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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: 2022-04-29 Fri 14:20</p>
<p class="date">Created: 2022-05-06 Fri 09:09</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-04-29 Fri 14:20 -->
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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="#orgca98111">1. Accessing sparse quantities</a>
<li><a href="#org1ce0257">1. Accessing sparse quantities</a>
<ul>
<li><a href="#orge447559">1.1. Fortran</a>
<li><a href="#org84ea310">1.1. Fortran</a>
<ul>
<li><a href="#org08f1df0">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orge0f630f">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgd7a4eb8">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org15d098b">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org7b460b4">1.1.5. Allocate memory</a></li>
<li><a href="#orga4a62c5">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orga9fca57">1.1.7. Read two-electron quantities</a>
<li><a href="#org0b390a0">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org1a2a689">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org55cbc0e">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgf79c4df">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgfdea5e6">1.1.5. Allocate memory</a></li>
<li><a href="#orgaf4e889">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org504e54d">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgf816175">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org6ff6f10">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org4212e44">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orga7f2023">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgf6bbd05">1.1.8. Compute the energy</a></li>
<li><a href="#org5da25c6">1.1.9. Terminate</a></li>
<li><a href="#orgcc1cc6d">1.1.8. Compute the energy</a></li>
<li><a href="#org63bafe5">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-orgca98111" class="outline-2">
<h2 id="orgca98111"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-org1ce0257" class="outline-2">
<h2 id="org1ce0257"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orge447559" class="outline-3">
<h3 id="orge447559"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org84ea310" class="outline-3">
<h3 id="org84ea310"><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-org08f1df0" class="outline-4">
<h4 id="org08f1df0"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org0b390a0" class="outline-4">
<h4 id="org0b390a0"><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-orge0f630f" class="outline-4">
<h4 id="orge0f630f"><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-org1a2a689" class="outline-4">
<h4 id="org1a2a689"><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-orgd7a4eb8" class="outline-4">
<h4 id="orgd7a4eb8"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org55cbc0e" class="outline-4">
<h4 id="org55cbc0e"><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-org15d098b" class="outline-4">
<h4 id="org15d098b"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgf79c4df" class="outline-4">
<h4 id="orgf79c4df"><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-org7b460b4" class="outline-4">
<h4 id="org7b460b4"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-orgfdea5e6" class="outline-4">
<h4 id="orgfdea5e6"><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-orga4a62c5" class="outline-4">
<h4 id="orga4a62c5"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgaf4e889" class="outline-4">
<h4 id="orgaf4e889"><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-orga9fca57" class="outline-4">
<h4 id="orga9fca57"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org504e54d" class="outline-4">
<h4 id="org504e54d"><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-orgf816175" class="outline-5">
<h5 id="orgf816175"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org4212e44" class="outline-5">
<h5 id="org4212e44"><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-org6ff6f10" class="outline-5">
<h5 id="org6ff6f10"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orga7f2023" class="outline-5">
<h5 id="orga7f2023"><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-orgf6bbd05" class="outline-4">
<h4 id="orgf6bbd05"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-orgcc1cc6d" class="outline-4">
<h4 id="orgcc1cc6d"><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-org5da25c6" class="outline-4">
<h4 id="org5da25c6"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org63bafe5" class="outline-4">
<h4 id="org63bafe5"><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: 2022-04-29 Fri 14:20</p>
<p class="date">Created: 2022-05-06 Fri 09:09</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>
<!-- 2022-04-29 Fri 14:20 -->
<!-- 2022-05-06 Fri 09:09 -->
<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: 2022-04-29 Fri 14:20</p>
<p class="date">Created: 2022-05-06 Fri 09:09</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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<head>
<!-- 2022-04-29 Fri 14:20 -->
<!-- 2022-05-06 Fri 09:09 -->
<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>
@ -311,23 +311,23 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgf4a9a90">1. Template for HDF5 definitions</a></li>
<li><a href="#orgc30c187">2. Template for HDF5 structures</a></li>
<li><a href="#orgf9e4e88">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgf49b4c1">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org0292bc8">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org336e3e8">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org2a242d0">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org5513971">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgc151942">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org64ae168">10. Source code for the determinant part</a></li>
<li><a href="#orgf6e20f8">11. Helper functions</a></li>
<li><a href="#org4715362">1. Template for HDF5 definitions</a></li>
<li><a href="#org123241f">2. Template for HDF5 structures</a></li>
