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README.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 22:34 -->
<!-- 2024-08-18 Sun 07:19 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -406,7 +406,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-08-17 Sat 22:34</p>
<p class="date">Created: 2024-08-18 Sun 07:19</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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examples.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 22:34 -->
<!-- 2024-08-18 Sun 07:19 -->
<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="#org4acaba2">1. Writing nuclear coordinates</a>
<li><a href="#org02f3987">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orge78b7ba">1.1. C</a></li>
<li><a href="#orgff248a9">1.2. Python</a></li>
<li><a href="#org30e3740">1.3. Fortran</a></li>
<li><a href="#orgd8f8958">1.1. C</a></li>
<li><a href="#org01e1120">1.2. Python</a></li>
<li><a href="#org8dcf8ea">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org8fa7bb9">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org4ece203">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org01ee2ad">2.1. Fortran</a>
<li><a href="#org21fb931">2.1. Fortran</a>
<ul>
<li><a href="#org8a76eb2">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org433dc5d">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org04e638d">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org72064c1">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgeb3c054">2.1.5. Allocate memory</a></li>
<li><a href="#orgad5a323">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org38d753d">2.1.7. Read two-electron quantities</a>
<li><a href="#org0627112">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org961ae15">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga6b5dad">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org2f946b6">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org2ba3c92">2.1.5. Allocate memory</a></li>
<li><a href="#orga1c595f">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org71fc885">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org1465f92">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgc4f3098">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org40badd0">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org9083781">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org6e82756">2.1.8. Compute the energy</a></li>
<li><a href="#orgfbf12c8">2.1.9. Terminate</a></li>
<li><a href="#org437f310">2.1.8. Compute the energy</a></li>
<li><a href="#orgf5267a7">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org14be920">2.2. Python</a>
<li><a href="#orge519e69">2.2. Python</a>
<ul>
<li><a href="#orgb2b2bd3">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org6bb4413">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org8395667">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org2891a39">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org44cfb64">2.2.5. Read two-electron quantities</a>
<li><a href="#orgb5ca49f">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org58beb35">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org7d8c550">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org9d397d3">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgb5f5f1d">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#orgf7de80e">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgbd4b68b">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#orgb0b5297">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org5cc6c26">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org8871732">2.2.6. Compute the energy</a></li>
<li><a href="#org1ea52fe">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orge07dc2d">3. Reading determinants</a>
<li><a href="#orgfdec62c">3. Reading determinants</a>
<ul>
<li><a href="#org19ecdb3">3.1. Fortran</a></li>
<li><a href="#org15a2aec">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org4acaba2" class="outline-2">
<h2 id="org4acaba2"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org02f3987" class="outline-2">
<h2 id="org02f3987"><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-orge78b7ba" class="outline-3">
<h3 id="orge78b7ba"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-orgd8f8958" class="outline-3">
<h3 id="orgd8f8958"><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-orgff248a9" class="outline-3">
<h3 id="orgff248a9"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org01e1120" class="outline-3">
<h3 id="org01e1120"><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-org30e3740" class="outline-3">
<h3 id="org30e3740"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-org8dcf8ea" class="outline-3">
<h3 id="org8dcf8ea"><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-org8fa7bb9" class="outline-2">
<h2 id="org8fa7bb9"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org4ece203" class="outline-2">
<h2 id="org4ece203"><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-org01ee2ad" class="outline-3">
<h3 id="org01ee2ad"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org21fb931" class="outline-3">
<h3 id="org21fb931"><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-org8a76eb2" class="outline-4">
<h4 id="org8a76eb2"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org0627112" class="outline-4">
<h4 id="org0627112"><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-org433dc5d" class="outline-4">
<h4 id="org433dc5d"><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-org961ae15" class="outline-4">
<h4 id="org961ae15"><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-org04e638d" class="outline-4">
<h4 id="org04e638d"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orga6b5dad" class="outline-4">
<h4 id="orga6b5dad"><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-org72064c1" class="outline-4">
<h4 id="org72064c1"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org2f946b6" class="outline-4">
