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README.html
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-07-01 Fri 13:17</p>
<p class="date">Created: 2022-07-01 Fri 13:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
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<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="#org397205a">1. Accessing sparse quantities (integrals)</a>
<li><a href="#org884383a">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#orgb7315d9">1.1. Fortran</a>
<li><a href="#org9be3f7d">1.1. Fortran</a>
<ul>
<li><a href="#org0048a2f">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orge05070d">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org2d6b0db">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org9ef0551">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgbc35b36">1.1.5. Allocate memory</a></li>
<li><a href="#orgad81f37">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org414029d">1.1.7. Read two-electron quantities</a>
<li><a href="#org0be275e">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgefacf80">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga80ba1d">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgc7d46d7">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org71b8ba4">1.1.5. Allocate memory</a></li>
<li><a href="#org5812034">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org86f8131">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgd917486">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org29ea948">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#orgea90c83">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org6596131">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org22de998">1.1.8. Compute the energy</a></li>
<li><a href="#org244f8f9">1.1.9. Terminate</a></li>
<li><a href="#org1c0b67d">1.1.8. Compute the energy</a></li>
<li><a href="#org8671090">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgb105959">2. Reading determinants</a>
<li><a href="#org5d527de">2. Reading determinants</a>
<ul>
<li><a href="#org25250c7">2.1. Fortran</a></li>
<li><a href="#org648c4da">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -365,12 +365,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org397205a" class="outline-2">
<h2 id="org397205a"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org884383a" class="outline-2">
<h2 id="org884383a"><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-orgb7315d9" class="outline-3">
<h3 id="orgb7315d9"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org9be3f7d" class="outline-3">
<h3 id="org9be3f7d"><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-org0048a2f" class="outline-4">
<h4 id="org0048a2f"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org0be275e" class="outline-4">
<h4 id="org0be275e"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div 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-orge05070d" class="outline-4">
<h4 id="orge05070d"><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-orgefacf80" class="outline-4">
<h4 id="orgefacf80"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div 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-org2d6b0db" class="outline-4">
<h4 id="org2d6b0db"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orga80ba1d" class="outline-4">
<h4 id="orga80ba1d"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div 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-org9ef0551" class="outline-4">
<h4 id="org9ef0551"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgc7d46d7" class="outline-4">
<h4 id="orgc7d46d7"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div 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-orgbc35b36" class="outline-4">
<h4 id="orgbc35b36"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org71b8ba4" class="outline-4">
<h4 id="org71b8ba4"><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-orgad81f37" class="outline-4">
<h4 id="orgad81f37"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org5812034" class="outline-4">
<h4 id="org5812034"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div 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-org414029d" class="outline-4">
<h4 id="org414029d"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org86f8131" class="outline-4">
<h4 id="org86f8131"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div 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-orgd917486" class="outline-5">
<h5 id="orgd917486"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgea90c83" class="outline-5">
<h5 id="orgea90c83"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div 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-org29ea948" class="outline-5">
<h5 id="org29ea948"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org6596131" class="outline-5">
<h5 id="org6596131"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div 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-org22de998" class="outline-4">
<h4 id="org22de998"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org1c0b67d" class="outline-4">
<h4 id="org1c0b67d"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div 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-org244f8f9" class="outline-4">
<h4 id="org244f8f9"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org8671090" class="outline-4">
<h4 id="org8671090"><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-orgb105959" class="outline-2">
<h2 id="orgb105959"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-org5d527de" class="outline-2">
<h2 id="org5d527de"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org25250c7" class="outline-3">
