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<div class="section" id="module-pymatgen.io.abinit.nodes">
<span id="pymatgen-io-abinit-nodes-module"></span><h1>pymatgen.io.abinit.nodes module<a class="headerlink" href="#module-pymatgen.io.abinit.nodes" title="Permalink to this headline">¶</a></h1>
<p>This module defines the Node class that is inherited by Task, Work and Flow objects.</p>
<dl class="class">
<dt id="pymatgen.io.abinit.nodes.Dependency">
<em class="property">class </em><code class="descname">Dependency</code><span class="sig-paren">(</span><em>node</em>, <em>exts=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Dependency"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Dependency" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>This object describes the dependencies among the nodes of a calculation.</p>
<p>A <cite>Dependency</cite> consists of a <cite>Node</cite> that produces a list of products (files)
that are used by the other nodes (<cite>Task</cite> or <cite>Work</cite>) to start the calculation.
One usually creates the object by calling work.register</p>
<p class="rubric">Example</p>
<p># Register the SCF task in work.
scf_task = work.register(scf_strategy)</p>
<p># Register the NSCF calculation and its dependency on the SCF run via deps.
nscf_task = work.register(nscf_strategy, deps={scf_task: “DEN”})</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>node</strong> – The task or the worfklow associated to the dependency or string with a filepath.</p></li>
<li><p><strong>exts</strong> – Extensions of the output files that are needed for running the other tasks.</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Dependency.apply_getters">
<code class="descname">apply_getters</code><span class="sig-paren">(</span><em>task</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Dependency.apply_getters"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Dependency.apply_getters" title="Permalink to this definition">¶</a></dt>
<dd><p>This function is called when we specify the task dependencies with the syntax:</p>
<blockquote>
<div><p>deps={node: “@property”}</p>
</div></blockquote>
<p>In this case the task has to the get <cite>property</cite> from <cite>node</cite> before starting the calculation.</p>
<p>At present, the following properties are supported:</p>
<blockquote>
<div><ul class="simple">
<li><p>@structure</p></li>
</ul>
</div></blockquote>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Dependency.connecting_vars">
<code class="descname">connecting_vars</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Dependency.connecting_vars"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Dependency.connecting_vars" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a dictionary with the variables that must be added to the
input file in order to connect this <a class="reference internal" href="#pymatgen.io.abinit.nodes.Node" title="pymatgen.io.abinit.nodes.Node"><code class="xref py py-class docutils literal notranslate"><span class="pre">Node</span></code></a> to its dependencies.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Dependency.get_filepaths_and_exts">
<code class="descname">get_filepaths_and_exts</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Dependency.get_filepaths_and_exts"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Dependency.get_filepaths_and_exts" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the paths of the output files produced by self and its extensions</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Dependency.info">
<code class="descname">info</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Dependency.info" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Dependency.node">
<code class="descname">node</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Dependency.node" title="Permalink to this definition">¶</a></dt>
<dd><p>The <a class="reference internal" href="#pymatgen.io.abinit.nodes.Node" title="pymatgen.io.abinit.nodes.Node"><code class="xref py py-class docutils literal notranslate"><span class="pre">Node</span></code></a> associated to the dependency.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Dependency.products">
<code class="descname">products</code><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Dependency.products"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Dependency.products" title="Permalink to this definition">¶</a></dt>
<dd><p>List of output files produces by self.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Dependency.status">
<code class="descname">status</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Dependency.status" title="Permalink to this definition">¶</a></dt>
<dd><p>The status of the dependency, i.e. the status of the <a class="reference internal" href="#pymatgen.io.abinit.nodes.Node" title="pymatgen.io.abinit.nodes.Node"><code class="xref py py-class docutils literal notranslate"><span class="pre">Node</span></code></a>.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.nodes.FileNode">
<em class="property">class </em><code class="descname">FileNode</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#FileNode"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.FileNode" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.io.abinit.nodes.Node" title="pymatgen.io.abinit.nodes.Node"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.io.abinit.nodes.Node</span></code></a></p>
