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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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<!-- 2023-01-07 Sat 17:42 -->
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<!-- 2023-01-08 Sun 11:14 -->
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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: 2023-01-07 Sat 17:42</p>
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||||
<p class="date">Created: 2023-01-08 Sun 11:14</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>
|
||||
</body>
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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>
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||||
<!-- 2023-01-07 Sat 17:42 -->
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||||
<!-- 2023-01-08 Sun 11:14 -->
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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="#org6f11ec9">1. Accessing sparse quantities (integrals)</a>
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<li><a href="#orgca3faa6">1. Accessing sparse quantities (integrals)</a>
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<ul>
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<li><a href="#org5ef5767">1.1. Fortran</a>
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<li><a href="#org7df6542">1.1. Fortran</a>
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||||
<ul>
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<li><a href="#orge176d5c">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org8fc2883">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="#orgd681f80">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org75bdf84">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org735bde0">1.1.5. Allocate memory</a></li>
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<li><a href="#orgb5715e0">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org0083f50">1.1.7. Read two-electron quantities</a>
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<li><a href="#org605e59e">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org03c32e2">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="#orgd6ad6b2">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org455e180">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orga77f271">1.1.5. Allocate memory</a></li>
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<li><a href="#orgaff8b86">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#orgaf0258b">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#org11a4ee4">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#orgec71676">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#org3a93a20">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org8553498">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="#org1fa50b6">1.1.8. Compute the energy</a></li>
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<li><a href="#orgd980f35">1.1.9. Terminate</a></li>
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<li><a href="#org4fa1cdc">1.1.8. Compute the energy</a></li>
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<li><a href="#org793d8fa">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="#org7b6e9dc">2. Reading determinants</a>
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<li><a href="#orgf2081a9">2. Reading determinants</a>
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<ul>
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<li><a href="#orgcb5d88b">2.1. Fortran</a></li>
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<li><a href="#org2fbd4d1">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-org6f11ec9" class="outline-2">
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<h2 id="org6f11ec9"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
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<div id="outline-container-orgca3faa6" class="outline-2">
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<h2 id="orgca3faa6"><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-org5ef5767" class="outline-3">
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<h3 id="org5ef5767"><span class="section-number-3">1.1</span> Fortran</h3>
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<div id="outline-container-org7df6542" class="outline-3">
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<h3 id="org7df6542"><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-orge176d5c" class="outline-4">
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<h4 id="orge176d5c"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-org605e59e" class="outline-4">
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<h4 id="org605e59e"><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-org8fc2883" class="outline-4">
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<h4 id="org8fc2883"><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-org03c32e2" class="outline-4">
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<h4 id="org03c32e2"><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-orgd681f80" class="outline-4">
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<h4 id="orgd681f80"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-orgd6ad6b2" class="outline-4">
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<h4 id="orgd6ad6b2"><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-org75bdf84" class="outline-4">
