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README.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-12-23 Thu 17:50 -->
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<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name=google-site-verification content=jdDnuP2rYGJVy8AHSd-8LkmOmvK_dyz5buZ98wilYII />
@ -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: 2021-12-23 Thu 17:50</p>
<p class="date">Created: 2022-01-05 Wed 12:58</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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examples.html
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<head>
<!-- 2021-12-23 Thu 17:50 -->
<!-- 2022-01-05 Wed 12:58 -->
<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="#org61b0d66">1. Accessing sparse quantities</a>
<li><a href="#org3160f12">1. Accessing sparse quantities</a>
<ul>
<li><a href="#org6535a64">1.1. Fortran</a>
<li><a href="#orgf6ba443">1.1. Fortran</a>
<ul>
<li><a href="#orgbec7c9d">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgd7d46b2">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orge565a2b">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org1615269">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org042d348">1.1.5. Allocate memory</a></li>
<li><a href="#orgbaf4ef7">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgec36213">1.1.7. Read two-electron quantities</a>
<li><a href="#org7e50186">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgbcad38e">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org485de44">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgcf86530">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org7db3733">1.1.5. Allocate memory</a></li>
<li><a href="#org45c07d7">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org7c109f8">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org9b14893">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orge63ad06">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org8f689dc">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgf412012">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org239a019">1.1.8. Compute the energy</a></li>
<li><a href="#orgfa5f1b1">1.1.9. Terminate</a></li>
<li><a href="#orgdfa7bcc">1.1.8. Compute the energy</a></li>
<li><a href="#org954f47d">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-org61b0d66" class="outline-2">
<h2 id="org61b0d66"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-org3160f12" class="outline-2">
<h2 id="org3160f12"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org6535a64" class="outline-3">
<h3 id="org6535a64"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-orgf6ba443" class="outline-3">
<h3 id="orgf6ba443"><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>
@ -413,8 +413,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgbec7c9d" class="outline-4">
<h4 id="orgbec7c9d"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org7e50186" class="outline-4">
<h4 id="org7e50186"><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>
@ -429,8 +429,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgd7d46b2" class="outline-4">
<h4 id="orgd7d46b2"><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-orgbcad38e" class="outline-4">
<h4 id="orgbcad38e"><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)
@ -446,8 +446,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orge565a2b" class="outline-4">
<h4 id="orge565a2b"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org485de44" class="outline-4">
<h4 id="org485de44"><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)
@ -461,8 +461,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org1615269" class="outline-4">
<h4 id="org1615269"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgcf86530" class="outline-4">
<h4 id="orgcf86530"><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)
@ -476,8 +476,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org042d348" class="outline-4">
<h4 id="org042d348"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org7db3733" class="outline-4">
<h4 id="org7db3733"><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) )
@ -489,8 +489,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-orgbaf4ef7" class="outline-4">
<h4 id="orgbaf4ef7"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org45c07d7" class="outline-4">
<h4 id="org45c07d7"><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)
@ -522,8 +522,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-orgec36213" class="outline-4">
<h4 id="orgec36213"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org7c109f8" class="outline-4">
<h4 id="org7c109f8"><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
@ -539,8 +539,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org9b14893" class="outline-5">
<h5 id="org9b14893"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org8f689dc" class="outline-5">
<h5 id="org8f689dc"><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)
@ -589,8 +589,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-orge63ad06" class="outline-5">
<h5 id="orge63ad06"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgf412012" class="outline-5">
<h5 id="orgf412012"><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)
@ -634,8 +634,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org239a019" class="outline-4">
<h4 id="org239a019"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-orgdfa7bcc" class="outline-4">
<h4 id="orgdfa7bcc"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div class="outline-text-4" id="text-1-1-8">
<p>
As \((n,m)\) 2D arrays are stored in memory as \((\n times m)\) 1D
@ -669,8 +669,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-orgfa5f1b1" class="outline-4">
<h4 id="orgfa5f1b1"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org954f47d" class="outline-4">
<h4 id="org954f47d"><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 )
@ -685,7 +685,7 @@ E = E + E_nn
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-12-23 Thu 17:50</p>
<p class="date">Created: 2022-01-05 Wed 12:58</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>
<!-- 2021-12-23 Thu 17:50 -->
<!-- 2022-01-05 Wed 12:58 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name=google-site-verification content=jdDnuP2rYGJVy8AHSd-8LkmOmvK_dyz5buZ98wilYII />
@ -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: 2021-12-23 Thu 17:50</p>
<p class="date">Created: 2022-01-05 Wed 12:58</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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templator_front.html
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templator_hdf5.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>
<!-- 2021-12-23 Thu 17:49 -->
<!-- 2022-01-05 Wed 12:58 -->
<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>
@ -311,29 +311,29 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org627961d">1. HDF5 back end</a>
<li><a href="#org29023f3">1. HDF5 back end</a>
<ul>
<li><a href="#org6a9fd3c">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org8b69565">1.2. Template for HDF5 structures</a></li>
