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README.html
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<head>
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -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: 2022-07-01 Fri 13:22</p>
<p class="date">Created: 2022-07-01 Fri 17:00</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-07-01 Fri 13:22 -->
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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="#org884383a">1. Accessing sparse quantities (integrals)</a>
<li><a href="#org054272b">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org9be3f7d">1.1. Fortran</a>
<li><a href="#org74d188d">1.1. Fortran</a>
<ul>
<li><a href="#org0be275e">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgefacf80">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga80ba1d">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgc7d46d7">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org71b8ba4">1.1.5. Allocate memory</a></li>
<li><a href="#org5812034">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org86f8131">1.1.7. Read two-electron quantities</a>
<li><a href="#orgc6a813e">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgd282ca6">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgf87e4b5">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orge639317">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org7f47ec4">1.1.5. Allocate memory</a></li>
<li><a href="#org6d8eff1">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgf296722">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgea90c83">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org6596131">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org8dd3990">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org9e8bf67">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org1c0b67d">1.1.8. Compute the energy</a></li>
<li><a href="#org8671090">1.1.9. Terminate</a></li>
<li><a href="#org15b912c">1.1.8. Compute the energy</a></li>
<li><a href="#org17b2769">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org5d527de">2. Reading determinants</a>
<li><a href="#org8fb944d">2. Reading determinants</a>
<ul>
<li><a href="#org648c4da">2.1. Fortran</a></li>
<li><a href="#org6aded94">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -365,12 +365,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org884383a" class="outline-2">
<h2 id="org884383a"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org054272b" class="outline-2">
<h2 id="org054272b"><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-org9be3f7d" class="outline-3">
<h3 id="org9be3f7d"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org74d188d" class="outline-3">
<h3 id="org74d188d"><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-org0be275e" class="outline-4">
<h4 id="org0be275e"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgc6a813e" class="outline-4">
<h4 id="orgc6a813e"><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-orgefacf80" class="outline-4">
<h4 id="orgefacf80"><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-orgd282ca6" class="outline-4">
<h4 id="orgd282ca6"><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-orga80ba1d" class="outline-4">
<h4 id="orga80ba1d"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgf87e4b5" class="outline-4">
<h4 id="orgf87e4b5"><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-orgc7d46d7" class="outline-4">
<h4 id="orgc7d46d7"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orge639317" class="outline-4">
<h4 id="orge639317"><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-org71b8ba4" class="outline-4">
<h4 id="org71b8ba4"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org7f47ec4" class="outline-4">
<h4 id="org7f47ec4"><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-org5812034" class="outline-4">
<h4 id="org5812034"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org6d8eff1" class="outline-4">
<h4 id="org6d8eff1"><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-org86f8131" class="outline-4">
<h4 id="org86f8131"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgf296722" class="outline-4">
<h4 id="orgf296722"><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-orgea90c83" class="outline-5">
<h5 id="orgea90c83"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org8dd3990" class="outline-5">
<h5 id="org8dd3990"><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-org6596131" class="outline-5">
<h5 id="org6596131"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org9e8bf67" class="outline-5">
<h5 id="org9e8bf67"><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-org1c0b67d" class="outline-4">
<h4 id="org1c0b67d"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org15b912c" class="outline-4">
<h4 id="org15b912c"><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-org8671090" class="outline-4">
<h4 id="org8671090"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org17b2769" class="outline-4">
<h4 id="org17b2769"><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-org5d527de" class="outline-2">
<h2 id="org5d527de"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-org8fb944d" class="outline-2">
<h2 id="org8fb944d"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org648c4da" class="outline-3">
<h3 id="org648c4da"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org6aded94" class="outline-3">
<h3 id="org6aded94"><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: 2022-07-01 Fri 13:22</p>
<p class="date">Created: 2022-07-01 Fri 17:00</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>
<!-- 2022-07-01 Fri 13:22 -->
<!-- 2022-07-01 Fri 17:00 -->
<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: 2022-07-01 Fri 13:22</p>
<p class="date">Created: 2022-07-01 Fri 17:00</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-07-01 Fri 13:22 -->
<!-- 2022-07-01 Fri 17:00 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>HDF5 back end</title>
@ -311,23 +311,23 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orge4577e1">1. Template for HDF5 definitions</a></li>
<li><a href="#orgf4de222">2. Template for HDF5 structures</a></li>
<li><a href="#org47cf1e6">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org8f10280">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org1bfa836">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orga005541">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgd3f47c7">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgaa30deb">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org9663538">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org078b330">10. Source code for the determinant part</a></li>
<li><a href="#orgadebb20">11. Helper functions</a></li>