<p>A Node that consists of a file. May be not yet existing</p>
<p>Mainly used to connect <code class="xref py py-class docutils literal notranslate"><span class="pre">Task</span></code> objects to external files produced in previous runs.</p>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.FileNode.abiopen">
<code class="descname">abiopen</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#FileNode.abiopen"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.FileNode.abiopen" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.FileNode.add_filechild">
<code class="descname">add_filechild</code><span class="sig-paren">(</span><em>node</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#FileNode.add_filechild"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.FileNode.add_filechild" title="Permalink to this definition">¶</a></dt>
<dd><p>Add a node (usually Task) to the children of this FileNode.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.FileNode.basename">
<code class="descname">basename</code><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#FileNode.basename"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.FileNode.basename" title="Permalink to this definition">¶</a></dt>
<dd><p>Basename of the file.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.FileNode.check_status">
<code class="descname">check_status</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#FileNode.check_status"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.FileNode.check_status" title="Permalink to this definition">¶</a></dt>
<dd><p>Check the status of the <cite>Node</cite>.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.FileNode.color_rgb">
<code class="descname">color_rgb</code><em class="property"> = array([0.4, 0.2, 1. ])</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.FileNode.color_rgb" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.FileNode.filechildren">
<code class="descname">filechildren</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.FileNode.filechildren" title="Permalink to this definition">¶</a></dt>
<dd><p>List with the children (nodes) of this FileNode.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.FileNode.get_results">
<code class="descname">get_results</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#FileNode.get_results"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.FileNode.get_results" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.FileNode.opath_from_ext">
<code class="descname">opath_from_ext</code><span class="sig-paren">(</span><em>ext</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#FileNode.opath_from_ext"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.FileNode.opath_from_ext" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.FileNode.open_gsr">
<code class="descname">open_gsr</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#FileNode.open_gsr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.FileNode.open_gsr" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.FileNode.products">
<code class="descname">products</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.FileNode.products" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.FileNode.status">
<code class="descname">status</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.FileNode.status" title="Permalink to this definition">¶</a></dt>
<dd><p>The status of the <cite>Node</cite>.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.nodes.GarbageCollector">
<em class="property">class </em><code class="descname">GarbageCollector</code><span class="sig-paren">(</span><em>exts</em>, <em>policy</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#GarbageCollector"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.GarbageCollector" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>This object stores information on the</p>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.nodes.GridFsFile">
<em class="property">class </em><code class="descname">GridFsFile</code><span class="sig-paren">(</span><em>path</em>, <em>fs_id=None</em>, <em>mode='b'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#GridFsFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.GridFsFile" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.collections.AttrDict</span></code></p>
<p>Information on a file that will stored in the MongoDb gridfs collection.</p>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord">
<em class="property">class </em><code class="descname">HistoryRecord</code><span class="sig-paren">(</span><em>level</em>, <em>pathname</em>, <em>lineno</em>, <em>msg</em>, <em>args</em>, <em>exc_info</em>, <em>func=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#HistoryRecord"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>A <cite>HistoryRecord</cite> instance represents an entry in the <a class="reference internal" href="#pymatgen.io.abinit.nodes.NodeHistory" title="pymatgen.io.abinit.nodes.NodeHistory"><code class="xref py py-class docutils literal notranslate"><span class="pre">NodeHistory</span></code></a>.</p>
<p><cite>HistoryRecord</cite> instances are created every time something is logged.
They contain all the information pertinent to the event being logged.
The main information passed in is in msg and args, which are combined
using str(msg) % args to create the message field of the record.
