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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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<!-- 2022-12-02 Fri 08:48 -->
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<!-- 2022-12-05 Mon 13:54 -->
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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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||||
@ -360,7 +360,7 @@ 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: 2022-12-02 Fri 08:48</p>
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||||
<p class="date">Created: 2022-12-05 Mon 13:54</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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@ -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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||||
<!-- 2022-12-02 Fri 08:48 -->
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||||
<!-- 2022-12-05 Mon 13:54 -->
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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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@ -346,31 +346,31 @@ 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="#org6b88d96">1. Accessing sparse quantities (integrals)</a>
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<li><a href="#org3f9dda8">1. Accessing sparse quantities (integrals)</a>
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<ul>
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<li><a href="#org77f2fef">1.1. Fortran</a>
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<li><a href="#org9d0d64e">1.1. Fortran</a>
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||||
<ul>
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||||
<li><a href="#org9d1ab54">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#orge5b9684">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="#org8bc95b2">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org5316411">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org7b3bf4c">1.1.5. Allocate memory</a></li>
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<li><a href="#orgcda4eee">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#orga0e50c4">1.1.7. Read two-electron quantities</a>
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<li><a href="#org65bdf81">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#orge49b5b2">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="#org6366bab">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org581ec8d">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orgfcee76e">1.1.5. Allocate memory</a></li>
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<li><a href="#org5d03b11">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org52fbc32">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#orgb6134a9">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org95156a4">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#org7ea4e98">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org12198e6">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="#orga2bfd9e">1.1.8. Compute the energy</a></li>
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<li><a href="#org926082a">1.1.9. Terminate</a></li>
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<li><a href="#org7eee29a">1.1.8. Compute the energy</a></li>
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<li><a href="#org0b619f1">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="#orgdbb7d24">2. Reading determinants</a>
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<li><a href="#org4ba481a">2. Reading determinants</a>
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<ul>
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<li><a href="#orgd2c50cf">2.1. Fortran</a></li>
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<li><a href="#org5b18ddb">2.1. Fortran</a></li>
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</ul>
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</li>
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</ul>
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@ -378,12 +378,12 @@ for the JavaScript code in this tag.
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</div>
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<div id="outline-container-org6b88d96" class="outline-2">
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<h2 id="org6b88d96"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
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<div id="outline-container-org3f9dda8" class="outline-2">
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<h2 id="org3f9dda8"><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-org77f2fef" class="outline-3">
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<h3 id="org77f2fef"><span class="section-number-3">1.1</span> Fortran</h3>
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<div id="outline-container-org9d0d64e" class="outline-3">
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<h3 id="org9d0d64e"><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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@ -429,8 +429,8 @@ 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-org9d1ab54" class="outline-4">
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<h4 id="org9d1ab54"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-org65bdf81" class="outline-4">
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<h4 id="org65bdf81"><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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@ -445,8 +445,8 @@ 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-orge5b9684" class="outline-4">
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<h4 id="orge5b9684"><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-orge49b5b2" class="outline-4">
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<h4 id="orge49b5b2"><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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@ -462,8 +462,8 @@ 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-org8bc95b2" class="outline-4">
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<h4 id="org8bc95b2"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-org6366bab" class="outline-4">
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<h4 id="org6366bab"><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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@ -477,8 +477,8 @@ 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-org5316411" class="outline-4">
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<h4 id="org5316411"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-org581ec8d" class="outline-4">
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<h4 id="org581ec8d"><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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@ -492,8 +492,8 @@ 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-org7b3bf4c" class="outline-4">
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<h4 id="org7b3bf4c"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div id="outline-container-orgfcee76e" class="outline-4">
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<h4 id="orgfcee76e"><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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@ -505,8 +505,8 @@ W(:,:,:,:) = 0.d0
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</div>
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</div>
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<div id="outline-container-orgcda4eee" class="outline-4">
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<h4 id="orgcda4eee"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div id="outline-container-org5d03b11" class="outline-4">
