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README.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-11-10 Sun 20:58 -->
<!-- 2024-11-20 Wed 14:29 -->
<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>
@ -339,6 +339,11 @@ the HDF5 library enabling fast read and write speeds. It is compatible with a
variety of platforms and has interfaces for Fortran, Python, and OCaml.
</p>
<p>
TREXIO can be downloaded here:
<a href="https://github.com/TREX-CoE/trexio/releases/latest">https://github.com/TREX-CoE/trexio/releases/latest</a>
</p>
<p>
If you use TREXIO, please cite this article published in the <a href="https://doi.org/10.1063/5.0148161">Journal of Chemical Physics</a>:
</p>
@ -406,7 +411,7 @@ 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: 2024-11-10 Sun 20:58</p>
<p class="date">Created: 2024-11-20 Wed 14:29</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

172
examples.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-11-10 Sun 20:58 -->
<!-- 2024-11-20 Wed 14:29 -->
<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="#orgbc7d4ef">1. Writing nuclear coordinates</a>
<li><a href="#org703cbe0">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orge193919">1.1. C</a></li>
<li><a href="#org984c61b">1.2. Python</a></li>
<li><a href="#org972a7a8">1.3. Fortran</a></li>
<li><a href="#org2697649">1.1. C</a></li>
<li><a href="#orgdf49152">1.2. Python</a></li>
<li><a href="#org55f1364">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org001bc48">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org018a800">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org7ef80cb">2.1. Fortran</a>
<li><a href="#org01cd0f1">2.1. Fortran</a>
<ul>
<li><a href="#org0428985">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org1d0d268">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org4b7d9d0">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orge93ca26">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgccf3405">2.1.5. Allocate memory</a></li>
<li><a href="#org523038b">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org2dc8a36">2.1.7. Read two-electron quantities</a>
<li><a href="#org28aaae1">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org9957b1c">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org7b78e2e">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org040c9c2">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgcca8755">2.1.5. Allocate memory</a></li>
<li><a href="#org73f4987">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org1f411df">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org41cd5ab">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org525aee1">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#orgb6bfe82">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org773fd81">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgbb2361c">2.1.8. Compute the energy</a></li>
<li><a href="#org681e674">2.1.9. Terminate</a></li>
<li><a href="#orgcbda434">2.1.8. Compute the energy</a></li>
<li><a href="#orgdfdf197">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org1f93a0c">2.2. Python</a>
<li><a href="#org7c6fa35">2.2. Python</a>
<ul>
<li><a href="#orgef696a9">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orge600dd4">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org4e0d9e8">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org4e54261">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org5149fa8">2.2.5. Read two-electron quantities</a>
<li><a href="#orgd2b043b">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgdb10521">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org32e90d8">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org7ebfbcf">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orga45424b">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#org13bb473">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org158ac39">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org40fffa0">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org1e6d0d6">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orga683d33">2.2.6. Compute the energy</a></li>
<li><a href="#orgc7e0b6b">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org16267de">3. Reading determinants</a>
<li><a href="#org57ffac6">3. Reading determinants</a>
<ul>
<li><a href="#org16a2e89">3.1. Fortran</a></li>
<li><a href="#org0144468">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgbc7d4ef" class="outline-2">
<h2 id="orgbc7d4ef"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org703cbe0" class="outline-2">
<h2 id="org703cbe0"><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-orge193919" class="outline-3">
<h3 id="orge193919"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org2697649" class="outline-3">
<h3 id="org2697649"><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-org984c61b" class="outline-3">
<h3 id="org984c61b"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-orgdf49152" class="outline-3">
<h3 id="orgdf49152"><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-org972a7a8" class="outline-3">
<h3 id="org972a7a8"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-org55f1364" class="outline-3">
<h3 id="org55f1364"><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-org001bc48" class="outline-2">
<h2 id="org001bc48"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org018a800" class="outline-2">
