TREX/trexio
1
0
Fork 0
mirror of https://github.com/TREX-CoE/trexio.git synced 2025-03-04 14:20:19 +01:00
Code Issues Projects Releases Wiki Activity

Deploying to gh-pages from @ TREX-CoE/trexio@4ed30a3c7a 🚀

Browse Source
This commit is contained in:
scemama 2022-12-27 16:09:06 +00:00
parent 289bf0b84e
commit b2a7ef0236
7 changed files with 676 additions and 544 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>
<!-- 2022-12-27 Tue 16:07 -->
<!-- 2022-12-27 Tue 16:09 -->
<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>
@ -360,7 +360,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-12-27 Tue 16:07</p>
<p class="date">Created: 2022-12-27 Tue 16:09</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

94
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>
<!-- 2022-12-27 Tue 16:07 -->
<!-- 2022-12-27 Tue 16:09 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Examples</title>
@ -346,31 +346,31 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org7323a59">1. Accessing sparse quantities (integrals)</a>
<li><a href="#org3e539ff">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org6737724">1.1. Fortran</a>
<li><a href="#org6c6893b">1.1. Fortran</a>
<ul>
<li><a href="#orgb9abeeb">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org7085900">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org7bbccbd">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org4111878">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org1dd2f79">1.1.5. Allocate memory</a></li>
<li><a href="#orgd7c8716">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgfb00001">1.1.7. Read two-electron quantities</a>
<li><a href="#org17a32b2">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org7b6515d">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org68d4564">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org8e9af98">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org827b5ce">1.1.5. Allocate memory</a></li>
<li><a href="#org6c9efc8">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org15f3ac5">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org1ad43c4">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org20970e5">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org5a1b228">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org940d3bc">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org6d18e2a">1.1.8. Compute the energy</a></li>
<li><a href="#org825f60d">1.1.9. Terminate</a></li>
<li><a href="#org12a3205">1.1.8. Compute the energy</a></li>
<li><a href="#orgf271abc">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org43201f3">2. Reading determinants</a>
<li><a href="#orge5dba12">2. Reading determinants</a>
<ul>
<li><a href="#orgd4b88e4">2.1. Fortran</a></li>
<li><a href="#org46ea76d">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -378,12 +378,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org7323a59" class="outline-2">
<h2 id="org7323a59"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org3e539ff" class="outline-2">
<h2 id="org3e539ff"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org6737724" class="outline-3">
<h3 id="org6737724"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org6c6893b" class="outline-3">
<h3 id="org6c6893b"><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>
@ -429,8 +429,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgb9abeeb" class="outline-4">
<h4 id="orgb9abeeb"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org17a32b2" class="outline-4">
<h4 id="org17a32b2"><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>
@ -445,8 +445,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org7085900" class="outline-4">
<h4 id="org7085900"><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-org7b6515d" class="outline-4">
<h4 id="org7b6515d"><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)
@ -462,8 +462,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org7bbccbd" class="outline-4">
<h4 id="org7bbccbd"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org68d4564" class="outline-4">
<h4 id="org68d4564"><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)
@ -477,8 +477,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org4111878" class="outline-4">
<h4 id="org4111878"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org8e9af98" class="outline-4">
<h4 id="org8e9af98"><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)
@ -492,8 +492,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org1dd2f79" class="outline-4">
<h4 id="org1dd2f79"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org827b5ce" class="outline-4">
<h4 id="org827b5ce"><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) )
@ -505,8 +505,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-orgd7c8716" class="outline-4">
<h4 id="orgd7c8716"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org6c9efc8" class="outline-4">
<h4 id="org6c9efc8"><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)
@ -538,8 +538,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-orgfb00001" class="outline-4">
<h4 id="orgfb00001"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org15f3ac5" class="outline-4">
<h4 id="org15f3ac5"><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
@ -555,8 +555,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org1ad43c4" class="outline-5">
<h5 id="org1ad43c4"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org5a1b228" class="outline-5">
<h5 id="org5a1b228"><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)
@ -605,8 +605,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-org20970e5" class="outline-5">
<h5 id="org20970e5"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org940d3bc" class="outline-5">
<h5 id="org940d3bc"><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)
