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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: 2022-09-26 Mon 15:11</p>
<p class="date">Created: 2022-09-27 Tue 11:56</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-09-26 Mon 15:11 -->
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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="#orgacdca06">1. Accessing sparse quantities (integrals)</a>
<li><a href="#org44da6df">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#orgb6460a3">1.1. Fortran</a>
<li><a href="#org18aa12a">1.1. Fortran</a>
<ul>
<li><a href="#orge24af2d">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org83bac8c">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org2734285">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgae37d13">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgbf27a51">1.1.5. Allocate memory</a></li>
<li><a href="#org50c32c9">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org0ced891">1.1.7. Read two-electron quantities</a>
<li><a href="#org7096488">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org94d0b6a">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgb7b3af8">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org22e2df2">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgebbdc8b">1.1.5. Allocate memory</a></li>
<li><a href="#org7a92517">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org934684b">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org74dc1da">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgc87abac">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org2f5edec">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgcf758b7">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org78ca9cd">1.1.8. Compute the energy</a></li>
<li><a href="#org68f8ccc">1.1.9. Terminate</a></li>
<li><a href="#org86b66fd">1.1.8. Compute the energy</a></li>
<li><a href="#orgfaf741b">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orga0dea8c">2. Reading determinants</a>
<li><a href="#org68675f4">2. Reading determinants</a>
<ul>
<li><a href="#orgdbec1c4">2.1. Fortran</a></li>
<li><a href="#org132f94d">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -365,12 +365,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgacdca06" class="outline-2">
<h2 id="orgacdca06"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org44da6df" class="outline-2">
<h2 id="org44da6df"><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-orgb6460a3" class="outline-3">
<h3 id="orgb6460a3"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org18aa12a" class="outline-3">
<h3 id="org18aa12a"><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-orge24af2d" class="outline-4">
<h4 id="orge24af2d"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org7096488" class="outline-4">
<h4 id="org7096488"><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-org83bac8c" class="outline-4">
<h4 id="org83bac8c"><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-org94d0b6a" class="outline-4">
<h4 id="org94d0b6a"><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-org2734285" class="outline-4">
<h4 id="org2734285"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgb7b3af8" class="outline-4">
<h4 id="orgb7b3af8"><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-orgae37d13" class="outline-4">
<h4 id="orgae37d13"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org22e2df2" class="outline-4">
<h4 id="org22e2df2"><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-orgbf27a51" class="outline-4">
<h4 id="orgbf27a51"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-orgebbdc8b" class="outline-4">
<h4 id="orgebbdc8b"><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-org50c32c9" class="outline-4">
<h4 id="org50c32c9"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org7a92517" class="outline-4">
<h4 id="org7a92517"><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-org0ced891" class="outline-4">
<h4 id="org0ced891"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org934684b" class="outline-4">
<h4 id="org934684b"><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-org74dc1da" class="outline-5">
<h5 id="org74dc1da"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org2f5edec" class="outline-5">
<h5 id="org2f5edec"><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-orgc87abac" class="outline-5">
<h5 id="orgc87abac"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgcf758b7" class="outline-5">
<h5 id="orgcf758b7"><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-org78ca9cd" class="outline-4">
<h4 id="org78ca9cd"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org86b66fd" class="outline-4">
<h4 id="org86b66fd"><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-org68f8ccc" class="outline-4">
<h4 id="org68f8ccc"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgfaf741b" class="outline-4">
<h4 id="orgfaf741b"><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-orga0dea8c" class="outline-2">
<h2 id="orga0dea8c"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-org68675f4" class="outline-2">
<h2 id="org68675f4"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgdbec1c4" class="outline-3">