<h2 id="org018a800"><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-org7ef80cb" class="outline-3">
<h3 id="org7ef80cb"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org01cd0f1" class="outline-3">
<h3 id="org01cd0f1"><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-org0428985" class="outline-4">
<h4 id="org0428985"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org28aaae1" class="outline-4">
<h4 id="org28aaae1"><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-org1d0d268" class="outline-4">
<h4 id="org1d0d268"><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-org9957b1c" class="outline-4">
<h4 id="org9957b1c"><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-org4b7d9d0" class="outline-4">
<h4 id="org4b7d9d0"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org7b78e2e" class="outline-4">
<h4 id="org7b78e2e"><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-orge93ca26" class="outline-4">
<h4 id="orge93ca26"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org040c9c2" class="outline-4">
<h4 id="org040c9c2"><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-orgccf3405" class="outline-4">
<h4 id="orgccf3405"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-orgcca8755" class="outline-4">
<h4 id="orgcca8755"><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-org523038b" class="outline-4">
<h4 id="org523038b"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org73f4987" class="outline-4">
<h4 id="org73f4987"><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-org2dc8a36" class="outline-4">
<h4 id="org2dc8a36"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org1f411df" class="outline-4">
<h4 id="org1f411df"><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-org41cd5ab" class="outline-5">
<h5 id="org41cd5ab"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgb6bfe82" class="outline-5">
<h5 id="orgb6bfe82"><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-org525aee1" class="outline-5">
<h5 id="org525aee1"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org773fd81" class="outline-5">
<h5 id="org773fd81"><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-orgbb2361c" class="outline-4">
<h4 id="orgbb2361c"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-orgcbda434" class="outline-4">
<h4 id="orgcbda434"><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-org681e674" class="outline-4">
<h4 id="org681e674"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-orgdfdf197" class="outline-4">
<h4 id="orgdfdf197"><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-org1f93a0c" class="outline-3">
<h3 id="org1f93a0c"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org7c6fa35" class="outline-3">
<h3 id="org7c6fa35"><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-orgef696a9" class="outline-4">
<h4 id="orgef696a9"><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-orgd2b043b" class="outline-4">
<h4 id="orgd2b043b"><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-orge600dd4" class="outline-4">
<h4 id="orge600dd4"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgdb10521" class="outline-4">
<h4 id="orgdb10521"><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-org4e0d9e8" class="outline-4">
<h4 id="org4e0d9e8"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org32e90d8" class="outline-4">
<h4 id="org32e90d8"><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-org4e54261" class="outline-4">
<h4 id="org4e54261"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org7ebfbcf" class="outline-4">
<h4 id="org7ebfbcf"><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-org5149fa8" class="outline-4">
<h4 id="org5149fa8"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-orga45424b" class="outline-4">
<h4 id="orga45424b"><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-org13bb473" class="outline-5">
<h5 id="org13bb473"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org40fffa0" class="outline-5">
<h5 id="org40fffa0"><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-org158ac39" class="outline-5">
<h5 id="org158ac39"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-org1e6d0d6" class="outline-5">
<h5 id="org1e6d0d6"><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-orga683d33" class="outline-4">
<h4 id="orga683d33"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-orgc7e0b6b" class="outline-4">
<h4 id="orgc7e0b6b"><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-org16267de" class="outline-2">
<h2 id="org16267de"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org57ffac6" class="outline-2">
<h2 id="org57ffac6"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org16a2e89" class="outline-3">
<h3 id="org16a2e89"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org0144468" class="outline-3">
<h3 id="org0144468"><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: 2024-11-10 Sun 20:58</p>
<p class="date">Created: 2024-11-20 Wed 14:29</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

9
index.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-11-10 Sun 20:58 -->
<!-- 2024-11-20 Wed 14:29 -->
<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>
@ -339,6 +339,11 @@ the HDF5 library enabling fast read and write speeds. It is compatible with a
variety of platforms and has interfaces for Fortran, Python, and OCaml.
