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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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<!-- 2022-10-04 Tue 15:14 -->
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<!-- 2022-10-04 Tue 15:30 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>TREXIO source code documentation</title>
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@ -347,7 +347,7 @@ and bug reports should be submitted at
|
||||
</div>
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||||
<div id="postamble" class="status">
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<p class="author">Author: TREX-CoE</p>
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||||
<p class="date">Created: 2022-10-04 Tue 15:14</p>
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||||
<p class="date">Created: 2022-10-04 Tue 15:30</p>
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||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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||||
</div>
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||||
</body>
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||||
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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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||||
<!-- 2022-10-04 Tue 15:14 -->
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||||
<!-- 2022-10-04 Tue 15:30 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>Examples</title>
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||||
@ -333,31 +333,31 @@ for the JavaScript code in this tag.
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||||
<h2>Table of Contents</h2>
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<div id="text-table-of-contents">
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<ul>
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<li><a href="#org49fef33">1. Accessing sparse quantities (integrals)</a>
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<li><a href="#org42c7818">1. Accessing sparse quantities (integrals)</a>
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<ul>
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<li><a href="#orgb224d18">1.1. Fortran</a>
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||||
<li><a href="#org1417273">1.1. Fortran</a>
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||||
<ul>
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||||
<li><a href="#orgd781927">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org2465fbf">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="#orgc19b206">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org06c0bba">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orgd2b8932">1.1.5. Allocate memory</a></li>
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<li><a href="#org3d060fd">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org3b9715c">1.1.7. Read two-electron quantities</a>
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<li><a href="#org6104921">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org0df0850">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="#org619ac0c">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org69319d5">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orga63b271">1.1.5. Allocate memory</a></li>
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<li><a href="#orgf917f8a">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org5a2eff4">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#org5baa0db">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#orgb7a5702">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#orgacd65fb">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org0445f9e">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="#orgc74fb12">1.1.8. Compute the energy</a></li>
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<li><a href="#org82e88ba">1.1.9. Terminate</a></li>
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<li><a href="#org1b2bcd8">1.1.8. Compute the energy</a></li>
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<li><a href="#orgf7d2f17">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="#orga749914">2. Reading determinants</a>
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<li><a href="#org8088931">2. Reading determinants</a>
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<ul>
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<li><a href="#org199ea60">2.1. Fortran</a></li>
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<li><a href="#orgff97007">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-org49fef33" class="outline-2">
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<h2 id="org49fef33"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
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<div id="outline-container-org42c7818" class="outline-2">
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||||
<h2 id="org42c7818"><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-orgb224d18" class="outline-3">
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<h3 id="orgb224d18"><span class="section-number-3">1.1</span> Fortran</h3>
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<div id="outline-container-org1417273" class="outline-3">
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<h3 id="org1417273"><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-orgd781927" class="outline-4">
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<h4 id="orgd781927"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-org6104921" class="outline-4">
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<h4 id="org6104921"><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-org2465fbf" class="outline-4">
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<h4 id="org2465fbf"><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-org0df0850" class="outline-4">
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<h4 id="org0df0850"><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-orgc19b206" class="outline-4">
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<h4 id="orgc19b206"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-org619ac0c" class="outline-4">
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<h4 id="org619ac0c"><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-org06c0bba" class="outline-4">
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||||
<h4 id="org06c0bba"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-org69319d5" class="outline-4">
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<h4 id="org69319d5"><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-orgd2b8932" class="outline-4">
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<h4 id="orgd2b8932"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div id="outline-container-orga63b271" class="outline-4">
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||||
<h4 id="orga63b271"><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-org3d060fd" class="outline-4">
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<h4 id="org3d060fd"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div id="outline-container-orgf917f8a" class="outline-4">
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<h4 id="orgf917f8a"><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-org3b9715c" class="outline-4">
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||||
<h4 id="org3b9715c"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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||||
<div id="outline-container-org5a2eff4" class="outline-4">
|
||||
<h4 id="org5a2eff4"><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-org5baa0db" class="outline-5">
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<h5 id="org5baa0db"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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||||
<div id="outline-container-orgacd65fb" class="outline-5">
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||||
