TREX/trexio
1
0
Fork 0
mirror of https://github.com/TREX-CoE/trexio.git synced 2024-11-03 20:54:07 +01:00
Code Issues Projects Releases Wiki Activity

Deploying to gh-pages from @ TREX-CoE/trexio@742f797d1a 🚀

Browse Source
This commit is contained in:
q-posev 2023-05-05 13:55:18 +00:00
parent 9ba69c565f
commit b5e0204744
9 changed files with 661 additions and 661 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>
<!-- 2023-05-05 Fri 13:26 -->
<!-- 2023-05-05 Fri 13:55 -->
<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>
@ -383,7 +383,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 13:26</p>
<p class="date">Created: 2023-05-05 Fri 13:55</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

172
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>
<!-- 2023-05-05 Fri 13:26 -->
<!-- 2023-05-05 Fri 13:55 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Examples</title>
@ -346,61 +346,61 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9dfef00">1. Writing nuclear coordinates</a>
<li><a href="#orgf591e8a">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#org8b56fff">1.1. C</a></li>
<li><a href="#org0eff649">1.2. Python</a></li>
<li><a href="#orgbabb19d">1.3. Fortran</a></li>
<li><a href="#org1ef4321">1.1. C</a></li>
<li><a href="#orgc58599e">1.2. Python</a></li>
<li><a href="#org0ae2465">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org5900dca">2. Accessing sparse quantities (integrals)</a>
<li><a href="#orga0b0b02">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org18b3b14">2.1. Fortran</a>
<li><a href="#org325bce5">2.1. Fortran</a>
<ul>
<li><a href="#org2ef38bd">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org654d081">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgeab1bd9">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgc43bd5a">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgb4139b1">2.1.5. Allocate memory</a></li>
<li><a href="#orgf013412">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org678442c">2.1.7. Read two-electron quantities</a>
<li><a href="#org2a985ab">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org3c69cd2">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgd48a4e8">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org042b9bd">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org0dd8ecc">2.1.5. Allocate memory</a></li>
<li><a href="#org5e7b57d">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org3319261">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org2ca5f9f">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org16227b7">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#orga3147ac">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgf45977d">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org09f8512">2.1.8. Compute the energy</a></li>
<li><a href="#orga20fffe">2.1.9. Terminate</a></li>
<li><a href="#org32e4150">2.1.8. Compute the energy</a></li>
<li><a href="#org4708c75">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org18201df">2.2. Python</a>
<li><a href="#orgb97ea94">2.2. Python</a>
<ul>
<li><a href="#orgce88bca">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgdaf305b">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#orgd885f8c">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org92e5969">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org83109cc">2.2.5. Read two-electron quantities</a>
<li><a href="#org99e10c4">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgf788474">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org8f37e57">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org6dc20c4">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgaa41903">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#orgb10896c">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgfe5e200">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org05effbd">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgc0b8a19">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org365296c">2.2.6. Compute the energy</a></li>
<li><a href="#orga9c9db9">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org0d11b50">3. Reading determinants</a>
<li><a href="#orgbe8eeb7">3. Reading determinants</a>
<ul>
<li><a href="#org3966b27">3.1. Fortran</a></li>
<li><a href="#org51f8d3c">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org9dfef00" class="outline-2">
<h2 id="org9dfef00"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-orgf591e8a" class="outline-2">
<h2 id="orgf591e8a"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div class="outline-text-2" id="text-1">
<p>
Here is a demonstration of how to use TREXIO to write the nuclear
@ -410,8 +410,8 @@ as well as the necessary TREXIO functions to perform these actions.
</p>
</div>
<div id="outline-container-org8b56fff" class="outline-3">
<h3 id="org8b56fff"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org1ef4321" class="outline-3">
<h3 id="org1ef4321"><span class="section-number-3">1.1</span> C</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #483d8b;">#include</span> <span style="color: #8b2252;">&lt;stdio.h&gt;</span>
@ -461,8 +461,8 @@ as well as the necessary TREXIO functions to perform these actions.
</div>
</div>
<div id="outline-container-org0eff649" class="outline-3">
<h3 id="org0eff649"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-orgc58599e" class="outline-3">
<h3 id="orgc58599e"><span class="section-number-3">1.2</span> Python</h3>
<div class="outline-text-3" id="text-1-2">
<p>
This code uses the TREXIO Python binding to create a new TREXIO file named
@ -509,8 +509,8 @@ coordinates of the system.
</div>
</div>
<div id="outline-container-orgbabb19d" class="outline-3">
<h3 id="orgbabb19d"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-org0ae2465" class="outline-3">
<h3 id="org0ae2465"><span class="section-number-3">1.3</span> Fortran</h3>
<div class="outline-text-3" id="text-1-3">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">trexio_water</span>
@ -567,12 +567,12 @@ coordinates of the system.
