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README.html
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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>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-21 Fri 11:33</p>
<p class="date">Created: 2022-01-24 Mon 17:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2022-01-21 Fri 11:33 -->
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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>
@ -333,24 +333,24 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org2100f3b">1. Accessing sparse quantities</a>
<li><a href="#orgacb424b">1. Accessing sparse quantities</a>
<ul>
<li><a href="#org5a95888">1.1. Fortran</a>
<li><a href="#org68425e2">1.1. Fortran</a>
<ul>
<li><a href="#org675aca3">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org921e888">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org9d6de53">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org1fc2715">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgc378548">1.1.5. Allocate memory</a></li>
<li><a href="#org7fffe3f">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgbae0f7a">1.1.7. Read two-electron quantities</a>
<li><a href="#org740c76f">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org1c2c3ca">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga7c53cc">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgdefc685">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org12c1cee">1.1.5. Allocate memory</a></li>
<li><a href="#org4c09e65">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org51207f7">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org3a8db52">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgd46abf2">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org0f68a1a">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org75754f5">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgf7b4d42">1.1.8. Compute the energy</a></li>
<li><a href="#orgd039657">1.1.9. Terminate</a></li>
<li><a href="#orgc4f3a55">1.1.8. Compute the energy</a></li>
<li><a href="#org89706f7">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
@ -360,12 +360,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org2100f3b" class="outline-2">
<h2 id="org2100f3b"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-orgacb424b" class="outline-2">
<h2 id="orgacb424b"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org5a95888" class="outline-3">
<h3 id="org5a95888"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org68425e2" class="outline-3">
<h3 id="org68425e2"><span class="section-number-3">1.1</span> Fortran</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
@ -411,8 +411,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org675aca3" class="outline-4">
<h4 id="org675aca3"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org740c76f" class="outline-4">
<h4 id="org740c76f"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div class="outline-text-4" id="text-1-1-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> i, j, k, l, m</span>
@ -427,8 +427,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org921e888" class="outline-4">
<h4 id="org921e888"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div id="outline-container-org1c2c3ca" class="outline-4">
<h4 id="org1c2c3ca"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div class="outline-text-4" id="text-1-1-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
@ -444,8 +444,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org9d6de53" class="outline-4">
<h4 id="org9d6de53"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orga7c53cc" class="outline-4">
<h4 id="orga7c53cc"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-1-1-3">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
@ -459,8 +459,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org1fc2715" class="outline-4">
<h4 id="org1fc2715"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgdefc685" class="outline-4">
<h4 id="orgdefc685"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-1-1-4">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
@ -474,8 +474,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgc378548" class="outline-4">
<h4 id="orgc378548"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org12c1cee" class="outline-4">
<h4 id="org12c1cee"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div class="outline-text-4" id="text-1-1-5">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
@ -487,8 +487,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-org7fffe3f" class="outline-4">
<h4 id="org7fffe3f"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org4c09e65" class="outline-4">
<h4 id="org4c09e65"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-1-1-6">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@ -520,8 +520,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-orgbae0f7a" class="outline-4">
<h4 id="orgbae0f7a"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org51207f7" class="outline-4">
<h4 id="org51207f7"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-1-1-7">
<p>
Reading is done with OpenMP. Each thread reads its own buffer, and
@ -537,8 +537,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org3a8db52" class="outline-5">
<h5 id="org3a8db52"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org0f68a1a" class="outline-5">
<h5 id="org0f68a1a"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-1-1-7-1">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
@ -587,8 +587,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-orgd46abf2" class="outline-5">
<h5 id="orgd46abf2"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org75754f5" class="outline-5">
<h5 id="org75754f5"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-1-1-7-2">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