<li><a href="#orgce116ae">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orge9d9e04">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org5bf214f">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgdb02241">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org2e57b58">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orga9102e5">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgcbc633c">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgbeec730">10. Source code for the determinant part</a></li>
<li><a href="#orga094401">11. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgf4a9a90" class="outline-2">
<h2 id="orgf4a9a90"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org4715362" class="outline-2">
<h2 id="org4715362"><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>
@ -339,8 +339,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgc30c187" class="outline-2">
<h2 id="orgc30c187"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org123241f" class="outline-2">
<h2 id="org123241f"><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> {
@ -353,8 +353,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgf9e4e88" class="outline-2">
<h2 id="orgf9e4e88"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgce116ae" class="outline-2">
<h2 id="orgce116ae"><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>
@ -459,8 +459,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgf49b4c1" class="outline-2">
<h2 id="orgf49b4c1"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orge9d9e04" class="outline-2">
<h2 id="orge9d9e04"><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>
@ -564,8 +564,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org0292bc8" class="outline-2">
<h2 id="org0292bc8"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org5bf214f" class="outline-2">
<h2 id="org5bf214f"><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>
@ -699,8 +699,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org336e3e8" class="outline-2">
<h2 id="org336e3e8"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orgdb02241" class="outline-2">
<h2 id="orgdb02241"><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
@ -903,8 +903,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org2a242d0" class="outline-2">
<h2 id="org2a242d0"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org2e57b58" class="outline-2">
<h2 id="org2e57b58"><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>
@ -1102,8 +1102,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org5513971" class="outline-2">
<h2 id="org5513971"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orga9102e5" class="outline-2">
<h2 id="orga9102e5"><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>
@ -1230,8 +1230,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-orgc151942" class="outline-2">
<h2 id="orgc151942"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgcbc633c" class="outline-2">
<h2 id="orgcbc633c"><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
@ -1271,8 +1271,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org64ae168" class="outline-2">
<h2 id="org64ae168"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div id="outline-container-orgbeec730" class="outline-2">
<h2 id="orgbeec730"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-10">
<p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1525,8 +1525,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-orgf6e20f8" class="outline-2">
<h2 id="orgf6e20f8"><span class="section-number-2">11</span> Helper functions</h2>
<div id="outline-container-orga094401" class="outline-2">
<h2 id="orga094401"><span class="section-number-2">11</span> Helper functions</h2>
<div class="outline-text-2" id="text-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1789,7 +1789,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-04-29 Fri 14:20</p>
<p class="date">Created: 2022-05-06 Fri 09:09</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

88
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>
<!-- 2022-04-29 Fri 14:20 -->
<!-- 2022-05-06 Fri 09:09 -->
<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>
@ -311,20 +311,20 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9c3f354">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgbfb31ce">2. Template for general structure in text back end</a></li>
<li><a href="#org292f468">3. Initialize function (constant part)</a></li>
<li><a href="#org0345f99">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgcd7e8c6">5. Template for text read a group</a></li>
<li><a href="#org366a5b1">6. Template for text flush a group</a></li>
<li><a href="#org82cfc38">7. Template for text free memory</a></li>
<li><a href="#orgeb8a677">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orge7ce255">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgf6b586a">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgfb48b7f">11. Template for has/read/write a string attribute</a></li>
<li><a href="#orgcea9da2">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org6758844">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org379dcb1">14. Source code for the determinant part</a></li>
<li><a href="#org209e5cc">1. Template for group-related structures in text back end</a></li>
<li><a href="#orga5df7f3">2. Template for general structure in text back end</a></li>
<li><a href="#org0ca6c48">3. Initialize function (constant part)</a></li>
<li><a href="#org2d39bde">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgbe90f33">5. Template for text read a group</a></li>
<li><a href="#orgfc1ceb1">6. Template for text flush a group</a></li>
<li><a href="#org06dfdb7">7. Template for text free memory</a></li>
<li><a href="#org2413d6d">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgc2c0a66">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org0bb7a0d">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgb588e9f">11. Template for has/read/write a string attribute</a></li>
<li><a href="#orga6a3b95">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org570b39a">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org68408be">14. Source code for the determinant part</a></li>
</ul>
</div>
</div>
@ -346,8 +346,8 @@ directory.
The file is written when closed, or when the flush function is called.
