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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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<head>
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<!-- 2022-07-08 Fri 16:14 -->
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<!-- 2022-07-11 Mon 13:34 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>TREXIO source code documentation</title>
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@ -347,7 +347,7 @@ and bug reports should be submitted at
|
||||
</div>
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<div id="postamble" class="status">
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<p class="author">Author: TREX-CoE</p>
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||||
<p class="date">Created: 2022-07-08 Fri 16:14</p>
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||||
<p class="date">Created: 2022-07-11 Mon 13:34</p>
|
||||
<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 @@
|
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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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||||
<!-- 2022-07-08 Fri 16:14 -->
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||||
<!-- 2022-07-11 Mon 13:34 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>Examples</title>
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@ -333,31 +333,31 @@ for the JavaScript code in this tag.
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||||
<h2>Table of Contents</h2>
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<div id="text-table-of-contents">
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<ul>
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<li><a href="#org1557606">1. Accessing sparse quantities (integrals)</a>
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<li><a href="#orga5740f0">1. Accessing sparse quantities (integrals)</a>
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<ul>
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<li><a href="#orgee17df4">1.1. Fortran</a>
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<li><a href="#orga6bcd76">1.1. Fortran</a>
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||||
<ul>
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||||
<li><a href="#orga60f184">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org69fb3eb">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="#org4e25c77">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#orgfd61bc7">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org02e2f13">1.1.5. Allocate memory</a></li>
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<li><a href="#orgb5d40e9">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org12e4147">1.1.7. Read two-electron quantities</a>
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<li><a href="#org69abbf6">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#orgd4978a8">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="#orgeb008ae">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org80c16eb">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org2036139">1.1.5. Allocate memory</a></li>
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<li><a href="#org8360aef">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org91b7a5c">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#org17e6823">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#orgf22cd29">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#orgc2f52ca">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org0030e77">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="#org1177385">1.1.8. Compute the energy</a></li>
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<li><a href="#orga3337c3">1.1.9. Terminate</a></li>
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<li><a href="#orgd77d65c">1.1.8. Compute the energy</a></li>
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<li><a href="#orgd60d946">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="#org1fc6517">2. Reading determinants</a>
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<li><a href="#org1d23d1c">2. Reading determinants</a>
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<ul>
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<li><a href="#orgb826171">2.1. Fortran</a></li>
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<li><a href="#org4778309">2.1. Fortran</a></li>
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</ul>
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</li>
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</ul>
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@ -365,12 +365,12 @@ for the JavaScript code in this tag.
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</div>
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<div id="outline-container-org1557606" class="outline-2">
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<h2 id="org1557606"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
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<div id="outline-container-orga5740f0" class="outline-2">
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||||
<h2 id="orga5740f0"><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-orgee17df4" class="outline-3">
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<h3 id="orgee17df4"><span class="section-number-3">1.1</span> Fortran</h3>
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<div id="outline-container-orga6bcd76" class="outline-3">
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<h3 id="orga6bcd76"><span class="section-number-3">1.1</span> Fortran</h3>
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<div class="outline-text-3" id="text-1-1">
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||||
<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
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@ -416,8 +416,8 @@ One needs to read from the TREXIO file:
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</div>
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</div>
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<div id="outline-container-orga60f184" class="outline-4">
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<h4 id="orga60f184"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-org69abbf6" class="outline-4">
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<h4 id="org69abbf6"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div class="outline-text-4" id="text-1-1-1">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> i, j, k, l, m</span>
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@ -432,8 +432,8 @@ One needs to read from the TREXIO file:
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</div>
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</div>
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<div id="outline-container-org69fb3eb" class="outline-4">
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<h4 id="org69fb3eb"><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-orgd4978a8" class="outline-4">
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<h4 id="orgd4978a8"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
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<div class="outline-text-4" id="text-1-1-2">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
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@ -449,8 +449,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-org4e25c77" class="outline-4">
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<h4 id="org4e25c77"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-orgeb008ae" class="outline-4">
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<h4 id="orgeb008ae"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div class="outline-text-4" id="text-1-1-3">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
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@ -464,8 +464,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-orgfd61bc7" class="outline-4">
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<h4 id="orgfd61bc7"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-org80c16eb" class="outline-4">
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<h4 id="org80c16eb"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div class="outline-text-4" id="text-1-1-4">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
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@ -479,8 +479,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-org02e2f13" class="outline-4">
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<h4 id="org02e2f13"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div id="outline-container-org2036139" class="outline-4">
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<h4 id="org2036139"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div class="outline-text-4" id="text-1-1-5">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
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@ -492,8 +492,8 @@ W(:,:,:,:) = 0.d0
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</div>
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</div>
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<div id="outline-container-orgb5d40e9" class="outline-4">
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<h4 id="orgb5d40e9"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div id="outline-container-org8360aef" class="outline-4">
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<h4 id="org8360aef"><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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@ -525,8 +525,8 @@ rc = trexio_read_rdm_1e(f, D)
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</div>
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</div>
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<div id="outline-container-org12e4147" class="outline-4">
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<h4 id="org12e4147"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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||||
<div id="outline-container-org91b7a5c" class="outline-4">
|
||||
<h4 id="org91b7a5c"><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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@ -542,8 +542,8 @@ to be protected in the critical section when modified.
