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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: 2022-06-28 Tue 08:16</p>
<p class="date">Created: 2022-07-01 Fri 08:36</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-06-28 Tue 08:16 -->
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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="#org9b82c10">1. Accessing sparse quantities (integrals)</a>
<li><a href="#org032657b">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org99b90c1">1.1. Fortran</a>
<li><a href="#org6309ffd">1.1. Fortran</a>
<ul>
<li><a href="#org562f316">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org9e58380">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org31f068a">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgfd84ca3">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org3006227">1.1.5. Allocate memory</a></li>
<li><a href="#org8817ee9">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org044144c">1.1.7. Read two-electron quantities</a>
<li><a href="#org5218905">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org135c221">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org56ef5fa">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org8480e26">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org9cf9b2e">1.1.5. Allocate memory</a></li>
<li><a href="#org3c351a4">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org2b67d3b">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgdc70d60">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org465d93b">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org6b4c72a">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org6e56b04">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgadfa968">1.1.8. Compute the energy</a></li>
<li><a href="#orgfd61ee3">1.1.9. Terminate</a></li>
<li><a href="#orge07ea64">1.1.8. Compute the energy</a></li>
<li><a href="#orgf2e9ff9">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org17f9fd4">2. Reading determinants</a>
<li><a href="#org7c691f3">2. Reading determinants</a>
<ul>
<li><a href="#orgd5bb71c">2.1. Fortran</a></li>
<li><a href="#org725040a">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -365,12 +365,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org9b82c10" class="outline-2">
<h2 id="org9b82c10"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org032657b" class="outline-2">
<h2 id="org032657b"><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-org99b90c1" class="outline-3">
<h3 id="org99b90c1"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org6309ffd" class="outline-3">
<h3 id="org6309ffd"><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-org562f316" class="outline-4">
<h4 id="org562f316"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org5218905" class="outline-4">
<h4 id="org5218905"><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-org9e58380" class="outline-4">
<h4 id="org9e58380"><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-org135c221" class="outline-4">
<h4 id="org135c221"><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-org31f068a" class="outline-4">
<h4 id="org31f068a"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org56ef5fa" class="outline-4">
<h4 id="org56ef5fa"><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-orgfd84ca3" class="outline-4">
<h4 id="orgfd84ca3"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org8480e26" class="outline-4">
<h4 id="org8480e26"><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-org3006227" class="outline-4">
<h4 id="org3006227"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org9cf9b2e" class="outline-4">
<h4 id="org9cf9b2e"><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-org8817ee9" class="outline-4">
<h4 id="org8817ee9"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org3c351a4" class="outline-4">
<h4 id="org3c351a4"><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-org044144c" class="outline-4">
<h4 id="org044144c"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org2b67d3b" class="outline-4">
<h4 id="org2b67d3b"><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-orgdc70d60" class="outline-5">
<h5 id="orgdc70d60"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org6b4c72a" class="outline-5">
<h5 id="org6b4c72a"><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-org465d93b" class="outline-5">
<h5 id="org465d93b"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org6e56b04" class="outline-5">
<h5 id="org6e56b04"><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-orgadfa968" class="outline-4">
<h4 id="orgadfa968"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-orge07ea64" class="outline-4">
<h4 id="orge07ea64"><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-orgfd61ee3" class="outline-4">
<h4 id="orgfd61ee3"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgf2e9ff9" class="outline-4">
<h4 id="orgf2e9ff9"><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-org17f9fd4" class="outline-2">
<h2 id="org17f9fd4"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-org7c691f3" class="outline-2">
<h2 id="org7c691f3"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgd5bb71c" class="outline-3">
<h3 id="orgd5bb71c"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org725040a" class="outline-3">
<h3 id="org725040a"><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: 2022-06-28 Tue 08:16</p>
<p class="date">Created: 2022-07-01 Fri 08:36</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>
<!-- 2022-06-28 Tue 08:16 -->
