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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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<!-- 2023-01-13 Fri 14:48 -->
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<!-- 2023-01-13 Fri 14:55 -->
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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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||||
@ -360,7 +360,7 @@ 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>
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||||
<p class="date">Created: 2023-01-13 Fri 14:48</p>
|
||||
<p class="date">Created: 2023-01-13 Fri 14:55</p>
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||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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</div>
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||||
</body>
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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">
|
||||
<head>
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||||
<!-- 2023-01-13 Fri 14:48 -->
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||||
<!-- 2023-01-13 Fri 14:55 -->
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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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@ -346,31 +346,31 @@ 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="#org905599a">1. Accessing sparse quantities (integrals)</a>
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<li><a href="#orgdc4e451">1. Accessing sparse quantities (integrals)</a>
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<ul>
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<li><a href="#orgc983130">1.1. Fortran</a>
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<li><a href="#orga054953">1.1. Fortran</a>
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||||
<ul>
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||||
<li><a href="#org5daa19d">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org851a6f0">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="#orgbb29f51">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org47de87a">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org2e21278">1.1.5. Allocate memory</a></li>
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<li><a href="#orgd0bdb37">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org40392a8">1.1.7. Read two-electron quantities</a>
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<li><a href="#org4a7841f">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org115e663">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="#orgde21c70">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org3a9899b">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org2e8e50d">1.1.5. Allocate memory</a></li>
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<li><a href="#org736d4d5">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#orga55c232">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#org71b0ee8">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org1de7c88">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#org010acf2">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org1342883">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="#orgf1d68d5">1.1.8. Compute the energy</a></li>
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<li><a href="#orgc9ab09c">1.1.9. Terminate</a></li>
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<li><a href="#org440a329">1.1.8. Compute the energy</a></li>
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<li><a href="#orgd0f973b">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="#org5b45ee2">2. Reading determinants</a>
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<li><a href="#orgf1a256d">2. Reading determinants</a>
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<ul>
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<li><a href="#org7d86640">2.1. Fortran</a></li>
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<li><a href="#org3a0836e">2.1. Fortran</a></li>
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</ul>
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</li>
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</ul>
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@ -378,12 +378,12 @@ for the JavaScript code in this tag.
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</div>
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<div id="outline-container-org905599a" class="outline-2">
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<h2 id="org905599a"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
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<div id="outline-container-orgdc4e451" class="outline-2">
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||||
<h2 id="orgdc4e451"><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-orgc983130" class="outline-3">
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<h3 id="orgc983130"><span class="section-number-3">1.1</span> Fortran</h3>
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<div id="outline-container-orga054953" class="outline-3">
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<h3 id="orga054953"><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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@ -429,8 +429,8 @@ 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-org5daa19d" class="outline-4">
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<h4 id="org5daa19d"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-org4a7841f" class="outline-4">
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<h4 id="org4a7841f"><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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@ -445,8 +445,8 @@ 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-org851a6f0" class="outline-4">
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<h4 id="org851a6f0"><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-org115e663" class="outline-4">
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<h4 id="org115e663"><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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@ -462,8 +462,8 @@ 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-orgbb29f51" class="outline-4">
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<h4 id="orgbb29f51"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-orgde21c70" class="outline-4">
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<h4 id="orgde21c70"><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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@ -477,8 +477,8 @@ 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-org47de87a" class="outline-4">
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<h4 id="org47de87a"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-org3a9899b" class="outline-4">
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<h4 id="org3a9899b"><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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@ -492,8 +492,8 @@ 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-org2e21278" class="outline-4">
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<h4 id="org2e21278"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div id="outline-container-org2e8e50d" class="outline-4">
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<h4 id="org2e8e50d"><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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@ -505,8 +505,8 @@ W(:,:,:,:) = 0.d0
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</div>
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</div>
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<div id="outline-container-orgd0bdb37" class="outline-4">
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<h4 id="orgd0bdb37"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div id="outline-container-org736d4d5" class="outline-4">
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<h4 id="org736d4d5"><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">
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<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
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@ -538,8 +538,8 @@ 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-org40392a8" class="outline-4">
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||||
<h4 id="org40392a8"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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<div id="outline-container-orga55c232" class="outline-4">
|
||||
<h4 id="orga55c232"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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<div class="outline-text-4" id="text-1-1-7">
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<p>
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Reading is done with OpenMP. Each thread reads its own buffer, and
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@ -555,8 +555,8 @@ 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-org71b0ee8" class="outline-5">