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</p>
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</div>
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<div id="outline-container-org17e6823" class="outline-5">
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<h5 id="org17e6823"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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||||
<div id="outline-container-orgc2f52ca" class="outline-5">
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<h5 id="orgc2f52ca"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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<div class="outline-text-5" id="text-1-1-7-1">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
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@ -592,8 +592,8 @@ icount = BUFSIZE
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</div>
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</div>
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<div id="outline-container-orgf22cd29" class="outline-5">
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<h5 id="orgf22cd29"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-org0030e77" class="outline-5">
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<h5 id="org0030e77"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div class="outline-text-5" id="text-1-1-7-2">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
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@ -637,8 +637,8 @@ icount = bufsize
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</div>
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</div>
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<div id="outline-container-org1177385" class="outline-4">
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<h4 id="org1177385"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div id="outline-container-orgd77d65c" class="outline-4">
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<h4 id="orgd77d65c"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div class="outline-text-4" id="text-1-1-8">
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<p>
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When the orbitals are real, we can use
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@ -684,8 +684,8 @@ E = E + E_nn
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</div>
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</div>
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<div id="outline-container-orga3337c3" class="outline-4">
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<h4 id="orga3337c3"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-orgd60d946" class="outline-4">
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<h4 id="orgd60d946"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div class="outline-text-4" id="text-1-1-9">
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<div class="org-src-container">
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<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
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@ -699,12 +699,12 @@ E = E + E_nn
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</div>
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<div id="outline-container-org1fc6517" class="outline-2">
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<h2 id="org1fc6517"><span class="section-number-2">2</span> Reading determinants</h2>
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<div id="outline-container-org1d23d1c" class="outline-2">
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<h2 id="org1d23d1c"><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-orgb826171" class="outline-3">
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<h3 id="orgb826171"><span class="section-number-3">2.1</span> Fortran</h3>
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<div id="outline-container-org4778309" class="outline-3">
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<h3 id="org4778309"><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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@ -783,7 +783,7 @@ 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>
|
||||
<p class="date">Created: 2022-07-08 Fri 16:14</p>
|
||||
<p class="date">Created: 2022-07-11 Mon 13:34</p>
|
||||
<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>
|
||||
<!-- 2022-07-08 Fri 16:14 -->
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||||
<!-- 2022-07-11 Mon 13:34 -->
|
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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" />
|
||||
<title>TREXIO source code documentation</title>
|
||||
@ -347,7 +347,7 @@ and bug reports should be submitted at
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-07-08 Fri 16:14</p>
|
||||
<p class="date">Created: 2022-07-11 Mon 13:34</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
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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<head>
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<!-- 2022-07-08 Fri 16:14 -->
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<!-- 2022-07-11 Mon 13:33 -->
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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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@ -311,24 +311,24 @@ 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="#orgea5c200">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#orga6eebb7">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgb8cc295">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orgdb0457f">4. Template for HDF5 has a group</a></li>
|
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<li><a href="#org2b33a39">5. Template for HDF5 has/read/write a numerical attribute</a></li>
