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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: 2023-09-15 Fri 14:31</p>
<p class="date">Created: 2023-09-19 Tue 12:46</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2023-09-15 Fri 14:31 -->
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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="#org3ee3e4b">1. Writing nuclear coordinates</a>
<li><a href="#org2743767">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#org9039b52">1.1. C</a></li>
<li><a href="#orgf4058e2">1.2. Python</a></li>
<li><a href="#org89405e9">1.3. Fortran</a></li>
<li><a href="#org21a7362">1.1. C</a></li>
<li><a href="#org263bcf0">1.2. Python</a></li>
<li><a href="#orgbfa7580">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org0d59102">2. Accessing sparse quantities (integrals)</a>
<li><a href="#orgb5791dc">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org1e9146a">2.1. Fortran</a>
<li><a href="#org7998c2b">2.1. Fortran</a>
<ul>
<li><a href="#org826c6ec">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org1d5fbb3">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgb6d8a48">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org652946f">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org7a04a85">2.1.5. Allocate memory</a></li>
<li><a href="#org9434ce8">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org2fb7d94">2.1.7. Read two-electron quantities</a>
<li><a href="#org0c204a2">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org68a46e0">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org8a4c9f1">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org06ab1b2">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org1abf616">2.1.5. Allocate memory</a></li>
<li><a href="#orgb6c21cb">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org239ae7c">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org2436eb2">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org556e149">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org59f21fa">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org12c3eb0">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgaf77725">2.1.8. Compute the energy</a></li>
<li><a href="#org39f8125">2.1.9. Terminate</a></li>
<li><a href="#orgc27f1e4">2.1.8. Compute the energy</a></li>
<li><a href="#org8cc35d7">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org87b29a9">2.2. Python</a>
<li><a href="#org40666d3">2.2. Python</a>
<ul>
<li><a href="#orgd3987e4">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga7245fd">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org68b8db3">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org4027261">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org851837d">2.2.5. Read two-electron quantities</a>
<li><a href="#org219c165">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org12c0017">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#orgf4f9d7a">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org8633e27">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgbb049be">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#orgf0513db">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgf1c21bd">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org1c8372f">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org748731a">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org014ab95">2.2.6. Compute the energy</a></li>
<li><a href="#org6bd9ec1">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org71026e7">3. Reading determinants</a>
<li><a href="#org392cd78">3. Reading determinants</a>
<ul>
<li><a href="#orgc47a844">3.1. Fortran</a></li>
<li><a href="#org2b511e8">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org3ee3e4b" class="outline-2">
<h2 id="org3ee3e4b"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org2743767" class="outline-2">
<h2 id="org2743767"><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-org9039b52" class="outline-3">
<h3 id="org9039b52"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org21a7362" class="outline-3">
<h3 id="org21a7362"><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-orgf4058e2" class="outline-3">
<h3 id="orgf4058e2"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org263bcf0" class="outline-3">
<h3 id="org263bcf0"><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-org89405e9" class="outline-3">
<h3 id="org89405e9"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orgbfa7580" class="outline-3">
<h3 id="orgbfa7580"><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-org0d59102" class="outline-2">
<h2 id="org0d59102"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orgb5791dc" class="outline-2">
<h2 id="orgb5791dc"><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-org1e9146a" class="outline-3">
<h3 id="org1e9146a"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org7998c2b" class="outline-3">
<h3 id="org7998c2b"><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-org826c6ec" class="outline-4">
<h4 id="org826c6ec"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org0c204a2" class="outline-4">
<h4 id="org0c204a2"><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-org1d5fbb3" class="outline-4">
<h4 id="org1d5fbb3"><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-org68a46e0" class="outline-4">
<h4 id="org68a46e0"><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-orgb6d8a48" class="outline-4">
<h4 id="orgb6d8a48"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org8a4c9f1" class="outline-4">
<h4 id="org8a4c9f1"><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-org652946f" class="outline-4">