<h4 id="org2f946b6"><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-orgeb3c054" class="outline-4">
<h4 id="orgeb3c054"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org2ba3c92" class="outline-4">
<h4 id="org2ba3c92"><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-orgad5a323" class="outline-4">
<h4 id="orgad5a323"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orga1c595f" class="outline-4">
<h4 id="orga1c595f"><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-org38d753d" class="outline-4">
<h4 id="org38d753d"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org71fc885" class="outline-4">
<h4 id="org71fc885"><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-org1465f92" class="outline-5">
<h5 id="org1465f92"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org40badd0" class="outline-5">
<h5 id="org40badd0"><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-orgc4f3098" class="outline-5">
<h5 id="orgc4f3098"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org9083781" class="outline-5">
<h5 id="org9083781"><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-org6e82756" class="outline-4">
<h4 id="org6e82756"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org437f310" class="outline-4">
<h4 id="org437f310"><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-orgfbf12c8" class="outline-4">
<h4 id="orgfbf12c8"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-orgf5267a7" class="outline-4">
<h4 id="orgf5267a7"><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-org14be920" class="outline-3">
<h3 id="org14be920"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-orge519e69" class="outline-3">
<h3 id="orge519e69"><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-orgb2b2bd3" class="outline-4">
<h4 id="orgb2b2bd3"><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-orgb5ca49f" class="outline-4">
<h4 id="orgb5ca49f"><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-org6bb4413" class="outline-4">
<h4 id="org6bb4413"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org58beb35" class="outline-4">
<h4 id="org58beb35"><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-org8395667" class="outline-4">
<h4 id="org8395667"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org7d8c550" class="outline-4">
<h4 id="org7d8c550"><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-org2891a39" class="outline-4">
<h4 id="org2891a39"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org9d397d3" class="outline-4">
<h4 id="org9d397d3"><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-org44cfb64" class="outline-4">
<h4 id="org44cfb64"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-orgb5f5f1d" class="outline-4">
<h4 id="orgb5f5f1d"><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-orgf7de80e" class="outline-5">
<h5 id="orgf7de80e"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgb0b5297" class="outline-5">
<h5 id="orgb0b5297"><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-orgbd4b68b" class="outline-5">
<h5 id="orgbd4b68b"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-org5cc6c26" class="outline-5">
<h5 id="org5cc6c26"><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-org8871732" class="outline-4">
<h4 id="org8871732"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org1ea52fe" class="outline-4">
<h4 id="org1ea52fe"><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-orge07dc2d" class="outline-2">
<h2 id="orge07dc2d"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-orgfdec62c" class="outline-2">
<h2 id="orgfdec62c"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org19ecdb3" class="outline-3">
<h3 id="org19ecdb3"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org15a2aec" class="outline-3">
<h3 id="org15a2aec"><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: 2024-08-17 Sat 22:34</p>
<p class="date">Created: 2024-08-18 Sun 07:19</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 22:34 -->
<!-- 2024-08-18 Sun 07:19 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -406,7 +406,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-08-17 Sat 22:34</p>
<p class="date">Created: 2024-08-18 Sun 07:19</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 22:34 -->
<!-- 2024-08-18 Sun 07:19 -->
<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: 2024-08-17 Sat 22:34</p>
<p class="date">Created: 2024-08-18 Sun 07:19</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 22:34 -->
<!-- 2024-08-18 Sun 07:19 -->
<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="#orgee189c5">1. Format specification</a>
<li><a href="#orgae0a0f6">1. Format specification</a>
<ul>
<li><a href="#orge570b15">1.1. Organization of the data</a></li>
<li><a href="#orga470e14">1.2. Data types</a></li>
<li><a href="#org98a6365">1.1. Organization of the data</a></li>
<li><a href="#orge3e5304">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#orgdedc8b9">2. The TREXIO library</a>
<li><a href="#org2787b17">2. The TREXIO library</a>
<ul>
<li><a href="#org1996960">2.1. The front-end</a></li>
<li><a href="#orgf825927">2.2. The back-end</a></li>
<li><a href="#org970165d">2.3. Supported languages</a></li>
<li><a href="#org41b4064">2.4. Source code generation and documentation</a></li>
<li><a href="#org1e87d90">2.5. Availability</a></li>
<li><a href="#orgbfe2d0e">2.1. The front-end</a></li>
<li><a href="#orgc012ebb">2.2. The back-end</a></li>
<li><a href="#org5966222">2.3. Supported languages</a></li>
<li><a href="#org6ae05ca">2.4. Source code generation and documentation</a></li>
<li><a href="#orgf6265e5">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgee189c5" class="outline-2">
<h2 id="orgee189c5"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-orgae0a0f6" class="outline-2">
<h2 id="orgae0a0f6"><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-orge570b15" class="outline-3">