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<li><a href="#org286dbf4">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
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<li><a href="#org5c459c5">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
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<li><a href="#org50f3489">8. Template for HDF5 has/read/write a dataset of strings</a></li>
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<li><a href="#org15e456f">9. Template for HDF5 has/read/write a string attribute</a></li>
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<li><a href="#org06fbf98">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
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<li><a href="#orge7d036c">11. Source code for the determinant part</a></li>
|
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<li><a href="#orga07a87f">12. Helper functions</a></li>
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<li><a href="#org6cc9f6d">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org7bf323f">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org6220c72">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org29614a8">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#org6a5054b">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org1d0c91d">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org374eaec">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#orgc91a4c2">8. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org9f6c421">9. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgf4818b3">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org6c9c271">11. Source code for the determinant part</a></li>
|
||||
<li><a href="#org26aff54">12. Helper functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgea5c200" class="outline-2">
|
||||
<h2 id="orgea5c200"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-org6cc9f6d" class="outline-2">
|
||||
<h2 id="org6cc9f6d"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #483d8b;">#define</span> $GROUP$_GROUP_NAME <span style="color: #8b2252;">"$group$"</span>
|
||||
@ -340,8 +340,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga6eebb7" class="outline-2">
|
||||
<h2 id="orga6eebb7"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-org7bf323f" class="outline-2">
|
||||
<h2 id="org7bf323f"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
|
||||
@ -361,8 +361,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb8cc295" class="outline-2">
|
||||
<h2 id="orgb8cc295"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-org6220c72" class="outline-2">
|
||||
<h2 id="org6220c72"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -467,8 +467,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdb0457f" class="outline-2">
|
||||
<h2 id="orgdb0457f"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
|
||||
<div id="outline-container-org29614a8" class="outline-2">
|
||||
<h2 id="org29614a8"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -498,8 +498,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2b33a39" class="outline-2">
|
||||
<h2 id="org2b33a39"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-org6a5054b" class="outline-2">
|
||||
<h2 id="org6a5054b"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -603,8 +603,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org286dbf4" class="outline-2">
|
||||
<h2 id="org286dbf4"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org1d0c91d" class="outline-2">
|
||||
<h2 id="org1d0c91d"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -738,8 +738,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5c459c5" class="outline-2">
|
||||
<h2 id="org5c459c5"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-org374eaec" class="outline-2">
|
||||
<h2 id="org374eaec"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<p>
|
||||
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
|
||||
@ -942,8 +942,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org50f3489" class="outline-2">
|
||||
<h2 id="org50f3489"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-orgc91a4c2" class="outline-2">
|
||||
<h2 id="orgc91a4c2"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div class="outline-text-2" id="text-8">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1141,8 +1141,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org15e456f" class="outline-2">
|
||||
<h2 id="org15e456f"><span class="section-number-2">9</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org9f6c421" class="outline-2">
|
||||
<h2 id="org9f6c421"><span class="section-number-2">9</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1269,8 +1269,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org06fbf98" class="outline-2">
|
||||
<h2 id="org06fbf98"><span class="section-number-2">10</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-orgf4818b3" class="outline-2">
|
||||
<h2 id="orgf4818b3"><span class="section-number-2">10</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<p>
|
||||
<b><b>Note:</b></b> in early versions of the HDF5 library (v < 1.10) unlinking an object was not working as expected
|
||||
@ -1310,8 +1310,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge7d036c" class="outline-2">
|
||||
<h2 id="orge7d036c"><span class="section-number-2">11</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org6c9c271" class="outline-2">
|
||||
<h2 id="org6c9c271"><span class="section-number-2">11</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
|
||||
@ -1564,8 +1564,8 @@ Size specifies the number of data items (e.g. determinants) to process.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga07a87f" class="outline-2">
|
||||
<h2 id="orga07a87f"><span class="section-number-2">12</span> Helper functions</h2>
|
||||
<div id="outline-container-org26aff54" class="outline-2">
