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README.html
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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>
@ -383,7 +383,7 @@ 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: 2023-04-03 Mon 20:54</p>
<p class="date">Created: 2023-04-12 Wed 13:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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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>Examples</title>
@ -346,46 +346,46 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9d5d734">1. Writing nuclear coordinates</a>
<li><a href="#org47edc39">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#org1df98d6">1.1. C</a></li>
<li><a href="#org230c1d6">1.2. Python</a></li>
<li><a href="#orge6bae2f">1.3. Fortran</a></li>
<li><a href="#orgec57731">1.1. C</a></li>
<li><a href="#org57689a0">1.2. Python</a></li>
<li><a href="#org62dcb50">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#orga9962e1">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org6ebf562">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org63ffa1c">2.1. Fortran</a>
<li><a href="#org39d97a1">2.1. Fortran</a>
<ul>
<li><a href="#org59e02b8">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgf526cd8">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgf1af9a7">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org218fe1b">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgbb3383e">2.1.5. Allocate memory</a></li>
<li><a href="#org7554e9f">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org594c3f0">2.1.7. Read two-electron quantities</a>
<li><a href="#org8ac08f6">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgb065c93">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org8aa260a">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgb2d5078">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orga79590f">2.1.5. Allocate memory</a></li>
<li><a href="#org3003c75">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org1af057c">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org6835b24">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org6793b3f">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org293f0a9">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgc457e1d">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org3d6b43b">2.1.8. Compute the energy</a></li>
<li><a href="#orgad0c1c5">2.1.9. Terminate</a></li>
<li><a href="#org0f26edb">2.1.8. Compute the energy</a></li>
<li><a href="#org9de132d">2.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org78fb748">3. Reading determinants</a>
<li><a href="#org3215352">3. Reading determinants</a>
<ul>
<li><a href="#org7191b6e">3.1. Fortran</a></li>
<li><a href="#orgcade163">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org9d5d734" class="outline-2">
<h2 id="org9d5d734"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org47edc39" class="outline-2">
<h2 id="org47edc39"><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
@ -395,8 +395,8 @@ as well as the necessary TREXIO functions to perform these actions.
</p>
</div>
<div id="outline-container-org1df98d6" class="outline-3">
<h3 id="org1df98d6"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-orgec57731" class="outline-3">
<h3 id="orgec57731"><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>
@ -446,8 +446,8 @@ as well as the necessary TREXIO functions to perform these actions.
</div>
</div>
<div id="outline-container-org230c1d6" class="outline-3">
<h3 id="org230c1d6"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org57689a0" class="outline-3">
<h3 id="org57689a0"><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
@ -494,8 +494,8 @@ coordinates of the system.
</div>
</div>
<div id="outline-container-orge6bae2f" class="outline-3">
<h3 id="orge6bae2f"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-org62dcb50" class="outline-3">
<h3 id="org62dcb50"><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>
@ -552,12 +552,12 @@ coordinates of the system.