<h3 id="orge570b15"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org98a6365" class="outline-3">
<h3 id="org98a6365"><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-orga470e14" class="outline-3">
<h3 id="orga470e14"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-orge3e5304" class="outline-3">
<h3 id="orge3e5304"><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-orgdedc8b9" class="outline-2">
<h2 id="orgdedc8b9"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-org2787b17" class="outline-2">
<h2 id="org2787b17"><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-org1996960" class="outline-3">
<h3 id="org1996960"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orgbfe2d0e" class="outline-3">
<h3 id="orgbfe2d0e"><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-orgf825927" class="outline-3">
<h3 id="orgf825927"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-orgc012ebb" class="outline-3">
<h3 id="orgc012ebb"><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-org970165d" class="outline-3">
<h3 id="org970165d"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org5966222" class="outline-3">
<h3 id="org5966222"><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-org41b4064" class="outline-3">
<h3 id="org41b4064"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org6ae05ca" class="outline-3">
<h3 id="org6ae05ca"><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-org1e87d90" class="outline-3">
<h3 id="org1e87d90"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-orgf6265e5" class="outline-3">
<h3 id="orgf6265e5"><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: 2024-08-17 Sat 22:34</p>
<p class="date">Created: 2024-08-18 Sun 07:19</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>
<!-- 2024-08-17 Sat 22:34 -->
<!-- 2024-08-18 Sun 07:19 -->
<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="#orga347775">1. Template for HDF5 definitions</a></li>
<li><a href="#org18cdb4e">2. Template for HDF5 structures</a></li>
<li><a href="#orgfcd93ea">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgd58ed6a">4. Template for HDF5 has a group</a></li>
<li><a href="#org77489a8">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orge93db81">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org7a467ba">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgd36a2cb">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org6e555dc">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org97a047d">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgefd1425">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org58cb9bc">12. Source code for the determinant part</a></li>
<li><a href="#orgeea9d56">13. Helper functions</a></li>
<li><a href="#org9a4507e">1. Template for HDF5 definitions</a></li>
<li><a href="#org5bfb8c0">2. Template for HDF5 structures</a></li>
<li><a href="#org0891d79">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgef651c2">4. Template for HDF5 has a group</a></li>
<li><a href="#org93877fc">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org5479739">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org493f64b">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgc441be4">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org1dd70fd">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgadb3af0">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org5e472b8">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org9db6846">12. Source code for the determinant part</a></li>
<li><a href="#orge6dbb6a">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orga347775" class="outline-2">
<h2 id="orga347775"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org9a4507e" class="outline-2">
<h2 id="org9a4507e"><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-org18cdb4e" class="outline-2">
<h2 id="org18cdb4e"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org5bfb8c0" class="outline-2">
<h2 id="org5bfb8c0"><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-orgfcd93ea" class="outline-2">
<h2 id="orgfcd93ea"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org0891d79" class="outline-2">
<h2 id="org0891d79"><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-orgd58ed6a" class="outline-2">
<h2 id="orgd58ed6a"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orgef651c2" class="outline-2">
<h2 id="orgef651c2"><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-org77489a8" class="outline-2">
<h2 id="org77489a8"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org93877fc" class="outline-2">
<h2 id="org93877fc"><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-orge93db81" class="outline-2">
<h2 id="orge93db81"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org5479739" class="outline-2">
<h2 id="org5479739"><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-org7a467ba" class="outline-2">
<h2 id="org7a467ba"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org493f64b" class="outline-2">
<h2 id="org493f64b"><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-orgd36a2cb" class="outline-2">
<h2 id="orgd36a2cb"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-orgc441be4" class="outline-2">
<h2 id="orgc441be4"><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-org6e555dc" class="outline-2">
<h2 id="org6e555dc"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org1dd70fd" class="outline-2">
<h2 id="org1dd70fd"><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-org97a047d" class="outline-2">
<h2 id="org97a047d"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgadb3af0" class="outline-2">
<h2 id="orgadb3af0"><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-orgefd1425" class="outline-2">
<h2 id="orgefd1425"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org5e472b8" class="outline-2">
<h2 id="org5e472b8"><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-org58cb9bc" class="outline-2">
<h2 id="org58cb9bc"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org9db6846" class="outline-2">
