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@ -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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<!-- 2022-07-12 Tue 17:36 -->
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<!-- 2022-07-26 Tue 12:07 -->
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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
|
||||
</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: 2022-07-12 Tue 17:36</p>
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||||
<p class="date">Created: 2022-07-26 Tue 12:07</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>
|
||||
</body>
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||||
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||||
@ -3,7 +3,7 @@
|
||||
"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">
|
||||
<head>
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||||
<!-- 2022-07-12 Tue 17:36 -->
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||||
<!-- 2022-07-26 Tue 12:07 -->
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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="#org2370452">1. Accessing sparse quantities (integrals)</a>
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<li><a href="#orgeb5a3bd">1. Accessing sparse quantities (integrals)</a>
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<ul>
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<li><a href="#orgff69caf">1.1. Fortran</a>
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<li><a href="#org87d9a1f">1.1. Fortran</a>
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||||
<ul>
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||||
<li><a href="#orgb6d531a">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#orgd9c959f">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="#org04f5b35">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org30a23b9">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orgc7bd5b5">1.1.5. Allocate memory</a></li>
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<li><a href="#orgacb8087">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org43bd810">1.1.7. Read two-electron quantities</a>
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<li><a href="#org86263da">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org8f04b13">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="#org3b5c6b7">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org9047854">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orgd202109">1.1.5. Allocate memory</a></li>
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<li><a href="#org3d77169">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#orga6a9dbe">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#orgd36f648">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org653643f">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#org10b4fee">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org7ef61d9">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="#org68be9da">1.1.8. Compute the energy</a></li>
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<li><a href="#orgf5d9010">1.1.9. Terminate</a></li>
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<li><a href="#orgf6d6bcb">1.1.8. Compute the energy</a></li>
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<li><a href="#org2e02579">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="#orgd7b7059">2. Reading determinants</a>
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<li><a href="#orgf43263d">2. Reading determinants</a>
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<ul>
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<li><a href="#org9336164">2.1. Fortran</a></li>
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<li><a href="#orgd2d0c85">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-org2370452" class="outline-2">
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<h2 id="org2370452"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
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<div id="outline-container-orgeb5a3bd" class="outline-2">
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||||
<h2 id="orgeb5a3bd"><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-orgff69caf" class="outline-3">
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<h3 id="orgff69caf"><span class="section-number-3">1.1</span> Fortran</h3>
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||||
<div id="outline-container-org87d9a1f" class="outline-3">
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||||
<h3 id="org87d9a1f"><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-orgb6d531a" class="outline-4">
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<h4 id="orgb6d531a"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-org86263da" class="outline-4">
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<h4 id="org86263da"><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-orgd9c959f" class="outline-4">
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<h4 id="orgd9c959f"><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-org8f04b13" class="outline-4">
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<h4 id="org8f04b13"><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-org04f5b35" class="outline-4">
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<h4 id="org04f5b35"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-org3b5c6b7" class="outline-4">
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<h4 id="org3b5c6b7"><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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||||
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||||
<div id="outline-container-org30a23b9" class="outline-4">
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<h4 id="org30a23b9"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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||||
<div id="outline-container-org9047854" class="outline-4">
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<h4 id="org9047854"><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-orgc7bd5b5" class="outline-4">
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||||
<h4 id="orgc7bd5b5"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div id="outline-container-orgd202109" class="outline-4">
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<h4 id="orgd202109"><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-orgacb8087" class="outline-4">
