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@ -3,7 +3,7 @@
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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<head>
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<!-- 2022-09-06 Tue 09:53 -->
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<!-- 2022-09-06 Tue 15:30 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>TREXIO source code documentation</title>
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||||
@ -347,7 +347,7 @@ and bug reports should be submitted at
|
||||
</div>
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||||
<div id="postamble" class="status">
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<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-09-06 Tue 09:53</p>
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||||
<p class="date">Created: 2022-09-06 Tue 15:30</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
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||||
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||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2022-09-06 Tue 09:53 -->
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||||
<!-- 2022-09-06 Tue 15:30 -->
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||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>Examples</title>
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||||
@ -333,31 +333,31 @@ for the JavaScript code in this tag.
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||||
<h2>Table of Contents</h2>
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||||
<div id="text-table-of-contents">
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||||
<ul>
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||||
<li><a href="#org6f808ca">1. Accessing sparse quantities (integrals)</a>
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<li><a href="#orga3cdf61">1. Accessing sparse quantities (integrals)</a>
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||||
<ul>
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<li><a href="#orgd4dfff5">1.1. Fortran</a>
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||||
<li><a href="#org5afcb5e">1.1. Fortran</a>
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||||
<ul>
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||||
<li><a href="#org47bd8b9">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org96b3387">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
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<li><a href="#org9757c39">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org780c82e">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org6f6e480">1.1.5. Allocate memory</a></li>
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<li><a href="#org64134e4">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#orgf6ba9ad">1.1.7. Read two-electron quantities</a>
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<li><a href="#org723256c">1.1.1. Declare Temporary variables</a></li>
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||||
<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>
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<li><a href="#orgcc2e7ea">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#orgaefa70b">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org9c26cb4">1.1.5. Allocate memory</a></li>
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<li><a href="#org086de1d">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#orgeb5ea18">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#org911e067">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#orgb83135b">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#org063f387">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org7aa5076">1.1.7.2. Reduced density matrix</a></li>
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</ul>
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</li>
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<li><a href="#orgcffff68">1.1.8. Compute the energy</a></li>
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<li><a href="#orgdc0ec1b">1.1.9. Terminate</a></li>
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<li><a href="#orgbd64619">1.1.8. Compute the energy</a></li>
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<li><a href="#orgb65a78d">1.1.9. Terminate</a></li>
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</ul>
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</li>
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</ul>
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</li>
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<li><a href="#org0d9fd26">2. Reading determinants</a>
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<li><a href="#orgc938429">2. Reading determinants</a>
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<ul>
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<li><a href="#orgebde94d">2.1. Fortran</a></li>
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<li><a href="#org09fbef9">2.1. Fortran</a></li>
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</ul>
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||||
</li>
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||||
</ul>
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||||
@ -365,12 +365,12 @@ for the JavaScript code in this tag.
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</div>
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||||
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||||
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||||
<div id="outline-container-org6f808ca" class="outline-2">
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<h2 id="org6f808ca"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
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<div id="outline-container-orga3cdf61" class="outline-2">
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||||
<h2 id="orga3cdf61"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
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<div class="outline-text-2" id="text-1">
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||||
</div>
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||||
<div id="outline-container-orgd4dfff5" class="outline-3">
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||||
<h3 id="orgd4dfff5"><span class="section-number-3">1.1</span> Fortran</h3>
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||||
<div id="outline-container-org5afcb5e" class="outline-3">
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||||
<h3 id="org5afcb5e"><span class="section-number-3">1.1</span> Fortran</h3>
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||||
<div class="outline-text-3" id="text-1-1">
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||||
<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
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@ -416,8 +416,8 @@ One needs to read from the TREXIO file:
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</div>
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</div>
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<div id="outline-container-org47bd8b9" class="outline-4">
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<h4 id="org47bd8b9"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-org723256c" class="outline-4">
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<h4 id="org723256c"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div class="outline-text-4" id="text-1-1-1">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> i, j, k, l, m</span>
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@ -432,8 +432,8 @@ One needs to read from the TREXIO file:
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</div>
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</div>
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<div id="outline-container-org96b3387" class="outline-4">
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<h4 id="org96b3387"><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>
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<div id="outline-container-orge82a820" class="outline-4">
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<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>
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<div class="outline-text-4" id="text-1-1-2">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
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@ -449,8 +449,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-org9757c39" class="outline-4">
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<h4 id="org9757c39"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-orgcc2e7ea" class="outline-4">
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<h4 id="orgcc2e7ea"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div class="outline-text-4" id="text-1-1-3">
