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README.html
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<head>
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<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>
@ -406,7 +406,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-08-17 Sat 21:10</p>
<p class="date">Created: 2024-08-17 Sat 21:34</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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examples.html
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<head>
<!-- 2024-08-17 Sat 21:10 -->
<!-- 2024-08-17 Sat 21:34 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Examples</title>
@ -346,61 +346,61 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgdaa5a50">1. Writing nuclear coordinates</a>
<li><a href="#orgb0d4ade">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#org6a37bb6">1.1. C</a></li>
<li><a href="#orga363f2c">1.2. Python</a></li>
<li><a href="#orgd4f3c30">1.3. Fortran</a></li>
<li><a href="#org5780c8a">1.1. C</a></li>
<li><a href="#org3928b01">1.2. Python</a></li>
<li><a href="#orge31a408">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org8d4efb3">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org164fcf9">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org34ac208">2.1. Fortran</a>
<li><a href="#org5e17234">2.1. Fortran</a>
<ul>
<li><a href="#orgf587bbc">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org57dfae9">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgc2095c4">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org4bf30b6">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org1a5c73e">2.1.5. Allocate memory</a></li>
<li><a href="#org39afffa">2.1.6. Read one-electron quantities</a></li>
<li><a href="#orgf05ef55">2.1.7. Read two-electron quantities</a>
<li><a href="#orgc929034">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgc45db07">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgc8bba04">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org7592f5e">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org6a726ae">2.1.5. Allocate memory</a></li>
<li><a href="#orgd6e10e9">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org732aa81">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org2727908">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org06b33fc">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org586e81d">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org4165d6b">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org76761db">2.1.8. Compute the energy</a></li>
<li><a href="#orgee137d3">2.1.9. Terminate</a></li>
<li><a href="#orgb9396c7">2.1.8. Compute the energy</a></li>
<li><a href="#org798cb40">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org4361c4a">2.2. Python</a>
<li><a href="#orgb3f1034">2.2. Python</a>
<ul>
<li><a href="#orgd451c51">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgdf8fc17">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#orgcae8df0">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org7faf886">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org57b1bc7">2.2.5. Read two-electron quantities</a>
<li><a href="#org080d174">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga0d87a8">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#orgca0d6a8">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org4d26a14">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgee8ad3e">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#orga0075cf">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org858aef5">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org2a31aa0">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orge892856">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org4e28e73">2.2.6. Compute the energy</a></li>
<li><a href="#org05f4d83">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgfba5da5">3. Reading determinants</a>
<li><a href="#orga9c174f">3. Reading determinants</a>
<ul>
<li><a href="#org0113114">3.1. Fortran</a></li>
<li><a href="#org44d4a16">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgdaa5a50" class="outline-2">
<h2 id="orgdaa5a50"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-orgb0d4ade" class="outline-2">
<h2 id="orgb0d4ade"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div class="outline-text-2" id="text-1">
<p>
Here is a demonstration of how to use TREXIO to write the nuclear
@ -410,8 +410,8 @@ as well as the necessary TREXIO functions to perform these actions.
</p>
</div>
<div id="outline-container-org6a37bb6" class="outline-3">
<h3 id="org6a37bb6"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org5780c8a" class="outline-3">
<h3 id="org5780c8a"><span class="section-number-3">1.1</span> C</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #483d8b;">#include</span> <span style="color: #8b2252;">&lt;stdio.h&gt;</span>
@ -461,8 +461,8 @@ as well as the necessary TREXIO functions to perform these actions.
</div>
</div>
<div id="outline-container-orga363f2c" class="outline-3">
<h3 id="orga363f2c"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org3928b01" class="outline-3">
<h3 id="org3928b01"><span class="section-number-3">1.2</span> Python</h3>
<div class="outline-text-3" id="text-1-2">
<p>
This code uses the TREXIO Python binding to create a new TREXIO file named
@ -509,8 +509,8 @@ coordinates of the system.
</div>
</div>
<div id="outline-container-orgd4f3c30" class="outline-3">
<h3 id="orgd4f3c30"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orge31a408" class="outline-3">
<h3 id="orge31a408"><span class="section-number-3">1.3</span> Fortran</h3>
<div class="outline-text-3" id="text-1-3">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">trexio_water</span>
@ -567,12 +567,12 @@ coordinates of the system.