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<h4 id="org75bdf84"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-org455e180" class="outline-4">
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<h4 id="org455e180"><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-org735bde0" class="outline-4">
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<h4 id="org735bde0"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div id="outline-container-orga77f271" class="outline-4">
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<h4 id="orga77f271"><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-orgb5715e0" class="outline-4">
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<h4 id="orgb5715e0"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div id="outline-container-orgaff8b86" class="outline-4">
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<h4 id="orgaff8b86"><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-org0083f50" class="outline-4">
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<h4 id="org0083f50"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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||||
<div id="outline-container-orgaf0258b" class="outline-4">
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||||
<h4 id="orgaf0258b"><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-org11a4ee4" class="outline-5">
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<h5 id="org11a4ee4"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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<div id="outline-container-org3a93a20" class="outline-5">
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<h5 id="org3a93a20"><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-orgec71676" class="outline-5">
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<h5 id="orgec71676"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-org8553498" class="outline-5">
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<h5 id="org8553498"><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-org1fa50b6" class="outline-4">
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<h4 id="org1fa50b6"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div id="outline-container-org4fa1cdc" class="outline-4">
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<h4 id="org4fa1cdc"><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-orgd980f35" class="outline-4">
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<h4 id="orgd980f35"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-org793d8fa" class="outline-4">
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<h4 id="org793d8fa"><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-org7b6e9dc" class="outline-2">
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<h2 id="org7b6e9dc"><span class="section-number-2">2</span> Reading determinants</h2>
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<div id="outline-container-orgf2081a9" class="outline-2">
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<h2 id="orgf2081a9"><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-orgcb5d88b" class="outline-3">
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<h3 id="orgcb5d88b"><span class="section-number-3">2.1</span> Fortran</h3>
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<div id="outline-container-org2fbd4d1" class="outline-3">
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<h3 id="org2fbd4d1"><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">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2023-01-07 Sat 17:42</p>
|
||||
<p class="date">Created: 2023-01-08 Sun 11:14</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 @@
|
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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>
|
||||
<!-- 2023-01-07 Sat 17:42 -->
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<!-- 2023-01-08 Sun 11:14 -->
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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: 2023-01-07 Sat 17:42</p>
|
||||
<p class="date">Created: 2023-01-08 Sun 11:14</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>
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<!-- 2023-01-07 Sat 17:42 -->
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<!-- 2023-01-08 Sun 11:14 -->
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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>
|
||||
<li><a href="#org0eca452">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org0493f3e">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgd5f9eaf">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org86ed23c">4. Template for HDF5 has a group</a></li>
|
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<li><a href="#orgac47e6d">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
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<li><a href="#orgfac5d04">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
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<li><a href="#orgbbe10ce">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
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<li><a href="#orge1fdfdc">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
|
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<li><a href="#org6a2479a">9. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org2ad08bc">10. Template for HDF5 has/read/write a string attribute</a></li>
|
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<li><a href="#orgf14fcf8">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org055a365">12. Source code for the determinant part</a></li>
