TREX/trexio
1
0
Fork 0
mirror of https://github.com/TREX-CoE/trexio.git synced 2024-10-02 14:31:05 +02:00
Code Issues Projects Releases Wiki Activity

Deploying to gh-pages from @ TREX-CoE/trexio@d8a37b26bf 🚀

Browse Source
This commit is contained in:
scemama 2023-06-02 12:58:36 +00:00
parent 7b26fb7fa3
commit d5c5fc1519
9 changed files with 666 additions and 662 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
README.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>
<!-- 2023-06-02 Fri 12:27 -->
<!-- 2023-06-02 Fri 12:58 -->
<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: 2023-06-02 Fri 12:27</p>
<p class="date">Created: 2023-06-02 Fri 12:58</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

172
examples.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>
<!-- 2023-06-02 Fri 12:27 -->
<!-- 2023-06-02 Fri 12:58 -->
<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="#orgbd92b82">1. Writing nuclear coordinates</a>
<li><a href="#org92f9c6c">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orgd59268a">1.1. C</a></li>
<li><a href="#orgbc92f58">1.2. Python</a></li>
<li><a href="#org6703c21">1.3. Fortran</a></li>
<li><a href="#org4501c83">1.1. C</a></li>
<li><a href="#orgf3d2f18">1.2. Python</a></li>
<li><a href="#orga6a9e60">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org98994d5">2. Accessing sparse quantities (integrals)</a>
<li><a href="#orgf2fc45e">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org4230447">2.1. Fortran</a>
<li><a href="#org8fa1343">2.1. Fortran</a>
<ul>
<li><a href="#org7c4d1b3">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orga08e347">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org9f91433">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org8931c14">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgfcc6547">2.1.5. Allocate memory</a></li>
<li><a href="#org1f5e0bb">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org49e4792">2.1.7. Read two-electron quantities</a>
<li><a href="#orgd53da35">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org6ad719a">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org3aef3f8">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgceac4ef">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orge16b2e2">2.1.5. Allocate memory</a></li>
<li><a href="#org478b894">2.1.6. Read one-electron quantities</a></li>
<li><a href="#orgb5dbd7f">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org08c9e97">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org45bd034">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org4f06313">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org784834e">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgf1db034">2.1.8. Compute the energy</a></li>
<li><a href="#org0532178">2.1.9. Terminate</a></li>
<li><a href="#org6148909">2.1.8. Compute the energy</a></li>
<li><a href="#org93c293d">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org26ff59b">2.2. Python</a>
<li><a href="#org52ad89b">2.2. Python</a>
<ul>
<li><a href="#org1c53adb">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgd5baac9">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org59b92a3">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org782399b">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org58d228b">2.2.5. Read two-electron quantities</a>
<li><a href="#org7e6f9d8">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgd9947f9">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org5bac3b4">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org1dc71bb">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgb5175f6">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#org8affef2">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgc6858ab">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#orgbdbeeb3">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgde7d7c4">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgc52ba92">2.2.6. Compute the energy</a></li>
<li><a href="#org81caab1">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orga24149d">3. Reading determinants</a>
<li><a href="#org6eca5d4">3. Reading determinants</a>
<ul>
<li><a href="#org37ccb46">3.1. Fortran</a></li>
<li><a href="#org3b0c755">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgbd92b82" class="outline-2">
<h2 id="orgbd92b82"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org92f9c6c" class="outline-2">
<h2 id="org92f9c6c"><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-orgd59268a" class="outline-3">
<h3 id="orgd59268a"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org4501c83" class="outline-3">
<h3 id="org4501c83"><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-orgbc92f58" class="outline-3">
<h3 id="orgbc92f58"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-orgf3d2f18" class="outline-3">
<h3 id="orgf3d2f18"><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-org6703c21" class="outline-3">
<h3 id="org6703c21"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orga6a9e60" class="outline-3">
