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marcoesters · Jan 4, 2018 · b809550 · b809550
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diff --git a/docs/index.html b/docs/index.html
@@ -179,7 +179,7 @@ <h2>Via conda (recommended)<a class="headerlink" href="#via-conda-recommended" t
 </pre></div>
 </div>
 <p>Pymatgen is under active development, and new features are added regularly. To
-upgrade pymatgen, use the following command:</p>
+upgrade pymatgen to the latest version, use the following command:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">upgrade</span> <span class="n">pymatgen</span>
 </pre></div>
 </div>

diff --git a/docs/pymatgen.io.abinit.nodes.html b/docs/pymatgen.io.abinit.nodes.html
@@ -297,7 +297,7 @@ <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="descname">ALL_STATUS</code><em class="property"> = [&lt;Status: Initialized, at 4750183816&gt;, &lt;Status: Locked, at 4713725128&gt;, &lt;Status: Ready, at 4686835528&gt;, &lt;Status: Submitted, at 4745525832&gt;, &lt;Status: Running, at 4752425288&gt;, &lt;Status: Done, at 4665926920&gt;, &lt;Status: AbiCritical, at 4686281800&gt;, &lt;Status: QCritical, at 4728965064&gt;, &lt;Status: Unconverged, at 4749064328&gt;, &lt;Status: Error, at 4749063368&gt;, &lt;Status: Completed, at 4749064264&gt;]</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.ALL_STATUS" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ALL_STATUS</code><em class="property"> = [&lt;Status: Initialized, at 4686755400&gt;, &lt;Status: Locked, at 4668696264&gt;, &lt;Status: Ready, at 4662404872&gt;, &lt;Status: Submitted, at 4716938120&gt;, &lt;Status: Running, at 4720948936&gt;, &lt;Status: Done, at 4714124168&gt;, &lt;Status: AbiCritical, at 4659968584&gt;, &lt;Status: QCritical, at 4662552456&gt;, &lt;Status: Unconverged, at 4714437640&gt;, &lt;Status: Error, at 4721657864&gt;, &lt;Status: Completed, at 4675297032&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">
@@ -314,57 +314,57 @@ <h3>Navigation</h3>
 
 <dl class="attribute">
 <dt id="pymatgen.io.abinit.nodes.Node.S_ABICRITICAL">
-<code class="descname">S_ABICRITICAL</code><em class="property"> = &lt;Status: AbiCritical, at 4686281800&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_ABICRITICAL" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_ABICRITICAL</code><em class="property"> = &lt;Status: AbiCritical, at 4659968584&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="descname">S_DONE</code><em class="property"> = &lt;Status: Done, at 4665926920&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_DONE" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_DONE</code><em class="property"> = &lt;Status: Done, at 4714124168&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="descname">S_ERROR</code><em class="property"> = &lt;Status: Error, at 4749063368&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_ERROR" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_ERROR</code><em class="property"> = &lt;Status: Error, at 4721657864&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="descname">S_INIT</code><em class="property"> = &lt;Status: Initialized, at 4750183816&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_INIT" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_INIT</code><em class="property"> = &lt;Status: Initialized, at 4686755400&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="descname">S_LOCKED</code><em class="property"> = &lt;Status: Locked, at 4713725128&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_LOCKED" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_LOCKED</code><em class="property"> = &lt;Status: Locked, at 4668696264&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="descname">S_OK</code><em class="property"> = &lt;Status: Completed, at 4749064264&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_OK" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_OK</code><em class="property"> = &lt;Status: Completed, at 4675297032&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="descname">S_QCRITICAL</code><em class="property"> = &lt;Status: QCritical, at 4728965064&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_QCRITICAL" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_QCRITICAL</code><em class="property"> = &lt;Status: QCritical, at 4662552456&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="descname">S_READY</code><em class="property"> = &lt;Status: Ready, at 4686835528&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_READY" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_READY</code><em class="property"> = &lt;Status: Ready, at 4662404872&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="descname">S_RUN</code><em class="property"> = &lt;Status: Running, at 4752425288&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_RUN" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_RUN</code><em class="property"> = &lt;Status: Running, at 4720948936&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="descname">S_SUB</code><em class="property"> = &lt;Status: Submitted, at 4745525832&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_SUB" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_SUB</code><em class="property"> = &lt;Status: Submitted, at 4716938120&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="descname">S_UNCONVERGED</code><em class="property"> = &lt;Status: Unconverged, at 4749064328&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.nodes.Node.S_UNCONVERGED" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_UNCONVERGED</code><em class="property"> = &lt;Status: Unconverged, at 4714437640&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">

