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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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||||
<!-- 2022-03-11 Fri 12:54 -->
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<!-- 2022-04-13 Wed 14:40 -->
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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: 2022-03-11 Fri 12:54</p>
|
||||
<p class="date">Created: 2022-04-13 Wed 14:40</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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||||
</div>
|
||||
</body>
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||||
|
||||
@ -3,7 +3,7 @@
|
||||
"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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||||
<!-- 2022-03-11 Fri 12:54 -->
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||||
<!-- 2022-04-13 Wed 14:40 -->
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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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@ -333,24 +333,24 @@ 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>
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||||
<li><a href="#org29e1b1d">1. Accessing sparse quantities</a>
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<li><a href="#orgb52be26">1. Accessing sparse quantities</a>
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<ul>
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||||
<li><a href="#orgacd44e2">1.1. Fortran</a>
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<li><a href="#org64925a5">1.1. Fortran</a>
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<ul>
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<li><a href="#org1ed3f46">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#orgb06a343">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="#orgd6fcb73">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#orgd070d3e">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org441fe30">1.1.5. Allocate memory</a></li>
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<li><a href="#org0f5e34c">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org5cf89ee">1.1.7. Read two-electron quantities</a>
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<li><a href="#orgafc7f4c">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#orge3620d4">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="#orgf770b43">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#orga9abfd7">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orgf8f96eb">1.1.5. Allocate memory</a></li>
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<li><a href="#org532fc04">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org2620568">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#orgdf7df26">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org1e875c6">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#orge3536c8">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#orgdf25aec">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="#org5810d9f">1.1.8. Compute the energy</a></li>
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<li><a href="#orgbb6b48d">1.1.9. Terminate</a></li>
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<li><a href="#org8977f5e">1.1.8. Compute the energy</a></li>
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<li><a href="#org028f8ba">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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@ -360,12 +360,12 @@ for the JavaScript code in this tag.
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</div>
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<div id="outline-container-org29e1b1d" class="outline-2">
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<h2 id="org29e1b1d"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
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||||
<div id="outline-container-orgb52be26" class="outline-2">
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||||
<h2 id="orgb52be26"><span class="section-number-2">1</span> Accessing sparse quantities</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-orgacd44e2" class="outline-3">
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<h3 id="orgacd44e2"><span class="section-number-3">1.1</span> Fortran</h3>
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||||
<div id="outline-container-org64925a5" class="outline-3">
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<h3 id="org64925a5"><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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@ -411,8 +411,8 @@ 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-org1ed3f46" class="outline-4">
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||||
<h4 id="org1ed3f46"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-orgafc7f4c" class="outline-4">
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<h4 id="orgafc7f4c"><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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@ -427,8 +427,8 @@ 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-orgb06a343" class="outline-4">
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<h4 id="orgb06a343"><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-orge3620d4" class="outline-4">
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<h4 id="orge3620d4"><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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@ -444,8 +444,8 @@ 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-orgd6fcb73" class="outline-4">
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<h4 id="orgd6fcb73"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-orgf770b43" class="outline-4">
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<h4 id="orgf770b43"><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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@ -459,8 +459,8 @@ 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-orgd070d3e" class="outline-4">
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||||
<h4 id="orgd070d3e"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-orga9abfd7" class="outline-4">
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||||
