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shyuep committed Sep 24, 2019
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22 changes: 1 addition & 21 deletions docs/index.html
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Expand Up @@ -191,24 +191,6 @@ <h2>Via conda (recommended)<a class="headerlink" href="#via-conda-recommended" t
</div>
<div class="section" id="via-pip">
<h2>Via pip<a class="headerlink" href="#via-pip" title="Permalink to this headline"></a></h2>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>Preparation</p>
<p>Before installing pymatgen, you may need to first install a few critical
dependencies manually.</p>
<ol class="arabic simple">
<li><p>It is highly recommended that you use Python&gt;=2.7.9 or latest 3.x. In
fact, unless you are very sure you have dependencies that require Python
2, it is highly recommended that you use latest Python 3.x.</p></li>
<li><p>Installation has been tested to be most successful with gcc. Use gcc
where possible and do “export CC=gcc” prior to installation.</p></li>
<li><p>Numpy’s distutils is needed to compile the spglib and pyhull
dependencies. Numpy should be the first thing you install.</p></li>
<li><p>One of the best things you can do is to use conda to manage all this.
The instructions for <a class="reference internal" href="#shared-cluster-installation">Shared cluster installation</a> pretty much
applies to any machine as well.</p></li>
</ol>
</div>
<p>The version at the Python Package Index (PyPI) is always the latest stable
release that is relatively bug-free. The easiest way to install pymatgen on
any system is to use pip:</p>
Expand Down Expand Up @@ -274,9 +256,7 @@ <h2>Shared cluster installation<a class="headerlink" href="#shared-cluster-insta
<p>If you are installing pymatgen on shared computing clusters, e.g., the XSEDE
or NERSC resources in the US, the best way is to use conda to perform a local
install. This guarantees the right version of python and all dependencies:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span># Here, Python 3.6+ is assumed.
# You can change the following to Miniconda2 if you prefer Python 2.7
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b

# Reload bash profile.
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24 changes: 12 additions & 12 deletions docs/pymatgen.io.abinit.nodes.html
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Expand Up @@ -309,7 +309,7 @@ <h3>Navigation</h3>
<p>Nodes are hashable and can be tested for equality</p>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.ALL_STATUS">
<code class="sig-name descname">ALL_STATUS</code><em class="property"> = [&lt;Status: Initialized, at 120768604192&gt;, &lt;Status: Locked, at 120771305216&gt;, &lt;Status: Ready, at 120771302976&gt;, &lt;Status: Submitted, at 120771303776&gt;, &lt;Status: Running, at 120771301776&gt;, &lt;Status: Done, at 120771301616&gt;, &lt;Status: AbiCritical, at 120771304176&gt;, &lt;Status: QCritical, at 120771304256&gt;, &lt;Status: Unconverged, at 120771303456&gt;, &lt;Status: Error, at 120771305376&gt;, &lt;Status: Completed, at 120771304576&gt;]</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.ALL_STATUS" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">ALL_STATUS</code><em class="property"> = [&lt;Status: Initialized, at 120815886576&gt;, &lt;Status: Locked, at 120815889856&gt;, &lt;Status: Ready, at 120815888016&gt;, &lt;Status: Submitted, at 120815889056&gt;, &lt;Status: Running, at 120815888336&gt;, &lt;Status: Done, at 120815888736&gt;, &lt;Status: AbiCritical, at 120815888816&gt;, &lt;Status: QCritical, at 120825309296&gt;, &lt;Status: Unconverged, at 120825308656&gt;, &lt;Status: Error, at 120816615248&gt;, &lt;Status: Completed, at 120816615168&gt;]</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.ALL_STATUS" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
Expand All @@ -326,57 +326,57 @@ <h3>Navigation</h3>

<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.S_ABICRITICAL">
<code class="sig-name descname">S_ABICRITICAL</code><em class="property"> = &lt;Status: AbiCritical, at 120771304176&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_ABICRITICAL" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_ABICRITICAL</code><em class="property"> = &lt;Status: AbiCritical, at 120815888816&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_ABICRITICAL" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.S_DONE">
<code class="sig-name descname">S_DONE</code><em class="property"> = &lt;Status: Done, at 120771301616&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_DONE" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_DONE</code><em class="property"> = &lt;Status: Done, at 120815888736&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_DONE" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.S_ERROR">
