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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>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-27 Mon 15:16</p>
<p class="date">Created: 2022-06-27 Mon 15:18</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-06-27 Mon 15:16 -->
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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>
@ -333,31 +333,31 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgfc46d48">1. Accessing sparse quantities (integrals)</a>
<li><a href="#org55b95b4">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#orgc50dfc2">1.1. Fortran</a>
<li><a href="#org5121153">1.1. Fortran</a>
<ul>
<li><a href="#org38e5311">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org9c5de5c">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orge8899e4">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgcbe0c2d">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org4d00415">1.1.5. Allocate memory</a></li>
<li><a href="#org94f4bdf">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org9485e9d">1.1.7. Read two-electron quantities</a>
<li><a href="#orgc4fc7ae">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org6dbea8f">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orge162ebe">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org24556f6">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orga981ebc">1.1.5. Allocate memory</a></li>
<li><a href="#org97913a3">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org061eebf">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgab5ff48">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org9509bc4">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org09c09b3">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orge31cc6f">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org03653d4">1.1.8. Compute the energy</a></li>
<li><a href="#org06dc4b9">1.1.9. Terminate</a></li>
<li><a href="#orgafc812a">1.1.8. Compute the energy</a></li>
<li><a href="#org5758af8">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orga62fa11">2. Reading determinants</a>
<li><a href="#orga1e04c8">2. Reading determinants</a>
<ul>
<li><a href="#org26ef9f9">2.1. Fortran</a></li>
<li><a href="#orga69c106">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -365,12 +365,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgfc46d48" class="outline-2">
<h2 id="orgfc46d48"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org55b95b4" class="outline-2">
<h2 id="org55b95b4"><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-orgc50dfc2" class="outline-3">
<h3 id="orgc50dfc2"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org5121153" class="outline-3">
<h3 id="org5121153"><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>
@ -416,8 +416,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org38e5311" class="outline-4">
<h4 id="org38e5311"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgc4fc7ae" class="outline-4">
<h4 id="orgc4fc7ae"><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>
@ -432,8 +432,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org9c5de5c" class="outline-4">
<h4 id="org9c5de5c"><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-org6dbea8f" class="outline-4">
<h4 id="org6dbea8f"><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)
@ -449,8 +449,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orge8899e4" class="outline-4">
<h4 id="orge8899e4"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orge162ebe" class="outline-4">
<h4 id="orge162ebe"><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)
@ -464,8 +464,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgcbe0c2d" class="outline-4">
<h4 id="orgcbe0c2d"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org24556f6" class="outline-4">
<h4 id="org24556f6"><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)
@ -479,8 +479,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org4d00415" class="outline-4">
<h4 id="org4d00415"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-orga981ebc" class="outline-4">
<h4 id="orga981ebc"><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) )
@ -492,8 +492,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-org94f4bdf" class="outline-4">
<h4 id="org94f4bdf"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org97913a3" class="outline-4">
<h4 id="org97913a3"><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)
@ -525,8 +525,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-org9485e9d" class="outline-4">
<h4 id="org9485e9d"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org061eebf" class="outline-4">
<h4 id="org061eebf"><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
@ -542,8 +542,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-orgab5ff48" class="outline-5">
<h5 id="orgab5ff48"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org09c09b3" class="outline-5">
<h5 id="org09c09b3"><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)
@ -592,8 +592,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-org9509bc4" class="outline-5">
<h5 id="org9509bc4"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orge31cc6f" class="outline-5">
<h5 id="orge31cc6f"><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)
@ -637,8 +637,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org03653d4" class="outline-4">
<h4 id="org03653d4"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-orgafc812a" class="outline-4">
<h4 id="orgafc812a"><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
@ -684,8 +684,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org06dc4b9" class="outline-4">
<h4 id="org06dc4b9"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org5758af8" class="outline-4">
