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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: 2022-07-04 Mon 12:36</p>
<p class="date">Created: 2022-07-04 Mon 14:01</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-07-04 Mon 12:36 -->
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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="#org5730e18">1. Accessing sparse quantities (integrals)</a>
<li><a href="#org929cb3b">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org8eceaec">1.1. Fortran</a>
<li><a href="#org20fa2df">1.1. Fortran</a>
<ul>
<li><a href="#orged0d83e">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org51a4061">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org758d47e">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org0dc52bf">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgf2a176f">1.1.5. Allocate memory</a></li>
<li><a href="#orgee3a274">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orge5f8c6b">1.1.7. Read two-electron quantities</a>
<li><a href="#orgc3e47cf">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgb721fc8">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgf525975">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org193f26d">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orge01712e">1.1.5. Allocate memory</a></li>
<li><a href="#orgdaa93f8">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgc145d57">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org00f390d">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org845fdc7">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org09e25b7">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org09de60a">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgf8af98c">1.1.8. Compute the energy</a></li>
<li><a href="#orge39c70c">1.1.9. Terminate</a></li>
<li><a href="#org92be323">1.1.8. Compute the energy</a></li>
<li><a href="#orgac18074">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org36f611f">2. Reading determinants</a>
<li><a href="#org9993e60">2. Reading determinants</a>
<ul>
<li><a href="#org04d2f60">2.1. Fortran</a></li>
<li><a href="#org591f91b">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -365,12 +365,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org5730e18" class="outline-2">
<h2 id="org5730e18"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org929cb3b" class="outline-2">
<h2 id="org929cb3b"><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-org8eceaec" class="outline-3">
<h3 id="org8eceaec"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org20fa2df" class="outline-3">
<h3 id="org20fa2df"><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-orged0d83e" class="outline-4">
<h4 id="orged0d83e"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgc3e47cf" class="outline-4">
<h4 id="orgc3e47cf"><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-org51a4061" class="outline-4">
<h4 id="org51a4061"><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-orgb721fc8" class="outline-4">
<h4 id="orgb721fc8"><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-org758d47e" class="outline-4">
<h4 id="org758d47e"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgf525975" class="outline-4">
<h4 id="orgf525975"><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-org0dc52bf" class="outline-4">
<h4 id="org0dc52bf"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org193f26d" class="outline-4">
<h4 id="org193f26d"><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-orgf2a176f" class="outline-4">
<h4 id="orgf2a176f"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-orge01712e" class="outline-4">
<h4 id="orge01712e"><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-orgee3a274" class="outline-4">
<h4 id="orgee3a274"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgdaa93f8" class="outline-4">
<h4 id="orgdaa93f8"><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-orge5f8c6b" class="outline-4">
<h4 id="orge5f8c6b"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgc145d57" class="outline-4">
<h4 id="orgc145d57"><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-org00f390d" class="outline-5">
<h5 id="org00f390d"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org09e25b7" class="outline-5">
<h5 id="org09e25b7"><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-org845fdc7" class="outline-5">
<h5 id="org845fdc7"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org09de60a" class="outline-5">
<h5 id="org09de60a"><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-orgf8af98c" class="outline-4">
<h4 id="orgf8af98c"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org92be323" class="outline-4">
<h4 id="org92be323"><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-orge39c70c" class="outline-4">
<h4 id="orge39c70c"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgac18074" class="outline-4">
<h4 id="orgac18074"><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-org36f611f" class="outline-2">
<h2 id="org36f611f"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-org9993e60" class="outline-2">
<h2 id="org9993e60"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org04d2f60" class="outline-3">
<h3 id="org04d2f60"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org591f91b" class="outline-3">
<h3 id="org591f91b"><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: 2022-07-04 Mon 12:36</p>
<p class="date">Created: 2022-07-04 Mon 14:01</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>
<!-- 2022-07-04 Mon 12:36 -->
<!-- 2022-07-04 Mon 14:01 -->
<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: 2022-07-04 Mon 12:36</p>
<p class="date">Created: 2022-07-04 Mon 14:01</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>
<!-- 2022-07-04 Mon 12:36 -->
<!-- 2022-07-04 Mon 14:01 -->
<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="#orga3b049d">1. Template for HDF5 definitions</a></li>
<li><a href="#org00ecec3">2. Template for HDF5 structures</a></li>
<li><a href="#orgb37df1a">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org303d7e9">4. Template for HDF5 has a group</a></li>
<li><a href="#org63183df">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org0151e23">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org2ab9be7">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org16f3c09">8. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org869fe5e">9. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org267fc08">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org4700f62">11. Source code for the determinant part</a></li>
