mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-12-24 13:23:44 +01:00
Deploying to gh-pages from @ TREX-CoE/trexio@24b1ce6b35 🚀
This commit is contained in:
q-posev
parent
c0b0449b7c
commit
3f8c54b04b
@ -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>
|
||||
<!-- 2022-05-06 Fri 09:09 -->
|
||||
<!-- 2022-05-18 Wed 09:56 -->
|
||||
<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: 2022-05-06 Fri 09:09</p>
|
||||
<p class="date">Created: 2022-05-18 Wed 09:56</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -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>
|
||||
<!-- 2022-05-06 Fri 09:09 -->
|
||||
<!-- 2022-05-18 Wed 09:56 -->
|
||||
<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="#org1ce0257">1. Accessing sparse quantities</a>
|
||||
<li><a href="#org37af446">1. Accessing sparse quantities</a>
|
||||
<ul>
|
||||
<li><a href="#org84ea310">1.1. Fortran</a>
|
||||
<li><a href="#org6d50677">1.1. Fortran</a>
|
||||
<ul>
|
||||
<li><a href="#org0b390a0">1.1.1. Declare Temporary variables</a></li>
|
||||
<li><a href="#org1a2a689">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
|
||||
<li><a href="#org55cbc0e">1.1.3. Read the nuclear repulsion energy</a></li>
|
||||
<li><a href="#orgf79c4df">1.1.4. Read the number of molecular orbitals</a></li>
|
||||
<li><a href="#orgfdea5e6">1.1.5. Allocate memory</a></li>
|
||||
<li><a href="#orgaf4e889">1.1.6. Read one-electron quantities</a></li>
|
||||
<li><a href="#org504e54d">1.1.7. Read two-electron quantities</a>
|
||||
<li><a href="#org6a86eda">1.1.1. Declare Temporary variables</a></li>
|
||||
<li><a href="#orgdf0fd07">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
|
||||
<li><a href="#orga4a5c6f">1.1.3. Read the nuclear repulsion energy</a></li>
|
||||
<li><a href="#org98a3bdc">1.1.4. Read the number of molecular orbitals</a></li>
|
||||
<li><a href="#org073da58">1.1.5. Allocate memory</a></li>
|
||||
<li><a href="#orgd7365b3">1.1.6. Read one-electron quantities</a></li>
|
||||
<li><a href="#org82a2dcf">1.1.7. Read two-electron quantities</a>
|
||||
<ul>
|
||||
<li><a href="#org4212e44">1.1.7.1. Electron repulsion integrals</a></li>
|
||||
<li><a href="#orga7f2023">1.1.7.2. Reduced density matrix</a></li>
|
||||
<li><a href="#org7567762">1.1.7.1. Electron repulsion integrals</a></li>
|
||||
<li><a href="#org6431bf8">1.1.7.2. Reduced density matrix</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgcc1cc6d">1.1.8. Compute the energy</a></li>
|
||||
<li><a href="#org63bafe5">1.1.9. Terminate</a></li>
|
||||
<li><a href="#org86fde4e">1.1.8. Compute the energy</a></li>
|
||||
<li><a href="#orgbdce9ba">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-org1ce0257" class="outline-2">
|
||||
<h2 id="org1ce0257"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
|
||||
<div id="outline-container-org37af446" class="outline-2">
|
||||
<h2 id="org37af446"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
</div>
|
||||
<div id="outline-container-org84ea310" class="outline-3">
|
||||
<h3 id="org84ea310"><span class="section-number-3">1.1</span> Fortran</h3>
|
||||
<div id="outline-container-org6d50677" class="outline-3">
|
||||
<h3 id="org6d50677"><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-org0b390a0" class="outline-4">
|
||||
<h4 id="org0b390a0"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
|
||||
<div id="outline-container-org6a86eda" class="outline-4">
|
||||
<h4 id="org6a86eda"><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-org1a2a689" class="outline-4">
|
||||
<h4 id="org1a2a689"><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-orgdf0fd07" class="outline-4">
|
||||
<h4 id="orgdf0fd07"><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-org55cbc0e" class="outline-4">
|
||||
<h4 id="org55cbc0e"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
|
||||
<div id="outline-container-orga4a5c6f" class="outline-4">
|
||||
<h4 id="orga4a5c6f"><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-orgf79c4df" class="outline-4">
|
||||
<h4 id="orgf79c4df"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
|
||||
<div id="outline-container-org98a3bdc" class="outline-4">
|
||||
<h4 id="org98a3bdc"><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-orgfdea5e6" class="outline-4">
|
||||
<h4 id="orgfdea5e6"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
|
||||
<div id="outline-container-org073da58" class="outline-4">
|
||||
<h4 id="org073da58"><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-orgaf4e889" class="outline-4">
|
||||
<h4 id="orgaf4e889"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
|
||||
<div id="outline-container-orgd7365b3" class="outline-4">
|
||||
<h4 id="orgd7365b3"><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-org504e54d" class="outline-4">
|
||||
<h4 id="org504e54d"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
|
||||
<div id="outline-container-org82a2dcf" class="outline-4">
|
||||
<h4 id="org82a2dcf"><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-org4212e44" class="outline-5">
|
||||
<h5 id="org4212e44"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
|
||||
<div id="outline-container-org7567762" class="outline-5">
|
||||
<h5 id="org7567762"><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-orga7f2023" class="outline-5">
|
||||
<h5 id="orga7f2023"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
|
||||
<div id="outline-container-org6431bf8" class="outline-5">
|
||||
<h5 id="org6431bf8"><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-orgcc1cc6d" class="outline-4">
