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README.html
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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>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: 2024-08-18 Sun 08:36</p>
<p class="date">Created: 2024-09-11 Wed 07:48</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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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>
<!-- 2024-08-18 Sun 08:36 -->
<!-- 2024-09-11 Wed 07:48 -->
<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="#org2282c8f">1. Writing nuclear coordinates</a>
<li><a href="#org650dd49">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orgf2d39e6">1.1. C</a></li>
<li><a href="#org2fa8914">1.2. Python</a></li>
<li><a href="#orga1a851f">1.3. Fortran</a></li>
<li><a href="#org7cc8d55">1.1. C</a></li>
<li><a href="#orgff42874">1.2. Python</a></li>
<li><a href="#orgaf5aefd">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org3a1fd29">2. Accessing sparse quantities (integrals)</a>
<li><a href="#orgd1396e1">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#orge83f5de">2.1. Fortran</a>
<li><a href="#org6d5821c">2.1. Fortran</a>
<ul>
<li><a href="#orgd57c8de">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgae0e97c">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga13feca">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org19dc70a">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgc4c12b1">2.1.5. Allocate memory</a></li>
<li><a href="#org8426bd0">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org0828d13">2.1.7. Read two-electron quantities</a>
<li><a href="#org50be0cc">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org589ff38">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org020d918">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgc04b581">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org5d32055">2.1.5. Allocate memory</a></li>
<li><a href="#orgc0fe39b">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org57d1c63">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org8afae0e">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org8822983">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org67950b9">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orga0e54bc">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org1467b52">2.1.8. Compute the energy</a></li>
<li><a href="#org069d19b">2.1.9. Terminate</a></li>
<li><a href="#orgf3d5f8b">2.1.8. Compute the energy</a></li>
<li><a href="#org9b55d42">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org9bb0c1f">2.2. Python</a>
<li><a href="#orgc92c763">2.2. Python</a>
<ul>
<li><a href="#orgd8493da">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org4688f3d">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#orgc4c34f5">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#orgab059c5">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orga9caf5f">2.2.5. Read two-electron quantities</a>
<li><a href="#org9468dab">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgc0e4c2d">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org090c025">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org751fb4d">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org5c77968">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#org7b5c547">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org0125f5f">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org3fd5977">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgeb2c791">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org72b7121">2.2.6. Compute the energy</a></li>
<li><a href="#org99dbbe6">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org62e684f">3. Reading determinants</a>
<li><a href="#orgca465b0">3. Reading determinants</a>
<ul>
<li><a href="#orgecaa9f9">3.1. Fortran</a></li>
<li><a href="#orge2c1198">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org2282c8f" class="outline-2">
<h2 id="org2282c8f"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org650dd49" class="outline-2">
<h2 id="org650dd49"><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-orgf2d39e6" class="outline-3">
<h3 id="orgf2d39e6"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org7cc8d55" class="outline-3">
<h3 id="org7cc8d55"><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-org2fa8914" class="outline-3">
<h3 id="org2fa8914"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-orgff42874" class="outline-3">
<h3 id="orgff42874"><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-orga1a851f" class="outline-3">
<h3 id="orga1a851f"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orgaf5aefd" class="outline-3">
<h3 id="orgaf5aefd"><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-org3a1fd29" class="outline-2">
<h2 id="org3a1fd29"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orgd1396e1" class="outline-2">
<h2 id="orgd1396e1"><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-orge83f5de" class="outline-3">
<h3 id="orge83f5de"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org6d5821c" class="outline-3">
<h3 id="org6d5821c"><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-orgd57c8de" class="outline-4">
<h4 id="orgd57c8de"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org50be0cc" class="outline-4">
<h4 id="org50be0cc"><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-orgae0e97c" class="outline-4">
<h4 id="orgae0e97c"><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-org589ff38" class="outline-4">
