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README.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 16:23 -->
<!-- 2024-08-17 Sat 16:24 -->
<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>
@ -406,7 +406,7 @@ 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: 2024-08-17 Sat 16:23</p>
<p class="date">Created: 2024-08-17 Sat 16:24</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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examples.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 16:23 -->
<!-- 2024-08-17 Sat 16:24 -->
<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="#org9e06a8b">1. Writing nuclear coordinates</a>
<li><a href="#org4432720">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orgb878a43">1.1. C</a></li>
<li><a href="#org0e7711e">1.2. Python</a></li>
<li><a href="#orgd0d1181">1.3. Fortran</a></li>
<li><a href="#orgc1050e9">1.1. C</a></li>
<li><a href="#org54162a4">1.2. Python</a></li>
<li><a href="#org11060c9">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#orgbe645f3">2. Accessing sparse quantities (integrals)</a>
<li><a href="#orga3a7444">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org567acb9">2.1. Fortran</a>
<li><a href="#org015deaa">2.1. Fortran</a>
<ul>
<li><a href="#orge6c947d">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org45b03e3">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org1e27d72">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org34f8a20">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgfa3088e">2.1.5. Allocate memory</a></li>
<li><a href="#org46e3a0b">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org72bde0f">2.1.7. Read two-electron quantities</a>
<li><a href="#org06f563d">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org786fa84">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org9a6a6a7">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgcf41425">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgd42d937">2.1.5. Allocate memory</a></li>
<li><a href="#org4f9762c">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org073952e">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org1eea73e">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org4ef2c3f">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org059585d">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org358cd9d">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org4b66373">2.1.8. Compute the energy</a></li>
<li><a href="#orge88e608">2.1.9. Terminate</a></li>
<li><a href="#org423cb4b">2.1.8. Compute the energy</a></li>
<li><a href="#org3c612b8">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org26ca29b">2.2. Python</a>
<li><a href="#org9413faf">2.2. Python</a>
<ul>
<li><a href="#org291ae5e">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga5bf50b">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#orgc7d6dd7">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org88e458e">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgff1bb69">2.2.5. Read two-electron quantities</a>
<li><a href="#orgd7371b7">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org34a2080">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org3147114">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org673dd51">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org990e4fd">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#orgc09d3cf">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgbc13001">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org2f7ddb9">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org9b06dc7">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org2f11685">2.2.6. Compute the energy</a></li>
<li><a href="#orgce3c601">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgfab9d63">3. Reading determinants</a>
<li><a href="#org550af38">3. Reading determinants</a>
<ul>
<li><a href="#orgc75816f">3.1. Fortran</a></li>
<li><a href="#org57bab0f">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org9e06a8b" class="outline-2">
<h2 id="org9e06a8b"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org4432720" class="outline-2">
<h2 id="org4432720"><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-orgb878a43" class="outline-3">
<h3 id="orgb878a43"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-orgc1050e9" class="outline-3">
<h3 id="orgc1050e9"><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-org0e7711e" class="outline-3">
<h3 id="org0e7711e"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org54162a4" class="outline-3">
<h3 id="org54162a4"><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-orgd0d1181" class="outline-3">
<h3 id="orgd0d1181"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-org11060c9" class="outline-3">
<h3 id="org11060c9"><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-orgbe645f3" class="outline-2">
<h2 id="orgbe645f3"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orga3a7444" class="outline-2">
<h2 id="orga3a7444"><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-org567acb9" class="outline-3">
<h3 id="org567acb9"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org015deaa" class="outline-3">
<h3 id="org015deaa"><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-orge6c947d" class="outline-4">
<h4 id="orge6c947d"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org06f563d" class="outline-4">
<h4 id="org06f563d"><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-org45b03e3" class="outline-4">
<h4 id="org45b03e3"><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-org786fa84" class="outline-4">
<h4 id="org786fa84"><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-org1e27d72" class="outline-4">
<h4 id="org1e27d72"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org9a6a6a7" class="outline-4">
<h4 id="org9a6a6a7"><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-org34f8a20" class="outline-4">
<h4 id="org34f8a20"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgcf41425" class="outline-4">
<h4 id="orgcf41425"><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-orgfa3088e" class="outline-4">
