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README.html
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<head>
<!-- 2022-01-24 Mon 17:22 -->
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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: 2022-01-24 Mon 17:22</p>
<p class="date">Created: 2022-01-25 Tue 15:19</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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examples.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<head>
<!-- 2022-01-24 Mon 17:22 -->
<!-- 2022-01-25 Tue 15:19 -->
<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="#orgacb424b">1. Accessing sparse quantities</a>
<li><a href="#org510b6d3">1. Accessing sparse quantities</a>
<ul>
<li><a href="#org68425e2">1.1. Fortran</a>
<li><a href="#org41943a1">1.1. Fortran</a>
<ul>
<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>
<li><a href="#orgc1fea90">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orge0221dd">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org8c86df5">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org98c6d4b">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orga2626ef">1.1.5. Allocate memory</a></li>
<li><a href="#org418387a">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orga4c8a95">1.1.7. Read two-electron quantities</a>
<ul>
<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>
<li><a href="#org0b5b544">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org83b7eab">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgc4f3a55">1.1.8. Compute the energy</a></li>
<li><a href="#org89706f7">1.1.9. Terminate</a></li>
<li><a href="#org4d88245">1.1.8. Compute the energy</a></li>
<li><a href="#orga2338f4">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-orgacb424b" class="outline-2">
<h2 id="orgacb424b"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-org510b6d3" class="outline-2">
<h2 id="org510b6d3"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org68425e2" class="outline-3">
<h3 id="org68425e2"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org41943a1" class="outline-3">
<h3 id="org41943a1"><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-org740c76f" class="outline-4">
<h4 id="org740c76f"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgc1fea90" class="outline-4">
<h4 id="orgc1fea90"><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-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 id="outline-container-orge0221dd" class="outline-4">
<h4 id="orge0221dd"><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-orga7c53cc" class="outline-4">
<h4 id="orga7c53cc"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org8c86df5" class="outline-4">
<h4 id="org8c86df5"><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-orgdefc685" class="outline-4">
<h4 id="orgdefc685"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org98c6d4b" class="outline-4">
<h4 id="org98c6d4b"><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-org12c1cee" class="outline-4">
<h4 id="org12c1cee"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-orga2626ef" class="outline-4">
<h4 id="orga2626ef"><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-org4c09e65" class="outline-4">
<h4 id="org4c09e65"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org418387a" class="outline-4">
<h4 id="org418387a"><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-org51207f7" class="outline-4">
<h4 id="org51207f7"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orga4c8a95" class="outline-4">
<h4 id="orga4c8a95"><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-org0f68a1a" class="outline-5">
<h5 id="org0f68a1a"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org0b5b544" class="outline-5">
<h5 id="org0b5b544"><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-org75754f5" class="outline-5">
<h5 id="org75754f5"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org83b7eab" class="outline-5">
<h5 id="org83b7eab"><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-orgc4f3a55" class="outline-4">
<h4 id="orgc4f3a55"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org4d88245" class="outline-4">
<h4 id="org4d88245"><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-org89706f7" class="outline-4">
<h4 id="org89706f7"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orga2338f4" class="outline-4">
<h4 id="orga2338f4"><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: 2022-01-24 Mon 17:22</p>
<p class="date">Created: 2022-01-25 Tue 15:19</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
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>
<!-- 2022-01-24 Mon 17:22 -->
<!-- 2022-01-25 Tue 15:19 -->
<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: 2022-01-24 Mon 17:22</p>
<p class="date">Created: 2022-01-25 Tue 15:19</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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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-24 Mon 17:22 -->
<!-- 2022-01-25 Tue 15:19 -->
<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>
@ -311,30 +311,23 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org296fc0b">1. HDF5 back end</a>
<ul>
<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>
<li><a href="#orgdd23018">1. Template for HDF5 definitions</a></li>
<li><a href="#orgf4ca766">2. Template for HDF5 structures</a></li>
<li><a href="#orgdd2fa5c">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org7f3dcbe">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orge503562">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgd7bf701">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org9503454">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org1a93155">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgad30cf3">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgdfe2065">10. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org296fc0b" class="outline-2">
<h2 id="org296fc0b"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-orgdd23018" class="outline-2">
<h2 id="orgdd23018"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div class="outline-text-2" id="text-1">
</div>
<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>
<span style="color: #483d8b;">#define</span> $GROUP_NUM$_NAME <span style="color: #8b2252;">"$group_num$"</span>
@ -345,9 +338,9 @@ for the JavaScript code in this tag.
