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<head>
<!-- 2022-01-25 Tue 16:21 -->
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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: 2022-01-25 Tue 16:21</p>
<p class="date">Created: 2022-01-26 Wed 13:01</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-01-25 Tue 16:21 -->
<!-- 2022-01-26 Wed 13:01 -->
<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="#org32639ae">1. Accessing sparse quantities</a>
<li><a href="#org2fa2f77">1. Accessing sparse quantities</a>
<ul>
<li><a href="#org164f6fc">1.1. Fortran</a>
<li><a href="#org947a74e">1.1. Fortran</a>
<ul>
<li><a href="#org670dae4">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgb10e756">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgbe4653a">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org707efc6">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org42e4c04">1.1.5. Allocate memory</a></li>
<li><a href="#org5ee299c">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org01ecc80">1.1.7. Read two-electron quantities</a>
<li><a href="#org366c25f">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org75e56c0">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga79dc32">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org16ce153">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org4161bbd">1.1.5. Allocate memory</a></li>
<li><a href="#org635230b">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orga2edfee">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org4121f02">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgae46824">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org0d49849">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org171f7e5">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org05b25de">1.1.8. Compute the energy</a></li>
<li><a href="#org81e0a1b">1.1.9. Terminate</a></li>
<li><a href="#orgde02804">1.1.8. Compute the energy</a></li>
<li><a href="#org3a156d0">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-org32639ae" class="outline-2">
<h2 id="org32639ae"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-org2fa2f77" class="outline-2">
<h2 id="org2fa2f77"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org164f6fc" class="outline-3">
<h3 id="org164f6fc"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org947a74e" class="outline-3">
<h3 id="org947a74e"><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-org670dae4" class="outline-4">
<h4 id="org670dae4"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org366c25f" class="outline-4">
<h4 id="org366c25f"><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-orgb10e756" class="outline-4">
<h4 id="orgb10e756"><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-org75e56c0" class="outline-4">
<h4 id="org75e56c0"><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-orgbe4653a" class="outline-4">
<h4 id="orgbe4653a"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orga79dc32" class="outline-4">
<h4 id="orga79dc32"><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-org707efc6" class="outline-4">
<h4 id="org707efc6"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org16ce153" class="outline-4">
<h4 id="org16ce153"><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-org42e4c04" class="outline-4">
<h4 id="org42e4c04"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org4161bbd" class="outline-4">
<h4 id="org4161bbd"><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-org5ee299c" class="outline-4">
<h4 id="org5ee299c"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org635230b" class="outline-4">
<h4 id="org635230b"><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-org01ecc80" class="outline-4">
<h4 id="org01ecc80"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orga2edfee" class="outline-4">
<h4 id="orga2edfee"><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-org4121f02" class="outline-5">
<h5 id="org4121f02"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org0d49849" class="outline-5">
<h5 id="org0d49849"><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-orgae46824" class="outline-5">
<h5 id="orgae46824"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org171f7e5" class="outline-5">
<h5 id="org171f7e5"><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-org05b25de" class="outline-4">
<h4 id="org05b25de"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-orgde02804" class="outline-4">
<h4 id="orgde02804"><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-org81e0a1b" class="outline-4">
<h4 id="org81e0a1b"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org3a156d0" class="outline-4">
<h4 id="org3a156d0"><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: 2022-01-25 Tue 16:21</p>
<p class="date">Created: 2022-01-26 Wed 13:01</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-25 Tue 16:21 -->
<!-- 2022-01-26 Wed 13:01 -->
<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: 2022-01-25 Tue 16:21</p>
<p class="date">Created: 2022-01-26 Wed 13:01</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2022-01-25 Tue 16:21 -->
<!-- 2022-01-26 Wed 13:01 -->
<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="#orge8a34dd">1. Template for HDF5 definitions</a></li>
<li><a href="#orgbfa6253">2. Template for HDF5 structures</a></li>
<li><a href="#org0dcab99">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org3f40e3a">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgc2e35ea">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org2d96545">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgcf896b0">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org53c7bdb">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org139c586">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org6cb0b56">10. Helper functions</a></li>
<li><a href="#org82287d3">1. Template for HDF5 definitions</a></li>
<li><a href="#org38502ed">2. Template for HDF5 structures</a></li>
<li><a href="#orge6f1036">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org3ecc216">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgb091c6f">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org99bff63">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org0595bab">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org0353bb1">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org2373d67">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org69555e2">10. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orge8a34dd" class="outline-2">
