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| | <h2> Contents </h2> |
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| | <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#coding">coding</a></li> |
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| | <section class="tex2jax_ignore mathjax_ignore" id="the-tutorial-2nd"> |
| | <h1>The tutorial 2nd<a class="headerlink" href="#the-tutorial-2nd" title="Link to this heading">#</a></h1> |
| | <p>Introduces the process for refining multi-phase systems.</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> |
| | <div class="cell docutils container"> |
| | <div class="cell_input docutils container"> |
| | <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> |
| | </div> |
| | </div> |
| | <div class="cell_output docutils container"> |
| | <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>██╗ ██╗██████╗ ███████╗███╗ ███╗ |
| | ██║ ██║██╔══██╗██╔════╝████╗ ████║ |
| | ██║ █╗ ██║██████╔╝█████╗ ██╔████╔██║ |
| | ██║███╗██║██╔═══╝ ██╔══╝ ██║╚██╔╝██║ |
| | ╚███╔███╔╝██║ ███████╗██║ ╚═╝ ██║ |
| | ╚══╝╚══╝ ╚═╝ ╚══════╝╚═╝ ╚═╝ |
| |
|
| | 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 11:11:54 | Have a great day. |
| | ==================================================================================================== |
| | </pre></div> |
| | </div> |
| | </div> |
| | </div> |
| | <blockquote> |
| | <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> |
| | </div></blockquote> |
| | <div class="cell docutils container"> |
| | <div class="cell_input docutils container"> |
| | <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> |
| | <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">22</span><span class="p">,</span><span class="n">poly_n</span><span class="o">=</span><span class="mi">8</span><span class="p">,</span><span class="n">bac_split</span><span class="o">=</span><span class="mi">8</span><span class="p">,</span><span class="n">bac_num</span><span class="o">=</span><span class="mi">600</span><span class="p">)</span> |
| | </pre></div> |
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| | <img alt="../../_images/7680f47f49a9945e5fbc83739b94877a360767ec80cfeb6f5d5dadaec0c20a62.png" src="../../_images/7680f47f49a9945e5fbc83739b94877a360767ec80cfeb6f5d5dadaec0c20a62.png" /> |
| | <img alt="../../_images/350eacfe86d4933fdfbbf4cdaede6f5202c37847400afaa29fc6b266efe8ff9e.png" src="../../_images/350eacfe86d4933fdfbbf4cdaede6f5202c37847400afaa29fc6b266efe8ff9e.png" /> |
| | <img alt="../../_images/75f1d073f3053cc85f0d230d73b75af79ff881f31ea9fc9796d091f4dfb4ea7c.png" src="../../_images/75f1d073f3053cc85f0d230d73b75af79ff881f31ea9fc9796d091f4dfb4ea7c.png" /> |
| | <img alt="../../_images/3f9788e3891be9e2c2a01f1802df05126c2975204c7b744dfcc710e71b151bb8.png" src="../../_images/3f9788e3891be9e2c2a01f1802df05126c2975204c7b744dfcc710e71b151bb8.png" /> |
| | <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>================================ |
| | </pre></div> |
| | </div> |
| | <div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span><Figure size 640x480 with 0 Axes> |
| | </pre></div> |
| | </div> |
| | </div> |
| | </div> |
| | <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 — <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> |
| | </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> files in the root directory. For example, if your structures are Mn₂O₃ and RuO₂, place files named <code class="docutils literal notranslate"><span class="pre">Mn2O3.cif</span></code> and <code class="docutils literal notranslate"><span class="pre">RuO2.cif</span></code> in the root directory as the reference phases.</p> |
| | <p>If you are unsure of the reference phases, you must first perform phase identification. For assistance, please visit our website: <a class="reference external" href="https://xqueryer.caobin.asia/">https://xqueryer.caobin.asia/</a></p> |
| | </div></blockquote> |
| | <div class="cell docutils container"> |
| | <div class="cell_input docutils container"> |
| | <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">MnO_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> |
| | </pre></div> |
| | </div> |
| | </div> |
| | <div class="cell_output docutils container"> |
| | <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> |
| | </div> |
| | <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> |
| | <div class="cell docutils container"> |
| | <div class="cell_input docutils container"> |
| | <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">RuO_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">'RuO2.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> |
| | </pre></div> |
| | </div> |
| | </div> |
| | <div class="cell_output docutils container"> |
| | <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>the space group of input crystal is : P 42/m n m |
| | cif file parse completed |
| | atom locations claculated by wyckoff site |
| | </pre></div> |
| | </div> |
| | <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 5 extinction peaks |
| | Diffraction condition judgment end ! |
| | The input crystal system is: Tetragonal | The initial lattice constants : 4.4968 4.4968 3.1049 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 generated.</strong></p> |
| | <p>Inside this folder, find the file named <code class="docutils literal notranslate"><span class="pre">xxxHKL.csv</span></code>. Copy it to the root directory and rename it sequentially as <code class="docutils literal notranslate"><span class="pre">peak0.csv</span></code>, <code class="docutils literal notranslate"><span class="pre">peak1.csv</span></code>, and so on. These files will be used in the refinement step.</p> |
| | </div></blockquote> |
| | <div class="cell docutils container"> |
| | <div class="cell_input docutils container"> |