</div>
</div>
<div id="outline-container-org8d4efb3" class="outline-2">
<h2 id="org8d4efb3"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org164fcf9" class="outline-2">
<h2 id="org164fcf9"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org34ac208" class="outline-3">
<h3 id="org34ac208"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org5e17234" class="outline-3">
<h3 id="org5e17234"><span class="section-number-3">2.1</span> Fortran</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
@ -618,8 +618,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgf587bbc" class="outline-4">
<h4 id="orgf587bbc"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgc929034" class="outline-4">
<h4 id="orgc929034"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div class="outline-text-4" id="text-2-1-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> i, j, k, l, m</span>
@ -634,8 +634,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org57dfae9" class="outline-4">
<h4 id="org57dfae9"><span class="section-number-4">2.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div id="outline-container-orgc45db07" class="outline-4">
<h4 id="orgc45db07"><span class="section-number-4">2.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div class="outline-text-4" id="text-2-1-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
@ -651,8 +651,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div>
</div>
<div id="outline-container-orgc2095c4" class="outline-4">
<h4 id="orgc2095c4"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgc8bba04" class="outline-4">
<h4 id="orgc8bba04"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-2-1-3">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
@ -666,8 +666,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div>
</div>
<div id="outline-container-org4bf30b6" class="outline-4">
<h4 id="org4bf30b6"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org7592f5e" class="outline-4">
<h4 id="org7592f5e"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-2-1-4">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
@ -681,8 +681,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div>
</div>
<div id="outline-container-org1a5c73e" class="outline-4">
<h4 id="org1a5c73e"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org6a726ae" class="outline-4">
<h4 id="org6a726ae"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div class="outline-text-4" id="text-2-1-5">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
@ -694,8 +694,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-org39afffa" class="outline-4">
<h4 id="org39afffa"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgd6e10e9" class="outline-4">
<h4 id="orgd6e10e9"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-2-1-6">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@ -727,8 +727,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-orgf05ef55" class="outline-4">
<h4 id="orgf05ef55"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org732aa81" class="outline-4">
<h4 id="org732aa81"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-2-1-7">
<p>
Reading is done with OpenMP. Each thread reads its own buffer, and
@ -744,8 +744,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org2727908" class="outline-5">
<h5 id="org2727908"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org586e81d" class="outline-5">
<h5 id="org586e81d"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-2-1-7-1">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
@ -794,8 +794,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-org06b33fc" class="outline-5">
<h5 id="org06b33fc"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org4165d6b" class="outline-5">
<h5 id="org4165d6b"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-2-1-7-2">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
@ -839,8 +839,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org76761db" class="outline-4">
<h4 id="org76761db"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-orgb9396c7" class="outline-4">
<h4 id="orgb9396c7"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div class="outline-text-4" id="text-2-1-8">
<p>
When the orbitals are real, we can use
@ -886,8 +886,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-orgee137d3" class="outline-4">
<h4 id="orgee137d3"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org798cb40" class="outline-4">
<h4 id="org798cb40"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div class="outline-text-4" id="text-2-1-9">
<div class="org-src-container">
<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
@ -899,8 +899,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org4361c4a" class="outline-3">
<h3 id="org4361c4a"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-orgb3f1034" class="outline-3">
<h3 id="orgb3f1034"><span class="section-number-3">2.2</span> Python</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">import</span> sys
@ -934,8 +934,8 @@ One needs to read from the TREXIO file:
</dl>
</div>
<div id="outline-container-orgd451c51" class="outline-4">
<h4 id="orgd451c51"><span class="section-number-4">2.2.1</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div id="outline-container-org080d174" class="outline-4">
<h4 id="org080d174"><span class="section-number-4">2.2.1</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div class="outline-text-4" id="text-2-2-1">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">filename</span> = sys.argv[1]
@ -945,8 +945,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgdf8fc17" class="outline-4">
<h4 id="orgdf8fc17"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orga0d87a8" class="outline-4">
<h4 id="orga0d87a8"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-2-2-2">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">E_nn</span> = trexio.read_nucleus_repulsion(f)
@ -955,8 +955,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgcae8df0" class="outline-4">
<h4 id="orgcae8df0"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgca0d6a8" class="outline-4">
<h4 id="orgca0d6a8"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-2-2-3">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">n</span> = trexio.read_mo_num(f)
@ -965,8 +965,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org7faf886" class="outline-4">
<h4 id="org7faf886"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org4d26a14" class="outline-4">
<h4 id="org4d26a14"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-2-2-4">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_mo_1e_int_core_hamiltonian(f):
@ -985,12 +985,12 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org57b1bc7" class="outline-4">