<h5 id="orgacd65fb"><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-orgb7a5702" class="outline-5">
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<h5 id="orgb7a5702"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-org0445f9e" class="outline-5">
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<h5 id="org0445f9e"><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-orgc74fb12" class="outline-4">
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<h4 id="orgc74fb12"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div id="outline-container-org1b2bcd8" class="outline-4">
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<h4 id="org1b2bcd8"><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-org82e88ba" class="outline-4">
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<h4 id="org82e88ba"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-orgf7d2f17" class="outline-4">
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<h4 id="orgf7d2f17"><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-orga749914" class="outline-2">
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<h2 id="orga749914"><span class="section-number-2">2</span> Reading determinants</h2>
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<div id="outline-container-org8088931" class="outline-2">
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<h2 id="org8088931"><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-org199ea60" class="outline-3">
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<h3 id="org199ea60"><span class="section-number-3">2.1</span> Fortran</h3>
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<div id="outline-container-orgff97007" class="outline-3">
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||||
<h3 id="orgff97007"><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">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-10-04 Tue 15:14</p>
|
||||
<p class="date">Created: 2022-10-04 Tue 15:30</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
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||||
|
||||
@ -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>
|
||||
<!-- 2022-10-04 Tue 15:14 -->
|
||||
<!-- 2022-10-04 Tue 15:30 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
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||||
<title>TREXIO source code documentation</title>
|
||||
@ -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: 2022-10-04 Tue 15:14</p>
|
||||
<p class="date">Created: 2022-10-04 Tue 15:30</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -3,7 +3,7 @@
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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||||
<head>
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||||
<!-- 2022-10-04 Tue 15:14 -->
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<!-- 2022-10-04 Tue 15:30 -->
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||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>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="#orgbe6e4a3">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org4d10685">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org9826774">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orgb7cb8d2">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#org5426a6e">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgd522468">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
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<li><a href="#org61c8d43">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
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<li><a href="#orgf987587">8. Template for HDF5 has/read/write a dataset of strings</a></li>
|
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<li><a href="#org4907da8">9. Template for HDF5 has/read/write a string attribute</a></li>
|
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<li><a href="#orgf503735">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org3849153">11. Source code for the determinant part</a></li>
|
||||
<li><a href="#org1ac17f9">12. Helper functions</a></li>
|
||||
<li><a href="#org1e1f226">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#orgb00a10b">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org1f5ce89">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org6e34dc9">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#orgacb9979">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org5cf4476">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgbf16202">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#org0c72410">8. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org01fd1b8">9. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#org0a14af1">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org6cff039">11. Source code for the determinant part</a></li>
|
||||
<li><a href="#orgdb62ea5">12. Helper functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgbe6e4a3" class="outline-2">
|
||||
<h2 id="orgbe6e4a3"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-org1e1f226" class="outline-2">
|
||||
<h2 id="org1e1f226"><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-org4d10685" class="outline-2">
|
||||
<h2 id="org4d10685"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-orgb00a10b" class="outline-2">
|
||||
<h2 id="orgb00a10b"><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-org9826774" class="outline-2">
|
||||
<h2 id="org9826774"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-org1f5ce89" class="outline-2">
|
||||
<h2 id="org1f5ce89"><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>
|
||||
@ -482,8 +482,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb7cb8d2" class="outline-2">
|
||||
<h2 id="orgb7cb8d2"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
|
||||
<div id="outline-container-org6e34dc9" class="outline-2">
|
||||
<h2 id="org6e34dc9"><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>
|
||||
@ -513,8 +513,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5426a6e" class="outline-2">
|
||||
<h2 id="org5426a6e"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-orgacb9979" class="outline-2">
|
||||
<h2 id="orgacb9979"><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>
|
||||
@ -618,8 +618,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd522468" class="outline-2">
|
||||
<h2 id="orgd522468"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org5cf4476" class="outline-2">
|
||||
<h2 id="org5cf4476"><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>
|
||||
@ -753,8 +753,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org61c8d43" class="outline-2">
|
||||
<h2 id="org61c8d43"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-orgbf16202" class="outline-2">
|
||||
<h2 id="orgbf16202"><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
|
||||
@ -957,8 +957,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf987587" class="outline-2">
|
||||
<h2 id="orgf987587"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org0c72410" class="outline-2">
|
||||
<h2 id="org0c72410"><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>
|
||||
@ -1156,8 +1156,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4907da8" class="outline-2">
|
||||
<h2 id="org4907da8"><span class="section-number-2">9</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org01fd1b8" class="outline-2">
|
||||
<h2 id="org01fd1b8"><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>
|
||||
@ -1284,8 +1284,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgf503735" class="outline-2">
|
||||
<h2 id="orgf503735"><span class="section-number-2">10</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-org0a14af1" class="outline-2">
|
||||
<h2 id="org0a14af1"><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
|
||||
@ -1325,8 +1325,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3849153" class="outline-2">
|
||||
<h2 id="org3849153"><span class="section-number-2">11</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org6cff039" class="outline-2">
|
||||
<h2 id="org6cff039"><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.
