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README.html
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<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-03 Fri 08:04</p>
<p class="date">Created: 2022-06-03 Fri 08:39</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>Examples</title>
@ -333,24 +333,24 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orge01f336">1. Accessing sparse quantities</a>
<li><a href="#orgcf71cb9">1. Accessing sparse quantities</a>
<ul>
<li><a href="#org4720a8b">1.1. Fortran</a>
<li><a href="#org5b12a9e">1.1. Fortran</a>
<ul>
<li><a href="#orga2128f7">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org6ffce8d">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgce65c3a">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org14fa0c4">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org180a43c">1.1.5. Allocate memory</a></li>
<li><a href="#org0921941">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org3110078">1.1.7. Read two-electron quantities</a>
<li><a href="#orgbcde88c">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgf6a7227">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga2a5e3f">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org9811c00">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgb5f3b14">1.1.5. Allocate memory</a></li>
<li><a href="#org2c4b30f">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgc2d1845">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org812218d">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orge216000">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org5752239">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgd65245f">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org609a04e">1.1.8. Compute the energy</a></li>
<li><a href="#org84f74c7">1.1.9. Terminate</a></li>
<li><a href="#orgc9091dd">1.1.8. Compute the energy</a></li>
<li><a href="#org875475b">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
@ -360,12 +360,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orge01f336" class="outline-2">
<h2 id="orge01f336"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-orgcf71cb9" class="outline-2">
<h2 id="orgcf71cb9"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org4720a8b" class="outline-3">
<h3 id="org4720a8b"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org5b12a9e" class="outline-3">
<h3 id="org5b12a9e"><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>
@ -411,8 +411,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orga2128f7" class="outline-4">
<h4 id="orga2128f7"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgbcde88c" class="outline-4">
<h4 id="orgbcde88c"><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>
@ -427,8 +427,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org6ffce8d" class="outline-4">
<h4 id="org6ffce8d"><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-orgf6a7227" class="outline-4">
<h4 id="orgf6a7227"><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)
@ -444,8 +444,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgce65c3a" class="outline-4">
<h4 id="orgce65c3a"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orga2a5e3f" class="outline-4">
<h4 id="orga2a5e3f"><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)
@ -459,8 +459,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org14fa0c4" class="outline-4">
<h4 id="org14fa0c4"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org9811c00" class="outline-4">
<h4 id="org9811c00"><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)
@ -474,8 +474,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org180a43c" class="outline-4">
<h4 id="org180a43c"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-orgb5f3b14" class="outline-4">
<h4 id="orgb5f3b14"><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) )
@ -487,8 +487,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-org0921941" class="outline-4">
<h4 id="org0921941"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org2c4b30f" class="outline-4">
<h4 id="org2c4b30f"><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)
@ -520,8 +520,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-org3110078" class="outline-4">
<h4 id="org3110078"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgc2d1845" class="outline-4">
<h4 id="orgc2d1845"><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
@ -537,8 +537,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org812218d" class="outline-5">
<h5 id="org812218d"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org5752239" class="outline-5">
<h5 id="org5752239"><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)
@ -587,8 +587,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-orge216000" class="outline-5">
<h5 id="orge216000"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgd65245f" class="outline-5">
<h5 id="orgd65245f"><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)
@ -632,8 +632,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org609a04e" class="outline-4">
<h4 id="org609a04e"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-orgc9091dd" class="outline-4">
<h4 id="orgc9091dd"><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
@ -679,8 +679,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org84f74c7" class="outline-4">
<h4 id="org84f74c7"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org875475b" class="outline-4">
<h4 id="org875475b"><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 )
@ -695,7 +695,7 @@ E = E + E_nn
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-03 Fri 08:04</p>
<p class="date">Created: 2022-06-03 Fri 08:39</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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index.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-06-03 Fri 08:04 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-03 Fri 08:04</p>