@ -650,8 +650,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org6d18e2a" class="outline-4">
<h4 id="org6d18e2a"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org12a3205" class="outline-4">
<h4 id="org12a3205"><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
@ -697,8 +697,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org825f60d" class="outline-4">
<h4 id="org825f60d"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgf271abc" class="outline-4">
<h4 id="orgf271abc"><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 )
@ -712,12 +712,12 @@ E = E + E_nn
</div>
<div id="outline-container-org43201f3" class="outline-2">
<h2 id="org43201f3"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-orge5dba12" class="outline-2">
<h2 id="orge5dba12"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgd4b88e4" class="outline-3">
<h3 id="orgd4b88e4"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org46ea76d" class="outline-3">
<h3 id="org46ea76d"><span class="section-number-3">2.1</span> Fortran</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
@ -796,7 +796,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-12-27 Tue 16:07</p>
<p class="date">Created: 2022-12-27 Tue 16:09</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>
<!-- 2022-12-27 Tue 16:07 -->
<!-- 2022-12-27 Tue 16:09 -->
<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>
@ -360,7 +360,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-12-27 Tue 16:07</p>
<p class="date">Created: 2022-12-27 Tue 16:09</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

626
templator_front.html
View File

File diff suppressed because it is too large Load Diff

82
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>
<!-- 2022-12-27 Tue 16:07 -->
<!-- 2022-12-27 Tue 16:08 -->
<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>
@ -324,25 +324,25 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org203f952">1. Template for HDF5 definitions</a></li>
<li><a href="#orgc7941d7">2. Template for HDF5 structures</a></li>
<li><a href="#org07d68c2">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org6445548">4. Template for HDF5 has a group</a></li>
<li><a href="#org099b17e">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org784910a">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org707e932">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org7fc21f0">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org720d400">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgfa96f64">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgefd0102">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org5cbd228">12. Source code for the determinant part</a></li>
<li><a href="#orge1abfdb">13. Helper functions</a></li>
<li><a href="#org336aa5c">1. Template for HDF5 definitions</a></li>
<li><a href="#org3afd2f5">2. Template for HDF5 structures</a></li>
<li><a href="#org029e8e2">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org9d3e986">4. Template for HDF5 has a group</a></li>
<li><a href="#org67a58b4">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org50d4aaf">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org5b10e24">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org105f9f5">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org11f25f6">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgbf7b501">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org429dd49">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgbe08380">12. Source code for the determinant part</a></li>
<li><a href="#orgc6e4d68">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org203f952" class="outline-2">
<h2 id="org203f952"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org336aa5c" class="outline-2">
<h2 id="org336aa5c"><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>
@ -354,8 +354,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgc7941d7" class="outline-2">
<h2 id="orgc7941d7"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org3afd2f5" class="outline-2">
<h2 id="org3afd2f5"><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
@ -375,8 +375,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org07d68c2" class="outline-2">
<h2 id="org07d68c2"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org029e8e2" class="outline-2">
<h2 id="org029e8e2"><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>
@ -496,8 +496,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org6445548" class="outline-2">
<h2 id="org6445548"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org9d3e986" class="outline-2">
<h2 id="org9d3e986"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -527,8 +527,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org099b17e" class="outline-2">
<h2 id="org099b17e"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org67a58b4" class="outline-2">
<h2 id="org67a58b4"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -632,8 +632,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org784910a" class="outline-2">
<h2 id="org784910a"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org50d4aaf" class="outline-2">
<h2 id="org50d4aaf"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -767,8 +767,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org707e932" class="outline-2">
<h2 id="org707e932"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org5b10e24" class="outline-2">
<h2 id="org5b10e24"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-7">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -971,8 +971,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org7fc21f0" class="outline-2">
<h2 id="org7fc21f0"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org105f9f5" class="outline-2">
<h2 id="org105f9f5"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div class="outline-text-2" id="text-8">
<p>
Chunked I/O in HDF5 for <code>buffered</code> data.
