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README.html
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<head>
<!-- 2023-01-13 Fri 14:55 -->
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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: 2023-01-13 Fri 14:55</p>
<p class="date">Created: 2023-01-19 Thu 00:32</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2023-01-13 Fri 14:55 -->
<!-- 2023-01-19 Thu 00:32 -->
<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="#orgdc4e451">1. Accessing sparse quantities (integrals)</a>
<li><a href="#orge1367c3">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#orga054953">1.1. Fortran</a>
<li><a href="#orgb27d9bb">1.1. Fortran</a>
<ul>
<li><a href="#org4a7841f">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org115e663">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgde21c70">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org3a9899b">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org2e8e50d">1.1.5. Allocate memory</a></li>
<li><a href="#org736d4d5">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orga55c232">1.1.7. Read two-electron quantities</a>
<li><a href="#org73addf3">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org6f375b2">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org9535f46">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org1400aeb">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgc9803e3">1.1.5. Allocate memory</a></li>
<li><a href="#org091a8bc">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org13293fa">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org010acf2">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org1342883">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#orgaadbd26">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org81dda01">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org440a329">1.1.8. Compute the energy</a></li>
<li><a href="#orgd0f973b">1.1.9. Terminate</a></li>
<li><a href="#org098730d">1.1.8. Compute the energy</a></li>
<li><a href="#org2c73760">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgf1a256d">2. Reading determinants</a>
<li><a href="#org09bd048">2. Reading determinants</a>
<ul>
<li><a href="#org3a0836e">2.1. Fortran</a></li>
<li><a href="#org19bb8c6">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -378,12 +378,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgdc4e451" class="outline-2">
<h2 id="orgdc4e451"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orge1367c3" class="outline-2">
<h2 id="orge1367c3"><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-orga054953" class="outline-3">
<h3 id="orga054953"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-orgb27d9bb" class="outline-3">
<h3 id="orgb27d9bb"><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-org4a7841f" class="outline-4">
<h4 id="org4a7841f"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org73addf3" class="outline-4">
<h4 id="org73addf3"><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-org115e663" class="outline-4">
<h4 id="org115e663"><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-org6f375b2" class="outline-4">
<h4 id="org6f375b2"><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-orgde21c70" class="outline-4">
<h4 id="orgde21c70"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org9535f46" class="outline-4">
<h4 id="org9535f46"><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-org3a9899b" class="outline-4">
<h4 id="org3a9899b"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org1400aeb" class="outline-4">
<h4 id="org1400aeb"><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-org2e8e50d" class="outline-4">
<h4 id="org2e8e50d"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-orgc9803e3" class="outline-4">
<h4 id="orgc9803e3"><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-org736d4d5" class="outline-4">
<h4 id="org736d4d5"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org091a8bc" class="outline-4">
<h4 id="org091a8bc"><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-orga55c232" class="outline-4">
<h4 id="orga55c232"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org13293fa" class="outline-4">
<h4 id="org13293fa"><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-org010acf2" class="outline-5">
<h5 id="org010acf2"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgaadbd26" class="outline-5">
<h5 id="orgaadbd26"><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-org1342883" class="outline-5">
<h5 id="org1342883"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org81dda01" class="outline-5">
<h5 id="org81dda01"><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-org440a329" class="outline-4">
<h4 id="org440a329"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org098730d" class="outline-4">
<h4 id="org098730d"><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-orgd0f973b" class="outline-4">
<h4 id="orgd0f973b"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org2c73760" class="outline-4">
<h4 id="org2c73760"><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-orgf1a256d" class="outline-2">
<h2 id="orgf1a256d"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-org09bd048" class="outline-2">
<h2 id="org09bd048"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org3a0836e" class="outline-3">
<h3 id="org3a0836e"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org19bb8c6" class="outline-3">
<h3 id="org19bb8c6"><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: 2023-01-13 Fri 14:55</p>
<p class="date">Created: 2023-01-19 Thu 00:32</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>
<!-- 2023-01-13 Fri 14:55 -->
<!-- 2023-01-19 Thu 00:32 -->
<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: 2023-01-13 Fri 14:55</p>
<p class="date">Created: 2023-01-19 Thu 00:32</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>