<h4 id="orgfa3088e"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-orgd42d937" class="outline-4">
<h4 id="orgd42d937"><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-org46e3a0b" class="outline-4">
<h4 id="org46e3a0b"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org4f9762c" class="outline-4">
<h4 id="org4f9762c"><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-org72bde0f" class="outline-4">
<h4 id="org72bde0f"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org073952e" class="outline-4">
<h4 id="org073952e"><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-org1eea73e" class="outline-5">
<h5 id="org1eea73e"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org059585d" class="outline-5">
<h5 id="org059585d"><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-org4ef2c3f" class="outline-5">
<h5 id="org4ef2c3f"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org358cd9d" class="outline-5">
<h5 id="org358cd9d"><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-org4b66373" class="outline-4">
<h4 id="org4b66373"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org423cb4b" class="outline-4">
<h4 id="org423cb4b"><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-orge88e608" class="outline-4">
<h4 id="orge88e608"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org3c612b8" class="outline-4">
<h4 id="org3c612b8"><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-org26ca29b" class="outline-3">
<h3 id="org26ca29b"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org9413faf" class="outline-3">
<h3 id="org9413faf"><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-org291ae5e" class="outline-4">
<h4 id="org291ae5e"><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-orgd7371b7" class="outline-4">
<h4 id="orgd7371b7"><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-orga5bf50b" class="outline-4">
<h4 id="orga5bf50b"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org34a2080" class="outline-4">
<h4 id="org34a2080"><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-orgc7d6dd7" class="outline-4">
<h4 id="orgc7d6dd7"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org3147114" class="outline-4">
<h4 id="org3147114"><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-org88e458e" class="outline-4">
<h4 id="org88e458e"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org673dd51" class="outline-4">
<h4 id="org673dd51"><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-orgff1bb69" class="outline-4">
<h4 id="orgff1bb69"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-org990e4fd" class="outline-4">
<h4 id="org990e4fd"><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-orgc09d3cf" class="outline-5">
<h5 id="orgc09d3cf"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org2f7ddb9" class="outline-5">
<h5 id="org2f7ddb9"><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-orgbc13001" class="outline-5">
<h5 id="orgbc13001"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-org9b06dc7" class="outline-5">
<h5 id="org9b06dc7"><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-org2f11685" class="outline-4">
<h4 id="org2f11685"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-orgce3c601" class="outline-4">
<h4 id="orgce3c601"><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-orgfab9d63" class="outline-2">
<h2 id="orgfab9d63"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org550af38" class="outline-2">
<h2 id="org550af38"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgc75816f" class="outline-3">
<h3 id="orgc75816f"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org57bab0f" class="outline-3">
<h3 id="org57bab0f"><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: 2024-08-17 Sat 16:23</p>
<p class="date">Created: 2024-08-17 Sat 16:24</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 16:23 -->
<!-- 2024-08-17 Sat 16:24 -->
<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>
@ -406,7 +406,7 @@ 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: 2024-08-17 Sat 16:23</p>
<p class="date">Created: 2024-08-17 Sat 16:24</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 16:23 -->
<!-- 2024-08-17 Sat 16:24 -->
<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: 2024-08-17 Sat 16:23</p>
<p class="date">Created: 2024-08-17 Sat 16:24</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
lib.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 16:23 -->
<!-- 2024-08-17 Sat 16:24 -->
<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="#org718c718">1. Format specification</a>
<li><a href="#org89953cc">1. Format specification</a>
<ul>
<li><a href="#org3aa6749">1.1. Organization of the data</a></li>
<li><a href="#org16b6cd5">1.2. Data types</a></li>
<li><a href="#org5952286">1.1. Organization of the data</a></li>
<li><a href="#org2715905">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#orgf861d79">2. The TREXIO library</a>
<li><a href="#org6aac0be">2. The TREXIO library</a>
<ul>
<li><a href="#org45c57da">2.1. The front-end</a></li>
<li><a href="#org409bf17">2.2. The back-end</a></li>
<li><a href="#org1b288f9">2.3. Supported languages</a></li>
<li><a href="#org2414377">2.4. Source code generation and documentation</a></li>
<li><a href="#org78915d6">2.5. Availability</a></li>
<li><a href="#org57378c4">2.1. The front-end</a></li>
<li><a href="#orgfa40b93">2.2. The back-end</a></li>
<li><a href="#orga71cfe0">2.3. Supported languages</a></li>
<li><a href="#org1e07e07">2.4. Source code generation and documentation</a></li>
<li><a href="#orgb31f629">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org718c718" class="outline-2">
<h2 id="org718c718"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org89953cc" class="outline-2">
<h2 id="org89953cc"><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-org3aa6749" class="outline-3">
<h3 id="org3aa6749"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org5952286" class="outline-3">
<h3 id="org5952286"><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-org16b6cd5" class="outline-3">
<h3 id="org16b6cd5"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org2715905" class="outline-3">