</div>
</div>
<div id="outline-container-orga9962e1" class="outline-2">
<h2 id="orga9962e1"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org6ebf562" class="outline-2">
<h2 id="org6ebf562"><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-org63ffa1c" class="outline-3">
<h3 id="org63ffa1c"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org39d97a1" class="outline-3">
<h3 id="org39d97a1"><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>
@ -603,8 +603,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org59e02b8" class="outline-4">
<h4 id="org59e02b8"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org8ac08f6" class="outline-4">
<h4 id="org8ac08f6"><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>
@ -619,8 +619,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgf526cd8" class="outline-4">
<h4 id="orgf526cd8"><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-orgb065c93" class="outline-4">
<h4 id="orgb065c93"><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)
@ -636,8 +636,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgf1af9a7" class="outline-4">
<h4 id="orgf1af9a7"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org8aa260a" class="outline-4">
<h4 id="org8aa260a"><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)
@ -651,8 +651,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org218fe1b" class="outline-4">
<h4 id="org218fe1b"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgb2d5078" class="outline-4">
<h4 id="orgb2d5078"><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)
@ -666,8 +666,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgbb3383e" class="outline-4">
<h4 id="orgbb3383e"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-orga79590f" class="outline-4">
<h4 id="orga79590f"><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) )
@ -679,8 +679,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-org7554e9f" class="outline-4">
<h4 id="org7554e9f"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org3003c75" class="outline-4">
<h4 id="org3003c75"><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)
@ -712,8 +712,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-org594c3f0" class="outline-4">
<h4 id="org594c3f0"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org1af057c" class="outline-4">
<h4 id="org1af057c"><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
@ -729,8 +729,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org6835b24" class="outline-5">
<h5 id="org6835b24"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org293f0a9" class="outline-5">
<h5 id="org293f0a9"><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)
@ -779,8 +779,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-org6793b3f" class="outline-5">
<h5 id="org6793b3f"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgc457e1d" class="outline-5">
<h5 id="orgc457e1d"><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)
@ -824,8 +824,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org3d6b43b" class="outline-4">
<h4 id="org3d6b43b"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org0f26edb" class="outline-4">
<h4 id="org0f26edb"><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
@ -871,8 +871,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-orgad0c1c5" class="outline-4">
<h4 id="orgad0c1c5"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org9de132d" class="outline-4">
<h4 id="org9de132d"><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 )
@ -885,12 +885,12 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org78fb748" class="outline-2">
<h2 id="org78fb748"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org3215352" class="outline-2">
<h2 id="org3215352"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org7191b6e" class="outline-3">
<h3 id="org7191b6e"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-orgcade163" class="outline-3">
<h3 id="orgcade163"><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>
@ -969,7 +969,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-04-03 Mon 20:54</p>
<p class="date">Created: 2023-04-12 Wed 13:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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index.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-04-03 Mon 20:54 -->
<!-- 2023-04-12 Wed 13:02 -->
<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>
@ -383,7 +383,7 @@ 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: 2023-04-03 Mon 20:54</p>
<p class="date">Created: 2023-04-12 Wed 13:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
intro.html
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<head>
<!-- 2023-04-03 Mon 20:54 -->
<!-- 2023-04-12 Wed 13:02 -->
<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: 2023-04-03 Mon 20:54</p>
<p class="date">Created: 2023-04-12 Wed 13:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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58
lib.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-04-03 Mon 20:54 -->
<!-- 2023-04-12 Wed 13:02 -->
<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="#org26b2686">1. Format specification</a>
<li><a href="#orgd69e8db">1. Format specification</a>
<ul>
<li><a href="#orgaae04f9">1.1. Organization of the data</a></li>
<li><a href="#org0e9702a">1.2. Data types</a></li>
<li><a href="#org9a119bf">1.1. Organization of the data</a></li>
<li><a href="#orgf5f2ad0">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#orgca8356c">2. The TREXIO library</a>
<li><a href="#orgd73fca5">2. The TREXIO library</a>
<ul>
<li><a href="#org539a2dd">2.1. The front-end</a></li>
<li><a href="#orgb0f042b">2.2. The back-end</a></li>
<li><a href="#org7105600">2.3. Supported languages</a></li>
<li><a href="#orgfab591a">2.4. Source code generation and documentation</a></li>
<li><a href="#org0c79543">2.5. Availability</a></li>
