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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 21:46</p>
<p class="date">Created: 2024-08-17 Sat 22:14</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 21:46 -->
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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>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="#orgd725e73">1. Writing nuclear coordinates</a>
<li><a href="#org279271c">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#org7825959">1.1. C</a></li>
<li><a href="#org13a38a9">1.2. Python</a></li>
<li><a href="#orgc836f9a">1.3. Fortran</a></li>
<li><a href="#org21d4211">1.1. C</a></li>
<li><a href="#org787e661">1.2. Python</a></li>
<li><a href="#orgf79b3c8">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org9e5f2cf">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org458fdb1">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org881e3ed">2.1. Fortran</a>
<li><a href="#orgbeee7a5">2.1. Fortran</a>
<ul>
<li><a href="#org0fc8c86">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgc49b374">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org5adddd5">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org7c73741">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgff88941">2.1.5. Allocate memory</a></li>
<li><a href="#orgb20379a">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org26b0a80">2.1.7. Read two-electron quantities</a>
<li><a href="#org27d7081">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org04fa5a7">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgfae163b">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgef5d1a5">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org43dc0b5">2.1.5. Allocate memory</a></li>
<li><a href="#org0d30306">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org1c27f74">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org505246e">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgb236370">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org7f5ffd4">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org99d0bd5">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org80c9e36">2.1.8. Compute the energy</a></li>
<li><a href="#orgec6ba20">2.1.9. Terminate</a></li>
<li><a href="#orgbf1a6b0">2.1.8. Compute the energy</a></li>
<li><a href="#org207c31e">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#orgacdf6b8">2.2. Python</a>
<li><a href="#org0c9da4b">2.2. Python</a>
<ul>
<li><a href="#org9fd5a75">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgb8b3646">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org5705f48">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org485c54c">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org5cd8eac">2.2.5. Read two-electron quantities</a>
<li><a href="#orgd41c2ea">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org87838aa">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#orgd22c0e7">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org31d522d">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org6af9300">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#org38fb2ff">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org9db6c5a">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#orgdf83e6a">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org8cc7b74">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org3eedf88">2.2.6. Compute the energy</a></li>
<li><a href="#org09ad6c2">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org7c0baa4">3. Reading determinants</a>
<li><a href="#org57ecb46">3. Reading determinants</a>
<ul>
<li><a href="#org7612e72">3.1. Fortran</a></li>
<li><a href="#org16687aa">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgd725e73" class="outline-2">
<h2 id="orgd725e73"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org279271c" class="outline-2">
<h2 id="org279271c"><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-org7825959" class="outline-3">
<h3 id="org7825959"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org21d4211" class="outline-3">
<h3 id="org21d4211"><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-org13a38a9" class="outline-3">
<h3 id="org13a38a9"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org787e661" class="outline-3">
<h3 id="org787e661"><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-orgc836f9a" class="outline-3">
<h3 id="orgc836f9a"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orgf79b3c8" class="outline-3">
<h3 id="orgf79b3c8"><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-org9e5f2cf" class="outline-2">
<h2 id="org9e5f2cf"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org458fdb1" class="outline-2">
<h2 id="org458fdb1"><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-org881e3ed" class="outline-3">
<h3 id="org881e3ed"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-orgbeee7a5" class="outline-3">
<h3 id="orgbeee7a5"><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-org0fc8c86" class="outline-4">
<h4 id="org0fc8c86"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org27d7081" class="outline-4">
<h4 id="org27d7081"><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-orgc49b374" class="outline-4">
<h4 id="orgc49b374"><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-org04fa5a7" class="outline-4">
<h4 id="org04fa5a7"><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-org5adddd5" class="outline-4">
<h4 id="org5adddd5"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgfae163b" class="outline-4">
