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README.html
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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>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-03-07 Mon 13:35</p>
<p class="date">Created: 2022-03-11 Fri 12:54</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2022-03-07 Mon 13:35 -->
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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>Examples</title>
@ -333,24 +333,24 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org7f845f5">1. Accessing sparse quantities</a>
<li><a href="#org29e1b1d">1. Accessing sparse quantities</a>
<ul>
<li><a href="#orgb07e860">1.1. Fortran</a>
<li><a href="#orgacd44e2">1.1. Fortran</a>
<ul>
<li><a href="#org0b8c7ec">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgad84218">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org4abb7cc">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgeca195b">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgb8bba21">1.1.5. Allocate memory</a></li>
<li><a href="#org0a9d94c">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgbe8668a">1.1.7. Read two-electron quantities</a>
<li><a href="#org1ed3f46">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgb06a343">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgd6fcb73">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgd070d3e">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org441fe30">1.1.5. Allocate memory</a></li>
<li><a href="#org0f5e34c">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org5cf89ee">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org823ffe3">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org6419b30">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#orgdf7df26">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org1e875c6">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org87e4b28">1.1.8. Compute the energy</a></li>
<li><a href="#org92207ae">1.1.9. Terminate</a></li>
<li><a href="#org5810d9f">1.1.8. Compute the energy</a></li>
<li><a href="#orgbb6b48d">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
@ -360,12 +360,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org7f845f5" class="outline-2">
<h2 id="org7f845f5"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-org29e1b1d" class="outline-2">
<h2 id="org29e1b1d"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orgb07e860" class="outline-3">
<h3 id="orgb07e860"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-orgacd44e2" class="outline-3">
<h3 id="orgacd44e2"><span class="section-number-3">1.1</span> Fortran</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
@ -411,8 +411,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org0b8c7ec" class="outline-4">
<h4 id="org0b8c7ec"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org1ed3f46" class="outline-4">
<h4 id="org1ed3f46"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div class="outline-text-4" id="text-1-1-1">
<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>
@ -427,8 +427,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgad84218" class="outline-4">
<h4 id="orgad84218"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div id="outline-container-orgb06a343" class="outline-4">
<h4 id="orgb06a343"><span class="section-number-4">1.1.2</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-1-1-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
@ -444,8 +444,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org4abb7cc" class="outline-4">
<h4 id="org4abb7cc"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgd6fcb73" class="outline-4">
<h4 id="orgd6fcb73"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-1-1-3">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
@ -459,8 +459,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgeca195b" class="outline-4">
<h4 id="orgeca195b"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgd070d3e" class="outline-4">
<h4 id="orgd070d3e"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-1-1-4">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
@ -474,8 +474,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgb8bba21" class="outline-4">
<h4 id="orgb8bba21"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org441fe30" class="outline-4">
<h4 id="org441fe30"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div class="outline-text-4" id="text-1-1-5">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
@ -487,8 +487,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-org0a9d94c" class="outline-4">
<h4 id="org0a9d94c"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org0f5e34c" class="outline-4">
<h4 id="org0f5e34c"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-1-1-6">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@ -520,8 +520,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-orgbe8668a" class="outline-4">
<h4 id="orgbe8668a"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org5cf89ee" class="outline-4">
<h4 id="org5cf89ee"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-1-1-7">
<p>
Reading is done with OpenMP. Each thread reads its own buffer, and
@ -537,8 +537,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org823ffe3" class="outline-5">
<h5 id="org823ffe3"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgdf7df26" class="outline-5">
<h5 id="orgdf7df26"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-1-1-7-1">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
@ -587,8 +587,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-org6419b30" class="outline-5">
<h5 id="org6419b30"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org1e875c6" class="outline-5">
<h5 id="org1e875c6"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-1-1-7-2">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
@ -632,8 +632,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org87e4b28" class="outline-4">
<h4 id="org87e4b28"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org5810d9f" class="outline-4">
<h4 id="org5810d9f"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div class="outline-text-4" id="text-1-1-8">
<p>
When the orbitals are real, we can use
@ -679,8 +679,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org92207ae" class="outline-4">
<h4 id="org92207ae"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgbb6b48d" class="outline-4">
<h4 id="orgbb6b48d"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div class="outline-text-4" id="text-1-1-9">
<div class="org-src-container">
<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
@ -695,7 +695,7 @@ E = E + E_nn
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-03-07 Mon 13:35</p>
<p class="date">Created: 2022-03-11 Fri 12:54</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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index.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>
<!-- 2022-03-07 Mon 13:35 -->
<!-- 2022-03-11 Fri 12:54 -->
<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>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-03-07 Mon 13:35</p>
<p class="date">Created: 2022-03-11 Fri 12:54</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-03-07 Mon 13:35 -->
<!-- 2022-03-11 Fri 12:54 -->
<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>
