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README.html
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<head>
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<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: 2024-11-10 Sun 20:35</p>
<p class="date">Created: 2024-11-10 Sun 20:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2024-11-10 Sun 20:35 -->
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<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="#orga7895b3">1. Writing nuclear coordinates</a>
<li><a href="#orga0063aa">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orgcfba583">1.1. C</a></li>
<li><a href="#orge36c535">1.2. Python</a></li>
<li><a href="#orgbfac495">1.3. Fortran</a></li>
<li><a href="#org7217a53">1.1. C</a></li>
<li><a href="#org38b1b28">1.2. Python</a></li>
<li><a href="#org7407679">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org84d912b">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org0c15b8e">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org8d8f6d5">2.1. Fortran</a>
<li><a href="#org719d9c1">2.1. Fortran</a>
<ul>
<li><a href="#org48cea96">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org23427af">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgcdd1da2">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgdaeb7ab">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org6a65096">2.1.5. Allocate memory</a></li>
<li><a href="#org9fed705">2.1.6. Read one-electron quantities</a></li>
<li><a href="#orgadebc3e">2.1.7. Read two-electron quantities</a>
<li><a href="#org82f22bc">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orge1eba2b">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgef2ebc5">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org2f0c3e8">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgde0974b">2.1.5. Allocate memory</a></li>
<li><a href="#org8de66c7">2.1.6. Read one-electron quantities</a></li>
<li><a href="#orgcf81609">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org04eaeb8">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org32d4c11">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org16d4e04">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org6cbfb24">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org62bdc6b">2.1.8. Compute the energy</a></li>
<li><a href="#orga08e49a">2.1.9. Terminate</a></li>
<li><a href="#org2ad18d9">2.1.8. Compute the energy</a></li>
<li><a href="#orgf5c1f39">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org8253e3b">2.2. Python</a>
<li><a href="#org7480326">2.2. Python</a>
<ul>
<li><a href="#orgf28dd42">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org331ea52">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org5d05daa">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org5f28d26">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org4bea6a9">2.2.5. Read two-electron quantities</a>
<li><a href="#org65f77da">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org2d5d0cf">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org18e4a34">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#orgf473c91">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org5c46c29">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#org86a19f6">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org00bde6f">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org535c348">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org76a8a96">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgf6d4ed4">2.2.6. Compute the energy</a></li>
<li><a href="#org5b0ece2">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgfc159ac">3. Reading determinants</a>
<li><a href="#orgee3e03c">3. Reading determinants</a>
<ul>
<li><a href="#org0f3b238">3.1. Fortran</a></li>
<li><a href="#orga82905e">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orga7895b3" class="outline-2">
<h2 id="orga7895b3"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-orga0063aa" class="outline-2">
<h2 id="orga0063aa"><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-orgcfba583" class="outline-3">
<h3 id="orgcfba583"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org7217a53" class="outline-3">
<h3 id="org7217a53"><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-orge36c535" class="outline-3">
<h3 id="orge36c535"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org38b1b28" class="outline-3">
<h3 id="org38b1b28"><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-orgbfac495" class="outline-3">
<h3 id="orgbfac495"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-org7407679" class="outline-3">
<h3 id="org7407679"><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-org84d912b" class="outline-2">
<h2 id="org84d912b"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org0c15b8e" class="outline-2">
<h2 id="org0c15b8e"><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-org8d8f6d5" class="outline-3">
<h3 id="org8d8f6d5"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org719d9c1" class="outline-3">
<h3 id="org719d9c1"><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-org48cea96" class="outline-4">
<h4 id="org48cea96"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org82f22bc" class="outline-4">
<h4 id="org82f22bc"><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-org23427af" class="outline-4">
<h4 id="org23427af"><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-orge1eba2b" class="outline-4">
<h4 id="orge1eba2b"><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-orgcdd1da2" class="outline-4">
<h4 id="orgcdd1da2"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgef2ebc5" class="outline-4">
<h4 id="orgef2ebc5"><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-orgdaeb7ab" class="outline-4">