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<div class="org-src-container">
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||||
<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
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@ -464,8 +464,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-org780c82e" class="outline-4">
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||||
<h4 id="org780c82e"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-orgaefa70b" class="outline-4">
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||||
<h4 id="orgaefa70b"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div class="outline-text-4" id="text-1-1-4">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
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@ -479,8 +479,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-org6f6e480" class="outline-4">
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||||
<h4 id="org6f6e480"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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||||
<div id="outline-container-org9c26cb4" class="outline-4">
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||||
<h4 id="org9c26cb4"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div class="outline-text-4" id="text-1-1-5">
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||||
<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
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@ -492,8 +492,8 @@ W(:,:,:,:) = 0.d0
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</div>
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</div>
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<div id="outline-container-org64134e4" class="outline-4">
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<h4 id="org64134e4"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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||||
<div id="outline-container-org086de1d" class="outline-4">
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||||
<h4 id="org086de1d"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
|
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<div class="outline-text-4" id="text-1-1-6">
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||||
<div class="org-src-container">
|
||||
<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
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@ -525,8 +525,8 @@ rc = trexio_read_rdm_1e(f, D)
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</div>
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</div>
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||||
<div id="outline-container-orgf6ba9ad" class="outline-4">
|
||||
<h4 id="orgf6ba9ad"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
|
||||
<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 class="outline-text-4" id="text-1-1-7">
|
||||
<p>
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||||
Reading is done with OpenMP. Each thread reads its own buffer, and
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||||
@ -542,8 +542,8 @@ to be protected in the critical section when modified.
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</p>
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</div>
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<div id="outline-container-org911e067" class="outline-5">
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||||
<h5 id="org911e067"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
|
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<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>
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<div class="outline-text-5" id="text-1-1-7-1">
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||||
<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
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@ -592,8 +592,8 @@ icount = BUFSIZE
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</div>
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</div>
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<div id="outline-container-orgb83135b" class="outline-5">
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<h5 id="orgb83135b"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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||||
<div id="outline-container-org7aa5076" class="outline-5">
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||||
<h5 id="org7aa5076"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div class="outline-text-5" id="text-1-1-7-2">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
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@ -637,8 +637,8 @@ icount = bufsize
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</div>
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</div>
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<div id="outline-container-orgcffff68" class="outline-4">
|
||||
<h4 id="orgcffff68"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
|
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<div id="outline-container-orgbd64619" class="outline-4">
|
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<h4 id="orgbd64619"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div class="outline-text-4" id="text-1-1-8">
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<p>
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When the orbitals are real, we can use
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@ -684,8 +684,8 @@ E = E + E_nn
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</div>
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</div>
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<div id="outline-container-orgdc0ec1b" class="outline-4">
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<h4 id="orgdc0ec1b"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-orgb65a78d" class="outline-4">
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||||
<h4 id="orgb65a78d"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div class="outline-text-4" id="text-1-1-9">
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||||
<div class="org-src-container">
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<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
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@ -699,12 +699,12 @@ E = E + E_nn
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</div>
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<div id="outline-container-org0d9fd26" class="outline-2">
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<h2 id="org0d9fd26"><span class="section-number-2">2</span> Reading determinants</h2>
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<div id="outline-container-orgc938429" class="outline-2">
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<h2 id="orgc938429"><span class="section-number-2">2</span> Reading determinants</h2>
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<div class="outline-text-2" id="text-2">
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||||
</div>
|
||||
<div id="outline-container-orgebde94d" class="outline-3">
|
||||
<h3 id="orgebde94d"><span class="section-number-3">2.1</span> Fortran</h3>
|
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<div id="outline-container-org09fbef9" class="outline-3">
|
||||
<h3 id="org09fbef9"><span class="section-number-3">2.1</span> Fortran</h3>
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||||
<div class="outline-text-3" id="text-2-1">
|
||||
<div class="org-src-container">
|
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<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
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@ -783,7 +783,7 @@ end
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||||
</div>
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||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-09-06 Tue 09:53</p>
|
||||
<p class="date">Created: 2022-09-06 Tue 15:30</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>
|
||||
<!-- 2022-09-06 Tue 09:53 -->
|
||||
<!-- 2022-09-06 Tue 15:30 -->
|
||||
<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 09:53</p>
|
||||
<p class="date">Created: 2022-09-06 Tue 15:30</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 @@
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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||||
<head>
|
||||
<!-- 2022-09-06 Tue 09:53 -->
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||||
<!-- 2022-09-06 Tue 15:30 -->
|
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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" />
|
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<title>HDF5 back end</title>
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@ -311,24 +311,24 @@ for the JavaScript code in this tag.