<h4 id="org652946f"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org06ab1b2" class="outline-4">
<h4 id="org06ab1b2"><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-org7a04a85" class="outline-4">
<h4 id="org7a04a85"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org1abf616" class="outline-4">
<h4 id="org1abf616"><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-org9434ce8" class="outline-4">
<h4 id="org9434ce8"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgb6c21cb" class="outline-4">
<h4 id="orgb6c21cb"><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-org2fb7d94" class="outline-4">
<h4 id="org2fb7d94"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org239ae7c" class="outline-4">
<h4 id="org239ae7c"><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-org2436eb2" class="outline-5">
<h5 id="org2436eb2"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org59f21fa" class="outline-5">
<h5 id="org59f21fa"><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-org556e149" class="outline-5">
<h5 id="org556e149"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org12c3eb0" class="outline-5">
<h5 id="org12c3eb0"><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-orgaf77725" class="outline-4">
<h4 id="orgaf77725"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-orgc27f1e4" class="outline-4">
<h4 id="orgc27f1e4"><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-org39f8125" class="outline-4">
<h4 id="org39f8125"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org8cc35d7" class="outline-4">
<h4 id="org8cc35d7"><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-org87b29a9" class="outline-3">
<h3 id="org87b29a9"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org40666d3" class="outline-3">
<h3 id="org40666d3"><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-orgd3987e4" class="outline-4">
<h4 id="orgd3987e4"><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-org219c165" class="outline-4">
<h4 id="org219c165"><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-orga7245fd" class="outline-4">
<h4 id="orga7245fd"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org12c0017" class="outline-4">
<h4 id="org12c0017"><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-org68b8db3" class="outline-4">
<h4 id="org68b8db3"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgf4f9d7a" class="outline-4">
<h4 id="orgf4f9d7a"><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-org4027261" class="outline-4">
<h4 id="org4027261"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org8633e27" class="outline-4">
<h4 id="org8633e27"><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-org851837d" class="outline-4">
<h4 id="org851837d"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-orgbb049be" class="outline-4">
<h4 id="orgbb049be"><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-orgf0513db" class="outline-5">
<h5 id="orgf0513db"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org1c8372f" class="outline-5">
<h5 id="org1c8372f"><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-orgf1c21bd" class="outline-5">
<h5 id="orgf1c21bd"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-org748731a" class="outline-5">
<h5 id="org748731a"><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-org014ab95" class="outline-4">
<h4 id="org014ab95"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org6bd9ec1" class="outline-4">
<h4 id="org6bd9ec1"><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-org71026e7" class="outline-2">
<h2 id="org71026e7"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org392cd78" class="outline-2">
<h2 id="org392cd78"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgc47a844" class="outline-3">
<h3 id="orgc47a844"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org2b511e8" class="outline-3">
<h3 id="org2b511e8"><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: 2023-09-15 Fri 14:31</p>
<p class="date">Created: 2023-09-19 Tue 12:46</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>
<!-- 2023-09-15 Fri 14:31 -->
<!-- 2023-09-19 Tue 12:46 -->
<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: 2023-09-15 Fri 14:31</p>
<p class="date">Created: 2023-09-19 Tue 12:46</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>
<!-- 2023-09-15 Fri 14:31 -->
<!-- 2023-09-19 Tue 12:46 -->
<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: 2023-09-15 Fri 14:31</p>
<p class="date">Created: 2023-09-19 Tue 12:46</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
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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>
<!-- 2023-09-15 Fri 14:31 -->
<!-- 2023-09-19 Tue 12:46 -->
<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="#org5cc9de1">1. Format specification</a>
<li><a href="#org6fe151c">1. Format specification</a>
<ul>
<li><a href="#org8152b31">1.1. Organization of the data</a></li>
<li><a href="#orgbafdde7">1.2. Data types</a></li>
<li><a href="#orgab452c8">1.1. Organization of the data</a></li>
<li><a href="#org1e7d255">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org239daeb">2. The TREXIO library</a>
<li><a href="#orgec9ce24">2. The TREXIO library</a>
<ul>
<li><a href="#org1c08c69">2.1. The front-end</a></li>
<li><a href="#org7297157">2.2. The back-end</a></li>
<li><a href="#orgd012f28">2.3. Supported languages</a></li>
<li><a href="#org44cb722">2.4. Source code generation and documentation</a></li>
<li><a href="#org750ced2">2.5. Availability</a></li>
<li><a href="#org7e86920">2.1. The front-end</a></li>
<li><a href="#org049b04e">2.2. The back-end</a></li>
<li><a href="#org99869bd">2.3. Supported languages</a></li>