<h4 id="orgdaeb7ab"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org2f0c3e8" class="outline-4">
<h4 id="org2f0c3e8"><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-org6a65096" class="outline-4">
<h4 id="org6a65096"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-orgde0974b" class="outline-4">
<h4 id="orgde0974b"><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-org9fed705" class="outline-4">
<h4 id="org9fed705"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org8de66c7" class="outline-4">
<h4 id="org8de66c7"><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-orgadebc3e" class="outline-4">
<h4 id="orgadebc3e"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgcf81609" class="outline-4">
<h4 id="orgcf81609"><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-org04eaeb8" class="outline-5">
<h5 id="org04eaeb8"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org16d4e04" class="outline-5">
<h5 id="org16d4e04"><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-org32d4c11" class="outline-5">
<h5 id="org32d4c11"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org6cbfb24" class="outline-5">
<h5 id="org6cbfb24"><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-org62bdc6b" class="outline-4">
<h4 id="org62bdc6b"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org2ad18d9" class="outline-4">
<h4 id="org2ad18d9"><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-orga08e49a" class="outline-4">
<h4 id="orga08e49a"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-orgf5c1f39" class="outline-4">
<h4 id="orgf5c1f39"><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-org8253e3b" class="outline-3">
<h3 id="org8253e3b"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org7480326" class="outline-3">
<h3 id="org7480326"><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-orgf28dd42" class="outline-4">
<h4 id="orgf28dd42"><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-org65f77da" class="outline-4">
<h4 id="org65f77da"><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-org331ea52" class="outline-4">
<h4 id="org331ea52"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org2d5d0cf" class="outline-4">
<h4 id="org2d5d0cf"><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-org5d05daa" class="outline-4">
<h4 id="org5d05daa"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org18e4a34" class="outline-4">
<h4 id="org18e4a34"><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-org5f28d26" class="outline-4">
<h4 id="org5f28d26"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-orgf473c91" class="outline-4">
<h4 id="orgf473c91"><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-org4bea6a9" class="outline-4">
<h4 id="org4bea6a9"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-org5c46c29" class="outline-4">
<h4 id="org5c46c29"><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-org86a19f6" class="outline-5">
<h5 id="org86a19f6"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org535c348" class="outline-5">
<h5 id="org535c348"><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-org00bde6f" class="outline-5">
<h5 id="org00bde6f"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-org76a8a96" class="outline-5">
<h5 id="org76a8a96"><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-orgf6d4ed4" class="outline-4">
<h4 id="orgf6d4ed4"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org5b0ece2" class="outline-4">
<h4 id="org5b0ece2"><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-orgfc159ac" class="outline-2">
<h2 id="orgfc159ac"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-orgee3e03c" class="outline-2">
<h2 id="orgee3e03c"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org0f3b238" class="outline-3">
<h3 id="org0f3b238"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-orga82905e" class="outline-3">
<h3 id="orga82905e"><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: 2024-11-10 Sun 20:35</p>
<p class="date">Created: 2024-11-10 Sun 20:47</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>
<!-- 2024-11-10 Sun 20:35 -->
<!-- 2024-11-10 Sun 20:47 -->
<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: 2024-11-10 Sun 20:35</p>
<p class="date">Created: 2024-11-10 Sun 20:47</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>
<!-- 2024-11-10 Sun 20:35 -->
<!-- 2024-11-10 Sun 20:47 -->
<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: 2024-11-10 Sun 20:35</p>
<p class="date">Created: 2024-11-10 Sun 20:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
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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>
<!-- 2024-11-10 Sun 20:35 -->
<!-- 2024-11-10 Sun 20:47 -->
<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="#orgdb4439c">1. Format specification</a>
<li><a href="#org24749ed">1. Format specification</a>
<ul>
<li><a href="#orge53005d">1.1. Organization of the data</a></li>
<li><a href="#orge2af44d">1.2. Data types</a></li>
<li><a href="#org4532cbc">1.1. Organization of the data</a></li>
<li><a href="#org2372df8">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org881f422">2. The TREXIO library</a>
<li><a href="#orga8b4f6f">2. The TREXIO library</a>
<ul>
<li><a href="#org3055d06">2.1. The front-end</a></li>
<li><a href="#org4dbeba7">2.2. The back-end</a></li>
<li><a href="#orgebbc000">2.3. Supported languages</a></li>
<li><a href="#org7814030">2.4. Source code generation and documentation</a></li>
<li><a href="#orgf7cd9cb">2.5. Availability</a></li>
<li><a href="#org18d2f8d">2.1. The front-end</a></li>
<li><a href="#orged54848">2.2. The back-end</a></li>
<li><a href="#org2d15c5c">2.3. Supported languages</a></li>
<li><a href="#orga389e86">2.4. Source code generation and documentation</a></li>