<li><a href="#orgef7297e">12. Helper functions</a></li>
<li><a href="#org304d291">1. Template for HDF5 definitions</a></li>
<li><a href="#org8e2f2d4">2. Template for HDF5 structures</a></li>
<li><a href="#orga409510">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgc1b2d94">4. Template for HDF5 has a group</a></li>
<li><a href="#org8d277c8">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgb18975a">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org3d782b3">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org3cd776d">8. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org1759c96">9. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org1a0cf4e">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org1c44b18">11. Source code for the determinant part</a></li>
<li><a href="#orgb447548">12. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orga3b049d" class="outline-2">
<h2 id="orga3b049d"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org304d291" class="outline-2">
<h2 id="org304d291"><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-org00ecec3" class="outline-2">
<h2 id="org00ecec3"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org8e2f2d4" class="outline-2">
<h2 id="org8e2f2d4"><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-orgb37df1a" class="outline-2">
<h2 id="orgb37df1a"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orga409510" class="outline-2">
<h2 id="orga409510"><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-org303d7e9" class="outline-2">
<h2 id="org303d7e9"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orgc1b2d94" class="outline-2">
<h2 id="orgc1b2d94"><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-org63183df" class="outline-2">
<h2 id="org63183df"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org8d277c8" class="outline-2">
<h2 id="org8d277c8"><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-org0151e23" class="outline-2">
<h2 id="org0151e23"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgb18975a" class="outline-2">
<h2 id="orgb18975a"><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-org2ab9be7" class="outline-2">
<h2 id="org2ab9be7"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org3d782b3" class="outline-2">
<h2 id="org3d782b3"><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-org16f3c09" class="outline-2">
<h2 id="org16f3c09"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org3cd776d" class="outline-2">
<h2 id="org3cd776d"><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-org869fe5e" class="outline-2">
<h2 id="org869fe5e"><span class="section-number-2">9</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org1759c96" class="outline-2">
<h2 id="org1759c96"><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-org267fc08" class="outline-2">
<h2 id="org267fc08"><span class="section-number-2">10</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org1a0cf4e" class="outline-2">
<h2 id="org1a0cf4e"><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-org4700f62" class="outline-2">
<h2 id="org4700f62"><span class="section-number-2">11</span> Source code for the determinant part</h2>
<div id="outline-container-org1c44b18" class="outline-2">
<h2 id="org1c44b18"><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-orgef7297e" class="outline-2">
<h2 id="orgef7297e"><span class="section-number-2">12</span> Helper functions</h2>
<div id="outline-container-orgb447548" class="outline-2">
<h2 id="orgb447548"><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: 2022-07-04 Mon 12:36</p>
<p class="date">Created: 2022-07-04 Mon 14:01</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>
<!-- 2022-07-04 Mon 12:36 -->
<!-- 2022-07-04 Mon 14:01 -->
<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="#orgfa149ea">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgc0ac678">2. Template for general structure in text back end</a></li>
<li><a href="#org9852f7d">3. Initialize function (constant part)</a></li>
<li><a href="#org310d2bf">4. Deinitialize function (templated part)</a></li>
<li><a href="#orge844be0">5. Template for text read a group</a></li>
<li><a href="#org4af4024">6. Template for text has a group</a></li>
<li><a href="#org262bb71">7. Template for text flush a group</a></li>
<li><a href="#org98f222d">8. Template for text free memory</a></li>
<li><a href="#org33cd7f1">9. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org22a3f54">10. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org19cef87">11. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgfbf774a">12. Template for has/read/write a string attribute</a></li>
<li><a href="#org41685a8">13. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org0c32725">14. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org58774dc">15. Source code for the determinant part</a></li>
<li><a href="#org7701447">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgb59ca2f">2. Template for general structure in text back end</a></li>
<li><a href="#org1e44237">3. Initialize function (constant part)</a></li>
<li><a href="#org9c77f44">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgb8b74ae">5. Template for text read a group</a></li>
<li><a href="#org4a5fbdb">6. Template for text has a group</a></li>
<li><a href="#orgac7aabf">7. Template for text flush a group</a></li>
<li><a href="#orgb6ea89b">8. Template for text free memory</a></li>
<li><a href="#org6a66c0e">9. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org1c770cf">10. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org7322a26">11. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org14b5812">12. Template for has/read/write a string attribute</a></li>
<li><a href="#org8a4e14b">13. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org800a171">14. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgc043d3b">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-orgfa149ea" class="outline-2">
<h2 id="orgfa149ea"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org7701447" class="outline-2">
<h2 id="org7701447"><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-orgc0ac678" class="outline-2">
<h2 id="orgc0ac678"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgb59ca2f" class="outline-2">
<h2 id="orgb59ca2f"><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-org9852f7d" class="outline-2">
<h2 id="org9852f7d"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org1e44237" class="outline-2">
