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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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<head>
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<!-- 2022-06-16 Thu 15:20 -->
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<!-- 2022-06-27 Mon 15:16 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>TREXIO source code documentation</title>
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@ -347,7 +347,7 @@ and bug reports should be submitted at
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</div>
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<div id="postamble" class="status">
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<p class="author">Author: TREX-CoE</p>
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<p class="date">Created: 2022-06-16 Thu 15:20</p>
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<p class="date">Created: 2022-06-27 Mon 15:16</p>
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<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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</div>
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</body>
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156
examples.html
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examples.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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<head>
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<!-- 2022-06-16 Thu 15:20 -->
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<!-- 2022-06-27 Mon 15:16 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>Examples</title>
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@ -333,39 +333,44 @@ for the JavaScript code in this tag.
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<h2>Table of Contents</h2>
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<div id="text-table-of-contents">
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<ul>
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<li><a href="#orgab17b52">1. Accessing sparse quantities</a>
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<li><a href="#orgfc46d48">1. Accessing sparse quantities (integrals)</a>
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<ul>
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<li><a href="#org3181d3f">1.1. Fortran</a>
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<li><a href="#orgc50dfc2">1.1. Fortran</a>
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<ul>
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<li><a href="#org7b49d62">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#orgddfc2aa">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
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<li><a href="#orgeb734b8">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#orgdd4e07d">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orgb62c7d7">1.1.5. Allocate memory</a></li>
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<li><a href="#org66047b1">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#orga9e0ec7">1.1.7. Read two-electron quantities</a>
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<li><a href="#org38e5311">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org9c5de5c">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
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<li><a href="#orge8899e4">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#orgcbe0c2d">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org4d00415">1.1.5. Allocate memory</a></li>
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<li><a href="#org94f4bdf">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org9485e9d">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#org8424b81">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#orgb190bc8">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#orgab5ff48">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org9509bc4">1.1.7.2. Reduced density matrix</a></li>
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</ul>
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</li>
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<li><a href="#orgbbc7be3">1.1.8. Compute the energy</a></li>
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<li><a href="#orgc2c66c9">1.1.9. Terminate</a></li>
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<li><a href="#org03653d4">1.1.8. Compute the energy</a></li>
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<li><a href="#org06dc4b9">1.1.9. Terminate</a></li>
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</ul>
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</li>
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</ul>
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</li>
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<li><a href="#orga62fa11">2. Reading determinants</a>
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<ul>
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<li><a href="#org26ef9f9">2.1. Fortran</a></li>
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</ul>
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</li>
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</ul>
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</div>
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</div>
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<div id="outline-container-orgab17b52" class="outline-2">
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<h2 id="orgab17b52"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
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<div id="outline-container-orgfc46d48" class="outline-2">
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<h2 id="orgfc46d48"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
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<div class="outline-text-2" id="text-1">
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</div>
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<div id="outline-container-org3181d3f" class="outline-3">
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<h3 id="org3181d3f"><span class="section-number-3">1.1</span> Fortran</h3>
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<div id="outline-container-orgc50dfc2" class="outline-3">
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<h3 id="orgc50dfc2"><span class="section-number-3">1.1</span> Fortran</h3>
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<div class="outline-text-3" id="text-1-1">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
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@ -411,8 +416,8 @@ One needs to read from the TREXIO file:
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</div>
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</div>
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<div id="outline-container-org7b49d62" class="outline-4">
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<h4 id="org7b49d62"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-org38e5311" class="outline-4">
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<h4 id="org38e5311"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div class="outline-text-4" id="text-1-1-1">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> i, j, k, l, m</span>