</p>
<p>
TREXIO can be downloaded here:
<a href="https://github.com/TREX-CoE/trexio/releases/latest">https://github.com/TREX-CoE/trexio/releases/latest</a>
</p>
<p>
If you use TREXIO, please cite this article published in the <a href="https://doi.org/10.1063/5.0148161">Journal of Chemical Physics</a>:
</p>
@ -406,7 +411,7 @@ 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: 2024-11-10 Sun 20:58</p>
<p class="date">Created: 2024-11-20 Wed 14:29</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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@ -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>
<!-- 2024-11-10 Sun 20:58 -->
<!-- 2024-11-20 Wed 14:29 -->
<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: 2024-11-10 Sun 20:58</p>
<p class="date">Created: 2024-11-20 Wed 14:29</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
lib.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-11-10 Sun 20:58 -->
<!-- 2024-11-20 Wed 14:29 -->
<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="#orgabd2c17">1. Format specification</a>
<li><a href="#org2526fb6">1. Format specification</a>
<ul>
<li><a href="#orgdb36ab3">1.1. Organization of the data</a></li>
<li><a href="#org9544493">1.2. Data types</a></li>
<li><a href="#org011f86a">1.1. Organization of the data</a></li>
<li><a href="#orgd68db31">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org00533d4">2. The TREXIO library</a>
<li><a href="#org2920936">2. The TREXIO library</a>
<ul>
<li><a href="#org0a35037">2.1. The front-end</a></li>
<li><a href="#orgcf3e066">2.2. The back-end</a></li>
<li><a href="#orgf5a26c6">2.3. Supported languages</a></li>
<li><a href="#orgbdb142c">2.4. Source code generation and documentation</a></li>
<li><a href="#org55e1894">2.5. Availability</a></li>
<li><a href="#orgbd6217a">2.1. The front-end</a></li>
<li><a href="#orgb19e73f">2.2. The back-end</a></li>
<li><a href="#orgae51329">2.3. Supported languages</a></li>
<li><a href="#org51afeed">2.4. Source code generation and documentation</a></li>
<li><a href="#org4a6c2f5">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgabd2c17" class="outline-2">
<h2 id="orgabd2c17"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org2526fb6" class="outline-2">
<h2 id="org2526fb6"><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-orgdb36ab3" class="outline-3">
<h3 id="orgdb36ab3"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org011f86a" class="outline-3">
<h3 id="org011f86a"><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-org9544493" class="outline-3">
<h3 id="org9544493"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-orgd68db31" class="outline-3">
<h3 id="orgd68db31"><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-org00533d4" class="outline-2">
<h2 id="org00533d4"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-org2920936" class="outline-2">
<h2 id="org2920936"><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-org0a35037" class="outline-3">
<h3 id="org0a35037"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orgbd6217a" class="outline-3">
<h3 id="orgbd6217a"><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-orgcf3e066" class="outline-3">
<h3 id="orgcf3e066"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-orgb19e73f" class="outline-3">
<h3 id="orgb19e73f"><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-orgf5a26c6" class="outline-3">
<h3 id="orgf5a26c6"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-orgae51329" class="outline-3">
<h3 id="orgae51329"><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-orgbdb142c" class="outline-3">
<h3 id="orgbdb142c"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org51afeed" class="outline-3">
<h3 id="org51afeed"><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-org55e1894" class="outline-3">
<h3 id="org55e1894"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org4a6c2f5" class="outline-3">
<h3 id="org4a6c2f5"><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: 2024-11-10 Sun 20:58</p>
<p class="date">Created: 2024-11-20 Wed 14:29</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>
<!-- 2024-11-10 Sun 20:58 -->
<!-- 2024-11-20 Wed 14:29 -->
<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="#orged00aff">1. Template for HDF5 definitions</a></li>
<li><a href="#org7a5272b">2. Template for HDF5 structures</a></li>
<li><a href="#orgef6ca8d">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orge679770">4. Template for HDF5 has a group</a></li>
<li><a href="#orgd9dcafb">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgd240efc">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org98cb1fb">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org2ef3abe">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org669f486">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgbca810b">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org28d4271">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org4fce3ea">12. Source code for the determinant part</a></li>
<li><a href="#orgea781f9">13. Helper functions</a></li>
<li><a href="#orga61cecb">1. Template for HDF5 definitions</a></li>
<li><a href="#org823852b">2. Template for HDF5 structures</a></li>
<li><a href="#org913e832">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org170345a">4. Template for HDF5 has a group</a></li>
<li><a href="#org4ba4f3f">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgd2da42f">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgc06b605">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgd3a80e4">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org8a2719c">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orga5cc59e">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orge417b11">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgfb701b1">12. Source code for the determinant part</a></li>
