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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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<head>
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<!-- 2023-01-08 Sun 16:18 -->
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<!-- 2023-01-10 Tue 17:49 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>TREXIO source code documentation</title>
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||||
@ -360,7 +360,7 @@ and bug reports should be submitted at
|
||||
</div>
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||||
<div id="postamble" class="status">
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<p class="author">Author: TREX-CoE</p>
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||||
<p class="date">Created: 2023-01-08 Sun 16:18</p>
|
||||
<p class="date">Created: 2023-01-10 Tue 17:49</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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||||
<!-- 2023-01-08 Sun 16:18 -->
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||||
<!-- 2023-01-10 Tue 17:49 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>Examples</title>
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@ -346,31 +346,31 @@ for the JavaScript code in this tag.
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||||
<h2>Table of Contents</h2>
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<div id="text-table-of-contents">
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<ul>
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<li><a href="#org9dea3e4">1. Accessing sparse quantities (integrals)</a>
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<li><a href="#orga189e8e">1. Accessing sparse quantities (integrals)</a>
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<ul>
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<li><a href="#orge49bfc0">1.1. Fortran</a>
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<li><a href="#orgeede694">1.1. Fortran</a>
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||||
<ul>
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<li><a href="#org8d7e2d4">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org2a717dd">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="#orgd7a6b52">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org79b36fa">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org1dc5aee">1.1.5. Allocate memory</a></li>
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<li><a href="#org9a2fb20">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org626d5c6">1.1.7. Read two-electron quantities</a>
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<li><a href="#org3547d55">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#orgae37673">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="#org210edbc">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org3fd170c">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org1b5ae00">1.1.5. Allocate memory</a></li>
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<li><a href="#orgd5d0065">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org874df27">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#org3a71a4c">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#orgd57c288">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#org81d0288">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#orgaf92d5f">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="#org64deb3c">1.1.8. Compute the energy</a></li>
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<li><a href="#orga2eab79">1.1.9. Terminate</a></li>
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<li><a href="#org1f8602d">1.1.8. Compute the energy</a></li>
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<li><a href="#org91c3901">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="#orgfe4c208">2. Reading determinants</a>
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<li><a href="#org611455e">2. Reading determinants</a>
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<ul>
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<li><a href="#org068cda0">2.1. Fortran</a></li>
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<li><a href="#orgd7ad5bd">2.1. Fortran</a></li>
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</ul>
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</li>
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</ul>
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@ -378,12 +378,12 @@ for the JavaScript code in this tag.
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</div>
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<div id="outline-container-org9dea3e4" class="outline-2">
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<h2 id="org9dea3e4"><span class="section-number-2">1</span> Accessing sparse quantities (integrals)</h2>
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<div id="outline-container-orga189e8e" class="outline-2">
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||||
<h2 id="orga189e8e"><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-orge49bfc0" class="outline-3">
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<h3 id="orge49bfc0"><span class="section-number-3">1.1</span> Fortran</h3>
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<div id="outline-container-orgeede694" class="outline-3">
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<h3 id="orgeede694"><span class="section-number-3">1.1</span> Fortran</h3>
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<div class="outline-text-3" id="text-1-1">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
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@ -429,8 +429,8 @@ One needs to read from the TREXIO file:
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</div>
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</div>
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<div id="outline-container-org8d7e2d4" class="outline-4">
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<h4 id="org8d7e2d4"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-org3547d55" class="outline-4">
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<h4 id="org3547d55"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div class="outline-text-4" id="text-1-1-1">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> i, j, k, l, m</span>
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@ -445,8 +445,8 @@ One needs to read from the TREXIO file:
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</div>
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</div>
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<div id="outline-container-org2a717dd" class="outline-4">
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<h4 id="org2a717dd"><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-orgae37673" class="outline-4">
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<h4 id="orgae37673"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
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<div class="outline-text-4" id="text-1-1-2">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
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@ -462,8 +462,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-orgd7a6b52" class="outline-4">
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<h4 id="orgd7a6b52"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-org210edbc" class="outline-4">
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<h4 id="org210edbc"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div class="outline-text-4" id="text-1-1-3">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
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@ -477,8 +477,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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||||
</div>
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<div id="outline-container-org79b36fa" class="outline-4">
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<h4 id="org79b36fa"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-org3fd170c" class="outline-4">
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<h4 id="org3fd170c"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div class="outline-text-4" id="text-1-1-4">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
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@ -492,8 +492,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-org1dc5aee" class="outline-4">
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||||
<h4 id="org1dc5aee"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div id="outline-container-org1b5ae00" class="outline-4">
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<h4 id="org1b5ae00"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div class="outline-text-4" id="text-1-1-5">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
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@ -505,8 +505,8 @@ W(:,:,:,:) = 0.d0
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</div>
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</div>
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<div id="outline-container-org9a2fb20" class="outline-4">
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<h4 id="org9a2fb20"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
|
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<div id="outline-container-orgd5d0065" class="outline-4">
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<h4 id="orgd5d0065"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div class="outline-text-4" id="text-1-1-6">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
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@ -538,8 +538,8 @@ rc = trexio_read_rdm_1e(f, D)
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</div>
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</div>
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<div id="outline-container-org626d5c6" class="outline-4">
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||||
<h4 id="org626d5c6"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
|
||||
<div id="outline-container-org874df27" class="outline-4">
|
||||
<h4 id="org874df27"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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<div class="outline-text-4" id="text-1-1-7">
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<p>
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Reading is done with OpenMP. Each thread reads its own buffer, and
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@ -555,8 +555,8 @@ to be protected in the critical section when modified.