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@ -427,8 +432,8 @@ One needs to read from the TREXIO file:
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</div>
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</div>
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<div id="outline-container-orgddfc2aa" class="outline-4">
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<h4 id="orgddfc2aa"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
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<div id="outline-container-org9c5de5c" class="outline-4">
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<h4 id="org9c5de5c"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
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<div class="outline-text-4" id="text-1-1-2">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
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@ -444,8 +449,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-orgeb734b8" class="outline-4">
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<h4 id="orgeb734b8"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-orge8899e4" class="outline-4">
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<h4 id="orge8899e4"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div class="outline-text-4" id="text-1-1-3">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
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@ -459,8 +464,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-orgdd4e07d" class="outline-4">
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<h4 id="orgdd4e07d"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-orgcbe0c2d" class="outline-4">
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<h4 id="orgcbe0c2d"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div class="outline-text-4" id="text-1-1-4">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
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@ -474,8 +479,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-orgb62c7d7" class="outline-4">
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<h4 id="orgb62c7d7"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div id="outline-container-org4d00415" class="outline-4">
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<h4 id="org4d00415"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div class="outline-text-4" id="text-1-1-5">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
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@ -487,8 +492,8 @@ W(:,:,:,:) = 0.d0
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</div>
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</div>
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<div id="outline-container-org66047b1" class="outline-4">
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<h4 id="org66047b1"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div id="outline-container-org94f4bdf" class="outline-4">
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<h4 id="org94f4bdf"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div class="outline-text-4" id="text-1-1-6">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
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@ -520,8 +525,8 @@ rc = trexio_read_rdm_1e(f, D)
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</div>
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</div>
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<div id="outline-container-orga9e0ec7" class="outline-4">
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<h4 id="orga9e0ec7"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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<div id="outline-container-org9485e9d" class="outline-4">
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<h4 id="org9485e9d"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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<div class="outline-text-4" id="text-1-1-7">
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<p>
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Reading is done with OpenMP. Each thread reads its own buffer, and
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@ -537,8 +542,8 @@ to be protected in the critical section when modified.
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</p>
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</div>
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<div id="outline-container-org8424b81" class="outline-5">
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<h5 id="org8424b81"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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<div id="outline-container-orgab5ff48" class="outline-5">
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<h5 id="orgab5ff48"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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<div class="outline-text-5" id="text-1-1-7-1">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
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@ -587,8 +592,8 @@ icount = BUFSIZE
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</div>
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</div>
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<div id="outline-container-orgb190bc8" class="outline-5">
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<h5 id="orgb190bc8"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-org9509bc4" class="outline-5">
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<h5 id="org9509bc4"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div class="outline-text-5" id="text-1-1-7-2">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
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@ -632,8 +637,8 @@ icount = bufsize
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</div>
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</div>
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<div id="outline-container-orgbbc7be3" class="outline-4">
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<h4 id="orgbbc7be3"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div id="outline-container-org03653d4" class="outline-4">
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<h4 id="org03653d4"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div class="outline-text-4" id="text-1-1-8">
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<p>
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When the orbitals are real, we can use
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@ -679,8 +684,8 @@ E = E + E_nn
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</div>
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</div>
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<div id="outline-container-orgc2c66c9" class="outline-4">
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<h4 id="orgc2c66c9"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-org06dc4b9" class="outline-4">
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<h4 id="org06dc4b9"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div class="outline-text-4" id="text-1-1-9">
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<div class="org-src-container">
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<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
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@ -692,10 +697,79 @@ E = E + E_nn
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</div>