<!-- 2023-01-13 Fri 14:55 -->
<!-- 2023-01-19 Thu 00:32 -->
<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="#org42285af">1. Template for HDF5 definitions</a></li>
<li><a href="#org0f65c98">2. Template for HDF5 structures</a></li>
<li><a href="#orga5b76ed">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org95dcebd">4. Template for HDF5 has a group</a></li>
<li><a href="#org2ec7d89">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org0911f6f">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orge65d6f7">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org39f8185">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org36af8af">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org38e9412">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org96793d1">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org4a6a8dc">12. Source code for the determinant part</a></li>
<li><a href="#orgb5512b8">13. Helper functions</a></li>
<li><a href="#orgeefe2d4">1. Template for HDF5 definitions</a></li>
<li><a href="#orge34dfc4">2. Template for HDF5 structures</a></li>
<li><a href="#org0008519">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org9ee8cf8">4. Template for HDF5 has a group</a></li>
<li><a href="#org9379e6f">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgc25d61c">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgb915dc4">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgc258e97">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgf42a28d">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgfdbe513">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgabbd4be">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgc1a6671">12. Source code for the determinant part</a></li>
<li><a href="#org9228d58">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org42285af" class="outline-2">
<h2 id="org42285af"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orgeefe2d4" class="outline-2">
<h2 id="orgeefe2d4"><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-org0f65c98" class="outline-2">
<h2 id="org0f65c98"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orge34dfc4" class="outline-2">
<h2 id="orge34dfc4"><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-orga5b76ed" class="outline-2">
<h2 id="orga5b76ed"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org0008519" class="outline-2">
<h2 id="org0008519"><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-org95dcebd" class="outline-2">
<h2 id="org95dcebd"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org9ee8cf8" class="outline-2">
<h2 id="org9ee8cf8"><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-org2ec7d89" class="outline-2">
<h2 id="org2ec7d89"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org9379e6f" class="outline-2">
<h2 id="org9379e6f"><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-org0911f6f" class="outline-2">
<h2 id="org0911f6f"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgc25d61c" class="outline-2">
<h2 id="orgc25d61c"><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>
@ -675,18 +675,21 @@ corresponding types for all back ends can be safely casted to
}
FREE(ddims);
/* <span style="color: #b22222;">Read dataset</span> */
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Dread(dset_id,
H5T_$GROUP_DSET_H5_DTYPE$,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
$group_dset$);
H5Sclose(dspace_id);
H5Dclose(dset_id);
/* <span style="color: #b22222;">High-level H5LT API. No need to deal with dataspaces and datatypes</span> */
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTread_dataset(f-&gt;$group$_group,
$GROUP_DSET$_NAME,
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;">return</span> TREXIO_SUCCESS;
}
</pre>
</div>
@ -707,7 +710,8 @@ corresponding types for all back ends can be safely casted to
<span style="color: #b22222;"> Consider using HDF5-native h5repack utility after deleting/overwriting big datasets.</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: #a020f0;">if</span> ((trexio_hdf5_has_$group_dset$(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> = 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;
}
@ -751,14 +755,13 @@ corresponding types for all back ends can be safely casted to
<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> (f-&gt;$group$_group == (<span style="color: #228b22;">hsize_t</span>) 0) <span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME);
/* <span style="color: #b22222;">H5LTfind_dataset returns 1 if dataset exists, 0 otherwise</span> */
<span style="color: #a020f0;">if</span> (status == 1){
<span style="color: #228b22;">htri_t</span> <span style="color: #a0522d;">exists</span> = H5Lexists(f-&gt;$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (exists &gt; 0) {
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (status == 0) {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
} <span style="color: #a020f0;">else</span> {
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (exists &lt; 0) {
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
} <span style="color: #a020f0;">else</span> {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
}
}
@ -767,8 +770,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orge65d6f7" class="outline-2">
<h2 id="orge65d6f7"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orgb915dc4" class="outline-2">
<h2 id="orgb915dc4"><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
@ -829,7 +832,7 @@ due to the fact that the sparse data will be written in chunks of user-defined s
<span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc_write</span> = TREXIO_FAILURE;
/* <span style="color: #b22222;">NOTE: chunk size is set upon creation of the HDF5 dataset and cannot be changed !</span> */
<span style="color: #a020f0;">if</span> ( H5LTfind_dataset(f-&gt;$group$_group, dset_index_name) != 1 ) {