</div>
</div>
<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 id="outline-container-orgf4ca766" class="outline-2">
<h2 id="orgf4ca766"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div class="outline-text-2" id="text-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> {
<span style="color: #228b22;">trexio_t</span> <span style="color: #a0522d;">parent</span> ;
@ -359,9 +352,9 @@ for the JavaScript code in this tag.
</div>
</div>
<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 id="outline-container-orgdd2fa5c" class="outline-2">
<h2 id="orgdd2fa5c"><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>
<span style="color: #0000ff;">trexio_hdf5_inquire</span>(<span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span>* <span style="color: #a0522d;">file_name</span>)
@ -399,6 +392,7 @@ for the JavaScript code in this tag.
// <span style="color: #b22222;">reading the existing file -&gt; open as RDONLY</span>
f-&gt;file_id = H5Fopen(file-&gt;file_name, H5F_ACC_RDONLY, H5P_DEFAULT);
<span style="color: #a020f0;">break</span>;
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'u'</span>:
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'w'</span>:
// <span style="color: #b22222;">writing the existing file -&gt; open as RDWRITE</span>
f-&gt;file_id = H5Fopen(file-&gt;file_name, H5F_ACC_RDWR, H5P_DEFAULT);
@ -411,6 +405,7 @@ for the JavaScript code in this tag.
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'r'</span>:
// <span style="color: #b22222;">reading non-existing file -&gt; error</span>
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'u'</span>:
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'w'</span>:
// <span style="color: #b22222;">writing non-existing file -&gt; create it</span>
f-&gt;file_id = H5Fcreate(file-&gt;file_name, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
@ -424,6 +419,7 @@ for the JavaScript code in this tag.
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'r'</span>:
f-&gt;$group$_group = H5Gopen(f-&gt;file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">break</span>;
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'u'</span>:
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'w'</span>:
<span style="color: #a020f0;">if</span> (f_exists == 1) {
f-&gt;$group$_group = H5Gopen(f-&gt;file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
@ -460,9 +456,9 @@ for the JavaScript code in this tag.
</div>
</div>
<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 id="outline-container-org7f3dcbe" class="outline-2">
<h2 id="org7f3dcbe"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</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>
<span style="color: #0000ff;">trexio_hdf5_read_$group_num$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, $group_num_dtype_double$* <span style="color: #a020f0;">const</span> num)
@ -501,29 +497,38 @@ for the JavaScript code in this tag.
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
/* <span style="color: #b22222;">Write the dimensioning variables </span>*/
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dtype</span> = H5Tcopy(H5T_$GROUP_NUM_H5_DTYPE$);
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace</span> = H5Screate(H5S_SCALAR);
/* <span style="color: #b22222;">Delete the attribute if it exists and if the file is open in UNSAFE mode </span>*/
<span style="color: #a020f0;">if</span> (trexio_hdf5_has_$group_num$(file) == TREXIO_SUCCESS &amp;&amp; file-&gt;mode == <span style="color: #8b2252;">'u'</span>) {
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status_del</span> = H5Adelete(f-&gt;$group$_group, $GROUP_NUM$_NAME);
<span style="color: #a020f0;">if</span> (status_del &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">num_id</span> = H5Acreate(f-&gt;$group$_group, $GROUP_NUM$_NAME,
dtype, dspace, H5P_DEFAULT, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (num_id &lt;= 0) {
H5Sclose(dspace);
H5Tclose(dtype);
/* <span style="color: #b22222;">Setup the dataspace </span>*/
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dtype_id</span> = H5Tcopy(H5T_$GROUP_NUM_H5_DTYPE$);
<span style="color: #a020f0;">if</span> (dtype_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace_id</span> = H5Screate(H5S_SCALAR);
<span style="color: #a020f0;">if</span> (dspace_id &lt;= 0) {
H5Tclose(dtype_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Awrite(num_id, dtype, &amp;(num));
<span style="color: #a020f0;">if</span> (status &lt; 0) {
H5Aclose(num_id);
H5Sclose(dspace);
H5Tclose(dtype);
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">num_id</span> = H5Acreate(f-&gt;$group$_group,
$GROUP_NUM$_NAME,
dtype_id, dspace_id,
H5P_DEFAULT, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (num_id &lt;= 0) {
H5Sclose(dspace_id);
H5Tclose(dtype_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
H5Sclose(dspace);
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Awrite(num_id, dtype_id, &amp;num);
H5Sclose(dspace_id);
H5Aclose(num_id);
H5Tclose(dtype);
H5Tclose(dtype_id);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
@ -555,9 +560,9 @@ for the JavaScript code in this tag.
