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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: 2022-07-28 Thu 11:50</p>
<p class="date">Created: 2022-07-28 Thu 13:21</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-07-28 Thu 11:50 -->
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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>
@ -333,31 +333,31 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org52c6638">1. Accessing sparse quantities (integrals)</a>
<li><a href="#org0106766">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org9b1a2c4">1.1. Fortran</a>
<li><a href="#org26cef2a">1.1. Fortran</a>
<ul>
<li><a href="#org5c800ba">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org113cdcb">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org40eb3bb">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgd151871">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org8314478">1.1.5. Allocate memory</a></li>
<li><a href="#orgdc01bad">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org8c4fad4">1.1.7. Read two-electron quantities</a>
<li><a href="#org5221ae9">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org5bd6307">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga945c4d">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org1fc5d2b">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org61edf7a">1.1.5. Allocate memory</a></li>
<li><a href="#orgfe711b2">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org82e6441">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgf6aeb99">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org56b40c1">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#orgc32375e">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org08121b2">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org859c25c">1.1.8. Compute the energy</a></li>
<li><a href="#org21eb957">1.1.9. Terminate</a></li>
<li><a href="#org15985c9">1.1.8. Compute the energy</a></li>
<li><a href="#org992dacd">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org10c5b21">2. Reading determinants</a>
<li><a href="#orgac16aef">2. Reading determinants</a>
<ul>
<li><a href="#orge7aea57">2.1. Fortran</a></li>
<li><a href="#org94a8eff">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -365,12 +365,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org52c6638" class="outline-2">
<h2 id="org52c6638"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org0106766" class="outline-2">
<h2 id="org0106766"><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-org9b1a2c4" class="outline-3">
<h3 id="org9b1a2c4"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org26cef2a" class="outline-3">
<h3 id="org26cef2a"><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>
@ -416,8 +416,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org5c800ba" class="outline-4">
<h4 id="org5c800ba"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org5221ae9" class="outline-4">
<h4 id="org5221ae9"><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>
@ -432,8 +432,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org113cdcb" class="outline-4">
<h4 id="org113cdcb"><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-org5bd6307" class="outline-4">
<h4 id="org5bd6307"><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)
@ -449,8 +449,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org40eb3bb" class="outline-4">
<h4 id="org40eb3bb"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orga945c4d" class="outline-4">
<h4 id="orga945c4d"><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)
@ -464,8 +464,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgd151871" class="outline-4">
<h4 id="orgd151871"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org1fc5d2b" class="outline-4">
<h4 id="org1fc5d2b"><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)
@ -479,8 +479,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org8314478" class="outline-4">
<h4 id="org8314478"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org61edf7a" class="outline-4">
<h4 id="org61edf7a"><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) )
@ -492,8 +492,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-orgdc01bad" class="outline-4">
<h4 id="orgdc01bad"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgfe711b2" class="outline-4">
<h4 id="orgfe711b2"><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)
@ -525,8 +525,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-org8c4fad4" class="outline-4">
<h4 id="org8c4fad4"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org82e6441" class="outline-4">
<h4 id="org82e6441"><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
@ -542,8 +542,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-orgf6aeb99" class="outline-5">
<h5 id="orgf6aeb99"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgc32375e" class="outline-5">
<h5 id="orgc32375e"><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)
@ -592,8 +592,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-org56b40c1" class="outline-5">
<h5 id="org56b40c1"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org08121b2" class="outline-5">
<h5 id="org08121b2"><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)
@ -637,8 +637,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org859c25c" class="outline-4">
<h4 id="org859c25c"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org15985c9" class="outline-4">
<h4 id="org15985c9"><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
@ -684,8 +684,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org21eb957" class="outline-4">
<h4 id="org21eb957"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org992dacd" class="outline-4">
<h4 id="org992dacd"><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 )
@ -699,12 +699,12 @@ E = E + E_nn
</div>
<div id="outline-container-org10c5b21" class="outline-2">
<h2 id="org10c5b21"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-orgac16aef" class="outline-2">