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<h4 id="orgacb8087"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div id="outline-container-org3d77169" class="outline-4">
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||||
<h4 id="org3d77169"><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-org43bd810" class="outline-4">
|
||||
<h4 id="org43bd810"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
|
||||
<div id="outline-container-orga6a9dbe" class="outline-4">
|
||||
<h4 id="orga6a9dbe"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
|
||||
<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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|
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<div id="outline-container-orgd36f648" class="outline-5">
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<h5 id="orgd36f648"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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||||
<div id="outline-container-org10b4fee" class="outline-5">
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||||
<h5 id="org10b4fee"><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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|
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<div id="outline-container-org653643f" class="outline-5">
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<h5 id="org653643f"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-org7ef61d9" class="outline-5">
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||||
<h5 id="org7ef61d9"><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-org68be9da" class="outline-4">
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||||
<h4 id="org68be9da"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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||||
<div id="outline-container-orgf6d6bcb" class="outline-4">
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||||
<h4 id="orgf6d6bcb"><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-orgf5d9010" class="outline-4">
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||||
<h4 id="orgf5d9010"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-org2e02579" class="outline-4">
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||||
<h4 id="org2e02579"><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-orgd7b7059" class="outline-2">
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<h2 id="orgd7b7059"><span class="section-number-2">2</span> Reading determinants</h2>
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<div id="outline-container-orgf43263d" class="outline-2">
|
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<h2 id="orgf43263d"><span class="section-number-2">2</span> Reading determinants</h2>
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<div class="outline-text-2" id="text-2">
|
||||
</div>
|
||||
<div id="outline-container-org9336164" class="outline-3">
|
||||
<h3 id="org9336164"><span class="section-number-3">2.1</span> Fortran</h3>
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||||
<div id="outline-container-orgd2d0c85" class="outline-3">
|
||||
<h3 id="orgd2d0c85"><span class="section-number-3">2.1</span> Fortran</h3>
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<div class="outline-text-3" id="text-2-1">
|
||||
<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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@ -783,7 +783,7 @@ end
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-07-12 Tue 17:36</p>
|
||||
<p class="date">Created: 2022-07-26 Tue 12:07</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>
|
||||
<!-- 2022-07-12 Tue 17:36 -->
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||||
<!-- 2022-07-26 Tue 12:07 -->
|
||||
<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: 2022-07-12 Tue 17:36</p>
|
||||
<p class="date">Created: 2022-07-26 Tue 12:07</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 @@
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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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||||
<!-- 2022-07-12 Tue 17:36 -->
|
||||
<!-- 2022-07-26 Tue 12:07 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
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<title>HDF5 back end</title>
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@ -311,24 +311,24 @@ for the JavaScript code in this tag.
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<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orgc0edf4b">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org335e9cd">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgd7cba9d">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org5302791">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#org479d41a">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgb61dee2">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
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<li><a href="#org967a42d">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
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<li><a href="#org94dc01c">8. Template for HDF5 has/read/write a dataset of strings</a></li>
|
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<li><a href="#org058c445">9. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgf3af49c">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org3d36fe4">11. Source code for the determinant part</a></li>
|
||||
<li><a href="#orgd8ffcaa">12. Helper functions</a></li>
|
||||
<li><a href="#orgc81183b">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#orgb75b36e">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orge459967">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org40fb719">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#orga64a2f2">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orga4f021b">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org9f65a6e">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#orgc6548dd">8. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org3739a82">9. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgd286137">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orgd6d47f6">11. Source code for the determinant part</a></li>
|
||||
<li><a href="#org5d1476c">12. Helper functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc0edf4b" class="outline-2">
|
||||
<h2 id="orgc0edf4b"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-orgc81183b" class="outline-2">
|
||||
<h2 id="orgc81183b"><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>
|
||||
@ -340,8 +340,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org335e9cd" class="outline-2">
