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README.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -360,7 +360,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-12-13 Tue 16:09</p>
<p class="date">Created: 2022-12-13 Tue 16:10</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-12-13 Tue 16:09 -->
<!-- 2022-12-13 Tue 16:10 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Examples</title>
@ -346,31 +346,31 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgc7394f9">1. Accessing sparse quantities (integrals)</a>
<li><a href="#orgfddc3b1">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#orgbb5c37d">1.1. Fortran</a>
<li><a href="#org9d1b8c9">1.1. Fortran</a>
<ul>
<li><a href="#org9c44353">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orge466609">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orge881812">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org63cc42c">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org5fdc731">1.1.5. Allocate memory</a></li>
<li><a href="#orga4fcf1d">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgade29d1">1.1.7. Read two-electron quantities</a>
<li><a href="#org1bab83f">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org4e1d5e2">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org0f920f8">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgeeab298">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org6923f37">1.1.5. Allocate memory</a></li>
<li><a href="#orgbcca21f">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org030a94e">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org612c9d7">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org7991bd6">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org0375961">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org498752b">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org45add8f">1.1.8. Compute the energy</a></li>
<li><a href="#orgc9de67d">1.1.9. Terminate</a></li>
<li><a href="#org749c8c1">1.1.8. Compute the energy</a></li>
<li><a href="#orgaad6518">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgc1627db">2. Reading determinants</a>
<li><a href="#orga08e7b0">2. Reading determinants</a>
<ul>
<li><a href="#orgeb7e4b8">2.1. Fortran</a></li>
<li><a href="#org1046bb7">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -378,12 +378,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgc7394f9" class="outline-2">
<h2 id="orgc7394f9"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orgfddc3b1" class="outline-2">
<h2 id="orgfddc3b1"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orgbb5c37d" class="outline-3">
<h3 id="orgbb5c37d"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org9d1b8c9" class="outline-3">
<h3 id="org9d1b8c9"><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>
@ -429,8 +429,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org9c44353" class="outline-4">
<h4 id="org9c44353"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org1bab83f" class="outline-4">
<h4 id="org1bab83f"><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>
@ -445,8 +445,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orge466609" class="outline-4">
<h4 id="orge466609"><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-org4e1d5e2" class="outline-4">
<h4 id="org4e1d5e2"><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)
@ -462,8 +462,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orge881812" class="outline-4">
<h4 id="orge881812"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org0f920f8" class="outline-4">
<h4 id="org0f920f8"><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)
@ -477,8 +477,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org63cc42c" class="outline-4">
<h4 id="org63cc42c"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgeeab298" class="outline-4">
<h4 id="orgeeab298"><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)
@ -492,8 +492,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org5fdc731" class="outline-4">
<h4 id="org5fdc731"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org6923f37" class="outline-4">
<h4 id="org6923f37"><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) )
@ -505,8 +505,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-orga4fcf1d" class="outline-4">
<h4 id="orga4fcf1d"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgbcca21f" class="outline-4">
<h4 id="orgbcca21f"><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)
@ -538,8 +538,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-orgade29d1" class="outline-4">
<h4 id="orgade29d1"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org030a94e" class="outline-4">
<h4 id="org030a94e"><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
@ -555,8 +555,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org612c9d7" class="outline-5">
<h5 id="org612c9d7"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org0375961" class="outline-5">
<h5 id="org0375961"><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)
@ -605,8 +605,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-org7991bd6" class="outline-5">
<h5 id="org7991bd6"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org498752b" class="outline-5">
<h5 id="org498752b"><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)
@ -650,8 +650,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org45add8f" class="outline-4">
<h4 id="org45add8f"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org749c8c1" class="outline-4">
<h4 id="org749c8c1"><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
@ -697,8 +697,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-orgc9de67d" class="outline-4">
<h4 id="orgc9de67d"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgaad6518" class="outline-4">
<h4 id="orgaad6518"><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 )
@ -712,12 +712,12 @@ E = E + E_nn
</div>
<div id="outline-container-orgc1627db" class="outline-2">
<h2 id="orgc1627db"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-orga08e7b0" class="outline-2">
<h2 id="orga08e7b0"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgeb7e4b8" class="outline-3">