<h4 id="orga9abfd7"><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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@ -474,8 +474,8 @@ 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-org441fe30" class="outline-4">
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<h4 id="org441fe30"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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||||
<div id="outline-container-orgf8f96eb" class="outline-4">
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||||
<h4 id="orgf8f96eb"><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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@ -487,8 +487,8 @@ W(:,:,:,:) = 0.d0
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</div>
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</div>
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<div id="outline-container-org0f5e34c" class="outline-4">
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<h4 id="org0f5e34c"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div id="outline-container-org532fc04" class="outline-4">
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||||
<h4 id="org532fc04"><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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@ -520,8 +520,8 @@ 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-org5cf89ee" class="outline-4">
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<h4 id="org5cf89ee"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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<div id="outline-container-org2620568" class="outline-4">
|
||||
<h4 id="org2620568"><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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@ -537,8 +537,8 @@ 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-orgdf7df26" class="outline-5">
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<h5 id="orgdf7df26"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
|
||||
<div id="outline-container-orge3536c8" class="outline-5">
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||||
<h5 id="orge3536c8"><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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@ -587,8 +587,8 @@ icount = BUFSIZE
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</div>
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</div>
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<div id="outline-container-org1e875c6" class="outline-5">
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<h5 id="org1e875c6"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-orgdf25aec" class="outline-5">
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<h5 id="orgdf25aec"><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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@ -632,8 +632,8 @@ icount = bufsize
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</div>
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</div>
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<div id="outline-container-org5810d9f" class="outline-4">
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<h4 id="org5810d9f"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div id="outline-container-org8977f5e" class="outline-4">
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<h4 id="org8977f5e"><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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@ -679,8 +679,8 @@ E = E + E_nn
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</div>
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</div>
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<div id="outline-container-orgbb6b48d" class="outline-4">
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<h4 id="orgbb6b48d"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-org028f8ba" class="outline-4">
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<h4 id="org028f8ba"><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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@ -695,7 +695,7 @@ E = E + E_nn
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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>
|
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<p class="date">Created: 2022-03-11 Fri 12:54</p>
|
||||
<p class="date">Created: 2022-04-13 Wed 14:40</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
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||||
|
||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2022-03-11 Fri 12:54 -->
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||||
<!-- 2022-04-13 Wed 14:40 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TREXIO source code documentation</title>
|
||||
@ -347,7 +347,7 @@ and bug reports should be submitted at
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-03-11 Fri 12:54</p>
|
||||
<p class="date">Created: 2022-04-13 Wed 14:40</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -3,7 +3,7 @@
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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||||
<head>
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<!-- 2022-03-11 Fri 12:54 -->
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||||
<!-- 2022-04-13 Wed 14:40 -->
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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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||||
@ -311,22 +311,22 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org365eb16">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org2767730">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org9e16a26">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org0162385">4. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgcb1e5bd">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org8bd2b5e">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#orga83dd5a">7. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org03c0bc2">8. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgc28c99a">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org8b88da2">10. Helper functions</a></li>
|
||||