<li><a href="#org4aacfb9">2.4. Source code generation and documentation</a></li>
<li><a href="#orgcbcf730">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org5cc9de1" class="outline-2">
<h2 id="org5cc9de1"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org6fe151c" class="outline-2">
<h2 id="org6fe151c"><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-org8152b31" class="outline-3">
<h3 id="org8152b31"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-orgab452c8" class="outline-3">
<h3 id="orgab452c8"><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-orgbafdde7" class="outline-3">
<h3 id="orgbafdde7"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org1e7d255" class="outline-3">
<h3 id="org1e7d255"><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-org239daeb" class="outline-2">
<h2 id="org239daeb"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orgec9ce24" class="outline-2">
<h2 id="orgec9ce24"><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-org1c08c69" class="outline-3">
<h3 id="org1c08c69"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-org7e86920" class="outline-3">
<h3 id="org7e86920"><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-org7297157" class="outline-3">
<h3 id="org7297157"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-org049b04e" class="outline-3">
<h3 id="org049b04e"><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-orgd012f28" class="outline-3">
<h3 id="orgd012f28"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org99869bd" class="outline-3">
<h3 id="org99869bd"><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-org44cb722" class="outline-3">
<h3 id="org44cb722"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org4aacfb9" class="outline-3">
<h3 id="org4aacfb9"><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-org750ced2" class="outline-3">
<h3 id="org750ced2"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-orgcbcf730" class="outline-3">
<h3 id="orgcbcf730"><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: 2023-09-15 Fri 14:31</p>
<p class="date">Created: 2023-09-19 Tue 12:46</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>
<!-- 2023-09-15 Fri 14:31 -->
<!-- 2023-09-19 Tue 12:46 -->
<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="#org9316cf1">1. Template for HDF5 definitions</a></li>
<li><a href="#orga1fd685">2. Template for HDF5 structures</a></li>
<li><a href="#orgaa7df7c">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org8929ec5">4. Template for HDF5 has a group</a></li>
<li><a href="#org060824f">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org5b62044">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org30343b6">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org6fe53a4">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org61980de">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org03de377">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org7f7d8a6">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgc0fb095">12. Source code for the determinant part</a></li>
<li><a href="#org2a1c16f">13. Helper functions</a></li>
<li><a href="#orgc366345">1. Template for HDF5 definitions</a></li>
<li><a href="#orgb01ada9">2. Template for HDF5 structures</a></li>
<li><a href="#org2395100">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org75bb1ce">4. Template for HDF5 has a group</a></li>
<li><a href="#org01443bd">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orga3619e6">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org8cbfcb9">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orge9b7fff">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgb76eb0d">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgd188669">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgcc3cc1c">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org1b5b5b0">12. Source code for the determinant part</a></li>
<li><a href="#orgd490a97">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org9316cf1" class="outline-2">
<h2 id="org9316cf1"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orgc366345" class="outline-2">
<h2 id="orgc366345"><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-orga1fd685" class="outline-2">
<h2 id="orga1fd685"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgb01ada9" class="outline-2">
<h2 id="orgb01ada9"><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-orgaa7df7c" class="outline-2">
<h2 id="orgaa7df7c"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org2395100" class="outline-2">
<h2 id="org2395100"><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-org8929ec5" class="outline-2">
<h2 id="org8929ec5"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org75bb1ce" class="outline-2">
<h2 id="org75bb1ce"><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-org060824f" class="outline-2">
<h2 id="org060824f"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org01443bd" class="outline-2">
<h2 id="org01443bd"><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-org5b62044" class="outline-2">
<h2 id="org5b62044"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orga3619e6" class="outline-2">
<h2 id="orga3619e6"><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-org30343b6" class="outline-2">
<h2 id="org30343b6"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org8cbfcb9" class="outline-2">
<h2 id="org8cbfcb9"><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-org6fe53a4" class="outline-2">
<h2 id="org6fe53a4"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-orge9b7fff" class="outline-2">
<h2 id="orge9b7fff"><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-org61980de" class="outline-2">