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</div>
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</div>
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<div id="outline-container-orga62fa11" class="outline-2">
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<h2 id="orga62fa11"><span class="section-number-2">2</span> Reading determinants</h2>
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<div class="outline-text-2" id="text-2">
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</div>
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<div id="outline-container-org26ef9f9" class="outline-3">
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<h3 id="org26ef9f9"><span class="section-number-3">2.1</span> Fortran</h3>
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<div class="outline-text-3" id="text-2-1">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
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<span style="color: #a020f0;">use</span> <span style="color: #0000ff;">trexio</span>
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<span style="color: #a020f0;">implicit</span> <span style="color: #228b22;">none</span>
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<span style="color: #228b22;">character</span>*(128) ::<span style="color: #a0522d;"> filename </span>! <span style="color: #b22222;">Name of the input file</span>
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<span style="color: #228b22;">integer</span>(trexio_exit_code) ::<span style="color: #a0522d;"> rc </span>! <span style="color: #b22222;">Return code for error checking</span>
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<span style="color: #228b22;">integer</span>(trexio_t) ::<span style="color: #a0522d;"> trex_determinant_file</span>
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<span style="color: #228b22;">integer</span>*8, <span style="color: #a020f0;">allocatable</span> ::<span style="color: #a0522d;"> buffer(:,:,:)</span>
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<span style="color: #228b22;">integer</span>(8) ::<span style="color: #a0522d;"> offset, icount, BUFSIZE</span>
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<span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> ndet, int64_num, m</span>
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<span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> occ_num_up, occ_num_dn</span>
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<span style="color: #228b22;">integer</span>, <span style="color: #a020f0;">allocatable</span> ::<span style="color: #a0522d;"> orb_list_up(:), orb_list_dn(:)</span>
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<span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
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trex_determinant_file = trexio_open(filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO, rc)
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<span style="color: #a020f0;">if</span> (rc /= TREXIO_SUCCESS) <span style="color: #a020f0;">then</span>
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<span style="color: #a020f0;">call</span> <span style="color: #0000ff;">trexio_string_of_error</span>(rc, err_msg)
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<span style="color: #a020f0;">print</span> *, <span style="color: #8b2252;">'Error opening TREXIO file: '</span>//<span style="color: #a020f0;">trim</span>(err_msg)
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<span style="color: #a020f0;">stop</span>
|
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<span style="color: #a020f0;">end if</span>
|
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|
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rc = trexio_read_determinant_num(trex_determinant_file, ndet)
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<span style="color: #a020f0;">print</span> *, <span style="color: #8b2252;">'ndet'</span>, ndet
|
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|
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rc = trexio_get_int64_num(trex_determinant_file, int64_num)
|
||||
<span style="color: #a020f0;">print</span> *, <span style="color: #8b2252;">'int64_num'</span>, int64_num
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|
||||
BUFSIZE = 1000_8
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<span style="color: #a020f0;">allocate</span>(buffer(int64_num, 2, BUFSIZE))
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<span style="color: #a020f0;">allocate</span>(orb_list_up(int64_num*64), orb_list_dn(int64_num*64))
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offset = 0_8
|
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icount = BUFSIZE
|
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<span style="color: #a020f0;">do while</span> (icount == BUFSIZE)
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<span style="color: #a020f0;">if</span> (offset < ndet) <span style="color: #a020f0;">then</span>
|
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rc = trexio_read_determinant_list(trex_determinant_file, offset, icount, buffer)
|
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offset = offset + icount
|
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<span style="color: #a020f0;">else</span>
|
||||
icount = 0
|
||||
<span style="color: #a020f0;">end if</span>
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<span style="color: #a020f0;">print</span> *, <span style="color: #8b2252;">'---'</span>
|
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<span style="color: #a020f0;">do</span> m=1,icount
|
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rc = trexio_to_orbital_list_up_dn(int64_num, buffer(1,1,m), <span style="color: #a020f0;">&</span>
|
||||
orb_list_up, orb_list_dn, occ_num_up, occ_num_dn)
|
||||
<span style="color: #a020f0;">print</span> <span style="color: #8b2252;">'(100(I3,X))'</span>, (orb_list_up(1:occ_num_up)), (orb_list_dn(1:occ_num_dn))
|
||||
<span style="color: #a020f0;">print</span> *, <span style="color: #8b2252;">''</span>
|
||||
<span style="color: #a020f0;">end do</span>
|
||||
<span style="color: #a020f0;">end do</span>
|
||||
|
||||
end
|
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</pre>
|
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</div>
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</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-06-16 Thu 15:20</p>
|
||||
<p class="date">Created: 2022-06-27 Mon 15:16</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2022-06-16 Thu 15:20 -->
|
||||
<!-- 2022-06-27 Mon 15:16 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TREXIO source code documentation</title>
|
||||
@ -347,7 +347,7 @@ and bug reports should be submitted at
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-06-16 Thu 15:20</p>
|
||||
<p class="date">Created: 2022-06-27 Mon 15:16</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2022-06-16 Thu 15:20 -->
|
||||
<!-- 2022-06-27 Mon 15:16 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>HDF5 back end</title>
|
||||