<!-- 2022-07-01 Fri 08:36 -->
<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: 2022-06-28 Tue 08:16</p>
<p class="date">Created: 2022-07-01 Fri 08:36</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>
<!-- 2022-06-28 Tue 08:16 -->
<!-- 2022-07-01 Fri 08:35 -->
<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="#org4da58d4">1. Template for HDF5 definitions</a></li>
<li><a href="#org8df2bc4">2. Template for HDF5 structures</a></li>
<li><a href="#orgdc1b22c">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org7000560">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgf224ab7">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgcced5ae">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgb2188bf">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orga658fae">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgfad8c26">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orge5b9474">10. Source code for the determinant part</a></li>
<li><a href="#orgfd1e449">11. Helper functions</a></li>
<li><a href="#org5eab87a">1. Template for HDF5 definitions</a></li>
<li><a href="#orgf9d56f8">2. Template for HDF5 structures</a></li>
<li><a href="#orga0a52f7">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org21afe16">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orga631422">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org258355c">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgd3f3ade">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org4eb0e71">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org364bdde">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org8b9aacd">10. Source code for the determinant part</a></li>
<li><a href="#orgb68b0b2">11. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org4da58d4" class="outline-2">
<h2 id="org4da58d4"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org5eab87a" class="outline-2">
<h2 id="org5eab87a"><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-org8df2bc4" class="outline-2">
<h2 id="org8df2bc4"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgf9d56f8" class="outline-2">
<h2 id="orgf9d56f8"><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-orgdc1b22c" class="outline-2">
<h2 id="orgdc1b22c"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orga0a52f7" class="outline-2">
<h2 id="orga0a52f7"><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-org7000560" class="outline-2">
<h2 id="org7000560"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org21afe16" class="outline-2">
<h2 id="org21afe16"><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-orgf224ab7" class="outline-2">
<h2 id="orgf224ab7"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orga631422" class="outline-2">
<h2 id="orga631422"><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-orgcced5ae" class="outline-2">
<h2 id="orgcced5ae"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org258355c" class="outline-2">
<h2 id="org258355c"><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-orgb2188bf" class="outline-2">
<h2 id="orgb2188bf"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgd3f3ade" class="outline-2">
<h2 id="orgd3f3ade"><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-orga658fae" class="outline-2">
<h2 id="orga658fae"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org4eb0e71" class="outline-2">
<h2 id="org4eb0e71"><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-orgfad8c26" class="outline-2">
<h2 id="orgfad8c26"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org364bdde" class="outline-2">
<h2 id="org364bdde"><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-orge5b9474" class="outline-2">
<h2 id="orge5b9474"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div id="outline-container-org8b9aacd" class="outline-2">
<h2 id="org8b9aacd"><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-orgfd1e449" class="outline-2">
<h2 id="orgfd1e449"><span class="section-number-2">11</span> Helper functions</h2>
<div id="outline-container-orgb68b0b2" class="outline-2">
<h2 id="orgb68b0b2"><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: 2022-06-28 Tue 08:16</p>
<p class="date">Created: 2022-07-01 Fri 08:35</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

88
templator_text.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>
<!-- 2022-06-28 Tue 08:16 -->
<!-- 2022-07-01 Fri 08:35 -->
<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="#org4e2c443">1. Template for group-related structures in text back end</a></li>
<li><a href="#org49c2435">2. Template for general structure in text back end</a></li>
<li><a href="#org33ec18a">3. Initialize function (constant part)</a></li>
<li><a href="#orgc5aabe0">4. Deinitialize function (templated part)</a></li>
<li><a href="#org0940142">5. Template for text read a group</a></li>
<li><a href="#orgf7e5fe6">6. Template for text flush a group</a></li>
<li><a href="#org380df5e">7. Template for text free memory</a></li>
<li><a href="#orgc6b1292">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org351f00d">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org5b7534f">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgffa7327">11. Template for has/read/write a string attribute</a></li>
<li><a href="#orgf7cd0b6">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org7504d03">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org850b07c">14. Source code for the determinant part</a></li>
<li><a href="#orgfb84825">1. Template for group-related structures in text back end</a></li>
