Merge pull request #59 from SMTG-UCL/master

synchronise with master

citation.cff

@@ -0,0 +1,19 @@
+cff-version: 1.2.0
+message: "If you use ThermoPlotter, please cite it as below:"
+authors:
+- family-names: "Spooner"
+  given-names: "Kieran B."
+  orcid: "https://orcid.org/0000-0002-4078-3148"
+- family-names: "Einhorn"
+  given-names: "Maud"
+  orcid: "https://orcid.org/0000-0003-0371-0262"
+- family-names: "Davies"
+  given-names: "Daniel W."
+  orcid: "https://orcid.org/0000-0003-4094-5992"
+- family-names: "Scanlon"
+  given-names: "David O."
+  orcid: "https://orcid.org/0000-0001-9174-8601"
+title: "ThermoPlotter: Streamlined Analysis of Thermoelectric Properties"
+version: 2.3.0
+date-released: 2022-10-12
+url: "https://github.com/SMTG-UCL/ThermoPlotter"

docs/_modules/tp/axes/large.html

@@ -84,18 +84,31 @@ <h1>Source code for tp.axes.large</h1><div class="highlight"><pre>
 <span class="sd">---------</span>
 
 <span class="sd">    one</span>
+
 <span class="sd">    one_colourbar</span>
+
 <span class="sd">    one_dos</span>
+<span class="sd">    </span>
 <span class="sd">    one_dos_colourbar</span>
+<span class="sd">    </span>
 <span class="sd">    two_h</span>
+<span class="sd">    </span>
 <span class="sd">    two_h_colourbars</span>
+<span class="sd">    </span>
 <span class="sd">    two_v</span>
+<span class="sd">    </span>
 <span class="sd">    two_v_colourbars</span>
+<span class="sd">    </span>
 <span class="sd">    three_h</span>
+<span class="sd">    </span>
 <span class="sd">    three_h_colourbars</span>
+<span class="sd">    </span>
 <span class="sd">    three_square</span>
+<span class="sd">    </span>
 <span class="sd">    three_square_colourbars</span>
+<span class="sd">    </span>
 <span class="sd">    four_square</span>
+<span class="sd">    </span>
 <span class="sd">    four_square_colourbars</span>
 <span class="sd">&quot;&quot;&quot;</span>
 

docs/_modules/tp/axes/small.html

@@ -83,18 +83,31 @@ <h1>Source code for tp.axes.small</h1><div class="highlight"><pre>
 <span class="sd">---------</span>
 
 <span class="sd">    one</span>
+<span class="sd">    </span>
 <span class="sd">    one_colourbar</span>
+<span class="sd">    </span>
 <span class="sd">    one_dos</span>
+<span class="sd">    </span>
 <span class="sd">    one_dos_colourbar</span>
+<span class="sd">    </span>
 <span class="sd">    two_h</span>
+<span class="sd">    </span>
 <span class="sd">    two_h_colourbars</span>
+<span class="sd">    </span>
 <span class="sd">    two_v</span>
+<span class="sd">    </span>
 <span class="sd">    two_v_colourbars</span>
+<span class="sd">    </span>
 <span class="sd">    three_h</span>
+<span class="sd">    </span>
 <span class="sd">    three_h_colourbars</span>
+<span class="sd">    </span>
 <span class="sd">    three_square</span>
+<span class="sd">    </span>
 <span class="sd">    three_square_colourbars</span>
+<span class="sd">    </span>
 <span class="sd">    four_square</span>
+<span class="sd">    </span>
 <span class="sd">    four_square_colourbars</span>
 <span class="sd">&quot;&quot;&quot;</span>
 

docs/_modules/tp/calculate.html

@@ -507,7 +507,7 @@ <h1>Source code for tp.calculate</h1><div class="highlight"><pre>
         <span class="n">zt</span> <span class="o">=</span> <span class="n">to_tp</span><span class="p">(</span><span class="s1">&#39;zt&#39;</span><span class="p">,</span> <span class="n">zt</span><span class="p">)</span>
         <span class="n">temperature</span> <span class="o">=</span> <span class="n">to_tp</span><span class="p">(</span><span class="s1">&#39;temperature&#39;</span><span class="p">,</span> <span class="n">temperature</span><span class="p">)</span>
 
-    <span class="n">mid</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">divide</span><span class="p">(</span><span class="n">pf</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">temperature</span><span class="p">)[:,</span> <span class="kc">None</span><span class="p">],</span> <span class="n">zt</span><span class="p">)</span>
+    <span class="n">mid</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">apply_along_axis</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">multiply</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">pf</span><span class="p">,</span> <span class="n">temperature</span><span class="p">)</span> <span class="o">/</span> <span class="n">zt</span>
     <span class="n">kl</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">subtract</span><span class="p">(</span><span class="n">mid</span><span class="p">,</span> <span class="n">electronic_thermal_conductivity</span><span class="p">)</span>
 