<span style="color: #a020f0;">if</span> (trexio_hdf5_has_$group_dset$(file) == TREXIO_HAS_NOT) {
/* <span style="color: #b22222;">If the file does not exist -&gt; create it and write</span> */
/* <span style="color: #b22222;">Create chunked dataset with index_dtype datatype and write indices into it</span> */
@ -955,14 +958,13 @@ 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: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
<span style="color: #a020f0;">if</span> (f-&gt;$group$_group == (<span style="color: #228b22;">hsize_t</span>) 0) <span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME <span style="color: #8b2252;">"_values"</span>);
/* <span style="color: #b22222;">H5LTfind_dataset returns 1 if dataset exists, 0 otherwise</span> */
<span style="color: #a020f0;">if</span> (status == 1){
<span style="color: #228b22;">htri_t</span> <span style="color: #a0522d;">exists</span> = H5Lexists(f-&gt;$group$_group, $GROUP_DSET$_NAME <span style="color: #8b2252;">"_values"</span>, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (exists &gt; 0) {
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (status == 0) {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
} <span style="color: #a020f0;">else</span> {
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (exists &lt; 0) {
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
} <span style="color: #a020f0;">else</span> {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
}
}
@ -971,8 +973,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org39f8185" class="outline-2">
<h2 id="org39f8185"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-orgc258e97" class="outline-2">
<h2 id="orgc258e97"><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.
@ -1026,7 +1028,7 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
<span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc_write</span> = TREXIO_FAILURE;
/* <span style="color: #b22222;">NOTE: chunk size is set upon creation of the HDF5 dataset and cannot be changed !</span> */
<span style="color: #a020f0;">if</span> ( H5LTfind_dataset(f-&gt;$group$_group, dset_name) != 1 ) {
<span style="color: #a020f0;">if</span> (trexio_hdf5_has_$group_dset$(file) == TREXIO_HAS_NOT) {
/* <span style="color: #b22222;">If the file does not exist -&gt; create it and write</span> */
/* <span style="color: #b22222;">Create chunked dataset with dtype datatype and write indices into it</span> */
@ -1092,14 +1094,13 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span> <span style="color: #a0522d;">dset_name</span>[256] = <span style="color: #8b2252;">"$group_dset$"</span>;
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTfind_dataset(f-&gt;$group$_group, dset_name);
/* <span style="color: #b22222;">H5LTfind_dataset returns 1 if dataset exists, 0 otherwise</span> */
<span style="color: #a020f0;">if</span> (status == 1){
<span style="color: #228b22;">htri_t</span> <span style="color: #a0522d;">exists</span> = H5Lexists(f-&gt;$group$_group, dset_name, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (exists &gt; 0) {
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (status == 0) {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
} <span style="color: #a020f0;">else</span> {
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (exists &lt; 0) {
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
} <span style="color: #a020f0;">else</span> {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
}
}
</pre>
@ -1107,8 +1108,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org36af8af" class="outline-2">
<h2 id="org36af8af"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgf42a28d" class="outline-2">
<h2 id="orgf42a28d"><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>
@ -1234,7 +1235,7 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
<span style="color: #b22222;"> Consider using HDF5-provided h5repack utility after deleting/overwriting big datasets.</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: #a020f0;">if</span> ( (trexio_hdf5_has_$group_dset$(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> = 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;
}
@ -1290,14 +1291,13 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
<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> (f-&gt;$group$_group == (<span style="color: #228b22;">hsize_t</span>) 0) <span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME);
/* <span style="color: #b22222;">H5LTfind_dataset returns 1 if dataset exists, 0 otherwise</span> */
<span style="color: #a020f0;">if</span> (status == 1){
<span style="color: #228b22;">htri_t</span> <span style="color: #a0522d;">exists</span> = H5Lexists(f-&gt;$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (exists &gt; 0) {
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (status == 0) {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
} <span style="color: #a020f0;">else</span> {
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (exists &lt; 0) {
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
} <span style="color: #a020f0;">else</span> {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
}
}
@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org38e9412" class="outline-2">
<h2 id="org38e9412"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgfdbe513" class="outline-2">
<h2 id="orgfdbe513"><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-org96793d1" class="outline-2">
<h2 id="org96793d1"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgabbd4be" class="outline-2">
<h2 id="orgabbd4be"><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-org4a6a8dc" class="outline-2">
<h2 id="org4a6a8dc"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-orgc1a6671" class="outline-2">
<h2 id="orgc1a6671"><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.