<h4 id="org5758af8"><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 )
@ -699,12 +699,12 @@ E = E + E_nn
</div>
<div id="outline-container-orga62fa11" class="outline-2">
<h2 id="orga62fa11"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-orga1e04c8" class="outline-2">
<h2 id="orga1e04c8"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org26ef9f9" class="outline-3">
<h3 id="org26ef9f9"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-orga69c106" class="outline-3">
<h3 id="orga69c106"><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>
@ -715,6 +715,8 @@ E = E + E_nn
<span style="color: #228b22;">character</span>*(128) ::<span style="color: #a0522d;"> filename </span>! <span style="color: #b22222;">Name of the input file</span>
<span style="color: #228b22;">integer</span>(trexio_exit_code) ::<span style="color: #a0522d;"> rc </span>! <span style="color: #b22222;">Return code for error checking</span>
<span style="color: #228b22;">integer</span>(trexio_t) ::<span style="color: #a0522d;"> trex_determinant_file</span>
<span style="color: #228b22;">character</span>*(128) ::<span style="color: #a0522d;"> err_msg </span>! <span style="color: #b22222;">Error message</span>
<span style="color: #228b22;">integer</span>*8, <span style="color: #a020f0;">allocatable</span> ::<span style="color: #a0522d;"> buffer(:,:,:)</span>
<span style="color: #228b22;">integer</span>(8) ::<span style="color: #a0522d;"> offset, icount, BUFSIZE</span>
@ -769,7 +771,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-27 Mon 15:16</p>
<p class="date">Created: 2022-06-27 Mon 15:18</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-06-27 Mon 15:16 -->
<!-- 2022-06-27 Mon 15:18 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-27 Mon 15:16</p>
<p class="date">Created: 2022-06-27 Mon 15:18</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>
<!-- 2022-06-27 Mon 15:16 -->
<!-- 2022-06-27 Mon 15:18 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>HDF5 back end</title>
@ -311,23 +311,23 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orge3f1f44">1. Template for HDF5 definitions</a></li>
<li><a href="#org047f996">2. Template for HDF5 structures</a></li>
<li><a href="#org1a5856d">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org71ce5b2">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org86be95e">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org2b692fc">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org7c97248">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org6a54f12">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org9ff3af7">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org4be2c66">10. Source code for the determinant part</a></li>
<li><a href="#orge9623d9">11. Helper functions</a></li>
<li><a href="#org5e479fc">1. Template for HDF5 definitions</a></li>
<li><a href="#org7d1f97f">2. Template for HDF5 structures</a></li>
<li><a href="#orgccf49bf">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgb0c113f">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org4db0049">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org7deb387">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org172ebd5">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org77aaa47">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org50eb215">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org7ac2b23">10. Source code for the determinant part</a></li>
<li><a href="#orgf3608ae">11. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orge3f1f44" class="outline-2">
<h2 id="orge3f1f44"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org5e479fc" class="outline-2">
<h2 id="org5e479fc"><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>
@ -339,8 +339,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org047f996" class="outline-2">
<h2 id="org047f996"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org7d1f97f" class="outline-2">
<h2 id="org7d1f97f"><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
@ -360,8 +360,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org1a5856d" class="outline-2">
<h2 id="org1a5856d"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgccf49bf" class="outline-2">
<h2 id="orgccf49bf"><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>
@ -466,8 +466,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org71ce5b2" class="outline-2">
<h2 id="org71ce5b2"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orgb0c113f" class="outline-2">
<h2 id="orgb0c113f"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org86be95e" class="outline-2">
<h2 id="org86be95e"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org4db0049" class="outline-2">
<h2 id="org4db0049"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -706,8 +706,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org2b692fc" class="outline-2">
<h2 id="org2b692fc"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org7deb387" class="outline-2">
<h2 id="org7deb387"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-6">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -910,8 +910,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org7c97248" class="outline-2">
<h2 id="org7c97248"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org172ebd5" class="outline-2">
<h2 id="org172ebd5"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1109,8 +1109,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org6a54f12" class="outline-2">
<h2 id="org6a54f12"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org77aaa47" class="outline-2">
<h2 id="org77aaa47"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1237,8 +1237,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-org9ff3af7" class="outline-2">
<h2 id="org9ff3af7"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org50eb215" class="outline-2">
