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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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<!-- 2022-06-27 Mon 15:18 -->
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<!-- 2022-06-28 Tue 08:16 -->
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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: 2022-06-27 Mon 15:18</p>
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<p class="date">Created: 2022-06-28 Tue 08:16</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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116
examples.html
116
examples.html
@ -3,7 +3,7 @@
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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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<!-- 2022-06-27 Mon 15:18 -->
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<!-- 2022-06-28 Tue 08:16 -->
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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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@ -333,31 +333,31 @@ 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="#org55b95b4">1. Accessing sparse quantities (integrals)</a>
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<li><a href="#org9b82c10">1. Accessing sparse quantities (integrals)</a>
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<ul>
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<li><a href="#org5121153">1.1. Fortran</a>
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<li><a href="#org99b90c1">1.1. Fortran</a>
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<ul>
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<li><a href="#orgc4fc7ae">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org6dbea8f">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="#orge162ebe">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org24556f6">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orga981ebc">1.1.5. Allocate memory</a></li>
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<li><a href="#org97913a3">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org061eebf">1.1.7. Read two-electron quantities</a>
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<li><a href="#org562f316">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org9e58380">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="#org31f068a">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#orgfd84ca3">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org3006227">1.1.5. Allocate memory</a></li>
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<li><a href="#org8817ee9">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org044144c">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#org09c09b3">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#orge31cc6f">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#orgdc70d60">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org465d93b">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="#orgafc812a">1.1.8. Compute the energy</a></li>
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<li><a href="#org5758af8">1.1.9. Terminate</a></li>
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<li><a href="#orgadfa968">1.1.8. Compute the energy</a></li>
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<li><a href="#orgfd61ee3">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="#orga1e04c8">2. Reading determinants</a>
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<li><a href="#org17f9fd4">2. Reading determinants</a>
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<ul>
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<li><a href="#orga69c106">2.1. Fortran</a></li>
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<li><a href="#orgd5bb71c">2.1. Fortran</a></li>
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</ul>
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</li>
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</ul>
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@ -365,12 +365,12 @@ for the JavaScript code in this tag.
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</div>
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<div id="outline-container-org55b95b4" class="outline-2">
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<h2 id="org55b95b4"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
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<div id="outline-container-org9b82c10" class="outline-2">
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<h2 id="org9b82c10"><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-org5121153" class="outline-3">
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<h3 id="org5121153"><span class="section-number-3">1.1</span> Fortran</h3>
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<div id="outline-container-org99b90c1" class="outline-3">
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<h3 id="org99b90c1"><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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@ -416,8 +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-orgc4fc7ae" class="outline-4">
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<h4 id="orgc4fc7ae"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-org562f316" class="outline-4">
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<h4 id="org562f316"><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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@ -432,8 +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-org6dbea8f" class="outline-4">
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<h4 id="org6dbea8f"><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-org9e58380" class="outline-4">
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<h4 id="org9e58380"><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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@ -449,8 +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-orge162ebe" class="outline-4">
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<h4 id="orge162ebe"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-org31f068a" class="outline-4">
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<h4 id="org31f068a"><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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@ -464,8 +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-org24556f6" class="outline-4">
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<h4 id="org24556f6"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-orgfd84ca3" class="outline-4">
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<h4 id="orgfd84ca3"><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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@ -479,8 +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-orga981ebc" class="outline-4">
