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    <h1>The tutorial 1st</h1>
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  <section class="tex2jax_ignore mathjax_ignore" id="the-tutorial-1st">
<h1>The tutorial 1st<a class="headerlink" href="#the-tutorial-1st" title="Link to this heading">#</a></h1>
<p>Demonstrates the basic operations involved in refinement.</p>
<section id="coding">
<h2>coding<a class="headerlink" href="#coding" title="Link to this heading">#</a></h2>
<blockquote>
<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>
</div></blockquote>
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<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># import PyXplore package</span>
<span class="kn">from</span> <span class="nn">PyXplore</span> <span class="kn">import</span> <span class="n">WPEM</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
</pre></div>
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>β–ˆβ–ˆβ•—    β–ˆβ–ˆβ•—β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ•— β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ•—β–ˆβ–ˆβ–ˆβ•—   β–ˆβ–ˆβ–ˆβ•—
β–ˆβ–ˆβ•‘    β–ˆβ–ˆβ•‘β–ˆβ–ˆβ•”β•β•β–ˆβ–ˆβ•—β–ˆβ–ˆβ•”β•β•β•β•β•β–ˆβ–ˆβ–ˆβ–ˆβ•— β–ˆβ–ˆβ–ˆβ–ˆβ•‘
β–ˆβ–ˆβ•‘ β–ˆβ•— β–ˆβ–ˆβ•‘β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ•”β•β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ•—  β–ˆβ–ˆβ•”β–ˆβ–ˆβ–ˆβ–ˆβ•”β–ˆβ–ˆβ•‘
β–ˆβ–ˆβ•‘β–ˆβ–ˆβ–ˆβ•—β–ˆβ–ˆβ•‘β–ˆβ–ˆβ•”β•β•β•β• β–ˆβ–ˆβ•”β•β•β•  β–ˆβ–ˆβ•‘β•šβ–ˆβ–ˆβ•”β•β–ˆβ–ˆβ•‘
β•šβ–ˆβ–ˆβ–ˆβ•”β–ˆβ–ˆβ–ˆβ•”β•β–ˆβ–ˆβ•‘     β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ•—β–ˆβ–ˆβ•‘ β•šβ•β• β–ˆβ–ˆβ•‘
 β•šβ•β•β•β•šβ•β•β• β•šβ•β•     β•šβ•β•β•β•β•β•β•β•šβ•β•     β•šβ•β•                                                  

A Diffraction Refinement Software : WPEM
Bin Cao, Advanced Materials Thrust, Hong Kong University of Science and Technology (Guangzhou)
URL : https://github.com/Bin-Cao/WPEM
Executed on : 2025-07-22 11:10:53  | Have a great day.
====================================================================================================
</pre></div>
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<blockquote>
<div><p><strong>2. Parse your diffraction data (<code class="docutils literal notranslate"><span class="pre">2ΞΈ</span></code>, intensity) and perform background processing.</strong></p>
</div></blockquote>
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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">&#39;intensity.csv&#39;</span><span class="p">,</span><span class="n">header</span><span class="o">=</span><span class="kc">None</span> <span class="p">)</span>
<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>
</pre></div>
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<img alt="../../_images/aef21596334ce6f490a2526bc5fad55f09e54a82db7a9cd1be5d6bbd153f14ff.png" src="../../_images/aef21596334ce6f490a2526bc5fad55f09e54a82db7a9cd1be5d6bbd153f14ff.png" />
<img alt="../../_images/16171239acea6bfcc15d02295c612fc20ca8c05252e8d4be1da7c0185068dd57.png" src="../../_images/16171239acea6bfcc15d02295c612fc20ca8c05252e8d4be1da7c0185068dd57.png" />
<img alt="../../_images/bd82c740555d0962c82da60bb973052160e8eb6ac62a5b2e7291124e8db988d0.png" src="../../_images/bd82c740555d0962c82da60bb973052160e8eb6ac62a5b2e7291124e8db988d0.png" />
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>================================
</pre></div>
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<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;Figure size 640x480 with 0 Axes&gt;
</pre></div>
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<blockquote>
<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>
</div></blockquote>
<blockquote>
<div><p><strong>Copy the two important files β€” <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> β€” 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>
</div></blockquote>
<blockquote>
<div><p><strong>4. After background subtraction, the next step is to parse the reference structure.</strong></p>
<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 Mnβ‚‚O₃, 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>
<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>
</div></blockquote>
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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">&#39;Mn2O3.cif&#39;</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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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>the space group of input crystal is : I 21 3
cif file parse completed
atom locations claculated by parsed cif file
</pre></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
extinction peaks are distinguished
There are 21 extinction peaks
Diffraction condition judgment end !
The input crystal system is: Cubic  |  The initial lattice constants : 9.41 9.41 9.41 90.0 90.0 90.0
</pre></div>
</div>
</div>
</div>
<blockquote>
<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>
<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 class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># The wavelength is set according to the actual light source</span>
<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>
<span class="c1"># The file name of non-background data (2theta-intensity data)</span>
<span class="n">no_bac_intensity_file</span> <span class="o">=</span> <span class="s2">&quot;no_bac_intensity.csv&quot;</span> 
<span class="c1"># The file name of raw/original data (2theta-intensity data)</span>
<span class="n">original_file</span> <span class="o">=</span> <span class="s2">&quot;intensity.csv&quot;</span>  
<span class="c1"># The file name of background data (2theta-intensity data)</span>
<span class="n">bacground_file</span> <span class="o">=</span> <span class="s2">&quot;bac.csv&quot;</span>  