</div>
</div>
<div id="outline-container-org5900dca" class="outline-2">
<h2 id="org5900dca"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orga0b0b02" class="outline-2">
<h2 id="orga0b0b02"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org18b3b14" class="outline-3">
<h3 id="org18b3b14"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org325bce5" class="outline-3">
<h3 id="org325bce5"><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;">print_energy</span>
@ -618,8 +618,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org2ef38bd" class="outline-4">
<h4 id="org2ef38bd"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org2a985ab" class="outline-4">
<h4 id="org2a985ab"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div class="outline-text-4" id="text-2-1-1">
<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>
@ -634,8 +634,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org654d081" class="outline-4">
<h4 id="org654d081"><span class="section-number-4">2.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div id="outline-container-org3c69cd2" class="outline-4">
<h4 id="org3c69cd2"><span class="section-number-4">2.1.2</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-2-1-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
@ -651,8 +651,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div>
</div>
<div id="outline-container-orgeab1bd9" class="outline-4">
<h4 id="orgeab1bd9"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgd48a4e8" class="outline-4">
<h4 id="orgd48a4e8"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-2-1-3">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
@ -666,8 +666,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div>
</div>
<div id="outline-container-orgc43bd5a" class="outline-4">
<h4 id="orgc43bd5a"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org042b9bd" class="outline-4">
<h4 id="org042b9bd"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-2-1-4">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
@ -681,8 +681,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div>
</div>
<div id="outline-container-orgb4139b1" class="outline-4">
<h4 id="orgb4139b1"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org0dd8ecc" class="outline-4">
<h4 id="org0dd8ecc"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div class="outline-text-4" id="text-2-1-5">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
@ -694,8 +694,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-orgf013412" class="outline-4">
<h4 id="orgf013412"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org5e7b57d" class="outline-4">
<h4 id="org5e7b57d"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-2-1-6">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@ -727,8 +727,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-org678442c" class="outline-4">
<h4 id="org678442c"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org3319261" class="outline-4">
<h4 id="org3319261"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-2-1-7">
<p>
Reading is done with OpenMP. Each thread reads its own buffer, and
@ -744,8 +744,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org2ca5f9f" class="outline-5">
<h5 id="org2ca5f9f"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orga3147ac" class="outline-5">
<h5 id="orga3147ac"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-2-1-7-1">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
@ -794,8 +794,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-org16227b7" class="outline-5">
<h5 id="org16227b7"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgf45977d" class="outline-5">
<h5 id="orgf45977d"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-2-1-7-2">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
@ -839,8 +839,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org09f8512" class="outline-4">
<h4 id="org09f8512"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org32e4150" class="outline-4">
<h4 id="org32e4150"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div class="outline-text-4" id="text-2-1-8">
<p>
When the orbitals are real, we can use
@ -886,8 +886,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-orga20fffe" class="outline-4">
<h4 id="orga20fffe"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org4708c75" class="outline-4">
<h4 id="org4708c75"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div class="outline-text-4" id="text-2-1-9">
<div class="org-src-container">
<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
@ -899,8 +899,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org18201df" class="outline-3">
<h3 id="org18201df"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-orgb97ea94" class="outline-3">
<h3 id="orgb97ea94"><span class="section-number-3">2.2</span> Python</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">import</span> sys
@ -934,8 +934,8 @@ One needs to read from the TREXIO file:
</dl>
</div>
<div id="outline-container-orgce88bca" class="outline-4">
<h4 id="orgce88bca"><span class="section-number-4">2.2.1</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div id="outline-container-org99e10c4" class="outline-4">
<h4 id="org99e10c4"><span class="section-number-4">2.2.1</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-2-2-1">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">filename</span> = sys.argv[1]
@ -945,8 +945,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgdaf305b" class="outline-4">
<h4 id="orgdaf305b"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgf788474" class="outline-4">
<h4 id="orgf788474"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-2-2-2">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">E_nn</span> = trexio.read_nucleus_repulsion(f)
@ -955,8 +955,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgd885f8c" class="outline-4">
<h4 id="orgd885f8c"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org8f37e57" class="outline-4">
<h4 id="org8f37e57"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-2-2-3">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">n</span> = trexio.read_mo_num(f)
@ -965,8 +965,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org92e5969" class="outline-4">
<h4 id="org92e5969"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org6dc20c4" class="outline-4">