|
||||
<h4 id="orgcc1cc6d"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
|
||||
<div id="outline-container-org86fde4e" class="outline-4">
|
||||
<h4 id="org86fde4e"><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-org63bafe5" class="outline-4">
|
||||
<h4 id="org63bafe5"><span class="section-number-4">1.1.9</span> Terminate</h4>
|
||||
<div id="outline-container-orgbdce9ba" class="outline-4">
|
||||
<h4 id="orgbdce9ba"><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: 2022-05-06 Fri 09:09</p>
|
||||
<p class="date">Created: 2022-05-18 Wed 09:56</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -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>
|
||||
<!-- 2022-05-06 Fri 09:09 -->
|
||||
<!-- 2022-05-18 Wed 09:56 -->
|
||||
<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: 2022-05-06 Fri 09:09</p>
|
||||
<p class="date">Created: 2022-05-18 Wed 09:56</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -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>
|
||||
<!-- 2022-05-06 Fri 09:09 -->
|
||||
<!-- 2022-05-18 Wed 09:56 -->
|
||||
<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="#org4715362">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org123241f">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgce116ae">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orge9d9e04">4. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org5bf214f">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgdb02241">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#org2e57b58">7. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orga9102e5">8. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgcbc633c">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orgbeec730">10. Source code for the determinant part</a></li>
|
||||
<li><a href="#orga094401">11. Helper functions</a></li>
|
||||
<li><a href="#org1a73ab0">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#orgb56a4cb">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgba2ac96">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orgd1b318c">4. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org3590ebe">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org360c1c3">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#org636694b">7. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org4e825d3">8. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#org0b4b28d">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org55a734d">10. Source code for the determinant part</a></li>
|
||||
<li><a href="#org0c6becf">11. Helper functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4715362" class="outline-2">
|
||||
<h2 id="org4715362"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-org1a73ab0" class="outline-2">
|
||||
<h2 id="org1a73ab0"><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-org123241f" class="outline-2">
|
||||
<h2 id="org123241f"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-orgb56a4cb" class="outline-2">
|
||||
<h2 id="orgb56a4cb"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_hdf5_s</span> {
|
||||
@ -353,8 +353,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgce116ae" class="outline-2">
|
||||
<h2 id="orgce116ae"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-orgba2ac96" class="outline-2">
|
||||
<h2 id="orgba2ac96"><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>
|
||||
@ -459,8 +459,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge9d9e04" class="outline-2">
|
||||
<h2 id="orge9d9e04"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-orgd1b318c" class="outline-2">
|
||||
<h2 id="orgd1b318c"><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>
|
||||
@ -564,8 +564,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5bf214f" class="outline-2">
|
||||
<h2 id="org5bf214f"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org3590ebe" class="outline-2">
|
||||
<h2 id="org3590ebe"><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>
|
||||
@ -699,8 +699,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdb02241" class="outline-2">
|
||||
<h2 id="orgdb02241"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-org360c1c3" class="outline-2">
|
||||
<h2 id="org360c1c3"><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
|
||||
@ -903,8 +903,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2e57b58" class="outline-2">
|
||||
<h2 id="org2e57b58"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org636694b" class="outline-2">
|
||||
<h2 id="org636694b"><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>
|
||||
@ -1102,8 +1102,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga9102e5" class="outline-2">
|
||||
<h2 id="orga9102e5"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org4e825d3" class="outline-2">
|
||||
<h2 id="org4e825d3"><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>
|
||||
@ -1230,8 +1230,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgcbc633c" class="outline-2">
|
||||
<h2 id="orgcbc633c"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-org0b4b28d" class="outline-2">
|
||||
<h2 id="org0b4b28d"><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 < 1.10) unlinking an object was not working as expected
|
||||
@ -1271,8 +1271,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgbeec730" class="outline-2">
|
||||
<h2 id="orgbeec730"><span class="section-number-2">10</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org55a734d" class="outline-2">
|
||||
<h2 id="org55a734d"><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.