|
||||
@ -1579,8 +1579,8 @@ Size specifies the number of data items (e.g. determinants) to process.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1ac17f9" class="outline-2">
|
||||
<h2 id="org1ac17f9"><span class="section-number-2">12</span> Helper functions</h2>
|
||||
<div id="outline-container-orgdb62ea5" class="outline-2">
|
||||
<h2 id="orgdb62ea5"><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>
|
||||
@ -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: 2022-10-04 Tue 15:14</p>
|
||||
<p class="date">Created: 2022-10-04 Tue 15:30</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2022-10-04 Tue 15:14 -->
|
||||
<!-- 2022-10-04 Tue 15:30 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TEXT back end</title>
|
||||
@ -311,22 +311,22 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orgf5c1ed6">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org4b42a8d">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org660af5c">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org8f56d5e">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orgd3e397d">5. Flush function (templated part)</a></li>
|
||||
<li><a href="#org2fa0dad">6. Template for text read a group</a></li>
|
||||
<li><a href="#orgf05eebf">7. Template for text has a group</a></li>
|
||||
<li><a href="#org189d95a">8. Template for text flush a group</a></li>
|
||||
<li><a href="#orgf5e640b">9. Template for text free memory</a></li>
|
||||
<li><a href="#orgb0d6d3a">10. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org0ee7477">11. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orge3edae2">12. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org40be1ff">13. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orga5d03a4">14. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org2972f34">15. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orgaf8ded5">16. Source code for the determinant part</a></li>
|
||||
<li><a href="#org9d62113">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#orgb74cc83">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org789af86">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org39c9237">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org023e4a5">5. Flush function (templated part)</a></li>
|
||||
<li><a href="#orgc580483">6. Template for text read a group</a></li>
|
||||
<li><a href="#orgc8936b4">7. Template for text has a group</a></li>
|
||||
<li><a href="#org4f6762c">8. Template for text flush a group</a></li>
|
||||
<li><a href="#org086a039">9. Template for text free memory</a></li>
|
||||
<li><a href="#orge565e65">10. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orga0d282a">11. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org31593bd">12. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgb84cebd">13. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org9bca428">14. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#orgb8dbd9a">15. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orgeb697cc">16. Source code for the determinant part</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -348,8 +348,8 @@ directory.
|
||||
The file is written when closed, or when the flush function is called.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-orgf5c1ed6" class="outline-2">
|
||||
<h2 id="orgf5c1ed6"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div id="outline-container-org9d62113" class="outline-2">
|
||||
<h2 id="org9d62113"><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 {
|
||||
@ -368,8 +368,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4b42a8d" class="outline-2">
|
||||
<h2 id="org4b42a8d"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div id="outline-container-orgb74cc83" class="outline-2">
|
||||
<h2 id="orgb74cc83"><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
|
||||
@ -389,8 +389,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org660af5c" class="outline-2">
|
||||
<h2 id="org660af5c"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div id="outline-container-org789af86" class="outline-2">
|
||||
<h2 id="org789af86"><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>
|
||||
@ -557,8 +557,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8f56d5e" class="outline-2">
|
||||
<h2 id="org8f56d5e"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div id="outline-container-org39c9237" class="outline-2">
|
||||
<h2 id="org39c9237"><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>
|
||||
@ -580,8 +580,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd3e397d" class="outline-2">
|
||||
<h2 id="orgd3e397d"><span class="section-number-2">5</span> Flush function (templated part)</h2>
|
||||
<div id="outline-container-org023e4a5" class="outline-2">
|
||||
<h2 id="org023e4a5"><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>
|
||||
@ -604,8 +604,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2fa0dad" class="outline-2">
|
||||
<h2 id="org2fa0dad"><span class="section-number-2">6</span> Template for text read a group</h2>
|
||||
<div id="outline-container-orgc580483" class="outline-2">
|
||||
<h2 id="orgc580483"><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*
|
||||
@ -831,8 +831,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf05eebf" class="outline-2">
|
||||
<h2 id="orgf05eebf"><span class="section-number-2">7</span> Template for text has a group</h2>
|
||||
<div id="outline-container-orgc8936b4" class="outline-2">
|
||||
<h2 id="orgc8936b4"><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>
|
||||
@ -872,8 +872,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org189d95a" class="outline-2">
|
||||
<h2 id="org189d95a"><span class="section-number-2">8</span> Template for text flush a group</h2>
|
||||
<div id="outline-container-org4f6762c" class="outline-2">
|
||||
<h2 id="org4f6762c"><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>
|
||||
@ -937,8 +937,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf5e640b" class="outline-2">
|
||||
<h2 id="orgf5e640b"><span class="section-number-2">9</span> Template for text free memory</h2>
|
||||
<div id="outline-container-org086a039" class="outline-2">
|
||||
<h2 id="org086a039"><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.
