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README.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<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: 2024-02-21 Wed 12:02</p>
<p class="date">Created: 2024-03-13 Wed 13:15</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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examples.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-02-21 Wed 12:02 -->
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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="#orgd2edb20">1. Writing nuclear coordinates</a>
<li><a href="#org9d28029">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orgd9f857e">1.1. C</a></li>
<li><a href="#org2594359">1.2. Python</a></li>
<li><a href="#orga66b14e">1.3. Fortran</a></li>
<li><a href="#org2f1cf59">1.1. C</a></li>
<li><a href="#org6ba82fa">1.2. Python</a></li>
<li><a href="#orgd0e548c">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org7e2b4a4">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org2724804">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org9a33d3a">2.1. Fortran</a>
<li><a href="#org9df903a">2.1. Fortran</a>
<ul>
<li><a href="#orgb754354">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgea2e656">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org336bc3f">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org53b8ff6">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org9441071">2.1.5. Allocate memory</a></li>
<li><a href="#orgc63d108">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org884ea5a">2.1.7. Read two-electron quantities</a>
<li><a href="#orgfebad1d">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org5c9805c">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org4f6ca6d">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org639e98c">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org7b5b464">2.1.5. Allocate memory</a></li>
<li><a href="#org7fc131f">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org3b58cba">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org8b04863">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org949d8da">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org1f79d7f">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgb087f6d">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org17402d7">2.1.8. Compute the energy</a></li>
<li><a href="#org5869f62">2.1.9. Terminate</a></li>
<li><a href="#org2d6f45c">2.1.8. Compute the energy</a></li>
<li><a href="#org6cea9a4">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org6f232fd">2.2. Python</a>
<li><a href="#org8359e53">2.2. Python</a>
<ul>
<li><a href="#org0e671c8">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org0bea0ea">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org14a550c">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#orgecba9b6">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org8ec9eeb">2.2.5. Read two-electron quantities</a>
<li><a href="#orgf6ab7ad">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgb0a3dbe">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org7ec8604">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org627a4bd">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org3c7ab4b">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#orgbc1521f">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org6a9d201">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org0ced04e">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org0ec3266">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org22a295a">2.2.6. Compute the energy</a></li>
<li><a href="#org6955673">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org0c79e58">3. Reading determinants</a>
<li><a href="#org6c6ac9d">3. Reading determinants</a>
<ul>
<li><a href="#org304eb10">3.1. Fortran</a></li>
<li><a href="#org884fe33">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgd2edb20" class="outline-2">
<h2 id="orgd2edb20"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org9d28029" class="outline-2">
<h2 id="org9d28029"><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-orgd9f857e" class="outline-3">
<h3 id="orgd9f857e"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org2f1cf59" class="outline-3">
<h3 id="org2f1cf59"><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-org2594359" class="outline-3">
<h3 id="org2594359"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org6ba82fa" class="outline-3">
<h3 id="org6ba82fa"><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-orga66b14e" class="outline-3">
<h3 id="orga66b14e"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orgd0e548c" class="outline-3">
<h3 id="orgd0e548c"><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-org7e2b4a4" class="outline-2">
<h2 id="org7e2b4a4"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org2724804" class="outline-2">
<h2 id="org2724804"><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-org9a33d3a" class="outline-3">
<h3 id="org9a33d3a"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org9df903a" class="outline-3">
<h3 id="org9df903a"><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-orgb754354" class="outline-4">
<h4 id="orgb754354"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgfebad1d" class="outline-4">
<h4 id="orgfebad1d"><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-orgea2e656" class="outline-4">