<h4 id="org6dc20c4"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-2-2-4">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_mo_1e_int_core_hamiltonian(f):
@ -985,12 +985,12 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org83109cc" class="outline-4">
<h4 id="org83109cc"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-orgaa41903" class="outline-4">
<h4 id="orgaa41903"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-2-2-5">
</div>
<div id="outline-container-orgb10896c" class="outline-5">
<h5 id="orgb10896c"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org05effbd" class="outline-5">
<h5 id="org05effbd"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-2-2-5-1">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_mo_2e_int_eri(f):
@ -1020,8 +1020,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgfe5e200" class="outline-5">
<h5 id="orgfe5e200"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-orgc0b8a19" class="outline-5">
<h5 id="orgc0b8a19"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-2-2-5-2">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_rdm_2e(f):
@ -1043,8 +1043,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org365296c" class="outline-4">
<h4 id="org365296c"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-orga9c9db9" class="outline-4">
<h4 id="orga9c9db9"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div class="outline-text-4" id="text-2-2-6">
<p>
When the orbitals are real, we can use
@ -1073,12 +1073,12 @@ E &=& E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle j | h | i \rangle\,
</div>
</div>
<div id="outline-container-org0d11b50" class="outline-2">
<h2 id="org0d11b50"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-orgbe8eeb7" class="outline-2">
<h2 id="orgbe8eeb7"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org3966b27" class="outline-3">
<h3 id="org3966b27"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org51f8d3c" class="outline-3">
<h3 id="org51f8d3c"><span class="section-number-3">3.1</span> Fortran</h3>
<div class="outline-text-3" id="text-3-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
@ -1157,7 +1157,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 13:26</p>
<p class="date">Created: 2023-05-05 Fri 13:55</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>
<!-- 2023-05-05 Fri 13:26 -->
<!-- 2023-05-05 Fri 13:55 -->
<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>
@ -383,7 +383,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 13:26</p>
<p class="date">Created: 2023-05-05 Fri 13:55</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
intro.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>
<!-- 2023-05-05 Fri 13:26 -->
<!-- 2023-05-05 Fri 13:55 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Motivation</title>
@ -384,7 +384,7 @@ still lacking, and the purpose of the TREXIO library is to fill this gap.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 13:26</p>
<p class="date">Created: 2023-05-05 Fri 13:55</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
lib.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>
<!-- 2023-05-05 Fri 13:26 -->
<!-- 2023-05-05 Fri 13:55 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>The TREXIO library</title>
@ -346,19 +346,19 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org5e20fa6">1. Format specification</a>
<li><a href="#org1b0275b">1. Format specification</a>
<ul>
<li><a href="#org9975962">1.1. Organization of the data</a></li>
<li><a href="#org957b61b">1.2. Data types</a></li>
<li><a href="#orga9a4fcc">1.1. Organization of the data</a></li>
<li><a href="#orgdf6c6f6">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org0320423">2. The TREXIO library</a>
<li><a href="#org8f6b1d8">2. The TREXIO library</a>
<ul>
<li><a href="#org0133483">2.1. The front-end</a></li>
<li><a href="#org5a84c6b">2.2. The back-end</a></li>
<li><a href="#org9ec9c9e">2.3. Supported languages</a></li>
<li><a href="#orgde44c44">2.4. Source code generation and documentation</a></li>
<li><a href="#org18fa05d">2.5. Availability</a></li>
<li><a href="#org87fd0a0">2.1. The front-end</a></li>
<li><a href="#orgdaabf53">2.2. The back-end</a></li>
<li><a href="#org24d1fa6">2.3. Supported languages</a></li>
<li><a href="#orgdc2de31">2.4. Source code generation and documentation</a></li>
<li><a href="#org7bad5e6">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org5e20fa6" class="outline-2">
<h2 id="org5e20fa6"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org1b0275b" class="outline-2">
<h2 id="org1b0275b"><span class="section-number-2">1</span> Format specification</h2>
<div class="outline-text-2" id="text-1">
</td>
<td>
@ -388,8 +388,8 @@ calculation are stored.
</p>
</div>
<div id="outline-container-org9975962" class="outline-3">
<h3 id="org9975962"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-orga9a4fcc" class="outline-3">
<h3 id="orga9a4fcc"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div class="outline-text-3" id="text-1-1">
<p>
The data in TREXIO are organized into <b>groups</b>, each containing
@ -405,8 +405,8 @@ number of nuclei.
</div>
</div>
<div id="outline-container-org957b61b" class="outline-3">
<h3 id="org957b61b"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-orgdf6c6f6" class="outline-3">
<h3 id="orgdf6c6f6"><span class="section-number-3">1.2</span> Data types</h3>
<div class="outline-text-3" id="text-1-2">
<p>
So that TREXIO can be used in any language, we use a limited number
@ -473,8 +473,8 @@ with the same name suffixed by <code>_im</code>.
</div>
</div>
<div id="outline-container-org0320423" class="outline-2">
<h2 id="org0320423"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-org8f6b1d8" class="outline-2">
<h2 id="org8f6b1d8"><span class="section-number-2">2</span> The TREXIO library</h2>
<div class="outline-text-2" id="text-2">
</td>
<td>
@ -497,8 +497,8 @@ interface between the library and the physical storage.
</p>
</div>
<div id="outline-container-org0133483" class="outline-3">
<h3 id="org0133483"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-org87fd0a0" class="outline-3">
<h3 id="org87fd0a0"><span class="section-number-3">2.1</span> The front-end</h3>
<div class="outline-text-3" id="text-2-1">
<p>
By using the TREXIO library, users can store and extract data in a
@ -539,8 +539,8 @@ made are safe.