|
||||
<li><a href="#org2ce68d7">13. Helper functions</a></li>
|
||||
<li><a href="#org0ed81e2">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org6654213">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orge36dd99">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orge1ef84e">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#org5c82ab6">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgd15be0f">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org7387d50">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#org017217c">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
|
||||
<li><a href="#orge5dc260">9. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orga3fc88b">10. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#org6fce6f6">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org880a5a7">12. Source code for the determinant part</a></li>
|
||||
<li><a href="#orgb181062">13. Helper functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0eca452" class="outline-2">
|
||||
<h2 id="org0eca452"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-org0ed81e2" class="outline-2">
|
||||
<h2 id="org0ed81e2"><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-org0493f3e" class="outline-2">
|
||||
<h2 id="org0493f3e"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-org6654213" class="outline-2">
|
||||
<h2 id="org6654213"><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-orgd5f9eaf" class="outline-2">
|
||||
<h2 id="orgd5f9eaf"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-orge36dd99" class="outline-2">
|
||||
<h2 id="orge36dd99"><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-org86ed23c" class="outline-2">
|
||||
<h2 id="org86ed23c"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
|
||||
<div id="outline-container-orge1ef84e" class="outline-2">
|
||||
<h2 id="orge1ef84e"><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-orgac47e6d" class="outline-2">
|
||||
<h2 id="orgac47e6d"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-org5c82ab6" class="outline-2">
|
||||
<h2 id="org5c82ab6"><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-orgfac5d04" class="outline-2">
|
||||
<h2 id="orgfac5d04"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-orgd15be0f" class="outline-2">
|
||||
<h2 id="orgd15be0f"><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-orgbbe10ce" class="outline-2">
|
||||
<h2 id="orgbbe10ce"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-org7387d50" class="outline-2">
|
||||
<h2 id="org7387d50"><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-orge1fdfdc" class="outline-2">
|
||||
<h2 id="orge1fdfdc"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
|
||||
<div id="outline-container-org017217c" class="outline-2">
|
||||
<h2 id="org017217c"><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-org6a2479a" class="outline-2">
|
||||
<h2 id="org6a2479a"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-orge5dc260" class="outline-2">
|
||||
<h2 id="orge5dc260"><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-org2ad08bc" class="outline-2">
|
||||
<h2 id="org2ad08bc"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-orga3fc88b" class="outline-2">
|
||||
<h2 id="orga3fc88b"><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-orgf14fcf8" class="outline-2">
|
||||
<h2 id="orgf14fcf8"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-org6fce6f6" class="outline-2">
|
||||
<h2 id="org6fce6f6"><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-org055a365" class="outline-2">
|
||||
<h2 id="org055a365"><span class="section-number-2">12</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org880a5a7" class="outline-2">
|
||||
<h2 id="org880a5a7"><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-org2ce68d7" class="outline-2">
|
||||
<h2 id="org2ce68d7"><span class="section-number-2">13</span> Helper functions</h2>
|
||||
<div id="outline-container-orgb181062" class="outline-2">
|
||||
<h2 id="orgb181062"><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: 2023-01-07 Sat 17:42</p>
|
||||
<p class="date">Created: 2023-01-08 Sun 11:14</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>
|
||||
<!-- 2023-01-07 Sat 17:42 -->
|
||||
<!-- 2023-01-08 Sun 11:14 -->
|
||||
<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="#org3b30361">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#orgfe7665c">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org3f4cede">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org2334b2f">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orgc014539">5. Flush function (templated part)</a></li>
|
||||
<li><a href="#org3e41945">6. Template for text read a group</a></li>
|
||||
<li><a href="#org2b33cee">7. Template for text has a group</a></li>
|
||||
<li><a href="#orge281ac8">8. Template for text flush a group</a></li>
|
||||
<li><a href="#orgebd3970">9. Template for text free memory</a></li>
|
||||
<li><a href="#org2b82a55">10. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org6d0cf06">11. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org9e47688">12. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org797ddd7">13. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org5143a69">14. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#orgad01383">15. Template for has/read/write a buffered vector</a></li>
|
||||
<li><a href="#orgfe52310">16. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org293c524">17. Source code for the determinant part</a></li>
