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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: 2022-09-06 Tue 15:30</p>
<p class="date">Created: 2022-09-10 Sat 19:17</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-09-06 Tue 15:30 -->
<!-- 2022-09-10 Sat 19:17 -->
<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="#orga3cdf61">1. Accessing sparse quantities (integrals)</a>
<li><a href="#org3b06fe6">1. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org5afcb5e">1.1. Fortran</a>
<li><a href="#org0936dd6">1.1. Fortran</a>
<ul>
<li><a href="#org723256c">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orge82a820">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgcc2e7ea">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgaefa70b">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org9c26cb4">1.1.5. Allocate memory</a></li>
<li><a href="#org086de1d">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgeb5ea18">1.1.7. Read two-electron quantities</a>
<li><a href="#org90ee005">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org6c9958b">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga611b9a">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org0cd8ba5">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org2d88141">1.1.5. Allocate memory</a></li>
<li><a href="#org4364cd5">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org99939c9">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org063f387">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org7aa5076">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org8a80b6d">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org03d9c73">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgbd64619">1.1.8. Compute the energy</a></li>
<li><a href="#orgb65a78d">1.1.9. Terminate</a></li>
<li><a href="#org2c4a694">1.1.8. Compute the energy</a></li>
<li><a href="#orgd333e21">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgc938429">2. Reading determinants</a>
<li><a href="#orgcdb37d7">2. Reading determinants</a>
<ul>
<li><a href="#org09fbef9">2.1. Fortran</a></li>
<li><a href="#org01dfd3d">2.1. Fortran</a></li>
</ul>
</li>
</ul>
@ -365,12 +365,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orga3cdf61" class="outline-2">
<h2 id="orga3cdf61"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org3b06fe6" class="outline-2">
<h2 id="org3b06fe6"><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-org5afcb5e" class="outline-3">
<h3 id="org5afcb5e"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org0936dd6" class="outline-3">
<h3 id="org0936dd6"><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-org723256c" class="outline-4">
<h4 id="org723256c"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org90ee005" class="outline-4">
<h4 id="org90ee005"><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-orge82a820" class="outline-4">
<h4 id="orge82a820"><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-org6c9958b" class="outline-4">
<h4 id="org6c9958b"><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-orgcc2e7ea" class="outline-4">
<h4 id="orgcc2e7ea"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orga611b9a" class="outline-4">
<h4 id="orga611b9a"><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-orgaefa70b" class="outline-4">
<h4 id="orgaefa70b"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org0cd8ba5" class="outline-4">
<h4 id="org0cd8ba5"><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-org9c26cb4" class="outline-4">
<h4 id="org9c26cb4"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org2d88141" class="outline-4">
<h4 id="org2d88141"><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-org086de1d" class="outline-4">
<h4 id="org086de1d"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org4364cd5" class="outline-4">
<h4 id="org4364cd5"><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-orgeb5ea18" class="outline-4">
<h4 id="orgeb5ea18"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org99939c9" class="outline-4">
<h4 id="org99939c9"><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-org063f387" class="outline-5">
<h5 id="org063f387"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org8a80b6d" class="outline-5">
<h5 id="org8a80b6d"><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-org7aa5076" class="outline-5">
<h5 id="org7aa5076"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org03d9c73" class="outline-5">
<h5 id="org03d9c73"><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-orgbd64619" class="outline-4">
<h4 id="orgbd64619"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org2c4a694" class="outline-4">
<h4 id="org2c4a694"><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-orgb65a78d" class="outline-4">
<h4 id="orgb65a78d"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgd333e21" class="outline-4">
<h4 id="orgd333e21"><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-orgc938429" class="outline-2">
<h2 id="orgc938429"><span class="section-number-2">2</span> Reading determinants</h2>
<div id="outline-container-orgcdb37d7" class="outline-2">
<h2 id="orgcdb37d7"><span class="section-number-2">2</span> Reading determinants</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org09fbef9" class="outline-3">
<h3 id="org09fbef9"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org01dfd3d" class="outline-3">
<h3 id="org01dfd3d"><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>
@ -783,7 +783,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-09-06 Tue 15:30</p>
<p class="date">Created: 2022-09-10 Sat 19:17</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>
<!-- 2022-09-06 Tue 15:30 -->
<!-- 2022-09-10 Sat 19:17 -->
<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: 2022-09-06 Tue 15:30</p>
<p class="date">Created: 2022-09-10 Sat 19:17</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>
<!-- 2022-09-06 Tue 15:30 -->
<!-- 2022-09-10 Sat 19:17 -->
<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>
@ -311,24 +311,24 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgdde78ca">1. Template for HDF5 definitions</a></li>
<li><a href="#orgf5394e0">2. Template for HDF5 structures</a></li>
<li><a href="#org7993876">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgd839def">4. Template for HDF5 has a group</a></li>
<li><a href="#org34edf43">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org03043a8">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org4394ce4">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org44413d5">8. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org23efd9f">9. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgc9aafae">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org12ef429">11. Source code for the determinant part</a></li>
<li><a href="#orga5d0f02">12. Helper functions</a></li>
<li><a href="#org2c2a074">1. Template for HDF5 definitions</a></li>
<li><a href="#orgb773e5b">2. Template for HDF5 structures</a></li>
<li><a href="#org39a4056">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgeb892e7">4. Template for HDF5 has a group</a></li>