diff --git a/docs/pymatgen.io.abinit.qjobs.html b/docs/pymatgen.io.abinit.qjobs.html
@@ -163,7 +163,7 @@ <h3>Navigation</h3>
 </table>
 <dl class="attribute">
 <dt id="pymatgen.io.abinit.qjobs.PbsProJob.PBSSTAT_TO_SLURM">
-<code class="descname">PBSSTAT_TO_SLURM</code><em class="property"> = defaultdict(&lt;function PbsProJob.&lt;lambda&gt;&gt;, {'E': &lt;JobStatus: FAILED, at 4750628616&gt;, 'F': &lt;JobStatus: COMPLETED, at 4750628744&gt;, 'Q': &lt;JobStatus: PENDING, at 4750627592&gt;, 'R': &lt;JobStatus: RUNNING, at 4750628936&gt;, 'S': &lt;JobStatus: SUSPENDED, at 4750628808&gt;})</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.PbsProJob.PBSSTAT_TO_SLURM" title="Permalink to this definition">¶</a></dt>
+<code class="descname">PBSSTAT_TO_SLURM</code><em class="property"> = defaultdict(&lt;function PbsProJob.&lt;lambda&gt;&gt;, {'E': &lt;JobStatus: FAILED, at 4694316744&gt;, 'F': &lt;JobStatus: COMPLETED, at 4694315720&gt;, 'Q': &lt;JobStatus: PENDING, at 4694317256&gt;, 'R': &lt;JobStatus: RUNNING, at 4694316808&gt;, 'S': &lt;JobStatus: SUSPENDED, at 4694315208&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">
@@ -208,57 +208,57 @@ <h3>Navigation</h3>
 
 <dl class="attribute">
 <dt id="pymatgen.io.abinit.qjobs.QueueJob.S_CANCELLED">
-<code class="descname">S_CANCELLED</code><em class="property"> = &lt;JobStatus: CANCELLED, at 4750628680&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_CANCELLED" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_CANCELLED</code><em class="property"> = &lt;JobStatus: CANCELLED, at 4694316104&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="descname">S_COMPLETED</code><em class="property"> = &lt;JobStatus: COMPLETED, at 4750628744&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_COMPLETED" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_COMPLETED</code><em class="property"> = &lt;JobStatus: COMPLETED, at 4694315720&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="descname">S_FAILED</code><em class="property"> = &lt;JobStatus: FAILED, at 4750628616&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_FAILED" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_FAILED</code><em class="property"> = &lt;JobStatus: FAILED, at 4694316744&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="descname">S_NODEFAIL</code><em class="property"> = &lt;JobStatus: NODEFAIL, at 4750629640&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_NODEFAIL" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_NODEFAIL</code><em class="property"> = &lt;JobStatus: NODEFAIL, at 4694317768&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="descname">S_PENDING</code><em class="property"> = &lt;JobStatus: PENDING, at 4750627592&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_PENDING" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_PENDING</code><em class="property"> = &lt;JobStatus: PENDING, at 4694317256&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="descname">S_PREEMPTED</code><em class="property"> = &lt;JobStatus: PREEMPTED, at 4750629704&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_PREEMPTED" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_PREEMPTED</code><em class="property"> = &lt;JobStatus: PREEMPTED, at 4694317064&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="descname">S_RESIZING</code><em class="property"> = &lt;JobStatus: RESIZING, at 4750628872&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_RESIZING" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_RESIZING</code><em class="property"> = &lt;JobStatus: RESIZING, at 4694316360&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="descname">S_RUNNING</code><em class="property"> = &lt;JobStatus: RUNNING, at 4750628936&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_RUNNING" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_RUNNING</code><em class="property"> = &lt;JobStatus: RUNNING, at 4694316808&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="descname">S_SUSPENDED</code><em class="property"> = &lt;JobStatus: SUSPENDED, at 4750628808&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_SUSPENDED" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_SUSPENDED</code><em class="property"> = &lt;JobStatus: SUSPENDED, at 4694315208&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="descname">S_TIMEOUT</code><em class="property"> = &lt;JobStatus: TIMEOUT, at 4750629768&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_TIMEOUT" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_TIMEOUT</code><em class="property"> = &lt;JobStatus: TIMEOUT, at 4694317000&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="descname">S_UNKNOWN</code><em class="property"> = &lt;JobStatus: UNKNOWN, at 4750627656&gt;</em><a class="headerlink" href="#pymatgen.io.abinit.qjobs.QueueJob.S_UNKNOWN" title="Permalink to this definition">¶</a></dt>
+<code class="descname">S_UNKNOWN</code><em class="property"> = &lt;JobStatus: UNKNOWN, at 4684708360&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">

