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README.html
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -360,7 +360,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-01-11 Wed 18:05</p>
<p class="date">Created: 2023-01-11 Wed 18:35</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2023-01-11 Wed 18:05 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Examples</title>
@ -346,31 +346,31 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org3116e49">1. Accessing sparse quantities (integrals)</a>
<li><a href="#orga60d003">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org11b427a">1.1. Fortran</a>
<li><a href="#org7717455">1.1. Fortran</a>
<ul>
<li><a href="#org6771b24">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org294b81d">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org2654075">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orge608318">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org2b64f65">1.1.5. Allocate memory</a></li>
<li><a href="#org9e678d3">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgf0e4ca5">1.1.7. Read two-electron quantities</a>
<li><a href="#orgd0c2770">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org27da21e">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orge8cdd7e">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orga60dad1">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org39d5608">1.1.5. Allocate memory</a></li>
<li><a href="#orgce94669">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orge879b46">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org15bb407">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org2e870ee">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org11d4eb4">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgeac937d">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgea929e5">1.1.8. Compute the energy</a></li>
<li><a href="#orga05f72e">1.1.9. Terminate</a></li>
<li><a href="#org8b870a9">1.1.8. Compute the energy</a></li>
<li><a href="#orgaa5e4c9">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orge203121">2. Reading determinants</a>
<li><a href="#org8f2616f">2. Reading determinants</a>
<ul>
<li><a href="#org9651988">2.1. Fortran</a></li>
<li><a href="#orgfa59962">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -378,12 +378,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org3116e49" class="outline-2">
<h2 id="org3116e49"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orga60d003" class="outline-2">
<h2 id="orga60d003"><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-org11b427a" class="outline-3">
<h3 id="org11b427a"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org7717455" class="outline-3">
<h3 id="org7717455"><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-org6771b24" class="outline-4">
<h4 id="org6771b24"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgd0c2770" class="outline-4">
<h4 id="orgd0c2770"><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-org294b81d" class="outline-4">
<h4 id="org294b81d"><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-org27da21e" class="outline-4">
<h4 id="org27da21e"><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-org2654075" class="outline-4">
<h4 id="org2654075"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orge8cdd7e" class="outline-4">
<h4 id="orge8cdd7e"><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-orge608318" class="outline-4">
<h4 id="orge608318"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orga60dad1" class="outline-4">
<h4 id="orga60dad1"><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-org2b64f65" class="outline-4">
<h4 id="org2b64f65"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org39d5608" class="outline-4">
<h4 id="org39d5608"><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-org9e678d3" class="outline-4">
<h4 id="org9e678d3"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgce94669" class="outline-4">
<h4 id="orgce94669"><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-orgf0e4ca5" class="outline-4">
<h4 id="orgf0e4ca5"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orge879b46" class="outline-4">
<h4 id="orge879b46"><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-org15bb407" class="outline-5">
<h5 id="org15bb407"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org11d4eb4" class="outline-5">
<h5 id="org11d4eb4"><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-org2e870ee" class="outline-5">
<h5 id="org2e870ee"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgeac937d" class="outline-5">
<h5 id="orgeac937d"><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-orgea929e5" class="outline-4">
<h4 id="orgea929e5"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org8b870a9" class="outline-4">
<h4 id="org8b870a9"><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-orga05f72e" class="outline-4">
<h4 id="orga05f72e"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgaa5e4c9" class="outline-4">
<h4 id="orgaa5e4c9"><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-orge203121" class="outline-2">
<h2 id="orge203121"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-org8f2616f" class="outline-2">
<h2 id="org8f2616f"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org9651988" class="outline-3">
<h3 id="org9651988"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-orgfa59962" class="outline-3">
<h3 id="orgfa59962"><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: 2023-01-11 Wed 18:05</p>
<p class="date">Created: 2023-01-11 Wed 18:35</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>
<!-- 2023-01-11 Wed 18:05 -->
<!-- 2023-01-11 Wed 18:35 -->
<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: 2023-01-11 Wed 18:05</p>
<p class="date">Created: 2023-01-11 Wed 18:35</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-01-11 Wed 18:05 -->
<!-- 2023-01-11 Wed 18:35 -->
<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="#org8a2eebc">1. Template for HDF5 definitions</a></li>