<h3 id="orgdbec1c4"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org132f94d" class="outline-3">
<h3 id="org132f94d"><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: 2022-09-26 Mon 15:11</p>
<p class="date">Created: 2022-09-27 Tue 11:56</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>
<!-- 2022-09-26 Mon 15:11 -->
<!-- 2022-09-27 Tue 11:56 -->
<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: 2022-09-26 Mon 15:11</p>
<p class="date">Created: 2022-09-27 Tue 11:56</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>
<!-- 2022-09-26 Mon 15:11 -->
<!-- 2022-09-27 Tue 11:56 -->
<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="#org500cb97">1. Template for HDF5 definitions</a></li>
<li><a href="#org657fa60">2. Template for HDF5 structures</a></li>
<li><a href="#org27ff7ed">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org2c689e9">4. Template for HDF5 has a group</a></li>
<li><a href="#orgfdc63e3">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org64de42d">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org7201e79">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org89ed6e7">8. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orga1eeb5c">9. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orga415456">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org16fefd5">11. Source code for the determinant part</a></li>
<li><a href="#org8241824">12. Helper functions</a></li>
<li><a href="#orge153bf8">1. Template for HDF5 definitions</a></li>
<li><a href="#org58f7a64">2. Template for HDF5 structures</a></li>
<li><a href="#orgd5c65b3">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgbd1d033">4. Template for HDF5 has a group</a></li>
<li><a href="#orgdedaf12">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgb51b363">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgeb25abf">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgaf238a3">8. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orge321d36">9. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgca94975">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org4666032">11. Source code for the determinant part</a></li>
<li><a href="#orga47882d">12. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org500cb97" class="outline-2">
<h2 id="org500cb97"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orge153bf8" class="outline-2">
<h2 id="orge153bf8"><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-org657fa60" class="outline-2">
<h2 id="org657fa60"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org58f7a64" class="outline-2">
<h2 id="org58f7a64"><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-org27ff7ed" class="outline-2">
<h2 id="org27ff7ed"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgd5c65b3" class="outline-2">
<h2 id="orgd5c65b3"><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>
@ -482,8 +482,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org2c689e9" class="outline-2">
<h2 id="org2c689e9"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orgbd1d033" class="outline-2">
<h2 id="orgbd1d033"><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>
@ -513,8 +513,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgfdc63e3" class="outline-2">
<h2 id="orgfdc63e3"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orgdedaf12" class="outline-2">
<h2 id="orgdedaf12"><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>
@ -618,8 +618,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org64de42d" class="outline-2">
<h2 id="org64de42d"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgb51b363" class="outline-2">
<h2 id="orgb51b363"><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>
@ -753,8 +753,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org7201e79" class="outline-2">
<h2 id="org7201e79"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orgeb25abf" class="outline-2">
<h2 id="orgeb25abf"><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
@ -957,8 +957,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org89ed6e7" class="outline-2">
<h2 id="org89ed6e7"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgaf238a3" class="outline-2">
<h2 id="orgaf238a3"><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>
@ -1156,8 +1156,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-orga1eeb5c" class="outline-2">
<h2 id="orga1eeb5c"><span class="section-number-2">9</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orge321d36" class="outline-2">
<h2 id="orge321d36"><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>
@ -1284,8 +1284,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-orga415456" class="outline-2">
<h2 id="orga415456"><span class="section-number-2">10</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgca94975" class="outline-2">
<h2 id="orgca94975"><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
@ -1325,8 +1325,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org16fefd5" class="outline-2">
<h2 id="org16fefd5"><span class="section-number-2">11</span> Source code for the determinant part</h2>
<div id="outline-container-org4666032" class="outline-2">
<h2 id="org4666032"><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.
