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README.html
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<head>
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -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: 2022-12-01 Thu 18:20</p>
<p class="date">Created: 2022-12-02 Fri 08:48</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-12-01 Thu 18:20 -->
<!-- 2022-12-02 Fri 08:48 -->
<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="#org2319ed2">1. Accessing sparse quantities (integrals)</a>
<li><a href="#org6b88d96">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org9566fea">1.1. Fortran</a>
<li><a href="#org77f2fef">1.1. Fortran</a>
<ul>
<li><a href="#orgf6f5710">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org75d2ef9">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgc52f491">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org4a9f1ad">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org7a548d3">1.1.5. Allocate memory</a></li>
<li><a href="#org5c60cd0">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org4c7d5ff">1.1.7. Read two-electron quantities</a>
<li><a href="#org9d1ab54">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orge5b9684">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org8bc95b2">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org5316411">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org7b3bf4c">1.1.5. Allocate memory</a></li>
<li><a href="#orgcda4eee">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orga0e50c4">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org1af921c">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgecf043f">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#orgb6134a9">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org95156a4">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgbbb0fc7">1.1.8. Compute the energy</a></li>
<li><a href="#org3ceecff">1.1.9. Terminate</a></li>
<li><a href="#orga2bfd9e">1.1.8. Compute the energy</a></li>
<li><a href="#org926082a">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org6e27917">2. Reading determinants</a>
<li><a href="#orgdbb7d24">2. Reading determinants</a>
<ul>
<li><a href="#org5f01b2d">2.1. Fortran</a></li>
<li><a href="#orgd2c50cf">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -378,12 +378,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org2319ed2" class="outline-2">
<h2 id="org2319ed2"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org6b88d96" class="outline-2">
<h2 id="org6b88d96"><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-org9566fea" class="outline-3">
<h3 id="org9566fea"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org77f2fef" class="outline-3">
<h3 id="org77f2fef"><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-orgf6f5710" class="outline-4">
<h4 id="orgf6f5710"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org9d1ab54" class="outline-4">
<h4 id="org9d1ab54"><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-org75d2ef9" class="outline-4">
<h4 id="org75d2ef9"><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-orge5b9684" class="outline-4">
<h4 id="orge5b9684"><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-orgc52f491" class="outline-4">
<h4 id="orgc52f491"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org8bc95b2" class="outline-4">
<h4 id="org8bc95b2"><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-org4a9f1ad" class="outline-4">
<h4 id="org4a9f1ad"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org5316411" class="outline-4">
<h4 id="org5316411"><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-org7a548d3" class="outline-4">
<h4 id="org7a548d3"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org7b3bf4c" class="outline-4">
<h4 id="org7b3bf4c"><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-org5c60cd0" class="outline-4">
<h4 id="org5c60cd0"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgcda4eee" class="outline-4">
<h4 id="orgcda4eee"><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-org4c7d5ff" class="outline-4">
<h4 id="org4c7d5ff"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orga0e50c4" class="outline-4">
<h4 id="orga0e50c4"><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-org1af921c" class="outline-5">
<h5 id="org1af921c"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgb6134a9" class="outline-5">
<h5 id="orgb6134a9"><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-orgecf043f" class="outline-5">
<h5 id="orgecf043f"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org95156a4" class="outline-5">
<h5 id="org95156a4"><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-orgbbb0fc7" class="outline-4">
<h4 id="orgbbb0fc7"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-orga2bfd9e" class="outline-4">
<h4 id="orga2bfd9e"><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-org3ceecff" class="outline-4">
<h4 id="org3ceecff"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org926082a" class="outline-4">
<h4 id="org926082a"><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-org6e27917" class="outline-2">
<h2 id="org6e27917"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-orgdbb7d24" class="outline-2">
<h2 id="orgdbb7d24"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org5f01b2d" class="outline-3">
<h3 id="org5f01b2d"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-orgd2c50cf" class="outline-3">
<h3 id="orgd2c50cf"><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: 2022-12-01 Thu 18:20</p>
<p class="date">Created: 2022-12-02 Fri 08:48</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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index.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-12-01 Thu 18:20 -->
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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: 2022-12-01 Thu 18:20</p>
<p class="date">Created: 2022-12-02 Fri 08:48</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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templator_hdf5.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-12-01 Thu 18:20 -->
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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>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="#org28015b0">1. Template for HDF5 definitions</a></li>
