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README.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -406,7 +406,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-08-17 Sat 18:03</p>
<p class="date">Created: 2024-08-17 Sat 18:21</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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<head>
<!-- 2024-08-17 Sat 18:03 -->
<!-- 2024-08-17 Sat 18:21 -->
<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="#org5a6539d">1. Writing nuclear coordinates</a>
<li><a href="#org9f3c0e6">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orga2702f2">1.1. C</a></li>
<li><a href="#orgce38555">1.2. Python</a></li>
<li><a href="#orgd6970e4">1.3. Fortran</a></li>
<li><a href="#orgd2e3fd2">1.1. C</a></li>
<li><a href="#org4bb9499">1.2. Python</a></li>
<li><a href="#org0088cb4">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#orgd164193">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org035e7d1">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#orgd54c3f3">2.1. Fortran</a>
<li><a href="#org58d5781">2.1. Fortran</a>
<ul>
<li><a href="#org47472fd">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgad076e7">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgf058bbb">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org954259f">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org70d55c6">2.1.5. Allocate memory</a></li>
<li><a href="#orgc7e2240">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org4997dfb">2.1.7. Read two-electron quantities</a>
<li><a href="#org0d5d44e">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org8f453eb">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org33e3268">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgbe44bae">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgb736c13">2.1.5. Allocate memory</a></li>
<li><a href="#org2b06b02">2.1.6. Read one-electron quantities</a></li>
<li><a href="#orgd06fe7e">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org607d6f2">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org39e4da1">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org619cd89">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orga37d07c">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org3ffac99">2.1.8. Compute the energy</a></li>
<li><a href="#org1893cbe">2.1.9. Terminate</a></li>
<li><a href="#org71c12b6">2.1.8. Compute the energy</a></li>
<li><a href="#orge07a2f2">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org14fc077">2.2. Python</a>
<li><a href="#org1d8a06f">2.2. Python</a>
<ul>
<li><a href="#org6ae597d">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org1c4d40f">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org39aae0f">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org6db07f6">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgdade61b">2.2.5. Read two-electron quantities</a>
<li><a href="#org608846d">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org10c4902">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#orgb439855">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org142a76f">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgf1911a9">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#org1ac9d5b">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org1bfeb6b">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#orgc0371c9">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org5ba8d2e">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org83bf4fb">2.2.6. Compute the energy</a></li>
<li><a href="#org5474e67">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgf6cbb98">3. Reading determinants</a>
<li><a href="#orgf41087c">3. Reading determinants</a>
<ul>
<li><a href="#org0df1027">3.1. Fortran</a></li>
<li><a href="#orgc84206d">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org5a6539d" class="outline-2">
<h2 id="org5a6539d"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org9f3c0e6" class="outline-2">
<h2 id="org9f3c0e6"><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-orga2702f2" class="outline-3">
<h3 id="orga2702f2"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-orgd2e3fd2" class="outline-3">
<h3 id="orgd2e3fd2"><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-orgce38555" class="outline-3">
<h3 id="orgce38555"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org4bb9499" class="outline-3">
<h3 id="org4bb9499"><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-orgd6970e4" class="outline-3">
<h3 id="orgd6970e4"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-org0088cb4" class="outline-3">
<h3 id="org0088cb4"><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-orgd164193" class="outline-2">
<h2 id="orgd164193"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org035e7d1" class="outline-2">
<h2 id="org035e7d1"><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-orgd54c3f3" class="outline-3">
<h3 id="orgd54c3f3"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org58d5781" class="outline-3">
<h3 id="org58d5781"><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-org47472fd" class="outline-4">
<h4 id="org47472fd"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org0d5d44e" class="outline-4">
<h4 id="org0d5d44e"><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-orgad076e7" class="outline-4">
<h4 id="orgad076e7"><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-org8f453eb" class="outline-4">
<h4 id="org8f453eb"><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-orgf058bbb" class="outline-4">
<h4 id="orgf058bbb"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org33e3268" class="outline-4">
<h4 id="org33e3268"><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-org954259f" class="outline-4">
<h4 id="org954259f"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgbe44bae" class="outline-4">
<h4 id="orgbe44bae"><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-org70d55c6" class="outline-4">
<h4 id="org70d55c6"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-orgb736c13" class="outline-4">
<h4 id="orgb736c13"><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-orgc7e2240" class="outline-4">
<h4 id="orgc7e2240"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org2b06b02" class="outline-4">
<h4 id="org2b06b02"><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-org4997dfb" class="outline-4">