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<h4 id="orga981ebc"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div id="outline-container-org3006227" class="outline-4">
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<h4 id="org3006227"><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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@ -492,8 +492,8 @@ W(:,:,:,:) = 0.d0
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</div>
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</div>
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<div id="outline-container-org97913a3" class="outline-4">
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<h4 id="org97913a3"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div id="outline-container-org8817ee9" class="outline-4">
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<h4 id="org8817ee9"><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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@ -525,8 +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-org061eebf" class="outline-4">
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||||
<h4 id="org061eebf"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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||||
<div id="outline-container-org044144c" class="outline-4">
|
||||
<h4 id="org044144c"><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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@ -542,8 +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-org09c09b3" class="outline-5">
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<h5 id="org09c09b3"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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<div id="outline-container-orgdc70d60" class="outline-5">
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<h5 id="orgdc70d60"><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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@ -592,8 +592,8 @@ icount = BUFSIZE
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</div>
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</div>
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<div id="outline-container-orge31cc6f" class="outline-5">
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<h5 id="orge31cc6f"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-org465d93b" class="outline-5">
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<h5 id="org465d93b"><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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@ -637,8 +637,8 @@ icount = bufsize
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</div>
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</div>
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<div id="outline-container-orgafc812a" class="outline-4">
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<h4 id="orgafc812a"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div id="outline-container-orgadfa968" class="outline-4">
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<h4 id="orgadfa968"><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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@ -684,8 +684,8 @@ E = E + E_nn
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</div>
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</div>
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<div id="outline-container-org5758af8" class="outline-4">
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<h4 id="org5758af8"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-orgfd61ee3" class="outline-4">
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<h4 id="orgfd61ee3"><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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@ -699,12 +699,12 @@ E = E + E_nn
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</div>
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<div id="outline-container-orga1e04c8" class="outline-2">
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<h2 id="orga1e04c8"><span class="section-number-2">2</span> Reading determinants</h2>
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<div id="outline-container-org17f9fd4" class="outline-2">
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<h2 id="org17f9fd4"><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-orga69c106" class="outline-3">
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<h3 id="orga69c106"><span class="section-number-3">2.1</span> Fortran</h3>
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<div id="outline-container-orgd5bb71c" class="outline-3">
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<h3 id="orgd5bb71c"><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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@ -712,10 +712,10 @@ E = E + E_nn
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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>
|
||||
<span style="color: #228b22;">character</span>*(128) ::<span style="color: #a0522d;"> err_msg </span>! <span style="color: #b22222;">Error message</span>
|
||||
<span style="color: #228b22;">character</span>*(128) ::<span style="color: #a0522d;"> filename </span>! <span style="color: #b22222;">Name of the input file</span>
|
||||
<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>
|
||||
<span style="color: #228b22;">integer</span>(trexio_t) ::<span style="color: #a0522d;"> trex_determinant_file </span>! <span style="color: #b22222;">TREXIO file handle</span>
|
||||
<span style="color: #228b22;">character</span>*(128) ::<span style="color: #a0522d;"> err_msg </span>! <span style="color: #b22222;">Error message</span>
|
||||
|
||||
|
||||
<span style="color: #228b22;">integer</span>*8, <span style="color: #a020f0;">allocatable</span> ::<span style="color: #a0522d;"> buffer(:,:,:)</span>
|
||||
@ -735,9 +735,19 @@ E = E + E_nn
|
||||
<span style="color: #a020f0;">end if</span>
|
||||
|
||||
rc = trexio_read_determinant_num(trex_determinant_file, ndet)
|
||||
<span style="color: #a020f0;">if</span> (rc /= TREXIO_SUCCESS) <span style="color: #a020f0;">then</span>
|
||||
<span style="color: #a020f0;">call</span> <span style="color: #0000ff;">trexio_string_of_error</span>(rc, err_msg)
|
||||
<span style="color: #a020f0;">print</span> *, <span style="color: #8b2252;">'Error reading determinant_num: '</span>//<span style="color: #a020f0;">trim</span>(err_msg)
|
||||
<span style="color: #a020f0;">stop</span>
|
||||
<span style="color: #a020f0;">end if</span>
|
||||
<span style="color: #a020f0;">print</span> *, <span style="color: #8b2252;">'ndet'</span>, ndet
|
||||
|
||||
rc = trexio_get_int64_num(trex_determinant_file, int64_num)
|
||||
<span style="color: #a020f0;">if</span> (rc /= TREXIO_SUCCESS) <span style="color: #a020f0;">then</span>
|
||||
<span style="color: #a020f0;">call</span> <span style="color: #0000ff;">trexio_string_of_error</span>(rc, err_msg)
|
||||
<span style="color: #a020f0;">print</span> *, <span style="color: #8b2252;">'Error reading int64_num: '</span>//<span style="color: #a020f0;">trim</span>(err_msg)