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</p>
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</div>
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<div id="outline-container-org3a71a4c" class="outline-5">
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<h5 id="org3a71a4c"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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||||
<div id="outline-container-org81d0288" class="outline-5">
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<h5 id="org81d0288"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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<div class="outline-text-5" id="text-1-1-7-1">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
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@ -605,8 +605,8 @@ icount = BUFSIZE
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</div>
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</div>
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<div id="outline-container-orgd57c288" class="outline-5">
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<h5 id="orgd57c288"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-orgaf92d5f" class="outline-5">
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||||
<h5 id="orgaf92d5f"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div class="outline-text-5" id="text-1-1-7-2">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
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@ -650,8 +650,8 @@ icount = bufsize
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</div>
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</div>
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<div id="outline-container-org64deb3c" class="outline-4">
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<h4 id="org64deb3c"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div id="outline-container-org1f8602d" class="outline-4">
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||||
<h4 id="org1f8602d"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div class="outline-text-4" id="text-1-1-8">
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<p>
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When the orbitals are real, we can use
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@ -697,8 +697,8 @@ E = E + E_nn
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</div>
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</div>
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<div id="outline-container-orga2eab79" class="outline-4">
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<h4 id="orga2eab79"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-org91c3901" class="outline-4">
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<h4 id="org91c3901"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div class="outline-text-4" id="text-1-1-9">
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<div class="org-src-container">
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<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
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@ -712,12 +712,12 @@ E = E + E_nn
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</div>
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<div id="outline-container-orgfe4c208" class="outline-2">
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<h2 id="orgfe4c208"><span class="section-number-2">2</span> Reading determinants</h2>
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<div id="outline-container-org611455e" class="outline-2">
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<h2 id="org611455e"><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-org068cda0" class="outline-3">
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<h3 id="org068cda0"><span class="section-number-3">2.1</span> Fortran</h3>
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<div id="outline-container-orgd7ad5bd" class="outline-3">
|
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<h3 id="orgd7ad5bd"><span class="section-number-3">2.1</span> Fortran</h3>
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<div class="outline-text-3" id="text-2-1">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
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@ -796,7 +796,7 @@ end
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</div>
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<div id="postamble" class="status">
|
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<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2023-01-08 Sun 16:18</p>
|
||||
<p class="date">Created: 2023-01-10 Tue 17:49</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>
|
||||
<!-- 2023-01-08 Sun 16:18 -->
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||||
<!-- 2023-01-10 Tue 17:49 -->
|
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
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<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TREXIO source code documentation</title>
|
||||
@ -360,7 +360,7 @@ and bug reports should be submitted at
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2023-01-08 Sun 16:18</p>
|
||||
<p class="date">Created: 2023-01-10 Tue 17:49</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -3,7 +3,7 @@
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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<head>
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||||
<!-- 2023-01-08 Sun 16:18 -->
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||||
<!-- 2023-01-10 Tue 17:49 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>HDF5 back end</title>
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@ -324,25 +324,25 @@ for the JavaScript code in this tag.
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<h2>Table of Contents</h2>
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<div id="text-table-of-contents">
|
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<ul>
|
||||
<li><a href="#org4114ab9">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org8fb0dbd">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgb7591f0">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orga1ae5e6">4. Template for HDF5 has a group</a></li>
|
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<li><a href="#org9943b52">5. Template for HDF5 has/read/write a numerical attribute</a></li>
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<li><a href="#org3ecd6ca">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
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<li><a href="#org29d65d0">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
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||||
<li><a href="#orgecfdc7b">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
|
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<li><a href="#orgf75b895">9. Template for HDF5 has/read/write a dataset of strings</a></li>
|
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<li><a href="#orgc63cc7b">10. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgbec10ca">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org87935e3">12. Source code for the determinant part</a></li>
|
||||
<li><a href="#org551bb02">13. Helper functions</a></li>
|
||||
<li><a href="#org8421c68">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#orga2f02cd">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org98b8469">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orgeda063f">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#org26b6753">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orge1e17d5">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orga30b06d">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#orgda093b8">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
|
||||
<li><a href="#orge1f0e76">9. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org79b0874">10. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#org74cb0b8">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orgb77748c">12. Source code for the determinant part</a></li>
|
||||
<li><a href="#org59bb536">13. Helper functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4114ab9" class="outline-2">
|
||||
<h2 id="org4114ab9"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-org8421c68" class="outline-2">
|
||||
<h2 id="org8421c68"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #483d8b;">#define</span> $GROUP$_GROUP_NAME <span style="color: #8b2252;">"$group$"</span>
|
||||
@ -354,8 +354,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8fb0dbd" class="outline-2">
|
||||
<h2 id="org8fb0dbd"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-orga2f02cd" class="outline-2">
|
||||
<h2 id="orga2f02cd"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
|
||||
@ -375,8 +375,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb7591f0" class="outline-2">
|
||||
<h2 id="orgb7591f0"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-org98b8469" class="outline-2">
|
||||
<h2 id="org98b8469"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -496,8 +496,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga1ae5e6" class="outline-2">
|
||||
<h2 id="orga1ae5e6"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
|
||||
<div id="outline-container-orgeda063f" class="outline-2">
|
||||
<h2 id="orgeda063f"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -527,8 +527,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9943b52" class="outline-2">
|
||||