@ -1579,8 +1579,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org8241824" class="outline-2">
<h2 id="org8241824"><span class="section-number-2">12</span> Helper functions</h2>
<div id="outline-container-orga47882d" class="outline-2">
<h2 id="orga47882d"><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>
@ -1843,7 +1843,7 @@ 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: 2022-09-26 Mon 15:11</p>
<p class="date">Created: 2022-09-27 Tue 11:56</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

100
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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>
<!-- 2022-09-26 Mon 15:11 -->
<!-- 2022-09-27 Tue 11:56 -->
<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>
@ -311,22 +311,22 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org228804f">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgaedb7c9">2. Template for general structure in text back end</a></li>
<li><a href="#orgbd5061c">3. Initialize function (constant part)</a></li>
<li><a href="#org2b1f48d">4. Deinitialize function (templated part)</a></li>
<li><a href="#org002dc8e">5. Flush function (templated part)</a></li>
<li><a href="#org56fad67">6. Template for text read a group</a></li>
<li><a href="#orgd1d9bb5">7. Template for text has a group</a></li>
<li><a href="#orgea01371">8. Template for text flush a group</a></li>
<li><a href="#org0d0a5a8">9. Template for text free memory</a></li>
<li><a href="#org89ffecc">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org5c8d484">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org74745b7">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org774b705">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org9012579">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orged1bd34">15. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org77ac1ba">16. Source code for the determinant part</a></li>
<li><a href="#org3b1666f">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgbd90ac3">2. Template for general structure in text back end</a></li>
<li><a href="#org2539998">3. Initialize function (constant part)</a></li>
<li><a href="#org61f873b">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgd969213">5. Flush function (templated part)</a></li>
<li><a href="#orge73fca4">6. Template for text read a group</a></li>
<li><a href="#org954ce1a">7. Template for text has a group</a></li>
<li><a href="#org7a9d65a">8. Template for text flush a group</a></li>
<li><a href="#org108ba92">9. Template for text free memory</a></li>
<li><a href="#orgc959f8e">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orga69b187">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org5f0efc2">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org55bf765">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org5b60ea0">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgdb14260">15. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgf5d8396">16. Source code for the determinant part</a></li>
</ul>
</div>
</div>
@ -348,8 +348,8 @@ directory.
The file is written when closed, or when the flush function is called.
</p>
<div id="outline-container-org228804f" class="outline-2">
<h2 id="org228804f"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org3b1666f" class="outline-2">
<h2 id="org3b1666f"><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 {
@ -368,8 +368,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orgaedb7c9" class="outline-2">
<h2 id="orgaedb7c9"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgbd90ac3" class="outline-2">
<h2 id="orgbd90ac3"><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
@ -389,8 +389,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgbd5061c" class="outline-2">
<h2 id="orgbd5061c"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org2539998" class="outline-2">
<h2 id="org2539998"><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>
@ -557,8 +557,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org2b1f48d" class="outline-2">
<h2 id="org2b1f48d"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org61f873b" class="outline-2">
<h2 id="org61f873b"><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>
@ -580,8 +580,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org002dc8e" class="outline-2">
<h2 id="org002dc8e"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-orgd969213" class="outline-2">
<h2 id="orgd969213"><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>
@ -604,8 +604,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org56fad67" class="outline-2">
<h2 id="org56fad67"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orge73fca4" class="outline-2">
<h2 id="orge73fca4"><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*
@ -831,8 +831,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgd1d9bb5" class="outline-2">
<h2 id="orgd1d9bb5"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org954ce1a" class="outline-2">
<h2 id="org954ce1a"><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>
@ -872,8 +872,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgea01371" class="outline-2">
<h2 id="orgea01371"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org7a9d65a" class="outline-2">
<h2 id="org7a9d65a"><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>
@ -937,8 +937,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org0d0a5a8" class="outline-2">
<h2 id="org0d0a5a8"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org108ba92" class="outline-2">
<h2 id="org108ba92"><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.
@ -1007,8 +1007,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org89ffecc" class="outline-2">
<h2 id="org89ffecc"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orgc959f8e" class="outline-2">
<h2 id="orgc959f8e"><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>
@ -1071,8 +1071,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org5c8d484" class="outline-2">
<h2 id="org5c8d484"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orga69b187" class="outline-2">
<h2 id="orga69b187"><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.
@ -1168,8 +1168,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org74745b7" class="outline-2">
<h2 id="org74745b7"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org5f0efc2" class="outline-2">
<h2 id="org5f0efc2"><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.