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<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orge07a788">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org53f7de8">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgb1290e3">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org470155d">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#orge991071">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org8140b69">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
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<li><a href="#org44b13c4">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
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<li><a href="#org690a0ed">8. Template for HDF5 has/read/write a dataset of strings</a></li>
|
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<li><a href="#orgf20c0c3">9. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#org64c9e2d">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org85d2099">11. Source code for the determinant part</a></li>
|
||||
<li><a href="#org41f3a38">12. Helper functions</a></li>
|
||||
<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>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge07a788" class="outline-2">
|
||||
<h2 id="orge07a788"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-orgdde78ca" class="outline-2">
|
||||
<h2 id="orgdde78ca"><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-org53f7de8" class="outline-2">
|
||||
<h2 id="org53f7de8"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-orgf5394e0" class="outline-2">
|
||||
<h2 id="orgf5394e0"><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-orgb1290e3" class="outline-2">
|
||||
<h2 id="orgb1290e3"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<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 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-org470155d" class="outline-2">
|
||||
<h2 id="org470155d"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
|
||||
<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 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-orge991071" class="outline-2">
|
||||
<h2 id="orge991071"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<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 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-org8140b69" class="outline-2">
|
||||
<h2 id="org8140b69"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<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 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-org44b13c4" class="outline-2">
|
||||
<h2 id="org44b13c4"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<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 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-org690a0ed" class="outline-2">
|
||||
<h2 id="org690a0ed"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<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 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-orgf20c0c3" class="outline-2">
|
||||
<h2 id="orgf20c0c3"><span class="section-number-2">9</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<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 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-org64c9e2d" class="outline-2">
|
||||
<h2 id="org64c9e2d"><span class="section-number-2">10</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<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 class="outline-text-2" id="text-10">
|
||||
<p>
|
||||
<b><b>Note:</b></b> in early versions of the HDF5 library (v < 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-org85d2099" class="outline-2">
|
||||
<h2 id="org85d2099"><span class="section-number-2">11</span> Source code for the determinant part</h2>
|
||||
<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 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-org41f3a38" class="outline-2">
|
||||
<h2 id="org41f3a38"><span class="section-number-2">12</span> Helper functions</h2>
|
||||
<div id="outline-container-orga5d0f02" class="outline-2">
|
||||
<h2 id="orga5d0f02"><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 09:53</p>
|
||||
<p class="date">Created: 2022-09-06 Tue 15:30</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>
|
||||
<!-- 2022-09-06 Tue 09:53 -->
|
||||
<!-- 2022-09-06 Tue 15:30 -->
|
||||
<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="#orgfe1a9b9">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org14eaad3">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org07f13fb">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org9b686fd">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org05d7d10">5. Template for text read a group</a></li>
|
||||
<li><a href="#orgdf07b7c">6. Template for text has a group</a></li>
|
||||
<li><a href="#org8c2ff41">7. Template for text flush a group</a></li>
|
||||
<li><a href="#orgb81a8b3">8. Template for text free memory</a></li>
|
||||
<li><a href="#org53234af">9. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org57d0eed">10. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgadb1e68">11. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgef58240">12. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org02766d8">13. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org2545cf4">14. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org178d54b">15. Source code for the determinant part</a></li>
|
||||
<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>
|
||||
</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-orgfe1a9b9" class="outline-2">
|
||||
<h2 id="orgfe1a9b9"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<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 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-org14eaad3" class="outline-2">
|
||||
<h2 id="org14eaad3"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<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 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-org07f13fb" class="outline-2">
|
||||
<h2 id="org07f13fb"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div id="outline-container-orgec1a52f" class="outline-2">
|
||||
<h2 id="orgec1a52f"><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-org9b686fd" class="outline-2">
|
||||
<h2 id="org9b686fd"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div id="outline-container-org8a3d118" class="outline-2">
|