The record also includes information such as when the record was created,
the source line where the logging call was made</p>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord.levelno">
<code class="descname">levelno</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord.levelno" title="Permalink to this definition">¶</a></dt>
<dd><p>Numeric logging level for the message (DEBUG, INFO, WARNING, ERROR, CRITICAL)</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord.levelname">
<code class="descname">levelname</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord.levelname" title="Permalink to this definition">¶</a></dt>
<dd><p>Text logging level for the message (“DEBUG”, “INFO”, “WARNING”, “ERROR”, “CRITICAL”)</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord.pathname">
<code class="descname">pathname</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord.pathname" title="Permalink to this definition">¶</a></dt>
<dd><p>Full pathname of the source file where the logging call was issued (if available)</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord.filename">
<code class="descname">filename</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord.filename" title="Permalink to this definition">¶</a></dt>
<dd><p>Filename portion of pathname</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord.module">
<code class="descname">module</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord.module" title="Permalink to this definition">¶</a></dt>
<dd><p>Module (name portion of filename)</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord.lineno">
<code class="descname">lineno</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord.lineno" title="Permalink to this definition">¶</a></dt>
<dd><p>Source line number where the logging call was issued (if available)</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord.func_name">
<code class="descname">func_name</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord.func_name" title="Permalink to this definition">¶</a></dt>
<dd><p>Function name</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord.created">
<code class="descname">created</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord.created" title="Permalink to this definition">¶</a></dt>
<dd><p>Time when the HistoryRecord was created (time.time() return value)</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord.asctime">
<code class="descname">asctime</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord.asctime" title="Permalink to this definition">¶</a></dt>
<dd><p>Textual time when the HistoryRecord was created</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord.message">
<code class="descname">message</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord.message" title="Permalink to this definition">¶</a></dt>
<dt>
<code class="descname">The result of record.getMessage(), computed just as the record is emitted</code></dt>
<dd></dd></dl>
<p>Initialize a logging record with interesting information.</p>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord.as_dict">
<code class="descname">as_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#HistoryRecord.as_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord.as_dict" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord.from_dict">
<em class="property">classmethod </em><code class="descname">from_dict</code><span class="sig-paren">(</span><em>d</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#HistoryRecord.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord.from_dict" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.HistoryRecord.get_message">
<code class="descname">get_message</code><span class="sig-paren">(</span><em>metadata=False</em>, <em>asctime=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#HistoryRecord.get_message"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.HistoryRecord.get_message" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the message after merging any user-supplied arguments with the message.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>metadata</strong> – True if function and module name should be added.</p></li>
<li><p><strong>asctime</strong> – True if time string should be added.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.nodes.Node">
<em class="property">class </em><code class="descname">Node</code><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Abstract base class defining the interface that must be
implemented by the nodes of the calculation.</p>
<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="descname">ALL_STATUS</code><em class="property"> = [<Status: Initialized, at 121034905800>, <Status: Locked, at 121035785544>, <Status: Ready, at 121035786504>, <Status: Submitted, at 121031587080>, <Status: Running, at 121045873416>, <Status: Done, at 121045872840>, <Status: AbiCritical, at 121029509192>, <Status: QCritical, at 121029512648>, <Status: Unconverged, at 121029510728>, <Status: Error, at 121029509704>, <Status: Completed, at 121038908232>]</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">
<dt id="pymatgen.io.abinit.nodes.Node.Error">
<code class="descname">Error</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.Error" title="Permalink to this definition">¶</a></dt>
<dd><p>alias of <a class="reference internal" href="#pymatgen.io.abinit.nodes.NodeError" title="pymatgen.io.abinit.nodes.NodeError"><code class="xref py py-class docutils literal notranslate"><span class="pre">NodeError</span></code></a></p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.Results">
<code class="descname">Results</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.Results" title="Permalink to this definition">¶</a></dt>
<dd><p>alias of <a class="reference internal" href="#pymatgen.io.abinit.nodes.NodeResults" title="pymatgen.io.abinit.nodes.NodeResults"><code class="xref py py-class docutils literal notranslate"><span class="pre">NodeResults</span></code></a></p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.S_ABICRITICAL">
<code class="descname">S_ABICRITICAL</code><em class="property"> = <Status: AbiCritical, at 121029509192></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="descname">S_DONE</code><em class="property"> = <Status: Done, at 121045872840></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="descname">S_ERROR</code><em class="property"> = <Status: Error, at 121029509704></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="descname">S_INIT</code><em class="property"> = <Status: Initialized, at 121034905800></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="descname">S_LOCKED</code><em class="property"> = <Status: Locked, at 121035785544></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="descname">S_OK</code><em class="property"> = <Status: Completed, at 121038908232></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="descname">S_QCRITICAL</code><em class="property"> = <Status: QCritical, at 121029512648></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="descname">S_READY</code><em class="property"> = <Status: Ready, at 121035786504></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="descname">S_RUN</code><em class="property"> = <Status: Running, at 121045873416></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="descname">S_SUB</code><em class="property"> = <Status: Submitted, at 121031587080></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="descname">S_UNCONVERGED</code><em class="property"> = <Status: Unconverged, at 121029510728></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">
<dt id="pymatgen.io.abinit.nodes.Node.SpectatorError">
<code class="descname">SpectatorError</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.SpectatorError" title="Permalink to this definition">¶</a></dt>
<dd><p>alias of <a class="reference internal" href="#pymatgen.io.abinit.nodes.SpectatorNodeError" title="pymatgen.io.abinit.nodes.SpectatorNodeError"><code class="xref py py-class docutils literal notranslate"><span class="pre">SpectatorNodeError</span></code></a></p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.add_deps">
<code class="descname">add_deps</code><span class="sig-paren">(</span><em>deps</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.add_deps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.add_deps" title="Permalink to this definition">¶</a></dt>
<dd><p>Add a list of dependencies to the <a class="reference internal" href="#pymatgen.io.abinit.nodes.Node" title="pymatgen.io.abinit.nodes.Node"><code class="xref py py-class docutils literal notranslate"><span class="pre">Node</span></code></a>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>deps</strong> – List of <a class="reference internal" href="#pymatgen.io.abinit.nodes.Dependency" title="pymatgen.io.abinit.nodes.Dependency"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dependency</span></code></a> objects specifying the dependencies of the node.