<h2 id="org61980de"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgb76eb0d" class="outline-2">
<h2 id="orgb76eb0d"><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-org03de377" class="outline-2">
<h2 id="org03de377"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgd188669" class="outline-2">
<h2 id="orgd188669"><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-org7f7d8a6" class="outline-2">
<h2 id="org7f7d8a6"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgcc3cc1c" class="outline-2">
<h2 id="orgcc3cc1c"><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-orgc0fb095" class="outline-2">
<h2 id="orgc0fb095"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org1b5b5b0" class="outline-2">
<h2 id="org1b5b5b0"><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-org2a1c16f" class="outline-2">
<h2 id="org2a1c16f"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgd490a97" class="outline-2">
<h2 id="orgd490a97"><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: 2023-09-15 Fri 14:31</p>
<p class="date">Created: 2023-09-19 Tue 12:46</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="#orgd1e9a84">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgb903120">2. Template for general structure in text back end</a></li>
<li><a href="#orgff58d0d">3. Initialize function (constant part)</a></li>
<li><a href="#orgdd18bd9">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgbe59957">5. Flush function (templated part)</a></li>
<li><a href="#org54cc82e">6. Template for text read a group</a></li>
<li><a href="#org3132075">7. Template for text has a group</a></li>
<li><a href="#org1069902">8. Template for text flush a group</a></li>
<li><a href="#org03b4a70">9. Template for text free memory</a></li>
<li><a href="#orga6bd9a2">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org471fa28">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org03378e9">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org20cd797">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org0c058d3">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgb853286">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgf1cc5bc">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgd37c0a1">17. Source code for the determinant part</a></li>
<li><a href="#orgf94cc45">1. Template for group-related structures in text back end</a></li>
<li><a href="#org2d38d40">2. Template for general structure in text back end</a></li>
<li><a href="#org5065e5f">3. Initialize function (constant part)</a></li>
<li><a href="#orga888da9">4. Deinitialize function (templated part)</a></li>
<li><a href="#org7b2998a">5. Flush function (templated part)</a></li>
<li><a href="#orgaba8be3">6. Template for text read a group</a></li>
<li><a href="#orgacfe879">7. Template for text has a group</a></li>
<li><a href="#org536d3a0">8. Template for text flush a group</a></li>
<li><a href="#orgb33355f">9. Template for text free memory</a></li>
<li><a href="#org9d30d4b">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgf5eca5c">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org24d56ee">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgaff81da">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org27c1280">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org3badef5">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org1c771d0">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgca1dde2">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-orgd1e9a84" class="outline-2">
<h2 id="orgd1e9a84"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orgf94cc45" class="outline-2">
<h2 id="orgf94cc45"><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-orgb903120" class="outline-2">
<h2 id="orgb903120"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org2d38d40" class="outline-2">
<h2 id="org2d38d40"><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-orgff58d0d" class="outline-2">
<h2 id="orgff58d0d"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org5065e5f" class="outline-2">
<h2 id="org5065e5f"><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-orgdd18bd9" class="outline-2">
<h2 id="orgdd18bd9"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orga888da9" class="outline-2">
<h2 id="orga888da9"><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-orgbe59957" class="outline-2">
<h2 id="orgbe59957"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org7b2998a" class="outline-2">
<h2 id="org7b2998a"><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-org54cc82e" class="outline-2">
<h2 id="org54cc82e"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orgaba8be3" class="outline-2">
<h2 id="orgaba8be3"><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-org3132075" class="outline-2">
<h2 id="org3132075"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-orgacfe879" class="outline-2">
<h2 id="orgacfe879"><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-org1069902" class="outline-2">
<h2 id="org1069902"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org536d3a0" class="outline-2">
<h2 id="org536d3a0"><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-org03b4a70" class="outline-2">
<h2 id="org03b4a70"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-orgb33355f" class="outline-2">
<h2 id="orgb33355f"><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-orga6bd9a2" class="outline-2">
<h2 id="orga6bd9a2"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org9d30d4b" class="outline-2">
<h2 id="org9d30d4b"><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-org471fa28" class="outline-2">
<h2 id="org471fa28"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgf5eca5c" class="outline-2">
