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README.html
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<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: 2022-06-03 Fri 07:50</p>
<p class="date">Created: 2022-06-03 Fri 07:52</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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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>Examples</title>
@ -333,24 +333,24 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgc59a7fe">1. Accessing sparse quantities</a>
<li><a href="#org2b0a3c0">1. Accessing sparse quantities</a>
<ul>
<li><a href="#org591fe9e">1.1. Fortran</a>
<li><a href="#orge33bde1">1.1. Fortran</a>
<ul>
<li><a href="#org97f6664">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org600570d">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org209f1f3">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgcc397ae">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orga37af36">1.1.5. Allocate memory</a></li>
<li><a href="#orgb20d6cb">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org2a736ad">1.1.7. Read two-electron quantities</a>
<li><a href="#orgc8440f3">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org319a7c0">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgd294e48">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgc3f7b93">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org2b36df3">1.1.5. Allocate memory</a></li>
<li><a href="#orgc85fe92">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgd8fead8">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgc2b43ec">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgea7c720">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#orgbe4da69">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgcac6ecf">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org0499bf9">1.1.8. Compute the energy</a></li>
<li><a href="#org92602b6">1.1.9. Terminate</a></li>
<li><a href="#org017d5b6">1.1.8. Compute the energy</a></li>
<li><a href="#orgd01af70">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
@ -360,12 +360,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgc59a7fe" class="outline-2">
<h2 id="orgc59a7fe"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-org2b0a3c0" class="outline-2">
<h2 id="org2b0a3c0"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org591fe9e" class="outline-3">
<h3 id="org591fe9e"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-orge33bde1" class="outline-3">
<h3 id="orge33bde1"><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>
@ -411,8 +411,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org97f6664" class="outline-4">
<h4 id="org97f6664"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgc8440f3" class="outline-4">
<h4 id="orgc8440f3"><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>
@ -427,8 +427,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org600570d" class="outline-4">
<h4 id="org600570d"><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-org319a7c0" class="outline-4">
<h4 id="org319a7c0"><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)
@ -444,8 +444,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org209f1f3" class="outline-4">
<h4 id="org209f1f3"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgd294e48" class="outline-4">
<h4 id="orgd294e48"><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)
@ -459,8 +459,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgcc397ae" class="outline-4">
<h4 id="orgcc397ae"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgc3f7b93" class="outline-4">
<h4 id="orgc3f7b93"><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)
@ -474,8 +474,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orga37af36" class="outline-4">
<h4 id="orga37af36"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org2b36df3" class="outline-4">
<h4 id="org2b36df3"><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) )
@ -487,8 +487,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-orgb20d6cb" class="outline-4">
<h4 id="orgb20d6cb"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgc85fe92" class="outline-4">
<h4 id="orgc85fe92"><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)
@ -520,8 +520,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-org2a736ad" class="outline-4">
<h4 id="org2a736ad"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgd8fead8" class="outline-4">
<h4 id="orgd8fead8"><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
@ -537,8 +537,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-orgc2b43ec" class="outline-5">
<h5 id="orgc2b43ec"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgbe4da69" class="outline-5">
<h5 id="orgbe4da69"><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)
@ -587,8 +587,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-orgea7c720" class="outline-5">
<h5 id="orgea7c720"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgcac6ecf" class="outline-5">
<h5 id="orgcac6ecf"><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)
@ -632,8 +632,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org0499bf9" class="outline-4">
<h4 id="org0499bf9"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org017d5b6" class="outline-4">
<h4 id="org017d5b6"><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
@ -679,8 +679,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org92602b6" class="outline-4">
<h4 id="org92602b6"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgd01af70" class="outline-4">
<h4 id="orgd01af70"><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 )
@ -695,7 +695,7 @@ E = E + E_nn
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-03 Fri 07:50</p>
<p class="date">Created: 2022-06-03 Fri 07:52</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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index.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-06-03 Fri 07:50 -->
<!-- 2022-06-03 Fri 07:52 -->
<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: 2022-06-03 Fri 07:50</p>
<p class="date">Created: 2022-06-03 Fri 07:52</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2022-06-03 Fri 07:50 -->