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<h5 id="org71b0ee8"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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<div id="outline-container-org010acf2" class="outline-5">
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<h5 id="org010acf2"><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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@ -605,8 +605,8 @@ icount = BUFSIZE
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</div>
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</div>
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<div id="outline-container-org1de7c88" class="outline-5">
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<h5 id="org1de7c88"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-org1342883" class="outline-5">
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<h5 id="org1342883"><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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@ -650,8 +650,8 @@ icount = bufsize
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</div>
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</div>
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<div id="outline-container-orgf1d68d5" class="outline-4">
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<h4 id="orgf1d68d5"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div id="outline-container-org440a329" class="outline-4">
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<h4 id="org440a329"><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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@ -697,8 +697,8 @@ E = E + E_nn
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</div>
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</div>
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<div id="outline-container-orgc9ab09c" class="outline-4">
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<h4 id="orgc9ab09c"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-orgd0f973b" class="outline-4">
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<h4 id="orgd0f973b"><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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@ -712,12 +712,12 @@ E = E + E_nn
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</div>
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<div id="outline-container-org5b45ee2" class="outline-2">
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<h2 id="org5b45ee2"><span class="section-number-2">2</span> Reading determinants</h2>
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<div id="outline-container-orgf1a256d" class="outline-2">
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<h2 id="orgf1a256d"><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>
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<div id="outline-container-org7d86640" class="outline-3">
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<h3 id="org7d86640"><span class="section-number-3">2.1</span> Fortran</h3>
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<div id="outline-container-org3a0836e" class="outline-3">
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<h3 id="org3a0836e"><span class="section-number-3">2.1</span> Fortran</h3>
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<div class="outline-text-3" id="text-2-1">
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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;">test</span>
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@ -796,7 +796,7 @@ end
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</div>
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<div id="postamble" class="status">
|
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<p class="author">Author: TREX-CoE</p>
|
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<p class="date">Created: 2023-01-13 Fri 14:48</p>
|
||||
<p class="date">Created: 2023-01-13 Fri 14:55</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
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</body>
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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">
|
||||
<head>
|
||||
<!-- 2023-01-13 Fri 14:48 -->
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<!-- 2023-01-13 Fri 14:55 -->
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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>
|
||||
@ -360,7 +360,7 @@ and bug reports should be submitted at
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2023-01-13 Fri 14:48</p>
|
||||
<p class="date">Created: 2023-01-13 Fri 14:55</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
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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>
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<!-- 2023-01-13 Fri 14:48 -->
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||||
<!-- 2023-01-13 Fri 14:55 -->
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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>HDF5 back end</title>
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@ -324,25 +324,25 @@ 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="#org18b6a82">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org5056794">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgd63cefb">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org14fb858">4. Template for HDF5 has a group</a></li>
|
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<li><a href="#org18b684f">5. Template for HDF5 has/read/write a numerical attribute</a></li>
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<li><a href="#org005e8f5">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
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<li><a href="#org7d8e066">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
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<li><a href="#org733f5ee">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
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<li><a href="#org2193b4b">9. Template for HDF5 has/read/write a dataset of strings</a></li>
|
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<li><a href="#org4f72873">10. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgc773567">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
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<li><a href="#org66e5e7e">12. Source code for the determinant part</a></li>
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<li><a href="#org8223ef3">13. Helper functions</a></li>
|
||||
<li><a href="#org42285af">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org0f65c98">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orga5b76ed">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org95dcebd">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#org2ec7d89">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org0911f6f">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orge65d6f7">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#org39f8185">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
|
||||
<li><a href="#org36af8af">9. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org38e9412">10. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#org96793d1">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org4a6a8dc">12. Source code for the determinant part</a></li>
|
||||
<li><a href="#orgb5512b8">13. Helper functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org18b6a82" class="outline-2">
|
||||
<h2 id="org18b6a82"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-org42285af" class="outline-2">
|
||||
<h2 id="org42285af"><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>
|
||||
@ -354,8 +354,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5056794" class="outline-2">
|
||||
<h2 id="org5056794"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-org0f65c98" class="outline-2">
|
||||
<h2 id="org0f65c98"><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
|
||||
@ -375,8 +375,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd63cefb" class="outline-2">
|
||||
<h2 id="orgd63cefb"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-orga5b76ed" class="outline-2">
|
||||
<h2 id="orga5b76ed"><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>
|
||||
@ -496,8 +496,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org14fb858" class="outline-2">
|
||||
<h2 id="org14fb858"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
|
||||
<div id="outline-container-org95dcebd" class="outline-2">
|
||||
<h2 id="org95dcebd"><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>
|
||||
@ -527,8 +527,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org18b684f" class="outline-2">
|
||||
<h2 id="org18b684f"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-org2ec7d89" class="outline-2">
|
||||
<h2 id="org2ec7d89"><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>
|
||||
@ -632,8 +632,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org005e8f5" class="outline-2">
|
||||
<h2 id="org005e8f5"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org0911f6f" class="outline-2">