<h2 id="org9943b52"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-org26b6753" class="outline-2">
|
||||
<h2 id="org26b6753"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -632,8 +632,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3ecd6ca" class="outline-2">
|
||||
<h2 id="org3ecd6ca"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-orge1e17d5" class="outline-2">
|
||||
<h2 id="orge1e17d5"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -767,8 +767,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org29d65d0" class="outline-2">
|
||||
<h2 id="org29d65d0"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-orga30b06d" class="outline-2">
|
||||
<h2 id="orga30b06d"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<p>
|
||||
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
|
||||
@ -971,8 +971,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgecfdc7b" class="outline-2">
|
||||
<h2 id="orgecfdc7b"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
|
||||
<div id="outline-container-orgda093b8" class="outline-2">
|
||||
<h2 id="orgda093b8"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
|
||||
<div class="outline-text-2" id="text-8">
|
||||
<p>
|
||||
Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
@ -1107,8 +1107,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf75b895" class="outline-2">
|
||||
<h2 id="orgf75b895"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-orge1f0e76" class="outline-2">
|
||||
<h2 id="orge1f0e76"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc63cc7b" class="outline-2">
|
||||
<h2 id="orgc63cc7b"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org79b0874" class="outline-2">
|
||||
<h2 id="org79b0874"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1434,8 +1434,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgbec10ca" class="outline-2">
|
||||
<h2 id="orgbec10ca"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-org74cb0b8" class="outline-2">
|
||||
<h2 id="org74cb0b8"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
<b><b>Note:</b></b> in early versions of the HDF5 library (v < 1.10) unlinking an object was not working as expected
|
||||
@ -1475,8 +1475,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org87935e3" class="outline-2">
|
||||
<h2 id="org87935e3"><span class="section-number-2">12</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-orgb77748c" class="outline-2">
|
||||
<h2 id="orgb77748c"><span class="section-number-2">12</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<p>
|
||||
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
|
||||
@ -1579,8 +1579,8 @@ Size specifies the number of data items (e.g. determinants) to process.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org551bb02" class="outline-2">
|
||||
<h2 id="org551bb02"><span class="section-number-2">13</span> Helper functions</h2>
|
||||
<div id="outline-container-org59bb536" class="outline-2">
|
||||
<h2 id="org59bb536"><span class="section-number-2">13</span> Helper functions</h2>
|
||||
<div class="outline-text-2" id="text-13">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1843,7 +1843,7 @@ Size specifies the number of data items (e.g. determinants) to process.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2023-01-08 Sun 16:18</p>
|
||||
<p class="date">Created: 2023-01-10 Tue 17:49</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2023-01-08 Sun 16:18 -->
|
||||
<!-- 2023-01-10 Tue 17:49 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TEXT back end</title>
|
||||
@ -324,23 +324,23 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orgc15fb97">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org3602a00">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org44b6c19">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#orgdd57d6a">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orgc6e1c9a">5. Flush function (templated part)</a></li>
|
||||
<li><a href="#orgb24c3d6">6. Template for text read a group</a></li>
|
||||
<li><a href="#org945ea13">7. Template for text has a group</a></li>
|
||||
<li><a href="#org3f399eb">8. Template for text flush a group</a></li>
|
||||
<li><a href="#orga9b3faf">9. Template for text free memory</a></li>
|
||||
<li><a href="#org545cca9">10. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org78d1c7f">11. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgb8dbfaf">12. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org77ec7be">13. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgb38701f">14. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org6f7b426">15. Template for has/read/write a buffered vector</a></li>
|
||||
<li><a href="#orgf3bbe13">16. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org3d5afec">17. Source code for the determinant part</a></li>
|
||||
<li><a href="#org795eb84">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org823b63a">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#orgdbd1106">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org57cdf82">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org877fc4e">5. Flush function (templated part)</a></li>
|
||||
<li><a href="#org3f8dd1f">6. Template for text read a group</a></li>
|
||||
<li><a href="#org191b7ac">7. Template for text has a group</a></li>
|
||||
<li><a href="#org99f6641">8. Template for text flush a group</a></li>
|
||||
<li><a href="#org7fa5136">9. Template for text free memory</a></li>
|
||||
<li><a href="#orgefffc95">10. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org725ea61">11. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org86c0ad1">12. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org33ccf87">13. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org14ffeee">14. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#orgb153999">15. Template for has/read/write a buffered vector</a></li>
|
||||
<li><a href="#orge99301c">16. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orgcf1c1cb">17. Source code for the determinant part</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -362,8 +362,8 @@ directory.
|
||||
The file is written when closed, or when the flush function is called.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-orgc15fb97" class="outline-2">
|
||||
<h2 id="orgc15fb97"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div id="outline-container-org795eb84" class="outline-2">
|
||||
<h2 id="org795eb84"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
|
||||
@ -382,8 +382,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3602a00" class="outline-2">
|
||||
<h2 id="org3602a00"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div id="outline-container-org823b63a" class="outline-2">
|
||||
<h2 id="org823b63a"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
|
||||
@ -403,8 +403,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org44b6c19" class="outline-2">
|
||||
<h2 id="org44b6c19"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div id="outline-container-orgdbd1106" class="outline-2">
|
||||
<h2 id="orgdbd1106"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">bool</span>
|
||||
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdd57d6a" class="outline-2">
|
||||
<h2 id="orgdd57d6a"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div id="outline-container-org57cdf82" class="outline-2">
|
||||
<h2 id="org57cdf82"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -594,8 +594,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc6e1c9a" class="outline-2">
|
||||
<h2 id="orgc6e1c9a"><span class="section-number-2">5</span> Flush function (templated part)</h2>
|
||||
<div id="outline-container-org877fc4e" class="outline-2">
|
||||
<h2 id="org877fc4e"><span class="section-number-2">5</span> Flush function (templated part)</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -618,8 +618,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb24c3d6" class="outline-2">
|
||||
<h2 id="orgb24c3d6"><span class="section-number-2">6</span> Template for text read a group</h2>
|
||||
<div id="outline-container-org3f8dd1f" class="outline-2">
|
||||
<h2 id="org3f8dd1f"><span class="section-number-2">6</span> Template for text read a group</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c">$group$_t*
|
||||
@ -845,8 +845,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org945ea13" class="outline-2">
|
||||
<h2 id="org945ea13"><span class="section-number-2">7</span> Template for text has a group</h2>
|
||||
<div id="outline-container-org191b7ac" class="outline-2">
|
||||
<h2 id="org191b7ac"><span class="section-number-2">7</span> Template for text has a group</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -886,8 +886,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3f399eb" class="outline-2">
|
||||
<h2 id="org3f399eb"><span class="section-number-2">8</span> Template for text flush a group</h2>
|
||||
<div id="outline-container-org99f6641" class="outline-2">
|
||||
<h2 id="org99f6641"><span class="section-number-2">8</span> Template for text flush a group</h2>
|
||||
<div class="outline-text-2" id="text-8">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -951,8 +951,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga9b3faf" class="outline-2">
|
||||
<h2 id="orga9b3faf"><span class="section-number-2">9</span> Template for text free memory</h2>
|
||||
<div id="outline-container-org7fa5136" class="outline-2">
|
||||
<h2 id="org7fa5136"><span class="section-number-2">9</span> Template for text free memory</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<p>
|
||||
Memory is allocated when reading. The following function frees memory.
