bring up-to-date

README.rst

@@ -13,13 +13,13 @@
     | |   |___   ___  |___  |_____   ___ :|___/  ___   |___   ___   ___  |___ \
     | |   |   | /   \ |   \ |  |  | /   \:|     /   |  |   \ /     /   \ |   \/
     | |   |   | |___/ |     |  |  | |   |:|     |   |  |     \___  |___/ |    \_____
-    | |   |   | \___  |     |  |  | \___/:|     \___|_ |         \ \___  |    :3.0.0\
+    | |   |   | \___  |     |  |  | \___/:|     \___|_ |         \ \___  |    :3.1.2\
     |____________________________________:_______________________/____________:_____/
 
 
-.. image:: https://app.travis-ci.com/SMTG-bham/ThermoParser.svg?branch=master
+.. image:: https://travis-ci.com/smtg-bham/ThermoParser.svg?branch=master
     :alt: The travis-ci badge
-    :target: https://app.travis-ci.com/SMTG-bham/ThermoParser
+    :target: https://travis-ci.com/smtg-bham/ThermoParser
 
 ThermoParser is a toolkit used to simplify the analysis of data
 produced by specialist materials science codes, centred around
@@ -46,7 +46,7 @@ ThermoParser can easily be installed with git and pip:
 
 .. code-block:: bash
 
-    git clone https://github.com/SMTG-bham/ThermoParser.git
+    git clone https://github.com/smtg-bham/ThermoParser.git
     cd ThermoParser
     pip install .
 
@@ -66,7 +66,7 @@ longer process is required:
 2. ``python3 -m pip install cython numpy``
 3. ``brew info hdf5`` to retrieve the path to your hdf5 install
 4. ``HDF5_DIR=YOUR_HDF5_PATH --no-build-isolation h5py``
-5. ``git clone https://github.com/SMTG-bham/ThermoParser.git``
+5. ``git clone https://github.com/smtg-bham/ThermoParser.git``
 6. ``cd ThermoParser``
 7. ``pip install --user -e .``
 

docs/_modules/index.html

@@ -78,7 +78,6 @@ <h1>All modules for which code is available</h1>
 <li><a href="tp/calculate.html">tp.calculate</a></li>
 <li><a href="tp/cli/options.html">tp.cli.options</a></li>
 <li><a href="tp/data/load.html">tp.data.load</a></li>
-<li><a href="tp/data/resolve.html">tp.data.resolve</a></li>
 <li><a href="tp/data/run.html">tp.data.run</a></li>
 <li><a href="tp/data/save.html">tp.data.save</a></li>
 <li><a href="tp/data/utilities.html">tp.data.utilities</a></li>

docs/_modules/tp/calculate.html

@@ -90,6 +90,8 @@ <h1>Source code for tp.calculate</h1><div class="highlight"><pre>
 <span class="sd">        particle lifetime.</span>
 <span class="sd">    mfp:</span>
 <span class="sd">        particle mean free path.</span>
+<span class="sd">    fd_occupation:</span>
+<span class="sd">        fermion occupation.</span>
 <span class="sd">    be_occupation:</span>
 <span class="sd">        boson occupation.</span>
 <span class="sd">    dfdde:</span>
@@ -233,9 +235,7 @@ <h1>Source code for tp.calculate</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">lifetime</span></div>
 
 <div class="viewcode-block" id="mfp"><a class="viewcode-back" href="../../tp.html#tp.calculate.mfp">[docs]</a><span class="k">def</span> <span class="nf">mfp</span><span class="p">(</span><span class="n">gamma</span><span class="p">,</span> <span class="n">group_velocity</span><span class="p">,</span> <span class="n">use_tprc</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    Calculates mean free path from imaginary self-energy (Gamma) and</span>
-<span class="sd">    group velocity.</span>
+    <span class="sd">&quot;&quot;&quot;Calculates mean free path from imaginary self-energy (Gamma) and group velocity.</span>
 
 <span class="sd">    Arguments</span>
 <span class="sd">    ---------</span>
@@ -266,6 +266,47 @@ <h1>Source code for tp.calculate</h1><div class="highlight"><pre>
 