<li><a href="#orgd93988b">2. Template for HDF5 structures</a></li>
<li><a href="#orgd6dd7ca">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org452d97d">4. Template for HDF5 has a group</a></li>
<li><a href="#orgae07204">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org519e292">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgbaa1263">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org5fc0c01">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org7ec92c7">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org9734933">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgf71dca6">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org5308856">12. Source code for the determinant part</a></li>
<li><a href="#org814ab10">13. Helper functions</a></li>
<li><a href="#org566b686">1. Template for HDF5 definitions</a></li>
<li><a href="#org1974247">2. Template for HDF5 structures</a></li>
<li><a href="#org9b8ebd2">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgd9ce991">4. Template for HDF5 has a group</a></li>
<li><a href="#org6836f9c">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org8f0d036">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org54ef246">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgd941e71">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgbb65636">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org28eaeee">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgd3b1cf1">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org3029933">12. Source code for the determinant part</a></li>
<li><a href="#orgafbeb7b">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org28015b0" class="outline-2">
<h2 id="org28015b0"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org566b686" class="outline-2">
<h2 id="org566b686"><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-orgd93988b" class="outline-2">
<h2 id="orgd93988b"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org1974247" class="outline-2">
<h2 id="org1974247"><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-orgd6dd7ca" class="outline-2">
<h2 id="orgd6dd7ca"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org9b8ebd2" class="outline-2">
<h2 id="org9b8ebd2"><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-org452d97d" class="outline-2">
<h2 id="org452d97d"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orgd9ce991" class="outline-2">
<h2 id="orgd9ce991"><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-orgae07204" class="outline-2">
<h2 id="orgae07204"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org6836f9c" class="outline-2">
<h2 id="org6836f9c"><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-org519e292" class="outline-2">
<h2 id="org519e292"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org8f0d036" class="outline-2">
<h2 id="org8f0d036"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -767,8 +767,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgbaa1263" class="outline-2">
<h2 id="orgbaa1263"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org54ef246" class="outline-2">
<h2 id="org54ef246"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-7">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -971,8 +971,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org5fc0c01" class="outline-2">
<h2 id="org5fc0c01"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-orgd941e71" class="outline-2">
<h2 id="orgd941e71"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div class="outline-text-2" id="text-8">
<p>
Chunked I/O in HDF5 for <code>buffered</code> data.
@ -1107,8 +1107,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org7ec92c7" class="outline-2">
<h2 id="org7ec92c7"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgbb65636" class="outline-2">
<h2 id="orgbb65636"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org9734933" class="outline-2">
<h2 id="org9734933"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org28eaeee" class="outline-2">
<h2 id="org28eaeee"><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-orgf71dca6" class="outline-2">
<h2 id="orgf71dca6"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgd3b1cf1" class="outline-2">
<h2 id="orgd3b1cf1"><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-org5308856" class="outline-2">
<h2 id="org5308856"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org3029933" class="outline-2">
<h2 id="org3029933"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-12">
<p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1579,8 +1579,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org814ab10" class="outline-2">
<h2 id="org814ab10"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgafbeb7b" class="outline-2">
<h2 id="orgafbeb7b"><span class="section-number-2">13</span> Helper functions</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1843,7 +1843,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-12-01 Thu 18:20</p>
<p class="date">Created: 2022-12-02 Fri 08:48</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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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>
<!-- 2022-12-01 Thu 18:20 -->
<!-- 2022-12-02 Fri 08:48 -->
<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="#orgab9a8cf">1. Template for group-related structures in text back end</a></li>
<li><a href="#org2732ee1">2. Template for general structure in text back end</a></li>
<li><a href="#org609bac6">3. Initialize function (constant part)</a></li>
<li><a href="#org19c424d">4. Deinitialize function (templated part)</a></li>
<li><a href="#org3f85835">5. Flush function (templated part)</a></li>
<li><a href="#org4db0173">6. Template for text read a group</a></li>
<li><a href="#orge1203b0">7. Template for text has a group</a></li>
<li><a href="#org55dbfd8">8. Template for text flush a group</a></li>
<li><a href="#org7289503">9. Template for text free memory</a></li>