<h3 id="org2715905"><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-orgf861d79" class="outline-2">
<h2 id="orgf861d79"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-org6aac0be" class="outline-2">
<h2 id="org6aac0be"><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-org45c57da" class="outline-3">
<h3 id="org45c57da"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-org57378c4" class="outline-3">
<h3 id="org57378c4"><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-org409bf17" class="outline-3">
<h3 id="org409bf17"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-orgfa40b93" class="outline-3">
<h3 id="orgfa40b93"><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-org1b288f9" class="outline-3">
<h3 id="org1b288f9"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-orga71cfe0" class="outline-3">
<h3 id="orga71cfe0"><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-org2414377" class="outline-3">
<h3 id="org2414377"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org1e07e07" class="outline-3">
<h3 id="org1e07e07"><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-org78915d6" class="outline-3">
<h3 id="org78915d6"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-orgb31f629" class="outline-3">
<h3 id="orgb31f629"><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: 2024-08-17 Sat 16:23</p>
<p class="date">Created: 2024-08-17 Sat 16:24</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 16:23 -->
<!-- 2024-08-17 Sat 16:24 -->
<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="#org44600c2">1. Template for HDF5 definitions</a></li>
<li><a href="#org98f18d2">2. Template for HDF5 structures</a></li>
<li><a href="#org75698f8">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgc009265">4. Template for HDF5 has a group</a></li>
<li><a href="#org62e5dd9">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgf6789b3">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgfa37abd">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org96d5811">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orge362d6c">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org839e9ea">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org2fa8bc6">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org0244c00">12. Source code for the determinant part</a></li>
<li><a href="#orgeed2df2">13. Helper functions</a></li>
<li><a href="#org4f9e110">1. Template for HDF5 definitions</a></li>
<li><a href="#org328fefe">2. Template for HDF5 structures</a></li>
<li><a href="#orgf016905">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgfc5d30a">4. Template for HDF5 has a group</a></li>
<li><a href="#org72c1db9">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgefc19c2">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgbfa2bbe">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgce6b670">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org7e9035c">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgc4d4a0d">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org042e3c6">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org31315a4">12. Source code for the determinant part</a></li>
<li><a href="#org3303df4">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org44600c2" class="outline-2">
<h2 id="org44600c2"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org4f9e110" class="outline-2">
<h2 id="org4f9e110"><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-org98f18d2" class="outline-2">
<h2 id="org98f18d2"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org328fefe" class="outline-2">
<h2 id="org328fefe"><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-org75698f8" class="outline-2">
<h2 id="org75698f8"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgf016905" class="outline-2">
<h2 id="orgf016905"><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-orgc009265" class="outline-2">
<h2 id="orgc009265"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orgfc5d30a" class="outline-2">
<h2 id="orgfc5d30a"><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-org62e5dd9" class="outline-2">
<h2 id="org62e5dd9"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org72c1db9" class="outline-2">
<h2 id="org72c1db9"><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-orgf6789b3" class="outline-2">
<h2 id="orgf6789b3"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgefc19c2" class="outline-2">
<h2 id="orgefc19c2"><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-orgfa37abd" class="outline-2">
<h2 id="orgfa37abd"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orgbfa2bbe" class="outline-2">
<h2 id="orgbfa2bbe"><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
@ -976,8 +976,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org96d5811" class="outline-2">
<h2 id="org96d5811"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-orgce6b670" class="outline-2">
<h2 id="orgce6b670"><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.
@ -1111,8 +1111,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-orge362d6c" class="outline-2">
<h2 id="orge362d6c"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org7e9035c" class="outline-2">
<h2 id="org7e9035c"><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>
@ -1309,8 +1309,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org839e9ea" class="outline-2">
<h2 id="org839e9ea"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgc4d4a0d" class="outline-2">
<h2 id="orgc4d4a0d"><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>
@ -1437,8 +1437,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
</div>
<div id="outline-container-org2fa8bc6" class="outline-2">
<h2 id="org2fa8bc6"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org042e3c6" class="outline-2">
<h2 id="org042e3c6"><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
@ -1478,8 +1478,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org0244c00" class="outline-2">
<h2 id="org0244c00"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org31315a4" class="outline-2">
<h2 id="org31315a4"><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.