|
||||
<h2 id="org26aff54"><span class="section-number-2">12</span> Helper functions</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1828,7 +1828,7 @@ Size specifies the number of data items (e.g. determinants) to process.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-07-08 Fri 16:14</p>
|
||||
<p class="date">Created: 2022-07-11 Mon 13:33</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2022-07-08 Fri 16:14 -->
|
||||
<!-- 2022-07-11 Mon 13:34 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TEXT back end</title>
|
||||
@ -311,21 +311,21 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org970f1d2">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#orgd668e68">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#orgeb45d9e">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org1855cec">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org4ea0c44">5. Template for text read a group</a></li>
|
||||
<li><a href="#orgf9fbafa">6. Template for text has a group</a></li>
|
||||
<li><a href="#org01130e2">7. Template for text flush a group</a></li>
|
||||
<li><a href="#org85d1874">8. Template for text free memory</a></li>
|
||||
<li><a href="#org747a9ed">9. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org167873f">10. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgaaed01c">11. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org2f2c34d">12. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org99df138">13. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#orge411de6">14. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org2f1ebbf">15. Source code for the determinant part</a></li>
|
||||
<li><a href="#org16c26ee">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org0dd26c1">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org8667df1">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#orga29cfb2">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org7ae7b54">5. Template for text read a group</a></li>
|
||||
<li><a href="#orga78175e">6. Template for text has a group</a></li>
|
||||
<li><a href="#org60e3043">7. Template for text flush a group</a></li>
|
||||
<li><a href="#org4523b5b">8. Template for text free memory</a></li>
|
||||
<li><a href="#orgfb7f2c5">9. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgcd1d6aa">10. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org7dee74c">11. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgd605018">12. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgafbe580">13. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org86b3019">14. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org7eed2f6">15. Source code for the determinant part</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -347,8 +347,8 @@ directory.
|
||||
The file is written when closed, or when the flush function is called.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-org970f1d2" class="outline-2">
|
||||
<h2 id="org970f1d2"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div id="outline-container-org16c26ee" class="outline-2">
|
||||
<h2 id="org16c26ee"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
|
||||
@ -367,8 +367,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd668e68" class="outline-2">
|
||||
<h2 id="orgd668e68"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div id="outline-container-org0dd26c1" class="outline-2">
|
||||
<h2 id="org0dd26c1"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
|
||||
@ -388,8 +388,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgeb45d9e" class="outline-2">
|
||||
<h2 id="orgeb45d9e"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div id="outline-container-org8667df1" class="outline-2">
|
||||
<h2 id="org8667df1"><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>
|
||||
@ -548,8 +548,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1855cec" class="outline-2">
|
||||
<h2 id="org1855cec"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div id="outline-container-orga29cfb2" class="outline-2">
|
||||
<h2 id="orga29cfb2"><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>
|
||||
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4ea0c44" class="outline-2">
|
||||
<h2 id="org4ea0c44"><span class="section-number-2">5</span> Template for text read a group</h2>
|
||||
<div id="outline-container-org7ae7b54" class="outline-2">
|
||||
<h2 id="org7ae7b54"><span class="section-number-2">5</span> Template for text read a group</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c">$group$_t*
|
||||
@ -798,8 +798,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf9fbafa" class="outline-2">
|
||||
<h2 id="orgf9fbafa"><span class="section-number-2">6</span> Template for text has a group</h2>
|
||||
<div id="outline-container-orga78175e" class="outline-2">
|
||||
<h2 id="orga78175e"><span class="section-number-2">6</span> Template for text has a group</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -839,8 +839,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org01130e2" class="outline-2">
|
||||
<h2 id="org01130e2"><span class="section-number-2">7</span> Template for text flush a group</h2>
|
||||
<div id="outline-container-org60e3043" class="outline-2">
|
||||
<h2 id="org60e3043"><span class="section-number-2">7</span> Template for text flush a group</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -904,8 +904,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org85d1874" class="outline-2">
|
||||
<h2 id="org85d1874"><span class="section-number-2">8</span> Template for text free memory</h2>
|
||||
<div id="outline-container-org4523b5b" class="outline-2">
|
||||
<h2 id="org4523b5b"><span class="section-number-2">8</span> Template for text free memory</h2>
|
||||
<div class="outline-text-2" id="text-8">
|
||||
<p>
|
||||
Memory is allocated when reading. The following function frees memory.