<li><a href="#org577d3c0">2.1. The front-end</a></li>
<li><a href="#orgf2e674c">2.2. The back-end</a></li>
<li><a href="#org6f264cf">2.3. Supported languages</a></li>
<li><a href="#orgcb82596">2.4. Source code generation and documentation</a></li>
<li><a href="#org81425f0">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org26b2686" class="outline-2">
<h2 id="org26b2686"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-orgd69e8db" class="outline-2">
<h2 id="orgd69e8db"><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-orgaae04f9" class="outline-3">
<h3 id="orgaae04f9"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org9a119bf" class="outline-3">
<h3 id="org9a119bf"><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-org0e9702a" class="outline-3">
<h3 id="org0e9702a"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-orgf5f2ad0" class="outline-3">
<h3 id="orgf5f2ad0"><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-orgca8356c" class="outline-2">
<h2 id="orgca8356c"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orgd73fca5" class="outline-2">
<h2 id="orgd73fca5"><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-org539a2dd" class="outline-3">
<h3 id="org539a2dd"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-org577d3c0" class="outline-3">
<h3 id="org577d3c0"><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-orgb0f042b" class="outline-3">
<h3 id="orgb0f042b"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-orgf2e674c" class="outline-3">
<h3 id="orgf2e674c"><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-org7105600" class="outline-3">
<h3 id="org7105600"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org6f264cf" class="outline-3">
<h3 id="org6f264cf"><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-orgfab591a" class="outline-3">
<h3 id="orgfab591a"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-orgcb82596" class="outline-3">
<h3 id="orgcb82596"><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-org0c79543" class="outline-3">
<h3 id="org0c79543"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org81425f0" class="outline-3">
<h3 id="org81425f0"><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: 2023-04-03 Mon 20:54</p>
<p class="date">Created: 2023-04-12 Wed 13:02</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>
<!-- 2023-04-03 Mon 20:53 -->
<!-- 2023-04-12 Wed 13:02 -->
<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="#orgbfaba02">1. Template for HDF5 definitions</a></li>
<li><a href="#org734f873">2. Template for HDF5 structures</a></li>
<li><a href="#orgbfde9df">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org408afad">4. Template for HDF5 has a group</a></li>
<li><a href="#orgdf7e3d0">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org395f2c0">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org93d7960">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org79609f9">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org70f39ad">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org97ce7be">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org6df6d52">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgcadd66f">12. Source code for the determinant part</a></li>
<li><a href="#org318750c">13. Helper functions</a></li>
<li><a href="#orge63c6aa">1. Template for HDF5 definitions</a></li>
<li><a href="#org592968e">2. Template for HDF5 structures</a></li>
<li><a href="#orgbea6521">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org7757730">4. Template for HDF5 has a group</a></li>
<li><a href="#org88a3d97">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org8be2a01">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org961571b">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org172b4f6">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org2ec0a12">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org98d57ea">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org95b11c8">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org624646f">12. Source code for the determinant part</a></li>
<li><a href="#orgf7c39c9">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgbfaba02" class="outline-2">
<h2 id="orgbfaba02"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orge63c6aa" class="outline-2">
<h2 id="orge63c6aa"><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-org734f873" class="outline-2">
<h2 id="org734f873"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org592968e" class="outline-2">
<h2 id="org592968e"><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-orgbfde9df" class="outline-2">
<h2 id="orgbfde9df"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgbea6521" class="outline-2">
<h2 id="orgbea6521"><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-org408afad" class="outline-2">
<h2 id="org408afad"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org7757730" class="outline-2">
<h2 id="org7757730"><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-orgdf7e3d0" class="outline-2">
<h2 id="orgdf7e3d0"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org88a3d97" class="outline-2">
<h2 id="org88a3d97"><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-org395f2c0" class="outline-2">
<h2 id="org395f2c0"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org8be2a01" class="outline-2">
<h2 id="org8be2a01"><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-org93d7960" class="outline-2">
<h2 id="org93d7960"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org961571b" class="outline-2">
<h2 id="org961571b"><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
@ -973,8 +973,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org79609f9" class="outline-2">
<h2 id="org79609f9"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org172b4f6" class="outline-2">
<h2 id="org172b4f6"><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.