<h2 id="orgac16aef"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orge7aea57" class="outline-3">
<h3 id="orge7aea57"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org94a8eff" class="outline-3">
<h3 id="org94a8eff"><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>
@ -783,7 +783,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-07-28 Thu 11:50</p>
<p class="date">Created: 2022-07-28 Thu 13:21</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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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>
<!-- 2022-07-28 Thu 11:50 -->
<!-- 2022-07-28 Thu 13:21 -->
<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: 2022-07-28 Thu 11:50</p>
<p class="date">Created: 2022-07-28 Thu 13:21</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-07-28 Thu 11:50 -->
<!-- 2022-07-28 Thu 13:21 -->
<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>
@ -311,24 +311,24 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org6a57229">1. Template for HDF5 definitions</a></li>
<li><a href="#org52f2c87">2. Template for HDF5 structures</a></li>
<li><a href="#org107e799">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org2642ccb">4. Template for HDF5 has a group</a></li>
<li><a href="#org6c969b0">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org27bc012">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org813cf9d">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org4924d87">8. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org39aed2c">9. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org11b4e93">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org0cf4e9f">11. Source code for the determinant part</a></li>
<li><a href="#org5e29390">12. Helper functions</a></li>
<li><a href="#org7ed1215">1. Template for HDF5 definitions</a></li>
<li><a href="#orgafee802">2. Template for HDF5 structures</a></li>
<li><a href="#org047f713">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org5cfe1ed">4. Template for HDF5 has a group</a></li>
<li><a href="#orgdfa9c04">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgf249e0d">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org7fc9ca2">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org73dd04f">8. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgfe580f3">9. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgb0db5cf">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org3d726ea">11. Source code for the determinant part</a></li>
<li><a href="#org4eb5c14">12. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org6a57229" class="outline-2">
<h2 id="org6a57229"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org7ed1215" class="outline-2">
<h2 id="org7ed1215"><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>
@ -340,8 +340,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org52f2c87" class="outline-2">
<h2 id="org52f2c87"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgafee802" class="outline-2">
<h2 id="orgafee802"><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
@ -361,8 +361,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org107e799" class="outline-2">
<h2 id="org107e799"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org047f713" class="outline-2">
<h2 id="org047f713"><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>
@ -467,8 +467,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org2642ccb" class="outline-2">
<h2 id="org2642ccb"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org5cfe1ed" class="outline-2">
<h2 id="org5cfe1ed"><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>
@ -498,8 +498,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org6c969b0" class="outline-2">
<h2 id="org6c969b0"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orgdfa9c04" class="outline-2">
<h2 id="orgdfa9c04"><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>
@ -603,8 +603,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org27bc012" class="outline-2">
<h2 id="org27bc012"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgf249e0d" class="outline-2">
<h2 id="orgf249e0d"><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>
@ -738,8 +738,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org813cf9d" class="outline-2">
<h2 id="org813cf9d"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org7fc9ca2" class="outline-2">
<h2 id="org7fc9ca2"><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
@ -942,8 +942,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org4924d87" class="outline-2">
<h2 id="org4924d87"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org73dd04f" class="outline-2">
<h2 id="org73dd04f"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of strings</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>
@ -1141,8 +1141,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org39aed2c" class="outline-2">
<h2 id="org39aed2c"><span class="section-number-2">9</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgfe580f3" class="outline-2">
<h2 id="orgfe580f3"><span class="section-number-2">9</span> Template for HDF5 has/read/write a string attribute</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>
@ -1269,8 +1269,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-org11b4e93" class="outline-2">
<h2 id="org11b4e93"><span class="section-number-2">10</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgb0db5cf" class="outline-2">
<h2 id="orgb0db5cf"><span class="section-number-2">10</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-10">
<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
@ -1310,8 +1310,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org0cf4e9f" class="outline-2">
<h2 id="org0cf4e9f"><span class="section-number-2">11</span> Source code for the determinant part</h2>
<div id="outline-container-org3d726ea" class="outline-2">