| | <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">"no_bac_intensity.csv"</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">"intensity.csv"</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">"bac.csv"</span> |
| |
|
| |
|
| | <span class="c1"># Input the initial lattice constants {a, b, c, α, β, γ}, 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">MnO_latt</span><span class="p">,</span><span class="n">RuO_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> |
| | </div> |
| | </div> |
| | <div class="cell_output docutils container"> |
| | <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Started at Tue Jul 22 11:12:11 2025 |
| |
|
| | Initialization |
| | -------------------------------------------------------------------------------- |
| | Diffraction indexs have been obtained by 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 |
| | The input crystal system is: Tetragonal | The initial lattice constants : 4.4968 4.4968 3.1049 90.0 90.0 90.0 |
| | —————————— Initilize the parameters by WPEM —————————— |
| | 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<?, ?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([ 9.41064, 9.41064, 9.41064, 90. , 90. , 90. ]), array([ 4.49679, 4.49679, 3.10478, 90. , 90. , 90. ])] |
| | </pre></div> |
| | </div> |
| | <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 20%|█████████ | 1/5 [00:12<00:50, 12.59s/it] |
| | </pre></div> |
| | </div> |
| | <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Rp:5.261 | Rwp:6.716 | Rsquare:5.517 |
| | </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([ 9.4107, 9.4107, 9.4107, 90. , 90. , 90. ]), array([ 4.49678, 4.49678, 3.10454, 90. , 90. , 90. ])] |
| | </pre></div> |
| | </div> |
| | <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 40%|██████████████████ | 2/5 [00:24<00:36, 12.27s/it] |
| | </pre></div> |
| | </div> |
| | <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Rp:5.112 | Rwp:6.474 | Rsquare:5.129 |
| | </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([ 9.41131, 9.41131, 9.41131, 90. , 90. , 90. ]), array([ 4.49676, 4.49676, 3.10435, 90. , 90. , 90. ])] |
| | </pre></div> |
| | </div> |
| | <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 60%|███████████████████████████ | 3/5 [00:36<00:24, 12.12s/it] |
| | </pre></div> |
| | </div> |
| | <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Rp:5.021 | Rwp:6.332 | Rsquare:4.872 |
| | </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 4-th iteration |
| | [array([ 9.41183, 9.41183, 9.41183, 90. , 90. , 90. ]), array([ 4.49678, 4.49678, 3.10416, 90. , 90. , 90. ])] |
| | </pre></div> |
| | </div> |
| | <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 80%|████████████████████████████████████ | 4/5 [00:48<00:12, 12.19s/it] |
| | </pre></div> |
| | </div> |
| | <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Rp:4.946 | Rwp:6.229 | Rsquare:4.704 |
| | </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 5-th iteration |
| | [array([ 9.41186, 9.41186, 9.41186, 90. , 90. , 90. ]), array([ 4.49683, 4.49683, 3.10397, 90. , 90. , 90. ])] |
| | </pre></div> |
| | </div> |
| | <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>100%|█████████████████████████████████████████████| 5/5 [01:01<00:00, 12.21s/it] |
| | </pre></div> |
| | </div> |
| | <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>100%|█████████████████████████████████████████████| 5/5 [01:01<00:00, 12.22s/it] |
| | </pre></div> |
| | </div> |
| | <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Rp:4.883 | Rwp:6.157 | Rsquare:4.598 |
| | </pre></div> |
| | </div> |
| | <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> |
| | </pre></div> |
| | </div> |
| | <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>After update the background : Rp = 2.960 | Rwp = 5.339 | Rsquare = 3.372 |
| | </pre></div> |
| | </div> |
| | <img alt="../../_images/b5a72fd26a03dfd34e3bfd3e93d7b3596685ab907d7206dc7e705bfced3c28c6.png" src="../../_images/b5a72fd26a03dfd34e3bfd3e93d7b3596685ab907d7206dc7e705bfced3c28c6.png" /> |
| | <img alt="../../_images/2349a84c851b39ab1defb4a22a91d64c6b6be3ca5ac1cb5e09339f5f1ab4f7da.png" src="../../_images/2349a84c851b39ab1defb4a22a91d64c6b6be3ca5ac1cb5e09339f5f1ab4f7da.png" /> |
| | <img alt="../../_images/23d9c635b98fe46659fb8811232e58dee1e996ab779c61be4eb3f9a226d9ede1.png" src="../../_images/23d9c635b98fe46659fb8811232e58dee1e996ab779c61be4eb3f9a226d9ede1.png" /> |
| | <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Mass fraction without structure factor estimate in % : [79.88104018906242, 20.11895981093757] |
| | Saved at the result documents |
| | 5-th iterations, reach the maximum number of iteration steps. |
| | Rp: 2.960 |
| | Rwp: 5.339 |
| |
|
| |
|
| | WPEM program running time : 0 hours 1 minute 7 second |
| | </pre></div> |
| | </div> |
| | <div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>('0 hours 1 minute 7 second ', |
| | [array([ 9.41186, 9.41186, 9.41186, 90. , 90. , 90. ]), |
| | array([ 4.49683, 4.49683, 3.10397, 90. , 90. , 90. ])]) |
| | </pre></div> |
| | </div> |
| | <div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span><Figure size 640x480 with 0 Axes> |
| | </pre></div> |
| | </div> |
| | </div> |
| | </div> |
| | <div class="admonition seealso"> |
| | <p class="admonition-title">See also</p> |
| | <p>For demonstration purposes, the code uses <code class="docutils literal notranslate"><span class="pre">iter_max</span> <span class="pre">=</span> <span class="pre">5</span></code> to reduce computational cost. However, for practical applications, it is recommended to set <code class="docutils literal notranslate"><span class="pre">iter_max</span></code> to at least 50 for more reliable results.</p> |
| | </div> |
| | </section> |
| | </section> |
| |
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