<li><a href="#org5bb5f04">2. Template for HDF5 structures</a></li>
<li><a href="#orged32647">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orge5ef551">4. Template for HDF5 has a group</a></li>
<li><a href="#org3ccd18b">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgeeef69b">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgd4aff47">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgc6d34e0">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org764e094">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org2c0ef69">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org242caa4">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgb33c539">12. Source code for the determinant part</a></li>
<li><a href="#org8b88671">13. Helper functions</a></li>
<li><a href="#orgdb82719">1. Template for HDF5 definitions</a></li>
<li><a href="#orga0440bb">2. Template for HDF5 structures</a></li>
<li><a href="#orgd6bfd76">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org817ec0a">4. Template for HDF5 has a group</a></li>
<li><a href="#org48539ab">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org06afb47">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orga2b4c68">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org1eb0ac7">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgc8924dc">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org4a07d68">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org185f5aa">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org4137ff0">12. Source code for the determinant part</a></li>
<li><a href="#orgee40fb1">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org8a2eebc" class="outline-2">
<h2 id="org8a2eebc"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orgdb82719" class="outline-2">
<h2 id="orgdb82719"><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-org5bb5f04" class="outline-2">
<h2 id="org5bb5f04"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orga0440bb" class="outline-2">
<h2 id="orga0440bb"><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-orged32647" class="outline-2">
<h2 id="orged32647"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgd6bfd76" class="outline-2">
<h2 id="orgd6bfd76"><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-orge5ef551" class="outline-2">
<h2 id="orge5ef551"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org817ec0a" class="outline-2">
<h2 id="org817ec0a"><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-org3ccd18b" class="outline-2">
<h2 id="org3ccd18b"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org48539ab" class="outline-2">
<h2 id="org48539ab"><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-orgeeef69b" class="outline-2">
<h2 id="orgeeef69b"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org06afb47" class="outline-2">
<h2 id="org06afb47"><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-orgd4aff47" class="outline-2">
<h2 id="orgd4aff47"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-orga2b4c68" class="outline-2">
<h2 id="orga2b4c68"><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-orgc6d34e0" class="outline-2">
<h2 id="orgc6d34e0"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org1eb0ac7" class="outline-2">
<h2 id="org1eb0ac7"><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-org764e094" class="outline-2">
<h2 id="org764e094"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgc8924dc" class="outline-2">
<h2 id="orgc8924dc"><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-org2c0ef69" class="outline-2">
<h2 id="org2c0ef69"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org4a07d68" class="outline-2">
<h2 id="org4a07d68"><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-org242caa4" class="outline-2">
<h2 id="org242caa4"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org185f5aa" class="outline-2">
<h2 id="org185f5aa"><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-orgb33c539" class="outline-2">
<h2 id="orgb33c539"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org4137ff0" class="outline-2">
<h2 id="org4137ff0"><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-org8b88671" class="outline-2">
<h2 id="org8b88671"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgee40fb1" class="outline-2">
<h2 id="orgee40fb1"><span class="section-number-2">13</span> Helper functions</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1843,7 +1843,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-01-11 Wed 18:05</p>
<p class="date">Created: 2023-01-11 Wed 18:35</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>
<!-- 2023-01-11 Wed 18:05 -->
<!-- 2023-01-11 Wed 18:35 -->
<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="#org9c7ab9b">1. Template for group-related structures in text back end</a></li>
<li><a href="#org29e342e">2. Template for general structure in text back end</a></li>
<li><a href="#org46e7551">3. Initialize function (constant part)</a></li>
<li><a href="#org377292c">4. Deinitialize function (templated part)</a></li>
<li><a href="#org9cb620a">5. Flush function (templated part)</a></li>
<li><a href="#org1eaf926">6. Template for text read a group</a></li>
<li><a href="#org44cf3fe">7. Template for text has a group</a></li>
<li><a href="#org3988727">8. Template for text flush a group</a></li>
<li><a href="#orgbea0746">9. Template for text free memory</a></li>
<li><a href="#orgdd7b25e">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org375b62d">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgba690bd">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org6ac1eed">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgeaca1cb">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgce8d8b4">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgdbb0f01">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org3b1e365">17. Source code for the determinant part</a></li>
<li><a href="#org6597cb3">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgcfb143d">2. Template for general structure in text back end</a></li>
