TREX/trexio
1
0
Fork 0
mirror of https://github.com/TREX-CoE/trexio.git synced 2024-12-25 05:43:53 +01:00
Code Issues Projects Releases Wiki Activity

Deploying to gh-pages from @ TREX-CoE/trexio@0bee7bb8d9 🚀

Browse Source
This commit is contained in:
scemama 2022-05-29 09:35:17 +00:00
parent 149842e4b7
commit 6592896785
7 changed files with 511 additions and 510 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>
<!-- 2022-05-25 Wed 08:09 -->
<!-- 2022-05-29 Sun 09:35 -->
<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: 2022-05-25 Wed 08:09</p>
<p class="date">Created: 2022-05-29 Sun 09:35</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>
<!-- 2022-05-25 Wed 08:09 -->
<!-- 2022-05-29 Sun 09:35 -->
<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="#org7f09ae3">1. Accessing sparse quantities</a>
<li><a href="#orgb823b57">1. Accessing sparse quantities</a>
<ul>
<li><a href="#orge385e6c">1.1. Fortran</a>
<li><a href="#org75fd4df">1.1. Fortran</a>
<ul>
<li><a href="#org9476572">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgb1a42e0">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org6db3515">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orge0e2709">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgf7d2393">1.1.5. Allocate memory</a></li>
<li><a href="#org26aeb59">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org3d38625">1.1.7. Read two-electron quantities</a>
<li><a href="#org520e7c1">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orga552273">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orge4d72c0">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orga21e480">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org85ab014">1.1.5. Allocate memory</a></li>
<li><a href="#org6750181">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgdbd5eef">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org33d54cb">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org8bf7780">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org3922096">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org4eed694">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org24974c8">1.1.8. Compute the energy</a></li>
<li><a href="#org64eec36">1.1.9. Terminate</a></li>
<li><a href="#org511fc42">1.1.8. Compute the energy</a></li>
<li><a href="#org05e581e">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-org7f09ae3" class="outline-2">
<h2 id="org7f09ae3"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-orgb823b57" class="outline-2">
<h2 id="orgb823b57"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orge385e6c" class="outline-3">
<h3 id="orge385e6c"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org75fd4df" class="outline-3">
<h3 id="org75fd4df"><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-org9476572" class="outline-4">
<h4 id="org9476572"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org520e7c1" class="outline-4">
<h4 id="org520e7c1"><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-orgb1a42e0" class="outline-4">
<h4 id="orgb1a42e0"><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-orga552273" class="outline-4">
<h4 id="orga552273"><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-org6db3515" class="outline-4">
<h4 id="org6db3515"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orge4d72c0" class="outline-4">
<h4 id="orge4d72c0"><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-orge0e2709" class="outline-4">
<h4 id="orge0e2709"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orga21e480" class="outline-4">
<h4 id="orga21e480"><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-orgf7d2393" class="outline-4">
<h4 id="orgf7d2393"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org85ab014" class="outline-4">
<h4 id="org85ab014"><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-org26aeb59" class="outline-4">
<h4 id="org26aeb59"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org6750181" class="outline-4">
<h4 id="org6750181"><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-org3d38625" class="outline-4">
<h4 id="org3d38625"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgdbd5eef" class="outline-4">
<h4 id="orgdbd5eef"><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-org33d54cb" class="outline-5">
<h5 id="org33d54cb"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org3922096" class="outline-5">
<h5 id="org3922096"><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-org8bf7780" class="outline-5">
<h5 id="org8bf7780"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org4eed694" class="outline-5">
<h5 id="org4eed694"><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-org24974c8" class="outline-4">
<h4 id="org24974c8"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org511fc42" class="outline-4">
<h4 id="org511fc42"><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-org64eec36" class="outline-4">
<h4 id="org64eec36"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org05e581e" class="outline-4">
<h4 id="org05e581e"><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: 2022-05-25 Wed 08:09</p>
<p class="date">Created: 2022-05-29 Sun 09:35</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>
<!-- 2022-05-25 Wed 08:09 -->
<!-- 2022-05-29 Sun 09:35 -->
<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: 2022-05-25 Wed 08:09</p>
<p class="date">Created: 2022-05-29 Sun 09:35</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

623
templator_front.html
View File

File diff suppressed because it is too large Load Diff

70
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>
<!-- 2022-05-25 Wed 08:09 -->
<!-- 2022-05-29 Sun 09:35 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>HDF5 back end</title>
@ -311,23 +311,23 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org415e764">1. Template for HDF5 definitions</a></li>
<li><a href="#org6054144">2. Template for HDF5 structures</a></li>