<h4 id="org57b1bc7"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-orgee8ad3e" class="outline-4">
<h4 id="orgee8ad3e"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-2-2-5">
</div>
<div id="outline-container-orga0075cf" class="outline-5">
<h5 id="orga0075cf"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org2a31aa0" class="outline-5">
<h5 id="org2a31aa0"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-2-2-5-1">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_mo_2e_int_eri(f):
@ -1020,8 +1020,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org858aef5" class="outline-5">
<h5 id="org858aef5"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-orge892856" class="outline-5">
<h5 id="orge892856"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-2-2-5-2">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_rdm_2e(f):
@ -1043,8 +1043,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org4e28e73" class="outline-4">
<h4 id="org4e28e73"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org05f4d83" class="outline-4">
<h4 id="org05f4d83"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div class="outline-text-4" id="text-2-2-6">
<p>
When the orbitals are real, we can use
@ -1073,12 +1073,12 @@ E &=& E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle j | h | i \rangle\,
</div>
</div>
<div id="outline-container-orgfba5da5" class="outline-2">
<h2 id="orgfba5da5"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-orga9c174f" class="outline-2">
<h2 id="orga9c174f"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org0113114" class="outline-3">
<h3 id="org0113114"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org44d4a16" class="outline-3">
<h3 id="org44d4a16"><span class="section-number-3">3.1</span> Fortran</h3>
<div class="outline-text-3" id="text-3-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
@ -1157,7 +1157,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-08-17 Sat 21:10</p>
<p class="date">Created: 2024-08-17 Sat 21:34</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
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@ -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>
<!-- 2024-08-17 Sat 21:10 -->
<!-- 2024-08-17 Sat 21:34 -->
<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>
@ -406,7 +406,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-08-17 Sat 21:10</p>
<p class="date">Created: 2024-08-17 Sat 21:34</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
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@ -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>
<!-- 2024-08-17 Sat 21:10 -->
<!-- 2024-08-17 Sat 21:34 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Motivation</title>
@ -384,7 +384,7 @@ still lacking, and the purpose of the TREXIO library is to fill this gap.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-08-17 Sat 21:10</p>
<p class="date">Created: 2024-08-17 Sat 21:34</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
lib.html
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@ -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>
<!-- 2024-08-17 Sat 21:10 -->
<!-- 2024-08-17 Sat 21:34 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>The TREXIO library</title>
@ -346,19 +346,19 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgc15e0ec">1. Format specification</a>
<li><a href="#org42d0eb5">1. Format specification</a>
<ul>
<li><a href="#org42226a0">1.1. Organization of the data</a></li>
<li><a href="#org31b6cb9">1.2. Data types</a></li>
<li><a href="#orga5b7631">1.1. Organization of the data</a></li>
<li><a href="#org1bd13c2">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#orgcd0a18a">2. The TREXIO library</a>
<li><a href="#orge77bbfd">2. The TREXIO library</a>
<ul>
<li><a href="#orgdfa65c1">2.1. The front-end</a></li>
<li><a href="#orgf9d6dae">2.2. The back-end</a></li>
<li><a href="#org0fa829a">2.3. Supported languages</a></li>
<li><a href="#org6ecdf16">2.4. Source code generation and documentation</a></li>
<li><a href="#org0658414">2.5. Availability</a></li>
<li><a href="#org196b4af">2.1. The front-end</a></li>
<li><a href="#orgcde50fa">2.2. The back-end</a></li>
<li><a href="#org9d89c6d">2.3. Supported languages</a></li>
<li><a href="#orgd851833">2.4. Source code generation and documentation</a></li>
<li><a href="#org2facf07">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgc15e0ec" class="outline-2">
<h2 id="orgc15e0ec"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org42d0eb5" class="outline-2">
<h2 id="org42d0eb5"><span class="section-number-2">1</span> Format specification</h2>
<div class="outline-text-2" id="text-1">
</td>
<td>
@ -388,8 +388,8 @@ calculation are stored.
</p>
</div>
<div id="outline-container-org42226a0" class="outline-3">
<h3 id="org42226a0"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-orga5b7631" class="outline-3">
<h3 id="orga5b7631"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div class="outline-text-3" id="text-1-1">
<p>
The data in TREXIO are organized into <b>groups</b>, each containing
@ -405,8 +405,8 @@ number of nuclei.
</div>
</div>
<div id="outline-container-org31b6cb9" class="outline-3">
<h3 id="org31b6cb9"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org1bd13c2" class="outline-3">
<h3 id="org1bd13c2"><span class="section-number-3">1.2</span> Data types</h3>
<div class="outline-text-3" id="text-1-2">
<p>
So that TREXIO can be used in any language, we use a limited number
@ -473,8 +473,8 @@ with the same name suffixed by <code>_im</code>.
</div>
</div>
<div id="outline-container-orgcd0a18a" class="outline-2">
<h2 id="orgcd0a18a"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orge77bbfd" class="outline-2">
<h2 id="orge77bbfd"><span class="section-number-2">2</span> The TREXIO library</h2>
<div class="outline-text-2" id="text-2">
</td>
<td>
@ -497,8 +497,8 @@ interface between the library and the physical storage.
</p>
</div>
<div id="outline-container-orgdfa65c1" class="outline-3">
<h3 id="orgdfa65c1"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-org196b4af" class="outline-3">
<h3 id="org196b4af"><span class="section-number-3">2.1</span> The front-end</h3>
<div class="outline-text-3" id="text-2-1">
<p>
By using the TREXIO library, users can store and extract data in a
@ -539,8 +539,8 @@ made are safe.
</div>
</div>
<div id="outline-container-orgf9d6dae" class="outline-3">
<h3 id="orgf9d6dae"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-orgcde50fa" class="outline-3">
<h3 id="orgcde50fa"><span class="section-number-3">2.2</span> The back-end</h3>
<div class="outline-text-3" id="text-2-2">
<p>
At present, TREXIO supports two back-ends: one relying only on the
@ -610,8 +610,8 @@ repositories.