<h2 id="org3d726ea"><span class="section-number-2">11</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-11">
<p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1564,8 +1564,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org5e29390" class="outline-2">
<h2 id="org5e29390"><span class="section-number-2">12</span> Helper functions</h2>
<div id="outline-container-org4eb5c14" class="outline-2">
<h2 id="org4eb5c14"><span class="section-number-2">12</span> Helper functions</h2>
<div class="outline-text-2" id="text-12">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1828,7 +1828,7 @@ 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: 2022-07-28 Thu 11:50</p>
<p class="date">Created: 2022-07-28 Thu 13:21</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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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>
<!-- 2022-07-28 Thu 11:50 -->
<!-- 2022-07-28 Thu 13:21 -->
<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>
@ -311,21 +311,21 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org6f1b301">1. Template for group-related structures in text back end</a></li>
<li><a href="#org483f360">2. Template for general structure in text back end</a></li>
<li><a href="#org9e4f4cc">3. Initialize function (constant part)</a></li>
<li><a href="#org3d9c5cd">4. Deinitialize function (templated part)</a></li>
<li><a href="#org9a0027c">5. Template for text read a group</a></li>
<li><a href="#org2d3bdcc">6. Template for text has a group</a></li>
<li><a href="#org13fb100">7. Template for text flush a group</a></li>
<li><a href="#orgc84ab8d">8. Template for text free memory</a></li>
<li><a href="#orgdb5dede">9. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org8d367b7">10. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org2bfe1f8">11. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org28a7228">12. Template for has/read/write a string attribute</a></li>
<li><a href="#orgc3668ab">13. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orga16bb1f">14. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org2142971">15. Source code for the determinant part</a></li>
<li><a href="#org22e9e9e">1. Template for group-related structures in text back end</a></li>
<li><a href="#org40d8371">2. Template for general structure in text back end</a></li>
<li><a href="#org35c1dd9">3. Initialize function (constant part)</a></li>
<li><a href="#orgbb7da55">4. Deinitialize function (templated part)</a></li>
<li><a href="#org33b4a6c">5. Template for text read a group</a></li>
<li><a href="#org2e41fbb">6. Template for text has a group</a></li>
<li><a href="#org7ba0c5b">7. Template for text flush a group</a></li>
<li><a href="#org203497f">8. Template for text free memory</a></li>
<li><a href="#org3ee6b47">9. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgba70a38">10. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org9ddb414">11. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org6e16906">12. Template for has/read/write a string attribute</a></li>
<li><a href="#org89eebfa">13. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org2b94da4">14. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org1159603">15. Source code for the determinant part</a></li>
</ul>
</div>
</div>
@ -347,8 +347,8 @@ directory.
The file is written when closed, or when the flush function is called.
</p>
<div id="outline-container-org6f1b301" class="outline-2">
<h2 id="org6f1b301"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org22e9e9e" class="outline-2">
<h2 id="org22e9e9e"><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 {
@ -367,8 +367,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org483f360" class="outline-2">
<h2 id="org483f360"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org40d8371" class="outline-2">
<h2 id="org40d8371"><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
@ -388,8 +388,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org9e4f4cc" class="outline-2">
<h2 id="org9e4f4cc"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org35c1dd9" class="outline-2">
<h2 id="org35c1dd9"><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>
@ -556,8 +556,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org3d9c5cd" class="outline-2">
<h2 id="org3d9c5cd"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgbb7da55" class="outline-2">
<h2 id="orgbb7da55"><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>
@ -579,8 +579,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org9a0027c" class="outline-2">
<h2 id="org9a0027c"><span class="section-number-2">5</span> Template for text read a group</h2>
<div id="outline-container-org33b4a6c" class="outline-2">
<h2 id="org33b4a6c"><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*
@ -806,8 +806,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org2d3bdcc" class="outline-2">
<h2 id="org2d3bdcc"><span class="section-number-2">6</span> Template for text has a group</h2>
<div id="outline-container-org2e41fbb" class="outline-2">
<h2 id="org2e41fbb"><span class="section-number-2">6</span> Template for text has 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>
@ -847,8 +847,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org13fb100" class="outline-2">
<h2 id="org13fb100"><span class="section-number-2">7</span> Template for text flush a group</h2>
<div id="outline-container-org7ba0c5b" class="outline-2">
<h2 id="org7ba0c5b"><span class="section-number-2">7</span> Template for text flush 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>
@ -912,8 +912,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgc84ab8d" class="outline-2">
<h2 id="orgc84ab8d"><span class="section-number-2">8</span> Template for text free memory</h2>
<div id="outline-container-org203497f" class="outline-2">
<h2 id="org203497f"><span class="section-number-2">8</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-8">
<p>
Memory is allocated when reading. The following function frees memory.