||||
<h2 id="org8a3d118"><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-org05d7d10" class="outline-2">
|
||||
<h2 id="org05d7d10"><span class="section-number-2">5</span> Template for text read a group</h2>
|
||||
<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 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-orgdf07b7c" class="outline-2">
|
||||
<h2 id="orgdf07b7c"><span class="section-number-2">6</span> Template for text has a group</h2>
|
||||
<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 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-org8c2ff41" class="outline-2">
|
||||
<h2 id="org8c2ff41"><span class="section-number-2">7</span> Template for text flush a group</h2>
|
||||
<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 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-orgb81a8b3" class="outline-2">
|
||||
<h2 id="orgb81a8b3"><span class="section-number-2">8</span> Template for text free memory</h2>
|
||||
<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 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-org53234af" class="outline-2">
|
||||
<h2 id="org53234af"><span class="section-number-2">9</span> Template for has/read/write a numerical attribute</h2>
|
||||
<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 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-org57d0eed" class="outline-2">
|
||||
<h2 id="org57d0eed"><span class="section-number-2">10</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<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 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-orgadb1e68" class="outline-2">
|
||||
<h2 id="orgadb1e68"><span class="section-number-2">11</span> Template for has/read/write a dataset of strings</h2>
|
||||
<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 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-orgef58240" class="outline-2">
|
||||
<h2 id="orgef58240"><span class="section-number-2">12</span> Template for has/read/write a string attribute</h2>
|
||||
<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 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-org02766d8" class="outline-2">
|
||||
<h2 id="org02766d8"><span class="section-number-2">13</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<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 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-org2545cf4" class="outline-2">
|
||||
<h2 id="org2545cf4"><span class="section-number-2">14</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<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 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-org178d54b" class="outline-2">
|
||||
<h2 id="org178d54b"><span class="section-number-2">15</span> Source code for the determinant part</h2>
|
||||
<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 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 09:53</p>
|
||||
<p class="date">Created: 2022-09-06 Tue 15:30</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
228
trex.html
228
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>
|
||||
<!-- 2022-09-06 Tue 09:53 -->
|
||||
<!-- 2022-09-06 Tue 15:30 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TREX Configuration file</title>
|
||||
@ -333,37 +333,38 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orgbdb92da">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org95687b9">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org9ffdd3d">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org7f7f96e">4. Effective core potentials (ecp group)</a>
|
||||
<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>
|
||||
<ul>
|
||||
<li><a href="#orgc79c3ff">4.1. Example</a></li>
|
||||
<li><a href="#org25267d9">4.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org1990ed1">5. Basis set (basis group)</a>
|
||||
<li><a href="#org8e99cf4">5. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#orga44e766">5.1. Example</a></li>
|
||||
<li><a href="#org0b9bb46">5.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgbe9bef7">6. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#org7e8b087">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="#org8ee0f97">7. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#orgb1e9c01">7. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#org5976458">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org840853e">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<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>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org3456367">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org03d2fc7">9. Excited states (state group)</a></li>
|
||||
<li><a href="#org00d2197">10. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org5931a0a">11. Cell (cell group)</a></li>
|
||||
<li><a href="#org7b2f9b9">12. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#org4842a3c">13. Quantum Monte Carlo data (qmc group)</a></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>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -417,8 +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-orgbdb92da" class="outline-2">
|
||||
<h2 id="orgbdb92da"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-org04dca1e" class="outline-2">
|
||||
<h2 id="org04dca1e"><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
|
||||
@ -428,7 +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="orgf8be5cb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2011cf3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -509,15 +510,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org95687b9" class="outline-2">
|
||||
<h2 id="org95687b9"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div id="outline-container-orge3b007b" class="outline-2">
|
||||
<h2 id="orge3b007b"><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="org036f80c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgad1e184" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -563,15 +564,15 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9ffdd3d" class="outline-2">
|
||||
<h2 id="org9ffdd3d"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div id="outline-container-org97a6b47" class="outline-2">
|
||||
<h2 id="org97a6b47"><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="org3aabc62" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org0be5b3b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -638,8 +639,8 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7f7f96e" class="outline-2">