<li><a href="#org64f81b8">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org78a63d4">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org7162046">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgbf07237">8. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org805bdb9">9. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orga663e3b">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgcd2ce71">11. Source code for the determinant part</a></li>
<li><a href="#org36ea9d0">12. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgdde78ca" class="outline-2">
<h2 id="orgdde78ca"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org2c2a074" class="outline-2">
<h2 id="org2c2a074"><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>
@ -340,8 +340,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgf5394e0" class="outline-2">
<h2 id="orgf5394e0"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgb773e5b" class="outline-2">
<h2 id="orgb773e5b"><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
@ -361,8 +361,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org7993876" class="outline-2">
<h2 id="org7993876"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org39a4056" class="outline-2">
<h2 id="org39a4056"><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>
@ -467,8 +467,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgd839def" class="outline-2">
<h2 id="orgd839def"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orgeb892e7" class="outline-2">
<h2 id="orgeb892e7"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -498,8 +498,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org34edf43" class="outline-2">
<h2 id="org34edf43"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org64f81b8" class="outline-2">
<h2 id="org64f81b8"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -603,8 +603,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org03043a8" class="outline-2">
<h2 id="org03043a8"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org78a63d4" class="outline-2">
<h2 id="org78a63d4"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -738,8 +738,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org4394ce4" class="outline-2">
<h2 id="org4394ce4"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org7162046" class="outline-2">
<h2 id="org7162046"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-7">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -942,8 +942,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org44413d5" class="outline-2">
<h2 id="org44413d5"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgbf07237" class="outline-2">
<h2 id="orgbf07237"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of strings</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>
@ -1141,8 +1141,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org23efd9f" class="outline-2">
<h2 id="org23efd9f"><span class="section-number-2">9</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org805bdb9" class="outline-2">
<h2 id="org805bdb9"><span class="section-number-2">9</span> Template for HDF5 has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1269,8 +1269,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-orgc9aafae" class="outline-2">
<h2 id="orgc9aafae"><span class="section-number-2">10</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orga663e3b" class="outline-2">
<h2 id="orga663e3b"><span class="section-number-2">10</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-10">
<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
@ -1310,8 +1310,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org12ef429" class="outline-2">
<h2 id="org12ef429"><span class="section-number-2">11</span> Source code for the determinant part</h2>
<div id="outline-container-orgcd2ce71" class="outline-2">
<h2 id="orgcd2ce71"><span class="section-number-2">11</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-11">
<p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1564,8 +1564,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-orga5d0f02" class="outline-2">
<h2 id="orga5d0f02"><span class="section-number-2">12</span> Helper functions</h2>
<div id="outline-container-org36ea9d0" class="outline-2">
<h2 id="org36ea9d0"><span class="section-number-2">12</span> Helper functions</h2>
<div class="outline-text-2" id="text-12">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1828,7 +1828,7 @@ 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: 2022-09-06 Tue 15:30</p>
<p class="date">Created: 2022-09-10 Sat 19:17</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

94
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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>
<!-- 2022-09-06 Tue 15:30 -->
<!-- 2022-09-10 Sat 19:17 -->
<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>
@ -311,21 +311,21 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org217f79d">1. Template for group-related structures in text back end</a></li>
<li><a href="#org5d66d68">2. Template for general structure in text back end</a></li>
<li><a href="#orgec1a52f">3. Initialize function (constant part)</a></li>
<li><a href="#org8a3d118">4. Deinitialize function (templated part)</a></li>
<li><a href="#org9728752">5. Template for text read a group</a></li>
<li><a href="#org0451132">6. Template for text has a group</a></li>
<li><a href="#org58d5eb4">7. Template for text flush a group</a></li>
<li><a href="#orge9fa97b">8. Template for text free memory</a></li>
<li><a href="#orgb64d3f3">9. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgf643307">10. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org08e0b64">11. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org926b6ab">12. Template for has/read/write a string attribute</a></li>
<li><a href="#orgaef5713">13. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org921b8f7">14. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgefaa8f4">15. Source code for the determinant part</a></li>
<li><a href="#org4b4e285">1. Template for group-related structures in text back end</a></li>
<li><a href="#org09ce75b">2. Template for general structure in text back end</a></li>
<li><a href="#org24ed5d6">3. Initialize function (constant part)</a></li>
<li><a href="#org1ac732f">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgf3c2a06">5. Template for text read a group</a></li>
<li><a href="#org7b43d0f">6. Template for text has a group</a></li>
<li><a href="#org78eaf67">7. Template for text flush a group</a></li>
<li><a href="#orga3848b3">8. Template for text free memory</a></li>
<li><a href="#orgb9d9f29">9. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org3864c3f">10. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgfe1ba96">11. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgd9ef705">12. Template for has/read/write a string attribute</a></li>
<li><a href="#org0e5a1ac">13. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org8d9cc43">14. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org8bfd6c6">15. Source code for the determinant part</a></li>
</ul>
</div>
</div>
@ -347,8 +347,8 @@ directory.
