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Aug 19, 2024
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Run black . without any manual modification #73

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11 changes: 7 additions & 4 deletions doc/examples/coreshellnp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,7 @@ def makeRecipe(stru1, stru2, datname):
# phases, we implicitly assume that the core-shell correlations contribute
# very little to the PDF.
from diffpy.srfit.pdf.characteristicfunctions import shellCF, sphericalCF

contribution.registerFunction(sphericalCF, name="f_CdS")
contribution.registerFunction(shellCF, name="f_ZnS")

Expand Down Expand Up @@ -137,10 +138,11 @@ def plotResults(recipe):
diff = g - gcalc + diffzero

import pylab
pylab.plot(r, g, 'bo', label="G(r) Data")
pylab.plot(r, gcalc, 'r-', label="G(r) Fit")
pylab.plot(r, diff, 'g-', label="G(r) diff")
pylab.plot(r, diffzero, 'k-')

pylab.plot(r, g, "bo", label="G(r) Data")
pylab.plot(r, gcalc, "r-", label="G(r) Fit")
pylab.plot(r, diff, "g-", label="G(r) diff")
pylab.plot(r, diffzero, "k-")
pylab.xlabel(r"$r (\AA)$")
pylab.ylabel(r"$G (\AA^{-2})$")
pylab.legend(loc=1)
Expand All @@ -162,6 +164,7 @@ def main():
stru2 = loadCrystal(znsciffile)
recipe = makeRecipe(stru1, stru2, data)
from diffpy.srfit.fitbase.fithook import PlotFitHook

recipe.pushFitHook(PlotFitHook())
recipe.fithooks[0].verbose = 3

Expand Down
18 changes: 11 additions & 7 deletions doc/examples/crystalpdf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@

####### Example Code


def makeRecipe(ciffile, datname):
"""Create a fitting recipe for crystalline PDF data."""

Expand All @@ -50,7 +51,7 @@ def makeRecipe(ciffile, datname):
parser = PDFParser()
parser.parseFile(datname)
profile.loadParsedData(parser)
profile.setCalculationRange(xmax = 20)
profile.setCalculationRange(xmax=20)

## The ProfileGenerator
# The PDFGenerator is for configuring and calculating a PDF profile. Here,
Expand All @@ -69,7 +70,7 @@ def makeRecipe(ciffile, datname):
# before.
contribution = FitContribution("nickel")
contribution.addProfileGenerator(generator)
contribution.setProfile(profile, xname = "r")
contribution.setProfile(profile, xname="r")

## Make the FitRecipe and add the FitContribution.
recipe = FitRecipe()
Expand All @@ -92,6 +93,7 @@ def makeRecipe(ciffile, datname):
# 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
Expand Down Expand Up @@ -121,6 +123,7 @@ def makeRecipe(ciffile, datname):
# Give the recipe away so it can be used!
return recipe


def plotResults(recipe):
"""Plot the results contained within a refined FitRecipe."""

Expand All @@ -132,19 +135,20 @@ def plotResults(recipe):
diff = g - gcalc + diffzero

import pylab
pylab.plot(r,g,'bo',label="G(r) Data")
pylab.plot(r, gcalc,'r-',label="G(r) Fit")
pylab.plot(r,diff,'g-',label="G(r) diff")
pylab.plot(r,diffzero,'k-')

pylab.plot(r, g, "bo", label="G(r) Data")
pylab.plot(r, gcalc, "r-", label="G(r) Fit")
pylab.plot(r, diff, "g-", label="G(r) diff")
pylab.plot(r, diffzero, "k-")
pylab.xlabel(r"$r (\AA)$")
pylab.ylabel(r"$G (\AA^{-2})$")
pylab.legend(loc=1)

pylab.show()
return

if __name__ == "__main__":

if __name__ == "__main__":
# Make the data and the recipe
ciffile = "data/ni.cif"
data = "data/ni-q27r100-neutron.gr"
Expand Down
71 changes: 36 additions & 35 deletions doc/examples/crystalpdfall.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,24 +28,26 @@

####### Example Code


def makeProfile(datafile):
"""Make an place data within a Profile."""
profile = Profile()
parser = PDFParser()
parser.parseFile(datafile)
profile.loadParsedData(parser)
profile.setCalculationRange(xmax = 20)
profile.setCalculationRange(xmax=20)
return profile


def makeContribution(name, generator, profile):
"""Make a FitContribution and add a generator and profile."""
contribution = FitContribution(name)
contribution.addProfileGenerator(generator)
contribution.setProfile(profile, xname = "r")
contribution.setProfile(profile, xname="r")
return contribution

def makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si,
xdata_sini):

def makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si, xdata_sini):
"""Create a fitting recipe for crystalline PDF data."""