|
||||
<span style="color: #a020f0;">stop</span>
|
||||
<span style="color: #a020f0;">end if</span>
|
||||
<span style="color: #a020f0;">print</span> *, <span style="color: #8b2252;">'int64_num'</span>, int64_num
|
||||
|
||||
BUFSIZE = 1000_8
|
||||
@ -760,7 +770,9 @@ E = E + E_nn
|
||||
<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>
|
||||
<span style="color: #a020f0;">end do</span>
|
||||
|
||||
<span style="color: #a020f0;">deallocate</span>(buffer, orb_list_dn, orb_list_up)
|
||||
|
||||
end
|
||||
</pre>
|
||||
@ -771,7 +783,7 @@ end
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-06-27 Mon 15:18</p>
|
||||
<p class="date">Created: 2022-06-28 Tue 08:16</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>
|
||||
<!-- 2022-06-27 Mon 15:18 -->
|
||||
<!-- 2022-06-28 Tue 08:16 -->
|
||||
<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: 2022-06-27 Mon 15:18</p>
|
||||
<p class="date">Created: 2022-06-28 Tue 08:16</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>
|
||||
<!-- 2022-06-27 Mon 15:18 -->
|
||||
<!-- 2022-06-28 Tue 08:16 -->
|
||||
<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="#org5e479fc">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org7d1f97f">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgccf49bf">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orgb0c113f">4. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org4db0049">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org7deb387">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#org172ebd5">7. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org77aaa47">8. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#org50eb215">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org7ac2b23">10. Source code for the determinant part</a></li>
|
||||
<li><a href="#orgf3608ae">11. Helper functions</a></li>
|
||||
<li><a href="#org4da58d4">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org8df2bc4">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgdc1b22c">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org7000560">4. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgf224ab7">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgcced5ae">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#orgb2188bf">7. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orga658fae">8. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgfad8c26">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orge5b9474">10. Source code for the determinant part</a></li>
|
||||
<li><a href="#orgfd1e449">11. Helper functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5e479fc" class="outline-2">
|
||||
<h2 id="org5e479fc"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-org4da58d4" class="outline-2">
|
||||
<h2 id="org4da58d4"><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-org7d1f97f" class="outline-2">
|
||||
<h2 id="org7d1f97f"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-org8df2bc4" class="outline-2">
|
||||
<h2 id="org8df2bc4"><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-orgccf49bf" class="outline-2">
|
||||
<h2 id="orgccf49bf"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-orgdc1b22c" class="outline-2">
|
||||
<h2 id="orgdc1b22c"><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-orgb0c113f" class="outline-2">
|
||||
<h2 id="orgb0c113f"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-org7000560" class="outline-2">
|
||||
<h2 id="org7000560"><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-org4db0049" class="outline-2">
|
||||
<h2 id="org4db0049"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-orgf224ab7" class="outline-2">
|
||||
<h2 id="orgf224ab7"><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-org7deb387" class="outline-2">
|
||||
<h2 id="org7deb387"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-orgcced5ae" class="outline-2">
|
||||
<h2 id="orgcced5ae"><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-org172ebd5" class="outline-2">
|
||||
<h2 id="org172ebd5"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-orgb2188bf" class="outline-2">
|
||||
<h2 id="orgb2188bf"><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-org77aaa47" class="outline-2">
|
||||
<h2 id="org77aaa47"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-orga658fae" class="outline-2">
|
||||
<h2 id="orga658fae"><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-org50eb215" class="outline-2">
|
||||
<h2 id="org50eb215"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-orgfad8c26" class="outline-2">
|
||||
<h2 id="orgfad8c26"><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-org7ac2b23" class="outline-2">
|
||||
<h2 id="org7ac2b23"><span class="section-number-2">10</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-orge5b9474" class="outline-2">
|
||||
<h2 id="orge5b9474"><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-orgf3608ae" class="outline-2">
|
||||
<h2 id="orgf3608ae"><span class="section-number-2">11</span> Helper functions</h2>
|
||||
<div id="outline-container-orgfd1e449" class="outline-2">
|
||||
<h2 id="orgfd1e449"><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: 2022-06-27 Mon 15:18</p>
|
||||
<p class="date">Created: 2022-06-28 Tue 08:16</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>
|
||||
<!-- 2022-06-27 Mon 15:18 -->
|
||||
<!-- 2022-06-28 Tue 08:16 -->
|
||||
<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="#org4552f4b">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#orgf2b012f">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org0465ec3">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org65d8227">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org74dfe0a">5. Template for text read a group</a></li>
|
||||
<li><a href="#orgae1f8c7">6. Template for text flush a group</a></li>
|
||||
<li><a href="#org51a2378">7. Template for text free memory</a></li>
|
||||
<li><a href="#org2a88c94">8. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org2a67e36">9. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgafddbbb">10. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org5186f30">11. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgd859cc0">12. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org3e0ee4c">13. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orgb03f2af">14. Source code for the determinant part</a></li>
|
||||
<li><a href="#org4e2c443">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org49c2435">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org33ec18a">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#orgc5aabe0">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org0940142">5. Template for text read a group</a></li>
|
||||
<li><a href="#orgf7e5fe6">6. Template for text flush a group</a></li>
|
||||
<li><a href="#org380df5e">7. Template for text free memory</a></li>
|
||||