<h4 id="orgea2e656"><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-org5c9805c" class="outline-4">
<h4 id="org5c9805c"><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-org336bc3f" class="outline-4">
<h4 id="org336bc3f"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org4f6ca6d" class="outline-4">
<h4 id="org4f6ca6d"><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-org53b8ff6" class="outline-4">
<h4 id="org53b8ff6"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org639e98c" class="outline-4">
<h4 id="org639e98c"><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-org9441071" class="outline-4">
<h4 id="org9441071"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org7b5b464" class="outline-4">
<h4 id="org7b5b464"><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-orgc63d108" class="outline-4">
<h4 id="orgc63d108"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org7fc131f" class="outline-4">
<h4 id="org7fc131f"><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-org884ea5a" class="outline-4">
<h4 id="org884ea5a"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org3b58cba" class="outline-4">
<h4 id="org3b58cba"><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-org8b04863" class="outline-5">
<h5 id="org8b04863"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org1f79d7f" class="outline-5">
<h5 id="org1f79d7f"><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-org949d8da" class="outline-5">
<h5 id="org949d8da"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgb087f6d" class="outline-5">
<h5 id="orgb087f6d"><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-org17402d7" class="outline-4">
<h4 id="org17402d7"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org2d6f45c" class="outline-4">
<h4 id="org2d6f45c"><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-org5869f62" class="outline-4">
<h4 id="org5869f62"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org6cea9a4" class="outline-4">
<h4 id="org6cea9a4"><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-org6f232fd" class="outline-3">
<h3 id="org6f232fd"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org8359e53" class="outline-3">
<h3 id="org8359e53"><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-org0e671c8" class="outline-4">
<h4 id="org0e671c8"><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-orgf6ab7ad" class="outline-4">
<h4 id="orgf6ab7ad"><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-org0bea0ea" class="outline-4">
<h4 id="org0bea0ea"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgb0a3dbe" class="outline-4">
<h4 id="orgb0a3dbe"><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-org14a550c" class="outline-4">
<h4 id="org14a550c"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org7ec8604" class="outline-4">
<h4 id="org7ec8604"><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-orgecba9b6" class="outline-4">
<h4 id="orgecba9b6"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org627a4bd" class="outline-4">
<h4 id="org627a4bd"><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-org8ec9eeb" class="outline-4">
<h4 id="org8ec9eeb"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-org3c7ab4b" class="outline-4">
<h4 id="org3c7ab4b"><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-orgbc1521f" class="outline-5">
<h5 id="orgbc1521f"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org0ced04e" class="outline-5">
<h5 id="org0ced04e"><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-org6a9d201" class="outline-5">
<h5 id="org6a9d201"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-org0ec3266" class="outline-5">
<h5 id="org0ec3266"><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-org22a295a" class="outline-4">
<h4 id="org22a295a"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org6955673" class="outline-4">
<h4 id="org6955673"><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-org0c79e58" class="outline-2">
<h2 id="org0c79e58"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org6c6ac9d" class="outline-2">
<h2 id="org6c6ac9d"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org304eb10" class="outline-3">
<h3 id="org304eb10"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org884fe33" class="outline-3">
<h3 id="org884fe33"><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: 2024-02-21 Wed 12:02</p>
<p class="date">Created: 2024-03-13 Wed 13:15</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>
<!-- 2024-02-21 Wed 12:02 -->
<!-- 2024-03-13 Wed 13:15 -->
<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: 2024-02-21 Wed 12:02</p>
<p class="date">Created: 2024-03-13 Wed 13:15</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>
<!-- 2024-02-21 Wed 12:02 -->
<!-- 2024-03-13 Wed 13:15 -->
<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: 2024-02-21 Wed 12:02</p>
<p class="date">Created: 2024-03-13 Wed 13:15</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>
<!-- 2024-02-21 Wed 12:02 -->
<!-- 2024-03-13 Wed 13:15 -->
<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="#org13eec7f">1. Format specification</a>
<li><a href="#org661ac98">1. Format specification</a>
<ul>
<li><a href="#orgd5ecbf4">1.1. Organization of the data</a></li>
<li><a href="#org88bab20">1.2. Data types</a></li>
<li><a href="#orga0f5002">1.1. Organization of the data</a></li>