<h4 id="orgfae163b"><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-org7c73741" class="outline-4">
<h4 id="org7c73741"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgef5d1a5" class="outline-4">
<h4 id="orgef5d1a5"><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-orgff88941" class="outline-4">
<h4 id="orgff88941"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org43dc0b5" class="outline-4">
<h4 id="org43dc0b5"><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-orgb20379a" class="outline-4">
<h4 id="orgb20379a"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org0d30306" class="outline-4">
<h4 id="org0d30306"><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-org26b0a80" class="outline-4">
<h4 id="org26b0a80"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org1c27f74" class="outline-4">
<h4 id="org1c27f74"><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-org505246e" class="outline-5">
<h5 id="org505246e"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org7f5ffd4" class="outline-5">
<h5 id="org7f5ffd4"><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-orgb236370" class="outline-5">
<h5 id="orgb236370"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org99d0bd5" class="outline-5">
<h5 id="org99d0bd5"><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-org80c9e36" class="outline-4">
<h4 id="org80c9e36"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-orgbf1a6b0" class="outline-4">
<h4 id="orgbf1a6b0"><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-orgec6ba20" class="outline-4">
<h4 id="orgec6ba20"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org207c31e" class="outline-4">
<h4 id="org207c31e"><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-orgacdf6b8" class="outline-3">
<h3 id="orgacdf6b8"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org0c9da4b" class="outline-3">
<h3 id="org0c9da4b"><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-org9fd5a75" class="outline-4">
<h4 id="org9fd5a75"><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-orgd41c2ea" class="outline-4">
<h4 id="orgd41c2ea"><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-orgb8b3646" class="outline-4">
<h4 id="orgb8b3646"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org87838aa" class="outline-4">
<h4 id="org87838aa"><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-org5705f48" class="outline-4">
<h4 id="org5705f48"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgd22c0e7" class="outline-4">
<h4 id="orgd22c0e7"><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-org485c54c" class="outline-4">
<h4 id="org485c54c"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org31d522d" class="outline-4">
<h4 id="org31d522d"><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-org5cd8eac" class="outline-4">
<h4 id="org5cd8eac"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-org6af9300" class="outline-4">
<h4 id="org6af9300"><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-org38fb2ff" class="outline-5">
<h5 id="org38fb2ff"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgdf83e6a" class="outline-5">
<h5 id="orgdf83e6a"><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-org9db6c5a" class="outline-5">
<h5 id="org9db6c5a"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-org8cc7b74" class="outline-5">
<h5 id="org8cc7b74"><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-org3eedf88" class="outline-4">
<h4 id="org3eedf88"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org09ad6c2" class="outline-4">
<h4 id="org09ad6c2"><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-org7c0baa4" class="outline-2">
<h2 id="org7c0baa4"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org57ecb46" class="outline-2">
<h2 id="org57ecb46"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org7612e72" class="outline-3">
<h3 id="org7612e72"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org16687aa" class="outline-3">
<h3 id="org16687aa"><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 21:46</p>
<p class="date">Created: 2024-08-17 Sat 22:14</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 21:46 -->
<!-- 2024-08-17 Sat 22:14 -->
<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 21:46</p>
<p class="date">Created: 2024-08-17 Sat 22:14</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 21:46 -->
<!-- 2024-08-17 Sat 22:14 -->
<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 21:46</p>
<p class="date">Created: 2024-08-17 Sat 22:14</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 21:46 -->
<!-- 2024-08-17 Sat 22:14 -->
<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="#org13d560b">1. Format specification</a>
<li><a href="#org806ec41">1. Format specification</a>
<ul>
<li><a href="#org6994202">1.1. Organization of the data</a></li>
<li><a href="#orge3cec39">1.2. Data types</a></li>
<li><a href="#org91a3771">1.1. Organization of the data</a></li>
<li><a href="#orgae366bc">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#orgbf8408c">2. The TREXIO library</a>
<li><a href="#org3ab2d35">2. The TREXIO library</a>
<ul>
<li><a href="#org7f6b64a">2.1. The front-end</a></li>
<li><a href="#org39fa350">2.2. The back-end</a></li>
<li><a href="#org8790fc0">2.3. Supported languages</a></li>
<li><a href="#org72bbbd6">2.4. Source code generation and documentation</a></li>
<li><a href="#org0d707d1">2.5. Availability</a></li>
<li><a href="#orgc7514fa">2.1. The front-end</a></li>
