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‎atomate/__init__.py‎

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__version__ = "0.9.3"
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__version__ = "0.9.4"

‎docs/_sources/changelog.rst.txt‎

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atomate Changelog
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=================
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**v0.9.4**
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* Fixes for new pymatgen (S. Blau, S.P. Ong)
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**v0.9.3**
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* Minor change to enforce storing chgcars, clean up old kwargs in MagneticOrderings workflow (M. Horton)

‎docs/_static/documentation_options.js‎

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var DOCUMENTATION_OPTIONS = {
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URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
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VERSION: '0.9.3',
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VERSION: '0.9.4',
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LANGUAGE: 'None',
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‎docs/atomate.common.firetasks.html‎

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<html xmlns="http://www.w3.org/1999/xhtml">
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<meta charset="utf-8" />
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<title>atomate.common.firetasks package &#8212; atomate 0.9.3 documentation</title>
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<title>atomate.common.firetasks package &#8212; atomate 0.9.4 documentation</title>
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<link rel="stylesheet" href="_static/nature.css" type="text/css" />
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<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
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<li class="right" >
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<a href="py-modindex.html" title="Python Module Index"
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>modules</a> |</li>
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<li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li>
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<li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="atomate.common.firetasks.tests.html">atomate.common.firetasks.tests package</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="atomate.common.firetasks.tests.html#submodules">Submodules</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atomate.common.firetasks.tests.html#module-atomate.common.firetasks.tests.test_glue_tasks">atomate.common.firetasks.tests.test_glue_tasks module</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atomate.common.firetasks.tests.html#atomate-common-firetasks-tests-test-glue-tasks-module">atomate.common.firetasks.tests.test_glue_tasks module</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atomate.common.firetasks.tests.html#module-atomate.common.firetasks.tests.test_parse_outputs">atomate.common.firetasks.tests.test_parse_outputs module</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atomate.common.firetasks.tests.html#module-atomate.common.firetasks.tests">Module contents</a></li>
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<dt>Required params:</dt><dd><p>name (str): descriptive name for this calculation file/dir</p>
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</dd>
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<dt>Optional params:</dt><dd><dl class="simple">
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<dt>filesystem (str or custom user format): name of filesystem. Supports env_chk. </dt><dd><p>defaults to None</p>
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<dt>filesystem (str or custom user format): name of filesystem. Supports env_chk.</dt><dd><p>defaults to None</p>
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</dd>
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<dt>path (str): The path to the directory containing the calculation. defaults to</dt><dd><p>current working directory.</p>
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</dd>
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to designate the stress from the last ionic_step. If the value
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is not a string or does not begin with “&gt;&gt;”, it is passed as is.</p>
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</dd>
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<dt>parse_class (str): string representation of complete path to a class </dt><dd><p>with which to parse the output, e. g. pymatgen.io.vasp.Vasprun
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<dt>parse_class (str): string representation of complete path to a class</dt><dd><p>with which to parse the output, e. g. pymatgen.io.vasp.Vasprun
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or pymatgen.io.feff.LDos.from_file, class must be MSONable</p>
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</dd>
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<dt>parse_kwargs (str): dict of kwargs for the parse class,</dt><dd><p>e. g. {“filename”: “vasprun.xml”, “parse_dos”: False,
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<dt>parse_kwargs (str): dict of kwargs for the parse class,</dt><dd><p>e. g. {“filename”: “vasprun.xml”, “parse_dos”: False,
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<li class="right" >
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<a href="py-modindex.html" title="Python Module Index"
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>modules</a> |</li>
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<li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li>
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<li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li>
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‎docs/atomate.common.firetasks.tests.html‎