<h3 id="orga6a9e60"><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-org98994d5" class="outline-2">
<h2 id="org98994d5"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orgf2fc45e" class="outline-2">
<h2 id="orgf2fc45e"><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-org4230447" class="outline-3">
<h3 id="org4230447"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org8fa1343" class="outline-3">
<h3 id="org8fa1343"><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-org7c4d1b3" class="outline-4">
<h4 id="org7c4d1b3"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgd53da35" class="outline-4">
<h4 id="orgd53da35"><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-orga08e347" class="outline-4">
<h4 id="orga08e347"><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-org6ad719a" class="outline-4">
<h4 id="org6ad719a"><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-org9f91433" class="outline-4">
<h4 id="org9f91433"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org3aef3f8" class="outline-4">
<h4 id="org3aef3f8"><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-org8931c14" class="outline-4">
<h4 id="org8931c14"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgceac4ef" class="outline-4">
<h4 id="orgceac4ef"><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-orgfcc6547" class="outline-4">
<h4 id="orgfcc6547"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-orge16b2e2" class="outline-4">
<h4 id="orge16b2e2"><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-org1f5e0bb" class="outline-4">
<h4 id="org1f5e0bb"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org478b894" class="outline-4">
<h4 id="org478b894"><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-org49e4792" class="outline-4">
<h4 id="org49e4792"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgb5dbd7f" class="outline-4">
<h4 id="orgb5dbd7f"><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-org08c9e97" class="outline-5">
<h5 id="org08c9e97"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org4f06313" class="outline-5">
<h5 id="org4f06313"><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-org45bd034" class="outline-5">
<h5 id="org45bd034"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org784834e" class="outline-5">
<h5 id="org784834e"><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-orgf1db034" class="outline-4">
<h4 id="orgf1db034"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org6148909" class="outline-4">
<h4 id="org6148909"><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-org0532178" class="outline-4">
<h4 id="org0532178"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org93c293d" class="outline-4">
<h4 id="org93c293d"><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-org26ff59b" class="outline-3">
<h3 id="org26ff59b"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org52ad89b" class="outline-3">
<h3 id="org52ad89b"><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-org1c53adb" class="outline-4">
<h4 id="org1c53adb"><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-org7e6f9d8" class="outline-4">
<h4 id="org7e6f9d8"><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-orgd5baac9" class="outline-4">
<h4 id="orgd5baac9"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgd9947f9" class="outline-4">
<h4 id="orgd9947f9"><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-org59b92a3" class="outline-4">
<h4 id="org59b92a3"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org5bac3b4" class="outline-4">
<h4 id="org5bac3b4"><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-org782399b" class="outline-4">
<h4 id="org782399b"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org1dc71bb" class="outline-4">
<h4 id="org1dc71bb"><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-org58d228b" class="outline-4">
<h4 id="org58d228b"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-orgb5175f6" class="outline-4">
<h4 id="orgb5175f6"><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-org8affef2" class="outline-5">
<h5 id="org8affef2"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgbdbeeb3" class="outline-5">
<h5 id="orgbdbeeb3"><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-orgc6858ab" class="outline-5">
<h5 id="orgc6858ab"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-orgde7d7c4" class="outline-5">
<h5 id="orgde7d7c4"><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-orgc52ba92" class="outline-4">
<h4 id="orgc52ba92"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org81caab1" class="outline-4">
<h4 id="org81caab1"><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-orga24149d" class="outline-2">
<h2 id="orga24149d"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org6eca5d4" class="outline-2">
<h2 id="org6eca5d4"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org37ccb46" class="outline-3">
<h3 id="org37ccb46"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org3b0c755" class="outline-3">
<h3 id="org3b0c755"><span class="section-number-3">3.1</span> Fortran</h3>
<div class="outline-text-3" id="text-3-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
