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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: 2023-01-20 Fri 08:33</p>
<p class="date">Created: 2023-02-16 Thu 08:31</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2023-01-20 Fri 08:33 -->
<!-- 2023-02-16 Thu 08:31 -->
<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="#org4311e88">1. Accessing sparse quantities (integrals)</a>
<li><a href="#org0ada7bb">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org76bc61c">1.1. Fortran</a>
<li><a href="#org2def822">1.1. Fortran</a>
<ul>
<li><a href="#org96a81b0">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org261598c">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org56b7553">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgdf7bda8">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orge617f6b">1.1.5. Allocate memory</a></li>
<li><a href="#orgb8d6c70">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org4e5b574">1.1.7. Read two-electron quantities</a>
<li><a href="#orge19a482">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgcefbbd9">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgd05b398">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgbfdeed9">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org0110ca9">1.1.5. Allocate memory</a></li>
<li><a href="#org46d6ccb">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgdcb4a96">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orge7faffe">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org7ebb1ab">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org69d43a9">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org01decab">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org458d680">1.1.8. Compute the energy</a></li>
<li><a href="#org5ab828c">1.1.9. Terminate</a></li>
<li><a href="#org0b229e7">1.1.8. Compute the energy</a></li>
<li><a href="#org607bde5">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgda4cb21">2. Reading determinants</a>
<li><a href="#org2c345eb">2. Reading determinants</a>
<ul>
<li><a href="#org0463da6">2.1. Fortran</a></li>
<li><a href="#orgf294611">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -378,12 +378,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org4311e88" class="outline-2">
<h2 id="org4311e88"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org0ada7bb" class="outline-2">
<h2 id="org0ada7bb"><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-org76bc61c" class="outline-3">
<h3 id="org76bc61c"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org2def822" class="outline-3">
<h3 id="org2def822"><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-org96a81b0" class="outline-4">
<h4 id="org96a81b0"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orge19a482" class="outline-4">
<h4 id="orge19a482"><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-org261598c" class="outline-4">
<h4 id="org261598c"><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-orgcefbbd9" class="outline-4">
<h4 id="orgcefbbd9"><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-org56b7553" class="outline-4">
<h4 id="org56b7553"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgd05b398" class="outline-4">
<h4 id="orgd05b398"><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-orgdf7bda8" class="outline-4">
<h4 id="orgdf7bda8"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgbfdeed9" class="outline-4">
<h4 id="orgbfdeed9"><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-orge617f6b" class="outline-4">
<h4 id="orge617f6b"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org0110ca9" class="outline-4">
<h4 id="org0110ca9"><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-orgb8d6c70" class="outline-4">
<h4 id="orgb8d6c70"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org46d6ccb" class="outline-4">
<h4 id="org46d6ccb"><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-org4e5b574" class="outline-4">
<h4 id="org4e5b574"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgdcb4a96" class="outline-4">
<h4 id="orgdcb4a96"><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-orge7faffe" class="outline-5">
<h5 id="orge7faffe"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org69d43a9" class="outline-5">
<h5 id="org69d43a9"><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-org7ebb1ab" class="outline-5">
<h5 id="org7ebb1ab"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org01decab" class="outline-5">
<h5 id="org01decab"><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-org458d680" class="outline-4">
<h4 id="org458d680"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org0b229e7" class="outline-4">
<h4 id="org0b229e7"><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-org5ab828c" class="outline-4">
<h4 id="org5ab828c"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org607bde5" class="outline-4">
<h4 id="org607bde5"><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-orgda4cb21" class="outline-2">
<h2 id="orgda4cb21"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-org2c345eb" class="outline-2">