|
||||
<h2 id="org0911f6f"><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>
|
||||
@ -767,8 +767,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7d8e066" class="outline-2">
|
||||
<h2 id="org7d8e066"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-orge65d6f7" class="outline-2">
|
||||
<h2 id="orge65d6f7"><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
|
||||
@ -971,8 +971,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org733f5ee" class="outline-2">
|
||||
<h2 id="org733f5ee"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
|
||||
<div id="outline-container-org39f8185" class="outline-2">
|
||||
<h2 id="org39f8185"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
|
||||
<div class="outline-text-2" id="text-8">
|
||||
<p>
|
||||
Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
@ -1107,8 +1107,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2193b4b" class="outline-2">
|
||||
<h2 id="org2193b4b"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org36af8af" class="outline-2">
|
||||
<h2 id="org36af8af"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</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>
|
||||
@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4f72873" class="outline-2">
|
||||
<h2 id="org4f72873"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org38e9412" class="outline-2">
|
||||
<h2 id="org38e9412"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1434,8 +1434,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgc773567" class="outline-2">
|
||||
<h2 id="orgc773567"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-org96793d1" class="outline-2">
|
||||
<h2 id="org96793d1"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
<b><b>Note:</b></b> in early versions of the HDF5 library (v < 1.10) unlinking an object was not working as expected
|
||||
@ -1475,8 +1475,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org66e5e7e" class="outline-2">
|
||||
<h2 id="org66e5e7e"><span class="section-number-2">12</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org4a6a8dc" class="outline-2">
|
||||
<h2 id="org4a6a8dc"><span class="section-number-2">12</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<p>
|
||||
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
|
||||
@ -1579,8 +1579,8 @@ Size specifies the number of data items (e.g. determinants) to process.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8223ef3" class="outline-2">
|
||||
<h2 id="org8223ef3"><span class="section-number-2">13</span> Helper functions</h2>
|
||||
<div id="outline-container-orgb5512b8" class="outline-2">
|
||||
<h2 id="orgb5512b8"><span class="section-number-2">13</span> Helper functions</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>
|
||||
@ -1843,7 +1843,7 @@ 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: 2023-01-13 Fri 14:48</p>
|
||||
<p class="date">Created: 2023-01-13 Fri 14:55</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>
|
||||
<!-- 2023-01-13 Fri 14:48 -->
|
||||
<!-- 2023-01-13 Fri 14:55 -->
|
||||
<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>
|
||||
@ -324,23 +324,23 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orgd5556fc">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org1dc4872">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#orge4fb8ef">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org65da595">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org7243234">5. Flush function (templated part)</a></li>
|
||||
<li><a href="#orgd60b2bc">6. Template for text read a group</a></li>
|
||||
<li><a href="#orged673ba">7. Template for text has a group</a></li>
|
||||
<li><a href="#orgb8f0824">8. Template for text flush a group</a></li>
|
||||
<li><a href="#orge9a6433">9. Template for text free memory</a></li>
|
||||
<li><a href="#orga4c329c">10. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org178cfee">11. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org575d148">12. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org85233cc">13. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orge6d4086">14. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org417bceb">15. Template for has/read/write a buffered vector</a></li>
|
||||
<li><a href="#org1e07bb5">16. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org2fc3520">17. Source code for the determinant part</a></li>
|
||||
<li><a href="#orgf67b369">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#orge24290c">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#orgadd15a8">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org49ff749">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orgd9ebc3b">5. Flush function (templated part)</a></li>
|
||||
<li><a href="#org300372a">6. Template for text read a group</a></li>
|
||||
<li><a href="#org679b845">7. Template for text has a group</a></li>
|
||||
<li><a href="#org3b9eb39">8. Template for text flush a group</a></li>
|
||||
<li><a href="#org20ba7d6">9. Template for text free memory</a></li>
|
||||
<li><a href="#orgaa63e03">10. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org6d7a7cf">11. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgd07ed1f">12. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org212c941">13. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgf3e8054">14. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#orga23edd5">15. Template for has/read/write a buffered vector</a></li>
|
||||
<li><a href="#orgac6fd0d">16. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org5b84477">17. Source code for the determinant part</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -362,8 +362,8 @@ directory.
|
||||
The file is written when closed, or when the flush function is called.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-orgd5556fc" class="outline-2">
|
||||
<h2 id="orgd5556fc"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div id="outline-container-orgf67b369" class="outline-2">
|
||||
<h2 id="orgf67b369"><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 {
|
||||
@ -382,8 +382,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1dc4872" class="outline-2">
|
||||
<h2 id="org1dc4872"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div id="outline-container-orge24290c" class="outline-2">
|
||||
<h2 id="orge24290c"><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
|
||||
@ -403,8 +403,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge4fb8ef" class="outline-2">
|
||||
<h2 id="orge4fb8ef"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div id="outline-container-orgadd15a8" class="outline-2">
|
||||
<h2 id="orgadd15a8"><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>
|
||||
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org65da595" class="outline-2">
|
||||
<h2 id="org65da595"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div id="outline-container-org49ff749" class="outline-2">
|
||||
<h2 id="org49ff749"><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>
|
||||
@ -594,8 +594,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7243234" class="outline-2">
|
||||
<h2 id="org7243234"><span class="section-number-2">5</span> Flush function (templated part)</h2>
|
||||
<div id="outline-container-orgd9ebc3b" class="outline-2">
|
||||
<h2 id="orgd9ebc3b"><span class="section-number-2">5</span> Flush function (templated part)</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>
|
||||
@ -618,8 +618,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd60b2bc" class="outline-2">
|
||||
<h2 id="orgd60b2bc"><span class="section-number-2">6</span> Template for text read a group</h2>
|
||||
<div id="outline-container-org300372a" class="outline-2">
|
||||
<h2 id="org300372a"><span class="section-number-2">6</span> Template for text read a group</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c">$group$_t*
|
||||
@ -845,8 +845,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orged673ba" class="outline-2">
|
||||
<h2 id="orged673ba"><span class="section-number-2">7</span> Template for text has a group</h2>
|
||||
<div id="outline-container-org679b845" class="outline-2">
|
||||
<h2 id="org679b845"><span class="section-number-2">7</span> Template for text has 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>
|
||||
@ -886,8 +886,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb8f0824" class="outline-2">
|
||||
<h2 id="orgb8f0824"><span class="section-number-2">8</span> Template for text flush a group</h2>
|
||||
<div id="outline-container-org3b9eb39" class="outline-2">
|
||||
<h2 id="org3b9eb39"><span class="section-number-2">8</span> Template for text flush a group</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>
|
||||
@ -951,8 +951,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge9a6433" class="outline-2">
|
||||
<h2 id="orge9a6433"><span class="section-number-2">9</span> Template for text free memory</h2>
|
||||
<div id="outline-container-org20ba7d6" class="outline-2">
|
||||
<h2 id="org20ba7d6"><span class="section-number-2">9</span> Template for text free memory</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<p>
|
||||
Memory is allocated when reading. The following function frees memory.