|
||||
<li><a href="#org9a59bff">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org841acea">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#orgf856c09">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org1654693">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orgd9408c9">5. Flush function (templated part)</a></li>
|
||||
<li><a href="#org4ca10e2">6. Template for text read a group</a></li>
|
||||
<li><a href="#org7b4ecdb">7. Template for text has a group</a></li>
|
||||
<li><a href="#org5d3eb5f">8. Template for text flush a group</a></li>
|
||||
<li><a href="#org0f8525a">9. Template for text free memory</a></li>
|
||||
<li><a href="#orgcf56a12">10. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org471a1a5">11. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org45ec95a">12. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org20b6106">13. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org4f481e2">14. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#orgbabbc67">15. Template for has/read/write a buffered vector</a></li>
|
||||
<li><a href="#orge792adf">16. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orgae766b1">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-org3b30361" class="outline-2">
|
||||
<h2 id="org3b30361"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div id="outline-container-org9a59bff" class="outline-2">
|
||||
<h2 id="org9a59bff"><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-orgfe7665c" class="outline-2">
|
||||
<h2 id="orgfe7665c"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div id="outline-container-org841acea" class="outline-2">
|
||||
<h2 id="org841acea"><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-org3f4cede" class="outline-2">
|
||||
<h2 id="org3f4cede"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div id="outline-container-orgf856c09" class="outline-2">
|
||||
<h2 id="orgf856c09"><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-org2334b2f" class="outline-2">
|
||||
<h2 id="org2334b2f"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div id="outline-container-org1654693" class="outline-2">
|
||||
<h2 id="org1654693"><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-orgc014539" class="outline-2">
|
||||
<h2 id="orgc014539"><span class="section-number-2">5</span> Flush function (templated part)</h2>
|
||||
<div id="outline-container-orgd9408c9" class="outline-2">
|
||||
<h2 id="orgd9408c9"><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-org3e41945" class="outline-2">
|
||||
<h2 id="org3e41945"><span class="section-number-2">6</span> Template for text read a group</h2>
|
||||
<div id="outline-container-org4ca10e2" class="outline-2">
|
||||
<h2 id="org4ca10e2"><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-org2b33cee" class="outline-2">
|
||||
<h2 id="org2b33cee"><span class="section-number-2">7</span> Template for text has a group</h2>
|
||||
<div id="outline-container-org7b4ecdb" class="outline-2">
|
||||
<h2 id="org7b4ecdb"><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-orge281ac8" class="outline-2">
|
||||
<h2 id="orge281ac8"><span class="section-number-2">8</span> Template for text flush a group</h2>
|
||||
<div id="outline-container-org5d3eb5f" class="outline-2">
|
||||
<h2 id="org5d3eb5f"><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-orgebd3970" class="outline-2">
|
||||
<h2 id="orgebd3970"><span class="section-number-2">9</span> Template for text free memory</h2>
|
||||
<div id="outline-container-org0f8525a" class="outline-2">
|
||||
<h2 id="org0f8525a"><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-org2b82a55" class="outline-2">
|
||||
<h2 id="org2b82a55"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-orgcf56a12" class="outline-2">
|
||||
<h2 id="orgcf56a12"><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-org6d0cf06" class="outline-2">
|
||||
<h2 id="org6d0cf06"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org471a1a5" class="outline-2">
|
||||
<h2 id="org471a1a5"><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-org9e47688" class="outline-2">
|
||||
<h2 id="org9e47688"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org45ec95a" class="outline-2">
|
||||
<h2 id="org45ec95a"><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-org797ddd7" class="outline-2">
|
||||
<h2 id="org797ddd7"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org20b6106" class="outline-2">
|
||||
<h2 id="org20b6106"><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-org5143a69" class="outline-2">
|
||||
<h2 id="org5143a69"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div id="outline-container-org4f481e2" class="outline-2">
|
||||
<h2 id="org4f481e2"><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-orgad01383" class="outline-2">
|
||||
<h2 id="orgad01383"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
|
||||
<div id="outline-container-orgbabbc67" class="outline-2">
|
||||
<h2 id="orgbabbc67"><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-orgfe52310" class="outline-2">
|
||||
<h2 id="orgfe52310"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-orge792adf" class="outline-2">
|
||||
<h2 id="orge792adf"><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-org293c524" class="outline-2">
|
||||
<h2 id="org293c524"><span class="section-number-2">17</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-orgae766b1" class="outline-2">
|
||||
<h2 id="orgae766b1"><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: 2023-01-07 Sat 17:42</p>
