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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 09:27 -->
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<!-- 2022-07-08 Fri 10:28 -->
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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 09:27</p>
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||||
<p class="date">Created: 2022-07-08 Fri 10:28</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 @@
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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 09:27 -->
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||||
<!-- 2022-07-08 Fri 10:28 -->
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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="#org8b535a2">1. Accessing sparse quantities (integrals)</a>
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<li><a href="#orgc4427cd">1. Accessing sparse quantities (integrals)</a>
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<ul>
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<li><a href="#orgfafed08">1.1. Fortran</a>
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<li><a href="#org5747596">1.1. Fortran</a>
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<ul>
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<li><a href="#org5f9626d">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org4438440">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="#orgc99063b">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org894f286">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orgd1c9769">1.1.5. Allocate memory</a></li>
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<li><a href="#orgc193864">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org19d9717">1.1.7. Read two-electron quantities</a>
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<li><a href="#org1e4c410">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#orga535004">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="#org58c1771">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#orgd6034ca">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orgb2f4760">1.1.5. Allocate memory</a></li>
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<li><a href="#org26f23e3">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#orge659810">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#orga94db4d">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org6f5838e">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#orgafa0ecb">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org6777df6">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="#orgea42011">1.1.8. Compute the energy</a></li>
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<li><a href="#org982ec92">1.1.9. Terminate</a></li>
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<li><a href="#orgf1ce2db">1.1.8. Compute the energy</a></li>
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<li><a href="#org7774231">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="#org5822055">2. Reading determinants</a>
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<li><a href="#org1283a83">2. Reading determinants</a>
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<ul>
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<li><a href="#org9bc9207">2.1. Fortran</a></li>
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<li><a href="#orge42477c">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-org8b535a2" class="outline-2">
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<h2 id="org8b535a2"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
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<div id="outline-container-orgc4427cd" class="outline-2">
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<h2 id="orgc4427cd"><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-orgfafed08" class="outline-3">
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<h3 id="orgfafed08"><span class="section-number-3">1.1</span> Fortran</h3>
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||||
<div id="outline-container-org5747596" class="outline-3">
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||||
<h3 id="org5747596"><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-org5f9626d" class="outline-4">
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<h4 id="org5f9626d"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-org1e4c410" class="outline-4">
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<h4 id="org1e4c410"><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-org4438440" class="outline-4">
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<h4 id="org4438440"><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-orga535004" class="outline-4">
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<h4 id="orga535004"><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-orgc99063b" class="outline-4">
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<h4 id="orgc99063b"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-org58c1771" class="outline-4">
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<h4 id="org58c1771"><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-org894f286" class="outline-4">
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||||
<h4 id="org894f286"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-orgd6034ca" class="outline-4">
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<h4 id="orgd6034ca"><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-orgd1c9769" class="outline-4">
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<h4 id="orgd1c9769"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div id="outline-container-orgb2f4760" class="outline-4">
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||||
<h4 id="orgb2f4760"><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-orgc193864" class="outline-4">
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<h4 id="orgc193864"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div id="outline-container-org26f23e3" class="outline-4">
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<h4 id="org26f23e3"><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-org19d9717" class="outline-4">
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<h4 id="org19d9717"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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||||
<div id="outline-container-orge659810" class="outline-4">
|
||||
<h4 id="orge659810"><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-orga94db4d" class="outline-5">
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<h5 id="orga94db4d"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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<div id="outline-container-orgafa0ecb" class="outline-5">
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<h5 id="orgafa0ecb"><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-org6f5838e" class="outline-5">