|
||||
<h2 id="org335e9cd"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-orgb75b36e" class="outline-2">
|
||||
<h2 id="orgb75b36e"><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
|
||||
@ -361,8 +361,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd7cba9d" class="outline-2">
|
||||
<h2 id="orgd7cba9d"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-orge459967" class="outline-2">
|
||||
<h2 id="orge459967"><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>
|
||||
@ -467,8 +467,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5302791" class="outline-2">
|
||||
<h2 id="org5302791"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
|
||||
<div id="outline-container-org40fb719" class="outline-2">
|
||||
<h2 id="org40fb719"><span class="section-number-2">4</span> Template for HDF5 has a group</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>
|
||||
@ -498,8 +498,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org479d41a" class="outline-2">
|
||||
<h2 id="org479d41a"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-orga64a2f2" class="outline-2">
|
||||
<h2 id="orga64a2f2"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</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>
|
||||
@ -603,8 +603,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb61dee2" class="outline-2">
|
||||
<h2 id="orgb61dee2"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-orga4f021b" class="outline-2">
|
||||
<h2 id="orga4f021b"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</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>
|
||||
@ -738,8 +738,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org967a42d" class="outline-2">
|
||||
<h2 id="org967a42d"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-org9f65a6e" class="outline-2">
|
||||
<h2 id="org9f65a6e"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<p>
|
||||
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
|
||||
@ -942,8 +942,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org94dc01c" class="outline-2">
|
||||
<h2 id="org94dc01c"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-orgc6548dd" class="outline-2">
|
||||
<h2 id="orgc6548dd"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of strings</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>
|
||||
@ -1141,8 +1141,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org058c445" class="outline-2">
|
||||
<h2 id="org058c445"><span class="section-number-2">9</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org3739a82" class="outline-2">
|
||||
<h2 id="org3739a82"><span class="section-number-2">9</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1269,8 +1269,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgf3af49c" class="outline-2">
|
||||
<h2 id="orgf3af49c"><span class="section-number-2">10</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-orgd286137" class="outline-2">
|
||||
<h2 id="orgd286137"><span class="section-number-2">10</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<p>
|
||||
<b><b>Note:</b></b> in early versions of the HDF5 library (v < 1.10) unlinking an object was not working as expected
|
||||
@ -1310,8 +1310,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3d36fe4" class="outline-2">
|
||||
<h2 id="org3d36fe4"><span class="section-number-2">11</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-orgd6d47f6" class="outline-2">
|
||||
<h2 id="orgd6d47f6"><span class="section-number-2">11</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
|
||||
@ -1564,8 +1564,8 @@ Size specifies the number of data items (e.g. determinants) to process.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd8ffcaa" class="outline-2">
|
||||
<h2 id="orgd8ffcaa"><span class="section-number-2">12</span> Helper functions</h2>
|
||||
<div id="outline-container-org5d1476c" class="outline-2">
|
||||
<h2 id="org5d1476c"><span class="section-number-2">12</span> Helper functions</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1828,7 +1828,7 @@ 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: 2022-07-12 Tue 17:36</p>
|
||||
<p class="date">Created: 2022-07-26 Tue 12:07</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>
|
||||
<!-- 2022-07-12 Tue 17:36 -->
|
||||
<!-- 2022-07-26 Tue 12:07 -->
|
||||
<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>
|
||||
@ -311,21 +311,21 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orgf75be0f">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org88dd90d">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#orgf45f487">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#orgfae3229">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orgb087b32">5. Template for text read a group</a></li>
|
||||
<li><a href="#org1027341">6. Template for text has a group</a></li>
|
||||
<li><a href="#org5216a51">7. Template for text flush a group</a></li>
|
||||
<li><a href="#orgdd1c2d1">8. Template for text free memory</a></li>
|
||||
<li><a href="#orga9d7ede">9. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orge4c69f1">10. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org3c87d6e">11. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org7004d75">12. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org6a0a77a">13. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#orgc187841">14. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org9be4932">15. Source code for the determinant part</a></li>
|
||||
<li><a href="#org09e751d">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org02ec6d4">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org656aed1">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#orgfb57ff4">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orga2a854a">5. Template for text read a group</a></li>
|
||||
<li><a href="#org0f057ef">6. Template for text has a group</a></li>
|
||||
<li><a href="#org7c9bf67">7. Template for text flush a group</a></li>
|
||||
<li><a href="#orgf2b3132">8. Template for text free memory</a></li>
|
||||
<li><a href="#org96096bc">9. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org62ecb8c">10. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgbe06b8a">11. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org32b8c0f">12. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org114c312">13. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#orge3e2b95">14. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org5a76866">15. Source code for the determinant part</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -347,8 +347,8 @@ directory.