|
||||
<p class="date">Created: 2023-01-08 Sun 11:14</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
246
trex.html
246
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>
|
||||
<!-- 2023-01-07 Sat 17:42 -->
|
||||
<!-- 2023-01-08 Sun 11:14 -->
|
||||
<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="#org9773af0">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#orgb0af61c">2. System</a>
|
||||
<li><a href="#orgb8e1b21">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org12c2fbd">2. System</a>
|
||||
<ul>
|
||||
<li><a href="#orgb883417">2.1. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org005cd4e">2.2. Cell (cell group)</a></li>
|
||||
<li><a href="#org37ccf5b">2.3. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#orgf4582b9">2.4. Electron (electron group)</a></li>
|
||||
<li><a href="#orgf8dff87">2.5. Ground or excited states (state group)</a></li>
|
||||
<li><a href="#orgf6aef26">2.1. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org1bb3a2c">2.2. Cell (cell group)</a></li>
|
||||
<li><a href="#orga8622aa">2.3. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#org2349df7">2.4. Electron (electron group)</a></li>
|
||||
<li><a href="#orge88cc99">2.5. Ground or excited states (state group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgc6d3cfd">3. Basis functions</a>
|
||||
<li><a href="#org907b8cc">3. Basis functions</a>
|
||||
<ul>
|
||||
<li><a href="#org079f7fa">3.1. Basis set (basis group)</a>
|
||||
<li><a href="#org356742a">3.1. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#org6afb634">3.1.1. Gaussian and Slater-type orbitals</a></li>
|
||||
<li><a href="#org919bd4c">3.1.2. Plane waves</a></li>
|
||||
<li><a href="#orgdbb87bb">3.1.3. Data definitions</a></li>
|
||||
<li><a href="#org340607e">3.1.4. Example</a></li>
|
||||
<li><a href="#orgec2ace0">3.1.1. Gaussian and Slater-type orbitals</a></li>
|
||||
<li><a href="#org4078870">3.1.2. Plane waves</a></li>
|
||||
<li><a href="#org166cec5">3.1.3. Data definitions</a></li>
|
||||
<li><a href="#org601bff7">3.1.4. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgc5599e1">3.2. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#org263e893">3.2. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#org9a1ecd4">3.2.1. Example</a></li>
|
||||
<li><a href="#orgab11cbc">3.2.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org21e7739">3.3. Numerical integration grid (grid group)</a></li>
|
||||
<li><a href="#org9f6ef4b">3.3. Numerical integration grid (grid group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org2f0046b">4. Orbitals</a>
|
||||
<li><a href="#org6e4cb9c">4. Orbitals</a>
|
||||
<ul>
|
||||
<li><a href="#org18a02df">4.1. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#orgd942381">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="#org94b7118">4.2. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org92a1557">4.2. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#orge1daf3d">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org1b06c7f">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#orgfc69492">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orgdc32cbd">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgd8fca50">5. Multi-determinant information</a>
|
||||
<li><a href="#orgd6762f3">5. Multi-determinant information</a>
|
||||
<ul>
|
||||
<li><a href="#org3bc24cd">5.1. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#orge3e338d">5.2. Configuration state functions (csf group)</a></li>
|
||||
<li><a href="#org019412f">5.3. Amplitudes (amplitude group)</a></li>
|
||||
<li><a href="#org344fb39">5.4. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#orge7140e5">5.1. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#orgfd4dc25">5.2. Configuration state functions (csf group)</a></li>
|
||||
<li><a href="#orge4981c3">5.3. Amplitudes (amplitude group)</a></li>
|
||||
<li><a href="#org7796df0">5.4. Reduced density matrices (rdm group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org346b604">6. Correlation factors</a>
|
||||
<li><a href="#org5442a12">6. Correlation factors</a>
|
||||
<ul>
|
||||
<li><a href="#org23a6fce">6.1. Jastrow factor (jastrow group)</a>
|
||||
<li><a href="#orgcb9e33b">6.1. Jastrow factor (jastrow group)</a>
|
||||
<ul>
|
||||
<li><a href="#org1f64d88">6.1.1. CHAMP</a></li>
|
||||
<li><a href="#orgfbc6158">6.1.2. Mu</a></li>
|
||||
<li><a href="#orgcc32e67">6.1.3. Table of values</a></li>
|
||||
<li><a href="#orgd5170f8">6.1.1. CHAMP</a></li>
|
||||
<li><a href="#org9a57e47">6.1.2. Mu</a></li>
|
||||
<li><a href="#orge9efeab">6.1.3. Table of values</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org5d0408f">7. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
<li><a href="#orga0c950a">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-org9773af0" class="outline-2">
|
||||
<h2 id="org9773af0"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-orgb8e1b21" class="outline-2">
|
||||
<h2 id="orgb8e1b21"><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="orgad9223f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga453c0f" 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-orgb0af61c" class="outline-2">
|
||||
<h2 id="orgb0af61c"><span class="section-number-2">2</span> System</h2>
|
||||
<div id="outline-container-org12c2fbd" class="outline-2">
|
||||
<h2 id="org12c2fbd"><span class="section-number-2">2</span> System</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
</div>
|
||||