<li><a href="#orgab9a42e">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org511078c">2. The TREXIO library</a>
<li><a href="#orga0324e6">2. The TREXIO library</a>
<ul>
<li><a href="#org3f66120">2.1. The front-end</a></li>
<li><a href="#orgd5640c2">2.2. The back-end</a></li>
<li><a href="#orgbfa4e81">2.3. Supported languages</a></li>
<li><a href="#orgf496f23">2.4. Source code generation and documentation</a></li>
<li><a href="#org180f8ab">2.5. Availability</a></li>
<li><a href="#orgc5d0490">2.1. The front-end</a></li>
<li><a href="#orge69743f">2.2. The back-end</a></li>
<li><a href="#org33b704e">2.3. Supported languages</a></li>
<li><a href="#org2ea78f8">2.4. Source code generation and documentation</a></li>
<li><a href="#org38ab5a0">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org13eec7f" class="outline-2">
<h2 id="org13eec7f"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org661ac98" class="outline-2">
<h2 id="org661ac98"><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-orgd5ecbf4" class="outline-3">
<h3 id="orgd5ecbf4"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-orga0f5002" class="outline-3">
<h3 id="orga0f5002"><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-org88bab20" class="outline-3">
<h3 id="org88bab20"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-orgab9a42e" class="outline-3">
<h3 id="orgab9a42e"><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-org511078c" class="outline-2">
<h2 id="org511078c"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orga0324e6" class="outline-2">
<h2 id="orga0324e6"><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-org3f66120" class="outline-3">
<h3 id="org3f66120"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orgc5d0490" class="outline-3">
<h3 id="orgc5d0490"><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-orgd5640c2" class="outline-3">
<h3 id="orgd5640c2"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-orge69743f" class="outline-3">
<h3 id="orge69743f"><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-orgbfa4e81" class="outline-3">
<h3 id="orgbfa4e81"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org33b704e" class="outline-3">
<h3 id="org33b704e"><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-orgf496f23" class="outline-3">
<h3 id="orgf496f23"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org2ea78f8" class="outline-3">
<h3 id="org2ea78f8"><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-org180f8ab" class="outline-3">
<h3 id="org180f8ab"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org38ab5a0" class="outline-3">
<h3 id="org38ab5a0"><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: 2024-02-21 Wed 12:02</p>
<p class="date">Created: 2024-03-13 Wed 13:15</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>
<!-- 2024-02-21 Wed 12:02 -->
<!-- 2024-03-13 Wed 13:15 -->
<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="#orgf9cf467">1. Template for HDF5 definitions</a></li>
<li><a href="#org63f1a10">2. Template for HDF5 structures</a></li>
<li><a href="#orgcfefec4">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org457a52f">4. Template for HDF5 has a group</a></li>
<li><a href="#org7c7569b">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org6dd0fad">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgb6fdc30">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgc51df09">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orga0ff7d2">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org4d30ad4">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org17af017">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org0b2af7e">12. Source code for the determinant part</a></li>
<li><a href="#org0d33b77">13. Helper functions</a></li>
<li><a href="#org635bd4a">1. Template for HDF5 definitions</a></li>
<li><a href="#org8e88073">2. Template for HDF5 structures</a></li>
<li><a href="#org3ec6d2a">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgeb2c7d8">4. Template for HDF5 has a group</a></li>
<li><a href="#org1ea277b">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgd8b32ac">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org9f833b4">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org8592181">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org03e0892">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orge407092">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgdba42b5">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org07ecab6">12. Source code for the determinant part</a></li>
<li><a href="#org6f703ab">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgf9cf467" class="outline-2">
<h2 id="orgf9cf467"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org635bd4a" class="outline-2">
<h2 id="org635bd4a"><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-org63f1a10" class="outline-2">
<h2 id="org63f1a10"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org8e88073" class="outline-2">
<h2 id="org8e88073"><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-orgcfefec4" class="outline-2">
<h2 id="orgcfefec4"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org3ec6d2a" class="outline-2">
<h2 id="org3ec6d2a"><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-org457a52f" class="outline-2">
<h2 id="org457a52f"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orgeb2c7d8" class="outline-2">