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<h5 id="org6f5838e"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-org6777df6" class="outline-5">
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<h5 id="org6777df6"><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-orgea42011" class="outline-4">
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<h4 id="orgea42011"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div id="outline-container-orgf1ce2db" class="outline-4">
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<h4 id="orgf1ce2db"><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-org982ec92" class="outline-4">
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<h4 id="org982ec92"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-org7774231" class="outline-4">
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<h4 id="org7774231"><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-org5822055" class="outline-2">
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<h2 id="org5822055"><span class="section-number-2">2</span> Reading determinants</h2>
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<div id="outline-container-org1283a83" class="outline-2">
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<h2 id="org1283a83"><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-org9bc9207" class="outline-3">
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<h3 id="org9bc9207"><span class="section-number-3">2.1</span> Fortran</h3>
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<div id="outline-container-orge42477c" class="outline-3">
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<h3 id="orge42477c"><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: 2022-07-08 Fri 09:27</p>
|
||||
<p class="date">Created: 2022-07-08 Fri 10:28</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 @@
|
||||
"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 09:27 -->
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<!-- 2022-07-08 Fri 10:28 -->
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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: 2022-07-08 Fri 09:27</p>
|
||||
<p class="date">Created: 2022-07-08 Fri 10:28</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 09:27 -->
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<!-- 2022-07-08 Fri 10:28 -->
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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="#org22832ac">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#orgec05919">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org6a5ac87">3. Template for HDF5 init/deinit</a></li>
|
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<li><a href="#orgecc33db">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#org99293ea">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
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<li><a href="#org1ee7de8">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
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<li><a href="#org615c9b9">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
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<li><a href="#org1b1e34d">8. Template for HDF5 has/read/write a dataset of strings</a></li>
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<li><a href="#org283924e">9. Template for HDF5 has/read/write a string attribute</a></li>
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<li><a href="#orgde6ad03">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
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<li><a href="#org5b6b77e">11. Source code for the determinant part</a></li>
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||||
<li><a href="#org7f8cade">12. Helper functions</a></li>
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<li><a href="#orgcc21784">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#orgfe46da2">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org9bf2595">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org891f746">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#org2ec9f6e">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org4d42d75">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
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<li><a href="#org3eff38c">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#org6e7417a">8. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgaded198">9. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#org1f0f206">10. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org8619474">11. Source code for the determinant part</a></li>
|
||||
<li><a href="#orgb2c882d">12. Helper functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org22832ac" class="outline-2">
|
||||
<h2 id="org22832ac"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-orgcc21784" class="outline-2">
|
||||
<h2 id="orgcc21784"><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-orgec05919" class="outline-2">
|
||||
<h2 id="orgec05919"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-orgfe46da2" class="outline-2">
|
||||
<h2 id="orgfe46da2"><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-org6a5ac87" class="outline-2">
|
||||
<h2 id="org6a5ac87"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-org9bf2595" class="outline-2">
|
||||
<h2 id="org9bf2595"><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-orgecc33db" class="outline-2">
|
||||
<h2 id="orgecc33db"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
|
||||
<div id="outline-container-org891f746" class="outline-2">
|
||||
<h2 id="org891f746"><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-org99293ea" class="outline-2">
|
||||
<h2 id="org99293ea"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-org2ec9f6e" class="outline-2">
|
||||
<h2 id="org2ec9f6e"><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-org1ee7de8" class="outline-2">
|
||||
<h2 id="org1ee7de8"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org4d42d75" class="outline-2">
|
||||
<h2 id="org4d42d75"><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-org615c9b9" class="outline-2">
|
||||
<h2 id="org615c9b9"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-org3eff38c" class="outline-2">
|
||||
<h2 id="org3eff38c"><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-org1b1e34d" class="outline-2">
|
||||
<h2 id="org1b1e34d"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org6e7417a" class="outline-2">
|
||||
<h2 id="org6e7417a"><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-org283924e" class="outline-2">
|
||||
<h2 id="org283924e"><span class="section-number-2">9</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-orgaded198" class="outline-2">
|
||||
<h2 id="orgaded198"><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-orgde6ad03" class="outline-2">
|
||||
<h2 id="orgde6ad03"><span class="section-number-2">10</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-org1f0f206" class="outline-2">
|
||||
<h2 id="org1f0f206"><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-org5b6b77e" class="outline-2">
|
||||