<h2 id="org1e44237"><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>
@ -548,8 +548,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org310d2bf" class="outline-2">
<h2 id="org310d2bf"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org9c77f44" class="outline-2">
<h2 id="org9c77f44"><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>
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orge844be0" class="outline-2">
<h2 id="orge844be0"><span class="section-number-2">5</span> Template for text read a group</h2>
<div id="outline-container-orgb8b74ae" class="outline-2">
<h2 id="orgb8b74ae"><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*
@ -796,8 +796,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org4af4024" class="outline-2">
<h2 id="org4af4024"><span class="section-number-2">6</span> Template for text has a group</h2>
<div id="outline-container-org4a5fbdb" class="outline-2">
<h2 id="org4a5fbdb"><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>
@ -837,8 +837,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org262bb71" class="outline-2">
<h2 id="org262bb71"><span class="section-number-2">7</span> Template for text flush a group</h2>
<div id="outline-container-orgac7aabf" class="outline-2">
<h2 id="orgac7aabf"><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>
@ -902,8 +902,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org98f222d" class="outline-2">
<h2 id="org98f222d"><span class="section-number-2">8</span> Template for text free memory</h2>
<div id="outline-container-orgb6ea89b" class="outline-2">
<h2 id="orgb6ea89b"><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.
@ -972,8 +972,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org33cd7f1" class="outline-2">
<h2 id="org33cd7f1"><span class="section-number-2">9</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org6a66c0e" class="outline-2">
<h2 id="org6a66c0e"><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>
@ -1036,8 +1036,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org22a3f54" class="outline-2">
<h2 id="org22a3f54"><span class="section-number-2">10</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org1c770cf" class="outline-2">
<h2 id="org1c770cf"><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.
@ -1133,8 +1133,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org19cef87" class="outline-2">
<h2 id="org19cef87"><span class="section-number-2">11</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org7322a26" class="outline-2">
<h2 id="org7322a26"><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.
@ -1235,8 +1235,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgfbf774a" class="outline-2">
<h2 id="orgfbf774a"><span class="section-number-2">12</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org14b5812" class="outline-2">
<h2 id="org14b5812"><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>
@ -1310,8 +1310,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org41685a8" class="outline-2">
<h2 id="org41685a8"><span class="section-number-2">13</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org8a4e14b" class="outline-2">
<h2 id="org8a4e14b"><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
@ -1601,8 +1601,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org0c32725" class="outline-2">
<h2 id="org0c32725"><span class="section-number-2">14</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org800a171" class="outline-2">
<h2 id="org800a171"><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>
@ -1630,8 +1630,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org58774dc" class="outline-2">
<h2 id="org58774dc"><span class="section-number-2">15</span> Source code for the determinant part</h2>
<div id="outline-container-orgc043d3b" class="outline-2">
<h2 id="orgc043d3b"><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
@ -2071,7 +2071,7 @@ 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: 2022-07-04 Mon 12:36</p>
<p class="date">Created: 2022-07-04 Mon 14:01</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>
<!-- 2022-07-04 Mon 12:36 -->
<!-- 2022-07-04 Mon 14:01 -->
<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="#org0caa118">1. Metadata (metadata group)</a></li>
<li><a href="#org60cf8cb">2. Electron (electron group)</a></li>
<li><a href="#org4ebe815">3. Nucleus (nucleus group)</a></li>
<li><a href="#org641326b">4. Effective core potentials (ecp group)</a>
<li><a href="#org2f7fa06">1. Metadata (metadata group)</a></li>
<li><a href="#orgcfd8478">2. Electron (electron group)</a></li>
<li><a href="#orgce929fb">3. Nucleus (nucleus group)</a></li>
<li><a href="#org162c6ed">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org1d67dba">4.1. Example</a></li>
<li><a href="#org7ea151b">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org9391469">5. Basis set (basis group)</a>
<li><a href="#orge8150db">5. Basis set (basis group)</a>
<ul>
<li><a href="#orgb219c39">5.1. Example</a></li>
<li><a href="#orgf040bd1">5.1. Example</a></li>
</ul>
</li>
<li><a href="#orgf953aec">6. Atomic orbitals (ao group)</a>
<li><a href="#org24ee7b7">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="#org55d7ba2">7. Molecular orbitals (mo group)</a>
<li><a href="#orgee40129">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org0eddf37">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgd3dd197">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgdc7477c">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgd0b6c51">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#orgea7a887">8. Slater determinants (determinant group)</a></li>
<li><a href="#org65af7de">9. Excited states (state group)</a></li>
<li><a href="#orgeff6d82">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org926d87a">11. Cell (cell group)</a></li>
<li><a href="#orga6ea213">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org64358e0">13. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org7272b21">8. Slater determinants (determinant group)</a></li>
<li><a href="#org214d29b">9. Excited states (state group)</a></li>
<li><a href="#org1842dc0">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org46187fc">11. Cell (cell group)</a></li>
<li><a href="#orgedb672c">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org130f3e9">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-org0caa118" class="outline-2">
<h2 id="org0caa118"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org2f7fa06" class="outline-2">
