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Introduced doc
2019-01-25 14:17:34 +01:00
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<div class="section" id="qp-create-ezfio">
<span id="id1"></span><h1>qp_create_ezfio<a class="headerlink" href="#qp-create-ezfio" title="Permalink to this headline"></a></h1>
<p>This command creates an <a class="reference external" href="http://gitlab.com/scemama/EZFIO">EZFIO</a> directory from a standard <cite>xyz</cite> file or
from a <cite>z-matrix</cite> file in Gaussian format.</p>
<div class="section" id="usage">
<h2>Usage<a class="headerlink" href="#usage" title="Permalink to this headline"></a></h2>
<div class="code bash highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">qp_create_ezfio</span> <span class="p">[</span><span class="o">-</span><span class="n">a</span><span class="p">]</span> <span class="o">-</span><span class="n">b</span> <span class="o">&lt;</span><span class="n">string</span><span class="o">&gt;</span> <span class="p">[</span><span class="o">-</span><span class="n">c</span> <span class="o">&lt;</span><span class="nb">int</span><span class="o">&gt;</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">d</span> <span class="o">&lt;</span><span class="nb">float</span><span class="o">&gt;</span><span class="p">]</span>
<span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">m</span> <span class="o">&lt;</span><span class="nb">int</span><span class="o">&gt;</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">o</span> <span class="n">EZFIO_DIR</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">p</span> <span class="o">&lt;</span><span class="n">string</span><span class="o">&gt;</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">x</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="p">]</span> <span class="n">FILE</span>
</pre></div>
</div>
<dl class="option">
<dt id="cmdoption-qp-create-ezfio-a">
<code class="descname">-a</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--au</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-qp-create-ezfio-a" title="Permalink to this definition"></a></dt>
<dd><p>If present, input geometry is in atomic units.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-qp-create-ezfio-b">
<code class="descname">-b</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--basis</code><code class="descclassname">=&lt;string&gt;</code><a class="headerlink" href="#cmdoption-qp-create-ezfio-b" title="Permalink to this definition"></a></dt>
<dd><p>Name of basis set. The basis set is defined as a single string if
all the atoms are taken from the same basis set, otherwise specific
elements can be defined as follows:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">-</span><span class="n">b</span> <span class="s2">&quot;cc-pcvdz | H:cc-pvdz | C:6-31g&quot;</span>
<span class="o">-</span><span class="n">b</span> <span class="s2">&quot;cc-pvtz | 1,H:sto-3g | 3,H:6-31g&quot;</span>
</pre></div>
</div>
<p>By default, the basis set is obtained from the local database of the.
<em>Quantum Package</em> This option is mandatory .</p>
<p>If <code class="docutils literal notranslate"><span class="pre">&lt;string&gt;</span></code> is set to <code class="docutils literal notranslate"><span class="pre">show</span></code>, the list of all available basis
sets is displayed.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-qp-create-ezfio-c">
<code class="descname">-c</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--charge</code><code class="descclassname">=&lt;int&gt;</code><a class="headerlink" href="#cmdoption-qp-create-ezfio-c" title="Permalink to this definition"></a></dt>
<dd><p>Total charge of the molecule. Default is 0.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-qp-create-ezfio-d">
<code class="descname">-d</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--dummy</code><code class="descclassname">=&lt;float&gt;</code><a class="headerlink" href="#cmdoption-qp-create-ezfio-d" title="Permalink to this definition"></a></dt>
<dd><p>Add dummy atoms (X) between atoms when the distance between two atoms
is less than <span class="math notranslate nohighlight">\(x \times \sum R_\mathrm{cov}\)</span>, the covalent radii
of the atoms. The default is x=0, so no dummy atom is added.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-qp-create-ezfio-h">
<code class="descname">-h</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--help</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-qp-create-ezfio-h" title="Permalink to this definition"></a></dt>
<dd><p>Print the help text and exit</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-qp-create-ezfio-m">
