TREX/trexio
1
0
Fork 0
mirror of https://github.com/TREX-CoE/trexio.git synced 2024-12-24 13:23:44 +01:00
Code Issues Projects Releases Wiki Activity

Deploying to gh-pages from @ TREX-CoE/trexio@5834244b30 🚀

Browse Source
This commit is contained in:
scemama 2022-02-23 15:12:17 +00:00
parent 787d82b209
commit ddf343f840
7 changed files with 429 additions and 437 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
README.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>
<!-- 2022-02-17 Thu 14:52 -->
<!-- 2022-02-23 Wed 15:12 -->
<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: 2022-02-17 Thu 14:52</p>
<p class="date">Created: 2022-02-23 Wed 15:12</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

82
examples.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>
<!-- 2022-02-17 Thu 14:52 -->
<!-- 2022-02-23 Wed 15:12 -->
<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="#orgd8dfc23">1. Accessing sparse quantities</a>
<li><a href="#orgcdf5a42">1. Accessing sparse quantities</a>
<ul>
<li><a href="#orgb03d2ec">1.1. Fortran</a>
<li><a href="#org93b4d8b">1.1. Fortran</a>
<ul>
<li><a href="#org5777051">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org70b4a3e">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org502cb41">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org46dd8e9">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgcd74845">1.1.5. Allocate memory</a></li>
<li><a href="#org0821c77">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orga0bbb64">1.1.7. Read two-electron quantities</a>
<li><a href="#org578d875">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgb5de91f">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgd7f9ea5">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orge5f82fe">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org9173e9c">1.1.5. Allocate memory</a></li>
<li><a href="#orgf58dd39">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgd8a0660">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org62931c4">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orga142491">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org70fe4ef">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org6ae140a">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgd02a02b">1.1.8. Compute the energy</a></li>
<li><a href="#orgfa9634e">1.1.9. Terminate</a></li>
<li><a href="#orge428ab4">1.1.8. Compute the energy</a></li>
<li><a href="#org4f16410">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-orgd8dfc23" class="outline-2">
<h2 id="orgd8dfc23"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-orgcdf5a42" class="outline-2">
<h2 id="orgcdf5a42"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orgb03d2ec" class="outline-3">
<h3 id="orgb03d2ec"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org93b4d8b" class="outline-3">
<h3 id="org93b4d8b"><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-org5777051" class="outline-4">
<h4 id="org5777051"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org578d875" class="outline-4">
<h4 id="org578d875"><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-org70b4a3e" class="outline-4">
<h4 id="org70b4a3e"><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-orgb5de91f" class="outline-4">
<h4 id="orgb5de91f"><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-org502cb41" class="outline-4">
<h4 id="org502cb41"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgd7f9ea5" class="outline-4">
<h4 id="orgd7f9ea5"><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-org46dd8e9" class="outline-4">
<h4 id="org46dd8e9"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orge5f82fe" class="outline-4">
<h4 id="orge5f82fe"><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-orgcd74845" class="outline-4">
<h4 id="orgcd74845"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org9173e9c" class="outline-4">
<h4 id="org9173e9c"><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-org0821c77" class="outline-4">
<h4 id="org0821c77"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgf58dd39" class="outline-4">
<h4 id="orgf58dd39"><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-orga0bbb64" class="outline-4">
<h4 id="orga0bbb64"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgd8a0660" class="outline-4">
<h4 id="orgd8a0660"><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-org62931c4" class="outline-5">
<h5 id="org62931c4"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org70fe4ef" class="outline-5">
<h5 id="org70fe4ef"><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-orga142491" class="outline-5">
<h5 id="orga142491"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org6ae140a" class="outline-5">
<h5 id="org6ae140a"><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-orgd02a02b" class="outline-4">
<h4 id="orgd02a02b"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-orge428ab4" class="outline-4">
<h4 id="orge428ab4"><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-orgfa9634e" class="outline-4">
<h4 id="orgfa9634e"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org4f16410" class="outline-4">
<h4 id="org4f16410"><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: 2022-02-17 Thu 14:52</p>
<p class="date">Created: 2022-02-23 Wed 15:12</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
index.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>
<!-- 2022-02-17 Thu 14:52 -->
<!-- 2022-02-23 Wed 15:12 -->
<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: 2022-02-17 Thu 14:52</p>
<p class="date">Created: 2022-02-23 Wed 15:12</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

494
templator_front.html
View File

File diff suppressed because it is too large Load Diff

64
templator_hdf5.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>
<!-- 2022-02-17 Thu 14:52 -->
<!-- 2022-02-23 Wed 15:12 -->
<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>
@ -311,22 +311,22 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgaf61c17">1. Template for HDF5 definitions</a></li>
<li><a href="#orgb23766f">2. Template for HDF5 structures</a></li>
<li><a href="#org7e9e586">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgb5c5409">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org2bebc81">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orga219828">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org27be479">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgde3fb51">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgf2128f5">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgf7edd6c">10. Helper functions</a></li>