<h2 id="org50eb215"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-9">
<p>
<b><b>Note:</b></b> in early versions of the HDF5 library (v &lt; 1.10) unlinking an object was not working as expected
@ -1278,8 +1278,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org4be2c66" class="outline-2">
<h2 id="org4be2c66"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div id="outline-container-org7ac2b23" class="outline-2">
<h2 id="org7ac2b23"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-10">
<p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1532,8 +1532,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-orge9623d9" class="outline-2">
<h2 id="orge9623d9"><span class="section-number-2">11</span> Helper functions</h2>
<div id="outline-container-orgf3608ae" class="outline-2">
<h2 id="orgf3608ae"><span class="section-number-2">11</span> Helper functions</h2>
<div class="outline-text-2" id="text-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1796,7 +1796,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-27 Mon 15:16</p>
<p class="date">Created: 2022-06-27 Mon 15:18</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

88
templator_text.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-06-27 Mon 15:16 -->
<!-- 2022-06-27 Mon 15:18 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
@ -311,20 +311,20 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org95837a5">1. Template for group-related structures in text back end</a></li>
<li><a href="#org8ba9330">2. Template for general structure in text back end</a></li>
<li><a href="#orge8e5969">3. Initialize function (constant part)</a></li>
<li><a href="#org5c77713">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgdc4b73a">5. Template for text read a group</a></li>
<li><a href="#org0bced25">6. Template for text flush a group</a></li>
<li><a href="#orgeec6aea">7. Template for text free memory</a></li>
<li><a href="#org54e3a37">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org857952c">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org4867c7a">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org1f121d1">11. Template for has/read/write a string attribute</a></li>
<li><a href="#orgbba877e">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgbc53fb1">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org88529a1">14. Source code for the determinant part</a></li>
<li><a href="#org4552f4b">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgf2b012f">2. Template for general structure in text back end</a></li>
<li><a href="#org0465ec3">3. Initialize function (constant part)</a></li>
<li><a href="#org65d8227">4. Deinitialize function (templated part)</a></li>
<li><a href="#org74dfe0a">5. Template for text read a group</a></li>
<li><a href="#orgae1f8c7">6. Template for text flush a group</a></li>
<li><a href="#org51a2378">7. Template for text free memory</a></li>
<li><a href="#org2a88c94">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org2a67e36">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgafddbbb">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org5186f30">11. Template for has/read/write a string attribute</a></li>
<li><a href="#orgd859cc0">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org3e0ee4c">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgb03f2af">14. Source code for the determinant part</a></li>
</ul>
</div>
</div>
@ -346,8 +346,8 @@ directory.
The file is written when closed, or when the flush function is called.
</p>
<div id="outline-container-org95837a5" class="outline-2">
<h2 id="org95837a5"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org4552f4b" class="outline-2">
<h2 id="org4552f4b"><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 {
@ -366,8 +366,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org8ba9330" class="outline-2">
<h2 id="org8ba9330"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgf2b012f" class="outline-2">
<h2 id="orgf2b012f"><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
@ -387,8 +387,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orge8e5969" class="outline-2">
<h2 id="orge8e5969"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org0465ec3" class="outline-2">
<h2 id="org0465ec3"><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;">trexio_exit_code</span>
@ -531,8 +531,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org5c77713" class="outline-2">
<h2 id="org5c77713"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org65d8227" class="outline-2">
<h2 id="org65d8227"><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>
@ -554,8 +554,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgdc4b73a" class="outline-2">
<h2 id="orgdc4b73a"><span class="section-number-2">5</span> Template for text read a group</h2>
<div id="outline-container-org74dfe0a" class="outline-2">
<h2 id="org74dfe0a"><span class="section-number-2">5</span> Template for text read a group</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -779,8 +779,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org0bced25" class="outline-2">
<h2 id="org0bced25"><span class="section-number-2">6</span> Template for text flush a group</h2>
<div id="outline-container-orgae1f8c7" class="outline-2">
<h2 id="orgae1f8c7"><span class="section-number-2">6</span> Template for text flush a group</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>
@ -844,8 +844,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgeec6aea" class="outline-2">
<h2 id="orgeec6aea"><span class="section-number-2">7</span> Template for text free memory</h2>
<div id="outline-container-org51a2378" class="outline-2">
<h2 id="org51a2378"><span class="section-number-2">7</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-7">
<p>
Memory is allocated when reading. The following function frees memory.
