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README.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>
<!-- 2024-08-10 Sat 15:35 -->
<!-- 2024-08-17 Sat 16:23 -->
<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: 2024-08-10 Sat 15:35</p>
<p class="date">Created: 2024-08-17 Sat 16:23</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>
<!-- 2024-08-10 Sat 15:35 -->
<!-- 2024-08-17 Sat 16:23 -->
<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="#org9bedbcb">1. Writing nuclear coordinates</a>
<li><a href="#org9e06a8b">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orgf06b480">1.1. C</a></li>
<li><a href="#org1c3e97c">1.2. Python</a></li>
<li><a href="#orga3910a3">1.3. Fortran</a></li>
<li><a href="#orgb878a43">1.1. C</a></li>
<li><a href="#org0e7711e">1.2. Python</a></li>
<li><a href="#orgd0d1181">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org9c6a236">2. Accessing sparse quantities (integrals)</a>
<li><a href="#orgbe645f3">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#orga02c846">2.1. Fortran</a>
<li><a href="#org567acb9">2.1. Fortran</a>
<ul>
<li><a href="#org7b9d693">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgcf5f86e">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org29b3e83">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org4323909">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgae95088">2.1.5. Allocate memory</a></li>
<li><a href="#org87346d6">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org7b5e4dd">2.1.7. Read two-electron quantities</a>
<li><a href="#orge6c947d">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org45b03e3">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org1e27d72">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org34f8a20">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgfa3088e">2.1.5. Allocate memory</a></li>
<li><a href="#org46e3a0b">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org72bde0f">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org838b667">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgf514305">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org1eea73e">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org4ef2c3f">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org9a1bb40">2.1.8. Compute the energy</a></li>
<li><a href="#org730108c">2.1.9. Terminate</a></li>
<li><a href="#org4b66373">2.1.8. Compute the energy</a></li>
<li><a href="#orge88e608">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org7ea1dc9">2.2. Python</a>
<li><a href="#org26ca29b">2.2. Python</a>
<ul>
<li><a href="#orgc9d9f60">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org32b1602">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org6097f3f">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#orgbc7f55b">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgbdd2fb5">2.2.5. Read two-electron quantities</a>
<li><a href="#org291ae5e">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga5bf50b">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#orgc7d6dd7">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org88e458e">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgff1bb69">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#org3b2c346">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org7239d84">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#orgc09d3cf">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgbc13001">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org24e7691">2.2.6. Compute the energy</a></li>
<li><a href="#org2f11685">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org145358b">3. Reading determinants</a>
<li><a href="#orgfab9d63">3. Reading determinants</a>
<ul>
<li><a href="#orgdc3ebe2">3.1. Fortran</a></li>
<li><a href="#orgc75816f">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org9bedbcb" class="outline-2">
<h2 id="org9bedbcb"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org9e06a8b" class="outline-2">
<h2 id="org9e06a8b"><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-orgf06b480" class="outline-3">
<h3 id="orgf06b480"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-orgb878a43" class="outline-3">
<h3 id="orgb878a43"><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-org1c3e97c" class="outline-3">
<h3 id="org1c3e97c"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org0e7711e" class="outline-3">
<h3 id="org0e7711e"><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-orga3910a3" class="outline-3">
<h3 id="orga3910a3"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orgd0d1181" class="outline-3">
<h3 id="orgd0d1181"><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-org9c6a236" class="outline-2">
<h2 id="org9c6a236"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orgbe645f3" class="outline-2">
<h2 id="orgbe645f3"><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-orga02c846" class="outline-3">
<h3 id="orga02c846"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org567acb9" class="outline-3">
<h3 id="org567acb9"><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-org7b9d693" class="outline-4">
<h4 id="org7b9d693"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orge6c947d" class="outline-4">
<h4 id="orge6c947d"><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-orgcf5f86e" class="outline-4">
<h4 id="orgcf5f86e"><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-org45b03e3" class="outline-4">