|
||||
@ -1021,8 +1021,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga4c329c" class="outline-2">
|
||||
<h2 id="orga4c329c"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-orgaa63e03" class="outline-2">
|
||||
<h2 id="orgaa63e03"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1085,8 +1085,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org178cfee" class="outline-2">
|
||||
<h2 id="org178cfee"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org6d7a7cf" class="outline-2">
|
||||
<h2 id="org6d7a7cf"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1182,8 +1182,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org575d148" class="outline-2">
|
||||
<h2 id="org575d148"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-orgd07ed1f" class="outline-2">
|
||||
<h2 id="orgd07ed1f"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1284,8 +1284,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org85233cc" class="outline-2">
|
||||
<h2 id="org85233cc"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org212c941" class="outline-2">
|
||||
<h2 id="org212c941"><span class="section-number-2">13</span> Template for has/read/write a string attribute</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>
|
||||
@ -1359,8 +1359,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orge6d4086" class="outline-2">
|
||||
<h2 id="orge6d4086"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div id="outline-container-orgf3e8054" class="outline-2">
|
||||
<h2 id="orgf3e8054"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div class="outline-text-2" id="text-14">
|
||||
<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
|
||||
@ -1650,8 +1650,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org417bceb" class="outline-2">
|
||||
<h2 id="org417bceb"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
|
||||
<div id="outline-container-orga23edd5" class="outline-2">
|
||||
<h2 id="orga23edd5"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</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 buffered I/O has to be decoupled
|
||||
@ -1881,8 +1881,8 @@ Size specifies the number of vector elements to be written.
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org1e07bb5" class="outline-2">
|
||||
<h2 id="org1e07bb5"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-orgac6fd0d" class="outline-2">
|
||||
<h2 id="orgac6fd0d"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-16">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1910,8 +1910,8 @@ Size specifies the number of vector elements to be written.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2fc3520" class="outline-2">
|
||||
<h2 id="org2fc3520"><span class="section-number-2">17</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org5b84477" class="outline-2">
|
||||
<h2 id="org5b84477"><span class="section-number-2">17</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-17">
|
||||
<p>
|
||||
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
|
||||
@ -2103,7 +2103,7 @@ 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: 2023-01-13 Fri 14:48</p>
|
||||
<p class="date">Created: 2023-01-13 Fri 14:55</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
244
trex.html
244
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>
|
||||
<!-- 2023-01-13 Fri 14:48 -->
|
||||
<!-- 2023-01-13 Fri 14:55 -->
|
||||
<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>
|
||||
@ -346,70 +346,70 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org400f57e">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org5d08e0a">2. System</a>
|
||||
<li><a href="#orgcc8c74f">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#orged65cbd">2. System</a>
|
||||
<ul>
|
||||
<li><a href="#orgca10043">2.1. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#orge26b227">2.2. Cell (cell group)</a></li>
|
||||
<li><a href="#org116ba34">2.3. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#org78b61e6">2.4. Electron (electron group)</a></li>
|
||||
<li><a href="#orgc4c2c51">2.5. Ground or excited states (state group)</a></li>
|
||||
<li><a href="#org6fe6199">2.1. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org9839d72">2.2. Cell (cell group)</a></li>
|
||||
<li><a href="#org7f084ed">2.3. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#org7686479">2.4. Electron (electron group)</a></li>
|
||||
<li><a href="#orgcb99efa">2.5. Ground or excited states (state group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org9d794c9">3. Basis functions</a>
|
||||
<li><a href="#org8636b4d">3. Basis functions</a>
|
||||
<ul>
|
||||
<li><a href="#org37eb01a">3.1. Basis set (basis group)</a>
|
||||
<li><a href="#orga201e4a">3.1. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#orge9960b3">3.1.1. Gaussian and Slater-type orbitals</a></li>
|
||||
<li><a href="#org3e6480a">3.1.2. Plane waves</a></li>
|
||||
<li><a href="#org2cb6d55">3.1.3. Data definitions</a></li>
|
||||
<li><a href="#orgbf0fe23">3.1.4. Example</a></li>
|
||||
<li><a href="#org4f59dfe">3.1.1. Gaussian and Slater-type orbitals</a></li>
|
||||
<li><a href="#orgfdb7ce7">3.1.2. Plane waves</a></li>
|
||||
<li><a href="#org4a17b48">3.1.3. Data definitions</a></li>
|
||||