@ -1157,7 +1157,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-06-02 Fri 12:27</p>
<p class="date">Created: 2023-06-02 Fri 12:58</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
index.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>
<!-- 2023-06-02 Fri 12:27 -->
<!-- 2023-06-02 Fri 12:58 -->
<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: 2023-06-02 Fri 12:27</p>
<p class="date">Created: 2023-06-02 Fri 12:58</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
intro.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>
<!-- 2023-06-02 Fri 12:27 -->
<!-- 2023-06-02 Fri 12:58 -->
<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: 2023-06-02 Fri 12:27</p>
<p class="date">Created: 2023-06-02 Fri 12:58</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
lib.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>
<!-- 2023-06-02 Fri 12:27 -->
<!-- 2023-06-02 Fri 12:58 -->
<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="#orgc5b1f19">1. Format specification</a>
<li><a href="#orga4ef44d">1. Format specification</a>
<ul>
<li><a href="#org828dc84">1.1. Organization of the data</a></li>
<li><a href="#orgcb95639">1.2. Data types</a></li>
<li><a href="#orgdbff06b">1.1. Organization of the data</a></li>
<li><a href="#orgf923f98">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org5badf27">2. The TREXIO library</a>
<li><a href="#org00a715e">2. The TREXIO library</a>
<ul>
<li><a href="#org5ab27e5">2.1. The front-end</a></li>
<li><a href="#org9cdfbaf">2.2. The back-end</a></li>
<li><a href="#org1bc716d">2.3. Supported languages</a></li>
<li><a href="#org79f0c69">2.4. Source code generation and documentation</a></li>
<li><a href="#orgac7831b">2.5. Availability</a></li>
<li><a href="#orgaa11cd8">2.1. The front-end</a></li>
<li><a href="#orgf713644">2.2. The back-end</a></li>
<li><a href="#orge4707f0">2.3. Supported languages</a></li>
<li><a href="#org40d69a7">2.4. Source code generation and documentation</a></li>
<li><a href="#org621f20c">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgc5b1f19" class="outline-2">
<h2 id="orgc5b1f19"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-orga4ef44d" class="outline-2">
<h2 id="orga4ef44d"><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-org828dc84" class="outline-3">
<h3 id="org828dc84"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-orgdbff06b" class="outline-3">
<h3 id="orgdbff06b"><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-orgcb95639" class="outline-3">
<h3 id="orgcb95639"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-orgf923f98" class="outline-3">
<h3 id="orgf923f98"><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-org5badf27" class="outline-2">
<h2 id="org5badf27"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-org00a715e" class="outline-2">
<h2 id="org00a715e"><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-org5ab27e5" class="outline-3">
<h3 id="org5ab27e5"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orgaa11cd8" class="outline-3">
<h3 id="orgaa11cd8"><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-org9cdfbaf" class="outline-3">
<h3 id="org9cdfbaf"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-orgf713644" class="outline-3">
<h3 id="orgf713644"><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-org1bc716d" class="outline-3">
<h3 id="org1bc716d"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-orge4707f0" class="outline-3">
<h3 id="orge4707f0"><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-org79f0c69" class="outline-3">
<h3 id="org79f0c69"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org40d69a7" class="outline-3">
<h3 id="org40d69a7"><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-orgac7831b" class="outline-3">
<h3 id="orgac7831b"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org621f20c" class="outline-3">
<h3 id="org621f20c"><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: 2023-06-02 Fri 12:27</p>
<p class="date">Created: 2023-06-02 Fri 12:58</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

650
templator_front.html
View File

File diff suppressed because it is too large Load Diff

82
templator_hdf5.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>
<!-- 2023-06-02 Fri 12:27 -->
<!-- 2023-06-02 Fri 12:58 -->
<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="#orgbc37d62">1. Template for HDF5 definitions</a></li>
<li><a href="#org21306e7">2. Template for HDF5 structures</a></li>
<li><a href="#org64394c0">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org72d62e6">4. Template for HDF5 has a group</a></li>
<li><a href="#orgb473618">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org3fc7ba1">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org3547c16">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org7f3c1a3">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgfd3c069">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org8123fcf">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org1c74ee6">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org7e9a838">12. Source code for the determinant part</a></li>