<h2 id="org5b6b77e"><span class="section-number-2">11</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org8619474" class="outline-2">
|
||||
<h2 id="org8619474"><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-org7f8cade" class="outline-2">
|
||||
<h2 id="org7f8cade"><span class="section-number-2">12</span> Helper functions</h2>
|
||||
<div id="outline-container-orgb2c882d" class="outline-2">
|
||||
<h2 id="orgb2c882d"><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 09:27</p>
|
||||
<p class="date">Created: 2022-07-08 Fri 10:28</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 09:27 -->
|
||||
<!-- 2022-07-08 Fri 10:28 -->
|
||||
<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="#org93f1ae5">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org13e703a">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org8be082b">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org7c2052d">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org99deda9">5. Template for text read a group</a></li>
|
||||
<li><a href="#orgd8de6fb">6. Template for text has a group</a></li>
|
||||
<li><a href="#org9d2b6e2">7. Template for text flush a group</a></li>
|
||||
<li><a href="#org9aff418">8. Template for text free memory</a></li>
|
||||
<li><a href="#org1593d66">9. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org0b4c3ac">10. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org83c7e26">11. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org00bf1e9">12. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgd717828">13. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org5fb3ad5">14. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org9145d29">15. Source code for the determinant part</a></li>
|
||||
<li><a href="#orga1f1196">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org6f326b7">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org15191fa">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org946838c">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org93c4012">5. Template for text read a group</a></li>
|
||||
<li><a href="#org043862c">6. Template for text has a group</a></li>
|
||||
<li><a href="#orgcb54dab">7. Template for text flush a group</a></li>
|
||||
<li><a href="#org42ee0c9">8. Template for text free memory</a></li>
|
||||
<li><a href="#org5277a19">9. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgdc158af">10. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org2e941ef">11. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgcf41f10">12. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org37e6a65">13. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org0e1863c">14. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org343b62c">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-org93f1ae5" class="outline-2">
|
||||
<h2 id="org93f1ae5"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div id="outline-container-orga1f1196" class="outline-2">
|
||||
<h2 id="orga1f1196"><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-org13e703a" class="outline-2">
|
||||
<h2 id="org13e703a"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div id="outline-container-org6f326b7" class="outline-2">
|
||||
<h2 id="org6f326b7"><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-org8be082b" class="outline-2">
|
||||
<h2 id="org8be082b"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div id="outline-container-org15191fa" class="outline-2">
|
||||
<h2 id="org15191fa"><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-org7c2052d" class="outline-2">
|
||||
<h2 id="org7c2052d"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div id="outline-container-org946838c" class="outline-2">
|
||||
<h2 id="org946838c"><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-org99deda9" class="outline-2">
|
||||
<h2 id="org99deda9"><span class="section-number-2">5</span> Template for text read a group</h2>
|
||||
<div id="outline-container-org93c4012" class="outline-2">
|
||||
<h2 id="org93c4012"><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*
|
||||
@ -704,13 +704,14 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
/* <span style="color: #b22222;">conventional fcanf with "%s" only return the string before the first space character</span>
|
||||
<span style="color: #b22222;"> * to read string with spaces use "%[^\n]" possible with space before or after, i.e. " %[^\n]"</span>
|
||||
<span style="color: #b22222;"> </span>*/
|
||||
rc = fscanf(f, <span style="color: #8b2252;">" %1023[^\n]"</span>, tmp_$group_dset$);
|
||||
rc = fscanf(f, <span style="color: #8b2252;">" %1023[^\n]"</span>, buffer);
|
||||
<span style="color: #a020f0;">if</span> (rc != 1) {
|
||||
trexio_text_free_read_$group$(buffer, f, file, $group$);
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
|
||||
}
|
||||
|
||||
<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">tmp_$group_dset$_len</span> = strlen($group$->$group_dset$[i]);
|
||||
<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">tmp_$group_dset$_len</span> = strlen(buffer);
|
||||
strncpy(tmp_$group_dset$, buffer, tmp_$group_dset$_len + 1);
|
||||
tmp_$group_dset$ += tmp_$group_dset$_len + 1;
|
||||
}
|
||||
}
|
||||
@ -768,14 +769,15 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
|
||||
}
|
||||
|
||||
rc = fscanf(f, <span style="color: #8b2252;">" %1023[^\n]"</span>, $group$->$group_str$);
|
||||
rc = fscanf(f, <span style="color: #8b2252;">" %1023[^\n]"</span>, buffer);
|
||||
<span style="color: #a020f0;">if</span> (rc != 1) {
|
||||
trexio_text_free_read_$group$(buffer, f, file, $group$);
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
|
||||
}
|
||||
/* <span style="color: #b22222;">Safer string conversion to avoid buffer overflow in fscanf </span>*/
|
||||
strncpy($group$->$group_str$, buffer, $group$->len_$group_str$);
|
||||
|
||||
}
|
||||
|
||||
// <span style="color: #b22222;">END REPEAT GROUP_ATTR_STR</span>
|
||||
} <span style="color: #a020f0;">else</span> {
|
||||
<span style="color: #a020f0;">continue</span>;
|
||||
@ -796,8 +798,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd8de6fb" class="outline-2">
|
||||
<h2 id="orgd8de6fb"><span class="section-number-2">6</span> Template for text has a group</h2>
|
||||
<div id="outline-container-org043862c" class="outline-2">
|
||||
<h2 id="org043862c"><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>
|
||||
@ -837,8 +839,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9d2b6e2" class="outline-2">
|
||||
<h2 id="org9d2b6e2"><span class="section-number-2">7</span> Template for text flush a group</h2>
|
||||
<div id="outline-container-orgcb54dab" class="outline-2">
|
||||
<h2 id="orgcb54dab"><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>
|
||||
@ -902,8 +904,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9aff418" class="outline-2">
|
||||
<h2 id="org9aff418"><span class="section-number-2">8</span> Template for text free memory</h2>
|
||||
<div id="outline-container-org42ee0c9" class="outline-2">
|
||||
<h2 id="org42ee0c9"><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.