@ -1270,8 +1270,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org774b705" class="outline-2">
<h2 id="org774b705"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org55bf765" class="outline-2">
<h2 id="org55bf765"><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>
@ -1345,8 +1345,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org9012579" class="outline-2">
<h2 id="org9012579"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org5b60ea0" class="outline-2">
<h2 id="org5b60ea0"><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
@ -1636,8 +1636,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-orged1bd34" class="outline-2">
<h2 id="orged1bd34"><span class="section-number-2">15</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgdb14260" class="outline-2">
<h2 id="orgdb14260"><span class="section-number-2">15</span> Template for text delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-15">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1665,8 +1665,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org77ac1ba" class="outline-2">
<h2 id="org77ac1ba"><span class="section-number-2">16</span> Source code for the determinant part</h2>
<div id="outline-container-orgf5d8396" class="outline-2">
<h2 id="orgf5d8396"><span class="section-number-2">16</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-16">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -2106,7 +2106,7 @@ 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: 2022-09-26 Mon 15:11</p>
<p class="date">Created: 2022-09-27 Tue 11:56</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

158
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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>
<!-- 2022-09-26 Mon 15:11 -->
<!-- 2022-09-27 Tue 11:56 -->
<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>
@ -333,38 +333,38 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9037426">1. Metadata (metadata group)</a></li>
<li><a href="#org44b5de4">2. Electron (electron group)</a></li>
<li><a href="#org5ed25cc">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgcbd75fc">4. Effective core potentials (ecp group)</a>
<li><a href="#org0edaf5a">1. Metadata (metadata group)</a></li>
<li><a href="#orge432d32">2. Electron (electron group)</a></li>
<li><a href="#org34cd45b">3. Nucleus (nucleus group)</a></li>
<li><a href="#org5b2f696">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orga020f8b">4.1. Example</a></li>
<li><a href="#org56b8cfa">4.1. Example</a></li>
</ul>
</li>
<li><a href="#orgdee963c">5. Basis set (basis group)</a>
<li><a href="#org83f05fd">5. Basis set (basis group)</a>
<ul>
<li><a href="#org845272a">5.1. Example</a></li>
<li><a href="#orgeede047">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org0db1500">6. Atomic orbitals (ao group)</a>
<li><a href="#org4541d8a">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="#orgc31075a">7. Molecular orbitals (mo group)</a>
<li><a href="#org273171a">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org56945f7">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org1a5da71">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org96a0e65">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgb8c905c">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org87e5834">8. Slater determinants (determinant group)</a></li>
<li><a href="#org39d2842">9. Configuration state functions (csf group)</a></li>
<li><a href="#orga8ace76">10. Excited states (state group)</a></li>
<li><a href="#orgc1edcb4">11. Reduced density matrices (rdm group)</a></li>
<li><a href="#org67e6a0c">12. Cell (cell group)</a></li>
<li><a href="#org5da502d">13. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org669742e">14. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org6a58413">8. Slater determinants (determinant group)</a></li>
<li><a href="#org9edf8dd">9. Configuration state functions (csf group)</a></li>
<li><a href="#org498ca03">10. Excited states (state group)</a></li>
<li><a href="#orgfe7b7d5">11. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgd253145">12. Cell (cell group)</a></li>
<li><a href="#org84abb3e">13. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org8565785">14. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -418,8 +418,8 @@ 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-org9037426" class="outline-2">
<h2 id="org9037426"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org0edaf5a" class="outline-2">
<h2 id="org0edaf5a"><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
@ -429,7 +429,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="org9e556ca" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb238415" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -510,15 +510,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-org44b5de4" class="outline-2">
<h2 id="org44b5de4"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orge432d32" class="outline-2">
<h2 id="orge432d32"><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="orgaacdbb8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc7548c3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -564,15 +564,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org5ed25cc" class="outline-2">
<h2 id="org5ed25cc"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org34cd45b" class="outline-2">
<h2 id="org34cd45b"><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="org137730a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org29c4b2b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -639,8 +639,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-orgcbd75fc" class="outline-2">
<h2 id="orgcbd75fc"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org5b2f696" class="outline-2">
<h2 id="org5b2f696"><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
@ -673,7 +673,7 @@ 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="org89aaa01" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org202260c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -775,8 +775,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-orga020f8b" class="outline-3">
<h3 id="orga020f8b"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org56b8cfa" class="outline-3">
<h3 id="org56b8cfa"><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
@ -839,8 +839,8 @@ power = [
</div>
</div>
<div id="outline-container-orgdee963c" class="outline-2">
<h2 id="orgdee963c"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org83f05fd" class="outline-2">
<h2 id="org83f05fd"><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
@ -893,7 +893,7 @@ 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="orgf20ada0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0a9bcfb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -987,8 +987,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-org845272a" class="outline-3">
<h3 id="org845272a"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-orgeede047" class="outline-3">
<h3 id="orgeede047"><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
@ -1066,8 +1066,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org0db1500" class="outline-2">
<h2 id="org0db1500"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org4541d8a" class="outline-2">
<h2 id="org4541d8a"><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
@ -1120,13 +1120,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#orgdee963c">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org83f05fd">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="org324596e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org34883b5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1178,8 +1178,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org7be852d" class="outline-3">
<h3 id="ao_one_e"><a id="org7be852d"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgc86eb12" class="outline-3">
<h3 id="ao_one_e"><a id="orgc86eb12"></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}}
@ -1196,7 +1196,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org8f4941d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org015be4a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1291,8 +1291,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org2c63560" class="outline-3">
<h3 id="ao_two_e"><a id="org2c63560"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org47498ae" class="outline-3">
<h3 id="ao_two_e"><a id="org47498ae"></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
@ -1313,7 +1313,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="orgd8a4ffe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org126980a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1353,10 +1353,10 @@ notation.