<li><a href="#orgd0203e7">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgdb4439c" class="outline-2">
<h2 id="orgdb4439c"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org24749ed" class="outline-2">
<h2 id="org24749ed"><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-orge53005d" class="outline-3">
<h3 id="orge53005d"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org4532cbc" class="outline-3">
<h3 id="org4532cbc"><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-orge2af44d" class="outline-3">
<h3 id="orge2af44d"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org2372df8" class="outline-3">
<h3 id="org2372df8"><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-org881f422" class="outline-2">
<h2 id="org881f422"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orga8b4f6f" class="outline-2">
<h2 id="orga8b4f6f"><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-org3055d06" class="outline-3">
<h3 id="org3055d06"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-org18d2f8d" class="outline-3">
<h3 id="org18d2f8d"><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-org4dbeba7" class="outline-3">
<h3 id="org4dbeba7"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-orged54848" class="outline-3">
<h3 id="orged54848"><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-orgebbc000" class="outline-3">
<h3 id="orgebbc000"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org2d15c5c" class="outline-3">
<h3 id="org2d15c5c"><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-org7814030" class="outline-3">
<h3 id="org7814030"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-orga389e86" class="outline-3">
<h3 id="orga389e86"><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-orgf7cd9cb" class="outline-3">
<h3 id="orgf7cd9cb"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-orgd0203e7" class="outline-3">
<h3 id="orgd0203e7"><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: 2024-11-10 Sun 20:35</p>
<p class="date">Created: 2024-11-10 Sun 20:47</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>
<!-- 2024-11-10 Sun 20:35 -->
<!-- 2024-11-10 Sun 20:47 -->
<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="#orgbe073b0">1. Template for HDF5 definitions</a></li>
<li><a href="#org3b4d8f7">2. Template for HDF5 structures</a></li>
<li><a href="#orga80ec15">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgdba20c1">4. Template for HDF5 has a group</a></li>
<li><a href="#orgdee6691">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgde276b6">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgb7fa278">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org1f76dca">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org5b3eb4f">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org768ddf6">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org7eaaca6">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org4827585">12. Source code for the determinant part</a></li>
<li><a href="#org857cb1c">13. Helper functions</a></li>
<li><a href="#org4975e35">1. Template for HDF5 definitions</a></li>
<li><a href="#orgb497c8a">2. Template for HDF5 structures</a></li>
<li><a href="#org3f6549d">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org2ebe4a6">4. Template for HDF5 has a group</a></li>
<li><a href="#org5948b02">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org12c6ecc">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org80c5272">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org7b8a603">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgc1a49da">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org9ef6900">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org68f52c8">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org8ed84c3">12. Source code for the determinant part</a></li>
<li><a href="#org110a986">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgbe073b0" class="outline-2">
<h2 id="orgbe073b0"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org4975e35" class="outline-2">
<h2 id="org4975e35"><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-org3b4d8f7" class="outline-2">
<h2 id="org3b4d8f7"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgb497c8a" class="outline-2">
<h2 id="orgb497c8a"><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-orga80ec15" class="outline-2">
<h2 id="orga80ec15"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org3f6549d" class="outline-2">
<h2 id="org3f6549d"><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-orgdba20c1" class="outline-2">
<h2 id="orgdba20c1"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org2ebe4a6" class="outline-2">
<h2 id="org2ebe4a6"><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-orgdee6691" class="outline-2">
<h2 id="orgdee6691"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org5948b02" class="outline-2">
<h2 id="org5948b02"><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-orgde276b6" class="outline-2">
<h2 id="orgde276b6"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org12c6ecc" class="outline-2">
<h2 id="org12c6ecc"><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-orgb7fa278" class="outline-2">
<h2 id="orgb7fa278"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org80c5272" class="outline-2">
<h2 id="org80c5272"><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-org1f76dca" class="outline-2">
<h2 id="org1f76dca"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org7b8a603" class="outline-2">
<h2 id="org7b8a603"><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-org5b3eb4f" class="outline-2">
<h2 id="org5b3eb4f"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgc1a49da" class="outline-2">