<li><a href="#org4b71194">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orged00aff" class="outline-2">
<h2 id="orged00aff"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orga61cecb" class="outline-2">
<h2 id="orga61cecb"><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-org7a5272b" class="outline-2">
<h2 id="org7a5272b"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org823852b" class="outline-2">
<h2 id="org823852b"><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-orgef6ca8d" class="outline-2">
<h2 id="orgef6ca8d"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org913e832" class="outline-2">
<h2 id="org913e832"><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-orge679770" class="outline-2">
<h2 id="orge679770"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org170345a" class="outline-2">
<h2 id="org170345a"><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-orgd9dcafb" class="outline-2">
<h2 id="orgd9dcafb"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org4ba4f3f" class="outline-2">
<h2 id="org4ba4f3f"><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-orgd240efc" class="outline-2">
<h2 id="orgd240efc"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgd2da42f" class="outline-2">
<h2 id="orgd2da42f"><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-org98cb1fb" class="outline-2">
<h2 id="org98cb1fb"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orgc06b605" class="outline-2">
<h2 id="orgc06b605"><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-org2ef3abe" class="outline-2">
<h2 id="org2ef3abe"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-orgd3a80e4" class="outline-2">
<h2 id="orgd3a80e4"><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-org669f486" class="outline-2">
<h2 id="org669f486"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org8a2719c" class="outline-2">
<h2 id="org8a2719c"><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-orgbca810b" class="outline-2">
<h2 id="orgbca810b"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orga5cc59e" class="outline-2">
<h2 id="orga5cc59e"><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-org28d4271" class="outline-2">
<h2 id="org28d4271"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orge417b11" class="outline-2">
<h2 id="orge417b11"><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-org4fce3ea" class="outline-2">
<h2 id="org4fce3ea"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-orgfb701b1" class="outline-2">
<h2 id="orgfb701b1"><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-orgea781f9" class="outline-2">
<h2 id="orgea781f9"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org4b71194" class="outline-2">
<h2 id="org4b71194"><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: 2024-11-10 Sun 20:58</p>
<p class="date">Created: 2024-11-20 Wed 14:29</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2024-11-10 Sun 20:58 -->
<!-- 2024-11-20 Wed 14:29 -->
<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="#orgf30df9d">1. Template for group-related structures in text back end</a></li>
<li><a href="#org9d0c0ea">2. Template for general structure in text back end</a></li>
<li><a href="#orgd2958a1">3. Initialize function (constant part)</a></li>
<li><a href="#orgbdd7c64">4. Deinitialize function (templated part)</a></li>
<li><a href="#orge4f54c4">5. Flush function (templated part)</a></li>
<li><a href="#org86cfabd">6. Template for text read a group</a></li>
<li><a href="#org88c308d">7. Template for text has a group</a></li>
<li><a href="#org8f3bde8">8. Template for text flush a group</a></li>
<li><a href="#org6f97e72">9. Template for text free memory</a></li>
<li><a href="#orgcdbce05">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org52c2a8c">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgf4e389e">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org887dc5c">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org178d59f">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgd3a9bc0">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgef6f2ba">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org0375352">17. Source code for the determinant part</a></li>
<li><a href="#org25be0d6">1. Template for group-related structures in text back end</a></li>
<li><a href="#org0b28003">2. Template for general structure in text back end</a></li>
<li><a href="#org1ab52a5">3. Initialize function (constant part)</a></li>
<li><a href="#org18c6599">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgdcd5de7">5. Flush function (templated part)</a></li>
<li><a href="#org1f92bcc">6. Template for text read a group</a></li>
<li><a href="#org92a0df2">7. Template for text has a group</a></li>
<li><a href="#org7ddae7a">8. Template for text flush a group</a></li>
<li><a href="#org4ddd40f">9. Template for text free memory</a></li>
<li><a href="#org0349813">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org96a15a3">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orge24957b">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org6cd9c37">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgfe5e297">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org7028212">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org23b8298">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org9e91c12">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-orgf30df9d" class="outline-2">
<h2 id="orgf30df9d"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org25be0d6" class="outline-2">
<h2 id="org25be0d6"><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-org9d0c0ea" class="outline-2">
<h2 id="org9d0c0ea"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org0b28003" class="outline-2">
<h2 id="org0b28003"><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-orgd2958a1" class="outline-2">