</div>
</div>
<div id="outline-container-org5a84c6b" class="outline-3">
<h3 id="org5a84c6b"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-orgdaabf53" class="outline-3">
<h3 id="orgdaabf53"><span class="section-number-3">2.2</span> The back-end</h3>
<div class="outline-text-3" id="text-2-2">
<p>
At present, TREXIO supports two back-ends: one relying only on the
@ -610,8 +610,8 @@ repositories.
</div>
</div>
<div id="outline-container-org9ec9c9e" class="outline-3">
<h3 id="org9ec9c9e"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org24d1fa6" class="outline-3">
<h3 id="org24d1fa6"><span class="section-number-3">2.3</span> Supported languages</h3>
<div class="outline-text-3" id="text-2-3">
<p>
One of the main benefits of using C as the interface for a library is
@ -668,8 +668,8 @@ via the Binder platform.
</div>
<div id="outline-container-orgde44c44" class="outline-3">
<h3 id="orgde44c44"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-orgdc2de31" class="outline-3">
<h3 id="orgdc2de31"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div class="outline-text-3" id="text-2-4">
<p>
Source code generation is a valuable technique that can significantly
@ -723,8 +723,8 @@ regardless of their programming skills.
</div>
</div>
<div id="outline-container-org18fa05d" class="outline-3">
<h3 id="org18fa05d"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org7bad5e6" class="outline-3">
<h3 id="org7bad5e6"><span class="section-number-3">2.5</span> Availability</h3>
<div class="outline-text-3" id="text-2-5">
<p>
The TREXIO library is designed to be portable and easy to install
@ -754,7 +754,7 @@ are available in Ubuntu 23.04.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 13:26</p>
<p class="date">Created: 2023-05-05 Fri 13:55</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

650
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>
<!-- 2023-05-05 Fri 13:26 -->
<!-- 2023-05-05 Fri 13:55 -->
<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="#org342c12f">1. Template for HDF5 definitions</a></li>
<li><a href="#org5a9192b">2. Template for HDF5 structures</a></li>
<li><a href="#orge9fcd69">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orge531263">4. Template for HDF5 has a group</a></li>
<li><a href="#org44200f7">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgb16da66">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org2ca9310">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgde42460">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org728f387">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgd14cd27">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgbcc85f0">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org24b6c95">12. Source code for the determinant part</a></li>
<li><a href="#org49f2a81">13. Helper functions</a></li>
<li><a href="#orga67a4fe">1. Template for HDF5 definitions</a></li>
<li><a href="#orgfea3999">2. Template for HDF5 structures</a></li>
<li><a href="#org40b92c5">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org9aa736f">4. Template for HDF5 has a group</a></li>
<li><a href="#org5793d1a">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org33e86e5">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org71e4ab0">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgb61ba1d">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org7681c9d">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org1b02d43">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org1330849">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org5887b37">12. Source code for the determinant part</a></li>
<li><a href="#orgb2a5d26">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org342c12f" class="outline-2">
<h2 id="org342c12f"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orga67a4fe" class="outline-2">
<h2 id="orga67a4fe"><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-org5a9192b" class="outline-2">
<h2 id="org5a9192b"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgfea3999" class="outline-2">
<h2 id="orgfea3999"><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-orge9fcd69" class="outline-2">
<h2 id="orge9fcd69"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org40b92c5" class="outline-2">
<h2 id="org40b92c5"><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-orge531263" class="outline-2">
<h2 id="orge531263"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org9aa736f" class="outline-2">
<h2 id="org9aa736f"><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-org44200f7" class="outline-2">
<h2 id="org44200f7"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org5793d1a" class="outline-2">
<h2 id="org5793d1a"><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-orgb16da66" class="outline-2">
<h2 id="orgb16da66"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org33e86e5" class="outline-2">
<h2 id="org33e86e5"><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>
@ -770,8 +770,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org2ca9310" class="outline-2">
<h2 id="org2ca9310"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org71e4ab0" class="outline-2">
<h2 id="org71e4ab0"><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
@ -973,8 +973,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-orgde42460" class="outline-2">
<h2 id="orgde42460"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-orgb61ba1d" class="outline-2">
<h2 id="orgb61ba1d"><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.
@ -1108,8 +1108,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org728f387" class="outline-2">
<h2 id="org728f387"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org7681c9d" class="outline-2">
<h2 id="org7681c9d"><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-orgd14cd27" class="outline-2">
<h2 id="orgd14cd27"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org1b02d43" class="outline-2">
<h2 id="org1b02d43"><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-orgbcc85f0" class="outline-2">
<h2 id="orgbcc85f0"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org1330849" class="outline-2">
<h2 id="org1330849"><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-org24b6c95" class="outline-2">
<h2 id="org24b6c95"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org5887b37" class="outline-2">
<h2 id="org5887b37"><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.