<h3 id="orgeb7e4b8"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org1046bb7" class="outline-3">
<h3 id="org1046bb7"><span class="section-number-3">2.1</span> Fortran</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
@ -796,7 +796,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-12-13 Tue 16:09</p>
<p class="date">Created: 2022-12-13 Tue 16:10</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>
<!-- 2022-12-13 Tue 16:09 -->
<!-- 2022-12-13 Tue 16:10 -->
<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>
@ -360,7 +360,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-12-13 Tue 16:09</p>
<p class="date">Created: 2022-12-13 Tue 16:10</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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templator_front.html
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orged474a5">1. Template for HDF5 definitions</a></li>
<li><a href="#org10a3b4a">2. Template for HDF5 structures</a></li>
<li><a href="#org5a002c4">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org9d10581">4. Template for HDF5 has a group</a></li>
<li><a href="#org4040a55">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org87b3285">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orga9c2d99">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org2458369">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org2c8d6c0">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org926bce3">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org7051ef1">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgfeba6e1">12. Source code for the determinant part</a></li>
<li><a href="#org4d76779">13. Helper functions</a></li>
<li><a href="#orgd34030b">1. Template for HDF5 definitions</a></li>
<li><a href="#org04e001e">2. Template for HDF5 structures</a></li>
<li><a href="#org5dfd60b">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org9438ff2">4. Template for HDF5 has a group</a></li>
<li><a href="#orgcd2b227">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgc7c8ec8">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orge28a579">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org3c69b87">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org45ed77c">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org1c5137f">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org0ab6955">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org58a543e">12. Source code for the determinant part</a></li>
<li><a href="#org229f9ae">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orged474a5" class="outline-2">
<h2 id="orged474a5"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orgd34030b" class="outline-2">
<h2 id="orgd34030b"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div class="outline-text-2" id="text-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #483d8b;">#define</span> $GROUP$_GROUP_NAME <span style="color: #8b2252;">"$group$"</span>
@ -354,8 +354,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org10a3b4a" class="outline-2">
<h2 id="org10a3b4a"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org04e001e" class="outline-2">
<h2 id="org04e001e"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div class="outline-text-2" id="text-2">
<p>
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
@ -375,8 +375,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org5a002c4" class="outline-2">
<h2 id="org5a002c4"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org5dfd60b" class="outline-2">
<h2 id="org5dfd60b"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -496,8 +496,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org9d10581" class="outline-2">
<h2 id="org9d10581"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org9438ff2" class="outline-2">
<h2 id="org9438ff2"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -527,8 +527,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org4040a55" class="outline-2">
<h2 id="org4040a55"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orgcd2b227" class="outline-2">
<h2 id="orgcd2b227"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -632,8 +632,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org87b3285" class="outline-2">
<h2 id="org87b3285"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgc7c8ec8" class="outline-2">
<h2 id="orgc7c8ec8"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -767,8 +767,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orga9c2d99" class="outline-2">
<h2 id="orga9c2d99"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orge28a579" class="outline-2">
<h2 id="orge28a579"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-7">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -971,8 +971,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org2458369" class="outline-2">
<h2 id="org2458369"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org3c69b87" class="outline-2">
<h2 id="org3c69b87"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div class="outline-text-2" id="text-8">
<p>
Chunked I/O in HDF5 for <code>buffered</code> data.
@ -1107,8 +1107,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org2c8d6c0" class="outline-2">
<h2 id="org2c8d6c0"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org45ed77c" class="outline-2">
<h2 id="org45ed77c"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org926bce3" class="outline-2">
<h2 id="org926bce3"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org1c5137f" class="outline-2">
<h2 id="org1c5137f"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1434,8 +1434,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
</div>
<div id="outline-container-org7051ef1" class="outline-2">
<h2 id="org7051ef1"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org0ab6955" class="outline-2">
<h2 id="org0ab6955"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-11">
<p>
<b><b>Note:</b></b> in early versions of the HDF5 library (v &lt; 1.10) unlinking an object was not working as expected
@ -1475,8 +1475,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-orgfeba6e1" class="outline-2">