<li><a href="#org2a42785">1. Template for HDF5 definitions</a></li>
<li><a href="#org835e1e5">2. Template for HDF5 structures</a></li>
<li><a href="#org7fa2668">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org43ddaf7">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orge73a169">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgd97bdcd">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orga546a4b">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org346f63c">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org8ee6fb7">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org7c1d0cb">10. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgaf61c17" class="outline-2">
<h2 id="orgaf61c17"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org2a42785" class="outline-2">
<h2 id="org2a42785"><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>
@ -338,8 +338,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgb23766f" class="outline-2">
<h2 id="orgb23766f"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org835e1e5" class="outline-2">
<h2 id="org835e1e5"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div class="outline-text-2" id="text-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_hdf5_s</span> {
@ -352,8 +352,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org7e9e586" class="outline-2">
<h2 id="org7e9e586"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org7fa2668" class="outline-2">
<h2 id="org7fa2668"><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>
@ -456,8 +456,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgb5c5409" class="outline-2">
<h2 id="orgb5c5409"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org43ddaf7" class="outline-2">
<h2 id="org43ddaf7"><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>
@ -560,8 +560,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org2bebc81" class="outline-2">
<h2 id="org2bebc81"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orge73a169" class="outline-2">
<h2 id="orge73a169"><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>
@ -694,8 +694,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orga219828" class="outline-2">
<h2 id="orga219828"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orgd97bdcd" class="outline-2">
<h2 id="orgd97bdcd"><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
@ -896,8 +896,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org27be479" class="outline-2">
<h2 id="org27be479"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orga546a4b" class="outline-2">
<h2 id="orga546a4b"><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>
@ -1094,8 +1094,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-orgde3fb51" class="outline-2">
<h2 id="orgde3fb51"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org346f63c" class="outline-2">
<h2 id="org346f63c"><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>
@ -1221,8 +1221,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-orgf2128f5" class="outline-2">
<h2 id="orgf2128f5"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org8ee6fb7" class="outline-2">
<h2 id="org8ee6fb7"><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
@ -1262,8 +1262,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-orgf7edd6c" class="outline-2">
<h2 id="orgf7edd6c"><span class="section-number-2">10</span> Helper functions</h2>
<div id="outline-container-org7c1d0cb" class="outline-2">
<h2 id="org7c1d0cb"><span class="section-number-2">10</span> Helper functions</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1524,7 +1524,7 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-02-17 Thu 14:52</p>
<p class="date">Created: 2022-02-23 Wed 15:12</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

88
templator_text.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>
<!-- 2022-02-17 Thu 14:52 -->
<!-- 2022-02-23 Wed 15:12 -->
<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>
@ -311,29 +311,29 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org239c3e9">1. TEXT back end</a>
<li><a href="#org5601add">1. TEXT back end</a>
<ul>
<li><a href="#org835d486">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org6cba301">1.2. Template for general structure in text back end</a></li>
<li><a href="#org92d0e22">1.3. Initialize function (constant part)</a></li>
<li><a href="#orga8f9fb5">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org5cb497c">1.5. Template for text read a group</a></li>
<li><a href="#orgefddb6c">1.6. Template for text flush a group</a></li>
<li><a href="#orge55590b">1.7. Template for text free memory</a></li>
<li><a href="#orgcfce45c">1.8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org604732d">1.9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgd25e859">1.10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgf91bf6e">1.11. Template for has/read/write a string attribute</a></li>
<li><a href="#orgd2cadca">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org60cca65">1.13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org4f1c5a1">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org34d622a">1.2. Template for general structure in text back end</a></li>
<li><a href="#org9e2706a">1.3. Initialize function (constant part)</a></li>
<li><a href="#org0acd23d">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orge49e2c6">1.5. Template for text read a group</a></li>
<li><a href="#org2b76d64">1.6. Template for text flush a group</a></li>
<li><a href="#org8fcb814">1.7. Template for text free memory</a></li>
<li><a href="#org49110b7">1.8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org3e987a4">1.9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orged1e947">1.10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org662f0f2">1.11. Template for has/read/write a string attribute</a></li>
<li><a href="#org5240e11">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgee124de">1.13. Template for text delete a group (UNSAFE mode)</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org239c3e9" class="outline-2">
<h2 id="org239c3e9"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-org5601add" class="outline-2">
<h2 id="org5601add"><span class="section-number-2">1</span> TEXT back end</h2>
<div class="outline-text-2" id="text-1">
<p>
The "file" produced by the text back end is a directory with one
@ -354,8 +354,8 @@ The file is written when closed, or when the flush function is called.