@ -311,23 +311,23 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orge9f6a0f">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org2c9bff7">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org892cb54">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org7899a5c">4. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org8ff7550">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org0bf1f27">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#org749b264">7. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org2fa726d">8. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#org3933942">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orge227156">10. Source code for the determinant part</a></li>
|
||||
<li><a href="#org3e62049">11. Helper functions</a></li>
|
||||
<li><a href="#orge3f1f44">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org047f996">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org1a5856d">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org71ce5b2">4. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org86be95e">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org2b692fc">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#org7c97248">7. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org6a54f12">8. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#org9ff3af7">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org4be2c66">10. Source code for the determinant part</a></li>
|
||||
<li><a href="#orge9623d9">11. Helper functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge9f6a0f" class="outline-2">
|
||||
<h2 id="orge9f6a0f"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-orge3f1f44" class="outline-2">
|
||||
<h2 id="orge3f1f44"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #483d8b;">#define</span> $GROUP$_GROUP_NAME <span style="color: #8b2252;">"$group$"</span>
|
||||
@ -339,8 +339,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2c9bff7" class="outline-2">
|
||||
<h2 id="org2c9bff7"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-org047f996" class="outline-2">
|
||||
<h2 id="org047f996"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
|
||||
@ -360,8 +360,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org892cb54" class="outline-2">
|
||||
<h2 id="org892cb54"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-org1a5856d" class="outline-2">
|
||||
<h2 id="org1a5856d"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -466,8 +466,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7899a5c" class="outline-2">
|
||||
<h2 id="org7899a5c"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-org71ce5b2" class="outline-2">
|
||||
<h2 id="org71ce5b2"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8ff7550" class="outline-2">
|
||||
<h2 id="org8ff7550"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org86be95e" class="outline-2">
|
||||
<h2 id="org86be95e"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -706,8 +706,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0bf1f27" class="outline-2">
|
||||
<h2 id="org0bf1f27"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-org2b692fc" class="outline-2">
|
||||
<h2 id="org2b692fc"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<p>
|
||||
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
|
||||
@ -910,8 +910,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org749b264" class="outline-2">
|
||||
<h2 id="org749b264"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org7c97248" class="outline-2">
|
||||
<h2 id="org7c97248"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1109,8 +1109,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2fa726d" class="outline-2">
|
||||
<h2 id="org2fa726d"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org6a54f12" class="outline-2">
|
||||
<h2 id="org6a54f12"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div class="outline-text-2" id="text-8">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1237,8 +1237,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org3933942" class="outline-2">
|
||||
<h2 id="org3933942"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-org9ff3af7" class="outline-2">
|
||||
<h2 id="org9ff3af7"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<p>
|
||||
<b><b>Note:</b></b> in early versions of the HDF5 library (v < 1.10) unlinking an object was not working as expected
|
||||
@ -1278,8 +1278,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge227156" class="outline-2">
|
||||
<h2 id="orge227156"><span class="section-number-2">10</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org4be2c66" class="outline-2">
|
||||
<h2 id="org4be2c66"><span class="section-number-2">10</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<p>
|
||||
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
|
||||
@ -1532,8 +1532,8 @@ Size specifies the number of data items (e.g. determinants) to process.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3e62049" class="outline-2">
|
||||
<h2 id="org3e62049"><span class="section-number-2">11</span> Helper functions</h2>
|
||||
<div id="outline-container-orge9623d9" class="outline-2">
|
||||
<h2 id="orge9623d9"><span class="section-number-2">11</span> Helper functions</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1796,7 +1796,7 @@ Size specifies the number of data items (e.g. determinants) to process.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-06-16 Thu 15:20</p>
|
||||
<p class="date">Created: 2022-06-27 Mon 15:16</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2022-06-16 Thu 15:20 -->
|
||||
<!-- 2022-06-27 Mon 15:16 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TEXT back end</title>
|
||||
@ -311,20 +311,20 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org07a98a4">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org39482aa">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org3252c3f">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#orgcb1b765">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org69ae094">5. Template for text read a group</a></li>
|
||||
<li><a href="#org75d7ccd">6. Template for text flush a group</a></li>
|
||||
<li><a href="#org57ebc40">7. Template for text free memory</a></li>
|
||||
<li><a href="#org48466ef">8. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgc4c810b">9. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgcdd7f94">10. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org395b4f8">11. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org90d0d62">12. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org0ece64c">13. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org14a2635">14. Source code for the determinant part</a></li>
|
||||
<li><a href="#org95837a5">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org8ba9330">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#orge8e5969">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org5c77713">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orgdc4b73a">5. Template for text read a group</a></li>
|
||||
<li><a href="#org0bced25">6. Template for text flush a group</a></li>
|
||||
<li><a href="#orgeec6aea">7. Template for text free memory</a></li>
|
||||
<li><a href="#org54e3a37">8. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org857952c">9. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org4867c7a">10. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org1f121d1">11. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgbba877e">12. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#orgbc53fb1">13. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org88529a1">14. Source code for the determinant part</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -346,8 +346,8 @@ directory.