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<h4 id="org5d03b11"><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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@ -538,8 +538,8 @@ 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-orga0e50c4" class="outline-4">
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||||
<h4 id="orga0e50c4"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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<div id="outline-container-org52fbc32" class="outline-4">
|
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<h4 id="org52fbc32"><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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@ -555,8 +555,8 @@ 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-orgb6134a9" class="outline-5">
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<h5 id="orgb6134a9"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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<div id="outline-container-org7ea4e98" class="outline-5">
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||||
<h5 id="org7ea4e98"><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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@ -605,8 +605,8 @@ icount = BUFSIZE
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</div>
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</div>
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<div id="outline-container-org95156a4" class="outline-5">
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<h5 id="org95156a4"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-org12198e6" class="outline-5">
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<h5 id="org12198e6"><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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@ -650,8 +650,8 @@ icount = bufsize
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</div>
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</div>
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<div id="outline-container-orga2bfd9e" class="outline-4">
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<h4 id="orga2bfd9e"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div id="outline-container-org7eee29a" class="outline-4">
|
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<h4 id="org7eee29a"><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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@ -697,8 +697,8 @@ E = E + E_nn
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</div>
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</div>
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<div id="outline-container-org926082a" class="outline-4">
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<h4 id="org926082a"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-org0b619f1" class="outline-4">
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<h4 id="org0b619f1"><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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@ -712,12 +712,12 @@ E = E + E_nn
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</div>
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<div id="outline-container-orgdbb7d24" class="outline-2">
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<h2 id="orgdbb7d24"><span class="section-number-2">2</span> Reading determinants</h2>
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<div id="outline-container-org4ba481a" class="outline-2">
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<h2 id="org4ba481a"><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-orgd2c50cf" class="outline-3">
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<h3 id="orgd2c50cf"><span class="section-number-3">2.1</span> Fortran</h3>
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<div id="outline-container-org5b18ddb" class="outline-3">
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<h3 id="org5b18ddb"><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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@ -796,7 +796,7 @@ end
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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: 2022-12-02 Fri 08:48</p>
|
||||
<p class="date">Created: 2022-12-05 Mon 13:54</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
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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">
|
||||
<head>
|
||||
<!-- 2022-12-02 Fri 08:48 -->
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<!-- 2022-12-05 Mon 13:54 -->
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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" />
|
||||
<title>TREXIO source code documentation</title>
|
||||
@ -360,7 +360,7 @@ and bug reports should be submitted at
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-12-02 Fri 08:48</p>
|
||||
<p class="date">Created: 2022-12-05 Mon 13:54</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
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</body>
|
||||
|
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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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||||
<!-- 2022-12-02 Fri 08:48 -->
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||||
<!-- 2022-12-05 Mon 13:54 -->
|
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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>HDF5 back end</title>
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@ -324,25 +324,25 @@ 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">
|
||||
<ul>
|
||||
<li><a href="#org566b686">1. Template for HDF5 definitions</a></li>
|
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<li><a href="#org1974247">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org9b8ebd2">3. Template for HDF5 init/deinit</a></li>
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<li><a href="#orgd9ce991">4. Template for HDF5 has a group</a></li>
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<li><a href="#org6836f9c">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
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<li><a href="#org8f0d036">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
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<li><a href="#org54ef246">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
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<li><a href="#orgd941e71">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
|
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<li><a href="#orgbb65636">9. Template for HDF5 has/read/write a dataset of strings</a></li>
|
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<li><a href="#org28eaeee">10. Template for HDF5 has/read/write a string attribute</a></li>
|
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<li><a href="#orgd3b1cf1">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
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<li><a href="#org3029933">12. Source code for the determinant part</a></li>
|
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<li><a href="#orgafbeb7b">13. Helper functions</a></li>
|
||||
<li><a href="#orgb677ea1">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org5d7617e">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgd46ccf6">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orgc9e1df9">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#orgd91936c">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org9cca20b">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org93eab8a">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#orgb71744f">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