<h4 id="org589ff38"><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-orga13feca" class="outline-4">
<h4 id="orga13feca"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org020d918" class="outline-4">
<h4 id="org020d918"><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-org19dc70a" class="outline-4">
<h4 id="org19dc70a"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgc04b581" class="outline-4">
<h4 id="orgc04b581"><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-orgc4c12b1" class="outline-4">
<h4 id="orgc4c12b1"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org5d32055" class="outline-4">
<h4 id="org5d32055"><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-org8426bd0" class="outline-4">
<h4 id="org8426bd0"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgc0fe39b" class="outline-4">
<h4 id="orgc0fe39b"><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-org0828d13" class="outline-4">
<h4 id="org0828d13"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org57d1c63" class="outline-4">
<h4 id="org57d1c63"><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-org8afae0e" class="outline-5">
<h5 id="org8afae0e"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org67950b9" class="outline-5">
<h5 id="org67950b9"><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-org8822983" class="outline-5">
<h5 id="org8822983"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orga0e54bc" class="outline-5">
<h5 id="orga0e54bc"><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-org1467b52" class="outline-4">
<h4 id="org1467b52"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-orgf3d5f8b" class="outline-4">
<h4 id="orgf3d5f8b"><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-org069d19b" class="outline-4">
<h4 id="org069d19b"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org9b55d42" class="outline-4">
<h4 id="org9b55d42"><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-org9bb0c1f" class="outline-3">
<h3 id="org9bb0c1f"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-orgc92c763" class="outline-3">
<h3 id="orgc92c763"><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-orgd8493da" class="outline-4">
<h4 id="orgd8493da"><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-org9468dab" class="outline-4">
<h4 id="org9468dab"><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-org4688f3d" class="outline-4">
<h4 id="org4688f3d"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgc0e4c2d" class="outline-4">
<h4 id="orgc0e4c2d"><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-orgc4c34f5" class="outline-4">
<h4 id="orgc4c34f5"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org090c025" class="outline-4">
<h4 id="org090c025"><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-orgab059c5" class="outline-4">
<h4 id="orgab059c5"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org751fb4d" class="outline-4">
<h4 id="org751fb4d"><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-orga9caf5f" class="outline-4">
<h4 id="orga9caf5f"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-org5c77968" class="outline-4">
<h4 id="org5c77968"><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-org7b5c547" class="outline-5">
<h5 id="org7b5c547"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org3fd5977" class="outline-5">
<h5 id="org3fd5977"><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-org0125f5f" class="outline-5">
<h5 id="org0125f5f"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-orgeb2c791" class="outline-5">
<h5 id="orgeb2c791"><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-org72b7121" class="outline-4">
<h4 id="org72b7121"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org99dbbe6" class="outline-4">
<h4 id="org99dbbe6"><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-org62e684f" class="outline-2">
<h2 id="org62e684f"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-orgca465b0" class="outline-2">
<h2 id="orgca465b0"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgecaa9f9" class="outline-3">
<h3 id="orgecaa9f9"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-orge2c1198" class="outline-3">
<h3 id="orge2c1198"><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: 2024-08-18 Sun 08:36</p>
<p class="date">Created: 2024-09-11 Wed 07:48</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>
<!-- 2024-08-18 Sun 08:36 -->
<!-- 2024-09-11 Wed 07:48 -->
<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: 2024-08-18 Sun 08:36</p>
<p class="date">Created: 2024-09-11 Wed 07:48</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>
<!-- 2024-08-18 Sun 08:36 -->
<!-- 2024-09-11 Wed 07:48 -->
<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: 2024-08-18 Sun 08:36</p>
<p class="date">Created: 2024-09-11 Wed 07:48</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
lib.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-18 Sun 08:36 -->
<!-- 2024-09-11 Wed 07:48 -->
<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="#org88eb5ed">1. Format specification</a>
<li><a href="#org11b6ebe">1. Format specification</a>
<ul>
<li><a href="#orgb9d2f42">1.1. Organization of the data</a></li>
<li><a href="#org9156a9d">1.2. Data types</a></li>
<li><a href="#orgfb77b3e">1.1. Organization of the data</a></li>
<li><a href="#org33c1aed">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org7f3e682">2. The TREXIO library</a>
<li><a href="#org334de05">2. The TREXIO library</a>
<ul>
<li><a href="#org0a53177">2.1. The front-end</a></li>