</div>
</div>
<div id="outline-container-org0fa829a" class="outline-3">
<h3 id="org0fa829a"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org9d89c6d" class="outline-3">
<h3 id="org9d89c6d"><span class="section-number-3">2.3</span> Supported languages</h3>
<div class="outline-text-3" id="text-2-3">
<p>
One of the main benefits of using C as the interface for a library is
@ -668,8 +668,8 @@ via the Binder platform.
</div>
<div id="outline-container-org6ecdf16" class="outline-3">
<h3 id="org6ecdf16"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-orgd851833" class="outline-3">
<h3 id="orgd851833"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div class="outline-text-3" id="text-2-4">
<p>
Source code generation is a valuable technique that can significantly
@ -723,8 +723,8 @@ regardless of their programming skills.
</div>
</div>
<div id="outline-container-org0658414" class="outline-3">
<h3 id="org0658414"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org2facf07" class="outline-3">
<h3 id="org2facf07"><span class="section-number-3">2.5</span> Availability</h3>
<div class="outline-text-3" id="text-2-5">
<p>
The TREXIO library is designed to be portable and easy to install
@ -754,7 +754,7 @@ are available in Ubuntu 23.04.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-08-17 Sat 21:10</p>
<p class="date">Created: 2024-08-17 Sat 21:34</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 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 21:10 -->
<!-- 2024-08-17 Sat 21:34 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>HDF5 back end</title>
@ -324,25 +324,25 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org2b2b310">1. Template for HDF5 definitions</a></li>
<li><a href="#org3286870">2. Template for HDF5 structures</a></li>
<li><a href="#orgb4bcddb">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org5777d5e">4. Template for HDF5 has a group</a></li>
<li><a href="#org1d35a74">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org098668e">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgc8bd132">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org4bbf91e">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org3c936e1">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgb46fc19">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgb4f5097">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org8b5c722">12. Source code for the determinant part</a></li>
<li><a href="#org77da9b9">13. Helper functions</a></li>
<li><a href="#org0d0a95c">1. Template for HDF5 definitions</a></li>
<li><a href="#orgdda4917">2. Template for HDF5 structures</a></li>
<li><a href="#orgfa55636">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org28775b0">4. Template for HDF5 has a group</a></li>
<li><a href="#orge463a65">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org07edcb2">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org357a7e6">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org9845813">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org981acb8">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgb393ba7">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgf4946f7">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgd7a62c9">12. Source code for the determinant part</a></li>
<li><a href="#orgb7b72ec">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org2b2b310" class="outline-2">
<h2 id="org2b2b310"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org0d0a95c" class="outline-2">
<h2 id="org0d0a95c"><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-org3286870" class="outline-2">
<h2 id="org3286870"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgdda4917" class="outline-2">
<h2 id="orgdda4917"><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-orgb4bcddb" class="outline-2">
<h2 id="orgb4bcddb"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgfa55636" class="outline-2">
<h2 id="orgfa55636"><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-org5777d5e" class="outline-2">
<h2 id="org5777d5e"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org28775b0" class="outline-2">
<h2 id="org28775b0"><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-org1d35a74" class="outline-2">
<h2 id="org1d35a74"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orge463a65" class="outline-2">
<h2 id="orge463a65"><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-org098668e" class="outline-2">
<h2 id="org098668e"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org07edcb2" class="outline-2">
<h2 id="org07edcb2"><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>
@ -770,8 +770,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgc8bd132" class="outline-2">
<h2 id="orgc8bd132"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org357a7e6" class="outline-2">
<h2 id="org357a7e6"><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
@ -976,8 +976,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org4bbf91e" class="outline-2">
<h2 id="org4bbf91e"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org9845813" class="outline-2">
<h2 id="org9845813"><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.
@ -1111,8 +1111,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org3c936e1" class="outline-2">
<h2 id="org3c936e1"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org981acb8" class="outline-2">
<h2 id="org981acb8"><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>
@ -1309,8 +1309,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-orgb46fc19" class="outline-2">
<h2 id="orgb46fc19"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgb393ba7" class="outline-2">
<h2 id="orgb393ba7"><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>
@ -1437,8 +1437,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
</div>
<div id="outline-container-orgb4f5097" class="outline-2">
<h2 id="orgb4f5097"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgf4946f7" class="outline-2">
<h2 id="orgf4946f7"><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 &lt; 1.10) unlinking an object was not working as expected
@ -1478,8 +1478,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org8b5c722" class="outline-2">
<h2 id="org8b5c722"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-orgd7a62c9" class="outline-2">
<h2 id="orgd7a62c9"><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.
