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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: 2022-10-06 Thu 13:35</p>
<p class="date">Created: 2022-10-07 Fri 09:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-10-06 Thu 13:35 -->
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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="#org59d1e48">1. Accessing sparse quantities (integrals)</a>
<li><a href="#orgcde88dd">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org7730943">1.1. Fortran</a>
<li><a href="#org6fce54a">1.1. Fortran</a>
<ul>
<li><a href="#org7aa71a5">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org2876687">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org76ecf7f">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org5d1651f">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org4dc7a33">1.1.5. Allocate memory</a></li>
<li><a href="#org603fe9d">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orge091f5d">1.1.7. Read two-electron quantities</a>
<li><a href="#org77cec33">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org1023293">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org30c2d7f">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org5d1cffb">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgfcd9bc4">1.1.5. Allocate memory</a></li>
<li><a href="#org9b6ac5b">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org91542f1">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org48e5b8a">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org75da222">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org44afa69">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org58f4842">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgd6ddd82">1.1.8. Compute the energy</a></li>
<li><a href="#orgd5fecc9">1.1.9. Terminate</a></li>
<li><a href="#org61fc2ac">1.1.8. Compute the energy</a></li>
<li><a href="#org6bc0967">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org551626c">2. Reading determinants</a>
<li><a href="#org7a69b1c">2. Reading determinants</a>
<ul>
<li><a href="#org3806827">2.1. Fortran</a></li>
<li><a href="#orgadcb0a1">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -365,12 +365,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org59d1e48" class="outline-2">
<h2 id="org59d1e48"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orgcde88dd" class="outline-2">
<h2 id="orgcde88dd"><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-org7730943" class="outline-3">
<h3 id="org7730943"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org6fce54a" class="outline-3">
<h3 id="org6fce54a"><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-org7aa71a5" class="outline-4">
<h4 id="org7aa71a5"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org77cec33" class="outline-4">
<h4 id="org77cec33"><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-org2876687" class="outline-4">
<h4 id="org2876687"><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-org1023293" class="outline-4">
<h4 id="org1023293"><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-org76ecf7f" class="outline-4">
<h4 id="org76ecf7f"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org30c2d7f" class="outline-4">
<h4 id="org30c2d7f"><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-org5d1651f" class="outline-4">
<h4 id="org5d1651f"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org5d1cffb" class="outline-4">
<h4 id="org5d1cffb"><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-org4dc7a33" class="outline-4">
<h4 id="org4dc7a33"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-orgfcd9bc4" class="outline-4">
<h4 id="orgfcd9bc4"><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-org603fe9d" class="outline-4">
<h4 id="org603fe9d"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org9b6ac5b" class="outline-4">
<h4 id="org9b6ac5b"><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-orge091f5d" class="outline-4">
<h4 id="orge091f5d"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org91542f1" class="outline-4">
<h4 id="org91542f1"><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-org48e5b8a" class="outline-5">
<h5 id="org48e5b8a"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org44afa69" class="outline-5">
<h5 id="org44afa69"><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-org75da222" class="outline-5">
<h5 id="org75da222"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org58f4842" class="outline-5">
<h5 id="org58f4842"><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-orgd6ddd82" class="outline-4">
<h4 id="orgd6ddd82"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org61fc2ac" class="outline-4">
<h4 id="org61fc2ac"><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-orgd5fecc9" class="outline-4">
<h4 id="orgd5fecc9"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org6bc0967" class="outline-4">
<h4 id="org6bc0967"><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-org551626c" class="outline-2">
<h2 id="org551626c"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-org7a69b1c" class="outline-2">
<h2 id="org7a69b1c"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org3806827" class="outline-3">
<h3 id="org3806827"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-orgadcb0a1" class="outline-3">
<h3 id="orgadcb0a1"><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: 2022-10-06 Thu 13:35</p>
<p class="date">Created: 2022-10-07 Fri 09:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-10-06 Thu 13:35 -->
<!-- 2022-10-07 Fri 09:47 -->
<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: 2022-10-06 Thu 13:35</p>
<p class="date">Created: 2022-10-07 Fri 09:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-10-06 Thu 13:35 -->
<!-- 2022-10-07 Fri 09:46 -->
<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>
@ -311,25 +311,25 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org246ffdc">1. Template for HDF5 definitions</a></li>
<li><a href="#org8317b02">2. Template for HDF5 structures</a></li>
<li><a href="#org460ee6c">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org355e79b">4. Template for HDF5 has a group</a></li>
<li><a href="#org0d92dcf">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgc550ebf">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org84f42be">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org3d27d6c">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgf8e608d">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org4422d26">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orge759da6">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org98c9a70">12. Source code for the determinant part</a></li>
<li><a href="#org8bc4db2">13. Helper functions</a></li>
<li><a href="#org7266d1a">1. Template for HDF5 definitions</a></li>
<li><a href="#org5c79ddc">2. Template for HDF5 structures</a></li>
<li><a href="#orgdb7c45f">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orge4664ad">4. Template for HDF5 has a group</a></li>