     <span class="k">if</span> <span class="n">use_tprc</span><span class="p">:</span>
@@ -633,7 +633,8 @@ <h1>Source code for tp.calculate</h1><div class="highlight"><pre>
                  <span class="n">data</span><span class="p">[</span><span class="s1">&#39;electronic_thermal_conductivity&#39;</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;zt&#39;</span><span class="p">],</span>
                  <span class="n">data</span><span class="p">[</span><span class="s1">&#39;temperature&#39;</span><span class="p">],</span> <span class="n">use_tprc</span><span class="o">=</span><span class="n">use_tprc</span><span class="p">)</span>
     <span class="n">data</span><span class="p">[</span><span class="s1">&#39;meta&#39;</span><span class="p">][</span><span class="s1">&#39;units&#39;</span><span class="p">][</span><span class="n">q</span><span class="p">]</span> <span class="o">=</span> <span class="n">tp</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">units</span><span class="p">(</span><span class="n">use_tprc</span><span class="o">=</span><span class="n">use_tprc</span><span class="p">)[</span><span class="n">q</span><span class="p">]</span>
-    <span class="n">data</span><span class="p">[</span><span class="s1">&#39;meta&#39;</span><span class="p">][</span><span class="s1">&#39;dimensions&#39;</span><span class="p">][</span><span class="n">q</span><span class="p">]</span> <span class="o">=</span> <span class="n">tp</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">dimensions</span><span class="p">()[</span><span class="n">q</span><span class="p">]</span>
+    <span class="n">data</span><span class="p">[</span><span class="s1">&#39;meta&#39;</span><span class="p">][</span><span class="s1">&#39;dimensions&#39;</span><span class="p">][</span><span class="n">q</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;meta&#39;</span><span class="p">][</span><span class="s1">&#39;dimensions&#39;</span><span class="p">][</span><span class="s1">&#39;seebeck&#39;</span><span class="p">]</span>
+
 
     <span class="k">return</span> <span class="n">data</span></div>
 
@@ -733,7 +734,8 @@ <h1>Source code for tp.calculate</h1><div class="highlight"><pre>
         <span class="n">data1</span><span class="p">,</span> <span class="n">data2</span> <span class="o">=</span> <span class="n">data2</span><span class="p">,</span> <span class="n">data1</span>
         <span class="n">keys1</span><span class="p">,</span> <span class="n">keys2</span> <span class="o">=</span> <span class="n">keys2</span><span class="p">,</span> <span class="n">keys1</span>
         <span class="n">axis1</span><span class="p">,</span> <span class="n">axis2</span> <span class="o">=</span> <span class="n">axis2</span><span class="p">,</span> <span class="n">axis1</span>
-    <span class="n">index</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">((</span><span class="n">data1</span><span class="p">[</span><span class="n">dependent</span><span class="p">]</span><span class="o">&gt;=</span><span class="n">data2</span><span class="p">[</span><span class="n">dependent</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">data1</span><span class="p">[</span><span class="n">dependent</span><span class="p">]</span><span class="o">&lt;=</span><span class="n">data2</span><span class="p">[</span><span class="n">dependent</span><span class="p">][</span><span class="o">-</span><span class="mi">1</span><span class="p">]))[</span><span class="mi">0</span><span class="p">]</span>
+    <span class="n">index</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">((</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">data1</span><span class="p">[</span><span class="n">dependent</span><span class="p">])</span><span class="o">&gt;=</span><span class="n">data2</span><span class="p">[</span><span class="n">dependent</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span> <span class="o">&amp;</span> \
+                     <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">data1</span><span class="p">[</span><span class="n">dependent</span><span class="p">])</span><span class="o">&lt;=</span><span class="n">data2</span><span class="p">[</span><span class="n">dependent</span><span class="p">][</span><span class="o">-</span><span class="mi">1</span><span class="p">]))[</span><span class="mi">0</span><span class="p">]</span>
 
     <span class="n">data1</span><span class="p">[</span><span class="n">dependent</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">data1</span><span class="p">[</span><span class="n">dependent</span><span class="p">])[</span><span class="n">index</span><span class="p">]</span>
     <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">keys1</span><span class="p">:</span>

docs/_modules/tp/cli/options.html

@@ -79,22 +79,39 @@ <h1>Source code for tp.cli.options</h1><div class="highlight"><pre>
 <span class="sd">---------</span>
 