<h2 id="orgd2958a1"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org1ab52a5" class="outline-2">
<h2 id="org1ab52a5"><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-orgbdd7c64" class="outline-2">
<h2 id="orgbdd7c64"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org18c6599" class="outline-2">
<h2 id="org18c6599"><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-orge4f54c4" class="outline-2">
<h2 id="orge4f54c4"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-orgdcd5de7" class="outline-2">
<h2 id="orgdcd5de7"><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-org86cfabd" class="outline-2">
<h2 id="org86cfabd"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org1f92bcc" class="outline-2">
<h2 id="org1f92bcc"><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-org88c308d" class="outline-2">
<h2 id="org88c308d"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org92a0df2" class="outline-2">
<h2 id="org92a0df2"><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-org8f3bde8" class="outline-2">
<h2 id="org8f3bde8"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org7ddae7a" class="outline-2">
<h2 id="org7ddae7a"><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-org6f97e72" class="outline-2">
<h2 id="org6f97e72"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org4ddd40f" class="outline-2">
<h2 id="org4ddd40f"><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-orgcdbce05" class="outline-2">
<h2 id="orgcdbce05"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org0349813" class="outline-2">
<h2 id="org0349813"><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-org52c2a8c" class="outline-2">
<h2 id="org52c2a8c"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org96a15a3" class="outline-2">
<h2 id="org96a15a3"><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-orgf4e389e" class="outline-2">
<h2 id="orgf4e389e"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orge24957b" class="outline-2">
<h2 id="orge24957b"><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-org887dc5c" class="outline-2">
<h2 id="org887dc5c"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org6cd9c37" class="outline-2">
<h2 id="org6cd9c37"><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-org178d59f" class="outline-2">
<h2 id="org178d59f"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orgfe5e297" class="outline-2">
<h2 id="orgfe5e297"><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-orgd3a9bc0" class="outline-2">
<h2 id="orgd3a9bc0"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org7028212" class="outline-2">
<h2 id="org7028212"><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-orgef6f2ba" class="outline-2">
<h2 id="orgef6f2ba"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org23b8298" class="outline-2">
<h2 id="org23b8298"><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-org0375352" class="outline-2">
<h2 id="org0375352"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org9e91c12" class="outline-2">
<h2 id="org9e91c12"><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: 2024-11-10 Sun 20:58</p>
<p class="date">Created: 2024-11-20 Wed 14:29</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

256
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<head>
<!-- 2024-11-10 Sun 20:58 -->
<!-- 2024-11-20 Wed 14:29 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Data stored in TREXIO</title>
@ -346,72 +346,72 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9b7190d">1. Metadata (metadata group)</a></li>
<li><a href="#orge23a35d">2. System</a>
<li><a href="#orgf8d8d25">1. Metadata (metadata group)</a></li>
<li><a href="#org14a605e">2. System</a>
<ul>
<li><a href="#org1559083">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org491ed03">2.2. Cell (cell group)</a></li>
<li><a href="#org6be64ea">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org9783d69">2.4. Electron (electron group)</a></li>
<li><a href="#org5787663">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org3827e71">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org8cfe6ae">2.2. Cell (cell group)</a></li>
<li><a href="#org52e7020">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org52396a0">2.4. Electron (electron group)</a></li>
<li><a href="#orgdae2c52">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org958f900">3. Basis functions</a>
<li><a href="#org5ee8a70">3. Basis functions</a>
<ul>
<li><a href="#orga103922">3.1. Basis set (basis group)</a>
<li><a href="#org1df5cc4">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orgb7f234d">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgb4c13ac">3.1.2. Numerical orbitals</a></li>
<li><a href="#org4cee4fb">3.1.3. Plane waves</a></li>
<li><a href="#orgf9319db">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org0bed9ea">3.1.5. Data definitions</a></li>
<li><a href="#orge9f04af">3.1.6. Example</a></li>
<li><a href="#orge1cb872">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgd109008">3.1.2. Numerical orbitals</a></li>
<li><a href="#orgb6781c0">3.1.3. Plane waves</a></li>
<li><a href="#org2af12ab">3.1.4. Oscillating orbitals</a></li>
<li><a href="#orgc341023">3.1.5. Data definitions</a></li>
<li><a href="#org919948a">3.1.6. Example</a></li>
</ul>
</li>
<li><a href="#orgc0d5f66">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org9d79234">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org1ea7071">3.2.1. Example</a></li>
<li><a href="#org3670ac7">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org64dba67">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org83e9fd6">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#orgf00657e">4. Orbitals</a>
<li><a href="#org7f7894a">4. Orbitals</a>
<ul>
<li><a href="#org30356d2">4.1. Atomic orbitals (ao group)</a>