<h2 id="orgc1a49da"><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-org768ddf6" class="outline-2">
<h2 id="org768ddf6"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org9ef6900" class="outline-2">
<h2 id="org9ef6900"><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-org7eaaca6" class="outline-2">
<h2 id="org7eaaca6"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org68f52c8" class="outline-2">
<h2 id="org68f52c8"><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-org4827585" class="outline-2">
<h2 id="org4827585"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org8ed84c3" class="outline-2">
<h2 id="org8ed84c3"><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-org857cb1c" class="outline-2">
<h2 id="org857cb1c"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org110a986" class="outline-2">
<h2 id="org110a986"><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: 2024-11-10 Sun 20:35</p>
<p class="date">Created: 2024-11-10 Sun 20:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<title>TEXT back end</title>
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org2d0c9a6">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgce29d73">2. Template for general structure in text back end</a></li>
<li><a href="#orgaff9007">3. Initialize function (constant part)</a></li>
<li><a href="#org789da6f">4. Deinitialize function (templated part)</a></li>
<li><a href="#org109e45e">5. Flush function (templated part)</a></li>
<li><a href="#org80eb647">6. Template for text read a group</a></li>
<li><a href="#org16b956d">7. Template for text has a group</a></li>
<li><a href="#org11ebfd1">8. Template for text flush a group</a></li>
<li><a href="#org64c9e97">9. Template for text free memory</a></li>
<li><a href="#org2a89a1c">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org6fbb1c1">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org3b4670c">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgd7ead5b">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org10c4559">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgec35c60">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org32fef60">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgdcb02f0">17. Source code for the determinant part</a></li>
<li><a href="#org6422c61">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgde8cb2f">2. Template for general structure in text back end</a></li>
<li><a href="#org0e24109">3. Initialize function (constant part)</a></li>
<li><a href="#org584e102">4. Deinitialize function (templated part)</a></li>
<li><a href="#org7cf20f1">5. Flush function (templated part)</a></li>
<li><a href="#orgaad0152">6. Template for text read a group</a></li>
<li><a href="#org0e1be31">7. Template for text has a group</a></li>
<li><a href="#org81a6c99">8. Template for text flush a group</a></li>
<li><a href="#org2a18398">9. Template for text free memory</a></li>
<li><a href="#org446719f">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org40f53a4">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org2667454">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org4146dcb">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgd179652">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org2e5f1bf">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org4c530a9">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgbab1411">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-org2d0c9a6" class="outline-2">
<h2 id="org2d0c9a6"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org6422c61" class="outline-2">
<h2 id="org6422c61"><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-orgce29d73" class="outline-2">
<h2 id="orgce29d73"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgde8cb2f" class="outline-2">
<h2 id="orgde8cb2f"><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-orgaff9007" class="outline-2">
<h2 id="orgaff9007"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org0e24109" class="outline-2">
<h2 id="org0e24109"><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-org789da6f" class="outline-2">
<h2 id="org789da6f"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org584e102" class="outline-2">
<h2 id="org584e102"><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-org109e45e" class="outline-2">
<h2 id="org109e45e"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org7cf20f1" class="outline-2">
<h2 id="org7cf20f1"><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-org80eb647" class="outline-2">
<h2 id="org80eb647"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orgaad0152" class="outline-2">
<h2 id="orgaad0152"><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>
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<h2 id="org16b956d"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org0e1be31" class="outline-2">
<h2 id="org0e1be31"><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-org11ebfd1" class="outline-2">
<h2 id="org11ebfd1"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org81a6c99" class="outline-2">
<h2 id="org81a6c99"><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-org64c9e97" class="outline-2">
<h2 id="org64c9e97"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org2a18398" class="outline-2">
<h2 id="org2a18398"><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-org2a89a1c" class="outline-2">
<h2 id="org2a89a1c"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org446719f" class="outline-2">
<h2 id="org446719f"><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-org6fbb1c1" class="outline-2">
<h2 id="org6fbb1c1"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org40f53a4" class="outline-2">
<h2 id="org40f53a4"><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-org3b4670c" class="outline-2">