|
||||
<h2 id="org7f7f96e"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<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 class="outline-text-2" id="text-4">
|
||||
<p>
|
||||
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
|
||||
@ -672,7 +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="org491299d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd6b5deb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -774,8 +775,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc79c3ff" class="outline-3">
|
||||
<h3 id="orgc79c3ff"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div id="outline-container-org25267d9" class="outline-3">
|
||||
<h3 id="org25267d9"><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
|
||||
@ -838,8 +839,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1990ed1" class="outline-2">
|
||||
<h2 id="org1990ed1"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div id="outline-container-org8e99cf4" class="outline-2">
|
||||
<h2 id="org8e99cf4"><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
|
||||
@ -892,7 +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="org453a2bb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org7928f34" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -986,8 +987,8 @@ All the basis set parameters are stored in one-dimensional arrays:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga44e766" class="outline-3">
|
||||
<h3 id="orga44e766"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div id="outline-container-org0b9bb46" class="outline-3">
|
||||
<h3 id="org0b9bb46"><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
|
||||
@ -1065,8 +1066,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgbe9bef7" class="outline-2">
|
||||
<h2 id="orgbe9bef7"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div id="outline-container-org7e8b087" class="outline-2">
|
||||
<h2 id="org7e8b087"><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
|
||||
@ -1119,13 +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="#org1990ed1">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#org8e99cf4">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="orgd154b68" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgccec6a7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1177,8 +1178,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org132022d" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org132022d"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<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 class="outline-text-3" id="text-ao_one_e">
|
||||
<ul class="org-ul">
|
||||
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
|
||||
@ -1195,7 +1196,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org15ca9f1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgbdffc10" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1290,8 +1291,8 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdc75ad8" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="orgdc75ad8"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<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 class="outline-text-3" id="text-ao_two_e">
|
||||
<p>
|
||||
The two-electron integrals for a two-electron operator \(\hat{O}\) are
|
||||
@ -1312,7 +1313,7 @@ notation.
|
||||
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
|
||||
</ul>
|
||||
|
||||
<table id="org6aad9ea" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2b922a2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1352,10 +1353,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8ee0f97" class="outline-2">
|
||||
<h2 id="org8ee0f97"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div id="outline-container-orgb1e9c01" class="outline-2">
|
||||
<h2 id="orgb1e9c01"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="orgcd5456f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org8a6af06" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1442,8 +1443,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5976458" class="outline-3">
|
||||
<h3 id="org5976458"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<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 class="outline-text-3" id="text-7-1">
|
||||
<p>
|
||||
The operators as the same as those defined in the
|
||||
@ -1451,7 +1452,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org73d8a93" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2649e6d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1546,8 +1547,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org840853e" class="outline-3">
|
||||
<h3 id="org840853e"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<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 class="outline-text-3" id="text-7-2">
|
||||
<p>
|
||||
The operators as the same as those defined in the
|
||||
@ -1555,7 +1556,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orgc9c55dd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga79a2b1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1595,8 +1596,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3456367" class="outline-2">
|
||||
<h2 id="org3456367"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
|
||||
<div id="outline-container-orgac2ee95" class="outline-2">
|
||||
<h2 id="orgac2ee95"><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 \(\Psi\)
|
||||
@ -1638,7 +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="orge096866" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org8e1ddbb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1684,17 +1685,86 @@ An illustration on how to read determinants is presented in the <a href="./examp
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org03d2fc7" class="outline-2">
|
||||
<h2 id="org03d2fc7"><span class="section-number-2">9</span> Excited states (state group)</h2>
|
||||
<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 class="outline-text-2" id="text-9">
|
||||
<p>
|
||||
The configuration interaction (CI) wave function \(\Psi\) can be
|
||||
expanded in the basis of <a href="https://en.wikipedia.org/wiki/Configuration_state_function">configuration state functions</a> (CSFs)
|
||||
\(\Psi_I\) as follows
|
||||
</p>
|
||||
|
||||
<p>
|
||||
\[
|
||||
\Psi = \sum_I C_I \psi_I.