|
||||
<li><a href="#orge11f92b">9. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orga717280">10. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#org62e1ea4">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org135e72e">12. Source code for the determinant part</a></li>
|
||||
<li><a href="#org2e42922">13. Helper functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org566b686" class="outline-2">
|
||||
<h2 id="org566b686"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-orgb677ea1" class="outline-2">
|
||||
<h2 id="orgb677ea1"><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>
|
||||
@ -354,8 +354,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1974247" class="outline-2">
|
||||
<h2 id="org1974247"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-org5d7617e" class="outline-2">
|
||||
<h2 id="org5d7617e"><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
|
||||
@ -375,8 +375,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9b8ebd2" class="outline-2">
|
||||
<h2 id="org9b8ebd2"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-orgd46ccf6" class="outline-2">
|
||||
<h2 id="orgd46ccf6"><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>
|
||||
@ -496,8 +496,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd9ce991" class="outline-2">
|
||||
<h2 id="orgd9ce991"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
|
||||
<div id="outline-container-orgc9e1df9" class="outline-2">
|
||||
<h2 id="orgc9e1df9"><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>
|
||||
@ -527,8 +527,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6836f9c" class="outline-2">
|
||||
<h2 id="org6836f9c"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-orgd91936c" class="outline-2">
|
||||
<h2 id="orgd91936c"><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>
|
||||
@ -632,8 +632,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8f0d036" class="outline-2">
|
||||
<h2 id="org8f0d036"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org9cca20b" class="outline-2">
|
||||
<h2 id="org9cca20b"><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>
|
||||
@ -767,8 +767,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org54ef246" class="outline-2">
|
||||
<h2 id="org54ef246"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-org93eab8a" class="outline-2">
|
||||
<h2 id="org93eab8a"><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
|
||||
@ -971,8 +971,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd941e71" class="outline-2">
|
||||
<h2 id="orgd941e71"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
|
||||
<div id="outline-container-orgb71744f" class="outline-2">
|
||||
<h2 id="orgb71744f"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
|
||||
<div class="outline-text-2" id="text-8">
|
||||
<p>
|
||||
Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
@ -1107,8 +1107,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgbb65636" class="outline-2">
|
||||
<h2 id="orgbb65636"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-orge11f92b" class="outline-2">
|
||||
<h2 id="orge11f92b"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</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>
|
||||
@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org28eaeee" class="outline-2">
|
||||
<h2 id="org28eaeee"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-orga717280" class="outline-2">
|
||||
<h2 id="orga717280"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1434,8 +1434,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgd3b1cf1" class="outline-2">
|
||||
<h2 id="orgd3b1cf1"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-org62e1ea4" class="outline-2">
|
||||
<h2 id="org62e1ea4"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
<b><b>Note:</b></b> in early versions of the HDF5 library (v < 1.10) unlinking an object was not working as expected
|
||||
@ -1475,8 +1475,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3029933" class="outline-2">
|
||||
<h2 id="org3029933"><span class="section-number-2">12</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org135e72e" class="outline-2">
|
||||
<h2 id="org135e72e"><span class="section-number-2">12</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<p>
|
||||
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
|
||||
@ -1579,8 +1579,8 @@ Size specifies the number of data items (e.g. determinants) to process.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgafbeb7b" class="outline-2">
|
||||
<h2 id="orgafbeb7b"><span class="section-number-2">13</span> Helper functions</h2>
|
||||
<div id="outline-container-org2e42922" class="outline-2">
|
||||
<h2 id="org2e42922"><span class="section-number-2">13</span> Helper functions</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>
|
||||
@ -1843,7 +1843,7 @@ 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: 2022-12-02 Fri 08:48</p>
|
||||
<p class="date">Created: 2022-12-05 Mon 13:54</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>
|
||||
<!-- 2022-12-02 Fri 08:48 -->
|
||||
<!-- 2022-12-05 Mon 13:54 -->
|
||||
<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>
|
||||
@ -324,23 +324,23 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org61721d1">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#orga76fb7f">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org5719d56">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#orgf5e4d10">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org4e7d6dc">5. Flush function (templated part)</a></li>
|
||||
<li><a href="#orgcade9d9">6. Template for text read a group</a></li>
|
||||
<li><a href="#org18c32dd">7. Template for text has a group</a></li>
|
||||
<li><a href="#org3d0015a">8. Template for text flush a group</a></li>
|
||||
<li><a href="#orgf19e278">9. Template for text free memory</a></li>
|
||||
<li><a href="#orga114128">10. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org4e882d1">11. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org2b1d924">12. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgf128167">13. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org048505f">14. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org3275562">15. Template for has/read/write a buffered vector</a></li>
|
||||
<li><a href="#orgdca7700">16. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orge0ad0b6">17. Source code for the determinant part</a></li>
|
||||
<li><a href="#org1cc3959">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org9b1391d">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org2e0469e">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#orgdf8b7b4">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orgdc275f7">5. Flush function (templated part)</a></li>
|
||||
<li><a href="#org9f17e82">6. Template for text read a group</a></li>
|
||||
<li><a href="#org5ab056c">7. Template for text has a group</a></li>
|
||||
<li><a href="#org209d84f">8. Template for text flush a group</a></li>
|
||||
<li><a href="#org0a06a91">9. Template for text free memory</a></li>
|
||||
<li><a href="#orgc073951">10. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgb5f82f4">11. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org268440c">12. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org9c2ba4d">13. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgc93dcc4">14. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org1020f22">15. Template for has/read/write a buffered vector</a></li>
|
||||
<li><a href="#orgdbbbf1b">16. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org27caedd">17. Source code for the determinant part</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -362,8 +362,8 @@ directory.