<li><a href="#org0d4475d">3.1.4. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgf9b3d6f">3.2. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#org6dbc63f">3.2. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#org6d034eb">3.2.1. Example</a></li>
|
||||
<li><a href="#org2c97923">3.2.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org9353080">3.3. Numerical integration grid (grid group)</a></li>
|
||||
<li><a href="#org4845372">3.3. Numerical integration grid (grid group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgb859c96">4. Orbitals</a>
|
||||
<li><a href="#orge2c6515">4. Orbitals</a>
|
||||
<ul>
|
||||
<li><a href="#org4255c4d">4.1. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#org7f7e206">4.1. Atomic orbitals (ao group)</a>
|
||||
<ul>
|
||||
<li><a href="#ao_one_e">4.1.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
|
||||
<li><a href="#ao_two_e">4.1.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org974e7a7">4.2. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org1600974">4.2. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#org8e8c832">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orge9d01be">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#org1ffde89">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org0487b24">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org418b92b">5. Multi-determinant information</a>
|
||||
<li><a href="#orgfa40d56">5. Multi-determinant information</a>
|
||||
<ul>
|
||||
<li><a href="#org01d223e">5.1. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org0193754">5.2. Configuration state functions (csf group)</a></li>
|
||||
<li><a href="#org416b269">5.3. Amplitudes (amplitude group)</a></li>
|
||||
<li><a href="#org87fe807">5.4. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org61d659d">5.1. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org28bd707">5.2. Configuration state functions (csf group)</a></li>
|
||||
<li><a href="#orgb24ec58">5.3. Amplitudes (amplitude group)</a></li>
|
||||
<li><a href="#orgf20085f">5.4. Reduced density matrices (rdm group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgdab52dd">6. Correlation factors</a>
|
||||
<li><a href="#orgca89c37">6. Correlation factors</a>
|
||||
<ul>
|
||||
<li><a href="#org2e8031e">6.1. Jastrow factor (jastrow group)</a>
|
||||
<li><a href="#org099f627">6.1. Jastrow factor (jastrow group)</a>
|
||||
<ul>
|
||||
<li><a href="#org9e0002e">6.1.1. CHAMP</a></li>
|
||||
<li><a href="#org1f5142f">6.1.2. Mu</a></li>
|
||||
<li><a href="#org9af8bbb">6.1.3. Table of values</a></li>
|
||||
<li><a href="#org919ef0a">6.1.1. CHAMP</a></li>
|
||||
<li><a href="#orgea8174d">6.1.2. Mu</a></li>
|
||||
<li><a href="#orgf11581f">6.1.3. Table of values</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgabc6f85">7. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
<li><a href="#org06d176e">7. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -477,8 +477,8 @@ in the variable, and the imaginary part will be stored in the variable
|
||||
with the same name suffixed by <code>_im</code>.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-org400f57e" class="outline-2">
|
||||
<h2 id="org400f57e"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-orgcc8c74f" class="outline-2">
|
||||
<h2 id="orgcc8c74f"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<p>
|
||||
As we expect TREXIO files to be archived in open-data repositories,
|
||||
@ -488,7 +488,7 @@ have participated to the creation of the file, a list of authors of
|
||||
the file, and a textual description.
|
||||
</p>
|
||||
|
||||
<table id="orgf45b147" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgdc7ee66" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -571,19 +571,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5d08e0a" class="outline-2">
|
||||
<h2 id="org5d08e0a"><span class="section-number-2">2</span> System</h2>
|
||||
<div id="outline-container-orged65cbd" class="outline-2">
|
||||
<h2 id="orged65cbd"><span class="section-number-2">2</span> System</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
</div>
|
||||
<div id="outline-container-orgca10043" class="outline-3">
|
||||
<h3 id="orgca10043"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
|
||||
<div id="outline-container-org6fe6199" class="outline-3">
|
||||
<h3 id="org6fe6199"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
|
||||
<div class="outline-text-3" id="text-2-1">
|
||||
<p>
|
||||
The nuclei are considered as fixed point charges. Coordinates are
|
||||
given in Cartesian \((x,y,z)\) format.
|
||||
</p>
|
||||
|
||||
<table id="org0914be0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org4ba8531" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -650,15 +650,15 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge26b227" class="outline-3">
|
||||
<h3 id="orge26b227"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
|
||||
<div id="outline-container-org9839d72" class="outline-3">
|
||||
<h3 id="org9839d72"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
|
||||
<div class="outline-text-3" id="text-2-2">
|
||||
<p>
|
||||
3 Lattice vectors to define a box containing the system, for example
|
||||
used in periodic calculations.