<p class="date">Created: 2022-06-03 Fri 08:39</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2022-06-03 Fri 08:04 -->
<!-- 2022-06-03 Fri 08:39 -->
<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="#org6abc5d7">1. Template for HDF5 definitions</a></li>
<li><a href="#orgb2ffbee">2. Template for HDF5 structures</a></li>
<li><a href="#orgbdc124e">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgb755321">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org6590cd7">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org9303c6d">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org12c4496">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgc824ff6">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgbd8f01e">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org5b9b629">10. Source code for the determinant part</a></li>
<li><a href="#orgccc0081">11. Helper functions</a></li>
<li><a href="#org49c4075">1. Template for HDF5 definitions</a></li>
<li><a href="#org87fb328">2. Template for HDF5 structures</a></li>
<li><a href="#org2f99c28">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgfb9b95b">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org9b7ef5b">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org0a9c2ae">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgb31c882">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org7fea7f6">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org20dc905">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orged8ae62">10. Source code for the determinant part</a></li>
<li><a href="#orgc376ec9">11. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org6abc5d7" class="outline-2">
<h2 id="org6abc5d7"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org49c4075" class="outline-2">
<h2 id="org49c4075"><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-orgb2ffbee" class="outline-2">
<h2 id="orgb2ffbee"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org87fb328" class="outline-2">
<h2 id="org87fb328"><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-orgbdc124e" class="outline-2">
<h2 id="orgbdc124e"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org2f99c28" class="outline-2">
<h2 id="org2f99c28"><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-orgb755321" class="outline-2">
<h2 id="orgb755321"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orgfb9b95b" class="outline-2">
<h2 id="orgfb9b95b"><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-org6590cd7" class="outline-2">
<h2 id="org6590cd7"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org9b7ef5b" class="outline-2">
<h2 id="org9b7ef5b"><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-org9303c6d" class="outline-2">
<h2 id="org9303c6d"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org0a9c2ae" class="outline-2">
<h2 id="org0a9c2ae"><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-org12c4496" class="outline-2">
<h2 id="org12c4496"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgb31c882" class="outline-2">
<h2 id="orgb31c882"><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-orgc824ff6" class="outline-2">
<h2 id="orgc824ff6"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org7fea7f6" class="outline-2">
<h2 id="org7fea7f6"><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-orgbd8f01e" class="outline-2">
<h2 id="orgbd8f01e"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org20dc905" class="outline-2">
<h2 id="org20dc905"><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-org5b9b629" class="outline-2">
<h2 id="org5b9b629"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div id="outline-container-orged8ae62" class="outline-2">
<h2 id="orged8ae62"><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-orgccc0081" class="outline-2">
<h2 id="orgccc0081"><span class="section-number-2">11</span> Helper functions</h2>
<div id="outline-container-orgc376ec9" class="outline-2">
<h2 id="orgc376ec9"><span class="section-number-2">11</span> Helper functions</h2>
<div class="outline-text-2" id="text-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1796,7 +1796,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-03 Fri 08:04</p>
<p class="date">Created: 2022-06-03 Fri 08:39</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

88
templator_text.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-06-03 Fri 08:04 -->
<!-- 2022-06-03 Fri 08:39 -->
<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="#org4f14c22">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgfeca5e6">2. Template for general structure in text back end</a></li>
<li><a href="#orgb193239">3. Initialize function (constant part)</a></li>
<li><a href="#org53b238b">4. Deinitialize function (templated part)</a></li>
<li><a href="#org85cc383">5. Template for text read a group</a></li>
<li><a href="#org9f22d3e">6. Template for text flush a group</a></li>
<li><a href="#org2170573">7. Template for text free memory</a></li>
<li><a href="#orgc420a41">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org0454855">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org5815346">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orge7605de">11. Template for has/read/write a string attribute</a></li>
<li><a href="#org8f70b40">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org7693a54">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org77cacd4">14. Source code for the determinant part</a></li>
<li><a href="#org9023685">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgd46fd94">2. Template for general structure in text back end</a></li>
<li><a href="#org1877b29">3. Initialize function (constant part)</a></li>