@ -1581,8 +1581,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-orgeed2df2" class="outline-2">
<h2 id="orgeed2df2"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org3303df4" class="outline-2">
<h2 id="org3303df4"><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>
@ -1850,7 +1850,7 @@ 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: 2024-08-17 Sat 16:23</p>
<p class="date">Created: 2024-08-17 Sat 16:24</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgd856766">1. Template for group-related structures in text back end</a></li>
<li><a href="#org17250c5">2. Template for general structure in text back end</a></li>
<li><a href="#org7a228b7">3. Initialize function (constant part)</a></li>
<li><a href="#org15f2876">4. Deinitialize function (templated part)</a></li>
<li><a href="#org7584c92">5. Flush function (templated part)</a></li>
<li><a href="#org807b3a8">6. Template for text read a group</a></li>
<li><a href="#org1c34cb3">7. Template for text has a group</a></li>
<li><a href="#org90edcd7">8. Template for text flush a group</a></li>
<li><a href="#org39532db">9. Template for text free memory</a></li>
<li><a href="#org412647e">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgd867664">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org056b4e7">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org4f5bb44">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org3ca6f34">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org2d670ca">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org10ec4ab">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orge975dc3">17. Source code for the determinant part</a></li>
<li><a href="#org3bcf7fb">1. Template for group-related structures in text back end</a></li>
<li><a href="#org3543a0b">2. Template for general structure in text back end</a></li>
<li><a href="#orgf1ecfd6">3. Initialize function (constant part)</a></li>
<li><a href="#orgb5d0f59">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgc55be76">5. Flush function (templated part)</a></li>
<li><a href="#orgab73191">6. Template for text read a group</a></li>
<li><a href="#orgf7c88ca">7. Template for text has a group</a></li>
<li><a href="#org0203335">8. Template for text flush a group</a></li>
<li><a href="#orgb7331db">9. Template for text free memory</a></li>
<li><a href="#org73c769d">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgc792520">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org7fb3475">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org078b87c">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgcae657a">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org665b61c">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org562e252">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org44e6d68">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-orgd856766" class="outline-2">
<h2 id="orgd856766"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org3bcf7fb" class="outline-2">
<h2 id="org3bcf7fb"><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-org17250c5" class="outline-2">
<h2 id="org17250c5"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org3543a0b" class="outline-2">
<h2 id="org3543a0b"><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-org7a228b7" class="outline-2">
<h2 id="org7a228b7"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-orgf1ecfd6" class="outline-2">
<h2 id="orgf1ecfd6"><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>
@ -601,8 +601,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org15f2876" class="outline-2">
<h2 id="org15f2876"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgb5d0f59" class="outline-2">
<h2 id="orgb5d0f59"><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>
@ -624,8 +624,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org7584c92" class="outline-2">
<h2 id="org7584c92"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-orgc55be76" class="outline-2">
<h2 id="orgc55be76"><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>
@ -648,8 +648,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org807b3a8" class="outline-2">
<h2 id="org807b3a8"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orgab73191" class="outline-2">
<h2 id="orgab73191"><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*
@ -875,8 +875,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org1c34cb3" class="outline-2">
<h2 id="org1c34cb3"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-orgf7c88ca" class="outline-2">
<h2 id="orgf7c88ca"><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>
@ -916,8 +916,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org90edcd7" class="outline-2">
<h2 id="org90edcd7"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org0203335" class="outline-2">
<h2 id="org0203335"><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>
@ -981,8 +981,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org39532db" class="outline-2">
<h2 id="org39532db"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-orgb7331db" class="outline-2">
<h2 id="orgb7331db"><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.
@ -1051,8 +1051,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org412647e" class="outline-2">
<h2 id="org412647e"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org73c769d" class="outline-2">
<h2 id="org73c769d"><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>
@ -1115,8 +1115,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orgd867664" class="outline-2">
<h2 id="orgd867664"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgc792520" class="outline-2">
<h2 id="orgc792520"><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.
@ -1212,8 +1212,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org056b4e7" class="outline-2">
<h2 id="org056b4e7"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org7fb3475" class="outline-2">
<h2 id="org7fb3475"><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.