<li><a href="#org9455874">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org1253718">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#orge867147">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org35f2c5a">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#org50c528a">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org381528d">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#org6ddfdf2">1.9. Helper functions</a></li>
<li><a href="#org1d75444">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org4e2d7b7">1.2. Template for HDF5 structures</a></li>
<li><a href="#org9951a49">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org248c864">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#orgdd8dff9">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org332b8ed">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#orga671666">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgb35260c">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#org472f553">1.9. Helper functions</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org627961d" class="outline-2">
<h2 id="org627961d"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-org29023f3" class="outline-2">
<h2 id="org29023f3"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org6a9fd3c" class="outline-3">
<h3 id="org6a9fd3c"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-org1d75444" class="outline-3">
<h3 id="org1d75444"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div class="outline-text-3" id="text-1-1">
<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>
@ -345,8 +345,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org8b69565" class="outline-3">
<h3 id="org8b69565"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-org4e2d7b7" class="outline-3">
<h3 id="org4e2d7b7"><span class="section-number-3">1.2</span> Template for HDF5 structures</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_hdf5_s</span> {
@ -360,8 +360,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org9455874" class="outline-3">
<h3 id="org9455874"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-org9951a49" class="outline-3">
<h3 id="org9951a49"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</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>
@ -441,8 +441,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org1253718" class="outline-3">
<h3 id="org1253718"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-org248c864" class="outline-3">
<h3 id="org248c864"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</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>
@ -536,8 +536,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orge867147" class="outline-3">
<h3 id="orge867147"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-orgdd8dff9" class="outline-3">
<h3 id="orgdd8dff9"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div class="outline-text-3" id="text-1-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -660,8 +660,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org35f2c5a" class="outline-3">
<h3 id="org35f2c5a"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of sparse data</h3>
<div id="outline-container-org332b8ed" class="outline-3">
<h3 id="org332b8ed"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of sparse data</h3>
<div class="outline-text-3" id="text-1-6">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -862,8 +862,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org50c528a" class="outline-3">
<h3 id="org50c528a"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-orga671666" class="outline-3">
<h3 id="orga671666"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div class="outline-text-3" id="text-1-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1068,8 +1068,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org381528d" class="outline-3">
<h3 id="org381528d"><span class="section-number-3">1.8</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-orgb35260c" class="outline-3">
<h3 id="orgb35260c"><span class="section-number-3">1.8</span> Template for HDF5 has/read/write the string 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>
@ -1192,8 +1192,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-org6ddfdf2" class="outline-3">
<h3 id="org6ddfdf2"><span class="section-number-3">1.9</span> Helper functions</h3>
<div id="outline-container-org472f553" class="outline-3">
<h3 id="org472f553"><span class="section-number-3">1.9</span> Helper functions</h3>
<div class="outline-text-3" id="text-1-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1443,7 +1443,7 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-12-23 Thu 17:49</p>
<p class="date">Created: 2022-01-05 Wed 12:58</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

82
templator_text.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>
<!-- 2021-12-23 Thu 17:50 -->
<!-- 2022-01-05 Wed 12:58 -->
<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>
@ -311,28 +311,28 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgc77e7c1">1. TEXT back end</a>
<li><a href="#org5a1a8ac">1. TEXT back end</a>
<ul>
<li><a href="#org460bce7">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org4f25bf7">1.2. Template for general structure in text back end</a></li>
<li><a href="#orgff7de1b">1.3. Initialize function (constant part)</a></li>
<li><a href="#org077000d">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org419edc1">1.5. Template for text read struct</a></li>
<li><a href="#org1abb408">1.6. Template for text flush struct</a></li>
<li><a href="#org653dd37">1.7. Template for text free memory</a></li>
<li><a href="#org9107cef">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#org8bc7d98">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org6823590">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org2a7a07c">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org17714f6">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org470e47b">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org9b13300">1.2. Template for general structure in text back end</a></li>
<li><a href="#org8f8ec6e">1.3. Initialize function (constant part)</a></li>
<li><a href="#org3296f37">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org7879e6c">1.5. Template for text read struct</a></li>
<li><a href="#orgcefa01e">1.6. Template for text flush struct</a></li>
<li><a href="#org0437b64">1.7. Template for text free memory</a></li>
<li><a href="#orgf0b4fe4">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orga871de0">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#orgf0927de">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org28258d0">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org2d06a42">1.12. Template for has/read/write the dataset of sparse data</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgc77e7c1" class="outline-2">
<h2 id="orgc77e7c1"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-org5a1a8ac" class="outline-2">
<h2 id="org5a1a8ac"><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
@ -353,8 +353,8 @@ The file is written when closed, or when the flush function is called.