|
||||
@ -1021,8 +1021,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org545cca9" class="outline-2">
|
||||
<h2 id="org545cca9"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-orgefffc95" class="outline-2">
|
||||
<h2 id="orgefffc95"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1085,8 +1085,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org78d1c7f" class="outline-2">
|
||||
<h2 id="org78d1c7f"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org725ea61" class="outline-2">
|
||||
<h2 id="org725ea61"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1182,8 +1182,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgb8dbfaf" class="outline-2">
|
||||
<h2 id="orgb8dbfaf"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org86c0ad1" class="outline-2">
|
||||
<h2 id="org86c0ad1"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1284,8 +1284,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org77ec7be" class="outline-2">
|
||||
<h2 id="org77ec7be"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org33ccf87" class="outline-2">
|
||||
<h2 id="org33ccf87"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
|
||||
<div class="outline-text-2" id="text-13">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1359,8 +1359,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgb38701f" class="outline-2">
|
||||
<h2 id="orgb38701f"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div id="outline-container-org14ffeee" class="outline-2">
|
||||
<h2 id="org14ffeee"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div class="outline-text-2" id="text-14">
|
||||
<p>
|
||||
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
|
||||
@ -1650,8 +1650,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6f7b426" class="outline-2">
|
||||
<h2 id="org6f7b426"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
|
||||
<div id="outline-container-orgb153999" class="outline-2">
|
||||
<h2 id="orgb153999"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
|
||||
<div class="outline-text-2" id="text-15">
|
||||
<p>
|
||||
Each array is stored in a separate <code>.txt</code> file due to the fact that buffered I/O has to be decoupled
|
||||
@ -1881,8 +1881,8 @@ Size specifies the number of vector elements to be written.
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgf3bbe13" class="outline-2">
|
||||
<h2 id="orgf3bbe13"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-orge99301c" class="outline-2">
|
||||
<h2 id="orge99301c"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-16">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1910,8 +1910,8 @@ Size specifies the number of vector elements to be written.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3d5afec" class="outline-2">
|
||||
<h2 id="org3d5afec"><span class="section-number-2">17</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-orgcf1c1cb" class="outline-2">
|
||||
<h2 id="orgcf1c1cb"><span class="section-number-2">17</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-17">
|
||||
<p>
|
||||
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
|
||||
@ -2103,7 +2103,7 @@ Size specifies the number of data items, e.g. determinants.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2023-01-08 Sun 16:18</p>
|
||||
<p class="date">Created: 2023-01-10 Tue 17:49</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
299
trex.html
299
trex.html
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2023-01-08 Sun 16:18 -->
|
||||
<!-- 2023-01-10 Tue 17:49 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TREX Configuration file</title>
|
||||
@ -346,70 +346,70 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orga572136">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org8f9f1fd">2. System</a>
|
||||
<li><a href="#orgc7ada1d">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org7b26f9e">2. System</a>
|
||||
<ul>
|
||||
<li><a href="#org76d91fb">2.1. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org9d5387e">2.2. Cell (cell group)</a></li>
|
||||
<li><a href="#org098e1e6">2.3. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#orgb04c3a4">2.4. Electron (electron group)</a></li>
|
||||
<li><a href="#org9c4025e">2.5. Ground or excited states (state group)</a></li>
|
||||
<li><a href="#org61770da">2.1. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#orgf21e92e">2.2. Cell (cell group)</a></li>
|
||||
<li><a href="#org8af6206">2.3. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#org5178785">2.4. Electron (electron group)</a></li>
|
||||
<li><a href="#orgc55c87c">2.5. Ground or excited states (state group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org9cda3b4">3. Basis functions</a>
|
||||
<li><a href="#org2e46b72">3. Basis functions</a>
|
||||
<ul>
|
||||
<li><a href="#org5df488e">3.1. Basis set (basis group)</a>
|
||||
<li><a href="#orgadc4355">3.1. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#org65abafc">3.1.1. Gaussian and Slater-type orbitals</a></li>
|
||||
<li><a href="#org426bb8f">3.1.2. Plane waves</a></li>
|
||||
<li><a href="#org94004b4">3.1.3. Data definitions</a></li>
|
||||
<li><a href="#org73af06e">3.1.4. Example</a></li>
|
||||
<li><a href="#orgc3d7a8f">3.1.1. Gaussian and Slater-type orbitals</a></li>
|
||||
<li><a href="#org6355bcc">3.1.2. Plane waves</a></li>
|
||||
<li><a href="#org035c9e1">3.1.3. Data definitions</a></li>
|
||||
<li><a href="#org42d7e8e">3.1.4. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org3b97897">3.2. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#orgf8232a7">3.2. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#org5e827b0">3.2.1. Example</a></li>
|
||||
<li><a href="#orgf30574f">3.2.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org9928563">3.3. Numerical integration grid (grid group)</a></li>
|
||||
<li><a href="#org5f99375">3.3. Numerical integration grid (grid group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org1b66a5c">4. Orbitals</a>
|
||||
<li><a href="#org12a8cfe">4. Orbitals</a>
|
||||
<ul>
|
||||
<li><a href="#org51b6564">4.1. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#org65a5f23">4.1. Atomic orbitals (ao group)</a>
|
||||
<ul>
|
||||
<li><a href="#ao_one_e">4.1.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
|
||||
<li><a href="#ao_two_e">4.1.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org900613b">4.2. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org8de6d94">4.2. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#org036a7ff">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org4e61a4b">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#orgb8d4a94">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org01ba9b5">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org0064387">5. Multi-determinant information</a>