|
||||
@ -972,8 +974,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1593d66" class="outline-2">
|
||||
<h2 id="org1593d66"><span class="section-number-2">9</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-org5277a19" class="outline-2">
|
||||
<h2 id="org5277a19"><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>
|
||||
@ -1036,8 +1038,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0b4c3ac" class="outline-2">
|
||||
<h2 id="org0b4c3ac"><span class="section-number-2">10</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-orgdc158af" class="outline-2">
|
||||
<h2 id="orgdc158af"><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.
|
||||
@ -1133,8 +1135,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org83c7e26" class="outline-2">
|
||||
<h2 id="org83c7e26"><span class="section-number-2">11</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org2e941ef" class="outline-2">
|
||||
<h2 id="org2e941ef"><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.
|
||||
@ -1235,8 +1237,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org00bf1e9" class="outline-2">
|
||||
<h2 id="org00bf1e9"><span class="section-number-2">12</span> Template for has/read/write a string attribute</h2>
|
||||
<div id="outline-container-orgcf41f10" class="outline-2">
|
||||
<h2 id="orgcf41f10"><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>
|
||||
@ -1310,8 +1312,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgd717828" class="outline-2">
|
||||
<h2 id="orgd717828"><span class="section-number-2">13</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div id="outline-container-org37e6a65" class="outline-2">
|
||||
<h2 id="org37e6a65"><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
|
||||
@ -1601,8 +1603,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5fb3ad5" class="outline-2">
|
||||
<h2 id="org5fb3ad5"><span class="section-number-2">14</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-org0e1863c" class="outline-2">
|
||||
<h2 id="org0e1863c"><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>
|
||||
@ -1630,8 +1632,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9145d29" class="outline-2">
|
||||
<h2 id="org9145d29"><span class="section-number-2">15</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-org343b62c" class="outline-2">
|
||||
<h2 id="org343b62c"><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
|
||||
@ -2071,7 +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 09:27</p>
|
||||
<p class="date">Created: 2022-07-08 Fri 10:28</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 09:27 -->
|
||||
<!-- 2022-07-08 Fri 10:28 -->
|
||||
<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="#orgfa4e1b7">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#orge952520">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org92bf20a">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#orgcba6c10">4. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#org0b597bc">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#orge1c999f">2. Electron (electron group)</a></li>
|
||||
<li><a href="#orged5c00d">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org8db0f38">4. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#org43dbf87">4.1. Example</a></li>
|
||||
<li><a href="#orga1b5fc5">4.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org812e12c">5. Basis set (basis group)</a>
|
||||
<li><a href="#org0fb1ce2">5. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#org34214c5">5.1. Example</a></li>
|
||||
<li><a href="#org0c19f3a">5.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org073d16b">6. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#orgb1943aa">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="#org8c91f6a">7. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#orge3cf408">7. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#org1cb9c8c">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org684577f">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#orgda7de53">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orgec60922">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgc40b3e6">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#orgf7ffcc0">9. Excited states (state group)</a></li>
|
||||
<li><a href="#org6731254">10. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#orgd21cfa9">11. Cell (cell group)</a></li>
|
||||
<li><a href="#org4a50621">12. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#orgde5c39d">13. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
<li><a href="#org89114a7">8. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#orge7794da">9. Excited states (state group)</a></li>
|
||||
<li><a href="#orgcc58a8d">10. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org30062e2">11. Cell (cell group)</a></li>
|
||||
<li><a href="#org19aaadc">12. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#orgd278416">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-orgfa4e1b7" class="outline-2">
|
||||
<h2 id="orgfa4e1b7"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-org0b597bc" class="outline-2">
|
||||
<h2 id="org0b597bc"><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="org7a36afa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgb60d684" 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-orge952520" class="outline-2">
|
||||
<h2 id="orge952520"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div id="outline-container-orge1c999f" class="outline-2">
|
||||
<h2 id="orge1c999f"><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="orgedc4ddf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgbaf8223" 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-org92bf20a" class="outline-2">
|
||||
<h2 id="org92bf20a"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div id="outline-container-orged5c00d" class="outline-2">
|
||||
<h2 id="orged5c00d"><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="org8a2923f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org478da3d" 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-orgcba6c10" class="outline-2">
|
||||
<h2 id="orgcba6c10"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div id="outline-container-org8db0f38" class="outline-2">
|
||||