</div>
</div>
<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 id="outline-container-orge503562" class="outline-2">
<h2 id="orge503562"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</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>
<span style="color: #0000ff;">trexio_hdf5_read_$group_dset$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, $group_dset_dtype$* <span style="color: #a020f0;">const</span> $group_dset$, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">rank</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint64_t</span>* <span style="color: #a0522d;">dims</span>)
@ -623,30 +628,41 @@ for the JavaScript code in this tag.
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
<span style="color: #a020f0;">if</span> ( H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME) != 1 ) {
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTmake_dataset(f-&gt;$group$_group,
$GROUP_DSET$_NAME,
(<span style="color: #228b22;">int</span>) rank, (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span>*) dims,
H5T_$GROUP_DSET_H5_DTYPE$,
$group_dset$);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
} <span style="color: #a020f0;">else</span> {
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span> = H5Dopen(f-&gt;$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Dwrite(dset_id,
H5T_$GROUP_DSET_H5_DTYPE$,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
$group_dset$);
H5Dclose(dset_id);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
/*
<span style="color: #b22222;"> Try to delete an existing dataset by unlinking it from the group (UNSAFE mode).</span>
<span style="color: #b22222;"> NOTE: In principle, HDF5 should see the deallocated (unused) file space and free it,</span>
<span style="color: #b22222;"> thus reducing the size of the HDF5 file. In practic, this is not always the case.</span>
<span style="color: #b22222;"> Consider using HDF5-native h5repack utility after deleting/overwriting big datasets.</span>
<span style="color: #b22222;"> </span>*/
<span style="color: #a020f0;">if</span> (H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME) == 1 &amp;&amp; file-&gt;mode == <span style="color: #8b2252;">'u'</span>) {
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status_del</span> = H5Ldelete(f-&gt;$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (status_del &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace_id</span> = H5Screate_simple( (<span style="color: #228b22;">int</span>) rank, (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span>*) dims, <span style="color: #008b8b;">NULL</span>);
<span style="color: #a020f0;">if</span> (dspace_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span> = H5Dcreate (f-&gt;$group$_group,
$GROUP_DSET$_NAME,
H5T_$GROUP_DSET_H5_DTYPE$,
dspace_id,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) {
H5Sclose(dspace_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Dwrite(dset_id,
H5T_$GROUP_DSET_H5_DTYPE$,
H5S_ALL,
dspace_id,
H5P_DEFAULT,
$group_dset$);
H5Dclose(dset_id);
H5Sclose(dspace_id);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
@ -678,9 +694,9 @@ for the JavaScript code in this tag.
</div>
</div>
<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">
<div id="outline-container-orgd7bf701" class="outline-2">
<h2 id="orgd7bf701"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-6">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
due to the fact that the sparse data will be written in chunks of user-defined size.