<li><a href="#org7a167a8">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org75e825e">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org379bf6e">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org3c56df5">4. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org98b03bd">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org5727110">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#orgca656f6">7. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgba53933">8. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgb0b0234">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org433ad94">10. Helper functions</a></li>
|
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</ul>
|
||||
</div>
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||||
</div>
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<div id="outline-container-org365eb16" class="outline-2">
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||||
<h2 id="org365eb16"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-org7a167a8" class="outline-2">
|
||||
<h2 id="org7a167a8"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
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||||
<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>
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@ -338,8 +338,8 @@ for the JavaScript code in this tag.
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||||
</div>
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||||
</div>
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||||
|
||||
<div id="outline-container-org2767730" class="outline-2">
|
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<h2 id="org2767730"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
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||||
<div id="outline-container-org75e825e" class="outline-2">
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||||
<h2 id="org75e825e"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
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||||
<div class="outline-text-2" id="text-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_hdf5_s</span> {
|
||||
@ -352,8 +352,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9e16a26" class="outline-2">
|
||||
<h2 id="org9e16a26"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-org379bf6e" class="outline-2">
|
||||
<h2 id="org379bf6e"><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>
|
||||
@ -456,8 +456,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0162385" class="outline-2">
|
||||
<h2 id="org0162385"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-org3c56df5" class="outline-2">
|
||||
<h2 id="org3c56df5"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</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>
|
||||
@ -560,8 +560,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgcb1e5bd" class="outline-2">
|
||||
<h2 id="orgcb1e5bd"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org98b03bd" class="outline-2">
|
||||
<h2 id="org98b03bd"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</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>
|
||||
@ -694,8 +694,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8bd2b5e" class="outline-2">
|
||||
<h2 id="org8bd2b5e"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-org5727110" class="outline-2">
|
||||
<h2 id="org5727110"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<p>
|
||||
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
|
||||
@ -717,7 +717,7 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
|
||||
|
||||
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">index_dtype</span>;
|
||||
<span style="color: #228b22;">void</span>* <span style="color: #a0522d;">index_p</span> = <span style="color: #008b8b;">NULL</span>;
|
||||
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">void</span>* <span style="color: #a0522d;">index_p</span>;
|
||||
<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">size_ranked</span> = (<span style="color: #228b22;">uint64_t</span>) size * $group_dset_rank$;
|
||||
/* <span style="color: #b22222;">Determine the optimal type for storing indices depending on the size_max (usually mo_num or ao_num) </span>*/
|
||||
<span style="color: #a020f0;">if</span> (size_max < UINT8_MAX) {
|
||||
@ -737,7 +737,7 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
index_p = index;
|
||||
index_dtype = H5T_NATIVE_UINT16;
|
||||
} <span style="color: #a020f0;">else</span> {
|
||||
index_p = (<span style="color: #228b22;">int32_t</span>*) index_sparse;
|
||||
index_p = (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int32_t</span>*) index_sparse;
|
||||
index_dtype = H5T_NATIVE_INT32;
|
||||
}
|
||||
|
||||
@ -896,8 +896,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga83dd5a" class="outline-2">
|
||||
<h2 id="orga83dd5a"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-orgca656f6" class="outline-2">
|
||||
<h2 id="orgca656f6"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</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>
|
||||
@ -1094,8 +1094,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org03c0bc2" class="outline-2">
|
||||
<h2 id="org03c0bc2"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-orgba53933" class="outline-2">
|
||||
<h2 id="orgba53933"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</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>
|
||||
@ -1221,8 +1221,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgc28c99a" class="outline-2">
|
||||
<h2 id="orgc28c99a"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-orgb0b0234" class="outline-2">
|
||||
<h2 id="orgb0b0234"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<p>
|
||||
<b><b>Note:</b></b> in early versions of the HDF5 library (v < 1.10) unlinking an object was not working as expected
|
||||
@ -1262,8 +1262,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8b88da2" class="outline-2">
|
||||
<h2 id="org8b88da2"><span class="section-number-2">10</span> Helper functions</h2>
|
||||
<div id="outline-container-org433ad94" class="outline-2">
|
||||
<h2 id="org433ad94"><span class="section-number-2">10</span> Helper functions</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>
|
||||
@ -1524,7 +1524,7 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-03-11 Fri 12:54</p>
|
||||
<p class="date">Created: 2022-04-13 Wed 14:40</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>
|
||||
<!-- 2022-03-11 Fri 12:54 -->
|
||||