|
||||
</p>
|
||||
|
||||
<table id="orgfe5b0d6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org72e4a48" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -732,15 +732,15 @@ used in periodic calculations.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org116ba34" class="outline-3">
|
||||
<h3 id="org116ba34"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
|
||||
<div id="outline-container-org7f084ed" class="outline-3">
|
||||
<h3 id="org7f084ed"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
|
||||
<div class="outline-text-3" id="text-2-3">
|
||||
<p>
|
||||
A single $k$-point per TREXIO file can be stored. The $k$-point is
|
||||
defined in this group.
|
||||
</p>
|
||||
|
||||
<table id="orgf2bc8ec" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org33742b4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -779,15 +779,15 @@ defined in this group.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org78b61e6" class="outline-3">
|
||||
<h3 id="org78b61e6"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
|
||||
<div id="outline-container-org7686479" class="outline-3">
|
||||
<h3 id="org7686479"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
|
||||
<div class="outline-text-3" id="text-2-4">
|
||||
<p>
|
||||
We consider wave functions expressed in the spin-free formalism, where
|
||||
the number of ↑ and ↓ electrons is fixed.
|
||||
</p>
|
||||
|
||||
<table id="org8d5f3c5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org75af6cf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -833,8 +833,8 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc4c2c51" class="outline-3">
|
||||
<h3 id="orgc4c2c51"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
|
||||
<div id="outline-container-orgcb99efa" class="outline-3">
|
||||
<h3 id="orgcb99efa"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
|
||||
<div class="outline-text-3" id="text-2-5">
|
||||
<p>
|
||||
This group contains information about excited states. Since only a
|
||||
@ -851,7 +851,7 @@ integrals, etc.
|
||||
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
|
||||
</p>
|
||||
|
||||
<table id="orgbc69651" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1da8a6b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -912,16 +912,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9d794c9" class="outline-2">
|
||||
<h2 id="org9d794c9"><span class="section-number-2">3</span> Basis functions</h2>
|
||||
<div id="outline-container-org8636b4d" class="outline-2">
|
||||
<h2 id="org8636b4d"><span class="section-number-2">3</span> Basis functions</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
</div>
|
||||
<div id="outline-container-org37eb01a" class="outline-3">
|
||||
<h3 id="org37eb01a"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
|
||||
<div id="outline-container-orga201e4a" class="outline-3">
|
||||
<h3 id="orga201e4a"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
|
||||
<div class="outline-text-3" id="text-3-1">
|
||||
</div>
|
||||
<div id="outline-container-orge9960b3" class="outline-4">
|
||||
<h4 id="orge9960b3"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
|
||||
<div id="outline-container-org4f59dfe" class="outline-4">
|
||||
<h4 id="org4f59dfe"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
|
||||
<div class="outline-text-4" id="text-3-1-1">
|
||||
<p>
|
||||
We consider here basis functions centered on nuclei. Hence, we enable
|
||||
@ -975,8 +975,8 @@ All the basis set parameters are stored in one-dimensional arrays.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3e6480a" class="outline-4">
|
||||
<h4 id="org3e6480a"><span class="section-number-4">3.1.2</span> Plane waves</h4>
|
||||
<div id="outline-container-orgfdb7ce7" class="outline-4">
|
||||
<h4 id="orgfdb7ce7"><span class="section-number-4">3.1.2</span> Plane waves</h4>
|
||||
<div class="outline-text-4" id="text-3-1-2">
|
||||
<p>
|
||||
A plane wave is defined as
|
||||
@ -997,10 +997,10 @@ plane waves.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2cb6d55" class="outline-4">
|
||||
<h4 id="org2cb6d55"><span class="section-number-4">3.1.3</span> Data definitions</h4>
|
||||
<div id="outline-container-org4a17b48" class="outline-4">
|
||||
<h4 id="org4a17b48"><span class="section-number-4">3.1.3</span> Data definitions</h4>
|
||||
<div class="outline-text-4" id="text-3-1-3">
|
||||
<table id="org63abc44" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd7290d4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1109,8 +1109,8 @@ plane waves.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgbf0fe23" class="outline-4">
|
||||
<h4 id="orgbf0fe23"><span class="section-number-4">3.1.4</span> Example</h4>
|
||||
<div id="outline-container-org0d4475d" class="outline-4">
|
||||
<h4 id="org0d4475d"><span class="section-number-4">3.1.4</span> Example</h4>
|
||||
<div class="outline-text-4" id="text-3-1-4">
|
||||
<p>
|
||||
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
|
||||
@ -1188,8 +1188,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf9b3d6f" class="outline-3">
|
||||
<h3 id="orgf9b3d6f"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
|
||||
<div id="outline-container-org6dbc63f" class="outline-3">
|
||||
<h3 id="org6dbc63f"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
|
||||
<div class="outline-text-3" id="text-3-2">
|
||||
<p>
|
||||
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
|
||||
@ -1221,7 +1221,7 @@ All 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="org16b164d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd2f9017" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1325,8 +1325,8 @@ If you encounter the aforementioned issue, please report it to our
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6d034eb" class="outline-4">
|
||||
<h4 id="org6d034eb"><span class="section-number-4">3.2.1</span> Example</h4>
|
||||
<div id="outline-container-org2c97923" class="outline-4">
|
||||
<h4 id="org2c97923"><span class="section-number-4">3.2.1</span> Example</h4>
|
||||
<div class="outline-text-4" id="text-3-2-1">
|
||||
<p>
|
||||
For example, consider H<sub>2</sub> molecule with the following
|
||||
@ -1389,8 +1389,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9353080" class="outline-3">
|
||||
<h3 id="org9353080"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
|
||||
<div id="outline-container-org4845372" class="outline-3">
|
||||
<h3 id="org4845372"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
|
||||
<div class="outline-text-3" id="text-3-3">
|
||||
<p>
|
||||
In some applications, such as DFT calculations, integrals have to
|
||||
@ -1405,7 +1405,7 @@ The structure of this group is adapted for the <a href="https://github.com/dftli
|
||||
Feel free to submit a PR if you find missing options/functionalities.