@ -1534,7 +1534,7 @@ Size specifies the number of data items (e.g. determinants) to process.
<span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc_write</span> = TREXIO_FAILURE;
/* <span style="color: #b22222;">NOTE: chunk size is set upon creation of the HDF5 dataset and cannot be changed !</span> */
<span style="color: #a020f0;">if</span> ( H5LTfind_dataset(f-&gt;determinant_group, dset_det_name) != 1 ) {
<span style="color: #a020f0;">if</span> ( trexio_hdf5_has_determinant_list(file) == TREXIO_HAS_NOT ) {
/* <span style="color: #b22222;">If the file does not exist -&gt; create it and write</span> */
/* <span style="color: #b22222;">Create chunked dataset with det_dtype datatype and write indices into it</span> */
@ -1564,14 +1564,13 @@ Size specifies the number of data items (e.g. determinants) to process.
<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> (f-&gt;determinant_group == (<span style="color: #228b22;">hsize_t</span>) 0) <span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTfind_dataset(f-&gt;determinant_group, <span style="color: #8b2252;">"determinant_list"</span>);
/* <span style="color: #b22222;">H5LTfind_dataset returns 1 if dataset exists, 0 otherwise</span> */
<span style="color: #a020f0;">if</span> (status == 1){
<span style="color: #228b22;">htri_t</span> <span style="color: #a0522d;">exists</span> = H5Lexists(f-&gt;determinant_group, <span style="color: #8b2252;">"determinant_list"</span>, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (exists &gt; 0) {
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (status == 0) {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
} <span style="color: #a020f0;">else</span> {
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (exists &lt; 0) {
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
} <span style="color: #a020f0;">else</span> {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
}
}
</pre>
@ -1579,8 +1578,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-orgb5512b8" class="outline-2">
<h2 id="orgb5512b8"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org9228d58" class="outline-2">
<h2 id="org9228d58"><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 +1842,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-01-13 Fri 14:55</p>
<p class="date">Created: 2023-01-19 Thu 00:32</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

106
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>
<!-- 2023-01-13 Fri 14:55 -->
<!-- 2023-01-19 Thu 00:32 -->
<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="#orgf67b369">1. Template for group-related structures in text back end</a></li>
<li><a href="#orge24290c">2. Template for general structure in text back end</a></li>
<li><a href="#orgadd15a8">3. Initialize function (constant part)</a></li>
<li><a href="#org49ff749">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgd9ebc3b">5. Flush function (templated part)</a></li>
<li><a href="#org300372a">6. Template for text read a group</a></li>
<li><a href="#org679b845">7. Template for text has a group</a></li>
<li><a href="#org3b9eb39">8. Template for text flush a group</a></li>
<li><a href="#org20ba7d6">9. Template for text free memory</a></li>
<li><a href="#orgaa63e03">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org6d7a7cf">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgd07ed1f">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org212c941">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgf3e8054">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orga23edd5">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgac6fd0d">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org5b84477">17. Source code for the determinant part</a></li>
<li><a href="#orgaf3b1e9">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgaa06d5b">2. Template for general structure in text back end</a></li>
<li><a href="#org4f6b05d">3. Initialize function (constant part)</a></li>
<li><a href="#orgfa491bc">4. Deinitialize function (templated part)</a></li>
<li><a href="#org9415b71">5. Flush function (templated part)</a></li>
<li><a href="#orge028bbe">6. Template for text read a group</a></li>
<li><a href="#orge45b19e">7. Template for text has a group</a></li>
<li><a href="#org45773f9">8. Template for text flush a group</a></li>
<li><a href="#org544a467">9. Template for text free memory</a></li>
<li><a href="#orgebfab88">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org7f1d502">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org5902d8a">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org36b7c19">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orga7add2f">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org854e766">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org8b5a8ca">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org73e0cce">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-orgf67b369" class="outline-2">
<h2 id="orgf67b369"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orgaf3b1e9" class="outline-2">
<h2 id="orgaf3b1e9"><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-orge24290c" class="outline-2">