<li><a href="#org0f39e32">2.2. The back-end</a></li>
<li><a href="#orgf5a0786">2.3. Supported languages</a></li>
<li><a href="#org27f7607">2.4. Source code generation and documentation</a></li>
<li><a href="#org81c2379">2.5. Availability</a></li>
<li><a href="#orge188c14">2.1. The front-end</a></li>
<li><a href="#orgb702c2b">2.2. The back-end</a></li>
<li><a href="#org0c14863">2.3. Supported languages</a></li>
<li><a href="#org700420b">2.4. Source code generation and documentation</a></li>
<li><a href="#org7f3a5c3">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org88eb5ed" class="outline-2">
<h2 id="org88eb5ed"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org11b6ebe" class="outline-2">
<h2 id="org11b6ebe"><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-orgb9d2f42" class="outline-3">
<h3 id="orgb9d2f42"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-orgfb77b3e" class="outline-3">
<h3 id="orgfb77b3e"><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-org9156a9d" class="outline-3">
<h3 id="org9156a9d"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org33c1aed" class="outline-3">
<h3 id="org33c1aed"><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-org7f3e682" class="outline-2">
<h2 id="org7f3e682"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-org334de05" class="outline-2">
<h2 id="org334de05"><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-org0a53177" class="outline-3">
<h3 id="org0a53177"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orge188c14" class="outline-3">
<h3 id="orge188c14"><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-org0f39e32" class="outline-3">
<h3 id="org0f39e32"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-orgb702c2b" class="outline-3">
<h3 id="orgb702c2b"><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-orgf5a0786" class="outline-3">
<h3 id="orgf5a0786"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org0c14863" class="outline-3">
<h3 id="org0c14863"><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-org27f7607" class="outline-3">
<h3 id="org27f7607"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org700420b" class="outline-3">
<h3 id="org700420b"><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-org81c2379" class="outline-3">
<h3 id="org81c2379"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org7f3a5c3" class="outline-3">
<h3 id="org7f3a5c3"><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: 2024-08-18 Sun 08:36</p>
<p class="date">Created: 2024-09-11 Wed 07:48</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>
<!-- 2024-08-18 Sun 08:36 -->
<!-- 2024-09-11 Wed 07:48 -->
<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="#orgc239058">1. Template for HDF5 definitions</a></li>
<li><a href="#orgba992d5">2. Template for HDF5 structures</a></li>
<li><a href="#org33c0628">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org217461b">4. Template for HDF5 has a group</a></li>
<li><a href="#org9b000e0">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgcf3f52f">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org4413714">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org6a201ae">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org8ae0c34">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgf337010">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgb5ecc73">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org94b8e7c">12. Source code for the determinant part</a></li>
<li><a href="#org55a05f6">13. Helper functions</a></li>
<li><a href="#org773feee">1. Template for HDF5 definitions</a></li>
<li><a href="#org0d4ab60">2. Template for HDF5 structures</a></li>
<li><a href="#org837769f">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org99b9913">4. Template for HDF5 has a group</a></li>
<li><a href="#orgcb15e76">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgb5fa749">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org7089504">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org02689ad">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org57692a7">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org587b3e2">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgf883918">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org8a9bd18">12. Source code for the determinant part</a></li>
<li><a href="#org6d02740">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgc239058" class="outline-2">
<h2 id="orgc239058"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org773feee" class="outline-2">
<h2 id="org773feee"><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-orgba992d5" class="outline-2">
<h2 id="orgba992d5"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org0d4ab60" class="outline-2">
<h2 id="org0d4ab60"><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-org33c0628" class="outline-2">
<h2 id="org33c0628"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org837769f" class="outline-2">
<h2 id="org837769f"><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-org217461b" class="outline-2">
<h2 id="org217461b"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org99b9913" class="outline-2">
<h2 id="org99b9913"><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-org9b000e0" class="outline-2">
<h2 id="org9b000e0"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orgcb15e76" class="outline-2">
<h2 id="orgcb15e76"><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-orgcf3f52f" class="outline-2">
<h2 id="orgcf3f52f"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgb5fa749" class="outline-2">