|
||||
</p>
|
||||
|
||||
<table id="org8df6818" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orge395a50" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1522,12 +1522,12 @@ Feel free to submit a PR if you find missing options/functionalities.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb859c96" class="outline-2">
|
||||
<h2 id="orgb859c96"><span class="section-number-2">4</span> Orbitals</h2>
|
||||
<div id="outline-container-orge2c6515" class="outline-2">
|
||||
<h2 id="orge2c6515"><span class="section-number-2">4</span> Orbitals</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
</div>
|
||||
<div id="outline-container-org4255c4d" class="outline-3">
|
||||
<h3 id="org4255c4d"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
|
||||
<div id="outline-container-org7f7e206" class="outline-3">
|
||||
<h3 id="org7f7e206"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
|
||||
<div class="outline-text-3" id="text-4-1">
|
||||
<p>
|
||||
Going from the atomic basis set to AOs implies a systematic
|
||||
@ -1580,13 +1580,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#org37eb01a">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#orga201e4a">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="orgf81416b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgb3870f7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1638,7 +1638,7 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6d99b2f" class="outline-4">
|
||||
<div id="outline-container-orgc975f3d" class="outline-4">
|
||||
<h4 id="ao_one_e"><span class="section-number-4">4.1.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h4>
|
||||
<div class="outline-text-4" id="text-ao_one_e">
|
||||
<ul class="org-ul">
|
||||
@ -1656,7 +1656,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orgf853313" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2756e2a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1751,7 +1751,7 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org32ad587" class="outline-4">
|
||||
<div id="outline-container-org0acd811" class="outline-4">
|
||||
<h4 id="ao_two_e"><span class="section-number-4">4.1.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h4>
|
||||
<div class="outline-text-4" id="text-ao_two_e">
|
||||
<p>
|
||||
@ -1783,7 +1783,7 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
\]
|
||||
</p>
|
||||
|
||||
<table id="orgb29e049" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org96a8e69" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1851,10 +1851,10 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org974e7a7" class="outline-3">
|
||||
<h3 id="org974e7a7"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
|
||||
<div id="outline-container-org1600974" class="outline-3">
|
||||
<h3 id="org1600974"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
|
||||
<div class="outline-text-3" id="text-4-2">
|
||||
<table id="org03d0101" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgff61c37" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1941,8 +1941,8 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8e8c832" class="outline-4">
|
||||
<h4 id="org8e8c832"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
|
||||
<div id="outline-container-org1ffde89" class="outline-4">
|
||||
<h4 id="org1ffde89"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
|
||||
<div class="outline-text-4" id="text-4-2-1">
|
||||
<p>
|
||||
The operators as the same as those defined in the
|
||||
@ -1950,7 +1950,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org7ca932c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org69b8290" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2045,8 +2045,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge9d01be" class="outline-4">
|
||||
<h4 id="orge9d01be"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
|
||||
<div id="outline-container-org0487b24" class="outline-4">
|
||||
<h4 id="org0487b24"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
|
||||
<div class="outline-text-4" id="text-4-2-2">
|
||||
<p>
|
||||
The operators are the same as those defined in the
|
||||
@ -2054,7 +2054,7 @@ The operators are the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org60eab8d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org69db9e4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2123,12 +2123,12 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org418b92b" class="outline-2">
|
||||
<h2 id="org418b92b"><span class="section-number-2">5</span> Multi-determinant information</h2>
|
||||
<div id="outline-container-orgfa40d56" class="outline-2">
|
||||
<h2 id="orgfa40d56"><span class="section-number-2">5</span> Multi-determinant information</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
</div>
|
||||
<div id="outline-container-org01d223e" class="outline-3">
|
||||
<h3 id="org01d223e"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
|
||||
<div id="outline-container-org61d659d" class="outline-3">
|
||||
<h3 id="org61d659d"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
|
||||
<div class="outline-text-3" id="text-5-1">
|
||||
<p>
|
||||
The configuration interaction (CI) wave function \(\Psi\)
|
||||
@ -2170,7 +2170,7 @@ 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="org8a9e095" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org00a23a1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2216,8 +2216,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0193754" class="outline-3">
|
||||
<h3 id="org0193754"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
|
||||
<div id="outline-container-org28bd707" class="outline-3">
|
||||
<h3 id="org28bd707"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
|
||||
<div class="outline-text-3" id="text-5-2">
|
||||
<p>
|
||||
The configuration interaction (CI) wave function \(\Psi\) can be
|
||||
@ -2239,7 +2239,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
|
||||
the basis of Slater determinants.