<h3 id="org25250c7"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org648c4da" class="outline-3">
<h3 id="org648c4da"><span class="section-number-3">2.1</span> Fortran</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
@ -783,7 +783,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-07-01 Fri 13:17</p>
<p class="date">Created: 2022-07-01 Fri 13:22</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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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-07-01 Fri 13:17 -->
<!-- 2022-07-01 Fri 13:22 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-07-01 Fri 13:17</p>
<p class="date">Created: 2022-07-01 Fri 13:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-07-01 Fri 13:17 -->
<!-- 2022-07-01 Fri 13:22 -->
<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="#orged5dea7">1. Template for HDF5 definitions</a></li>
<li><a href="#org3254610">2. Template for HDF5 structures</a></li>
<li><a href="#org0e57cf3">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org8f11cc1">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgb4a0ccb">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org98b26e9">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org857c675">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org406c461">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org95a7436">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgbc4c629">10. Source code for the determinant part</a></li>
<li><a href="#orgf13002e">11. Helper functions</a></li>
<li><a href="#orge4577e1">1. Template for HDF5 definitions</a></li>
<li><a href="#orgf4de222">2. Template for HDF5 structures</a></li>
<li><a href="#org47cf1e6">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org8f10280">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org1bfa836">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orga005541">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgd3f47c7">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgaa30deb">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org9663538">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org078b330">10. Source code for the determinant part</a></li>
<li><a href="#orgadebb20">11. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orged5dea7" class="outline-2">
<h2 id="orged5dea7"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orge4577e1" class="outline-2">
<h2 id="orge4577e1"><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-org3254610" class="outline-2">
<h2 id="org3254610"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgf4de222" class="outline-2">
<h2 id="orgf4de222"><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-org0e57cf3" class="outline-2">
<h2 id="org0e57cf3"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org47cf1e6" class="outline-2">
<h2 id="org47cf1e6"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div 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-org8f11cc1" class="outline-2">
<h2 id="org8f11cc1"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org8f10280" class="outline-2">
<h2 id="org8f10280"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div 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-orgb4a0ccb" class="outline-2">
<h2 id="orgb4a0ccb"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org1bfa836" class="outline-2">
<h2 id="org1bfa836"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div 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-org98b26e9" class="outline-2">
<h2 id="org98b26e9"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orga005541" class="outline-2">
<h2 id="orga005541"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div 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-org857c675" class="outline-2">
<h2 id="org857c675"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgd3f47c7" class="outline-2">
<h2 id="orgd3f47c7"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div 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-org406c461" class="outline-2">
<h2 id="org406c461"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgaa30deb" class="outline-2">
<h2 id="orgaa30deb"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div 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-org95a7436" class="outline-2">
<h2 id="org95a7436"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org9663538" class="outline-2">
<h2 id="org9663538"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div 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-orgbc4c629" class="outline-2">
<h2 id="orgbc4c629"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div id="outline-container-org078b330" class="outline-2">
<h2 id="org078b330"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div 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-orgf13002e" class="outline-2">
<h2 id="orgf13002e"><span class="section-number-2">11</span> Helper functions</h2>
<div id="outline-container-orgadebb20" class="outline-2">
<h2 id="orgadebb20"><span class="section-number-2">11</span> Helper functions</h2>
<div class="outline-text-2" id="text-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1796,7 +1796,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-07-01 Fri 13:17</p>
<p class="date">Created: 2022-07-01 Fri 13:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

88
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-07-01 Fri 13:17 -->
<!-- 2022-07-01 Fri 13:22 -->
<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="#org1214f71">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgca2c1c7">2. Template for general structure in text back end</a></li>