<code class="descname">-m</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--multiplicity</code><code class="descclassname">=&lt;int&gt;</code><a class="headerlink" href="#cmdoption-qp-create-ezfio-m" title="Permalink to this definition"></a></dt>
<dd><p>Spin multiplicity <span class="math notranslate nohighlight">\(2S+1\)</span> of the molecule. Default is 1.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-qp-create-ezfio-o">
<code class="descname">-o</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--output</code><code class="descclassname">=EZFIO_DIR</code><a class="headerlink" href="#cmdoption-qp-create-ezfio-o" title="Permalink to this definition"></a></dt>
<dd><p>Name of the created <a class="reference external" href="http://gitlab.com/scemama/EZFIO">EZFIO</a> directory.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-qp-create-ezfio-p">
<code class="descname">-p</code><code class="descclassname"> &lt;string&gt;</code><code class="descclassname">, </code><code class="descname">--pseudo</code><code class="descclassname">=&lt;string&gt;</code><a class="headerlink" href="#cmdoption-qp-create-ezfio-p" title="Permalink to this definition"></a></dt>
<dd><p>Name of the pseudo-potential. Follows the same conventions as the basis set.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-qp-create-ezfio-x">
<code class="descname">-x</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--cart</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-qp-create-ezfio-x" title="Permalink to this definition"></a></dt>
<dd><p>Compute <abbr title="Atomic Orbitals">AOs</abbr> in the Cartesian basis set (6d, 10f, …)</p>
</dd></dl>
</div>
<div class="section" id="using-custom-atomic-basis-sets">
<h2>Using custom atomic basis sets<a class="headerlink" href="#using-custom-atomic-basis-sets" title="Permalink to this headline"></a></h2>
<p>If a file with the same name as the basis set exists, this file will
be read. For example, if the file containing the basis set is named
<code class="docutils literal notranslate"><span class="pre">custom.basis</span></code>, and the <em>xyz</em> geometry is in <code class="docutils literal notranslate"><span class="pre">molecule.xyz</span></code>, the
following should be used:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">qp_create_ezfio</span> <span class="o">-</span><span class="n">b</span> <span class="n">custom</span><span class="o">.</span><span class="n">basis</span> <span class="n">molecule</span><span class="o">.</span><span class="n">xyz</span>
</pre></div>
</div>
<p>Basis set files should be given in <a class="reference external" href="https://www.msg.chem.iastate.edu/gamess/">GAMESS</a> format, where the full
names of the atoms are given, and the basis sets for each element are
separated by a blank line. Here is an example</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">HYDROGEN</span>
<span class="n">S</span> <span class="mi">3</span>
<span class="mi">1</span> <span class="mf">13.0100000</span> <span class="mf">0.0196850</span>
<span class="mi">2</span> <span class="mf">1.9620000</span> <span class="mf">0.1379770</span>
<span class="mi">3</span> <span class="mf">0.4446000</span> <span class="mf">0.4781480</span>
<span class="n">S</span> <span class="mi">1</span>
<span class="mi">1</span> <span class="mf">0.1220000</span> <span class="mf">1.0000000</span>
<span class="n">P</span> <span class="mi">1</span>
<span class="mi">1</span> <span class="mf">0.7270000</span> <span class="mf">1.0000000</span>
<span class="n">BORON</span>
<span class="n">S</span> <span class="mi">8</span>
<span class="mi">1</span> <span class="mf">4570.0000000</span> <span class="mf">0.0006960</span>
<span class="mi">2</span> <span class="mf">685.9000000</span> <span class="mf">0.0053530</span>
<span class="mi">3</span> <span class="mf">156.5000000</span> <span class="mf">0.0271340</span>
<span class="mi">4</span> <span class="mf">44.4700000</span> <span class="mf">0.1013800</span>
<span class="mi">5</span> <span class="mf">14.4800000</span> <span class="mf">0.2720550</span>
<span class="mi">6</span> <span class="mf">5.1310000</span> <span class="mf">0.4484030</span>
<span class="mi">7</span> <span class="mf">1.8980000</span> <span class="mf">0.2901230</span>
<span class="mi">8</span> <span class="mf">0.3329000</span> <span class="mf">0.0143220</span>
<span class="n">S</span> <span class="mi">8</span>
<span class="mi">1</span> <span class="mf">4570.0000000</span> <span class="o">-</span><span class="mf">0.0001390</span>
<span class="mi">2</span> <span class="mf">685.9000000</span> <span class="o">-</span><span class="mf">0.0010970</span>