@ -311,22 +311,22 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org5d129b0">1. Template for HDF5 definitions</a></li>
<li><a href="#org518b515">2. Template for HDF5 structures</a></li>
<li><a href="#org19b7a39">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org32fc9ea">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgae773d1">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org75401cf">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org5899cf9">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org6c12128">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgd5eb638">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgdd237f1">10. Helper functions</a></li>
<li><a href="#org365eb16">1. Template for HDF5 definitions</a></li>
<li><a href="#org2767730">2. Template for HDF5 structures</a></li>
<li><a href="#org9e16a26">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org0162385">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgcb1e5bd">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org8bd2b5e">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orga83dd5a">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org03c0bc2">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgc28c99a">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org8b88da2">10. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org5d129b0" class="outline-2">
<h2 id="org5d129b0"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org365eb16" class="outline-2">
<h2 id="org365eb16"><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>
@ -338,8 +338,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org518b515" class="outline-2">
<h2 id="org518b515"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org2767730" class="outline-2">
<h2 id="org2767730"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div class="outline-text-2" id="text-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_hdf5_s</span> {
@ -352,8 +352,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org19b7a39" class="outline-2">
<h2 id="org19b7a39"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org9e16a26" class="outline-2">
<h2 id="org9e16a26"><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>
@ -456,8 +456,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org32fc9ea" class="outline-2">
<h2 id="org32fc9ea"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org0162385" class="outline-2">
<h2 id="org0162385"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</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>
@ -560,8 +560,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgae773d1" class="outline-2">
<h2 id="orgae773d1"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgcb1e5bd" class="outline-2">
<h2 id="orgcb1e5bd"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</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>
@ -694,8 +694,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org75401cf" class="outline-2">
<h2 id="org75401cf"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org8bd2b5e" class="outline-2">
<h2 id="org8bd2b5e"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-6">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -896,8 +896,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org5899cf9" class="outline-2">
<h2 id="org5899cf9"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orga83dd5a" class="outline-2">
<h2 id="orga83dd5a"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</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>
@ -1094,8 +1094,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org6c12128" class="outline-2">
<h2 id="org6c12128"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org03c0bc2" class="outline-2">
<h2 id="org03c0bc2"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</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>
@ -1221,8 +1221,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-orgd5eb638" class="outline-2">
<h2 id="orgd5eb638"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgc28c99a" class="outline-2">
<h2 id="orgc28c99a"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-9">
<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
@ -1262,8 +1262,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-orgdd237f1" class="outline-2">
<h2 id="orgdd237f1"><span class="section-number-2">10</span> Helper functions</h2>
<div id="outline-container-org8b88da2" class="outline-2">
<h2 id="org8b88da2"><span class="section-number-2">10</span> Helper functions</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>
@ -1524,7 +1524,7 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-03-07 Mon 13:35</p>
<p class="date">Created: 2022-03-11 Fri 12:54</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

88
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<head>
<!-- 2022-03-07 Mon 13:35 -->
<!-- 2022-03-11 Fri 12:54 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
@ -311,29 +311,29 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org0cb7198">1. TEXT back end</a>
<li><a href="#orge60f291">1. TEXT back end</a>
<ul>
<li><a href="#orgf92a83c">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#orgcce8194">1.2. Template for general structure in text back end</a></li>
<li><a href="#org204ce78">1.3. Initialize function (constant part)</a></li>
<li><a href="#orgab80d68">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orgd8fdb7b">1.5. Template for text read a group</a></li>
<li><a href="#org2d92d1c">1.6. Template for text flush a group</a></li>
<li><a href="#org1c827b5">1.7. Template for text free memory</a></li>
<li><a href="#org010467e">1.8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgbab6653">1.9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org5d761b7">1.10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org6258e10">1.11. Template for has/read/write a string attribute</a></li>
<li><a href="#org0053650">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org37a6097">1.13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org262b8be">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org538aa5a">1.2. Template for general structure in text back end</a></li>
<li><a href="#org183d11d">1.3. Initialize function (constant part)</a></li>
<li><a href="#org645e4c0">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orgdba238b">1.5. Template for text read a group</a></li>
<li><a href="#org20ee9d7">1.6. Template for text flush a group</a></li>
<li><a href="#org7c3aa5e">1.7. Template for text free memory</a></li>
<li><a href="#orgca242c4">1.8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgbfc74fc">1.9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org7e79bd9">1.10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orga3f41cb">1.11. Template for has/read/write a string attribute</a></li>
<li><a href="#org83e4363">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orga67ea82">1.13. Template for text delete a group (UNSAFE mode)</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org0cb7198" class="outline-2">
<h2 id="org0cb7198"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-orge60f291" class="outline-2">
<h2 id="orge60f291"><span class="section-number-2">1</span> TEXT back end</h2>
<div class="outline-text-2" id="text-1">
<p>
The "file" produced by the text back end is a directory with one
@ -354,8 +354,8 @@ The file is written when closed, or when the flush function is called.