@ -914,8 +914,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org54e3a37" class="outline-2">
<h2 id="org54e3a37"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org2a88c94" class="outline-2">
<h2 id="org2a88c94"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -978,8 +978,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org857952c" class="outline-2">
<h2 id="org857952c"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org2a67e36" class="outline-2">
<h2 id="org2a67e36"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-9">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1075,8 +1075,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org4867c7a" class="outline-2">
<h2 id="org4867c7a"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgafddbbb" class="outline-2">
<h2 id="orgafddbbb"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-10">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1177,8 +1177,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org1f121d1" class="outline-2">
<h2 id="org1f121d1"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org5186f30" class="outline-2">
<h2 id="org5186f30"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1252,8 +1252,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgbba877e" class="outline-2">
<h2 id="orgbba877e"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orgd859cc0" class="outline-2">
<h2 id="orgd859cc0"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-12">
<p>
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
@ -1526,8 +1526,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-orgbc53fb1" class="outline-2">
<h2 id="orgbc53fb1"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org3e0ee4c" class="outline-2">
<h2 id="org3e0ee4c"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</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>
@ -1555,8 +1555,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org88529a1" class="outline-2">
<h2 id="org88529a1"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div id="outline-container-orgb03f2af" class="outline-2">
<h2 id="orgb03f2af"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-14">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -1960,7 +1960,7 @@ Size specifies the number of data items, e.g. determinants.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-27 Mon 15:16</p>
<p class="date">Created: 2022-06-27 Mon 15:18</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

150
trex.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-06-27 Mon 15:16 -->
<!-- 2022-06-27 Mon 15:18 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREX Configuration file</title>
@ -333,37 +333,37 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org0917011">1. Metadata (metadata group)</a></li>
<li><a href="#orgc590047">2. Electron (electron group)</a></li>
<li><a href="#org048edc1">3. Nucleus (nucleus group)</a></li>
<li><a href="#org1a9c956">4. Effective core potentials (ecp group)</a>
<li><a href="#org2eb785f">1. Metadata (metadata group)</a></li>
<li><a href="#orgc0b522d">2. Electron (electron group)</a></li>
<li><a href="#org0aaa67a">3. Nucleus (nucleus group)</a></li>
<li><a href="#org44967bd">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org0a97abb">4.1. Example</a></li>
<li><a href="#orgbb35f47">4.1. Example</a></li>
</ul>
</li>
<li><a href="#orge397838">5. Basis set (basis group)</a>
<li><a href="#org0a4adea">5. Basis set (basis group)</a>
<ul>
<li><a href="#orgd9f9d51">5.1. Example</a></li>
<li><a href="#org166bca7">5.1. Example</a></li>
</ul>
</li>
<li><a href="#orgd430435">6. Atomic orbitals (ao group)</a>
<li><a href="#org4c85e23">6. Atomic orbitals (ao group)</a>
<ul>
<li><a href="#ao_one_e">6.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
<li><a href="#ao_two_e">6.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org3658e4a">7. Molecular orbitals (mo group)</a>
<li><a href="#orgab9d1bc">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org29e1126">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org5336375">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org30a0074">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org75dfb1b">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org31de853">8. Slater determinants (determinant group)</a></li>
<li><a href="#org8945d84">9. Excited states (state group)</a></li>
<li><a href="#org7b178c5">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org0ee8dc3">11. Cell (cell group)</a></li>
<li><a href="#orgc1d4760">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org09c1290">13. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org648f813">8. Slater determinants (determinant group)</a></li>
<li><a href="#org3a63206">9. Excited states (state group)</a></li>
<li><a href="#org341b9a4">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org8bba62a">11. Cell (cell group)</a></li>
<li><a href="#org069ce74">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org89b4829">13. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -413,8 +413,8 @@ the <a href="./examples.html">examples</a>.