diff --git a/docs/pymatgen.io.abinit.tasks.html b/docs/pymatgen.io.abinit.tasks.html
@@ -80,7 +80,7 @@ <h3>Navigation</h3>
 </table>
 <dl class="attribute">
 <dt id="pymatgen.io.abinit.tasks.TaskManager.ENTRIES">
-<code class="descname">ENTRIES</code><em class="property"> = {'batch_adapter', 'db_connector', 'qadapters', 'policy'}</em><a class="headerlink" href="#pymatgen.io.abinit.tasks.TaskManager.ENTRIES" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ENTRIES</code><em class="property"> = {'batch_adapter', 'qadapters', 'db_connector', 'policy'}</em><a class="headerlink" href="#pymatgen.io.abinit.tasks.TaskManager.ENTRIES" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="attribute">

diff --git a/docs/pymatgen.io.adf.html b/docs/pymatgen.io.adf.html
@@ -162,7 +162,7 @@ <h3>Navigation</h3>
 
 <dl class="attribute">
 <dt id="pymatgen.io.adf.AdfKey.block_keys">
-<code class="descname">block_keys</code><em class="property"> = {'RELATIVISTIC', 'GEOMETRY', 'UNITS', 'SYMMETRY', 'CHARGE', 'OCCUPATIONS', 'SAVE', 'A1FIT', 'UNRESTRICTED', 'ZLMFIT', 'ANALYTICALFREQ', 'BASIS', 'SCF', 'EXACTDENSITY', 'TOTALENERGY', 'ATOMS', 'INTEGRATION', 'XC', 'TITLE'}</em><a class="headerlink" href="#pymatgen.io.adf.AdfKey.block_keys" title="Permalink to this definition">¶</a></dt>
+<code class="descname">block_keys</code><em class="property"> = {'CHARGE', 'UNITS', 'TITLE', 'SYMMETRY', 'RELATIVISTIC', 'TOTALENERGY', 'ZLMFIT', 'ANALYTICALFREQ', 'XC', 'ATOMS', 'SCF', 'UNRESTRICTED', 'SAVE', 'GEOMETRY', 'INTEGRATION', 'BASIS', 'OCCUPATIONS', 'EXACTDENSITY', 'A1FIT'}</em><a class="headerlink" href="#pymatgen.io.adf.AdfKey.block_keys" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="classmethod">

diff --git a/docs/pymatgen.io.qchem.html b/docs/pymatgen.io.qchem.html
@@ -269,7 +269,7 @@ <h3>Navigation</h3>
 
 <dl class="attribute">
 <dt id="pymatgen.io.qchem.QcTask.optional_keywords_list">
-<code class="descname">optional_keywords_list</code><em class="property"> = {'force_field_params', 'intracule', 'swap_occupied_virtual', 'pcm', 'basis2', 'localized_diabatization', 'efp_params', 'aux_basis', 'opt', 'occupied', 'nbo', 'empirical_dispersion', 'ecp', 'efp_fragments', 'svp', 'xc_functional', 'plots', 'qm_atoms', 'solvent', 'pcm_solvent', 'isotopes', 'velocity', 'alist', 'basis', 'cdft', 'external_charges', 'svpirf', 'multipole_field', 'van_der_waals'}</em><a class="headerlink" href="#pymatgen.io.qchem.QcTask.optional_keywords_list" title="Permalink to this definition">¶</a></dt>
+<code class="descname">optional_keywords_list</code><em class="property"> = {'external_charges', 'solvent', 'empirical_dispersion', 'pcm', 'svpirf', 'ecp', 'alist', 'xc_functional', 'pcm_solvent', 'svp', 'multipole_field', 'aux_basis', 'occupied', 'qm_atoms', 'efp_params', 'nbo', 'basis2', 'force_field_params', 'van_der_waals', 'cdft', 'swap_occupied_virtual', 'opt', 'basis', 'intracule', 'velocity', 'isotopes', 'localized_diabatization', 'efp_fragments', 'plots'}</em><a class="headerlink" href="#pymatgen.io.qchem.QcTask.optional_keywords_list" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="method">

diff --git a/docs_rst/index.rst b/docs_rst/index.rst
@@ -135,7 +135,7 @@ pymatgen can be installed from the `matsci channel on Anaconda cloud
    conda install --channel matsci pymatgen
 
 Pymatgen is under active development, and new features are added regularly. To
-upgrade pymatgen, use the following command::
+upgrade pymatgen to the latest version, use the following command::
 
    conda upgrade pymatgen