|
||||
The file is written when closed, or when the flush function is called.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-org61721d1" class="outline-2">
|
||||
<h2 id="org61721d1"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div id="outline-container-org1cc3959" class="outline-2">
|
||||
<h2 id="org1cc3959"><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 {
|
||||
@ -382,8 +382,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga76fb7f" class="outline-2">
|
||||
<h2 id="orga76fb7f"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div id="outline-container-org9b1391d" class="outline-2">
|
||||
<h2 id="org9b1391d"><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
|
||||
@ -403,8 +403,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5719d56" class="outline-2">
|
||||
<h2 id="org5719d56"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div id="outline-container-org2e0469e" class="outline-2">
|
||||
<h2 id="org2e0469e"><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>
|
||||
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf5e4d10" class="outline-2">
|
||||
<h2 id="orgf5e4d10"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div id="outline-container-orgdf8b7b4" class="outline-2">
|
||||
<h2 id="orgdf8b7b4"><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>
|
||||
@ -594,8 +594,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4e7d6dc" class="outline-2">
|
||||
<h2 id="org4e7d6dc"><span class="section-number-2">5</span> Flush function (templated part)</h2>
|
||||
<div id="outline-container-orgdc275f7" class="outline-2">
|
||||
<h2 id="orgdc275f7"><span class="section-number-2">5</span> Flush function (templated part)</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>
|
||||
@ -618,8 +618,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgcade9d9" class="outline-2">
|
||||
<h2 id="orgcade9d9"><span class="section-number-2">6</span> Template for text read a group</h2>
|
||||
<div id="outline-container-org9f17e82" class="outline-2">
|
||||
<h2 id="org9f17e82"><span class="section-number-2">6</span> Template for text read a group</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c">$group$_t*
|
||||
@ -845,8 +845,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org18c32dd" class="outline-2">
|
||||
<h2 id="org18c32dd"><span class="section-number-2">7</span> Template for text has a group</h2>
|
||||
<div id="outline-container-org5ab056c" class="outline-2">
|
||||
<h2 id="org5ab056c"><span class="section-number-2">7</span> Template for text has 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>
|
||||
@ -886,8 +886,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3d0015a" class="outline-2">
|
||||
<h2 id="org3d0015a"><span class="section-number-2">8</span> Template for text flush a group</h2>
|
||||
<div id="outline-container-org209d84f" class="outline-2">
|
||||
<h2 id="org209d84f"><span class="section-number-2">8</span> Template for text flush a group</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>
|
||||
@ -951,8 +951,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf19e278" class="outline-2">
|
||||
<h2 id="orgf19e278"><span class="section-number-2">9</span> Template for text free memory</h2>
|
||||
<div id="outline-container-org0a06a91" class="outline-2">
|
||||
<h2 id="org0a06a91"><span class="section-number-2">9</span> Template for text free memory</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<p>
|
||||
Memory is allocated when reading. The following function frees memory.