@ -632,8 +632,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-orgf7b4d42" class="outline-4">
<h4 id="orgf7b4d42"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-orgc4f3a55" class="outline-4">
<h4 id="orgc4f3a55"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div class="outline-text-4" id="text-1-1-8">
<p>
When the orbitals are real, we can use
@ -679,8 +679,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-orgd039657" class="outline-4">
<h4 id="orgd039657"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org89706f7" class="outline-4">
<h4 id="org89706f7"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div class="outline-text-4" id="text-1-1-9">
<div class="org-src-container">
<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
@ -695,7 +695,7 @@ E = E + E_nn
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-21 Fri 11:33</p>
<p class="date">Created: 2022-01-24 Mon 17:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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index.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-21 Fri 11:33 -->
<!-- 2022-01-24 Mon 17:22 -->
<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>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-21 Fri 11:33</p>
<p class="date">Created: 2022-01-24 Mon 17:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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templator_front.html
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templator_hdf5.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-21 Fri 11:33 -->
<!-- 2022-01-24 Mon 17:22 -->
<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>
@ -311,29 +311,29 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org6aeed92">1. HDF5 back end</a>
<li><a href="#org296fc0b">1. HDF5 back end</a>
<ul>
<li><a href="#org5c79978">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org1fe8d16">1.2. Template for HDF5 structures</a></li>
<li><a href="#org857b698">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgeedb644">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org11a7705">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org6d287dd">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#org9829b69">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgb4c3604">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#org6721a21">1.9. Helper functions</a></li>
<li><a href="#orgcbf5324">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org1362474">1.2. Template for HDF5 structures</a></li>
<li><a href="#org6fb743f">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org1e43f1f">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#orgcbd0458">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#orgeb6cfbd">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#org97b0074">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org06de11a">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#orgeb3710c">1.9. Helper functions</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org6aeed92" class="outline-2">
<h2 id="org6aeed92"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-org296fc0b" class="outline-2">
<h2 id="org296fc0b"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org5c79978" class="outline-3">
<h3 id="org5c79978"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-orgcbf5324" class="outline-3">
<h3 id="orgcbf5324"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div class="outline-text-3" id="text-1-1">
<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>
@ -345,8 +345,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org1fe8d16" class="outline-3">
<h3 id="org1fe8d16"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-org1362474" class="outline-3">
<h3 id="org1362474"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div class="outline-text-3" id="text-1-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_hdf5_s</span> {
@ -359,8 +359,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org857b698" class="outline-3">
<h3 id="org857b698"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-org6fb743f" class="outline-3">
<h3 id="org6fb743f"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div class="outline-text-3" id="text-1-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -460,8 +460,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgeedb644" class="outline-3">
<h3 id="orgeedb644"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-org1e43f1f" class="outline-3">
<h3 id="org1e43f1f"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div class="outline-text-3" id="text-1-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -555,8 +555,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org11a7705" class="outline-3">
<h3 id="org11a7705"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-orgcbd0458" class="outline-3">
<h3 id="orgcbd0458"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div class="outline-text-3" id="text-1-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -678,8 +678,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org6d287dd" class="outline-3">
<h3 id="org6d287dd"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of sparse data</h3>
<div id="outline-container-orgeb6cfbd" class="outline-3">
<h3 id="orgeb6cfbd"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of sparse data</h3>
<div class="outline-text-3" id="text-1-6">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -880,8 +880,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org9829b69" class="outline-3">
<h3 id="org9829b69"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-org97b0074" class="outline-3">
<h3 id="org97b0074"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div class="outline-text-3" id="text-1-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1085,8 +1085,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-orgb4c3604" class="outline-3">