@ -1578,8 +1578,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org49f2a81" class="outline-2">
<h2 id="org49f2a81"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgb2a5d26" class="outline-2">
<h2 id="orgb2a5d26"><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>
@ -1842,7 +1842,7 @@ 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: 2023-05-05 Fri 13:26</p>
<p class="date">Created: 2023-05-05 Fri 13:55</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>
<!-- 2023-05-05 Fri 13:26 -->
<!-- 2023-05-05 Fri 13:55 -->
<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="#org1a16ade">1. Template for group-related structures in text back end</a></li>
<li><a href="#orge2937d5">2. Template for general structure in text back end</a></li>
<li><a href="#org62319b7">3. Initialize function (constant part)</a></li>
<li><a href="#org1a517f0">4. Deinitialize function (templated part)</a></li>
<li><a href="#org303cad9">5. Flush function (templated part)</a></li>
<li><a href="#orgbc4fede">6. Template for text read a group</a></li>
<li><a href="#org6fc7599">7. Template for text has a group</a></li>
<li><a href="#orgb23d9aa">8. Template for text flush a group</a></li>
<li><a href="#orge112ae1">9. Template for text free memory</a></li>
<li><a href="#orgc0c1424">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org3941f91">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orge82536b">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgee1a4f7">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org5abd367">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org5694b85">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org9b97492">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org96c6aff">17. Source code for the determinant part</a></li>
<li><a href="#org68e9a8f">1. Template for group-related structures in text back end</a></li>
<li><a href="#org25a4484">2. Template for general structure in text back end</a></li>
<li><a href="#org3ea3fc0">3. Initialize function (constant part)</a></li>
<li><a href="#org9493a90">4. Deinitialize function (templated part)</a></li>
<li><a href="#org5697cc4">5. Flush function (templated part)</a></li>
<li><a href="#org36a5ddd">6. Template for text read a group</a></li>
<li><a href="#org8962244">7. Template for text has a group</a></li>
<li><a href="#org00a57f4">8. Template for text flush a group</a></li>
<li><a href="#orgce0b083">9. Template for text free memory</a></li>
<li><a href="#org2d6d1a8">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org0d2f228">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org7f31bc9">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org77c2309">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgac967d9">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org078582a">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org39835b7">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org869c063">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-org1a16ade" class="outline-2">
<h2 id="org1a16ade"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org68e9a8f" class="outline-2">
<h2 id="org68e9a8f"><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-orge2937d5" class="outline-2">
<h2 id="orge2937d5"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org25a4484" class="outline-2">
<h2 id="org25a4484"><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-org62319b7" class="outline-2">
<h2 id="org62319b7"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org3ea3fc0" class="outline-2">
<h2 id="org3ea3fc0"><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>
@ -597,8 +597,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org1a517f0" class="outline-2">
<h2 id="org1a517f0"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org9493a90" class="outline-2">
<h2 id="org9493a90"><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>
@ -620,8 +620,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org303cad9" class="outline-2">
<h2 id="org303cad9"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org5697cc4" class="outline-2">
<h2 id="org5697cc4"><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>
@ -644,8 +644,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-orgbc4fede" class="outline-2">
<h2 id="orgbc4fede"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org36a5ddd" class="outline-2">
<h2 id="org36a5ddd"><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*
@ -871,8 +871,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org6fc7599" class="outline-2">
<h2 id="org6fc7599"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org8962244" class="outline-2">
<h2 id="org8962244"><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>
@ -912,8 +912,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgb23d9aa" class="outline-2">
<h2 id="orgb23d9aa"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org00a57f4" class="outline-2">
<h2 id="org00a57f4"><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>
@ -977,8 +977,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orge112ae1" class="outline-2">
<h2 id="orge112ae1"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-orgce0b083" class="outline-2">
<h2 id="orgce0b083"><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.
@ -1047,8 +1047,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orgc0c1424" class="outline-2">
<h2 id="orgc0c1424"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org2d6d1a8" class="outline-2">
<h2 id="org2d6d1a8"><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>
@ -1111,8 +1111,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org3941f91" class="outline-2">
<h2 id="org3941f91"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org0d2f228" class="outline-2">
<h2 id="org0d2f228"><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.
@ -1208,8 +1208,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orge82536b" class="outline-2">
<h2 id="orge82536b"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org7f31bc9" class="outline-2">
<h2 id="org7f31bc9"><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.