<h2 id="orgeb2c7d8"><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-org7c7569b" class="outline-2">
<h2 id="org7c7569b"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org1ea277b" class="outline-2">
<h2 id="org1ea277b"><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-org6dd0fad" class="outline-2">
<h2 id="org6dd0fad"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgd8b32ac" class="outline-2">
<h2 id="orgd8b32ac"><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-orgb6fdc30" class="outline-2">
<h2 id="orgb6fdc30"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org9f833b4" class="outline-2">
<h2 id="org9f833b4"><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-orgc51df09" class="outline-2">
<h2 id="orgc51df09"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org8592181" class="outline-2">
<h2 id="org8592181"><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-orga0ff7d2" class="outline-2">
<h2 id="orga0ff7d2"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org03e0892" class="outline-2">
<h2 id="org03e0892"><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-org4d30ad4" class="outline-2">
<h2 id="org4d30ad4"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orge407092" class="outline-2">
<h2 id="orge407092"><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-org17af017" class="outline-2">
<h2 id="org17af017"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgdba42b5" class="outline-2">
<h2 id="orgdba42b5"><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-org0b2af7e" class="outline-2">
<h2 id="org0b2af7e"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org07ecab6" class="outline-2">
<h2 id="org07ecab6"><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-org0d33b77" class="outline-2">
<h2 id="org0d33b77"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org6f703ab" class="outline-2">
<h2 id="org6f703ab"><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: 2024-02-21 Wed 12:02</p>
<p class="date">Created: 2024-03-13 Wed 13:15</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org142b727">1. Template for group-related structures in text back end</a></li>
<li><a href="#org597a3c9">2. Template for general structure in text back end</a></li>
<li><a href="#org61c5841">3. Initialize function (constant part)</a></li>
<li><a href="#orgb97d4fc">4. Deinitialize function (templated part)</a></li>
<li><a href="#org9894658">5. Flush function (templated part)</a></li>
<li><a href="#orge2d9eb7">6. Template for text read a group</a></li>
<li><a href="#orgdcd4013">7. Template for text has a group</a></li>
<li><a href="#orgdd61e4f">8. Template for text flush a group</a></li>
<li><a href="#orgada9814">9. Template for text free memory</a></li>
<li><a href="#org337b892">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgd133012">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org23c6179">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org156f7d6">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org71db391">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org53520e2">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgd092bca">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org887b7da">17. Source code for the determinant part</a></li>
<li><a href="#orgb4fae5c">1. Template for group-related structures in text back end</a></li>
<li><a href="#org9da3ede">2. Template for general structure in text back end</a></li>
<li><a href="#org6ee0bb1">3. Initialize function (constant part)</a></li>
<li><a href="#orgad0c8e8">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgd5b48e8">5. Flush function (templated part)</a></li>
<li><a href="#org0168538">6. Template for text read a group</a></li>
<li><a href="#org21b2392">7. Template for text has a group</a></li>
<li><a href="#orgbad4453">8. Template for text flush a group</a></li>
<li><a href="#org92981e0">9. Template for text free memory</a></li>
<li><a href="#org5793154">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org10f1441">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org295c77c">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org985aaed">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgb99ab70">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orga4ca407">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgbe7be25">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org0a5e869">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-org142b727" class="outline-2">
<h2 id="org142b727"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orgb4fae5c" class="outline-2">
<h2 id="orgb4fae5c"><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-org597a3c9" class="outline-2">
<h2 id="org597a3c9"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org9da3ede" class="outline-2">
<h2 id="org9da3ede"><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-org61c5841" class="outline-2">
<h2 id="org61c5841"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org6ee0bb1" class="outline-2">
<h2 id="org6ee0bb1"><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-orgb97d4fc" class="outline-2">
<h2 id="orgb97d4fc"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgad0c8e8" class="outline-2">
<h2 id="orgad0c8e8"><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-org9894658" class="outline-2">
<h2 id="org9894658"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-orgd5b48e8" class="outline-2">