|
||||
@ -1525,8 +1525,8 @@ Size specifies the number of data items (e.g. determinants) to process.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga094401" class="outline-2">
|
||||
<h2 id="orga094401"><span class="section-number-2">11</span> Helper functions</h2>
|
||||
<div id="outline-container-org0c6becf" class="outline-2">
|
||||
<h2 id="org0c6becf"><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>
|
||||
@ -1789,7 +1789,7 @@ 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: 2022-05-06 Fri 09:09</p>
|
||||
<p class="date">Created: 2022-05-18 Wed 09:56</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -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>
|
||||
<!-- 2022-05-06 Fri 09:09 -->
|
||||
<!-- 2022-05-18 Wed 09:56 -->
|
||||
<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="#org209e5cc">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#orga5df7f3">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org0ca6c48">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org2d39bde">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orgbe90f33">5. Template for text read a group</a></li>
|
||||
<li><a href="#orgfc1ceb1">6. Template for text flush a group</a></li>
|
||||
<li><a href="#org06dfdb7">7. Template for text free memory</a></li>
|
||||
<li><a href="#org2413d6d">8. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgc2c0a66">9. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org0bb7a0d">10. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgb588e9f">11. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orga6a3b95">12. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org570b39a">13. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org68408be">14. Source code for the determinant part</a></li>
|
||||
<li><a href="#org02786e9">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org5ce48d7">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org5eebf3a">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org1fa0258">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org6bdb0ff">5. Template for text read a group</a></li>
|
||||
<li><a href="#org4935693">6. Template for text flush a group</a></li>
|
||||
<li><a href="#org81b0478">7. Template for text free memory</a></li>
|
||||
<li><a href="#orgc4cf68f">8. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgc63e851">9. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgf4d3dda">10. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org7822561">11. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org43c9d82">12. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org20d868f">13. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org9bf2c90">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-org209e5cc" class="outline-2">
|
||||
<h2 id="org209e5cc"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div id="outline-container-org02786e9" class="outline-2">
|
||||
<h2 id="org02786e9"><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-orga5df7f3" class="outline-2">
|
||||
<h2 id="orga5df7f3"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div id="outline-container-org5ce48d7" class="outline-2">
|
||||
<h2 id="org5ce48d7"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_text_s</span> {
|
||||
@ -380,8 +380,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0ca6c48" class="outline-2">
|
||||
<h2 id="org0ca6c48"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div id="outline-container-org5eebf3a" class="outline-2">
|
||||
<h2 id="org5eebf3a"><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>
|
||||
@ -524,8 +524,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2d39bde" class="outline-2">
|
||||
<h2 id="org2d39bde"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div id="outline-container-org1fa0258" class="outline-2">
|
||||
<h2 id="org1fa0258"><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>
|
||||
@ -547,8 +547,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgbe90f33" class="outline-2">
|
||||
<h2 id="orgbe90f33"><span class="section-number-2">5</span> Template for text read a group</h2>
|
||||
<div id="outline-container-org6bdb0ff" class="outline-2">
|
||||
<h2 id="org6bdb0ff"><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*
|
||||
@ -849,8 +849,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgfc1ceb1" class="outline-2">
|
||||
<h2 id="orgfc1ceb1"><span class="section-number-2">6</span> Template for text flush a group</h2>
|
||||
<div id="outline-container-org4935693" class="outline-2">
|
||||
<h2 id="org4935693"><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>
|
||||
@ -914,8 +914,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org06dfdb7" class="outline-2">
|
||||
<h2 id="org06dfdb7"><span class="section-number-2">7</span> Template for text free memory</h2>
|
||||
<div id="outline-container-org81b0478" class="outline-2">
|
||||
<h2 id="org81b0478"><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.