</p>
</div>
<div id="outline-container-org460bce7" class="outline-3">
<h3 id="org460bce7"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-org470e47b" class="outline-3">
<h3 id="org470e47b"><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 {
@ -373,8 +373,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org4f25bf7" class="outline-3">
<h3 id="org4f25bf7"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org9b13300" class="outline-3">
<h3 id="org9b13300"><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> {
@ -387,8 +387,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orgff7de1b" class="outline-3">
<h3 id="orgff7de1b"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-org8f8ec6e" class="outline-3">
<h3 id="org8f8ec6e"><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>
@ -519,8 +519,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org077000d" class="outline-3">
<h3 id="org077000d"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-org3296f37" class="outline-3">
<h3 id="org3296f37"><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>
@ -542,8 +542,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org419edc1" class="outline-3">
<h3 id="org419edc1"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-org7879e6c" class="outline-3">
<h3 id="org7879e6c"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div class="outline-text-3" id="text-1-5">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -835,8 +835,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org1abb408" class="outline-3">
<h3 id="org1abb408"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-orgcefa01e" class="outline-3">
<h3 id="orgcefa01e"><span class="section-number-3">1.6</span> Template for text flush struct</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>
@ -901,8 +901,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org653dd37" class="outline-3">
<h3 id="org653dd37"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-org0437b64" class="outline-3">
<h3 id="org0437b64"><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.
@ -947,8 +947,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-org9107cef" class="outline-3">
<h3 id="org9107cef"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-orgf0b4fe4" class="outline-3">
<h3 id="orgf0b4fe4"><span class="section-number-3">1.8</span> Template for has/read/write the 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>
@ -1011,8 +1011,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-org8bc7d98" class="outline-3">
<h3 id="org8bc7d98"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-orga871de0" class="outline-3">
<h3 id="orga871de0"><span class="section-number-3">1.9</span> Template for has/read/write the 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.
@ -1108,8 +1108,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org6823590" class="outline-3">
<h3 id="org6823590"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-orgf0927de" class="outline-3">
<h3 id="orgf0927de"><span class="section-number-3">1.10</span> Template for has/read/write the 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.
@ -1210,8 +1210,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org2a7a07c" class="outline-3">
<h3 id="org2a7a07c"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-org28258d0" class="outline-3">
<h3 id="org28258d0"><span class="section-number-3">1.11</span> Template for has/read/write the 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>
@ -1285,8 +1285,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org17714f6" class="outline-3">
<h3 id="org17714f6"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div id="outline-container-org2d06a42" class="outline-3">
<h3 id="org2d06a42"><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
@ -1563,7 +1563,7 @@ 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: 2021-12-23 Thu 17:50</p>
<p class="date">Created: 2022-01-05 Wed 12:58</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

116
trex.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>
<!-- 2021-12-23 Thu 17:50 -->
<!-- 2022-01-05 Wed 12:58 -->
<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="#org721885b">1. Metadata (metadata group)</a></li>
<li><a href="#org69d05fd">2. Electron (electron group)</a></li>
<li><a href="#org10943bb">3. Nucleus (nucleus group)</a></li>
<li><a href="#org354636d">4. Effective core potentials (ecp group)</a>
<li><a href="#org1815fc4">1. Metadata (metadata group)</a></li>
<li><a href="#orgf6bf34b">2. Electron (electron group)</a></li>
<li><a href="#org7c2ba42">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgb6d374e">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org1087ae1">4.1. Example</a></li>
<li><a href="#org8e56c0d">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org8b65da1">5. Basis set (basis group)</a>
<li><a href="#orga5f2098">5. Basis set (basis group)</a>
<ul>
<li><a href="#org95a8957">5.1. Example</a></li>
<li><a href="#org95270df">5.1. Example</a></li>
</ul>
</li>
<li><a href="#orgd95749e">6. Atomic orbitals (ao group)</a>
<li><a href="#org7df0aa7">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="#org8861cfe">7. Molecular orbitals (mo group)</a>
<li><a href="#org3d8d144">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org4ee4f08">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org4b2c19f">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org078333c">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org66bf651">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org7e8c53d">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org50dd1bf">9. Reduced density matrices (rdm group)</a></li>
<li><a href="#org0b4b5ad">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org71500ab">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-org721885b" class="outline-2">
<h2 id="org721885b"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org1815fc4" class="outline-2">
<h2 id="org1815fc4"><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="org94cef9f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org926a548" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -487,15 +487,15 @@ authors of the file, and a textual description.