@ -1310,8 +1310,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgee1a4f7" class="outline-2">
<h2 id="orgee1a4f7"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org77c2309" class="outline-2">
<h2 id="org77c2309"><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>
@ -1385,8 +1385,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org5abd367" class="outline-2">
<h2 id="org5abd367"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orgac967d9" class="outline-2">
<h2 id="orgac967d9"><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
@ -1676,8 +1676,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org5694b85" class="outline-2">
<h2 id="org5694b85"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org078582a" class="outline-2">
<h2 id="org078582a"><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
@ -1907,8 +1907,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-org9b97492" class="outline-2">
<h2 id="org9b97492"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org39835b7" class="outline-2">
<h2 id="org39835b7"><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>
@ -1936,8 +1936,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-org96c6aff" class="outline-2">
<h2 id="org96c6aff"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org869c063" class="outline-2">
<h2 id="org869c063"><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
@ -2129,7 +2129,7 @@ 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: 2023-05-05 Fri 13:26</p>
<p class="date">Created: 2023-05-05 Fri 13:55</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

242
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>
<!-- 2023-05-05 Fri 13:26 -->
<!-- 2023-05-05 Fri 13:55 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Data stored in TREXIO</title>
@ -346,70 +346,70 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org5bb2bf7">1. Metadata (metadata group)</a></li>
<li><a href="#orgdec8afa">2. System</a>
<li><a href="#org632e5d4">1. Metadata (metadata group)</a></li>
<li><a href="#orga0e498f">2. System</a>
<ul>
<li><a href="#orgab20162">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#orgbedbbc1">2.2. Cell (cell group)</a></li>
<li><a href="#org639c83e">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orge97d5ab">2.4. Electron (electron group)</a></li>
<li><a href="#org764b2ab">2.5. Ground or excited states (state group)</a></li>
<li><a href="#orgd840d70">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org8e33219">2.2. Cell (cell group)</a></li>
<li><a href="#orgf92ba2a">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgfb60eed">2.4. Electron (electron group)</a></li>
<li><a href="#orga5c2c88">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#orga28058c">3. Basis functions</a>
<li><a href="#org773b3d9">3. Basis functions</a>
<ul>
<li><a href="#org901e9ff">3.1. Basis set (basis group)</a>
<li><a href="#orgd880119">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orge525d1b">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org838fc4f">3.1.2. Plane waves</a></li>
<li><a href="#org758c3ac">3.1.3. Data definitions</a></li>
<li><a href="#org10c6fd5">3.1.4. Example</a></li>
<li><a href="#org5ca1a86">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgd4a0ba5">3.1.2. Plane waves</a></li>
<li><a href="#orgcaf51c4">3.1.3. Data definitions</a></li>
<li><a href="#org091614b">3.1.4. Example</a></li>
</ul>
</li>
<li><a href="#orgb7a063c">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org7d5fdbf">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org8eb1bd9">3.2.1. Example</a></li>
<li><a href="#orgeb17000">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org432a90b">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#orgb003432">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org05201bd">4. Orbitals</a>
<li><a href="#org7ecd9e3">4. Orbitals</a>
<ul>
<li><a href="#org410e19f">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org7bcbd57">4.1. Atomic orbitals (ao group)</a>
<ul>
<li><a href="#ao_one_e">4.1.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
<li><a href="#ao_two_e">4.1.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org45ec2ac">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org970c183">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orga01eaed">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgec94027">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgd2c63e0">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org551c669">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org80182f0">5. Multi-determinant information</a>
<li><a href="#org61a77be">5. Multi-determinant information</a>
<ul>
<li><a href="#org32e39f4">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org200b5d9">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org521ac87">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgdb2da53">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org91c6ee0">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org8e1a335">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org5c63afb">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgc74eb08">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org3dd8d5a">6. Correlation factors</a>
<li><a href="#org6d8a6f3">6. Correlation factors</a>
<ul>
<li><a href="#org59799e0">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org2f23b5c">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org17c1bca">6.1.1. CHAMP</a></li>
<li><a href="#org796bc7e">6.1.2. Mu</a></li>
<li><a href="#org754bd19">6.1.3. Table of values</a></li>
<li><a href="#orgbd3f27c">6.1.1. CHAMP</a></li>
<li><a href="#org86be907">6.1.2. Mu</a></li>
<li><a href="#org3b3dad9">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgf0b0717">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org5cdbf95">7. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -422,8 +422,8 @@ is reversed in the produced <code>trex.json</code> configuration file as the
library is written in C.
</p>
<div id="outline-container-org5bb2bf7" class="outline-2">
<h2 id="org5bb2bf7"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org632e5d4" class="outline-2">
<h2 id="org632e5d4"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect TREXIO files to be archived in open-data repositories,
@ -433,7 +433,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
</p>
<table id="org1a25f5e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd0443d8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -516,19 +516,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
</div>
</div>
<div id="outline-container-orgdec8afa" class="outline-2">
<h2 id="orgdec8afa"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-orga0e498f" class="outline-2">
<h2 id="orga0e498f"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgab20162" class="outline-3">
<h3 id="orgab20162"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orgd840d70" class="outline-3">
<h3 id="orgd840d70"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div class="outline-text-3" id="text-2-1">
<p>
The nuclei are considered as fixed point charges. Coordinates are
given in Cartesian \((x,y,z)\) format.