|
||||
@ -1021,8 +1021,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga114128" class="outline-2">
|
||||
<h2 id="orga114128"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-orgc073951" class="outline-2">
|
||||
<h2 id="orgc073951"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1085,8 +1085,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4e882d1" class="outline-2">
|
||||
<h2 id="org4e882d1"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-orgb5f82f4" class="outline-2">
|
||||
<h2 id="orgb5f82f4"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1182,8 +1182,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org2b1d924" class="outline-2">
|
||||
<h2 id="org2b1d924"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org268440c" class="outline-2">
|
||||
<h2 id="org268440c"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1284,8 +1284,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgf128167" class="outline-2">
|
||||
<h2 id="orgf128167"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org9c2ba4d" class="outline-2">
|
||||
<h2 id="org9c2ba4d"><span class="section-number-2">13</span> Template for has/read/write a string attribute</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>
|
||||
@ -1359,8 +1359,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org048505f" class="outline-2">
|
||||
<h2 id="org048505f"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div id="outline-container-orgc93dcc4" class="outline-2">
|
||||
<h2 id="orgc93dcc4"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div class="outline-text-2" id="text-14">
|
||||
<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
|
||||
@ -1650,8 +1650,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3275562" class="outline-2">
|
||||
<h2 id="org3275562"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
|
||||
<div id="outline-container-org1020f22" class="outline-2">
|
||||
<h2 id="org1020f22"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</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 buffered I/O has to be decoupled
|
||||
@ -1881,8 +1881,8 @@ Size specifies the number of vector elements to be written.
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgdca7700" class="outline-2">
|
||||
<h2 id="orgdca7700"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-orgdbbbf1b" class="outline-2">
|
||||
<h2 id="orgdbbbf1b"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-16">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1910,8 +1910,8 @@ Size specifies the number of vector elements to be written.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge0ad0b6" class="outline-2">
|
||||
<h2 id="orge0ad0b6"><span class="section-number-2">17</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org27caedd" class="outline-2">
|
||||
<h2 id="org27caedd"><span class="section-number-2">17</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-17">
|
||||
<p>
|
||||
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
|
||||
@ -2103,7 +2103,7 @@ 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: 2022-12-02 Fri 08:48</p>
|
||||
<p class="date">Created: 2022-12-05 Mon 13:54</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
161
trex.html
161
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>
|
||||
<!-- 2022-12-02 Fri 08:48 -->
|
||||
<!-- 2022-12-05 Mon 13:54 -->
|
||||
<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>
|
||||
@ -346,38 +346,38 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org353b04b">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org34d836f">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org4f71b4b">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org1a4d1e1">4. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#org9fc011b">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#orgfe585c9">2. Electron (electron group)</a></li>
|
||||
<li><a href="#orgf548aec">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#orga17f95f">4. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#org81687cd">4.1. Example</a></li>
|
||||
<li><a href="#org8955dc4">4.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org3635982">5. Basis set (basis group)</a>
|
||||
<li><a href="#orga46b2ed">5. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#org99c9b1d">5.1. Example</a></li>
|
||||
<li><a href="#org9892ba5">5.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org641a3f3">6. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#orgbe720e6">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="#orgc596a7d">7. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org096fdcd">7. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#org029e862">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orgca729b2">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#org87738f0">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orge897684">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org5581892">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org58b3eb8">9. Configuration state functions (csf group)</a></li>
|
||||
<li><a href="#org275a5d7">10. Excited states (state group)</a></li>
|
||||
<li><a href="#org03f970d">11. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org695f3b7">12. Cell (cell group)</a></li>
|
||||
<li><a href="#org52561de">13. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#org647ace5">14. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
<li><a href="#org148f3fd">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org8e7abf4">9. Configuration state functions (csf group)</a></li>
|
||||
<li><a href="#org4afded7">10. Excited states (state group)</a></li>
|
||||
<li><a href="#org6dbe4ee">11. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#orgd43c6df">12. Cell (cell group)</a></li>
|
||||
<li><a href="#org689e2e6">13. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#orgb956cad">14. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -439,8 +439,8 @@ For determinant lists (integer bit fields), the <code>special</code> attribute i
|
||||
This means that the source code is not produced by the generator, but hand-written.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-org353b04b" class="outline-2">
|
||||
<h2 id="org353b04b"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-org9fc011b" class="outline-2">
|
||||
<h2 id="org9fc011b"><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
|
||||
@ -450,7 +450,7 @@ which have participated to the creation of the file, a list of
|
||||
authors of the file, and a textual description.