@ -1107,8 +1107,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org720d400" class="outline-2">
<h2 id="org720d400"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org11f25f6" class="outline-2">
<h2 id="org11f25f6"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-orgfa96f64" class="outline-2">
<h2 id="orgfa96f64"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgbf7b501" class="outline-2">
<h2 id="orgbf7b501"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1434,8 +1434,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
</div>
<div id="outline-container-orgefd0102" class="outline-2">
<h2 id="orgefd0102"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org429dd49" class="outline-2">
<h2 id="org429dd49"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-11">
<p>
<b><b>Note:</b></b> in early versions of the HDF5 library (v &lt; 1.10) unlinking an object was not working as expected
@ -1475,8 +1475,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org5cbd228" class="outline-2">
<h2 id="org5cbd228"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-orgbe08380" class="outline-2">
<h2 id="orgbe08380"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-12">
<p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1579,8 +1579,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-orge1abfdb" class="outline-2">
<h2 id="orge1abfdb"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgc6e4d68" class="outline-2">
<h2 id="orgc6e4d68"><span class="section-number-2">13</span> Helper functions</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1843,7 +1843,7 @@ 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: 2022-12-27 Tue 16:07</p>
<p class="date">Created: 2022-12-27 Tue 16:08</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

106
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>
<!-- 2022-12-27 Tue 16:07 -->
<!-- 2022-12-27 Tue 16:08 -->
<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>
@ -324,23 +324,23 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orga17e734">1. Template for group-related structures in text back end</a></li>
<li><a href="#org72d47ca">2. Template for general structure in text back end</a></li>
<li><a href="#org1aec4a4">3. Initialize function (constant part)</a></li>
<li><a href="#orgb827100">4. Deinitialize function (templated part)</a></li>
<li><a href="#org54dcca0">5. Flush function (templated part)</a></li>
<li><a href="#org3960f7e">6. Template for text read a group</a></li>
<li><a href="#org274a283">7. Template for text has a group</a></li>
<li><a href="#org2b650d7">8. Template for text flush a group</a></li>
<li><a href="#orge491474">9. Template for text free memory</a></li>
<li><a href="#orge01ce81">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orga6f1702">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org1802d4f">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgc42c38f">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgf2f6434">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgbd52584">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org8c20dff">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org1d182ef">17. Source code for the determinant part</a></li>
<li><a href="#orgfecbc65">1. Template for group-related structures in text back end</a></li>
<li><a href="#org2917919">2. Template for general structure in text back end</a></li>
<li><a href="#org575450f">3. Initialize function (constant part)</a></li>
<li><a href="#orgb699b14">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgcf469e8">5. Flush function (templated part)</a></li>
<li><a href="#org174076f">6. Template for text read a group</a></li>
<li><a href="#org99e2956">7. Template for text has a group</a></li>
<li><a href="#orge044981">8. Template for text flush a group</a></li>
<li><a href="#org0e2b2b4">9. Template for text free memory</a></li>
<li><a href="#orgc611a38">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org8ce6ec8">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org7bfa4ba">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org9cc788c">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org256e3a4">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgb2e3a6b">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgfe3fb88">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org8bb2ca7">17. Source code for the determinant part</a></li>
</ul>
</div>
</div>
@ -362,8 +362,8 @@ directory.
The file is written when closed, or when the flush function is called.
</p>
<div id="outline-container-orga17e734" class="outline-2">
<h2 id="orga17e734"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orgfecbc65" class="outline-2">
<h2 id="orgfecbc65"><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 {
@ -382,8 +382,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org72d47ca" class="outline-2">
<h2 id="org72d47ca"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org2917919" class="outline-2">
<h2 id="org2917919"><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
@ -403,8 +403,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org1aec4a4" class="outline-2">
<h2 id="org1aec4a4"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org575450f" class="outline-2">
<h2 id="org575450f"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">bool</span>
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgb827100" class="outline-2">
<h2 id="orgb827100"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgb699b14" class="outline-2">
<h2 id="orgb699b14"><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>
@ -594,8 +594,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org54dcca0" class="outline-2">
<h2 id="org54dcca0"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-orgcf469e8" class="outline-2">
<h2 id="orgcf469e8"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -618,8 +618,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org3960f7e" class="outline-2">
<h2 id="org3960f7e"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org174076f" class="outline-2">
<h2 id="org174076f"><span class="section-number-2">6</span> Template for text read a group</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -845,8 +845,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org274a283" class="outline-2">
<h2 id="org274a283"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org99e2956" class="outline-2">
<h2 id="org99e2956"><span class="section-number-2">7</span> Template for text has a group</h2>
<div class="outline-text-2" id="text-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -886,8 +886,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org2b650d7" class="outline-2">
<h2 id="org2b650d7"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-orge044981" class="outline-2">
<h2 id="orge044981"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div class="outline-text-2" id="text-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -951,8 +951,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orge491474" class="outline-2">
<h2 id="orge491474"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org0e2b2b4" class="outline-2">
<h2 id="org0e2b2b4"><span class="section-number-2">9</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-9">
<p>
Memory is allocated when reading. The following function frees memory.