<li><a href="#org7406ebf">3. Initialize function (constant part)</a></li>
<li><a href="#orgbce22cf">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgbe42ff8">5. Flush function (templated part)</a></li>
<li><a href="#orgf81c11b">6. Template for text read a group</a></li>
<li><a href="#orgcee0b6f">7. Template for text has a group</a></li>
<li><a href="#org46ff19f">8. Template for text flush a group</a></li>
<li><a href="#orga987fe0">9. Template for text free memory</a></li>
<li><a href="#org61c96e3">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org537e0d0">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org8bc36f6">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orge6df78a">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org2c1a45d">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgd3e76fa">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org3c47dad">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org6d532fb">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-org9c7ab9b" class="outline-2">
<h2 id="org9c7ab9b"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org6597cb3" class="outline-2">
<h2 id="org6597cb3"><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-org29e342e" class="outline-2">
<h2 id="org29e342e"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgcfb143d" class="outline-2">
<h2 id="orgcfb143d"><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-org46e7551" class="outline-2">
<h2 id="org46e7551"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org7406ebf" class="outline-2">
<h2 id="org7406ebf"><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-org377292c" class="outline-2">
<h2 id="org377292c"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgbce22cf" class="outline-2">
<h2 id="orgbce22cf"><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-org9cb620a" class="outline-2">
<h2 id="org9cb620a"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-orgbe42ff8" class="outline-2">
<h2 id="orgbe42ff8"><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-org1eaf926" class="outline-2">
<h2 id="org1eaf926"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orgf81c11b" class="outline-2">
<h2 id="orgf81c11b"><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-org44cf3fe" class="outline-2">
<h2 id="org44cf3fe"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-orgcee0b6f" class="outline-2">
<h2 id="orgcee0b6f"><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-org3988727" class="outline-2">
<h2 id="org3988727"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org46ff19f" class="outline-2">
<h2 id="org46ff19f"><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-orgbea0746" class="outline-2">
<h2 id="orgbea0746"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-orga987fe0" class="outline-2">
<h2 id="orga987fe0"><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-orgdd7b25e" class="outline-2">
<h2 id="orgdd7b25e"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org61c96e3" class="outline-2">
<h2 id="org61c96e3"><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-org375b62d" class="outline-2">
<h2 id="org375b62d"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org537e0d0" class="outline-2">
<h2 id="org537e0d0"><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-orgba690bd" class="outline-2">
<h2 id="orgba690bd"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org8bc36f6" class="outline-2">
<h2 id="org8bc36f6"><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-org6ac1eed" class="outline-2">
<h2 id="org6ac1eed"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orge6df78a" class="outline-2">
<h2 id="orge6df78a"><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-orgeaca1cb" class="outline-2">
<h2 id="orgeaca1cb"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org2c1a45d" class="outline-2">
<h2 id="org2c1a45d"><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-orgce8d8b4" class="outline-2">
<h2 id="orgce8d8b4"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-orgd3e76fa" class="outline-2">
<h2 id="orgd3e76fa"><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-orgdbb0f01" class="outline-2">
<h2 id="orgdbb0f01"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org3c47dad" class="outline-2">
<h2 id="org3c47dad"><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-org3b1e365" class="outline-2">
<h2 id="org3b1e365"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org6d532fb" class="outline-2">
<h2 id="org6d532fb"><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: 2023-01-11 Wed 18:05</p>
<p class="date">Created: 2023-01-11 Wed 18:35</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2023-01-11 Wed 18:05 -->
<!-- 2023-01-11 Wed 18:35 -->
<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="#org9456e81">1. Metadata (metadata group)</a></li>
<li><a href="#org59dc001">2. System</a>
<li><a href="#orga668de9">1. Metadata (metadata group)</a></li>
<li><a href="#orgac61218">2. System</a>
<ul>
<li><a href="#org023296c">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#orgc99253a">2.2. Cell (cell group)</a></li>
<li><a href="#org52e2903">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org5328431">2.4. Electron (electron group)</a></li>
<li><a href="#org8a7ef1d">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org8ccb9c3">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org670d159">2.2. Cell (cell group)</a></li>
<li><a href="#org4eff854">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org518ff1d">2.4. Electron (electron group)</a></li>
<li><a href="#org4cb1621">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#orgfc9e6f6">3. Basis functions</a>
<li><a href="#org364d828">3. Basis functions</a>
<ul>
<li><a href="#orgeff6825">3.1. Basis set (basis group)</a>
<li><a href="#orgfb4b5d0">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orgff7fb94">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgda6a94e">3.1.2. Plane waves</a></li>
<li><a href="#org469fd27">3.1.3. Data definitions</a></li>
<li><a href="#orge26b4cd">3.1.4. Example</a></li>