<li><a href="#org85375ec">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org29236f8">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org2a0a12b">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org8aed55d">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgb1b1ab5">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgf1998e3">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org22f8d12">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org16d5f52">12. Source code for the determinant part</a></li>
<li><a href="#orgd261ce1">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org246ffdc" class="outline-2">
<h2 id="org246ffdc"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org7266d1a" class="outline-2">
<h2 id="org7266d1a"><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>
@ -341,8 +341,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org8317b02" class="outline-2">
<h2 id="org8317b02"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org5c79ddc" class="outline-2">
<h2 id="org5c79ddc"><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
@ -362,8 +362,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org460ee6c" class="outline-2">
<h2 id="org460ee6c"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgdb7c45f" class="outline-2">
<h2 id="orgdb7c45f"><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>
@ -483,8 +483,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org355e79b" class="outline-2">
<h2 id="org355e79b"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orge4664ad" class="outline-2">
<h2 id="orge4664ad"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -514,8 +514,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org0d92dcf" class="outline-2">
<h2 id="org0d92dcf"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org85375ec" class="outline-2">
<h2 id="org85375ec"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -619,8 +619,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgc550ebf" class="outline-2">
<h2 id="orgc550ebf"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org29236f8" class="outline-2">
<h2 id="org29236f8"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -754,8 +754,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org84f42be" class="outline-2">
<h2 id="org84f42be"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org2a0a12b" class="outline-2">
<h2 id="org2a0a12b"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-7">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -958,8 +958,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org3d27d6c" class="outline-2">
<h2 id="org3d27d6c"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org8aed55d" class="outline-2">
<h2 id="org8aed55d"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div class="outline-text-2" id="text-8">
<p>
Chunked I/O in HDF5 for <code>buffered</code> data.
@ -1094,8 +1094,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-orgf8e608d" class="outline-2">
<h2 id="orgf8e608d"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgb1b1ab5" class="outline-2">
<h2 id="orgb1b1ab5"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1293,8 +1293,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org4422d26" class="outline-2">
<h2 id="org4422d26"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgf1998e3" class="outline-2">
<h2 id="orgf1998e3"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1421,8 +1421,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
</div>
<div id="outline-container-orge759da6" class="outline-2">
<h2 id="orge759da6"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org22f8d12" class="outline-2">
<h2 id="org22f8d12"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-11">
<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
@ -1462,8 +1462,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org98c9a70" class="outline-2">
<h2 id="org98c9a70"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org16d5f52" class="outline-2">
<h2 id="org16d5f52"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-12">
<p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1566,8 +1566,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org8bc4db2" class="outline-2">
<h2 id="org8bc4db2"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgd261ce1" class="outline-2">
<h2 id="orgd261ce1"><span class="section-number-2">13</span> Helper functions</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>
@ -1830,7 +1830,7 @@ 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: 2022-10-06 Thu 13:35</p>
<p class="date">Created: 2022-10-07 Fri 09:46</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>
<!-- 2022-10-06 Thu 13:35 -->
<!-- 2022-10-07 Fri 09:47 -->
<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>
@ -311,23 +311,23 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org78bd9f1">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgd8c09cf">2. Template for general structure in text back end</a></li>
<li><a href="#org44fd165">3. Initialize function (constant part)</a></li>
<li><a href="#org214c263">4. Deinitialize function (templated part)</a></li>
<li><a href="#org436e771">5. Flush function (templated part)</a></li>
<li><a href="#orgb7d31b8">6. Template for text read a group</a></li>
<li><a href="#org79f1647">7. Template for text has a group</a></li>
<li><a href="#org219178b">8. Template for text flush a group</a></li>
<li><a href="#orgf2232d0">9. Template for text free memory</a></li>
<li><a href="#org7034821">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org8a2f19d">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org4cd23dc">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orge0f79f8">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgf66c25c">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgad47a68">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org21b9574">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgf02d803">17. Source code for the determinant part</a></li>
<li><a href="#orga3106ae">1. Template for group-related structures in text back end</a></li>
<li><a href="#org93ee287">2. Template for general structure in text back end</a></li>
<li><a href="#orga166c4d">3. Initialize function (constant part)</a></li>
<li><a href="#org51034ec">4. Deinitialize function (templated part)</a></li>
<li><a href="#org5cd1823">5. Flush function (templated part)</a></li>
<li><a href="#org31dcd63">6. Template for text read a group</a></li>
<li><a href="#org7b9599e">7. Template for text has a group</a></li>
<li><a href="#orgb5947bb">8. Template for text flush a group</a></li>
<li><a href="#org9935d9b">9. Template for text free memory</a></li>
<li><a href="#org3513e68">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org82f1c44">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgaec00ae">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org8be155e">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgcd6bc0c">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org51f47fd">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org974f669">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgba8bc93">17. Source code for the determinant part</a></li>
</ul>
</div>
</div>
@ -349,8 +349,8 @@ directory.