<h2 id="orge8a34dd"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org82287d3" class="outline-2">
<h2 id="org82287d3"><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-orgbfa6253" class="outline-2">
<h2 id="orgbfa6253"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org38502ed" class="outline-2">
<h2 id="org38502ed"><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-org0dcab99" class="outline-2">
<h2 id="org0dcab99"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orge6f1036" class="outline-2">
<h2 id="orge6f1036"><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-org3f40e3a" class="outline-2">
<h2 id="org3f40e3a"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org3ecc216" class="outline-2">
<h2 id="org3ecc216"><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-orgc2e35ea" class="outline-2">
<h2 id="orgc2e35ea"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgb091c6f" class="outline-2">
<h2 id="orgb091c6f"><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-org2d96545" class="outline-2">
<h2 id="org2d96545"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org99bff63" class="outline-2">
<h2 id="org99bff63"><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-orgcf896b0" class="outline-2">
<h2 id="orgcf896b0"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org0595bab" class="outline-2">
<h2 id="org0595bab"><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-org53c7bdb" class="outline-2">
<h2 id="org53c7bdb"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org0353bb1" class="outline-2">
<h2 id="org0353bb1"><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-org139c586" class="outline-2">
<h2 id="org139c586"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org2373d67" class="outline-2">
<h2 id="org2373d67"><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-org6cb0b56" class="outline-2">
<h2 id="org6cb0b56"><span class="section-number-2">10</span> Helper functions</h2>
<div id="outline-container-org69555e2" class="outline-2">
<h2 id="org69555e2"><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: 2022-01-25 Tue 16:21</p>
<p class="date">Created: 2022-01-26 Wed 13:01</p>
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-25 Tue 16:21 -->
<!-- 2022-01-26 Wed 13:01 -->
<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="#orgfec1a8f">1. TEXT back end</a>
<li><a href="#orgc192b3f">1. TEXT back end</a>
<ul>
<li><a href="#org36a9c8c">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org7671c79">1.2. Template for general structure in text back end</a></li>
<li><a href="#org8b5cddc">1.3. Initialize function (constant part)</a></li>
<li><a href="#org61d363c">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orgbb9ee56">1.5. Template for text read a group</a></li>
<li><a href="#org914cf2c">1.6. Template for text flush a group</a></li>
<li><a href="#org2e9a83a">1.7. Template for text free memory</a></li>
<li><a href="#orgf374949">1.8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org75f2880">1.9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org7a47ed6">1.10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orga461d87">1.11. Template for has/read/write a string attribute</a></li>
<li><a href="#orga200d85">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgfb775ff">1.13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org747c854">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#orged4e898">1.2. Template for general structure in text back end</a></li>
<li><a href="#org3112c15">1.3. Initialize function (constant part)</a></li>
<li><a href="#org3336043">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orgc14d4eb">1.5. Template for text read a group</a></li>
<li><a href="#org9fd6257">1.6. Template for text flush a group</a></li>
<li><a href="#org3c88c5d">1.7. Template for text free memory</a></li>
<li><a href="#org862c647">1.8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org0edba12">1.9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org2c7e745">1.10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org53b2b80">1.11. Template for has/read/write a string attribute</a></li>
<li><a href="#orge99fe0a">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org72a171b">1.13. Template for text delete a group (UNSAFE mode)</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgfec1a8f" class="outline-2">
<h2 id="orgfec1a8f"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-orgc192b3f" class="outline-2">
<h2 id="orgc192b3f"><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-org36a9c8c" class="outline-3">
<h3 id="org36a9c8c"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-org747c854" class="outline-3">
<h3 id="org747c854"><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-org7671c79" class="outline-3">
<h3 id="org7671c79"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-orged4e898" class="outline-3">
<h3 id="orged4e898"><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-org8b5cddc" class="outline-3">
<h3 id="org8b5cddc"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-org3112c15" class="outline-3">
<h3 id="org3112c15"><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-org61d363c" class="outline-3">
<h3 id="org61d363c"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-org3336043" class="outline-3">
<h3 id="org3336043"><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-orgbb9ee56" class="outline-3">
<h3 id="orgbb9ee56"><span class="section-number-3">1.5</span> Template for text read a group</h3>
<div id="outline-container-orgc14d4eb" class="outline-3">
<h3 id="orgc14d4eb"><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*
@ -848,8 +848,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org914cf2c" class="outline-3">
<h3 id="org914cf2c"><span class="section-number-3">1.6</span> Template for text flush a group</h3>
<div id="outline-container-org9fd6257" class="outline-3">
<h3 id="org9fd6257"><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>
@ -913,8 +913,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org2e9a83a" class="outline-3">
<h3 id="org2e9a83a"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-org3c88c5d" class="outline-3">
<h3 id="org3c88c5d"><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.
