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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>
@ -383,7 +383,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 14:45</p>
<p class="date">Created: 2023-05-05 Fri 15:07</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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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-05-05 Fri 14:45 -->
<!-- 2023-05-05 Fri 15:07 -->
<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="#org536dda9">1. Writing nuclear coordinates</a>
<li><a href="#org27507be">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orgfc47556">1.1. C</a></li>
<li><a href="#org4267a2e">1.2. Python</a></li>
<li><a href="#orgb5c2133">1.3. Fortran</a></li>
<li><a href="#orgf326493">1.1. C</a></li>
<li><a href="#org1632430">1.2. Python</a></li>
<li><a href="#orge3bb3ec">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#orge6ce014">2. Accessing sparse quantities (integrals)</a>
<li><a href="#orgb041a38">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org52b7df1">2.1. Fortran</a>
<li><a href="#org32cdec9">2.1. Fortran</a>
<ul>
<li><a href="#org992e739">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org153c45f">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org80ee466">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orga65aa45">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orge425c78">2.1.5. Allocate memory</a></li>
<li><a href="#orga68a823">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org79107fd">2.1.7. Read two-electron quantities</a>
<li><a href="#org2db18e1">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org500a779">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org5ab5ec9">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgcac60f2">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org2079b6a">2.1.5. Allocate memory</a></li>
<li><a href="#org95f7389">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org5d2d798">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org02ef1ef">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgb7bdfe9">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#orgb7f1ec9">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org90880c4">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgef8d5d3">2.1.8. Compute the energy</a></li>
<li><a href="#org1743e1f">2.1.9. Terminate</a></li>
<li><a href="#orgf58d154">2.1.8. Compute the energy</a></li>
<li><a href="#org0ba516e">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#orgfc1b7ae">2.2. Python</a>
<li><a href="#org33c5fb8">2.2. Python</a>
<ul>
<li><a href="#orgf683d9c">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org657de5c">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org643541e">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#orgcc05277">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org7d57d95">2.2.5. Read two-electron quantities</a>
<li><a href="#orgc66a7e3">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org6b2c1fd">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org47faf76">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org1b2a7bf">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org57d061d">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#org8c5bc1d">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org65897a7">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org97de0f4">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgbcd70a2">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org2a7c785">2.2.6. Compute the energy</a></li>
<li><a href="#orge2685cb">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org292df64">3. Reading determinants</a>
<li><a href="#orgcb306c5">3. Reading determinants</a>
<ul>
<li><a href="#org3b06bec">3.1. Fortran</a></li>
<li><a href="#org4d33010">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org536dda9" class="outline-2">
<h2 id="org536dda9"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org27507be" class="outline-2">
<h2 id="org27507be"><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-orgfc47556" class="outline-3">
<h3 id="orgfc47556"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-orgf326493" class="outline-3">
<h3 id="orgf326493"><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-org4267a2e" class="outline-3">
<h3 id="org4267a2e"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org1632430" class="outline-3">
<h3 id="org1632430"><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-orgb5c2133" class="outline-3">
<h3 id="orgb5c2133"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orge3bb3ec" class="outline-3">
<h3 id="orge3bb3ec"><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-orge6ce014" class="outline-2">
<h2 id="orge6ce014"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orgb041a38" class="outline-2">
<h2 id="orgb041a38"><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-org52b7df1" class="outline-3">
<h3 id="org52b7df1"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org32cdec9" class="outline-3">
<h3 id="org32cdec9"><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-org992e739" class="outline-4">
<h4 id="org992e739"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org2db18e1" class="outline-4">
<h4 id="org2db18e1"><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-org153c45f" class="outline-4">
<h4 id="org153c45f"><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-org500a779" class="outline-4">
<h4 id="org500a779"><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-org80ee466" class="outline-4">
<h4 id="org80ee466"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org5ab5ec9" class="outline-4">
<h4 id="org5ab5ec9"><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-orga65aa45" class="outline-4">
<h4 id="orga65aa45"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgcac60f2" class="outline-4">