<li><a href="#orgd5fdf51">2.2. The back-end</a></li>
<li><a href="#org784b951">2.3. Supported languages</a></li>
<li><a href="#org888c239">2.4. Source code generation and documentation</a></li>
<li><a href="#orgbfb929e">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org13d560b" class="outline-2">
<h2 id="org13d560b"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org806ec41" class="outline-2">
<h2 id="org806ec41"><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-org6994202" class="outline-3">
<h3 id="org6994202"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org91a3771" class="outline-3">
<h3 id="org91a3771"><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-orge3cec39" class="outline-3">
<h3 id="orge3cec39"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-orgae366bc" class="outline-3">
<h3 id="orgae366bc"><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-orgbf8408c" class="outline-2">
<h2 id="orgbf8408c"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-org3ab2d35" class="outline-2">
<h2 id="org3ab2d35"><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-org7f6b64a" class="outline-3">
<h3 id="org7f6b64a"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orgc7514fa" class="outline-3">
<h3 id="orgc7514fa"><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-org39fa350" class="outline-3">
<h3 id="org39fa350"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-orgd5fdf51" class="outline-3">
<h3 id="orgd5fdf51"><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-org8790fc0" class="outline-3">
<h3 id="org8790fc0"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org784b951" class="outline-3">
<h3 id="org784b951"><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-org72bbbd6" class="outline-3">
<h3 id="org72bbbd6"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org888c239" class="outline-3">
<h3 id="org888c239"><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-org0d707d1" class="outline-3">
<h3 id="org0d707d1"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-orgbfb929e" class="outline-3">
<h3 id="orgbfb929e"><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 21:46</p>
<p class="date">Created: 2024-08-17 Sat 22:14</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 21:46 -->
<!-- 2024-08-17 Sat 22:14 -->
<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="#org1948631">1. Template for HDF5 definitions</a></li>
<li><a href="#org723d83f">2. Template for HDF5 structures</a></li>
<li><a href="#org0032fd2">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orge890c13">4. Template for HDF5 has a group</a></li>
<li><a href="#org83c8599">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org72814f5">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgf1974e3">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org26f0e0b">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgd87d4bf">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org1c1bf80">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgb72557e">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org7ce9838">12. Source code for the determinant part</a></li>
<li><a href="#org022caf2">13. Helper functions</a></li>
<li><a href="#org398ff0c">1. Template for HDF5 definitions</a></li>
<li><a href="#orgf0f8c79">2. Template for HDF5 structures</a></li>
<li><a href="#org96f5d07">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org66e629a">4. Template for HDF5 has a group</a></li>
<li><a href="#org61b6068">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org3cd9232">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orge7ec5d3">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgb9e3424">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org46bb0d8">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org47d7dca">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org1f3774b">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orga6eb649">12. Source code for the determinant part</a></li>
<li><a href="#orgd06ddb7">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org1948631" class="outline-2">
<h2 id="org1948631"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org398ff0c" class="outline-2">
<h2 id="org398ff0c"><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-org723d83f" class="outline-2">
<h2 id="org723d83f"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgf0f8c79" class="outline-2">
<h2 id="orgf0f8c79"><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-org0032fd2" class="outline-2">
<h2 id="org0032fd2"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org96f5d07" class="outline-2">
<h2 id="org96f5d07"><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-orge890c13" class="outline-2">
<h2 id="orge890c13"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org66e629a" class="outline-2">
<h2 id="org66e629a"><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-org83c8599" class="outline-2">
<h2 id="org83c8599"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org61b6068" class="outline-2">
<h2 id="org61b6068"><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-org72814f5" class="outline-2">
<h2 id="org72814f5"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org3cd9232" class="outline-2">
<h2 id="org3cd9232"><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-orgf1974e3" class="outline-2">
<h2 id="orgf1974e3"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orge7ec5d3" class="outline-2">
<h2 id="orge7ec5d3"><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-org26f0e0b" class="outline-2">