@ -1108,8 +1108,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org70f39ad" class="outline-2">
<h2 id="org70f39ad"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org2ec0a12" class="outline-2">
<h2 id="org2ec0a12"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org97ce7be" class="outline-2">
<h2 id="org97ce7be"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org98d57ea" class="outline-2">
<h2 id="org98d57ea"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1434,8 +1434,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
</div>
<div id="outline-container-org6df6d52" class="outline-2">
<h2 id="org6df6d52"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org95b11c8" class="outline-2">
<h2 id="org95b11c8"><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
@ -1475,8 +1475,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-orgcadd66f" class="outline-2">
<h2 id="orgcadd66f"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org624646f" class="outline-2">
<h2 id="org624646f"><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.
@ -1578,8 +1578,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org318750c" class="outline-2">
<h2 id="org318750c"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgf7c39c9" class="outline-2">
<h2 id="orgf7c39c9"><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>
@ -1842,7 +1842,7 @@ 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: 2023-04-03 Mon 20:53</p>
<p class="date">Created: 2023-04-12 Wed 13:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

138
templator_text.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-04-03 Mon 20:54 -->
<!-- 2023-04-12 Wed 13:02 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
@ -324,23 +324,23 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgb6ee06a">1. Template for group-related structures in text back end</a></li>
<li><a href="#org1f01927">2. Template for general structure in text back end</a></li>
<li><a href="#orga3431cc">3. Initialize function (constant part)</a></li>
<li><a href="#orgfbbb17d">4. Deinitialize function (templated part)</a></li>
<li><a href="#org84c59a9">5. Flush function (templated part)</a></li>
<li><a href="#org078ef71">6. Template for text read a group</a></li>
<li><a href="#orgc8b151c">7. Template for text has a group</a></li>
<li><a href="#org61154fe">8. Template for text flush a group</a></li>
<li><a href="#orge607f21">9. Template for text free memory</a></li>
<li><a href="#org6181eff">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org7a325d1">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orga5d00cc">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org8118b90">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org8cc0a59">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgbfb86f1">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org841eeb0">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgf271006">17. Source code for the determinant part</a></li>
<li><a href="#org040a756">1. Template for group-related structures in text back end</a></li>
<li><a href="#org9a7ae81">2. Template for general structure in text back end</a></li>
<li><a href="#org2c0459b">3. Initialize function (constant part)</a></li>
<li><a href="#org1314919">4. Deinitialize function (templated part)</a></li>
<li><a href="#org36a067b">5. Flush function (templated part)</a></li>
<li><a href="#org44b5509">6. Template for text read a group</a></li>
<li><a href="#orgefd419d">7. Template for text has a group</a></li>
<li><a href="#orga270dd9">8. Template for text flush a group</a></li>
<li><a href="#orgf42a71f">9. Template for text free memory</a></li>
<li><a href="#orgcf9040f">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgb2fb342">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org2a5c459">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org1ae4941">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org4c48140">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgea7bafd">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgefc3ff5">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org1fcee54">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-orgb6ee06a" class="outline-2">
<h2 id="orgb6ee06a"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org040a756" class="outline-2">
<h2 id="org040a756"><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-org1f01927" class="outline-2">
<h2 id="org1f01927"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org9a7ae81" class="outline-2">
<h2 id="org9a7ae81"><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-orga3431cc" class="outline-2">
<h2 id="orga3431cc"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org2c0459b" class="outline-2">
<h2 id="org2c0459b"><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>
@ -436,10 +436,10 @@ corresponding types for all back ends can be safely casted to
<span style="color: #a020f0;">if</span> (file_exists) {
<span style="color: #228b22;">bool</span> <span style="color: #a0522d;">is_a_directory</span> = <span style="color: #008b8b;">false</span>;
<span style="color: #483d8b;">#ifdef</span> S_IFDIR
<span style="color: #483d8b;">#if</span> <span style="color: #483d8b;">defined</span>(S_IFDIR)
is_a_directory = st.st_mode &amp; S_IFDIR;
<span style="color: #483d8b;">#elif</span> S_ISDIR
is_a_directory = S_ISDIR(s.st_mode);
<span style="color: #483d8b;">#elif</span> <span style="color: #483d8b;">defined</span>(S_ISDIR)
is_a_directory = S_ISDIR(st.st_mode);
<span style="color: #483d8b;">#else</span>
printf(<span style="color: #8b2252;">"Some important macros are missing for directory handling.\n"</span>);
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
@ -454,6 +454,32 @@ corresponding types for all back ends can be safely casted to
</pre>
</div>
<p>
On non-POSIX file systems, the function <code>mkdtemp</code> might is not defined.