<h2 id="orgfeba6e1"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org58a543e" class="outline-2">
<h2 id="org58a543e"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-12">
<p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1579,8 +1579,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org4d76779" class="outline-2">
<h2 id="org4d76779"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org229f9ae" class="outline-2">
<h2 id="org229f9ae"><span class="section-number-2">13</span> Helper functions</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>

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@ -324,23 +324,23 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgd36d627">1. Template for group-related structures in text back end</a></li>
<li><a href="#org392910c">2. Template for general structure in text back end</a></li>
<li><a href="#org68ea668">3. Initialize function (constant part)</a></li>
<li><a href="#org64ed749">4. Deinitialize function (templated part)</a></li>
<li><a href="#org79af832">5. Flush function (templated part)</a></li>
<li><a href="#org976b1ce">6. Template for text read a group</a></li>
<li><a href="#org4f6bce9">7. Template for text has a group</a></li>
<li><a href="#orga6932e6">8. Template for text flush a group</a></li>
<li><a href="#org48d0a44">9. Template for text free memory</a></li>
<li><a href="#org8e3090e">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgbb45c62">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgb04410c">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org8291626">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgefd4e4b">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgecf45c1">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org6a196a4">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org377b939">17. Source code for the determinant part</a></li>
<li><a href="#org0dd83e7">1. Template for group-related structures in text back end</a></li>
<li><a href="#org8a452ca">2. Template for general structure in text back end</a></li>
<li><a href="#org413d152">3. Initialize function (constant part)</a></li>
<li><a href="#orgbcc1b0f">4. Deinitialize function (templated part)</a></li>
<li><a href="#org47ac91d">5. Flush function (templated part)</a></li>
<li><a href="#org1a29416">6. Template for text read a group</a></li>
<li><a href="#orgbff7a05">7. Template for text has a group</a></li>
<li><a href="#org48e4dec">8. Template for text flush a group</a></li>
<li><a href="#org011ecac">9. Template for text free memory</a></li>
<li><a href="#org2422bc5">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org3e9c97b">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org710ebfc">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org59e623c">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org24e320e">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgdde7a4e">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org37c5e00">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org00faa46">17. Source code for the determinant part</a></li>
</ul>
</div>
</div>
@ -362,8 +362,8 @@ directory.
The file is written when closed, or when the flush function is called.
</p>
<div id="outline-container-orgd36d627" class="outline-2">
<h2 id="orgd36d627"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org0dd83e7" class="outline-2">
<h2 id="org0dd83e7"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div class="outline-text-2" id="text-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
@ -382,8 +382,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org392910c" class="outline-2">
<h2 id="org392910c"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org8a452ca" class="outline-2">
<h2 id="org8a452ca"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div class="outline-text-2" id="text-2">
<p>
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
@ -403,8 +403,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org68ea668" class="outline-2">
<h2 id="org68ea668"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org413d152" class="outline-2">
<h2 id="org413d152"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">bool</span>
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org64ed749" class="outline-2">
<h2 id="org64ed749"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgbcc1b0f" class="outline-2">
<h2 id="orgbcc1b0f"><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>
@ -594,8 +594,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org79af832" class="outline-2">
<h2 id="org79af832"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org47ac91d" class="outline-2">
<h2 id="org47ac91d"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -618,8 +618,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org976b1ce" class="outline-2">
<h2 id="org976b1ce"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org1a29416" class="outline-2">
<h2 id="org1a29416"><span class="section-number-2">6</span> Template for text read a group</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -845,8 +845,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org4f6bce9" class="outline-2">
<h2 id="org4f6bce9"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-orgbff7a05" class="outline-2">
<h2 id="orgbff7a05"><span class="section-number-2">7</span> Template for text has a group</h2>
<div class="outline-text-2" id="text-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -886,8 +886,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orga6932e6" class="outline-2">
<h2 id="orga6932e6"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org48e4dec" class="outline-2">
<h2 id="org48e4dec"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div class="outline-text-2" id="text-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -951,8 +951,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org48d0a44" class="outline-2">
<h2 id="org48d0a44"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org011ecac" class="outline-2">
<h2 id="org011ecac"><span class="section-number-2">9</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-9">
<p>
Memory is allocated when reading. The following function frees memory.