</p>
<table id="orgc4241b8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org86edaef" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -595,15 +595,15 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-orgbedbbc1" class="outline-3">
<h3 id="orgbedbbc1"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org8e33219" class="outline-3">
<h3 id="org8e33219"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div class="outline-text-3" id="text-2-2">
<p>
3 Lattice vectors to define a box containing the system, for example
used in periodic calculations.
</p>
<table id="orgfdfc27e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6e704ef" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -677,15 +677,15 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-org639c83e" class="outline-3">
<h3 id="org639c83e"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-orgf92ba2a" class="outline-3">
<h3 id="orgf92ba2a"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div class="outline-text-3" id="text-2-3">
<p>
A single $k$-point per TREXIO file can be stored. The $k$-point is
defined in this group.
</p>
<table id="org00c74ba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6322505" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -724,8 +724,8 @@ defined in this group.
</div>
</div>
<div id="outline-container-orge97d5ab" class="outline-3">
<h3 id="orge97d5ab"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-orgfb60eed" class="outline-3">
<h3 id="orgfb60eed"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div class="outline-text-3" id="text-2-4">
<p>
The chemical system consists of nuclei and electrons, where the
@ -744,7 +744,7 @@ the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org345e32b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9645b92" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -790,8 +790,8 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org764b2ab" class="outline-3">
<h3 id="org764b2ab"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-orga5c2c88" class="outline-3">
<h3 id="orga5c2c88"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div class="outline-text-3" id="text-2-5">
<p>
This group contains information about excited states. Since only a
@ -808,7 +808,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="org8e79840" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfe9cacf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -869,16 +869,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-orga28058c" class="outline-2">
<h2 id="orga28058c"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org773b3d9" class="outline-2">
<h2 id="org773b3d9"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org901e9ff" class="outline-3">
<h3 id="org901e9ff"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-orgd880119" class="outline-3">
<h3 id="orgd880119"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div class="outline-text-3" id="text-3-1">
</div>
<div id="outline-container-orge525d1b" class="outline-4">
<h4 id="orge525d1b"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org5ca1a86" class="outline-4">
<h4 id="org5ca1a86"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div class="outline-text-4" id="text-3-1-1">
<p>
We consider here basis functions centered on nuclei. Hence, it is
@ -932,8 +932,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-org838fc4f" class="outline-4">
<h4 id="org838fc4f"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div id="outline-container-orgd4a0ba5" class="outline-4">
<h4 id="orgd4a0ba5"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div class="outline-text-4" id="text-3-1-2">
<p>
A plane wave is defined as
@ -954,10 +954,10 @@ plane waves.
</div>
</div>
<div id="outline-container-org758c3ac" class="outline-4">
<h4 id="org758c3ac"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div id="outline-container-orgcaf51c4" class="outline-4">
<h4 id="orgcaf51c4"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-3">
<table id="orgbb97434" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb0e6b97" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1066,8 +1066,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org10c6fd5" class="outline-4">
<h4 id="org10c6fd5"><span class="section-number-4">3.1.4</span> Example</h4>
<div id="outline-container-org091614b" class="outline-4">
<h4 id="org091614b"><span class="section-number-4">3.1.4</span> Example</h4>
<div class="outline-text-4" id="text-3-1-4">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1145,8 +1145,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgb7a063c" class="outline-3">
<h3 id="orgb7a063c"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org7d5fdbf" class="outline-3">
<h3 id="org7d5fdbf"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div class="outline-text-3" id="text-3-2">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -1180,7 +1180,7 @@ where \(Z_\text{eff}\) is the effective nuclear charge of the center.
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="org27b7339" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org26c3977" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1284,8 +1284,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-org8eb1bd9" class="outline-4">
<h4 id="org8eb1bd9"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orgeb17000" class="outline-4">
<h4 id="orgeb17000"><span class="section-number-4">3.2.1</span> Example</h4>
<div class="outline-text-4" id="text-3-2-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -1348,8 +1348,8 @@ power = [
</div>
</div>
<div id="outline-container-org432a90b" class="outline-3">
<h3 id="org432a90b"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-orgb003432" class="outline-3">
<h3 id="orgb003432"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div class="outline-text-3" id="text-3-3">
<p>
In some applications, such as DFT calculations, integrals have to
@ -1364,7 +1364,7 @@ The structure of this group is adapted for the <a href="https://github.com/dftli
Feel free to submit a PR if you find missing options/functionalities.