<h2 id="orgb5fa749"><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-org4413714" class="outline-2">
<h2 id="org4413714"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org7089504" class="outline-2">
<h2 id="org7089504"><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-org6a201ae" class="outline-2">
<h2 id="org6a201ae"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org02689ad" class="outline-2">
<h2 id="org02689ad"><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-org8ae0c34" class="outline-2">
<h2 id="org8ae0c34"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org57692a7" class="outline-2">
<h2 id="org57692a7"><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-orgf337010" class="outline-2">
<h2 id="orgf337010"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org587b3e2" class="outline-2">
<h2 id="org587b3e2"><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-orgb5ecc73" class="outline-2">
<h2 id="orgb5ecc73"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgf883918" class="outline-2">
<h2 id="orgf883918"><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-org94b8e7c" class="outline-2">
<h2 id="org94b8e7c"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org8a9bd18" class="outline-2">
<h2 id="org8a9bd18"><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-org55a05f6" class="outline-2">
<h2 id="org55a05f6"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org6d02740" class="outline-2">
<h2 id="org6d02740"><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: 2024-08-18 Sun 08:36</p>
<p class="date">Created: 2024-09-11 Wed 07:48</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<title>TEXT back end</title>
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org71021b2">1. Template for group-related structures in text back end</a></li>
<li><a href="#org2c81a5a">2. Template for general structure in text back end</a></li>
<li><a href="#org3bc0c7c">3. Initialize function (constant part)</a></li>
<li><a href="#org4b60b38">4. Deinitialize function (templated part)</a></li>
<li><a href="#org85ea294">5. Flush function (templated part)</a></li>
<li><a href="#orgcaed7c7">6. Template for text read a group</a></li>
<li><a href="#orgfae2069">7. Template for text has a group</a></li>
<li><a href="#orgac42915">8. Template for text flush a group</a></li>
<li><a href="#org88e3a7e">9. Template for text free memory</a></li>
<li><a href="#org0580c05">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org178a837">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org6615379">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org18a26c1">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org900abba">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgb42c42f">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org170b455">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org1b54148">17. Source code for the determinant part</a></li>
<li><a href="#org2d30503">1. Template for group-related structures in text back end</a></li>
<li><a href="#org8c7568e">2. Template for general structure in text back end</a></li>
<li><a href="#org457c467">3. Initialize function (constant part)</a></li>
<li><a href="#orgf141f43">4. Deinitialize function (templated part)</a></li>
<li><a href="#org035528e">5. Flush function (templated part)</a></li>
<li><a href="#org9a3c737">6. Template for text read a group</a></li>
<li><a href="#org7fa4607">7. Template for text has a group</a></li>
<li><a href="#org941ac76">8. Template for text flush a group</a></li>
<li><a href="#org7d211e5">9. Template for text free memory</a></li>
<li><a href="#org0e37415">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org163aa3b">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgd1ccf8e">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org26596fe">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org4ca3a2f">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgccbd1bb">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgafdd779">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org0c20522">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-org71021b2" class="outline-2">
<h2 id="org71021b2"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org2d30503" class="outline-2">
<h2 id="org2d30503"><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-org2c81a5a" class="outline-2">
<h2 id="org2c81a5a"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org8c7568e" class="outline-2">
<h2 id="org8c7568e"><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-org3bc0c7c" class="outline-2">
<h2 id="org3bc0c7c"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org457c467" class="outline-2">
<h2 id="org457c467"><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-org4b60b38" class="outline-2">
<h2 id="org4b60b38"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgf141f43" class="outline-2">
<h2 id="orgf141f43"><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-org85ea294" class="outline-2">
<h2 id="org85ea294"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org035528e" class="outline-2">
<h2 id="org035528e"><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-orgcaed7c7" class="outline-2">
<h2 id="orgcaed7c7"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org9a3c737" class="outline-2">
<h2 id="org9a3c737"><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-orgfae2069" class="outline-2">
<h2 id="orgfae2069"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org7fa4607" class="outline-2">
