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Rare installation fix and minor docs updates #93

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Mar 21, 2024
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Rare installation fix and minor docs updates #93

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a485603
Merge pull request #92 from SMTG-Bham/master
kbspooner Mar 20, 2024
f7f199b
fix rare installation bug and docs updates
Mar 21, 2024
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2 changes: 1 addition & 1 deletion README.rst
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Expand Up @@ -13,7 +13,7 @@
| | |___ ___ |___ |_____ ___ :|___/ ___ |___ ___ ___ |___ \
| | | | / \ | \ | | | / \:| / | | \ / / \ | \/
| | | | |___/ | | | | | |:| | | | \___ |___/ | \_____
| | | | \___ | | | | \___/:| \___|_ | \ \___ | :3.1.2\
| | | | \___ | | | | \___/:| \___|_ | \ \___ | :3.1.3\
|____________________________________:_______________________/____________:_____/


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2 changes: 1 addition & 1 deletion docs/gallery.html
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Expand Up @@ -129,7 +129,7 @@ <h2>Note:<a class="headerlink" href="#note" title="Permalink to this headline">
<code class="docutils literal notranslate"><span class="pre">ztmap</span></code> heatmap (the power factor <code class="docutils literal notranslate"><span class="pre">pfmap</span></code> is also available):</p>
<a class="reference external image-reference" href="https://smtg-bham.github.io/ThermoParser/heatmaps.html"><img alt="A heatmap of ZT against carrier concentration and temperature" src="_images/ztmap1.png" /></a>
<p>Click on the plot to see the script, or one could use</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="sb">`</span>tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c <span class="s1">&#39;#800080&#39;</span> -d x
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="sb">`</span>tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c <span class="s1">&#39;#800080&#39;</span> -d x --discrete
</pre></div>
</div>
<p>A related plot we hope people find useful for screening materials to
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10 changes: 6 additions & 4 deletions docs/heatmaps.html
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Expand Up @@ -89,7 +89,7 @@ <h1>Heatmaps<a class="headerlink" href="#heatmaps" title="Permalink to this head
<img alt="ZT against carrier concentration and temperature." src="_images/ztmap1.png" />
<p>This shows the classic ZT against carrier concentration and temperature
heatmap. This can be plotted at the command line with:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="sb">`</span>tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c <span class="s1">&#39;#800080&#39;</span> -d x
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="sb">`</span>tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c <span class="s1">&#39;#800080&#39;</span> -d x --discrete
</pre></div>
</div>
<p>and in python with:</p>
Expand Down Expand Up @@ -118,7 +118,8 @@ <h1>Heatmaps<a class="headerlink" href="#heatmaps" title="Permalink to this head
23
24
25
26</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="ch">#!/usr/bin/env python3</span>
26
27</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="ch">#!/usr/bin/env python3</span>

<span class="kn">from</span> <span class="nn">os</span> <span class="kn">import</span> <span class="n">path</span>
<span class="kn">import</span> <span class="nn">tp</span>
Expand All @@ -139,8 +140,9 @@ <h1>Heatmaps<a class="headerlink" href="#heatmaps" title="Permalink to this head
<span class="n">kdata</span> <span class="o">=</span> <span class="n">tp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">load</span><span class="o">.</span><span class="n">phono3py</span><span class="p">(</span><span class="n">kfile</span><span class="p">)</span>

<span class="c1"># Add</span>
<span class="hll"><span class="n">tp</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">heatmap</span><span class="o">.</span><span class="n">add_ztmap</span><span class="p">(</span><span class="n">ax</span><span class="p">,</span> <span class="n">adata</span><span class="p">,</span> <span class="n">kdata</span><span class="p">,</span> <span class="n">direction</span><span class="o">=</span><span class="n">direction</span><span class="p">,</span> <span class="n">colour</span><span class="o">=</span><span class="n">colour</span><span class="p">)</span>
</span>
<span class="hll"><span class="n">tp</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">heatmap</span><span class="o">.</span><span class="n">add_ztmap</span><span class="p">(</span><span class="n">ax</span><span class="p">,</span> <span class="n">adata</span><span class="p">,</span> <span class="n">kdata</span><span class="p">,</span> <span class="n">direction</span><span class="o">=</span><span class="n">direction</span><span class="p">,</span> <span class="n">colour</span><span class="o">=</span><span class="n">colour</span><span class="p">,</span>
</span> <span class="n">discrete</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>

<span class="c1"># Save</span>
<span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s1">&#39;ztmap.pdf&#39;</span><span class="p">)</span>
<span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s1">&#39;ztmap.png&#39;</span><span class="p">)</span>
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6 changes: 3 additions & 3 deletions docs/index.html
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Expand Up @@ -76,7 +76,7 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">