<h2 id="org26f0e0b"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-orgb9e3424" class="outline-2">
<h2 id="orgb9e3424"><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-orgd87d4bf" class="outline-2">
<h2 id="orgd87d4bf"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org46bb0d8" class="outline-2">
<h2 id="org46bb0d8"><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-org1c1bf80" class="outline-2">
<h2 id="org1c1bf80"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org47d7dca" class="outline-2">
<h2 id="org47d7dca"><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-orgb72557e" class="outline-2">
<h2 id="orgb72557e"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org1f3774b" class="outline-2">
<h2 id="org1f3774b"><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-org7ce9838" class="outline-2">
<h2 id="org7ce9838"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-orga6eb649" class="outline-2">
<h2 id="orga6eb649"><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-org022caf2" class="outline-2">
<h2 id="org022caf2"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgd06ddb7" class="outline-2">
<h2 id="orgd06ddb7"><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 21:46</p>
<p class="date">Created: 2024-08-17 Sat 22:14</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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<title>TEXT back end</title>
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgbf8f180">1. Template for group-related structures in text back end</a></li>
<li><a href="#org7e5241d">2. Template for general structure in text back end</a></li>
<li><a href="#org074feb5">3. Initialize function (constant part)</a></li>
<li><a href="#org681e2d9">4. Deinitialize function (templated part)</a></li>
<li><a href="#org374d741">5. Flush function (templated part)</a></li>
<li><a href="#org3c33330">6. Template for text read a group</a></li>
<li><a href="#org481deb9">7. Template for text has a group</a></li>
<li><a href="#org2d5c1a4">8. Template for text flush a group</a></li>
<li><a href="#org39fc3c4">9. Template for text free memory</a></li>
<li><a href="#org79bdfca">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org0371062">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orge0ceca0">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org4245147">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org18195e3">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org96bfbf5">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org831bfb5">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org18de444">17. Source code for the determinant part</a></li>
<li><a href="#org3911ecf">1. Template for group-related structures in text back end</a></li>
<li><a href="#org570dddb">2. Template for general structure in text back end</a></li>
<li><a href="#org3b1a432">3. Initialize function (constant part)</a></li>
<li><a href="#org5056eab">4. Deinitialize function (templated part)</a></li>
<li><a href="#org8813c4d">5. Flush function (templated part)</a></li>
<li><a href="#orgd71d6a9">6. Template for text read a group</a></li>
<li><a href="#org54ccb28">7. Template for text has a group</a></li>
<li><a href="#org1e9901b">8. Template for text flush a group</a></li>
<li><a href="#org6c5ea6a">9. Template for text free memory</a></li>
<li><a href="#orgca0b510">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org87fc4fa">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org31ac4b8">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org2a08ec3">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org91e3818">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org74aad51">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orge4b2ea5">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org2ae2e5a">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-orgbf8f180" class="outline-2">
<h2 id="orgbf8f180"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org3911ecf" class="outline-2">
<h2 id="org3911ecf"><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-org7e5241d" class="outline-2">
<h2 id="org7e5241d"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org570dddb" class="outline-2">
<h2 id="org570dddb"><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-org074feb5" class="outline-2">
<h2 id="org074feb5"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org3b1a432" class="outline-2">
<h2 id="org3b1a432"><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-org681e2d9" class="outline-2">
<h2 id="org681e2d9"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org5056eab" class="outline-2">
<h2 id="org5056eab"><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-org374d741" class="outline-2">
<h2 id="org374d741"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org8813c4d" class="outline-2">
<h2 id="org8813c4d"><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-org3c33330" class="outline-2">
<h2 id="org3c33330"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orgd71d6a9" class="outline-2">
<h2 id="orgd71d6a9"><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-org481deb9" class="outline-2">
<h2 id="org481deb9"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org54ccb28" class="outline-2">
<h2 id="org54ccb28"><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-org2d5c1a4" class="outline-2">
<h2 id="org2d5c1a4"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org1e9901b" class="outline-2">
<h2 id="org1e9901b"><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-org39fc3c4" class="outline-2">