<h2 id="org8db0f38"><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="org37e74c4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org285d96d" 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-org43dbf87" class="outline-3">
|
||||
<h3 id="org43dbf87"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div id="outline-container-orga1b5fc5" class="outline-3">
|
||||
<h3 id="orga1b5fc5"><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-org812e12c" class="outline-2">
|
||||
<h2 id="org812e12c"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div id="outline-container-org0fb1ce2" class="outline-2">
|
||||
<h2 id="org0fb1ce2"><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="orgdaf325b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org18a289d" 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-org34214c5" class="outline-3">
|
||||
<h3 id="org34214c5"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div id="outline-container-org0c19f3a" class="outline-3">
|
||||
<h3 id="org0c19f3a"><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-org073d16b" class="outline-2">
|
||||
<h2 id="org073d16b"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div id="outline-container-orgb1943aa" class="outline-2">
|
||||
<h2 id="orgb1943aa"><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="#org812e12c">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#org0fb1ce2">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="org151e6e1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org646dcb5" 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-org9b629ee" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org9b629ee"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div id="outline-container-org2d38f32" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org2d38f32"></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="org7e7f63f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgbf8ee73" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1290,8 +1290,8 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7bccde8" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org7bccde8"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div id="outline-container-orge8dfb15" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="orge8dfb15"></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="org93c80eb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org8d8dd29" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1352,10 +1352,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8c91f6a" class="outline-2">
|
||||
<h2 id="org8c91f6a"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div id="outline-container-orge3cf408" class="outline-2">
|
||||
<h2 id="orge3cf408"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="orgdfe73c9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgdebdcca" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1442,8 +1442,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1cb9c8c" class="outline-3">
|
||||
<h3 id="org1cb9c8c"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div id="outline-container-orgda7de53" class="outline-3">
|
||||
<h3 id="orgda7de53"><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="org10876e7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org4e3aece" 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-org684577f" class="outline-3">
|
||||
<h3 id="org684577f"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div id="outline-container-orgec60922" class="outline-3">
|
||||
<h3 id="orgec60922"><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="org664f9e4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org207aa4a" 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-orgc40b3e6" class="outline-2">
|
||||
<h2 id="orgc40b3e6"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
|
||||
<div id="outline-container-org89114a7" class="outline-2">
|
||||
<h2 id="org89114a7"><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="org6739d80" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgb69079d" 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-orgf7ffcc0" class="outline-2">
|
||||
<h2 id="orgf7ffcc0"><span class="section-number-2">9</span> Excited states (state group)</h2>
|
||||
<div id="outline-container-orge7794da" class="outline-2">
|
||||
<h2 id="orge7794da"><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="org097046b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgb1afb32" 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-org6731254" class="outline-2">
|
||||
<h2 id="org6731254"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
|
||||
<div id="outline-container-orgcc58a8d" class="outline-2">
|
||||
<h2 id="orgcc58a8d"><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="org2bc2966" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org90381c2" 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-orgd21cfa9" class="outline-2">
|
||||
<h2 id="orgd21cfa9"><span class="section-number-2">11</span> Cell (cell group)</h2>
|
||||
<div id="outline-container-org30062e2" class="outline-2">
|
||||
<h2 id="org30062e2"><span class="section-number-2">11</span> Cell (cell group)</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<table id="org23abf7a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org544d124" 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-org4a50621" class="outline-2">
|
||||
<h2 id="org4a50621"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div id="outline-container-org19aaadc" class="outline-2">
|
||||
<h2 id="org19aaadc"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<table id="orgaaa55f6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org7dcc4bd" 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-orgde5c39d" class="outline-2">
|
||||
<h2 id="orgde5c39d"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div id="outline-container-orgd278416" class="outline-2">
|
||||
<h2 id="orgd278416"><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="orga134204" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1ffe5d5" 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 09:27</p>
|
||||
<p class="date">Created: 2022-07-08 Fri 10:28</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