<a class="reference external image-reference" href="https://smtg-bham.github.io/ThermoParser/"><img alt="The ThermoParser logo, which looks like &quot;TP&quot;" class="align-center" src="figures/tp-logo-header.png" /></a>
<a class="reference external image-reference" href="https://smtg-bham.github.io/ThermoParser/"><img alt="The ThermoParser logo, which looks like &quot;TP&quot;" class="align-center" src="_images/tp-logo-header.png" /></a>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span> <span class="n">________</span>
<span class="o">/////</span> \\\\
\<span class="n">________</span><span class="o">/</span><span class="n">________________________________________________________________</span>
Expand All @@ -85,7 +85,7 @@
<span class="o">|</span> <span class="o">|</span> <span class="o">|</span><span class="n">___</span> <span class="n">___</span> <span class="o">|</span><span class="n">___</span> <span class="o">|</span><span class="n">_____</span> <span class="n">___</span> <span class="p">:</span><span class="o">|</span><span class="n">___</span><span class="o">/</span> <span class="n">___</span> <span class="o">|</span><span class="n">___</span> <span class="n">___</span> <span class="n">___</span> <span class="o">|</span><span class="n">___</span> \
<span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">/</span> \ <span class="o">|</span> \ <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">/</span> \<span class="p">:</span><span class="o">|</span> <span class="o">/</span> <span class="o">|</span> <span class="o">|</span> \ <span class="o">/</span> <span class="o">/</span> \ <span class="o">|</span> \<span class="o">/</span>
<span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span><span class="n">___</span><span class="o">/</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span><span class="p">:</span><span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> \<span class="n">___</span> <span class="o">|</span><span class="n">___</span><span class="o">/</span> <span class="o">|</span> \<span class="n">_____</span>
<span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> \<span class="n">___</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> \<span class="n">___</span><span class="o">/</span><span class="p">:</span><span class="o">|</span> \<span class="n">___</span><span class="o">|</span><span class="n">_</span> <span class="o">|</span> \ \<span class="n">___</span> <span class="o">|</span> <span class="p">:</span><span class="mf">3.1</span><span class="o">.</span><span class="mi">2</span>\
<span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> \<span class="n">___</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> \<span class="n">___</span><span class="o">/</span><span class="p">:</span><span class="o">|</span> \<span class="n">___</span><span class="o">|</span><span class="n">_</span> <span class="o">|</span> \ \<span class="n">___</span> <span class="o">|</span> <span class="p">:</span><span class="mf">3.1</span><span class="o">.</span><span class="mi">3</span>\
<span class="o">|</span><span class="n">____________________________________</span><span class="p">:</span><span class="n">_______________________</span><span class="o">/</span><span class="n">____________</span><span class="p">:</span><span class="n">_____</span><span class="o">/</span>
</pre></div>
</div>
Expand All @@ -102,7 +102,7 @@
also contains a suite of command-line tools which can retrieve specific
data, save derived properties and plot graphs in a single command.</p>
<p>Click on the image to go to the <a class="reference external" href="https://smtg-bham.github.io/ThermoParser/gallery.html">gallery</a>!</p>
<a class="reference external image-reference" href="https://smtg-bham.github.io/ThermoParser/gallery.html"><img alt="A phonon dispersion where widened bands show phonon scattering" src="figures/wideband.png" /></a>
<a class="reference external image-reference" href="https://smtg-bham.github.io/ThermoParser/gallery.html"><img alt="A phonon dispersion where widened bands show phonon scattering" src="_images/wideband.png" /></a>
<div class="section" id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
<p>ThermoParser can easily be installed with git and pip:</p>
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3 changes: 2 additions & 1 deletion examples/heatmaps/plot-zt.py
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Expand Up @@ -19,7 +19,8 @@
kdata = tp.data.load.phono3py(kfile)

# Add
tp.plot.heatmap.add_ztmap(ax, adata, kdata, direction=direction, colour=colour)
tp.plot.heatmap.add_ztmap(ax, adata, kdata, direction=direction, colour=colour,
discrete=True)

# Save
fig.savefig('ztmap.pdf')
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2 changes: 1 addition & 1 deletion examples/heatmaps/plot-zt.sh
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@@ -1 +1 @@
`tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c '#800080' -d x
`tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c '#800080' -d x --discrete
4 changes: 3 additions & 1 deletion requirements.txt
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Expand Up @@ -4,4 +4,6 @@ matplotlib
numpy >=1.14.3
pymatgen >=2020.1.28
pyyaml
scipy
scipy
setuptools
wheel
6 changes: 3 additions & 3 deletions setup.py
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Expand Up @@ -3,10 +3,10 @@
__name__ = 'ThermoParser'
__author__ = 'Kieran B. Spooner'
__copyright__ = 'Copyright Scanlon Materials Theory Group (2024)'
__version__ = '3.1.2'
__version__ = '3.1.3'
__maintainer__ = 'Kieran B. Spooner'
__email__ = 'k.b.spooner@bham.ac.uk'
__date__ = 'March 5th 2024'
__date__ = 'March 21st 2024'

import os
import setuptools
Expand Down Expand Up @@ -61,7 +61,7 @@ def __init__(self, *args, **kwargs):
'amset boltztrap tp te matplotlib vasp transport',
test_suite='setup.load_test_suite',
install_requires=['click', 'h5py', 'matplotlib', 'numpy', 'pymatgen',
'pyyaml', 'scipy'],
'pyyaml', 'scipy', 'setuptools', 'wheel'],
extras_require={'docs': ['sphinx', 'sphinx_rtd_theme'],
'tests': ['unitest']},
python_requires='>=3.6',
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