 <span class="sd">    direction_option</span>
+<span class="sd">    </span>
 <span class="sd">    directions_option</span>
+<span class="sd">    </span>
 <span class="sd">    doping_type_option</span>
+<span class="sd">    </span>
 <span class="sd">    doping_option</span>
+<span class="sd">    </span>
 <span class="sd">    dopings_option</span>
+<span class="sd">    </span>
 <span class="sd">    dos_function</span>
+<span class="sd">    </span>
 <span class="sd">    input_argument</span>
+<span class="sd">    </span>
 <span class="sd">    inputs_function</span>
+<span class="sd">    </span>
 <span class="sd">    interpolate_options</span>
+<span class="sd">    </span>
 <span class="sd">    kpoints_options</span>
+<span class="sd">    </span>
 <span class="sd">    legend_options</span>
+<span class="sd">    </span>
 <span class="sd">    line_options</span>
+<span class="sd">    </span>
 <span class="sd">    fill_options</span>
+<span class="sd">    </span>
 <span class="sd">    plot_io_function</span>
+<span class="sd">    </span>
 <span class="sd">    temperature_option</span>
+<span class="sd">    </span>
 <span class="sd">    verbose_option</span>
+<span class="sd">    </span>
 <span class="sd">    xy_limit_options</span>
+<span class="sd">    </span>
 <span class="sd">    c_limit_options</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
@@ -104,7 +121,7 @@ <h1>Source code for tp.cli.options</h1><div class="highlight"><pre>
     <span class="sd">&quot;&quot;&quot;Option for singular option for anisotropic data.&quot;&quot;&quot;</span>
 
     <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">&#39;-d&#39;</span><span class="p">,</span> <span class="s1">&#39;--direction&#39;</span><span class="p">,</span>
-                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Direction(s) for anisotropic data.&#39;</span><span class="p">,</span>
+                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Direction for anisotropic data.&#39;</span><span class="p">,</span>
                      <span class="nb">type</span><span class="o">=</span><span class="n">click</span><span class="o">.</span><span class="n">Choice</span><span class="p">([</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">,</span> <span class="s1">&#39;c&#39;</span><span class="p">,</span>
                                         <span class="s1">&#39;x&#39;</span><span class="p">,</span> <span class="s1">&#39;y&#39;</span><span class="p">,</span> <span class="s1">&#39;z&#39;</span><span class="p">,</span>
                                         <span class="s1">&#39;average&#39;</span><span class="p">,</span> <span class="s1">&#39;avg&#39;</span><span class="p">,</span>
@@ -176,7 +193,7 @@ <h1>Source code for tp.cli.options</h1><div class="highlight"><pre>
                          <span class="nb">type</span><span class="o">=</span><span class="n">click</span><span class="o">.</span><span class="n">Path</span><span class="p">(</span><span class="n">file_okay</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">dir_okay</span><span class="o">=</span><span class="kc">False</span><span class="p">),</span>
                          <span class="n">default</span><span class="o">=</span><span class="s1">&#39;POSCAR&#39;</span><span class="p">,</span>
                          <span class="n">show_default</span><span class="o">=</span><span class="kc">True</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span>
-        <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">&#39;-a&#39;</span><span class="p">,</span> <span class="s1">&#39;--atoms&#39;</span><span class="p">,</span>
+        <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">&#39;--atoms&#39;</span><span class="p">,</span>
                          <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Atoms in POSCAR order. Repeated names have &#39;</span>
                               <span class="s1">&#39;their contributions summed, or different names &#39;</span>
                               <span class="s1">&#39;can be used to separate environments. E.g. &#39;</span>
@@ -385,16 +402,16 @@ <h1>Source code for tp.cli.options</h1><div class="highlight"><pre>
     <span class="sd">&quot;&quot;&quot;Options for x and y axes limits.&quot;&quot;&quot;</span>
 
     <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">&#39;--xmin&#39;</span><span class="p">,</span>
-                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Override minimum x.&#39;</span><span class="p">,</span>
+                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Override minimum x-axis value.&#39;</span><span class="p">,</span>
                      <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span>
     <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">&#39;--xmax&#39;</span><span class="p">,</span>
-                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Override maximum x.&#39;</span><span class="p">,</span>
+                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Override maximum x-axis value.&#39;</span><span class="p">,</span>
                      <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span>
     <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">&#39;--ymin&#39;</span><span class="p">,</span>
-                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Override minimum y.&#39;</span><span class="p">,</span>
+                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Override minimum y-axis value.&#39;</span><span class="p">,</span>
                      <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span>
     <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">&#39;--ymax&#39;</span><span class="p">,</span>
-                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Override maximum y.&#39;</span><span class="p">,</span>
+                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Override maximum y-axis value.&#39;</span><span class="p">,</span>
                      <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span>
 
     <span class="k">return</span> <span class="n">f</span></div>
@@ -403,10 +420,10 @@ <h1>Source code for tp.cli.options</h1><div class="highlight"><pre>
     <span class="sd">&quot;&quot;&quot;Options for colour axes limits.&quot;&quot;&quot;</span>
 
     <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">&#39;--cmin&#39;</span><span class="p">,</span>
-                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Override minimum colour value.&#39;</span><span class="p">,</span>
+                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Override minimum colour-axis value.&#39;</span><span class="p">,</span>
                      <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span>
     <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">&#39;--cmax&#39;</span><span class="p">,</span>
-                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Override maximum colour value.&#39;</span><span class="p">,</span>
+                     <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Override maximum colour-axis value.&#39;</span><span class="p">,</span>
                      <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span>
 
     <span class="k">return</span> <span class="n">f</span></div>