</p>
</div>
<div id="outline-container-orgf92a83c" class="outline-3">
<h3 id="orgf92a83c"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-org262b8be" class="outline-3">
<h3 id="org262b8be"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
@ -374,8 +374,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orgcce8194" class="outline-3">
<h3 id="orgcce8194"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org538aa5a" class="outline-3">
<h3 id="org538aa5a"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div class="outline-text-3" id="text-1-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_text_s</span> {
@ -388,8 +388,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org204ce78" class="outline-3">
<h3 id="org204ce78"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-org183d11d" class="outline-3">
<h3 id="org183d11d"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div class="outline-text-3" id="text-1-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -532,8 +532,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orgab80d68" class="outline-3">
<h3 id="orgab80d68"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-org645e4c0" class="outline-3">
<h3 id="org645e4c0"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div class="outline-text-3" id="text-1-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -555,8 +555,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orgd8fdb7b" class="outline-3">
<h3 id="orgd8fdb7b"><span class="section-number-3">1.5</span> Template for text read a group</h3>
<div id="outline-container-orgdba238b" class="outline-3">
<h3 id="orgdba238b"><span class="section-number-3">1.5</span> Template for text read a group</h3>
<div class="outline-text-3" id="text-1-5">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -857,8 +857,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org2d92d1c" class="outline-3">
<h3 id="org2d92d1c"><span class="section-number-3">1.6</span> Template for text flush a group</h3>
<div id="outline-container-org20ee9d7" class="outline-3">
<h3 id="org20ee9d7"><span class="section-number-3">1.6</span> Template for text flush a group</h3>
<div class="outline-text-3" id="text-1-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -922,8 +922,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org1c827b5" class="outline-3">
<h3 id="org1c827b5"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-org7c3aa5e" class="outline-3">
<h3 id="org7c3aa5e"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div class="outline-text-3" id="text-1-7">
<p>
Memory is allocated when reading. The following function frees memory.
@ -970,8 +970,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-org010467e" class="outline-3">
<h3 id="org010467e"><span class="section-number-3">1.8</span> Template for has/read/write a numerical attribute</h3>
<div id="outline-container-orgca242c4" class="outline-3">
<h3 id="orgca242c4"><span class="section-number-3">1.8</span> Template for has/read/write a numerical attribute</h3>
<div class="outline-text-3" id="text-1-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1034,8 +1034,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-orgbab6653" class="outline-3">
<h3 id="orgbab6653"><span class="section-number-3">1.9</span> Template for has/read/write a dataset of numerical data</h3>
<div id="outline-container-orgbfc74fc" class="outline-3">
<h3 id="orgbfc74fc"><span class="section-number-3">1.9</span> Template for has/read/write a dataset of numerical data</h3>
<div class="outline-text-3" id="text-1-9">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1131,8 +1131,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org5d761b7" class="outline-3">
<h3 id="org5d761b7"><span class="section-number-3">1.10</span> Template for has/read/write a dataset of strings</h3>
<div id="outline-container-org7e79bd9" class="outline-3">
<h3 id="org7e79bd9"><span class="section-number-3">1.10</span> Template for has/read/write a dataset of strings</h3>
<div class="outline-text-3" id="text-1-10">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1233,8 +1233,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org6258e10" class="outline-3">
<h3 id="org6258e10"><span class="section-number-3">1.11</span> Template for has/read/write a string attribute</h3>
<div id="outline-container-orga3f41cb" class="outline-3">
<h3 id="orga3f41cb"><span class="section-number-3">1.11</span> Template for has/read/write a string attribute</h3>
<div class="outline-text-3" id="text-1-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1308,8 +1308,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org0053650" class="outline-3">
<h3 id="org0053650"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div id="outline-container-org83e4363" class="outline-3">
<h3 id="org83e4363"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div class="outline-text-3" id="text-1-12">
<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
@ -1583,8 +1583,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org37a6097" class="outline-3">
<h3 id="org37a6097"><span class="section-number-3">1.13</span> Template for text delete a group (UNSAFE mode)</h3>
<div id="outline-container-orga67ea82" class="outline-3">