<h4 id="orgcac60f2"><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-orge425c78" class="outline-4">
<h4 id="orge425c78"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org2079b6a" class="outline-4">
<h4 id="org2079b6a"><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-orga68a823" class="outline-4">
<h4 id="orga68a823"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org95f7389" class="outline-4">
<h4 id="org95f7389"><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-org79107fd" class="outline-4">
<h4 id="org79107fd"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org5d2d798" class="outline-4">
<h4 id="org5d2d798"><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-org02ef1ef" class="outline-5">
<h5 id="org02ef1ef"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgb7f1ec9" class="outline-5">
<h5 id="orgb7f1ec9"><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-orgb7bdfe9" class="outline-5">
<h5 id="orgb7bdfe9"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org90880c4" class="outline-5">
<h5 id="org90880c4"><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-orgef8d5d3" class="outline-4">
<h4 id="orgef8d5d3"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-orgf58d154" class="outline-4">
<h4 id="orgf58d154"><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-org1743e1f" class="outline-4">
<h4 id="org1743e1f"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org0ba516e" class="outline-4">
<h4 id="org0ba516e"><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-orgfc1b7ae" class="outline-3">
<h3 id="orgfc1b7ae"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org33c5fb8" class="outline-3">
<h3 id="org33c5fb8"><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-orgf683d9c" class="outline-4">
<h4 id="orgf683d9c"><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-orgc66a7e3" class="outline-4">
<h4 id="orgc66a7e3"><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-org657de5c" class="outline-4">
<h4 id="org657de5c"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org6b2c1fd" class="outline-4">
<h4 id="org6b2c1fd"><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-org643541e" class="outline-4">
<h4 id="org643541e"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org47faf76" class="outline-4">
<h4 id="org47faf76"><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-orgcc05277" class="outline-4">
<h4 id="orgcc05277"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org1b2a7bf" class="outline-4">
<h4 id="org1b2a7bf"><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-org7d57d95" class="outline-4">
<h4 id="org7d57d95"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-org57d061d" class="outline-4">
<h4 id="org57d061d"><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-org8c5bc1d" class="outline-5">
<h5 id="org8c5bc1d"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org97de0f4" class="outline-5">
<h5 id="org97de0f4"><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-org65897a7" class="outline-5">
<h5 id="org65897a7"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-orgbcd70a2" class="outline-5">
<h5 id="orgbcd70a2"><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-org2a7c785" class="outline-4">
<h4 id="org2a7c785"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-orge2685cb" class="outline-4">
<h4 id="orge2685cb"><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-org292df64" class="outline-2">
<h2 id="org292df64"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-orgcb306c5" class="outline-2">
<h2 id="orgcb306c5"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org3b06bec" class="outline-3">
<h3 id="org3b06bec"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org4d33010" class="outline-3">
<h3 id="org4d33010"><span class="section-number-3">3.1</span> Fortran</h3>
<div class="outline-text-3" id="text-3-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
@ -1157,7 +1157,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 14:45</p>
<p class="date">Created: 2023-05-05 Fri 15:07</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>
<!-- 2023-05-05 Fri 14:45 -->
<!-- 2023-05-05 Fri 15:07 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -383,7 +383,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 14:45</p>
<p class="date">Created: 2023-05-05 Fri 15:07</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>
<!-- 2023-05-05 Fri 14:45 -->
<!-- 2023-05-05 Fri 15:07 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Motivation</title>
@ -384,7 +384,7 @@ still lacking, and the purpose of the TREXIO library is to fill this gap.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 14:45</p>
<p class="date">Created: 2023-05-05 Fri 15:07</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>
<!-- 2023-05-05 Fri 14:45 -->
<!-- 2023-05-05 Fri 15:07 -->
<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="#org0bc1f7e">1. Format specification</a>
<li><a href="#orgddd2676">1. Format specification</a>
<ul>
<li><a href="#org7c430d7">1.1. Organization of the data</a></li>
<li><a href="#org2ba69be">1.2. Data types</a></li>
<li><a href="#orgc617628">1.1. Organization of the data</a></li>
<li><a href="#org95ff4de">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org565a14f">2. The TREXIO library</a>
<li><a href="#orgb2b028f">2. The TREXIO library</a>
<ul>
<li><a href="#orge6c4001">2.1. The front-end</a></li>
<li><a href="#org895d1d7">2.2. The back-end</a></li>
<li><a href="#org1e3d161">2.3. Supported languages</a></li>
<li><a href="#org24f4c15">2.4. Source code generation and documentation</a></li>
<li><a href="#org3618aec">2.5. Availability</a></li>
<li><a href="#orgfb6c54e">2.1. The front-end</a></li>
<li><a href="#org02c3894">2.2. The back-end</a></li>
<li><a href="#orge18d6ea">2.3. Supported languages</a></li>
<li><a href="#org295ead1">2.4. Source code generation and documentation</a></li>
<li><a href="#org0e518c5">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org0bc1f7e" class="outline-2">