<h3 id="orgb4c3604"><span class="section-number-3">1.8</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-org06de11a" class="outline-3">
<h3 id="org06de11a"><span class="section-number-3">1.8</span> Template for HDF5 has/read/write the string attribute</h3>
<div class="outline-text-3" id="text-1-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1208,8 +1208,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-org6721a21" class="outline-3">
<h3 id="org6721a21"><span class="section-number-3">1.9</span> Helper functions</h3>
<div id="outline-container-orgeb3710c" class="outline-3">
<h3 id="orgeb3710c"><span class="section-number-3">1.9</span> Helper functions</h3>
<div class="outline-text-3" id="text-1-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1471,7 +1471,7 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-21 Fri 11:33</p>
<p class="date">Created: 2022-01-24 Mon 17:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

82
templator_text.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-21 Fri 11:33 -->
<!-- 2022-01-24 Mon 17:22 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
@ -311,28 +311,28 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org2bf6565">1. TEXT back end</a>
<li><a href="#orge38e1d2">1. TEXT back end</a>
<ul>
<li><a href="#org68d139b">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#orgb6ad1c8">1.2. Template for general structure in text back end</a></li>
<li><a href="#orgcb4f142">1.3. Initialize function (constant part)</a></li>
<li><a href="#org9bfc752">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orge22acfc">1.5. Template for text read struct</a></li>
<li><a href="#org0960c37">1.6. Template for text flush struct</a></li>
<li><a href="#orge4d6b83">1.7. Template for text free memory</a></li>
<li><a href="#org13436e7">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orga01dc32">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#orga6e0e20">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org1eb10f3">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org0eb6313">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgfb08429">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org35452f8">1.2. Template for general structure in text back end</a></li>
<li><a href="#org13b5fd7">1.3. Initialize function (constant part)</a></li>
<li><a href="#org5876a02">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orgf13b5c9">1.5. Template for text read struct</a></li>
<li><a href="#orgb973239">1.6. Template for text flush struct</a></li>
<li><a href="#org2877301">1.7. Template for text free memory</a></li>
<li><a href="#org7e6af7e">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#org4ae2244">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org5e429ca">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#orge6ea6a3">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org247f33d">1.12. Template for has/read/write the dataset of sparse data</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org2bf6565" class="outline-2">
<h2 id="org2bf6565"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-orge38e1d2" class="outline-2">
<h2 id="orge38e1d2"><span class="section-number-2">1</span> TEXT back end</h2>
<div class="outline-text-2" id="text-1">
<p>
The "file" produced by the text back end is a directory with one
@ -353,8 +353,8 @@ The file is written when closed, or when the flush function is called.
</p>
</div>
<div id="outline-container-org68d139b" class="outline-3">
<h3 id="org68d139b"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-orgfb08429" class="outline-3">
<h3 id="orgfb08429"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
@ -373,8 +373,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orgb6ad1c8" class="outline-3">
<h3 id="orgb6ad1c8"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org35452f8" class="outline-3">
<h3 id="org35452f8"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div class="outline-text-3" id="text-1-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_text_s</span> {
@ -387,8 +387,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orgcb4f142" class="outline-3">
<h3 id="orgcb4f142"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-org13b5fd7" class="outline-3">
<h3 id="org13b5fd7"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div class="outline-text-3" id="text-1-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -531,8 +531,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org9bfc752" class="outline-3">
<h3 id="org9bfc752"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-org5876a02" class="outline-3">
<h3 id="org5876a02"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div class="outline-text-3" id="text-1-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -554,8 +554,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orge22acfc" class="outline-3">
<h3 id="orge22acfc"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-orgf13b5c9" class="outline-3">
<h3 id="orgf13b5c9"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div class="outline-text-3" id="text-1-5">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -847,8 +847,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org0960c37" class="outline-3">
<h3 id="org0960c37"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-orgb973239" class="outline-3">
<h3 id="orgb973239"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div class="outline-text-3" id="text-1-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -913,8 +913,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orge4d6b83" class="outline-3">
<h3 id="orge4d6b83"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-org2877301" class="outline-3">
<h3 id="org2877301"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div class="outline-text-3" id="text-1-7">
<p>
Memory is allocated when reading. The following function frees memory.