|
||||
The file is written when closed, or when the flush function is called.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-orgf75be0f" class="outline-2">
|
||||
<h2 id="orgf75be0f"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div id="outline-container-org09e751d" class="outline-2">
|
||||
<h2 id="org09e751d"><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 {
|
||||
@ -367,8 +367,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org88dd90d" class="outline-2">
|
||||
<h2 id="org88dd90d"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div id="outline-container-org02ec6d4" class="outline-2">
|
||||
<h2 id="org02ec6d4"><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
|
||||
@ -388,8 +388,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf45f487" class="outline-2">
|
||||
<h2 id="orgf45f487"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div id="outline-container-org656aed1" class="outline-2">
|
||||
<h2 id="org656aed1"><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;">bool</span>
|
||||
@ -556,8 +556,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgfae3229" class="outline-2">
|
||||
<h2 id="orgfae3229"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div id="outline-container-orgfb57ff4" class="outline-2">
|
||||
<h2 id="orgfb57ff4"><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>
|
||||
@ -579,8 +579,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb087b32" class="outline-2">
|
||||
<h2 id="orgb087b32"><span class="section-number-2">5</span> Template for text read a group</h2>
|
||||
<div id="outline-container-orga2a854a" class="outline-2">
|
||||
<h2 id="orga2a854a"><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*
|
||||
@ -806,8 +806,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1027341" class="outline-2">
|
||||
<h2 id="org1027341"><span class="section-number-2">6</span> Template for text has a group</h2>
|
||||
<div id="outline-container-org0f057ef" class="outline-2">
|
||||
<h2 id="org0f057ef"><span class="section-number-2">6</span> Template for text has 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>
|
||||
@ -847,8 +847,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5216a51" class="outline-2">
|
||||
<h2 id="org5216a51"><span class="section-number-2">7</span> Template for text flush a group</h2>
|
||||
<div id="outline-container-org7c9bf67" class="outline-2">
|
||||
<h2 id="org7c9bf67"><span class="section-number-2">7</span> Template for text flush a group</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>
|
||||
@ -912,8 +912,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdd1c2d1" class="outline-2">
|
||||
<h2 id="orgdd1c2d1"><span class="section-number-2">8</span> Template for text free memory</h2>
|
||||
<div id="outline-container-orgf2b3132" class="outline-2">
|
||||
<h2 id="orgf2b3132"><span class="section-number-2">8</span> Template for text free memory</h2>
|
||||
<div class="outline-text-2" id="text-8">
|
||||
<p>
|
||||
Memory is allocated when reading. The following function frees memory.
|
||||
@ -982,8 +982,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga9d7ede" class="outline-2">
|
||||
<h2 id="orga9d7ede"><span class="section-number-2">9</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-org96096bc" class="outline-2">
|
||||
<h2 id="org96096bc"><span class="section-number-2">9</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1046,8 +1046,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge4c69f1" class="outline-2">
|
||||
<h2 id="orge4c69f1"><span class="section-number-2">10</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org62ecb8c" class="outline-2">
|
||||
<h2 id="org62ecb8c"><span class="section-number-2">10</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1143,8 +1143,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org3c87d6e" class="outline-2">
|
||||
<h2 id="org3c87d6e"><span class="section-number-2">11</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-orgbe06b8a" class="outline-2">
|
||||
<h2 id="orgbe06b8a"><span class="section-number-2">11</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1245,8 +1245,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org7004d75" class="outline-2">
|
||||
<h2 id="org7004d75"><span class="section-number-2">12</span> Template for has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org32b8c0f" class="outline-2">
|
||||
<h2 id="org32b8c0f"><span class="section-number-2">12</span> Template for has/read/write a string attribute</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1320,8 +1320,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org6a0a77a" class="outline-2">
|
||||
<h2 id="org6a0a77a"><span class="section-number-2">13</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div id="outline-container-org114c312" class="outline-2">
|
||||
<h2 id="org114c312"><span class="section-number-2">13</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div class="outline-text-2" id="text-13">
|
||||
<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
|
||||
@ -1611,8 +1611,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc187841" class="outline-2">
|
||||
<h2 id="orgc187841"><span class="section-number-2">14</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-orge3e2b95" class="outline-2">
|
||||
<h2 id="orge3e2b95"><span class="section-number-2">14</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-14">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1640,8 +1640,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9be4932" class="outline-2">
|
||||
<h2 id="org9be4932"><span class="section-number-2">15</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org5a76866" class="outline-2">
|
||||
<h2 id="org5a76866"><span class="section-number-2">15</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-15">
|
||||
<p>
|
||||
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
|
||||
@ -2081,7 +2081,7 @@ 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: 2022-07-12 Tue 17:36</p>
|
||||
<p class="date">Created: 2022-07-26 Tue 12:07</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>
|
||||
<!-- 2022-07-12 Tue 17:36 -->
|
||||
<!-- 2022-07-26 Tue 12:07 -->
|
||||
<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="#org90b7a29">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org50b7365">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org3b3903e">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#orgceb82d2">4. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#orgb13a2ef">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org517fe02">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org0759ca2">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org1c8a520">4. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#org24e7094">4.1. Example</a></li>
