Merge pull request #90 from SMTG-Bham/bug-fix

Bug fix

README.rst

@@ -162,7 +162,9 @@ while contributions can be made using the `fork and pull`_ approach.
 Contributions should include comprehensive docstrings, and where
 appropriate `examples`_, further `documentation`_ and `tests`_ are greatly
 appreciated. Documentation uses the `sphinx`_ package, and can be built from
-the ``docs`` directory with ``sphinx-build -b html src/ .``.
+the ``docs`` directory with ``sphinx-build -b html src/ .``. In order to build
+the docs, download the extra dependencies with, e.g., ``pip install .[docs]``
+from the ThermoParser directory.
 
 .. _issue tracker: https://github.com/smtg-bham/ThermoParser/issues
 .. _fork and pull: https://guides.github.com/activities/forking
@@ -173,7 +175,9 @@ Testing
 -------
 
 Tests use the `unittest`_ package, and can be run from the test directory
-with ``python3 -m unittest``.
+with ``python3 -m unittest``. If you don't already have unittest installed, it
+can be directly with ``pip install unitest`` or, e.g., ``pip install .[tests]``
+from the ThermoParser directory.
 
 .. _unittest: https://docs.python.org/3/library/unittest.html
 

docs/_sources/gallery.rst.txt

@@ -54,9 +54,8 @@ from either a python script or the command line, such as the classic
 
 Click on the plot to see the script, or one could use
 
-.. code-block:: bash
-
-   tp plot ztmap boltztrap.hdf5 -k kappa-m<xxx>.hdf5 -c '#800080' -d x
+.. literalinclude:: ../../examples/heatmaps/plot-zt.sh
+   :language: bash
 
 A related plot we hope people find useful for screening materials to
 run three+ phonon calculations on is the ``kappa-target`` plot, which
@@ -67,9 +66,8 @@ ZT, in this case 2.
    :alt: A heatmap of target lattice thermal conductivity against carrier concentration and temperature
    :target: https://smtg-bham.github.io/ThermoParser/heatmaps.html
 
-.. code-block:: bash
-
-   tp plot kappa-target boltztrap.hdf5 -c '#008080' -d x
+.. literalinclude:: ../../examples/heatmaps/plot-kappa-target.sh
+   :language: bash
 
 Or on the analytical end of the process, ``zdiff`` and ``pfdiff`` allow
 comparison among different datasets.
@@ -78,9 +76,8 @@ comparison among different datasets.
    :alt: A heatmap of differentce in ZT against carrier concentration and temperature
    :target: https://smtg-bham.github.io/ThermoParser/heatmaps.html
 
-.. code-block:: bash
-
-   tp plot ztdiff <x>/boltztrap.hdf5 <y>/boltztrap.hdf5 -k <x>/kappa-m<xxx>.hdf5 <y>/kappa-m<yyy>.hdf5 -l <x> <y>
+.. literalinclude:: ../../examples/heatmaps/plot-ztdiff.sh
+   :language: bash
 
 Slightly more complex plots also with command line scripts are the
 phonon dispersions, which can be overlayed and plotted with DoSs.
@@ -89,17 +86,15 @@ phonon dispersions, which can be overlayed and plotted with DoSs.
    :alt: A plot converging phonon dispersions against supercell size
    :target: https://smtg-bham.github.io/ThermoParser/phonons.html
 
-.. code-block:: bash
-
-   tp plot phonons <list of band.yamls> -l <list of labels> -t 'Supercell\ Size'
+.. literalinclude:: ../../examples/phonons/plot-multiphon.sh
+   :language: bash
 
 .. image:: figures/phonons.png
    :alt: A phonon dispersion and DoS
    :target: https://smtg-bham.github.io/ThermoParser/phonons.html
 
-.. code-block:: bash
-
-   tp plot phonons band.yaml -c '#ff8000' -d projected_dos.dat --doscolour '#ffff00' '#00ffff'
+.. literalinclude:: ../../examples/phonons/plot-phonons.sh
+   :language: bash
 
 This is where some of the more useful functions of ``ThermoParser``
 come in, e.g. the rescaling of the x axis in the former plot, and the
@@ -111,11 +106,15 @@ e.g. Phonopy or maintain multiple data files.
    :alt: A DoS plot without and with gaussian smearing (sigma=0.2)
    :target: https://smtg-bham.github.io/ThermoParser/dos.html
 