or dictionary mapping nodes to file extensions e.g. {task: “DEN”}</p>
</dd>
</dl>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.nodes.Node.as_node">
<em class="property">classmethod </em><code class="descname">as_node</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.as_node"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.as_node" title="Permalink to this definition">¶</a></dt>
<dd><p>Convert obj into a Node instance.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>obj if obj is a Node instance,
cast obj to <a class="reference internal" href="#pymatgen.io.abinit.nodes.FileNode" title="pymatgen.io.abinit.nodes.FileNode"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNode</span></code></a> instance of obj is a string.
None if obj is None</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.check_status">
<code class="descname">check_status</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.check_status"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.check_status" title="Permalink to this definition">¶</a></dt>
<dd><p>Check the status of the <cite>Node</cite>.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.color_hex">
<code class="descname">color_hex</code><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.color_hex"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.color_hex" title="Permalink to this definition">¶</a></dt>
<dd><p>//en.wikipedia.org/wiki/Web_colors#Hex_triplet</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>Node color as Hex Triplet https</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.color_rgb">
<code class="descname">color_rgb</code><em class="property"> = array([0.41176471, 0.41176471, 0.41176471])</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.color_rgb" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.corrections">
<code class="descname">corrections</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.corrections" title="Permalink to this definition">¶</a></dt>
<dd><p>List of dictionaries with infornation on the actions performed to solve <cite>AbiCritical</cite> Events.
Each dictionary contains the <cite>AbinitEvent</cite> who triggered the correction and
a human-readable message with the description of the operation performed.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.depends_on">
<code class="descname">depends_on</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.depends_on"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.depends_on" title="Permalink to this definition">¶</a></dt>
<dd><p>True if this node depends on the other node.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.deps">
<code class="descname">deps</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.deps" title="Permalink to this definition">¶</a></dt>
<dd><p>List of <a class="reference internal" href="#pymatgen.io.abinit.nodes.Dependency" title="pymatgen.io.abinit.nodes.Dependency"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dependency</span></code></a> objects defining the dependencies
of this <cite>Node</cite>. Empty list if this <a class="reference internal" href="#pymatgen.io.abinit.nodes.Node" title="pymatgen.io.abinit.nodes.Node"><code class="xref py py-class docutils literal notranslate"><span class="pre">Node</span></code></a> does not have dependencies.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.deps_status">
<code class="descname">deps_status</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.deps_status" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a list with the status of the dependencies.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.event_handlers">
<code class="descname">event_handlers</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.event_handlers" title="Permalink to this definition">¶</a></dt>
<dd><p>The list of handlers registered for this node.
If the node is not a <cite>Flow</cite> and does not have its own list of
<cite>handlers</cite> the handlers registered at the level of the flow are returned.</p>
<p>This trick allows one to registered different handlers at the level of the Task
for testing purposes. By default, we have a common list of handlers for all the nodes in the flow.
This choice facilitates the automatic installation of the handlers when we use callbacks to generate
new Works and Tasks!</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.finalized">
<code class="descname">finalized</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.finalized" title="Permalink to this definition">¶</a></dt>
<dd><p>True if the <cite>Node</cite> has been finalized.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.gc">
<code class="descname">gc</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.gc" title="Permalink to this definition">¶</a></dt>
<dd><p>Garbage collector. None if garbage collection is deactivated.