</p>
</div>
<div id="outline-container-org835d486" class="outline-3">
<h3 id="org835d486"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-org4f1c5a1" class="outline-3">
<h3 id="org4f1c5a1"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
@ -374,8 +374,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org6cba301" class="outline-3">
<h3 id="org6cba301"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org34d622a" class="outline-3">
<h3 id="org34d622a"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div class="outline-text-3" id="text-1-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_text_s</span> {
@ -388,8 +388,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org92d0e22" class="outline-3">
<h3 id="org92d0e22"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-org9e2706a" class="outline-3">
<h3 id="org9e2706a"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div class="outline-text-3" id="text-1-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -532,8 +532,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orga8f9fb5" class="outline-3">
<h3 id="orga8f9fb5"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-org0acd23d" class="outline-3">
<h3 id="org0acd23d"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div class="outline-text-3" id="text-1-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -555,8 +555,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org5cb497c" class="outline-3">
<h3 id="org5cb497c"><span class="section-number-3">1.5</span> Template for text read a group</h3>
<div id="outline-container-orge49e2c6" class="outline-3">
<h3 id="orge49e2c6"><span class="section-number-3">1.5</span> Template for text read a group</h3>
<div class="outline-text-3" id="text-1-5">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -857,8 +857,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgefddb6c" class="outline-3">
<h3 id="orgefddb6c"><span class="section-number-3">1.6</span> Template for text flush a group</h3>
<div id="outline-container-org2b76d64" class="outline-3">
<h3 id="org2b76d64"><span class="section-number-3">1.6</span> Template for text flush a group</h3>
<div class="outline-text-3" id="text-1-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -922,8 +922,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orge55590b" class="outline-3">
<h3 id="orge55590b"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-org8fcb814" class="outline-3">
<h3 id="org8fcb814"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div class="outline-text-3" id="text-1-7">
<p>
Memory is allocated when reading. The following function frees memory.