|
||||
<li><a href="#orgd571d38">5. Multi-determinant information</a>
|
||||
<ul>
|
||||
<li><a href="#orgaaa44c6">5.1. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#orgb449073">5.2. Configuration state functions (csf group)</a></li>
|
||||
<li><a href="#org85695c2">5.3. Amplitudes (amplitude group)</a></li>
|
||||
<li><a href="#org8ef00b9">5.4. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org10d5905">5.1. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org5b834f3">5.2. Configuration state functions (csf group)</a></li>
|
||||
<li><a href="#org156dc71">5.3. Amplitudes (amplitude group)</a></li>
|
||||
<li><a href="#org06b983e">5.4. Reduced density matrices (rdm group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org755c905">6. Correlation factors</a>
|
||||
<li><a href="#org64d89be">6. Correlation factors</a>
|
||||
<ul>
|
||||
<li><a href="#orgf79852a">6.1. Jastrow factor (jastrow group)</a>
|
||||
<li><a href="#org259da9b">6.1. Jastrow factor (jastrow group)</a>
|
||||
<ul>
|
||||
<li><a href="#org0154324">6.1.1. CHAMP</a></li>
|
||||
<li><a href="#org3780a2e">6.1.2. Mu</a></li>
|
||||
<li><a href="#org9666375">6.1.3. Table of values</a></li>
|
||||
<li><a href="#orga671d59">6.1.1. CHAMP</a></li>
|
||||
<li><a href="#orge77cb4c">6.1.2. Mu</a></li>
|
||||
<li><a href="#orga3940d4">6.1.3. Table of values</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org58a4acc">7. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
<li><a href="#org93ec000">7. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -477,8 +477,8 @@ in the variable, and the imaginary part will be stored in the variable
|
||||
with the same name suffixed by <code>_im</code>.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-orga572136" class="outline-2">
|
||||
<h2 id="orga572136"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-orgc7ada1d" class="outline-2">
|
||||
<h2 id="orgc7ada1d"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<p>
|
||||
As we expect TREXIO files to be archived in open-data repositories,
|
||||
@ -488,7 +488,7 @@ have participated to the creation of the file, a list of authors of
|
||||
the file, and a textual description.
|
||||
</p>
|
||||
|
||||
<table id="orgf52dc47" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org6027ac8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -571,19 +571,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8f9f1fd" class="outline-2">
|
||||
<h2 id="org8f9f1fd"><span class="section-number-2">2</span> System</h2>
|
||||
<div id="outline-container-org7b26f9e" class="outline-2">
|
||||
<h2 id="org7b26f9e"><span class="section-number-2">2</span> System</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
</div>
|
||||
<div id="outline-container-org76d91fb" class="outline-3">
|
||||
<h3 id="org76d91fb"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
|
||||
<div id="outline-container-org61770da" class="outline-3">
|
||||
<h3 id="org61770da"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
|
||||
<div class="outline-text-3" id="text-2-1">
|
||||
<p>
|
||||
The nuclei are considered as fixed point charges. Coordinates are
|
||||
given in Cartesian \((x,y,z)\) format.
|
||||
</p>
|
||||
|
||||
<table id="org4a743cf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgf3d3c76" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -650,15 +650,15 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9d5387e" class="outline-3">
|
||||
<h3 id="org9d5387e"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
|
||||
<div id="outline-container-orgf21e92e" class="outline-3">
|
||||
<h3 id="orgf21e92e"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
|
||||
<div class="outline-text-3" id="text-2-2">
|
||||
<p>
|
||||
3 Lattice vectors to define a box containing the system, for example
|
||||
used in periodic calculations.
|
||||
</p>
|
||||
|
||||
<table id="org0cfd8d2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga99ffbc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -683,36 +683,64 @@ used in periodic calculations.
|
||||
<td class="org-left"><code>a</code></td>
|
||||
<td class="org-left"><code>float</code></td>
|
||||
<td class="org-left"><code>(3)</code></td>
|
||||
<td class="org-left">First lattice vector</td>
|
||||
<td class="org-left">First real space lattice vector</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>b</code></td>
|
||||
<td class="org-left"><code>float</code></td>
|
||||
<td class="org-left"><code>(3)</code></td>
|
||||
<td class="org-left">Second lattice vector</td>
|
||||
<td class="org-left">Second real space lattice vector</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>c</code></td>
|
||||
<td class="org-left"><code>float</code></td>
|
||||
<td class="org-left"><code>(3)</code></td>
|
||||
<td class="org-left">Third lattice vector</td>
|
||||
<td class="org-left">Third real space lattice vector</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>G_a</code></td>
|
||||
<td class="org-left"><code>float</code></td>
|
||||
<td class="org-left"><code>(3)</code></td>
|
||||
<td class="org-left">First reciprocal space lattice vector</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>G_b</code></td>
|
||||
<td class="org-left"><code>float</code></td>
|
||||
<td class="org-left"><code>(3)</code></td>
|
||||
<td class="org-left">Second reciprocal space lattice vector</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>G_c</code></td>
|
||||
<td class="org-left"><code>float</code></td>
|
||||
<td class="org-left"><code>(3)</code></td>
|
||||
<td class="org-left">Third reciprocal space lattice vector</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>two_pi</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left"><code>0</code> or <code>1</code>. If <code>two_pi=1</code>, \(2\pi\) is included in the reciprocal vectors.</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org098e1e6" class="outline-3">
|
||||
<h3 id="org098e1e6"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
|
||||
<div id="outline-container-org8af6206" class="outline-3">
|
||||
<h3 id="org8af6206"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
|
||||
<div class="outline-text-3" id="text-2-3">
|
||||
<p>
|
||||
A single $k$-point per TREXIO file can be stored. The $k$-point is
|
||||
defined in this group.