@ -1314,8 +1314,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org4f5bb44" class="outline-2">
<h2 id="org4f5bb44"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org078b87c" class="outline-2">
<h2 id="org078b87c"><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>
@ -1389,8 +1389,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org3ca6f34" class="outline-2">
<h2 id="org3ca6f34"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orgcae657a" class="outline-2">
<h2 id="orgcae657a"><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
@ -1680,8 +1680,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org2d670ca" class="outline-2">
<h2 id="org2d670ca"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org665b61c" class="outline-2">
<h2 id="org665b61c"><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
@ -1911,8 +1911,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-org10ec4ab" class="outline-2">
<h2 id="org10ec4ab"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org562e252" class="outline-2">
<h2 id="org562e252"><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>
@ -1940,8 +1940,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-orge975dc3" class="outline-2">
<h2 id="orge975dc3"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org44e6d68" class="outline-2">
<h2 id="org44e6d68"><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
@ -2133,7 +2133,7 @@ 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: 2024-08-17 Sat 16:23</p>
<p class="date">Created: 2024-08-17 Sat 16:24</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2024-08-17 Sat 16:23 -->
<!-- 2024-08-17 Sat 16:24 -->
<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>
@ -346,72 +346,72 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgc9144cd">1. Metadata (metadata group)</a></li>
<li><a href="#org3b0b96c">2. System</a>
<li><a href="#org2652472">1. Metadata (metadata group)</a></li>
<li><a href="#org6163624">2. System</a>
<ul>
<li><a href="#orgaf29d0f">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org5c21f6b">2.2. Cell (cell group)</a></li>
<li><a href="#org6ae3162">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org0748bfd">2.4. Electron (electron group)</a></li>
<li><a href="#org3ee9861">2.5. Ground or excited states (state group)</a></li>
<li><a href="#orgc150c7f">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#orgcd918b7">2.2. Cell (cell group)</a></li>
<li><a href="#org861574d">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org207cea2">2.4. Electron (electron group)</a></li>
<li><a href="#org9b4b120">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org5eb0c45">3. Basis functions</a>
<li><a href="#orgd9238b2">3. Basis functions</a>
<ul>
<li><a href="#org86915a5">3.1. Basis set (basis group)</a>
<li><a href="#orgafbe142">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org4a90815">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgcdd12bd">3.1.2. Numerical orbitals</a></li>
<li><a href="#orgec0af68">3.1.3. Plane waves</a></li>
<li><a href="#orge71171e">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org11c91c1">3.1.5. Data definitions</a></li>
<li><a href="#org36c09d6">3.1.6. Example</a></li>
<li><a href="#orgb74215c">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org8b56a2a">3.1.2. Numerical orbitals</a></li>
<li><a href="#orgd21b8f4">3.1.3. Plane waves</a></li>
<li><a href="#orgcac8d26">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org4f9170e">3.1.5. Data definitions</a></li>
<li><a href="#orga45f777">3.1.6. Example</a></li>
</ul>
</li>
<li><a href="#org7b84c1d">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org95f8e98">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org7e8c7ae">3.2.1. Example</a></li>
<li><a href="#org09e92eb">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#orgb387550">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#orga721df8">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#orgd125fe0">4. Orbitals</a>
<li><a href="#org0073650">4. Orbitals</a>
<ul>
<li><a href="#org33b91d1">4.1. Atomic orbitals (ao group)</a>
<li><a href="#orgb73da54">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="#org77ca964">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org5e1e585">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org4c79f67">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orge937947">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgf2569a6">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org306118f">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgb26260a">5. Multi-determinant information</a>
<li><a href="#org6d8ef92">5. Multi-determinant information</a>
<ul>
<li><a href="#org92fd042">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgabb4cb5">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org307362a">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orge03b148">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org3c8d556">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgaad53ff">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orge367e4d">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org1aeea13">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#orgb316b75">6. Correlation factors</a>
<li><a href="#org3fca32a">6. Correlation factors</a>
<ul>
<li><a href="#org4e5282b">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org888bfcf">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org89f15d6">6.1.1. CHAMP</a></li>
<li><a href="#orgedbd8fa">6.1.2. Mu</a></li>
<li><a href="#org0859c27">6.1.3. Table of values</a></li>
<li><a href="#org3f14853">6.1.1. CHAMP</a></li>
<li><a href="#org91b1355">6.1.2. Mu</a></li>
<li><a href="#org504318b">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org530e2d9">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org25faab1">7. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -433,8 +433,8 @@ contiguous in memory. In the row-major representation, <code>A[i,j]</code> and
<code>A[i,j+1]</code> are contiguous.