<h2 id="orgd5b48e8"><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-orge2d9eb7" class="outline-2">
<h2 id="orge2d9eb7"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org0168538" class="outline-2">
<h2 id="org0168538"><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-orgdcd4013" class="outline-2">
<h2 id="orgdcd4013"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org21b2392" class="outline-2">
<h2 id="org21b2392"><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-orgdd61e4f" class="outline-2">
<h2 id="orgdd61e4f"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-orgbad4453" class="outline-2">
<h2 id="orgbad4453"><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-orgada9814" class="outline-2">
<h2 id="orgada9814"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org92981e0" class="outline-2">
<h2 id="org92981e0"><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-org337b892" class="outline-2">
<h2 id="org337b892"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org5793154" class="outline-2">
<h2 id="org5793154"><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-orgd133012" class="outline-2">
<h2 id="orgd133012"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org10f1441" class="outline-2">
<h2 id="org10f1441"><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-org23c6179" class="outline-2">
<h2 id="org23c6179"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org295c77c" class="outline-2">
<h2 id="org295c77c"><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-org156f7d6" class="outline-2">
<h2 id="org156f7d6"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org985aaed" class="outline-2">
<h2 id="org985aaed"><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-org71db391" class="outline-2">
<h2 id="org71db391"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orgb99ab70" class="outline-2">
<h2 id="orgb99ab70"><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-org53520e2" class="outline-2">
<h2 id="org53520e2"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-orga4ca407" class="outline-2">
<h2 id="orga4ca407"><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-orgd092bca" class="outline-2">
<h2 id="orgd092bca"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgbe7be25" class="outline-2">
<h2 id="orgbe7be25"><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-org887b7da" class="outline-2">
<h2 id="org887b7da"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org0a5e869" class="outline-2">
<h2 id="org0a5e869"><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: 2024-02-21 Wed 12:02</p>
<p class="date">Created: 2024-03-13 Wed 13:15</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2024-02-21 Wed 12:02 -->
<!-- 2024-03-13 Wed 13:15 -->
<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="#org5629722">1. Metadata (metadata group)</a></li>
<li><a href="#org66a086a">2. System</a>
<li><a href="#orga5b0934">1. Metadata (metadata group)</a></li>
<li><a href="#orga6ef707">2. System</a>
<ul>
<li><a href="#org7e7984d">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org6d66c86">2.2. Cell (cell group)</a></li>
<li><a href="#orgb97b4a9">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgaef2f03">2.4. Electron (electron group)</a></li>
<li><a href="#org2d99a33">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org721cefe">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org07004a2">2.2. Cell (cell group)</a></li>
<li><a href="#orgf757b30">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org09a7b84">2.4. Electron (electron group)</a></li>
<li><a href="#org2bac8b4">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org9cec117">3. Basis functions</a>
<li><a href="#org5c2f3d5">3. Basis functions</a>
<ul>
<li><a href="#org7a18dee">3.1. Basis set (basis group)</a>
<li><a href="#orgc14ee0a">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org501d562">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org87d2155">3.1.2. Numerical orbitals</a></li>
<li><a href="#orgcf60e8e">3.1.3. Plane waves</a></li>
<li><a href="#org86983c2">3.1.4. Data definitions</a></li>
<li><a href="#org5c465c4">3.1.5. Example</a></li>
<li><a href="#orgdd8565f">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org058a19f">3.1.2. Numerical orbitals</a></li>
<li><a href="#orgcf71100">3.1.3. Plane waves</a></li>
<li><a href="#org7ebd447">3.1.4. Data definitions</a></li>
<li><a href="#org3c3b7f2">3.1.5. Example</a></li>
</ul>
</li>
<li><a href="#orgda1e305">3.2. Effective core potentials (ecp group)</a>
<li><a href="#orgb0a0b23">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org71940d3">3.2.1. Example</a></li>
<li><a href="#org9ed565a">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#orgcbf84f7">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org750011c">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org08f08eb">4. Orbitals</a>
<li><a href="#orgfdedbe2">4. Orbitals</a>
<ul>
<li><a href="#org221cd4d">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org4d3c3fa">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="#orgc4a5b4f">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org5a7d4b4">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orga16bd3f">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org089e9b0">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org2269586">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org90d0ad3">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org9c53bf0">5. Multi-determinant information</a>
