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<p>Demonstrates the basic operations involved in refinement.</p> |
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<div><p><strong>1. Save your diffraction data to the root directory and rename the file to <code class="docutils literal notranslate"><span class="pre">intensity.csv</span></code>.</strong></p> |
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<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># import PyXplore package</span> |
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<span class="kn">from</span> <span class="nn">PyXplore</span> <span class="kn">import</span> <span class="n">WPEM</span> |
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<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span> |
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</pre></div> |
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</div> |
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</div> |
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<div class="cell_output docutils container"> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>██╗ ██╗██████╗ ███████╗███╗ ███╗ |
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██║ ██║██╔══██╗██╔════╝████╗ ████║ |
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██║ █╗ ██║██████╔╝█████╗ ██╔████╔██║ |
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██║███╗██║██╔═══╝ ██╔══╝ ██║╚██╔╝██║ |
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╚███╔███╔╝██║ ███████╗██║ ╚═╝ ██║ |
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╚══╝╚══╝ ╚═╝ ╚══════╝╚═╝ ╚═╝ |
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A Diffraction Refinement Software : WPEM |
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Bin Cao, Advanced Materials Thrust, Hong Kong University of Science and Technology (Guangzhou) |
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URL : https://github.com/Bin-Cao/WPEM |
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Executed on : 2025-07-22 11:10:53 | Have a great day. |
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==================================================================================================== |
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</pre></div> |
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</div> |
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</div> |
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</div> |
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<blockquote> |
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<div><p><strong>2. Parse your diffraction data (<code class="docutils literal notranslate"><span class="pre">2θ</span></code>, intensity) and perform background processing.</strong></p> |
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</div></blockquote> |
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<div class="cell docutils container"> |
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<div class="cell_input docutils container"> |
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<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">intensity_csv</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="sa">r</span><span class="s1">'intensity.csv'</span><span class="p">,</span><span class="n">header</span><span class="o">=</span><span class="kc">None</span> <span class="p">)</span> |
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<span class="n">var</span> <span class="o">=</span> <span class="n">WPEM</span><span class="o">.</span><span class="n">BackgroundFit</span><span class="p">(</span><span class="n">intensity_csv</span><span class="p">,</span><span class="n">lowAngleRange</span><span class="o">=</span><span class="mi">17</span><span class="p">,</span><span class="n">poly_n</span><span class="o">=</span><span class="mi">13</span><span class="p">,</span><span class="n">bac_split</span><span class="o">=</span><span class="mi">16</span><span class="p">,</span><span class="n">bac_num</span><span class="o">=</span><span class="mi">300</span><span class="p">)</span> |
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</pre></div> |
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</div> |
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</div> |
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<div class="cell_output docutils container"> |
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<img alt="../../_images/aef21596334ce6f490a2526bc5fad55f09e54a82db7a9cd1be5d6bbd153f14ff.png" src="../../_images/aef21596334ce6f490a2526bc5fad55f09e54a82db7a9cd1be5d6bbd153f14ff.png" /> |
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<img alt="../../_images/16171239acea6bfcc15d02295c612fc20ca8c05252e8d4be1da7c0185068dd57.png" src="../../_images/16171239acea6bfcc15d02295c612fc20ca8c05252e8d4be1da7c0185068dd57.png" /> |
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<img alt="../../_images/bd82c740555d0962c82da60bb973052160e8eb6ac62a5b2e7291124e8db988d0.png" src="../../_images/bd82c740555d0962c82da60bb973052160e8eb6ac62a5b2e7291124e8db988d0.png" /> |
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<img alt="../../_images/11049e0b7d8aafa36de7c37dfe510fdeca704dcf18e8ccc5a933a5e75f64b536.png" src="../../_images/11049e0b7d8aafa36de7c37dfe510fdeca704dcf18e8ccc5a933a5e75f64b536.png" /> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>================================ |
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</pre></div> |
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</div> |
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<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span><Figure size 640x480 with 0 Axes> |
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</pre></div> |
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</div> |
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</div> |
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</div> |
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<blockquote> |
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<div><p><strong>3. After running the code, a new folder named <code class="docutils literal notranslate"><span class="pre">ConvertedDocuments</span></code> will be created in the root directory. This folder contains the background information.</strong></p> |
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</div></blockquote> |
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<blockquote> |
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<div><p><strong>Copy the two important files — <code class="docutils literal notranslate"><span class="pre">bac.csv</span></code> and <code class="docutils literal notranslate"><span class="pre">no_bac_intensity.csv</span></code> — from <code class="docutils literal notranslate"><span class="pre">ConvertedDocuments</span></code> into the root directory, as they are required for the next steps.</strong></p> |