<li><a href="#orgc329b08">13. Helper functions</a></li>
<li><a href="#org59669e5">1. Template for HDF5 definitions</a></li>
<li><a href="#org47473d9">2. Template for HDF5 structures</a></li>
<li><a href="#org836855a">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgb029ac7">4. Template for HDF5 has a group</a></li>
<li><a href="#org57f2b46">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org9657411">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org2ebf4ae">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org0a0487d">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org415c986">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgbdddcfd">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org709f130">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgdbf6e8d">12. Source code for the determinant part</a></li>
<li><a href="#orge4cf2f1">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgbc37d62" class="outline-2">
<h2 id="orgbc37d62"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org59669e5" class="outline-2">
<h2 id="org59669e5"><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-org21306e7" class="outline-2">
<h2 id="org21306e7"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org47473d9" class="outline-2">
<h2 id="org47473d9"><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-org64394c0" class="outline-2">
<h2 id="org64394c0"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org836855a" class="outline-2">
<h2 id="org836855a"><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-org72d62e6" class="outline-2">
<h2 id="org72d62e6"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orgb029ac7" class="outline-2">
<h2 id="orgb029ac7"><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-orgb473618" class="outline-2">
<h2 id="orgb473618"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org57f2b46" class="outline-2">
<h2 id="org57f2b46"><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-org3fc7ba1" class="outline-2">
<h2 id="org3fc7ba1"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org9657411" class="outline-2">
<h2 id="org9657411"><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-org3547c16" class="outline-2">
<h2 id="org3547c16"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org2ebf4ae" class="outline-2">
<h2 id="org2ebf4ae"><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-org7f3c1a3" class="outline-2">
<h2 id="org7f3c1a3"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org0a0487d" class="outline-2">
<h2 id="org0a0487d"><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-orgfd3c069" class="outline-2">
<h2 id="orgfd3c069"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org415c986" class="outline-2">
<h2 id="org415c986"><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-org8123fcf" class="outline-2">
<h2 id="org8123fcf"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgbdddcfd" class="outline-2">
<h2 id="orgbdddcfd"><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-org1c74ee6" class="outline-2">
<h2 id="org1c74ee6"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org709f130" class="outline-2">
<h2 id="org709f130"><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-org7e9a838" class="outline-2">
<h2 id="org7e9a838"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-orgdbf6e8d" class="outline-2">
<h2 id="orgdbf6e8d"><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-orgc329b08" class="outline-2">
<h2 id="orgc329b08"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orge4cf2f1" class="outline-2">
<h2 id="orge4cf2f1"><span class="section-number-2">13</span> Helper functions</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1850,7 +1850,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-06-02 Fri 12:27</p>
<p class="date">Created: 2023-06-02 Fri 12:58</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

112
templator_text.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>
<!-- 2023-06-02 Fri 12:27 -->
<!-- 2023-06-02 Fri 12:58 -->
<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="#org20545cc">1. Template for group-related structures in text back end</a></li>
<li><a href="#org86fbc9d">2. Template for general structure in text back end</a></li>
<li><a href="#orgad0eeb6">3. Initialize function (constant part)</a></li>
<li><a href="#org95ba4ea">4. Deinitialize function (templated part)</a></li>
<li><a href="#org48ad9db">5. Flush function (templated part)</a></li>
<li><a href="#org1e2cb98">6. Template for text read a group</a></li>
<li><a href="#org149a6fd">7. Template for text has a group</a></li>
<li><a href="#org9176052">8. Template for text flush a group</a></li>
<li><a href="#org324a3c1">9. Template for text free memory</a></li>
<li><a href="#orgc88982c">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org66c2ab8">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org1127cec">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgfa9b3c3">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgd07f427">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org248f7d9">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org10701ab">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org1afd9ee">17. Source code for the determinant part</a></li>