-The right-hand plot can be plotted with:
+The left-hand plot can be plotted with:
+
+.. literalinclude:: ../../examples/dos/plot-dos-total.sh
+   :language: bash
 
-.. code-block:: bash
+And the right-hand plot can be plotted with:
 
-   tp plot dos projected_dos.dat --atoms "Ba Sn O O_2 2" --sigma 0.2 --location 1 -c magenta -c cyan -c red -c orange
+.. literalinclude:: ../../examples/dos/plot-dos-smeared.sh
+   :language: bash
 
 There are command-line scripts, but the main functionality is
 intended as a python package, which enables much more customisable
@@ -141,9 +140,8 @@ latter shows the same data, but in a more quantitative way.
    :alt: A phonon dispersion where widened bands show phonon scattering
    :target: https://smtg-bham.github.io/ThermoParser/prophon.html
 
-.. code-block:: bash
-
-   tp plot wideband band.yaml kappa-m<xxx>.hdf5 -c '#000000' '#ff0000' -s dark_background
+.. literalinclude:: ../../examples/projected-phonons/plot-wideband.sh
+   :language: bash
 
 .. image:: figures/prophon.png
    :alt: A phonon dispersion where dark colours show phonn scattering
@@ -157,13 +155,12 @@ because thats long... many of these outlined in the `tutorials`_, and some are
 demonstrated in this line plot, which is not available as a python command,
 but is easily scripted or plotted at the command line:
 
-.. image:: avg-rates.png
+.. image:: ../../examples/avg-rates/avg-rates.png
    :alt: A plot of weighted average scattering rates against temperature and carrier concnetration.
    :target: https://smtg-bham.github.io/ThermoParser/avg-rates.html
 
-.. code-block::
-
-   tp plot avg-rates ../data/basno3/mesh_75x75x75.h5 -t 1000 -n -1e19 --location 2 --large -c red -c blue -c magenta
+.. literalinclude:: ../../examples/avg-rates/plot-avg-rates.sh
+   :language: bash
 
 It shows the k-point and Fermi-Dirac weighted scattering rates against
 temperature and carrier concentration, to give an accurate picture of their

docs/avg-rates.html

@@ -86,13 +86,13 @@
 
   <div class="section" id="average-rates">
 <h1>Average Rates<a class="headerlink" href="#average-rates" title="Permalink to this headline">¶</a></h1>
-<img alt="A plot of weighted average scattering rates against temperature and carrier concnetration." src="_images/avg-rates.png" />
+<img alt="A plot of weighted average scattering rates against temperature and carrier concnetration." src="_images/avg-rates1.png" />
 <p>This shows the average scattering rates against temperature, averaged
 across k-points and weighted by the derivative of the Fermi-Dirac
 distribution, as they are when calculating the conductivity, thereby
 giving a representative image of the effect the scattering processes
 play in the material. This can be plotted at the command line with:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">tp</span> <span class="n">plot</span> <span class="n">avg</span><span class="o">-</span><span class="n">rates</span> <span class="o">../</span><span class="n">data</span><span class="o">/</span><span class="n">basno3</span><span class="o">/</span><span class="n">mesh_75x75x75</span><span class="o">.</span><span class="n">h5</span> <span class="o">-</span><span class="n">t</span> <span class="mi">1000</span> <span class="o">-</span><span class="n">n</span> <span class="o">-</span><span class="mf">1e19</span> <span class="o">--</span><span class="n">location</span> <span class="mi">2</span> <span class="o">--</span><span class="n">large</span> <span class="o">-</span><span class="n">c</span> <span class="n">red</span> <span class="o">-</span><span class="n">c</span> <span class="n">blue</span> <span class="o">-</span><span class="n">c</span> <span class="n">magenta</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>tp plot avg-rates ../data/basno3/mesh_75x75x75.h5 -t <span class="m">1000</span> -n -1e19 --location <span class="m">2</span> --large -c red -c blue -c magenta
 </pre></div>
 </div>
 <p>If rates are included in the file but are very low, you may want to