<h4 id="org4997dfb"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgd06fe7e" class="outline-4">
<h4 id="orgd06fe7e"><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-org607d6f2" class="outline-5">
<h5 id="org607d6f2"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org619cd89" class="outline-5">
<h5 id="org619cd89"><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-org39e4da1" class="outline-5">
<h5 id="org39e4da1"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orga37d07c" class="outline-5">
<h5 id="orga37d07c"><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-org3ffac99" class="outline-4">
<h4 id="org3ffac99"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org71c12b6" class="outline-4">
<h4 id="org71c12b6"><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-org1893cbe" class="outline-4">
<h4 id="org1893cbe"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-orge07a2f2" class="outline-4">
<h4 id="orge07a2f2"><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-org14fc077" class="outline-3">
<h3 id="org14fc077"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org1d8a06f" class="outline-3">
<h3 id="org1d8a06f"><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-org6ae597d" class="outline-4">
<h4 id="org6ae597d"><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-org608846d" class="outline-4">
<h4 id="org608846d"><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-org1c4d40f" class="outline-4">
<h4 id="org1c4d40f"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org10c4902" class="outline-4">
<h4 id="org10c4902"><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-org39aae0f" class="outline-4">
<h4 id="org39aae0f"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgb439855" class="outline-4">
<h4 id="orgb439855"><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-org6db07f6" class="outline-4">
<h4 id="org6db07f6"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org142a76f" class="outline-4">
<h4 id="org142a76f"><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-orgdade61b" class="outline-4">
<h4 id="orgdade61b"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-orgf1911a9" class="outline-4">
<h4 id="orgf1911a9"><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-org1ac9d5b" class="outline-5">
<h5 id="org1ac9d5b"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgc0371c9" class="outline-5">
<h5 id="orgc0371c9"><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-org1bfeb6b" class="outline-5">
<h5 id="org1bfeb6b"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-org5ba8d2e" class="outline-5">
<h5 id="org5ba8d2e"><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-org83bf4fb" class="outline-4">
<h4 id="org83bf4fb"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org5474e67" class="outline-4">
<h4 id="org5474e67"><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-orgf6cbb98" class="outline-2">
<h2 id="orgf6cbb98"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-orgf41087c" class="outline-2">
<h2 id="orgf41087c"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org0df1027" class="outline-3">
<h3 id="org0df1027"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-orgc84206d" class="outline-3">
<h3 id="orgc84206d"><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 18:03</p>
<p class="date">Created: 2024-08-17 Sat 18:21</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 18:03 -->
<!-- 2024-08-17 Sat 18:21 -->
<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 18:03</p>
<p class="date">Created: 2024-08-17 Sat 18:21</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 18:03 -->
<!-- 2024-08-17 Sat 18:21 -->
<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 18:03</p>
<p class="date">Created: 2024-08-17 Sat 18:21</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 18:03 -->
<!-- 2024-08-17 Sat 18:21 -->
<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="#org8162f66">1. Format specification</a>
<li><a href="#org4872fac">1. Format specification</a>
<ul>
<li><a href="#orgf8ad9e0">1.1. Organization of the data</a></li>
<li><a href="#orgbdd8e48">1.2. Data types</a></li>
<li><a href="#org9ab2355">1.1. Organization of the data</a></li>
<li><a href="#org3bfeeab">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org834b1e6">2. The TREXIO library</a>
<li><a href="#orgee682df">2. The TREXIO library</a>
<ul>
<li><a href="#org2e15c75">2.1. The front-end</a></li>
<li><a href="#org00c029e">2.2. The back-end</a></li>
<li><a href="#org6cc6c19">2.3. Supported languages</a></li>
<li><a href="#orgbde06bf">2.4. Source code generation and documentation</a></li>
<li><a href="#org336ff50">2.5. Availability</a></li>
<li><a href="#org0dc8d98">2.1. The front-end</a></li>
<li><a href="#org555ea09">2.2. The back-end</a></li>
<li><a href="#org17b9c0a">2.3. Supported languages</a></li>
<li><a href="#orgc33801d">2.4. Source code generation and documentation</a></li>
<li><a href="#org6d3def6">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org8162f66" class="outline-2">
<h2 id="org8162f66"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org4872fac" class="outline-2">
<h2 id="org4872fac"><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-orgf8ad9e0" class="outline-3">
<h3 id="orgf8ad9e0"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org9ab2355" class="outline-3">
<h3 id="org9ab2355"><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-orgbdd8e48" class="outline-3">
<h3 id="orgbdd8e48"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org3bfeeab" class="outline-3">
<h3 id="org3bfeeab"><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-org834b1e6" class="outline-2">
<h2 id="org834b1e6"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orgee682df" class="outline-2">
<h2 id="orgee682df"><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-org2e15c75" class="outline-3">
<h3 id="org2e15c75"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-org0dc8d98" class="outline-3">
<h3 id="org0dc8d98"><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-org00c029e" class="outline-3">
<h3 id="org00c029e"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-org555ea09" class="outline-3">
<h3 id="org555ea09"><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-org6cc6c19" class="outline-3">
<h3 id="org6cc6c19"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org17b9c0a" class="outline-3">