@ -959,8 +959,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-org13436e7" class="outline-3">
<h3 id="org13436e7"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-org7e6af7e" class="outline-3">
<h3 id="org7e6af7e"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div class="outline-text-3" id="text-1-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1023,8 +1023,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-orga01dc32" class="outline-3">
<h3 id="orga01dc32"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-org4ae2244" class="outline-3">
<h3 id="org4ae2244"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div class="outline-text-3" id="text-1-9">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1120,8 +1120,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orga6e0e20" class="outline-3">
<h3 id="orga6e0e20"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-org5e429ca" class="outline-3">
<h3 id="org5e429ca"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div class="outline-text-3" id="text-1-10">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1222,8 +1222,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org1eb10f3" class="outline-3">
<h3 id="org1eb10f3"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-orge6ea6a3" class="outline-3">
<h3 id="orge6ea6a3"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div class="outline-text-3" id="text-1-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1297,8 +1297,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org0eb6313" class="outline-3">
<h3 id="org0eb6313"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div id="outline-container-org247f33d" class="outline-3">
<h3 id="org247f33d"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div class="outline-text-3" id="text-1-12">
<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
@ -1575,7 +1575,7 @@ User provides indices and values of the sparse array as two separate variables.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-21 Fri 11:33</p>
<p class="date">Created: 2022-01-24 Mon 17:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

116
trex.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-21 Fri 11:33 -->
<!-- 2022-01-24 Mon 17:22 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREX Configuration file</title>
@ -333,33 +333,33 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org5271fe4">1. Metadata (metadata group)</a></li>
<li><a href="#orgcefd04e">2. Electron (electron group)</a></li>
<li><a href="#org824cc40">3. Nucleus (nucleus group)</a></li>
<li><a href="#org2781dbd">4. Effective core potentials (ecp group)</a>
<li><a href="#org67be512">1. Metadata (metadata group)</a></li>
<li><a href="#org3e95b37">2. Electron (electron group)</a></li>
<li><a href="#orgba6a084">3. Nucleus (nucleus group)</a></li>
<li><a href="#orga47d7f9">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org66d0b7f">4.1. Example</a></li>
<li><a href="#orgb42ac10">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org31cafdb">5. Basis set (basis group)</a>
<li><a href="#org9769ac1">5. Basis set (basis group)</a>
<ul>
<li><a href="#org84d7629">5.1. Example</a></li>
<li><a href="#orgc749b8c">5.1. Example</a></li>
</ul>
</li>
<li><a href="#orgca3a397">6. Atomic orbitals (ao group)</a>
<li><a href="#org793b44d">6. Atomic orbitals (ao group)</a>
<ul>
<li><a href="#ao_one_e">6.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
<li><a href="#ao_two_e">6.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#orga285b50">7. Molecular orbitals (mo group)</a>
<li><a href="#org15c7250">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org1633812">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org8dc9ea7">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org3b49505">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgced8595">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#orgfa01dd4">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#orgd609cb3">9. Reduced density matrices (rdm group)</a></li>
<li><a href="#org250ed58">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org037f311">9. Reduced density matrices (rdm group)</a></li>
</ul>
</div>
</div>
@ -409,8 +409,8 @@ fetched using multiple function calls to perform I/O on buffers.
</p>
<div id="outline-container-org5271fe4" class="outline-2">
<h2 id="org5271fe4"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org67be512" class="outline-2">
<h2 id="org67be512"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect our files to be archived in open-data repositories, we
@ -420,7 +420,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="org8f46b8c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbef8356" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -487,15 +487,15 @@ authors of the file, and a textual description.
</div>
</div>
<div id="outline-container-orgcefd04e" class="outline-2">
<h2 id="orgcefd04e"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org3e95b37" class="outline-2">
<h2 id="org3e95b37"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div class="outline-text-2" id="text-2">
<p>
We consider wave functions expressed in the spin-free formalism, where
the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="orgd09ac06" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org14d2718" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -534,15 +534,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org824cc40" class="outline-2">
<h2 id="org824cc40"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-orgba6a084" class="outline-2">
<h2 id="orgba6a084"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div class="outline-text-2" id="text-3">
<p>
The nuclei are considered as fixed point charges. Coordinates are
given in Cartesian \((x,y,z)\) format.
</p>
<table id="org5708791" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org757305b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -609,8 +609,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org2781dbd" class="outline-2">
<h2 id="org2781dbd"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orga47d7f9" class="outline-2">
<h2 id="orga47d7f9"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div class="outline-text-2" id="text-4">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -643,7 +643,7 @@ The functions \(V_{A\ell}\) are parameterized as:
See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.4984046</a> or <a href="https://doi.org/10.1063/1.5121006">https://doi.org/10.1063/1.5121006</a> for more info.
