Add changes for efb6fac

_sources/use.rst.txt

@@ -596,6 +596,7 @@ The output depends on the value of ``-V``, which can be:
       There is no way to change this behavior.
     + By default, the program also include the base tensors calculated in the process.
       The ``-S`` option prevents this (that may be useful in the case of electric field differentiation)
+    + If you want to add results to existing ``molecule_nd.h5`` file, you can use the ```--append`` option.
     + Projection over normal mode of all the geometrical derivatives is requested via the ``-p`` option, but you can also request that the cartesian hessian used to do so is different, with the ``-H`` option (which accepts FCHK and dalton archives with cartesian hessian in it as argument).
 
 

api.html

@@ -856,14 +856,15 @@ <h1>Code documentation<a class="headerlink" href="#code-documentation" title="Li
 
 <dl class="py class">
 <dt class="sig sig-object py" id="nachos.core.baking.Baker">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">nachos.core.baking.</span></span><span class="sig-name descname"><span class="pre">Baker</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">recipe</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">storage</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">directory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#nachos.core.baking.Baker" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">nachos.core.baking.</span></span><span class="sig-name descname"><span class="pre">Baker</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">recipe</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">storage</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">directory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">original_cf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#nachos.core.baking.Baker" title="Link to this definition"></a></dt>
 <dd><p>Baker class to finally perform the numerical differentiation</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>recipe</strong> (<a class="reference internal" href="#nachos.core.files.Recipe" title="nachos.core.files.Recipe"><em>nachos.core.files.Recipe</em></a>) – a recipe</p></li>
 <li><p><strong>storage</strong> (<a class="reference internal" href="#nachos.core.files.ComputationalResults" title="nachos.core.files.ComputationalResults"><em>nachos.core.files.ComputationalResults</em></a>) – storage of results</p></li>
 <li><p><strong>directory</strong> (<em>str</em>) – working directory</p></li>
+<li><p><strong>original_cf</strong> (<em>qcip_tools.chemistry_files.chemistry_datafile.ChemistryDataFile</em>) – Originak chemistry file to append to</p></li>
 </ul>
 </dd>
 </dl>

genindex.html

@@ -104,6 +104,13 @@ <h2 id="Symbols">Symbols</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li>
+    --append
+
+      <ul>
+        <li><a href="use.html#cmdoption-nachos_bake-a">nachos_bake command line option</a>
+</li>
+      </ul></li>
+      <li>
     --basis-set
 
       <ul>
@@ -419,6 +426,13 @@ <h2 id="Symbols">Symbols</h2>
 
       <ul>
         <li><a href="use.html#cmdoption-nachos_shake-A">nachos_shake command line option</a>
+</li>
+      </ul></li>
+      <li>
+    -a
+
+      <ul>
+        <li><a href="use.html#cmdoption-nachos_bake-a">nachos_bake command line option</a>
 </li>
       </ul></li>
       <li>
@@ -995,6 +1009,8 @@ <h2 id="N">N</h2>
     nachos_bake command line option
 
       <ul>
+        <li><a href="use.html#cmdoption-nachos_bake-a">--append</a>
+</li>
         <li><a href="use.html#cmdoption-nachos_bake-d">--data</a>
 </li>
         <li><a href="use.html#cmdoption-nachos_bake-S">--do-not-steal</a>
@@ -1016,6 +1032,8 @@ <h2 id="N">N</h2>
         <li><a href="use.html#cmdoption-nachos_bake-V">--verbose</a>
 </li>
         <li><a href="use.html#cmdoption-nachos_bake-v">--version</a>
+</li>
+        <li><a href="use.html#cmdoption-nachos_bake-a">-a</a>
 </li>
         <li><a href="use.html#cmdoption-nachos_bake-d">-d</a>
 </li>

use.html

@@ -947,7 +947,7 @@ <h3>nachos_cook<a class="headerlink" href="#id3" title="Link to this heading">
 <h3>nachos_bake<a class="headerlink" href="#id4" title="Link to this heading"></a></h3>
 <p>From h5 file, perform numerical differentiation</p>
 <div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">usage: nachos_bake [-h] [-v] [-r RECIPE] [-d DATA] [-o OUTPUT] [-V VERBOSE]</span>
-<span class="go">                   [-S] [-O ONLY] [-p] [-H HESSIAN] [-R ROMBERG]</span>
+<span class="go">                   [-S] [-O ONLY] [-p] [-H HESSIAN] [-R ROMBERG] [-a]</span>
 </pre></div>
 </div>
 <dl class="std option">
@@ -1016,6 +1016,12 @@ <h3>nachos_bake<a class="headerlink" href="#id4" title="Link to this heading">
 <dd><p>Bypass detection and force a value in the triangle. Must be of the form <cite>k;m</cite>.</p>
 </dd></dl>
 
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-nachos_bake-a">
+<span id="cmdoption-nachos_bake-append"></span><span class="sig-name descname"><span class="pre">-a</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--append</span></span><span class="sig-prename descclassname"></span><a class="headerlink" href="#cmdoption-nachos_bake-a" title="Link to this definition"></a></dt>
+<dd><p>Append to existing H5 file</p>
+</dd></dl>
+
 </section>
 <p>The <code class="docutils literal notranslate"><span class="pre">-O</span></code> option to control what is actually differentiated.
 It expects a semicolon list like the <code class="docutils literal notranslate"><span class="pre">--differentiation</span></code> option of <code class="docutils literal notranslate"><span class="pre">nachos_make</span></code> (<a class="reference internal" href="#nachos-make-note-2"><span class="std std-ref">see above</span></a>), but you don’t have to provide the number of time if you want the number in the recipe to be used.</p>
@@ -1047,6 +1053,7 @@ <h3>nachos_bake<a class="headerlink" href="#id4" title="Link to this heading">
 There is no way to change this behavior.</p></li>
 <li><p>By default, the program also include the base tensors calculated in the process.
 The <code class="docutils literal notranslate"><span class="pre">-S</span></code> option prevents this (that may be useful in the case of electric field differentiation)</p></li>
+<li><p>If you want to add results to existing <code class="docutils literal notranslate"><span class="pre">molecule_nd.h5</span></code> file, you can use the <code class="docutils literal notranslate"><span class="pre">`--append</span></code> option.</p></li>
 <li><p>Projection over normal mode of all the geometrical derivatives is requested via the <code class="docutils literal notranslate"><span class="pre">-p</span></code> option, but you can also request that the cartesian hessian used to do so is different, with the <code class="docutils literal notranslate"><span class="pre">-H</span></code> option (which accepts FCHK and dalton archives with cartesian hessian in it as argument).</p></li>
 </ul>
 </div>