The file is written when closed, or when the flush function is called.
</p>
<div id="outline-container-org217f79d" class="outline-2">
<h2 id="org217f79d"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org4b4e285" class="outline-2">
<h2 id="org4b4e285"><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 {
@ -367,8 +367,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org5d66d68" class="outline-2">
<h2 id="org5d66d68"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org09ce75b" class="outline-2">
<h2 id="org09ce75b"><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
@ -388,8 +388,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgec1a52f" class="outline-2">
<h2 id="orgec1a52f"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org24ed5d6" class="outline-2">
<h2 id="org24ed5d6"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">bool</span>
@ -556,8 +556,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org8a3d118" class="outline-2">
<h2 id="org8a3d118"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org1ac732f" class="outline-2">
<h2 id="org1ac732f"><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>
@ -579,8 +579,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org9728752" class="outline-2">
<h2 id="org9728752"><span class="section-number-2">5</span> Template for text read a group</h2>
<div id="outline-container-orgf3c2a06" class="outline-2">
<h2 id="orgf3c2a06"><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*
@ -806,8 +806,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org0451132" class="outline-2">
<h2 id="org0451132"><span class="section-number-2">6</span> Template for text has a group</h2>
<div id="outline-container-org7b43d0f" class="outline-2">
<h2 id="org7b43d0f"><span class="section-number-2">6</span> Template for text has 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>
@ -847,8 +847,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org58d5eb4" class="outline-2">
<h2 id="org58d5eb4"><span class="section-number-2">7</span> Template for text flush a group</h2>
<div id="outline-container-org78eaf67" class="outline-2">
<h2 id="org78eaf67"><span class="section-number-2">7</span> Template for text flush a group</h2>
<div class="outline-text-2" id="text-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -912,8 +912,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orge9fa97b" class="outline-2">
<h2 id="orge9fa97b"><span class="section-number-2">8</span> Template for text free memory</h2>
<div id="outline-container-orga3848b3" class="outline-2">
<h2 id="orga3848b3"><span class="section-number-2">8</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-8">
<p>
Memory is allocated when reading. The following function frees memory.
