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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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||||
<!-- 2022-02-16 Wed 13:52 -->
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<!-- 2022-02-17 Thu 14:52 -->
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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>
|
||||
<p class="date">Created: 2022-02-16 Wed 13:52</p>
|
||||
<p class="date">Created: 2022-02-17 Thu 14:52</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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||||
<!-- 2022-02-16 Wed 13:52 -->
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||||
<!-- 2022-02-17 Thu 14:52 -->
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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="#org7e0e2cd">1. Accessing sparse quantities</a>
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<li><a href="#orgd8dfc23">1. Accessing sparse quantities</a>
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<ul>
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<li><a href="#org1ae5306">1.1. Fortran</a>
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<li><a href="#orgb03d2ec">1.1. Fortran</a>
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<ul>
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<li><a href="#orga06ba65">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org26fbd98">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="#org581bc5f">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org86c4bf6">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org29cf69a">1.1.5. Allocate memory</a></li>
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<li><a href="#org49a3da8">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org844a9ca">1.1.7. Read two-electron quantities</a>
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<li><a href="#org5777051">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org70b4a3e">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="#org502cb41">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org46dd8e9">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orgcd74845">1.1.5. Allocate memory</a></li>
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<li><a href="#org0821c77">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#orga0bbb64">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#org7febd4e">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#orge7e02eb">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#org62931c4">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#orga142491">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="#orgb23857e">1.1.8. Compute the energy</a></li>
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<li><a href="#org4cec77e">1.1.9. Terminate</a></li>
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<li><a href="#orgd02a02b">1.1.8. Compute the energy</a></li>
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<li><a href="#orgfa9634e">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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||||
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<div id="outline-container-org7e0e2cd" class="outline-2">
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<h2 id="org7e0e2cd"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
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<div id="outline-container-orgd8dfc23" class="outline-2">
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||||
<h2 id="orgd8dfc23"><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-org1ae5306" class="outline-3">
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<h3 id="org1ae5306"><span class="section-number-3">1.1</span> Fortran</h3>
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||||
<div id="outline-container-orgb03d2ec" class="outline-3">
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<h3 id="orgb03d2ec"><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-orga06ba65" class="outline-4">
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<h4 id="orga06ba65"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-org5777051" class="outline-4">
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||||
<h4 id="org5777051"><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-org26fbd98" class="outline-4">
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<h4 id="org26fbd98"><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-org70b4a3e" class="outline-4">
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<h4 id="org70b4a3e"><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-org581bc5f" class="outline-4">
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<h4 id="org581bc5f"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-org502cb41" class="outline-4">
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<h4 id="org502cb41"><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-org86c4bf6" class="outline-4">
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<h4 id="org86c4bf6"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-org46dd8e9" class="outline-4">
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<h4 id="org46dd8e9"><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-org29cf69a" class="outline-4">
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<h4 id="org29cf69a"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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||||
<div id="outline-container-orgcd74845" class="outline-4">
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||||
<h4 id="orgcd74845"><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-org49a3da8" class="outline-4">
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<h4 id="org49a3da8"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div id="outline-container-org0821c77" class="outline-4">
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<h4 id="org0821c77"><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-org844a9ca" class="outline-4">
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||||
<h4 id="org844a9ca"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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<div id="outline-container-orga0bbb64" class="outline-4">
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||||
<h4 id="orga0bbb64"><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-org7febd4e" class="outline-5">
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<h5 id="org7febd4e"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
|
||||
<div id="outline-container-org62931c4" class="outline-5">
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||||
<h5 id="org62931c4"><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-orge7e02eb" class="outline-5">
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<h5 id="orge7e02eb"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-orga142491" class="outline-5">
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<h5 id="orga142491"><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-orgb23857e" class="outline-4">