<h2 id="org3b4670c"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org2667454" class="outline-2">
<h2 id="org2667454"><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-orgd7ead5b" class="outline-2">
<h2 id="orgd7ead5b"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org4146dcb" class="outline-2">
<h2 id="org4146dcb"><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-org10c4559" class="outline-2">
<h2 id="org10c4559"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orgd179652" class="outline-2">
<h2 id="orgd179652"><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-orgec35c60" class="outline-2">
<h2 id="orgec35c60"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org2e5f1bf" class="outline-2">
<h2 id="org2e5f1bf"><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-org32fef60" class="outline-2">
<h2 id="org32fef60"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org4c530a9" class="outline-2">
<h2 id="org4c530a9"><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-orgdcb02f0" class="outline-2">
<h2 id="orgdcb02f0"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-orgbab1411" class="outline-2">
<h2 id="orgbab1411"><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: 2024-11-10 Sun 20:35</p>
<p class="date">Created: 2024-11-10 Sun 20:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2024-11-10 Sun 20:35 -->
<!-- 2024-11-10 Sun 20:47 -->
<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="#orgb212b99">1. Metadata (metadata group)</a></li>
<li><a href="#org26ef7e7">2. System</a>
<li><a href="#orga7fa706">1. Metadata (metadata group)</a></li>
<li><a href="#org53548d3">2. System</a>
<ul>
<li><a href="#orgb0c3425">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org7f5277a">2.2. Cell (cell group)</a></li>
<li><a href="#org92769df">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org86e10ee">2.4. Electron (electron group)</a></li>
<li><a href="#org65c9225">2.5. Ground or excited states (state group)</a></li>
<li><a href="#orgb284c96">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org25bf4ac">2.2. Cell (cell group)</a></li>
<li><a href="#org7b91861">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org2b02cff">2.4. Electron (electron group)</a></li>
<li><a href="#orgfd4ec3b">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org3f34c56">3. Basis functions</a>
<li><a href="#org2c8ca9c">3. Basis functions</a>
<ul>
<li><a href="#orgc12921f">3.1. Basis set (basis group)</a>
<li><a href="#org31d29fb">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orgd40fd9b">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org72acd5b">3.1.2. Numerical orbitals</a></li>
<li><a href="#org28cccc1">3.1.3. Plane waves</a></li>
<li><a href="#org680942d">3.1.4. Oscillating orbitals</a></li>
<li><a href="#orgb1e6733">3.1.5. Data definitions</a></li>
<li><a href="#org8b071e9">3.1.6. Example</a></li>
<li><a href="#orge78fa30">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgbab6309">3.1.2. Numerical orbitals</a></li>
<li><a href="#org02a96f5">3.1.3. Plane waves</a></li>
<li><a href="#org03fbd82">3.1.4. Oscillating orbitals</a></li>
<li><a href="#orgce234ac">3.1.5. Data definitions</a></li>
<li><a href="#org3c7a467">3.1.6. Example</a></li>
</ul>
</li>
<li><a href="#org6022f88">3.2. Effective core potentials (ecp group)</a>
<li><a href="#orgf1dd44e">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org10353f5">3.2.1. Example</a></li>
<li><a href="#orgc29a1b5">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org6d15b80">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org824b46b">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org5f6d955">4. Orbitals</a>
<li><a href="#org3cb5787">4. Orbitals</a>
<ul>
<li><a href="#org443945d">4.1. Atomic orbitals (ao group)</a>
<li><a href="#orgafcc2f7">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="#org6b7ba1d">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org0be8e19">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org9146472">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgd8a2283">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orga0de663">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org5debbe7">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org6a57b68">5. Multi-determinant information</a>
<li><a href="#org8ccc8fd">5. Multi-determinant information</a>
<ul>
<li><a href="#org4f3b627">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org126c7b5">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org1cf50ae">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgb29d8ca">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org8164463">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgd44dbf7">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org331f139">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org57c7587">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org0389182">6. Correlation factors</a>
<li><a href="#org77d143d">6. Correlation factors</a>
<ul>
<li><a href="#org132f17e">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org5c8b28b">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#orgc347941">6.1.1. CHAMP</a></li>
<li><a href="#org300b39c">6.1.2. Mu</a></li>
<li><a href="#orgec4f907">6.1.3. Table of values</a></li>
<li><a href="#org40d278e">6.1.1. CHAMP</a></li>
<li><a href="#org1952be9">6.1.2. Mu</a></li>
<li><a href="#orgc092ce0">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org6df3502">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#orgb3338a4">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-orgb212b99" class="outline-2">
<h2 id="orgb212b99"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orga7fa706" class="outline-2">