<h4 id="org45b03e3"><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-org29b3e83" class="outline-4">
<h4 id="org29b3e83"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org1e27d72" class="outline-4">
<h4 id="org1e27d72"><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-org4323909" class="outline-4">
<h4 id="org4323909"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org34f8a20" class="outline-4">
<h4 id="org34f8a20"><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-orgae95088" class="outline-4">
<h4 id="orgae95088"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-orgfa3088e" class="outline-4">
<h4 id="orgfa3088e"><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-org87346d6" class="outline-4">
<h4 id="org87346d6"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org46e3a0b" class="outline-4">
<h4 id="org46e3a0b"><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-org7b5e4dd" class="outline-4">
<h4 id="org7b5e4dd"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org72bde0f" class="outline-4">
<h4 id="org72bde0f"><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-org838b667" class="outline-5">
<h5 id="org838b667"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org1eea73e" class="outline-5">
<h5 id="org1eea73e"><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-orgf514305" class="outline-5">
<h5 id="orgf514305"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org4ef2c3f" class="outline-5">
<h5 id="org4ef2c3f"><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-org9a1bb40" class="outline-4">
<h4 id="org9a1bb40"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org4b66373" class="outline-4">
<h4 id="org4b66373"><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-org730108c" class="outline-4">
<h4 id="org730108c"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-orge88e608" class="outline-4">
<h4 id="orge88e608"><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-org7ea1dc9" class="outline-3">
<h3 id="org7ea1dc9"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org26ca29b" class="outline-3">
<h3 id="org26ca29b"><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-orgc9d9f60" class="outline-4">
<h4 id="orgc9d9f60"><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-org291ae5e" class="outline-4">
<h4 id="org291ae5e"><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-org32b1602" class="outline-4">
<h4 id="org32b1602"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orga5bf50b" class="outline-4">
<h4 id="orga5bf50b"><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-org6097f3f" class="outline-4">
<h4 id="org6097f3f"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgc7d6dd7" class="outline-4">
<h4 id="orgc7d6dd7"><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-orgbc7f55b" class="outline-4">
<h4 id="orgbc7f55b"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org88e458e" class="outline-4">
<h4 id="org88e458e"><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-orgbdd2fb5" class="outline-4">
<h4 id="orgbdd2fb5"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-orgff1bb69" class="outline-4">
<h4 id="orgff1bb69"><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-org3b2c346" class="outline-5">
<h5 id="org3b2c346"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgc09d3cf" class="outline-5">
<h5 id="orgc09d3cf"><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-org7239d84" class="outline-5">
<h5 id="org7239d84"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-orgbc13001" class="outline-5">
<h5 id="orgbc13001"><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-org24e7691" class="outline-4">
<h4 id="org24e7691"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org2f11685" class="outline-4">
<h4 id="org2f11685"><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-org145358b" class="outline-2">
<h2 id="org145358b"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-orgfab9d63" class="outline-2">
<h2 id="orgfab9d63"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgdc3ebe2" class="outline-3">
<h3 id="orgdc3ebe2"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-orgc75816f" class="outline-3">
<h3 id="orgc75816f"><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: 2024-08-10 Sat 15:35</p>
<p class="date">Created: 2024-08-17 Sat 16:23</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>
<!-- 2024-08-10 Sat 15:35 -->
<!-- 2024-08-17 Sat 16:23 -->
<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: 2024-08-10 Sat 15:35</p>
<p class="date">Created: 2024-08-17 Sat 16:23</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>
<!-- 2024-08-10 Sat 15:35 -->
<!-- 2024-08-17 Sat 16:23 -->
<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: 2024-08-10 Sat 15:35</p>
<p class="date">Created: 2024-08-17 Sat 16:23</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>
<!-- 2024-08-10 Sat 15:35 -->
<!-- 2024-08-17 Sat 16:23 -->
<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="#org354084e">1. Format specification</a>
<li><a href="#org718c718">1. Format specification</a>
<ul>
<li><a href="#orgd0348ad">1.1. Organization of the data</a></li>
<li><a href="#org4cf8d61">1.2. Data types</a></li>
<li><a href="#org3aa6749">1.1. Organization of the data</a></li>
<li><a href="#org16b6cd5">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org46e06de">2. The TREXIO library</a>
<li><a href="#orgf861d79">2. The TREXIO library</a>
<ul>
<li><a href="#org04be9ab">2.1. The front-end</a></li>
<li><a href="#orgb42f8ad">2.2. The back-end</a></li>