<h2 id="orge24290c"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgaa06d5b" class="outline-2">
<h2 id="orgaa06d5b"><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-orgadd15a8" class="outline-2">
<h2 id="orgadd15a8"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org4f6b05d" class="outline-2">
<h2 id="org4f6b05d"><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-org49ff749" class="outline-2">
<h2 id="org49ff749"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgfa491bc" class="outline-2">
<h2 id="orgfa491bc"><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-orgd9ebc3b" class="outline-2">
<h2 id="orgd9ebc3b"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org9415b71" class="outline-2">
<h2 id="org9415b71"><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-org300372a" class="outline-2">
<h2 id="org300372a"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orge028bbe" class="outline-2">
<h2 id="orge028bbe"><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-org679b845" class="outline-2">
<h2 id="org679b845"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-orge45b19e" class="outline-2">
<h2 id="orge45b19e"><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-org3b9eb39" class="outline-2">
<h2 id="org3b9eb39"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org45773f9" class="outline-2">
<h2 id="org45773f9"><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-org20ba7d6" class="outline-2">
<h2 id="org20ba7d6"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org544a467" class="outline-2">
<h2 id="org544a467"><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-orgaa63e03" class="outline-2">
<h2 id="orgaa63e03"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orgebfab88" class="outline-2">
<h2 id="orgebfab88"><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-org6d7a7cf" class="outline-2">
<h2 id="org6d7a7cf"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org7f1d502" class="outline-2">
<h2 id="org7f1d502"><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-orgd07ed1f" class="outline-2">
<h2 id="orgd07ed1f"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org5902d8a" class="outline-2">
<h2 id="org5902d8a"><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-org212c941" class="outline-2">
<h2 id="org212c941"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org36b7c19" class="outline-2">
<h2 id="org36b7c19"><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-orgf3e8054" class="outline-2">
<h2 id="orgf3e8054"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orga7add2f" class="outline-2">
<h2 id="orga7add2f"><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-orga23edd5" class="outline-2">
<h2 id="orga23edd5"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org854e766" class="outline-2">
<h2 id="org854e766"><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-orgac6fd0d" class="outline-2">
<h2 id="orgac6fd0d"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org8b5a8ca" class="outline-2">
<h2 id="org8b5a8ca"><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-org5b84477" class="outline-2">
<h2 id="org5b84477"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org73e0cce" class="outline-2">
<h2 id="org73e0cce"><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: 2023-01-13 Fri 14:55</p>
<p class="date">Created: 2023-01-19 Thu 00:32</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

244
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>
<!-- 2023-01-13 Fri 14:55 -->
<!-- 2023-01-19 Thu 00:32 -->
<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>
@ -346,70 +346,70 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgcc8c74f">1. Metadata (metadata group)</a></li>
<li><a href="#orged65cbd">2. System</a>
<li><a href="#orgdfa5587">1. Metadata (metadata group)</a></li>
<li><a href="#orgc491583">2. System</a>
<ul>
<li><a href="#org6fe6199">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org9839d72">2.2. Cell (cell group)</a></li>
<li><a href="#org7f084ed">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org7686479">2.4. Electron (electron group)</a></li>
<li><a href="#orgcb99efa">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org07b01cd">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org1170aab">2.2. Cell (cell group)</a></li>
<li><a href="#orgc5efe6e">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org0ec07cf">2.4. Electron (electron group)</a></li>
<li><a href="#orge2aa5d3">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org8636b4d">3. Basis functions</a>
<li><a href="#org04cd872">3. Basis functions</a>
<ul>
<li><a href="#orga201e4a">3.1. Basis set (basis group)</a>
<li><a href="#orgd85a8ff">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org4f59dfe">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgfdb7ce7">3.1.2. Plane waves</a></li>
<li><a href="#org4a17b48">3.1.3. Data definitions</a></li>
<li><a href="#org0d4475d">3.1.4. Example</a></li>
<li><a href="#org893c7e1">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org7164e23">3.1.2. Plane waves</a></li>
<li><a href="#orgf6a795e">3.1.3. Data definitions</a></li>