<li><a href="#org8ede420">2. Template for general structure in text back end</a></li>
<li><a href="#org9ce99c9">3. Initialize function (constant part)</a></li>
<li><a href="#org961496d">4. Deinitialize function (templated part)</a></li>
<li><a href="#org609dcc6">5. Template for text read a group</a></li>
<li><a href="#org5300420">6. Template for text flush a group</a></li>
<li><a href="#org415064d">7. Template for text free memory</a></li>
<li><a href="#org5e83460">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgfff45d0">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org74ae362">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org67ac364">11. Template for has/read/write a string attribute</a></li>
<li><a href="#org66ec6f9">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org808cf6c">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org934856f">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-org4e2c443" class="outline-2">
<h2 id="org4e2c443"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orgfb84825" class="outline-2">
<h2 id="orgfb84825"><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-org49c2435" class="outline-2">
<h2 id="org49c2435"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org8ede420" class="outline-2">
<h2 id="org8ede420"><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-org33ec18a" class="outline-2">
<h2 id="org33ec18a"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org9ce99c9" class="outline-2">
<h2 id="org9ce99c9"><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-orgc5aabe0" class="outline-2">
<h2 id="orgc5aabe0"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org961496d" class="outline-2">
<h2 id="org961496d"><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-org0940142" class="outline-2">
<h2 id="org0940142"><span class="section-number-2">5</span> Template for text read a group</h2>
<div id="outline-container-org609dcc6" class="outline-2">
<h2 id="org609dcc6"><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-orgf7e5fe6" class="outline-2">
<h2 id="orgf7e5fe6"><span class="section-number-2">6</span> Template for text flush a group</h2>
<div id="outline-container-org5300420" class="outline-2">
<h2 id="org5300420"><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-org380df5e" class="outline-2">
<h2 id="org380df5e"><span class="section-number-2">7</span> Template for text free memory</h2>
<div id="outline-container-org415064d" class="outline-2">
<h2 id="org415064d"><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-orgc6b1292" class="outline-2">
<h2 id="orgc6b1292"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org5e83460" class="outline-2">
<h2 id="org5e83460"><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-org351f00d" class="outline-2">
<h2 id="org351f00d"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgfff45d0" class="outline-2">
<h2 id="orgfff45d0"><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-org5b7534f" class="outline-2">
<h2 id="org5b7534f"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org74ae362" class="outline-2">
<h2 id="org74ae362"><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-orgffa7327" class="outline-2">
<h2 id="orgffa7327"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org67ac364" class="outline-2">
<h2 id="org67ac364"><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-orgf7cd0b6" class="outline-2">
<h2 id="orgf7cd0b6"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org66ec6f9" class="outline-2">
<h2 id="org66ec6f9"><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-org7504d03" class="outline-2">
<h2 id="org7504d03"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org808cf6c" class="outline-2">
<h2 id="org808cf6c"><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-org850b07c" class="outline-2">
<h2 id="org850b07c"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div id="outline-container-org934856f" class="outline-2">
<h2 id="org934856f"><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: 2022-06-28 Tue 08:16</p>
<p class="date">Created: 2022-07-01 Fri 08:35</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

171
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>
<!-- 2022-06-28 Tue 08:16 -->
<!-- 2022-07-01 Fri 08:36 -->
<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="#org75f3edf">1. Metadata (metadata group)</a></li>
<li><a href="#org45f60fe">2. Electron (electron group)</a></li>
<li><a href="#orgce900f7">3. Nucleus (nucleus group)</a></li>
<li><a href="#org7a648de">4. Effective core potentials (ecp group)</a>
<li><a href="#org9d90889">1. Metadata (metadata group)</a></li>
<li><a href="#org872ebf0">2. Electron (electron group)</a></li>
<li><a href="#org503c284">3. Nucleus (nucleus group)</a></li>
<li><a href="#org754c012">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org7ab7b1e">4.1. Example</a></li>
<li><a href="#orgfbf2c28">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org1bbccb1">5. Basis set (basis group)</a>
<li><a href="#org5c8d759">5. Basis set (basis group)</a>
<ul>
<li><a href="#org5ce2b74">5.1. Example</a></li>
<li><a href="#orgfb79566">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org1922695">6. Atomic orbitals (ao group)</a>
<li><a href="#org9d900a9">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="#org76c76cc">7. Molecular orbitals (mo group)</a>
<li><a href="#org29d8f6d">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org121026b">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgf37f115">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgd4fcf97">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org0503bd7">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#orgb38e06b">8. Slater determinants (determinant group)</a></li>