<div id="outline-container-orgb883417" class="outline-3">
|
||||
<h3 id="orgb883417"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
|
||||
<div id="outline-container-orgf6aef26" class="outline-3">
|
||||
<h3 id="orgf6aef26"><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="org29bfc44" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org17f39ba" 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-org005cd4e" class="outline-3">
|
||||
<h3 id="org005cd4e"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
|
||||
<div id="outline-container-org1bb3a2c" class="outline-3">
|
||||
<h3 id="org1bb3a2c"><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="org5164a11" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org9b14fbc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -704,15 +704,15 @@ used in periodic calculations.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org37ccf5b" class="outline-3">
|
||||
<h3 id="org37ccf5b"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
|
||||
<div id="outline-container-orga8622aa" class="outline-3">
|
||||
<h3 id="orga8622aa"><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="org807b56e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org0c6fbe4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -751,15 +751,15 @@ defined in this group.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf4582b9" class="outline-3">
|
||||
<h3 id="orgf4582b9"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
|
||||
<div id="outline-container-org2349df7" class="outline-3">
|
||||
<h3 id="org2349df7"><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="org4256241" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1dc32a8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -805,8 +805,8 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf8dff87" class="outline-3">
|
||||
<h3 id="orgf8dff87"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
|
||||
<div id="outline-container-orge88cc99" class="outline-3">
|
||||
<h3 id="orge88cc99"><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
|
||||
@ -823,7 +823,7 @@ integrals, etc.
|
||||
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
|
||||
</p>
|
||||
|
||||
<table id="org5317245" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga5b89d2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -884,16 +884,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc6d3cfd" class="outline-2">
|
||||
<h2 id="orgc6d3cfd"><span class="section-number-2">3</span> Basis functions</h2>
|
||||
<div id="outline-container-org907b8cc" class="outline-2">
|
||||
<h2 id="org907b8cc"><span class="section-number-2">3</span> Basis functions</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
</div>
|
||||
<div id="outline-container-org079f7fa" class="outline-3">
|
||||
<h3 id="org079f7fa"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
|
||||
<div id="outline-container-org356742a" class="outline-3">
|
||||
<h3 id="org356742a"><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-org6afb634" class="outline-4">
|
||||
<h4 id="org6afb634"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
|
||||
<div id="outline-container-orgec2ace0" class="outline-4">
|
||||
<h4 id="orgec2ace0"><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
|
||||
@ -947,8 +947,8 @@ All the basis set parameters are stored in one-dimensional arrays.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org919bd4c" class="outline-4">
|
||||
<h4 id="org919bd4c"><span class="section-number-4">3.1.2</span> Plane waves</h4>
|
||||
<div id="outline-container-org4078870" class="outline-4">
|
||||
<h4 id="org4078870"><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
|
||||
@ -968,10 +968,10 @@ cutoff <code>e_cut</code> is the only input data relevant to plane waves.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdbb87bb" class="outline-4">
|
||||
<h4 id="orgdbb87bb"><span class="section-number-4">3.1.3</span> Data definitions</h4>
|
||||
<div id="outline-container-org166cec5" class="outline-4">
|
||||
<h4 id="org166cec5"><span class="section-number-4">3.1.3</span> Data definitions</h4>
|
||||
<div class="outline-text-4" id="text-3-1-3">
|
||||
<table id="orgce785f8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1b40f12" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1080,8 +1080,8 @@ cutoff <code>e_cut</code> is the only input data relevant to plane waves.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org340607e" class="outline-4">
|
||||
<h4 id="org340607e"><span class="section-number-4">3.1.4</span> Example</h4>
|
||||
<div id="outline-container-org601bff7" class="outline-4">
|
||||
<h4 id="org601bff7"><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
|
||||
@ -1159,8 +1159,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc5599e1" class="outline-3">
|
||||
<h3 id="orgc5599e1"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
|
||||
<div id="outline-container-org263e893" class="outline-3">
|
||||
<h3 id="org263e893"><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
|
||||
@ -1193,7 +1193,7 @@ 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="org1a19db3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orge3e4774" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1298,8 +1298,8 @@ If you encounter the aforementioned issue, please report it to our
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9a1ecd4" class="outline-4">
|
||||
<h4 id="org9a1ecd4"><span class="section-number-4">3.2.1</span> Example</h4>
|
||||