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</div></blockquote> |
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<blockquote> |
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<div><p><strong>4. After background subtraction, the next step is to parse the reference structure.</strong></p> |
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<p>Save the reference <code class="docutils literal notranslate"><span class="pre">.cif</span></code> file in the root directory. For example, if the structure is Mn₂O₃, place a file named <code class="docutils literal notranslate"><span class="pre">Mn2O3.cif</span></code> in the root directory as the reference phase.</p> |
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<p>If you are unsure of the reference phase, you must perform phase identification first. Please visit our website for assistance: <a class="reference external" href="https://xqueryer.caobin.asia/">https://xqueryer.caobin.asia/</a></p> |
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</div></blockquote> |
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<div class="cell docutils container"> |
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<div class="cell_input docutils container"> |
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<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">latt</span><span class="p">,</span> <span class="n">AtomCoordinates</span><span class="p">,</span><span class="n">des</span> <span class="o">=</span> <span class="n">WPEM</span><span class="o">.</span><span class="n">CIFpreprocess</span><span class="p">(</span><span class="n">filepath</span><span class="o">=</span><span class="s1">'Mn2O3.cif'</span><span class="p">,</span><span class="n">two_theta_range</span><span class="o">=</span><span class="p">(</span><span class="mi">15</span><span class="p">,</span><span class="mi">75</span><span class="p">))</span> |
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</pre></div> |
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</div> |
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</div> |
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<div class="cell_output docutils container"> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>the space group of input crystal is : I 21 3 |
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cif file parse completed |
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atom locations claculated by parsed cif file |
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</pre></div> |
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</div> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>retrieval of all reciprocal vectors satisfying the diffraction geometry is done |
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extinction peaks are distinguished |
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There are 21 extinction peaks |
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Diffraction condition judgment end ! |
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The input crystal system is: Cubic | The initial lattice constants : 9.41 9.41 9.41 90.0 90.0 90.0 |
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</pre></div> |
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</div> |
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</div> |
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</div> |
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<blockquote> |
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<div><p><strong>5. After running the code, a new folder named <code class="docutils literal notranslate"><span class="pre">output_xrd</span></code> will be created.</strong></p> |
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<p>Inside this folder, locate the file named <code class="docutils literal notranslate"><span class="pre">xxxHKL.csv</span></code>, copy it to the root directory, and rename it to <code class="docutils literal notranslate"><span class="pre">peak0.csv</span></code>. This file will be used in the refinement step.</p> |
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</div></blockquote> |
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<div class="cell docutils container"> |
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<div class="cell_input docutils container"> |
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<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># The wavelength is set according to the actual light source</span> |
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<span class="n">wavelength</span> <span class="o">=</span> <span class="p">[</span><span class="mf">1.540593</span><span class="p">,</span> <span class="mf">1.544414</span><span class="p">]</span> |
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<span class="c1"># The file name of non-background data (2theta-intensity data)</span> |
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<span class="n">no_bac_intensity_file</span> <span class="o">=</span> <span class="s2">"no_bac_intensity.csv"</span> |
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<span class="c1"># The file name of raw/original data (2theta-intensity data)</span> |
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<span class="n">original_file</span> <span class="o">=</span> <span class="s2">"intensity.csv"</span> |
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<span class="c1"># The file name of background data (2theta-intensity data)</span> |
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<span class="n">bacground_file</span> <span class="o">=</span> <span class="s2">"bac.csv"</span> |
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<span class="c1"># Input the initial lattice constants {a, b, c, α, β, γ}, whose values need to be assumed at initialization.</span> |
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<span class="n">Lattice_constants</span> <span class="o">=</span> <span class="p">[</span><span class="n">latt</span><span class="p">,]</span> |
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<span class="c1"># Execute the model</span> |
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<span class="n">WPEM</span><span class="o">.</span><span class="n">XRDfit</span><span class="p">(</span> |
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<span class="n">wavelength</span><span class="p">,</span> <span class="n">var</span><span class="p">,</span> <span class="n">Lattice_constants</span><span class="p">,</span><span class="n">no_bac_intensity_file</span><span class="p">,</span> <span class="n">original_file</span><span class="p">,</span> <span class="n">bacground_file</span><span class="p">,</span> |