@ -1021,8 +1021,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org8e3090e" class="outline-2">
<h2 id="org8e3090e"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org2422bc5" class="outline-2">
<h2 id="org2422bc5"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1085,8 +1085,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orgbb45c62" class="outline-2">
<h2 id="orgbb45c62"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org3e9c97b" class="outline-2">
<h2 id="org3e9c97b"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-11">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1182,8 +1182,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgb04410c" class="outline-2">
<h2 id="orgb04410c"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org710ebfc" class="outline-2">
<h2 id="org710ebfc"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-12">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1284,8 +1284,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org8291626" class="outline-2">
<h2 id="org8291626"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org59e623c" class="outline-2">
<h2 id="org59e623c"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1359,8 +1359,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgefd4e4b" class="outline-2">
<h2 id="orgefd4e4b"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org24e320e" class="outline-2">
<h2 id="org24e320e"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-14">
<p>
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
@ -1650,8 +1650,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-orgecf45c1" class="outline-2">
<h2 id="orgecf45c1"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-orgdde7a4e" class="outline-2">
<h2 id="orgdde7a4e"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div class="outline-text-2" id="text-15">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that buffered I/O has to be decoupled
@ -1881,8 +1881,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-org6a196a4" class="outline-2">
<h2 id="org6a196a4"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org37c5e00" class="outline-2">
<h2 id="org37c5e00"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-16">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1910,8 +1910,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-org377b939" class="outline-2">
<h2 id="org377b939"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org00faa46" class="outline-2">
<h2 id="org00faa46"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-17">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled

154
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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>
<!-- 2022-12-13 Tue 16:09 -->
<!-- 2022-12-13 Tue 16:10 -->
<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>
@ -346,38 +346,38 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org386724a">1. Metadata (metadata group)</a></li>
<li><a href="#orgdb3b43a">2. Electron (electron group)</a></li>
<li><a href="#orga952471">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgef9392e">4. Effective core potentials (ecp group)</a>
<li><a href="#orgc0b7ad2">1. Metadata (metadata group)</a></li>
<li><a href="#org18889b8">2. Electron (electron group)</a></li>
<li><a href="#org0087f85">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgc70756d">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgc6f3ffa">4.1. Example</a></li>
<li><a href="#org902cc0a">4.1. Example</a></li>
</ul>
</li>
<li><a href="#orgd4da5fc">5. Basis set (basis group)</a>
<li><a href="#orgef69be3">5. Basis set (basis group)</a>
<ul>
<li><a href="#orga9ae56b">5.1. Example</a></li>
<li><a href="#org28374ca">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org7512c0a">6. Atomic orbitals (ao group)</a>
<li><a href="#org4910989">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="#orgede8270">7. Molecular orbitals (mo group)</a>
<li><a href="#orga1e8ae3">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orge058064">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgaba70e8">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgea5dbf4">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org63def0b">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#orgab751af">8. Slater determinants (determinant group)</a></li>
<li><a href="#org4434ab1">9. Configuration state functions (csf group)</a></li>
<li><a href="#org0623e66">10. Excited states (state group)</a></li>
<li><a href="#orgb0c1706">11. Reduced density matrices (rdm group)</a></li>
<li><a href="#org38ce760">12. Cell (cell group)</a></li>
<li><a href="#org8e203f3">13. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orge6c6fe5">14. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#orgac67ff5">8. Slater determinants (determinant group)</a></li>
<li><a href="#org8cb782b">9. Configuration state functions (csf group)</a></li>
<li><a href="#orgfb3a4c1">10. Excited states (state group)</a></li>
<li><a href="#orgd24b81a">11. Reduced density matrices (rdm group)</a></li>
<li><a href="#org71d238c">12. Cell (cell group)</a></li>
<li><a href="#org437a801">13. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgcd97803">14. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -439,8 +439,8 @@ For determinant lists (integer bit fields), the <code>special</code> attribute i
This means that the source code is not produced by the generator, but hand-written.
</p>
<div id="outline-container-org386724a" class="outline-2">
<h2 id="org386724a"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgc0b7ad2" class="outline-2">
<h2 id="orgc0b7ad2"><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
@ -450,7 +450,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="orgac86ee5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb136653" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -531,15 +531,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-orgdb3b43a" class="outline-2">
<h2 id="orgdb3b43a"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org18889b8" class="outline-2">
<h2 id="org18889b8"><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="orgfee0bcc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org03dde79" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -585,15 +585,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orga952471" class="outline-2">
<h2 id="orga952471"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org0087f85" class="outline-2">
<h2 id="org0087f85"><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="org7da5d7f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2396bba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -660,8 +660,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-orgef9392e" class="outline-2">
<h2 id="orgef9392e"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orgc70756d" class="outline-2">
<h2 id="orgc70756d"><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
@ -694,7 +694,7 @@ 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="orgb2c1e2a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org57c1418" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -796,8 +796,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-orgc6f3ffa" class="outline-3">
<h3 id="orgc6f3ffa"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org902cc0a" class="outline-3">
<h3 id="org902cc0a"><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
@ -860,8 +860,8 @@ power = [
</div>
</div>
<div id="outline-container-orgd4da5fc" class="outline-2">
<h2 id="orgd4da5fc"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-orgef69be3" class="outline-2">
<h2 id="orgef69be3"><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
@ -914,7 +914,7 @@ 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="org09598d8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc5f9821" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1015,8 +1015,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-orga9ae56b" class="outline-3">
<h3 id="orga9ae56b"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org28374ca" class="outline-3">
<h3 id="org28374ca"><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
@ -1094,8 +1094,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org7512c0a" class="outline-2">
<h2 id="org7512c0a"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org4910989" class="outline-2">
<h2 id="org4910989"><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
@ -1148,13 +1148,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#orgd4da5fc">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#orgef69be3">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="org677f0a2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb46bbcb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1206,7 +1206,7 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-orgc63db46" class="outline-3">
<div id="outline-container-orgf3c6853" class="outline-3">
<h3 id="ao_one_e"><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">
@ -1224,7 +1224,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org5918787" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0e73fc2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1319,7 +1319,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org68480a1" class="outline-3">
<div id="outline-container-orgb00de5e" class="outline-3">
<h3 id="ao_two_e"><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>
@ -1341,7 +1341,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org94af0fd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org58acacf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1381,10 +1381,10 @@ notation.