<!-- 2022-04-13 Wed 14:40 -->
|
||||
<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>
|
||||
@ -311,29 +311,29 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orge60f291">1. TEXT back end</a>
|
||||
<li><a href="#org5b833fc">1. TEXT back end</a>
|
||||
<ul>
|
||||
<li><a href="#org262b8be">1.1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org538aa5a">1.2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org183d11d">1.3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org645e4c0">1.4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orgdba238b">1.5. Template for text read a group</a></li>
|
||||
<li><a href="#org20ee9d7">1.6. Template for text flush a group</a></li>
|
||||
<li><a href="#org7c3aa5e">1.7. Template for text free memory</a></li>
|
||||
<li><a href="#orgca242c4">1.8. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgbfc74fc">1.9. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org7e79bd9">1.10. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orga3f41cb">1.11. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org83e4363">1.12. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#orga67ea82">1.13. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orga30ee45">1.1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org91e9c45">1.2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org633d4d5">1.3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org12fe8bb">1.4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orga3c5bca">1.5. Template for text read a group</a></li>
|
||||
<li><a href="#org01f0f8a">1.6. Template for text flush a group</a></li>
|
||||
<li><a href="#orgf5681e4">1.7. Template for text free memory</a></li>
|
||||
<li><a href="#orga35665f">1.8. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org07daeef">1.9. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgf307d5b">1.10. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org61baf9b">1.11. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org1699abb">1.12. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org71c7d7f">1.13. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge60f291" class="outline-2">
|
||||
<h2 id="orge60f291"><span class="section-number-2">1</span> TEXT back end</h2>
|
||||
<div id="outline-container-org5b833fc" class="outline-2">
|
||||
<h2 id="org5b833fc"><span class="section-number-2">1</span> TEXT back end</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<p>
|
||||
The "file" produced by the text back end is a directory with one
|
||||
@ -354,8 +354,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org262b8be" class="outline-3">
|
||||
<h3 id="org262b8be"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
|
||||
<div id="outline-container-orga30ee45" class="outline-3">
|
||||
<h3 id="orga30ee45"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
|
||||
<div class="outline-text-3" id="text-1-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
|
||||
@ -374,8 +374,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org538aa5a" class="outline-3">
|
||||
<h3 id="org538aa5a"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
|
||||
<div id="outline-container-org91e9c45" class="outline-3">
|
||||
<h3 id="org91e9c45"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
|
||||
<div class="outline-text-3" id="text-1-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_text_s</span> {
|
||||
@ -388,8 +388,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org183d11d" class="outline-3">
|
||||
<h3 id="org183d11d"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
|
||||
<div id="outline-container-org633d4d5" class="outline-3">
|
||||
<h3 id="org633d4d5"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
|
||||
<div class="outline-text-3" id="text-1-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -532,8 +532,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org645e4c0" class="outline-3">
|
||||
<h3 id="org645e4c0"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
|
||||
<div id="outline-container-org12fe8bb" class="outline-3">
|
||||
<h3 id="org12fe8bb"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
|
||||
<div class="outline-text-3" id="text-1-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -555,8 +555,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdba238b" class="outline-3">
|
||||
<h3 id="orgdba238b"><span class="section-number-3">1.5</span> Template for text read a group</h3>
|
||||
<div id="outline-container-orga3c5bca" class="outline-3">
|
||||
<h3 id="orga3c5bca"><span class="section-number-3">1.5</span> Template for text read a group</h3>
|
||||
<div class="outline-text-3" id="text-1-5">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c">$group$_t*
|
||||
@ -857,8 +857,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org20ee9d7" class="outline-3">
|
||||
<h3 id="org20ee9d7"><span class="section-number-3">1.6</span> Template for text flush a group</h3>
|
||||
<div id="outline-container-org01f0f8a" class="outline-3">
|
||||
<h3 id="org01f0f8a"><span class="section-number-3">1.6</span> Template for text flush a group</h3>
|
||||
<div class="outline-text-3" id="text-1-6">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -922,8 +922,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7c3aa5e" class="outline-3">
|
||||
<h3 id="org7c3aa5e"><span class="section-number-3">1.7</span> Template for text free memory</h3>
|
||||
<div id="outline-container-orgf5681e4" class="outline-3">
|
||||
<h3 id="orgf5681e4"><span class="section-number-3">1.7</span> Template for text free memory</h3>
|
||||
<div class="outline-text-3" id="text-1-7">
|
||||
<p>
|
||||
Memory is allocated when reading. The following function frees memory.
|
||||
@ -970,8 +970,8 @@ Memory is allocated when reading. The following function frees memory.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgca242c4" class="outline-3">
|
||||
<h3 id="orgca242c4"><span class="section-number-3">1.8</span> Template for has/read/write a numerical attribute</h3>
|
||||
<div id="outline-container-orga35665f" class="outline-3">
|
||||
<h3 id="orga35665f"><span class="section-number-3">1.8</span> Template for has/read/write a numerical attribute</h3>
|
||||
