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2.0
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<li class="toctree-l1"><a class="reference internal" href="../intro/selected_ci.html">Selected Configuration Interaction</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Quick-start guide</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#hands-on">Hands on</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#create-the-ezfio-database">Create the EZFIO database</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#run-a-hartree-fock-calculation">Run a Hartree-Fock calculation</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#choose-the-target-mo-space">Choose the target <abbr title="Molecular Orbital">MO</abbr> space</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#run-the-cipsi-calculation">Run the <abbr title="Configuration Interaction using a Perturbative Selection">CIPSI</abbr> calculation</a></li>
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<li class="toctree-l1"><a class="reference internal" href="printing.html">Printing the near-<abbr title="Full Configuration Interaction">FCI</abbr> wave function</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../appendix/research.html">Some research made with the <em>Quantum Package</em></a></li>
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<li class="toctree-l1"><a class="reference internal" href="../appendix/contributors.html">Contributors</a></li>
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<div class="section" id="quick-start-guide">
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<h1>Quick-start guide<a class="headerlink" href="#quick-start-guide" title="Permalink to this headline">¶</a></h1>
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<p>This tutorial should teach you everything you need to get started with
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the the basics of the <em>Quantum Package</em>. As an example, we will run a frozen core
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<abbr title="Configuration Interaction using a Perturbative Selection">CIPSI</abbr> calculation on the HCN molecule in the 631-G basis set.</p>
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<div class="section" id="demo-video">
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<h2>Demo video<a class="headerlink" href="#demo-video" title="Permalink to this headline">¶</a></h2>
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</div>
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<div class="section" id="hands-on">
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<h2>Hands on<a class="headerlink" href="#hands-on" title="Permalink to this headline">¶</a></h2>
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<div class="admonition important">
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<p class="first admonition-title">Important</p>
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<p class="last">Before using the <em>Quantum Package</em>, it is required to source the file
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<code class="file docutils literal notranslate"><span class="pre">quantum_package.rc</span></code> if it has not been done already in the
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current shell.</p>
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</div>
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<div class="section" id="create-the-ezfio-database">
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<h3>Create the EZFIO database<a class="headerlink" href="#create-the-ezfio-database" title="Permalink to this headline">¶</a></h3>
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<p>The data relative to calculations are stored in an <a class="reference external" href="http://gitlab.com/scemama/EZFIO">EZFIO</a> database.
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<a class="reference external" href="http://gitlab.com/scemama/EZFIO">EZFIO</a> is a hierarchical data format which uses the hierarchy of the
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file system to organize the data, as files stored in a directory. The
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data in the <a class="reference external" href="http://gitlab.com/scemama/EZFIO">EZFIO</a> directory are stored as plain text files, so it can
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be opened with any text editor.
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To access the data of the <a class="reference external" href="http://gitlab.com/scemama/EZFIO">EZFIO</a> database, the APIs (Fortran, <a class="reference external" href="http://www.python.org">Python</a>,
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<a class="reference external" href="http://ocaml.org/">OCaml</a> or Bash) provided by <a class="reference external" href="http://gitlab.com/scemama/EZFIO">EZFIO</a> should be used, or tools using
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these APIs such as <a class="reference internal" href="qp_edit.html#qp-edit"><span class="std std-ref">qp_edit</span></a> provided with the <em>Quantum Package</em>.</p>
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<p>First, create an <cite>xyz</cite> file containing the coordinates of the molecule.
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The file <code class="file docutils literal notranslate"><span class="pre">hcn.xyz</span></code> contains:</p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="mi">3</span>
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<span class="n">HCN</span> <span class="n">molecule</span>
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<span class="n">C</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
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<span class="n">H</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">1.064</span>
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<span class="n">N</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">1.156</span>
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</pre></div>
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</div>
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<p>This xyz file is now used with the <a class="reference internal" href="qp_create_ezfio_from_xyz.html#qp-create-ezfio"><span class="std std-ref">qp_create_ezfio</span></a> command to
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create an <a class="reference external" href="http://gitlab.com/scemama/EZFIO">EZFIO</a> database with the 6-31G basis set:</p>
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<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="s2">"6-31G"</span> <span class="n">hcn</span><span class="o">.</span><span class="n">xyz</span> <span class="o">-</span><span class="n">o</span> <span class="n">hcn</span>
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</pre></div>
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</div>
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<p>The EZFIO database now contains data relative to the nuclear coordinates
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and the atomic basis set:</p>
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<div class="code bash highlight-default notranslate"><div class="highlight"><pre><span></span>$ ls hcn
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ao_basis/ electrons/ ezfio/ nuclei/ pseudo/
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</pre></div>
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</div>
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</div>
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<div class="section" id="run-a-hartree-fock-calculation">
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<h3>Run a Hartree-Fock calculation<a class="headerlink" href="#run-a-hartree-fock-calculation" title="Permalink to this headline">¶</a></h3>
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<p>The program <a class="reference internal" href="qp_run.html#qp-run"><span class="std std-ref">qp_run</span></a> is the driver program of the <em>Quantum Package</em>. To run a
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<abbr title="Self Consistent Field">SCF</abbr> calculation, just run</p>
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<div class="code bash highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">qp_run</span> <span class="n">scf</span> <span class="n">hcn</span>
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</pre></div>
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</div>
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<p>The expected energy is <code class="docutils literal notranslate"><span class="pre">-92.827856698</span></code> au.</p>
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<div class="admonition seealso">
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<p class="first admonition-title">See also</p>
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<p class="last">The documentation of the <span class="xref std std-ref">hartree_fock</span> module and that of the <code class="xref c c-func docutils literal notranslate"><span class="pre">scf()</span></code> program.</p>
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</div>
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<p>This creates the <abbr title="Molecular Orbitals">MOs</abbr> in the <a class="reference external" href="http://gitlab.com/scemama/EZFIO">EZFIO</a> database that will be used to
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perform any other post-SCF method. The <em>Quantum Package</em> does not handle symmetry and
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the <abbr title="Molecular Orbitals">MOs</abbr> are stored by increasing order of Fock energies.</p>
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</div>
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<div class="section" id="choose-the-target-mo-space">
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<h3>Choose the target <abbr title="Molecular Orbital">MO</abbr> space<a class="headerlink" href="#choose-the-target-mo-space" title="Permalink to this headline">¶</a></h3>
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<p>Now, modify to <a class="reference external" href="http://gitlab.com/scemama/EZFIO">EZFIO</a> database to make <abbr title="Configuration Interaction using a Perturbative Selection">CIPSI</abbr> calculation in the
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full set of valence <abbr title="Molecular Orbitals">MOs</abbr>, keeping the core <abbr title="Molecular Orbitals">MOs</abbr> frozen. The simple
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command <a class="reference internal" href="qp_set_frozen_core.html#qp-set-frozen-core"><span class="std std-ref">qp_set_frozen_core</span></a> does this automatically:</p>
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<div class="code bash highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">qp_set_frozen_core</span> <span class="n">hcn</span>
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</pre></div>
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</div>
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<p>The general command to specify core and active orbitals is <a class="reference internal" href="qp_set_mo_class.html#qp-set-mo-class"><span class="std std-ref">qp_set_mo_class</span></a>.