</div>
</div>
<div id="outline-container-orgede8270" class="outline-2">
<h2 id="orgede8270"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orga1e8ae3" class="outline-2">
<h2 id="orga1e8ae3"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org46679d5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8c2e21d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1471,8 +1471,8 @@ notation.
</table>
</div>
<div id="outline-container-orge058064" class="outline-3">
<h3 id="orge058064"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-orgea5dbf4" class="outline-3">
<h3 id="orgea5dbf4"><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
@ -1480,7 +1480,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org71e7b6e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org431c9fb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1575,8 +1575,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgaba70e8" class="outline-3">
<h3 id="orgaba70e8"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org63def0b" class="outline-3">
<h3 id="org63def0b"><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 are the same as those defined in the
@ -1594,7 +1594,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org4f4ee46" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb22b4ab" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1662,8 +1662,8 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-orgab751af" class="outline-2">
<h2 id="orgab751af"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-orgac67ff5" class="outline-2">
<h2 id="orgac67ff5"><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 \(\Psi\)
@ -1705,7 +1705,7 @@ produced by the code generator.
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
</p>
<table id="orgbaf0809" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4eab1d6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1751,8 +1751,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org4434ab1" class="outline-2">
<h2 id="org4434ab1"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
<div id="outline-container-org8cb782b" class="outline-2">
<h2 id="org8cb782b"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
<div class="outline-text-2" id="text-9">
<p>
The configuration interaction (CI) wave function \(\Psi\) can be
@ -1774,7 +1774,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org1e78ee5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbf97586" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1820,8 +1820,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org0623e66" class="outline-2">
<h2 id="org0623e66"><span class="section-number-2">10</span> Excited states (state group)</h2>
<div id="outline-container-orgfb3a4c1" class="outline-2">
<h2 id="orgfb3a4c1"><span class="section-number-2">10</span> Excited states (state group)</h2>
<div class="outline-text-2" id="text-10">
<p>
This group contains information about excited state. Since TREXIO version 2.3.0
@ -1836,7 +1836,7 @@ The <code>id</code> and <code>current_label</code> attributes have to be specifi
(containing both ground and excited state data).
</p>
<table id="orgea8c221" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdc0d596" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1896,8 +1896,8 @@ The <code>id</code> and <code>current_label</code> attributes have to be specifi
</div>
</div>
<div id="outline-container-orgb0c1706" class="outline-2">
<h2 id="orgb0c1706"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orgd24b81a" class="outline-2">
<h2 id="orgd24b81a"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-11">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1972,7 +1972,7 @@ expressed in a basis of a one-electron function
\(g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)\).
</p>
<table id="orge195de6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9595729" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2123,10 +2123,10 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org38ce760" class="outline-2">
<h2 id="org38ce760"><span class="section-number-2">12</span> Cell (cell group)</h2>
<div id="outline-container-org71d238c" class="outline-2">
<h2 id="org71d238c"><span class="section-number-2">12</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-12">
<table id="org1d40d86" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5fa9fac" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2172,10 +2172,10 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org8e203f3" class="outline-2">
<h2 id="org8e203f3"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-org437a801" class="outline-2">
<h2 id="org437a801"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-13">
<table id="org94b650f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4d256a5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2214,8 +2214,8 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-orge6c6fe5" class="outline-2">
<h2 id="orge6c6fe5"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-orgcd97803" class="outline-2">
<h2 id="orgcd97803"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-14">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -2229,7 +2229,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orgf252d1f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf8b8864" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2284,7 +2284,7 @@ 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: 2022-12-13 Tue 16:09</p>
<p class="date">Created: 2022-12-13 Tue 16:10</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>