@ -961,8 +961,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-orgf374949" class="outline-3">
<h3 id="orgf374949"><span class="section-number-3">1.8</span> Template for has/read/write a numerical attribute</h3>
<div id="outline-container-org862c647" class="outline-3">
<h3 id="org862c647"><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>
@ -1025,8 +1025,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-org75f2880" class="outline-3">
<h3 id="org75f2880"><span class="section-number-3">1.9</span> Template for has/read/write a dataset of numerical data</h3>
<div id="outline-container-org0edba12" class="outline-3">
<h3 id="org0edba12"><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.
@ -1122,8 +1122,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org7a47ed6" class="outline-3">
<h3 id="org7a47ed6"><span class="section-number-3">1.10</span> Template for has/read/write a dataset of strings</h3>
<div id="outline-container-org2c7e745" class="outline-3">
<h3 id="org2c7e745"><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.
@ -1224,8 +1224,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orga461d87" class="outline-3">
<h3 id="orga461d87"><span class="section-number-3">1.11</span> Template for has/read/write a string attribute</h3>
<div id="outline-container-org53b2b80" class="outline-3">
<h3 id="org53b2b80"><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>
@ -1299,8 +1299,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orga200d85" class="outline-3">
<h3 id="orga200d85"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div id="outline-container-orge99fe0a" class="outline-3">
<h3 id="orge99fe0a"><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
@ -1574,8 +1574,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-orgfb775ff" class="outline-3">
<h3 id="orgfb775ff"><span class="section-number-3">1.13</span> Template for text delete a group (UNSAFE mode)</h3>
<div id="outline-container-org72a171b" class="outline-3">
<h3 id="org72a171b"><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>
@ -1606,7 +1606,7 @@ 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: 2022-01-25 Tue 16:21</p>
<p class="date">Created: 2022-01-26 Wed 13:01</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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trex.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-25 Tue 16:21 -->
<!-- 2022-01-26 Wed 13:01 -->
<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="#org61b7a53">1. Metadata (metadata group)</a></li>
<li><a href="#org36dd79d">2. Electron (electron group)</a></li>
<li><a href="#orgf04d938">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgc647318">4. Effective core potentials (ecp group)</a>
<li><a href="#org6e08fed">1. Metadata (metadata group)</a></li>
<li><a href="#org42e3d4c">2. Electron (electron group)</a></li>
<li><a href="#org74d3277">3. Nucleus (nucleus group)</a></li>
<li><a href="#org9ba4489">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgd18edde">4.1. Example</a></li>
<li><a href="#org7319394">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org5ef6dfd">5. Basis set (basis group)</a>
<li><a href="#org115015d">5. Basis set (basis group)</a>
<ul>
<li><a href="#orgb9563f7">5.1. Example</a></li>
<li><a href="#org72b3a07">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org386b75b">6. Atomic orbitals (ao group)</a>
<li><a href="#org06e5c81">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="#orgb07f1be">7. Molecular orbitals (mo group)</a>
<li><a href="#orgfb50666">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgbe3af15">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org297af2d">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org7978980">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orga4df715">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org04051d9">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org3a2b3b2">9. Reduced density matrices (rdm group)</a></li>
<li><a href="#org1122e55">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#orgb21aa37">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-org61b7a53" class="outline-2">
<h2 id="org61b7a53"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org6e08fed" class="outline-2">
<h2 id="org6e08fed"><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="org575978b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd127ced" 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-org36dd79d" class="outline-2">
<h2 id="org36dd79d"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org42e3d4c" class="outline-2">
<h2 id="org42e3d4c"><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="org6613526" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3215a8a" 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-orgf04d938" class="outline-2">
<h2 id="orgf04d938"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org74d3277" class="outline-2">
<h2 id="org74d3277"><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="org458701d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org27ac488" 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-orgc647318" class="outline-2">