In that case, we define an alternate one, which is not as safe as the original one.
</p>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #483d8b;">#if</span> <span style="color: #483d8b;">defined</span> _POSIX_C_SOURCE &amp;&amp; (_POSIX_C_SOURCE - 0) &gt;= 200809L
<span style="color: #483d8b;">#else</span>
<span style="color: #228b22;">char</span>* <span style="color: #0000ff;">mkdtemp</span>(<span style="color: #228b22;">char</span>* <span style="color: #a0522d;">template</span>) {
<span style="color: #228b22;">char</span>* <span style="color: #a0522d;">dir</span> = <span style="color: #008b8b;">NULL</span>;
dir = tmpnam(dir);
<span style="color: #a020f0;">if</span> (dir == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
<span style="color: #a020f0;">if</span> (mkdir(dir, S_IRWXU | S_IRWXG | S_IRWXO) != 0) {
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
}
strcpy(template, dir);
<span style="color: #a020f0;">return</span> template;
}
<span style="color: #483d8b;">#endif</span>
</pre>
</div>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_text_init</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>)
@ -571,8 +597,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgfbbb17d" class="outline-2">
<h2 id="orgfbbb17d"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org1314919" class="outline-2">
<h2 id="org1314919"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -594,8 +620,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org84c59a9" class="outline-2">
<h2 id="org84c59a9"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org36a067b" class="outline-2">
<h2 id="org36a067b"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -618,8 +644,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org078ef71" class="outline-2">
<h2 id="org078ef71"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org44b5509" class="outline-2">
<h2 id="org44b5509"><span class="section-number-2">6</span> Template for text read a group</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -845,8 +871,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgc8b151c" class="outline-2">
<h2 id="orgc8b151c"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-orgefd419d" class="outline-2">
<h2 id="orgefd419d"><span class="section-number-2">7</span> Template for text has a group</h2>
<div class="outline-text-2" id="text-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -886,8 +912,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org61154fe" class="outline-2">
<h2 id="org61154fe"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-orga270dd9" class="outline-2">
<h2 id="orga270dd9"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div class="outline-text-2" id="text-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -951,8 +977,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orge607f21" class="outline-2">
<h2 id="orge607f21"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-orgf42a71f" class="outline-2">
<h2 id="orgf42a71f"><span class="section-number-2">9</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-9">
<p>
Memory is allocated when reading. The following function frees memory.
@ -1021,8 +1047,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org6181eff" class="outline-2">
<h2 id="org6181eff"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orgcf9040f" class="outline-2">
<h2 id="orgcf9040f"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1085,8 +1111,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org7a325d1" class="outline-2">
<h2 id="org7a325d1"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgb2fb342" class="outline-2">
<h2 id="orgb2fb342"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-11">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1182,8 +1208,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orga5d00cc" class="outline-2">
<h2 id="orga5d00cc"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org2a5c459" class="outline-2">
<h2 id="org2a5c459"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-12">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1284,8 +1310,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org8118b90" class="outline-2">
<h2 id="org8118b90"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org1ae4941" class="outline-2">
<h2 id="org1ae4941"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1359,8 +1385,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org8cc0a59" class="outline-2">
<h2 id="org8cc0a59"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org4c48140" class="outline-2">
<h2 id="org4c48140"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-14">
<p>
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
@ -1650,8 +1676,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-orgbfb86f1" class="outline-2">
<h2 id="orgbfb86f1"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-orgea7bafd" class="outline-2">
<h2 id="orgea7bafd"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div class="outline-text-2" id="text-15">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that buffered I/O has to be decoupled