<h2 id="org39fc3c4"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org6c5ea6a" class="outline-2">
<h2 id="org6c5ea6a"><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-org79bdfca" class="outline-2">
<h2 id="org79bdfca"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orgca0b510" class="outline-2">
<h2 id="orgca0b510"><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-org0371062" class="outline-2">
<h2 id="org0371062"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org87fc4fa" class="outline-2">
<h2 id="org87fc4fa"><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-orge0ceca0" class="outline-2">
<h2 id="orge0ceca0"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org31ac4b8" class="outline-2">
<h2 id="org31ac4b8"><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-org4245147" class="outline-2">
<h2 id="org4245147"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org2a08ec3" class="outline-2">
<h2 id="org2a08ec3"><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-org18195e3" class="outline-2">
<h2 id="org18195e3"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org91e3818" class="outline-2">
<h2 id="org91e3818"><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-org96bfbf5" class="outline-2">
<h2 id="org96bfbf5"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org74aad51" class="outline-2">
<h2 id="org74aad51"><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-org831bfb5" class="outline-2">
<h2 id="org831bfb5"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orge4b2ea5" class="outline-2">
<h2 id="orge4b2ea5"><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-org18de444" class="outline-2">
<h2 id="org18de444"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org2ae2e5a" class="outline-2">
<h2 id="org2ae2e5a"><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 21:46</p>
<p class="date">Created: 2024-08-17 Sat 22:14</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2024-08-17 Sat 21:46 -->
<!-- 2024-08-17 Sat 22:14 -->
<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="#org20dadf8">1. Metadata (metadata group)</a></li>
<li><a href="#orgac71bff">2. System</a>
<li><a href="#orgb2c0526">1. Metadata (metadata group)</a></li>
<li><a href="#org1789373">2. System</a>
<ul>
<li><a href="#org4b8d43f">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org9125949">2.2. Cell (cell group)</a></li>
<li><a href="#orge7b769a">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orga50cae8">2.4. Electron (electron group)</a></li>
<li><a href="#org027a84f">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org8a6b2b5">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#orgcd5e2b5">2.2. Cell (cell group)</a></li>
<li><a href="#org6f36870">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org43d63d6">2.4. Electron (electron group)</a></li>
<li><a href="#org24a887c">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org8ead50a">3. Basis functions</a>
<li><a href="#org9409aa3">3. Basis functions</a>
<ul>
<li><a href="#org1328fb8">3.1. Basis set (basis group)</a>
<li><a href="#orgd2483d4">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org661c9ff">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgc179b79">3.1.2. Numerical orbitals</a></li>
<li><a href="#org5afe37f">3.1.3. Plane waves</a></li>
<li><a href="#orgaf61dba">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org173fc7c">3.1.5. Data definitions</a></li>
<li><a href="#org9815bdd">3.1.6. Example</a></li>
<li><a href="#orgd15bcdc">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org78027f8">3.1.2. Numerical orbitals</a></li>
<li><a href="#org00ee33a">3.1.3. Plane waves</a></li>
<li><a href="#org3ea2b13">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org5c30afc">3.1.5. Data definitions</a></li>
<li><a href="#org3c45827">3.1.6. Example</a></li>
</ul>
</li>
<li><a href="#org867d0c4">3.2. Effective core potentials (ecp group)</a>
<li><a href="#orgb807462">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgf9e589d">3.2.1. Example</a></li>
<li><a href="#orgb267530">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org0907a64">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#orgbeaccff">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org37c2e05">4. Orbitals</a>
<li><a href="#org5741d89">4. Orbitals</a>
<ul>
<li><a href="#org52b4075">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org1c48573">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="#org90be400">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org3c5dca8">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org96f732a">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org80bb8ad">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orge3a3c11">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgd374776">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org4d39725">5. Multi-determinant information</a>
<li><a href="#org369fc5f">5. Multi-determinant information</a>
<ul>
<li><a href="#org0d1b2b5">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org9e8b37a">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgcb681ae">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org3dec9ee">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org887434b">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org044e21d">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org5322831">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgf3a418d">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#orgcaf5bf0">6. Correlation factors</a>