docs/cumkappa.html

@@ -97,7 +97,7 @@ <h1>Cumulative Lattice Thermal Conductivity<a class="headerlink" href="#cumulati
 to 100 nanometers may reduce the lattice thermal conductivity by around
 40 %.</p>
 <p>The right plot can be plotted at the command line with:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">tp</span> <span class="n">plot</span> <span class="n">cumkappa</span> <span class="o">../</span><span class="n">data</span><span class="o">/</span><span class="n">zno</span><span class="o">/</span><span class="n">kappa</span><span class="o">-</span><span class="n">m404021</span><span class="o">.</span><span class="n">hdf5</span> <span class="o">--</span><span class="n">mfp</span> <span class="o">--</span><span class="n">percent</span> <span class="o">-</span><span class="n">d</span> <span class="n">x</span> <span class="o">-</span><span class="n">d</span> <span class="n">y</span> <span class="o">-</span><span class="n">c</span> <span class="s1">&#39;#59c605&#39;</span> <span class="o">-</span><span class="n">c</span> <span class="s1">&#39;#ffcf06&#39;</span> <span class="o">--</span><span class="n">nofill</span> <span class="o">--</span><span class="n">xmarkers</span> <span class="mf">1e-7</span> <span class="o">-</span><span class="n">l</span> <span class="n">x</span> <span class="o">-</span><span class="n">l</span> <span class="n">y</span> <span class="o">--</span><span class="n">location</span> <span class="ow">in</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>tp plot cumkappa ../data/zno/kappa-m404021.hdf5 --mfp --percent -d x -d y -c <span class="s1">&#39;#59c605&#39;</span> -c <span class="s1">&#39;#ffcf06&#39;</span> --nofill --xmarkers 1e-7 -l x -l y --location in
 </pre></div>
 </div>
 <p>And while the layering of the DoS plot is not yet supported at the

docs/dos.html

@@ -90,11 +90,11 @@ <h1>Density of States (DoS)<a class="headerlink" href="#density-of-states-dos" t
 <p>This shows a two densities of states (DoSs), which show the density of phonon
 modes at particular frequencies.</p>
 <p>The left plot can be generated by:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">tp</span> <span class="n">plot</span> <span class="n">dos</span> <span class="o">../</span><span class="n">data</span><span class="o">/</span><span class="n">basno3</span><span class="o">/</span><span class="n">projected_dos</span><span class="o">.</span><span class="n">dat</span> <span class="o">--</span><span class="n">total</span> <span class="o">--</span><span class="n">nolegend</span> <span class="o">-</span><span class="n">c</span> <span class="n">pink</span> <span class="o">-</span><span class="n">c</span> <span class="n">cyan</span> <span class="o">-</span><span class="n">c</span> <span class="n">red</span> <span class="o">-</span><span class="n">p</span> <span class="o">../</span><span class="n">data</span><span class="o">/</span><span class="n">basno3</span><span class="o">/</span><span class="n">POSCAR</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>tp plot dos ../data/basno3/projected_dos.dat --total --nolegend -c pink -c cyan -c red -p ../data/basno3/POSCAR
 </pre></div>
 </div>
 <p>And the right plot by:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">tp</span> <span class="n">plot</span> <span class="n">dos</span> <span class="o">../</span><span class="n">data</span><span class="o">/</span><span class="n">basno3</span><span class="o">/</span><span class="n">projected_dos</span><span class="o">.</span><span class="n">dat</span> <span class="o">--</span><span class="n">atoms</span> <span class="s2">&quot;Ba Sn O O_2 2&quot;</span> <span class="o">--</span><span class="n">sigma</span> <span class="mf">0.2</span> <span class="o">--</span><span class="n">location</span> <span class="mi">1</span> <span class="o">-</span><span class="n">c</span> <span class="n">magenta</span> <span class="o">-</span><span class="n">c</span> <span class="n">cyan</span> <span class="o">-</span><span class="n">c</span> <span class="n">red</span> <span class="o">-</span><span class="n">c</span> <span class="n">orange</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>tp plot dos ../data/basno3/projected_dos.dat --atoms <span class="s2">&quot;Ba Sn O O_2 2&quot;</span> --sigma <span class="m">0</span>.2 --location <span class="m">1</span> -c magenta -c cyan -c red -c orange
 </pre></div>
 </div>
 <p>Or the whole thing in python with:</p>