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<h4 id="orgb23857e"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div id="outline-container-orgd02a02b" class="outline-4">
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<h4 id="orgd02a02b"><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-org4cec77e" class="outline-4">
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<h4 id="org4cec77e"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-orgfa9634e" class="outline-4">
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<h4 id="orgfa9634e"><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: 2022-02-16 Wed 13:52</p>
|
||||
<p class="date">Created: 2022-02-17 Thu 14:52</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">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2022-02-16 Wed 13:52 -->
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||||
<!-- 2022-02-17 Thu 14:52 -->
|
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<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>
|
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<p class="date">Created: 2022-02-16 Wed 13:52</p>
|
||||
<p class="date">Created: 2022-02-17 Thu 14:52</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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||||
<!-- 2022-02-16 Wed 13:52 -->
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||||
<!-- 2022-02-17 Thu 14:52 -->
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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>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="#orgb1e560f">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org416f7d4">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org62d7fa7">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orgbfe05db">4. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgb698d7f">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org9f925b2">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#org7c4d338">7. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgdff8d75">8. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#org8243dac">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org2ebf198">10. Helper functions</a></li>
|
||||
<li><a href="#orgaf61c17">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#orgb23766f">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org7e9e586">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orgb5c5409">4. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org2bebc81">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orga219828">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#org27be479">7. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgde3fb51">8. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgf2128f5">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orgf7edd6c">10. Helper functions</a></li>
|
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</ul>
|
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</div>
|
||||
</div>
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|
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<div id="outline-container-orgb1e560f" class="outline-2">
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<h2 id="orgb1e560f"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-orgaf61c17" class="outline-2">
|
||||
<h2 id="orgaf61c17"><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">
|
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<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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||||
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||||
<div id="outline-container-org416f7d4" class="outline-2">
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||||
<h2 id="org416f7d4"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-orgb23766f" class="outline-2">
|
||||
<h2 id="orgb23766f"><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-org62d7fa7" class="outline-2">
|
||||
<h2 id="org62d7fa7"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-org7e9e586" class="outline-2">
|
||||
<h2 id="org7e9e586"><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-orgbfe05db" class="outline-2">
|
||||
<h2 id="orgbfe05db"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-orgb5c5409" class="outline-2">
|
||||
<h2 id="orgb5c5409"><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-orgb698d7f" class="outline-2">
|
||||
<h2 id="orgb698d7f"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org2bebc81" class="outline-2">
|
||||
<h2 id="org2bebc81"><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-org9f925b2" class="outline-2">
|
||||
<h2 id="org9f925b2"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-orga219828" class="outline-2">
|
||||
<h2 id="orga219828"><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
|
||||
@ -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-org7c4d338" class="outline-2">
|
||||
<h2 id="org7c4d338"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org27be479" class="outline-2">
|
||||
<h2 id="org27be479"><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-orgdff8d75" class="outline-2">
|
||||
<h2 id="orgdff8d75"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-orgde3fb51" class="outline-2">
|
||||
<h2 id="orgde3fb51"><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-org8243dac" class="outline-2">
|
||||
<h2 id="org8243dac"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-orgf2128f5" class="outline-2">
|
||||
<h2 id="orgf2128f5"><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-org2ebf198" class="outline-2">
|
||||
<h2 id="org2ebf198"><span class="section-number-2">10</span> Helper functions</h2>
|
||||
<div id="outline-container-orgf7edd6c" class="outline-2">
|
||||
<h2 id="orgf7edd6c"><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: 2022-02-16 Wed 13:52</p>
|
||||
<p class="date">Created: 2022-02-17 Thu 14:52</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>
|
||||
<!-- 2022-02-16 Wed 13:52 -->
|
||||
<!-- 2022-02-17 Thu 14:52 -->
|
||||
<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="#org2b283a5">1. TEXT back end</a>
|
||||
<li><a href="#org239c3e9">1. TEXT back end</a>
|
||||
<ul>
|
||||
<li><a href="#org3c6a7b3">1.1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org1e07007">1.2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#orgad02bfb">1.3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org76d4a60">1.4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org70c9ff7">1.5. Template for text read a group</a></li>
|
||||
<li><a href="#org4e4514c">1.6. Template for text flush a group</a></li>
|
||||
<li><a href="#org5198ec7">1.7. Template for text free memory</a></li>
|
||||
<li><a href="#orgb097852">1.8. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org3df4185">1.9. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgb6b7c3a">1.10. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org98e611c">1.11. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgaceea75">1.12. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org0b87886">1.13. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#org835d486">1.1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org6cba301">1.2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org92d0e22">1.3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#orga8f9fb5">1.4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org5cb497c">1.5. Template for text read a group</a></li>