The file is written when closed, or when the flush function is called.
</p>
<div id="outline-container-org78bd9f1" class="outline-2">
<h2 id="org78bd9f1"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orga3106ae" class="outline-2">
<h2 id="orga3106ae"><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 {
@ -369,8 +369,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orgd8c09cf" class="outline-2">
<h2 id="orgd8c09cf"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org93ee287" class="outline-2">
<h2 id="org93ee287"><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
@ -390,8 +390,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org44fd165" class="outline-2">
<h2 id="org44fd165"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-orga166c4d" class="outline-2">
<h2 id="orga166c4d"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">bool</span>
@ -558,8 +558,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org214c263" class="outline-2">
<h2 id="org214c263"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org51034ec" class="outline-2">
<h2 id="org51034ec"><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>
@ -581,8 +581,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org436e771" class="outline-2">
<h2 id="org436e771"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org5cd1823" class="outline-2">
<h2 id="org5cd1823"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -605,8 +605,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgb7d31b8" class="outline-2">
<h2 id="orgb7d31b8"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org31dcd63" class="outline-2">
<h2 id="org31dcd63"><span class="section-number-2">6</span> Template for text read a group</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -832,8 +832,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org79f1647" class="outline-2">
<h2 id="org79f1647"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org7b9599e" class="outline-2">
<h2 id="org7b9599e"><span class="section-number-2">7</span> Template for text has a group</h2>
<div class="outline-text-2" id="text-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -873,8 +873,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org219178b" class="outline-2">
<h2 id="org219178b"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-orgb5947bb" class="outline-2">
<h2 id="orgb5947bb"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div class="outline-text-2" id="text-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -938,8 +938,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgf2232d0" class="outline-2">
<h2 id="orgf2232d0"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org9935d9b" class="outline-2">
<h2 id="org9935d9b"><span class="section-number-2">9</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-9">
<p>
Memory is allocated when reading. The following function frees memory.
@ -1008,8 +1008,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org7034821" class="outline-2">
<h2 id="org7034821"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org3513e68" class="outline-2">
<h2 id="org3513e68"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1072,8 +1072,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org8a2f19d" class="outline-2">
<h2 id="org8a2f19d"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org82f1c44" class="outline-2">
<h2 id="org82f1c44"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-11">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1169,8 +1169,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org4cd23dc" class="outline-2">
<h2 id="org4cd23dc"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgaec00ae" class="outline-2">
<h2 id="orgaec00ae"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-12">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1271,8 +1271,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orge0f79f8" class="outline-2">
<h2 id="orge0f79f8"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org8be155e" class="outline-2">
<h2 id="org8be155e"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1346,8 +1346,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgf66c25c" class="outline-2">
<h2 id="orgf66c25c"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orgcd6bc0c" class="outline-2">
<h2 id="orgcd6bc0c"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-14">
<p>
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
@ -1637,8 +1637,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-orgad47a68" class="outline-2">
<h2 id="orgad47a68"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org51f47fd" class="outline-2">
<h2 id="org51f47fd"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div class="outline-text-2" id="text-15">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that buffered I/O has to be decoupled
@ -1868,8 +1868,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-org21b9574" class="outline-2">
<h2 id="org21b9574"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org974f669" class="outline-2">
<h2 id="org974f669"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-16">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1897,8 +1897,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-orgf02d803" class="outline-2">
<h2 id="orgf02d803"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-orgba8bc93" class="outline-2">
<h2 id="orgba8bc93"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-17">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -2090,7 +2090,7 @@ 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: 2022-10-06 Thu 13:35</p>
<p class="date">Created: 2022-10-07 Fri 09:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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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>TREX Configuration file</title>
@ -333,38 +333,38 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org7c9c73c">1. Metadata (metadata group)</a></li>
<li><a href="#org6b7505d">2. Electron (electron group)</a></li>
<li><a href="#orgc5286a4">3. Nucleus (nucleus group)</a></li>
<li><a href="#org4377a79">4. Effective core potentials (ecp group)</a>
<li><a href="#org5bf6321">1. Metadata (metadata group)</a></li>
<li><a href="#org158a20b">2. Electron (electron group)</a></li>
<li><a href="#orgd0fe14f">3. Nucleus (nucleus group)</a></li>
<li><a href="#org846923a">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org2bdb917">4.1. Example</a></li>