@ -880,9 +896,9 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<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 id="outline-container-org9503454" class="outline-2">
<h2 id="org9503454"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</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>
<span style="color: #0000ff;">trexio_hdf5_read_$group_dset$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #228b22;">char</span>* <span style="color: #a020f0;">const</span> $group_dset$, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">rank</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint64_t</span>* <span style="color: #a0522d;">dims</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">max_str_len</span>)
@ -1000,6 +1016,18 @@ due to the fact that the sparse data will be written in chunks of user-defined s
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
/*
<span style="color: #b22222;"> Try to delete an existing dataset by unlinking it from the group (UNSAFE mode).</span>
<span style="color: #b22222;"> NOTE: In principle, HDF5 should see the deallocated (unused) file space and free it,</span>
<span style="color: #b22222;"> thus reducing the size of the HDF5 file. In practic, this is not always the case.</span>
<span style="color: #b22222;"> Consider using HDF5-provided h5repack utility after deleting/overwriting big datasets.</span>
<span style="color: #b22222;"> </span>*/
<span style="color: #a020f0;">if</span> (H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME) == 1 &amp;&amp; file-&gt;mode == <span style="color: #8b2252;">'u'</span>) {
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status_del</span> = H5Ldelete(f-&gt;$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (status_del &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span>;
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span>;
@ -1010,49 +1038,30 @@ due to the fact that the sparse data will be written in chunks of user-defined s
status = H5Tset_size (memtype, H5T_VARIABLE);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">if</span> ( H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME) != 1 ) {
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace</span> = H5Screate_simple( (<span style="color: #228b22;">int</span>) rank, (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span>*) dims, <span style="color: #008b8b;">NULL</span>);
<span style="color: #a020f0;">if</span> (dspace &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
/* <span style="color: #b22222;">code to create dataset </span>*/
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">filetype</span> = H5Tcopy (H5T_FORTRAN_S1);
<span style="color: #a020f0;">if</span> (filetype &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
/* <span style="color: #b22222;">code to create dataset </span>*/
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">filetype</span> = H5Tcopy (H5T_FORTRAN_S1);
<span style="color: #a020f0;">if</span> (filetype &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
status = H5Tset_size (filetype, H5T_VARIABLE);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
status = H5Tset_size (filetype, H5T_VARIABLE);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace</span> = H5Screate_simple( (<span style="color: #228b22;">int</span>) rank, (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span>*) dims, <span style="color: #008b8b;">NULL</span>);
<span style="color: #a020f0;">if</span> (dspace &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
dset_id = H5Dcreate (f-&gt;$group$_group, $GROUP_DSET$_NAME, filetype, dspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
dset_id = H5Dcreate (f-&gt;$group$_group, $GROUP_DSET$_NAME, filetype, dspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
status = H5Dwrite (dset_id, memtype,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
$group_dset$);
status = H5Dwrite (dset_id, memtype,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
$group_dset$);
H5Dclose (dset_id);
H5Sclose (dspace);
H5Tclose (filetype);
H5Tclose (memtype);
H5Dclose (dset_id);
H5Sclose (dspace);
H5Tclose (filetype);
H5Tclose (memtype);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
} <span style="color: #a020f0;">else</span> {
dset_id = H5Dopen(f-&gt;$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
/* <span style="color: #b22222;">code to write dataset </span>*/
status = H5Dwrite(dset_id, memtype,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
$group_dset$);
H5Dclose(dset_id);
H5Tclose(memtype);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
@ -1085,9 +1094,9 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<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 id="outline-container-org1a93155" class="outline-2">
<h2 id="org1a93155"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</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>
<span style="color: #0000ff;">trexio_hdf5_read_$group_str$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #228b22;">char</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">str</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">max_str_len</span>)
@ -1140,8 +1149,13 @@ due to the fact that the sparse data will be written in chunks of user-defined s
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
/* <span style="color: #b22222;">Delete the attribute if it exists and if the file is open in UNSAFE mode </span>*/
<span style="color: #a020f0;">if</span> (trexio_hdf5_has_$group_str$(file) == TREXIO_SUCCESS &amp;&amp; file-&gt;mode == <span style="color: #8b2252;">'u'</span>) {
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status_del</span> = H5Adelete(f-&gt;$group$_group, $GROUP_STR$_NAME);
<span style="color: #a020f0;">if</span> (status_del &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
/* <span style="color: #b22222;">Setup the dataspace </span>*/
/* <span style="color: #b22222;">Setup the datatype for variable length string </span>*/
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dtype_id</span> = H5Tcopy(H5T_C_S1);
<span style="color: #a020f0;">if</span> (dtype_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
@ -1154,12 +1168,15 @@ due to the fact that the sparse data will be written in chunks of user-defined s
status = H5Tset_strpad(dtype_id, H5T_STR_NULLTERM);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
/* <span style="color: #b22222;">Setup the dataspace </span>*/
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace_id</span> = H5Screate(H5S_SCALAR);
<span style="color: #a020f0;">if</span> (dspace_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
/* <span style="color: #b22222;">Create the $group_str$ attribute of $group$ group </span>*/
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">str_id</span> = H5Acreate(f-&gt;$group$_group, $GROUP_STR$_NAME, dtype_id, dspace_id,
H5P_DEFAULT, H5P_DEFAULT);
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">str_id</span> = H5Acreate(f-&gt;$group$_group,
$GROUP_STR$_NAME,
dtype_id, dspace_id,
H5P_DEFAULT, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (str_id &lt;= 0) {
H5Sclose(dspace_id);
@ -1168,18 +1185,14 @@ due to the fact that the sparse data will be written in chunks of user-defined s
}
status = H5Awrite(str_id, dtype_id, str);
<span style="color: #a020f0;">if</span> (status &lt; 0) {
H5Aclose(str_id);
H5Sclose(dspace_id);
H5Tclose(dtype_id);
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
H5Aclose(str_id);
H5Sclose(dspace_id);
H5Tclose(dtype_id);
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
</div>
@ -1208,9 +1221,50 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<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 id="outline-container-orgad30cf3" class="outline-2">
<h2 id="orgad30cf3"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-9">
<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
and the associated memory was not necessarily freed (see <a href="https://stackoverflow.com/questions/1124994/removing-data-from-a-hdf5-file">this StackOverflow discussion</a> for example).