</p>
<table id="orgda71739" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org770cf4c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -741,8 +741,8 @@ The latter causes issues when written before <code>ang_mom</code> in the TREXIO
</p>
</div>
<div id="outline-container-org66d0b7f" class="outline-3">
<h3 id="org66d0b7f"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-orgb42ac10" class="outline-3">
<h3 id="orgb42ac10"><span class="section-number-3">4.1</span> Example</h3>
<div class="outline-text-3" id="text-4-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -805,8 +805,8 @@ power = [
</div>
</div>
<div id="outline-container-org31cafdb" class="outline-2">
<h2 id="org31cafdb"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org9769ac1" class="outline-2">
<h2 id="org9769ac1"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div class="outline-text-2" id="text-5">
<p>
We consider here basis functions centered on nuclei. Hence, we enable
@ -859,7 +859,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).
All the basis set parameters are stored in one-dimensional arrays:
</p>
<table id="orgcf8afe3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7be90af" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -953,8 +953,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-org84d7629" class="outline-3">
<h3 id="org84d7629"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-orgc749b8c" class="outline-3">
<h3 id="orgc749b8c"><span class="section-number-3">5.1</span> Example</h3>
<div class="outline-text-3" id="text-5-1">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1032,8 +1032,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgca3a397" class="outline-2">
<h2 id="orgca3a397"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org793b44d" class="outline-2">
<h2 id="org793b44d"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div class="outline-text-2" id="text-6">
<p>
Going from the atomic basis set to AOs implies a systematic
@ -1086,13 +1086,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org31cafdb">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org9769ac1">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
normalization factor of the atomic orbitals in spherical coordinates.
The normalization factor of the \(xy\) function which should be
introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</p>
<table id="orgb7ee3e5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3ddcdaa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1144,8 +1144,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org57b1061" class="outline-3">
<h3 id="ao_one_e"><a id="org57b1061"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgb9191c9" class="outline-3">
<h3 id="ao_one_e"><a id="orgb9191c9"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_one_e">
<ul class="org-ul">
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
@ -1163,7 +1163,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
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<table id="org2aecfd1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1230,8 +1230,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgbf8fd49" class="outline-3">
<h3 id="ao_two_e"><a id="orgbf8fd49"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org6aeee3d" class="outline-3">
<h3 id="ao_two_e"><a id="org6aeee3d"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_two_e">
<p>
The two-electron integrals for a two-electron operator \(\hat{O}\) are
@ -1252,7 +1252,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
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<table id="orgdef6991" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1292,10 +1292,10 @@ notation.
</div>
</div>
<div id="outline-container-orga285b50" class="outline-2">
<h2 id="orga285b50"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org15c7250" class="outline-2">
<h2 id="org15c7250"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org4566220" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf720360" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1361,8 +1361,8 @@ notation.
</table>
</div>
<div id="outline-container-org1633812" class="outline-3">
<h3 id="org1633812"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org3b49505" class="outline-3">
<h3 id="org3b49505"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-1">
<p>
The operators as the same as those defined in the
@ -1370,7 +1370,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org4da72c6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org720caa1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1437,8 +1437,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org8dc9ea7" class="outline-3">
<h3 id="org8dc9ea7"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orgced8595" class="outline-3">
<h3 id="orgced8595"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-2">
<p>
The operators as the same as those defined in the
@ -1446,7 +1446,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org2965362" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5ab3f27" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1486,11 +1486,11 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgfa01dd4" class="outline-2">
<h2 id="orgfa01dd4"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-org250ed58" class="outline-2">
<h2 id="org250ed58"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-orgd609cb3" class="outline-2">
<h2 id="orgd609cb3"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org037f311" class="outline-2">
<h2 id="org037f311"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1543,7 +1543,7 @@ The total energy can be computed as:
\]
</p>
<table id="orga3178c0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbfeeafe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1626,7 +1626,7 @@ The total energy can be computed as:
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-21 Fri 11:33</p>
<p class="date">Created: 2022-01-24 Mon 17:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>