<h2 id="org0bc1f7e"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-orgddd2676" class="outline-2">
<h2 id="orgddd2676"><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-org7c430d7" class="outline-3">
<h3 id="org7c430d7"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-orgc617628" class="outline-3">
<h3 id="orgc617628"><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-org2ba69be" class="outline-3">
<h3 id="org2ba69be"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org95ff4de" class="outline-3">
<h3 id="org95ff4de"><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-org565a14f" class="outline-2">
<h2 id="org565a14f"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orgb2b028f" class="outline-2">
<h2 id="orgb2b028f"><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-orge6c4001" class="outline-3">
<h3 id="orge6c4001"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orgfb6c54e" class="outline-3">
<h3 id="orgfb6c54e"><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-org895d1d7" class="outline-3">
<h3 id="org895d1d7"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-org02c3894" class="outline-3">
<h3 id="org02c3894"><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-org1e3d161" class="outline-3">
<h3 id="org1e3d161"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-orge18d6ea" class="outline-3">
<h3 id="orge18d6ea"><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-org24f4c15" class="outline-3">
<h3 id="org24f4c15"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org295ead1" class="outline-3">
<h3 id="org295ead1"><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-org3618aec" class="outline-3">
<h3 id="org3618aec"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org0e518c5" class="outline-3">
<h3 id="org0e518c5"><span class="section-number-3">2.5</span> Availability</h3>
<div class="outline-text-3" id="text-2-5">
<p>
The TREXIO library is designed to be portable and easy to install
@ -754,7 +754,7 @@ are available in Ubuntu 23.04.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 14:45</p>
<p class="date">Created: 2023-05-05 Fri 15:07</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>
<!-- 2023-05-05 Fri 14:45 -->
<!-- 2023-05-05 Fri 15:06 -->
<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="#orga002589">1. Template for HDF5 definitions</a></li>
<li><a href="#org2f35e85">2. Template for HDF5 structures</a></li>
<li><a href="#org5a6ce88">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org98c4ec1">4. Template for HDF5 has a group</a></li>
<li><a href="#org3e4e365">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgdafbbca">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgf64310e">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org85baef5">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org65746e7">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org2fe086a">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org3e42400">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orga5c62ac">12. Source code for the determinant part</a></li>
<li><a href="#org9f0b0da">13. Helper functions</a></li>
<li><a href="#orgedcaac5">1. Template for HDF5 definitions</a></li>
<li><a href="#orge85628d">2. Template for HDF5 structures</a></li>
<li><a href="#org5c4f5d4">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org67327ca">4. Template for HDF5 has a group</a></li>
<li><a href="#orga224940">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgf64fcb7">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgf2e9b6c">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org51e08c5">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org31dfb24">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org46460ae">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org62d67a8">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgf5e2309">12. Source code for the determinant part</a></li>
<li><a href="#orge103bdb">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orga002589" class="outline-2">
<h2 id="orga002589"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orgedcaac5" class="outline-2">
<h2 id="orgedcaac5"><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-org2f35e85" class="outline-2">
<h2 id="org2f35e85"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orge85628d" class="outline-2">
<h2 id="orge85628d"><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-org5a6ce88" class="outline-2">
<h2 id="org5a6ce88"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org5c4f5d4" class="outline-2">
<h2 id="org5c4f5d4"><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-org98c4ec1" class="outline-2">
<h2 id="org98c4ec1"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org67327ca" class="outline-2">
<h2 id="org67327ca"><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-org3e4e365" class="outline-2">
<h2 id="org3e4e365"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orga224940" class="outline-2">
<h2 id="orga224940"><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-orgdafbbca" class="outline-2">
<h2 id="orgdafbbca"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgf64fcb7" class="outline-2">
<h2 id="orgf64fcb7"><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-orgf64310e" class="outline-2">
<h2 id="orgf64310e"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orgf2e9b6c" class="outline-2">
<h2 id="orgf2e9b6c"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-7">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -973,8 +973,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org85baef5" class="outline-2">
<h2 id="org85baef5"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org51e08c5" class="outline-2">
<h2 id="org51e08c5"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div class="outline-text-2" id="text-8">
<p>
Chunked I/O in HDF5 for <code>buffered</code> data.