<li><a href="#orgb268a8c">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgf57f831">2. Template for general structure in text back end</a></li>
<li><a href="#orgd1b8f5b">3. Initialize function (constant part)</a></li>
<li><a href="#org7152864">4. Deinitialize function (templated part)</a></li>
<li><a href="#org4256ccc">5. Flush function (templated part)</a></li>
<li><a href="#org0a7f482">6. Template for text read a group</a></li>
<li><a href="#org84e0036">7. Template for text has a group</a></li>
<li><a href="#orgcbe7b3a">8. Template for text flush a group</a></li>
<li><a href="#orgc2c8f89">9. Template for text free memory</a></li>
<li><a href="#orge9d36a9">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgcd047ca">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org7f3a42a">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org5445b40">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org540af38">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orge7725b4">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org02da001">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org0c3b96a">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-org20545cc" class="outline-2">
<h2 id="org20545cc"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orgb268a8c" class="outline-2">
<h2 id="orgb268a8c"><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-org86fbc9d" class="outline-2">
<h2 id="org86fbc9d"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgf57f831" class="outline-2">
<h2 id="orgf57f831"><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-orgad0eeb6" class="outline-2">
<h2 id="orgad0eeb6"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-orgd1b8f5b" class="outline-2">
<h2 id="orgd1b8f5b"><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>
@ -460,7 +460,11 @@ In that case, we define an alternate one, which is not as safe as the original o
</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
<pre class="src src-c"><span style="color: #483d8b;">#if</span> /* <span style="color: #b22222;">Since glibc 2.19:</span> */ _DEFAULT_SOURCE \
|| /* <span style="color: #b22222;">Glibc 2.19 and earlier:</span> */ _BSD_SOURCE \
|| /* <span style="color: #b22222;">Since glibc 2.10:</span> */ _POSIX_C_SOURCE &gt;= 200809L
/* <span style="color: #b22222;">mkdtemp is defined</span> */
<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>) {
@ -597,8 +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-org95ba4ea" class="outline-2">
<h2 id="org95ba4ea"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org7152864" class="outline-2">
<h2 id="org7152864"><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>
@ -620,8 +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-org48ad9db" class="outline-2">
<h2 id="org48ad9db"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org4256ccc" class="outline-2">
<h2 id="org4256ccc"><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>
@ -644,8 +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-org1e2cb98" class="outline-2">
<h2 id="org1e2cb98"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org0a7f482" class="outline-2">
<h2 id="org0a7f482"><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*
@ -871,8 +875,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org149a6fd" class="outline-2">
<h2 id="org149a6fd"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org84e0036" class="outline-2">
<h2 id="org84e0036"><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>
@ -912,8 +916,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org9176052" class="outline-2">
<h2 id="org9176052"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-orgcbe7b3a" class="outline-2">
<h2 id="orgcbe7b3a"><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>
@ -977,8 +981,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org324a3c1" class="outline-2">
<h2 id="org324a3c1"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-orgc2c8f89" class="outline-2">
<h2 id="orgc2c8f89"><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.
@ -1047,8 +1051,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orgc88982c" class="outline-2">
<h2 id="orgc88982c"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orge9d36a9" class="outline-2">
<h2 id="orge9d36a9"><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>
@ -1111,8 +1115,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org66c2ab8" class="outline-2">
<h2 id="org66c2ab8"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgcd047ca" class="outline-2">
<h2 id="orgcd047ca"><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.
@ -1208,8 +1212,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org1127cec" class="outline-2">
<h2 id="org1127cec"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org7f3a42a" class="outline-2">
<h2 id="org7f3a42a"><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.