</p>
<div id="outline-container-orgc9144cd" class="outline-2">
<h2 id="orgc9144cd"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org2652472" class="outline-2">
<h2 id="org2652472"><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,
@ -444,7 +444,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
</p>
<table id="orgabb21b1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2807601" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -537,19 +537,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
</div>
</div>
<div id="outline-container-org3b0b96c" class="outline-2">
<h2 id="org3b0b96c"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org6163624" class="outline-2">
<h2 id="org6163624"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgaf29d0f" class="outline-3">
<h3 id="orgaf29d0f"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orgc150c7f" class="outline-3">
<h3 id="orgc150c7f"><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="orgdd30748" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org57275ca" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -634,15 +634,15 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org5c21f6b" class="outline-3">
<h3 id="org5c21f6b"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-orgcd918b7" class="outline-3">
<h3 id="orgcd918b7"><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="orgdc07ab3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgda3208d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -726,10 +726,10 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-org6ae3162" class="outline-3">
<h3 id="org6ae3162"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org861574d" class="outline-3">
<h3 id="org861574d"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div class="outline-text-3" id="text-2-3">
<table id="orgdb80ddb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgca43468" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -789,8 +789,8 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-org0748bfd" class="outline-3">
<h3 id="org0748bfd"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org207cea2" class="outline-3">
<h3 id="org207cea2"><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
@ -809,7 +809,7 @@ the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org1d0d494" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9be2b7d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -861,8 +861,8 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org3ee9861" class="outline-3">
<h3 id="org3ee9861"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org9b4b120" class="outline-3">
<h3 id="org9b4b120"><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
@ -879,7 +879,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="orgc9b0730" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd957ef0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -956,16 +956,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-org5eb0c45" class="outline-2">
<h2 id="org5eb0c45"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-orgd9238b2" class="outline-2">
<h2 id="orgd9238b2"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org86915a5" class="outline-3">
<h3 id="org86915a5"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-orgafbe142" class="outline-3">
<h3 id="orgafbe142"><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-org4a90815" class="outline-4">
<h4 id="org4a90815"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-orgb74215c" class="outline-4">
<h4 id="orgb74215c"><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
@ -1019,8 +1019,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-orgcdd12bd" class="outline-4">
<h4 id="orgcdd12bd"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-org8b56a2a" class="outline-4">
<h4 id="org8b56a2a"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div class="outline-text-4" id="text-3-1-2">
<p>
Trexio supports numerical atom centered orbitals. The implementation is
@ -1084,8 +1084,8 @@ reimplement them with consideration for its specific needs.
</div>
</div>
<div id="outline-container-orgec0af68" class="outline-4">
<h4 id="orgec0af68"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-orgd21b8f4" class="outline-4">
<h4 id="orgd21b8f4"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div class="outline-text-4" id="text-3-1-3">
<p>
A plane wave is defined as
@ -1106,8 +1106,8 @@ plane waves.
</div>
</div>
<div id="outline-container-orge71171e" class="outline-4">
<h4 id="orge71171e"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div id="outline-container-orgcac8d26" class="outline-4">
<h4 id="orgcac8d26"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div class="outline-text-4" id="text-3-1-4">
<p>
Basis functions can be made oscillating as
@ -1129,10 +1129,10 @@ Oscillation kind can be:
</div>
</div>
<div id="outline-container-org11c91c1" class="outline-4">
<h4 id="org11c91c1"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div id="outline-container-org4f9170e" class="outline-4">
<h4 id="org4f9170e"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-5">
<table id="org38dbb8e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfb31119" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1384,8 +1384,8 @@ Oscillation kind can be:
</div>
</div>
<div id="outline-container-org36c09d6" class="outline-4">
<h4 id="org36c09d6"><span class="section-number-4">3.1.6</span> Example</h4>
<div id="outline-container-orga45f777" class="outline-4">
<h4 id="orga45f777"><span class="section-number-4">3.1.6</span> Example</h4>
<div class="outline-text-4" id="text-3-1-6">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1463,8 +1463,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org7b84c1d" class="outline-3">
<h3 id="org7b84c1d"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org95f8e98" class="outline-3">
<h3 id="org95f8e98"><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
@ -1498,7 +1498,7 @@ 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="org38a89b0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf52ee7a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1613,8 +1613,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-org7e8c7ae" class="outline-4">
<h4 id="org7e8c7ae"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-org09e92eb" class="outline-4">
<h4 id="org09e92eb"><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
@ -1677,8 +1677,8 @@ power = [
</div>
</div>
<div id="outline-container-orgb387550" class="outline-3">
<h3 id="orgb387550"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-orga721df8" class="outline-3">
<h3 id="orga721df8"><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
@ -1693,7 +1693,7 @@ 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="org763bc6a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org414c7a5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1826,12 +1826,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-orgd125fe0" class="outline-2">