<li><a href="#org95a6daf">3.1.4. Example</a></li>
</ul>
</li>
<li><a href="#org6dbc63f">3.2. Effective core potentials (ecp group)</a>
<li><a href="#orgb2a0189">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org2c97923">3.2.1. Example</a></li>
<li><a href="#orgb392da1">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org4845372">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org0767572">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#orge2c6515">4. Orbitals</a>
<li><a href="#orge564fed">4. Orbitals</a>
<ul>
<li><a href="#org7f7e206">4.1. Atomic orbitals (ao group)</a>
<li><a href="#orgccd8dbe">4.1. Atomic orbitals (ao group)</a>
<ul>
<li><a href="#ao_one_e">4.1.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
<li><a href="#ao_two_e">4.1.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org1600974">4.2. Molecular orbitals (mo group)</a>
<li><a href="#orgfbf930d">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org1ffde89">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org0487b24">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgaf240b4">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orga4b20f4">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgfa40d56">5. Multi-determinant information</a>
<li><a href="#org176d372">5. Multi-determinant information</a>
<ul>
<li><a href="#org61d659d">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org28bd707">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgb24ec58">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgf20085f">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org4d3d76f">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org02850cf">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgc4ade84">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgae01d67">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#orgca89c37">6. Correlation factors</a>
<li><a href="#org7fe8ced">6. Correlation factors</a>
<ul>
<li><a href="#org099f627">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#orgdbcf159">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org919ef0a">6.1.1. CHAMP</a></li>
<li><a href="#orgea8174d">6.1.2. Mu</a></li>
<li><a href="#orgf11581f">6.1.3. Table of values</a></li>
<li><a href="#orgdb43028">6.1.1. CHAMP</a></li>
<li><a href="#org87f6d5e">6.1.2. Mu</a></li>
<li><a href="#org0da47d7">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org06d176e">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org3e678f1">7. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -477,8 +477,8 @@ in the variable, and the imaginary part will be stored in the variable
with the same name suffixed by <code>_im</code>.
</p>
<div id="outline-container-orgcc8c74f" class="outline-2">
<h2 id="orgcc8c74f"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgdfa5587" class="outline-2">
<h2 id="orgdfa5587"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect TREXIO files to be archived in open-data repositories,
@ -488,7 +488,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
</p>
<table id="orgdc7ee66" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1f6ef89" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -571,19 +571,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
</div>
</div>
<div id="outline-container-orged65cbd" class="outline-2">
<h2 id="orged65cbd"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-orgc491583" class="outline-2">
<h2 id="orgc491583"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org6fe6199" class="outline-3">
<h3 id="org6fe6199"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org07b01cd" class="outline-3">
<h3 id="org07b01cd"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div class="outline-text-3" id="text-2-1">
<p>
The nuclei are considered as fixed point charges. Coordinates are
given in Cartesian \((x,y,z)\) format.
</p>
<table id="org4ba8531" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8e19fb6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -650,15 +650,15 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org9839d72" class="outline-3">
<h3 id="org9839d72"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org1170aab" class="outline-3">
<h3 id="org1170aab"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div class="outline-text-3" id="text-2-2">
<p>
3 Lattice vectors to define a box containing the system, for example
used in periodic calculations.
</p>
<table id="org72e4a48" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga47cee4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -732,15 +732,15 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-org7f084ed" class="outline-3">
<h3 id="org7f084ed"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-orgc5efe6e" class="outline-3">
<h3 id="orgc5efe6e"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div class="outline-text-3" id="text-2-3">
<p>
A single $k$-point per TREXIO file can be stored. The $k$-point is
defined in this group.
</p>
<table id="org33742b4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8db587d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -779,15 +779,15 @@ defined in this group.