@ -1581,8 +1581,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org77da9b9" class="outline-2">
<h2 id="org77da9b9"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgb7b72ec" class="outline-2">
<h2 id="orgb7b72ec"><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>
@ -1850,7 +1850,7 @@ 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: 2024-08-17 Sat 21:10</p>
<p class="date">Created: 2024-08-17 Sat 21:34</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgee29158">1. Template for group-related structures in text back end</a></li>
<li><a href="#org493f4e2">2. Template for general structure in text back end</a></li>
<li><a href="#org7d1a3f0">3. Initialize function (constant part)</a></li>
<li><a href="#orga171ad8">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgc1ca74e">5. Flush function (templated part)</a></li>
<li><a href="#org7b7af11">6. Template for text read a group</a></li>
<li><a href="#orgb3338b7">7. Template for text has a group</a></li>
<li><a href="#org60123cc">8. Template for text flush a group</a></li>
<li><a href="#org988958c">9. Template for text free memory</a></li>
<li><a href="#org14d2381">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org24d08d7">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgf71e4e8">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgfcc6b93">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org2824152">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org3dfa98a">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org52a3027">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org2aebf1a">17. Source code for the determinant part</a></li>
<li><a href="#org2f4117b">1. Template for group-related structures in text back end</a></li>
<li><a href="#org78adf0e">2. Template for general structure in text back end</a></li>
<li><a href="#org86f166e">3. Initialize function (constant part)</a></li>
<li><a href="#org8a29574">4. Deinitialize function (templated part)</a></li>
<li><a href="#org3e150da">5. Flush function (templated part)</a></li>
<li><a href="#org1c348f8">6. Template for text read a group</a></li>
<li><a href="#org4205a4e">7. Template for text has a group</a></li>
<li><a href="#org46fec83">8. Template for text flush a group</a></li>
<li><a href="#org9fa337d">9. Template for text free memory</a></li>
<li><a href="#org9cadde2">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgd9625d1">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org39b423b">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgd073162">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org6bcd0bd">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org472e0b9">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgb0f4223">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org5ede353">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-orgee29158" class="outline-2">
<h2 id="orgee29158"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org2f4117b" class="outline-2">
<h2 id="org2f4117b"><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-org493f4e2" class="outline-2">
<h2 id="org493f4e2"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org78adf0e" class="outline-2">
<h2 id="org78adf0e"><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-org7d1a3f0" class="outline-2">
<h2 id="org7d1a3f0"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org86f166e" class="outline-2">
<h2 id="org86f166e"><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>
@ -601,8 +601,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-orga171ad8" class="outline-2">
<h2 id="orga171ad8"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org8a29574" class="outline-2">
<h2 id="org8a29574"><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>
@ -624,8 +624,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-orgc1ca74e" class="outline-2">
<h2 id="orgc1ca74e"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org3e150da" class="outline-2">
<h2 id="org3e150da"><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>
@ -648,8 +648,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org7b7af11" class="outline-2">
<h2 id="org7b7af11"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org1c348f8" class="outline-2">
<h2 id="org1c348f8"><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*
@ -875,8 +875,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgb3338b7" class="outline-2">
<h2 id="orgb3338b7"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org4205a4e" class="outline-2">
<h2 id="org4205a4e"><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>
@ -916,8 +916,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org60123cc" class="outline-2">
<h2 id="org60123cc"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org46fec83" class="outline-2">
<h2 id="org46fec83"><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>
@ -981,8 +981,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org988958c" class="outline-2">
<h2 id="org988958c"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org9fa337d" class="outline-2">
<h2 id="org9fa337d"><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.
@ -1051,8 +1051,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org14d2381" class="outline-2">
<h2 id="org14d2381"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org9cadde2" class="outline-2">
<h2 id="org9cadde2"><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>
@ -1115,8 +1115,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org24d08d7" class="outline-2">
<h2 id="org24d08d7"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgd9625d1" class="outline-2">
<h2 id="orgd9625d1"><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.
@ -1212,8 +1212,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgf71e4e8" class="outline-2">
<h2 id="orgf71e4e8"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org39b423b" class="outline-2">
<h2 id="org39b423b"><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.