<div class="outline-text-3" id="text-1-8">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1034,8 +1034,8 @@ Memory is allocated when reading. The following function frees memory.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgbfc74fc" class="outline-3">
|
||||
<h3 id="orgbfc74fc"><span class="section-number-3">1.9</span> Template for has/read/write a dataset of numerical data</h3>
|
||||
<div id="outline-container-org07daeef" class="outline-3">
|
||||
<h3 id="org07daeef"><span class="section-number-3">1.9</span> Template for has/read/write a dataset of numerical data</h3>
|
||||
<div class="outline-text-3" id="text-1-9">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1131,8 +1131,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org7e79bd9" class="outline-3">
|
||||
<h3 id="org7e79bd9"><span class="section-number-3">1.10</span> Template for has/read/write a dataset of strings</h3>
|
||||
<div id="outline-container-orgf307d5b" class="outline-3">
|
||||
<h3 id="orgf307d5b"><span class="section-number-3">1.10</span> Template for has/read/write a dataset of strings</h3>
|
||||
<div class="outline-text-3" id="text-1-10">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1233,8 +1233,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orga3f41cb" class="outline-3">
|
||||
<h3 id="orga3f41cb"><span class="section-number-3">1.11</span> Template for has/read/write a string attribute</h3>
|
||||
<div id="outline-container-org61baf9b" class="outline-3">
|
||||
<h3 id="org61baf9b"><span class="section-number-3">1.11</span> Template for has/read/write a string attribute</h3>
|
||||
<div class="outline-text-3" id="text-1-11">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1308,8 +1308,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org83e4363" class="outline-3">
|
||||
<h3 id="org83e4363"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
|
||||
<div id="outline-container-org1699abb" class="outline-3">
|
||||
<h3 id="org1699abb"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
|
||||
<div class="outline-text-3" id="text-1-12">
|
||||
<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
|
||||
@ -1583,8 +1583,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga67ea82" class="outline-3">
|
||||
<h3 id="orga67ea82"><span class="section-number-3">1.13</span> Template for text delete a group (UNSAFE mode)</h3>
|
||||
<div id="outline-container-org71c7d7f" class="outline-3">
|
||||
<h3 id="org71c7d7f"><span class="section-number-3">1.13</span> Template for text delete a group (UNSAFE mode)</h3>
|
||||
<div class="outline-text-3" id="text-1-13">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1615,7 +1615,7 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-03-11 Fri 12:54</p>
|
||||
<p class="date">Created: 2022-04-13 Wed 14:40</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -8,7 +8,7 @@
|
||||
#+INFOJS_OPT: toc:t mouse:underline path:org-info.js
|
||||
#+HTML_HEAD: <link rel="stylesheet" title="Standard" href="trexio.css" type="text/css" />
|
||||
|
||||
#+STARTUP: align fold nodlcheck hidestars oddeven lognotestate
|
||||
#+STARTUP: align nodlcheck hidestars oddeven lognotestate
|
||||
#+AUTHOR: TREX-CoE
|
||||
#+LANGUAGE: en
|
||||
|
||||
|
||||
210
trex.html
210
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>
|
||||
<!-- 2022-03-11 Fri 12:54 -->
|
||||
<!-- 2022-04-13 Wed 14:40 -->
|
||||
<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>
|
||||
@ -333,33 +333,34 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org56d8986">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#orgb1f499e">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org5cc8a82">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org35661b1">4. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#org43da47e">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org6992d6e">2. Electron (electron group)</a></li>
|
||||
<li><a href="#orgabfd33b">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#orgce25685">4. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#orgf0c1d1a">4.1. Example</a></li>
|
||||
<li><a href="#org048c36b">4.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgddc4bdf">5. Basis set (basis group)</a>
|
||||
<li><a href="#orgd8244eb">5. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#orge85c802">5.1. Example</a></li>
|
||||
<li><a href="#org5412e10">5.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org25757ac">6. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#org1baedc9">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="#orgb2e4d24">7. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org8adb423">7. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#org2a64258">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orgc2bf608">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#orgb5fa684">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orgd0a95a6">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org02d15d9">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
|
||||
<li><a href="#org9a6fddf">9. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org8c5ddc1">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
|
||||
<li><a href="#orga4cddb0">9. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org5b8bdc9">10. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -367,18 +368,12 @@ for the JavaScript code in this tag.
|
||||
This page contains information about the general structure of the
|
||||
TREXIO library. The source code of the library can be automatically
|
||||
generated based on the contents of the <code>trex.json</code> configuration file,
|
||||
which itself is compiled from different sections (groups) presented
|
||||
which itself is generated from different sections (groups) presented
|
||||
below.
|
||||
</p>
|
||||
|
||||
<p>
|
||||
For more information about the automatic generation on the source code
|
||||
or regarding possible modifications, please contact the TREXIO
|
||||
developers.
|
||||
</p>
|
||||
|
||||
<p>
|
||||
All quantities are saved in TREXIO file in atomic units. The
|
||||
All quantities are saved in TREXIO files in atomic units. The
|
||||
dimensions of the arrays in the tables below are given in column-major
|
||||
order (as in Fortran), and the ordering of the dimensions is reversed
|
||||
in the produced <code>trex.json</code> configuration file as the library is
|
||||
@ -389,7 +384,7 @@ written in C.