</div>
</div>
<div id="outline-container-org7686479" class="outline-3">
<h3 id="org7686479"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org0ec07cf" class="outline-3">
<h3 id="org0ec07cf"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div class="outline-text-3" id="text-2-4">
<p>
We consider wave functions expressed in the spin-free formalism, where
the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org75af6cf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3ded15c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -833,8 +833,8 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgcb99efa" class="outline-3">
<h3 id="orgcb99efa"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-orge2aa5d3" class="outline-3">
<h3 id="orge2aa5d3"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div class="outline-text-3" id="text-2-5">
<p>
This group contains information about excited states. Since only a
@ -851,7 +851,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="org1da8a6b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org43b0acb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -912,16 +912,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-org8636b4d" class="outline-2">
<h2 id="org8636b4d"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org04cd872" class="outline-2">
<h2 id="org04cd872"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orga201e4a" class="outline-3">
<h3 id="orga201e4a"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-orgd85a8ff" class="outline-3">
<h3 id="orgd85a8ff"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div class="outline-text-3" id="text-3-1">
</div>
<div id="outline-container-org4f59dfe" class="outline-4">
<h4 id="org4f59dfe"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org893c7e1" class="outline-4">
<h4 id="org893c7e1"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div class="outline-text-4" id="text-3-1-1">
<p>
We consider here basis functions centered on nuclei. Hence, we enable
@ -975,8 +975,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-orgfdb7ce7" class="outline-4">
<h4 id="orgfdb7ce7"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div id="outline-container-org7164e23" class="outline-4">
<h4 id="org7164e23"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div class="outline-text-4" id="text-3-1-2">
<p>
A plane wave is defined as
@ -997,10 +997,10 @@ plane waves.
</div>
</div>
<div id="outline-container-org4a17b48" class="outline-4">
<h4 id="org4a17b48"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div id="outline-container-orgf6a795e" class="outline-4">
<h4 id="orgf6a795e"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-3">
<table id="orgd7290d4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd73da09" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1109,8 +1109,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org0d4475d" class="outline-4">
<h4 id="org0d4475d"><span class="section-number-4">3.1.4</span> Example</h4>
<div id="outline-container-org95a6daf" class="outline-4">
<h4 id="org95a6daf"><span class="section-number-4">3.1.4</span> Example</h4>
<div class="outline-text-4" id="text-3-1-4">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1188,8 +1188,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org6dbc63f" class="outline-3">
<h3 id="org6dbc63f"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-orgb2a0189" class="outline-3">
<h3 id="orgb2a0189"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div class="outline-text-3" id="text-3-2">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -1221,7 +1221,7 @@ All 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="orgd2f9017" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0d31c6a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1325,8 +1325,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-org2c97923" class="outline-4">
<h4 id="org2c97923"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orgb392da1" class="outline-4">
<h4 id="orgb392da1"><span class="section-number-4">3.2.1</span> Example</h4>
<div class="outline-text-4" id="text-3-2-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -1389,8 +1389,8 @@ power = [
</div>
</div>
<div id="outline-container-org4845372" class="outline-3">
<h3 id="org4845372"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org0767572" class="outline-3">
<h3 id="org0767572"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div class="outline-text-3" id="text-3-3">
<p>
In some applications, such as DFT calculations, integrals have to
@ -1405,7 +1405,7 @@ The structure of this group is adapted for the <a href="https://github.com/dftli
Feel free to submit a PR if you find missing options/functionalities.
</p>
<table id="orge395a50" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdc44959" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1522,12 +1522,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-orge2c6515" class="outline-2">
<h2 id="orge2c6515"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-orge564fed" class="outline-2">
<h2 id="orge564fed"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org7f7e206" class="outline-3">
<h3 id="org7f7e206"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-orgccd8dbe" class="outline-3">
<h3 id="orgccd8dbe"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div class="outline-text-3" id="text-4-1">
<p>
Going from the atomic basis set to AOs implies a systematic
@ -1580,13 +1580,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#orga201e4a">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#orgd85a8ff">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="orgb3870f7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org49a00c4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1638,7 +1638,7 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-orgc975f3d" class="outline-4">
<div id="outline-container-org4b12b15" class="outline-4">
<h4 id="ao_one_e"><span class="section-number-4">4.1.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_one_e">
<ul class="org-ul">
@ -1656,7 +1656,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org2756e2a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org500603c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1751,7 +1751,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org0acd811" class="outline-4">
<div id="outline-container-orgc0aea73" class="outline-4">
<h4 id="ao_two_e"><span class="section-number-4">4.1.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_two_e">
<p>
@ -1783,7 +1783,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org96a8e69" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4475d93" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1851,10 +1851,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org1600974" class="outline-3">
<h3 id="org1600974"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-orgfbf930d" class="outline-3">
<h3 id="orgfbf930d"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="orgff61c37" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7628e3b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1941,8 +1941,8 @@ The Cholesky decomposition of the integrals can also be stored:
</table>
</div>
<div id="outline-container-org1ffde89" class="outline-4">
<h4 id="org1ffde89"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-orgaf240b4" class="outline-4">
<h4 id="orgaf240b4"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-1">
<p>
The operators as the same as those defined in the
@ -1950,7 +1950,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org69b8290" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3b71fcc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2045,8 +2045,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org0487b24" class="outline-4">
<h4 id="org0487b24"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-orga4b20f4" class="outline-4">
<h4 id="orga4b20f4"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-2">
<p>
The operators are the same as those defined in the
@ -2054,7 +2054,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org69db9e4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org43f34d3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2123,12 +2123,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgfa40d56" class="outline-2">
<h2 id="orgfa40d56"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org176d372" class="outline-2">
<h2 id="org176d372"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org61d659d" class="outline-3">
<h3 id="org61d659d"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org4d3d76f" class="outline-3">
<h3 id="org4d3d76f"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div class="outline-text-3" id="text-5-1">
<p>
The configuration interaction (CI) wave function \(\Psi\)
@ -2170,7 +2170,7 @@ produced by the code generator.