<h2 id="orga7fa706"><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="org062c702" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgba81053" 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-org26ef7e7" class="outline-2">
<h2 id="org26ef7e7"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org53548d3" class="outline-2">
<h2 id="org53548d3"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgb0c3425" class="outline-3">
<h3 id="orgb0c3425"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orgb284c96" class="outline-3">
<h3 id="orgb284c96"><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="org46914e5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org20526da" 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-org7f5277a" class="outline-3">
<h3 id="org7f5277a"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org25bf4ac" class="outline-3">
<h3 id="org25bf4ac"><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="orgfe73ebc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf148687" 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-org92769df" class="outline-3">
<h3 id="org92769df"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org7b91861" class="outline-3">
<h3 id="org7b91861"><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="orgbe2c4bb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org58abe42" 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-org86e10ee" class="outline-3">
<h3 id="org86e10ee"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org2b02cff" class="outline-3">
<h3 id="org2b02cff"><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="orgcd8b1a8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5068a0a" 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-org65c9225" class="outline-3">
<h3 id="org65c9225"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-orgfd4ec3b" class="outline-3">
<h3 id="orgfd4ec3b"><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="org9beffc7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb519830" 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-org3f34c56" class="outline-2">
<h2 id="org3f34c56"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org2c8ca9c" class="outline-2">
<h2 id="org2c8ca9c"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgc12921f" class="outline-3">
<h3 id="orgc12921f"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org31d29fb" class="outline-3">
<h3 id="org31d29fb"><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-orgd40fd9b" class="outline-4">
<h4 id="orgd40fd9b"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-orge78fa30" class="outline-4">
<h4 id="orge78fa30"><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-org72acd5b" class="outline-4">
<h4 id="org72acd5b"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-orgbab6309" class="outline-4">
<h4 id="orgbab6309"><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-org28cccc1" class="outline-4">
<h4 id="org28cccc1"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-org02a96f5" class="outline-4">
<h4 id="org02a96f5"><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-org680942d" class="outline-4">
<h4 id="org680942d"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div id="outline-container-org03fbd82" class="outline-4">
<h4 id="org03fbd82"><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-orgb1e6733" class="outline-4">
<h4 id="orgb1e6733"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div id="outline-container-orgce234ac" class="outline-4">
<h4 id="orgce234ac"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-5">
<table id="org09bfdb9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org181606e" 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-org8b071e9" class="outline-4">
<h4 id="org8b071e9"><span class="section-number-4">3.1.6</span> Example</h4>
<div id="outline-container-org3c7a467" class="outline-4">
<h4 id="org3c7a467"><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-org6022f88" class="outline-3">
<h3 id="org6022f88"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-orgf1dd44e" class="outline-3">
<h3 id="orgf1dd44e"><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="org4f00a98" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org41b145d" 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-org10353f5" class="outline-4">
<h4 id="org10353f5"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orgc29a1b5" class="outline-4">
<h4 id="orgc29a1b5"><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-org6d15b80" class="outline-3">
<h3 id="org6d15b80"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org824b46b" class="outline-3">
<h3 id="org824b46b"><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="org3c166b7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2a99ffc" 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-org5f6d955" class="outline-2">
<h2 id="org5f6d955"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org3cb5787" class="outline-2">
<h2 id="org3cb5787"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org443945d" class="outline-3">
<h3 id="org443945d"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-orgafcc2f7" class="outline-3">
<h3 id="orgafcc2f7"><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
@ -1918,7 +1918,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="org9a620ba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge6fc1c7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1977,7 +1977,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-orgfe40734" class="outline-4">
<div id="outline-container-org0d4fb94" 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">
@ -1995,7 +1995,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgaf700f5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4f2db9e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2103,7 +2103,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org1eb6e2b" class="outline-4">