|
||||
TREXIO currently supports <code>int</code>, <code>float</code> and <code>str</code> types for both
|
||||
single attributes and arrays. Note, that some attributes might have
|
||||
<code>dim</code> type (e.g. <code>num</code> of the <code>nucleus</code> group). This type is treated
|
||||
exactly the same as <code>int</code> with the only difference that <code>dim</code>
|
||||
exactly in the same way as <code>int</code> with the only difference that <code>dim</code>
|
||||
variables cannot be negative. This additional constraint is required
|
||||
because <code>dim</code> attributes are used internally to allocate memory and to
|
||||
check array boundaries in the memory-safe API. Most of the times, the
|
||||
@ -397,8 +392,8 @@ check array boundaries in the memory-safe API. Most of the times, the
|
||||
</p>
|
||||
|
||||
<p>
|
||||
In Fortran, the arrays are 1-based and in most other languages the
|
||||
arrays are 0-based. Hence, we introduce the <code>index</code> type which is an
|
||||
In Fortran, arrays are 1-based and in most other languages the
|
||||
arrays are 0-based. Hence, we introduce the <code>index</code> type which is a
|
||||
1-based <code>int</code> in the Fortran interface and 0-based otherwise.
|
||||
</p>
|
||||
|
||||
@ -406,11 +401,13 @@ arrays are 0-based. Hence, we introduce the <code>index</code> type which is an
|
||||
For sparse data structures such as electron replusion integrals,
|
||||
the data can be too large to fit in memory and the data needs to be
|
||||
fetched using multiple function calls to perform I/O on buffers.
|
||||
For more information on how to read/write sparse data structures, see
|
||||
the <a href="./examples.html">examples</a>.
|
||||
</p>
|
||||
|
||||
|
||||
<div id="outline-container-org56d8986" class="outline-2">
|
||||
<h2 id="org56d8986"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-org43da47e" class="outline-2">
|
||||
<h2 id="org43da47e"><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
|
||||
@ -420,7 +417,7 @@ which have participated to the creation of the file, a list of
|
||||
authors of the file, and a textual description.
|
||||
</p>
|
||||
|
||||
<table id="org73b5985" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgbbe7e1e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -501,15 +498,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb1f499e" class="outline-2">
|
||||
<h2 id="orgb1f499e"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div id="outline-container-org6992d6e" class="outline-2">
|
||||
<h2 id="org6992d6e"><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="orgff31774" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgbe41d44" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -530,6 +527,13 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left"><code>num</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Number of electrons</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>up_num</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
@ -548,15 +552,15 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5cc8a82" class="outline-2">
|
||||
<h2 id="org5cc8a82"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div id="outline-container-orgabfd33b" class="outline-2">
|
||||
<h2 id="orgabfd33b"><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="orgc04c3a1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgc4f4b69" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -623,8 +627,8 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org35661b1" class="outline-2">
|
||||
<h2 id="org35661b1"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div id="outline-container-orgce25685" class="outline-2">
|
||||
<h2 id="orgce25685"><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
|
||||
@ -657,7 +661,7 @@ 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="orge084345" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgc6c6f68" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -759,8 +763,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf0c1d1a" class="outline-3">
|
||||
<h3 id="orgf0c1d1a"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div id="outline-container-org048c36b" class="outline-3">
|
||||
<h3 id="org048c36b"><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
|
||||
@ -823,8 +827,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgddc4bdf" class="outline-2">
|
||||
<h2 id="orgddc4bdf"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div id="outline-container-orgd8244eb" class="outline-2">
|
||||
<h2 id="orgd8244eb"><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
|
||||
@ -877,7 +881,7 @@ 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="orga494916" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org270f4b7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -971,8 +975,8 @@ All the basis set parameters are stored in one-dimensional arrays:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge85c802" class="outline-3">
|
||||
<h3 id="orge85c802"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div id="outline-container-org5412e10" class="outline-3">
|
||||
<h3 id="org5412e10"><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
|
||||
@ -1050,8 +1054,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org25757ac" class="outline-2">
|
||||
<h2 id="org25757ac"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div id="outline-container-org1baedc9" class="outline-2">
|
||||
<h2 id="org1baedc9"><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
|
||||
@ -1104,13 +1108,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#orgddc4bdf">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#orgd8244eb">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="org2b3af66" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd4885d3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1162,8 +1166,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1268404" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org1268404"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div id="outline-container-orgdb31d9f" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="orgdb31d9f"></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}}
|
||||
@ -1180,7 +1184,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org1589284" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgd7a5387" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1240,8 +1244,8 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdb9d958" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="orgdb9d958"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div id="outline-container-org8ab253a" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org8ab253a"></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
|
||||
@ -1262,7 +1266,7 @@ notation.