<h2 id="org2c345eb"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org0463da6" class="outline-3">
<h3 id="org0463da6"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-orgf294611" class="outline-3">
<h3 id="orgf294611"><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: 2023-01-20 Fri 08:33</p>
<p class="date">Created: 2023-02-16 Thu 08:31</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>
<!-- 2023-01-20 Fri 08:33 -->
<!-- 2023-02-16 Thu 08:31 -->
<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: 2023-01-20 Fri 08:33</p>
<p class="date">Created: 2023-02-16 Thu 08:31</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-01-20 Fri 08:33 -->
<!-- 2023-02-16 Thu 08:31 -->
<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="#org3988b92">1. Template for HDF5 definitions</a></li>
<li><a href="#org6cb742c">2. Template for HDF5 structures</a></li>
<li><a href="#orgde2ed9b">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgc426a0a">4. Template for HDF5 has a group</a></li>
<li><a href="#org746ffe9">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org251d221">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org91c83ec">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org5b86179">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org4b479eb">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org4fdd96c">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org90d58ae">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org1ee22b2">12. Source code for the determinant part</a></li>
<li><a href="#org98cd99b">13. Helper functions</a></li>
<li><a href="#orgf5ffd52">1. Template for HDF5 definitions</a></li>
<li><a href="#org0eb6385">2. Template for HDF5 structures</a></li>
<li><a href="#orgd17ce03">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orge31791e">4. Template for HDF5 has a group</a></li>
<li><a href="#orgf8a7e04">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org63fa7ef">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org51eca4f">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org4dc838b">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgb8d7595">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org4b60a49">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org2d247a4">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org315ad20">12. Source code for the determinant part</a></li>
<li><a href="#org89fa238">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org3988b92" class="outline-2">
<h2 id="org3988b92"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orgf5ffd52" class="outline-2">
<h2 id="orgf5ffd52"><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-org6cb742c" class="outline-2">
<h2 id="org6cb742c"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org0eb6385" class="outline-2">
<h2 id="org0eb6385"><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-orgde2ed9b" class="outline-2">
<h2 id="orgde2ed9b"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgd17ce03" class="outline-2">
<h2 id="orgd17ce03"><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-orgc426a0a" class="outline-2">
<h2 id="orgc426a0a"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orge31791e" class="outline-2">
<h2 id="orge31791e"><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-org746ffe9" class="outline-2">
<h2 id="org746ffe9"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orgf8a7e04" class="outline-2">
<h2 id="orgf8a7e04"><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-org251d221" class="outline-2">
<h2 id="org251d221"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org63fa7ef" class="outline-2">
<h2 id="org63fa7ef"><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>
@ -770,8 +770,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org91c83ec" class="outline-2">
<h2 id="org91c83ec"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org51eca4f" class="outline-2">
<h2 id="org51eca4f"><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
@ -973,8 +973,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org5b86179" class="outline-2">
<h2 id="org5b86179"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org4dc838b" class="outline-2">
<h2 id="org4dc838b"><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.
@ -1108,8 +1108,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org4b479eb" class="outline-2">
<h2 id="org4b479eb"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgb8d7595" class="outline-2">
<h2 id="orgb8d7595"><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-org4fdd96c" class="outline-2">
<h2 id="org4fdd96c"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org4b60a49" class="outline-2">
<h2 id="org4b60a49"><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-org90d58ae" class="outline-2">
<h2 id="org90d58ae"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org2d247a4" class="outline-2">
<h2 id="org2d247a4"><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-org1ee22b2" class="outline-2">
<h2 id="org1ee22b2"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org315ad20" class="outline-2">
<h2 id="org315ad20"><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.