<h3 id="orga67ea82"><span class="section-number-3">1.13</span> Template for text delete a group (UNSAFE mode)</h3>
<div class="outline-text-3" id="text-1-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1615,7 +1615,7 @@ User provides indices and values of the sparse array as two separate variables.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-03-07 Mon 13:35</p>
<p class="date">Created: 2022-03-11 Fri 12:54</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

122
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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>
<!-- 2022-03-07 Mon 13:35 -->
<!-- 2022-03-11 Fri 12:54 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREX Configuration file</title>
@ -333,33 +333,33 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org59e1053">1. Metadata (metadata group)</a></li>
<li><a href="#orgddeb0d4">2. Electron (electron group)</a></li>
<li><a href="#org96e72aa">3. Nucleus (nucleus group)</a></li>
<li><a href="#org252e582">4. Effective core potentials (ecp group)</a>
<li><a href="#org56d8986">1. Metadata (metadata group)</a></li>
<li><a href="#orgb1f499e">2. Electron (electron group)</a></li>
<li><a href="#org5cc8a82">3. Nucleus (nucleus group)</a></li>
<li><a href="#org35661b1">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org00154f3">4.1. Example</a></li>
<li><a href="#orgf0c1d1a">4.1. Example</a></li>
</ul>
</li>
<li><a href="#orgd1d7570">5. Basis set (basis group)</a>
<li><a href="#orgddc4bdf">5. Basis set (basis group)</a>
<ul>
<li><a href="#orga32ce7e">5.1. Example</a></li>
<li><a href="#orge85c802">5.1. Example</a></li>
</ul>
</li>
<li><a href="#orgb478849">6. Atomic orbitals (ao group)</a>
<li><a href="#org25757ac">6. Atomic orbitals (ao group)</a>
<ul>
<li><a href="#ao_one_e">6.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
<li><a href="#ao_two_e">6.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org28a3703">7. Molecular orbitals (mo group)</a>
<li><a href="#orgb2e4d24">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgdbe274d">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org2b40dbd">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org2a64258">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgc2bf608">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#orgdd25863">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org7111e75">9. Reduced density matrices (rdm group)</a></li>
<li><a href="#org02d15d9">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org9a6fddf">9. Reduced density matrices (rdm group)</a></li>
</ul>
</div>
</div>
@ -409,8 +409,8 @@ fetched using multiple function calls to perform I/O on buffers.
</p>
<div id="outline-container-org59e1053" class="outline-2">
<h2 id="org59e1053"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org56d8986" class="outline-2">
<h2 id="org56d8986"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect our files to be archived in open-data repositories, we
@ -420,7 +420,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="org3a11137" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org73b5985" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -501,15 +501,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-orgddeb0d4" class="outline-2">
<h2 id="orgddeb0d4"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orgb1f499e" class="outline-2">
<h2 id="orgb1f499e"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div class="outline-text-2" id="text-2">
<p>
We consider wave functions expressed in the spin-free formalism, where
the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org5e89249" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgff31774" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -548,15 +548,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org96e72aa" class="outline-2">
<h2 id="org96e72aa"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org5cc8a82" class="outline-2">
<h2 id="org5cc8a82"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div class="outline-text-2" id="text-3">
<p>
The nuclei are considered as fixed point charges. Coordinates are
given in Cartesian \((x,y,z)\) format.
</p>
<table id="orgba6cc71" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc04c3a1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -623,8 +623,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org252e582" class="outline-2">
<h2 id="org252e582"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org35661b1" class="outline-2">
<h2 id="org35661b1"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div class="outline-text-2" id="text-4">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -657,7 +657,7 @@ The functions \(V_{A\ell}\) are parameterized as:
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="orgf7c178a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge084345" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -751,12 +751,16 @@ ECP that replaces the core electrons.
<b>Note for developers</b>: avoid having variables with similar prefix in their name.
HDF5 back end might cause issues due to the way <code>find_dataset</code> function works.
For example, in the ECP group we use <code>max_ang_mom</code> and not <code>ang_mom_max</code>.