<li><a href="#org80193ee">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org82c1d66">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org576aebd">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org2411c23">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgcfd7a26">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org843f230">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org4d2acd7">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org71815ba">17. Source code for the determinant part</a></li>
<li><a href="#org61721d1">1. Template for group-related structures in text back end</a></li>
<li><a href="#orga76fb7f">2. Template for general structure in text back end</a></li>
<li><a href="#org5719d56">3. Initialize function (constant part)</a></li>
<li><a href="#orgf5e4d10">4. Deinitialize function (templated part)</a></li>
<li><a href="#org4e7d6dc">5. Flush function (templated part)</a></li>
<li><a href="#orgcade9d9">6. Template for text read a group</a></li>
<li><a href="#org18c32dd">7. Template for text has a group</a></li>
<li><a href="#org3d0015a">8. Template for text flush a group</a></li>
<li><a href="#orgf19e278">9. Template for text free memory</a></li>
<li><a href="#orga114128">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org4e882d1">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org2b1d924">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgf128167">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org048505f">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org3275562">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgdca7700">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orge0ad0b6">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-orgab9a8cf" class="outline-2">
<h2 id="orgab9a8cf"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org61721d1" class="outline-2">
<h2 id="org61721d1"><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-org2732ee1" class="outline-2">
<h2 id="org2732ee1"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orga76fb7f" class="outline-2">
<h2 id="orga76fb7f"><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-org609bac6" class="outline-2">
<h2 id="org609bac6"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org5719d56" class="outline-2">
<h2 id="org5719d56"><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-org19c424d" class="outline-2">
<h2 id="org19c424d"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgf5e4d10" class="outline-2">
<h2 id="orgf5e4d10"><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-org3f85835" class="outline-2">
<h2 id="org3f85835"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org4e7d6dc" class="outline-2">
<h2 id="org4e7d6dc"><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-org4db0173" class="outline-2">
<h2 id="org4db0173"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orgcade9d9" class="outline-2">
<h2 id="orgcade9d9"><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-orge1203b0" class="outline-2">
<h2 id="orge1203b0"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org18c32dd" class="outline-2">
<h2 id="org18c32dd"><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-org55dbfd8" class="outline-2">
<h2 id="org55dbfd8"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org3d0015a" class="outline-2">
<h2 id="org3d0015a"><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-org7289503" class="outline-2">
<h2 id="org7289503"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-orgf19e278" class="outline-2">
<h2 id="orgf19e278"><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-org80193ee" class="outline-2">
<h2 id="org80193ee"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orga114128" class="outline-2">
<h2 id="orga114128"><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-org82c1d66" class="outline-2">
<h2 id="org82c1d66"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org4e882d1" class="outline-2">
<h2 id="org4e882d1"><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-org576aebd" class="outline-2">
<h2 id="org576aebd"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org2b1d924" class="outline-2">
<h2 id="org2b1d924"><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-org2411c23" class="outline-2">
<h2 id="org2411c23"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orgf128167" class="outline-2">
<h2 id="orgf128167"><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-orgcfd7a26" class="outline-2">
<h2 id="orgcfd7a26"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org048505f" class="outline-2">
<h2 id="org048505f"><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-org843f230" class="outline-2">
<h2 id="org843f230"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org3275562" class="outline-2">
<h2 id="org3275562"><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-org4d2acd7" class="outline-2">
<h2 id="org4d2acd7"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgdca7700" class="outline-2">
<h2 id="orgdca7700"><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-org71815ba" class="outline-2">
<h2 id="org71815ba"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-orge0ad0b6" class="outline-2">
<h2 id="orge0ad0b6"><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: 2022-12-01 Thu 18:20</p>
<p class="date">Created: 2022-12-02 Fri 08:48</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-12-01 Thu 18:20 -->
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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>TREX Configuration file</title>
@ -346,38 +346,38 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9084e47">1. Metadata (metadata group)</a></li>
<li><a href="#org0079050">2. Electron (electron group)</a></li>
<li><a href="#org6af4211">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgae1cb45">4. Effective core potentials (ecp group)</a>
<li><a href="#org353b04b">1. Metadata (metadata group)</a></li>
<li><a href="#org34d836f">2. Electron (electron group)</a></li>
<li><a href="#org4f71b4b">3. Nucleus (nucleus group)</a></li>
<li><a href="#org1a4d1e1">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org12a08ea">4.1. Example</a></li>
<li><a href="#org81687cd">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org53ba67b">5. Basis set (basis group)</a>
<li><a href="#org3635982">5. Basis set (basis group)</a>
<ul>
<li><a href="#orgaa057e8">5.1. Example</a></li>
<li><a href="#org99c9b1d">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org7a073c2">6. Atomic orbitals (ao group)</a>