|
||||
<li><a href="#orgefddb6c">1.6. Template for text flush a group</a></li>
|
||||
<li><a href="#orge55590b">1.7. Template for text free memory</a></li>
|
||||
<li><a href="#orgcfce45c">1.8. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org604732d">1.9. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgd25e859">1.10. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgf91bf6e">1.11. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgd2cadca">1.12. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org60cca65">1.13. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2b283a5" class="outline-2">
|
||||
<h2 id="org2b283a5"><span class="section-number-2">1</span> TEXT back end</h2>
|
||||
<div id="outline-container-org239c3e9" class="outline-2">
|
||||
<h2 id="org239c3e9"><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-org3c6a7b3" class="outline-3">
|
||||
<h3 id="org3c6a7b3"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
|
||||
<div id="outline-container-org835d486" class="outline-3">
|
||||
<h3 id="org835d486"><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-org1e07007" class="outline-3">
|
||||
<h3 id="org1e07007"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
|
||||
<div id="outline-container-org6cba301" class="outline-3">
|
||||
<h3 id="org6cba301"><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-orgad02bfb" class="outline-3">
|
||||
<h3 id="orgad02bfb"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
|
||||
<div id="outline-container-org92d0e22" class="outline-3">
|
||||
<h3 id="org92d0e22"><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-org76d4a60" class="outline-3">
|
||||
<h3 id="org76d4a60"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
|
||||
<div id="outline-container-orga8f9fb5" class="outline-3">
|
||||
<h3 id="orga8f9fb5"><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-org70c9ff7" class="outline-3">
|
||||
<h3 id="org70c9ff7"><span class="section-number-3">1.5</span> Template for text read a group</h3>
|
||||
<div id="outline-container-org5cb497c" class="outline-3">
|
||||
<h3 id="org5cb497c"><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-org4e4514c" class="outline-3">
|
||||
<h3 id="org4e4514c"><span class="section-number-3">1.6</span> Template for text flush a group</h3>
|
||||
<div id="outline-container-orgefddb6c" class="outline-3">
|
||||
<h3 id="orgefddb6c"><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-org5198ec7" class="outline-3">
|
||||
<h3 id="org5198ec7"><span class="section-number-3">1.7</span> Template for text free memory</h3>
|
||||
<div id="outline-container-orge55590b" class="outline-3">
|
||||
<h3 id="orge55590b"><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-orgb097852" class="outline-3">
|
||||
<h3 id="orgb097852"><span class="section-number-3">1.8</span> Template for has/read/write a numerical attribute</h3>
|
||||
<div id="outline-container-orgcfce45c" class="outline-3">
|
||||
<h3 id="orgcfce45c"><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-org3df4185" class="outline-3">
|
||||
<h3 id="org3df4185"><span class="section-number-3">1.9</span> Template for has/read/write a dataset of numerical data</h3>
|
||||
<div id="outline-container-org604732d" class="outline-3">
|
||||
<h3 id="org604732d"><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-orgb6b7c3a" class="outline-3">
|
||||
<h3 id="orgb6b7c3a"><span class="section-number-3">1.10</span> Template for has/read/write a dataset of strings</h3>
|
||||
<div id="outline-container-orgd25e859" class="outline-3">
|
||||
<h3 id="orgd25e859"><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-org98e611c" class="outline-3">
|
||||
<h3 id="org98e611c"><span class="section-number-3">1.11</span> Template for has/read/write a string attribute</h3>
|
||||
<div id="outline-container-orgf91bf6e" class="outline-3">
|
||||
<h3 id="orgf91bf6e"><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-orgaceea75" class="outline-3">
|
||||
<h3 id="orgaceea75"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
|
||||
<div id="outline-container-orgd2cadca" class="outline-3">
|
||||
<h3 id="orgd2cadca"><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-org0b87886" class="outline-3">
|
||||
<h3 id="org0b87886"><span class="section-number-3">1.13</span> Template for text delete a group (UNSAFE mode)</h3>
|
||||
<div id="outline-container-org60cca65" class="outline-3">
|
||||
<h3 id="org60cca65"><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: 2022-02-16 Wed 13:52</p>
|
||||
<p class="date">Created: 2022-02-17 Thu 14:52</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
116
trex.html
116
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>
|
||||
<!-- 2022-02-16 Wed 13:52 -->
|
||||
<!-- 2022-02-17 Thu 14:52 -->
|
||||
<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 +333,33 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org3a8ad6a">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org2f05f94">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org70c2027">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#orgd2b2dd0">4. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#org72195c8">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org5c67572">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org0f6133e">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org34ee8c0">4. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#orge301a99">4.1. Example</a></li>
|
||||
<li><a href="#org153262e">4.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org74a3a63">5. Basis set (basis group)</a>
|
||||
<li><a href="#org44b264f">5. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#org615c5d4">5.1. Example</a></li>
|
||||
<li><a href="#org4d09113">5.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org072996e">6. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#orgeed6add">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="#org9781300">7. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org9ab9e65">7. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#orgd258c0b">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orgb9f5c74">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#orga8221b5">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orgb666f26">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org4baa7ea">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
|
||||
<li><a href="#orgc1cf92e">9. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org7f512fe">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
|
||||
<li><a href="#org9ff4e63">9. Reduced density matrices (rdm group)</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -409,8 +409,8 @@ fetched using multiple function calls to perform I/O on buffers.
