdxs=[0,1,2],
                  basisvecs=2.5*np.array([1,0,0]), kvecs=np.array([0,0,1.5]),
                  ffparamkey='Mn2')

# Create and prep the magnetic structure
mstr = magStructure()

# 需要导入模块: from diffpy.srfit.fitbase import Profile [as 别名]
# 或者: from diffpy.srfit.fitbase.Profile import setCalculationRange [as 别名]
def makeRecipe(ciffile, xdatname, ndatname):
    """Create a fitting recipe for crystalline PDF data."""

    ## The Profiles
    # We need a profile for each data set. This means that we will need two
    # FitContributions as well.
    xprofile = Profile()
    nprofile = Profile()

    # Load data and add it to the proper Profile.
    parser = PDFParser()
    parser.parseFile(xdatname)
    xprofile.loadParsedData(parser)
    xprofile.setCalculationRange(xmax = 20)

    parser = PDFParser()
    parser.parseFile(ndatname)
    nprofile.loadParsedData(parser)
    nprofile.setCalculationRange(xmax = 20)

    ## The ProfileGenerators
    # We need one of these for the x-ray data.
    xgenerator = PDFGenerator("G")
    stru = CreateCrystalFromCIF(file(ciffile))
    xgenerator.setStructure(stru)

    # And we need one for the neutron data. We want to refine the same
    # structure object in each PDFGenerator. This would suggest that we add the
    # same Crystal to each. However, if we do that then we will have two
    # Parameters for each Crystal data member (two Parameters for the "a"
    # lattice parameter, etc.), held in different ObjCrystCrystalParSets, each
    # managed by its own PDFGenerator. Thus, changes made to the Crystal
    # through one PDFGenerator will not be known to the other PDFGenerator
    # since their ObjCrystCrystalParSets don't know about each other. The
    # solution is to share ObjCrystCrystalParSets rather than Crystals. This
    # way there is only one Parameter for each Crystal data member. (An
    # alternative to this is to constrain each structure Parameter to be varied
    # to the same variable. The present approach is easier and less error
    # prone.)
    #
    # Tell the neutron PDFGenerator to use the phase from the x-ray
    # PDFGenerator.
    ngenerator = PDFGenerator("G")
    ngenerator.setPhase(xgenerator.phase)

    ## The FitContributions
    # We associate the x-ray PDFGenerator and Profile in one FitContribution...
    xcontribution = FitContribution("xnickel")
    xcontribution.addProfileGenerator(xgenerator)
    xcontribution.setProfile(xprofile, xname = "r")
    # and the neutron objects in another.
    ncontribution = FitContribution("nnickel")
    ncontribution.addProfileGenerator(ngenerator)
    ncontribution.setProfile(nprofile, xname = "r")

    # This example is different than the previous ones in that we are composing
    # a residual function from other residuals (one for the x-ray contribution
    # and one for the neutron contribution). The relative magnitude of these
    # residuals effectively determines the influence of each contribution over
    # the fit. This is a problem in this case because the x-ray data has
    # uncertainty values associated with it (on the order of 1e-4), and the
    # chi^2 residual is proportional to 1 / uncertainty**2. The neutron has no
    # uncertainty, so it's chi^2 is proportional to 1. Thus, my optimizing
    # chi^2 we would give the neutron data practically no weight in the fit. To
    # get around this, we will optimize a different metric.
    #
    # The contribution's residual can be either chi^2, Rw^2, or custom crafted.
    # In this case, we should minimize Rw^2 of each contribution so that each
    # one can contribute roughly equally to the fit.
    xcontribution.setResidualEquation("resv")
    ncontribution.setResidualEquation("resv")

    # Make the FitRecipe and add the FitContributions.
    recipe = FitRecipe()
    recipe.addContribution(xcontribution)
    recipe.addContribution(ncontribution)

    # Now we vary and constrain Parameters as before.
    recipe.addVar(xgenerator.scale, 1, "xscale")
    recipe.addVar(ngenerator.scale, 1, "nscale")
    recipe.addVar(xgenerator.qdamp, 0.01, "xqdamp")
    recipe.addVar(ngenerator.qdamp, 0.01, "nqdamp")
    # delta2 is a non-structual material propery. Thus, we constrain together
    # delta2 Parameter from each PDFGenerator.
    delta2 = recipe.newVar("delta2", 2)
    recipe.constrain(xgenerator.delta2, delta2)
    recipe.constrain(ngenerator.delta2, delta2)

    # We only need to constrain phase properties once since there is a single
    # ObjCrystCrystalParSet for the Crystal.
    phase = xgenerator.phase
    for par in phase.sgpars:
        recipe.addVar(par)
    recipe.B11_0 = 0.1

    # Give the recipe away so it can be used!
    return recipe