|
||||
The file is written when closed, or when the flush function is called.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-org07a98a4" class="outline-2">
|
||||
<h2 id="org07a98a4"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div id="outline-container-org95837a5" class="outline-2">
|
||||
<h2 id="org95837a5"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
|
||||
@ -366,8 +366,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org39482aa" class="outline-2">
|
||||
<h2 id="org39482aa"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div id="outline-container-org8ba9330" class="outline-2">
|
||||
<h2 id="org8ba9330"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
|
||||
@ -387,8 +387,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3252c3f" class="outline-2">
|
||||
<h2 id="org3252c3f"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div id="outline-container-orge8e5969" class="outline-2">
|
||||
<h2 id="orge8e5969"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -531,8 +531,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgcb1b765" class="outline-2">
|
||||
<h2 id="orgcb1b765"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div id="outline-container-org5c77713" class="outline-2">
|
||||
<h2 id="org5c77713"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -554,8 +554,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org69ae094" class="outline-2">
|
||||
<h2 id="org69ae094"><span class="section-number-2">5</span> Template for text read a group</h2>
|
||||
<div id="outline-container-orgdc4b73a" class="outline-2">
|
||||
<h2 id="orgdc4b73a"><span class="section-number-2">5</span> Template for text read a group</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c">$group$_t*
|
||||
@ -779,8 +779,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org75d7ccd" class="outline-2">
|
||||
<h2 id="org75d7ccd"><span class="section-number-2">6</span> Template for text flush a group</h2>
|
||||
<div id="outline-container-org0bced25" class="outline-2">
|
||||
<h2 id="org0bced25"><span class="section-number-2">6</span> Template for text flush a group</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -844,8 +844,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org57ebc40" class="outline-2">
|
||||
<h2 id="org57ebc40"><span class="section-number-2">7</span> Template for text free memory</h2>
|
||||
<div id="outline-container-orgeec6aea" class="outline-2">
|
||||
<h2 id="orgeec6aea"><span class="section-number-2">7</span> Template for text free memory</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<p>
|
||||
Memory is allocated when reading. The following function frees memory.