@ -1108,8 +1108,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org65746e7" class="outline-2">
<h2 id="org65746e7"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org31dfb24" class="outline-2">
<h2 id="org31dfb24"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org2fe086a" class="outline-2">
<h2 id="org2fe086a"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org46460ae" class="outline-2">
<h2 id="org46460ae"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1434,8 +1434,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
</div>
<div id="outline-container-org3e42400" class="outline-2">
<h2 id="org3e42400"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org62d67a8" class="outline-2">
<h2 id="org62d67a8"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-11">
<p>
<b><b>Note:</b></b> in early versions of the HDF5 library (v &lt; 1.10) unlinking an object was not working as expected
@ -1475,8 +1475,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-orga5c62ac" class="outline-2">
<h2 id="orga5c62ac"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-orgf5e2309" class="outline-2">
<h2 id="orgf5e2309"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-12">
<p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1578,8 +1578,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org9f0b0da" class="outline-2">
<h2 id="org9f0b0da"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orge103bdb" class="outline-2">
<h2 id="orge103bdb"><span class="section-number-2">13</span> Helper functions</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1842,7 +1842,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 14:45</p>
<p class="date">Created: 2023-05-05 Fri 15:06</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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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="#orge6c388f">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgb5051ae">2. Template for general structure in text back end</a></li>
<li><a href="#orgb219a28">3. Initialize function (constant part)</a></li>
<li><a href="#org0fed843">4. Deinitialize function (templated part)</a></li>
<li><a href="#org5608cd8">5. Flush function (templated part)</a></li>
<li><a href="#org80c0694">6. Template for text read a group</a></li>
<li><a href="#orgb20703e">7. Template for text has a group</a></li>
<li><a href="#orge378ee4">8. Template for text flush a group</a></li>
<li><a href="#org85569f1">9. Template for text free memory</a></li>
<li><a href="#org0802e37">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgdadcae2">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgea2a758">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org933fce8">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org93c5e9f">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org59fbe77">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org9bc722c">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org8ff2f99">17. Source code for the determinant part</a></li>
<li><a href="#orgf430d51">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgb3b7c76">2. Template for general structure in text back end</a></li>
<li><a href="#org4dac12e">3. Initialize function (constant part)</a></li>
<li><a href="#org78c0131">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgc26645c">5. Flush function (templated part)</a></li>
<li><a href="#org7657bd4">6. Template for text read a group</a></li>
<li><a href="#orgf6f68a5">7. Template for text has a group</a></li>
<li><a href="#org75793ff">8. Template for text flush a group</a></li>
<li><a href="#org3d4d0f9">9. Template for text free memory</a></li>
<li><a href="#org23d0fb0">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orga3f6af4">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org5b730be">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org808e6a3">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgaf4675b">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org6bd265c">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orge3149cc">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgbfdf875">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-orge6c388f" class="outline-2">
<h2 id="orge6c388f"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orgf430d51" class="outline-2">
<h2 id="orgf430d51"><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-orgb5051ae" class="outline-2">
<h2 id="orgb5051ae"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgb3b7c76" class="outline-2">
<h2 id="orgb3b7c76"><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-orgb219a28" class="outline-2">
<h2 id="orgb219a28"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org4dac12e" class="outline-2">
<h2 id="org4dac12e"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">bool</span>
@ -597,8 +597,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org0fed843" class="outline-2">
<h2 id="org0fed843"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org78c0131" class="outline-2">
<h2 id="org78c0131"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -620,8 +620,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org5608cd8" class="outline-2">
<h2 id="org5608cd8"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-orgc26645c" class="outline-2">
<h2 id="orgc26645c"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -644,8 +644,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org80c0694" class="outline-2">
<h2 id="org80c0694"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org7657bd4" class="outline-2">
<h2 id="org7657bd4"><span class="section-number-2">6</span> Template for text read a group</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -871,8 +871,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgb20703e" class="outline-2">
<h2 id="orgb20703e"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-orgf6f68a5" class="outline-2">
<h2 id="orgf6f68a5"><span class="section-number-2">7</span> Template for text has a group</h2>
<div class="outline-text-2" id="text-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -912,8 +912,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orge378ee4" class="outline-2">
<h2 id="orge378ee4"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org75793ff" class="outline-2">
<h2 id="org75793ff"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div class="outline-text-2" id="text-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -977,8 +977,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org85569f1" class="outline-2">
<h2 id="org85569f1"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org3d4d0f9" class="outline-2">
<h2 id="org3d4d0f9"><span class="section-number-2">9</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-9">
<p>
Memory is allocated when reading. The following function frees memory.