<li><a href="#org2d4c4ac">1. Template for HDF5 definitions</a></li>
<li><a href="#org049f1c6">2. Template for HDF5 structures</a></li>
<li><a href="#org4bb5622">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org55f383c">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org848e098">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgbe96f11">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org655bf37">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org1c47e07">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org99ed368">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org370d80f">10. Source code for the determinant part</a></li>
<li><a href="#org1816027">11. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orge4577e1" class="outline-2">
<h2 id="orge4577e1"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org2d4c4ac" class="outline-2">
<h2 id="org2d4c4ac"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div class="outline-text-2" id="text-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #483d8b;">#define</span> $GROUP$_GROUP_NAME <span style="color: #8b2252;">"$group$"</span>
@ -339,8 +339,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgf4de222" class="outline-2">
<h2 id="orgf4de222"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org049f1c6" class="outline-2">
<h2 id="org049f1c6"><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
@ -360,8 +360,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org47cf1e6" class="outline-2">
<h2 id="org47cf1e6"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org4bb5622" class="outline-2">
<h2 id="org4bb5622"><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>
@ -466,8 +466,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org8f10280" class="outline-2">
<h2 id="org8f10280"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org55f383c" class="outline-2">
<h2 id="org55f383c"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org1bfa836" class="outline-2">
<h2 id="org1bfa836"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org848e098" class="outline-2">
<h2 id="org848e098"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -706,8 +706,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orga005541" class="outline-2">
<h2 id="orga005541"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orgbe96f11" class="outline-2">
<h2 id="orgbe96f11"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-6">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -910,8 +910,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-orgd3f47c7" class="outline-2">
<h2 id="orgd3f47c7"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org655bf37" class="outline-2">
<h2 id="org655bf37"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1109,8 +1109,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-orgaa30deb" class="outline-2">
<h2 id="orgaa30deb"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org1c47e07" class="outline-2">
<h2 id="org1c47e07"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1237,8 +1237,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-org9663538" class="outline-2">
<h2 id="org9663538"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org99ed368" class="outline-2">
<h2 id="org99ed368"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-9">
<p>
<b><b>Note:</b></b> in early versions of the HDF5 library (v &lt; 1.10) unlinking an object was not working as expected
@ -1278,8 +1278,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org078b330" class="outline-2">
<h2 id="org078b330"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div id="outline-container-org370d80f" class="outline-2">
<h2 id="org370d80f"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-10">
<p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1532,8 +1532,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-orgadebb20" class="outline-2">
<h2 id="orgadebb20"><span class="section-number-2">11</span> Helper functions</h2>
<div id="outline-container-org1816027" class="outline-2">
<h2 id="org1816027"><span class="section-number-2">11</span> Helper functions</h2>
<div class="outline-text-2" id="text-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1796,7 +1796,7 @@ 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: 2022-07-01 Fri 13:22</p>
<p class="date">Created: 2022-07-01 Fri 17:00</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

88
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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>
<!-- 2022-07-01 Fri 13:22 -->
<!-- 2022-07-01 Fri 17:00 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
@ -311,20 +311,20 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org647c01a">1. Template for group-related structures in text back end</a></li>
<li><a href="#org0388489">2. Template for general structure in text back end</a></li>
<li><a href="#orge3a8b35">3. Initialize function (constant part)</a></li>
<li><a href="#org1ebea73">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgc34d686">5. Template for text read a group</a></li>
<li><a href="#org6f6c893">6. Template for text flush a group</a></li>
<li><a href="#orge3d8f5a">7. Template for text free memory</a></li>
<li><a href="#orgee2471f">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgbb73003">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org779b83f">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orga40ed6b">11. Template for has/read/write a string attribute</a></li>
<li><a href="#org9ca02b6">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org9000691">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org8aa8e4e">14. Source code for the determinant part</a></li>
<li><a href="#orgee3c736">1. Template for group-related structures in text back end</a></li>
<li><a href="#orge8e3db4">2. Template for general structure in text back end</a></li>
<li><a href="#orgb011dcb">3. Initialize function (constant part)</a></li>
<li><a href="#org5aba818">4. Deinitialize function (templated part)</a></li>
<li><a href="#org7ae56d8">5. Template for text read a group</a></li>
<li><a href="#orgd961d2d">6. Template for text flush a group</a></li>
<li><a href="#org4c394a9">7. Template for text free memory</a></li>
<li><a href="#orgcba114b">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org6dfd8a1">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgd8bf893">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org48500c4">11. Template for has/read/write a string attribute</a></li>
<li><a href="#org5208c3b">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgc19a4d2">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org015831b">14. Source code for the determinant part</a></li>
</ul>
</div>
</div>
@ -346,8 +346,8 @@ directory.
The file is written when closed, or when the flush function is called.