<li><a href="#org36e99af">9. Excited states (state group)</a></li>
<li><a href="#org3f306dc">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org4467f13">11. Cell (cell group)</a></li>
<li><a href="#orgc367fea">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgedd1906">13. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org36e5c50">8. Slater determinants (determinant group)</a></li>
<li><a href="#org4cffc11">9. Excited states (state group)</a></li>
<li><a href="#org01c946e">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org9e97832">11. Cell (cell group)</a></li>
<li><a href="#org3b1c62d">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org56420ad">13. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -412,9 +412,13 @@ For more information on how to read/write sparse data structures, see
the <a href="./examples.html">examples</a>.
</p>
<p>
For determinants, the <code>special</code> attribute is present in the type. This
means that the source code is not produced by the generator, but hand-written.
</p>
<div id="outline-container-org75f3edf" class="outline-2">
<h2 id="org75f3edf"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org9d90889" class="outline-2">
<h2 id="org9d90889"><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
@ -424,7 +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="orgbc51bca" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0b7412c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -505,15 +509,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-org45f60fe" class="outline-2">
<h2 id="org45f60fe"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org872ebf0" class="outline-2">
<h2 id="org872ebf0"><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="org4639a3a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org182f380" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -559,15 +563,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgce900f7" class="outline-2">
<h2 id="orgce900f7"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org503c284" class="outline-2">
<h2 id="org503c284"><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="orga7418b6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1cb4218" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -634,8 +638,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org7a648de" class="outline-2">
<h2 id="org7a648de"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org754c012" class="outline-2">
<h2 id="org754c012"><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
@ -668,7 +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="orge6d02c7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org93a79c3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -770,8 +774,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-org7ab7b1e" class="outline-3">
<h3 id="org7ab7b1e"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-orgfbf2c28" class="outline-3">
<h3 id="orgfbf2c28"><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
@ -834,8 +838,8 @@ power = [
</div>
</div>
<div id="outline-container-org1bbccb1" class="outline-2">
<h2 id="org1bbccb1"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org5c8d759" class="outline-2">
<h2 id="org5c8d759"><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
@ -888,7 +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="org681ad23" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2c493c6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -982,8 +986,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-org5ce2b74" class="outline-3">
<h3 id="org5ce2b74"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-orgfb79566" class="outline-3">
<h3 id="orgfb79566"><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
@ -1061,8 +1065,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org1922695" class="outline-2">
<h2 id="org1922695"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org9d900a9" class="outline-2">
<h2 id="org9d900a9"><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
@ -1115,13 +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="#org1bbccb1">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org5c8d759">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="org9a01349" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org58965e9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1173,8 +1177,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-orgae1604c" class="outline-3">
<h3 id="ao_one_e"><a id="orgae1604c"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgce54fee" class="outline-3">
<h3 id="ao_one_e"><a id="orgce54fee"></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}}
@ -1191,7 +1195,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgd86073c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org916b132" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1286,8 +1290,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orge809d65" class="outline-3">
<h3 id="ao_two_e"><a id="orge809d65"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org00dc2f3" class="outline-3">
<h3 id="ao_two_e"><a id="org00dc2f3"></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
@ -1308,7 +1312,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org5ceeaea" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org886de0d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1348,10 +1352,10 @@ notation.