<li><a href="#org069853e">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgc0ec4a1">3.1.2. Plane waves</a></li>
<li><a href="#org758fa05">3.1.3. Data definitions</a></li>
<li><a href="#org5a55a23">3.1.4. Example</a></li>
</ul>
</li>
<li><a href="#org7451a8c">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org3c95d37">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org6eb7d7c">3.2.1. Example</a></li>
<li><a href="#org823893e">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org6515cd7">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#orga6c7216">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org7d7bfac">4. Orbitals</a>
<li><a href="#org6eaf1d0">4. Orbitals</a>
<ul>
<li><a href="#orgd0af6c0">4.1. Atomic orbitals (ao group)</a>
<li><a href="#orgd9f8d69">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="#orgd0c73d8">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org3bc5f59">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org81c75dd">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orga959c75">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orga317863">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org504572a">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgc22aaf8">5. Multi-determinant information</a>
<li><a href="#org3902688">5. Multi-determinant information</a>
<ul>
<li><a href="#org109e00c">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org48f81a0">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orga878796">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgcd2ad7f">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org08663a4">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org34beca9">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgdd8d096">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org12fe87d">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org43b581d">6. Correlation factors</a>
<li><a href="#org705019a">6. Correlation factors</a>
<ul>
<li><a href="#org4e2a1e0">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org320793f">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#orgbe89846">6.1.1. CHAMP</a></li>
<li><a href="#orga5bb7e8">6.1.2. Mu</a></li>
<li><a href="#orga278e84">6.1.3. Table of values</a></li>
<li><a href="#orgae1b3d1">6.1.1. CHAMP</a></li>
<li><a href="#org9909f84">6.1.2. Mu</a></li>
<li><a href="#org84472dc">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgb938556">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org36923e1">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-org9456e81" class="outline-2">
<h2 id="org9456e81"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orga668de9" class="outline-2">
<h2 id="orga668de9"><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="org732bc8c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgaa0a743" 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-org59dc001" class="outline-2">
<h2 id="org59dc001"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-orgac61218" class="outline-2">
<h2 id="orgac61218"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org023296c" class="outline-3">
<h3 id="org023296c"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org8ccb9c3" class="outline-3">
<h3 id="org8ccb9c3"><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="org675154c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org82ba13b" 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-orgc99253a" class="outline-3">
<h3 id="orgc99253a"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org670d159" class="outline-3">
<h3 id="org670d159"><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="org9a4c1ea" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org16fc6a2" 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-org52e2903" class="outline-3">
<h3 id="org52e2903"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org4eff854" class="outline-3">
<h3 id="org4eff854"><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="org239776f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org776141a" 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-org5328431" class="outline-3">
<h3 id="org5328431"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org518ff1d" class="outline-3">
<h3 id="org518ff1d"><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="orgd53a19f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org16ca417" 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-org8a7ef1d" class="outline-3">
<h3 id="org8a7ef1d"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org4cb1621" class="outline-3">
<h3 id="org4cb1621"><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="org67af526" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7da175d" 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-orgfc9e6f6" class="outline-2">
<h2 id="orgfc9e6f6"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org364d828" class="outline-2">
<h2 id="org364d828"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgeff6825" class="outline-3">
<h3 id="orgeff6825"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-orgfb4b5d0" class="outline-3">
<h3 id="orgfb4b5d0"><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-orgff7fb94" class="outline-4">
<h4 id="orgff7fb94"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org069853e" class="outline-4">
<h4 id="org069853e"><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-orgda6a94e" class="outline-4">
<h4 id="orgda6a94e"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div id="outline-container-orgc0ec4a1" class="outline-4">
<h4 id="orgc0ec4a1"><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-org469fd27" class="outline-4">
<h4 id="org469fd27"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div id="outline-container-org758fa05" class="outline-4">
<h4 id="org758fa05"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-3">
<table id="orgfb8c3af" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4ebd115" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1109,8 +1109,8 @@ plane waves.