<li><a href="#orgca4ef9d">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="#org22c9f7b">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org23e7c1f">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org6c6bf62">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org3802a31">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgbc59f2e">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org1016bb8">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org2051391">5. Multi-determinant information</a>
<li><a href="#org4532d32">5. Multi-determinant information</a>
<ul>
<li><a href="#org5767991">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org131751b">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org257bedd">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org936b661">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org4f1fe06">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org81f8f3b">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgd2bc3f5">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org490e538">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#orge90ca4a">6. Correlation factors</a>
<li><a href="#org04a685b">6. Correlation factors</a>
<ul>
<li><a href="#org2f7f5f8">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org24b6615">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#orgfce725d">6.1.1. CHAMP</a></li>
<li><a href="#org9ab7ae0">6.1.2. Mu</a></li>
<li><a href="#org8fa9ac0">6.1.3. Table of values</a></li>
<li><a href="#org9c3bf5e">6.1.1. CHAMP</a></li>
<li><a href="#org9ea0da8">6.1.2. Mu</a></li>
<li><a href="#org8a19129">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org2b0868d">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org03a46d4">7. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -433,8 +433,8 @@ contiguous in memory. In the row-major representation, <code>A[i,j]</code> and
<code>A[i,j+1]</code> are contiguous.
</p>
<div id="outline-container-org9b7190d" class="outline-2">
<h2 id="org9b7190d"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgf8d8d25" class="outline-2">
<h2 id="orgf8d8d25"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect TREXIO files to be archived in open-data repositories,
@ -444,7 +444,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
</p>
<table id="org72c8c49" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge2021d3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -537,19 +537,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
</div>
</div>
<div id="outline-container-orge23a35d" class="outline-2">
<h2 id="orge23a35d"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org14a605e" class="outline-2">
<h2 id="org14a605e"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org1559083" class="outline-3">
<h3 id="org1559083"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org3827e71" class="outline-3">
<h3 id="org3827e71"><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="org88dc5d0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org441d99b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -634,15 +634,15 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org491ed03" class="outline-3">
<h3 id="org491ed03"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org8cfe6ae" class="outline-3">
<h3 id="org8cfe6ae"><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="org95ab323" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfd1f0e9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -726,10 +726,10 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-org6be64ea" class="outline-3">
<h3 id="org6be64ea"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org52e7020" class="outline-3">
<h3 id="org52e7020"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div class="outline-text-3" id="text-2-3">
<table id="org6e4cd7e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org70b4351" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -789,8 +789,8 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-org9783d69" class="outline-3">
<h3 id="org9783d69"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org52396a0" class="outline-3">
<h3 id="org52396a0"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div class="outline-text-3" id="text-2-4">
<p>
The chemical system consists of nuclei and electrons, where the
@ -809,7 +809,7 @@ the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org4dc792c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org33c70ed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -861,8 +861,8 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org5787663" class="outline-3">
<h3 id="org5787663"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-orgdae2c52" class="outline-3">
<h3 id="orgdae2c52"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div class="outline-text-3" id="text-2-5">
<p>
This group contains information about excited states. Since only a
@ -879,7 +879,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="orgcb56cf9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org077f9eb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -956,16 +956,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-org958f900" class="outline-2">
<h2 id="org958f900"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org5ee8a70" class="outline-2">
<h2 id="org5ee8a70"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orga103922" class="outline-3">
<h3 id="orga103922"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org1df5cc4" class="outline-3">
<h3 id="org1df5cc4"><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-orgb7f234d" class="outline-4">
<h4 id="orgb7f234d"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-orge1cb872" class="outline-4">
<h4 id="orge1cb872"><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
@ -1008,7 +1008,7 @@ this normalization factor is not required, \(f_{ks}=1\).