<!-- 2022-06-03 Fri 07:52 -->
<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="#orgd21c09d">1. Template for HDF5 definitions</a></li>
<li><a href="#orgf154928">2. Template for HDF5 structures</a></li>
<li><a href="#orgc205952">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgefc48cf">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org1b3d255">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org80a8fcd">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgc86d817">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orga089ca2">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgc2d9063">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org7e76698">10. Source code for the determinant part</a></li>
<li><a href="#orgc64dbca">11. Helper functions</a></li>
<li><a href="#orgd715ed3">1. Template for HDF5 definitions</a></li>
<li><a href="#org4694773">2. Template for HDF5 structures</a></li>
<li><a href="#orge8bb9c7">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org6a9bd4b">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org5dd5ef6">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org93df72b">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgcfa1482">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orga462aab">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org75e2945">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orga09edad">10. Source code for the determinant part</a></li>
<li><a href="#org3f51525">11. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgd21c09d" class="outline-2">
<h2 id="orgd21c09d"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orgd715ed3" class="outline-2">
<h2 id="orgd715ed3"><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-orgf154928" class="outline-2">
<h2 id="orgf154928"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org4694773" class="outline-2">
<h2 id="org4694773"><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-orgc205952" class="outline-2">
<h2 id="orgc205952"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orge8bb9c7" class="outline-2">
<h2 id="orge8bb9c7"><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-orgefc48cf" class="outline-2">
<h2 id="orgefc48cf"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org6a9bd4b" class="outline-2">
<h2 id="org6a9bd4b"><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-org1b3d255" class="outline-2">
<h2 id="org1b3d255"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org5dd5ef6" class="outline-2">
<h2 id="org5dd5ef6"><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-org80a8fcd" class="outline-2">
<h2 id="org80a8fcd"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org93df72b" class="outline-2">
<h2 id="org93df72b"><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-orgc86d817" class="outline-2">
<h2 id="orgc86d817"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgcfa1482" class="outline-2">
<h2 id="orgcfa1482"><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-orga089ca2" class="outline-2">
<h2 id="orga089ca2"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orga462aab" class="outline-2">
<h2 id="orga462aab"><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-orgc2d9063" class="outline-2">
<h2 id="orgc2d9063"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org75e2945" class="outline-2">
<h2 id="org75e2945"><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-org7e76698" class="outline-2">
<h2 id="org7e76698"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div id="outline-container-orga09edad" class="outline-2">
<h2 id="orga09edad"><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-orgc64dbca" class="outline-2">
<h2 id="orgc64dbca"><span class="section-number-2">11</span> Helper functions</h2>
<div id="outline-container-org3f51525" class="outline-2">
<h2 id="org3f51525"><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: 2022-06-03 Fri 07:50</p>
<p class="date">Created: 2022-06-03 Fri 07:52</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

88
templator_text.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-06-03 Fri 07:50 -->
<!-- 2022-06-03 Fri 07:52 -->
<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="#org03edc32">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgeafc0b7">2. Template for general structure in text back end</a></li>
<li><a href="#org52a864c">3. Initialize function (constant part)</a></li>
<li><a href="#org4588e43">4. Deinitialize function (templated part)</a></li>
<li><a href="#org87c6ab0">5. Template for text read a group</a></li>
<li><a href="#org374a8f3">6. Template for text flush a group</a></li>
<li><a href="#org88451c8">7. Template for text free memory</a></li>
<li><a href="#orga4d96d5">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org28a8d19">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgfe6fc47">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org41112b3">11. Template for has/read/write a string attribute</a></li>
<li><a href="#orgf06f64f">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org9728148">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org5942ccc">14. Source code for the determinant part</a></li>
<li><a href="#org4ffb75f">1. Template for group-related structures in text back end</a></li>
<li><a href="#org6dea98c">2. Template for general structure in text back end</a></li>
<li><a href="#orgc295d93">3. Initialize function (constant part)</a></li>
<li><a href="#org41970db">4. Deinitialize function (templated part)</a></li>
<li><a href="#org7c5b555">5. Template for text read a group</a></li>
<li><a href="#org8b3fa0c">6. Template for text flush a group</a></li>
<li><a href="#org43a4f82">7. Template for text free memory</a></li>
<li><a href="#org9a04a88">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org6cc11e0">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org5eda6db">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgb7ec02c">11. Template for has/read/write a string attribute</a></li>
<li><a href="#org1a92014">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org946767c">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgd9a35b5">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-org03edc32" class="outline-2">