</div>
</div>
<div id="outline-container-orge26b4cd" class="outline-4">
<h4 id="orge26b4cd"><span class="section-number-4">3.1.4</span> Example</h4>
<div id="outline-container-org5a55a23" class="outline-4">
<h4 id="org5a55a23"><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-org7451a8c" class="outline-3">
<h3 id="org7451a8c"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org3c95d37" class="outline-3">
<h3 id="org3c95d37"><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="orgc549ffd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgec61feb" 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-org6eb7d7c" class="outline-4">
<h4 id="org6eb7d7c"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-org823893e" class="outline-4">
<h4 id="org823893e"><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-org6515cd7" class="outline-3">
<h3 id="org6515cd7"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-orga6c7216" class="outline-3">
<h3 id="orga6c7216"><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="org3914930" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf513d1d" 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-org7d7bfac" class="outline-2">
<h2 id="org7d7bfac"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org6eaf1d0" class="outline-2">
<h2 id="org6eaf1d0"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-orgd0af6c0" class="outline-3">
<h3 id="orgd0af6c0"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-orgd9f8d69" class="outline-3">
<h3 id="orgd9f8d69"><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="#orgeff6825">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#orgfb4b5d0">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="org1aa544d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd41dcc5" 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-org9b55047" class="outline-4">
<div id="outline-container-org202d247" 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="org1f6aad1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc5fc351" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1751,7 +1751,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orga7634d8" class="outline-4">
<div id="outline-container-orga5337b0" 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="org85bfea2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org173f242" 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-orgd0c73d8" class="outline-3">
<h3 id="orgd0c73d8"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org3bc5f59" class="outline-3">
<h3 id="org3bc5f59"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org47e66cd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org588d643" 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-org81c75dd" class="outline-4">
<h4 id="org81c75dd"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-orga317863" class="outline-4">
<h4 id="orga317863"><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="orgdc10c3c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org69b542d" 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-orga959c75" class="outline-4">
<h4 id="orga959c75"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org504572a" class="outline-4">
<h4 id="org504572a"><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="org8382c3a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3aab7ce" 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-orgc22aaf8" class="outline-2">
<h2 id="orgc22aaf8"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org3902688" class="outline-2">
<h2 id="org3902688"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org109e00c" class="outline-3">
<h3 id="org109e00c"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org08663a4" class="outline-3">
<h3 id="org08663a4"><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="org20e7068" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbdc4e91" 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-org48f81a0" class="outline-3">
<h3 id="org48f81a0"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org34beca9" class="outline-3">
<h3 id="org34beca9"><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="org262f231" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org98ae853" 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-orga878796" class="outline-3">
<h3 id="orga878796"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orgdd8d096" class="outline-3">
<h3 id="orgdd8d096"><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="org9615176" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgac49339" 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-orgcd2ad7f" class="outline-3">
<h3 id="orgcd2ad7f"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org12fe87d" class="outline-3">
<h3 id="org12fe87d"><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="orgc1229a2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org124dc04" 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-org43b581d" class="outline-2">
<h2 id="org43b581d"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org705019a" class="outline-2">
<h2 id="org705019a"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org4e2a1e0" class="outline-3">
<h3 id="org4e2a1e0"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org320793f" class="outline-3">
<h3 id="org320793f"><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-orgbe89846" class="outline-4">
<h4 id="orgbe89846"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orgae1b3d1" class="outline-4">
<h4 id="orgae1b3d1"><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-orga5bb7e8" class="outline-4">
<h4 id="orga5bb7e8"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org9909f84" class="outline-4">
<h4 id="org9909f84"><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-orga278e84" class="outline-4">
<h4 id="orga278e84"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div id="outline-container-org84472dc" class="outline-4">
<h4 id="org84472dc"><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="orge097aa2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc525af1" 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-orgb938556" class="outline-2">
<h2 id="orgb938556"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org36923e1" class="outline-2">
<h2 id="org36923e1"><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="org5462265" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org46d8926" 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: 2023-01-11 Wed 18:05</p>
<p class="date">Created: 2023-01-11 Wed 18:35</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>