     <span class="k">return</span> <span class="n">mfp</span></div>
 
+<div class="viewcode-block" id="fd_occupation"><a class="viewcode-back" href="../../tp.html#tp.calculate.fd_occupation">[docs]</a><span class="k">def</span> <span class="nf">fd_occupation</span><span class="p">(</span><span class="n">energy</span><span class="p">,</span> <span class="n">temperature</span><span class="p">,</span> <span class="n">fermi_level</span><span class="p">,</span> <span class="n">use_tprc</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;Calculates Fermi-Dirac occupation.</span>
+
+<span class="sd">    Assumes singly-occupied bands: double as necessary.</span>
+
+<span class="sd">    Arguments</span>
+<span class="sd">    ---------</span>
+
+<span class="sd">        energy : array-like or float</span>
+<span class="sd">            energies (by default in eV).</span>
+<span class="sd">        temperature : array-like or float</span>
+<span class="sd">            temperature (by default in K).</span>
+<span class="sd">        fermi_level : array-like or float</span>
+<span class="sd">            fermi level (by default in eV).</span>
+
+<span class="sd">        use_tprc : bool, optional</span>
+<span class="sd">            use custom unit conversions. Default: True.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+
+<span class="sd">        array-like</span>
+<span class="sd">            occupations.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">kb</span> <span class="o">=</span> <span class="n">physical_constants</span><span class="p">[</span><span class="s1">&#39;Boltzmann constant in eV/K&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+
+    <span class="k">if</span> <span class="n">use_tprc</span><span class="p">:</span>
+        <span class="n">energy</span> <span class="o">=</span> <span class="n">to_tp</span><span class="p">(</span><span class="s1">&#39;energy&#39;</span><span class="p">,</span> <span class="n">energy</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">fermi_level</span> <span class="o">=</span> <span class="n">to_tp</span><span class="p">(</span><span class="s1">&#39;fermi_level&#39;</span><span class="p">,</span> <span class="n">fermi_level</span><span class="p">)</span>
+
+    <span class="n">occupation</span> <span class="o">=</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">divide</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">add</span><span class="o">.</span><span class="n">outer</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">fermi_level</span><span class="p">),</span>
+                                                <span class="n">energy</span><span class="p">),</span>
+                  <span class="n">kb</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="p">:,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">]))</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">**</span> <span class="o">-</span><span class="mi">1</span>
+
+    <span class="k">if</span> <span class="n">use_tprc</span><span class="p">:</span>
+        <span class="n">occupation</span> <span class="o">=</span> <span class="n">from_tp</span><span class="p">(</span><span class="s1">&#39;occupation&#39;</span><span class="p">,</span> <span class="n">occupation</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">occupation</span></div>
+
 <div class="viewcode-block" id="be_occupation"><a class="viewcode-back" href="../../tp.html#tp.calculate.be_occupation">[docs]</a><span class="k">def</span> <span class="nf">be_occupation</span><span class="p">(</span><span class="n">frequency</span><span class="p">,</span> <span class="n">temperature</span><span class="p">,</span> <span class="n">use_tprc</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Calculates Bose-Einstein occupation.</span>
 
@@ -295,15 +336,15 @@ <h1>Source code for tp.calculate</h1><div class="highlight"><pre>
         <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">frequency</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">frequency</span><span class="p">)</span>
-    <span class="n">occupation</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">expm1</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">divide</span><span class="o">.</span><span class="n">outer</span><span class="p">(</span><span class="n">kb</span> <span class="o">*</span> <span class="n">temperature</span><span class="p">,</span>
+    <span class="n">occupation</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">expm1</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">divide</span><span class="o">.</span><span class="n">outer</span><span class="p">(</span><span class="n">kb</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="n">frequency</span> <span class="o">*</span> <span class="mf">1e12</span> <span class="o">*</span> <span class="n">hbar</span><span class="p">)</span> <span class="o">**</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span> <span class="o">**</span> <span class="o">-</span><span class="mi">1</span>
 
     <span class="k">if</span> <span class="n">use_tprc</span><span class="p">:</span>
         <span class="n">occupation</span> <span class="o">=</span> <span class="n">from_tp</span><span class="p">(</span><span class="s1">&#39;occupation&#39;</span><span class="p">,</span> <span class="n">occupation</span><span class="p">)</span>
 
     <span class="k">return</span> <span class="n">occupation</span></div>
 
-<div class="viewcode-block" id="dfdde"><a class="viewcode-back" href="../../tp.html#tp.calculate.dfdde">[docs]</a><span class="k">def</span> <span class="nf">dfdde</span><span class="p">(</span><span class="n">energy</span><span class="p">,</span> <span class="n">fermi_level</span><span class="p">,</span> <span class="n">temperature</span><span class="p">,</span> <span class="n">doping</span><span class="p">,</span> <span class="n">amset_order</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+<div class="viewcode-block" id="dfdde"><a class="viewcode-back" href="../../tp.html#tp.calculate.dfdde">[docs]</a><span class="k">def</span> <span class="nf">dfdde</span><span class="p">(</span><span class="n">energy</span><span class="p">,</span> <span class="n">fermi_level</span><span class="p">,</span> <span class="n">temperature</span><span class="p">,</span> <span class="n">amset_order</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
           <span class="n">use_tprc</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Derivative of the Fermi-Dirac distribution wrt energy.</span>
 
@@ -316,8 +357,6 @@ <h1>Source code for tp.calculate</h1><div class="highlight"><pre>
 <span class="sd">            fermi level per temperature and dopant (by default in eV).</span>
 <span class="sd">        temperature : array-like</span>
 <span class="sd">            temperatures (by default in K).</span>
-<span class="sd">        doping : array-like</span>
-<span class="sd">            doping concentrations (by default in cm-3).</span>
 
 <span class="sd">        amset_order : bool, optional</span>
 <span class="sd">            doping index before temperature index. Default: False.</span>
@@ -337,7 +376,6 @@ <h1>Source code for tp.calculate</h1><div class="highlight"><pre>
         <span class="n">energy</span> <span class="o">=</span> <span class="n">to_tp</span><span class="p">(</span><span class="s1">&#39;energy&#39;</span><span class="p">,</span> <span class="n">energy</span><span class="p">)</span>
         <span class="n">fermi_level</span> <span class="o">=</span> <span class="n">to_tp</span><span class="p">(</span><span class="s1">&#39;energy&#39;</span><span class="p">,</span> <span class="n">fermi_level</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">doping</span> <span class="o">=</span> <span class="n">to_tp</span><span class="p">(</span><span class="s1">&#39;doping&#39;</span><span class="p">,</span> <span class="n">doping</span><span class="p">)</span>
 
     <span class="n">kbt</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">multiply</span><span class="p">(</span><span class="n">kb</span><span class="p">,</span> <span class="n">temperature</span><span class="p">)</span>
     <span class="n">de</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">subtract</span><span class="o">.</span><span class="n">outer</span><span class="p">(</span><span class="n">fermi_level</span><span class="p">,</span> <span class="n">energy</span><span class="p">)</span>