Use flow.set_garbage_collector to initialize the object.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.get_children">
<code class="descname">get_children</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.get_children"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.get_children" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the list of nodes in the <code class="xref py py-class docutils literal notranslate"><span class="pre">Flow</span></code> that depends on this <a class="reference internal" href="#pymatgen.io.abinit.nodes.Node" title="pymatgen.io.abinit.nodes.Node"><code class="xref py py-class docutils literal notranslate"><span class="pre">Node</span></code></a></p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>This routine assumes the entire flow has been allocated.</p>
</div>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.get_graphviz_dirtree">
<code class="descname">get_graphviz_dirtree</code><span class="sig-paren">(</span><em>engine='automatic'</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.get_graphviz_dirtree"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.get_graphviz_dirtree" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate directory graph in the DOT language. The graph show the files and directories
in the node workdir.</p>
<p>Returns: graphviz.Digraph <<a class="reference external" href="https://graphviz.readthedocs.io/en/stable/api.html#digraph">https://graphviz.readthedocs.io/en/stable/api.html#digraph</a>></p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.get_parents">
<code class="descname">get_parents</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.get_parents"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.get_parents" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the list of nodes in the <code class="xref py py-class docutils literal notranslate"><span class="pre">Flow</span></code> required by this <a class="reference internal" href="#pymatgen.io.abinit.nodes.Node" title="pymatgen.io.abinit.nodes.Node"><code class="xref py py-class docutils literal notranslate"><span class="pre">Node</span></code></a></p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.get_vars_dataframe">
<code class="descname">get_vars_dataframe</code><span class="sig-paren">(</span><em>*varnames</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.get_vars_dataframe"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.get_vars_dataframe" title="Permalink to this definition">¶</a></dt>
<dd><p>Return pandas DataFrame with the value of the variables specified in <cite>varnames</cite>.
Can be used for task/works/flow. It’s recursive!</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.in_spectator_mode">
<code class="descname">in_spectator_mode</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.in_spectator_mode" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.install_event_handlers">
<code class="descname">install_event_handlers</code><span class="sig-paren">(</span><em>categories=None</em>, <em>handlers=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.install_event_handlers"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.install_event_handlers" title="Permalink to this definition">¶</a></dt>
<dd><p>Install the <cite>EventHandlers for this `Node</cite>. If no argument is provided
the default list of handlers is installed.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>categories</strong> – List of categories to install e.g. base + can_change_physics</p></li>
<li><p><strong>handlers</strong> – explicit list of <code class="xref py py-class docutils literal notranslate"><span class="pre">EventHandler</span></code> instances.
This is the most flexible way to install handlers.</p></li>
</ul>
</dd>
</dl>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>categories and handlers are mutually exclusive.</p>
</div>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.is_file">
<code class="descname">is_file</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.is_file" title="Permalink to this definition">¶</a></dt>
<dd><p>True if this node is a file</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.is_flow">
<code class="descname">is_flow</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.is_flow" title="Permalink to this definition">¶</a></dt>
<dd><p>True if this node is a Flow</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.is_task">
<code class="descname">is_task</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.is_task" title="Permalink to this definition">¶</a></dt>
<dd><p>True if this node is a Task</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.is_work">
<code class="descname">is_work</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.is_work" title="Permalink to this definition">¶</a></dt>
<dd><p>True if this node is a Work</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.isinstance">
<code class="descname">isinstance</code><span class="sig-paren">(</span><em>class_or_string</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.isinstance"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.isinstance" title="Permalink to this definition">¶</a></dt>
<dd><p>Check whether the node is a instance of <cite>class_or_string</cite>.
Unlinke the standard isinstance builtin, the method accepts either a class or a string.
In the later case, the string is compared with self.__class__.__name__ (case insensitive).</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.log_correction">
<code class="descname">log_correction</code><span class="sig-paren">(</span><em>event</em>, <em>action</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.log_correction"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.log_correction" title="Permalink to this definition">¶</a></dt>
<dd><p>This method should be called once we have fixed the problem associated to this event.