<h2 id="orgf5eca5c"><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-org03378e9" class="outline-2">
<h2 id="org03378e9"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org24d56ee" class="outline-2">
<h2 id="org24d56ee"><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-org20cd797" class="outline-2">
<h2 id="org20cd797"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orgaff81da" class="outline-2">
<h2 id="orgaff81da"><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-org0c058d3" class="outline-2">
<h2 id="org0c058d3"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org27c1280" class="outline-2">
<h2 id="org27c1280"><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-orgb853286" class="outline-2">
<h2 id="orgb853286"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org3badef5" class="outline-2">
<h2 id="org3badef5"><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-orgf1cc5bc" class="outline-2">
<h2 id="orgf1cc5bc"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org1c771d0" class="outline-2">
<h2 id="org1c771d0"><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-orgd37c0a1" class="outline-2">
<h2 id="orgd37c0a1"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-orgca1dde2" class="outline-2">
<h2 id="orgca1dde2"><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: 2023-09-15 Fri 14:31</p>
<p class="date">Created: 2023-09-19 Tue 12:46</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2023-09-15 Fri 14:31 -->
<!-- 2023-09-19 Tue 12:46 -->
<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>
@ -346,71 +346,71 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org4cb9603">1. Metadata (metadata group)</a></li>
<li><a href="#orgcc9c7a3">2. System</a>
<li><a href="#org15a419c">1. Metadata (metadata group)</a></li>
<li><a href="#orgd4e0b7b">2. System</a>
<ul>
<li><a href="#org6b92fa9">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org0aa8a9e">2.2. Cell (cell group)</a></li>
<li><a href="#orga5b79e9">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org611d525">2.4. Electron (electron group)</a></li>
<li><a href="#orgf0c9f6e">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org6b1abed">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org31ae268">2.2. Cell (cell group)</a></li>
<li><a href="#org4f7e70b">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgb2d131f">2.4. Electron (electron group)</a></li>
<li><a href="#org784df97">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#orgfbc0244">3. Basis functions</a>
<li><a href="#orgb1e38f8">3. Basis functions</a>
<ul>
<li><a href="#orga7b97e8">3.1. Basis set (basis group)</a>
<li><a href="#org8d00bf1">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org036fd30">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org3a69e90">3.1.2. Numerical orbitals</a></li>
<li><a href="#orgf2fc8bf">3.1.3. Plane waves</a></li>
<li><a href="#org6ac48d6">3.1.4. Data definitions</a></li>
<li><a href="#org3259b54">3.1.5. Example</a></li>
<li><a href="#orge1a2fa3">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org8325fba">3.1.2. Numerical orbitals</a></li>
<li><a href="#orgb23ecf2">3.1.3. Plane waves</a></li>
<li><a href="#org8570665">3.1.4. Data definitions</a></li>
<li><a href="#org82dc3e8">3.1.5. Example</a></li>
</ul>
</li>
<li><a href="#org2de5247">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org4000d74">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org6ab625e">3.2.1. Example</a></li>
<li><a href="#org518db35">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#orga3fd182">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#orgf6d2a6e">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org7bbaba5">4. Orbitals</a>
<li><a href="#org2ca991a">4. Orbitals</a>
<ul>
<li><a href="#org478a585">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org30bfd09">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="#orgfa0d1c2">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org400c464">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgd1a7298">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org7d1a8ef">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org24704ae">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orga15552f">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org92a8837">5. Multi-determinant information</a>
<li><a href="#orgc57652d">5. Multi-determinant information</a>
<ul>
<li><a href="#org0e75b2b">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgea1c4ee">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org0a6d760">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org1a481cf">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org80d576e">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgeaa0fae">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgb3dd45a">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgb755c04">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org2c09e57">6. Correlation factors</a>
<li><a href="#org3468cfd">6. Correlation factors</a>
<ul>
<li><a href="#orga409880">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#orgd688fc3">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org84f1286">6.1.1. CHAMP</a></li>
<li><a href="#orgbf2a3b1">6.1.2. Mu</a></li>
<li><a href="#orga9f2a9f">6.1.3. Table of values</a></li>
<li><a href="#org4b02e4b">6.1.1. CHAMP</a></li>
<li><a href="#org8c69533">6.1.2. Mu</a></li>
<li><a href="#org5741440">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org977925f">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org7909b5c">7. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -423,8 +423,8 @@ is reversed in the produced <code>trex.json</code> configuration file as the
library is written in C.