</p>
<p>
Some codes assume that the basis function are normalized. This
Some codes assume that the basis functions are normalized. This
implies the computation of an extra normalization factor, \(\mathcal{N}_s\).
If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).
</p>
@ -1019,8 +1019,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-orgb4c13ac" class="outline-4">
<h4 id="orgb4c13ac"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-orgd109008" class="outline-4">
<h4 id="orgd109008"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div class="outline-text-4" id="text-3-1-2">
<p>
Trexio supports numerical atom centered orbitals. The implementation is
@ -1084,8 +1084,8 @@ reimplement them with consideration for its specific needs.
</div>
</div>
<div id="outline-container-org4cee4fb" class="outline-4">
<h4 id="org4cee4fb"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-orgb6781c0" class="outline-4">
<h4 id="orgb6781c0"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div class="outline-text-4" id="text-3-1-3">
<p>
A plane wave is defined as
@ -1106,8 +1106,8 @@ plane waves.
</div>
</div>
<div id="outline-container-orgf9319db" class="outline-4">
<h4 id="orgf9319db"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div id="outline-container-org2af12ab" class="outline-4">
<h4 id="org2af12ab"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div class="outline-text-4" id="text-3-1-4">
<p>
Basis functions can be made oscillating as
@ -1129,10 +1129,10 @@ Oscillation kind can be:
</div>
</div>
<div id="outline-container-org0bed9ea" class="outline-4">
<h4 id="org0bed9ea"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div id="outline-container-orgc341023" class="outline-4">
<h4 id="orgc341023"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-5">
<table id="orgfdb83ff" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org332525a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1384,8 +1384,8 @@ Oscillation kind can be:
</div>
</div>
<div id="outline-container-orge9f04af" class="outline-4">
<h4 id="orge9f04af"><span class="section-number-4">3.1.6</span> Example</h4>
<div id="outline-container-org919948a" class="outline-4">
<h4 id="org919948a"><span class="section-number-4">3.1.6</span> Example</h4>
<div class="outline-text-4" id="text-3-1-6">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1463,8 +1463,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgc0d5f66" class="outline-3">
<h3 id="orgc0d5f66"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org9d79234" class="outline-3">
<h3 id="org9d79234"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div class="outline-text-3" id="text-3-2">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -1498,7 +1498,7 @@ where \(Z_\text{eff}\) is the effective nuclear charge of the center.
See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.4984046</a> or <a href="https://doi.org/10.1063/1.5121006">https://doi.org/10.1063/1.5121006</a> for more info.
</p>
<table id="orga60db7a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd66178e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1613,8 +1613,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-org1ea7071" class="outline-4">
<h4 id="org1ea7071"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-org3670ac7" class="outline-4">
<h4 id="org3670ac7"><span class="section-number-4">3.2.1</span> Example</h4>
<div class="outline-text-4" id="text-3-2-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -1677,8 +1677,8 @@ power = [
</div>
</div>
<div id="outline-container-org64dba67" class="outline-3">
<h3 id="org64dba67"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org83e9fd6" class="outline-3">
<h3 id="org83e9fd6"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div class="outline-text-3" id="text-3-3">
<p>
In some applications, such as DFT calculations, integrals have to
@ -1693,7 +1693,7 @@ The structure of this group is adapted for the <a href="https://github.com/dftli
Feel free to submit a PR if you find missing options/functionalities.