<li><a href="#org00f3be5">2.3. Supported languages</a></li>
<li><a href="#orgda9ce78">2.4. Source code generation and documentation</a></li>
<li><a href="#orgf81f3c4">2.5. Availability</a></li>
<li><a href="#org45c57da">2.1. The front-end</a></li>
<li><a href="#org409bf17">2.2. The back-end</a></li>
<li><a href="#org1b288f9">2.3. Supported languages</a></li>
<li><a href="#org2414377">2.4. Source code generation and documentation</a></li>
<li><a href="#org78915d6">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org354084e" class="outline-2">
<h2 id="org354084e"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org718c718" class="outline-2">
<h2 id="org718c718"><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-orgd0348ad" class="outline-3">
<h3 id="orgd0348ad"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org3aa6749" class="outline-3">
<h3 id="org3aa6749"><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-org4cf8d61" class="outline-3">
<h3 id="org4cf8d61"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org16b6cd5" class="outline-3">
<h3 id="org16b6cd5"><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-org46e06de" class="outline-2">
<h2 id="org46e06de"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orgf861d79" class="outline-2">
<h2 id="orgf861d79"><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-org04be9ab" class="outline-3">
<h3 id="org04be9ab"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-org45c57da" class="outline-3">
<h3 id="org45c57da"><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-orgb42f8ad" class="outline-3">
<h3 id="orgb42f8ad"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-org409bf17" class="outline-3">
<h3 id="org409bf17"><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-org00f3be5" class="outline-3">
<h3 id="org00f3be5"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org1b288f9" class="outline-3">
<h3 id="org1b288f9"><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-orgda9ce78" class="outline-3">
<h3 id="orgda9ce78"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org2414377" class="outline-3">
<h3 id="org2414377"><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-orgf81f3c4" class="outline-3">
<h3 id="orgf81f3c4"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org78915d6" class="outline-3">
<h3 id="org78915d6"><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: 2024-08-10 Sat 15:35</p>
<p class="date">Created: 2024-08-17 Sat 16:23</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>
<!-- 2024-08-10 Sat 15:35 -->
<!-- 2024-08-17 Sat 16:23 -->
<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="#orgcadea36">1. Template for HDF5 definitions</a></li>
<li><a href="#orgcd3b453">2. Template for HDF5 structures</a></li>
<li><a href="#org9123777">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgeabc0a0">4. Template for HDF5 has a group</a></li>
<li><a href="#orgbbc768d">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org01e6401">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgd5c041e">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org7f9a338">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org1a36573">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org186f27c">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org3af6451">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orga1540d9">12. Source code for the determinant part</a></li>
<li><a href="#org7aa0503">13. Helper functions</a></li>
<li><a href="#org44600c2">1. Template for HDF5 definitions</a></li>
<li><a href="#org98f18d2">2. Template for HDF5 structures</a></li>
<li><a href="#org75698f8">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgc009265">4. Template for HDF5 has a group</a></li>
<li><a href="#org62e5dd9">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgf6789b3">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgfa37abd">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org96d5811">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orge362d6c">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org839e9ea">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org2fa8bc6">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org0244c00">12. Source code for the determinant part</a></li>
<li><a href="#orgeed2df2">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgcadea36" class="outline-2">
<h2 id="orgcadea36"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org44600c2" class="outline-2">
<h2 id="org44600c2"><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-orgcd3b453" class="outline-2">
<h2 id="orgcd3b453"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org98f18d2" class="outline-2">
<h2 id="org98f18d2"><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-org9123777" class="outline-2">
<h2 id="org9123777"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org75698f8" class="outline-2">
<h2 id="org75698f8"><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-orgeabc0a0" class="outline-2">
<h2 id="orgeabc0a0"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orgc009265" class="outline-2">
<h2 id="orgc009265"><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-orgbbc768d" class="outline-2">
<h2 id="orgbbc768d"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org62e5dd9" class="outline-2">
<h2 id="org62e5dd9"><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-org01e6401" class="outline-2">
<h2 id="org01e6401"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgf6789b3" class="outline-2">