|
||||
</p>
|
||||
|
||||
<table id="org9a8b3ae" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org0488c44" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -531,15 +531,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org34d836f" class="outline-2">
|
||||
<h2 id="org34d836f"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div id="outline-container-orgfe585c9" class="outline-2">
|
||||
<h2 id="orgfe585c9"><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="orga25fbf6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org06dfde9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -585,15 +585,15 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4f71b4b" class="outline-2">
|
||||
<h2 id="org4f71b4b"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div id="outline-container-orgf548aec" class="outline-2">
|
||||
<h2 id="orgf548aec"><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="orge32a82e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org294dd3d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -660,8 +660,8 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1a4d1e1" class="outline-2">
|
||||
<h2 id="org1a4d1e1"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div id="outline-container-orga17f95f" class="outline-2">
|
||||
<h2 id="orga17f95f"><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
|
||||
@ -694,7 +694,7 @@ 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="org6b6f336" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgc60dc6c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -796,8 +796,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org81687cd" class="outline-3">
|
||||
<h3 id="org81687cd"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div id="outline-container-org8955dc4" class="outline-3">
|
||||
<h3 id="org8955dc4"><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
|
||||
@ -860,8 +860,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3635982" class="outline-2">
|
||||
<h2 id="org3635982"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div id="outline-container-orga46b2ed" class="outline-2">
|
||||
<h2 id="orga46b2ed"><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
|
||||
@ -914,7 +914,7 @@ 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="org2c6acd0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org8b608e6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -977,6 +977,13 @@ All the basis set parameters are stored in one-dimensional arrays:
|
||||
<td class="org-left">Normalization factor of each shell (\(\mathcal{N}_s\))</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>r_power</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
<td class="org-left"><code>(basis.shell_num)</code></td>
|
||||
<td class="org-left">Power to which \(r\) is raised (\(n_s\))</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>shell_index</code></td>
|
||||
<td class="org-left"><code>index</code></td>
|
||||
@ -1008,8 +1015,8 @@ All the basis set parameters are stored in one-dimensional arrays:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org99c9b1d" class="outline-3">
|
||||
<h3 id="org99c9b1d"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div id="outline-container-org9892ba5" class="outline-3">
|
||||
<h3 id="org9892ba5"><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
|
||||
@ -1087,8 +1094,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org641a3f3" class="outline-2">
|
||||
<h2 id="org641a3f3"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div id="outline-container-orgbe720e6" class="outline-2">
|
||||
<h2 id="orgbe720e6"><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
|
||||
@ -1141,13 +1148,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#org3635982">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#orga46b2ed">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="org051419e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org38a1d25" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1199,7 +1206,7 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5d9a674" class="outline-3">
|
||||
<div id="outline-container-orgaef044e" class="outline-3">
|
||||
<h3 id="ao_one_e"><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">
|
||||
@ -1217,7 +1224,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orgcb26697" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org894e5c8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1312,7 +1319,7 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga31de14" class="outline-3">
|
||||
<div id="outline-container-org5712739" class="outline-3">
|
||||
<h3 id="ao_two_e"><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>
|
||||
@ -1334,7 +1341,7 @@ notation.