<li><a href="#org49ebf70">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org0233771">5. Basis set (basis group)</a>
<li><a href="#org7712c7a">5. Basis set (basis group)</a>
<ul>
<li><a href="#orgdc9e405">5.1. Example</a></li>
<li><a href="#org163f057">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org5d37b3d">6. Atomic orbitals (ao group)</a>
<li><a href="#orgf862398">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="#org27eb989">7. Molecular orbitals (mo group)</a>
<li><a href="#orgdc42359">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org9794d0b">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgca36d07">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org1bd2c6c">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org5e2a6ca">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org68e3033">8. Slater determinants (determinant group)</a></li>
<li><a href="#org689e4f7">9. Configuration state functions (csf group)</a></li>
<li><a href="#org898ce1d">10. Excited states (state group)</a></li>
<li><a href="#orge93dc97">11. Reduced density matrices (rdm group)</a></li>
<li><a href="#org2dd29e9">12. Cell (cell group)</a></li>
<li><a href="#orgdf2d928">13. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org773d882">14. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#orgfd419e6">8. Slater determinants (determinant group)</a></li>
<li><a href="#orga422e83">9. Configuration state functions (csf group)</a></li>
<li><a href="#org1e89f93">10. Excited states (state group)</a></li>
<li><a href="#orgb3658ed">11. Reduced density matrices (rdm group)</a></li>
<li><a href="#orge7a4d29">12. Cell (cell group)</a></li>
<li><a href="#org39c8715">13. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgecd3b29">14. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -426,8 +426,8 @@ For determinant lists (integer bit fields), the <code>special</code> attribute i
This means that the source code is not produced by the generator, but hand-written.
</p>
<div id="outline-container-org7c9c73c" class="outline-2">
<h2 id="org7c9c73c"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org5bf6321" class="outline-2">
<h2 id="org5bf6321"><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
@ -437,7 +437,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="orgbd8a047" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdc371fa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -518,15 +518,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-org6b7505d" class="outline-2">
<h2 id="org6b7505d"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org158a20b" class="outline-2">
<h2 id="org158a20b"><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="org09a208a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9e3f7b5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -572,15 +572,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgc5286a4" class="outline-2">
<h2 id="orgc5286a4"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-orgd0fe14f" class="outline-2">
<h2 id="orgd0fe14f"><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="orgf8aa393" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org43eb6a8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -647,8 +647,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org4377a79" class="outline-2">
<h2 id="org4377a79"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org846923a" class="outline-2">
<h2 id="org846923a"><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
@ -681,7 +681,7 @@ 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="orgcc9670a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdaf15ec" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -783,8 +783,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-org2bdb917" class="outline-3">
<h3 id="org2bdb917"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org49ebf70" class="outline-3">
<h3 id="org49ebf70"><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
@ -847,8 +847,8 @@ power = [
</div>
</div>
<div id="outline-container-org0233771" class="outline-2">
<h2 id="org0233771"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org7712c7a" class="outline-2">
<h2 id="org7712c7a"><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
@ -901,7 +901,7 @@ 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="org402c4c0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcccdef1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -995,8 +995,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-orgdc9e405" class="outline-3">
<h3 id="orgdc9e405"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org163f057" class="outline-3">
<h3 id="org163f057"><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
@ -1074,8 +1074,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org5d37b3d" class="outline-2">
<h2 id="org5d37b3d"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-orgf862398" class="outline-2">
<h2 id="orgf862398"><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
@ -1128,13 +1128,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org0233771">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org7712c7a">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="org24c8e11" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbc1f77f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1186,8 +1186,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org4c98bf7" class="outline-3">
<h3 id="ao_one_e"><a id="org4c98bf7"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orge3dba40" class="outline-3">
<h3 id="ao_one_e"><a id="orge3dba40"></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}}
@ -1204,7 +1204,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org018befe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd2f6123" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1299,8 +1299,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org3bd21d5" class="outline-3">
<h3 id="ao_two_e"><a id="org3bd21d5"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org893c5cc" class="outline-3">
<h3 id="ao_two_e"><a id="org893c5cc"></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
@ -1321,7 +1321,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org4e86641" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org263dd79" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1361,10 +1361,10 @@ notation.