<h2 id="orgc647318"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org9ba4489" class="outline-2">
<h2 id="org9ba4489"><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="orgf970f8e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgffe14e0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -755,8 +755,8 @@ The latter causes issues when written before <code>ang_mom</code> in the TREXIO
</p>
</div>
<div id="outline-container-orgd18edde" class="outline-3">
<h3 id="orgd18edde"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org7319394" class="outline-3">
<h3 id="org7319394"><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 +819,8 @@ power = [
</div>
</div>
<div id="outline-container-org5ef6dfd" class="outline-2">
<h2 id="org5ef6dfd"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org115015d" class="outline-2">
<h2 id="org115015d"><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 +873,7 @@ 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="orgc608224" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf7fddea" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -967,8 +967,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-orgb9563f7" class="outline-3">
<h3 id="orgb9563f7"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org72b3a07" class="outline-3">
<h3 id="org72b3a07"><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 +1046,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org386b75b" class="outline-2">
<h2 id="org386b75b"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org06e5c81" class="outline-2">
<h2 id="org06e5c81"><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 +1100,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org5ef6dfd">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org115015d">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="orgd0c3c83" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge04a086" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1158,8 +1158,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-orgfc78fb9" class="outline-3">
<h3 id="ao_one_e"><a id="orgfc78fb9"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org62a2e27" class="outline-3">
<h3 id="ao_one_e"><a id="org62a2e27"></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}}
@ -1177,7 +1177,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgfef975f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org87eef34" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1244,8 +1244,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org0b9cdb7" class="outline-3">
<h3 id="ao_two_e"><a id="org0b9cdb7"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org2d9c57a" class="outline-3">
<h3 id="ao_two_e"><a id="org2d9c57a"></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
@ -1266,7 +1266,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org526ecc9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2e2aa4b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1306,10 +1306,10 @@ notation.
</div>
</div>
<div id="outline-container-orgb07f1be" class="outline-2">
<h2 id="orgb07f1be"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgfb50666" class="outline-2">
<h2 id="orgfb50666"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org6f69e1e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5b0430a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1375,8 +1375,8 @@ notation.
</table>
</div>
<div id="outline-container-orgbe3af15" class="outline-3">
<h3 id="orgbe3af15"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org7978980" class="outline-3">
<h3 id="org7978980"><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
@ -1384,7 +1384,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org9834cae" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3a9b766" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1451,8 +1451,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org297af2d" class="outline-3">
<h3 id="org297af2d"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orga4df715" class="outline-3">
<h3 id="orga4df715"><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
@ -1460,7 +1460,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org94cc137" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org34d3b1b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1500,11 +1500,11 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org04051d9" class="outline-2">
<h2 id="org04051d9"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-org1122e55" class="outline-2">
<h2 id="org1122e55"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-org3a2b3b2" class="outline-2">
<h2 id="org3a2b3b2"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orgb21aa37" class="outline-2">
<h2 id="orgb21aa37"><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
@ -1557,7 +1557,7 @@ The total energy can be computed as:
\]
</p>
<table id="org5e61037" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbbdba8a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1640,7 +1640,7 @@ The total energy can be computed as:
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-25 Tue 16:21</p>
<p class="date">Created: 2022-01-26 Wed 13:01</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>