</p>
<div id="outline-container-org4cb9603" class="outline-2">
<h2 id="org4cb9603"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org15a419c" class="outline-2">
<h2 id="org15a419c"><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,
@ -434,7 +434,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
</p>
<table id="org71e389b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb4a0f75" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -517,19 +517,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
</div>
</div>
<div id="outline-container-orgcc9c7a3" class="outline-2">
<h2 id="orgcc9c7a3"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-orgd4e0b7b" class="outline-2">
<h2 id="orgd4e0b7b"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org6b92fa9" class="outline-3">
<h3 id="org6b92fa9"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org6b1abed" class="outline-3">
<h3 id="org6b1abed"><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="orgfc0284a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge5b226b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -596,15 +596,15 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org0aa8a9e" class="outline-3">
<h3 id="org0aa8a9e"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org31ae268" class="outline-3">
<h3 id="org31ae268"><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="org32eebd8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdcc132e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -678,15 +678,15 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-orga5b79e9" class="outline-3">
<h3 id="orga5b79e9"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org4f7e70b" class="outline-3">
<h3 id="org4f7e70b"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div class="outline-text-3" id="text-2-3">
<p>
A single $k$-point per TREXIO file can be stored. The $k$-point is
defined in this group.
</p>
<table id="org4e9dc5f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4dc67c1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -725,8 +725,8 @@ defined in this group.
</div>
</div>
<div id="outline-container-org611d525" class="outline-3">
<h3 id="org611d525"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-orgb2d131f" class="outline-3">
<h3 id="orgb2d131f"><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
@ -745,7 +745,7 @@ the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org8295a20" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org507c313" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -791,8 +791,8 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgf0c9f6e" class="outline-3">
<h3 id="orgf0c9f6e"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org784df97" class="outline-3">
<h3 id="org784df97"><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
@ -809,7 +809,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="org278efc6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc525e99" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -877,16 +877,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-orgfbc0244" class="outline-2">
<h2 id="orgfbc0244"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-orgb1e38f8" class="outline-2">
<h2 id="orgb1e38f8"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orga7b97e8" class="outline-3">
<h3 id="orga7b97e8"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org8d00bf1" class="outline-3">
<h3 id="org8d00bf1"><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-org036fd30" class="outline-4">
<h4 id="org036fd30"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-orge1a2fa3" class="outline-4">
<h4 id="orge1a2fa3"><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
@ -940,8 +940,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-org3a69e90" class="outline-4">
<h4 id="org3a69e90"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-org8325fba" class="outline-4">
<h4 id="org8325fba"><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
@ -1005,8 +1005,8 @@ reimplement them with consideration for its specific needs.
</div>
</div>
<div id="outline-container-orgf2fc8bf" class="outline-4">
<h4 id="orgf2fc8bf"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-orgb23ecf2" class="outline-4">
<h4 id="orgb23ecf2"><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
@ -1027,10 +1027,10 @@ plane waves.
</div>
</div>
<div id="outline-container-org6ac48d6" class="outline-4">
<h4 id="org6ac48d6"><span class="section-number-4">3.1.4</span> Data definitions</h4>
<div id="outline-container-org8570665" class="outline-4">
<h4 id="org8570665"><span class="section-number-4">3.1.4</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-4">
<table id="orgcee1cc6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge04bd17" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1250,8 +1250,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org3259b54" class="outline-4">
<h4 id="org3259b54"><span class="section-number-4">3.1.5</span> Example</h4>
<div id="outline-container-org82dc3e8" class="outline-4">
<h4 id="org82dc3e8"><span class="section-number-4">3.1.5</span> Example</h4>
<div class="outline-text-4" id="text-3-1-5">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1329,8 +1329,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org2de5247" class="outline-3">
<h3 id="org2de5247"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org4000d74" class="outline-3">
<h3 id="org4000d74"><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
@ -1364,7 +1364,7 @@ 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="orgc79bd3f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7c655c7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1468,8 +1468,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-org6ab625e" class="outline-4">
<h4 id="org6ab625e"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-org518db35" class="outline-4">
<h4 id="org518db35"><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
@ -1532,8 +1532,8 @@ power = [
</div>
</div>
<div id="outline-container-orga3fd182" class="outline-3">
<h3 id="orga3fd182"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-orgf6d2a6e" class="outline-3">
<h3 id="orgf6d2a6e"><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
@ -1548,7 +1548,7 @@ 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="org8ae2f45" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb954f75" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1665,12 +1665,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-org7bbaba5" class="outline-2">
<h2 id="org7bbaba5"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org2ca991a" class="outline-2">