<span class="mi">3</span> <span class="mf">156.5000000</span> <span class="o">-</span><span class="mf">0.0054440</span>
<span class="mi">4</span> <span class="mf">44.4700000</span> <span class="o">-</span><span class="mf">0.0219160</span>
<span class="mi">5</span> <span class="mf">14.4800000</span> <span class="o">-</span><span class="mf">0.0597510</span>
<span class="mi">6</span> <span class="mf">5.1310000</span> <span class="o">-</span><span class="mf">0.1387320</span>
<span class="mi">7</span> <span class="mf">1.8980000</span> <span class="o">-</span><span class="mf">0.1314820</span>
<span class="mi">8</span> <span class="mf">0.3329000</span> <span class="mf">0.5395260</span>
<span class="n">S</span> <span class="mi">1</span>
<span class="mi">1</span> <span class="mf">0.1043000</span> <span class="mf">1.0000000</span>
<span class="n">P</span> <span class="mi">3</span>
<span class="mi">1</span> <span class="mf">6.0010000</span> <span class="mf">0.0354810</span>
<span class="mi">2</span> <span class="mf">1.2410000</span> <span class="mf">0.1980720</span>
<span class="mi">3</span> <span class="mf">0.3364000</span> <span class="mf">0.5052300</span>
<span class="n">P</span> <span class="mi">1</span>
<span class="mi">1</span> <span class="mf">0.0953800</span> <span class="mf">1.0000000</span>
<span class="n">D</span> <span class="mi">1</span>
<span class="mi">1</span> <span class="mf">0.3430000</span> <span class="mf">1.0000000</span>
</pre></div>
</div>
</div>
<div class="section" id="using-custom-pseudo-potentials">
<h2>Using custom pseudo-potentials<a class="headerlink" href="#using-custom-pseudo-potentials" title="Permalink to this headline"></a></h2>
<p>As for the basis set, if a file with the same name as the
pseudo-potential exists, this file will be read. For example, if the
file containing the custom pseudo-potential is named <code class="docutils literal notranslate"><span class="pre">custom.pseudo</span></code>,
the basis set is named <code class="docutils literal notranslate"><span class="pre">custom.basis</span></code>, and the <em>xyz</em> geometry is in
<code class="docutils literal notranslate"><span class="pre">molecule.xyz</span></code>, the following command should be used</p>
<div class="code bash highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">qp_create_ezfio</span> <span class="o">-</span><span class="n">b</span> <span class="n">custom</span><span class="o">.</span><span class="n">basis</span> <span class="o">-</span><span class="n">p</span> <span class="n">custom</span><span class="o">.</span><span class="n">pseudo</span> <span class="n">molecule</span><span class="o">.</span><span class="n">xyz</span>
</pre></div>
</div>
<p>Pseudo-potential files should be given in a format very close to
<a class="reference external" href="https://www.msg.chem.iastate.edu/gamess/">GAMESS</a> format. The first line should be formatted as <code class="docutils literal notranslate"><span class="pre">%s</span> <span class="pre">GEN</span> <span class="pre">%d</span> <span class="pre">%d</span></code>
where the first string is the chemical symbol, the first integer is
the number of core electrons to be removed and the second integer is
LMAX+1 as in <a class="reference external" href="https://www.msg.chem.iastate.edu/gamess/">GAMESS</a> format. The pseudo-potential for each element are
separated by a blank line. Here is an example</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Ne</span> <span class="n">GEN</span> <span class="mi">2</span> <span class="mi">1</span>
<span class="mi">3</span>
<span class="mf">8.00000000</span> <span class="mi">1</span> <span class="mf">10.74945199</span>
<span class="mf">85.99561593</span> <span class="mi">3</span> <span class="mf">10.19801460</span>
<span class="o">-</span><span class="mf">56.79004456</span> <span class="mi">2</span> <span class="mf">10.18694048</span>
<span class="mi">1</span>
<span class="mf">55.11144535</span> <span class="mi">2</span> <span class="mf">12.85042963</span>
<span class="n">F</span> <span class="n">GEN</span> <span class="mi">2</span> <span class="mi">1</span>
<span class="mi">3</span>
<span class="mf">7.00000000</span> <span class="mi">1</span> <span class="mf">11.39210685</span>
<span class="mf">79.74474797</span> <span class="mi">3</span> <span class="mf">10.74911370</span>
<span class="o">-</span><span class="mf">49.45159098</span> <span class="mi">2</span> <span class="mf">10.45120693</span>
<span class="mi">1</span>
<span class="mf">50.25646328</span> <span class="mi">2</span> <span class="mf">11.30345826</span>
</pre></div>
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