@ -1578,8 +1578,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org98cd99b" class="outline-2">
<h2 id="org98cd99b"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org89fa238" class="outline-2">
<h2 id="org89fa238"><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>
@ -1842,7 +1842,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-01-20 Fri 08:33</p>
<p class="date">Created: 2023-02-16 Thu 08:31</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2023-01-20 Fri 08:33 -->
<!-- 2023-02-16 Thu 08:31 -->
<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="#org67c187e">1. Template for group-related structures in text back end</a></li>
<li><a href="#org6c0d1e7">2. Template for general structure in text back end</a></li>
<li><a href="#orgfb8c6ac">3. Initialize function (constant part)</a></li>
<li><a href="#org1bc2676">4. Deinitialize function (templated part)</a></li>
<li><a href="#org59c4c52">5. Flush function (templated part)</a></li>
<li><a href="#org754ab78">6. Template for text read a group</a></li>
<li><a href="#org11b6a61">7. Template for text has a group</a></li>
<li><a href="#org7820997">8. Template for text flush a group</a></li>
<li><a href="#org6c28a47">9. Template for text free memory</a></li>
<li><a href="#org296d50a">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org16a7ea9">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org07fc8be">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org805c590">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgbe5bc8c">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org78882d0">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgfa85033">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org6dcc538">17. Source code for the determinant part</a></li>
<li><a href="#orga640ee0">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgc330155">2. Template for general structure in text back end</a></li>
<li><a href="#org44d0b5b">3. Initialize function (constant part)</a></li>
<li><a href="#orgad27d10">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgd43e45e">5. Flush function (templated part)</a></li>
<li><a href="#orgd54b267">6. Template for text read a group</a></li>
<li><a href="#orgbb4eb72">7. Template for text has a group</a></li>
<li><a href="#org516f934">8. Template for text flush a group</a></li>
<li><a href="#orgc1a5739">9. Template for text free memory</a></li>
<li><a href="#org6ade7f3">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org6eb727a">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgd47ed4e">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org813c770">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org927a9d2">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org18d8e7c">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgc9f8921">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org28743d8">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-org67c187e" class="outline-2">
<h2 id="org67c187e"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orga640ee0" class="outline-2">
<h2 id="orga640ee0"><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-org6c0d1e7" class="outline-2">
<h2 id="org6c0d1e7"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgc330155" class="outline-2">
<h2 id="orgc330155"><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-orgfb8c6ac" class="outline-2">
<h2 id="orgfb8c6ac"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org44d0b5b" class="outline-2">
<h2 id="org44d0b5b"><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-org1bc2676" class="outline-2">
<h2 id="org1bc2676"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgad27d10" class="outline-2">
<h2 id="orgad27d10"><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-org59c4c52" class="outline-2">
<h2 id="org59c4c52"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-orgd43e45e" class="outline-2">
<h2 id="orgd43e45e"><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-org754ab78" class="outline-2">
<h2 id="org754ab78"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orgd54b267" class="outline-2">
<h2 id="orgd54b267"><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-org11b6a61" class="outline-2">
<h2 id="org11b6a61"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-orgbb4eb72" class="outline-2">
<h2 id="orgbb4eb72"><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-org7820997" class="outline-2">
<h2 id="org7820997"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org516f934" class="outline-2">
<h2 id="org516f934"><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-org6c28a47" class="outline-2">
<h2 id="org6c28a47"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-orgc1a5739" class="outline-2">
<h2 id="orgc1a5739"><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-org296d50a" class="outline-2">
<h2 id="org296d50a"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org6ade7f3" class="outline-2">
<h2 id="org6ade7f3"><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-org16a7ea9" class="outline-2">
<h2 id="org16a7ea9"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org6eb727a" class="outline-2">
<h2 id="org6eb727a"><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-org07fc8be" class="outline-2">
<h2 id="org07fc8be"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgd47ed4e" class="outline-2">
<h2 id="orgd47ed4e"><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-org805c590" class="outline-2">
<h2 id="org805c590"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org813c770" class="outline-2">
<h2 id="org813c770"><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-orgbe5bc8c" class="outline-2">
<h2 id="orgbe5bc8c"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org927a9d2" class="outline-2">
<h2 id="org927a9d2"><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-org78882d0" class="outline-2">
<h2 id="org78882d0"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org18d8e7c" class="outline-2">
<h2 id="org18d8e7c"><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-orgfa85033" class="outline-2">
<h2 id="orgfa85033"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgc9f8921" class="outline-2">
<h2 id="orgc9f8921"><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-org6dcc538" class="outline-2">
<h2 id="org6dcc538"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org28743d8" class="outline-2">
<h2 id="org28743d8"><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: 2023-01-20 Fri 08:33</p>