<li><a href="#org119b4b6">4. Deinitialize function (templated part)</a></li>
<li><a href="#org0583867">5. Template for text read a group</a></li>
<li><a href="#orgaa91bf7">6. Template for text flush a group</a></li>
<li><a href="#org465c7c8">7. Template for text free memory</a></li>
<li><a href="#org847b96a">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgfef2e89">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org5f2cd24">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org6e08cbb">11. Template for has/read/write a string attribute</a></li>
<li><a href="#orgf3c19d0">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgea536bc">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgfdb13bc">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-org4f14c22" class="outline-2">
<h2 id="org4f14c22"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org9023685" class="outline-2">
<h2 id="org9023685"><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-orgfeca5e6" class="outline-2">
<h2 id="orgfeca5e6"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgd46fd94" class="outline-2">
<h2 id="orgd46fd94"><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-orgb193239" class="outline-2">
<h2 id="orgb193239"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org1877b29" class="outline-2">
<h2 id="org1877b29"><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-org53b238b" class="outline-2">
<h2 id="org53b238b"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org119b4b6" class="outline-2">
<h2 id="org119b4b6"><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-org85cc383" class="outline-2">
<h2 id="org85cc383"><span class="section-number-2">5</span> Template for text read a group</h2>
<div id="outline-container-org0583867" class="outline-2">
<h2 id="org0583867"><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-org9f22d3e" class="outline-2">
<h2 id="org9f22d3e"><span class="section-number-2">6</span> Template for text flush a group</h2>
<div id="outline-container-orgaa91bf7" class="outline-2">
<h2 id="orgaa91bf7"><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-org2170573" class="outline-2">
<h2 id="org2170573"><span class="section-number-2">7</span> Template for text free memory</h2>
<div id="outline-container-org465c7c8" class="outline-2">
<h2 id="org465c7c8"><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-orgc420a41" class="outline-2">
<h2 id="orgc420a41"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org847b96a" class="outline-2">
<h2 id="org847b96a"><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-org0454855" class="outline-2">
<h2 id="org0454855"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgfef2e89" class="outline-2">
<h2 id="orgfef2e89"><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-org5815346" class="outline-2">
<h2 id="org5815346"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org5f2cd24" class="outline-2">
<h2 id="org5f2cd24"><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-orge7605de" class="outline-2">
<h2 id="orge7605de"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org6e08cbb" class="outline-2">
<h2 id="org6e08cbb"><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-org8f70b40" class="outline-2">
<h2 id="org8f70b40"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orgf3c19d0" class="outline-2">
<h2 id="orgf3c19d0"><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-org7693a54" class="outline-2">
<h2 id="org7693a54"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgea536bc" class="outline-2">
<h2 id="orgea536bc"><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-org77cacd4" class="outline-2">
<h2 id="org77cacd4"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div id="outline-container-orgfdb13bc" class="outline-2">
<h2 id="orgfdb13bc"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-14">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -1960,7 +1960,7 @@ Size specifies the number of data items, e.g. determinants.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-03 Fri 08:04</p>
<p class="date">Created: 2022-06-03 Fri 08:39</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

150
trex.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-06-03 Fri 08:04 -->
<!-- 2022-06-03 Fri 08:39 -->
<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="#org0d0cb4e">1. Metadata (metadata group)</a></li>
<li><a href="#org0e3a614">2. Electron (electron group)</a></li>
<li><a href="#org5ecb93a">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgf7a8b04">4. Effective core potentials (ecp group)</a>
<li><a href="#org01f9da1">1. Metadata (metadata group)</a></li>
<li><a href="#org8f46be0">2. Electron (electron group)</a></li>
<li><a href="#orgaac74d9">3. Nucleus (nucleus group)</a></li>
<li><a href="#org8048c72">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgbfe48ca">4.1. Example</a></li>
<li><a href="#org9a71608">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org919fc3a">5. Basis set (basis group)</a>
<li><a href="#orge93c6d0">5. Basis set (basis group)</a>
<ul>
<li><a href="#org33e54f9">5.1. Example</a></li>
<li><a href="#org3bab2d7">5.1. Example</a></li>
</ul>
</li>
<li><a href="#orgc38036d">6. Atomic orbitals (ao group)</a>
<li><a href="#orge41851a">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="#org96b8540">7. Molecular orbitals (mo group)</a>
<li><a href="#org1eab1ab">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org761be00">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgddc84d0">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org1e287b7">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgf31c3c1">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org5697589">8. Slater determinants (determinant group)</a></li>
<li><a href="#orga8294db">9. Excited states (state group)</a></li>