|
||||
<li><a href="#org1102ef7">4.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org4c9e68b">5. Basis set (basis group)</a>
|
||||
<li><a href="#org02a38f7">5. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#orgd2a8d73">5.1. Example</a></li>
|
||||
<li><a href="#org4cfb045">5.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgd56973b">6. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#org11ca494">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="#org853010c">7. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org4b50e99">7. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#org55fbe81">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org3bd70ce">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#orgea29cf1">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orgf5bbbda">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org156ae36">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org5572c73">9. Excited states (state group)</a></li>
|
||||
<li><a href="#org8f43cab">10. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org7a98824">11. Cell (cell group)</a></li>
|
||||
<li><a href="#org97a548b">12. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#orgdff9310">13. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
<li><a href="#org45e5940">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org6b5c562">9. Excited states (state group)</a></li>
|
||||
<li><a href="#org1ac5326">10. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#orgcf789da">11. Cell (cell group)</a></li>
|
||||
<li><a href="#org31d7540">12. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#orgaa0dcae">13. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -417,8 +417,8 @@ For determinants, the <code>special</code> attribute is present in the type. Thi
|
||||
means that the source code is not produced by the generator, but hand-written.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-org90b7a29" class="outline-2">
|
||||
<h2 id="org90b7a29"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-orgb13a2ef" class="outline-2">
|
||||
<h2 id="orgb13a2ef"><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
|
||||
@ -428,7 +428,7 @@ which have participated to the creation of the file, a list of
|
||||
authors of the file, and a textual description.
|
||||
</p>
|
||||
|
||||
<table id="org7cf6049" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgaadc7ca" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -509,15 +509,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org50b7365" class="outline-2">
|
||||
<h2 id="org50b7365"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div id="outline-container-org517fe02" class="outline-2">
|
||||
<h2 id="org517fe02"><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="org10359bf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgc866849" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -563,15 +563,15 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3b3903e" class="outline-2">
|
||||
<h2 id="org3b3903e"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div id="outline-container-org0759ca2" class="outline-2">
|
||||
<h2 id="org0759ca2"><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="org55a235b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2b3940c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -638,8 +638,8 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgceb82d2" class="outline-2">
|
||||
<h2 id="orgceb82d2"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div id="outline-container-org1c8a520" class="outline-2">
|
||||
<h2 id="org1c8a520"><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
|
||||
@ -672,7 +672,7 @@ 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="orgbf8ebbf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga706a8f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -774,8 +774,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org24e7094" class="outline-3">
|
||||
<h3 id="org24e7094"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div id="outline-container-org1102ef7" class="outline-3">
|
||||
<h3 id="org1102ef7"><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
|
||||
@ -838,8 +838,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4c9e68b" class="outline-2">
|
||||
<h2 id="org4c9e68b"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div id="outline-container-org02a38f7" class="outline-2">
|
||||
<h2 id="org02a38f7"><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
|
||||
@ -892,7 +892,7 @@ 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="org981e154" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgfd5bf5c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -986,8 +986,8 @@ All the basis set parameters are stored in one-dimensional arrays:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd2a8d73" class="outline-3">
|
||||
<h3 id="orgd2a8d73"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div id="outline-container-org4cfb045" class="outline-3">
|
||||
<h3 id="org4cfb045"><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
|
||||
@ -1065,8 +1065,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd56973b" class="outline-2">
|
||||
<h2 id="orgd56973b"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div id="outline-container-org11ca494" class="outline-2">
|
||||
<h2 id="org11ca494"><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
|
||||
@ -1119,13 +1119,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#org4c9e68b">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#org02a38f7">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="org6ddbc14" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgdda94dd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1177,8 +1177,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org64a4fa8" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org64a4fa8"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div id="outline-container-orgbd68786" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="orgbd68786"></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}}
|
||||
@ -1195,7 +1195,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orgb4c3b62" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1c0d77e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1290,8 +1290,8 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org55b8b3b" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org55b8b3b"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div id="outline-container-org08dad02" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org08dad02"></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
|
||||
@ -1312,7 +1312,7 @@ notation.