|
||||
@ -974,8 +974,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org747a9ed" class="outline-2">
|
||||
<h2 id="org747a9ed"><span class="section-number-2">9</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-orgfb7f2c5" class="outline-2">
|
||||
<h2 id="orgfb7f2c5"><span class="section-number-2">9</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1038,8 +1038,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org167873f" class="outline-2">
|
||||
<h2 id="org167873f"><span class="section-number-2">10</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-orgcd1d6aa" class="outline-2">
|
||||
<h2 id="orgcd1d6aa"><span class="section-number-2">10</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1135,8 +1135,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgaaed01c" class="outline-2">
|
||||
<h2 id="orgaaed01c"><span class="section-number-2">11</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org7dee74c" class="outline-2">
|
||||
<h2 id="org7dee74c"><span class="section-number-2">11</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1237,8 +1237,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org2f2c34d" class="outline-2">
|
||||
<h2 id="org2f2c34d"><span class="section-number-2">12</span> Template for has/read/write a string attribute</h2>
|
||||
<div id="outline-container-orgd605018" class="outline-2">
|
||||
<h2 id="orgd605018"><span class="section-number-2">12</span> Template for has/read/write a string attribute</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1312,8 +1312,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org99df138" class="outline-2">
|
||||
<h2 id="org99df138"><span class="section-number-2">13</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div id="outline-container-orgafbe580" class="outline-2">
|
||||
<h2 id="orgafbe580"><span class="section-number-2">13</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div class="outline-text-2" id="text-13">
|
||||
<p>
|
||||
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
|
||||
@ -1603,8 +1603,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge411de6" class="outline-2">
|
||||
<h2 id="orge411de6"><span class="section-number-2">14</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-org86b3019" class="outline-2">
|
||||
<h2 id="org86b3019"><span class="section-number-2">14</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-14">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1632,8 +1632,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2f1ebbf" class="outline-2">
|
||||
<h2 id="org2f1ebbf"><span class="section-number-2">15</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org7eed2f6" class="outline-2">
|
||||
<h2 id="org7eed2f6"><span class="section-number-2">15</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-15">
|
||||
<p>
|
||||
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
|
||||
@ -2073,7 +2073,7 @@ Size specifies the number of data items, e.g. determinants.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-07-08 Fri 16:14</p>
|
||||
<p class="date">Created: 2022-07-11 Mon 13:34</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
150
trex.html
150
trex.html
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2022-07-08 Fri 16:14 -->
|
||||
<!-- 2022-07-11 Mon 13:34 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TREX Configuration file</title>
|
||||
@ -333,37 +333,37 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org7b34e97">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#orgcb093a1">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org5686cf0">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org6884584">4. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#orgdfc2f04">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org9c9f90b">2. Electron (electron group)</a></li>
|
||||
<li><a href="#orgf30588d">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#orgb28197a">4. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#org3b51b1b">4.1. Example</a></li>
|
||||
<li><a href="#orgc940cff">4.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orga495bbd">5. Basis set (basis group)</a>
|
||||
<li><a href="#org934bc00">5. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#org04cbf57">5.1. Example</a></li>
|
||||
<li><a href="#org0173011">5.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org0c98027">6. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#org2f761cf">6. Atomic orbitals (ao group)</a>
|
||||
<ul>
|
||||
<li><a href="#ao_one_e">6.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
|
||||
<li><a href="#ao_two_e">6.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org5fbfe92">7. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org321d4ab">7. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#org1f4bf48">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org3a81663">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#org67dcd4e">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org69e3470">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org7ffd2e9">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org750ac7e">9. Excited states (state group)</a></li>
|
||||
<li><a href="#orgebd2914">10. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org14d557a">11. Cell (cell group)</a></li>
|
||||
<li><a href="#org8b9af32">12. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#orgc9a1e3c">13. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
<li><a href="#org2f3a5fb">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#orge963548">9. Excited states (state group)</a></li>
|
||||
<li><a href="#org81b795a">10. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#orgbbe58b8">11. Cell (cell group)</a></li>
|
||||
<li><a href="#orgf4cc4b0">12. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#org8bf2b31">13. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -417,8 +417,8 @@ For determinants, the <code>special</code> attribute is present in the type. Thi
|
||||
means that the source code is not produced by the generator, but hand-written.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-org7b34e97" class="outline-2">
|
||||
<h2 id="org7b34e97"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-orgdfc2f04" class="outline-2">
|
||||
<h2 id="orgdfc2f04"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<p>
|
||||
As we expect our files to be archived in open-data repositories, we
|
||||
@ -428,7 +428,7 @@ which have participated to the creation of the file, a list of
|
||||
authors of the file, and a textual description.