<li><a href="#org0d9ac4b">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org442c5d4">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgc49d9af">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org1fec6fe">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org3062a8d">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgb214495">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orge08f8c7">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org20dd6d2">10. Source code for the determinant part</a></li>
<li><a href="#org2608fd1">11. Helper functions</a></li>
<li><a href="#orgd987e65">1. Template for HDF5 definitions</a></li>
<li><a href="#orged9951b">2. Template for HDF5 structures</a></li>
<li><a href="#orgb46430e">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgd8286bb">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org3b3ab06">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org5d532e9">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org5bad79c">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org999b27e">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org9d1b5ca">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgeb13048">10. Source code for the determinant part</a></li>
<li><a href="#orgdcbe7e9">11. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org415e764" class="outline-2">
<h2 id="org415e764"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orgd987e65" class="outline-2">
<h2 id="orgd987e65"><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-org6054144" class="outline-2">
<h2 id="org6054144"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orged9951b" class="outline-2">
<h2 id="orged9951b"><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-org0d9ac4b" class="outline-2">
<h2 id="org0d9ac4b"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgb46430e" class="outline-2">
<h2 id="orgb46430e"><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-org442c5d4" class="outline-2">
<h2 id="org442c5d4"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orgd8286bb" class="outline-2">
<h2 id="orgd8286bb"><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-orgc49d9af" class="outline-2">
<h2 id="orgc49d9af"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org3b3ab06" class="outline-2">
<h2 id="org3b3ab06"><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-org1fec6fe" class="outline-2">
<h2 id="org1fec6fe"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org5d532e9" class="outline-2">
<h2 id="org5d532e9"><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-org3062a8d" class="outline-2">
<h2 id="org3062a8d"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org5bad79c" class="outline-2">
<h2 id="org5bad79c"><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-orgb214495" class="outline-2">
<h2 id="orgb214495"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org999b27e" class="outline-2">
<h2 id="org999b27e"><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-orge08f8c7" class="outline-2">
<h2 id="orge08f8c7"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org9d1b5ca" class="outline-2">
<h2 id="org9d1b5ca"><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-org20dd6d2" class="outline-2">
<h2 id="org20dd6d2"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div id="outline-container-orgeb13048" class="outline-2">
<h2 id="orgeb13048"><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-org2608fd1" class="outline-2">
<h2 id="org2608fd1"><span class="section-number-2">11</span> Helper functions</h2>
<div id="outline-container-orgdcbe7e9" class="outline-2">
<h2 id="orgdcbe7e9"><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: 2022-05-25 Wed 08:09</p>
<p class="date">Created: 2022-05-29 Sun 09:35</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>
<!-- 2022-05-25 Wed 08:09 -->
<!-- 2022-05-29 Sun 09:35 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
@ -311,20 +311,20 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org2fe21f3">1. Template for group-related structures in text back end</a></li>
<li><a href="#org71b1f2d">2. Template for general structure in text back end</a></li>
<li><a href="#org2a3fe4a">3. Initialize function (constant part)</a></li>
<li><a href="#orgc2c0d8d">4. Deinitialize function (templated part)</a></li>
<li><a href="#orge55e9fd">5. Template for text read a group</a></li>
<li><a href="#org17bd233">6. Template for text flush a group</a></li>
<li><a href="#orgf3195b5">7. Template for text free memory</a></li>
<li><a href="#org3c5f12f">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orga19ca3d">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgcbb9add">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgf098f0b">11. Template for has/read/write a string attribute</a></li>
<li><a href="#orgcf3f519">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org615f838">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org97dfada">14. Source code for the determinant part</a></li>
<li><a href="#orgeb275ff">1. Template for group-related structures in text back end</a></li>
<li><a href="#org4bdc6e9">2. Template for general structure in text back end</a></li>
<li><a href="#org76b1309">3. Initialize function (constant part)</a></li>
<li><a href="#org615534a">4. Deinitialize function (templated part)</a></li>
<li><a href="#org8e71808">5. Template for text read a group</a></li>
<li><a href="#org3881a37">6. Template for text flush a group</a></li>
<li><a href="#org2b552b8">7. Template for text free memory</a></li>
<li><a href="#org36ba7a6">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orga8ac1f2">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgaa204dc">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org3aed297">11. Template for has/read/write a string attribute</a></li>
<li><a href="#org4b9b879">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org3f2f1bd">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org14f0bd7">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-org2fe21f3" class="outline-2">
<h2 id="org2fe21f3"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orgeb275ff" class="outline-2">