<li><a href="#org641a3f3">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="#org6617b7a">7. Molecular orbitals (mo group)</a>
<li><a href="#orgc596a7d">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org0cb1ed8">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org304482e">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org029e862">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgca729b2">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org8f33879">8. Slater determinants (determinant group)</a></li>
<li><a href="#org0cdc8fe">9. Configuration state functions (csf group)</a></li>
<li><a href="#orgef1389f">10. Excited states (state group)</a></li>
<li><a href="#org621cf81">11. Reduced density matrices (rdm group)</a></li>
<li><a href="#org67fd674">12. Cell (cell group)</a></li>
<li><a href="#org821a9c6">13. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org4a41efa">14. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org5581892">8. Slater determinants (determinant group)</a></li>
<li><a href="#org58b3eb8">9. Configuration state functions (csf group)</a></li>
<li><a href="#org275a5d7">10. Excited states (state group)</a></li>
<li><a href="#org03f970d">11. Reduced density matrices (rdm group)</a></li>
<li><a href="#org695f3b7">12. Cell (cell group)</a></li>
<li><a href="#org52561de">13. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org647ace5">14. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -439,8 +439,8 @@ For determinant lists (integer bit fields), the <code>special</code> attribute i
This means that the source code is not produced by the generator, but hand-written.
</p>
<div id="outline-container-org9084e47" class="outline-2">
<h2 id="org9084e47"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org353b04b" class="outline-2">
<h2 id="org353b04b"><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
@ -450,7 +450,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="org088daed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9a8b3ae" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -531,15 +531,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-org0079050" class="outline-2">
<h2 id="org0079050"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org34d836f" class="outline-2">
<h2 id="org34d836f"><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="orgddfa06b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga25fbf6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -585,15 +585,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org6af4211" class="outline-2">
<h2 id="org6af4211"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org4f71b4b" class="outline-2">
<h2 id="org4f71b4b"><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="org0ad98c8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge32a82e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -660,8 +660,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-orgae1cb45" class="outline-2">
<h2 id="orgae1cb45"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org1a4d1e1" class="outline-2">
<h2 id="org1a4d1e1"><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
@ -694,7 +694,7 @@ 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="org29f6312" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6b6f336" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -796,8 +796,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-org12a08ea" class="outline-3">
<h3 id="org12a08ea"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org81687cd" class="outline-3">
<h3 id="org81687cd"><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
@ -860,8 +860,8 @@ power = [
</div>
</div>
<div id="outline-container-org53ba67b" class="outline-2">
<h2 id="org53ba67b"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org3635982" class="outline-2">
<h2 id="org3635982"><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
@ -914,7 +914,7 @@ 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="org1ce2302" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2c6acd0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1008,8 +1008,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-orgaa057e8" class="outline-3">
<h3 id="orgaa057e8"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org99c9b1d" class="outline-3">
<h3 id="org99c9b1d"><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
@ -1087,8 +1087,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org7a073c2" class="outline-2">
<h2 id="org7a073c2"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org641a3f3" class="outline-2">
<h2 id="org641a3f3"><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
@ -1141,13 +1141,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org53ba67b">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org3635982">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="orgf42513a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org051419e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1199,7 +1199,7 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org81770c7" class="outline-3">
<div id="outline-container-org5d9a674" class="outline-3">
<h3 id="ao_one_e"><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">
@ -1217,7 +1217,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org8dce719" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcb26697" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1312,7 +1312,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgbbaff9c" class="outline-3">
<div id="outline-container-orga31de14" class="outline-3">
<h3 id="ao_two_e"><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>
@ -1334,7 +1334,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org9fa36c9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orged7096c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1374,10 +1374,10 @@ notation.
</div>
</div>
<div id="outline-container-org6617b7a" class="outline-2">
<h2 id="org6617b7a"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgc596a7d" class="outline-2">
<h2 id="orgc596a7d"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org7c22ae8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5b5e5b5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1464,8 +1464,8 @@ notation.