<h2 id="org9db6846"><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-orgeea9d56" class="outline-2">
<h2 id="orgeea9d56"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orge6dbb6a" class="outline-2">
<h2 id="orge6dbb6a"><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: 2024-08-17 Sat 22:34</p>
<p class="date">Created: 2024-08-18 Sun 07:19</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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<title>TEXT back end</title>
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org777dba7">1. Template for group-related structures in text back end</a></li>
<li><a href="#org7d65493">2. Template for general structure in text back end</a></li>
<li><a href="#org571cc2c">3. Initialize function (constant part)</a></li>
<li><a href="#orgc404102">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgf76767f">5. Flush function (templated part)</a></li>
<li><a href="#org60578e2">6. Template for text read a group</a></li>
<li><a href="#org81e80c1">7. Template for text has a group</a></li>
<li><a href="#orgd62ecfa">8. Template for text flush a group</a></li>
<li><a href="#orgba58a3b">9. Template for text free memory</a></li>
<li><a href="#org8519ec2">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org839b28c">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org533e75b">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgdb53d01">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org9fd692f">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org61ab13f">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org96fb7fd">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgce057d8">17. Source code for the determinant part</a></li>
<li><a href="#orga606586">1. Template for group-related structures in text back end</a></li>
<li><a href="#org7b6646b">2. Template for general structure in text back end</a></li>
<li><a href="#org35e8976">3. Initialize function (constant part)</a></li>
<li><a href="#org8a92ec5">4. Deinitialize function (templated part)</a></li>
<li><a href="#org170d15f">5. Flush function (templated part)</a></li>
<li><a href="#orgabc1a69">6. Template for text read a group</a></li>
<li><a href="#org90be663">7. Template for text has a group</a></li>
<li><a href="#orgbdb6745">8. Template for text flush a group</a></li>
<li><a href="#orga10deb6">9. Template for text free memory</a></li>
<li><a href="#orga52bd92">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org5f6747c">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org3e13f86">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgc24e41a">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org9b08a69">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgabb0374">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org80804e1">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgfb4cdad">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-org777dba7" class="outline-2">
<h2 id="org777dba7"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orga606586" class="outline-2">
<h2 id="orga606586"><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-org7d65493" class="outline-2">
<h2 id="org7d65493"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org7b6646b" class="outline-2">
<h2 id="org7b6646b"><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-org571cc2c" class="outline-2">
<h2 id="org571cc2c"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org35e8976" class="outline-2">
<h2 id="org35e8976"><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-orgc404102" class="outline-2">
<h2 id="orgc404102"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org8a92ec5" class="outline-2">
<h2 id="org8a92ec5"><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-orgf76767f" class="outline-2">
<h2 id="orgf76767f"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org170d15f" class="outline-2">
<h2 id="org170d15f"><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-org60578e2" class="outline-2">
<h2 id="org60578e2"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orgabc1a69" class="outline-2">
<h2 id="orgabc1a69"><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-org81e80c1" class="outline-2">
<h2 id="org81e80c1"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org90be663" class="outline-2">
<h2 id="org90be663"><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-orgd62ecfa" class="outline-2">
<h2 id="orgd62ecfa"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-orgbdb6745" class="outline-2">
<h2 id="orgbdb6745"><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-orgba58a3b" class="outline-2">
<h2 id="orgba58a3b"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-orga10deb6" class="outline-2">
<h2 id="orga10deb6"><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-org8519ec2" class="outline-2">
<h2 id="org8519ec2"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orga52bd92" class="outline-2">
<h2 id="orga52bd92"><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-org839b28c" class="outline-2">
<h2 id="org839b28c"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org5f6747c" class="outline-2">
<h2 id="org5f6747c"><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-org533e75b" class="outline-2">
<h2 id="org533e75b"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org3e13f86" class="outline-2">
<h2 id="org3e13f86"><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-orgdb53d01" class="outline-2">
<h2 id="orgdb53d01"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orgc24e41a" class="outline-2">
<h2 id="orgc24e41a"><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-org9fd692f" class="outline-2">
<h2 id="org9fd692f"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org9b08a69" class="outline-2">
<h2 id="org9b08a69"><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-org61ab13f" class="outline-2">