<li><a href="#orgbe0d7fe">6. Correlation factors</a>
<ul>
<li><a href="#orgd87602c">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#orgd8bdfbd">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org869d195">6.1.1. CHAMP</a></li>
<li><a href="#org467e614">6.1.2. Mu</a></li>
<li><a href="#org4769e34">6.1.3. Table of values</a></li>
<li><a href="#org96b2cc5">6.1.1. CHAMP</a></li>
<li><a href="#org49f952e">6.1.2. Mu</a></li>
<li><a href="#orgf0471f1">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org7c93e57">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org68df45e">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-org20dadf8" class="outline-2">
<h2 id="org20dadf8"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgb2c0526" class="outline-2">
<h2 id="orgb2c0526"><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="orge823461" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0a9acb1" 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-orgac71bff" class="outline-2">
<h2 id="orgac71bff"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org1789373" class="outline-2">
<h2 id="org1789373"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org4b8d43f" class="outline-3">
<h3 id="org4b8d43f"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org8a6b2b5" class="outline-3">
<h3 id="org8a6b2b5"><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="orgdc6fbfa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga53a6b6" 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-org9125949" class="outline-3">
<h3 id="org9125949"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-orgcd5e2b5" class="outline-3">
<h3 id="orgcd5e2b5"><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="org36af743" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5eca599" 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-orge7b769a" class="outline-3">
<h3 id="orge7b769a"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org6f36870" class="outline-3">
<h3 id="org6f36870"><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="org3091e29" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org719a128" 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-orga50cae8" class="outline-3">
<h3 id="orga50cae8"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org43d63d6" class="outline-3">
<h3 id="org43d63d6"><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="org37ca3d1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbc00ba2" 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-org027a84f" class="outline-3">
<h3 id="org027a84f"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org24a887c" class="outline-3">
<h3 id="org24a887c"><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="org3ca47e9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3d2c6ec" 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-org8ead50a" class="outline-2">
<h2 id="org8ead50a"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org9409aa3" class="outline-2">
<h2 id="org9409aa3"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org1328fb8" class="outline-3">
<h3 id="org1328fb8"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-orgd2483d4" class="outline-3">
<h3 id="orgd2483d4"><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-org661c9ff" class="outline-4">
<h4 id="org661c9ff"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-orgd15bcdc" class="outline-4">
<h4 id="orgd15bcdc"><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-orgc179b79" class="outline-4">
<h4 id="orgc179b79"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-org78027f8" class="outline-4">
<h4 id="org78027f8"><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-org5afe37f" class="outline-4">
<h4 id="org5afe37f"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-org00ee33a" class="outline-4">
<h4 id="org00ee33a"><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-orgaf61dba" class="outline-4">
<h4 id="orgaf61dba"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div id="outline-container-org3ea2b13" class="outline-4">
<h4 id="org3ea2b13"><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-org173fc7c" class="outline-4">
<h4 id="org173fc7c"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div id="outline-container-org5c30afc" class="outline-4">
<h4 id="org5c30afc"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-5">
<table id="orgdb916c0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8346b69" 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-org9815bdd" class="outline-4">
<h4 id="org9815bdd"><span class="section-number-4">3.1.6</span> Example</h4>
<div id="outline-container-org3c45827" class="outline-4">
<h4 id="org3c45827"><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-org867d0c4" class="outline-3">
<h3 id="org867d0c4"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-orgb807462" class="outline-3">
<h3 id="orgb807462"><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="org62a66f7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgec71ddc" 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-orgf9e589d" class="outline-4">
<h4 id="orgf9e589d"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orgb267530" class="outline-4">
<h4 id="orgb267530"><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-org0907a64" class="outline-3">
<h3 id="org0907a64"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-orgbeaccff" class="outline-3">