<h3 id="org17b9c0a"><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-orgbde06bf" class="outline-3">
<h3 id="orgbde06bf"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-orgc33801d" class="outline-3">
<h3 id="orgc33801d"><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-org336ff50" class="outline-3">
<h3 id="org336ff50"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org6d3def6" class="outline-3">
<h3 id="org6d3def6"><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 18:03</p>
<p class="date">Created: 2024-08-17 Sat 18:21</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 18:03 -->
<!-- 2024-08-17 Sat 18:21 -->
<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="#orgf5141a1">1. Template for HDF5 definitions</a></li>
<li><a href="#org1a0fb71">2. Template for HDF5 structures</a></li>
<li><a href="#org392171f">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgef41d6e">4. Template for HDF5 has a group</a></li>
<li><a href="#org9ea785c">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org8405a77">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org91ca8cd">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org9e9afe1">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org67e0005">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgc8fabe5">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgc791435">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org43d799e">12. Source code for the determinant part</a></li>
<li><a href="#org279afff">13. Helper functions</a></li>
<li><a href="#orgbcb3727">1. Template for HDF5 definitions</a></li>
<li><a href="#orgd42b60c">2. Template for HDF5 structures</a></li>
<li><a href="#org1a054c0">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orge11fbb8">4. Template for HDF5 has a group</a></li>
<li><a href="#orgd20ef17">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org10010b7">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgc642f19">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org0273e32">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orge031f61">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orge5eaaa6">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org3ba3747">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orga7200ba">12. Source code for the determinant part</a></li>
<li><a href="#org616e8cd">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgf5141a1" class="outline-2">
<h2 id="orgf5141a1"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orgbcb3727" class="outline-2">
<h2 id="orgbcb3727"><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-org1a0fb71" class="outline-2">
<h2 id="org1a0fb71"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgd42b60c" class="outline-2">
<h2 id="orgd42b60c"><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-org392171f" class="outline-2">
<h2 id="org392171f"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org1a054c0" class="outline-2">
<h2 id="org1a054c0"><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-orgef41d6e" class="outline-2">
<h2 id="orgef41d6e"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orge11fbb8" class="outline-2">
<h2 id="orge11fbb8"><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-org9ea785c" class="outline-2">
<h2 id="org9ea785c"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orgd20ef17" class="outline-2">
<h2 id="orgd20ef17"><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-org8405a77" class="outline-2">
<h2 id="org8405a77"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org10010b7" class="outline-2">
<h2 id="org10010b7"><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-org91ca8cd" class="outline-2">
<h2 id="org91ca8cd"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orgc642f19" class="outline-2">
<h2 id="orgc642f19"><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-org9e9afe1" class="outline-2">
<h2 id="org9e9afe1"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org0273e32" class="outline-2">
<h2 id="org0273e32"><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-org67e0005" class="outline-2">
<h2 id="org67e0005"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orge031f61" class="outline-2">
<h2 id="orge031f61"><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-orgc8fabe5" class="outline-2">
<h2 id="orgc8fabe5"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orge5eaaa6" class="outline-2">
<h2 id="orge5eaaa6"><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-orgc791435" class="outline-2">
<h2 id="orgc791435"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org3ba3747" class="outline-2">
<h2 id="org3ba3747"><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-org43d799e" class="outline-2">
<h2 id="org43d799e"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-orga7200ba" class="outline-2">
<h2 id="orga7200ba"><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-org279afff" class="outline-2">
<h2 id="org279afff"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org616e8cd" class="outline-2">
<h2 id="org616e8cd"><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 18:03</p>
<p class="date">Created: 2024-08-17 Sat 18:21</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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<head>
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>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="#orge659216">1. Template for group-related structures in text back end</a></li>
<li><a href="#org6f12885">2. Template for general structure in text back end</a></li>
<li><a href="#org4b01cb8">3. Initialize function (constant part)</a></li>
<li><a href="#orge48217d">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgaf9a832">5. Flush function (templated part)</a></li>
<li><a href="#orgb61391d">6. Template for text read a group</a></li>
<li><a href="#orgcf672ab">7. Template for text has a group</a></li>
<li><a href="#orgc02e253">8. Template for text flush a group</a></li>
<li><a href="#org3293594">9. Template for text free memory</a></li>
<li><a href="#orga9cd313">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgf875e42">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgeb998c8">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgc6258e1">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org76b515e">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org6a85ab2">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org34c32fc">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orge7007de">17. Source code for the determinant part</a></li>