</p>
<div id="outline-container-org9c3f354" class="outline-2">
<h2 id="org9c3f354"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org209e5cc" class="outline-2">
<h2 id="org209e5cc"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div class="outline-text-2" id="text-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
@ -366,8 +366,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orgbfb31ce" class="outline-2">
<h2 id="orgbfb31ce"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orga5df7f3" class="outline-2">
<h2 id="orga5df7f3"><span class="section-number-2">2</span> Template for general structure in text back end</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_text_s</span> {
@ -380,8 +380,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org292f468" class="outline-2">
<h2 id="org292f468"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org0ca6c48" class="outline-2">
<h2 id="org0ca6c48"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -524,8 +524,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org0345f99" class="outline-2">
<h2 id="org0345f99"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org2d39bde" class="outline-2">
<h2 id="org2d39bde"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -547,8 +547,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orgcd7e8c6" class="outline-2">
<h2 id="orgcd7e8c6"><span class="section-number-2">5</span> Template for text read a group</h2>
<div id="outline-container-orgbe90f33" class="outline-2">
<h2 id="orgbe90f33"><span class="section-number-2">5</span> Template for text read a group</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -849,8 +849,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org366a5b1" class="outline-2">
<h2 id="org366a5b1"><span class="section-number-2">6</span> Template for text flush a group</h2>
<div id="outline-container-orgfc1ceb1" class="outline-2">
<h2 id="orgfc1ceb1"><span class="section-number-2">6</span> Template for text flush a group</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -914,8 +914,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org82cfc38" class="outline-2">
<h2 id="org82cfc38"><span class="section-number-2">7</span> Template for text free memory</h2>
<div id="outline-container-org06dfdb7" class="outline-2">
<h2 id="org06dfdb7"><span class="section-number-2">7</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-7">
<p>
Memory is allocated when reading. The following function frees memory.
@ -962,8 +962,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-orgeb8a677" class="outline-2">
<h2 id="orgeb8a677"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org2413d6d" class="outline-2">
<h2 id="org2413d6d"><span class="section-number-2">8</span> Template for has/read/write a numerical 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>
@ -1026,8 +1026,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-orge7ce255" class="outline-2">
<h2 id="orge7ce255"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgc2c0a66" class="outline-2">
<h2 id="orgc2c0a66"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-9">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1123,8 +1123,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgf6b586a" class="outline-2">
<h2 id="orgf6b586a"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org0bb7a0d" class="outline-2">
<h2 id="org0bb7a0d"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-10">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1225,8 +1225,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgfb48b7f" class="outline-2">
<h2 id="orgfb48b7f"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orgb588e9f" class="outline-2">
<h2 id="orgb588e9f"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1300,8 +1300,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgcea9da2" class="outline-2">
<h2 id="orgcea9da2"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orga6a3b95" class="outline-2">
<h2 id="orga6a3b95"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-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
@ -1575,8 +1575,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org6758844" class="outline-2">
<h2 id="org6758844"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org570b39a" class="outline-2">
<h2 id="org570b39a"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1604,8 +1604,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org379dcb1" class="outline-2">
<h2 id="org379dcb1"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div id="outline-container-org68408be" class="outline-2">
<h2 id="org68408be"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-14">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -2009,7 +2009,7 @@ Size specifies the number of data items, e.g. determinants.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-04-29 Fri 14:20</p>
<p class="date">Created: 2022-05-06 Fri 09:09</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

134
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>
<!-- 2022-04-29 Fri 14:20 -->
<!-- 2022-05-06 Fri 09:09 -->
<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>
@ -333,35 +333,35 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgf0c185d">1. Metadata (metadata group)</a></li>
<li><a href="#org26456a5">2. Electron (electron group)</a></li>
<li><a href="#org3795725">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgb99052a">4. Effective core potentials (ecp group)</a>
<li><a href="#org7298043">1. Metadata (metadata group)</a></li>
<li><a href="#org6719728">2. Electron (electron group)</a></li>
<li><a href="#orgfce12b6">3. Nucleus (nucleus group)</a></li>
<li><a href="#org2215159">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgdb10996">4.1. Example</a></li>
<li><a href="#org27dbd85">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org7361efb">5. Basis set (basis group)</a>
<li><a href="#org2c04851">5. Basis set (basis group)</a>
<ul>
<li><a href="#orgd1e4da5">5.1. Example</a></li>
<li><a href="#orgc237734">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org12faf86">6. Atomic orbitals (ao group)</a>
<li><a href="#orgb2196d3">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="#orgeced7cb">7. Molecular orbitals (mo group)</a>
<li><a href="#org57bef24">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orge0ac2ff">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgd34b29e">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org7502a33">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orga2d1fd1">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org9ab7e92">8. Slater determinants (determinant group)</a></li>
<li><a href="#org09fe11a">9. Excited states (state group)</a></li>
<li><a href="#org724db1e">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org50f0a2c">11. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#orge6c9ce0">8. Slater determinants (determinant group)</a></li>
<li><a href="#orge377fa1">9. Excited states (state group)</a></li>
<li><a href="#orgb32bbd4">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#orge3ff0a0">11. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -407,8 +407,8 @@ the <a href="./examples.html">examples</a>.
