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‎.buildinfo‎

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# Sphinx build info version 1
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# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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config: 73080f2f80c5c857268e5728fb5a359d
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config: ef272f409fa0d83ba87a930e5dc91fde
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tags: 645f666f9bcd5a90fca523b33c5a78b7

‎_downloads/013300f3620019485548697445e5b47a/Ni.stru‎

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title structure Ni FCC
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format pdffit
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scale 1.000000
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sharp 0.000000, 1.000000, 0.000000
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spcgr Fm-3m
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cell 3.520000, 3.520000, 3.520000, 90.000000, 90.000000, 90.000000
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dcell 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000
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ncell 1, 1, 1, 4
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atoms
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NI 0.00000000 0.00000000 0.00000000 1.0000
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0.00000000 0.00000000 0.00000000 0.0000
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0.00126651 0.00126651 0.00126651
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0.00000000 0.00000000 0.00000000
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0.00000000 0.00000000 0.00000000
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0.00000000 0.00000000 0.00000000
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NI 0.00000000 0.50000000 0.50000000 1.0000
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0.00000000 0.00000000 0.00000000 0.0000
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0.00126651 0.00126651 0.00126651
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0.00000000 0.00000000 0.00000000
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0.00000000 0.00000000 0.00000000
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0.00000000 0.00000000 0.00000000
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NI 0.50000000 0.00000000 0.50000000 1.0000
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0.00000000 0.00000000 0.00000000 0.0000
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0.00126651 0.00126651 0.00126651
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0.00000000 0.00000000 0.00000000
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0.00000000 0.00000000 0.00000000
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0.00000000 0.00000000 0.00000000
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NI 0.50000000 0.50000000 0.00000000 1.0000
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0.00000000 0.00000000 0.00000000 0.0000
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0.00126651 0.00126651 0.00126651
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0.00000000 0.00000000 0.00000000
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0.00000000 0.00000000 0.00000000
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0.00000000 0.00000000 0.00000000

‎_downloads/019d6e377cbbff298dd5aa4d545daaec/Ni_refinement.py‎

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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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"""Perform simple refinement of Ni structure to the experimental x-ray PDF.
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Save fitted curve, refined structure and results summary.
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"""
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import matplotlib.pyplot as plt
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import numpy
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from diffpy.pdffit2 import PdfFit
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# Create new PDF calculator object.
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pf = PdfFit()
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# Load data ------------------------------------------------------------------
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# Load experimental x-ray PDF data
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qmax = 30.0 # Q-cutoff used in PDF calculation in 1/A
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qdamp = 0.01 # instrument Q-resolution factor, responsible for PDF decay
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pf.read_data("Ni-xray.gr", "X", qmax, qdamp)
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# Load nickel structure, must be in PDFFIT or DISCUS format
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pf.read_struct("Ni.stru")
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# Configure Refinement -------------------------------------------------------
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# Refine lattice parameters a, b, c.
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# Make them all equal to parameter @1.
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pf.constrain(pf.lat(1), "@1")
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pf.constrain(pf.lat(2), "@1")
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pf.constrain(pf.lat(3), "@1")
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# set initial value of parameter @1
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pf.setpar(1, pf.lat(1))
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# Refine phase scale factor. Right side can have formulas.
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pf.constrain("pscale", "@20 * 2")
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pf.setpar(20, pf.getvar(pf.pscale) / 2.0)
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# Refine PDF damping due to instrument Q-resolution.
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# Left side can be also passed as a reference to PdfFit object
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pf.constrain(pf.qdamp, "@21")
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pf.setpar(21, 0.03)
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# Refine sharpening factor for correlated motion of close atoms.
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pf.constrain(pf.delta2, 22)
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pf.setpar(22, 0.0003)
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# Set all temperature factors isotropic and equal to @4
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for idx in range(1, 5):
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pf.constrain(pf.u11(idx), "@4")
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pf.constrain(pf.u22(idx), "@4")
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pf.constrain(pf.u33(idx), "@4")
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pf.setpar(4, pf.u11(1))
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# Refine ---------------------------------------------------------------------
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pf.pdfrange(1, 1.5, 19.99)
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pf.refine()
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# Save results ---------------------------------------------------------------
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pf.save_pdf(1, "Ni_refinement.fgr")
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pf.save_struct(1, "Ni_refinement.rstr")
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pf.save_res("Ni_refinement.res")
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# Plot results ---------------------------------------------------------------
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# obtain data from PdfFit calculator object
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r = pf.getR()
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Gobs = pf.getpdf_obs()
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Gfit = pf.getpdf_fit()
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# calculate difference curve
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Gdiff = numpy.array(Gobs) - numpy.array(Gfit)
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Gdiff_baseline = -10
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plt.plot(r, Gobs, "ko")
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plt.plot(r, Gfit, "b-")
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plt.plot(r, Gdiff + Gdiff_baseline, "r-")
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plt.xlabel("r (Å)")
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plt.ylabel("G (Å$^{-2}$)")
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plt.title("Fit of nickel to x-ray experimental PDF")
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# display plot window, this must be the last command in the script
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plt.show()

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