<h2 id="org03edc32"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org4ffb75f" class="outline-2">
<h2 id="org4ffb75f"><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-orgeafc0b7" class="outline-2">
<h2 id="orgeafc0b7"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org6dea98c" class="outline-2">
<h2 id="org6dea98c"><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-org52a864c" class="outline-2">
<h2 id="org52a864c"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-orgc295d93" class="outline-2">
<h2 id="orgc295d93"><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-org4588e43" class="outline-2">
<h2 id="org4588e43"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org41970db" class="outline-2">
<h2 id="org41970db"><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-org87c6ab0" class="outline-2">
<h2 id="org87c6ab0"><span class="section-number-2">5</span> Template for text read a group</h2>
<div id="outline-container-org7c5b555" class="outline-2">
<h2 id="org7c5b555"><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-org374a8f3" class="outline-2">
<h2 id="org374a8f3"><span class="section-number-2">6</span> Template for text flush a group</h2>
<div id="outline-container-org8b3fa0c" class="outline-2">
<h2 id="org8b3fa0c"><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-org88451c8" class="outline-2">
<h2 id="org88451c8"><span class="section-number-2">7</span> Template for text free memory</h2>
<div id="outline-container-org43a4f82" class="outline-2">
<h2 id="org43a4f82"><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-orga4d96d5" class="outline-2">
<h2 id="orga4d96d5"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org9a04a88" class="outline-2">
<h2 id="org9a04a88"><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-org28a8d19" class="outline-2">
<h2 id="org28a8d19"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org6cc11e0" class="outline-2">
<h2 id="org6cc11e0"><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-orgfe6fc47" class="outline-2">
<h2 id="orgfe6fc47"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org5eda6db" class="outline-2">
<h2 id="org5eda6db"><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-org41112b3" class="outline-2">
<h2 id="org41112b3"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orgb7ec02c" class="outline-2">
<h2 id="orgb7ec02c"><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-orgf06f64f" class="outline-2">
<h2 id="orgf06f64f"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org1a92014" class="outline-2">
<h2 id="org1a92014"><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-org9728148" class="outline-2">
<h2 id="org9728148"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org946767c" class="outline-2">
<h2 id="org946767c"><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-org5942ccc" class="outline-2">
<h2 id="org5942ccc"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div id="outline-container-orgd9a35b5" class="outline-2">
<h2 id="orgd9a35b5"><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: 2022-06-03 Fri 07:50</p>
<p class="date">Created: 2022-06-03 Fri 07:52</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

150
trex.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>
<!-- 2022-06-03 Fri 07:50 -->
<!-- 2022-06-03 Fri 07:52 -->
<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="#org3252880">1. Metadata (metadata group)</a></li>
<li><a href="#org4b52101">2. Electron (electron group)</a></li>
<li><a href="#org14cc67b">3. Nucleus (nucleus group)</a></li>
<li><a href="#orga30d309">4. Effective core potentials (ecp group)</a>
<li><a href="#org6300f73">1. Metadata (metadata group)</a></li>
<li><a href="#orge914361">2. Electron (electron group)</a></li>
<li><a href="#org8d192de">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgae8c47e">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org9788d03">4.1. Example</a></li>
<li><a href="#orge079e3d">4.1. Example</a></li>
</ul>
</li>
<li><a href="#orgf710972">5. Basis set (basis group)</a>
<li><a href="#orge1b8f06">5. Basis set (basis group)</a>
<ul>
<li><a href="#org874395b">5.1. Example</a></li>
<li><a href="#orgc195865">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org86a8a0f">6. Atomic orbitals (ao group)</a>
<li><a href="#orgd49676c">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="#org3ac2528">7. Molecular orbitals (mo group)</a>
<li><a href="#org8275048">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgb05a088">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orga3d72a3">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org0a71e05">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org3893c95">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org0f20932">8. Slater determinants (determinant group)</a></li>
<li><a href="#org96965b3">9. Excited states (state group)</a></li>
<li><a href="#orged44ed8">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgc07dae2">11. Cell (cell group)</a></li>
<li><a href="#orgf0e2c1d">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org1140887">13. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org3c92e88">8. Slater determinants (determinant group)</a></li>
<li><a href="#org0889db2">9. Excited states (state group)</a></li>
<li><a href="#orgbc74f20">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org585adb5">11. Cell (cell group)</a></li>
<li><a href="#org53f1718">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org4265157">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-org3252880" class="outline-2">
<h2 id="org3252880"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org6300f73" class="outline-2">
<h2 id="org6300f73"><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="org7bb12ba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgac1e090" 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-org4b52101" class="outline-2">
<h2 id="org4b52101"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orge914361" class="outline-2">