|
||||
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
|
||||
</ul>
|
||||
|
||||
<table id="orgd34360c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org24e2de2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1302,10 +1306,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb2e4d24" class="outline-2">
|
||||
<h2 id="orgb2e4d24"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div id="outline-container-org8adb423" class="outline-2">
|
||||
<h2 id="org8adb423"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="orgfc34de6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org6a35a08" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1371,8 +1375,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2a64258" class="outline-3">
|
||||
<h3 id="org2a64258"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div id="outline-container-orgb5fa684" class="outline-3">
|
||||
<h3 id="orgb5fa684"><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
|
||||
@ -1380,7 +1384,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org3d74cc1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org22b4a6d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1440,8 +1444,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc2bf608" class="outline-3">
|
||||
<h3 id="orgc2bf608"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div id="outline-container-orgd0a95a6" class="outline-3">
|
||||
<h3 id="orgd0a95a6"><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
|
||||
@ -1449,7 +1453,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org3bab743" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org848a240" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1489,11 +1493,11 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org02d15d9" class="outline-2">
|
||||
<h2 id="org02d15d9"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
|
||||
<div id="outline-container-org8c5ddc1" class="outline-2">
|
||||
<h2 id="org8c5ddc1"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
|
||||
</div>
|
||||
<div id="outline-container-org9a6fddf" class="outline-2">
|
||||
<h2 id="org9a6fddf"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
|
||||
<div id="outline-container-orga4cddb0" class="outline-2">
|
||||
<h2 id="orga4cddb0"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<p>
|
||||
The reduced density matrices are defined in the basis of molecular
|
||||
@ -1546,7 +1550,7 @@ The total energy can be computed as:
|
||||
\]
|
||||
</p>
|
||||
|
||||
<table id="org46f5bb4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2755768" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1626,10 +1630,78 @@ The total energy can be computed as:
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5b8bdc9" class="outline-2">
|
||||
<h2 id="org5b8bdc9"><span class="section-number-2">10</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
<p>
|
||||
In quantum Monte Carlo calculations, the wave function is evaluated
|
||||
at points of the 3N-dimensional space. Some algorithms require multiple
|
||||
independent <i>walkers</i>, so it is possible to store multiple coordinates,
|
||||
as well as some quantities evaluated at those points.
|
||||
</p>
|
||||
|
||||
<p>
|
||||
By convention, the electron coordinates contain first all the electrons
|
||||
of $↑$-spin and then all the $↓$-spin.
|
||||
</p>
|
||||
|
||||
<table id="orgf08a6c3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
<col class="org-left" />
|
||||
|
||||
<col class="org-left" />
|
||||
|
||||
<col class="org-left" />
|
||||
|
||||
<col class="org-left" />
|
||||
</colgroup>
|
||||
<thead>
|
||||
<tr>
|
||||
<th scope="col" class="org-left">Variable</th>
|
||||
<th scope="col" class="org-left">Type</th>
|
||||
<th scope="col" class="org-left">Dimensions</th>
|
||||
<th scope="col" class="org-left">Description</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left"><code>num</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Number of 3N-dimensional points</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>point</code></td>
|
||||
<td class="org-left"><code>float</code></td>
|
||||
<td class="org-left"><code>(3, electron.num, qmc.num)</code></td>
|
||||
<td class="org-left">3N-dimensional points</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>psi</code></td>
|
||||
<td class="org-left"><code>float</code></td>
|
||||
<td class="org-left"><code>(qmc.num)</code></td>
|
||||
<td class="org-left">Wave function evaluated at the points</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>e_loc</code></td>
|
||||
<td class="org-left"><code>float</code></td>
|
||||
<td class="org-left"><code>(qmc.num)</code></td>
|
||||
<td class="org-left">Local energy evaluated at the points</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-03-11 Fri 12:54</p>
|
||||
<p class="date">Created: 2022-04-13 Wed 14:40</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
Loading…
Reference in New Issue
Block a user