</div>
</div>
<div id="outline-container-org76c76cc" class="outline-2">
<h2 id="org76c76cc"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org29d8f6d" class="outline-2">
<h2 id="org29d8f6d"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org266a5c1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2832668" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1424,8 +1428,8 @@ notation.
</table>
</div>
<div id="outline-container-org121026b" class="outline-3">
<h3 id="org121026b"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-orgd4fcf97" class="outline-3">
<h3 id="orgd4fcf97"><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
@ -1433,7 +1437,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org12ba11e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org70bf3b7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1528,8 +1532,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgf37f115" class="outline-3">
<h3 id="orgf37f115"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org0503bd7" class="outline-3">
<h3 id="org0503bd7"><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
@ -1537,7 +1541,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org9fbb1b7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5807466" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1577,8 +1581,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgb38e06b" class="outline-2">
<h2 id="orgb38e06b"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-org36e5c50" class="outline-2">
<h2 id="org36e5c50"><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 \(\Psi\)
@ -1602,16 +1606,25 @@ in the memory.
<p>
\[
D_I = \alpha_1 \alpha_2 \ldots \alpha_{n\uparrow} \beta_1 \beta_2 \ldots \beta_{n\downarrow}
D_I = \alpha_1 \alpha_2 \ldots \alpha_{n_\uparrow} \beta_1 \beta_2 \ldots \beta_{n_\downarrow}
\]
</p>
<p>
where \(\alpha\) and \(\beta\) denote $&uarr;$-spin and $&darr;$-spin electrons, respectively,
\(n\uparrow\) and \(n\downarrow\) correspond to <code>electron.up_num</code> and <code>electron.dn_num</code>, respectively.
where \(\alpha\) and \(\beta\) denote &uarr;-spin and &darr;-spin electrons, respectively,
\(n_\uparrow\) and \(n_\downarrow\) correspond to <code>electron.up_num</code> and <code>electron.dn_num</code>, respectively.
</p>
<table id="org3588963" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<p>
Note: the <code>special</code> attribute is present in the types, meaning that the source node is not
produced by the code generator.
</p>
<p>
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
</p>
<table id="org45dad5e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1657,8 +1670,8 @@ where \(\alpha\) and \(\beta\) denote $&uarr;$-spin and $&darr;$-spin electrons,
</div>
</div>
<div id="outline-container-org36e99af" class="outline-2">
<h2 id="org36e99af"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div id="outline-container-org4cffc11" class="outline-2">
<h2 id="org4cffc11"><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.
@ -1667,7 +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="orgbb6e38a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7a0617c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1706,8 +1719,8 @@ determinants. This is the goal of the present group
</div>
</div>
<div id="outline-container-org3f306dc" class="outline-2">
<h2 id="org3f306dc"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org01c946e" class="outline-2">
<h2 id="org01c946e"><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
@ -1715,7 +1728,7 @@ orbitals.
</p>
<p>
The $&uarr;$-spin and $&darr;$-spin components of the one-body
The &uarr;-spin and &darr;-spin components of the one-body
density matrix are given by
</p>
\begin{eqnarray*}
@ -1760,7 +1773,7 @@ The total energy can be computed as:
\]
</p>
<table id="org1cff17f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0f3b380" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1841,10 +1854,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org4467f13" class="outline-2">
<h2 id="org4467f13"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div id="outline-container-org9e97832" class="outline-2">
<h2 id="org9e97832"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-11">
<table id="org730dfbb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge3c67c1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1890,10 +1903,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-orgc367fea" class="outline-2">
<h2 id="orgc367fea"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-org3b1c62d" class="outline-2">
<h2 id="org3b1c62d"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-12">
<table id="orgfbcee5a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgee93b25" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1932,8 +1945,8 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-orgedd1906" class="outline-2">
<h2 id="orgedd1906"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org56420ad" class="outline-2">
<h2 id="org56420ad"><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
@ -1947,7 +1960,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orgf7346cd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org04fc26d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2002,7 +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: 2022-06-28 Tue 08:16</p>
<p class="date">Created: 2022-07-01 Fri 08:36</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>