<li><a href="#org27d6043">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgc27da88">2. Template for general structure in text back end</a></li>
<li><a href="#org29b947e">3. Initialize function (constant part)</a></li>
<li><a href="#org31463c8">4. Deinitialize function (templated part)</a></li>
<li><a href="#org852beab">5. Flush function (templated part)</a></li>
<li><a href="#org271620b">6. Template for text read a group</a></li>
<li><a href="#org3896045">7. Template for text has a group</a></li>
<li><a href="#org7798ea5">8. Template for text flush a group</a></li>
<li><a href="#org54ec02b">9. Template for text free memory</a></li>
<li><a href="#org86d8fa9">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgfc5e407">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org7d65f11">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgd664e35">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orga629e09">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org1ad2544">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgc610051">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org4f81bfa">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-orge659216" class="outline-2">
<h2 id="orge659216"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org27d6043" class="outline-2">
<h2 id="org27d6043"><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-org6f12885" class="outline-2">
<h2 id="org6f12885"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgc27da88" class="outline-2">
<h2 id="orgc27da88"><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-org4b01cb8" class="outline-2">
<h2 id="org4b01cb8"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org29b947e" class="outline-2">
<h2 id="org29b947e"><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-orge48217d" class="outline-2">
<h2 id="orge48217d"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org31463c8" class="outline-2">
<h2 id="org31463c8"><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-orgaf9a832" class="outline-2">
<h2 id="orgaf9a832"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org852beab" class="outline-2">
<h2 id="org852beab"><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-orgb61391d" class="outline-2">
<h2 id="orgb61391d"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org271620b" class="outline-2">
<h2 id="org271620b"><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-orgcf672ab" class="outline-2">
<h2 id="orgcf672ab"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org3896045" class="outline-2">
<h2 id="org3896045"><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-orgc02e253" class="outline-2">
<h2 id="orgc02e253"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org7798ea5" class="outline-2">
<h2 id="org7798ea5"><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-org3293594" class="outline-2">
<h2 id="org3293594"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org54ec02b" class="outline-2">
<h2 id="org54ec02b"><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-orga9cd313" class="outline-2">
<h2 id="orga9cd313"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org86d8fa9" class="outline-2">
<h2 id="org86d8fa9"><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-orgf875e42" class="outline-2">
<h2 id="orgf875e42"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgfc5e407" class="outline-2">
<h2 id="orgfc5e407"><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-orgeb998c8" class="outline-2">
<h2 id="orgeb998c8"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org7d65f11" class="outline-2">
<h2 id="org7d65f11"><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-orgc6258e1" class="outline-2">
<h2 id="orgc6258e1"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orgd664e35" class="outline-2">
<h2 id="orgd664e35"><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-org76b515e" class="outline-2">
<h2 id="org76b515e"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orga629e09" class="outline-2">
<h2 id="orga629e09"><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-org6a85ab2" class="outline-2">
<h2 id="org6a85ab2"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org1ad2544" class="outline-2">
<h2 id="org1ad2544"><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-org34c32fc" class="outline-2">
<h2 id="org34c32fc"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgc610051" class="outline-2">
<h2 id="orgc610051"><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-orge7007de" class="outline-2">
<h2 id="orge7007de"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org4f81bfa" class="outline-2">
<h2 id="org4f81bfa"><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 18:03</p>
<p class="date">Created: 2024-08-17 Sat 18:21</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2024-08-17 Sat 18:03 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>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="#org94caca2">1. Metadata (metadata group)</a></li>
<li><a href="#orgeb7de11">2. System</a>
<li><a href="#org8a4975a">1. Metadata (metadata group)</a></li>
<li><a href="#org50fb2b5">2. System</a>
<ul>
<li><a href="#orgb9ee81c">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org2d8b0fe">2.2. Cell (cell group)</a></li>
<li><a href="#org4a04a42">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org4d73644">2.4. Electron (electron group)</a></li>
<li><a href="#org60065c0">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org4b9311a">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org167de68">2.2. Cell (cell group)</a></li>
<li><a href="#org0822385">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org1ffe785">2.4. Electron (electron group)</a></li>
<li><a href="#org6218718">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org39077fc">3. Basis functions</a>
<li><a href="#orgaed65e6">3. Basis functions</a>
<ul>
<li><a href="#orgfdf7c85">3.1. Basis set (basis group)</a>
<li><a href="#org1df82ba">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orgb9f5fb7">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org7c972ca">3.1.2. Numerical orbitals</a></li>
<li><a href="#org9dce27e">3.1.3. Plane waves</a></li>
<li><a href="#org6292747">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org2019d8d">3.1.5. Data definitions</a></li>