<li><a href="#orga78f1e0">5. Multi-determinant information</a>
<ul>
<li><a href="#orgec8f447">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgc4c3083">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org8bfbeb7">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org597f84c">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgabe7ef6">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org859f95a">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgc75ae3d">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org07ac3a8">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org59dacd2">6. Correlation factors</a>
<li><a href="#org338541d">6. Correlation factors</a>
<ul>
<li><a href="#org2eee619">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#orgea46819">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org35455a9">6.1.1. CHAMP</a></li>
<li><a href="#org279f650">6.1.2. Mu</a></li>
<li><a href="#orgc27511b">6.1.3. Table of values</a></li>
<li><a href="#orgedc051e">6.1.1. CHAMP</a></li>
<li><a href="#org3961af4">6.1.2. Mu</a></li>
<li><a href="#orgaa8d94f">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgd2f738b">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org4d8cb71">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-org5629722" class="outline-2">
<h2 id="org5629722"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orga5b0934" class="outline-2">
<h2 id="orga5b0934"><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="org9415f3a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org06f2909" 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-org66a086a" class="outline-2">
<h2 id="org66a086a"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-orga6ef707" class="outline-2">
<h2 id="orga6ef707"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org7e7984d" class="outline-3">
<h3 id="org7e7984d"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org721cefe" class="outline-3">
<h3 id="org721cefe"><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="org6aa21cd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb89ab60" 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-org6d66c86" class="outline-3">
<h3 id="org6d66c86"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org07004a2" class="outline-3">
<h3 id="org07004a2"><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="orgec6d92c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org99ecbb7" 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-orgb97b4a9" class="outline-3">
<h3 id="orgb97b4a9"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-orgf757b30" class="outline-3">
<h3 id="orgf757b30"><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="org095e378" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9e9b8f2" 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-orgaef2f03" class="outline-3">
<h3 id="orgaef2f03"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org09a7b84" class="outline-3">
<h3 id="org09a7b84"><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="org95d6c70" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org553bdf2" 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-org2d99a33" class="outline-3">
<h3 id="org2d99a33"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org2bac8b4" class="outline-3">
<h3 id="org2bac8b4"><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="orgc659f22" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org93a866b" 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-org9cec117" class="outline-2">
<h2 id="org9cec117"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org5c2f3d5" class="outline-2">
<h2 id="org5c2f3d5"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org7a18dee" class="outline-3">
<h3 id="org7a18dee"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-orgc14ee0a" class="outline-3">
<h3 id="orgc14ee0a"><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-org501d562" class="outline-4">
<h4 id="org501d562"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-orgdd8565f" class="outline-4">
<h4 id="orgdd8565f"><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-org87d2155" class="outline-4">
<h4 id="org87d2155"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-org058a19f" class="outline-4">
<h4 id="org058a19f"><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
@ -964,10 +964,10 @@ Laplacian easily as follows:
<p>
\[
\grad_{x_i} \phi = \frac{x_i}{r^2}\left u\prime(r) - \frac{u(r)}{r}\right
\nabla_{x_i} \phi = \frac{x_i}{r^2}\left( u^\prime\left(r\right) - \frac{u\left(r\right)}{r}\right)
\]
\[
\Delta \phi = \frac{1}{r^3}\left x^2 u''(r) + \left3x^2-r^2\right \left \frac{u(r)}{r^2} - \frac{u'(r)}{r}\right \right
\Delta \phi = \frac{1}{r^3}\left(x^2 u^{\prime\prime}(r) + \left( 3x^2-r^2\right) \left( \frac{u(r)}{r^2} - \frac{u'(r)}{r}\right) \right)
\]
</p>
@ -995,7 +995,7 @@ A radius is converted to this scale by (note the zero-indexing)
\]
where
\[
c = \log\left \frac{r_1}{r_0}\right.
c = \log\left(\frac{r_1}{r_0}\right)
\]
For convenience, this conversion and functions to evaluate the splines
are provided with trexio. Since these implementations are not adapted to
@ -1005,8 +1005,8 @@ reimplement them with consideration for its specific needs.