<li><a href="#orgc6b1292">8. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org351f00d">9. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org5b7534f">10. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgffa7327">11. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgf7cd0b6">12. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org7504d03">13. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org850b07c">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-org4552f4b" class="outline-2">
|
||||
<h2 id="org4552f4b"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div id="outline-container-org4e2c443" class="outline-2">
|
||||
<h2 id="org4e2c443"><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-orgf2b012f" class="outline-2">
|
||||
<h2 id="orgf2b012f"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div id="outline-container-org49c2435" class="outline-2">
|
||||
<h2 id="org49c2435"><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-org0465ec3" class="outline-2">
|
||||
<h2 id="org0465ec3"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div id="outline-container-org33ec18a" class="outline-2">
|
||||
<h2 id="org33ec18a"><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-org65d8227" class="outline-2">
|
||||
<h2 id="org65d8227"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div id="outline-container-orgc5aabe0" class="outline-2">
|
||||
<h2 id="orgc5aabe0"><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-org74dfe0a" class="outline-2">
|
||||
<h2 id="org74dfe0a"><span class="section-number-2">5</span> Template for text read a group</h2>
|
||||
<div id="outline-container-org0940142" class="outline-2">
|
||||
<h2 id="org0940142"><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-orgae1f8c7" class="outline-2">
|
||||
<h2 id="orgae1f8c7"><span class="section-number-2">6</span> Template for text flush a group</h2>
|
||||
<div id="outline-container-orgf7e5fe6" class="outline-2">
|
||||
<h2 id="orgf7e5fe6"><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-org51a2378" class="outline-2">
|
||||
<h2 id="org51a2378"><span class="section-number-2">7</span> Template for text free memory</h2>
|
||||
<div id="outline-container-org380df5e" class="outline-2">
|
||||
<h2 id="org380df5e"><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-org2a88c94" class="outline-2">
|
||||
<h2 id="org2a88c94"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-orgc6b1292" class="outline-2">
|
||||
<h2 id="orgc6b1292"><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-org2a67e36" class="outline-2">
|
||||
<h2 id="org2a67e36"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org351f00d" class="outline-2">
|
||||
<h2 id="org351f00d"><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-orgafddbbb" class="outline-2">
|
||||
<h2 id="orgafddbbb"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org5b7534f" class="outline-2">
|
||||
<h2 id="org5b7534f"><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-org5186f30" class="outline-2">
|
||||
<h2 id="org5186f30"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
|
||||
<div id="outline-container-orgffa7327" class="outline-2">
|
||||
<h2 id="orgffa7327"><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-orgd859cc0" class="outline-2">
|
||||
<h2 id="orgd859cc0"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div id="outline-container-orgf7cd0b6" class="outline-2">
|
||||
<h2 id="orgf7cd0b6"><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-org3e0ee4c" class="outline-2">
|
||||
<h2 id="org3e0ee4c"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-org7504d03" class="outline-2">
|
||||
<h2 id="org7504d03"><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-orgb03f2af" class="outline-2">
|
||||
<h2 id="orgb03f2af"><span class="section-number-2">14</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org850b07c" class="outline-2">
|
||||
<h2 id="org850b07c"><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: 2022-06-27 Mon 15:18</p>
|
||||
<p class="date">Created: 2022-06-28 Tue 08:16</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>
|
||||
<!-- 2022-06-27 Mon 15:18 -->
|
||||
<!-- 2022-06-28 Tue 08:16 -->
|
||||
<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="#org2eb785f">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#orgc0b522d">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org0aaa67a">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org44967bd">4. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#org75f3edf">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org45f60fe">2. Electron (electron group)</a></li>
|
||||
<li><a href="#orgce900f7">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org7a648de">4. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#orgbb35f47">4.1. Example</a></li>
|
||||
<li><a href="#org7ab7b1e">4.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org0a4adea">5. Basis set (basis group)</a>
|
||||
<li><a href="#org1bbccb1">5. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#org166bca7">5.1. Example</a></li>
|
||||
<li><a href="#org5ce2b74">5.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org4c85e23">6. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#org1922695">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="#orgab9d1bc">7. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org76c76cc">7. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#org30a0074">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org75dfb1b">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#org121026b">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orgf37f115">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org648f813">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org3a63206">9. Excited states (state group)</a></li>
|
||||
<li><a href="#org341b9a4">10. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org8bba62a">11. Cell (cell group)</a></li>
|
||||
<li><a href="#org069ce74">12. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#org89b4829">13. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
<li><a href="#orgb38e06b">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org36e99af">9. Excited states (state group)</a></li>
|
||||
<li><a href="#org3f306dc">10. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org4467f13">11. Cell (cell group)</a></li>
|
||||
<li><a href="#orgc367fea">12. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#orgedd1906">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-org2eb785f" class="outline-2">
|
||||
<h2 id="org2eb785f"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-org75f3edf" class="outline-2">
|
||||
<h2 id="org75f3edf"><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="orgda3c7c3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgbc51bca" 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-orgc0b522d" class="outline-2">
|
||||
<h2 id="orgc0b522d"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div id="outline-container-org45f60fe" class="outline-2">
|
||||