<h2 id="orgf6789b3"><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-orgd5c041e" class="outline-2">
<h2 id="orgd5c041e"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orgfa37abd" class="outline-2">
<h2 id="orgfa37abd"><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-org7f9a338" class="outline-2">
<h2 id="org7f9a338"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org96d5811" class="outline-2">
<h2 id="org96d5811"><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-org1a36573" class="outline-2">
<h2 id="org1a36573"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orge362d6c" class="outline-2">
<h2 id="orge362d6c"><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-org186f27c" class="outline-2">
<h2 id="org186f27c"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org839e9ea" class="outline-2">
<h2 id="org839e9ea"><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-org3af6451" class="outline-2">
<h2 id="org3af6451"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org2fa8bc6" class="outline-2">
<h2 id="org2fa8bc6"><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-orga1540d9" class="outline-2">
<h2 id="orga1540d9"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org0244c00" class="outline-2">
<h2 id="org0244c00"><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-org7aa0503" class="outline-2">
<h2 id="org7aa0503"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgeed2df2" class="outline-2">
<h2 id="orgeed2df2"><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: 2024-08-10 Sat 15:35</p>
<p class="date">Created: 2024-08-17 Sat 16:23</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org5807130">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgb1ccdc6">2. Template for general structure in text back end</a></li>
<li><a href="#org055baad">3. Initialize function (constant part)</a></li>
<li><a href="#org77dc166">4. Deinitialize function (templated part)</a></li>
<li><a href="#org42068f6">5. Flush function (templated part)</a></li>
<li><a href="#org3a67691">6. Template for text read a group</a></li>
<li><a href="#org0b84f3e">7. Template for text has a group</a></li>
<li><a href="#orgf0c4591">8. Template for text flush a group</a></li>
<li><a href="#org1db95d5">9. Template for text free memory</a></li>
<li><a href="#orgf41193a">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org53235f4">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org3eb14ad">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org1cc8067">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org3416f6f">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orga8c86a1">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org33103e0">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org3322880">17. Source code for the determinant part</a></li>
<li><a href="#orgd856766">1. Template for group-related structures in text back end</a></li>
<li><a href="#org17250c5">2. Template for general structure in text back end</a></li>
<li><a href="#org7a228b7">3. Initialize function (constant part)</a></li>
<li><a href="#org15f2876">4. Deinitialize function (templated part)</a></li>
<li><a href="#org7584c92">5. Flush function (templated part)</a></li>
<li><a href="#org807b3a8">6. Template for text read a group</a></li>
<li><a href="#org1c34cb3">7. Template for text has a group</a></li>
<li><a href="#org90edcd7">8. Template for text flush a group</a></li>
<li><a href="#org39532db">9. Template for text free memory</a></li>
<li><a href="#org412647e">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgd867664">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org056b4e7">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org4f5bb44">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org3ca6f34">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org2d670ca">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org10ec4ab">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orge975dc3">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-org5807130" class="outline-2">
<h2 id="org5807130"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orgd856766" class="outline-2">
<h2 id="orgd856766"><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-orgb1ccdc6" class="outline-2">
<h2 id="orgb1ccdc6"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org17250c5" class="outline-2">
<h2 id="org17250c5"><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-org055baad" class="outline-2">
<h2 id="org055baad"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org7a228b7" class="outline-2">
<h2 id="org7a228b7"><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-org77dc166" class="outline-2">
<h2 id="org77dc166"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org15f2876" class="outline-2">
<h2 id="org15f2876"><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-org42068f6" class="outline-2">
<h2 id="org42068f6"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org7584c92" class="outline-2">
<h2 id="org7584c92"><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-org3a67691" class="outline-2">
<h2 id="org3a67691"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org807b3a8" class="outline-2">
<h2 id="org807b3a8"><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>
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<h2 id="org0b84f3e"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org1c34cb3" class="outline-2">