<p class="date">Created: 2023-02-16 Thu 08:31</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2023-01-20 Fri 08:33 -->
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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>
@ -346,70 +346,70 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgf5947a9">1. Metadata (metadata group)</a></li>
<li><a href="#org0107e79">2. System</a>
<li><a href="#org33ce91d">1. Metadata (metadata group)</a></li>
<li><a href="#org70a683c">2. System</a>
<ul>
<li><a href="#org59df8d3">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#orgc68f3d6">2.2. Cell (cell group)</a></li>
<li><a href="#org99fb2d1">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgb4fa8ec">2.4. Electron (electron group)</a></li>
<li><a href="#org43af937">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org92d6f0a">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org5b8f3d8">2.2. Cell (cell group)</a></li>
<li><a href="#org2f9c849">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org5d3e21f">2.4. Electron (electron group)</a></li>
<li><a href="#orgca11162">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org2f5bb1b">3. Basis functions</a>
<li><a href="#org5ca96fe">3. Basis functions</a>
<ul>
<li><a href="#org8894185">3.1. Basis set (basis group)</a>
<li><a href="#orgd28bb5b">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orgbc77273">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orge3821dd">3.1.2. Plane waves</a></li>
<li><a href="#org18cf71e">3.1.3. Data definitions</a></li>
<li><a href="#org75250e2">3.1.4. Example</a></li>
<li><a href="#org827b6e4">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org0212469">3.1.2. Plane waves</a></li>
<li><a href="#orga2715ca">3.1.3. Data definitions</a></li>
<li><a href="#org38f5e8d">3.1.4. Example</a></li>
</ul>
</li>
<li><a href="#org0971e33">3.2. Effective core potentials (ecp group)</a>
<li><a href="#orgb395003">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org0787b65">3.2.1. Example</a></li>
<li><a href="#orge49cb3b">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org835e311">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org8a449f8">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org2cd0abc">4. Orbitals</a>
<li><a href="#org312e279">4. Orbitals</a>
<ul>
<li><a href="#orgf4e79e0">4.1. Atomic orbitals (ao group)</a>
<li><a href="#orge8a94c0">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="#org9e9672a">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org784c310">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org2138a2e">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org6c83b34">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgcb6f756">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org107f204">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgaee9eec">5. Multi-determinant information</a>
<li><a href="#orgd8b5719">5. Multi-determinant information</a>
<ul>
<li><a href="#org86be6e0">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgcef0dd2">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgc7268e4">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org527dedf">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org1f9bd75">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgb43c55b">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgc58d4a0">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org56a57e1">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org7154ccd">6. Correlation factors</a>
<li><a href="#org3bfd9bc">6. Correlation factors</a>
<ul>
<li><a href="#org1aca633">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#orgbfcbb42">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org674c039">6.1.1. CHAMP</a></li>
<li><a href="#org98bca38">6.1.2. Mu</a></li>
<li><a href="#org41080b3">6.1.3. Table of values</a></li>
<li><a href="#orgb47e682">6.1.1. CHAMP</a></li>
<li><a href="#orgb962d45">6.1.2. Mu</a></li>
<li><a href="#orgab4862f">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgd435a34">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org8e6038b">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-orgf5947a9" class="outline-2">
<h2 id="orgf5947a9"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org33ce91d" class="outline-2">
<h2 id="org33ce91d"><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="org9043411" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd42ddd1" 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-org0107e79" class="outline-2">
<h2 id="org0107e79"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org70a683c" class="outline-2">
<h2 id="org70a683c"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org59df8d3" class="outline-3">
<h3 id="org59df8d3"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org92d6f0a" class="outline-3">
<h3 id="org92d6f0a"><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="orge221f43" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6aa242a" 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-orgc68f3d6" class="outline-3">
<h3 id="orgc68f3d6"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org5b8f3d8" class="outline-3">
<h3 id="org5b8f3d8"><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="orgaf16f31" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8cc056f" 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-org99fb2d1" class="outline-3">
<h3 id="org99fb2d1"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org2f9c849" class="outline-3">
<h3 id="org2f9c849"><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="orgf618775" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd21ff56" 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-orgb4fa8ec" class="outline-3">
<h3 id="orgb4fa8ec"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org5d3e21f" class="outline-3">
<h3 id="org5d3e21f"><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="org4ed9b6d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf25a63e" 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-org43af937" class="outline-3">
<h3 id="org43af937"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-orgca11162" class="outline-3">
<h3 id="orgca11162"><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="orgd51761f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9290cb9" 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-org2f5bb1b" class="outline-2">
<h2 id="org2f5bb1b"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org5ca96fe" class="outline-2">
<h2 id="org5ca96fe"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org8894185" class="outline-3">