@ -1881,8 +1907,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-org841eeb0" class="outline-2">
<h2 id="org841eeb0"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgefc3ff5" class="outline-2">
<h2 id="orgefc3ff5"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-16">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1910,8 +1936,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-orgf271006" class="outline-2">
<h2 id="orgf271006"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org1fcee54" class="outline-2">
<h2 id="org1fcee54"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-17">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -2103,7 +2129,7 @@ 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: 2023-04-03 Mon 20:54</p>
<p class="date">Created: 2023-04-12 Wed 13:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

242
trex.html
View File

@ -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>
<!-- 2023-04-03 Mon 20:54 -->
<!-- 2023-04-12 Wed 13:02 -->
<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>
@ -346,70 +346,70 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org80f93fd">1. Metadata (metadata group)</a></li>
<li><a href="#org5bc0a4d">2. System</a>
<li><a href="#org931a1a7">1. Metadata (metadata group)</a></li>
<li><a href="#org9490e25">2. System</a>
<ul>
<li><a href="#org62aa6af">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#orgba8e50b">2.2. Cell (cell group)</a></li>
<li><a href="#orge55730f">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org88cf9f0">2.4. Electron (electron group)</a></li>
<li><a href="#orgfd4cfce">2.5. Ground or excited states (state group)</a></li>
<li><a href="#orgd263158">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org1e9a2e0">2.2. Cell (cell group)</a></li>
<li><a href="#org108077b">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org61d5805">2.4. Electron (electron group)</a></li>
<li><a href="#org41af6a0">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org6a1719b">3. Basis functions</a>
<li><a href="#org4da7900">3. Basis functions</a>
<ul>
<li><a href="#org5347405">3.1. Basis set (basis group)</a>
<li><a href="#org577bce4">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org7b5f19b">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org2432a24">3.1.2. Plane waves</a></li>
<li><a href="#org573ee0e">3.1.3. Data definitions</a></li>
<li><a href="#org45dc71c">3.1.4. Example</a></li>
<li><a href="#orgf8c0772">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orga0284c4">3.1.2. Plane waves</a></li>
<li><a href="#org93388ad">3.1.3. Data definitions</a></li>
<li><a href="#org695c598">3.1.4. Example</a></li>
</ul>
</li>
<li><a href="#org1dfd4ec">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org6d54c17">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org049c22e">3.2.1. Example</a></li>
<li><a href="#orgb7fe0ba">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#orge0ca080">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org7a12d22">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org0b1b41d">4. Orbitals</a>
<li><a href="#orga82e74f">4. Orbitals</a>
<ul>
<li><a href="#org6ec1462">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org8c6861e">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="#org946e8ec">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org677aec3">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgc34777a">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org7306d2a">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org02fbc92">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orge145863">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgd6efd11">5. Multi-determinant information</a>
<li><a href="#org85898df">5. Multi-determinant information</a>
<ul>
<li><a href="#org014b055">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orga2b8b8d">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org2a0d639">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org4622701">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org6e75fa6">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org692d1b1">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgb2265b1">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org73c553f">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org20e7752">6. Correlation factors</a>
<li><a href="#org6c7ecbc">6. Correlation factors</a>
<ul>
<li><a href="#org3ae8246">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org35807bd">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#orge4748b3">6.1.1. CHAMP</a></li>
<li><a href="#orgadccaf8">6.1.2. Mu</a></li>
<li><a href="#org866d644">6.1.3. Table of values</a></li>
<li><a href="#orge87d13d">6.1.1. CHAMP</a></li>
<li><a href="#org7b89c22">6.1.2. Mu</a></li>
<li><a href="#org4c18469">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org8315dcf">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org08ba4f2">7. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -422,8 +422,8 @@ is reversed in the produced <code>trex.json</code> configuration file as the
library is written in C.