@ -982,8 +982,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orgdb5dede" class="outline-2">
<h2 id="orgdb5dede"><span class="section-number-2">9</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org3ee6b47" class="outline-2">
<h2 id="org3ee6b47"><span class="section-number-2">9</span> Template for has/read/write a numerical attribute</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>
@ -1046,8 +1046,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org8d367b7" class="outline-2">
<h2 id="org8d367b7"><span class="section-number-2">10</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgba70a38" class="outline-2">
<h2 id="orgba70a38"><span class="section-number-2">10</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-10">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1143,8 +1143,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org2bfe1f8" class="outline-2">
<h2 id="org2bfe1f8"><span class="section-number-2">11</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org9ddb414" class="outline-2">
<h2 id="org9ddb414"><span class="section-number-2">11</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-11">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1245,8 +1245,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org28a7228" class="outline-2">
<h2 id="org28a7228"><span class="section-number-2">12</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org6e16906" class="outline-2">
<h2 id="org6e16906"><span class="section-number-2">12</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-12">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1320,8 +1320,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgc3668ab" class="outline-2">
<h2 id="orgc3668ab"><span class="section-number-2">13</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org89eebfa" class="outline-2">
<h2 id="org89eebfa"><span class="section-number-2">13</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-13">
<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
@ -1611,8 +1611,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-orga16bb1f" class="outline-2">
<h2 id="orga16bb1f"><span class="section-number-2">14</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org2b94da4" class="outline-2">
<h2 id="org2b94da4"><span class="section-number-2">14</span> Template for text delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-14">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1640,8 +1640,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org2142971" class="outline-2">
<h2 id="org2142971"><span class="section-number-2">15</span> Source code for the determinant part</h2>
<div id="outline-container-org1159603" class="outline-2">
<h2 id="org1159603"><span class="section-number-2">15</span> Source code for the determinant part</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 determinant I/O has to be decoupled
@ -2081,7 +2081,7 @@ 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: 2022-07-28 Thu 11:50</p>
<p class="date">Created: 2022-07-28 Thu 13:21</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

150
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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>
<!-- 2022-07-28 Thu 11:50 -->
<!-- 2022-07-28 Thu 13:21 -->
<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>
@ -333,37 +333,37 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org5616564">1. Metadata (metadata group)</a></li>
<li><a href="#org81e1d34">2. Electron (electron group)</a></li>
<li><a href="#orgaa99e7b">3. Nucleus (nucleus group)</a></li>
<li><a href="#org0e63431">4. Effective core potentials (ecp group)</a>
<li><a href="#org8fae003">1. Metadata (metadata group)</a></li>
<li><a href="#orga52be2a">2. Electron (electron group)</a></li>
<li><a href="#orga12b1b0">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgdab3dea">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org7a10252">4.1. Example</a></li>
<li><a href="#org45208fc">4.1. Example</a></li>
</ul>
</li>
<li><a href="#orgfbee7c3">5. Basis set (basis group)</a>
<li><a href="#org24a2127">5. Basis set (basis group)</a>
<ul>
<li><a href="#org5d46282">5.1. Example</a></li>
<li><a href="#org2b8cb50">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org3643ce9">6. Atomic orbitals (ao group)</a>
<li><a href="#orgec8847b">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="#org5d46e89">7. Molecular orbitals (mo group)</a>
<li><a href="#org2f6e62e">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgf72b0b6">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org169f192">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org5d32869">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org486d37c">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org93c2ce0">8. Slater determinants (determinant group)</a></li>
<li><a href="#org4327538">9. Excited states (state group)</a></li>
<li><a href="#orge1a7b0e">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgc79c0a1">11. Cell (cell group)</a></li>
<li><a href="#org8c4d404">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orga1f1553">13. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org28bd0a0">8. Slater determinants (determinant group)</a></li>
<li><a href="#org1323cb1">9. Excited states (state group)</a></li>
<li><a href="#orgee26a54">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org3b2a113">11. Cell (cell group)</a></li>
<li><a href="#org5e20456">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org61bc6bf">13. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -417,8 +417,8 @@ For determinants, the <code>special</code> attribute is present in the type. Thi
means that the source code is not produced by the generator, but hand-written.