|
||||
</p>
|
||||
|
||||
<table id="orgda40a73" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orge0c7469" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2285,8 +2285,8 @@ the basis of Slater determinants.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org416b269" class="outline-3">
|
||||
<h3 id="org416b269"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
|
||||
<div id="outline-container-orgb24ec58" class="outline-3">
|
||||
<h3 id="orgb24ec58"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
|
||||
<div class="outline-text-3" id="text-5-3">
|
||||
<p>
|
||||
The wave function may be expressed in terms of action of the cluster
|
||||
@ -2357,7 +2357,7 @@ The order of the indices is chosen such that
|
||||
<li>\(\dots\)</li>
|
||||
</ul>
|
||||
|
||||
<table id="org5c1d1b9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgc86d064" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2438,8 +2438,8 @@ The order of the indices is chosen such that
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org87fe807" class="outline-3">
|
||||
<h3 id="org87fe807"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
|
||||
<div id="outline-container-orgf20085f" class="outline-3">
|
||||
<h3 id="orgf20085f"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
|
||||
<div class="outline-text-3" id="text-5-4">
|
||||
<p>
|
||||
The reduced density matrices are defined in the basis of molecular
|
||||
@ -2514,7 +2514,7 @@ expressed in a basis of a one-electron function
|
||||
\(g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)\).
|
||||
</p>
|
||||
|
||||
<table id="org367037c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgacb787b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2666,12 +2666,12 @@ expressed in a basis of a one-electron function
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdab52dd" class="outline-2">
|
||||
<h2 id="orgdab52dd"><span class="section-number-2">6</span> Correlation factors</h2>
|
||||
<div id="outline-container-orgca89c37" class="outline-2">
|
||||
<h2 id="orgca89c37"><span class="section-number-2">6</span> Correlation factors</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
</div>
|
||||
<div id="outline-container-org2e8031e" class="outline-3">
|
||||
<h3 id="org2e8031e"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
|
||||
<div id="outline-container-org099f627" class="outline-3">
|
||||
<h3 id="org099f627"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
|
||||
<div class="outline-text-3" id="text-6-1">
|
||||
<p>
|
||||
The Jastrow factor is an $N$-electron function to which the CI
|
||||
@ -2696,8 +2696,8 @@ following:
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9e0002e" class="outline-4">
|
||||
<h4 id="org9e0002e"><span class="section-number-4">6.1.1</span> CHAMP</h4>
|
||||
<div id="outline-container-org919ef0a" class="outline-4">
|
||||
<h4 id="org919ef0a"><span class="section-number-4">6.1.1</span> CHAMP</h4>
|
||||
<div class="outline-text-4" id="text-6-1-1">
|
||||
<p>
|
||||
The first form of Jastrow factor is the one used in
|
||||
@ -2774,8 +2774,8 @@ The terms \(J_{\text{ee}}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to en
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1f5142f" class="outline-4">
|
||||
<h4 id="org1f5142f"><span class="section-number-4">6.1.2</span> Mu</h4>
|
||||
<div id="outline-container-orgea8174d" class="outline-4">
|
||||
<h4 id="orgea8174d"><span class="section-number-4">6.1.2</span> Mu</h4>
|
||||
<div class="outline-text-4" id="text-6-1-2">
|
||||
<p>
|
||||
<a href="https://aip.scitation.org/doi/10.1063/5.0044683">Mu-Jastrow</a> is based on a one-parameter correlation factor that has
|
||||
@ -2872,10 +2872,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9af8bbb" class="outline-4">
|
||||
<h4 id="org9af8bbb"><span class="section-number-4">6.1.3</span> Table of values</h4>
|
||||
<div id="outline-container-orgf11581f" class="outline-4">
|
||||
<h4 id="orgf11581f"><span class="section-number-4">6.1.3</span> Table of values</h4>
|
||||
<div class="outline-text-4" id="text-6-1-3">
|
||||
<table id="orgf1238cc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org7d30c55" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2979,8 +2979,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgabc6f85" class="outline-2">
|
||||
<h2 id="orgabc6f85"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div id="outline-container-org06d176e" class="outline-2">
|
||||
<h2 id="org06d176e"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<p>
|
||||
In quantum Monte Carlo calculations, the wave function is evaluated
|
||||
@ -2994,7 +2994,7 @@ By convention, the electron coordinates contain first all the electrons
|
||||
of $↑$-spin and then all the $↓$-spin.
|
||||
</p>
|
||||
|
||||
<table id="org076b0eb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd5fc427" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -3049,7 +3049,7 @@ of $↑$-spin and then all the $↓$-spin.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2023-01-13 Fri 14:48</p>
|
||||
<p class="date">Created: 2023-01-13 Fri 14:55</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user