<code class="sig-name descname">S_ERROR</code><em class="property"> = &lt;Status: Error, at 120771305376&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_ERROR" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_ERROR</code><em class="property"> = &lt;Status: Error, at 120816615248&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_ERROR" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.S_INIT">
<code class="sig-name descname">S_INIT</code><em class="property"> = &lt;Status: Initialized, at 120768604192&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_INIT" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_INIT</code><em class="property"> = &lt;Status: Initialized, at 120815886576&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_INIT" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.S_LOCKED">
<code class="sig-name descname">S_LOCKED</code><em class="property"> = &lt;Status: Locked, at 120771305216&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_LOCKED" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_LOCKED</code><em class="property"> = &lt;Status: Locked, at 120815889856&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_LOCKED" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.S_OK">
<code class="sig-name descname">S_OK</code><em class="property"> = &lt;Status: Completed, at 120771304576&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_OK" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_OK</code><em class="property"> = &lt;Status: Completed, at 120816615168&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_OK" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.S_QCRITICAL">
<code class="sig-name descname">S_QCRITICAL</code><em class="property"> = &lt;Status: QCritical, at 120771304256&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_QCRITICAL" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_QCRITICAL</code><em class="property"> = &lt;Status: QCritical, at 120825309296&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_QCRITICAL" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.S_READY">
<code class="sig-name descname">S_READY</code><em class="property"> = &lt;Status: Ready, at 120771302976&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_READY" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_READY</code><em class="property"> = &lt;Status: Ready, at 120815888016&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_READY" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.S_RUN">
<code class="sig-name descname">S_RUN</code><em class="property"> = &lt;Status: Running, at 120771301776&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_RUN" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_RUN</code><em class="property"> = &lt;Status: Running, at 120815888336&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_RUN" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.S_SUB">
<code class="sig-name descname">S_SUB</code><em class="property"> = &lt;Status: Submitted, at 120771303776&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_SUB" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_SUB</code><em class="property"> = &lt;Status: Submitted, at 120815889056&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_SUB" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.S_UNCONVERGED">
<code class="sig-name descname">S_UNCONVERGED</code><em class="property"> = &lt;Status: Unconverged, at 120771303456&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_UNCONVERGED" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_UNCONVERGED</code><em class="property"> = &lt;Status: Unconverged, at 120825308656&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_UNCONVERGED" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
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24 changes: 12 additions & 12 deletions docs/pymatgen.io.abinit.qjobs.html
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Expand Up @@ -141,7 +141,7 @@ <h3>Navigation</h3>
</dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.qjobs.PbsProJob.PBSSTAT_TO_SLURM">
<code class="sig-name descname">PBSSTAT_TO_SLURM</code><em class="property"> = {'E': &lt;JobStatus: FAILED, at 120775450448&gt;, 'F': &lt;JobStatus: COMPLETED, at 120775449248&gt;, 'Q': &lt;JobStatus: PENDING, at 120775450704&gt;, 'R': &lt;JobStatus: RUNNING, at 120775447008&gt;, 'S': &lt;JobStatus: SUSPENDED, at 120775449648&gt;}</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.PbsProJob.PBSSTAT_TO_SLURM" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">PBSSTAT_TO_SLURM</code><em class="property"> = {'E': &lt;JobStatus: FAILED, at 120822872496&gt;, 'F': &lt;JobStatus: COMPLETED, at 120822873936&gt;, 'Q': &lt;JobStatus: PENDING, at 120816575424&gt;, 'R': &lt;JobStatus: RUNNING, at 120816576544&gt;, 'S': &lt;JobStatus: SUSPENDED, at 120822873616&gt;}</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.PbsProJob.PBSSTAT_TO_SLURM" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
Expand Down Expand Up @@ -183,57 +183,57 @@ <h3>Navigation</h3>

<dl class="attribute">
<dt id="pymatgen.io.abinit.qjobs.QueueJob.S_CANCELLED">