## The Profiles
Expand Down Expand Up @@ -81,8 +83,7 @@ def makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si,
xcontribution_ni = makeContribution("xnickel", xgenerator_ni, xprofile_ni)
xcontribution_si = makeContribution("xsilicon", xgenerator_si, xprofile_si)
ncontribution_ni = makeContribution("nnickel", ngenerator_ni, nprofile_ni)
xcontribution_sini = makeContribution("xsini", xgenerator_sini_ni,
xprofile_sini)
xcontribution_sini = makeContribution("xsini", xgenerator_sini_ni, xprofile_sini)
xcontribution_sini.addProfileGenerator(xgenerator_sini_si)
xcontribution_sini.setEquation("scale * (xG_sini_ni + xG_sini_si)")

Expand All @@ -101,22 +102,22 @@ def makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si,

# Now we vary and constrain Parameters as before.
for par in phase_ni.sgpars:
recipe.addVar(par, name = par.name + "_ni")
recipe.addVar(par, name=par.name + "_ni")
delta2_ni = recipe.newVar("delta2_ni", 2.5)
recipe.constrain(xgenerator_ni.delta2, delta2_ni)
recipe.constrain(ngenerator_ni.delta2, delta2_ni)
recipe.constrain(xgenerator_sini_ni.delta2, delta2_ni)

for par in phase_si.sgpars:
recipe.addVar(par, name = par.name + "_si")
recipe.addVar(par, name=par.name + "_si")
delta2_si = recipe.newVar("delta2_si", 2.5)
recipe.constrain(xgenerator_si.delta2, delta2_si)
recipe.constrain(xgenerator_sini_si.delta2, delta2_si)

# Now the experimental parameters
recipe.addVar(xgenerator_ni.scale, name = "xscale_ni")
recipe.addVar(xgenerator_si.scale, name = "xscale_si")
recipe.addVar(ngenerator_ni.scale, name = "nscale_ni")
recipe.addVar(xgenerator_ni.scale, name="xscale_ni")
recipe.addVar(xgenerator_si.scale, name="xscale_si")
recipe.addVar(ngenerator_ni.scale, name="nscale_ni")
recipe.addVar(xcontribution_sini.scale, 1.0, "xscale_sini")
recipe.newVar("pscale_sini_ni", 0.8)
recipe.constrain(xgenerator_sini_ni.scale, "pscale_sini_ni")
Expand All @@ -133,6 +134,7 @@ def makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si,
# Give the recipe away so it can be used!
return recipe


def plotResults(recipe):
"""Plot the results contained within a refined FitRecipe."""

Expand All @@ -141,67 +143,67 @@ def plotResults(recipe):
xr_ni = xnickel.profile.x
xg_ni = xnickel.profile.y
xgcalc_ni = xnickel.profile.ycalc
xdiffzero_ni = -0.8 * max(xg_ni) * numpy.ones_like(xg_ni)
xdiffzero_ni = -0.8 * max(xg_ni) * numpy.ones_like(xg_ni)
xdiff_ni = xg_ni - xgcalc_ni + xdiffzero_ni

xsilicon = recipe.xsilicon
xr_si = xsilicon.profile.x
xg_si = xsilicon.profile.y
xgcalc_si = xsilicon.profile.ycalc
xdiffzero_si = -0.8 * max(xg_si) * numpy.ones_like(xg_si)
xdiffzero_si = -0.8 * max(xg_si) * numpy.ones_like(xg_si)
xdiff_si = xg_si - xgcalc_si + xdiffzero_si

nnickel = recipe.nnickel
nr_ni = nnickel.profile.x
ng_ni = nnickel.profile.y
ngcalc_ni = nnickel.profile.ycalc
ndiffzero_ni = -0.8 * max(ng_ni) * numpy.ones_like(ng_ni)
ndiffzero_ni = -0.8 * max(ng_ni) * numpy.ones_like(ng_ni)
ndiff_ni = ng_ni - ngcalc_ni + ndiffzero_ni

xsini = recipe.xsini
xr_sini = xsini.profile.x
xg_sini = xsini.profile.y
xgcalc_sini = xsini.profile.ycalc
xdiffzero_sini = -0.8 * max(xg_sini) * numpy.ones_like(xg_sini)
xdiffzero_sini = -0.8 * max(xg_sini) * numpy.ones_like(xg_sini)
xdiff_sini = xg_sini - xgcalc_sini + xdiffzero_sini


import pylab

pylab.subplot(2, 2, 1)
pylab.plot(xr_ni,xg_ni,'bo',label="G(r) x-ray nickel Data")
pylab.plot(xr_ni,xgcalc_ni,'r-',label="G(r) x-ray nickel Fit")
pylab.plot(xr_ni,xdiff_ni,'g-',label="G(r) x-ray nickel diff")
pylab.plot(xr_ni,xdiffzero_ni,'k-')
pylab.plot(xr_ni, xg_ni, "bo", label="G(r) x-ray nickel Data")
pylab.plot(xr_ni, xgcalc_ni, "r-", label="G(r) x-ray nickel Fit")
pylab.plot(xr_ni, xdiff_ni, "g-", label="G(r) x-ray nickel diff")
pylab.plot(xr_ni, xdiffzero_ni, "k-")
pylab.xlabel(r"$r (\AA)$")
pylab.ylabel(r"$G (\AA^{-2})$")
pylab.legend(loc=1)