|
||||
</p>
|
||||
|
||||
<table id="orgad92505" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgfa47eeb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -751,15 +779,15 @@ defined in this group.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb04c3a4" class="outline-3">
|
||||
<h3 id="orgb04c3a4"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
|
||||
<div id="outline-container-org5178785" class="outline-3">
|
||||
<h3 id="org5178785"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
|
||||
<div class="outline-text-3" id="text-2-4">
|
||||
<p>
|
||||
We consider wave functions expressed in the spin-free formalism, where
|
||||
the number of ↑ and ↓ electrons is fixed.
|
||||
</p>
|
||||
|
||||
<table id="org6848f1a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2a698b3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -805,8 +833,8 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9c4025e" class="outline-3">
|
||||
<h3 id="org9c4025e"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
|
||||
<div id="outline-container-orgc55c87c" class="outline-3">
|
||||
<h3 id="orgc55c87c"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
|
||||
<div class="outline-text-3" id="text-2-5">
|
||||
<p>
|
||||
This group contains information about excited states. Since only a
|
||||
@ -823,7 +851,7 @@ integrals, etc.
|
||||
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
|
||||
</p>
|
||||
|
||||
<table id="org4519461" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1cdd4e4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -884,16 +912,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9cda3b4" class="outline-2">
|
||||
<h2 id="org9cda3b4"><span class="section-number-2">3</span> Basis functions</h2>
|
||||
<div id="outline-container-org2e46b72" class="outline-2">
|
||||
<h2 id="org2e46b72"><span class="section-number-2">3</span> Basis functions</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
</div>
|
||||
<div id="outline-container-org5df488e" class="outline-3">
|
||||
<h3 id="org5df488e"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
|
||||
<div id="outline-container-orgadc4355" class="outline-3">
|
||||
<h3 id="orgadc4355"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
|
||||
<div class="outline-text-3" id="text-3-1">
|
||||
</div>
|
||||
<div id="outline-container-org65abafc" class="outline-4">
|
||||
<h4 id="org65abafc"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
|
||||
<div id="outline-container-orgc3d7a8f" class="outline-4">
|
||||
<h4 id="orgc3d7a8f"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
|
||||
<div class="outline-text-4" id="text-3-1-1">
|
||||
<p>
|
||||
We consider here basis functions centered on nuclei. Hence, we enable
|
||||
@ -947,8 +975,8 @@ All the basis set parameters are stored in one-dimensional arrays.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org426bb8f" class="outline-4">
|
||||
<h4 id="org426bb8f"><span class="section-number-4">3.1.2</span> Plane waves</h4>
|
||||
<div id="outline-container-org6355bcc" class="outline-4">
|
||||
<h4 id="org6355bcc"><span class="section-number-4">3.1.2</span> Plane waves</h4>
|
||||
<div class="outline-text-4" id="text-3-1-2">
|
||||
<p>
|
||||
A plane wave is defined as
|
||||
@ -956,22 +984,23 @@ A plane wave is defined as
|
||||
|
||||
<p>
|
||||
\[
|
||||
\chi_j(r) = \exp \left( -i \mathbf{k}_j \mathbf{r} \right)
|
||||
\chi_j(\mathbf{r}) = \exp \left( -i \mathbf{G}_j \cdot \mathbf{r} \right)
|
||||
\]
|
||||
</p>
|
||||
|
||||
<p>
|
||||
The basis set is defined as the array of $k$-points in the
|
||||
reciprocal space, defined in the <code>pbc</code> group. The kinetic energy
|
||||
cutoff <code>e_cut</code> is the only input data relevant to plane waves.
|
||||
reciprocal space \(\mathbf{G}_j\), defined in the <code>pbc</code> group. The
|
||||
kinetic energy cutoff <code>e_cut</code> is the only input data relevant to
|
||||
plane waves.
|
||||
</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org94004b4" class="outline-4">
|
||||
<h4 id="org94004b4"><span class="section-number-4">3.1.3</span> Data definitions</h4>
|
||||
<div id="outline-container-org035c9e1" class="outline-4">
|
||||
<h4 id="org035c9e1"><span class="section-number-4">3.1.3</span> Data definitions</h4>
|
||||
<div class="outline-text-4" id="text-3-1-3">
|
||||
<table id="orgd1fd181" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga6d61fa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1080,8 +1109,8 @@ cutoff <code>e_cut</code> is the only input data relevant to plane waves.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org73af06e" class="outline-4">
|
||||
<h4 id="org73af06e"><span class="section-number-4">3.1.4</span> Example</h4>
|
||||
<div id="outline-container-org42d7e8e" class="outline-4">
|
||||
<h4 id="org42d7e8e"><span class="section-number-4">3.1.4</span> Example</h4>
|
||||
<div class="outline-text-4" id="text-3-1-4">
|
||||
<p>
|
||||
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
|
||||
@ -1145,7 +1174,7 @@ exponent =
|
||||
coefficient =
|
||||
[ 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, 1.0, 1.0, 1.0,
|
||||
0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, 1.0, 1.0, 1.0 ]
|
||||
`
|
||||
|
||||
prim_factor =
|
||||
[ 1.0006253235944540e+01, 2.4169531573445120e+00, 7.9610924849766440e-01
|
||||
3.0734305383061117e-01, 1.2929684417481876e-01, 3.0734305383061117e-01,
|
||||
@ -1159,8 +1188,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3b97897" class="outline-3">
|
||||
<h3 id="org3b97897"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
|
||||
<div id="outline-container-orgf8232a7" class="outline-3">
|
||||
<h3 id="orgf8232a7"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
|
||||
<div class="outline-text-3" id="text-3-2">
|
||||
<p>
|
||||
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
|
||||
@ -1168,9 +1197,8 @@ core electrons of atom \(A\) can be expressed as
|
||||
\[
|
||||
V_A^{\text{ECP}} =
|
||||
V_{A \ell_{\max}+1} +
|
||||
\sum_{\ell=0}^{\ell_{\max}}
|
||||
\sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \left[
|
||||
V_{A \ell} - V_{A \ell_{\max}+1} \right] \langle Y_{\ell m} |
|
||||
\sum_{\ell=0}^{\ell_{\max}} V_{A \ell}
|
||||
\sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \langle Y_{\ell m} |
|
||||
\]
|
||||
</p>
|
||||
|
||||
@ -1180,20 +1208,20 @@ while the remaining terms correspond to the non-local channel projections.