|
||||
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
|
||||
</ul>
|
||||
|
||||
<table id="org0725781" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org32a5378" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1352,10 +1352,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org853010c" class="outline-2">
|
||||
<h2 id="org853010c"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div id="outline-container-org4b50e99" class="outline-2">
|
||||
<h2 id="org4b50e99"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="orgc2ce685" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org17c2714" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1442,8 +1442,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org55fbe81" class="outline-3">
|
||||
<h3 id="org55fbe81"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div id="outline-container-orgea29cf1" class="outline-3">
|
||||
<h3 id="orgea29cf1"><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
|
||||
@ -1451,7 +1451,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orgbc2b2e0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga44e2e3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1546,8 +1546,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3bd70ce" class="outline-3">
|
||||
<h3 id="org3bd70ce"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div id="outline-container-orgf5bbbda" class="outline-3">
|
||||
<h3 id="orgf5bbbda"><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
|
||||
@ -1555,7 +1555,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orgfd8a05a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org89588ed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1595,8 +1595,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org156ae36" class="outline-2">
|
||||
<h2 id="org156ae36"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
|
||||
<div id="outline-container-org45e5940" class="outline-2">
|
||||
<h2 id="org45e5940"><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 \(\Psi\)
|
||||
@ -1638,7 +1638,7 @@ produced by the code generator.
|
||||
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
|
||||
</p>
|
||||
|
||||
<table id="orga0f3b9b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org21b93ca" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1684,8 +1684,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5572c73" class="outline-2">
|
||||
<h2 id="org5572c73"><span class="section-number-2">9</span> Excited states (state group)</h2>
|
||||
<div id="outline-container-org6b5c562" class="outline-2">
|
||||
<h2 id="org6b5c562"><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.
|
||||
@ -1694,7 +1694,7 @@ correspond to excited state wave functions for the same set of
|
||||
determinants. This is the goal of the present group
|
||||
</p>
|
||||
|
||||
<table id="org26e439a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org0f6e604" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1733,8 +1733,8 @@ determinants. This is the goal of the present group
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8f43cab" class="outline-2">
|
||||
<h2 id="org8f43cab"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
|
||||
<div id="outline-container-org1ac5326" class="outline-2">
|
||||
<h2 id="org1ac5326"><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
|
||||
@ -1787,7 +1787,7 @@ The total energy can be computed as:
|
||||
\]
|
||||
</p>
|
||||
|
||||
<table id="org2a0edc4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1f7c917" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1868,10 +1868,10 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7a98824" class="outline-2">
|
||||
<h2 id="org7a98824"><span class="section-number-2">11</span> Cell (cell group)</h2>
|
||||
<div id="outline-container-orgcf789da" class="outline-2">
|
||||
<h2 id="orgcf789da"><span class="section-number-2">11</span> Cell (cell group)</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<table id="org038116b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org595bd1c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1917,10 +1917,10 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org97a548b" class="outline-2">
|
||||
<h2 id="org97a548b"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div id="outline-container-org31d7540" class="outline-2">
|
||||
<h2 id="org31d7540"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<table id="org0f8e3d3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org98837cb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1959,8 +1959,8 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdff9310" class="outline-2">
|
||||
<h2 id="orgdff9310"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div id="outline-container-orgaa0dcae" class="outline-2">
|
||||
<h2 id="orgaa0dcae"><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
|
||||
@ -1974,7 +1974,7 @@ By convention, the electron coordinates contain first all the electrons
|
||||
of $↑$-spin and then all the $↓$-spin.
|
||||
</p>
|
||||
|
||||
<table id="org2078cd1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org581bef3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2029,7 +2029,7 @@ of $↑$-spin and then all the $↓$-spin.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-07-12 Tue 17:36</p>
|
||||
<p class="date">Created: 2022-07-26 Tue 12:07</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