<h2 id="org1c34cb3"><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-orgf0c4591" class="outline-2">
<h2 id="orgf0c4591"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org90edcd7" class="outline-2">
<h2 id="org90edcd7"><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-org1db95d5" class="outline-2">
<h2 id="org1db95d5"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org39532db" class="outline-2">
<h2 id="org39532db"><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-orgf41193a" class="outline-2">
<h2 id="orgf41193a"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org412647e" class="outline-2">
<h2 id="org412647e"><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-org53235f4" class="outline-2">
<h2 id="org53235f4"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgd867664" class="outline-2">
<h2 id="orgd867664"><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-org3eb14ad" class="outline-2">
<h2 id="org3eb14ad"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org056b4e7" class="outline-2">
<h2 id="org056b4e7"><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-org1cc8067" class="outline-2">
<h2 id="org1cc8067"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org4f5bb44" class="outline-2">
<h2 id="org4f5bb44"><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-org3416f6f" class="outline-2">
<h2 id="org3416f6f"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org3ca6f34" class="outline-2">
<h2 id="org3ca6f34"><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-orga8c86a1" class="outline-2">
<h2 id="orga8c86a1"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org2d670ca" class="outline-2">
<h2 id="org2d670ca"><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-org33103e0" class="outline-2">
<h2 id="org33103e0"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org10ec4ab" class="outline-2">
<h2 id="org10ec4ab"><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-org3322880" class="outline-2">
<h2 id="org3322880"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-orge975dc3" class="outline-2">
<h2 id="orge975dc3"><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: 2024-08-10 Sat 15:35</p>
<p class="date">Created: 2024-08-17 Sat 16:23</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2024-08-10 Sat 15:35 -->
<!-- 2024-08-17 Sat 16:23 -->
<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="#org9f9a808">1. Metadata (metadata group)</a></li>
<li><a href="#org805c7b0">2. System</a>
<li><a href="#orgc9144cd">1. Metadata (metadata group)</a></li>
<li><a href="#org3b0b96c">2. System</a>
<ul>
<li><a href="#org466ab7c">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org81d183e">2.2. Cell (cell group)</a></li>
<li><a href="#orgaaaf11c">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orge804afa">2.4. Electron (electron group)</a></li>
<li><a href="#orgc5e4a35">2.5. Ground or excited states (state group)</a></li>
<li><a href="#orgaf29d0f">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org5c21f6b">2.2. Cell (cell group)</a></li>
<li><a href="#org6ae3162">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org0748bfd">2.4. Electron (electron group)</a></li>
<li><a href="#org3ee9861">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org1d0b592">3. Basis functions</a>
<li><a href="#org5eb0c45">3. Basis functions</a>
<ul>
<li><a href="#orgecd410b">3.1. Basis set (basis group)</a>
<li><a href="#org86915a5">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org4536fd0">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orge128561">3.1.2. Numerical orbitals</a></li>
<li><a href="#org0523ef1">3.1.3. Plane waves</a></li>
<li><a href="#org01ec8b2">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org3f89575">3.1.5. Data definitions</a></li>
<li><a href="#org6feb722">3.1.6. Example</a></li>
<li><a href="#org4a90815">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgcdd12bd">3.1.2. Numerical orbitals</a></li>
<li><a href="#orgec0af68">3.1.3. Plane waves</a></li>
<li><a href="#orge71171e">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org11c91c1">3.1.5. Data definitions</a></li>
<li><a href="#org36c09d6">3.1.6. Example</a></li>
</ul>
</li>
<li><a href="#org219911b">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org7b84c1d">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgb884365">3.2.1. Example</a></li>
<li><a href="#org7e8c7ae">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org94afc53">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#orgb387550">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#orga882b33">4. Orbitals</a>
<li><a href="#orgd125fe0">4. Orbitals</a>
<ul>
<li><a href="#org36435c7">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org33b91d1">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="#org6dff09d">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org77ca964">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org5581608">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgb51a4dd">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org4c79f67">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orge937947">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org6b9e941">5. Multi-determinant information</a>
<li><a href="#orgb26260a">5. Multi-determinant information</a>
<ul>