<h2 id="org45f60fe"><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="org737725b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org4639a3a" 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-org0aaa67a" class="outline-2">
|
||||
<h2 id="org0aaa67a"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div id="outline-container-orgce900f7" class="outline-2">
|
||||
<h2 id="orgce900f7"><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="org8165391" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga7418b6" 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-org44967bd" class="outline-2">
|
||||
<h2 id="org44967bd"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div id="outline-container-org7a648de" class="outline-2">
|
||||
<h2 id="org7a648de"><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="orgcf52957" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orge6d02c7" 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-orgbb35f47" class="outline-3">
|
||||
<h3 id="orgbb35f47"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div id="outline-container-org7ab7b1e" class="outline-3">
|
||||
<h3 id="org7ab7b1e"><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-org0a4adea" class="outline-2">
|
||||
<h2 id="org0a4adea"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div id="outline-container-org1bbccb1" class="outline-2">
|
||||
<h2 id="org1bbccb1"><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="org257e528" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org681ad23" 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-org166bca7" class="outline-3">
|
||||
<h3 id="org166bca7"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div id="outline-container-org5ce2b74" class="outline-3">
|
||||
<h3 id="org5ce2b74"><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-org4c85e23" class="outline-2">
|
||||
<h2 id="org4c85e23"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div id="outline-container-org1922695" class="outline-2">
|
||||
<h2 id="org1922695"><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="#org0a4adea">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#org1bbccb1">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="orge057762" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org9a01349" 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-org34dbf62" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org34dbf62"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div id="outline-container-orgae1604c" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="orgae1604c"></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="org97b409a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd86073c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1286,8 +1286,8 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8e444af" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org8e444af"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div id="outline-container-orge809d65" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="orge809d65"></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="org6223c2a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org5ceeaea" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1348,10 +1348,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgab9d1bc" class="outline-2">
|
||||
<h2 id="orgab9d1bc"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div id="outline-container-org76c76cc" class="outline-2">
|
||||
<h2 id="org76c76cc"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="orgce1c0ad" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org266a5c1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1424,8 +1424,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org30a0074" class="outline-3">
|
||||
<h3 id="org30a0074"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div id="outline-container-org121026b" class="outline-3">
|
||||
<h3 id="org121026b"><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="orge1384c0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org12ba11e" 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-org75dfb1b" class="outline-3">
|
||||
<h3 id="org75dfb1b"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div id="outline-container-orgf37f115" class="outline-3">
|
||||
<h3 id="orgf37f115"><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="orgaf36671" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org9fbb1b7" 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-org648f813" class="outline-2">
|
||||
<h2 id="org648f813"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
|
||||
<div id="outline-container-orgb38e06b" class="outline-2">
|
||||
<h2 id="orgb38e06b"><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="org24745f7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org3588963" 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-org3a63206" class="outline-2">
|
||||
<h2 id="org3a63206"><span class="section-number-2">9</span> Excited states (state group)</h2>
|
||||
<div id="outline-container-org36e99af" class="outline-2">
|
||||
<h2 id="org36e99af"><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="org0fb4b65" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgbb6e38a" 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-org341b9a4" class="outline-2">
|
||||
<h2 id="org341b9a4"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
|
||||
<div id="outline-container-org3f306dc" class="outline-2">
|
||||
<h2 id="org3f306dc"><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="orgda2dea0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1cff17f" 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-org8bba62a" class="outline-2">
|
||||
<h2 id="org8bba62a"><span class="section-number-2">11</span> Cell (cell group)</h2>
|
||||
<div id="outline-container-org4467f13" class="outline-2">
|
||||
<h2 id="org4467f13"><span class="section-number-2">11</span> Cell (cell group)</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<table id="orgc91b9a5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org730dfbb" 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-org069ce74" class="outline-2">
|
||||
<h2 id="org069ce74"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div id="outline-container-orgc367fea" class="outline-2">
|
||||
<h2 id="orgc367fea"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<table id="orgbee2fc2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgfbcee5a" 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-org89b4829" class="outline-2">
|
||||
<h2 id="org89b4829"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div id="outline-container-orgedd1906" class="outline-2">
|
||||
<h2 id="orgedd1906"><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="org420185e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgf7346cd" 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: 2022-06-27 Mon 15:18</p>
|
||||
<p class="date">Created: 2022-06-28 Tue 08:16</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
Loading…
Reference in New Issue
Block a user