|
||||
@ -962,8 +962,8 @@ Memory is allocated when reading. The following function frees memory.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2413d6d" class="outline-2">
|
||||
<h2 id="org2413d6d"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-orgc4cf68f" class="outline-2">
|
||||
<h2 id="orgc4cf68f"><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>
|
||||
@ -1026,8 +1026,8 @@ Memory is allocated when reading. The following function frees memory.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc2c0a66" class="outline-2">
|
||||
<h2 id="orgc2c0a66"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-orgc63e851" class="outline-2">
|
||||
<h2 id="orgc63e851"><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.
|
||||
@ -1123,8 +1123,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org0bb7a0d" class="outline-2">
|
||||
<h2 id="org0bb7a0d"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-orgf4d3dda" class="outline-2">
|
||||
<h2 id="orgf4d3dda"><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.
|
||||
@ -1225,8 +1225,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgb588e9f" class="outline-2">
|
||||
<h2 id="orgb588e9f"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org7822561" class="outline-2">
|
||||
<h2 id="org7822561"><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>
|
||||
@ -1300,8 +1300,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orga6a3b95" class="outline-2">
|
||||
<h2 id="orga6a3b95"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div id="outline-container-org43c9d82" class="outline-2">
|
||||
<h2 id="org43c9d82"><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
|
||||
@ -1575,8 +1575,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org570b39a" class="outline-2">
|
||||
<h2 id="org570b39a"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-org20d868f" class="outline-2">
|
||||
<h2 id="org20d868f"><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>
|
||||
@ -1604,8 +1604,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org68408be" class="outline-2">
|
||||
<h2 id="org68408be"><span class="section-number-2">14</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org9bf2c90" class="outline-2">
|
||||
<h2 id="org9bf2c90"><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
|
||||
@ -2009,7 +2009,7 @@ 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: 2022-05-06 Fri 09:09</p>
|
||||
<p class="date">Created: 2022-05-18 Wed 09:56</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
192
trex.html
192
trex.html
@ -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>
|
||||
<!-- 2022-05-06 Fri 09:09 -->
|
||||
<!-- 2022-05-18 Wed 09:56 -->
|
||||
<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>
|
||||
@ -333,35 +333,35 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org7298043">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org6719728">2. Electron (electron group)</a></li>
|
||||
<li><a href="#orgfce12b6">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org2215159">4. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#org39aecf0">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#orgff3c918">2. Electron (electron group)</a></li>
|
||||
<li><a href="#orgbfedf30">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#orgbe51561">4. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#org27dbd85">4.1. Example</a></li>
|
||||
<li><a href="#orgff9b62d">4.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org2c04851">5. Basis set (basis group)</a>
|
||||
<li><a href="#orgaaf6f48">5. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#orgc237734">5.1. Example</a></li>
|
||||
<li><a href="#orga640d2e">5.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgb2196d3">6. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#org08b6ff6">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="#org57bef24">7. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org06d529b">7. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#org7502a33">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orga2d1fd1">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#orgc8965f7">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org6a396a6">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orge6c9ce0">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#orge377fa1">9. Excited states (state group)</a></li>
|
||||
<li><a href="#orgb32bbd4">10. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#orge3ff0a0">11. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
<li><a href="#org9e29804">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#orgc4c49d3">9. Excited states (state group)</a></li>
|
||||
<li><a href="#org2436c98">10. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#orgf0f0e0c">11. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -390,6 +390,10 @@ variables cannot be negative. This additional constraint is required
|
||||
because <code>dim</code> attributes are used internally to allocate memory and to
|
||||
check array boundaries in the memory-safe API. Most of the times, the
|
||||
<code>dim</code> variables contain the <code>num</code> suffix.
|
||||
You may also encounter some <code>dim readonly</code> variables.
|
||||
It means that the value is automatically computed and written by the
|
||||
TREXIO library, thus it is read-only and cannot be (over)written by the
|
||||
user.
|
||||
</p>
|
||||
|
||||
<p>
|
||||
@ -407,8 +411,8 @@ the <a href="./examples.html">examples</a>.
|
||||
</p>
|
||||
|
||||
|
||||
<div id="outline-container-org7298043" class="outline-2">
|
||||
<h2 id="org7298043"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-org39aecf0" class="outline-2">
|
||||
<h2 id="org39aecf0"><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
|
||||
@ -418,7 +422,7 @@ which have participated to the creation of the file, a list of
|
||||
authors of the file, and a textual description.