</p>
<div id="outline-container-org80f93fd" class="outline-2">
<h2 id="org80f93fd"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org931a1a7" class="outline-2">
<h2 id="org931a1a7"><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,
@ -433,7 +433,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
</p>
<table id="org51788ee" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org18c0144" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -516,19 +516,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
</div>
</div>
<div id="outline-container-org5bc0a4d" class="outline-2">
<h2 id="org5bc0a4d"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org9490e25" class="outline-2">
<h2 id="org9490e25"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org62aa6af" class="outline-3">
<h3 id="org62aa6af"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orgd263158" class="outline-3">
<h3 id="orgd263158"><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="org83d6ee1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf7c38d9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -595,15 +595,15 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-orgba8e50b" class="outline-3">
<h3 id="orgba8e50b"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org1e9a2e0" class="outline-3">
<h3 id="org1e9a2e0"><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="org6b329b1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd5f0b93" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -677,15 +677,15 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-orge55730f" class="outline-3">
<h3 id="orge55730f"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org108077b" class="outline-3">
<h3 id="org108077b"><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="org7aaadb7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8883d91" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -724,8 +724,8 @@ defined in this group.
</div>
</div>
<div id="outline-container-org88cf9f0" class="outline-3">
<h3 id="org88cf9f0"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org61d5805" class="outline-3">
<h3 id="org61d5805"><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
@ -744,7 +744,7 @@ the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="orgb2ea49e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcdceab4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -790,8 +790,8 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgfd4cfce" class="outline-3">
<h3 id="orgfd4cfce"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org41af6a0" class="outline-3">
<h3 id="org41af6a0"><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
@ -808,7 +808,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="org9a0f0b9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5f02641" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -869,16 +869,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-org6a1719b" class="outline-2">
<h2 id="org6a1719b"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org4da7900" class="outline-2">
<h2 id="org4da7900"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org5347405" class="outline-3">
<h3 id="org5347405"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org577bce4" class="outline-3">
<h3 id="org577bce4"><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-org7b5f19b" class="outline-4">
<h4 id="org7b5f19b"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-orgf8c0772" class="outline-4">
<h4 id="orgf8c0772"><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
@ -932,8 +932,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-org2432a24" class="outline-4">
<h4 id="org2432a24"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div id="outline-container-orga0284c4" class="outline-4">
<h4 id="orga0284c4"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div class="outline-text-4" id="text-3-1-2">
<p>
A plane wave is defined as
@ -954,10 +954,10 @@ plane waves.
</div>
</div>
<div id="outline-container-org573ee0e" class="outline-4">
<h4 id="org573ee0e"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div id="outline-container-org93388ad" class="outline-4">
<h4 id="org93388ad"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-3">
<table id="org151c985" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbd1c2d4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1066,8 +1066,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org45dc71c" class="outline-4">
<h4 id="org45dc71c"><span class="section-number-4">3.1.4</span> Example</h4>
<div id="outline-container-org695c598" class="outline-4">
<h4 id="org695c598"><span class="section-number-4">3.1.4</span> Example</h4>
<div class="outline-text-4" id="text-3-1-4">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1145,8 +1145,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org1dfd4ec" class="outline-3">
<h3 id="org1dfd4ec"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org6d54c17" class="outline-3">
<h3 id="org6d54c17"><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
@ -1180,7 +1180,7 @@ 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="orga00b54c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1292c58" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1284,8 +1284,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-org049c22e" class="outline-4">
<h4 id="org049c22e"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orgb7fe0ba" class="outline-4">
<h4 id="orgb7fe0ba"><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
@ -1348,8 +1348,8 @@ power = [
</div>
</div>
<div id="outline-container-orge0ca080" class="outline-3">
<h3 id="orge0ca080"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org7a12d22" class="outline-3">
<h3 id="org7a12d22"><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
@ -1364,7 +1364,7 @@ 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="orgb74a6fb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc260c9d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1481,12 +1481,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-org0b1b41d" class="outline-2">
<h2 id="org0b1b41d"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-orga82e74f" class="outline-2">
<h2 id="orga82e74f"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org6ec1462" class="outline-3">
<h3 id="org6ec1462"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org8c6861e" class="outline-3">
<h3 id="org8c6861e"><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