Nevertheless, some space might remain occupied even after deleting the associated object in recent version.
To take the best use of the deleted file space, we recommend to write the deleted group within the same session
(i.e. before closing the TREXIO file).
</p>
<p>
In principle, one can use HDF5-provided <code>h5repack</code> binary, which copies all existing objects from one file into another.
Thus, any corrupted/lost file space will remain in the first file. The use of <code>h5repack</code> is highly encouraged.
</p>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_delete_$group$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>)
{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
// <span style="color: #b22222;">delete the link to the existing group: this should free the associated space</span>
H5Gclose(f-&gt;$group$_group);
f-&gt;$group$_group = 0;
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Ldelete(f-&gt;file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
// <span style="color: #b22222;">re-create the group (with the new link ?)</span>
f-&gt;$group$_group = H5Gcreate(f-&gt;file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (f-&gt;$group$_group &lt;= 0L) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
</div>
</div>
</div>
<div id="outline-container-orgdfe2065" class="outline-2">
<h2 id="orgdfe2065"><span class="section-number-2">10</span> Helper functions</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>
<span style="color: #0000ff;">trexio_hdf5_create_write_dset_sparse</span> (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">group_id</span>,
@ -1468,10 +1522,9 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-24 Mon 17:22</p>
<p class="date">Created: 2022-01-25 Tue 15:19</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

117
templator_text.html
View File

@ -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>
<!-- 2022-01-24 Mon 17:22 -->
<!-- 2022-01-25 Tue 15:19 -->
<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 +311,29 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orge38e1d2">1. TEXT back end</a>
<li><a href="#org4e1f8e8">1. TEXT back end</a>
<ul>
<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>
<li><a href="#orgd0a84ce">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org0441f3a">1.2. Template for general structure in text back end</a></li>
<li><a href="#org1f36fbb">1.3. Initialize function (constant part)</a></li>
<li><a href="#org56f6fd2">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orgda7da3c">1.5. Template for text read a group</a></li>
<li><a href="#org6229363">1.6. Template for text flush a group</a></li>
<li><a href="#org50f5721">1.7. Template for text free memory</a></li>
<li><a href="#org6b3bffb">1.8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org866dd99">1.9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org908ec28">1.10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org88d7458">1.11. Template for has/read/write a string attribute</a></li>
<li><a href="#org857d53e">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org58ff87c">1.13. Template for text delete a group (UNSAFE mode)</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orge38e1d2" class="outline-2">
<h2 id="orge38e1d2"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-org4e1f8e8" class="outline-2">
<h2 id="org4e1f8e8"><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 +354,8 @@ The file is written when closed, or when the flush function is called.
</p>
</div>
<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 id="outline-container-orgd0a84ce" class="outline-3">
<h3 id="orgd0a84ce"><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 +374,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<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 id="outline-container-org0441f3a" class="outline-3">
<h3 id="org0441f3a"><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 +388,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<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 id="outline-container-org1f36fbb" class="outline-3">
<h3 id="org1f36fbb"><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 +532,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<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 id="outline-container-org56f6fd2" class="outline-3">
<h3 id="org56f6fd2"><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 +555,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<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 id="outline-container-orgda7da3c" class="outline-3">
<h3 id="orgda7da3c"><span class="section-number-3">1.5</span> Template for text read a group</h3>
<div class="outline-text-3" id="text-1-5">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -847,8 +848,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<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 id="outline-container-org6229363" class="outline-3">
<h3 id="org6229363"><span class="section-number-3">1.6</span> Template for text flush a group</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>
@ -860,12 +861,11 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
<span style="color: #a020f0;">if</span> (file-&gt;parent.mode == <span style="color: #8b2252;">'r'</span>) <span style="color: #a020f0;">return</span> TREXIO_READONLY;
$group$_t* $group$ = file-&gt;$group$;
<span style="color: #a020f0;">if</span> ($group$ == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
<span style="color: #a020f0;">if</span> ($group$-&gt;to_flush == 0) <span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
assert (file-&gt;parent.mode == <span style="color: #8b2252;">'w'</span>);
assert (file-&gt;parent.mode == <span style="color: #8b2252;">'w'</span> || file-&gt;parent.mode == <span style="color: #8b2252;">'u'</span>);
<span style="color: #228b22;">FILE</span>* <span style="color: #a0522d;">f</span> = fopen($group$-&gt;file_name, <span style="color: #8b2252;">"w"</span>);
<span style="color: #a020f0;">if</span> (f == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
@ -913,8 +913,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<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 id="outline-container-org50f5721" class="outline-3">
<h3 id="org50f5721"><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.