@ -982,8 +982,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orgb64d3f3" class="outline-2">
<h2 id="orgb64d3f3"><span class="section-number-2">9</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orgb9d9f29" class="outline-2">
<h2 id="orgb9d9f29"><span class="section-number-2">9</span> Template for has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1046,8 +1046,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orgf643307" class="outline-2">
<h2 id="orgf643307"><span class="section-number-2">10</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org3864c3f" class="outline-2">
<h2 id="org3864c3f"><span class="section-number-2">10</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-10">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1143,8 +1143,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org08e0b64" class="outline-2">
<h2 id="org08e0b64"><span class="section-number-2">11</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgfe1ba96" class="outline-2">
<h2 id="orgfe1ba96"><span class="section-number-2">11</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-11">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1245,8 +1245,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org926b6ab" class="outline-2">
<h2 id="org926b6ab"><span class="section-number-2">12</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orgd9ef705" class="outline-2">
<h2 id="orgd9ef705"><span class="section-number-2">12</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-12">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1320,8 +1320,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgaef5713" class="outline-2">
<h2 id="orgaef5713"><span class="section-number-2">13</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org0e5a1ac" class="outline-2">
<h2 id="org0e5a1ac"><span class="section-number-2">13</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-13">
<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
@ -1611,8 +1611,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org921b8f7" class="outline-2">
<h2 id="org921b8f7"><span class="section-number-2">14</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org8d9cc43" class="outline-2">
<h2 id="org8d9cc43"><span class="section-number-2">14</span> Template for text delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-14">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1640,8 +1640,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-orgefaa8f4" class="outline-2">
<h2 id="orgefaa8f4"><span class="section-number-2">15</span> Source code for the determinant part</h2>
<div id="outline-container-org8bfd6c6" class="outline-2">
<h2 id="org8bfd6c6"><span class="section-number-2">15</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-15">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -2081,7 +2081,7 @@ 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: 2022-09-06 Tue 15:30</p>
<p class="date">Created: 2022-09-10 Sat 19:17</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

158
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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>
<!-- 2022-09-06 Tue 15:30 -->
<!-- 2022-09-10 Sat 19:17 -->
<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>
@ -333,38 +333,38 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org04dca1e">1. Metadata (metadata group)</a></li>
<li><a href="#orge3b007b">2. Electron (electron group)</a></li>
<li><a href="#org97a6b47">3. Nucleus (nucleus group)</a></li>
<li><a href="#org7a11291">4. Effective core potentials (ecp group)</a>
<li><a href="#org09b781b">1. Metadata (metadata group)</a></li>
<li><a href="#org5f3b096">2. Electron (electron group)</a></li>
<li><a href="#org449c33c">3. Nucleus (nucleus group)</a></li>
<li><a href="#org8da4bf9">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org25267d9">4.1. Example</a></li>
<li><a href="#orgcda760a">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org8e99cf4">5. Basis set (basis group)</a>
<li><a href="#org46397f8">5. Basis set (basis group)</a>
<ul>
<li><a href="#org0b9bb46">5.1. Example</a></li>
<li><a href="#orgdc37331">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org7e8b087">6. Atomic orbitals (ao group)</a>
<li><a href="#orgd70a99e">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="#orgb1e9c01">7. Molecular orbitals (mo group)</a>
<li><a href="#orgb58ed66">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgeb8856d">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org8472701">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org6491ba6">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgb2307a0">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#orgac2ee95">8. Slater determinants (determinant group)</a></li>
<li><a href="#orgf104a13">9. Configuration state functions (csf group)</a></li>
<li><a href="#org34234ac">10. Excited states (state group)</a></li>
<li><a href="#org9d1f7c6">11. Reduced density matrices (rdm group)</a></li>
<li><a href="#org1e8829a">12. Cell (cell group)</a></li>
<li><a href="#org5dc87ff">13. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org8350cdd">14. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org967cbc3">8. Slater determinants (determinant group)</a></li>
<li><a href="#orgfcff64a">9. Configuration state functions (csf group)</a></li>
<li><a href="#orgfe7d5d1">10. Excited states (state group)</a></li>
<li><a href="#org8bf66f2">11. Reduced density matrices (rdm group)</a></li>
<li><a href="#org38cdb28">12. Cell (cell group)</a></li>
<li><a href="#org316851a">13. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgc0944b0">14. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -418,8 +418,8 @@ For determinants, the <code>special</code> attribute is present in the type. Thi
means that the source code is not produced by the generator, but hand-written.
</p>
<div id="outline-container-org04dca1e" class="outline-2">
<h2 id="org04dca1e"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org09b781b" class="outline-2">
<h2 id="org09b781b"><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
@ -429,7 +429,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="org2011cf3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org819261f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -510,15 +510,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-orge3b007b" class="outline-2">
<h2 id="orge3b007b"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org5f3b096" class="outline-2">
<h2 id="org5f3b096"><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="orgad1e184" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org57abf34" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -564,15 +564,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org97a6b47" class="outline-2">
<h2 id="org97a6b47"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org449c33c" class="outline-2">
<h2 id="org449c33c"><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="org0be5b3b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8c6386b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -639,8 +639,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org7a11291" class="outline-2">
<h2 id="org7a11291"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org8da4bf9" class="outline-2">
<h2 id="org8da4bf9"><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
@ -673,7 +673,7 @@ 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="orgd6b5deb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgba0ce66" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -775,8 +775,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-org25267d9" class="outline-3">
<h3 id="org25267d9"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-orgcda760a" class="outline-3">
<h3 id="orgcda760a"><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
@ -839,8 +839,8 @@ power = [
</div>
</div>
<div id="outline-container-org8e99cf4" class="outline-2">
<h2 id="org8e99cf4"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org46397f8" class="outline-2">
<h2 id="org46397f8"><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
@ -893,7 +893,7 @@ 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="org7928f34" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org36f46f8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -987,8 +987,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-org0b9bb46" class="outline-3">
<h3 id="org0b9bb46"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-orgdc37331" class="outline-3">
<h3 id="orgdc37331"><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
@ -1066,8 +1066,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org7e8b087" class="outline-2">
<h2 id="org7e8b087"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-orgd70a99e" class="outline-2">
<h2 id="orgd70a99e"><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
@ -1120,13 +1120,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org8e99cf4">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org46397f8">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="orgccec6a7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0017345" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1178,8 +1178,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org33f991e" class="outline-3">
<h3 id="ao_one_e"><a id="org33f991e"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgf1974df" class="outline-3">
<h3 id="ao_one_e"><a id="orgf1974df"></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}}
@ -1196,7 +1196,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgbdffc10" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9d15fda" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1291,8 +1291,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgd699c29" class="outline-3">
<h3 id="ao_two_e"><a id="orgd699c29"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org97d074d" class="outline-3">
<h3 id="ao_two_e"><a id="org97d074d"></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
@ -1313,7 +1313,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org2b922a2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org225f8f7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1353,10 +1353,10 @@ notation.