It adds a new entry in the correction history of the node.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>event</strong> – <code class="xref py py-class docutils literal notranslate"><span class="pre">AbinitEvent</span></code> that triggered the correction.</p></li>
<li><p><strong>action</strong> (<em>str</em>) – Human-readable string with info on the action perfomed to solve the problem.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.name">
<code class="descname">name</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.name" title="Permalink to this definition">¶</a></dt>
<dd><p>The name of the node
(only used for facilitating its identification in the user interface).</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.node_id">
<code class="descname">node_id</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.node_id" title="Permalink to this definition">¶</a></dt>
<dd><p>Node identifier.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.num_corrections">
<code class="descname">num_corrections</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.num_corrections" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.relworkdir">
<code class="descname">relworkdir</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.relworkdir" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a relative version of the workdir</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.remove_deps">
<code class="descname">remove_deps</code><span class="sig-paren">(</span><em>deps</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.remove_deps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.remove_deps" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove a list of dependencies from the <a class="reference internal" href="#pymatgen.io.abinit.nodes.Node" title="pymatgen.io.abinit.nodes.Node"><code class="xref py py-class docutils literal notranslate"><span class="pre">Node</span></code></a>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>deps</strong> – List of <a class="reference internal" href="#pymatgen.io.abinit.nodes.Dependency" title="pymatgen.io.abinit.nodes.Dependency"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dependency</span></code></a> objects specifying the dependencies of the node.</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.send_signal">
<code class="descname">send_signal</code><span class="sig-paren">(</span><em>signal</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.send_signal"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.send_signal" title="Permalink to this definition">¶</a></dt>
<dd><p>Send signal from this node to all connected receivers unless the node is in spectator mode.</p>
<p>signal – (hashable) signal value, see <cite>dispatcher</cite> connect for details</p>
<p>Return a list of tuple pairs [(receiver, response), … ]
or None if the node is in spectator mode.</p>
<p>if any receiver raises an error, the error propagates back
through send, terminating the dispatch loop, so it is quite
possible to not have all receivers called if a raises an error.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.set_gc">
<code class="descname">set_gc</code><span class="sig-paren">(</span><em>gc</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.set_gc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.set_gc" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the garbage collector.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.set_name">
<code class="descname">set_name</code><span class="sig-paren">(</span><em>name</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.set_name"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.set_name" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the name of the Node.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.set_node_id">
<code class="descname">set_node_id</code><span class="sig-paren">(</span><em>node_id</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.set_node_id"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.set_node_id" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the node identifier. Use it carefully!</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.show_event_handlers">
<code class="descname">show_event_handlers</code><span class="sig-paren">(</span><em>stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'></em>, <em>verbose=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.show_event_handlers"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.show_event_handlers" title="Permalink to this definition">¶</a></dt>
<dd><p>Print to <cite>stream</cite> the event handlers installed for this flow.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Node.status">
<code class="descname">status</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.status" title="Permalink to this definition">¶</a></dt>
<dd><p>The status of the <cite>Node</cite>.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Node.str_deps">
<code class="descname">str_deps</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Node.str_deps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.str_deps" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the string representation of the dependencies of the node.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.nodes.NodeCorrections">
<em class="property">class </em><code class="descname">NodeCorrections</code><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeCorrections"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeCorrections" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></p>
<p>Iterable storing the correctios performed by the <code class="xref py py-class docutils literal notranslate"><span class="pre">EventHandler</span></code></p>
</dd></dl>
<dl class="exception">
<dt id="pymatgen.io.abinit.nodes.NodeError">
<em class="property">exception </em><code class="descname">NodeError</code><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeError" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
<p>Base Exception raised by <a class="reference internal" href="#pymatgen.io.abinit.nodes.Node" title="pymatgen.io.abinit.nodes.Node"><code class="xref py py-class docutils literal notranslate"><span class="pre">Node</span></code></a> subclasses</p>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.nodes.NodeHistory">
<em class="property">class </em><code class="descname">NodeHistory</code><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeHistory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeHistory" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">collections.deque</span></code></p>
<p>Logger-like object</p>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.NodeHistory.critical">
<code class="descname">critical</code><span class="sig-paren">(</span><em>msg</em>, <em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeHistory.critical"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeHistory.critical" title="Permalink to this definition">¶</a></dt>
<dd><p>Log ‘msg % args’ with the critical severity level</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.NodeHistory.info">
<code class="descname">info</code><span class="sig-paren">(</span><em>msg</em>, <em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeHistory.info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeHistory.info" title="Permalink to this definition">¶</a></dt>