@ -1047,8 +1047,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org0802e37" class="outline-2">
<h2 id="org0802e37"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org23d0fb0" class="outline-2">
<h2 id="org23d0fb0"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1111,8 +1111,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orgdadcae2" class="outline-2">
<h2 id="orgdadcae2"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orga3f6af4" class="outline-2">
<h2 id="orga3f6af4"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-11">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1208,8 +1208,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgea2a758" class="outline-2">
<h2 id="orgea2a758"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org5b730be" class="outline-2">
<h2 id="org5b730be"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-12">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1310,8 +1310,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org933fce8" class="outline-2">
<h2 id="org933fce8"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org808e6a3" class="outline-2">
<h2 id="org808e6a3"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1385,8 +1385,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org93c5e9f" class="outline-2">
<h2 id="org93c5e9f"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orgaf4675b" class="outline-2">
<h2 id="orgaf4675b"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-14">
<p>
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
@ -1676,8 +1676,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org59fbe77" class="outline-2">
<h2 id="org59fbe77"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org6bd265c" class="outline-2">
<h2 id="org6bd265c"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div class="outline-text-2" id="text-15">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that buffered I/O has to be decoupled
@ -1907,8 +1907,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-org9bc722c" class="outline-2">
<h2 id="org9bc722c"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orge3149cc" class="outline-2">
<h2 id="orge3149cc"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-16">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1936,8 +1936,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-org8ff2f99" class="outline-2">
<h2 id="org8ff2f99"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-orgbfdf875" class="outline-2">
<h2 id="orgbfdf875"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-17">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -2129,7 +2129,7 @@ Size specifies the number of data items, e.g. determinants.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 14:45</p>
<p class="date">Created: 2023-05-05 Fri 15:07</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2023-05-05 Fri 14:45 -->
<!-- 2023-05-05 Fri 15:07 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Data stored in TREXIO</title>
@ -346,70 +346,70 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgcaaaa06">1. Metadata (metadata group)</a></li>
<li><a href="#orge59c383">2. System</a>
<li><a href="#orgd3b4d9c">1. Metadata (metadata group)</a></li>
<li><a href="#org83dca7c">2. System</a>
<ul>
<li><a href="#org8547a6d">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#orgffacbce">2.2. Cell (cell group)</a></li>
<li><a href="#org9b99d8d">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org65bd804">2.4. Electron (electron group)</a></li>
<li><a href="#orgefe38ae">2.5. Ground or excited states (state group)</a></li>
<li><a href="#orga495e24">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#orgdb22d3d">2.2. Cell (cell group)</a></li>
<li><a href="#org0c8c6fd">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgb5720d6">2.4. Electron (electron group)</a></li>
<li><a href="#orgfe35c6e">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org5ef0ba5">3. Basis functions</a>
<li><a href="#org9c6d95e">3. Basis functions</a>
<ul>
<li><a href="#org35e79fe">3.1. Basis set (basis group)</a>
<li><a href="#org0b5580a">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org3619022">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org4b68421">3.1.2. Plane waves</a></li>
<li><a href="#org6728ad0">3.1.3. Data definitions</a></li>
<li><a href="#org70296c0">3.1.4. Example</a></li>
<li><a href="#org00ada3a">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgff88257">3.1.2. Plane waves</a></li>
<li><a href="#org5d8215a">3.1.3. Data definitions</a></li>
<li><a href="#org9a0eb25">3.1.4. Example</a></li>
</ul>
</li>
<li><a href="#org817e079">3.2. Effective core potentials (ecp group)</a>
<li><a href="#orgf472f6b">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org0ef9e37">3.2.1. Example</a></li>
<li><a href="#org0cef604">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org1172c85">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#orgc4b1862">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org5d2537a">4. Orbitals</a>
<li><a href="#orgbfaa7c4">4. Orbitals</a>
<ul>
<li><a href="#org60eeb5e">4.1. Atomic orbitals (ao group)</a>
<li><a href="#orgcd11163">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="#org8ee5a85">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org7015cbb">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org1e235bb">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org6668af5">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org3d298a4">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgbe34546">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org7e1415e">5. Multi-determinant information</a>
<li><a href="#orgf274c5f">5. Multi-determinant information</a>
<ul>