</p>
<table id="orgec5c5b1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4ac7018" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1481,12 +1481,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-org05201bd" class="outline-2">
<h2 id="org05201bd"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org7ecd9e3" class="outline-2">
<h2 id="org7ecd9e3"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org410e19f" class="outline-3">
<h3 id="org410e19f"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org7bcbd57" class="outline-3">
<h3 id="org7bcbd57"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div class="outline-text-3" id="text-4-1">
<p>
AOs are defined as
@ -1567,7 +1567,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="org9d268f5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge8e32fe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1619,7 +1619,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-orgb12a5c1" class="outline-4">
<div id="outline-container-orge24facc" class="outline-4">
<h4 id="ao_one_e"><span class="section-number-4">4.1.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_one_e">
<ul class="org-ul">
@ -1637,7 +1637,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org16852d0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org300dbee" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1732,7 +1732,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org07d1b52" class="outline-4">
<div id="outline-container-orgfa9eb4d" class="outline-4">
<h4 id="ao_two_e"><span class="section-number-4">4.1.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_two_e">
<p>
@ -1758,7 +1758,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="orge73dcb9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4494170" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1826,10 +1826,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org45ec2ac" class="outline-3">
<h3 id="org45ec2ac"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org970c183" class="outline-3">
<h3 id="org970c183"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org88b7678" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3c131e1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1916,8 +1916,8 @@ The Cholesky decomposition of the integrals can also be stored:
</table>
</div>
<div id="outline-container-orga01eaed" class="outline-4">
<h4 id="orga01eaed"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-orgd2c63e0" class="outline-4">
<h4 id="orgd2c63e0"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-1">
<p>
The operators as the same as those defined in the
@ -1925,7 +1925,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org228f5a0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc81d801" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2020,8 +2020,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgec94027" class="outline-4">
<h4 id="orgec94027"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org551c669" class="outline-4">
<h4 id="org551c669"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-2">
<p>
The operators are the same as those defined in the
@ -2029,7 +2029,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org02006bd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgee4ea22" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2098,12 +2098,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org80182f0" class="outline-2">
<h2 id="org80182f0"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org61a77be" class="outline-2">
<h2 id="org61a77be"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org32e39f4" class="outline-3">
<h3 id="org32e39f4"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org91c6ee0" class="outline-3">
<h3 id="org91c6ee0"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div class="outline-text-3" id="text-5-1">
<p>
The configuration interaction (CI) wave function \(\Psi\)
@ -2145,7 +2145,7 @@ 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="org2b60400" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9ef07e4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2191,8 +2191,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org200b5d9" class="outline-3">
<h3 id="org200b5d9"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org8e1a335" class="outline-3">
<h3 id="org8e1a335"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div class="outline-text-3" id="text-5-2">
<p>
The configuration interaction (CI) wave function \(\Psi\) can be
@ -2214,7 +2214,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="orga058679" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9c302a3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2260,8 +2260,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org521ac87" class="outline-3">
<h3 id="org521ac87"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org5c63afb" class="outline-3">
<h3 id="org5c63afb"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div class="outline-text-3" id="text-5-3">
<p>
The wave function may be expressed in terms of action of the cluster
@ -2332,7 +2332,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org0a1a96e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8e5a254" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2413,8 +2413,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-orgdb2da53" class="outline-3">
<h3 id="orgdb2da53"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-orgc74eb08" class="outline-3">
<h3 id="orgc74eb08"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div class="outline-text-3" id="text-5-4">
<p>
The reduced density matrices are defined in the basis of molecular
@ -2486,7 +2486,7 @@ 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="org6367256" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org262ebfa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2617,12 +2617,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org3dd8d5a" class="outline-2">
<h2 id="org3dd8d5a"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org6d8a6f3" class="outline-2">
<h2 id="org6d8a6f3"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org59799e0" class="outline-3">
<h3 id="org59799e0"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org2f23b5c" class="outline-3">
<h3 id="org2f23b5c"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div class="outline-text-3" id="text-6-1">
<p>
The Jastrow factor is an $N$-electron function which multiplies the CI
@ -2647,8 +2647,8 @@ following:
</ul>
</div>
<div id="outline-container-org17c1bca" class="outline-4">
<h4 id="org17c1bca"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orgbd3f27c" class="outline-4">
<h4 id="orgbd3f27c"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div class="outline-text-4" id="text-6-1-1">
<p>
The first form of Jastrow factor is the one used in
@ -2749,8 +2749,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-org796bc7e" class="outline-4">
<h4 id="org796bc7e"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org86be907" class="outline-4">
<h4 id="org86be907"><span class="section-number-4">6.1.2</span> Mu</h4>
<div class="outline-text-4" id="text-6-1-2">
<p>
<a href="https://aip.scitation.org/doi/10.1063/5.0044683">Mu-Jastrow</a> is based on a one-parameter correlation factor that has
@ -2847,10 +2847,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org754bd19" class="outline-4">
<h4 id="org754bd19"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div id="outline-container-org3b3dad9" class="outline-4">
<h4 id="org3b3dad9"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div class="outline-text-4" id="text-6-1-3">
<table id="orgd55076e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1f4c38d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2954,8 +2954,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-orgf0b0717" class="outline-2">
<h2 id="orgf0b0717"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org5cdbf95" class="outline-2">
<h2 id="org5cdbf95"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-7">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -2969,7 +2969,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="org62fcdf1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd5def7d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3024,7 +3024,7 @@ 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: 2023-05-05 Fri 13:26</p>
<p class="date">Created: 2023-05-05 Fri 13:55</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>