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
</p>
<table id="org00a23a1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc3b8afc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2216,8 +2216,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org28bd707" class="outline-3">
<h3 id="org28bd707"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org02850cf" class="outline-3">
<h3 id="org02850cf"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div class="outline-text-3" id="text-5-2">
<p>
The configuration interaction (CI) wave function \(\Psi\) can be
@ -2239,7 +2239,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="orge0c7469" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3bf7236" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2285,8 +2285,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-orgb24ec58" class="outline-3">
<h3 id="orgb24ec58"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orgc4ade84" class="outline-3">
<h3 id="orgc4ade84"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div class="outline-text-3" id="text-5-3">
<p>
The wave function may be expressed in terms of action of the cluster
@ -2357,7 +2357,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="orgc86d064" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf20702d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2438,8 +2438,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-orgf20085f" class="outline-3">
<h3 id="orgf20085f"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-orgae01d67" class="outline-3">
<h3 id="orgae01d67"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div class="outline-text-3" id="text-5-4">
<p>
The reduced density matrices are defined in the basis of molecular
@ -2514,7 +2514,7 @@ expressed in a basis of a one-electron function
\(g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)\).
</p>
<table id="orgacb787b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org02d2043" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2666,12 +2666,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-orgca89c37" class="outline-2">
<h2 id="orgca89c37"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org7fe8ced" class="outline-2">
<h2 id="org7fe8ced"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org099f627" class="outline-3">
<h3 id="org099f627"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-orgdbcf159" class="outline-3">
<h3 id="orgdbcf159"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div class="outline-text-3" id="text-6-1">
<p>
The Jastrow factor is an $N$-electron function to which the CI
@ -2696,8 +2696,8 @@ following:
</ul>
</div>
<div id="outline-container-org919ef0a" class="outline-4">
<h4 id="org919ef0a"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orgdb43028" class="outline-4">
<h4 id="orgdb43028"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div class="outline-text-4" id="text-6-1-1">
<p>
The first form of Jastrow factor is the one used in
@ -2774,8 +2774,8 @@ The terms \(J_{\text{ee}}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to en
</div>
</div>
<div id="outline-container-orgea8174d" class="outline-4">
<h4 id="orgea8174d"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org87f6d5e" class="outline-4">
<h4 id="org87f6d5e"><span class="section-number-4">6.1.2</span> Mu</h4>
<div class="outline-text-4" id="text-6-1-2">
<p>
<a href="https://aip.scitation.org/doi/10.1063/5.0044683">Mu-Jastrow</a> is based on a one-parameter correlation factor that has
@ -2872,10 +2872,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-orgf11581f" class="outline-4">
<h4 id="orgf11581f"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div id="outline-container-org0da47d7" class="outline-4">
<h4 id="org0da47d7"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div class="outline-text-4" id="text-6-1-3">
<table id="org7d30c55" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbba4555" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2979,8 +2979,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org06d176e" class="outline-2">
<h2 id="org06d176e"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org3e678f1" class="outline-2">
<h2 id="org3e678f1"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-7">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -2994,7 +2994,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orgd5fc427" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf809d9d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3049,7 +3049,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-01-13 Fri 14:55</p>
<p class="date">Created: 2023-01-19 Thu 00:32</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>