<dd><p>Log ‘msg % args’ with the info severity level</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.NodeHistory.to_string">
<code class="descname">to_string</code><span class="sig-paren">(</span><em>metadata=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeHistory.to_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeHistory.to_string" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a string with the history. Set metadata to True to have info on function and module.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.NodeHistory.warning">
<code class="descname">warning</code><span class="sig-paren">(</span><em>msg</em>, <em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeHistory.warning"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeHistory.warning" title="Permalink to this definition">¶</a></dt>
<dd><p>Log ‘msg % args’ with the warning severity level</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.nodes.NodeResults">
<em class="property">class </em><code class="descname">NodeResults</code><span class="sig-paren">(</span><em>node</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeResults"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeResults" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.json.MSONable</span></code></p>
<p>Dictionary used to store the most important results produced by a <a class="reference internal" href="#pymatgen.io.abinit.nodes.Node" title="pymatgen.io.abinit.nodes.Node"><code class="xref py py-class docutils literal notranslate"><span class="pre">Node</span></code></a>.</p>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.NodeResults.JSON_SCHEMA">
<code class="descname">JSON_SCHEMA</code><em class="property"> = {'properties': {'exceptions': {'required': True, 'type': 'array'}, 'files': {'required': True, 'type': 'object'}, 'in': {'description': 'dictionary with input parameters', 'required': True, 'type': 'object'}, 'node_class': {'required': True, 'type': 'string'}, 'node_finalized': {'required': True, 'type': 'boolean'}, 'node_history': {'required': True, 'type': 'array'}, 'node_id': {'required': True, 'type': 'integer'}, 'node_name': {'required': True, 'type': 'string'}, 'node_status': {'required': True, 'type': 'string'}, 'out': {'description': 'dictionary with the output results', 'required': True, 'type': 'object'}}, 'type': 'object'}</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeResults.JSON_SCHEMA" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.NodeResults.as_dict">
<code class="descname">as_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeResults.as_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeResults.as_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>A JSON serializable dict representation of an object.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.NodeResults.exceptions">
<code class="descname">exceptions</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeResults.exceptions" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.nodes.NodeResults.from_dict">
<em class="property">classmethod </em><code class="descname">from_dict</code><span class="sig-paren">(</span><em>d</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeResults.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeResults.from_dict" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.nodes.NodeResults.from_node">
<em class="property">classmethod </em><code class="descname">from_node</code><span class="sig-paren">(</span><em>node</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeResults.from_node"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeResults.from_node" title="Permalink to this definition">¶</a></dt>
<dd><p>Initialize an instance of <cite>NodeResults</cite> from a <cite>Node</cite> subclass.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.NodeResults.gridfs_files">
<code class="descname">gridfs_files</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeResults.gridfs_files" title="Permalink to this definition">¶</a></dt>
<dd><p>List with the absolute paths of the files to be put in GridFs.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.NodeResults.json_dump">
<code class="descname">json_dump</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeResults.json_dump"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeResults.json_dump" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.nodes.NodeResults.json_load">
<em class="property">classmethod </em><code class="descname">json_load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeResults.json_load"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeResults.json_load" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.NodeResults.push_exceptions">
<code class="descname">push_exceptions</code><span class="sig-paren">(</span><em>*exceptions</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeResults.push_exceptions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeResults.push_exceptions" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.NodeResults.register_gridfs_files">
<code class="descname">register_gridfs_files</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeResults.register_gridfs_files"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeResults.register_gridfs_files" title="Permalink to this definition">¶</a></dt>
<dd><p>This function registers the files that will be saved in GridFS.
kwargs is a dictionary mapping the key associated to the file (usually the extension)
to the absolute path. By default, files are assumed to be in binary form, for formatted files
one should pass a tuple (“filepath”, “t”).</p>
<p>Example:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">results</span><span class="o">.</span><span class="n">register_gridfs</span><span class="p">(</span><span class="n">GSR</span><span class="o">=</span><span class="s2">"path/to/GSR.nc"</span><span class="p">,</span> <span class="n">text_file</span><span class="o">=</span><span class="p">(</span><span class="s2">"/path/to/txt_file"</span><span class="p">,</span> <span class="s2">"t"</span><span class="p">))</span>
</pre></div>
</div>
<p>The GSR file is a binary file, whereas text_file is a text file.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.NodeResults.update_collection">
<code class="descname">update_collection</code><span class="sig-paren">(</span><em>collection</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeResults.update_collection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeResults.update_collection" title="Permalink to this definition">¶</a></dt>
<dd><p>Update a mongodb collection.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.NodeResults.validate_json_schema">
<code class="descname">validate_json_schema</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#NodeResults.validate_json_schema"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.NodeResults.validate_json_schema" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.nodes.Product">
<em class="property">class </em><code class="descname">Product</code><span class="sig-paren">(</span><em>ext</em>, <em>path</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Product"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Product" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>A product represents an output file produced by ABINIT instance.