|
||||
</p>
|
||||
|
||||
|
||||
<div id="outline-container-org3a8ad6a" class="outline-2">
|
||||
<h2 id="org3a8ad6a"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-org72195c8" class="outline-2">
|
||||
<h2 id="org72195c8"><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 +420,7 @@ which have participated to the creation of the file, a list of
|
||||
authors of the file, and a textual description.
|
||||
</p>
|
||||
|
||||
<table id="orgabd6d58" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org6dc8a6b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -501,15 +501,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2f05f94" class="outline-2">
|
||||
<h2 id="org2f05f94"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div id="outline-container-org5c67572" class="outline-2">
|
||||
<h2 id="org5c67572"><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="orga4de617" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org4258d4a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -548,15 +548,15 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org70c2027" class="outline-2">
|
||||
<h2 id="org70c2027"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div id="outline-container-org0f6133e" class="outline-2">
|
||||
<h2 id="org0f6133e"><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="org9a473ab" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2477139" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -623,8 +623,8 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd2b2dd0" class="outline-2">
|
||||
<h2 id="orgd2b2dd0"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div id="outline-container-org34ee8c0" class="outline-2">
|
||||
<h2 id="org34ee8c0"><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 +657,7 @@ 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="org76c244b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2403ae0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -755,8 +755,8 @@ The latter causes issues when written before <code>ang_mom</code> in the TREXIO
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge301a99" class="outline-3">
|
||||
<h3 id="orge301a99"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div id="outline-container-org153262e" class="outline-3">
|
||||
<h3 id="org153262e"><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
|
||||
@ -819,8 +819,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org74a3a63" class="outline-2">
|
||||
<h2 id="org74a3a63"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div id="outline-container-org44b264f" class="outline-2">
|
||||
<h2 id="org44b264f"><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
|
||||
@ -873,7 +873,7 @@ 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="org0b5051d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org23bedb9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -967,8 +967,8 @@ All the basis set parameters are stored in one-dimensional arrays:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org615c5d4" class="outline-3">
|
||||
<h3 id="org615c5d4"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div id="outline-container-org4d09113" class="outline-3">
|
||||
<h3 id="org4d09113"><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
|
||||
@ -1046,8 +1046,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org072996e" class="outline-2">
|
||||
<h2 id="org072996e"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div id="outline-container-orgeed6add" class="outline-2">
|
||||
<h2 id="orgeed6add"><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
|
||||
@ -1100,13 +1100,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#org74a3a63">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#org44b264f">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="org084943a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org352fd6a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1158,8 +1158,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org832b8db" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org832b8db"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div id="outline-container-org07f6428" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org07f6428"></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}}
|
||||
@ -1177,7 +1177,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orgc569c13" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org41fdf72" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1244,8 +1244,8 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org317e5f8" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org317e5f8"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div id="outline-container-org1c389cc" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org1c389cc"></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
|
||||
@ -1266,7 +1266,7 @@ notation.
|
||||
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
|
||||
</ul>
|
||||
|
||||
<table id="org2c308db" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org72979f2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1306,10 +1306,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9781300" class="outline-2">
|
||||
<h2 id="org9781300"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div id="outline-container-org9ab9e65" class="outline-2">
|
||||
<h2 id="org9ab9e65"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="orgedd33a3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org34e4ed5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1375,8 +1375,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd258c0b" class="outline-3">
|
||||
<h3 id="orgd258c0b"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div id="outline-container-orga8221b5" class="outline-3">
|
||||
<h3 id="orga8221b5"><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
|
||||
@ -1384,7 +1384,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org38894b9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org7e925ed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1451,8 +1451,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb9f5c74" class="outline-3">
|
||||
<h3 id="orgb9f5c74"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div id="outline-container-orgb666f26" class="outline-3">
|
||||
<h3 id="orgb666f26"><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
|
||||
@ -1460,7 +1460,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orgede5f9d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgc0742d3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1500,11 +1500,11 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4baa7ea" class="outline-2">
|
||||
<h2 id="org4baa7ea"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
|
||||
<div id="outline-container-org7f512fe" class="outline-2">
|
||||
<h2 id="org7f512fe"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
|
||||
</div>
|
||||
<div id="outline-container-orgc1cf92e" class="outline-2">
|
||||
<h2 id="orgc1cf92e"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
|
||||
<div id="outline-container-org9ff4e63" class="outline-2">
|
||||
<h2 id="org9ff4e63"><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
|
||||
@ -1557,7 +1557,7 @@ The total energy can be computed as:
|
||||
\]
|
||||
</p>
|
||||
|
||||
<table id="org601923e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org317d59e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1640,7 +1640,7 @@ The total energy can be computed as:
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-02-16 Wed 13:52</p>
|
||||
<p class="date">Created: 2022-02-17 Thu 14:52</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