<h3 id="org8894185"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-orgd28bb5b" class="outline-3">
<h3 id="orgd28bb5b"><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-orgbc77273" class="outline-4">
<h4 id="orgbc77273"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org827b6e4" class="outline-4">
<h4 id="org827b6e4"><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-orge3821dd" class="outline-4">
<h4 id="orge3821dd"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div id="outline-container-org0212469" class="outline-4">
<h4 id="org0212469"><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-org18cf71e" class="outline-4">
<h4 id="org18cf71e"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div id="outline-container-orga2715ca" class="outline-4">
<h4 id="orga2715ca"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-3">
<table id="org54ca4ab" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5a62610" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1109,8 +1109,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org75250e2" class="outline-4">
<h4 id="org75250e2"><span class="section-number-4">3.1.4</span> Example</h4>
<div id="outline-container-org38f5e8d" class="outline-4">
<h4 id="org38f5e8d"><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-org0971e33" class="outline-3">
<h3 id="org0971e33"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-orgb395003" class="outline-3">
<h3 id="orgb395003"><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
@ -1210,7 +1210,7 @@ while the remaining terms correspond to the non-local channel projections.
<p>
All the functions \(V_{A\ell}\) are parameterized as:
\[
V_{A \ell}(\mathbf{r}) =
V_{A \ell}(\mathbf{r}) =
\sum_{q=1}^{N_{q \ell}}
\beta_{A q \ell}\, |\mathbf{r}-\mathbf{R}_{A}|^{n_{A q \ell}}\,
e^{-\alpha_{A q \ell} |\mathbf{r}-\mathbf{R}_{A}|^2 }
@ -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="org3e2d469" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge41735c" 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-org0787b65" class="outline-4">
<h4 id="org0787b65"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orge49cb3b" class="outline-4">
<h4 id="orge49cb3b"><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-org835e311" class="outline-3">
<h3 id="org835e311"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org8a449f8" class="outline-3">
<h3 id="org8a449f8"><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="orgeb78ddb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org393430d" 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-org2cd0abc" class="outline-2">
<h2 id="org2cd0abc"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org312e279" class="outline-2">
<h2 id="org312e279"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-orgf4e79e0" class="outline-3">
<h3 id="orgf4e79e0"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-orge8a94c0" class="outline-3">
<h3 id="orge8a94c0"><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="#org8894185">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#orgd28bb5b">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="orgd863625" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd888ed2" 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-orgdcb2fe1" class="outline-4">
<div id="outline-container-orgb594dc9" 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="org479e30e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org53c5ab9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1751,7 +1751,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org97ec15b" class="outline-4">
<div id="outline-container-orga3a2567" 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="org8f008fe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf3bd6f0" 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-org9e9672a" class="outline-3">
<h3 id="org9e9672a"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org784c310" class="outline-3">
<h3 id="org784c310"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org7642620" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org195bdf3" 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-org2138a2e" class="outline-4">
<h4 id="org2138a2e"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-orgcb6f756" class="outline-4">
<h4 id="orgcb6f756"><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="org4f6570e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge2a805b" 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-org6c83b34" class="outline-4">
<h4 id="org6c83b34"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org107f204" class="outline-4">
<h4 id="org107f204"><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="orgc0d7bbc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgee4f335" 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-orgaee9eec" class="outline-2">
<h2 id="orgaee9eec"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-orgd8b5719" class="outline-2">
<h2 id="orgd8b5719"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org86be6e0" class="outline-3">
<h3 id="org86be6e0"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org1f9bd75" class="outline-3">
<h3 id="org1f9bd75"><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="org5890dfa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org72b5bd1" 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-orgcef0dd2" class="outline-3">
<h3 id="orgcef0dd2"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-orgb43c55b" class="outline-3">
<h3 id="orgb43c55b"><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="orgcf5d5f8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org117f756" 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-orgc7268e4" class="outline-3">
<h3 id="orgc7268e4"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orgc58d4a0" class="outline-3">
<h3 id="orgc58d4a0"><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
@ -2305,7 +2305,7 @@ on a reference wave function \(\Psi\), where \(\hat{T}_1\) is the single excitat
<p>
\[
\hat{T}_1 = \sum_{ia} t_{i}^{a}\, \hat{a}^\dagger_a \hat{a}_i,
\hat{T}_1 = \sum_{ia} t_{i}^{a}\, \hat{a}^\dagger_a \hat{a}_i,
\]
</p>
@ -2341,7 +2341,7 @@ and coupled-cluster wave functions are of the form
</p>
<p>
The reference wave function is stored using the <code>determinant</code> and/or
The reference wave function is stored using the <code>determinant</code> and/or
<code>csf</code> groups, and the amplitudes are stored using the current group.
