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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>
@ -360,7 +360,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-01-02 Mon 15:08</p>
<p class="date">Created: 2023-01-04 Wed 09:11</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2023-01-02 Mon 15:08 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Examples</title>
@ -346,31 +346,31 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9ca1a8f">1. Accessing sparse quantities (integrals)</a>
<li><a href="#orge6f22b8">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#orgcf91e4f">1.1. Fortran</a>
<li><a href="#org16952b4">1.1. Fortran</a>
<ul>
<li><a href="#org36097df">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org8b873d1">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org01e9761">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orge5f8cd1">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org7269f46">1.1.5. Allocate memory</a></li>
<li><a href="#org3f30613">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgcdfb977">1.1.7. Read two-electron quantities</a>
<li><a href="#orgd7f8bfe">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org6dd8616">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga3cb154">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgda5ba92">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org83d9440">1.1.5. Allocate memory</a></li>
<li><a href="#org99addd3">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgd782dc8">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgd9d9b3e">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org7c967d7">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#orgd74d93a">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org640be86">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgd09d6b4">1.1.8. Compute the energy</a></li>
<li><a href="#orgde89e26">1.1.9. Terminate</a></li>
<li><a href="#orgc19d4ab">1.1.8. Compute the energy</a></li>
<li><a href="#orgf75bc85">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org69f1abc">2. Reading determinants</a>
<li><a href="#orgdc875b1">2. Reading determinants</a>
<ul>
<li><a href="#org0be05a6">2.1. Fortran</a></li>
<li><a href="#orga99b162">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -378,12 +378,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org9ca1a8f" class="outline-2">
<h2 id="org9ca1a8f"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orge6f22b8" class="outline-2">
<h2 id="orge6f22b8"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orgcf91e4f" class="outline-3">
<h3 id="orgcf91e4f"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org16952b4" class="outline-3">
<h3 id="org16952b4"><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>
@ -429,8 +429,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org36097df" class="outline-4">
<h4 id="org36097df"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgd7f8bfe" class="outline-4">
<h4 id="orgd7f8bfe"><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>
@ -445,8 +445,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org8b873d1" class="outline-4">
<h4 id="org8b873d1"><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-org6dd8616" class="outline-4">
<h4 id="org6dd8616"><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)
@ -462,8 +462,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org01e9761" class="outline-4">
<h4 id="org01e9761"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orga3cb154" class="outline-4">
<h4 id="orga3cb154"><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)
@ -477,8 +477,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orge5f8cd1" class="outline-4">
<h4 id="orge5f8cd1"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgda5ba92" class="outline-4">
<h4 id="orgda5ba92"><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)
@ -492,8 +492,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org7269f46" class="outline-4">
<h4 id="org7269f46"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org83d9440" class="outline-4">
<h4 id="org83d9440"><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) )
@ -505,8 +505,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-org3f30613" class="outline-4">
<h4 id="org3f30613"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org99addd3" class="outline-4">
<h4 id="org99addd3"><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)
@ -538,8 +538,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-orgcdfb977" class="outline-4">
<h4 id="orgcdfb977"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgd782dc8" class="outline-4">
<h4 id="orgd782dc8"><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
@ -555,8 +555,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-orgd9d9b3e" class="outline-5">
<h5 id="orgd9d9b3e"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgd74d93a" class="outline-5">
<h5 id="orgd74d93a"><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)
@ -605,8 +605,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-org7c967d7" class="outline-5">
<h5 id="org7c967d7"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org640be86" class="outline-5">
<h5 id="org640be86"><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)
@ -650,8 +650,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-orgd09d6b4" class="outline-4">
<h4 id="orgd09d6b4"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-orgc19d4ab" class="outline-4">
<h4 id="orgc19d4ab"><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
@ -697,8 +697,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-orgde89e26" class="outline-4">
<h4 id="orgde89e26"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgf75bc85" class="outline-4">
