def make_generator(
config: GenConfig) -> Union[PDFGenerator, DebyePDFGenerator]:
"""
Build a generator according to the information in the GenConfig.
Parameters
----------
config : GenConfig
A configuration instance for generator building.
Returns
-------
generator: PDFGenerator or DebyePDFGenerator
A generator built from GenConfig.
"""
name = config.name
stru: Structure = loadStructure(config.stru_file)
ncpu = config.ncpu
if config.debye:
generator = DebyePDFGenerator(name)
else:
generator = PDFGenerator(name)
generator.setStructure(stru, periodic=config.periodic)
if ncpu:
pool = multiprocessing.Pool(ncpu)
generator.parallel(ncpu, mapfunc=pool.imap_unordered)
else:
pass
return generator
def make_generator(genconfig: GenConfig) -> Union[PDFGenerator, DebyePDFGenerator]:
"""
Build a generator according to the information in the GenConfig.
Parameters
----------
genconfig : GenConfig
A configuration instance for generator building.
Returns
-------
generator: PDFGenerator or DebyePDFGenerator
A generator built from GenConfig.
"""
generator = DebyePDFGenerator(genconfig.name) if genconfig.debye else PDFGenerator(genconfig.name)
generator.setStructure(genconfig.structure, periodic=genconfig.structure)
ncpu = genconfig.ncpu
if ncpu:
pool = multiprocessing.Pool(ncpu)
generator.parallel(ncpu, mapfunc=pool.imap_unordered)
return generator
def makeRecipe(stru1, stru2, stru3, 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, xmax = 40, dx = 0.01)
## The ProfileGenerator
generator_MEF_Cryst_B = PDFGenerator("G_MEF_Cryst_B")
generator_MEF_Cryst_B.setStructure(stru1, periodic = True)
generator_MEF_Mole_B = DebyePDFGenerator("G_MEF_Mole_B")
generator_MEF_Mole_B.setStructure(stru2, periodic = False)
generator_MEF_Intra = DebyePDFGenerator("G_MEF_Intra")
generator_MEF_Intra.setStructure(stru3, periodic = False)
## The FitContribution
# Add both generators to the FitContribution. Add the Profile. This will
# send the metadata to the generators.
contribution = FitContribution("MEF")
contribution.addProfileGenerator(generator_MEF_Cryst_B)
contribution.addProfileGenerator(generator_MEF_Mole_B)
contribution.addProfileGenerator(generator_MEF_Intra)
contribution.setProfile(profile, xname = "r")
#write down the fit equation:
#(G_MEF_Cryst_B - G_MEF_Mole_B) gives the intermolecular PDF, using a larger atomic displacement parameter
#G_MEF_Intra gives intramolecular PDF, using a smaller atomic displacement parameter.
#The sum of both parts gives the total PDF.
contribution.setEquation("scale * (G_MEF_Cryst_B - G_MEF_Mole_B + G_MEF_Intra)")
# Make the FitRecipe and add the FitContribution.
recipe = FitRecipe()
recipe.addContribution(contribution)