@ -1314,8 +1314,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgfcc6b93" class="outline-2">
<h2 id="orgfcc6b93"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orgd073162" class="outline-2">
<h2 id="orgd073162"><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>
@ -1389,8 +1389,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org2824152" class="outline-2">
<h2 id="org2824152"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org6bcd0bd" class="outline-2">
<h2 id="org6bcd0bd"><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
@ -1680,8 +1680,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org3dfa98a" class="outline-2">
<h2 id="org3dfa98a"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org472e0b9" class="outline-2">
<h2 id="org472e0b9"><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
@ -1911,8 +1911,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-org52a3027" class="outline-2">
<h2 id="org52a3027"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgb0f4223" class="outline-2">
<h2 id="orgb0f4223"><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>
@ -1940,8 +1940,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-org2aebf1a" class="outline-2">
<h2 id="org2aebf1a"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org5ede353" class="outline-2">
<h2 id="org5ede353"><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
@ -2133,7 +2133,7 @@ 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: 2024-08-17 Sat 21:10</p>
<p class="date">Created: 2024-08-17 Sat 21:34</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2024-08-17 Sat 21:10 -->
<!-- 2024-08-17 Sat 21:34 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Data stored in TREXIO</title>
@ -346,72 +346,72 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org8f9db0b">1. Metadata (metadata group)</a></li>
<li><a href="#orgcfa5e58">2. System</a>
<li><a href="#org26bb2c9">1. Metadata (metadata group)</a></li>
<li><a href="#org1cd8dc4">2. System</a>
<ul>
<li><a href="#org00d16c2">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org1e5ca44">2.2. Cell (cell group)</a></li>
<li><a href="#org31e2b20">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org9bfbdaa">2.4. Electron (electron group)</a></li>
<li><a href="#orge9f4feb">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org97059c1">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org0bd70ae">2.2. Cell (cell group)</a></li>
<li><a href="#org2f32fe4">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgefda9b1">2.4. Electron (electron group)</a></li>
<li><a href="#org143e1ea">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org7faf911">3. Basis functions</a>
<li><a href="#org5df781e">3. Basis functions</a>
<ul>
<li><a href="#orgdbe0adc">3.1. Basis set (basis group)</a>
<li><a href="#orgfa416a1">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orgb6004ad">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org60d6b19">3.1.2. Numerical orbitals</a></li>
<li><a href="#org651535e">3.1.3. Plane waves</a></li>
<li><a href="#org5a0d49a">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org9ddc89b">3.1.5. Data definitions</a></li>
<li><a href="#org958dcda">3.1.6. Example</a></li>
<li><a href="#org5c8b5e9">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org5719733">3.1.2. Numerical orbitals</a></li>
<li><a href="#org7303e43">3.1.3. Plane waves</a></li>
<li><a href="#orgc0b8964">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org2430ecf">3.1.5. Data definitions</a></li>
<li><a href="#org91e1984">3.1.6. Example</a></li>
</ul>
</li>
<li><a href="#org6c02eb7">3.2. Effective core potentials (ecp group)</a>
<li><a href="#orgdfe0ae6">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgd98565a">3.2.1. Example</a></li>
<li><a href="#orgadfa52c">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org5b664c6">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#orgaf126a1">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#orga715209">4. Orbitals</a>
<li><a href="#org0b487b0">4. Orbitals</a>
<ul>
<li><a href="#orgc64539a">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org80e6026">4.1. Atomic orbitals (ao group)</a>
<ul>
<li><a href="#ao_one_e">4.1.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
<li><a href="#ao_two_e">4.1.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org36fe15d">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org0ff7b23">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org4ba3f50">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org8b3e4b1">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org2f67fe4">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org6dd1dd4">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgf16e97f">5. Multi-determinant information</a>
<li><a href="#org0e97bf4">5. Multi-determinant information</a>
<ul>
<li><a href="#org154acc4">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org7133942">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org97684cb">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org5759ff3">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org6b991ce">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org1d37f79">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orge3b0f50">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org7477541">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#orge244381">6. Correlation factors</a>
<li><a href="#org6aee6b8">6. Correlation factors</a>
<ul>
<li><a href="#org53811b4">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org555aa39">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org594c3ff">6.1.1. CHAMP</a></li>
<li><a href="#orga00b5c0">6.1.2. Mu</a></li>
<li><a href="#org0574858">6.1.3. Table of values</a></li>
<li><a href="#orgf17b063">6.1.1. CHAMP</a></li>
<li><a href="#orgb574be8">6.1.2. Mu</a></li>
<li><a href="#org7a99f9b">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org283b8af">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#orgb2dd188">7. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -433,8 +433,8 @@ contiguous in memory. In the row-major representation, <code>A[i,j]</code> and
<code>A[i,j+1]</code> are contiguous.
</p>
<div id="outline-container-org8f9db0b" class="outline-2">
<h2 id="org8f9db0b"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org26bb2c9" class="outline-2">
<h2 id="org26bb2c9"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect TREXIO files to be archived in open-data repositories,
@ -444,7 +444,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
</p>
<table id="org72e6cd0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf67b149" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -537,19 +537,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
</div>
</div>
<div id="outline-container-orgcfa5e58" class="outline-2">
<h2 id="orgcfa5e58"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org1cd8dc4" class="outline-2">
<h2 id="org1cd8dc4"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org00d16c2" class="outline-3">
<h3 id="org00d16c2"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org97059c1" class="outline-3">
<h3 id="org97059c1"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div class="outline-text-3" id="text-2-1">
<p>
The nuclei are considered as fixed point charges. Coordinates are
given in Cartesian \((x,y,z)\) format.
</p>
<table id="orgab077a8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgeab663c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -634,15 +634,15 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org1e5ca44" class="outline-3">
<h3 id="org1e5ca44"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org0bd70ae" class="outline-3">
<h3 id="org0bd70ae"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div class="outline-text-3" id="text-2-2">
<p>
3 Lattice vectors to define a box containing the system, for example
used in periodic calculations.