<h2 id="org7fa4607"><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-orgac42915" class="outline-2">
<h2 id="orgac42915"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org941ac76" class="outline-2">
<h2 id="org941ac76"><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-org88e3a7e" class="outline-2">
<h2 id="org88e3a7e"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org7d211e5" class="outline-2">
<h2 id="org7d211e5"><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-org0580c05" class="outline-2">
<h2 id="org0580c05"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org0e37415" class="outline-2">
<h2 id="org0e37415"><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-org178a837" class="outline-2">
<h2 id="org178a837"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org163aa3b" class="outline-2">
<h2 id="org163aa3b"><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-org6615379" class="outline-2">
<h2 id="org6615379"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgd1ccf8e" class="outline-2">
<h2 id="orgd1ccf8e"><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-org18a26c1" class="outline-2">
<h2 id="org18a26c1"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org26596fe" class="outline-2">
<h2 id="org26596fe"><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-org900abba" class="outline-2">
<h2 id="org900abba"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org4ca3a2f" class="outline-2">
<h2 id="org4ca3a2f"><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-orgb42c42f" class="outline-2">
<h2 id="orgb42c42f"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-orgccbd1bb" class="outline-2">
<h2 id="orgccbd1bb"><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-org170b455" class="outline-2">
<h2 id="org170b455"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgafdd779" class="outline-2">
<h2 id="orgafdd779"><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-org1b54148" class="outline-2">
<h2 id="org1b54148"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org0c20522" class="outline-2">
<h2 id="org0c20522"><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: 2024-08-18 Sun 08:36</p>
<p class="date">Created: 2024-09-11 Wed 07:48</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2024-08-18 Sun 08:36 -->
<!-- 2024-09-11 Wed 07:48 -->
<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="#orga72911c">1. Metadata (metadata group)</a></li>
<li><a href="#org90d40eb">2. System</a>
<li><a href="#org9376afb">1. Metadata (metadata group)</a></li>
<li><a href="#orgc1f8d2a">2. System</a>
<ul>
<li><a href="#org3031d83">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org337b9a3">2.2. Cell (cell group)</a></li>
<li><a href="#org91e2f26">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgb8d30c4">2.4. Electron (electron group)</a></li>
<li><a href="#orga5b40d8">2.5. Ground or excited states (state group)</a></li>
<li><a href="#orgb276560">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org5aff943">2.2. Cell (cell group)</a></li>
<li><a href="#org3a79a88">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org7da76af">2.4. Electron (electron group)</a></li>
<li><a href="#org4c2c910">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#orgdff748d">3. Basis functions</a>
<li><a href="#org1d38261">3. Basis functions</a>
<ul>
<li><a href="#org2f6e469">3.1. Basis set (basis group)</a>
<li><a href="#org9bd214c">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org6d1a859">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org98084aa">3.1.2. Numerical orbitals</a></li>
<li><a href="#orgd42ecf5">3.1.3. Plane waves</a></li>
<li><a href="#org141baa3">3.1.4. Oscillating orbitals</a></li>
<li><a href="#orgaea8e31">3.1.5. Data definitions</a></li>
<li><a href="#orgd5e5dcc">3.1.6. Example</a></li>
<li><a href="#org8d40771">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org3547bc7">3.1.2. Numerical orbitals</a></li>
<li><a href="#org71e0301">3.1.3. Plane waves</a></li>
<li><a href="#org70fa0bf">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org9604b5c">3.1.5. Data definitions</a></li>
<li><a href="#org62c9f0a">3.1.6. Example</a></li>
</ul>
</li>
<li><a href="#orge8dffe1">3.2. Effective core potentials (ecp group)</a>
<li><a href="#orgd4223a5">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgc9ffb9a">3.2.1. Example</a></li>
<li><a href="#orgb2ec6d9">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#orge24fcf0">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#orgc2ea03a">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org9049320">4. Orbitals</a>
<li><a href="#orgf4d461e">4. Orbitals</a>
<ul>
<li><a href="#orga4cf8c9">4.1. Atomic orbitals (ao group)</a>
<li><a href="#orgaac0227">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="#org275fe83">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org1cb1416">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org9a4316e">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org2bed550">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orge2617d2">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org214c22e">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgd7fbd6c">5. Multi-determinant information</a>
<li><a href="#orge09f052">5. Multi-determinant information</a>
<ul>