<h2 id="orgeb275ff"><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-org71b1f2d" class="outline-2">
<h2 id="org71b1f2d"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org4bdc6e9" class="outline-2">
<h2 id="org4bdc6e9"><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-org2a3fe4a" class="outline-2">
<h2 id="org2a3fe4a"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org76b1309" class="outline-2">
<h2 id="org76b1309"><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-orgc2c0d8d" class="outline-2">
<h2 id="orgc2c0d8d"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org615534a" class="outline-2">
<h2 id="org615534a"><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-orge55e9fd" class="outline-2">
<h2 id="orge55e9fd"><span class="section-number-2">5</span> Template for text read a group</h2>
<div id="outline-container-org8e71808" class="outline-2">
<h2 id="org8e71808"><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-org17bd233" class="outline-2">
<h2 id="org17bd233"><span class="section-number-2">6</span> Template for text flush a group</h2>
<div id="outline-container-org3881a37" class="outline-2">
<h2 id="org3881a37"><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-orgf3195b5" class="outline-2">
<h2 id="orgf3195b5"><span class="section-number-2">7</span> Template for text free memory</h2>
<div id="outline-container-org2b552b8" class="outline-2">
<h2 id="org2b552b8"><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-org3c5f12f" class="outline-2">
<h2 id="org3c5f12f"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org36ba7a6" class="outline-2">
<h2 id="org36ba7a6"><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-orga19ca3d" class="outline-2">
<h2 id="orga19ca3d"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orga8ac1f2" class="outline-2">
<h2 id="orga8ac1f2"><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-orgcbb9add" class="outline-2">
<h2 id="orgcbb9add"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgaa204dc" class="outline-2">
<h2 id="orgaa204dc"><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-orgf098f0b" class="outline-2">
<h2 id="orgf098f0b"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org3aed297" class="outline-2">
<h2 id="org3aed297"><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-orgcf3f519" class="outline-2">
<h2 id="orgcf3f519"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org4b9b879" class="outline-2">
<h2 id="org4b9b879"><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-org615f838" class="outline-2">
<h2 id="org615f838"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org3f2f1bd" class="outline-2">
<h2 id="org3f2f1bd"><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-org97dfada" class="outline-2">
<h2 id="org97dfada"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div id="outline-container-org14f0bd7" class="outline-2">
<h2 id="org14f0bd7"><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: 2022-05-25 Wed 08:09</p>
<p class="date">Created: 2022-05-29 Sun 09:35</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>
<!-- 2022-05-25 Wed 08:09 -->
<!-- 2022-05-29 Sun 09:35 -->
<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="#org12fffe5">1. Metadata (metadata group)</a></li>
<li><a href="#org88cb927">2. Electron (electron group)</a></li>
<li><a href="#orge84df97">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgd30433c">4. Effective core potentials (ecp group)</a>
<li><a href="#orgb6f8868">1. Metadata (metadata group)</a></li>
<li><a href="#org878b403">2. Electron (electron group)</a></li>
<li><a href="#orgfa88b69">3. Nucleus (nucleus group)</a></li>
<li><a href="#org4ddafb2">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org3421d84">4.1. Example</a></li>
<li><a href="#orgf784e5e">4.1. Example</a></li>
</ul>
</li>
<li><a href="#orgbb4b684">5. Basis set (basis group)</a>
<li><a href="#orga5fffc8">5. Basis set (basis group)</a>
<ul>
<li><a href="#org83f0165">5.1. Example</a></li>
<li><a href="#org3bbb004">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org5f49723">6. Atomic orbitals (ao group)</a>
<li><a href="#orgce3182a">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="#org0a80907">7. Molecular orbitals (mo group)</a>
<li><a href="#org4baba03">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org4f19d65">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org599d1a9">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgfada648">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org37c0a71">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org7f332a8">8. Slater determinants (determinant group)</a></li>
<li><a href="#orgce9f1c3">9. Excited states (state group)</a></li>
<li><a href="#org67d5b39">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgb8eb0d3">11. Cell (cell group)</a></li>
<li><a href="#org2313ffb">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org2b1668e">13. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org0258065">8. Slater determinants (determinant group)</a></li>
<li><a href="#orgb64b8a4">9. Excited states (state group)</a></li>
<li><a href="#orga35ed54">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org9f18e1b">11. Cell (cell group)</a></li>
<li><a href="#org5c34c17">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org0d4ac51">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-org12fffe5" class="outline-2">
<h2 id="org12fffe5"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgb6f8868" class="outline-2">
<h2 id="orgb6f8868"><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="org87db0fd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org00dc3b3" 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-org88cb927" class="outline-2">
<h2 id="org88cb927"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org878b403" class="outline-2">
<h2 id="org878b403"><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="orgb10fcdf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org46b4b40" 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-orge84df97" class="outline-2">