@ -970,8 +970,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-orgcfce45c" class="outline-3">
<h3 id="orgcfce45c"><span class="section-number-3">1.8</span> Template for has/read/write a numerical attribute</h3>
<div id="outline-container-org49110b7" class="outline-3">
<h3 id="org49110b7"><span class="section-number-3">1.8</span> Template for has/read/write a numerical attribute</h3>
<div class="outline-text-3" id="text-1-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1034,8 +1034,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-org604732d" class="outline-3">
<h3 id="org604732d"><span class="section-number-3">1.9</span> Template for has/read/write a dataset of numerical data</h3>
<div id="outline-container-org3e987a4" class="outline-3">
<h3 id="org3e987a4"><span class="section-number-3">1.9</span> Template for has/read/write a dataset of numerical data</h3>
<div class="outline-text-3" id="text-1-9">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1131,8 +1131,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgd25e859" class="outline-3">
<h3 id="orgd25e859"><span class="section-number-3">1.10</span> Template for has/read/write a dataset of strings</h3>
<div id="outline-container-orged1e947" class="outline-3">
<h3 id="orged1e947"><span class="section-number-3">1.10</span> Template for has/read/write a dataset of strings</h3>
<div class="outline-text-3" id="text-1-10">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1233,8 +1233,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgf91bf6e" class="outline-3">
<h3 id="orgf91bf6e"><span class="section-number-3">1.11</span> Template for has/read/write a string attribute</h3>
<div id="outline-container-org662f0f2" class="outline-3">
<h3 id="org662f0f2"><span class="section-number-3">1.11</span> Template for has/read/write a string attribute</h3>
<div class="outline-text-3" id="text-1-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1308,8 +1308,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgd2cadca" class="outline-3">
<h3 id="orgd2cadca"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div id="outline-container-org5240e11" class="outline-3">
<h3 id="org5240e11"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div class="outline-text-3" id="text-1-12">
<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
@ -1583,8 +1583,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org60cca65" class="outline-3">
<h3 id="org60cca65"><span class="section-number-3">1.13</span> Template for text delete a group (UNSAFE mode)</h3>
<div id="outline-container-orgee124de" class="outline-3">
<h3 id="orgee124de"><span class="section-number-3">1.13</span> Template for text delete a group (UNSAFE mode)</h3>
<div class="outline-text-3" id="text-1-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1615,7 +1615,7 @@ User provides indices and values of the sparse array as two separate variables.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-02-17 Thu 14:52</p>
<p class="date">Created: 2022-02-23 Wed 15:12</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

130
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>
<!-- 2022-02-17 Thu 14:52 -->
<!-- 2022-02-23 Wed 15:12 -->
<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>
@ -333,33 +333,33 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org72195c8">1. Metadata (metadata group)</a></li>
<li><a href="#org5c67572">2. Electron (electron group)</a></li>
<li><a href="#org0f6133e">3. Nucleus (nucleus group)</a></li>
<li><a href="#org34ee8c0">4. Effective core potentials (ecp group)</a>
<li><a href="#org50e4627">1. Metadata (metadata group)</a></li>
<li><a href="#org5719122">2. Electron (electron group)</a></li>
<li><a href="#org1a47377">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgbd6d2c1">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org153262e">4.1. Example</a></li>
<li><a href="#orgfbc232a">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org44b264f">5. Basis set (basis group)</a>
<li><a href="#org202f03d">5. Basis set (basis group)</a>
<ul>
<li><a href="#org4d09113">5.1. Example</a></li>
<li><a href="#org60c165f">5.1. Example</a></li>
</ul>
</li>
<li><a href="#orgeed6add">6. Atomic orbitals (ao group)</a>
<li><a href="#org36f9a25">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="#org9ab9e65">7. Molecular orbitals (mo group)</a>
<li><a href="#org637bc17">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orga8221b5">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgb666f26">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgb1bfa66">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgd264573">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org7f512fe">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org9ff4e63">9. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgfff9a77">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org46e0ece">9. Reduced density matrices (rdm group)</a></li>
</ul>
</div>
</div>
@ -409,8 +409,8 @@ fetched using multiple function calls to perform I/O on buffers.
</p>
<div id="outline-container-org72195c8" class="outline-2">
<h2 id="org72195c8"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org50e4627" class="outline-2">
<h2 id="org50e4627"><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
@ -420,7 +420,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="org6dc8a6b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3f9056b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -501,15 +501,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-org5c67572" class="outline-2">
<h2 id="org5c67572"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org5719122" class="outline-2">
<h2 id="org5719122"><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="org4258d4a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org44daeb5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -548,15 +548,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org0f6133e" class="outline-2">
<h2 id="org0f6133e"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org1a47377" class="outline-2">
<h2 id="org1a47377"><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="org2477139" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org725c8ef" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -623,8 +623,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org34ee8c0" class="outline-2">
<h2 id="org34ee8c0"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orgbd6d2c1" class="outline-2">