<h2 id="org61ab13f"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-orgabb0374" class="outline-2">
<h2 id="orgabb0374"><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-org96fb7fd" class="outline-2">
<h2 id="org96fb7fd"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org80804e1" class="outline-2">
<h2 id="org80804e1"><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-orgce057d8" class="outline-2">
<h2 id="orgce057d8"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-orgfb4cdad" class="outline-2">
<h2 id="orgfb4cdad"><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: 2024-08-17 Sat 22:34</p>
<p class="date">Created: 2024-08-18 Sun 07:19</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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<head>
<!-- 2024-08-17 Sat 22:34 -->
<!-- 2024-08-18 Sun 07:19 -->
<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="#org4cdb392">1. Metadata (metadata group)</a></li>
<li><a href="#org286b347">2. System</a>
<li><a href="#org60b68bd">1. Metadata (metadata group)</a></li>
<li><a href="#orgf4ebc3f">2. System</a>
<ul>
<li><a href="#org67d1f12">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org3427164">2.2. Cell (cell group)</a></li>
<li><a href="#org65eef5e">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org0569fdf">2.4. Electron (electron group)</a></li>
<li><a href="#orge8e1efb">2.5. Ground or excited states (state group)</a></li>
<li><a href="#orge9bd170">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org48cff78">2.2. Cell (cell group)</a></li>
<li><a href="#org1a19300">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgd6b290c">2.4. Electron (electron group)</a></li>
<li><a href="#org2f3e9ff">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#orge869178">3. Basis functions</a>
<li><a href="#org9647358">3. Basis functions</a>
<ul>
<li><a href="#org39ec48f">3.1. Basis set (basis group)</a>
<li><a href="#orgc8d6c9e">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org1f428fa">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org5dfade1">3.1.2. Numerical orbitals</a></li>
<li><a href="#orge0e144a">3.1.3. Plane waves</a></li>
<li><a href="#org457d6fc">3.1.4. Oscillating orbitals</a></li>
<li><a href="#orge04bb6e">3.1.5. Data definitions</a></li>
<li><a href="#org30ad417">3.1.6. Example</a></li>
<li><a href="#orgeaaf4ee">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org68a8fbf">3.1.2. Numerical orbitals</a></li>
<li><a href="#org0d76324">3.1.3. Plane waves</a></li>
<li><a href="#org2a0d023">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org7c4e1bd">3.1.5. Data definitions</a></li>
<li><a href="#org0e03ff1">3.1.6. Example</a></li>
</ul>
</li>
<li><a href="#orgf5e76ee">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org8ee8d62">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org92fb84d">3.2.1. Example</a></li>
<li><a href="#orgd0fd1a6">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org27821eb">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org29663e9">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org0990aad">4. Orbitals</a>
<li><a href="#org64cba32">4. Orbitals</a>
<ul>
<li><a href="#org9d32bda">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org68eed98">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="#org9420bcf">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org7c8fa47">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org79a917f">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org7f01ecc">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgc2491fe">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgeca6f3d">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org3329317">5. Multi-determinant information</a>
<li><a href="#orgf2cd851">5. Multi-determinant information</a>
<ul>
<li><a href="#orgc8febdb">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org3c9cb78">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org75cae19">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org7e74614">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org1b76801">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgbc62c3a">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org139f642">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org1e58c6b">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#orga731208">6. Correlation factors</a>
<li><a href="#org0e13ef2">6. Correlation factors</a>
<ul>
<li><a href="#org12b1213">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#orgf729caf">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org25dd6f1">6.1.1. CHAMP</a></li>
<li><a href="#org15a66ea">6.1.2. Mu</a></li>
<li><a href="#orgfa50d7a">6.1.3. Table of values</a></li>
<li><a href="#orgbb4fcff">6.1.1. CHAMP</a></li>
<li><a href="#org4f150bb">6.1.2. Mu</a></li>
<li><a href="#orgd2f16f5">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org4c31c11">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org17d8bff">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-org4cdb392" class="outline-2">
<h2 id="org4cdb392"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org60b68bd" class="outline-2">
<h2 id="org60b68bd"><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="org45b0c1c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2dae8b0" 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-org286b347" class="outline-2">
<h2 id="org286b347"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-orgf4ebc3f" class="outline-2">
<h2 id="orgf4ebc3f"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org67d1f12" class="outline-3">
<h3 id="org67d1f12"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orge9bd170" class="outline-3">
<h3 id="orge9bd170"><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="orgbb2b621" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org149549f" 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-org3427164" class="outline-3">
<h3 id="org3427164"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org48cff78" class="outline-3">