</p>
<div id="outline-container-org5616564" class="outline-2">
<h2 id="org5616564"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org8fae003" class="outline-2">
<h2 id="org8fae003"><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
@ -428,7 +428,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="org7949a13" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc13548e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -509,15 +509,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-org81e1d34" class="outline-2">
<h2 id="org81e1d34"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orga52be2a" class="outline-2">
<h2 id="orga52be2a"><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="org106c53f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0a66865" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -563,15 +563,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgaa99e7b" class="outline-2">
<h2 id="orgaa99e7b"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-orga12b1b0" class="outline-2">
<h2 id="orga12b1b0"><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="org18785e4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf94341e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -638,8 +638,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org0e63431" class="outline-2">
<h2 id="org0e63431"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orgdab3dea" class="outline-2">
<h2 id="orgdab3dea"><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
@ -672,7 +672,7 @@ 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="org5de2895" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb5fa80b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -774,8 +774,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-org7a10252" class="outline-3">
<h3 id="org7a10252"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org45208fc" class="outline-3">
<h3 id="org45208fc"><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
@ -838,8 +838,8 @@ power = [
</div>
</div>
<div id="outline-container-orgfbee7c3" class="outline-2">
<h2 id="orgfbee7c3"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org24a2127" class="outline-2">
<h2 id="org24a2127"><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
@ -892,7 +892,7 @@ 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="org7e2ddbb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgab86063" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -986,8 +986,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-org5d46282" class="outline-3">
<h3 id="org5d46282"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org2b8cb50" class="outline-3">
<h3 id="org2b8cb50"><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
@ -1065,8 +1065,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org3643ce9" class="outline-2">
<h2 id="org3643ce9"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-orgec8847b" class="outline-2">
<h2 id="orgec8847b"><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
@ -1119,13 +1119,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#orgfbee7c3">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org24a2127">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="org247a970" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0643290" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1177,8 +1177,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org11a3d67" class="outline-3">
<h3 id="ao_one_e"><a id="org11a3d67"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgb240cb5" class="outline-3">
<h3 id="ao_one_e"><a id="orgb240cb5"></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}}
@ -1195,7 +1195,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgc28972f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgac16db6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1290,8 +1290,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org1fccbc1" class="outline-3">
<h3 id="ao_two_e"><a id="org1fccbc1"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org4ceef5e" class="outline-3">
<h3 id="ao_two_e"><a id="org4ceef5e"></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
@ -1312,7 +1312,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org9894992" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3b49736" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1352,10 +1352,10 @@ notation.
</div>
</div>
<div id="outline-container-org5d46e89" class="outline-2">
<h2 id="org5d46e89"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org2f6e62e" class="outline-2">
<h2 id="org2f6e62e"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org15cff2f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga37bb7f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1442,8 +1442,8 @@ notation.
</table>
</div>
<div id="outline-container-orgf72b0b6" class="outline-3">
<h3 id="orgf72b0b6"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org5d32869" class="outline-3">
<h3 id="org5d32869"><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
@ -1451,7 +1451,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org3123822" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb1ab55d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1546,8 +1546,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org169f192" class="outline-3">
<h3 id="org169f192"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org486d37c" class="outline-3">
<h3 id="org486d37c"><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
@ -1555,7 +1555,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org272d5a8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org795a8bf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1595,8 +1595,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org93c2ce0" class="outline-2">
<h2 id="org93c2ce0"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-org28bd0a0" class="outline-2">
<h2 id="org28bd0a0"><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 \(\Psi\)
@ -1638,7 +1638,7 @@ 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="org0ba9ffa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org04bf37b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1684,8 +1684,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org4327538" class="outline-2">
<h2 id="org4327538"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div id="outline-container-org1323cb1" class="outline-2">
<h2 id="org1323cb1"><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.
@ -1694,7 +1694,7 @@ correspond to excited state wave functions for the same set of
determinants. This is the goal of the present group
</p>
<table id="orgaaed6a1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge9e66e1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1733,8 +1733,8 @@ determinants. This is the goal of the present group
</div>
</div>
<div id="outline-container-orge1a7b0e" class="outline-2">
<h2 id="orge1a7b0e"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orgee26a54" class="outline-2">
<h2 id="orgee26a54"><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
@ -1787,7 +1787,7 @@ The total energy can be computed as:
\]
</p>
<table id="org3c855e8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org94f1b69" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1868,10 +1868,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-orgc79c0a1" class="outline-2">
<h2 id="orgc79c0a1"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div id="outline-container-org3b2a113" class="outline-2">
<h2 id="org3b2a113"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-11">
<table id="orgf3f8eac" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga0eaa4f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1917,10 +1917,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org8c4d404" class="outline-2">
<h2 id="org8c4d404"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-org5e20456" class="outline-2">
<h2 id="org5e20456"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-12">
<table id="org87da593" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb74989f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1959,8 +1959,8 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-orga1f1553" class="outline-2">
<h2 id="orga1f1553"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org61bc6bf" class="outline-2">
<h2 id="org61bc6bf"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-13">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -1974,7 +1974,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orgf2e457d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9cc54a1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2029,7 +2029,7 @@ 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: 2022-07-28 Thu 11:50</p>
<p class="date">Created: 2022-07-28 Thu 13:21</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>