@ -1567,7 +1567,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="org4c8cbe7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2d815d8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1619,7 +1619,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org1850405" class="outline-4">
<div id="outline-container-org7bc03b7" 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">
@ -1637,7 +1637,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgf2474fe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1dbd2df" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1732,7 +1732,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org123f8dd" class="outline-4">
<div id="outline-container-org6b35232" 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>
@ -1758,7 +1758,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="orgd7b6aea" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6115593" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1826,10 +1826,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org946e8ec" class="outline-3">
<h3 id="org946e8ec"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org677aec3" class="outline-3">
<h3 id="org677aec3"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="orgfda7572" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3b04a26" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1916,8 +1916,8 @@ The Cholesky decomposition of the integrals can also be stored:
</table>
</div>
<div id="outline-container-orgc34777a" class="outline-4">
<h4 id="orgc34777a"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org02fbc92" class="outline-4">
<h4 id="org02fbc92"><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
@ -1925,7 +1925,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgb5fac64" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0446e3b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2020,8 +2020,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org7306d2a" class="outline-4">
<h4 id="org7306d2a"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-orge145863" class="outline-4">
<h4 id="orge145863"><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
@ -2029,7 +2029,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orge395df7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfcf1018" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2098,12 +2098,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgd6efd11" class="outline-2">
<h2 id="orgd6efd11"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org85898df" class="outline-2">
<h2 id="org85898df"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org014b055" class="outline-3">
<h3 id="org014b055"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org6e75fa6" class="outline-3">
<h3 id="org6e75fa6"><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 \(\Psi\)
@ -2145,7 +2145,7 @@ 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="orgddb6b62" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2adc71f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2191,8 +2191,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-orga2b8b8d" class="outline-3">
<h3 id="orga2b8b8d"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org692d1b1" class="outline-3">
<h3 id="org692d1b1"><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
@ -2214,7 +2214,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org4241d95" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org15d99b9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2260,8 +2260,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org2a0d639" class="outline-3">
<h3 id="org2a0d639"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orgb2265b1" class="outline-3">
<h3 id="orgb2265b1"><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
@ -2332,7 +2332,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org4d1b853" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9437cbe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2413,8 +2413,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-org4622701" class="outline-3">
<h3 id="org4622701"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org73c553f" class="outline-3">
<h3 id="org73c553f"><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
@ -2486,7 +2486,7 @@ 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="org880b11c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6f6dc8d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2617,12 +2617,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org20e7752" class="outline-2">
<h2 id="org20e7752"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org6c7ecbc" class="outline-2">
<h2 id="org6c7ecbc"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org3ae8246" class="outline-3">
<h3 id="org3ae8246"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org35807bd" class="outline-3">
<h3 id="org35807bd"><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
@ -2647,8 +2647,8 @@ following:
</ul>
</div>
<div id="outline-container-orge4748b3" class="outline-4">
<h4 id="orge4748b3"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orge87d13d" class="outline-4">
<h4 id="orge87d13d"><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
@ -2749,8 +2749,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-orgadccaf8" class="outline-4">
<h4 id="orgadccaf8"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org7b89c22" class="outline-4">
<h4 id="org7b89c22"><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
@ -2847,10 +2847,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org866d644" class="outline-4">
<h4 id="org866d644"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div id="outline-container-org4c18469" class="outline-4">
<h4 id="org4c18469"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div class="outline-text-4" id="text-6-1-3">
<table id="org5e5d7eb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc15b832" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2954,8 +2954,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org8315dcf" class="outline-2">
<h2 id="org8315dcf"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org08ba4f2" class="outline-2">
<h2 id="org08ba4f2"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-7">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -2969,7 +2969,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="org34fcd3b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4d06ce6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3024,7 +3024,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-04-03 Mon 20:54</p>
<p class="date">Created: 2023-04-12 Wed 13:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>