<h3 id="org48cff78"><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="org1d6493e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org520745e" 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-org65eef5e" class="outline-3">
<h3 id="org65eef5e"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org1a19300" class="outline-3">
<h3 id="org1a19300"><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="orgb26b117" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org668bc83" 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-org0569fdf" class="outline-3">
<h3 id="org0569fdf"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-orgd6b290c" class="outline-3">
<h3 id="orgd6b290c"><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="orge43b88c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0533a24" 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-orge8e1efb" class="outline-3">
<h3 id="orge8e1efb"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org2f3e9ff" class="outline-3">
<h3 id="org2f3e9ff"><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="orgabcb0e9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2fe2001" 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-orge869178" class="outline-2">
<h2 id="orge869178"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org9647358" class="outline-2">
<h2 id="org9647358"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org39ec48f" class="outline-3">
<h3 id="org39ec48f"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-orgc8d6c9e" class="outline-3">
<h3 id="orgc8d6c9e"><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-org1f428fa" class="outline-4">
<h4 id="org1f428fa"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-orgeaaf4ee" class="outline-4">
<h4 id="orgeaaf4ee"><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
@ -1019,8 +1019,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-org5dfade1" class="outline-4">
<h4 id="org5dfade1"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-org68a8fbf" class="outline-4">
<h4 id="org68a8fbf"><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-orge0e144a" class="outline-4">
<h4 id="orge0e144a"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-org0d76324" class="outline-4">
<h4 id="org0d76324"><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-org457d6fc" class="outline-4">
<h4 id="org457d6fc"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div id="outline-container-org2a0d023" class="outline-4">
<h4 id="org2a0d023"><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-orge04bb6e" class="outline-4">
<h4 id="orge04bb6e"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div id="outline-container-org7c4e1bd" class="outline-4">
<h4 id="org7c4e1bd"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-5">
<table id="org062843d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0eae3ae" 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-org30ad417" class="outline-4">
<h4 id="org30ad417"><span class="section-number-4">3.1.6</span> Example</h4>
<div id="outline-container-org0e03ff1" class="outline-4">
<h4 id="org0e03ff1"><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-orgf5e76ee" class="outline-3">
<h3 id="orgf5e76ee"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org8ee8d62" class="outline-3">
<h3 id="org8ee8d62"><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="org2b3e167" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9415df6" 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-org92fb84d" class="outline-4">
<h4 id="org92fb84d"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orgd0fd1a6" class="outline-4">
<h4 id="orgd0fd1a6"><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-org27821eb" class="outline-3">
<h3 id="org27821eb"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org29663e9" class="outline-3">
<h3 id="org29663e9"><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="org9a1e86b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc174b20" 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-org0990aad" class="outline-2">
<h2 id="org0990aad"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org64cba32" class="outline-2">
<h2 id="org64cba32"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org9d32bda" class="outline-3">
<h3 id="org9d32bda"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org68eed98" class="outline-3">
<h3 id="org68eed98"><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
@ -1912,7 +1912,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="org5d9a840" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga36a0a5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1971,7 +1971,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org116b250" class="outline-4">
<div id="outline-container-org82e4d0d" 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">
@ -1989,7 +1989,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org3fc29f3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0620fb8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2097,7 +2097,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org3dec393" class="outline-4">
<div id="outline-container-orgf6bf24d" 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>
@ -2123,7 +2123,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org6bbd3e8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfd22c33" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2200,10 +2200,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org9420bcf" class="outline-3">
<h3 id="org9420bcf"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org7c8fa47" class="outline-3">
<h3 id="org7c8fa47"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="orgdd16ab2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbe9d043" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2319,8 +2319,8 @@ is the number of spin-orbitals, twice the number of spatial orbitals.