</p>
<table id="orgdfd9542" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb183f51" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1826,12 +1826,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-orgf00657e" class="outline-2">
<h2 id="orgf00657e"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org7f7894a" class="outline-2">
<h2 id="org7f7894a"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org30356d2" class="outline-3">
<h3 id="org30356d2"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-orgca4ef9d" class="outline-3">
<h3 id="orgca4ef9d"><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
@ -1918,7 +1918,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="org7d5339b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3765ceb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1977,7 +1977,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org304acc5" class="outline-4">
<div id="outline-container-org53bb93f" 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">
@ -1995,7 +1995,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org3e70231" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfb31c91" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2103,7 +2103,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgab8a897" class="outline-4">
<div id="outline-container-orgd1c5d1c" 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>
@ -2129,7 +2129,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org66056d2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgba68d2f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2206,10 +2206,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org22c9f7b" class="outline-3">
<h3 id="org22c9f7b"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org23e7c1f" class="outline-3">
<h3 id="org23e7c1f"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="orgd0a2e7d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9e9772e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2325,8 +2325,8 @@ is the number of spin-orbitals, twice the number of spatial orbitals.
</div>
<div id="outline-container-org6c6bf62" class="outline-4">
<h4 id="org6c6bf62"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-orgbc59f2e" class="outline-4">
<h4 id="orgbc59f2e"><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
@ -2334,7 +2334,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org4443540" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge9e6171" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2442,8 +2442,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org3802a31" class="outline-4">
<h4 id="org3802a31"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org1016bb8" class="outline-4">
<h4 id="org1016bb8"><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
@ -2451,7 +2451,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org4b70a2f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3e54d94" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2529,12 +2529,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org2051391" class="outline-2">
<h2 id="org2051391"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org4532d32" class="outline-2">
<h2 id="org4532d32"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org5767991" class="outline-3">
<h3 id="org5767991"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org4f1fe06" class="outline-3">
<h3 id="org4f1fe06"><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 \(\Psi\)
@ -2576,7 +2576,7 @@ 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="orgfc786c4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2883770" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2628,8 +2628,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org131751b" class="outline-3">
<h3 id="org131751b"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org81f8f3b" class="outline-3">
<h3 id="org81f8f3b"><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
@ -2651,7 +2651,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="orgdf779f9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf86b809" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2703,8 +2703,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org257bedd" class="outline-3">
<h3 id="org257bedd"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orgd2bc3f5" class="outline-3">
<h3 id="orgd2bc3f5"><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
@ -2775,7 +2775,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org6a315ba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc1848e3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2867,8 +2867,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-org936b661" class="outline-3">
<h3 id="org936b661"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org490e538" class="outline-3">
<h3 id="org490e538"><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
@ -2940,7 +2940,7 @@ 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="org6763ad2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcbfce0c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3105,12 +3105,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-orge90ca4a" class="outline-2">
<h2 id="orge90ca4a"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org04a685b" class="outline-2">
<h2 id="org04a685b"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org2f7f5f8" class="outline-3">
<h3 id="org2f7f5f8"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
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<h3 id="org24b6615"><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
@ -3135,8 +3135,8 @@ following:
</ul>
</div>
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<h4 id="orgfce725d"><span class="section-number-4">6.1.1</span> CHAMP</h4>
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<h4 id="org9c3bf5e"><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
@ -3237,8 +3237,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
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<h4 id="org9ab7ae0"><span class="section-number-4">6.1.2</span> Mu</h4>
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<h4 id="org9ea0da8"><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
@ -3335,10 +3335,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
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<h4 id="org8fa9ac0"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="org8a19129"><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="org78d4011" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8b59b1c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3456,8 +3456,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
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<h2 id="org2b0868d"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org03a46d4"><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
@ -3471,7 +3471,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="org95f09b4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
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<colgroup>
@ -3533,7 +3533,7 @@ 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: 2024-11-10 Sun 20:58</p>
<p class="date">Created: 2024-11-20 Wed 14:29</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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