<li><a href="#orgd9c7b89">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org961fd18">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org0342b7a">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org8bad848">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgc65df6c">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org02f0dc7">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org64b0eb5">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org8ac7631">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org013fe8a">6. Correlation factors</a>
<li><a href="#orgc65f042">6. Correlation factors</a>
<ul>
<li><a href="#org2fe5417">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org4b855e9">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#orgf3c4a37">6.1.1. CHAMP</a></li>
<li><a href="#org493832c">6.1.2. Mu</a></li>
<li><a href="#org6b73482">6.1.3. Table of values</a></li>
<li><a href="#org85208e7">6.1.1. CHAMP</a></li>
<li><a href="#org3d4776b">6.1.2. Mu</a></li>
<li><a href="#org3ae71a8">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orged92bfd">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org3096f46">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-orga72911c" class="outline-2">
<h2 id="orga72911c"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org9376afb" class="outline-2">
<h2 id="org9376afb"><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="org3671334" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8d55b40" 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-org90d40eb" class="outline-2">
<h2 id="org90d40eb"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-orgc1f8d2a" class="outline-2">
<h2 id="orgc1f8d2a"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org3031d83" class="outline-3">
<h3 id="org3031d83"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orgb276560" class="outline-3">
<h3 id="orgb276560"><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="orgc2b329f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2024a49" 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-org337b9a3" class="outline-3">
<h3 id="org337b9a3"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org5aff943" class="outline-3">
<h3 id="org5aff943"><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="orgd5fd5d1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge4a81cb" 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-org91e2f26" class="outline-3">
<h3 id="org91e2f26"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org3a79a88" class="outline-3">
<h3 id="org3a79a88"><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="orga9d9848" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge90c1d4" 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-orgb8d30c4" class="outline-3">
<h3 id="orgb8d30c4"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org7da76af" class="outline-3">
<h3 id="org7da76af"><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="org68b0f07" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org076cb45" 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-orga5b40d8" class="outline-3">
<h3 id="orga5b40d8"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org4c2c910" class="outline-3">
<h3 id="org4c2c910"><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="org413a505" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbad4111" 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-orgdff748d" class="outline-2">
<h2 id="orgdff748d"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org1d38261" class="outline-2">
<h2 id="org1d38261"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org2f6e469" class="outline-3">
<h3 id="org2f6e469"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org9bd214c" class="outline-3">
<h3 id="org9bd214c"><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-org6d1a859" class="outline-4">
<h4 id="org6d1a859"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org8d40771" class="outline-4">
<h4 id="org8d40771"><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-org98084aa" class="outline-4">
<h4 id="org98084aa"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-org3547bc7" class="outline-4">
<h4 id="org3547bc7"><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-orgd42ecf5" class="outline-4">
<h4 id="orgd42ecf5"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-org71e0301" class="outline-4">
<h4 id="org71e0301"><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-org141baa3" class="outline-4">
<h4 id="org141baa3"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div id="outline-container-org70fa0bf" class="outline-4">
<h4 id="org70fa0bf"><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-orgaea8e31" class="outline-4">
<h4 id="orgaea8e31"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div id="outline-container-org9604b5c" class="outline-4">
<h4 id="org9604b5c"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-5">
<table id="org59a5c53" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org12988ff" 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-orgd5e5dcc" class="outline-4">
<h4 id="orgd5e5dcc"><span class="section-number-4">3.1.6</span> Example</h4>
<div id="outline-container-org62c9f0a" class="outline-4">
<h4 id="org62c9f0a"><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-orge8dffe1" class="outline-3">
<h3 id="orge8dffe1"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-orgd4223a5" class="outline-3">
<h3 id="orgd4223a5"><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="orga37f1e8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3184e26" 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-orgc9ffb9a" class="outline-4">
<h4 id="orgc9ffb9a"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orgb2ec6d9" class="outline-4">