<h2 id="org2ca991a"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org478a585" class="outline-3">
<h3 id="org478a585"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org30bfd09" class="outline-3">
<h3 id="org30bfd09"><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
@ -1751,7 +1751,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="org551daff" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org97002ab" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1803,7 +1803,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org86f8a74" class="outline-4">
<div id="outline-container-orga240d0a" 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">
@ -1821,7 +1821,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org79c6f89" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org137c670" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1916,7 +1916,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org9952b3a" class="outline-4">
<div id="outline-container-org077063f" 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>
@ -1942,7 +1942,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="orgfc642a8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org65c5e9d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2010,10 +2010,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-orgfa0d1c2" class="outline-3">
<h3 id="orgfa0d1c2"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org400c464" class="outline-3">
<h3 id="org400c464"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org4ca4481" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org56cdd5f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2100,8 +2100,8 @@ The Cholesky decomposition of the integrals can also be stored:
</table>
</div>
<div id="outline-container-orgd1a7298" class="outline-4">
<h4 id="orgd1a7298"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org24704ae" class="outline-4">
<h4 id="org24704ae"><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
@ -2109,7 +2109,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org263384a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge850ea5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2204,8 +2204,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org7d1a8ef" class="outline-4">
<h4 id="org7d1a8ef"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-orga15552f" class="outline-4">
<h4 id="orga15552f"><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
@ -2213,7 +2213,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orge77c9a3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8fb3043" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2282,12 +2282,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org92a8837" class="outline-2">
<h2 id="org92a8837"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-orgc57652d" class="outline-2">
<h2 id="orgc57652d"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org0e75b2b" class="outline-3">
<h3 id="org0e75b2b"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org80d576e" class="outline-3">
<h3 id="org80d576e"><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 \(\Psi\)
@ -2329,7 +2329,7 @@ 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="orgcce5f83" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org311a1d7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2375,8 +2375,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-orgea1c4ee" class="outline-3">
<h3 id="orgea1c4ee"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-orgeaa0fae" class="outline-3">
<h3 id="orgeaa0fae"><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
@ -2398,7 +2398,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org9bce722" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbf22ae8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2444,8 +2444,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org0a6d760" class="outline-3">
<h3 id="org0a6d760"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orgb3dd45a" class="outline-3">
<h3 id="orgb3dd45a"><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
@ -2516,7 +2516,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org7154561" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org66b46a0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2597,8 +2597,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-org1a481cf" class="outline-3">
<h3 id="org1a481cf"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-orgb755c04" class="outline-3">
<h3 id="orgb755c04"><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
@ -2670,7 +2670,7 @@ 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="org3f422cb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6102a7f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2801,12 +2801,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org2c09e57" class="outline-2">
<h2 id="org2c09e57"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org3468cfd" class="outline-2">
<h2 id="org3468cfd"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-orga409880" class="outline-3">
<h3 id="orga409880"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-orgd688fc3" class="outline-3">
<h3 id="orgd688fc3"><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
@ -2831,8 +2831,8 @@ following:
</ul>
</div>
<div id="outline-container-org84f1286" class="outline-4">
<h4 id="org84f1286"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org4b02e4b" class="outline-4">
<h4 id="org4b02e4b"><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
@ -2933,8 +2933,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-orgbf2a3b1" class="outline-4">
<h4 id="orgbf2a3b1"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org8c69533" class="outline-4">
<h4 id="org8c69533"><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
@ -3031,10 +3031,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
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<h4 id="orga9f2a9f"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="org5741440"><span class="section-number-4">6.1.3</span> Table of values</h4>
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@ -3138,8 +3138,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h2 id="org977925f"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org7909b5c"><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
@ -3153,7 +3153,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3208,7 +3208,7 @@ 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: 2023-09-15 Fri 14:31</p>
<p class="date">Created: 2023-09-19 Tue 12:46</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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