<h2 id="orge914361"><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="org69dea59" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga7f0051" 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-org14cc67b" class="outline-2">
<h2 id="org14cc67b"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org8d192de" class="outline-2">
<h2 id="org8d192de"><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="orgf6fd47a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2d7abfe" 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-orga30d309" class="outline-2">
<h2 id="orga30d309"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orgae8c47e" class="outline-2">
<h2 id="orgae8c47e"><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="org9b377bf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org712148a" 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-org9788d03" class="outline-3">
<h3 id="org9788d03"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-orge079e3d" class="outline-3">
<h3 id="orge079e3d"><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-orgf710972" class="outline-2">
<h2 id="orgf710972"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-orge1b8f06" class="outline-2">
<h2 id="orge1b8f06"><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="orgc26f475" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8022526" 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-org874395b" class="outline-3">
<h3 id="org874395b"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-orgc195865" class="outline-3">
<h3 id="orgc195865"><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-org86a8a0f" class="outline-2">
<h2 id="org86a8a0f"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-orgd49676c" class="outline-2">
<h2 id="orgd49676c"><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="#orgf710972">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#orge1b8f06">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="org1b4c26e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3db2cb9" 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-orgc9dde95" class="outline-3">
<h3 id="ao_one_e"><a id="orgc9dde95"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org4a77a0e" class="outline-3">
<h3 id="ao_one_e"><a id="org4a77a0e"></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="org4ebfef0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org63357eb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1286,8 +1286,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgb5d2f72" class="outline-3">
<h3 id="ao_two_e"><a id="orgb5d2f72"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org6109ddb" class="outline-3">
<h3 id="ao_two_e"><a id="org6109ddb"></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="org72427b9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0df1438" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1348,10 +1348,10 @@ notation.
</div>
</div>
<div id="outline-container-org3ac2528" class="outline-2">
<h2 id="org3ac2528"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org8275048" class="outline-2">
<h2 id="org8275048"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="orgb1fb83d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfb80842" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1424,8 +1424,8 @@ notation.
</table>
</div>
<div id="outline-container-orgb05a088" class="outline-3">
<h3 id="orgb05a088"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org0a71e05" class="outline-3">
<h3 id="org0a71e05"><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="orge043ebb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org57528eb" 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-orga3d72a3" class="outline-3">
<h3 id="orga3d72a3"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org3893c95" class="outline-3">
<h3 id="org3893c95"><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="org93f9cc9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org64112e0" 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-org0f20932" class="outline-2">
<h2 id="org0f20932"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-org3c92e88" class="outline-2">
<h2 id="org3c92e88"><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="org736e622" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge5d30f1" 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-org96965b3" class="outline-2">
<h2 id="org96965b3"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div id="outline-container-org0889db2" class="outline-2">
<h2 id="org0889db2"><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="org773cdae" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge042b4e" 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-orged44ed8" class="outline-2">
<h2 id="orged44ed8"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orgbc74f20" class="outline-2">
<h2 id="orgbc74f20"><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="orga8743a6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3bf6972" 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-orgc07dae2" class="outline-2">
<h2 id="orgc07dae2"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div id="outline-container-org585adb5" class="outline-2">
<h2 id="org585adb5"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-11">
<table id="org90740b8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd492386" 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-orgf0e2c1d" class="outline-2">
<h2 id="orgf0e2c1d"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-org53f1718" class="outline-2">
<h2 id="org53f1718"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-12">
<table id="org3b917d6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org428c623" 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-org1140887" class="outline-2">
<h2 id="org1140887"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org4265157" class="outline-2">
<h2 id="org4265157"><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="org0dc4fe8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org184a78c" 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: 2022-06-03 Fri 07:50</p>
<p class="date">Created: 2022-06-03 Fri 07:52</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>