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<span class="n">subset_number</span><span class="o">=</span><span class="mi">11</span><span class="p">,</span><span class="n">low_bound</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span><span class="n">up_bound</span><span class="o">=</span><span class="mi">70</span><span class="p">,</span><span class="n">bta</span> <span class="o">=</span> <span class="mf">0.85</span><span class="p">,</span><span class="n">iter_max</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span> <span class="n">asy_C</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span><span class="n">InitializationEpoch</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> |
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<span class="p">)</span> |
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</pre></div> |
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</div> |
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</div> |
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<div class="cell_output docutils container"> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Started at Tue Jul 22 11:11:09 2025 |
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Initialization |
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-------------------------------------------------------------------------------- |
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The input HKL document is matched with WPEM |
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Diffraction indexs have been obtained by WPEM |
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The input crystal system is: Cubic | The initial lattice constants : 9.41 9.41 9.41 90.0 90.0 90.0 |
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—————————— Initilize the parameters by WPEM —————————— |
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Parameter initialization has been completed |
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</pre></div> |
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</div> |
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 0%| | 0/5 [00:00<?, ?it/s] |
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</pre></div> |
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</div> |
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING:tensorflow:From /Users/jacob/miniconda3/lib/python3.9/site-packages/tensorflow/python/util/deprecation.py:576: calling function (from tensorflow.python.eager.polymorphic_function.polymorphic_function) with experimental_relax_shapes is deprecated and will be removed in a future version. |
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Instructions for updating: |
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experimental_relax_shapes is deprecated, use reduce_retracing instead |
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</pre></div> |
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</div> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WPEM 1-th iteration |
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[array([ 9.40989, 9.40989, 9.40989, 90. , 90. , 90. ])] |
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</pre></div> |
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</div> |
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 20%|█████████ | 1/5 [00:07<00:28, 7.05s/it] |
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</pre></div> |
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</div> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Rp:3.603 | Rwp:5.039 | Rsquare:4.349 |
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</pre></div> |
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</div> |
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING:tensorflow:From /Users/jacob/miniconda3/lib/python3.9/site-packages/tensorflow/python/util/deprecation.py:576: calling function (from tensorflow.python.eager.polymorphic_function.polymorphic_function) with experimental_relax_shapes is deprecated and will be removed in a future version. |
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Instructions for updating: |
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experimental_relax_shapes is deprecated, use reduce_retracing instead |
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</pre></div> |
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</div> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WPEM 2-th iteration |
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[array([ 9.40961, 9.40961, 9.40961, 90. , 90. , 90. ])] |
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</pre></div> |
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</div> |
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 40%|██████████████████ | 2/5 [00:13<00:20, 6.89s/it] |
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</pre></div> |
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</div> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Rp:3.385 | Rwp:4.664 | Rsquare:3.518 |
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</pre></div> |
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</div> |
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING:tensorflow:From /Users/jacob/miniconda3/lib/python3.9/site-packages/tensorflow/python/util/deprecation.py:576: calling function (from tensorflow.python.eager.polymorphic_function.polymorphic_function) with experimental_relax_shapes is deprecated and will be removed in a future version. |
|
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Instructions for updating: |
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experimental_relax_shapes is deprecated, use reduce_retracing instead |
|
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</pre></div> |
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</div> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WPEM 3-th iteration |
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[array([ 9.40934, 9.40934, 9.40934, 90. , 90. , 90. ])] |
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</pre></div> |
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</div> |
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 60%|███████████████████████████ | 3/5 [00:20<00:13, 6.75s/it] |
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</pre></div> |
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</div> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Rp:3.241 | Rwp:4.423 | Rsquare:3.047 |
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</pre></div> |
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</div> |
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING:tensorflow:From /Users/jacob/miniconda3/lib/python3.9/site-packages/tensorflow/python/util/deprecation.py:576: calling function (from tensorflow.python.eager.polymorphic_function.polymorphic_function) with experimental_relax_shapes is deprecated and will be removed in a future version. |