|
||||
</p>
|
||||
|
||||
<p>
|
||||
The functions \(V_{A\ell}\) are parameterized as:
|
||||
All the functions \(V_{A\ell}\) are parameterized as:
|
||||
\[
|
||||
V_{A \ell}(\mathbf{r}) =
|
||||
V_{A \ell}(\mathbf{r}) =
|
||||
\sum_{q=1}^{N_{q \ell}}
|
||||
\beta_{A q \ell}\, |\mathbf{r}-\mathbf{R}_{A}|^{n_{A q \ell}}\,
|
||||
e^{-\alpha_{A q \ell} |\mathbf{r}-\mathbf{R}_{A}|^2 }
|
||||
\]
|
||||
\].
|
||||
</p>
|
||||
|
||||
<p>
|
||||
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="org84c7e18" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org7d37916" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1272,7 +1300,6 @@ See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.49
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
|
||||
<p>
|
||||
There might be some confusion in the meaning of the \(\ell_{\max}\).
|
||||
It can be attributed to the maximum angular momentum occupied in
|
||||
@ -1298,8 +1325,8 @@ If you encounter the aforementioned issue, please report it to our
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5e827b0" class="outline-4">
|
||||
<h4 id="org5e827b0"><span class="section-number-4">3.2.1</span> Example</h4>
|
||||
<div id="outline-container-orgf30574f" class="outline-4">
|
||||
<h4 id="orgf30574f"><span class="section-number-4">3.2.1</span> Example</h4>
|
||||
<div class="outline-text-4" id="text-3-2-1">
|
||||
<p>
|
||||
For example, consider H<sub>2</sub> molecule with the following
|
||||
@ -1362,8 +1389,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9928563" class="outline-3">
|
||||
<h3 id="org9928563"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
|
||||
<div id="outline-container-org5f99375" class="outline-3">
|
||||
<h3 id="org5f99375"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
|
||||
<div class="outline-text-3" id="text-3-3">
|
||||
<p>
|
||||
In some applications, such as DFT calculations, integrals have to
|
||||
@ -1378,7 +1405,7 @@ The structure of this group is adapted for the <a href="https://github.com/dftli
|
||||
Feel free to submit a PR if you find missing options/functionalities.
|
||||
</p>
|
||||
|
||||
<table id="org58dd313" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org3b9ba0c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1495,12 +1522,12 @@ Feel free to submit a PR if you find missing options/functionalities.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1b66a5c" class="outline-2">
|
||||
<h2 id="org1b66a5c"><span class="section-number-2">4</span> Orbitals</h2>
|
||||
<div id="outline-container-org12a8cfe" class="outline-2">
|
||||
<h2 id="org12a8cfe"><span class="section-number-2">4</span> Orbitals</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
</div>
|
||||
<div id="outline-container-org51b6564" class="outline-3">
|
||||
<h3 id="org51b6564"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
|
||||
<div id="outline-container-org65a5f23" class="outline-3">
|
||||
<h3 id="org65a5f23"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
|
||||
<div class="outline-text-3" id="text-4-1">
|
||||
<p>
|
||||
Going from the atomic basis set to AOs implies a systematic
|
||||
@ -1553,13 +1580,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#org5df488e">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#orgadc4355">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="orgcbb68fa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1181316" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1611,7 +1638,7 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org325c272" class="outline-4">
|
||||
<div id="outline-container-orgcefaef9" class="outline-4">
|
||||
<h4 id="ao_one_e"><span class="section-number-4">4.1.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h4>
|
||||
<div class="outline-text-4" id="text-ao_one_e">
|
||||
<ul class="org-ul">
|
||||
@ -1629,7 +1656,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org26c20b3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org8e121e4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1724,7 +1751,7 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgfff87a4" class="outline-4">
|
||||
<div id="outline-container-org2194460" class="outline-4">
|
||||
<h4 id="ao_two_e"><span class="section-number-4">4.1.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h4>
|
||||
<div class="outline-text-4" id="text-ao_two_e">
|
||||
<p>
|
||||
@ -1756,7 +1783,7 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
\]
|
||||
</p>
|
||||
|
||||
<table id="orgb690c36" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1af3a3b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1824,10 +1851,10 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org900613b" class="outline-3">
|
||||
<h3 id="org900613b"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
|
||||
<div id="outline-container-org8de6d94" class="outline-3">
|
||||
<h3 id="org8de6d94"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
|
||||
<div class="outline-text-3" id="text-4-2">
|
||||
<table id="orgdea473f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgb126628" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1914,8 +1941,8 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org036a7ff" class="outline-4">
|
||||
<h4 id="org036a7ff"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
|
||||
<div id="outline-container-orgb8d4a94" class="outline-4">
|
||||
<h4 id="orgb8d4a94"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
|
||||
<div class="outline-text-4" id="text-4-2-1">
|
||||
<p>
|
||||
The operators as the same as those defined in the
|
||||
@ -1923,7 +1950,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orgf64c2bc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org306d4c8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2018,8 +2045,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4e61a4b" class="outline-4">
|
||||
<h4 id="org4e61a4b"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
|
||||
<div id="outline-container-org01ba9b5" class="outline-4">
|
||||
<h4 id="org01ba9b5"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
|
||||
<div class="outline-text-4" id="text-4-2-2">
|
||||
<p>
|
||||
The operators are the same as those defined in the
|
||||
@ -2027,7 +2054,7 @@ The operators are the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org4effce0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgf36ff4a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2096,12 +2123,12 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0064387" class="outline-2">
|
||||
<h2 id="org0064387"><span class="section-number-2">5</span> Multi-determinant information</h2>
|
||||
<div id="outline-container-orgd571d38" class="outline-2">
|
||||
<h2 id="orgd571d38"><span class="section-number-2">5</span> Multi-determinant information</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
</div>
|
||||
<div id="outline-container-orgaaa44c6" class="outline-3">
|
||||
<h3 id="orgaaa44c6"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
|
||||
<div id="outline-container-org10d5905" class="outline-3">
|
||||
<h3 id="org10d5905"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
|
||||
<div class="outline-text-3" id="text-5-1">
|
||||
<p>
|
||||
The configuration interaction (CI) wave function \(\Psi\)
|
||||
@ -2143,7 +2170,7 @@ produced by the code generator.