<li><a href="#org825ec5c">3.1.6. Example</a></li>
<li><a href="#orgdcc1e52">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org23c313c">3.1.2. Numerical orbitals</a></li>
<li><a href="#org8abc728">3.1.3. Plane waves</a></li>
<li><a href="#org0f623f8">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org3d0f3ce">3.1.5. Data definitions</a></li>
<li><a href="#org4fa80fb">3.1.6. Example</a></li>
</ul>
</li>
<li><a href="#org70a3f5e">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org129015e">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org29be9f3">3.2.1. Example</a></li>
<li><a href="#orgc022dd0">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#orgab4b16d">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org6e097d0">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#orgc10e12e">4. Orbitals</a>
<li><a href="#orge30ffe2">4. Orbitals</a>
<ul>
<li><a href="#org7fdefc6">4.1. Atomic orbitals (ao group)</a>
<li><a href="#orged04750">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="#org81b7f6d">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org4a7c23e">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org3f03e58">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org474d5b2">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orge5defd6">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org6021e9f">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgd190335">5. Multi-determinant information</a>
<li><a href="#orgd4b11f2">5. Multi-determinant information</a>
<ul>
<li><a href="#org19a3330">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org45ebe7e">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org7e75a15">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org185e834">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgf292756">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org1c4d9a6">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orge613877">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org475bc52">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#orge1bedc3">6. Correlation factors</a>
<li><a href="#org0f7499f">6. Correlation factors</a>
<ul>
<li><a href="#orgca118e3">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org667d1ea">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org68746d1">6.1.1. CHAMP</a></li>
<li><a href="#org4e24d13">6.1.2. Mu</a></li>
<li><a href="#org40ef2c2">6.1.3. Table of values</a></li>
<li><a href="#org1d4ce4c">6.1.1. CHAMP</a></li>
<li><a href="#org8d7f208">6.1.2. Mu</a></li>
<li><a href="#orge2f046d">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org5343b08">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org9bd95de">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-org94caca2" class="outline-2">
<h2 id="org94caca2"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org8a4975a" class="outline-2">
<h2 id="org8a4975a"><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="org9f5b350" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org28459d5" 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-orgeb7de11" class="outline-2">
<h2 id="orgeb7de11"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org50fb2b5" class="outline-2">
<h2 id="org50fb2b5"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgb9ee81c" class="outline-3">
<h3 id="orgb9ee81c"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org4b9311a" class="outline-3">
<h3 id="org4b9311a"><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="org523db2c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org27fd4e6" 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-org2d8b0fe" class="outline-3">
<h3 id="org2d8b0fe"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org167de68" class="outline-3">
<h3 id="org167de68"><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="org7e2e0ae" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4cd8f9d" 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-org4a04a42" class="outline-3">
<h3 id="org4a04a42"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org0822385" class="outline-3">
<h3 id="org0822385"><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="org5956aa2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf63e602" 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-org4d73644" class="outline-3">
<h3 id="org4d73644"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org1ffe785" class="outline-3">
<h3 id="org1ffe785"><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="org650c9c6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org76304b6" 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-org60065c0" class="outline-3">
<h3 id="org60065c0"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org6218718" class="outline-3">
<h3 id="org6218718"><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="org63a1079" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7ee52e7" 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-org39077fc" class="outline-2">
<h2 id="org39077fc"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-orgaed65e6" class="outline-2">
<h2 id="orgaed65e6"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgfdf7c85" class="outline-3">
<h3 id="orgfdf7c85"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org1df82ba" class="outline-3">
<h3 id="org1df82ba"><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-orgb9f5fb7" class="outline-4">
<h4 id="orgb9f5fb7"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-orgdcc1e52" class="outline-4">
<h4 id="orgdcc1e52"><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-org7c972ca" class="outline-4">
<h4 id="org7c972ca"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-org23c313c" class="outline-4">
<h4 id="org23c313c"><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-org9dce27e" class="outline-4">
<h4 id="org9dce27e"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-org8abc728" class="outline-4">
<h4 id="org8abc728"><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-org6292747" class="outline-4">
<h4 id="org6292747"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div id="outline-container-org0f623f8" class="outline-4">
<h4 id="org0f623f8"><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-org2019d8d" class="outline-4">
<h4 id="org2019d8d"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div id="outline-container-org3d0f3ce" class="outline-4">