|
||||
@ -914,8 +914,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org48466ef" class="outline-2">
|
||||
<h2 id="org48466ef"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-org54e3a37" class="outline-2">
|
||||
<h2 id="org54e3a37"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div class="outline-text-2" id="text-8">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -978,8 +978,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc4c810b" class="outline-2">
|
||||
<h2 id="orgc4c810b"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org857952c" class="outline-2">
|
||||
<h2 id="org857952c"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1075,8 +1075,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgcdd7f94" class="outline-2">
|
||||
<h2 id="orgcdd7f94"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org4867c7a" class="outline-2">
|
||||
<h2 id="org4867c7a"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1177,8 +1177,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org395b4f8" class="outline-2">
|
||||
<h2 id="org395b4f8"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org1f121d1" class="outline-2">
|
||||
<h2 id="org1f121d1"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1252,8 +1252,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org90d0d62" class="outline-2">
|
||||
<h2 id="org90d0d62"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div id="outline-container-orgbba877e" class="outline-2">
|
||||
<h2 id="orgbba877e"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<p>
|
||||
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
|
||||
@ -1526,8 +1526,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0ece64c" class="outline-2">
|
||||
<h2 id="org0ece64c"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-orgbc53fb1" class="outline-2">
|
||||
<h2 id="orgbc53fb1"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-13">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1555,8 +1555,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org14a2635" class="outline-2">
|
||||
<h2 id="org14a2635"><span class="section-number-2">14</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org88529a1" class="outline-2">
|
||||
<h2 id="org88529a1"><span class="section-number-2">14</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-14">
|
||||
<p>
|
||||
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
|
||||
@ -1960,7 +1960,7 @@ Size specifies the number of data items, e.g. determinants.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-06-16 Thu 15:20</p>
|
||||
<p class="date">Created: 2022-06-27 Mon 15:16</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
150
trex.html
150
trex.html
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2022-06-16 Thu 15:20 -->
|
||||
<!-- 2022-06-27 Mon 15:16 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TREX Configuration file</title>
|
||||
@ -333,37 +333,37 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orgc98157b">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org6f76b6e">2. Electron (electron group)</a></li>
|
||||
<li><a href="#orgac182eb">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#orgf70cf0c">4. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#org0917011">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#orgc590047">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org048edc1">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org1a9c956">4. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#orgaa32ede">4.1. Example</a></li>
|
||||
<li><a href="#org0a97abb">4.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org1371c4b">5. Basis set (basis group)</a>
|
||||
<li><a href="#orge397838">5. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#orgbf532ab">5.1. Example</a></li>
|
||||
<li><a href="#orgd9f9d51">5.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgb956148">6. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#orgd430435">6. Atomic orbitals (ao group)</a>
|
||||
<ul>
|
||||
<li><a href="#ao_one_e">6.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
|
||||
<li><a href="#ao_two_e">6.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org84fad74">7. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org3658e4a">7. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#org4ca8797">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org8be84e9">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#org29e1126">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org5336375">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgcfb1606">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org08f365d">9. Excited states (state group)</a></li>
|
||||
<li><a href="#org79b5e15">10. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org35c56e1">11. Cell (cell group)</a></li>
|
||||
<li><a href="#org0e7aa9b">12. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#orgdc82494">13. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
<li><a href="#org31de853">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org8945d84">9. Excited states (state group)</a></li>
|
||||
<li><a href="#org7b178c5">10. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org0ee8dc3">11. Cell (cell group)</a></li>
|
||||
<li><a href="#orgc1d4760">12. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#org09c1290">13. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -413,8 +413,8 @@ the <a href="./examples.html">examples</a>.
|
||||
</p>
|
||||
|
||||
|
||||
<div id="outline-container-orgc98157b" class="outline-2">
|
||||
<h2 id="orgc98157b"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-org0917011" class="outline-2">
|
||||
<h2 id="org0917011"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<p>
|
||||
As we expect our files to be archived in open-data repositories, we
|
||||
@ -424,7 +424,7 @@ which have participated to the creation of the file, a list of
|
||||
authors of the file, and a textual description.
|
||||
</p>
|
||||
|
||||
<table id="org37159bd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd3e696f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -505,15 +505,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6f76b6e" class="outline-2">
|
||||
<h2 id="org6f76b6e"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div id="outline-container-orgc590047" class="outline-2">
|
||||
<h2 id="orgc590047"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
We consider wave functions expressed in the spin-free formalism, where
|
||||
the number of ↑ and ↓ electrons is fixed.
|
||||
</p>
|
||||
|
||||
<table id="org7b12c50" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgbdd5bc2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -559,15 +559,15 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgac182eb" class="outline-2">
|
||||
<h2 id="orgac182eb"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div id="outline-container-org048edc1" class="outline-2">
|
||||
<h2 id="org048edc1"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
<p>
|
||||
The nuclei are considered as fixed point charges. Coordinates are
|
||||
given in Cartesian \((x,y,z)\) format.