</div>
</div>
<div id="outline-container-orgc31075a" class="outline-2">
<h2 id="orgc31075a"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org273171a" class="outline-2">
<h2 id="org273171a"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org6b1d05c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0472fcc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1443,8 +1443,8 @@ notation.
</table>
</div>
<div id="outline-container-org56945f7" class="outline-3">
<h3 id="org56945f7"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org96a0e65" class="outline-3">
<h3 id="org96a0e65"><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
@ -1452,7 +1452,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgcd21131" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org996cda9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1547,8 +1547,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org1a5da71" class="outline-3">
<h3 id="org1a5da71"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orgb8c905c" class="outline-3">
<h3 id="orgb8c905c"><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
@ -1556,7 +1556,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org1e792b7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb6bf735" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1596,8 +1596,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org87e5834" class="outline-2">
<h2 id="org87e5834"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-org6a58413" class="outline-2">
<h2 id="org6a58413"><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 \(\Psi\)
@ -1639,7 +1639,7 @@ 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="org817938f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb511327" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1685,8 +1685,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org39d2842" class="outline-2">
<h2 id="org39d2842"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
<div id="outline-container-org9edf8dd" class="outline-2">
<h2 id="org9edf8dd"><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
@ -1708,7 +1708,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="orge506aff" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2dfa53e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1754,8 +1754,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-orga8ace76" class="outline-2">
<h2 id="orga8ace76"><span class="section-number-2">10</span> Excited states (state group)</h2>
<div id="outline-container-org498ca03" class="outline-2">
<h2 id="org498ca03"><span class="section-number-2">10</span> Excited states (state group)</h2>
<div class="outline-text-2" id="text-10">
<p>
By default, the <code>determinant</code> group corresponds to the ground state.
@ -1764,7 +1764,7 @@ correspond to excited state wave functions for the same set of
determinants. This is the goal of the present group
</p>
<table id="orgea4942e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org505ea9a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1803,8 +1803,8 @@ determinants. This is the goal of the present group
</div>
</div>
<div id="outline-container-orgc1edcb4" class="outline-2">
<h2 id="orgc1edcb4"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orgfe7b7d5" class="outline-2">
<h2 id="orgfe7b7d5"><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
@ -1857,7 +1857,7 @@ The total energy can be computed as:
\]
</p>
<table id="org31adbcc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org729e93e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1938,10 +1938,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org67e6a0c" class="outline-2">
<h2 id="org67e6a0c"><span class="section-number-2">12</span> Cell (cell group)</h2>
<div id="outline-container-orgd253145" class="outline-2">
<h2 id="orgd253145"><span class="section-number-2">12</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-12">
<table id="org984c7b5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9f8814a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1987,10 +1987,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org5da502d" class="outline-2">
<h2 id="org5da502d"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-org84abb3e" class="outline-2">
<h2 id="org84abb3e"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-13">
<table id="orgb53a9d8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc80df37" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2029,8 +2029,8 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org669742e" class="outline-2">
<h2 id="org669742e"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org8565785" class="outline-2">
<h2 id="org8565785"><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
@ -2044,7 +2044,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="org229a0de" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd7d2a27" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2099,7 +2099,7 @@ 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: 2022-09-26 Mon 15:11</p>
<p class="date">Created: 2022-09-27 Tue 11:56</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>