<h3 id="orgbeaccff"><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="org4780e1a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdbfa325" 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-org37c2e05" class="outline-2">
<h2 id="org37c2e05"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org5741d89" class="outline-2">
<h2 id="org5741d89"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org52b4075" class="outline-3">
<h3 id="org52b4075"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org1c48573" class="outline-3">
<h3 id="org1c48573"><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="org22ff984" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2c0dc70" 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-orgc7eab7e" class="outline-4">
<div id="outline-container-orgdabc4d8" 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="orgbe128d2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org68b305b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2097,7 +2097,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgfce0763" class="outline-4">
<div id="outline-container-org731a19d" 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="org0e291a3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge51ad18" 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-org90be400" class="outline-3">
<h3 id="org90be400"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org3c5dca8" class="outline-3">
<h3 id="org3c5dca8"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org947ad9e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9df3d75" 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-org96f732a" class="outline-4">
<h4 id="org96f732a"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-orge3a3c11" class="outline-4">
<h4 id="orge3a3c11"><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="orgf7ce504" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc9bfdab" 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-org80bb8ad" class="outline-4">
<h4 id="org80bb8ad"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-orgd374776" class="outline-4">
<h4 id="orgd374776"><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="org137f769" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga286a8e" 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-org4d39725" class="outline-2">
<h2 id="org4d39725"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org369fc5f" class="outline-2">
<h2 id="org369fc5f"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org0d1b2b5" class="outline-3">
<h3 id="org0d1b2b5"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org887434b" class="outline-3">
<h3 id="org887434b"><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="org2aa0e4f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2074188" 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-org9e8b37a" class="outline-3">
<h3 id="org9e8b37a"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org044e21d" class="outline-3">
<h3 id="org044e21d"><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="org2607e12" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf802a91" 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-orgcb681ae" class="outline-3">
<h3 id="orgcb681ae"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org5322831" class="outline-3">
<h3 id="org5322831"><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="org9443c42" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org77527a9" 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-org3dec9ee" class="outline-3">
<h3 id="org3dec9ee"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-orgf3a418d" class="outline-3">
<h3 id="orgf3a418d"><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="org2c0a6f9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbbf0882" 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-orgcaf5bf0" class="outline-2">
<h2 id="orgcaf5bf0"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-orgbe0d7fe" class="outline-2">
<h2 id="orgbe0d7fe"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-orgd87602c" class="outline-3">
<h3 id="orgd87602c"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-orgd8bdfbd" class="outline-3">
<h3 id="orgd8bdfbd"><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-org869d195" class="outline-4">
<h4 id="org869d195"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org96b2cc5" class="outline-4">
<h4 id="org96b2cc5"><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-org467e614" class="outline-4">
<h4 id="org467e614"><span class="section-number-4">6.1.2</span> Mu</h4>
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<h4 id="org49f952e"><span class="section-number-4">6.1.2</span> Mu</h4>
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<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="org4769e34"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="orgf0471f1"><span class="section-number-4">6.1.3</span> Table of values</h4>
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@ -3450,8 +3450,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h2 id="org7c93e57"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org68df45e"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<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.
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@ -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 21:46</p>
<p class="date">Created: 2024-08-17 Sat 22:14</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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