<li><a href="#org0c2ba0b">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org6b05344">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgec89971">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org061c33c">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org4b83365">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org3b22088">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org8c6ec71">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org99f4e2a">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org047e4af">6. Correlation factors</a>
<li><a href="#orgf886aff">6. Correlation factors</a>
<ul>
<li><a href="#orgce7b419">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org6ba38b7">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org61b22dd">6.1.1. CHAMP</a></li>
<li><a href="#org401825b">6.1.2. Mu</a></li>
<li><a href="#org1248c48">6.1.3. Table of values</a></li>
<li><a href="#org532697e">6.1.1. CHAMP</a></li>
<li><a href="#orgafe6f62">6.1.2. Mu</a></li>
<li><a href="#orge6da841">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgcd34f07">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#orgcdac528">7. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -422,8 +422,8 @@ is reversed in the produced <code>trex.json</code> configuration file as the
library is written in C.
</p>
<div id="outline-container-orgcaaaa06" class="outline-2">
<h2 id="orgcaaaa06"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgd3b4d9c" class="outline-2">
<h2 id="orgd3b4d9c"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect TREXIO files to be archived in open-data repositories,
@ -433,7 +433,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
</p>
<table id="orgd7ac698" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb57d269" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -516,19 +516,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
</div>
</div>
<div id="outline-container-orge59c383" class="outline-2">
<h2 id="orge59c383"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org83dca7c" class="outline-2">
<h2 id="org83dca7c"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org8547a6d" class="outline-3">
<h3 id="org8547a6d"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orga495e24" class="outline-3">
<h3 id="orga495e24"><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="org7c6b684" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orged0a759" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -595,15 +595,15 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-orgffacbce" class="outline-3">
<h3 id="orgffacbce"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-orgdb22d3d" class="outline-3">
<h3 id="orgdb22d3d"><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="org95bad80" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfed3b63" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -677,15 +677,15 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-org9b99d8d" class="outline-3">
<h3 id="org9b99d8d"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org0c8c6fd" class="outline-3">
<h3 id="org0c8c6fd"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div class="outline-text-3" id="text-2-3">
<p>
A single $k$-point per TREXIO file can be stored. The $k$-point is
defined in this group.
</p>
<table id="orgf38f950" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2529442" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -724,8 +724,8 @@ defined in this group.
</div>
</div>
<div id="outline-container-org65bd804" class="outline-3">
<h3 id="org65bd804"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-orgb5720d6" class="outline-3">
<h3 id="orgb5720d6"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div class="outline-text-3" id="text-2-4">
<p>
The chemical system consists of nuclei and electrons, where the
@ -744,7 +744,7 @@ the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org6822419" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org29f6d01" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -790,8 +790,8 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgefe38ae" class="outline-3">
<h3 id="orgefe38ae"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-orgfe35c6e" class="outline-3">
<h3 id="orgfe35c6e"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div class="outline-text-3" id="text-2-5">
<p>
This group contains information about excited states. Since only a
@ -808,7 +808,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="orgc1b9df5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd4af6b3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -869,16 +869,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-org5ef0ba5" class="outline-2">
<h2 id="org5ef0ba5"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org9c6d95e" class="outline-2">
<h2 id="org9c6d95e"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org35e79fe" class="outline-3">
<h3 id="org35e79fe"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org0b5580a" class="outline-3">
<h3 id="org0b5580a"><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-org3619022" class="outline-4">
<h4 id="org3619022"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org00ada3a" class="outline-4">
<h4 id="org00ada3a"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div class="outline-text-4" id="text-3-1-1">
<p>
We consider here basis functions centered on nuclei. Hence, it is
@ -932,8 +932,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-org4b68421" class="outline-4">
<h4 id="org4b68421"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div id="outline-container-orgff88257" class="outline-4">
<h4 id="orgff88257"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div class="outline-text-4" id="text-3-1-2">
<p>
A plane wave is defined as
@ -954,10 +954,10 @@ plane waves.