@ -1310,8 +1314,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgfa9b3c3" class="outline-2">
<h2 id="orgfa9b3c3"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org5445b40" class="outline-2">
<h2 id="org5445b40"><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>
@ -1385,8 +1389,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgd07f427" class="outline-2">
<h2 id="orgd07f427"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org540af38" class="outline-2">
<h2 id="org540af38"><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
@ -1676,8 +1680,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org248f7d9" class="outline-2">
<h2 id="org248f7d9"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-orge7725b4" class="outline-2">
<h2 id="orge7725b4"><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
@ -1907,8 +1911,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-org10701ab" class="outline-2">
<h2 id="org10701ab"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org02da001" class="outline-2">
<h2 id="org02da001"><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>
@ -1936,8 +1940,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-org1afd9ee" class="outline-2">
<h2 id="org1afd9ee"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org0c3b96a" class="outline-2">
<h2 id="org0c3b96a"><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
@ -2129,7 +2133,7 @@ Size specifies the number of data items, e.g. determinants.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-06-02 Fri 12:27</p>
<p class="date">Created: 2023-06-02 Fri 12:58</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>
<!-- 2023-06-02 Fri 12:27 -->
<!-- 2023-06-02 Fri 12:58 -->
<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="#org5c94fbd">1. Metadata (metadata group)</a></li>
<li><a href="#org8ed5864">2. System</a>
<li><a href="#org31afad0">1. Metadata (metadata group)</a></li>
<li><a href="#orgab3fc9d">2. System</a>
<ul>
<li><a href="#org7979d8a">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org5e0f449">2.2. Cell (cell group)</a></li>
<li><a href="#org6a4d1a8">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orge0eef0e">2.4. Electron (electron group)</a></li>
<li><a href="#orgf316dc5">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org6e5f610">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#orgc67117e">2.2. Cell (cell group)</a></li>
<li><a href="#orgec1ac69">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org959bab5">2.4. Electron (electron group)</a></li>
<li><a href="#orgf4a7dc0">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org9022ae2">3. Basis functions</a>
<li><a href="#orgcd73058">3. Basis functions</a>
<ul>
<li><a href="#org8e63b24">3.1. Basis set (basis group)</a>
<li><a href="#org3b6369a">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org3ba03ac">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org36c2a0b">3.1.2. Plane waves</a></li>
<li><a href="#org63ca6dc">3.1.3. Data definitions</a></li>
<li><a href="#orge0102be">3.1.4. Example</a></li>
<li><a href="#orgb8f9a77">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org43e4aa8">3.1.2. Plane waves</a></li>
<li><a href="#orgeb78806">3.1.3. Data definitions</a></li>
<li><a href="#orge49d793">3.1.4. Example</a></li>
</ul>
</li>
<li><a href="#org3525dab">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org8fef59c">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org96ca313">3.2.1. Example</a></li>
<li><a href="#orgf3419a1">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#orga026e7e">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org04ff51d">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#orgdfa3f45">4. Orbitals</a>
<li><a href="#org7ba73e6">4. Orbitals</a>
<ul>
<li><a href="#orgdc3be1f">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org7c203a1">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="#orgad6646c">4.2. Molecular orbitals (mo group)</a>
<li><a href="#orgab081d3">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org17c72f4">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org10095da">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgf8442b4">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgfbed630">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org402203a">5. Multi-determinant information</a>
<li><a href="#org0250294">5. Multi-determinant information</a>
<ul>
<li><a href="#org7da8ce8">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org61f4e38">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org120d8a0">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org5167fa5">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgf68f7b8">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org4adc6c8">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org0d003ca">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgfc0534d">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org092f3d5">6. Correlation factors</a>
<li><a href="#orgd71d670">6. Correlation factors</a>
<ul>
<li><a href="#orgbfdd9a6">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#orgf608ff6">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org5824caa">6.1.1. CHAMP</a></li>
<li><a href="#org4fccb68">6.1.2. Mu</a></li>
<li><a href="#org0a52336">6.1.3. Table of values</a></li>
<li><a href="#org2af13ac">6.1.1. CHAMP</a></li>
<li><a href="#org58fd4e9">6.1.2. Mu</a></li>
<li><a href="#orgb8db84f">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgcb02d1e">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org05b6d6c">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-org5c94fbd" class="outline-2">
<h2 id="org5c94fbd"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org31afad0" class="outline-2">
<h2 id="org31afad0"><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="org6f5ec38" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0541602" 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-org8ed5864" class="outline-2">