<h4 id="orgf75bc85"><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 )
@ -712,12 +712,12 @@ E = E + E_nn
</div>
<div id="outline-container-org69f1abc" class="outline-2">
<h2 id="org69f1abc"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-orgdc875b1" class="outline-2">
<h2 id="orgdc875b1"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org0be05a6" class="outline-3">
<h3 id="org0be05a6"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-orga99b162" class="outline-3">
<h3 id="orga99b162"><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;">test</span>
@ -796,7 +796,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-01-02 Mon 15:08</p>
<p class="date">Created: 2023-01-04 Wed 09:11</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>
<!-- 2023-01-02 Mon 15:08 -->
<!-- 2023-01-04 Wed 09:11 -->
<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>
@ -360,7 +360,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-01-02 Mon 15:08</p>
<p class="date">Created: 2023-01-04 Wed 09:11</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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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>
<!-- 2023-01-02 Mon 15:08 -->
<!-- 2023-01-04 Wed 09:11 -->
<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="#orgb5fcc4f">1. Template for HDF5 definitions</a></li>
<li><a href="#org5dd17e9">2. Template for HDF5 structures</a></li>
<li><a href="#org955a848">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orge6dcf2b">4. Template for HDF5 has a group</a></li>
<li><a href="#org37047c2">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orge430c0c">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org2bd2a43">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgdae39f4">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orga4d5b07">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org936d766">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org1967515">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org92b8d4f">12. Source code for the determinant part</a></li>
<li><a href="#orgbd2d4d9">13. Helper functions</a></li>
<li><a href="#orgaf9edee">1. Template for HDF5 definitions</a></li>
<li><a href="#org5ee59ab">2. Template for HDF5 structures</a></li>
<li><a href="#orgeb30ef4">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org5d9e351">4. Template for HDF5 has a group</a></li>
<li><a href="#org7974169">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orge6c88ea">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orga19f4b6">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org66288d9">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgf5a9fd6">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org1af13eb">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgf1f4350">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org8e17ea4">12. Source code for the determinant part</a></li>
<li><a href="#org699cbad">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgb5fcc4f" class="outline-2">
<h2 id="orgb5fcc4f"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orgaf9edee" class="outline-2">
<h2 id="orgaf9edee"><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-org5dd17e9" class="outline-2">
<h2 id="org5dd17e9"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org5ee59ab" class="outline-2">
<h2 id="org5ee59ab"><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-org955a848" class="outline-2">
<h2 id="org955a848"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgeb30ef4" class="outline-2">
<h2 id="orgeb30ef4"><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-orge6dcf2b" class="outline-2">
<h2 id="orge6dcf2b"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org5d9e351" class="outline-2">
<h2 id="org5d9e351"><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-org37047c2" class="outline-2">
<h2 id="org37047c2"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org7974169" class="outline-2">
<h2 id="org7974169"><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-orge430c0c" class="outline-2">
<h2 id="orge430c0c"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orge6c88ea" class="outline-2">
<h2 id="orge6c88ea"><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>
@ -767,8 +767,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org2bd2a43" class="outline-2">
<h2 id="org2bd2a43"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orga19f4b6" class="outline-2">
<h2 id="orga19f4b6"><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
@ -971,8 +971,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-orgdae39f4" class="outline-2">
<h2 id="orgdae39f4"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org66288d9" class="outline-2">
<h2 id="org66288d9"><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.
@ -1107,8 +1107,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-orga4d5b07" class="outline-2">
<h2 id="orga4d5b07"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgf5a9fd6" class="outline-2">
<h2 id="orgf5a9fd6"><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-org936d766" class="outline-2">
<h2 id="org936d766"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org1af13eb" class="outline-2">
<h2 id="org1af13eb"><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-org1967515" class="outline-2">
<h2 id="org1967515"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgf1f4350" class="outline-2">
<h2 id="orgf1f4350"><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-org92b8d4f" class="outline-2">
<h2 id="org92b8d4f"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org8e17ea4" class="outline-2">
<h2 id="org8e17ea4"><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.