<h2 id="org2f7fa06"><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="org8e25e55" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orged00870" 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-org60cf8cb" class="outline-2">
<h2 id="org60cf8cb"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orgcfd8478" class="outline-2">
<h2 id="orgcfd8478"><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="org6b06e6c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org310a257" 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-org4ebe815" class="outline-2">
<h2 id="org4ebe815"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-orgce929fb" class="outline-2">
<h2 id="orgce929fb"><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="orgdc338ee" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7b4e30c" 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-org641326b" class="outline-2">
<h2 id="org641326b"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org162c6ed" class="outline-2">
<h2 id="org162c6ed"><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="org7165628" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1b45f41" 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-org1d67dba" class="outline-3">
<h3 id="org1d67dba"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org7ea151b" class="outline-3">
<h3 id="org7ea151b"><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-org9391469" class="outline-2">
<h2 id="org9391469"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-orge8150db" class="outline-2">
<h2 id="orge8150db"><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="org8ef08e5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5685ee3" 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-orgb219c39" class="outline-3">
<h3 id="orgb219c39"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-orgf040bd1" class="outline-3">
<h3 id="orgf040bd1"><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-orgf953aec" class="outline-2">
<h2 id="orgf953aec"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org24ee7b7" class="outline-2">
<h2 id="org24ee7b7"><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="#org9391469">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#orge8150db">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="orgf671a14" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbf7951c" 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-org6301f20" class="outline-3">
<h3 id="ao_one_e"><a id="org6301f20"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgf5d0296" class="outline-3">
<h3 id="ao_one_e"><a id="orgf5d0296"></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="org521cb9b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org27d5510" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1290,8 +1290,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgbac32f2" class="outline-3">
<h3 id="ao_two_e"><a id="orgbac32f2"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-orga34500f" class="outline-3">
<h3 id="ao_two_e"><a id="orga34500f"></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="org3658fef" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb19b307" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1352,10 +1352,10 @@ notation.
</div>
</div>
<div id="outline-container-org55d7ba2" class="outline-2">
<h2 id="org55d7ba2"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgee40129" class="outline-2">
<h2 id="orgee40129"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org661600e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6a5df95" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1442,8 +1442,8 @@ notation.
</table>
</div>
<div id="outline-container-org0eddf37" class="outline-3">
<h3 id="org0eddf37"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-orgdc7477c" class="outline-3">
<h3 id="orgdc7477c"><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="orgbbd2e90" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3445b5b" 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-orgd3dd197" class="outline-3">
<h3 id="orgd3dd197"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orgd0b6c51" class="outline-3">
<h3 id="orgd0b6c51"><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="org0147526" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgde066e6" 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-orgea7a887" class="outline-2">
<h2 id="orgea7a887"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-org7272b21" class="outline-2">
<h2 id="org7272b21"><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="orgbaece4b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1496085" 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-org65af7de" class="outline-2">
<h2 id="org65af7de"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div id="outline-container-org214d29b" class="outline-2">
<h2 id="org214d29b"><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="orgceff4e4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org72b1747" 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-orgeff6d82" class="outline-2">
<h2 id="orgeff6d82"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org1842dc0" class="outline-2">
<h2 id="org1842dc0"><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="orga6c8445" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org89f9fb1" 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-org926d87a" class="outline-2">
<h2 id="org926d87a"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div id="outline-container-org46187fc" class="outline-2">
<h2 id="org46187fc"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-11">
<table id="org257d398" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdc5b925" 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-orga6ea213" class="outline-2">
<h2 id="orga6ea213"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-orgedb672c" class="outline-2">
<h2 id="orgedb672c"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-12">
<table id="org942d04d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6851dd1" 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-org64358e0" class="outline-2">
<h2 id="org64358e0"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org130f3e9" class="outline-2">
<h2 id="org130f3e9"><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="org21c6367" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgde64cf6" 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: 2022-07-04 Mon 12:36</p>
<p class="date">Created: 2022-07-04 Mon 14:01</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>