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<html xmlns="http://www.w3.org/1999/xhtml">
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<li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li>
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<li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li>
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<div class="section" id="submodules">
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<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline"></a></h2>
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</div>
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<div class="section" id="module-atomate.common.firetasks.tests.test_glue_tasks">
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<span id="atomate-common-firetasks-tests-test-glue-tasks-module"></span><h2>atomate.common.firetasks.tests.test_glue_tasks module<a class="headerlink" href="#module-atomate.common.firetasks.tests.test_glue_tasks" title="Permalink to this headline"></a></h2>
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<dl class="class">
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<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc">
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<em class="property">class </em><code class="sig-prename descclassname">atomate.common.firetasks.tests.test_glue_tasks.</code><code class="sig-name descname">TestCopyFilesFromCalcLoc</code><span class="sig-paren">(</span><em class="sig-param">methodName='runTest'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc" title="Permalink to this definition"></a></dt>
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<dd><p>Bases: <a class="reference internal" href="atomate.utils.html#atomate.utils.testing.AtomateTest" title="atomate.utils.testing.AtomateTest"><code class="xref py py-class docutils literal notranslate"><span class="pre">atomate.utils.testing.AtomateTest</span></code></a></p>
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<dl class="method">
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<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc.setUpClass">
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<em class="property">classmethod </em><code class="sig-name descname">setUpClass</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc.setUpClass" title="Permalink to this definition"></a></dt>
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<dd><p>Hook method for setting up class fixture before running tests in the class.</p>
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<dl class="method">
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<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc.test_copyfilesfromcalcloc">
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<code class="sig-name descname">test_copyfilesfromcalcloc</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc.test_copyfilesfromcalcloc" title="Permalink to this definition"></a></dt>
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<dd></dd></dl>
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<dl class="class">
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<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestCreateFolder">
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<em class="property">class </em><code class="sig-prename descclassname">atomate.common.firetasks.tests.test_glue_tasks.</code><code class="sig-name descname">TestCreateFolder</code><span class="sig-paren">(</span><em class="sig-param">methodName='runTest'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestCreateFolder" title="Permalink to this definition"></a></dt>
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<dd><p>Bases: <a class="reference internal" href="atomate.utils.html#atomate.utils.testing.AtomateTest" title="atomate.utils.testing.AtomateTest"><code class="xref py py-class docutils literal notranslate"><span class="pre">atomate.utils.testing.AtomateTest</span></code></a></p>
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<dl class="method">
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<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestCreateFolder.test_createfolder">
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<code class="sig-name descname">test_createfolder</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestCreateFolder.test_createfolder" title="Permalink to this definition"></a></dt>
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<dd></dd></dl>
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<dl class="class">
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<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestDeleteFiles">
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<em class="property">class </em><code class="sig-prename descclassname">atomate.common.firetasks.tests.test_glue_tasks.</code><code class="sig-name descname">TestDeleteFiles</code><span class="sig-paren">(</span><em class="sig-param">methodName='runTest'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestDeleteFiles" title="Permalink to this definition"></a></dt>
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<dd><p>Bases: <a class="reference internal" href="atomate.utils.html#atomate.utils.testing.AtomateTest" title="atomate.utils.testing.AtomateTest"><code class="xref py py-class docutils literal notranslate"><span class="pre">atomate.utils.testing.AtomateTest</span></code></a></p>
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<dl class="method">
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<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestDeleteFiles.test_cleanupfiles">
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<code class="sig-name descname">test_cleanupfiles</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestDeleteFiles.test_cleanupfiles" title="Permalink to this definition"></a></dt>
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<dd></dd></dl>
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<dl class="class">
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<em class="property">class </em><code class="sig-prename descclassname">atomate.common.firetasks.tests.test_glue_tasks.</code><code class="sig-name descname">TestPassCalcLocs</code><span class="sig-paren">(</span><em class="sig-param">methodName='runTest'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestPassCalcLocs" title="Permalink to this definition"></a></dt>
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<dd><p>Bases: <a class="reference internal" href="atomate.utils.html#atomate.utils.testing.AtomateTest" title="atomate.utils.testing.AtomateTest"><code class="xref py py-class docutils literal notranslate"><span class="pre">atomate.utils.testing.AtomateTest</span></code></a></p>
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<code class="sig-name descname">test_passcalclocs</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestPassCalcLocs.test_passcalclocs" title="Permalink to this definition"></a></dt>
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<div class="section" id="atomate-common-firetasks-tests-test-glue-tasks-module">
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<h2>atomate.common.firetasks.tests.test_glue_tasks module<a class="headerlink" href="#atomate-common-firetasks-tests-test-glue-tasks-module" title="Permalink to this headline"></a></h2>
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<div class="section" id="module-atomate.common.firetasks.tests.test_parse_outputs">
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<span id="atomate-common-firetasks-tests-test-parse-outputs-module"></span><h2>atomate.common.firetasks.tests.test_parse_outputs module<a class="headerlink" href="#module-atomate.common.firetasks.tests.test_parse_outputs" title="Permalink to this headline"></a></h2>
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<ul>
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<li><a class="reference internal" href="#">atomate.common.firetasks.tests package</a><ul>
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<li><a class="reference internal" href="#submodules">Submodules</a></li>
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<li><a class="reference internal" href="#module-atomate.common.firetasks.tests.test_glue_tasks">atomate.common.firetasks.tests.test_glue_tasks module</a></li>
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<li><a class="reference internal" href="#atomate-common-firetasks-tests-test-glue-tasks-module">atomate.common.firetasks.tests.test_glue_tasks module</a></li>
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<li><a class="reference internal" href="#module-atomate.common.firetasks.tests.test_parse_outputs">atomate.common.firetasks.tests.test_parse_outputs module</a></li>
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<li><a class="reference internal" href="#module-atomate.common.firetasks.tests">Module contents</a></li>
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</ul>
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<li class="right" >
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<a href="py-modindex.html" title="Python Module Index"
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>modules</a> |</li>
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<li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li>
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<li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li>
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‎docs/atomate.common.html‎

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<li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li>
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<li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li>
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<li class="toctree-l2"><a class="reference internal" href="atomate.common.firetasks.html#subpackages">Subpackages</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="atomate.common.firetasks.tests.html">atomate.common.firetasks.tests package</a><ul>
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<li class="toctree-l4"><a class="reference internal" href="atomate.common.firetasks.tests.html#submodules">Submodules</a></li>
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<li class="toctree-l4"><a class="reference internal" href="atomate.common.firetasks.tests.html#module-atomate.common.firetasks.tests.test_glue_tasks">atomate.common.firetasks.tests.test_glue_tasks module</a></li>
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<li class="toctree-l4"><a class="reference internal" href="atomate.common.firetasks.tests.html#atomate-common-firetasks-tests-test-glue-tasks-module">atomate.common.firetasks.tests.test_glue_tasks module</a></li>
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<li class="toctree-l4"><a class="reference internal" href="atomate.common.firetasks.tests.html#module-atomate.common.firetasks.tests.test_parse_outputs">atomate.common.firetasks.tests.test_parse_outputs module</a></li>
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‎docs/atomate.feff.firetasks.html‎

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<p>This module defines tasks to run FEFF.</p>
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<p>This module defines tasks for writing FEFF input sets.</p>
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<em class="property">class </em><code class="sig-prename descclassname">atomate.feff.firetasks.write_inputs.</code><code class="sig-name descname">WriteEXAFSPaths</code><span class="sig-paren">(</span><em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.feff.firetasks.write_inputs.WriteEXAFSPaths" title="Permalink to this definition"></a></dt>
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<a href="py-modindex.html" title="Python Module Index"
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<li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li>
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