</div>
</div>
<div id="outline-container-orgcf60e8e" class="outline-4">
<h4 id="orgcf60e8e"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-orgcf71100" class="outline-4">
<h4 id="orgcf71100"><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-org86983c2" class="outline-4">
<h4 id="org86983c2"><span class="section-number-4">3.1.4</span> Data definitions</h4>
<div id="outline-container-org7ebd447" class="outline-4">
<h4 id="org7ebd447"><span class="section-number-4">3.1.4</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-4">
<table id="orgbd90b59" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgac016b5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1250,8 +1250,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org5c465c4" class="outline-4">
<h4 id="org5c465c4"><span class="section-number-4">3.1.5</span> Example</h4>
<div id="outline-container-org3c3b7f2" class="outline-4">
<h4 id="org3c3b7f2"><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-orgda1e305" class="outline-3">
<h3 id="orgda1e305"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-orgb0a0b23" class="outline-3">
<h3 id="orgb0a0b23"><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="orgd9a2afa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org51040dc" 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-org71940d3" class="outline-4">
<h4 id="org71940d3"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-org9ed565a" class="outline-4">
<h4 id="org9ed565a"><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-orgcbf84f7" class="outline-3">
<h3 id="orgcbf84f7"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org750011c" class="outline-3">
<h3 id="org750011c"><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="orgc36ef0d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org57a8de1" 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-org08f08eb" class="outline-2">
<h2 id="org08f08eb"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-orgfdedbe2" class="outline-2">
<h2 id="orgfdedbe2"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org221cd4d" class="outline-3">
<h3 id="org221cd4d"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org4d3c3fa" class="outline-3">
<h3 id="org4d3c3fa"><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="org075a0e9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbde2546" 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-orgb38ccd4" class="outline-4">
<div id="outline-container-org5e576cd" 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="orgb3fdb3a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org831c829" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1916,7 +1916,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgd5342e6" class="outline-4">
<div id="outline-container-orgc0e9800" 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="org3e2f7ff" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org64759a6" 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-orgc4a5b4f" class="outline-3">
<h3 id="orgc4a5b4f"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org5a7d4b4" class="outline-3">
<h3 id="org5a7d4b4"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org3a9bba8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2b02c52" 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-orga16bd3f" class="outline-4">
<h4 id="orga16bd3f"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org2269586" class="outline-4">
<h4 id="org2269586"><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="org309f533" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org107c60a" 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-org089e9b0" class="outline-4">
<h4 id="org089e9b0"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org90d0ad3" class="outline-4">
<h4 id="org90d0ad3"><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="org6ea2c3d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb895003" 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-org9c53bf0" class="outline-2">
<h2 id="org9c53bf0"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-orga78f1e0" class="outline-2">
<h2 id="orga78f1e0"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-orgec8f447" class="outline-3">
<h3 id="orgec8f447"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-orgabe7ef6" class="outline-3">
<h3 id="orgabe7ef6"><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="org00349a9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcf29d19" 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-orgc4c3083" class="outline-3">
<h3 id="orgc4c3083"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org859f95a" class="outline-3">
<h3 id="org859f95a"><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="orgf959ca4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0e450a5" 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-org8bfbeb7" class="outline-3">
<h3 id="org8bfbeb7"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orgc75ae3d" class="outline-3">
<h3 id="orgc75ae3d"><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="orgf4b26fd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org11401e3" 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-org597f84c" class="outline-3">
<h3 id="org597f84c"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org07ac3a8" class="outline-3">
<h3 id="org07ac3a8"><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="org25bee64" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org34e56df" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2815,12 +2815,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org59dacd2" class="outline-2">
<h2 id="org59dacd2"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org338541d" class="outline-2">
<h2 id="org338541d"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org2eee619" class="outline-3">
<h3 id="org2eee619"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-orgea46819" class="outline-3">
<h3 id="orgea46819"><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
@ -2845,8 +2845,8 @@ following:
</ul>
</div>
<div id="outline-container-org35455a9" class="outline-4">
<h4 id="org35455a9"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orgedc051e" class="outline-4">
<h4 id="orgedc051e"><span class="section-number-4">6.1.1</span> CHAMP</h4>
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<p>
The first form of Jastrow factor is the one used in
@ -2947,8 +2947,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
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<h4 id="org279f650"><span class="section-number-4">6.1.2</span> Mu</h4>
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<h4 id="org3961af4"><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
@ -3045,10 +3045,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h4 id="orgc27511b"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="orgaa8d94f"><span class="section-number-4">6.1.3</span> Table of values</h4>
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@ -3152,8 +3152,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h2 id="orgd2f738b"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org4d8cb71"><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
@ -3167,7 +3167,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3222,7 +3222,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
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<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-02-21 Wed 12:02</p>
<p class="date">Created: 2024-03-13 Wed 13:15</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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