</p>
<div id="outline-container-orgf0c185d" class="outline-2">
<h2 id="orgf0c185d"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org7298043" class="outline-2">
<h2 id="org7298043"><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
@ -418,7 +418,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="org745310b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9b49cbd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -499,15 +499,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-org26456a5" class="outline-2">
<h2 id="org26456a5"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org6719728" class="outline-2">
<h2 id="org6719728"><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="orgd287ae1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org25fad49" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -553,15 +553,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org3795725" class="outline-2">
<h2 id="org3795725"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-orgfce12b6" class="outline-2">
<h2 id="orgfce12b6"><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="org18baaf4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org22433c4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -628,8 +628,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-orgb99052a" class="outline-2">
<h2 id="orgb99052a"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org2215159" class="outline-2">
<h2 id="org2215159"><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
@ -662,7 +662,7 @@ 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="org19f76a6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge48112b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -764,8 +764,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-orgdb10996" class="outline-3">
<h3 id="orgdb10996"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org27dbd85" class="outline-3">
<h3 id="org27dbd85"><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
@ -828,8 +828,8 @@ power = [
</div>
</div>
<div id="outline-container-org7361efb" class="outline-2">
<h2 id="org7361efb"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org2c04851" class="outline-2">
<h2 id="org2c04851"><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
@ -882,7 +882,7 @@ 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="org2bd7321" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org96b0133" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -976,8 +976,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-orgd1e4da5" class="outline-3">
<h3 id="orgd1e4da5"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-orgc237734" class="outline-3">
<h3 id="orgc237734"><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
@ -1055,8 +1055,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org12faf86" class="outline-2">
<h2 id="org12faf86"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-orgb2196d3" class="outline-2">
<h2 id="orgb2196d3"><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
@ -1109,13 +1109,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org7361efb">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org2c04851">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="orgc4dc32a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7452ebd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1167,8 +1167,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org0280e53" class="outline-3">
<h3 id="ao_one_e"><a id="org0280e53"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org497b2e8" class="outline-3">
<h3 id="ao_one_e"><a id="org497b2e8"></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}}
@ -1185,7 +1185,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgc0d2456" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5749a1d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1245,8 +1245,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org6c0e26d" class="outline-3">
<h3 id="ao_two_e"><a id="org6c0e26d"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-orgad00540" class="outline-3">
<h3 id="ao_two_e"><a id="orgad00540"></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
@ -1267,7 +1267,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="orga248999" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb77f2a8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1307,10 +1307,10 @@ notation.
</div>
</div>
<div id="outline-container-orgeced7cb" class="outline-2">
<h2 id="orgeced7cb"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org57bef24" class="outline-2">
<h2 id="org57bef24"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org9c038de" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbf1edd5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1376,8 +1376,8 @@ notation.
</table>
</div>
<div id="outline-container-orge0ac2ff" class="outline-3">
<h3 id="orge0ac2ff"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org7502a33" class="outline-3">
<h3 id="org7502a33"><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
@ -1385,7 +1385,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org546274c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org81b9d8e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1445,8 +1445,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgd34b29e" class="outline-3">
<h3 id="orgd34b29e"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orga2d1fd1" class="outline-3">
<h3 id="orga2d1fd1"><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
@ -1454,7 +1454,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org4a0ff86" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org53d504a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1494,8 +1494,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org9ab7e92" class="outline-2">
<h2 id="org9ab7e92"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-orge6c9ce0" class="outline-2">
<h2 id="orge6c9ce0"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div class="outline-text-2" id="text-8">
<p>
The configuration interaction (CI) wave function \(\Psi\)
@ -1560,7 +1560,7 @@ Internally, bit fields for \(\alpha\) and \(\beta\) electrons are stored separat
which is why the <code>determinant.list</code> attribute has a second dimension.
</p>
<table id="orge4370a9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org878ec70" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1606,8 +1606,8 @@ which is why the <code>determinant.list</code> attribute has a second dimension.
</div>
</div>
<div id="outline-container-org09fe11a" class="outline-2">
<h2 id="org09fe11a"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div id="outline-container-orge377fa1" class="outline-2">
<h2 id="orge377fa1"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div class="outline-text-2" id="text-9">
<p>
By default, the <code>determinant</code> group corresponds to the ground state.
@ -1616,7 +1616,7 @@ correspond to excited state wave functions for the same set of
determinants. This is the goal of the present group
</p>
<table id="org8cf36a7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org155ab99" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1655,8 +1655,8 @@ determinants. This is the goal of the present group
</div>
</div>
<div id="outline-container-org724db1e" class="outline-2">
<h2 id="org724db1e"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orgb32bbd4" class="outline-2">
<h2 id="orgb32bbd4"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-10">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1709,7 +1709,7 @@ The total energy can be computed as:
\]
</p>
<table id="org7fc114e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgabab98d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1790,8 +1790,8 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org50f0a2c" class="outline-2">
<h2 id="org50f0a2c"><span class="section-number-2">11</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-orge3ff0a0" class="outline-2">
<h2 id="orge3ff0a0"><span class="section-number-2">11</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-11">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -1805,7 +1805,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="org594a8e2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd3ceca7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1860,7 +1860,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-04-29 Fri 14:20</p>
<p class="date">Created: 2022-05-06 Fri 09:09</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>