<h2 id="org8ed5864"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-orgab3fc9d" class="outline-2">
<h2 id="orgab3fc9d"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org7979d8a" class="outline-3">
<h3 id="org7979d8a"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org6e5f610" class="outline-3">
<h3 id="org6e5f610"><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="org8ecee12" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org52df6b1" 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-org5e0f449" class="outline-3">
<h3 id="org5e0f449"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-orgc67117e" class="outline-3">
<h3 id="orgc67117e"><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="org44d7771" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org33e46ac" 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-org6a4d1a8" class="outline-3">
<h3 id="org6a4d1a8"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-orgec1ac69" class="outline-3">
<h3 id="orgec1ac69"><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="org9033350" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9a32cfe" 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-orge0eef0e" class="outline-3">
<h3 id="orge0eef0e"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org959bab5" class="outline-3">
<h3 id="org959bab5"><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="org282735e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9dcf962" 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-orgf316dc5" class="outline-3">
<h3 id="orgf316dc5"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-orgf4a7dc0" class="outline-3">
<h3 id="orgf4a7dc0"><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="org303f3bc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org81a6bff" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -876,16 +876,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-org9022ae2" class="outline-2">
<h2 id="org9022ae2"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-orgcd73058" class="outline-2">
<h2 id="orgcd73058"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org8e63b24" class="outline-3">
<h3 id="org8e63b24"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org3b6369a" class="outline-3">
<h3 id="org3b6369a"><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-org3ba03ac" class="outline-4">
<h4 id="org3ba03ac"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-orgb8f9a77" class="outline-4">
<h4 id="orgb8f9a77"><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
@ -939,8 +939,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-org36c2a0b" class="outline-4">
<h4 id="org36c2a0b"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div id="outline-container-org43e4aa8" class="outline-4">
<h4 id="org43e4aa8"><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
@ -961,10 +961,10 @@ plane waves.
</div>
</div>
<div id="outline-container-org63ca6dc" class="outline-4">
<h4 id="org63ca6dc"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div id="outline-container-orgeb78806" class="outline-4">
<h4 id="orgeb78806"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-3">
<table id="org99dcba0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc3c94bd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1073,8 +1073,8 @@ plane waves.
</div>
</div>
<div id="outline-container-orge0102be" class="outline-4">
<h4 id="orge0102be"><span class="section-number-4">3.1.4</span> Example</h4>
<div id="outline-container-orge49d793" class="outline-4">
<h4 id="orge49d793"><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
@ -1152,8 +1152,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org3525dab" class="outline-3">
<h3 id="org3525dab"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org8fef59c" class="outline-3">
<h3 id="org8fef59c"><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
@ -1187,7 +1187,7 @@ 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="org12f7df8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdef2909" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1291,8 +1291,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-org96ca313" class="outline-4">
<h4 id="org96ca313"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orgf3419a1" class="outline-4">
<h4 id="orgf3419a1"><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
@ -1355,8 +1355,8 @@ power = [
</div>
</div>
<div id="outline-container-orga026e7e" class="outline-3">
<h3 id="orga026e7e"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org04ff51d" class="outline-3">
<h3 id="org04ff51d"><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
@ -1371,7 +1371,7 @@ 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="org4c74e95" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga3e6f9f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1488,12 +1488,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-orgdfa3f45" class="outline-2">
<h2 id="orgdfa3f45"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org7ba73e6" class="outline-2">
<h2 id="org7ba73e6"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-orgdc3be1f" class="outline-3">
<h3 id="orgdc3be1f"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org7c203a1" class="outline-3">
<h3 id="org7c203a1"><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
@ -1574,7 +1574,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="org3c85e8c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1b1d725" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1626,7 +1626,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org43d1d8d" class="outline-4">
<div id="outline-container-org3ec59e4" 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">
@ -1644,7 +1644,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgf0805e7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org054d04e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1739,7 +1739,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org356029c" class="outline-4">