|
||||
</p>
|
||||
|
||||
<table id="org02fbb69" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgce45cc6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -634,8 +634,8 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf70cf0c" class="outline-2">
|
||||
<h2 id="orgf70cf0c"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div id="outline-container-org1a9c956" class="outline-2">
|
||||
<h2 id="org1a9c956"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
<p>
|
||||
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
|
||||
@ -668,7 +668,7 @@ The functions \(V_{A\ell}\) are parameterized as:
|
||||
See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.4984046</a> or <a href="https://doi.org/10.1063/1.5121006">https://doi.org/10.1063/1.5121006</a> for more info.
|
||||
</p>
|
||||
|
||||
<table id="orga21e7aa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org260d650" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -770,8 +770,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgaa32ede" class="outline-3">
|
||||
<h3 id="orgaa32ede"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div id="outline-container-org0a97abb" class="outline-3">
|
||||
<h3 id="org0a97abb"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div class="outline-text-3" id="text-4-1">
|
||||
<p>
|
||||
For example, consider H<sub>2</sub> molecule with the following
|
||||
@ -834,8 +834,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1371c4b" class="outline-2">
|
||||
<h2 id="org1371c4b"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div id="outline-container-orge397838" class="outline-2">
|
||||
<h2 id="orge397838"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
<p>
|
||||
We consider here basis functions centered on nuclei. Hence, we enable
|
||||
@ -888,7 +888,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).
|
||||
All the basis set parameters are stored in one-dimensional arrays:
|
||||
</p>
|
||||
|
||||
<table id="org710b215" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org657b385" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -982,8 +982,8 @@ All the basis set parameters are stored in one-dimensional arrays:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgbf532ab" class="outline-3">
|
||||
<h3 id="orgbf532ab"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div id="outline-container-orgd9f9d51" class="outline-3">
|
||||
<h3 id="orgd9f9d51"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div class="outline-text-3" id="text-5-1">
|
||||
<p>
|
||||
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
|
||||
@ -1061,8 +1061,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb956148" class="outline-2">
|
||||
<h2 id="orgb956148"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div id="outline-container-orgd430435" class="outline-2">
|
||||
<h2 id="orgd430435"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<p>
|
||||
Going from the atomic basis set to AOs implies a systematic
|
||||
@ -1115,13 +1115,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#org1371c4b">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#orge397838">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
normalization factor of the atomic orbitals in spherical coordinates.
|
||||
The normalization factor of the \(xy\) function which should be
|
||||
introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</p>
|
||||
|
||||
<table id="org721e71b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org4d38da9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1173,8 +1173,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd40844c" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="orgd40844c"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div id="outline-container-org222ab37" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org222ab37"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div class="outline-text-3" id="text-ao_one_e">
|
||||
<ul class="org-ul">
|
||||
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
|
||||
@ -1191,7 +1191,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orge46c38d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgac62a1e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1286,8 +1286,8 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org61e7028" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org61e7028"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div id="outline-container-org5bb07fd" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org5bb07fd"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div class="outline-text-3" id="text-ao_two_e">
|
||||
<p>
|
||||
The two-electron integrals for a two-electron operator \(\hat{O}\) are
|
||||
@ -1308,7 +1308,7 @@ notation.