</p>
<table id="orgb7d2990" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6dbbe0c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -726,10 +726,10 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-org31e2b20" class="outline-3">
<h3 id="org31e2b20"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org2f32fe4" class="outline-3">
<h3 id="org2f32fe4"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div class="outline-text-3" id="text-2-3">
<table id="org6887395" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0cbde75" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -789,8 +789,8 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-org9bfbdaa" class="outline-3">
<h3 id="org9bfbdaa"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-orgefda9b1" class="outline-3">
<h3 id="orgefda9b1"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div class="outline-text-3" id="text-2-4">
<p>
The chemical system consists of nuclei and electrons, where the
@ -809,7 +809,7 @@ the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org3bb3310" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org009ef9a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -861,8 +861,8 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orge9f4feb" class="outline-3">
<h3 id="orge9f4feb"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org143e1ea" class="outline-3">
<h3 id="org143e1ea"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div class="outline-text-3" id="text-2-5">
<p>
This group contains information about excited states. Since only a
@ -879,7 +879,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="orgef4993d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org559471a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -956,16 +956,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-org7faf911" class="outline-2">
<h2 id="org7faf911"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org5df781e" class="outline-2">
<h2 id="org5df781e"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgdbe0adc" class="outline-3">
<h3 id="orgdbe0adc"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-orgfa416a1" class="outline-3">
<h3 id="orgfa416a1"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div class="outline-text-3" id="text-3-1">
</div>
<div id="outline-container-orgb6004ad" class="outline-4">
<h4 id="orgb6004ad"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org5c8b5e9" class="outline-4">
<h4 id="org5c8b5e9"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div class="outline-text-4" id="text-3-1-1">
<p>
We consider here basis functions centered on nuclei. Hence, it is
@ -1019,8 +1019,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-org60d6b19" class="outline-4">
<h4 id="org60d6b19"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-org5719733" class="outline-4">
<h4 id="org5719733"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div class="outline-text-4" id="text-3-1-2">
<p>
Trexio supports numerical atom centered orbitals. The implementation is
@ -1084,8 +1084,8 @@ reimplement them with consideration for its specific needs.
</div>
</div>
<div id="outline-container-org651535e" class="outline-4">
<h4 id="org651535e"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-org7303e43" class="outline-4">
<h4 id="org7303e43"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div class="outline-text-4" id="text-3-1-3">
<p>
A plane wave is defined as
@ -1106,8 +1106,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org5a0d49a" class="outline-4">
<h4 id="org5a0d49a"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div id="outline-container-orgc0b8964" class="outline-4">
<h4 id="orgc0b8964"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div class="outline-text-4" id="text-3-1-4">
<p>
Basis functions can be made oscillating as
@ -1129,10 +1129,10 @@ Oscillation kind can be:
</div>
</div>
<div id="outline-container-org9ddc89b" class="outline-4">
<h4 id="org9ddc89b"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div id="outline-container-org2430ecf" class="outline-4">
<h4 id="org2430ecf"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-5">
<table id="org3dcc8fe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf085278" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1384,8 +1384,8 @@ Oscillation kind can be:
</div>
</div>
<div id="outline-container-org958dcda" class="outline-4">
<h4 id="org958dcda"><span class="section-number-4">3.1.6</span> Example</h4>
<div id="outline-container-org91e1984" class="outline-4">
<h4 id="org91e1984"><span class="section-number-4">3.1.6</span> Example</h4>
<div class="outline-text-4" id="text-3-1-6">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1463,8 +1463,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org6c02eb7" class="outline-3">
<h3 id="org6c02eb7"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-orgdfe0ae6" class="outline-3">
<h3 id="orgdfe0ae6"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div class="outline-text-3" id="text-3-2">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -1498,7 +1498,7 @@ where \(Z_\text{eff}\) is the effective nuclear charge of the center.
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="org4033af6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org87911df" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1613,8 +1613,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-orgd98565a" class="outline-4">
<h4 id="orgd98565a"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orgadfa52c" class="outline-4">
<h4 id="orgadfa52c"><span class="section-number-4">3.2.1</span> Example</h4>
<div class="outline-text-4" id="text-3-2-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -1677,8 +1677,8 @@ power = [
</div>
</div>
<div id="outline-container-org5b664c6" class="outline-3">
<h3 id="org5b664c6"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-orgaf126a1" class="outline-3">
<h3 id="orgaf126a1"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div class="outline-text-3" id="text-3-3">
<p>
In some applications, such as DFT calculations, integrals have to
@ -1693,7 +1693,7 @@ The structure of this group is adapted for the <a href="https://github.com/dftli
Feel free to submit a PR if you find missing options/functionalities.