</div>
</div>
<div id="outline-container-org6728ad0" class="outline-4">
<h4 id="org6728ad0"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div id="outline-container-org5d8215a" class="outline-4">
<h4 id="org5d8215a"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-3">
<table id="org2a4ab46" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org756757b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1066,8 +1066,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org70296c0" class="outline-4">
<h4 id="org70296c0"><span class="section-number-4">3.1.4</span> Example</h4>
<div id="outline-container-org9a0eb25" class="outline-4">
<h4 id="org9a0eb25"><span class="section-number-4">3.1.4</span> Example</h4>
<div class="outline-text-4" id="text-3-1-4">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1145,8 +1145,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org817e079" class="outline-3">
<h3 id="org817e079"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-orgf472f6b" class="outline-3">
<h3 id="orgf472f6b"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div class="outline-text-3" id="text-3-2">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -1180,7 +1180,7 @@ where \(Z_\text{eff}\) is the effective nuclear charge of the center.
See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.4984046</a> or <a href="https://doi.org/10.1063/1.5121006">https://doi.org/10.1063/1.5121006</a> for more info.
</p>
<table id="orgb17f854" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org25040e8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1284,8 +1284,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-org0ef9e37" class="outline-4">
<h4 id="org0ef9e37"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-org0cef604" class="outline-4">
<h4 id="org0cef604"><span class="section-number-4">3.2.1</span> Example</h4>
<div class="outline-text-4" id="text-3-2-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -1348,8 +1348,8 @@ power = [
</div>
</div>
<div id="outline-container-org1172c85" class="outline-3">
<h3 id="org1172c85"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-orgc4b1862" class="outline-3">
<h3 id="orgc4b1862"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div class="outline-text-3" id="text-3-3">
<p>
In some applications, such as DFT calculations, integrals have to
@ -1364,7 +1364,7 @@ The structure of this group is adapted for the <a href="https://github.com/dftli
Feel free to submit a PR if you find missing options/functionalities.
</p>
<table id="org6d52246" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge8d045e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1481,12 +1481,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-org5d2537a" class="outline-2">
<h2 id="org5d2537a"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-orgbfaa7c4" class="outline-2">
<h2 id="orgbfaa7c4"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org60eeb5e" class="outline-3">
<h3 id="org60eeb5e"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-orgcd11163" class="outline-3">
<h3 id="orgcd11163"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div class="outline-text-3" id="text-4-1">
<p>
AOs are defined as
@ -1567,7 +1567,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="orgf4827d7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org85a0451" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1619,7 +1619,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org64540da" class="outline-4">
<div id="outline-container-org35896e2" class="outline-4">
<h4 id="ao_one_e"><span class="section-number-4">4.1.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_one_e">
<ul class="org-ul">
@ -1637,7 +1637,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org428fd41" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5215c2b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1732,7 +1732,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org8bfd1a0" class="outline-4">
<div id="outline-container-orgeabead3" class="outline-4">
<h4 id="ao_two_e"><span class="section-number-4">4.1.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_two_e">
<p>
@ -1758,7 +1758,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org807276f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc638c43" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1826,10 +1826,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org8ee5a85" class="outline-3">
<h3 id="org8ee5a85"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org7015cbb" class="outline-3">
<h3 id="org7015cbb"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="orgb90e8fa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc80ea33" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1916,8 +1916,8 @@ The Cholesky decomposition of the integrals can also be stored:
</table>
</div>
<div id="outline-container-org1e235bb" class="outline-4">
<h4 id="org1e235bb"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org3d298a4" class="outline-4">
<h4 id="org3d298a4"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-1">
<p>
The operators as the same as those defined in the
@ -1925,7 +1925,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org8c47767" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd39a9bb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2020,8 +2020,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org6668af5" class="outline-4">
<h4 id="org6668af5"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-orgbe34546" class="outline-4">
<h4 id="orgbe34546"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-2">
<p>
The operators are the same as those defined in the
@ -2029,7 +2029,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org3a74244" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org809dfbb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2098,12 +2098,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org7e1415e" class="outline-2">
<h2 id="org7e1415e"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-orgf274c5f" class="outline-2">
<h2 id="orgf274c5f"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org0c2ba0b" class="outline-3">
<h3 id="org0c2ba0b"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org4b83365" class="outline-3">
<h3 id="org4b83365"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div class="outline-text-3" id="text-5-1">
<p>
The configuration interaction (CI) wave function \(\Psi\)
@ -2145,7 +2145,7 @@ produced by the code generator.