<h2 id="orgbd6d2c1"><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
@ -657,7 +657,7 @@ 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="org2403ae0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfbc68e6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -755,8 +755,8 @@ The latter causes issues when written before <code>ang_mom</code> in the TREXIO
</p>
</div>
<div id="outline-container-org153262e" class="outline-3">
<h3 id="org153262e"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-orgfbc232a" class="outline-3">
<h3 id="orgfbc232a"><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
@ -819,8 +819,8 @@ power = [
</div>
</div>
<div id="outline-container-org44b264f" class="outline-2">
<h2 id="org44b264f"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org202f03d" class="outline-2">
<h2 id="org202f03d"><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
@ -873,7 +873,7 @@ 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="org23bedb9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga9ae10a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -967,8 +967,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-org4d09113" class="outline-3">
<h3 id="org4d09113"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org60c165f" class="outline-3">
<h3 id="org60c165f"><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
@ -1046,8 +1046,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgeed6add" class="outline-2">
<h2 id="orgeed6add"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org36f9a25" class="outline-2">
<h2 id="org36f9a25"><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
@ -1100,13 +1100,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org44b264f">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org202f03d">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="org352fd6a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdc1b7fa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1158,8 +1158,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org07f6428" class="outline-3">
<h3 id="ao_one_e"><a id="org07f6428"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgf969f56" class="outline-3">
<h3 id="ao_one_e"><a id="orgf969f56"></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}}
@ -1167,8 +1167,7 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
\mathbf{r}_i \vert} \] : electron-nucleus attractive potential,</li>
<li>\[ \hat{T}_{\text{e}} =
\sum_{i=1}^{N_\text{elec}} -\frac{1}{2}\hat{\Delta}_i \] : electronic kinetic energy</li>
<li>\(\hat{h} = \hat{T}_\text{e} + \hat{V}_\text{ne} +
\hat{V}_\text{ecp,l} + \hat{V}_\text{ecp,nl}\) : core electronic Hamiltonian</li>
<li>\(\hat{h} = \hat{T}_\text{e} + \hat{V}_\text{ne} + \hat{V}_\text{ECP}\) : core electronic Hamiltonian</li>
</ul>
<p>
@ -1177,7 +1176,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org41fdf72" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org90d60d1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1220,17 +1219,10 @@ over atomic orbitals.
</tr>
<tr>
<td class="org-left"><code>ecp_local</code></td>
<td class="org-left"><code>ecp</code></td>
<td class="org-left"><code>float</code></td>
<td class="org-left"><code>(ao.num, ao.num)</code></td>
<td class="org-left">\(\langle p \vert \hat{V}_{\text{ecp,l}} \vert q \rangle\)</td>
</tr>
<tr>
<td class="org-left"><code>ecp_non_local</code></td>
<td class="org-left"><code>float</code></td>
<td class="org-left"><code>(ao.num, ao.num)</code></td>
<td class="org-left">\(\langle p \vert \hat{V}_{\text{ecp,nl}} \vert q \rangle\)</td>
<td class="org-left">\(\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle\)</td>
</tr>
<tr>
@ -1244,8 +1236,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org1c389cc" class="outline-3">
<h3 id="ao_two_e"><a id="org1c389cc"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-orga079855" class="outline-3">
<h3 id="ao_two_e"><a id="orga079855"></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
@ -1266,7 +1258,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org72979f2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfbd6955" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1306,10 +1298,10 @@ notation.
</div>
</div>
<div id="outline-container-org9ab9e65" class="outline-2">
<h2 id="org9ab9e65"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org637bc17" class="outline-2">
<h2 id="org637bc17"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org34e4ed5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb7c2e6a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1375,8 +1367,8 @@ notation.
</table>
</div>
<div id="outline-container-orga8221b5" class="outline-3">
<h3 id="orga8221b5"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-orgb1bfa66" class="outline-3">
<h3 id="orgb1bfa66"><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
@ -1384,7 +1376,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org7e925ed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgebfac04" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1451,8 +1443,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgb666f26" class="outline-3">
<h3 id="orgb666f26"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orgd264573" class="outline-3">
<h3 id="orgd264573"><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
@ -1460,7 +1452,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgc0742d3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd1d6c78" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1500,11 +1492,11 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org7f512fe" class="outline-2">
<h2 id="org7f512fe"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-orgfff9a77" class="outline-2">
<h2 id="orgfff9a77"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-org9ff4e63" class="outline-2">
<h2 id="org9ff4e63"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org46e0ece" class="outline-2">
<h2 id="org46e0ece"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1557,7 +1549,7 @@ The total energy can be computed as:
\]
</p>
<table id="org317d59e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org87815d3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1640,7 +1632,7 @@ The total energy can be computed as:
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-02-17 Thu 14:52</p>
<p class="date">Created: 2022-02-23 Wed 15:12</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>