The attributes with the <code>exp</code> suffix correspond to exponentialized operators.
</p>
@ -2357,7 +2357,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="orgd754ef9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9bcca6b" 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-org527dedf" class="outline-3">
<h3 id="org527dedf"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org56a57e1" class="outline-3">
<h3 id="org56a57e1"><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
@ -2462,8 +2462,7 @@ and the spin-summed one-body density matrix is
</p>
<p>
The \(\uparrow \uparrow\), \(\downarrow \downarrow\), \(\uparrow \downarrow\), \(\downarrow \uparrow\)
components of the two-body density matrix are given by
The \(\uparrow \uparrow\), \(\downarrow \downarrow\), \(\uparrow \downarrow\) components of the two-body density matrix are given by
</p>
\begin{eqnarray*}
\Gamma_{ijkl}^{\uparrow \uparrow} &=&
@ -2472,17 +2471,21 @@ components of the two-body density matrix are given by
\langle \Psi | \hat{a}^{\dagger}_{k\beta}\, \hat{a}^{\dagger}_{l\beta} \hat{a}_{j\beta}\, \hat{a}_{i\beta} | \Psi \rangle \\
\Gamma_{ijkl}^{\uparrow \downarrow} &=&
\langle \Psi | \hat{a}^{\dagger}_{k\alpha}\, \hat{a}^{\dagger}_{l\beta} \hat{a}_{j\beta}\, \hat{a}_{i\alpha} | \Psi \rangle \\
\Gamma_{ijkl}^{\downarrow \uparrow} &=&
\langle \Psi | \hat{a}^{\dagger}_{k\beta}\, \hat{a}^{\dagger}_{l\alpha} \hat{a}_{j\alpha}\, \hat{a}_{i\beta} | \Psi \rangle \\
\end{eqnarray*}
<p>
and the spin-summed one-body density matrix is
\[
\Gamma_{ijkl} = \Gamma_{ijkl}^{\uparrow \uparrow} +
\Gamma_{ijkl}^{\downarrow \downarrow} + \Gamma_{ijkl}^{\uparrow \downarrow} +
\Gamma_{ijkl}^{\downarrow \uparrow}
\Gamma_{ijkl}^{\downarrow \downarrow} + \Gamma_{ijkl}^{\uparrow \downarrow}.
\]
The density matrices are normalized such that
</p>
\begin{eqnarray*}
\sum_{ij} \Gamma_{ijij}^{\uparrow \uparrow} & = & N_\uparrow\, (N_\uparrow-1)/2 \\
\sum_{ij} \Gamma_{ijij}^{\downarrow \downarrow} & = & N_\downarrow\, (N_\downarrow-1)/2 \\
\sum_{ij} \Gamma_{ijij}^{\uparrow \downarrow} & = & N_\uparrow\, N_\downarrow \\
\sum_{ij} \Gamma_{ijij} & = & (N_\uparrow+N_\downarrow)\, (N_\uparrow+N_\downarrow-1)/2.