@ -1021,8 +1021,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orge01ce81" class="outline-2">
<h2 id="orge01ce81"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orgc611a38" class="outline-2">
<h2 id="orgc611a38"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1085,8 +1085,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orga6f1702" class="outline-2">
<h2 id="orga6f1702"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org8ce6ec8" class="outline-2">
<h2 id="org8ce6ec8"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-11">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1182,8 +1182,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org1802d4f" class="outline-2">
<h2 id="org1802d4f"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org7bfa4ba" class="outline-2">
<h2 id="org7bfa4ba"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-12">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1284,8 +1284,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgc42c38f" class="outline-2">
<h2 id="orgc42c38f"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org9cc788c" class="outline-2">
<h2 id="org9cc788c"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1359,8 +1359,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgf2f6434" class="outline-2">
<h2 id="orgf2f6434"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org256e3a4" class="outline-2">
<h2 id="org256e3a4"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-14">
<p>
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
@ -1650,8 +1650,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-orgbd52584" class="outline-2">
<h2 id="orgbd52584"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-orgb2e3a6b" class="outline-2">
<h2 id="orgb2e3a6b"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div class="outline-text-2" id="text-15">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that buffered I/O has to be decoupled
@ -1881,8 +1881,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-org8c20dff" class="outline-2">
<h2 id="org8c20dff"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgfe3fb88" class="outline-2">
<h2 id="orgfe3fb88"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-16">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1910,8 +1910,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-org1d182ef" class="outline-2">
<h2 id="org1d182ef"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org8bb2ca7" class="outline-2">
<h2 id="org8bb2ca7"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-17">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -2103,7 +2103,7 @@ 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: 2022-12-27 Tue 16:07</p>
<p class="date">Created: 2022-12-27 Tue 16:08</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

304
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>
<!-- 2022-12-27 Tue 16:07 -->
<!-- 2022-12-27 Tue 16:09 -->
<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>
@ -346,41 +346,42 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org22780b3">1. Metadata (metadata group)</a></li>
<li><a href="#org83ef57e">2. Electron (electron group)</a></li>
<li><a href="#org0c148fd">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgd8edbf3">4. Effective core potentials (ecp group)</a>
<li><a href="#org97c50da">1. Metadata (metadata group)</a></li>
<li><a href="#org7c3d07b">2. Electron (electron group)</a></li>
<li><a href="#org767b4ec">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgadd2b2f">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org30571c2">4.1. Example</a></li>
<li><a href="#org6c18282">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org576a90b">5. Basis set (basis group)</a>
<li><a href="#org265705a">5. Basis set (basis group)</a>
<ul>
<li><a href="#orgc0173b7">5.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgcd31c84">5.2. Plane waves</a></li>
<li><a href="#org3546c5b">5.3. Data definitions</a></li>
<li><a href="#org48152cb">5.4. Example</a></li>
<li><a href="#org2b46187">5.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgd0d2056">5.2. Plane waves</a></li>
<li><a href="#org9761dcd">5.3. Data definitions</a></li>
<li><a href="#orgaf18fc7">5.4. Example</a></li>
</ul>
</li>
<li><a href="#orgf167e44">6. Atomic orbitals (ao group)</a>
<li><a href="#org79cc588">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="#orgb863b31">7. Molecular orbitals (mo group)</a>
<li><a href="#orge7a8b69">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org3a94888">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org511073f">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org5bfcf19">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org49fb8ca">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org4790589">8. Slater determinants (determinant group)</a></li>
<li><a href="#org16fa608">9. Configuration state functions (csf group)</a></li>
<li><a href="#org8f1a1eb">10. Excited states (state group)</a></li>
<li><a href="#org45f477c">11. Reduced density matrices (rdm group)</a></li>
<li><a href="#org8ade16b">12. Cell (cell group)</a></li>
<li><a href="#orgd2292b1">13. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org7291fcb">14. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#orgaa485c5">8. Slater determinants (determinant group)</a></li>
<li><a href="#orgca180c6">9. Configuration state functions (csf group)</a></li>
<li><a href="#orga268384">10. Excited states (state group)</a></li>
<li><a href="#org1df921a">11. Reduced density matrices (rdm group)</a></li>
<li><a href="#org4d0e96c">12. Cell (cell group)</a></li>
<li><a href="#org2d7097b">13. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orga8a5165">14. Numerical integration grid (grid group)</a></li>
<li><a href="#org3b756ea">15. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -442,8 +443,8 @@ For determinant lists (integer bit fields), the <code>special</code> attribute i
This means that the source code is not produced by the generator, but hand-written.