<li><a href="#org232ff2e">3. Initialize function (constant part)</a></li>
<li><a href="#org40277a8">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgdc5ac31">5. Template for text read a group</a></li>
<li><a href="#orgd5ca60e">6. Template for text flush a group</a></li>
<li><a href="#orgac44663">7. Template for text free memory</a></li>
<li><a href="#orge2586fa">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgaa74ed0">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org3f7fcb6">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org826f6bd">11. Template for has/read/write a string attribute</a></li>
<li><a href="#org243609b">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org212d7ac">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org97a3ef5">14. Source code for the determinant part</a></li>
<li><a href="#org647c01a">1. Template for group-related structures in text back end</a></li>
<li><a href="#org0388489">2. Template for general structure in text back end</a></li>
<li><a href="#orge3a8b35">3. Initialize function (constant part)</a></li>
<li><a href="#org1ebea73">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgc34d686">5. Template for text read a group</a></li>
<li><a href="#org6f6c893">6. Template for text flush a group</a></li>
<li><a href="#orge3d8f5a">7. Template for text free memory</a></li>
<li><a href="#orgee2471f">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgbb73003">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org779b83f">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orga40ed6b">11. Template for has/read/write a string attribute</a></li>
<li><a href="#org9ca02b6">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org9000691">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org8aa8e4e">14. Source code for the determinant part</a></li>
</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-org1214f71" class="outline-2">
<h2 id="org1214f71"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org647c01a" class="outline-2">
<h2 id="org647c01a"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div 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-orgca2c1c7" class="outline-2">
<h2 id="orgca2c1c7"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org0388489" class="outline-2">
<h2 id="org0388489"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div 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-org232ff2e" class="outline-2">
<h2 id="org232ff2e"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-orge3a8b35" class="outline-2">
<h2 id="orge3a8b35"><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-org40277a8" class="outline-2">
<h2 id="org40277a8"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org1ebea73" class="outline-2">
<h2 id="org1ebea73"><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-orgdc5ac31" class="outline-2">
<h2 id="orgdc5ac31"><span class="section-number-2">5</span> Template for text read a group</h2>
<div id="outline-container-orgc34d686" class="outline-2">
<h2 id="orgc34d686"><span class="section-number-2">5</span> Template for text read a group</h2>
<div 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-orgd5ca60e" class="outline-2">
<h2 id="orgd5ca60e"><span class="section-number-2">6</span> Template for text flush a group</h2>
<div id="outline-container-org6f6c893" class="outline-2">
<h2 id="org6f6c893"><span class="section-number-2">6</span> Template for text flush a group</h2>
<div 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-orgac44663" class="outline-2">
<h2 id="orgac44663"><span class="section-number-2">7</span> Template for text free memory</h2>
<div id="outline-container-orge3d8f5a" class="outline-2">
<h2 id="orge3d8f5a"><span class="section-number-2">7</span> Template for text free memory</h2>
<div 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-orge2586fa" class="outline-2">
<h2 id="orge2586fa"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orgee2471f" class="outline-2">
<h2 id="orgee2471f"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
<div 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-orgaa74ed0" class="outline-2">
<h2 id="orgaa74ed0"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgbb73003" class="outline-2">
<h2 id="orgbb73003"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div 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-org3f7fcb6" class="outline-2">
<h2 id="org3f7fcb6"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org779b83f" class="outline-2">
<h2 id="org779b83f"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div 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-org826f6bd" class="outline-2">
<h2 id="org826f6bd"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orga40ed6b" class="outline-2">
<h2 id="orga40ed6b"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div 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-org243609b" class="outline-2">
<h2 id="org243609b"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org9ca02b6" class="outline-2">
<h2 id="org9ca02b6"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div 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-org212d7ac" class="outline-2">
<h2 id="org212d7ac"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org9000691" class="outline-2">
<h2 id="org9000691"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
<div 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-org97a3ef5" class="outline-2">
<h2 id="org97a3ef5"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div id="outline-container-org8aa8e4e" class="outline-2">