qdamp = 0.02902
generator_MEF_Cryst_B.qdamp.value = qdamp
generator_MEF_Mole_B.qdamp.value = qdamp
generator_MEF_Intra.qdamp.value = qdamp
# Vary the gloabal scale as well.
recipe.addVar(contribution.scale, 1)
#############################################################################################
############### First the MEF_Cryst_B parameters ############################################
#############################################################################################
phase_MEF_Cryst_B = generator_MEF_Cryst_B.phase
lat = phase_MEF_Cryst_B.getLattice()
atoms = phase_MEF_Cryst_B.getScatterers()
recipe.newVar("Uiso_Inter", 0.05, tag = "T1")
recipe.newVar("lat_a", 14.556, tag = "lat")
recipe.newVar("lat_b", 6.811, tag = "lat")
recipe.newVar("lat_c", 7.657, tag = "lat")
recipe.newVar("alpha", 119.57, tag = "lat")
recipe.newVar("beta", 103.93, tag = "lat")
recipe.newVar("gamma", 91.30, tag = "lat")
recipe.constrain(lat.a, "lat_a")
recipe.constrain(lat.b, "lat_b")
recipe.constrain(lat.c, "lat_c")
recipe.constrain(lat.alpha, "alpha")
recipe.constrain(lat.beta, "beta")
recipe.constrain(lat.gamma, "gamma")
for atom in atoms:
if atom.element.title() == "N":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "O":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "C":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "H":
recipe.constrain(atom.Uiso, "Uiso_Inter")
generator_MEF_Cryst_B.delta2.value = 0
#############################################################################################
############### Second the MEF_Mole_B parameters ############################################
#############################################################################################
phase_MEF_Mole_B = generator_MEF_Mole_B.phase
generator_MEF_Mole_B.setQmin(0.0)
generator_MEF_Mole_B.setQmax(24.0)
recipe.newVar("zoom_Mole_B", 1, tag = "lat2")
lat = phase_MEF_Mole_B.getLattice()
recipe.constrain(lat.a, "zoom_Mole_B")
recipe.constrain(lat.b, "zoom_Mole_B")
recipe.constrain(lat.c, "zoom_Mole_B")
# Constrain fractional xyz parameters
atoms = phase_MEF_Mole_B.getScatterers()
# Constrain ADPs
for atom in atoms:
if atom.element.title() == "C":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "O":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "N":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "H":
recipe.constrain(atom.Uiso, "Uiso_Inter")
generator_MEF_Mole_B.delta2.value = 0
#############################################################################################
############### Third the intra molecule parameters##########################################
#############################################################################################
phase_MEF_Intra = generator_MEF_Intra.phase
generator_MEF_Intra.setQmin(0.0)
generator_MEF_Intra.setQmax(24.0)
recipe.newVar("zoom_Intra", 1, tag = "lat3")
lat = phase_MEF_Intra.getLattice()
recipe.constrain(lat.a, "zoom_Intra")
recipe.constrain(lat.b, "zoom_Intra")
recipe.constrain(lat.c, "zoom_Intra")
# Constrain fractional xyz parameters
atoms = phase_MEF_Intra.getScatterers()
# Constrain ADPs
recipe.newVar("Uiso_Intra", 0.005, tag = "T2")
for atom in atoms:
if atom.element.title() == "C":
recipe.constrain(atom.Uiso, "Uiso_Intra")
elif atom.element.title() == "O":
recipe.constrain(atom.Uiso, "Uiso_Intra")
elif atom.element.title() == "N":
recipe.constrain(atom.Uiso, "Uiso_Intra")
elif atom.element.title() == "H":
recipe.constrain(atom.Uiso, "Uiso_Intra")
generator_MEF_Intra.delta2.value = 0
# Give the recipe away so it can be used!
return recipe
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
def makeRecipe(stru1, stru2, stru3, 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, xmax=20, dx=0.01)
## The ProfileGenerator
generator_ROY_Cryst_B = PDFGenerator("G_ROY_Cryst_B")
generator_ROY_Cryst_B.setStructure(stru1, periodic=True)
generator_ROY_Mole_B = DebyePDFGenerator("G_ROY_Mole_B")
generator_ROY_Mole_B.setStructure(stru2, periodic=False)
generator_ROY_Intra = DebyePDFGenerator("G_ROY_Intra")
generator_ROY_Intra.setStructure(stru3, periodic=False)
## The FitContribution
# Add both generators to the FitContribution. Add the Profile. This will
# send the metadata to the generators.
contribution = FitContribution("ROY")
contribution.addProfileGenerator(generator_ROY_Cryst_B)
contribution.addProfileGenerator(generator_ROY_Mole_B)
contribution.addProfileGenerator(generator_ROY_Intra)
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.
#from diffpy.srfit.pdf.characteristicfunctions import sphericalCF
#contribution.registerFunction(sphericalCF, name = "f_IMC")
contribution.setEquation(
"scale * (G_ROY_Cryst_B - G_ROY_Mole_B + G_ROY_Intra)")
# Make the FitRecipe and add the FitContribution.
recipe = FitRecipe()
recipe.addContribution(contribution)