|
||||
@ -1007,8 +1007,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb0d6d3a" class="outline-2">
|
||||
<h2 id="orgb0d6d3a"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-orge565e65" class="outline-2">
|
||||
<h2 id="orge565e65"><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>
|
||||
@ -1071,8 +1071,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0ee7477" class="outline-2">
|
||||
<h2 id="org0ee7477"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-orga0d282a" class="outline-2">
|
||||
<h2 id="orga0d282a"><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.
|
||||
@ -1168,8 +1168,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orge3edae2" class="outline-2">
|
||||
<h2 id="orge3edae2"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org31593bd" class="outline-2">
|
||||
<h2 id="org31593bd"><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.
|
||||
@ -1270,8 +1270,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org40be1ff" class="outline-2">
|
||||
<h2 id="org40be1ff"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
|
||||
<div id="outline-container-orgb84cebd" class="outline-2">
|
||||
<h2 id="orgb84cebd"><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>
|
||||
@ -1345,8 +1345,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orga5d03a4" class="outline-2">
|
||||
<h2 id="orga5d03a4"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div id="outline-container-org9bca428" class="outline-2">
|
||||
<h2 id="org9bca428"><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
|
||||
@ -1636,8 +1636,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2972f34" class="outline-2">
|
||||
<h2 id="org2972f34"><span class="section-number-2">15</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-orgb8dbd9a" class="outline-2">
|
||||
<h2 id="orgb8dbd9a"><span class="section-number-2">15</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-15">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1665,8 +1665,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgaf8ded5" class="outline-2">
|
||||
<h2 id="orgaf8ded5"><span class="section-number-2">16</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-orgeb697cc" class="outline-2">
|
||||
<h2 id="orgeb697cc"><span class="section-number-2">16</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-16">
|
||||
<p>
|
||||
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
|
||||
@ -2106,7 +2106,7 @@ 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: 2022-10-04 Tue 15:14</p>
|
||||
<p class="date">Created: 2022-10-04 Tue 15:30</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
158
trex.html
158
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>
|
||||
<!-- 2022-10-04 Tue 15:14 -->
|
||||
<!-- 2022-10-04 Tue 15:30 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TREX Configuration file</title>
|
||||
@ -333,38 +333,38 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org1b42896">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org82d93d0">2. Electron (electron group)</a></li>
|
||||
<li><a href="#orgcd3484d">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org51efd35">4. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#orgcfb3c67">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#orga4b5862">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org2d50454">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org97a33ae">4. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#orgcea614d">4.1. Example</a></li>
|
||||
<li><a href="#orgf7a6b1a">4.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org3c7cac4">5. Basis set (basis group)</a>
|
||||
<li><a href="#orgd6c1173">5. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#orgb5f87d0">5.1. Example</a></li>
|
||||
<li><a href="#org6fe9c1d">5.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orga0a4481">6. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#org0da7d13">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="#orgcafc15c">7. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org45503ff">7. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#orgc5e76f6">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org3ab6018">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#orgcec550d">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org9fc2375">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org5e96f40">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#orgb5239a8">9. Configuration state functions (csf group)</a></li>
|
||||
<li><a href="#org9120e33">10. Excited states (state group)</a></li>
|
||||
<li><a href="#org76b8e9b">11. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org9d8b688">12. Cell (cell group)</a></li>
|
||||
<li><a href="#orgeb373af">13. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#org453661e">14. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
<li><a href="#orgd129c28">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org984dea8">9. Configuration state functions (csf group)</a></li>
|
||||
<li><a href="#org3b3fd1d">10. Excited states (state group)</a></li>
|
||||
<li><a href="#orga37907c">11. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org3fd50f4">12. Cell (cell group)</a></li>
|
||||
<li><a href="#org0724618">13. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#orgdae0106">14. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -418,8 +418,8 @@ For determinants, the <code>special</code> attribute is present in the type. Thi
|
||||
means that the source code is not produced by the generator, but hand-written.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-org1b42896" class="outline-2">
|
||||
<h2 id="org1b42896"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-orgcfb3c67" class="outline-2">
|
||||
<h2 id="orgcfb3c67"><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
|
||||
@ -429,7 +429,7 @@ which have participated to the creation of the file, a list of
|
||||
authors of the file, and a textual description.