|
||||
</p>
|
||||
|
||||
<table id="org9b49cbd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org684fbce" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -499,15 +503,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6719728" class="outline-2">
|
||||
<h2 id="org6719728"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div id="outline-container-orgff3c918" class="outline-2">
|
||||
<h2 id="orgff3c918"><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 ↑ and ↓ electrons is fixed.
|
||||
</p>
|
||||
|
||||
<table id="org25fad49" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgfdcc5eb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -553,15 +557,15 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgfce12b6" class="outline-2">
|
||||
<h2 id="orgfce12b6"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div id="outline-container-orgbfedf30" class="outline-2">
|
||||
<h2 id="orgbfedf30"><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="org22433c4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org9f075ea" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -628,8 +632,8 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2215159" class="outline-2">
|
||||
<h2 id="org2215159"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div id="outline-container-orgbe51561" class="outline-2">
|
||||
<h2 id="orgbe51561"><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
|
||||
@ -662,7 +666,7 @@ 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="orge48112b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1ce1f68" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -764,8 +768,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org27dbd85" class="outline-3">
|
||||
<h3 id="org27dbd85"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div id="outline-container-orgff9b62d" class="outline-3">
|
||||
<h3 id="orgff9b62d"><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
|
||||
@ -828,8 +832,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2c04851" class="outline-2">
|
||||
<h2 id="org2c04851"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div id="outline-container-orgaaf6f48" class="outline-2">
|
||||
<h2 id="orgaaf6f48"><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
|
||||
@ -882,7 +886,7 @@ 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="org96b0133" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org3fa290a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -976,8 +980,8 @@ All the basis set parameters are stored in one-dimensional arrays:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc237734" class="outline-3">
|
||||
<h3 id="orgc237734"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div id="outline-container-orga640d2e" class="outline-3">
|
||||
<h3 id="orga640d2e"><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
|
||||
@ -1055,8 +1059,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb2196d3" class="outline-2">
|
||||
<h2 id="orgb2196d3"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div id="outline-container-org08b6ff6" class="outline-2">
|
||||
<h2 id="org08b6ff6"><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
|
||||
@ -1109,13 +1113,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#org2c04851">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#orgaaf6f48">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="org7452ebd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgb9d94de" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1167,8 +1171,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org497b2e8" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org497b2e8"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div id="outline-container-org13b9379" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org13b9379"></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}}
|
||||
@ -1185,7 +1189,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org5749a1d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orge6a80c7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1245,8 +1249,8 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgad00540" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="orgad00540"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div id="outline-container-orgb1d52f8" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="orgb1d52f8"></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
|
||||
@ -1267,7 +1271,7 @@ notation.
|
||||
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
|
||||
</ul>
|
||||
|
||||
<table id="orgb77f2a8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgf561b5a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1307,10 +1311,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org57bef24" class="outline-2">
|
||||
<h2 id="org57bef24"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div id="outline-container-org06d529b" class="outline-2">
|
||||
<h2 id="org06d529b"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="orgbf1edd5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org11aabf8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1376,8 +1380,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7502a33" class="outline-3">
|
||||
<h3 id="org7502a33"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div id="outline-container-orgc8965f7" class="outline-3">
|
||||
<h3 id="orgc8965f7"><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
|
||||
@ -1385,7 +1389,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org81b9d8e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org4232212" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1445,8 +1449,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga2d1fd1" class="outline-3">
|
||||
<h3 id="orga2d1fd1"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div id="outline-container-org6a396a6" class="outline-3">
|
||||
<h3 id="org6a396a6"><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
|
||||
@ -1454,7 +1458,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org53d504a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org9560f2a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1494,8 +1498,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge6c9ce0" class="outline-2">
|
||||
<h2 id="orge6c9ce0"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
|
||||
<div id="outline-container-org9e29804" class="outline-2">
|
||||
<h2 id="org9e29804"><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 \(\Psi\)
|
||||
@ -1504,63 +1508,31 @@ can be expanded in the basis of Slater determinants \(D_I\) as follows
|
||||
|
||||
<p>
|
||||
\[
|
||||
</p>
|
||||
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
<col class="org-left" />
|
||||
|
||||
<col class="org-left" />
|
||||
</colgroup>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left">Ψ> = ∑<sub>I</sub> C<sub>I</sub></td>
|
||||
<td class="org-left">D<sub>I</sub>></td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>
|
||||
\]
|
||||
\Psi = \sum_I C_I D_I
|
||||
\]
|
||||
</p>
|
||||
|
||||
<p>
|
||||
For relatively small expansions, a given determinant can be represented as a list of <code>mo.num</code> occupation numbers.