</p>
<div id="outline-container-org22780b3" class="outline-2">
<h2 id="org22780b3"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org97c50da" class="outline-2">
<h2 id="org97c50da"><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
@ -453,7 +454,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="org8c2526f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org34160c8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -534,15 +535,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-org83ef57e" class="outline-2">
<h2 id="org83ef57e"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org7c3d07b" class="outline-2">
<h2 id="org7c3d07b"><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="org7476886" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbfcdd00" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -588,15 +589,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org0c148fd" class="outline-2">
<h2 id="org0c148fd"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org767b4ec" class="outline-2">
<h2 id="org767b4ec"><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="orgf7a22b3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb020f38" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -663,8 +664,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-orgd8edbf3" class="outline-2">
<h2 id="orgd8edbf3"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orgadd2b2f" class="outline-2">
<h2 id="orgadd2b2f"><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
@ -697,7 +698,7 @@ 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="org254be10" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org20d7b71" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -799,8 +800,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-org30571c2" class="outline-3">
<h3 id="org30571c2"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org6c18282" class="outline-3">
<h3 id="org6c18282"><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
@ -863,12 +864,12 @@ power = [
</div>
</div>
<div id="outline-container-org576a90b" class="outline-2">
<h2 id="org576a90b"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org265705a" class="outline-2">
<h2 id="org265705a"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-orgc0173b7" class="outline-3">
<h3 id="orgc0173b7"><span class="section-number-3">5.1</span> Gaussian and Slater-type orbitals</h3>
<div id="outline-container-org2b46187" class="outline-3">
<h3 id="org2b46187"><span class="section-number-3">5.1</span> Gaussian and Slater-type orbitals</h3>
<div class="outline-text-3" id="text-5-1">
<p>
We consider here basis functions centered on nuclei. Hence, we enable
@ -922,8 +923,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-orgcd31c84" class="outline-3">
<h3 id="orgcd31c84"><span class="section-number-3">5.2</span> Plane waves</h3>
<div id="outline-container-orgd0d2056" class="outline-3">
<h3 id="orgd0d2056"><span class="section-number-3">5.2</span> Plane waves</h3>
<div class="outline-text-3" id="text-5-2">
<p>
A plane wave is defined as
@ -943,10 +944,10 @@ cutoff <code>e_cut</code> is the only input data relevant to plane waves.
</div>
</div>
<div id="outline-container-org3546c5b" class="outline-3">
<h3 id="org3546c5b"><span class="section-number-3">5.3</span> Data definitions</h3>
<div id="outline-container-org9761dcd" class="outline-3">
<h3 id="org9761dcd"><span class="section-number-3">5.3</span> Data definitions</h3>
<div class="outline-text-3" id="text-5-3">
<table id="org074568b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1676bd0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1055,8 +1056,8 @@ cutoff <code>e_cut</code> is the only input data relevant to plane waves.
</div>
</div>
<div id="outline-container-org48152cb" class="outline-3">
<h3 id="org48152cb"><span class="section-number-3">5.4</span> Example</h3>
<div id="outline-container-orgaf18fc7" class="outline-3">
<h3 id="orgaf18fc7"><span class="section-number-3">5.4</span> Example</h3>
<div class="outline-text-3" id="text-5-4">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1134,8 +1135,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgf167e44" class="outline-2">
<h2 id="orgf167e44"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org79cc588" class="outline-2">
<h2 id="org79cc588"><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
@ -1188,13 +1189,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org576a90b">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org265705a">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="org9242b15" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8c2d8a7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1246,7 +1247,7 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org93fd21f" class="outline-3">
<div id="outline-container-org5bb805f" class="outline-3">
<h3 id="ao_one_e"><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">
@ -1264,7 +1265,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgb76c157" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org67f74dd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1359,7 +1360,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgae0d905" class="outline-3">
<div id="outline-container-orgcdba85a" class="outline-3">
<h3 id="ao_two_e"><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>
@ -1381,7 +1382,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org760f4e4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org70ee7d7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1421,10 +1422,10 @@ notation.