<h2 id="orge84df97"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-orgfa88b69" class="outline-2">
<h2 id="orgfa88b69"><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="orgec6d319" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc5a9e9a" 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-orgd30433c" class="outline-2">
<h2 id="orgd30433c"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org4ddafb2" class="outline-2">
<h2 id="org4ddafb2"><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="org955cc10" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd71aeb9" 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-org3421d84" class="outline-3">
<h3 id="org3421d84"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-orgf784e5e" class="outline-3">
<h3 id="orgf784e5e"><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-orgbb4b684" class="outline-2">
<h2 id="orgbb4b684"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-orga5fffc8" class="outline-2">
<h2 id="orga5fffc8"><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="orgcf531d2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2a11d67" 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-org83f0165" class="outline-3">
<h3 id="org83f0165"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org3bbb004" class="outline-3">
<h3 id="org3bbb004"><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-org5f49723" class="outline-2">
<h2 id="org5f49723"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-orgce3182a" class="outline-2">
<h2 id="orgce3182a"><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="#orgbb4b684">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#orga5fffc8">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="org7e9fd8b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9ff2bd1" 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-org5cc5480" class="outline-3">
<h3 id="ao_one_e"><a id="org5cc5480"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org6b26f73" class="outline-3">
<h3 id="ao_one_e"><a id="org6b26f73"></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="orgc3d277d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org74a58e4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1286,8 +1286,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org4ea5918" class="outline-3">
<h3 id="ao_two_e"><a id="org4ea5918"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-orgd3212ce" class="outline-3">
<h3 id="ao_two_e"><a id="orgd3212ce"></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="orgc28406b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org63ecf35" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1348,10 +1348,10 @@ notation.
</div>
</div>
<div id="outline-container-org0a80907" class="outline-2">
<h2 id="org0a80907"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org4baba03" class="outline-2">
<h2 id="org4baba03"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org465f8b3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb9cfa11" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1424,8 +1424,8 @@ notation.
</table>
</div>
<div id="outline-container-org4f19d65" class="outline-3">
<h3 id="org4f19d65"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-orgfada648" class="outline-3">
<h3 id="orgfada648"><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="org3ecae69" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf0be913" 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-org599d1a9" class="outline-3">
<h3 id="org599d1a9"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org37c0a71" class="outline-3">
<h3 id="org37c0a71"><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="org1643a41" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org774a79f" 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-org7f332a8" class="outline-2">
<h2 id="org7f332a8"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-org0258065" class="outline-2">
<h2 id="org0258065"><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="org42e2812" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga13cf10" 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-orgce9f1c3" class="outline-2">
<h2 id="orgce9f1c3"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div id="outline-container-orgb64b8a4" class="outline-2">
<h2 id="orgb64b8a4"><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="org849cd04" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb40c2fe" 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-org67d5b39" class="outline-2">
<h2 id="org67d5b39"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orga35ed54" class="outline-2">
<h2 id="orga35ed54"><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="orgd03b829" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4371d49" 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-orgb8eb0d3" class="outline-2">
<h2 id="orgb8eb0d3"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div id="outline-container-org9f18e1b" class="outline-2">
<h2 id="org9f18e1b"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-11">
<table id="orgdcec9ea" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga96a3f0" 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-org2313ffb" class="outline-2">
<h2 id="org2313ffb"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-org5c34c17" class="outline-2">
<h2 id="org5c34c17"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-12">
<table id="org9536e70" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org937fba7" 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-org2b1668e" class="outline-2">
<h2 id="org2b1668e"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org0d4ac51" class="outline-2">
<h2 id="org0d4ac51"><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="orged821ab" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga58de5b" 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: 2022-05-25 Wed 08:09</p>
<p class="date">Created: 2022-05-29 Sun 09:35</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>