@ -951,6 +951,8 @@ Memory is allocated when reading. The following function frees memory.
// <span style="color: #b22222;">END REPEAT GROUP_ATTR_STR</span>
FREE ($group$);
file-&gt;$group$ = <span style="color: #008b8b;">NULL</span>;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
@ -959,8 +961,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<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 id="outline-container-org6b3bffb" class="outline-3">
<h3 id="org6b3bffb"><span class="section-number-3">1.8</span> Template for has/read/write a 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 +1025,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<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 id="outline-container-org866dd99" class="outline-3">
<h3 id="org866dd99"><span class="section-number-3">1.9</span> Template for has/read/write a 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 +1122,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<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 id="outline-container-org908ec28" class="outline-3">
<h3 id="org908ec28"><span class="section-number-3">1.10</span> Template for has/read/write a 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 +1224,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<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 id="outline-container-org88d7458" class="outline-3">
<h3 id="org88d7458"><span class="section-number-3">1.11</span> Template for has/read/write a 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 +1299,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<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 id="outline-container-org857d53e" class="outline-3">
<h3 id="org857d53e"><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
@ -1571,11 +1573,40 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
</div>
<div id="outline-container-org58ff87c" class="outline-3">
<h3 id="org58ff87c"><span class="section-number-3">1.13</span> Template for text delete a group (UNSAFE mode)</h3>
<div class="outline-text-3" id="text-1-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_text_delete_$group$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>)
{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #228b22;">trexio_text_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_text_t</span>*) file;
$group$_t* $group$ = trexio_text_read_$group$(f);
<span style="color: #a020f0;">if</span> ($group$ == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #228b22;">int</span> <span style="color: #a0522d;">rc</span> = remove($group$-&gt;file_name);
<span style="color: #a020f0;">if</span> (rc == -1) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
$group$-&gt;to_flush = 0;
<span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc_free</span> = trexio_text_free_$group$(f);
<span style="color: #a020f0;">if</span> (rc_free != TREXIO_SUCCESS) <span style="color: #a020f0;">return</span> rc_free;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
</div>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-24 Mon 17:22</p>
<p class="date">Created: 2022-01-25 Tue 15:19</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

130
trex.html
View File

@ -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>
<!-- 2022-01-24 Mon 17:22 -->
<!-- 2022-01-25 Tue 15:19 -->
<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="#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>
<li><a href="#org30cfbb9">1. Metadata (metadata group)</a></li>
<li><a href="#orgac328f5">2. Electron (electron group)</a></li>
<li><a href="#org5fafbd7">3. Nucleus (nucleus group)</a></li>
<li><a href="#org4d8bba8">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgb42ac10">4.1. Example</a></li>
<li><a href="#org917e096">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org9769ac1">5. Basis set (basis group)</a>
<li><a href="#org3c9f450">5. Basis set (basis group)</a>
<ul>
<li><a href="#orgc749b8c">5.1. Example</a></li>
<li><a href="#org205694a">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org793b44d">6. Atomic orbitals (ao group)</a>
<li><a href="#org1c1146c">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="#org15c7250">7. Molecular orbitals (mo group)</a>
<li><a href="#orgbfdc0e2">7. Molecular orbitals (mo group)</a>
<ul>
<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>
<li><a href="#orga06ee7b">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org2d578b9">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</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>
<li><a href="#orgf9b0d2d">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#orgfa4ea16">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-org67be512" class="outline-2">
<h2 id="org67be512"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org30cfbb9" class="outline-2">
<h2 id="org30cfbb9"><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="orgbef8356" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org55ec242" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -482,20 +482,34 @@ authors of the file, and a textual description.