|
||||
</p>
|
||||
|
||||
<table id="orgfcfc452" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgb9e4e89" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -509,15 +509,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgcb093a1" class="outline-2">
|
||||
<h2 id="orgcb093a1"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div id="outline-container-org9c9f90b" class="outline-2">
|
||||
<h2 id="org9c9f90b"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
We consider wave functions expressed in the spin-free formalism, where
|
||||
the number of ↑ and ↓ electrons is fixed.
|
||||
</p>
|
||||
|
||||
<table id="org4899550" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga260fc9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -563,15 +563,15 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5686cf0" class="outline-2">
|
||||
<h2 id="org5686cf0"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div id="outline-container-orgf30588d" class="outline-2">
|
||||
<h2 id="orgf30588d"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
<p>
|
||||
The nuclei are considered as fixed point charges. Coordinates are
|
||||
given in Cartesian \((x,y,z)\) format.
|
||||
</p>
|
||||
|
||||
<table id="org4297f86" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1dd82b7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -638,8 +638,8 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6884584" class="outline-2">
|
||||
<h2 id="org6884584"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div id="outline-container-orgb28197a" class="outline-2">
|
||||
<h2 id="orgb28197a"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
<p>
|
||||
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
|
||||
@ -672,7 +672,7 @@ 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="org61ddf74" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgb4f2760" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -774,8 +774,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3b51b1b" class="outline-3">
|
||||
<h3 id="org3b51b1b"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div id="outline-container-orgc940cff" class="outline-3">
|
||||
<h3 id="orgc940cff"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div class="outline-text-3" id="text-4-1">
|
||||
<p>
|
||||
For example, consider H<sub>2</sub> molecule with the following
|
||||
@ -838,8 +838,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga495bbd" class="outline-2">
|
||||
<h2 id="orga495bbd"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div id="outline-container-org934bc00" class="outline-2">
|
||||
<h2 id="org934bc00"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
<p>
|
||||
We consider here basis functions centered on nuclei. Hence, we enable
|
||||
@ -892,7 +892,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).
|
||||
All the basis set parameters are stored in one-dimensional arrays:
|
||||
</p>
|
||||
|
||||
<table id="orgdf5e6af" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org065631f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -986,8 +986,8 @@ All the basis set parameters are stored in one-dimensional arrays:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org04cbf57" class="outline-3">
|
||||
<h3 id="org04cbf57"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div id="outline-container-org0173011" class="outline-3">
|
||||
<h3 id="org0173011"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div class="outline-text-3" id="text-5-1">
|
||||
<p>
|
||||
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
|
||||
@ -1065,8 +1065,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0c98027" class="outline-2">
|
||||
<h2 id="org0c98027"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div id="outline-container-org2f761cf" class="outline-2">
|
||||
<h2 id="org2f761cf"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<p>
|
||||
Going from the atomic basis set to AOs implies a systematic
|
||||
@ -1119,13 +1119,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#orga495bbd">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#org934bc00">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="org2dd8963" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org3a5a772" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1177,8 +1177,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org13abe79" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org13abe79"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div id="outline-container-orga321405" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="orga321405"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div class="outline-text-3" id="text-ao_one_e">
|
||||
<ul class="org-ul">
|
||||
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
|
||||
@ -1195,7 +1195,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org2625af0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org78c2f01" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1290,8 +1290,8 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2db6eeb" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org2db6eeb"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div id="outline-container-org5f75933" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org5f75933"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div class="outline-text-3" id="text-ao_two_e">
|
||||
<p>
|
||||
The two-electron integrals for a two-electron operator \(\hat{O}\) are
|
||||
@ -1312,7 +1312,7 @@ notation.