</div>
</div>
<div id="outline-container-orgb863b31" class="outline-2">
<h2 id="orgb863b31"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orge7a8b69" class="outline-2">
<h2 id="orge7a8b69"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="orga632309" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5bfe709" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1511,8 +1512,8 @@ notation.
</table>
</div>
<div id="outline-container-org3a94888" class="outline-3">
<h3 id="org3a94888"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org5bfcf19" class="outline-3">
<h3 id="org5bfcf19"><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
@ -1520,7 +1521,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org9977be4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org687acdb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1615,8 +1616,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org511073f" class="outline-3">
<h3 id="org511073f"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org49fb8ca" class="outline-3">
<h3 id="org49fb8ca"><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 are the same as those defined in the
@ -1634,7 +1635,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org93973d0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0aa7ed7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1702,8 +1703,8 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org4790589" class="outline-2">
<h2 id="org4790589"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-orgaa485c5" class="outline-2">
<h2 id="orgaa485c5"><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 \(\Psi\)
@ -1745,7 +1746,7 @@ produced by the code generator.
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
</p>
<table id="org6f4e818" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3e3d332" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1791,8 +1792,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org16fa608" class="outline-2">
<h2 id="org16fa608"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
<div id="outline-container-orgca180c6" class="outline-2">
<h2 id="orgca180c6"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
<div class="outline-text-2" id="text-9">
<p>
The configuration interaction (CI) wave function \(\Psi\) can be
@ -1814,7 +1815,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org8ee75f5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1840138" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1860,8 +1861,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org8f1a1eb" class="outline-2">
<h2 id="org8f1a1eb"><span class="section-number-2">10</span> Excited states (state group)</h2>
<div id="outline-container-orga268384" class="outline-2">
<h2 id="orga268384"><span class="section-number-2">10</span> Excited states (state group)</h2>
<div class="outline-text-2" id="text-10">
<p>
This group contains information about excited states. Since only a
@ -1878,7 +1879,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="orga1e08bf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org23b4257" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1938,8 +1939,8 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-org45f477c" class="outline-2">
<h2 id="org45f477c"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org1df921a" class="outline-2">
<h2 id="org1df921a"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-11">
<p>
The reduced density matrices are defined in the basis of molecular
@ -2014,7 +2015,7 @@ expressed in a basis of a one-electron function
\(g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)\).
</p>
<table id="orgc35191c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfa0ad36" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2165,15 +2166,15 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org8ade16b" class="outline-2">
<h2 id="org8ade16b"><span class="section-number-2">12</span> Cell (cell group)</h2>
<div id="outline-container-org4d0e96c" class="outline-2">
<h2 id="org4d0e96c"><span class="section-number-2">12</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-12">
<p>
3 Lattice vectors to define a box containing the system, for example
used in periodic calculations.
</p>
<table id="org43f68c2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf14434e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2219,15 +2220,15 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-orgd2292b1" class="outline-2">
<h2 id="orgd2292b1"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-org2d7097b" class="outline-2">
<h2 id="org2d7097b"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-13">
<p>
A single $k$-point per TREXIO file can be stored. The $k$-point is
defined in this group.
</p>
<table id="org87a85cc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org62bc2f9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2266,10 +2267,141 @@ defined in this group.
</div>
</div>
<div id="outline-container-org7291fcb" class="outline-2">
<h2 id="org7291fcb"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-orga8a5165" class="outline-2">
<h2 id="orga8a5165"><span class="section-number-2">14</span> Numerical integration grid (grid group)</h2>
<div class="outline-text-2" id="text-14">
<p>
The molecular integrals have to be computed numerically on a grid in many applications.