pylab.subplot(2, 2, 2)
pylab.plot(xr_si,xg_si,'bo',label="G(r) x-ray silicon Data")
pylab.plot(xr_si,xgcalc_si,'r-',label="G(r) x-ray silicon Fit")
pylab.plot(xr_si,xdiff_si,'g-',label="G(r) x-ray silicon diff")
pylab.plot(xr_si,xdiffzero_si,'k-')
pylab.plot(xr_si, xg_si, "bo", label="G(r) x-ray silicon Data")
pylab.plot(xr_si, xgcalc_si, "r-", label="G(r) x-ray silicon Fit")
pylab.plot(xr_si, xdiff_si, "g-", label="G(r) x-ray silicon diff")
pylab.plot(xr_si, xdiffzero_si, "k-")
pylab.legend(loc=1)

pylab.subplot(2, 2, 3)
pylab.plot(nr_ni,ng_ni,'bo',label="G(r) neutron nickel Data")
pylab.plot(nr_ni,ngcalc_ni,'r-',label="G(r) neutron nickel Fit")
pylab.plot(nr_ni,ndiff_ni,'g-',label="G(r) neutron nickel diff")
pylab.plot(nr_ni,ndiffzero_ni,'k-')
pylab.plot(nr_ni, ng_ni, "bo", label="G(r) neutron nickel Data")
pylab.plot(nr_ni, ngcalc_ni, "r-", label="G(r) neutron nickel Fit")
pylab.plot(nr_ni, ndiff_ni, "g-", label="G(r) neutron nickel diff")
pylab.plot(nr_ni, ndiffzero_ni, "k-")
pylab.legend(loc=1)

pylab.subplot(2, 2, 4)
pylab.plot(xr_sini,xg_sini,'bo',label="G(r) x-ray sini Data")
pylab.plot(xr_sini,xgcalc_sini,'r-',label="G(r) x-ray sini Fit")
pylab.plot(xr_sini,xdiff_sini,'g-',label="G(r) x-ray sini diff")
pylab.plot(xr_sini,xdiffzero_sini,'k-')
pylab.plot(xr_sini, xg_sini, "bo", label="G(r) x-ray sini Data")
pylab.plot(xr_sini, xgcalc_sini, "r-", label="G(r) x-ray sini Fit")
pylab.plot(xr_sini, xdiff_sini, "g-", label="G(r) x-ray sini diff")
pylab.plot(xr_sini, xdiffzero_sini, "k-")
pylab.legend(loc=1)

pylab.show()
return

if __name__ == "__main__":

if __name__ == "__main__":
# Make the data and the recipe
ciffile_ni = "data/ni.cif"
ciffile_si = "data/si.cif"
Expand All @@ -211,8 +213,7 @@ def plotResults(recipe):
xdata_sini = "data/si90ni10-q27r60-xray.gr"

# Make the recipe
recipe = makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si,
xdata_sini)
recipe = makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si, xdata_sini)

# Optimize
scipyOptimize(recipe)
Expand Down
9 changes: 5 additions & 4 deletions doc/examples/crystalpdfobjcryst.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@

####### Example Code


def makeRecipe(ciffile, datname):
"""Create a fitting recipe for crystalline PDF data."""

Expand All @@ -43,7 +44,7 @@ def makeRecipe(ciffile, datname):
parser = PDFParser()
parser.parseFile(datname)
profile.loadParsedData(parser)
profile.setCalculationRange(xmax = 20)
profile.setCalculationRange(xmax=20)

## The ProfileGenerator
# This time we use the CreateCrystalFromCIF method of pyobjcryst.crystal to
Expand All @@ -57,7 +58,7 @@ def makeRecipe(ciffile, datname):
## The FitContribution
contribution = FitContribution("nickel")
contribution.addProfileGenerator(generator)
contribution.setProfile(profile, xname = "r")
contribution.setProfile(profile, xname="r")

# Make the FitRecipe and add the FitContribution.
recipe = FitRecipe()
Expand Down Expand Up @@ -86,7 +87,7 @@ def makeRecipe(ciffile, datname):
for par in phase.sgpars:
recipe.addVar(par)
# set the initial thermal factor to a non-zero value
assert hasattr(recipe, 'B11_0')
assert hasattr(recipe, "B11_0")
recipe.B11_0 = 0.1

# We now select non-structural parameters to refine.
Expand All @@ -100,8 +101,8 @@ def makeRecipe(ciffile, datname):
# Give the recipe away so it can be used!
return recipe

if __name__ == "__main__":

if __name__ == "__main__":
# Make the data and the recipe
ciffile = "data/si.cif"
data = "data/si-q27r60-xray.gr"
Expand Down
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