|
||||
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
|
||||
</ul>
|
||||
|
||||
<table id="orgaec987c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2324726" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1352,10 +1352,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5fbfe92" class="outline-2">
|
||||
<h2 id="org5fbfe92"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div id="outline-container-org321d4ab" class="outline-2">
|
||||
<h2 id="org321d4ab"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="orgc690e28" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd9159e0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1442,8 +1442,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1f4bf48" class="outline-3">
|
||||
<h3 id="org1f4bf48"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div id="outline-container-org67dcd4e" class="outline-3">
|
||||
<h3 id="org67dcd4e"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div class="outline-text-3" id="text-7-1">
|
||||
<p>
|
||||
The operators as the same as those defined in the
|
||||
@ -1451,7 +1451,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org2adc0ed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org713b6ba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1546,8 +1546,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3a81663" class="outline-3">
|
||||
<h3 id="org3a81663"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div id="outline-container-org69e3470" class="outline-3">
|
||||
<h3 id="org69e3470"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div class="outline-text-3" id="text-7-2">
|
||||
<p>
|
||||
The operators as the same as those defined in the
|
||||
@ -1555,7 +1555,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org340cf2c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgea43ca0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1595,8 +1595,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7ffd2e9" class="outline-2">
|
||||
<h2 id="org7ffd2e9"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
|
||||
<div id="outline-container-org2f3a5fb" class="outline-2">
|
||||
<h2 id="org2f3a5fb"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
|
||||
<div class="outline-text-2" id="text-8">
|
||||
<p>
|
||||
The configuration interaction (CI) wave function \(\Psi\)
|
||||
@ -1638,7 +1638,7 @@ 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="org2f8227f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgf1d351f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1684,8 +1684,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org750ac7e" class="outline-2">
|
||||
<h2 id="org750ac7e"><span class="section-number-2">9</span> Excited states (state group)</h2>
|
||||
<div id="outline-container-orge963548" class="outline-2">
|
||||
<h2 id="orge963548"><span class="section-number-2">9</span> Excited states (state group)</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<p>
|
||||
By default, the <code>determinant</code> group corresponds to the ground state.
|
||||
@ -1694,7 +1694,7 @@ correspond to excited state wave functions for the same set of
|
||||
determinants. This is the goal of the present group
|
||||
</p>
|
||||
|
||||
<table id="org0fc333d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgabb862d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1733,8 +1733,8 @@ determinants. This is the goal of the present group
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgebd2914" class="outline-2">
|
||||
<h2 id="orgebd2914"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
|
||||
<div id="outline-container-org81b795a" class="outline-2">
|
||||
<h2 id="org81b795a"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<p>
|
||||
The reduced density matrices are defined in the basis of molecular
|
||||
@ -1787,7 +1787,7 @@ The total energy can be computed as:
|
||||
\]
|
||||
</p>
|
||||
|
||||
<table id="orgb585c96" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2bb9e3f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1868,10 +1868,10 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org14d557a" class="outline-2">
|
||||
<h2 id="org14d557a"><span class="section-number-2">11</span> Cell (cell group)</h2>
|
||||
<div id="outline-container-orgbbe58b8" class="outline-2">
|
||||
<h2 id="orgbbe58b8"><span class="section-number-2">11</span> Cell (cell group)</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<table id="org97347d8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org8479eba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1917,10 +1917,10 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8b9af32" class="outline-2">
|
||||
<h2 id="org8b9af32"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div id="outline-container-orgf4cc4b0" class="outline-2">
|
||||
<h2 id="orgf4cc4b0"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<table id="org0453ff6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1451aae" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1959,8 +1959,8 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc9a1e3c" class="outline-2">
|
||||
<h2 id="orgc9a1e3c"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div id="outline-container-org8bf2b31" class="outline-2">
|
||||
<h2 id="org8bf2b31"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div class="outline-text-2" id="text-13">
|
||||
<p>
|
||||
In quantum Monte Carlo calculations, the wave function is evaluated
|
||||
@ -1974,7 +1974,7 @@ By convention, the electron coordinates contain first all the electrons
|
||||
of $↑$-spin and then all the $↓$-spin.
|
||||
</p>
|
||||
|
||||
<table id="orgc08be08" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org3ff9669" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2029,7 +2029,7 @@ of $↑$-spin and then all the $↓$-spin.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-07-08 Fri 16:14</p>
|
||||
<p class="date">Created: 2022-07-11 Mon 13:34</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