@ -1579,8 +1579,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-orgbd2d4d9" class="outline-2">
<h2 id="orgbd2d4d9"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org699cbad" class="outline-2">
<h2 id="org699cbad"><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>
@ -1843,7 +1843,7 @@ 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: 2023-01-02 Mon 15:08</p>
<p class="date">Created: 2023-01-04 Wed 09:11</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

106
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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>
<!-- 2023-01-02 Mon 15:08 -->
<!-- 2023-01-04 Wed 09:11 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
@ -324,23 +324,23 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgecb9847">1. Template for group-related structures in text back end</a></li>
<li><a href="#org98d3e4a">2. Template for general structure in text back end</a></li>
<li><a href="#org20e971f">3. Initialize function (constant part)</a></li>
<li><a href="#org4a77764">4. Deinitialize function (templated part)</a></li>
<li><a href="#org15c51fa">5. Flush function (templated part)</a></li>
<li><a href="#orgb015c3a">6. Template for text read a group</a></li>
<li><a href="#orgd59bb7e">7. Template for text has a group</a></li>
<li><a href="#org0fd7251">8. Template for text flush a group</a></li>
<li><a href="#org2435d76">9. Template for text free memory</a></li>
<li><a href="#org5987ec4">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org94bce44">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgf723fbc">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orga5e9032">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org8c210fb">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org97857ff">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgb4f7f27">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org799adc9">17. Source code for the determinant part</a></li>
<li><a href="#org43edccd">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgcf3c781">2. Template for general structure in text back end</a></li>
<li><a href="#orgd4f5ed6">3. Initialize function (constant part)</a></li>
<li><a href="#org0c140ed">4. Deinitialize function (templated part)</a></li>
<li><a href="#org4ffd7ad">5. Flush function (templated part)</a></li>
<li><a href="#org27999a0">6. Template for text read a group</a></li>
<li><a href="#org4f1cfa3">7. Template for text has a group</a></li>
<li><a href="#orgb243fc8">8. Template for text flush a group</a></li>
<li><a href="#org39da28e">9. Template for text free memory</a></li>
<li><a href="#orge1c7ba8">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org4a13709">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org0ba2fc5">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org0d27a0e">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org14a3e8f">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgc6a84b3">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgb68de95">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orge6da6aa">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-orgecb9847" class="outline-2">
<h2 id="orgecb9847"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org43edccd" class="outline-2">
<h2 id="org43edccd"><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-org98d3e4a" class="outline-2">
<h2 id="org98d3e4a"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgcf3c781" class="outline-2">
<h2 id="orgcf3c781"><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-org20e971f" class="outline-2">
<h2 id="org20e971f"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-orgd4f5ed6" class="outline-2">
<h2 id="orgd4f5ed6"><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>
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org4a77764" class="outline-2">
<h2 id="org4a77764"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org0c140ed" class="outline-2">
<h2 id="org0c140ed"><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>
@ -594,8 +594,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org15c51fa" class="outline-2">
<h2 id="org15c51fa"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org4ffd7ad" class="outline-2">
<h2 id="org4ffd7ad"><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>
@ -618,8 +618,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgb015c3a" class="outline-2">
<h2 id="orgb015c3a"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org27999a0" class="outline-2">
<h2 id="org27999a0"><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*
@ -845,8 +845,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgd59bb7e" class="outline-2">
<h2 id="orgd59bb7e"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org4f1cfa3" class="outline-2">
<h2 id="org4f1cfa3"><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>
@ -886,8 +886,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org0fd7251" class="outline-2">
<h2 id="org0fd7251"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-orgb243fc8" class="outline-2">
<h2 id="orgb243fc8"><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>
@ -951,8 +951,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org2435d76" class="outline-2">
<h2 id="org2435d76"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org39da28e" class="outline-2">
<h2 id="org39da28e"><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.
@ -1021,8 +1021,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org5987ec4" class="outline-2">
<h2 id="org5987ec4"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orge1c7ba8" class="outline-2">
<h2 id="orge1c7ba8"><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>
@ -1085,8 +1085,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org94bce44" class="outline-2">
<h2 id="org94bce44"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org4a13709" class="outline-2">
<h2 id="org4a13709"><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.
@ -1182,8 +1182,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgf723fbc" class="outline-2">
<h2 id="orgf723fbc"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org0ba2fc5" class="outline-2">
<h2 id="org0ba2fc5"><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.
@ -1284,8 +1284,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orga5e9032" class="outline-2">
<h2 id="orga5e9032"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org0d27a0e" class="outline-2">
<h2 id="org0d27a0e"><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>
@ -1359,8 +1359,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org8c210fb" class="outline-2">
<h2 id="org8c210fb"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org14a3e8f" class="outline-2">
<h2 id="org14a3e8f"><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
@ -1650,8 +1650,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org97857ff" class="outline-2">
<h2 id="org97857ff"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-orgc6a84b3" class="outline-2">
<h2 id="orgc6a84b3"><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
@ -1881,8 +1881,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-orgb4f7f27" class="outline-2">
<h2 id="orgb4f7f27"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgb68de95" class="outline-2">
<h2 id="orgb68de95"><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>
@ -1910,8 +1910,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-org799adc9" class="outline-2">
<h2 id="org799adc9"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-orge6da6aa" class="outline-2">
<h2 id="orge6da6aa"><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
@ -2103,7 +2103,7 @@ 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: 2023-01-02 Mon 15:08</p>
<p class="date">Created: 2023-01-04 Wed 09:11</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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