|
||||
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
|
||||
</ul>
|
||||
|
||||
<table id="orgd8d104d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org294e72d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1348,10 +1348,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org84fad74" class="outline-2">
|
||||
<h2 id="org84fad74"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div id="outline-container-org3658e4a" class="outline-2">
|
||||
<h2 id="org3658e4a"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="orgdfd5d28" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgc21563d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1424,8 +1424,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4ca8797" class="outline-3">
|
||||
<h3 id="org4ca8797"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div id="outline-container-org29e1126" class="outline-3">
|
||||
<h3 id="org29e1126"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div class="outline-text-3" id="text-7-1">
|
||||
<p>
|
||||
The operators as the same as those defined in the
|
||||
@ -1433,7 +1433,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org06f940e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd3dd34e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1528,8 +1528,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8be84e9" class="outline-3">
|
||||
<h3 id="org8be84e9"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div id="outline-container-org5336375" class="outline-3">
|
||||
<h3 id="org5336375"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div class="outline-text-3" id="text-7-2">
|
||||
<p>
|
||||
The operators as the same as those defined in the
|
||||
@ -1537,7 +1537,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org7d65746" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgafcad66" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1577,8 +1577,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgcfb1606" class="outline-2">
|
||||
<h2 id="orgcfb1606"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
|
||||
<div id="outline-container-org31de853" class="outline-2">
|
||||
<h2 id="org31de853"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
|
||||
<div class="outline-text-2" id="text-8">
|
||||
<p>
|
||||
The configuration interaction (CI) wave function \(\Psi\)
|
||||
@ -1611,7 +1611,7 @@ where \(\alpha\) and \(\beta\) denote $↑$-spin and $↓$-spin electrons,
|
||||
\(n\uparrow\) and \(n\downarrow\) correspond to <code>electron.up_num</code> and <code>electron.dn_num</code>, respectively.
|
||||
</p>
|
||||
|
||||
<table id="org20508c6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org9b7f654" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1657,8 +1657,8 @@ where \(\alpha\) and \(\beta\) denote $↑$-spin and $↓$-spin electrons,
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org08f365d" class="outline-2">
|
||||
<h2 id="org08f365d"><span class="section-number-2">9</span> Excited states (state group)</h2>
|
||||
<div id="outline-container-org8945d84" class="outline-2">
|
||||
<h2 id="org8945d84"><span class="section-number-2">9</span> Excited states (state group)</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<p>
|
||||
By default, the <code>determinant</code> group corresponds to the ground state.
|
||||
@ -1667,7 +1667,7 @@ correspond to excited state wave functions for the same set of
|
||||
determinants. This is the goal of the present group
|
||||
</p>
|
||||
|
||||
<table id="org04ac219" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgcfb70ed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1706,8 +1706,8 @@ determinants. This is the goal of the present group
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org79b5e15" class="outline-2">
|
||||
<h2 id="org79b5e15"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
|
||||
<div id="outline-container-org7b178c5" class="outline-2">
|
||||
<h2 id="org7b178c5"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<p>
|
||||
The reduced density matrices are defined in the basis of molecular
|
||||
@ -1760,7 +1760,7 @@ The total energy can be computed as:
|
||||
\]
|
||||
</p>
|
||||
|
||||
<table id="org3148dac" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org08c39bb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1841,10 +1841,10 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org35c56e1" class="outline-2">
|
||||
<h2 id="org35c56e1"><span class="section-number-2">11</span> Cell (cell group)</h2>
|
||||
<div id="outline-container-org0ee8dc3" class="outline-2">
|
||||
<h2 id="org0ee8dc3"><span class="section-number-2">11</span> Cell (cell group)</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<table id="orgd0de25a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgcb4937b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1890,10 +1890,10 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0e7aa9b" class="outline-2">
|
||||
<h2 id="org0e7aa9b"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div id="outline-container-orgc1d4760" class="outline-2">
|
||||
<h2 id="orgc1d4760"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<table id="orge172734" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org40a9ab8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1932,8 +1932,8 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdc82494" class="outline-2">
|
||||
<h2 id="orgdc82494"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div id="outline-container-org09c1290" class="outline-2">
|
||||
<h2 id="org09c1290"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div class="outline-text-2" id="text-13">
|
||||
<p>
|
||||
In quantum Monte Carlo calculations, the wave function is evaluated
|
||||
@ -1947,7 +1947,7 @@ By convention, the electron coordinates contain first all the electrons
|
||||
of $↑$-spin and then all the $↓$-spin.
|
||||
</p>
|
||||
|
||||
<table id="orga3ffdb3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orge31bce9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2002,7 +2002,7 @@ of $↑$-spin and then all the $↓$-spin.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-06-16 Thu 15:20</p>
|
||||
<p class="date">Created: 2022-06-27 Mon 15:16</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
Loading…
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Reference in New Issue
Block a user