The latter causes issues when written before <code>ang_mom</code> in the TREXIO file.
The latter causes issues when written before the <code>ang_mom</code> array in the TREXIO file.
<b>Update</b>: in fact, the aforementioned issue has only been observed when using HDF5 version 1.10.4
installed via <code>apt-get</code>. Installing the same version from the <code>conda-forge</code> channel and running it in
an isolated <code>conda</code> environment works just fine. Thus, it seems to be a bug in the <code>apt</code>-provided package.
If you encounter the aforementioned issue, please report it to our <a href="https://github.com/TREX-CoE/trexio/issues">issue tracker on GitHub</a>.
</p>
</div>
<div id="outline-container-org00154f3" class="outline-3">
<h3 id="org00154f3"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-orgf0c1d1a" class="outline-3">
<h3 id="orgf0c1d1a"><span class="section-number-3">4.1</span> Example</h3>
<div class="outline-text-3" id="text-4-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -819,8 +823,8 @@ power = [
</div>
</div>
<div id="outline-container-orgd1d7570" class="outline-2">
<h2 id="orgd1d7570"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-orgddc4bdf" class="outline-2">
<h2 id="orgddc4bdf"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div class="outline-text-2" id="text-5">
<p>
We consider here basis functions centered on nuclei. Hence, we enable
@ -873,7 +877,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).
All the basis set parameters are stored in one-dimensional arrays:
</p>
<table id="org0de34ac" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga494916" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -967,8 +971,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-orga32ce7e" class="outline-3">
<h3 id="orga32ce7e"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-orge85c802" class="outline-3">
<h3 id="orge85c802"><span class="section-number-3">5.1</span> Example</h3>
<div class="outline-text-3" id="text-5-1">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1046,8 +1050,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgb478849" class="outline-2">
<h2 id="orgb478849"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org25757ac" class="outline-2">
<h2 id="org25757ac"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div class="outline-text-2" id="text-6">
<p>
Going from the atomic basis set to AOs implies a systematic
@ -1100,13 +1104,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#orgd1d7570">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#orgddc4bdf">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
normalization factor of the atomic orbitals in spherical coordinates.
The normalization factor of the \(xy\) function which should be
introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</p>
<table id="org411213f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2b3af66" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1158,8 +1162,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-orgb93fd52" class="outline-3">
<h3 id="ao_one_e"><a id="orgb93fd52"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org1268404" class="outline-3">
<h3 id="ao_one_e"><a id="org1268404"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_one_e">
<ul class="org-ul">
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
@ -1176,7 +1180,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org2646263" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1589284" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1236,8 +1240,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org6f69d7d" class="outline-3">
<h3 id="ao_two_e"><a id="org6f69d7d"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-orgdb9d958" class="outline-3">
<h3 id="ao_two_e"><a id="orgdb9d958"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_two_e">
<p>
The two-electron integrals for a two-electron operator \(\hat{O}\) are
@ -1258,7 +1262,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org1767d7a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd34360c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1298,10 +1302,10 @@ notation.
</div>
</div>
<div id="outline-container-org28a3703" class="outline-2">
<h2 id="org28a3703"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgb2e4d24" class="outline-2">
<h2 id="orgb2e4d24"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org0180a6e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfc34de6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1367,8 +1371,8 @@ notation.
</table>
</div>
<div id="outline-container-orgdbe274d" class="outline-3">
<h3 id="orgdbe274d"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org2a64258" class="outline-3">
<h3 id="org2a64258"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-1">
<p>
The operators as the same as those defined in the
@ -1376,7 +1380,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org457d614" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3d74cc1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1436,8 +1440,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org2b40dbd" class="outline-3">
<h3 id="org2b40dbd"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orgc2bf608" class="outline-3">
<h3 id="orgc2bf608"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-2">
<p>
The operators as the same as those defined in the
@ -1445,7 +1449,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgaeb1be0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3bab743" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1485,11 +1489,11 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgdd25863" class="outline-2">
<h2 id="orgdd25863"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-org02d15d9" class="outline-2">
<h2 id="org02d15d9"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-org7111e75" class="outline-2">
<h2 id="org7111e75"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org9a6fddf" class="outline-2">
<h2 id="org9a6fddf"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1542,7 +1546,7 @@ The total energy can be computed as:
\]
</p>
<table id="org003f2db" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org46f5bb4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1625,7 +1629,7 @@ The total energy can be computed as:
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-03-07 Mon 13:35</p>
<p class="date">Created: 2022-03-11 Fri 12:54</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>