<div id="outline-container-org5518c64" 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>
@ -2129,7 +2129,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org487104c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0975647" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2206,10 +2206,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org6b7ba1d" class="outline-3">
<h3 id="org6b7ba1d"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org0be8e19" class="outline-3">
<h3 id="org0be8e19"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="orgd37270d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org36d0881" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2325,8 +2325,8 @@ is the number of spin-orbitals, twice the number of spatial orbitals.
</div>
<div id="outline-container-org9146472" class="outline-4">
<h4 id="org9146472"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-orga0de663" class="outline-4">
<h4 id="orga0de663"><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
@ -2334,7 +2334,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orge47db26" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbd719ad" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2442,8 +2442,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgd8a2283" class="outline-4">
<h4 id="orgd8a2283"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org5debbe7" class="outline-4">
<h4 id="org5debbe7"><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
@ -2451,7 +2451,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgb8868c0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9b97562" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2529,12 +2529,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org6a57b68" class="outline-2">
<h2 id="org6a57b68"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org8ccc8fd" class="outline-2">
<h2 id="org8ccc8fd"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org4f3b627" class="outline-3">
<h3 id="org4f3b627"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org8164463" class="outline-3">
<h3 id="org8164463"><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 \(\Psi\)
@ -2576,7 +2576,7 @@ 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="org2a048fe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org641da61" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2628,8 +2628,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org126c7b5" class="outline-3">
<h3 id="org126c7b5"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-orgd44dbf7" class="outline-3">
<h3 id="orgd44dbf7"><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
@ -2651,7 +2651,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org0088437" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org45785ec" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2703,8 +2703,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org1cf50ae" class="outline-3">
<h3 id="org1cf50ae"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org331f139" class="outline-3">
<h3 id="org331f139"><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
@ -2775,7 +2775,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org2fae4c9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6608689" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2867,8 +2867,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-orgb29d8ca" class="outline-3">
<h3 id="orgb29d8ca"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org57c7587" class="outline-3">
<h3 id="org57c7587"><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
@ -2940,7 +2940,7 @@ 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="org46136dc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4ddfa2b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3105,12 +3105,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org0389182" class="outline-2">
<h2 id="org0389182"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org77d143d" class="outline-2">
<h2 id="org77d143d"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org132f17e" class="outline-3">
<h3 id="org132f17e"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org5c8b28b" class="outline-3">
<h3 id="org5c8b28b"><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
@ -3135,8 +3135,8 @@ following:
</ul>
</div>
<div id="outline-container-orgc347941" class="outline-4">
<h4 id="orgc347941"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org40d278e" class="outline-4">
<h4 id="org40d278e"><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
@ -3237,8 +3237,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-org300b39c" class="outline-4">
<h4 id="org300b39c"><span class="section-number-4">6.1.2</span> Mu</h4>
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<h4 id="org1952be9"><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
@ -3335,10 +3335,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h4 id="orgec4f907"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="orgc092ce0"><span class="section-number-4">6.1.3</span> Table of values</h4>
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@ -3456,8 +3456,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h2 id="org6df3502"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="orgb3338a4"><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
@ -3471,7 +3471,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3533,7 +3533,7 @@ 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: 2024-11-10 Sun 20:35</p>
<p class="date">Created: 2024-11-10 Sun 20:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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