This file is needed to start another <cite>Task</cite> or another <cite>Work</cite>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ext</strong> – ABINIT file extension</p></li>
<li><p><strong>path</strong> – (asbolute) filepath</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.io.abinit.nodes.Product.connecting_vars">
<code class="descname">connecting_vars</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Product.connecting_vars"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Product.connecting_vars" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a dictionary with the ABINIT variables that
must be used to make the code use this file.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Product.filepath">
<code class="descname">filepath</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Product.filepath" title="Permalink to this definition">¶</a></dt>
<dd><p>Absolute path of the file.</p>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.nodes.Product.from_file">
<em class="property">classmethod </em><code class="descname">from_file</code><span class="sig-paren">(</span><em>filepath</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Product.from_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Product.from_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Build a <a class="reference internal" href="#pymatgen.io.abinit.nodes.Product" title="pymatgen.io.abinit.nodes.Product"><code class="xref py py-class docutils literal notranslate"><span class="pre">Product</span></code></a> instance from a filepath.</p>
</dd></dl>
</dd></dl>
<dl class="exception">
<dt id="pymatgen.io.abinit.nodes.SpectatorNodeError">
<em class="property">exception </em><code class="descname">SpectatorNodeError</code><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#SpectatorNodeError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.SpectatorNodeError" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.io.abinit.nodes.NodeError" title="pymatgen.io.abinit.nodes.NodeError"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.io.abinit.nodes.NodeError</span></code></a></p>
<p>Exception raised by <a class="reference internal" href="#pymatgen.io.abinit.nodes.Node" title="pymatgen.io.abinit.nodes.Node"><code class="xref py py-class docutils literal notranslate"><span class="pre">Node</span></code></a> methods when the node is in spectator mode
and we are calling a method with side effects.</p>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.nodes.Status">
<em class="property">class </em><code class="descname">Status</code><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Status"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Status" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></p>
<p>This object is an integer representing the status of the <cite>Node</cite>.</p>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.nodes.Status.all_status_strings">
<em class="property">classmethod </em><code class="descname">all_status_strings</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Status.all_status_strings"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Status.all_status_strings" title="Permalink to this definition">¶</a></dt>
<dd><p>List of strings with all possible values status.</p>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.nodes.Status.as_status">
<em class="property">classmethod </em><code class="descname">as_status</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Status.as_status"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Status.as_status" title="Permalink to this definition">¶</a></dt>
<dd><p>Convert obj into Status.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Status.color_opts">
<code class="descname">color_opts</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Status.color_opts" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Status.colored">
<code class="descname">colored</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Status.colored" title="Permalink to this definition">¶</a></dt>
<dd><p>Return colorized text used to print the status if the stream supports it.</p>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.nodes.Status.from_string">
<em class="property">classmethod </em><code class="descname">from_string</code><span class="sig-paren">(</span><em>s</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#Status.from_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.Status.from_string" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a <cite>Status</cite> instance from its string representation.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.nodes.Status.is_critical">
<code class="descname">is_critical</code><a class="headerlink" href="#pymatgen.io.abinit.nodes.Status.is_critical" title="Permalink to this definition">¶</a></dt>
<dd><p>True if status is critical.</p>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.io.abinit.nodes.check_spectator">
<code class="descname">check_spectator</code><span class="sig-paren">(</span><em>node_method</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#check_spectator"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.check_spectator" title="Permalink to this definition">¶</a></dt>
<dd><p>Decorator for <a class="reference internal" href="#pymatgen.io.abinit.nodes.Node" title="pymatgen.io.abinit.nodes.Node"><code class="xref py py-class docutils literal notranslate"><span class="pre">Node</span></code></a> methods. Raise <cite>SpectatorNodeError</cite>.</p>
</dd></dl>
<dl class="function">
<dt id="pymatgen.io.abinit.nodes.get_newnode_id">
<code class="descname">get_newnode_id</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#get_newnode_id"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.get_newnode_id" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a new node identifier used for <code class="xref py py-class docutils literal notranslate"><span class="pre">Task</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">Work</span></code> and <code class="xref py py-class docutils literal notranslate"><span class="pre">Flow</span></code> objects.</p>
</dd></dl>
<dl class="function">
<dt id="pymatgen.io.abinit.nodes.init_counter">
<code class="descname">init_counter</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#init_counter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.init_counter" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="function">
<dt id="pymatgen.io.abinit.nodes.save_lastnode_id">
<code class="descname">save_lastnode_id</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/nodes.html#save_lastnode_id"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.nodes.save_lastnode_id" title="Permalink to this definition">¶</a></dt>
<dd><p>Save the id of the last node created.</p>
</dd></dl>
</div>
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