<h2 id="orgd125fe0"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org0073650" class="outline-2">
<h2 id="org0073650"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org33b91d1" class="outline-3">
<h3 id="org33b91d1"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-orgb73da54" class="outline-3">
<h3 id="orgb73da54"><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
@ -1912,7 +1912,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="org5d1a8c4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org03948c1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1971,7 +1971,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org44b9e1b" class="outline-4">
<div id="outline-container-org3558e34" 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">
@ -1989,7 +1989,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org1f1c3b1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgceed872" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2097,7 +2097,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org0f7477b" class="outline-4">
<div id="outline-container-org3047e63" 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>
@ -2123,7 +2123,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="orgf2bf2b9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4adc64a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2200,10 +2200,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org77ca964" class="outline-3">
<h3 id="org77ca964"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org5e1e585" class="outline-3">
<h3 id="org5e1e585"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org2ba2152" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1c6e7c9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2319,8 +2319,8 @@ is the number of spin-orbitals, twice the number of spatial orbitals.
</div>
<div id="outline-container-org4c79f67" class="outline-4">
<h4 id="org4c79f67"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-orgf2569a6" class="outline-4">
<h4 id="orgf2569a6"><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
@ -2328,7 +2328,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org769394f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2f74ca6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2436,8 +2436,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orge937947" class="outline-4">
<h4 id="orge937947"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org306118f" class="outline-4">
<h4 id="org306118f"><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
@ -2445,7 +2445,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgff00368" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9841fc8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2523,12 +2523,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgb26260a" class="outline-2">
<h2 id="orgb26260a"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org6d8ef92" class="outline-2">
<h2 id="org6d8ef92"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org92fd042" class="outline-3">
<h3 id="org92fd042"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org3c8d556" class="outline-3">
<h3 id="org3c8d556"><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 \(\Psi\)
@ -2570,7 +2570,7 @@ 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="org195ed0e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd6d9e4d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2622,8 +2622,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-orgabb4cb5" class="outline-3">
<h3 id="orgabb4cb5"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-orgaad53ff" class="outline-3">
<h3 id="orgaad53ff"><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
@ -2645,7 +2645,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org7e182e7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org613d041" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2697,8 +2697,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org307362a" class="outline-3">
<h3 id="org307362a"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orge367e4d" class="outline-3">
<h3 id="orge367e4d"><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
@ -2769,7 +2769,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org2221953" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgeffae88" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2861,8 +2861,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-orge03b148" class="outline-3">
<h3 id="orge03b148"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org1aeea13" class="outline-3">
<h3 id="org1aeea13"><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
@ -2934,7 +2934,7 @@ 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="org44783e9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5d7fd52" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3099,12 +3099,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-orgb316b75" class="outline-2">
<h2 id="orgb316b75"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org3fca32a" class="outline-2">
<h2 id="org3fca32a"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org4e5282b" class="outline-3">
<h3 id="org4e5282b"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org888bfcf" class="outline-3">
<h3 id="org888bfcf"><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
@ -3129,8 +3129,8 @@ following:
</ul>
</div>
<div id="outline-container-org89f15d6" class="outline-4">
<h4 id="org89f15d6"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org3f14853" class="outline-4">
<h4 id="org3f14853"><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
@ -3231,8 +3231,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-orgedbd8fa" class="outline-4">
<h4 id="orgedbd8fa"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org91b1355" class="outline-4">
<h4 id="org91b1355"><span class="section-number-4">6.1.2</span> Mu</h4>
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<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
@ -3329,10 +3329,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h4 id="org0859c27"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="org504318b"><span class="section-number-4">6.1.3</span> Table of values</h4>
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@ -3450,8 +3450,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h2 id="org530e2d9"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org25faab1"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -3465,7 +3465,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3527,7 +3527,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
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<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-08-17 Sat 16:23</p>
<p class="date">Created: 2024-08-17 Sat 16:24</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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