</div>
<div id="outline-container-org79a917f" class="outline-4">
<h4 id="org79a917f"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-orgc2491fe" class="outline-4">
<h4 id="orgc2491fe"><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
@ -2328,7 +2328,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgd787b6c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgeb9e898" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2436,8 +2436,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org7f01ecc" class="outline-4">
<h4 id="org7f01ecc"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-orgeca6f3d" class="outline-4">
<h4 id="orgeca6f3d"><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
@ -2445,7 +2445,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org480b397" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0120ed9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2523,12 +2523,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org3329317" class="outline-2">
<h2 id="org3329317"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-orgf2cd851" class="outline-2">
<h2 id="orgf2cd851"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-orgc8febdb" class="outline-3">
<h3 id="orgc8febdb"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org1b76801" class="outline-3">
<h3 id="org1b76801"><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 \(\Psi\)
@ -2570,7 +2570,7 @@ 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="orgc5a6cd5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org67c6a4c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2622,8 +2622,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org3c9cb78" class="outline-3">
<h3 id="org3c9cb78"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-orgbc62c3a" class="outline-3">
<h3 id="orgbc62c3a"><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
@ -2645,7 +2645,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org1355184" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc474878" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2697,8 +2697,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org75cae19" class="outline-3">
<h3 id="org75cae19"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org139f642" class="outline-3">
<h3 id="org139f642"><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
@ -2769,7 +2769,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org0c79740" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0ffb43e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2861,8 +2861,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-org7e74614" class="outline-3">
<h3 id="org7e74614"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org1e58c6b" class="outline-3">
<h3 id="org1e58c6b"><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
@ -2934,7 +2934,7 @@ 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="orgfe8f5e5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org66dd505" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3099,12 +3099,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-orga731208" class="outline-2">
<h2 id="orga731208"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org0e13ef2" class="outline-2">
<h2 id="org0e13ef2"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org12b1213" class="outline-3">
<h3 id="org12b1213"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-orgf729caf" class="outline-3">
<h3 id="orgf729caf"><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
@ -3129,8 +3129,8 @@ following:
</ul>
</div>
<div id="outline-container-org25dd6f1" class="outline-4">
<h4 id="org25dd6f1"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orgbb4fcff" class="outline-4">
<h4 id="orgbb4fcff"><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
@ -3231,8 +3231,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-org15a66ea" class="outline-4">
<h4 id="org15a66ea"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org4f150bb" class="outline-4">
<h4 id="org4f150bb"><span class="section-number-4">6.1.2</span> Mu</h4>
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<p>
<a href="https://aip.scitation.org/doi/10.1063/5.0044683">Mu-Jastrow</a> is based on a one-parameter correlation factor that has
@ -3329,10 +3329,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h4 id="orgfa50d7a"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="orgd2f16f5"><span class="section-number-4">6.1.3</span> Table of values</h4>
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@ -3450,8 +3450,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h2 id="org4c31c11"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org17d8bff"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -3465,7 +3465,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3527,7 +3527,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
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<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-08-17 Sat 22:34</p>
<p class="date">Created: 2024-08-18 Sun 07:19</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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