|
||||
\]
|
||||
</p>
|
||||
|
||||
<p>
|
||||
Each CSF is a linear combination of Slater determinants. Slater
|
||||
determinants are stored in the <code>determinant</code> section. In this group
|
||||
we store the CI coefficients in the basis of CSFs, and the
|
||||
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">
|
||||
|
||||
|
||||
<colgroup>
|
||||
<col class="org-left" />
|
||||
|
||||
<col class="org-left" />
|
||||
|
||||
<col class="org-left" />
|
||||
|
||||
<col class="org-left" />
|
||||
</colgroup>
|
||||
<thead>
|
||||
<tr>
|
||||
<th scope="col" class="org-left">Variable</th>
|
||||
<th scope="col" class="org-left">Type</th>
|
||||
<th scope="col" class="org-left">Dimensions</th>
|
||||
<th scope="col" class="org-left">Description</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left"><code>num</code></td>
|
||||
<td class="org-left"><code>dim readonly</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Number of CSFs</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>coefficient</code></td>
|
||||
<td class="org-left"><code>float special</code></td>
|
||||
<td class="org-left"><code>(state.num,csf.num)</code></td>
|
||||
<td class="org-left">Coefficients of the CSFs from the CI expansion</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>det_coefficient</code></td>
|
||||
<td class="org-left"><code>float sparse</code></td>
|
||||
<td class="org-left"><code>(determinant.num,csf.num)</code></td>
|
||||
<td class="org-left">Projection on the determinant basis</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</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 class="outline-text-2" id="text-10">
|
||||
<p>
|
||||
By default, the <code>determinant</code> group corresponds to the ground state.
|
||||
However, it should be also possible to store the coefficients that
|
||||
correspond to excited state wave functions for the same set of
|
||||
determinants. This is the goal of the present group
|
||||
</p>
|
||||
|
||||
<table id="org0579377" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org404a2b0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1733,9 +1803,9 @@ determinants. This is the goal of the present group
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org00d2197" class="outline-2">
|
||||
<h2 id="org00d2197"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<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 class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
The reduced density matrices are defined in the basis of molecular
|
||||
orbitals.
|
||||
@ -1787,7 +1857,7 @@ The total energy can be computed as:
|
||||
\]
|
||||
</p>
|
||||
|
||||
<table id="org34c5289" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgf1f1a6b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1868,10 +1938,10 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5931a0a" class="outline-2">
|
||||
<h2 id="org5931a0a"><span class="section-number-2">11</span> Cell (cell group)</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<table id="orgb72b404" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<div id="outline-container-org1e8829a" class="outline-2">
|
||||
<h2 id="org1e8829a"><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">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1917,10 +1987,10 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7b2f9b9" class="outline-2">
|
||||
<h2 id="org7b2f9b9"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<table id="orge842095" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<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 class="outline-text-2" id="text-13">
|
||||
<table id="org83b5a0e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1959,9 +2029,9 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4842a3c" class="outline-2">
|
||||
<h2 id="org4842a3c"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div class="outline-text-2" id="text-13">
|
||||
<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 class="outline-text-2" id="text-14">
|
||||
<p>
|
||||
In quantum Monte Carlo calculations, the wave function is evaluated
|
||||
at points of the 3N-dimensional space. Some algorithms require multiple
|
||||
@ -1974,7 +2044,7 @@ By convention, the electron coordinates contain first all the electrons
|
||||
of $↑$-spin and then all the $↓$-spin.
|
||||
</p>
|
||||
|
||||
<table id="org7969b9d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org6c9d57c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2029,7 +2099,7 @@ of $↑$-spin and then all the $↓$-spin.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-09-06 Tue 09:53</p>
|
||||
<p class="date">Created: 2022-09-06 Tue 15:30</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