</p>
<table id="org4e8baa9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8d1d694" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1826,12 +1826,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-orga715209" class="outline-2">
<h2 id="orga715209"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org0b487b0" class="outline-2">
<h2 id="org0b487b0"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-orgc64539a" class="outline-3">
<h3 id="orgc64539a"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org80e6026" class="outline-3">
<h3 id="org80e6026"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div class="outline-text-3" id="text-4-1">
<p>
AOs are defined as
@ -1912,7 +1912,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="orga6cc10e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org540174d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1971,7 +1971,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org9df7de3" class="outline-4">
<div id="outline-container-org1c8d668" class="outline-4">
<h4 id="ao_one_e"><span class="section-number-4">4.1.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_one_e">
<ul class="org-ul">
@ -1989,7 +1989,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgb1084ff" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgba5fb95" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2097,7 +2097,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgce48b25" class="outline-4">
<div id="outline-container-orgf257213" class="outline-4">
<h4 id="ao_two_e"><span class="section-number-4">4.1.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_two_e">
<p>
@ -2123,7 +2123,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org2f42821" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org478d937" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2200,10 +2200,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org36fe15d" class="outline-3">
<h3 id="org36fe15d"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org0ff7b23" class="outline-3">
<h3 id="org0ff7b23"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org6dd05ac" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org296e1f2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2319,8 +2319,8 @@ is the number of spin-orbitals, twice the number of spatial orbitals.
</div>
<div id="outline-container-org4ba3f50" class="outline-4">
<h4 id="org4ba3f50"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org2f67fe4" class="outline-4">
<h4 id="org2f67fe4"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-1">
<p>
The operators as the same as those defined in the
@ -2328,7 +2328,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org892e0e9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8238da2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2436,8 +2436,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org8b3e4b1" class="outline-4">
<h4 id="org8b3e4b1"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org6dd1dd4" class="outline-4">
<h4 id="org6dd1dd4"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-2">
<p>
The operators are the same as those defined in the
@ -2445,7 +2445,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgc59d48d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org51761a5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2523,12 +2523,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgf16e97f" class="outline-2">
<h2 id="orgf16e97f"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org0e97bf4" class="outline-2">
<h2 id="org0e97bf4"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org154acc4" class="outline-3">
<h3 id="org154acc4"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org6b991ce" class="outline-3">
<h3 id="org6b991ce"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div class="outline-text-3" id="text-5-1">
<p>
The configuration interaction (CI) wave function \(\Psi\)
@ -2570,7 +2570,7 @@ 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="orgbeca308" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb9ca281" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2622,8 +2622,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org7133942" class="outline-3">
<h3 id="org7133942"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org1d37f79" class="outline-3">
<h3 id="org1d37f79"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div class="outline-text-3" id="text-5-2">
<p>
The configuration interaction (CI) wave function \(\Psi\) can be
@ -2645,7 +2645,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org13ad3ee" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc14df1f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2697,8 +2697,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org97684cb" class="outline-3">
<h3 id="org97684cb"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orge3b0f50" class="outline-3">
<h3 id="orge3b0f50"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div class="outline-text-3" id="text-5-3">
<p>
The wave function may be expressed in terms of action of the cluster
@ -2769,7 +2769,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="orgebd7aa6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb71141c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2861,8 +2861,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-org5759ff3" class="outline-3">
<h3 id="org5759ff3"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org7477541" class="outline-3">
<h3 id="org7477541"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div class="outline-text-3" id="text-5-4">
<p>
The reduced density matrices are defined in the basis of molecular
@ -2934,7 +2934,7 @@ 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="org4289ed7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9ffcae8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3099,12 +3099,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-orge244381" class="outline-2">
<h2 id="orge244381"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org6aee6b8" class="outline-2">
<h2 id="org6aee6b8"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org53811b4" class="outline-3">
<h3 id="org53811b4"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org555aa39" class="outline-3">
<h3 id="org555aa39"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div class="outline-text-3" id="text-6-1">
<p>
The Jastrow factor is an $N$-electron function which multiplies the CI
@ -3129,8 +3129,8 @@ following:
</ul>
</div>
<div id="outline-container-org594c3ff" class="outline-4">
<h4 id="org594c3ff"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orgf17b063" class="outline-4">
<h4 id="orgf17b063"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div class="outline-text-4" id="text-6-1-1">
<p>
The first form of Jastrow factor is the one used in
@ -3231,8 +3231,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-orga00b5c0" class="outline-4">
<h4 id="orga00b5c0"><span class="section-number-4">6.1.2</span> Mu</h4>
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<h4 id="orgb574be8"><span class="section-number-4">6.1.2</span> Mu</h4>
<div class="outline-text-4" id="text-6-1-2">
<p>
<a href="https://aip.scitation.org/doi/10.1063/5.0044683">Mu-Jastrow</a> is based on a one-parameter correlation factor that has
@ -3329,10 +3329,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h4 id="org0574858"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div id="outline-container-org7a99f9b" class="outline-4">
<h4 id="org7a99f9b"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div class="outline-text-4" id="text-6-1-3">
<table id="org2c9f470" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
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<colgroup>
@ -3450,8 +3450,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<div id="outline-container-org283b8af" class="outline-2">
<h2 id="org283b8af"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-orgb2dd188" class="outline-2">
<h2 id="orgb2dd188"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-7">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -3465,7 +3465,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orgf4bd04c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
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<colgroup>
@ -3527,7 +3527,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
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<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-08-17 Sat 21:10</p>
<p class="date">Created: 2024-08-17 Sat 21:34</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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