|
||||
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
|
||||
</p>
|
||||
|
||||
<table id="orgaa1eb49" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1845af3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2189,8 +2216,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb449073" class="outline-3">
|
||||
<h3 id="orgb449073"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
|
||||
<div id="outline-container-org5b834f3" class="outline-3">
|
||||
<h3 id="org5b834f3"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
|
||||
<div class="outline-text-3" id="text-5-2">
|
||||
<p>
|
||||
The configuration interaction (CI) wave function \(\Psi\) can be
|
||||
@ -2212,7 +2239,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
|
||||
the basis of Slater determinants.
|
||||
</p>
|
||||
|
||||
<table id="orgf85216e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgcae2fee" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2258,8 +2285,8 @@ the basis of Slater determinants.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org85695c2" class="outline-3">
|
||||
<h3 id="org85695c2"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
|
||||
<div id="outline-container-org156dc71" class="outline-3">
|
||||
<h3 id="org156dc71"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
|
||||
<div class="outline-text-3" id="text-5-3">
|
||||
<p>
|
||||
The wave function may be expressed in terms of action of the cluster
|
||||
@ -2330,7 +2357,7 @@ The order of the indices is chosen such that
|
||||
<li>\(\dots\)</li>
|
||||
</ul>
|
||||
|
||||
<table id="org8f49580" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd066f47" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2411,8 +2438,8 @@ The order of the indices is chosen such that
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8ef00b9" class="outline-3">
|
||||
<h3 id="org8ef00b9"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
|
||||
<div id="outline-container-org06b983e" class="outline-3">
|
||||
<h3 id="org06b983e"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
|
||||
<div class="outline-text-3" id="text-5-4">
|
||||
<p>
|
||||
The reduced density matrices are defined in the basis of molecular
|
||||
@ -2487,7 +2514,7 @@ expressed in a basis of a one-electron function
|
||||
\(g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)\).
|
||||
</p>
|
||||
|
||||
<table id="org1cb8247" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orge146b8c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2639,12 +2666,12 @@ expressed in a basis of a one-electron function
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org755c905" class="outline-2">
|
||||
<h2 id="org755c905"><span class="section-number-2">6</span> Correlation factors</h2>
|
||||
<div id="outline-container-org64d89be" class="outline-2">
|
||||
<h2 id="org64d89be"><span class="section-number-2">6</span> Correlation factors</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
</div>
|
||||
<div id="outline-container-orgf79852a" class="outline-3">
|
||||
<h3 id="orgf79852a"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
|
||||
<div id="outline-container-org259da9b" class="outline-3">
|
||||
<h3 id="org259da9b"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
|
||||
<div class="outline-text-3" id="text-6-1">
|
||||
<p>
|
||||
The Jastrow factor is an $N$-electron function to which the CI
|
||||
@ -2669,8 +2696,8 @@ following:
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0154324" class="outline-4">
|
||||
<h4 id="org0154324"><span class="section-number-4">6.1.1</span> CHAMP</h4>
|
||||
<div id="outline-container-orga671d59" class="outline-4">
|
||||
<h4 id="orga671d59"><span class="section-number-4">6.1.1</span> CHAMP</h4>
|
||||
<div class="outline-text-4" id="text-6-1-1">
|
||||
<p>
|
||||
The first form of Jastrow factor is the one used in
|
||||
@ -2747,8 +2774,8 @@ The terms \(J_{\text{ee}}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to en
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3780a2e" class="outline-4">
|
||||
<h4 id="org3780a2e"><span class="section-number-4">6.1.2</span> Mu</h4>
|
||||
<div id="outline-container-orge77cb4c" class="outline-4">
|
||||
<h4 id="orge77cb4c"><span class="section-number-4">6.1.2</span> Mu</h4>
|
||||
<div class="outline-text-4" id="text-6-1-2">
|
||||
<p>
|
||||
<a href="https://aip.scitation.org/doi/10.1063/5.0044683">Mu-Jastrow</a> is based on a one-parameter correlation factor that has
|
||||
@ -2845,10 +2872,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9666375" class="outline-4">
|
||||
<h4 id="org9666375"><span class="section-number-4">6.1.3</span> Table of values</h4>
|
||||
<div id="outline-container-orga3940d4" class="outline-4">
|
||||
<h4 id="orga3940d4"><span class="section-number-4">6.1.3</span> Table of values</h4>
|
||||
<div class="outline-text-4" id="text-6-1-3">
|
||||
<table id="org0088c26" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org766ca54" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2952,8 +2979,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org58a4acc" class="outline-2">
|
||||
<h2 id="org58a4acc"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div id="outline-container-org93ec000" class="outline-2">
|
||||
<h2 id="org93ec000"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<p>
|
||||
In quantum Monte Carlo calculations, the wave function is evaluated
|
||||
@ -2967,7 +2994,7 @@ By convention, the electron coordinates contain first all the electrons
|
||||
of $↑$-spin and then all the $↓$-spin.
|
||||
</p>
|
||||
|
||||
<table id="org82652f5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgf226068" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -3022,7 +3049,7 @@ of $↑$-spin and then all the $↓$-spin.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2023-01-08 Sun 16:18</p>
|
||||
<p class="date">Created: 2023-01-10 Tue 17:49</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