<code class="sig-name descname">S_CANCELLED</code><em class="property"> = &lt;JobStatus: CANCELLED, at 120775449968&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_CANCELLED" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_CANCELLED</code><em class="property"> = &lt;JobStatus: CANCELLED, at 120822871856&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_CANCELLED" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.qjobs.QueueJob.S_COMPLETED">
<code class="sig-name descname">S_COMPLETED</code><em class="property"> = &lt;JobStatus: COMPLETED, at 120775449248&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_COMPLETED" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_COMPLETED</code><em class="property"> = &lt;JobStatus: COMPLETED, at 120822873936&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_COMPLETED" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.qjobs.QueueJob.S_FAILED">
<code class="sig-name descname">S_FAILED</code><em class="property"> = &lt;JobStatus: FAILED, at 120775450448&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_FAILED" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_FAILED</code><em class="property"> = &lt;JobStatus: FAILED, at 120822872496&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_FAILED" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.qjobs.QueueJob.S_NODEFAIL">
<code class="sig-name descname">S_NODEFAIL</code><em class="property"> = &lt;JobStatus: NODEFAIL, at 120775448688&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_NODEFAIL" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_NODEFAIL</code><em class="property"> = &lt;JobStatus: NODEFAIL, at 120822872016&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_NODEFAIL" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.qjobs.QueueJob.S_PENDING">
<code class="sig-name descname">S_PENDING</code><em class="property"> = &lt;JobStatus: PENDING, at 120775450704&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_PENDING" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_PENDING</code><em class="property"> = &lt;JobStatus: PENDING, at 120816575424&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_PENDING" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.qjobs.QueueJob.S_PREEMPTED">
<code class="sig-name descname">S_PREEMPTED</code><em class="property"> = &lt;JobStatus: PREEMPTED, at 120775450288&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_PREEMPTED" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_PREEMPTED</code><em class="property"> = &lt;JobStatus: PREEMPTED, at 120822870096&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_PREEMPTED" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.qjobs.QueueJob.S_RESIZING">
<code class="sig-name descname">S_RESIZING</code><em class="property"> = &lt;JobStatus: RESIZING, at 120775450528&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_RESIZING" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_RESIZING</code><em class="property"> = &lt;JobStatus: RESIZING, at 120816574944&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_RESIZING" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.qjobs.QueueJob.S_RUNNING">
<code class="sig-name descname">S_RUNNING</code><em class="property"> = &lt;JobStatus: RUNNING, at 120775447008&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_RUNNING" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_RUNNING</code><em class="property"> = &lt;JobStatus: RUNNING, at 120816576544&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_RUNNING" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.qjobs.QueueJob.S_SUSPENDED">
<code class="sig-name descname">S_SUSPENDED</code><em class="property"> = &lt;JobStatus: SUSPENDED, at 120775449648&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_SUSPENDED" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_SUSPENDED</code><em class="property"> = &lt;JobStatus: SUSPENDED, at 120822873616&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_SUSPENDED" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.qjobs.QueueJob.S_TIMEOUT">
<code class="sig-name descname">S_TIMEOUT</code><em class="property"> = &lt;JobStatus: TIMEOUT, at 120775450208&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_TIMEOUT" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_TIMEOUT</code><em class="property"> = &lt;JobStatus: TIMEOUT, at 120822873776&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_TIMEOUT" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="pymatgen.io.abinit.qjobs.QueueJob.S_UNKNOWN">
<code class="sig-name descname">S_UNKNOWN</code><em class="property"> = &lt;JobStatus: UNKNOWN, at 120775452304&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_UNKNOWN" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">S_UNKNOWN</code><em class="property"> = &lt;JobStatus: UNKNOWN, at 120816577104&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_UNKNOWN" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="method">
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2 changes: 1 addition & 1 deletion docs/searchindex.js
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