<li><a href="#org259d4ed">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orge25a66d">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org45a3460">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org34c288d">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org92fd042">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgabb4cb5">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org307362a">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orge03b148">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org5d3eeef">6. Correlation factors</a>
<li><a href="#orgb316b75">6. Correlation factors</a>
<ul>
<li><a href="#org94dbff9">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org4e5282b">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org1757967">6.1.1. CHAMP</a></li>
<li><a href="#org085395a">6.1.2. Mu</a></li>
<li><a href="#org893e9d6">6.1.3. Table of values</a></li>
<li><a href="#org89f15d6">6.1.1. CHAMP</a></li>
<li><a href="#orgedbd8fa">6.1.2. Mu</a></li>
<li><a href="#org0859c27">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org7fd911a">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org530e2d9">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-org9f9a808" class="outline-2">
<h2 id="org9f9a808"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgc9144cd" class="outline-2">
<h2 id="orgc9144cd"><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="orgbb2536f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgabb21b1" 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-org805c7b0" class="outline-2">
<h2 id="org805c7b0"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org3b0b96c" class="outline-2">
<h2 id="org3b0b96c"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org466ab7c" class="outline-3">
<h3 id="org466ab7c"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orgaf29d0f" class="outline-3">
<h3 id="orgaf29d0f"><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="org6faafd1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdd30748" 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-org81d183e" class="outline-3">
<h3 id="org81d183e"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org5c21f6b" class="outline-3">
<h3 id="org5c21f6b"><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="orgdcd04f7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdc07ab3" 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-orgaaaf11c" class="outline-3">
<h3 id="orgaaaf11c"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org6ae3162" class="outline-3">
<h3 id="org6ae3162"><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="org8208f5a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdb80ddb" 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-orge804afa" class="outline-3">
<h3 id="orge804afa"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org0748bfd" class="outline-3">
<h3 id="org0748bfd"><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="org311fb7d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1d0d494" 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-orgc5e4a35" class="outline-3">
<h3 id="orgc5e4a35"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org3ee9861" class="outline-3">
<h3 id="org3ee9861"><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="org7ae06db" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc9b0730" 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-org1d0b592" class="outline-2">
<h2 id="org1d0b592"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org5eb0c45" class="outline-2">
<h2 id="org5eb0c45"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgecd410b" class="outline-3">
<h3 id="orgecd410b"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org86915a5" class="outline-3">
<h3 id="org86915a5"><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-org4536fd0" class="outline-4">
<h4 id="org4536fd0"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org4a90815" class="outline-4">
<h4 id="org4a90815"><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-orge128561" class="outline-4">
<h4 id="orge128561"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-orgcdd12bd" class="outline-4">
<h4 id="orgcdd12bd"><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-org0523ef1" class="outline-4">
<h4 id="org0523ef1"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-orgec0af68" class="outline-4">
<h4 id="orgec0af68"><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-org01ec8b2" class="outline-4">
<h4 id="org01ec8b2"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div id="outline-container-orge71171e" class="outline-4">
<h4 id="orge71171e"><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-org3f89575" class="outline-4">
<h4 id="org3f89575"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div id="outline-container-org11c91c1" class="outline-4">
<h4 id="org11c91c1"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-5">
<table id="org41f5c37" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org38dbb8e" 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-org6feb722" class="outline-4">
<h4 id="org6feb722"><span class="section-number-4">3.1.6</span> Example</h4>
<div id="outline-container-org36c09d6" class="outline-4">
<h4 id="org36c09d6"><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-org219911b" class="outline-3">
<h3 id="org219911b"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org7b84c1d" class="outline-3">
<h3 id="org7b84c1d"><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="org2138b41" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org38a89b0" 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-orgb884365" class="outline-4">