<h4 id="org3d0f3ce"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-5">
<table id="org8b49718" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgac3de75" 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-org825ec5c" class="outline-4">
<h4 id="org825ec5c"><span class="section-number-4">3.1.6</span> Example</h4>
<div id="outline-container-org4fa80fb" class="outline-4">
<h4 id="org4fa80fb"><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-org70a3f5e" class="outline-3">
<h3 id="org70a3f5e"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org129015e" class="outline-3">
<h3 id="org129015e"><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="org5a5856e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgde3808f" 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-org29be9f3" class="outline-4">
<h4 id="org29be9f3"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orgc022dd0" class="outline-4">
<h4 id="orgc022dd0"><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-orgab4b16d" class="outline-3">
<h3 id="orgab4b16d"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org6e097d0" class="outline-3">
<h3 id="org6e097d0"><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="org5dcdd22" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org65c490f" 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-orgc10e12e" class="outline-2">
<h2 id="orgc10e12e"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-orge30ffe2" class="outline-2">
<h2 id="orge30ffe2"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org7fdefc6" class="outline-3">
<h3 id="org7fdefc6"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-orged04750" class="outline-3">
<h3 id="orged04750"><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="orgd681f8f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf481049" 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-orgda88468" class="outline-4">
<div id="outline-container-orgedb4eef" 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="orgf09de71" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb116b53" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2097,7 +2097,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org916a03d" class="outline-4">
<div id="outline-container-org7955ff9" 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="orgbb4852b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbca30c4" 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-org81b7f6d" class="outline-3">
<h3 id="org81b7f6d"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org4a7c23e" class="outline-3">
<h3 id="org4a7c23e"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="orgf9c84b8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org85b21a9" 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-org3f03e58" class="outline-4">
<h4 id="org3f03e58"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-orge5defd6" class="outline-4">
<h4 id="orge5defd6"><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="org0dc121b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5d96b7d" 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-org474d5b2" class="outline-4">
<h4 id="org474d5b2"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org6021e9f" class="outline-4">
<h4 id="org6021e9f"><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="orgd77fb01" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3b4fef0" 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-orgd190335" class="outline-2">
<h2 id="orgd190335"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-orgd4b11f2" class="outline-2">
<h2 id="orgd4b11f2"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org19a3330" class="outline-3">
<h3 id="org19a3330"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-orgf292756" class="outline-3">
<h3 id="orgf292756"><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="org27790e0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdaf23a6" 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-org45ebe7e" class="outline-3">
<h3 id="org45ebe7e"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org1c4d9a6" class="outline-3">
<h3 id="org1c4d9a6"><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="org129effe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgab3575f" 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-org7e75a15" class="outline-3">
<h3 id="org7e75a15"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orge613877" class="outline-3">
<h3 id="orge613877"><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="org2b483c8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8d70817" 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-org185e834" class="outline-3">
<h3 id="org185e834"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org475bc52" class="outline-3">
<h3 id="org475bc52"><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="org31894d0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org64783ab" 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-orge1bedc3" class="outline-2">
<h2 id="orge1bedc3"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org0f7499f" class="outline-2">
<h2 id="org0f7499f"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-orgca118e3" class="outline-3">
<h3 id="orgca118e3"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org667d1ea" class="outline-3">
<h3 id="org667d1ea"><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-org68746d1" class="outline-4">
<h4 id="org68746d1"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org1d4ce4c" class="outline-4">
<h4 id="org1d4ce4c"><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-org4e24d13" class="outline-4">
<h4 id="org4e24d13"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org8d7f208" class="outline-4">
<h4 id="org8d7f208"><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="org40ef2c2"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="orge2f046d"><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="org5343b08"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org9bd95de"><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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<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-08-17 Sat 18:03</p>
<p class="date">Created: 2024-08-17 Sat 18:21</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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