\end{eqnarray*}
<p>
The total energy can be computed as:
@ -2514,7 +2517,7 @@ 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="orgabe2b22" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org076b848" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2584,13 +2587,6 @@ expressed in a basis of a one-electron function
<td class="org-left">&uarr;&darr; component of the two-body reduced density matrix</td>
</tr>
<tr>
<td class="org-left"><code>2e_dnup</code></td>
<td class="org-left"><code>float sparse</code></td>
<td class="org-left"><code>(mo.num, mo.num, mo.num, mo.num)</code></td>
<td class="org-left">&darr;&uarr; component of the two-body reduced density matrix</td>
</tr>
<tr>
<td class="org-left"><code>2e_cholesky_num</code></td>
<td class="org-left"><code>dim</code></td>
@ -2646,32 +2642,18 @@ expressed in a basis of a one-electron function
<td class="org-left"><code>(mo.num, mo.num, rdm.2e_updn_cholesky_num)</code></td>
<td class="org-left">Cholesky decomposition of the two-body RDM (&uarr;&darr;)</td>
</tr>
<tr>
<td class="org-left"><code>2e_dnup_cholesky_num</code></td>
<td class="org-left"><code>dim</code></td>
<td class="org-left">&#xa0;</td>
<td class="org-left">Number of Cholesky vectors</td>
</tr>
<tr>
<td class="org-left"><code>2e_dnup_cholesky</code></td>
<td class="org-left"><code>float sparse</code></td>
<td class="org-left"><code>(mo.num, mo.num, rdm.2e_dnup_cholesky_num)</code></td>
<td class="org-left">Cholesky decomposition of the two-body RDM (&darr;&uarr;)</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
<div id="outline-container-org7154ccd" class="outline-2">
<h2 id="org7154ccd"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org3bfd9bc" class="outline-2">
<h2 id="org3bfd9bc"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org1aca633" class="outline-3">
<h3 id="org1aca633"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-orgbfcbb42" class="outline-3">
<h3 id="orgbfcbb42"><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 +2678,8 @@ following:
</ul>
</div>
<div id="outline-container-org674c039" class="outline-4">
<h4 id="org674c039"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orgb47e682" class="outline-4">
<h4 id="orgb47e682"><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 +2756,8 @@ The terms \(J_{\text{ee}}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to en
</div>
</div>
<div id="outline-container-org98bca38" class="outline-4">
<h4 id="org98bca38"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-orgb962d45" class="outline-4">
<h4 id="orgb962d45"><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
@ -2784,12 +2766,12 @@ correlation factor imposes the electron-electron cusp and it is
built such that the leading order in \(1/r_{12}\) of the effective
two-electron potential reproduces the long-range interaction of the
range-separated density functional theory. Its analytical
expression reads
expression reads
</p>
<p>
\[
J(\mathbf{r}, \mathbf{R}) = J_{\text{eeN}}(\mathbf{r}, \mathbf{R}) +
J(\mathbf{r}, \mathbf{R}) = J_{\text{eeN}}(\mathbf{r}, \mathbf{R}) +
J_{\text{eN}}(\mathbf{r}, \mathbf{R})
\].
</p>
@ -2800,7 +2782,7 @@ The electron-electron cusp is incorporated in the three-body term.
<p>
\[
J_\text{eeN} (\mathbf{r}, \mathbf{R}) =
J_\text{eeN} (\mathbf{r}, \mathbf{R}) =
\sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \, u\left(\mu, r_{ij}\right) \,
\Pi_{\alpha=1}^{N_{\text{nucl}}} \, E_\alpha({R}_{i\alpha}) \, E_\alpha({R}_{j\alpha})
\]
@ -2842,8 +2824,8 @@ Mu-Jastrow factor becomes a two-body Jastrow factor:
<p>
\[
J_{\text{ee}}(\mathbf{r}) =
\sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \, u\left(\mu, r_{ij}\right)
J_{\text{ee}}(\mathbf{r}) =
\sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \, u\left(\mu, r_{ij}\right)
\]
</p>
@ -2872,10 +2854,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org41080b3" class="outline-4">
<h4 id="org41080b3"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div id="outline-container-orgab4862f" class="outline-4">
<h4 id="orgab4862f"><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="orga72f177" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org430db76" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2979,8 +2961,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-orgd435a34" class="outline-2">
<h2 id="orgd435a34"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org8e6038b" class="outline-2">
<h2 id="org8e6038b"><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 +2976,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orgc13c65b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0125719" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3049,7 +3031,7 @@ 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: 2023-01-20 Fri 08:33</p>
<p class="date">Created: 2023-02-16 Thu 08:31</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>