</p>
<div id="outline-container-org647c01a" class="outline-2">
<h2 id="org647c01a"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orgee3c736" class="outline-2">
<h2 id="orgee3c736"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div class="outline-text-2" id="text-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
@ -366,8 +366,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org0388489" class="outline-2">
<h2 id="org0388489"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orge8e3db4" class="outline-2">
<h2 id="orge8e3db4"><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
@ -387,8 +387,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orge3a8b35" class="outline-2">
<h2 id="orge3a8b35"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-orgb011dcb" class="outline-2">
<h2 id="orgb011dcb"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -531,8 +531,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org1ebea73" class="outline-2">
<h2 id="org1ebea73"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org5aba818" class="outline-2">
<h2 id="org5aba818"><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>
@ -554,8 +554,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgc34d686" class="outline-2">
<h2 id="orgc34d686"><span class="section-number-2">5</span> Template for text read a group</h2>
<div id="outline-container-org7ae56d8" class="outline-2">
<h2 id="org7ae56d8"><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*
@ -779,8 +779,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org6f6c893" class="outline-2">
<h2 id="org6f6c893"><span class="section-number-2">6</span> Template for text flush a group</h2>
<div id="outline-container-orgd961d2d" class="outline-2">
<h2 id="orgd961d2d"><span class="section-number-2">6</span> Template for text flush a group</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -844,8 +844,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orge3d8f5a" class="outline-2">
<h2 id="orge3d8f5a"><span class="section-number-2">7</span> Template for text free memory</h2>
<div id="outline-container-org4c394a9" class="outline-2">
<h2 id="org4c394a9"><span class="section-number-2">7</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-7">
<p>
Memory is allocated when reading. The following function frees memory.
@ -914,8 +914,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orgee2471f" class="outline-2">
<h2 id="orgee2471f"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orgcba114b" class="outline-2">
<h2 id="orgcba114b"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -978,8 +978,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orgbb73003" class="outline-2">
<h2 id="orgbb73003"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org6dfd8a1" class="outline-2">
<h2 id="org6dfd8a1"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-9">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1075,8 +1075,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org779b83f" class="outline-2">
<h2 id="org779b83f"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgd8bf893" class="outline-2">
<h2 id="orgd8bf893"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-10">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1177,8 +1177,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orga40ed6b" class="outline-2">
<h2 id="orga40ed6b"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org48500c4" class="outline-2">
<h2 id="org48500c4"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1252,8 +1252,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org9ca02b6" class="outline-2">
<h2 id="org9ca02b6"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org5208c3b" class="outline-2">
<h2 id="org5208c3b"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-12">
<p>
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
@ -1526,8 +1526,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org9000691" class="outline-2">
<h2 id="org9000691"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgc19a4d2" class="outline-2">
<h2 id="orgc19a4d2"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1555,8 +1555,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org8aa8e4e" class="outline-2">
<h2 id="org8aa8e4e"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div id="outline-container-org015831b" class="outline-2">
<h2 id="org015831b"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-14">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -1960,7 +1960,7 @@ 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: 2022-07-01 Fri 13:22</p>
<p class="date">Created: 2022-07-01 Fri 17:00</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

150
trex.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-07-01 Fri 13:22 -->
<!-- 2022-07-01 Fri 17:00 -->
<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="#orgc7dcaf3">1. Metadata (metadata group)</a></li>
<li><a href="#org27e8836">2. Electron (electron group)</a></li>
<li><a href="#orgd36cfa9">3. Nucleus (nucleus group)</a></li>
<li><a href="#org0f7ef9a">4. Effective core potentials (ecp group)</a>
<li><a href="#org87fd8b4">1. Metadata (metadata group)</a></li>
<li><a href="#orgee117f4">2. Electron (electron group)</a></li>
<li><a href="#org0f1b9cd">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgcc5b4e5">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org0d5d8f6">4.1. Example</a></li>
<li><a href="#org448c314">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org496421b">5. Basis set (basis group)</a>
<li><a href="#org495a768">5. Basis set (basis group)</a>
<ul>
<li><a href="#org6eb141c">5.1. Example</a></li>
<li><a href="#orgf1d5188">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org1351cfc">6. Atomic orbitals (ao group)</a>
<li><a href="#org391e743">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="#org93ecdc1">7. Molecular orbitals (mo group)</a>
<li><a href="#org7f6ada6">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org2b7d31d">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org67fb79a">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org932ac48">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org62075e9">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org564073f">8. Slater determinants (determinant group)</a></li>
<li><a href="#org650e5ea">9. Excited states (state group)</a></li>
<li><a href="#org5afc119">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org54ab114">11. Cell (cell group)</a></li>
<li><a href="#orge57764b">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org7f09c3f">13. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org971f5b7">8. Slater determinants (determinant group)</a></li>
<li><a href="#org685658b">9. Excited states (state group)</a></li>
<li><a href="#org95cdcba">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org8ba41e0">11. Cell (cell group)</a></li>
<li><a href="#orgde40f5d">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org0c9a7d5">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-orgc7dcaf3" class="outline-2">
<h2 id="orgc7dcaf3"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org87fd8b4" class="outline-2">
<h2 id="org87fd8b4"><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="org2e0efdd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0b10d6c" 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-org27e8836" class="outline-2">