|
||||
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
|
||||
</ul>
|
||||
|
||||
<table id="orged7096c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org3ee0f0a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1374,10 +1381,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc596a7d" class="outline-2">
|
||||
<h2 id="orgc596a7d"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div id="outline-container-org096fdcd" class="outline-2">
|
||||
<h2 id="org096fdcd"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="org5b5e5b5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgab8dd83" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1464,8 +1471,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org029e862" class="outline-3">
|
||||
<h3 id="org029e862"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div id="outline-container-org87738f0" class="outline-3">
|
||||
<h3 id="org87738f0"><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
|
||||
@ -1473,7 +1480,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org3e34a27" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org984d05c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1568,8 +1575,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgca729b2" class="outline-3">
|
||||
<h3 id="orgca729b2"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div id="outline-container-orge897684" class="outline-3">
|
||||
<h3 id="orge897684"><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 are the same as those defined in the
|
||||
@ -1587,7 +1594,7 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
\]
|
||||
</p>
|
||||
|
||||
<table id="org7c0d98f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga0f4f6c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1655,8 +1662,8 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5581892" class="outline-2">
|
||||
<h2 id="org5581892"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
|
||||
<div id="outline-container-org148f3fd" class="outline-2">
|
||||
<h2 id="org148f3fd"><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 \(\Psi\)
|
||||
@ -1698,7 +1705,7 @@ 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="orgf3792da" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga215844" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1744,8 +1751,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org58b3eb8" class="outline-2">
|
||||
<h2 id="org58b3eb8"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
|
||||
<div id="outline-container-org8e7abf4" class="outline-2">
|
||||
<h2 id="org8e7abf4"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<p>
|
||||
The configuration interaction (CI) wave function \(\Psi\) can be
|
||||
@ -1767,7 +1774,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
|
||||
the basis of Slater determinants.
|
||||
</p>
|
||||
|
||||
<table id="org24af018" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org4ce99d6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1813,8 +1820,8 @@ the basis of Slater determinants.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org275a5d7" class="outline-2">
|
||||
<h2 id="org275a5d7"><span class="section-number-2">10</span> Excited states (state group)</h2>
|
||||
<div id="outline-container-org4afded7" class="outline-2">
|
||||
<h2 id="org4afded7"><span class="section-number-2">10</span> Excited states (state group)</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<p>
|
||||
This group contains information about excited state. Since TREXIO version 2.3.0
|
||||
@ -1829,7 +1836,7 @@ The <code>id</code> and <code>current_label</code> attributes have to be specifi
|
||||
(containing both ground and excited state data).
|
||||
</p>
|
||||
|
||||
<table id="org0378449" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org747b897" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1889,8 +1896,8 @@ The <code>id</code> and <code>current_label</code> attributes have to be specifi
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org03f970d" class="outline-2">
|
||||
<h2 id="org03f970d"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
|
||||
<div id="outline-container-org6dbe4ee" class="outline-2">
|
||||
<h2 id="org6dbe4ee"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
The reduced density matrices are defined in the basis of molecular
|
||||
@ -1965,7 +1972,7 @@ expressed in a basis of a one-electron function
|
||||
\(g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)\).
|
||||
</p>
|
||||
|
||||
<table id="orgcc83ee8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org7934970" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2116,10 +2123,10 @@ expressed in a basis of a one-electron function
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org695f3b7" class="outline-2">
|
||||
<h2 id="org695f3b7"><span class="section-number-2">12</span> Cell (cell group)</h2>
|
||||
<div id="outline-container-orgd43c6df" class="outline-2">
|
||||
<h2 id="orgd43c6df"><span class="section-number-2">12</span> Cell (cell group)</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<table id="org8694241" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org42cd4db" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2165,10 +2172,10 @@ expressed in a basis of a one-electron function
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org52561de" class="outline-2">
|
||||
<h2 id="org52561de"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div id="outline-container-org689e2e6" class="outline-2">
|
||||
<h2 id="org689e2e6"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div class="outline-text-2" id="text-13">
|
||||
<table id="orgd62d417" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgcda20eb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2207,8 +2214,8 @@ expressed in a basis of a one-electron function
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org647ace5" class="outline-2">
|
||||
<h2 id="org647ace5"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div id="outline-container-orgb956cad" class="outline-2">
|
||||
<h2 id="orgb956cad"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div class="outline-text-2" id="text-14">
|
||||
<p>
|
||||
In quantum Monte Carlo calculations, the wave function is evaluated
|
||||
@ -2222,7 +2229,7 @@ By convention, the electron coordinates contain first all the electrons
|
||||
of $↑$-spin and then all the $↓$-spin.
|
||||
</p>
|
||||
|
||||
<table id="org67c3254" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org9b4f895" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2277,7 +2284,7 @@ of $↑$-spin and then all the $↓$-spin.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-12-02 Fri 08:48</p>
|
||||
<p class="date">Created: 2022-12-05 Mon 13:54</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user