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
</p>
<table id="org174c779" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga3f4c8d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2191,8 +2191,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org6b05344" class="outline-3">
<h3 id="org6b05344"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org3b22088" class="outline-3">
<h3 id="org3b22088"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div class="outline-text-3" id="text-5-2">
<p>
The configuration interaction (CI) wave function \(\Psi\) can be
@ -2214,7 +2214,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org050d276" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgab39e36" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2260,8 +2260,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-orgec89971" class="outline-3">
<h3 id="orgec89971"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org8c6ec71" class="outline-3">
<h3 id="org8c6ec71"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div class="outline-text-3" id="text-5-3">
<p>
The wave function may be expressed in terms of action of the cluster
@ -2332,7 +2332,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="orgcacf103" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org28f54aa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2413,8 +2413,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-org061c33c" class="outline-3">
<h3 id="org061c33c"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org99f4e2a" class="outline-3">
<h3 id="org99f4e2a"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div class="outline-text-3" id="text-5-4">
<p>
The reduced density matrices are defined in the basis of molecular
@ -2486,7 +2486,7 @@ expressed in a basis of a one-electron function
\(g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)\).
</p>
<table id="org0092eb0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org879eaee" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2617,12 +2617,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org047e4af" class="outline-2">
<h2 id="org047e4af"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-orgf886aff" class="outline-2">
<h2 id="orgf886aff"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-orgce7b419" class="outline-3">
<h3 id="orgce7b419"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org6ba38b7" class="outline-3">
<h3 id="org6ba38b7"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div class="outline-text-3" id="text-6-1">
<p>
The Jastrow factor is an $N$-electron function which multiplies the CI
@ -2647,8 +2647,8 @@ following:
</ul>
</div>
<div id="outline-container-org61b22dd" class="outline-4">
<h4 id="org61b22dd"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org532697e" class="outline-4">
<h4 id="org532697e"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div class="outline-text-4" id="text-6-1-1">
<p>
The first form of Jastrow factor is the one used in
@ -2749,8 +2749,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-org401825b" class="outline-4">
<h4 id="org401825b"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-orgafe6f62" class="outline-4">
<h4 id="orgafe6f62"><span class="section-number-4">6.1.2</span> Mu</h4>
<div class="outline-text-4" id="text-6-1-2">
<p>
<a href="https://aip.scitation.org/doi/10.1063/5.0044683">Mu-Jastrow</a> is based on a one-parameter correlation factor that has
@ -2847,10 +2847,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org1248c48" class="outline-4">
<h4 id="org1248c48"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div id="outline-container-orge6da841" class="outline-4">
<h4 id="orge6da841"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div class="outline-text-4" id="text-6-1-3">
<table id="org5f1b10b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org10545db" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2954,8 +2954,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-orgcd34f07" class="outline-2">
<h2 id="orgcd34f07"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-orgcdac528" class="outline-2">
<h2 id="orgcdac528"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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In quantum Monte Carlo calculations, the wave function is evaluated
@ -2969,7 +2969,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3024,7 +3024,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
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<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-05 Fri 14:45</p>
<p class="date">Created: 2023-05-05 Fri 15:07</p>
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