<h4 id="orgb2ec6d9"><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-orge24fcf0" class="outline-3">
<h3 id="orge24fcf0"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-orgc2ea03a" class="outline-3">
<h3 id="orgc2ea03a"><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="orgd5eec1c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2820ce0" 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-org9049320" class="outline-2">
<h2 id="org9049320"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-orgf4d461e" class="outline-2">
<h2 id="orgf4d461e"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-orga4cf8c9" class="outline-3">
<h3 id="orga4cf8c9"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-orgaac0227" class="outline-3">
<h3 id="orgaac0227"><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="org1cd94cc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge372a9d" 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-orga97f094" class="outline-4">
<div id="outline-container-org2a76381" 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="orgd3d286a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc734c72" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2097,7 +2097,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgb09500a" class="outline-4">
<div id="outline-container-org2aa510c" 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="orgb637d60" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgaa24d56" 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-org275fe83" class="outline-3">
<h3 id="org275fe83"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org1cb1416" class="outline-3">
<h3 id="org1cb1416"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org81b3ad4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge9a4e63" 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-org9a4316e" class="outline-4">
<h4 id="org9a4316e"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-orge2617d2" class="outline-4">
<h4 id="orge2617d2"><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="org362bf27" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org576411f" 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-org2bed550" class="outline-4">
<h4 id="org2bed550"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org214c22e" class="outline-4">
<h4 id="org214c22e"><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="org3a43b57" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4acf5ad" 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-orgd7fbd6c" class="outline-2">
<h2 id="orgd7fbd6c"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-orge09f052" class="outline-2">
<h2 id="orge09f052"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-orgd9c7b89" class="outline-3">
<h3 id="orgd9c7b89"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-orgc65df6c" class="outline-3">
<h3 id="orgc65df6c"><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="orgbc066b6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb46f92a" 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-org961fd18" class="outline-3">
<h3 id="org961fd18"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org02f0dc7" class="outline-3">
<h3 id="org02f0dc7"><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="orgf39aa49" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbd2cb38" 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-org0342b7a" class="outline-3">
<h3 id="org0342b7a"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org64b0eb5" class="outline-3">
<h3 id="org64b0eb5"><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="org265a7e9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0fe9ccc" 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-org8bad848" class="outline-3">
<h3 id="org8bad848"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org8ac7631" class="outline-3">
<h3 id="org8ac7631"><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="org64aed9c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org27e4346" 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-org013fe8a" class="outline-2">
<h2 id="org013fe8a"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-orgc65f042" class="outline-2">
<h2 id="orgc65f042"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org2fe5417" class="outline-3">
<h3 id="org2fe5417"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org4b855e9" class="outline-3">
<h3 id="org4b855e9"><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-orgf3c4a37" class="outline-4">
<h4 id="orgf3c4a37"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org85208e7" class="outline-4">
<h4 id="org85208e7"><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-org493832c" class="outline-4">
<h4 id="org493832c"><span class="section-number-4">6.1.2</span> Mu</h4>
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<h4 id="org3d4776b"><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="org6b73482"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="org3ae71a8"><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="orged92bfd"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org3096f46"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-7">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -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: 2024-08-18 Sun 08:36</p>
<p class="date">Created: 2024-09-11 Wed 07:48</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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