<div id="outline-container-orgab11cbc" class="outline-4">
|
||||
<h4 id="orgab11cbc"><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
|
||||
@ -1362,8 +1362,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org21e7739" class="outline-3">
|
||||
<h3 id="org21e7739"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
|
||||
<div id="outline-container-org9f6ef4b" class="outline-3">
|
||||
<h3 id="org9f6ef4b"><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
|
||||
@ -1378,7 +1378,7 @@ 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="orgdf774d1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orge43b3c4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1495,12 +1495,12 @@ Feel free to submit a PR if you find missing options/functionalities.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2f0046b" class="outline-2">
|
||||
<h2 id="org2f0046b"><span class="section-number-2">4</span> Orbitals</h2>
|
||||
<div id="outline-container-org6e4cb9c" class="outline-2">
|
||||
<h2 id="org6e4cb9c"><span class="section-number-2">4</span> Orbitals</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
</div>
|
||||
<div id="outline-container-org18a02df" class="outline-3">
|
||||
<h3 id="org18a02df"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
|
||||
<div id="outline-container-orgd942381" class="outline-3">
|
||||
<h3 id="orgd942381"><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
|
||||
@ -1553,13 +1553,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#org079f7fa">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#org356742a">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="org45b1b72" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org6341352" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1611,7 +1611,7 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgde26214" class="outline-4">
|
||||
<div id="outline-container-orge95191d" 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">
|
||||
@ -1629,7 +1629,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org3059f6d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org08cf8dd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1724,7 +1724,7 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org14646f1" class="outline-4">
|
||||
<div id="outline-container-orge3aadd0" 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>
|
||||
@ -1756,7 +1756,7 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
\]
|
||||
</p>
|
||||
|
||||
<table id="org672aac0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgea6fc88" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1824,10 +1824,10 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org94b7118" class="outline-3">
|
||||
<h3 id="org94b7118"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
|
||||
<div id="outline-container-org92a1557" class="outline-3">
|
||||
<h3 id="org92a1557"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
|
||||
<div class="outline-text-3" id="text-4-2">
|
||||
<table id="orga18cb30" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org03e9822" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1914,8 +1914,8 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge1daf3d" class="outline-4">
|
||||
<h4 id="orge1daf3d"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
|
||||
<div id="outline-container-orgfc69492" class="outline-4">
|
||||
<h4 id="orgfc69492"><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
|
||||
@ -1923,7 +1923,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org739f7f1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgc6d8bcd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2018,8 +2018,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1b06c7f" class="outline-4">
|
||||
<h4 id="org1b06c7f"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
|
||||
<div id="outline-container-orgdc32cbd" class="outline-4">
|
||||
<h4 id="orgdc32cbd"><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
|
||||
@ -2027,7 +2027,7 @@ The operators are the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org91173a3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1d6e8e1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2096,12 +2096,12 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd8fca50" class="outline-2">
|
||||
<h2 id="orgd8fca50"><span class="section-number-2">5</span> Multi-determinant information</h2>
|
||||
<div id="outline-container-orgd6762f3" class="outline-2">
|
||||
<h2 id="orgd6762f3"><span class="section-number-2">5</span> Multi-determinant information</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
</div>
|
||||
<div id="outline-container-org3bc24cd" class="outline-3">
|
||||
<h3 id="org3bc24cd"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
|
||||
<div id="outline-container-orge7140e5" class="outline-3">
|
||||
<h3 id="orge7140e5"><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 \(\Psi\)
|
||||
@ -2143,7 +2143,7 @@ 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="orgc9d3fe0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd81c73c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2189,8 +2189,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge3e338d" class="outline-3">
|
||||
<h3 id="orge3e338d"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
|
||||
<div id="outline-container-orgfd4dc25" class="outline-3">
|
||||
<h3 id="orgfd4dc25"><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
|
||||
@ -2212,7 +2212,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
|
||||
the basis of Slater determinants.