|
||||
</p>
|
||||
|
||||
<table id="orgbac21e3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org0a21c09" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -510,15 +510,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org82d93d0" class="outline-2">
|
||||
<h2 id="org82d93d0"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div id="outline-container-orga4b5862" class="outline-2">
|
||||
<h2 id="orga4b5862"><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="orgf15b344" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org5bf7a54" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -564,15 +564,15 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgcd3484d" class="outline-2">
|
||||
<h2 id="orgcd3484d"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div id="outline-container-org2d50454" class="outline-2">
|
||||
<h2 id="org2d50454"><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="org36df01a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org9182fd4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -639,8 +639,8 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org51efd35" class="outline-2">
|
||||
<h2 id="org51efd35"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div id="outline-container-org97a33ae" class="outline-2">
|
||||
<h2 id="org97a33ae"><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
|
||||
@ -673,7 +673,7 @@ The functions \(V_{A\ell}\) are parameterized as:
|
||||
See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.4984046</a> or <a href="https://doi.org/10.1063/1.5121006">https://doi.org/10.1063/1.5121006</a> for more info.
|
||||
</p>
|
||||
|
||||
<table id="org647a474" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org71f0ead" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -775,8 +775,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgcea614d" class="outline-3">
|
||||
<h3 id="orgcea614d"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div id="outline-container-orgf7a6b1a" class="outline-3">
|
||||
<h3 id="orgf7a6b1a"><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
|
||||
@ -839,8 +839,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3c7cac4" class="outline-2">
|
||||
<h2 id="org3c7cac4"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div id="outline-container-orgd6c1173" class="outline-2">
|
||||
<h2 id="orgd6c1173"><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
|
||||
@ -893,7 +893,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).
|
||||
All the basis set parameters are stored in one-dimensional arrays:
|
||||
</p>
|
||||
|
||||
<table id="orgb92538e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org25d85a6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -987,8 +987,8 @@ All the basis set parameters are stored in one-dimensional arrays:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb5f87d0" class="outline-3">
|
||||
<h3 id="orgb5f87d0"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div id="outline-container-org6fe9c1d" class="outline-3">
|
||||
<h3 id="org6fe9c1d"><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
|
||||
@ -1066,8 +1066,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga0a4481" class="outline-2">
|
||||
<h2 id="orga0a4481"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div id="outline-container-org0da7d13" class="outline-2">
|
||||
<h2 id="org0da7d13"><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
|
||||
@ -1120,13 +1120,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#org3c7cac4">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#orgd6c1173">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="orgbdb67ba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org70a7808" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1178,8 +1178,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb95a805" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="orgb95a805"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div id="outline-container-orgab675b8" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="orgab675b8"></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}}
|
||||
@ -1196,7 +1196,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org312ddb7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org4a086f5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1291,8 +1291,8 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6a5a1b7" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org6a5a1b7"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div id="outline-container-org2b5510e" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org2b5510e"></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
|
||||
@ -1313,7 +1313,7 @@ notation.