<li><a href="#org06515ca">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org1fb27dd">11. Cell (cell group)</a></li>
<li><a href="#org714aeb1">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org3f640c2">13. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org39535bb">8. Slater determinants (determinant group)</a></li>
<li><a href="#org075153f">9. Excited states (state group)</a></li>
<li><a href="#org5ddec4d">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgfc26547">11. Cell (cell group)</a></li>
<li><a href="#org7ae3a14">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orge47d2ff">13. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -413,8 +413,8 @@ the <a href="./examples.html">examples</a>.
</p>
<div id="outline-container-org0d0cb4e" class="outline-2">
<h2 id="org0d0cb4e"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org01f9da1" class="outline-2">
<h2 id="org01f9da1"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect our files to be archived in open-data repositories, we
@ -424,7 +424,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="org589c62a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5a4ab12" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -505,15 +505,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-org0e3a614" class="outline-2">
<h2 id="org0e3a614"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org8f46be0" class="outline-2">
<h2 id="org8f46be0"><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="org040e829" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3020480" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -559,15 +559,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org5ecb93a" class="outline-2">
<h2 id="org5ecb93a"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-orgaac74d9" class="outline-2">
<h2 id="orgaac74d9"><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="orge6a0235" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgeb5d2db" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -634,8 +634,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-orgf7a8b04" class="outline-2">
<h2 id="orgf7a8b04"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org8048c72" class="outline-2">
<h2 id="org8048c72"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div class="outline-text-2" id="text-4">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -668,7 +668,7 @@ 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="org168903a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org999a742" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -770,8 +770,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-orgbfe48ca" class="outline-3">
<h3 id="orgbfe48ca"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org9a71608" class="outline-3">
<h3 id="org9a71608"><span class="section-number-3">4.1</span> Example</h3>
<div class="outline-text-3" id="text-4-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -834,8 +834,8 @@ power = [
</div>
</div>
<div id="outline-container-org919fc3a" class="outline-2">
<h2 id="org919fc3a"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-orge93c6d0" class="outline-2">
<h2 id="orge93c6d0"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div class="outline-text-2" id="text-5">
<p>
We consider here basis functions centered on nuclei. Hence, we enable
@ -888,7 +888,7 @@ 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="orgca2f263" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga221744" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -982,8 +982,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-org33e54f9" class="outline-3">
<h3 id="org33e54f9"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org3bab2d7" class="outline-3">
<h3 id="org3bab2d7"><span class="section-number-3">5.1</span> Example</h3>
<div class="outline-text-3" id="text-5-1">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1061,8 +1061,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgc38036d" class="outline-2">
<h2 id="orgc38036d"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-orge41851a" class="outline-2">
<h2 id="orge41851a"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div class="outline-text-2" id="text-6">
<p>
Going from the atomic basis set to AOs implies a systematic
@ -1115,13 +1115,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org919fc3a">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#orge93c6d0">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="org41505e1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2a89083" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1173,8 +1173,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org5fb3e76" class="outline-3">
<h3 id="ao_one_e"><a id="org5fb3e76"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org64ecd2e" class="outline-3">
<h3 id="ao_one_e"><a id="org64ecd2e"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_one_e">
<ul class="org-ul">
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
@ -1191,7 +1191,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgdf50f91" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org37105a9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1286,8 +1286,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org809d897" class="outline-3">
<h3 id="ao_two_e"><a id="org809d897"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-orge50cb5c" class="outline-3">
<h3 id="ao_two_e"><a id="orge50cb5c"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_two_e">
<p>
The two-electron integrals for a two-electron operator \(\hat{O}\) are
@ -1308,7 +1308,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="orgab48bee" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org09a57c2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1348,10 +1348,10 @@ notation.