</div>
</div>
<div id="outline-container-orgb1e9c01" class="outline-2">
<h2 id="orgb1e9c01"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgb58ed66" class="outline-2">
<h2 id="orgb58ed66"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org8a6af06" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1b780b7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1443,8 +1443,8 @@ notation.
</table>
</div>
<div id="outline-container-orgeb8856d" class="outline-3">
<h3 id="orgeb8856d"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org6491ba6" class="outline-3">
<h3 id="org6491ba6"><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
@ -1452,7 +1452,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org2649e6d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb51d089" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1547,8 +1547,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org8472701" class="outline-3">
<h3 id="org8472701"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orgb2307a0" class="outline-3">
<h3 id="orgb2307a0"><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
@ -1556,7 +1556,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orga79a2b1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5475a55" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1596,8 +1596,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgac2ee95" class="outline-2">
<h2 id="orgac2ee95"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-org967cbc3" class="outline-2">
<h2 id="org967cbc3"><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 \(\Psi\)
@ -1639,7 +1639,7 @@ produced by the code generator.
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
</p>
<table id="org8e1ddbb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8169614" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1685,8 +1685,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-orgf104a13" class="outline-2">
<h2 id="orgf104a13"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
<div id="outline-container-orgfcff64a" class="outline-2">
<h2 id="orgfcff64a"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
<div class="outline-text-2" id="text-9">
<p>
The configuration interaction (CI) wave function \(\Psi\) can be
@ -1708,7 +1708,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="orgfed4116" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org517e77f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1754,8 +1754,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org34234ac" class="outline-2">
<h2 id="org34234ac"><span class="section-number-2">10</span> Excited states (state group)</h2>
<div id="outline-container-orgfe7d5d1" class="outline-2">
<h2 id="orgfe7d5d1"><span class="section-number-2">10</span> Excited states (state group)</h2>
<div class="outline-text-2" id="text-10">
<p>
By default, the <code>determinant</code> group corresponds to the ground state.
@ -1764,7 +1764,7 @@ correspond to excited state wave functions for the same set of
determinants. This is the goal of the present group
</p>
<table id="org404a2b0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb87296a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1803,8 +1803,8 @@ determinants. This is the goal of the present group
</div>
</div>
<div id="outline-container-org9d1f7c6" class="outline-2">
<h2 id="org9d1f7c6"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org8bf66f2" class="outline-2">
<h2 id="org8bf66f2"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-11">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1857,7 +1857,7 @@ The total energy can be computed as:
\]
</p>
<table id="orgf1f1a6b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3c36387" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1938,10 +1938,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org1e8829a" class="outline-2">
<h2 id="org1e8829a"><span class="section-number-2">12</span> Cell (cell group)</h2>
<div id="outline-container-org38cdb28" class="outline-2">
<h2 id="org38cdb28"><span class="section-number-2">12</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-12">
<table id="org7c2bbe3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5506427" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1987,10 +1987,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org5dc87ff" class="outline-2">
<h2 id="org5dc87ff"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-org316851a" class="outline-2">
<h2 id="org316851a"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-13">
<table id="org83b5a0e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org12de937" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2029,8 +2029,8 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org8350cdd" class="outline-2">
<h2 id="org8350cdd"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-orgc0944b0" class="outline-2">
<h2 id="orgc0944b0"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-14">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -2044,7 +2044,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="org6c9d57c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6938f00" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2099,7 +2099,7 @@ 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: 2022-09-06 Tue 15:30</p>
<p class="date">Created: 2022-09-10 Sat 19:17</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>