</p>
<div id="outline-container-org0917011" class="outline-2">
<h2 id="org0917011"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org2eb785f" class="outline-2">
<h2 id="org2eb785f"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect our files to be archived in open-data repositories, we
@ -424,7 +424,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="orgd3e696f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgda3c7c3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -505,15 +505,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-orgc590047" class="outline-2">
<h2 id="orgc590047"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orgc0b522d" class="outline-2">
<h2 id="orgc0b522d"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div class="outline-text-2" id="text-2">
<p>
We consider wave functions expressed in the spin-free formalism, where
the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="orgbdd5bc2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org737725b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -559,15 +559,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org048edc1" class="outline-2">
<h2 id="org048edc1"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org0aaa67a" class="outline-2">
<h2 id="org0aaa67a"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div class="outline-text-2" id="text-3">
<p>
The nuclei are considered as fixed point charges. Coordinates are
given in Cartesian \((x,y,z)\) format.
</p>
<table id="orgce45cc6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8165391" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -634,8 +634,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org1a9c956" class="outline-2">
<h2 id="org1a9c956"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org44967bd" class="outline-2">
<h2 id="org44967bd"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div class="outline-text-2" id="text-4">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -668,7 +668,7 @@ The functions \(V_{A\ell}\) are parameterized as:
See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.4984046</a> or <a href="https://doi.org/10.1063/1.5121006">https://doi.org/10.1063/1.5121006</a> for more info.
</p>
<table id="org260d650" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcf52957" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -770,8 +770,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-org0a97abb" class="outline-3">
<h3 id="org0a97abb"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-orgbb35f47" class="outline-3">
<h3 id="orgbb35f47"><span class="section-number-3">4.1</span> Example</h3>
<div class="outline-text-3" id="text-4-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -834,8 +834,8 @@ power = [
</div>
</div>
<div id="outline-container-orge397838" class="outline-2">
<h2 id="orge397838"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org0a4adea" class="outline-2">
<h2 id="org0a4adea"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div class="outline-text-2" id="text-5">
<p>
We consider here basis functions centered on nuclei. Hence, we enable
@ -888,7 +888,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).
All the basis set parameters are stored in one-dimensional arrays:
</p>
<table id="org657b385" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org257e528" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -982,8 +982,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-orgd9f9d51" class="outline-3">
<h3 id="orgd9f9d51"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org166bca7" class="outline-3">
<h3 id="org166bca7"><span class="section-number-3">5.1</span> Example</h3>
<div class="outline-text-3" id="text-5-1">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1061,8 +1061,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgd430435" class="outline-2">
<h2 id="orgd430435"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org4c85e23" class="outline-2">
<h2 id="org4c85e23"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div class="outline-text-2" id="text-6">
<p>
Going from the atomic basis set to AOs implies a systematic
@ -1115,13 +1115,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#orge397838">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org0a4adea">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="org4d38da9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge057762" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1173,8 +1173,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org222ab37" class="outline-3">
<h3 id="ao_one_e"><a id="org222ab37"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org34dbf62" class="outline-3">
<h3 id="ao_one_e"><a id="org34dbf62"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_one_e">
<ul class="org-ul">
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
@ -1191,7 +1191,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgac62a1e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org97b409a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1286,8 +1286,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org5bb07fd" class="outline-3">
<h3 id="ao_two_e"><a id="org5bb07fd"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org8e444af" class="outline-3">
<h3 id="ao_two_e"><a id="org8e444af"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_two_e">
<p>
The two-electron integrals for a two-electron operator \(\hat{O}\) are
@ -1308,7 +1308,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org294e72d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6223c2a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1348,10 +1348,10 @@ notation.