<div id="outline-container-orge1c5e44" 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>
@ -1765,7 +1765,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org881ddfb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org10a7376" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1833,10 +1833,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-orgad6646c" class="outline-3">
<h3 id="orgad6646c"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-orgab081d3" class="outline-3">
<h3 id="orgab081d3"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org8ac5cac" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgacf2bc4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1923,8 +1923,8 @@ The Cholesky decomposition of the integrals can also be stored:
</table>
</div>
<div id="outline-container-org17c72f4" class="outline-4">
<h4 id="org17c72f4"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-orgf8442b4" class="outline-4">
<h4 id="orgf8442b4"><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
@ -1932,7 +1932,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org2b0db20" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org34c28c1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2027,8 +2027,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org10095da" class="outline-4">
<h4 id="org10095da"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-orgfbed630" class="outline-4">
<h4 id="orgfbed630"><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
@ -2036,7 +2036,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org327da58" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4ad79b6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2105,12 +2105,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org402203a" class="outline-2">
<h2 id="org402203a"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org0250294" class="outline-2">
<h2 id="org0250294"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org7da8ce8" class="outline-3">
<h3 id="org7da8ce8"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-orgf68f7b8" class="outline-3">
<h3 id="orgf68f7b8"><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 \(\Psi\)
@ -2152,7 +2152,7 @@ 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="org1009c21" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd7c97f3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2198,8 +2198,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org61f4e38" class="outline-3">
<h3 id="org61f4e38"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org4adc6c8" class="outline-3">
<h3 id="org4adc6c8"><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
@ -2221,7 +2221,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="orgaad8e0a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge4a45cd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2267,8 +2267,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org120d8a0" class="outline-3">
<h3 id="org120d8a0"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org0d003ca" class="outline-3">
<h3 id="org0d003ca"><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
@ -2339,7 +2339,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="orgf79e786" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org442d786" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2420,8 +2420,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-org5167fa5" class="outline-3">
<h3 id="org5167fa5"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-orgfc0534d" class="outline-3">
<h3 id="orgfc0534d"><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
@ -2493,7 +2493,7 @@ 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="orgbe6d6b3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org39eaf71" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2624,12 +2624,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org092f3d5" class="outline-2">
<h2 id="org092f3d5"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-orgd71d670" class="outline-2">
<h2 id="orgd71d670"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-orgbfdd9a6" class="outline-3">
<h3 id="orgbfdd9a6"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-orgf608ff6" class="outline-3">
<h3 id="orgf608ff6"><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
@ -2654,8 +2654,8 @@ following:
</ul>
</div>
<div id="outline-container-org5824caa" class="outline-4">
<h4 id="org5824caa"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org2af13ac" class="outline-4">
<h4 id="org2af13ac"><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
@ -2756,8 +2756,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-org4fccb68" class="outline-4">
<h4 id="org4fccb68"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org58fd4e9" class="outline-4">
<h4 id="org58fd4e9"><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
@ -2854,10 +2854,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org0a52336" class="outline-4">
<h4 id="org0a52336"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div id="outline-container-orgb8db84f" class="outline-4">
<h4 id="orgb8db84f"><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="org1c0c5b5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org50f2fa5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2961,8 +2961,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-orgcb02d1e" class="outline-2">
<h2 id="orgcb02d1e"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org05b6d6c" class="outline-2">
<h2 id="org05b6d6c"><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
@ -2976,7 +2976,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="org68dd316" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org84efc56" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3031,7 +3031,7 @@ 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: 2023-06-02 Fri 12:27</p>
<p class="date">Created: 2023-06-02 Fri 12:58</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>