|
||||
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
|
||||
</ul>
|
||||
|
||||
<table id="org29fd064" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orge89ece0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1353,10 +1353,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgcafc15c" class="outline-2">
|
||||
<h2 id="orgcafc15c"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div id="outline-container-org45503ff" class="outline-2">
|
||||
<h2 id="org45503ff"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="orge9dd888" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd105e00" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1443,8 +1443,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc5e76f6" class="outline-3">
|
||||
<h3 id="orgc5e76f6"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div id="outline-container-orgcec550d" class="outline-3">
|
||||
<h3 id="orgcec550d"><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
|
||||
@ -1452,7 +1452,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org14202ed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org3dfe259" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1547,8 +1547,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3ab6018" class="outline-3">
|
||||
<h3 id="org3ab6018"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div id="outline-container-org9fc2375" class="outline-3">
|
||||
<h3 id="org9fc2375"><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
|
||||
@ -1556,7 +1556,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orgad73612" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org93b3ee2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1596,8 +1596,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5e96f40" class="outline-2">
|
||||
<h2 id="org5e96f40"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
|
||||
<div id="outline-container-orgd129c28" class="outline-2">
|
||||
<h2 id="orgd129c28"><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 \(\Psi\)
|
||||
@ -1639,7 +1639,7 @@ produced by the code generator.
|
||||
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
|
||||
</p>
|
||||
|
||||
<table id="org2bbe4a2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orge480ea8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1685,8 +1685,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb5239a8" class="outline-2">
|
||||
<h2 id="orgb5239a8"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
|
||||
<div id="outline-container-org984dea8" class="outline-2">
|
||||
<h2 id="org984dea8"><span class="section-number-2">9</span> Configuration state functions (csf group)</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<p>
|
||||
The configuration interaction (CI) wave function \(\Psi\) can be
|
||||
@ -1708,7 +1708,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
|
||||
the basis of Slater determinants.
|
||||
</p>
|
||||
|
||||
<table id="orgedf3605" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org42b53ec" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1754,8 +1754,8 @@ the basis of Slater determinants.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9120e33" class="outline-2">
|
||||
<h2 id="org9120e33"><span class="section-number-2">10</span> Excited states (state group)</h2>
|
||||
<div id="outline-container-org3b3fd1d" class="outline-2">
|
||||
<h2 id="org3b3fd1d"><span class="section-number-2">10</span> Excited states (state group)</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<p>
|
||||
By default, the <code>determinant</code> group corresponds to the ground state.
|
||||
@ -1764,7 +1764,7 @@ correspond to excited state wave functions for the same set of
|
||||
determinants. This is the goal of the present group
|
||||
</p>
|
||||
|
||||
<table id="orgb16eac1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org5673aae" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1803,8 +1803,8 @@ determinants. This is the goal of the present group
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org76b8e9b" class="outline-2">
|
||||
<h2 id="org76b8e9b"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
|
||||
<div id="outline-container-orga37907c" class="outline-2">
|
||||
<h2 id="orga37907c"><span class="section-number-2">11</span> Reduced density matrices (rdm group)</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
The reduced density matrices are defined in the basis of molecular
|
||||
@ -1857,7 +1857,7 @@ The total energy can be computed as:
|
||||
\]
|
||||
</p>
|
||||
|
||||
<table id="org3bae6a7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgc54848e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1938,10 +1938,10 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9d8b688" class="outline-2">
|
||||
<h2 id="org9d8b688"><span class="section-number-2">12</span> Cell (cell group)</h2>
|
||||
<div id="outline-container-org3fd50f4" class="outline-2">
|
||||
<h2 id="org3fd50f4"><span class="section-number-2">12</span> Cell (cell group)</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<table id="orgc8db2c4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org31b804e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1987,10 +1987,10 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgeb373af" class="outline-2">
|
||||
<h2 id="orgeb373af"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div id="outline-container-org0724618" class="outline-2">
|
||||
<h2 id="org0724618"><span class="section-number-2">13</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div class="outline-text-2" id="text-13">
|
||||
<table id="orgf4f627d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org335a3b3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2029,8 +2029,8 @@ The total energy can be computed as:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org453661e" class="outline-2">
|
||||
<h2 id="org453661e"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div id="outline-container-orgdae0106" class="outline-2">
|
||||
<h2 id="orgdae0106"><span class="section-number-2">14</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div class="outline-text-2" id="text-14">
|
||||
<p>
|
||||
In quantum Monte Carlo calculations, the wave function is evaluated
|
||||
@ -2044,7 +2044,7 @@ By convention, the electron coordinates contain first all the electrons
|
||||
of $↑$-spin and then all the $↓$-spin.
|
||||
</p>
|
||||
|
||||
<table id="orgb8ad3be" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org76b1072" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2099,7 +2099,7 @@ of $↑$-spin and then all the $↓$-spin.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-10-04 Tue 15:14</p>
|
||||
<p class="date">Created: 2022-10-04 Tue 15:30</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
Loading…
Reference in New Issue
Block a user