|
||||
</p>
|
||||
|
||||
<table id="org579712e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgaa3f3be" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2258,8 +2258,8 @@ the basis of Slater determinants.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org019412f" class="outline-3">
|
||||
<h3 id="org019412f"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
|
||||
<div id="outline-container-orge4981c3" class="outline-3">
|
||||
<h3 id="orge4981c3"><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
|
||||
@ -2330,7 +2330,7 @@ The order of the indices is chosen such that
|
||||
<li>\(\dots\)</li>
|
||||
</ul>
|
||||
|
||||
<table id="orgcbbefe5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org473bef1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2411,8 +2411,8 @@ The order of the indices is chosen such that
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org344fb39" class="outline-3">
|
||||
<h3 id="org344fb39"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
|
||||
<div id="outline-container-org7796df0" class="outline-3">
|
||||
<h3 id="org7796df0"><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
|
||||
@ -2487,7 +2487,7 @@ 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="org2015f8b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgbbfaaeb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2639,12 +2639,12 @@ expressed in a basis of a one-electron function
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org346b604" class="outline-2">
|
||||
<h2 id="org346b604"><span class="section-number-2">6</span> Correlation factors</h2>
|
||||
<div id="outline-container-org5442a12" class="outline-2">
|
||||
<h2 id="org5442a12"><span class="section-number-2">6</span> Correlation factors</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
</div>
|
||||
<div id="outline-container-org23a6fce" class="outline-3">
|
||||
<h3 id="org23a6fce"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
|
||||
<div id="outline-container-orgcb9e33b" class="outline-3">
|
||||
<h3 id="orgcb9e33b"><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
|
||||
@ -2669,8 +2669,8 @@ following:
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1f64d88" class="outline-4">
|
||||
<h4 id="org1f64d88"><span class="section-number-4">6.1.1</span> CHAMP</h4>
|
||||
<div id="outline-container-orgd5170f8" class="outline-4">
|
||||
<h4 id="orgd5170f8"><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
|
||||
@ -2747,8 +2747,8 @@ The terms \(J_{\text{ee}}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to en
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgfbc6158" class="outline-4">
|
||||
<h4 id="orgfbc6158"><span class="section-number-4">6.1.2</span> Mu</h4>
|
||||
<div id="outline-container-org9a57e47" class="outline-4">
|
||||
<h4 id="org9a57e47"><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
|
||||
@ -2780,7 +2780,7 @@ The electron-electron cusp is incorporated in the three-body term.
|
||||
</p>
|
||||
|
||||
<p>
|
||||
\(u\) is an electron-electron function given by the symetric function
|
||||
\(u\) is an electron-electron function given by the symmetric function
|
||||
</p>
|
||||
|
||||
<p>
|
||||
@ -2845,10 +2845,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgcc32e67" class="outline-4">
|
||||
<h4 id="orgcc32e67"><span class="section-number-4">6.1.3</span> Table of values</h4>
|
||||
<div id="outline-container-orge9efeab" class="outline-4">
|
||||
<h4 id="orge9efeab"><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="org811a25c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgbe0767d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2952,8 +2952,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5d0408f" class="outline-2">
|
||||
<h2 id="org5d0408f"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div id="outline-container-orga0c950a" class="outline-2">
|
||||
<h2 id="orga0c950a"><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
|
||||
@ -2967,7 +2967,7 @@ By convention, the electron coordinates contain first all the electrons
|
||||
of $↑$-spin and then all the $↓$-spin.
|
||||
</p>
|
||||
|
||||
<table id="orgfe35447" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgf096874" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -3022,7 +3022,7 @@ of $↑$-spin and then all the $↓$-spin.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2023-01-07 Sat 17:42</p>
|
||||
<p class="date">Created: 2023-01-08 Sun 11:14</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