|
||||
However, this requires a lot of extra memory and would be technically impossible for larger expansions
|
||||
(<code>millions of determinants). This is why the determinants are stored as bit fields in the TREXIO file
|
||||
(see ~int bitfield</code> type in the table below). By default, the chemist notation is used, namely
|
||||
For relatively small expansions, a given determinant can be represented as a list of occupied orbitals.
|
||||
However, this becomes unfeasible for larger expansions and requires more advanced data structures.
|
||||
The bit field representation is used here, namely a given determinant is represented as \(N_{\text{int}}\)
|
||||
64-bit integers where j-th bit is set to 1 if there is an electron in the j-th orbital and 0 otherwise.
|
||||
This gives access to larger determinant expansions by optimising the storage of the determinant lists
|
||||
in the memory.
|
||||
</p>
|
||||
|
||||
<p>
|
||||
\[
|
||||
</p>
|
||||
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
<col class="org-left" />
|
||||
|
||||
<col class="org-left" />
|
||||
</colgroup>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left">D<sub>I</sub> > =</td>
|
||||
<td class="org-left">α<sub>1</sub> α<sub>2</sub> \ldots α<sub>n↑</sub> β<sub>1</sub> β<sub>2</sub> \ldots β<sub>n↓</sub> ></td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>
|
||||
\]
|
||||
D_I = \alpha_1 \alpha_2 \ldots \alpha_{n\uparrow} \beta_1 \beta_2 \ldots \beta_{n\downarrow}
|
||||
\]
|
||||
</p>
|
||||
|
||||
<p>
|
||||
where \(\alpha\) and \(\beta\) denote $↑$-spin and $↓$-spin electrons, respectively,
|
||||
\(n\uparrow\) and \(n\downarrow\) correspond to <code>electron.up_num</code> and <code>electron.dn_num</code>, respectively.
|
||||
Internally, bit fields for \(\alpha\) and \(\beta\) electrons are stored separately,
|
||||
which is why the <code>determinant.list</code> attribute has a second dimension.
|
||||
</p>
|
||||
|
||||
<table id="org878ec70" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga095b19" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1583,7 +1555,7 @@ which is why the <code>determinant.list</code> attribute has a second dimension.
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left"><code>num</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"><code>dim readonly</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Number of determinants</td>
|
||||
</tr>
|
||||
@ -1606,8 +1578,8 @@ which is why the <code>determinant.list</code> attribute has a second dimension.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge377fa1" class="outline-2">
|
||||
<h2 id="orge377fa1"><span class="section-number-2">9</span> Excited states (state group)</h2>
|
||||
<div id="outline-container-orgc4c49d3" class="outline-2">
|
||||
<h2 id="orgc4c49d3"><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.
|
||||
@ -1616,7 +1588,7 @@ correspond to excited state wave functions for the same set of
|
||||
determinants. This is the goal of the present group
|
||||
</p>
|
||||
|
||||
<table id="org155ab99" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2e3a6c3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1655,8 +1627,8 @@ determinants. This is the goal of the present group
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb32bbd4" class="outline-2">
|
||||
<h2 id="orgb32bbd4"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
|
||||
<div id="outline-container-org2436c98" class="outline-2">
|
||||
<h2 id="org2436c98"><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
|
||||
@ -1709,7 +1681,7 @@ The total energy can be computed as:
|
||||
\]
|
||||
</p>
|
||||
|
||||
<table id="orgabab98d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd99ebcc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1790,8 +1762,8 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge3ff0a0" class="outline-2">
|
||||
<h2 id="orge3ff0a0"><span class="section-number-2">11</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div id="outline-container-orgf0f0e0c" class="outline-2">
|
||||
<h2 id="orgf0f0e0c"><span class="section-number-2">11</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
In quantum Monte Carlo calculations, the wave function is evaluated
|
||||
@ -1805,7 +1777,7 @@ By convention, the electron coordinates contain first all the electrons
|
||||
of $↑$-spin and then all the $↓$-spin.
|
||||
</p>
|
||||
|
||||
<table id="orgd3ceca7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org0c7c2a2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1860,7 +1832,7 @@ of $↑$-spin and then all the $↓$-spin.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-05-06 Fri 09:09</p>
|
||||
<p class="date">Created: 2022-05-18 Wed 09:56</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
Loading…
Reference in New Issue
Block a user