<td class="org-left">&#xa0;</td>
<td class="org-left">Text describing the content of file</td>
</tr>
<tr>
<td class="org-left"><code>unsafe</code></td>
<td class="org-left"><code>int</code></td>
<td class="org-left">&#xa0;</td>
<td class="org-left"><code>1</code>: true, <code>0</code>: false</td>
</tr>
</tbody>
</table>
<p>
<b><b>Note:</b></b> <code>unsafe</code> attribute of the <code>metadata</code> group indicates whether the file has been previously opened with <code>'u'</code> mode.
It is automatically written in the file upon the first unsafe opening.
If the user has checked that the TREXIO file is valid (e.g. using <code>trexio-tools</code>) after unsafe operations,
then the <code>unsafe</code> attribute value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>0</code>.
</p>
</div>
</div>
<div id="outline-container-org3e95b37" class="outline-2">
<h2 id="org3e95b37"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orgac328f5" class="outline-2">
<h2 id="orgac328f5"><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="org14d2718" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge9e1e7c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -534,15 +548,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgba6a084" class="outline-2">
<h2 id="orgba6a084"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org5fafbd7" class="outline-2">
<h2 id="org5fafbd7"><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="org757305b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0196fbf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -609,8 +623,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<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 id="outline-container-org4d8bba8" class="outline-2">
<h2 id="org4d8bba8"><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 +657,7 @@ 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="org770cf4c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5be31a3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -741,8 +755,8 @@ The latter causes issues when written before <code>ang_mom</code> in the TREXIO
</p>
</div>
<div id="outline-container-orgb42ac10" class="outline-3">
<h3 id="orgb42ac10"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org917e096" class="outline-3">
<h3 id="org917e096"><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 +819,8 @@ power = [
</div>
</div>
<div id="outline-container-org9769ac1" class="outline-2">
<h2 id="org9769ac1"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org3c9f450" class="outline-2">
<h2 id="org3c9f450"><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 +873,7 @@ 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="org7be90af" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5a9e73b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -953,8 +967,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-orgc749b8c" class="outline-3">
<h3 id="orgc749b8c"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org205694a" class="outline-3">
<h3 id="org205694a"><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 +1046,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org793b44d" class="outline-2">
<h2 id="org793b44d"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org1c1146c" class="outline-2">
<h2 id="org1c1146c"><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 +1100,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org9769ac1">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org3c9f450">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="org3ddcdaa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge6a6e3b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1144,8 +1158,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<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 id="outline-container-org42ebd61" class="outline-3">
<h3 id="ao_one_e"><a id="org42ebd61"></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 +1177,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org2aecfd1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7c6775a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1230,8 +1244,8 @@ over atomic orbitals.
</div>
</div>
<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 id="outline-container-org04ad7a5" class="outline-3">
<h3 id="ao_two_e"><a id="org04ad7a5"></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 +1266,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="orgdef6991" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1f9a94c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1292,10 +1306,10 @@ notation.
</div>
</div>
<div id="outline-container-org15c7250" class="outline-2">
<h2 id="org15c7250"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgbfdc0e2" class="outline-2">
<h2 id="orgbfdc0e2"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="orgf720360" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga3583de" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1361,8 +1375,8 @@ notation.
</table>
</div>
<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 id="outline-container-orga06ee7b" class="outline-3">
<h3 id="orga06ee7b"><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 +1384,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org720caa1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga01718a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1437,8 +1451,8 @@ the basis of molecular orbitals.
</div>
</div>
<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 id="outline-container-org2d578b9" class="outline-3">
<h3 id="org2d578b9"><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 +1460,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org5ab3f27" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4e043b1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1486,11 +1500,11 @@ the basis of molecular orbitals.
</div>
</div>
<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 id="outline-container-orgf9b0d2d" class="outline-2">
<h2 id="orgf9b0d2d"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<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 id="outline-container-orgfa4ea16" class="outline-2">
<h2 id="orgfa4ea16"><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 +1557,7 @@ The total energy can be computed as:
\]
</p>
<table id="orgbfeeafe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb2f33a2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1626,7 +1640,7 @@ The total energy can be computed as:
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-24 Mon 17:22</p>
<p class="date">Created: 2022-01-25 Tue 15:19</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>