</div>
</div>
<div id="outline-container-org96b8540" class="outline-2">
<h2 id="org96b8540"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org1eab1ab" class="outline-2">
<h2 id="org1eab1ab"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="orge39dada" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8439ad6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1424,8 +1424,8 @@ notation.
</table>
</div>
<div id="outline-container-org761be00" class="outline-3">
<h3 id="org761be00"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org1e287b7" class="outline-3">
<h3 id="org1e287b7"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-1">
<p>
The operators as the same as those defined in the
@ -1433,7 +1433,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org31cfbd7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgce42a11" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1528,8 +1528,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgddc84d0" class="outline-3">
<h3 id="orgddc84d0"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orgf31c3c1" class="outline-3">
<h3 id="orgf31c3c1"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-2">
<p>
The operators as the same as those defined in the
@ -1537,7 +1537,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org0193665" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgac447df" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1577,8 +1577,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org5697589" class="outline-2">
<h2 id="org5697589"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-org39535bb" class="outline-2">
<h2 id="org39535bb"><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 \(\Psi\)
@ -1611,7 +1611,7 @@ where \(\alpha\) and \(\beta\) denote $&uarr;$-spin and $&darr;$-spin electrons,
\(n\uparrow\) and \(n\downarrow\) correspond to <code>electron.up_num</code> and <code>electron.dn_num</code>, respectively.
</p>
<table id="org0eaa590" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga7b6793" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1657,8 +1657,8 @@ where \(\alpha\) and \(\beta\) denote $&uarr;$-spin and $&darr;$-spin electrons,
</div>
</div>
<div id="outline-container-orga8294db" class="outline-2">
<h2 id="orga8294db"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div id="outline-container-org075153f" class="outline-2">
<h2 id="org075153f"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div class="outline-text-2" id="text-9">
<p>
By default, the <code>determinant</code> group corresponds to the ground state.
@ -1667,7 +1667,7 @@ correspond to excited state wave functions for the same set of
determinants. This is the goal of the present group
</p>
<table id="orgffbde17" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc68e2ee" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1706,8 +1706,8 @@ determinants. This is the goal of the present group
</div>
</div>
<div id="outline-container-org06515ca" class="outline-2">
<h2 id="org06515ca"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org5ddec4d" class="outline-2">
<h2 id="org5ddec4d"><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
@ -1760,7 +1760,7 @@ The total energy can be computed as:
\]
</p>
<table id="orgfb29fa8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8e47266" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1841,10 +1841,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org1fb27dd" class="outline-2">
<h2 id="org1fb27dd"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div id="outline-container-orgfc26547" class="outline-2">
<h2 id="orgfc26547"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-11">
<table id="org75c2fd1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org142a156" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1890,10 +1890,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org714aeb1" class="outline-2">
<h2 id="org714aeb1"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-org7ae3a14" class="outline-2">
<h2 id="org7ae3a14"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-12">
<table id="orge966db8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcf5bf34" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1932,8 +1932,8 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org3f640c2" class="outline-2">
<h2 id="org3f640c2"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-orge47d2ff" class="outline-2">
<h2 id="orge47d2ff"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-13">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -1947,7 +1947,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orge7ef917" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9f14476" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2002,7 +2002,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-03 Fri 08:04</p>
<p class="date">Created: 2022-06-03 Fri 08:39</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>