</div>
</div>
<div id="outline-container-org69d05fd" class="outline-2">
<h2 id="org69d05fd"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orgf6bf34b" class="outline-2">
<h2 id="orgf6bf34b"><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="org0ecb5b9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgad512a1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -534,15 +534,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org10943bb" class="outline-2">
<h2 id="org10943bb"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org7c2ba42" class="outline-2">
<h2 id="org7c2ba42"><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="org11c864f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbb02f85" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -609,8 +609,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org354636d" class="outline-2">
<h2 id="org354636d"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orgb6d374e" class="outline-2">
<h2 id="orgb6d374e"><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
@ -643,7 +643,7 @@ 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="org9d1ffdc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7cb59ee" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -741,8 +741,8 @@ The latter causes issues when written before <code>ang_mom</code> in the TREXIO
</p>
</div>
<div id="outline-container-org1087ae1" class="outline-3">
<h3 id="org1087ae1"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org8e56c0d" class="outline-3">
<h3 id="org8e56c0d"><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
@ -805,8 +805,8 @@ power = [
</div>
</div>
<div id="outline-container-org8b65da1" class="outline-2">
<h2 id="org8b65da1"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-orga5f2098" class="outline-2">
<h2 id="orga5f2098"><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
@ -859,7 +859,7 @@ 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="orgad677b5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf49d33e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -953,8 +953,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-org95a8957" class="outline-3">
<h3 id="org95a8957"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org95270df" class="outline-3">
<h3 id="org95270df"><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
@ -1032,8 +1032,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgd95749e" class="outline-2">
<h2 id="orgd95749e"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org7df0aa7" class="outline-2">
<h2 id="org7df0aa7"><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
@ -1081,13 +1081,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org8b65da1">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#orga5f2098">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="org27fcc9f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org46e3da2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1139,8 +1139,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org1c23f2f" class="outline-3">
<h3 id="ao_one_e"><a id="org1c23f2f"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org3c7a8f8" class="outline-3">
<h3 id="ao_one_e"><a id="org3c7a8f8"></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}}
@ -1158,7 +1158,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org15f0c84" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgce26774" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1225,8 +1225,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgbbf6192" class="outline-3">
<h3 id="ao_two_e"><a id="orgbbf6192"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-orgbe9c219" class="outline-3">
<h3 id="ao_two_e"><a id="orgbe9c219"></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
@ -1247,7 +1247,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org9ecb890" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org48bb774" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1287,10 +1287,10 @@ notation.
</div>
</div>
<div id="outline-container-org8861cfe" class="outline-2">
<h2 id="org8861cfe"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org3d8d144" class="outline-2">
<h2 id="org3d8d144"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="orgae1fe9e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcdf0cc8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1356,8 +1356,8 @@ notation.
</table>
</div>
<div id="outline-container-org4ee4f08" class="outline-3">
<h3 id="org4ee4f08"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org078333c" class="outline-3">
<h3 id="org078333c"><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
@ -1365,7 +1365,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org605ba8b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org61f73f1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1432,8 +1432,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org4b2c19f" class="outline-3">
<h3 id="org4b2c19f"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org66bf651" class="outline-3">
<h3 id="org66bf651"><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
@ -1441,7 +1441,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgc92474c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7066b59" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1481,13 +1481,13 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org7e8c53d" class="outline-2">
<h2 id="org7e8c53d"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-org0b4b5ad" class="outline-2">
<h2 id="org0b4b5ad"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-org50dd1bf" class="outline-2">
<h2 id="org50dd1bf"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org71500ab" class="outline-2">
<h2 id="org71500ab"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
<table id="orge96736a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfb09daf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1563,7 +1563,7 @@ the basis of molecular orbitals.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-12-23 Thu 17:50</p>
<p class="date">Created: 2022-01-05 Wed 12:58</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>