qdamp = 0.02902
generator_ROY_Cryst_B.qdamp.value = qdamp
generator_ROY_Mole_B.qdamp.value = qdamp
generator_ROY_Intra.qdamp.value = qdamp
qbroad = 0.017315
generator_ROY_Cryst_B.qbroad.value = qbroad
generator_ROY_Mole_B.qbroad.value = qbroad
generator_ROY_Intra.qbroad.value = qbroad
# Vary the gloabal scale as well.
recipe.addVar(contribution.scale, 1)
#############################################################################################
############### First the ROY_Cryst_B parameters ############################################
#############################################################################################
phase_ROY_Cryst_B = generator_ROY_Cryst_B.phase
lat = phase_ROY_Cryst_B.getLattice()
atoms = phase_ROY_Cryst_B.getScatterers()
recipe.newVar("Uiso_Inter", 0.05, tag="T1")
recipe.newVar("lat_a", 3.9453, tag="lat")
recipe.newVar("lat_b", 18.685, tag="lat")
recipe.newVar("lat_c", 16.3948, tag="lat")
#recipe.newVar("alpha", 90, tag = "lat")
recipe.newVar("beta", 93.83, tag="lat")
#recipe.newVar("gamma", 90, tag = "lat")
recipe.constrain(lat.a, "lat_a")
recipe.constrain(lat.b, "lat_b")
recipe.constrain(lat.c, "lat_c")
#recipe.constrain(lat.alpha, "alpha")
recipe.constrain(lat.beta, "beta")
#recipe.constrain(lat.gamma, "gamma")
for atom in atoms:
if atom.element.title() == "N":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "O":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "C":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "H":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "S":
recipe.constrain(atom.Uiso, "Uiso_Inter")
generator_ROY_Cryst_B.delta2.value = 0
# recipe.addVar(generator_IMC_Cryst_B.delta2, name = "delta2_IMC_Cryst_B", value =
# 0, tag = "delta")
#############################################################################################
############### Second the ROY_Mole_B parameters ############################################
#############################################################################################
phase_ROY_Mole_B = generator_ROY_Mole_B.phase
generator_ROY_Mole_B.setQmin(0.0)
generator_ROY_Mole_B.setQmax(24.0)
recipe.newVar("zoom_Mole_B", 1, tag="lat2")
lat = phase_ROY_Mole_B.getLattice()
recipe.constrain(lat.a, "zoom_Mole_B")
recipe.constrain(lat.b, "zoom_Mole_B")
recipe.constrain(lat.c, "zoom_Mole_B")
# Constrain fractional xyz parameters
atoms = phase_ROY_Mole_B.getScatterers()
# Constrain ADPs
#recipe.newVar("Uiso_Inter", 0.05, tag = "T2")
for atom in atoms:
if atom.element.title() == "C":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "O":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "N":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "H":
recipe.constrain(atom.Uiso, "Uiso_Inter")
elif atom.element.title() == "S":
recipe.constrain(atom.Uiso, "Uiso_Inter")
generator_ROY_Mole_B.delta2.value = 0
# recipe.addVar(generator_IMC_Mole_B.delta2, name = "delta2_IMC_Mole_B", value
# = 5.66086478091, tag = "delta")
#############################################################################################
############### Third the intra molecule parameters##########################################
#############################################################################################
phase_ROY_Intra = generator_ROY_Intra.phase
generator_ROY_Intra.setQmin(0.0)
generator_ROY_Intra.setQmax(24.0)
recipe.newVar("zoom_Intra", 1, tag="lat3")
lat = phase_ROY_Intra.getLattice()
recipe.constrain(lat.a, "zoom_Intra")
recipe.constrain(lat.b, "zoom_Intra")
recipe.constrain(lat.c, "zoom_Intra")
# Constrain fractional xyz parameters
atoms = phase_ROY_Intra.getScatterers()
# Constrain ADPs
recipe.newVar("Uiso_Intra", 0.005, tag="T2")
for atom in atoms:
if atom.element.title() == "C":
recipe.constrain(atom.Uiso, "Uiso_Intra")
elif atom.element.title() == "O":
recipe.constrain(atom.Uiso, "Uiso_Intra")
elif atom.element.title() == "N":
recipe.constrain(atom.Uiso, "Uiso_Intra")
elif atom.element.title() == "H":
recipe.constrain(atom.Uiso, "Uiso_Intra")
elif atom.element.title() == "S":
recipe.constrain(atom.Uiso, "Uiso_Intra")
generator_ROY_Intra.delta2.value = 0
# Give the recipe away so it can be used!
return recipe