</table>
</div>
<div id="outline-container-org0cb1ed8" class="outline-3">
<h3 id="org0cb1ed8"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org029e862" class="outline-3">
<h3 id="org029e862"><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
@ -1473,7 +1473,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org884388a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3e34a27" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1568,8 +1568,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org304482e" class="outline-3">
<h3 id="org304482e"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orgca729b2" class="outline-3">
<h3 id="orgca729b2"><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 are the same as those defined in the
@ -1587,7 +1587,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="orga4fac98" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7c0d98f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1632,7 +1632,7 @@ The Cholesky decomposition of the integrals can also be stored:
<tr>
<td class="org-left"><code>eri_cholesky</code></td>
<td class="org-left"><code>float sparse</code></td>
<td class="org-left"><code>(mo.num, mo.num, rdm.2e_cholesky_num)</code></td>
<td class="org-left"><code>(mo.num, mo.num, mo_2e_int.eri_cholesky_num)</code></td>
<td class="org-left">Cholesky decomposition of the ERI</td>
</tr>
@ -1646,7 +1646,7 @@ The Cholesky decomposition of the integrals can also be stored:
<tr>
<td class="org-left"><code>eri_lr_cholesky</code></td>
<td class="org-left"><code>float sparse</code></td>
<td class="org-left"><code>(mo.num, mo.num, rdm.2e_cholesky_num)</code></td>
<td class="org-left"><code>(mo.num, mo.num, mo_2e_int.eri_lr_cholesky_num)</code></td>
<td class="org-left">Cholesky decomposition of the long range ERI</td>
</tr>
</tbody>
@ -1655,8 +1655,8 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org8f33879" class="outline-2">
<h2 id="org8f33879"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-org5581892" class="outline-2">
<h2 id="org5581892"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div class="outline-text-2" id="text-8">
<p>
The configuration interaction (CI) wave function \(\Psi\)
@ -1698,7 +1698,7 @@ 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="orgf2f7c67" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf3792da" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1744,8 +1744,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org0cdc8fe" class="outline-2">
<h2 id="org0cdc8fe"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
<div id="outline-container-org58b3eb8" class="outline-2">
<h2 id="org58b3eb8"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
<div class="outline-text-2" id="text-9">
<p>
The configuration interaction (CI) wave function \(\Psi\) can be
@ -1767,7 +1767,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org2b9e692" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org24af018" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1813,8 +1813,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-orgef1389f" class="outline-2">
<h2 id="orgef1389f"><span class="section-number-2">10</span> Excited states (state group)</h2>
<div id="outline-container-org275a5d7" class="outline-2">
<h2 id="org275a5d7"><span class="section-number-2">10</span> Excited states (state group)</h2>
<div class="outline-text-2" id="text-10">
<p>
This group contains information about excited state. Since TREXIO version 2.3.0
@ -1829,7 +1829,7 @@ The <code>id</code> and <code>current_label</code> attributes have to be specifi
(containing both ground and excited state data).
</p>
<table id="org5d7fe36" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0378449" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1889,8 +1889,8 @@ The <code>id</code> and <code>current_label</code> attributes have to be specifi
</div>
</div>
<div id="outline-container-org621cf81" class="outline-2">
<h2 id="org621cf81"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org03f970d" class="outline-2">
<h2 id="org03f970d"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-11">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1965,7 +1965,7 @@ 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="org1264d51" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcc83ee8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2116,10 +2116,10 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org67fd674" class="outline-2">
<h2 id="org67fd674"><span class="section-number-2">12</span> Cell (cell group)</h2>
<div id="outline-container-org695f3b7" class="outline-2">
<h2 id="org695f3b7"><span class="section-number-2">12</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-12">
<table id="org406e544" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8694241" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2165,10 +2165,10 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org821a9c6" class="outline-2">
<h2 id="org821a9c6"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-org52561de" class="outline-2">
<h2 id="org52561de"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-13">
<table id="orgda0b833" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd62d417" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2207,8 +2207,8 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org4a41efa" class="outline-2">
<h2 id="org4a41efa"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org647ace5" class="outline-2">
<h2 id="org647ace5"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-14">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -2222,7 +2222,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="org8bd07f0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org67c3254" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2277,7 +2277,7 @@ 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: 2022-12-01 Thu 18:20</p>
<p class="date">Created: 2022-12-02 Fri 08:48</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>