<h4 id="orgb884365"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-org7e8c7ae" class="outline-4">
<h4 id="org7e8c7ae"><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-org94afc53" class="outline-3">
<h3 id="org94afc53"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-orgb387550" class="outline-3">
<h3 id="orgb387550"><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="orgd89e705" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org763bc6a" 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-orga882b33" class="outline-2">
<h2 id="orga882b33"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-orgd125fe0" class="outline-2">
<h2 id="orgd125fe0"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org36435c7" class="outline-3">
<h3 id="org36435c7"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org33b91d1" class="outline-3">
<h3 id="org33b91d1"><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="org0e9e271" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5d1a8c4" 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-orgf13532d" class="outline-4">
<div id="outline-container-org44b9e1b" 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="orgb639500" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1f1c3b1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2097,7 +2097,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org6d3b5f9" class="outline-4">
<div id="outline-container-org0f7477b" 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="org92ca757" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf2bf2b9" 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-org6dff09d" class="outline-3">
<h3 id="org6dff09d"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org77ca964" class="outline-3">
<h3 id="org77ca964"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="orgd1796f8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2ba2152" 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-org5581608" class="outline-4">
<h4 id="org5581608"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org4c79f67" class="outline-4">
<h4 id="org4c79f67"><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="orga8bacf0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org769394f" 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-orgb51a4dd" class="outline-4">
<h4 id="orgb51a4dd"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-orge937947" class="outline-4">
<h4 id="orge937947"><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="org8b81977" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgff00368" 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-org6b9e941" class="outline-2">
<h2 id="org6b9e941"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-orgb26260a" class="outline-2">
<h2 id="orgb26260a"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org259d4ed" class="outline-3">
<h3 id="org259d4ed"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org92fd042" class="outline-3">
<h3 id="org92fd042"><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="org5c00002" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org195ed0e" 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-orge25a66d" class="outline-3">
<h3 id="orge25a66d"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-orgabb4cb5" class="outline-3">
<h3 id="orgabb4cb5"><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="org4299b80" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7e182e7" 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-org45a3460" class="outline-3">
<h3 id="org45a3460"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org307362a" class="outline-3">
<h3 id="org307362a"><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="org30e9fb8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2221953" 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-org34c288d" class="outline-3">
<h3 id="org34c288d"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-orge03b148" class="outline-3">
<h3 id="orge03b148"><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="org4b522d0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org44783e9" 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-org5d3eeef" class="outline-2">
<h2 id="org5d3eeef"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-orgb316b75" class="outline-2">
<h2 id="orgb316b75"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org94dbff9" class="outline-3">
<h3 id="org94dbff9"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org4e5282b" class="outline-3">
<h3 id="org4e5282b"><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-org1757967" class="outline-4">
<h4 id="org1757967"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org89f15d6" class="outline-4">
<h4 id="org89f15d6"><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-org085395a" class="outline-4">
<h4 id="org085395a"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-orgedbd8fa" class="outline-4">
<h4 id="orgedbd8fa"><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="org893e9d6"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="org0859c27"><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="org7fd911a"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org530e2d9"><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: 2024-08-10 Sat 15:35</p>
<p class="date">Created: 2024-08-17 Sat 16:23</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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