<span class="c1"># Input the initial lattice constants {a, b, c, Ξ±, Ξ², Ξ³}, whose values need to be assumed at initialization.</span>
<span class="n">Lattice_constants</span> <span class="o">=</span> <span class="p">[</span><span class="n">latt</span><span class="p">,]</span>

<span class="c1"># Execute the model</span>

<span class="n">WPEM</span><span class="o">.</span><span class="n">XRDfit</span><span class="p">(</span>
    <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> 
    <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> 
    <span class="p">)</span>
</pre></div>
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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 

Initialization
--------------------------------------------------------------------------------
The input HKL document is matched with WPEM
Diffraction indexs have been obtained by WPEM


The input crystal system is: Cubic  |  The initial lattice constants : 9.41 9.41 9.41 90.0 90.0 90.0
β€”β€”β€”β€”β€”β€”β€”β€”β€”β€” Initilize the parameters by WPEM β€”β€”β€”β€”β€”β€”β€”β€”β€”β€”
Parameter initialization has been completed 
</pre></div>
</div>
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>  0%|                                                     | 0/5 [00:00&lt;?, ?it/s]
</pre></div>
</div>
<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.
Instructions for updating:
experimental_relax_shapes is deprecated, use reduce_retracing instead
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WPEM 1-th iteration
[array([ 9.40989,  9.40989,  9.40989, 90.     , 90.     , 90.     ])]
</pre></div>
</div>
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 20%|β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ                                    | 1/5 [00:07&lt;00:28,  7.05s/it]
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Rp:3.603 | Rwp:5.039 | Rsquare:4.349
</pre></div>
</div>
<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.
Instructions for updating:
experimental_relax_shapes is deprecated, use reduce_retracing instead
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WPEM 2-th iteration
[array([ 9.40961,  9.40961,  9.40961, 90.     , 90.     , 90.     ])]
</pre></div>
</div>
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 40%|β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ                           | 2/5 [00:13&lt;00:20,  6.89s/it]
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Rp:3.385 | Rwp:4.664 | Rsquare:3.518
</pre></div>
</div>
<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.
Instructions for updating:
experimental_relax_shapes is deprecated, use reduce_retracing instead
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WPEM 3-th iteration
[array([ 9.40934,  9.40934,  9.40934, 90.     , 90.     , 90.     ])]
</pre></div>
</div>
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 60%|β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ                  | 3/5 [00:20&lt;00:13,  6.75s/it]
</pre></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
</pre></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.
Instructions for updating:
experimental_relax_shapes is deprecated, use reduce_retracing instead
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WPEM 4-th iteration
[array([ 9.40913,  9.40913,  9.40913, 90.     , 90.     , 90.     ])]
</pre></div>
</div>
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 80%|β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ         | 4/5 [00:27&lt;00:06,  6.70s/it]
</pre></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
</pre></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.
Instructions for updating:
experimental_relax_shapes is deprecated, use reduce_retracing instead
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WPEM 5-th iteration
[array([ 9.40901,  9.40901,  9.40901, 90.     , 90.     , 90.     ])]
</pre></div>
</div>
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>100%|β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ| 5/5 [00:33&lt;00:00,  6.65s/it]
</pre></div>
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>100%|β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ| 5/5 [00:33&lt;00:00,  6.72s/it]
</pre></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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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>
</pre></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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<img alt="../../_images/775928bcfdc02036451df7b0bec83cb51ef9e3dc96a7c68f96ebb63ff7f2f43a.png" src="../../_images/775928bcfdc02036451df7b0bec83cb51ef9e3dc96a7c68f96ebb63ff7f2f43a.png" />
<img alt="../../_images/71c85b5daec8a90059dbf2f5589b75579eaba24753816838cff228188dab8aa6.png" src="../../_images/71c85b5daec8a90059dbf2f5589b75579eaba24753816838cff228188dab8aa6.png" />
<img alt="../../_images/190307293664ee80df15ed5b3a02370514e177dd9b071a827e3f4f0697d46f73.png" src="../../_images/190307293664ee80df15ed5b3a02370514e177dd9b071a827e3f4f0697d46f73.png" />
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Mass fraction without structure factor estimate in % : [100.0] 
 Saved at the result documents
5-th iterations, reach the maximum number of iteration steps.
 Rp: 1.555
Rwp: 3.076 


WPEM program running time :  0 hours 0 minute  38 second  
</pre></div>
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<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>(&#39;0 hours 0 minute  38 second  &#39;,
 [array([ 9.40901,  9.40901,  9.40901, 90.     , 90.     , 90.     ])])
</pre></div>
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<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;Figure size 640x480 with 0 Axes&gt;
</pre></div>
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<blockquote>
<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>
<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>
</div></blockquote>
<div class="admonition seealso">
<p class="admonition-title">See also</p>
<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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