</div>
</div>
<div id="outline-container-org27eb989" class="outline-2">
<h2 id="org27eb989"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgdc42359" class="outline-2">
<h2 id="orgdc42359"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="orgbe48c84" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga042705" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1451,8 +1451,8 @@ notation.
</table>
</div>
<div id="outline-container-org9794d0b" class="outline-3">
<h3 id="org9794d0b"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org1bd2c6c" class="outline-3">
<h3 id="org1bd2c6c"><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
@ -1460,7 +1460,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgea44942" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org29f9cbb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1555,8 +1555,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgca36d07" class="outline-3">
<h3 id="orgca36d07"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org5e2a6ca" class="outline-3">
<h3 id="org5e2a6ca"><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
@ -1564,7 +1564,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org60c7037" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdba8257" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1604,8 +1604,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org68e3033" class="outline-2">
<h2 id="org68e3033"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-orgfd419e6" class="outline-2">
<h2 id="orgfd419e6"><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 \(\Psi\)
@ -1647,7 +1647,7 @@ 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="org4bfa01d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge38a36f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1693,8 +1693,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org689e4f7" class="outline-2">
<h2 id="org689e4f7"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
<div id="outline-container-orga422e83" class="outline-2">
<h2 id="orga422e83"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
<div class="outline-text-2" id="text-9">
<p>
The configuration interaction (CI) wave function \(\Psi\) can be
@ -1716,7 +1716,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org32a1175" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org247808e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1762,8 +1762,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org898ce1d" class="outline-2">
<h2 id="org898ce1d"><span class="section-number-2">10</span> Excited states (state group)</h2>
<div id="outline-container-org1e89f93" class="outline-2">
<h2 id="org1e89f93"><span class="section-number-2">10</span> Excited states (state group)</h2>
<div class="outline-text-2" id="text-10">
<p>
This group contains information about excited state. Since TREXIO version 2.3.0
@ -1778,7 +1778,7 @@ The <code>id</code> and <code>current_label</code> attributes have to be specifi
(containing both ground and excited state data).
</p>
<table id="org65ab8ed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb6e0c76" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1838,8 +1838,8 @@ The <code>id</code> and <code>current_label</code> attributes have to be specifi
</div>
</div>
<div id="outline-container-orge93dc97" class="outline-2">
<h2 id="orge93dc97"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orgb3658ed" class="outline-2">
<h2 id="orgb3658ed"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-11">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1892,7 +1892,7 @@ The total energy can be computed as:
\]
</p>
<table id="org13d8cf3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5b82902" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1973,10 +1973,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org2dd29e9" class="outline-2">
<h2 id="org2dd29e9"><span class="section-number-2">12</span> Cell (cell group)</h2>
<div id="outline-container-orge7a4d29" class="outline-2">
<h2 id="orge7a4d29"><span class="section-number-2">12</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-12">
<table id="orga81c0ae" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org08e70e1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2022,10 +2022,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-orgdf2d928" class="outline-2">
<h2 id="orgdf2d928"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-org39c8715" class="outline-2">
<h2 id="org39c8715"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-13">
<table id="org38577ad" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org537e2c3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2064,8 +2064,8 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org773d882" class="outline-2">
<h2 id="org773d882"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-orgecd3b29" class="outline-2">
<h2 id="orgecd3b29"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-14">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -2079,7 +2079,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="org1f3e44b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge8c3196" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2134,7 +2134,7 @@ 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: 2022-10-06 Thu 13:35</p>
<p class="date">Created: 2022-10-07 Fri 09:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>