</div>
</div>
<div id="outline-container-org3658e4a" class="outline-2">
<h2 id="org3658e4a"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgab9d1bc" class="outline-2">
<h2 id="orgab9d1bc"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="orgc21563d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgce1c0ad" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1424,8 +1424,8 @@ notation.
</table>
</div>
<div id="outline-container-org29e1126" class="outline-3">
<h3 id="org29e1126"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org30a0074" class="outline-3">
<h3 id="org30a0074"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-1">
<p>
The operators as the same as those defined in the
@ -1433,7 +1433,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgd3dd34e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge1384c0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1528,8 +1528,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org5336375" class="outline-3">
<h3 id="org5336375"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org75dfb1b" class="outline-3">
<h3 id="org75dfb1b"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-2">
<p>
The operators as the same as those defined in the
@ -1537,7 +1537,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgafcad66" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgaf36671" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1577,8 +1577,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org31de853" class="outline-2">
<h2 id="org31de853"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-org648f813" class="outline-2">
<h2 id="org648f813"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div class="outline-text-2" id="text-8">
<p>
The configuration interaction (CI) wave function \(\Psi\)
@ -1611,7 +1611,7 @@ where \(\alpha\) and \(\beta\) denote $&uarr;$-spin and $&darr;$-spin electrons,
\(n\uparrow\) and \(n\downarrow\) correspond to <code>electron.up_num</code> and <code>electron.dn_num</code>, respectively.
</p>
<table id="org9b7f654" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org24745f7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1657,8 +1657,8 @@ where \(\alpha\) and \(\beta\) denote $&uarr;$-spin and $&darr;$-spin electrons,
</div>
</div>
<div id="outline-container-org8945d84" class="outline-2">
<h2 id="org8945d84"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div id="outline-container-org3a63206" class="outline-2">
<h2 id="org3a63206"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div class="outline-text-2" id="text-9">
<p>
By default, the <code>determinant</code> group corresponds to the ground state.
@ -1667,7 +1667,7 @@ correspond to excited state wave functions for the same set of
determinants. This is the goal of the present group
</p>
<table id="orgcfb70ed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0fb4b65" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1706,8 +1706,8 @@ determinants. This is the goal of the present group
</div>
</div>
<div id="outline-container-org7b178c5" class="outline-2">
<h2 id="org7b178c5"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org341b9a4" class="outline-2">
<h2 id="org341b9a4"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-10">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1760,7 +1760,7 @@ The total energy can be computed as:
\]
</p>
<table id="org08c39bb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgda2dea0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1841,10 +1841,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org0ee8dc3" class="outline-2">
<h2 id="org0ee8dc3"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div id="outline-container-org8bba62a" class="outline-2">
<h2 id="org8bba62a"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-11">
<table id="orgcb4937b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc91b9a5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1890,10 +1890,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-orgc1d4760" class="outline-2">
<h2 id="orgc1d4760"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-org069ce74" class="outline-2">
<h2 id="org069ce74"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-12">
<table id="org40a9ab8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbee2fc2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1932,8 +1932,8 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org09c1290" class="outline-2">
<h2 id="org09c1290"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org89b4829" class="outline-2">
<h2 id="org89b4829"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-13">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -1947,7 +1947,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orge31bce9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org420185e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2002,7 +2002,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-27 Mon 15:16</p>
<p class="date">Created: 2022-06-27 Mon 15:18</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>