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Instructions for updating: |
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experimental_relax_shapes is deprecated, use reduce_retracing instead |
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</pre></div> |
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</div> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WPEM 4-th iteration |
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[array([ 9.40913, 9.40913, 9.40913, 90. , 90. , 90. ])] |
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</pre></div> |
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</div> |
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 80%|████████████████████████████████████ | 4/5 [00:27<00:06, 6.70s/it] |
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</pre></div> |
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</div> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Rp:3.140 | Rwp:4.243 | Rsquare:2.758 |
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</pre></div> |
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</div> |
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING:tensorflow:From /Users/jacob/miniconda3/lib/python3.9/site-packages/tensorflow/python/util/deprecation.py:576: calling function (from tensorflow.python.eager.polymorphic_function.polymorphic_function) with experimental_relax_shapes is deprecated and will be removed in a future version. |
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Instructions for updating: |
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experimental_relax_shapes is deprecated, use reduce_retracing instead |
|
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</pre></div> |
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</div> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WPEM 5-th iteration |
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[array([ 9.40901, 9.40901, 9.40901, 90. , 90. , 90. ])] |
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</pre></div> |
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</div> |
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>100%|█████████████████████████████████████████████| 5/5 [00:33<00:00, 6.65s/it] |
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</pre></div> |
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</div> |
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>100%|█████████████████████████████████████████████| 5/5 [00:33<00:00, 6.72s/it] |
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</pre></div> |
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</div> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Rp:3.062 | Rwp:4.109 | Rsquare:2.577 |
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</pre></div> |
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</div> |
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> |
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</pre></div> |
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</div> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>After update the background : Rp = 1.555 | Rwp = 3.076 | Rsquare = 1.690 |
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</pre></div> |
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</div> |
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<img alt="../../_images/775928bcfdc02036451df7b0bec83cb51ef9e3dc96a7c68f96ebb63ff7f2f43a.png" src="../../_images/775928bcfdc02036451df7b0bec83cb51ef9e3dc96a7c68f96ebb63ff7f2f43a.png" /> |
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<img alt="../../_images/71c85b5daec8a90059dbf2f5589b75579eaba24753816838cff228188dab8aa6.png" src="../../_images/71c85b5daec8a90059dbf2f5589b75579eaba24753816838cff228188dab8aa6.png" /> |
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<img alt="../../_images/190307293664ee80df15ed5b3a02370514e177dd9b071a827e3f4f0697d46f73.png" src="../../_images/190307293664ee80df15ed5b3a02370514e177dd9b071a827e3f4f0697d46f73.png" /> |
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Mass fraction without structure factor estimate in % : [100.0] |
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Saved at the result documents |
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5-th iterations, reach the maximum number of iteration steps. |
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Rp: 1.555 |
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Rwp: 3.076 |
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WPEM program running time : 0 hours 0 minute 38 second |
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</pre></div> |
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</div> |
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<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>('0 hours 0 minute 38 second ', |
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[array([ 9.40901, 9.40901, 9.40901, 90. , 90. , 90. ])]) |
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</pre></div> |
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</div> |
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<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span><Figure size 640x480 with 0 Axes> |
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</pre></div> |
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</div> |
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</div> |
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</div> |
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<blockquote> |
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<div><p><strong>6. The refinement results will be saved in the folder <code class="docutils literal notranslate"><span class="pre">WPEMFittingResults</span></code>.</strong></p> |
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<p>For automated refinement and system integration, please refer to my repository: <a class="reference external" href="https://github.com/Bin-Cao/Ares">Ares</a>.</p> |
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</div></blockquote> |
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<div class="admonition seealso"> |
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<p class="admonition-title">See also</p> |
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<p>Details on the parameters and output files can be found in the documentation booklet for <strong>PyXplore</strong>. For more information, see the introduction in the <code class="docutils literal notranslate"><span class="pre">PyWPEM</span></code> repository: <a class="github reference external" href="https://github.com/Bin-Cao/PyWPEM">Bin-Cao/PyWPEM</a>.</p> |
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