A common choice for the angular grid is the one proposed by Lebedev and Laikov
[Russian Academy of Sciences Doklady Mathematics, Volume 59, Number 3, 1999, pages 477-481].
For the radial grids, many approaches have been developed over the years.
</p>
<p>
The structure of this group is adapted for the <a href="https://github.com/dftlibs/numgrid">numgrid</a> library.
Feel free to submit a PR if you find missing options/functionalities.
</p>
<table id="orgb19af79" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
</colgroup>
<thead>
<tr>
<th scope="col" class="org-left">Variable</th>
<th scope="col" class="org-left">Type</th>
<th scope="col" class="org-left">Dimensions</th>
<th scope="col" class="org-left">Description</th>
</tr>
</thead>
<tbody>
<tr>
<td class="org-left"><code>description</code></td>
<td class="org-left"><code>str</code></td>
<td class="org-left">&#xa0;</td>
<td class="org-left">Details about the used quadratures can go here</td>
</tr>
<tr>
<td class="org-left"><code>rad_precision</code></td>
<td class="org-left"><code>float</code></td>
<td class="org-left">&#xa0;</td>
<td class="org-left">Radial precision parameter (not used in some schemes like Krack-Köster)</td>
</tr>
<tr>
<td class="org-left"><code>num</code></td>
<td class="org-left"><code>dim</code></td>
<td class="org-left">&#xa0;</td>
<td class="org-left">Number of grid points</td>
</tr>
<tr>
<td class="org-left"><code>max_ang_num</code></td>
<td class="org-left"><code>int</code></td>
<td class="org-left">&#xa0;</td>
<td class="org-left">Maximum number of angular grid points (for pruning)</td>
</tr>
<tr>
<td class="org-left"><code>min_ang_num</code></td>
<td class="org-left"><code>int</code></td>
<td class="org-left">&#xa0;</td>
<td class="org-left">Minimum number of angular grid points (for pruning)</td>
</tr>
<tr>
<td class="org-left"><code>coord</code></td>
<td class="org-left"><code>float</code></td>
<td class="org-left"><code>(grid.num)</code></td>
<td class="org-left">Discretized coordinate space</td>
</tr>
<tr>
<td class="org-left"><code>weight</code></td>
<td class="org-left"><code>float</code></td>
<td class="org-left"><code>(grid.num)</code></td>
<td class="org-left">Grid weights according to a given partitioning (e.g. Becke)</td>
</tr>
<tr>
<td class="org-left"><code>ang_num</code></td>
<td class="org-left"><code>dim</code></td>
<td class="org-left">&#xa0;</td>
<td class="org-left">Number of angular integration points (if used)</td>
</tr>
<tr>
<td class="org-left"><code>ang_coord</code></td>
<td class="org-left"><code>float</code></td>
<td class="org-left"><code>(grid.ang_num)</code></td>
<td class="org-left">Discretized angular space (if used)</td>
</tr>
<tr>
<td class="org-left"><code>ang_weight</code></td>
<td class="org-left"><code>float</code></td>
<td class="org-left"><code>(grid.ang_num)</code></td>
<td class="org-left">Angular grid weights (if used)</td>
</tr>
<tr>
<td class="org-left"><code>rad_num</code></td>
<td class="org-left"><code>dim</code></td>
<td class="org-left">&#xa0;</td>
<td class="org-left">Number of radial integration points (if used)</td>
</tr>
<tr>
<td class="org-left"><code>rad_coord</code></td>
<td class="org-left"><code>float</code></td>
<td class="org-left"><code>(grid.rad_num)</code></td>
<td class="org-left">Discretized radial space (if used)</td>
</tr>
<tr>
<td class="org-left"><code>rad_weight</code></td>
<td class="org-left"><code>float</code></td>
<td class="org-left"><code>(grid.rad_num)</code></td>
<td class="org-left">Radial grid weights (if used)</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-org3b756ea" class="outline-2">
<h2 id="org3b756ea"><span class="section-number-2">15</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-15">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
at points of the 3N-dimensional space. Some algorithms require multiple
independent <i>walkers</i>, so it is possible to store multiple coordinates,
@ -2281,7 +2413,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orgd33e500" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org495cf25" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2336,7 +2468,7 @@ 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: 2022-12-27 Tue 16:07</p>
<p class="date">Created: 2022-12-27 Tue 16:09</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>