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In the case of HCN molecule in the 631G basis, one has 20 <abbr title="Molecular Orbitals">MOs</abbr> in total and the two first orbitals are frozen:</p>
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<div class="code highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">qp_set_mo_class</span> <span class="o">-</span><span class="n">core</span> <span class="s2">"[1-2]"</span> <span class="o">-</span><span class="n">act</span> <span class="s2">"[3-20]"</span> <span class="n">hcn</span>
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</pre></div>
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</div>
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</div>
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<div class="section" id="run-the-cipsi-calculation">
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<h3>Run the <abbr title="Configuration Interaction using a Perturbative Selection">CIPSI</abbr> calculation<a class="headerlink" href="#run-the-cipsi-calculation" title="Permalink to this headline">¶</a></h3>
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<p>We will now use the <abbr title="Configuration Interaction using a Perturbative Selection">CIPSI</abbr> algorithm to estimate the <abbr title="Full Configuration Interaction">FCI</abbr> energy.</p>
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<div class="code highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">qp_run</span> <span class="n">fci</span> <span class="n">hcn</span> <span class="o">|</span> <span class="n">tee</span> <span class="n">hcn</span><span class="o">.</span><span class="n">fci</span><span class="o">.</span><span class="n">out</span>
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</pre></div>
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</div>
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<p>The program will start with a single determinant and will iteratively:</p>
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<ul class="simple">
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<li>Select the most important determinants from the external space and add them to the
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internal space</li>
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<li>Add all the necessary determinants to allow the eigenvector of <span class="math notranslate nohighlight">\(\hat H\)</span> to be
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also an eigenstate of <span class="math notranslate nohighlight">\(\widehat{S^2}\)</span></li>
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<li>Diagonalize <span class="math notranslate nohighlight">\(\hat H\)</span> in the enlarged internal space</li>
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<li>Compute (stochastically) the second-order perturbative contribution to the energy</li>
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<li>Extrapolate the variational energy by fitting
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<span class="math notranslate nohighlight">\(E=E_\text{FCI} - \alpha\, E_\text{PT2}\)</span></li>
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</ul>
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<p>By default, the program will stop when more than one million determinants have
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entered in the internal space, or when the <abbr title="Second order perturbative correction">PT2</abbr> energy is below <span class="math notranslate nohighlight">\(10^{-4}\)</span>.</p>
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<p>To have a pictural illustration of the convergence of the <abbr title="Configuration Interaction using a Perturbative Selection">CIPSI</abbr> algorithm, just run</p>
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<div class="code highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">qp_e_conv_fci</span> <span class="n">hcn</span><span class="o">.</span><span class="n">fci</span><span class="o">.</span><span class="n">out</span>
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</pre></div>
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</div>
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<p>This will create the files “hcn.fci.out.conv” containing the data of the convergence of the energy that can be plotted, together with the file “hcn.fci.out.conv.1.eps” which is obtained from the gnuplot plot file “hcn.fci.out.conv.plt”.</p>
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<p>The estimated <abbr title="Full Configuration Interaction">FCI</abbr> energy of HCN is <code class="docutils literal notranslate"><span class="pre">-93.0501</span></code> au.</p>
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<div class="admonition seealso">
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<p class="first admonition-title">See also</p>
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<p class="last">The documentation of the <a class="reference internal" href="../programs/fci.html#fci"><span class="std std-ref">fci</span></a> module and that of the <code class="xref c c-func docutils literal notranslate"><span class="pre">fci()</span></code> program.</p>
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</div>
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<hr class="docutils" />
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<p>TODO</p>
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<div class="admonition important">
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<p class="first admonition-title">Important</p>
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<p>TODO</p>
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<img alt="http://craniointernational.com/wp-content/uploads/2018/01/work-in-progress.jpg" src="http://craniointernational.com/wp-content/uploads/2018/01/work-in-progress.jpg" />
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<ul class="last simple">
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<li>Parameters for Hartree-Fock</li>
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<li>Parameters for Davidson</li>
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<li>Running in parallel</li>
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</ul>
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</div>
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