<h2 id="org8aa8e4e"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-14">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -1960,7 +1960,7 @@ Size specifies the number of data items, e.g. determinants.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-07-01 Fri 13:17</p>
<p class="date">Created: 2022-07-01 Fri 13:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

150
trex.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-07-01 Fri 13:17 -->
<!-- 2022-07-01 Fri 13:22 -->
<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="#org133bcb2">1. Metadata (metadata group)</a></li>
<li><a href="#org36d3049">2. Electron (electron group)</a></li>
<li><a href="#orgdd5d6b9">3. Nucleus (nucleus group)</a></li>
<li><a href="#org7e1b09f">4. Effective core potentials (ecp group)</a>
<li><a href="#orgc7dcaf3">1. Metadata (metadata group)</a></li>
<li><a href="#org27e8836">2. Electron (electron group)</a></li>
<li><a href="#orgd36cfa9">3. Nucleus (nucleus group)</a></li>
<li><a href="#org0f7ef9a">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org3dff1ab">4.1. Example</a></li>
<li><a href="#org0d5d8f6">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org013989a">5. Basis set (basis group)</a>
<li><a href="#org496421b">5. Basis set (basis group)</a>
<ul>
<li><a href="#orgbe9369d">5.1. Example</a></li>
<li><a href="#org6eb141c">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org6e39d88">6. Atomic orbitals (ao group)</a>
<li><a href="#org1351cfc">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="#orged5fbb2">7. Molecular orbitals (mo group)</a>
<li><a href="#org93ecdc1">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org340cd19">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org930748c">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org2b7d31d">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org67fb79a">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#orgdbff2a9">8. Slater determinants (determinant group)</a></li>
<li><a href="#org455059c">9. Excited states (state group)</a></li>
<li><a href="#org67f7cfd">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org37f8aa6">11. Cell (cell group)</a></li>
<li><a href="#orgc016fb1">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgd970e6d">13. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org564073f">8. Slater determinants (determinant group)</a></li>
<li><a href="#org650e5ea">9. Excited states (state group)</a></li>
<li><a href="#org5afc119">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org54ab114">11. Cell (cell group)</a></li>
<li><a href="#orge57764b">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org7f09c3f">13. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -417,8 +417,8 @@ For determinants, the <code>special</code> attribute is present in the type. Thi
means that the source code is not produced by the generator, but hand-written.
</p>
<div id="outline-container-org133bcb2" class="outline-2">
<h2 id="org133bcb2"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgc7dcaf3" class="outline-2">
<h2 id="orgc7dcaf3"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect our files to be archived in open-data repositories, we
@ -428,7 +428,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="orgbab3efa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2e0efdd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -509,15 +509,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-org36d3049" class="outline-2">
<h2 id="org36d3049"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org27e8836" class="outline-2">
<h2 id="org27e8836"><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="org687efff" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbda8a39" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -563,15 +563,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgdd5d6b9" class="outline-2">
<h2 id="orgdd5d6b9"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-orgd36cfa9" class="outline-2">
<h2 id="orgd36cfa9"><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="org62aa021" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org014d005" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -638,8 +638,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org7e1b09f" class="outline-2">
<h2 id="org7e1b09f"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org0f7ef9a" class="outline-2">
<h2 id="org0f7ef9a"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div class="outline-text-2" id="text-4">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -672,7 +672,7 @@ The functions \(V_{A\ell}\) are parameterized as:
See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.4984046</a> or <a href="https://doi.org/10.1063/1.5121006">https://doi.org/10.1063/1.5121006</a> for more info.
</p>
<table id="org1576238" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7580788" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -774,8 +774,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-org3dff1ab" class="outline-3">
<h3 id="org3dff1ab"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org0d5d8f6" class="outline-3">
<h3 id="org0d5d8f6"><span class="section-number-3">4.1</span> Example</h3>
<div class="outline-text-3" id="text-4-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -838,8 +838,8 @@ power = [
</div>
</div>
<div id="outline-container-org013989a" class="outline-2">
<h2 id="org013989a"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org496421b" class="outline-2">
<h2 id="org496421b"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div class="outline-text-2" id="text-5">
<p>
We consider here basis functions centered on nuclei. Hence, we enable
@ -892,7 +892,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).