<h2 id="org27e8836"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orgee117f4" class="outline-2">
<h2 id="orgee117f4"><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="orgbda8a39" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0a14137" 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-orgd36cfa9" class="outline-2">
<h2 id="orgd36cfa9"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org0f1b9cd" class="outline-2">
<h2 id="org0f1b9cd"><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="org014d005" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org56cd3f3" 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-org0f7ef9a" class="outline-2">
<h2 id="org0f7ef9a"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orgcc5b4e5" class="outline-2">
<h2 id="orgcc5b4e5"><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="org7580788" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org39b861a" 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-org0d5d8f6" class="outline-3">
<h3 id="org0d5d8f6"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org448c314" class="outline-3">
<h3 id="org448c314"><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-org496421b" class="outline-2">
<h2 id="org496421b"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org495a768" class="outline-2">
<h2 id="org495a768"><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="org23c35f9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org331baa2" 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-org6eb141c" class="outline-3">
<h3 id="org6eb141c"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-orgf1d5188" class="outline-3">
<h3 id="orgf1d5188"><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-org1351cfc" class="outline-2">
<h2 id="org1351cfc"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org391e743" class="outline-2">
<h2 id="org391e743"><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="#org496421b">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org495a768">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="orgf4caf7b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga085532" 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-org2682c68" class="outline-3">
<h3 id="ao_one_e"><a id="org2682c68"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgf340726" class="outline-3">
<h3 id="ao_one_e"><a id="orgf340726"></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="orge80df7e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgee44cd0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1290,8 +1290,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org8c771de" class="outline-3">
<h3 id="ao_two_e"><a id="org8c771de"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-orgc140cca" class="outline-3">
<h3 id="ao_two_e"><a id="orgc140cca"></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="org5861337" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdf397fe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1352,10 +1352,10 @@ notation.
</div>
</div>
<div id="outline-container-org93ecdc1" class="outline-2">
<h2 id="org93ecdc1"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org7f6ada6" class="outline-2">
<h2 id="org7f6ada6"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org75df1c2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2fb3718" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1428,8 +1428,8 @@ notation.
</table>
</div>
<div id="outline-container-org2b7d31d" class="outline-3">
<h3 id="org2b7d31d"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org932ac48" class="outline-3">
<h3 id="org932ac48"><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
@ -1437,7 +1437,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org8c31e41" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf614d3e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1532,8 +1532,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org67fb79a" class="outline-3">
<h3 id="org67fb79a"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org62075e9" class="outline-3">
<h3 id="org62075e9"><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
@ -1541,7 +1541,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org1975100" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcda8801" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1581,8 +1581,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org564073f" class="outline-2">
<h2 id="org564073f"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-org971f5b7" class="outline-2">
<h2 id="org971f5b7"><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 \(\Psi\)
@ -1624,7 +1624,7 @@ 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="org7fd9639" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org069dce1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1670,8 +1670,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org650e5ea" class="outline-2">
<h2 id="org650e5ea"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div id="outline-container-org685658b" class="outline-2">
<h2 id="org685658b"><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.
@ -1680,7 +1680,7 @@ correspond to excited state wave functions for the same set of
determinants. This is the goal of the present group
</p>
<table id="org2582ea3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb508e5a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1719,8 +1719,8 @@ determinants. This is the goal of the present group
</div>
</div>
<div id="outline-container-org5afc119" class="outline-2">
<h2 id="org5afc119"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org95cdcba" class="outline-2">
<h2 id="org95cdcba"><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
@ -1773,7 +1773,7 @@ The total energy can be computed as:
\]
</p>
<table id="org88e8703" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org66345c9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1854,10 +1854,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org54ab114" class="outline-2">
<h2 id="org54ab114"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div id="outline-container-org8ba41e0" class="outline-2">
<h2 id="org8ba41e0"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-11">
<table id="org8a1cf8a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org59d7a8d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1903,10 +1903,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-orge57764b" class="outline-2">
<h2 id="orge57764b"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-orgde40f5d" class="outline-2">
<h2 id="orgde40f5d"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-12">
<table id="org43dd9bf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9b50d11" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1945,8 +1945,8 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org7f09c3f" class="outline-2">
<h2 id="org7f09c3f"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org0c9a7d5" class="outline-2">
<h2 id="org0c9a7d5"><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
@ -1960,7 +1960,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="org44b619e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org058ab86" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2015,7 +2015,7 @@ 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: 2022-07-01 Fri 13:22</p>
<p class="date">Created: 2022-07-01 Fri 17:00</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>