All the basis set parameters are stored in one-dimensional arrays:
</p>
<table id="org141eae5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org23c35f9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -986,8 +986,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-orgbe9369d" class="outline-3">
<h3 id="orgbe9369d"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org6eb141c" class="outline-3">
<h3 id="org6eb141c"><span class="section-number-3">5.1</span> Example</h3>
<div class="outline-text-3" id="text-5-1">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1065,8 +1065,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org6e39d88" class="outline-2">
<h2 id="org6e39d88"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org1351cfc" class="outline-2">
<h2 id="org1351cfc"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div class="outline-text-2" id="text-6">
<p>
Going from the atomic basis set to AOs implies a systematic
@ -1119,13 +1119,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org013989a">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org496421b">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="org89a2e96" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf4caf7b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1177,8 +1177,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-orgafb7103" class="outline-3">
<h3 id="ao_one_e"><a id="orgafb7103"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org2682c68" class="outline-3">
<h3 id="ao_one_e"><a id="org2682c68"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_one_e">
<ul class="org-ul">
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
@ -1195,7 +1195,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org615b4fa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge80df7e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1290,8 +1290,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgb2219fe" class="outline-3">
<h3 id="ao_two_e"><a id="orgb2219fe"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org8c771de" class="outline-3">
<h3 id="ao_two_e"><a id="org8c771de"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_two_e">
<p>
The two-electron integrals for a two-electron operator \(\hat{O}\) are
@ -1312,7 +1312,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org2b3cfda" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5861337" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1352,10 +1352,10 @@ notation.
</div>
</div>
<div id="outline-container-orged5fbb2" class="outline-2">
<h2 id="orged5fbb2"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org93ecdc1" class="outline-2">
<h2 id="org93ecdc1"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org30f6331" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org75df1c2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1428,8 +1428,8 @@ notation.
</table>
</div>
<div id="outline-container-org340cd19" class="outline-3">
<h3 id="org340cd19"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org2b7d31d" class="outline-3">
<h3 id="org2b7d31d"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-1">
<p>
The operators as the same as those defined in the
@ -1437,7 +1437,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org8fd2ca7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8c31e41" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1532,8 +1532,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org930748c" class="outline-3">
<h3 id="org930748c"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org67fb79a" class="outline-3">
<h3 id="org67fb79a"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-2">
<p>
The operators as the same as those defined in the
@ -1541,7 +1541,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org394fd63" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1975100" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1581,8 +1581,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgdbff2a9" class="outline-2">
<h2 id="orgdbff2a9"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-org564073f" class="outline-2">
<h2 id="org564073f"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div class="outline-text-2" id="text-8">
<p>
The configuration interaction (CI) wave function \(\Psi\)
@ -1624,7 +1624,7 @@ produced by the code generator.
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
</p>
<table id="orgc1733a6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7fd9639" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1670,8 +1670,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org455059c" class="outline-2">
<h2 id="org455059c"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div id="outline-container-org650e5ea" class="outline-2">
<h2 id="org650e5ea"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div class="outline-text-2" id="text-9">
<p>
By default, the <code>determinant</code> group corresponds to the ground state.
@ -1680,7 +1680,7 @@ correspond to excited state wave functions for the same set of
determinants. This is the goal of the present group
</p>
<table id="org661e93d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2582ea3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1719,8 +1719,8 @@ determinants. This is the goal of the present group
</div>
</div>
<div id="outline-container-org67f7cfd" class="outline-2">
<h2 id="org67f7cfd"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org5afc119" class="outline-2">
<h2 id="org5afc119"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-10">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1773,7 +1773,7 @@ The total energy can be computed as:
\]
</p>
<table id="org1225656" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org88e8703" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1854,10 +1854,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org37f8aa6" class="outline-2">
<h2 id="org37f8aa6"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div id="outline-container-org54ab114" class="outline-2">
<h2 id="org54ab114"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-11">
<table id="org9428a45" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8a1cf8a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1903,10 +1903,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-orgc016fb1" class="outline-2">
<h2 id="orgc016fb1"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-orge57764b" class="outline-2">
<h2 id="orge57764b"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-12">
<table id="org28d1de4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org43dd9bf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1945,8 +1945,8 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-orgd970e6d" class="outline-2">
<h2 id="orgd970e6d"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org7f09c3f" class="outline-2">
<h2 id="org7f09c3f"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-13">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -1960,7 +1960,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orgdc8e147" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org44b619e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2015,7 +2015,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-07-01 Fri 13:17</p>
<p class="date">Created: 2022-07-01 Fri 13:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>