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6
README.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-05-18 Tue 10:33 -->
<!-- 2021-05-18 Tue 23:32 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>QMCkl source code documentation</title>
@ -320,6 +320,8 @@ for the JavaScript code in this tag.
<li><a href="./qmckl_electron.html">Electrons</a></li>
<li><a href="./qmckl_ao.html">Atomic Orbitals</a></li>
<li><a href="./qmckl_distance.html">Inter-particle distances</a></li>
<li><a href="./qmckl_utils.html">Utility functions</a></li>
<li><a href="./qmckl_tests.html">Data for Tests</a></li>
</ul>
@ -350,7 +352,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX CoE</p>
<p class="date">Created: 2021-05-18 Tue 10:33</p>
<p class="date">Created: 2021-05-18 Tue 23:32</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

102
qmckl.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-05-18 Tue 10:33 -->
<!-- 2021-05-18 Tue 23:32 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Introduction</title>
@ -333,30 +333,30 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org8732f54">1. Using QMCkl</a></li>
<li><a href="#org72375bf">2. Developing in QMCkl</a>
<li><a href="#orgd1006c4">1. Using QMCkl</a></li>
<li><a href="#orga0b07a9">2. Developing in QMCkl</a>
<ul>
<li><a href="#org2fd5baf">2.1. Literate programming</a></li>
<li><a href="#orgeca8f61">2.2. Source code editing</a></li>
<li><a href="#org6344806">2.3. Choice of the programming language</a></li>
<li><a href="#org18c6ca4">2.4. Coding rules</a></li>
<li><a href="#org7c2077d">2.5. Design of the library</a></li>
<li><a href="#org05b95f0">2.6. Naming conventions</a></li>
<li><a href="#org8da24c9">2.7. Application programming interface</a></li>
<li><a href="#org0b94751">2.8. Global state</a></li>
<li><a href="#org3e8524f">2.9. Headers</a></li>
<li><a href="#org6a0c67f">2.10. Low-level functions</a></li>
<li><a href="#org5ef4513">2.11. High-level functions</a></li>
<li><a href="#orgaca373f">2.12. Numerical precision</a></li>
<li><a href="#orgd9442d3">2.13. Algorithms</a></li>
<li><a href="#orgf235310">2.1. Literate programming</a></li>
<li><a href="#org2efd276">2.2. Source code editing</a></li>
<li><a href="#org91a43fd">2.3. Choice of the programming language</a></li>
<li><a href="#org0bb366f">2.4. Coding rules</a></li>
<li><a href="#orgd5dd075">2.5. Design of the library</a></li>
<li><a href="#org7092a15">2.6. Naming conventions</a></li>
<li><a href="#org0811a18">2.7. Application programming interface</a></li>
<li><a href="#orgd4e885b">2.8. Global state</a></li>
<li><a href="#orgd9d3690">2.9. Headers</a></li>
<li><a href="#org19e4e9e">2.10. Low-level functions</a></li>
<li><a href="#org64e0a70">2.11. High-level functions</a></li>
<li><a href="#org96f36d7">2.12. Numerical precision</a></li>
<li><a href="#org9785916">2.13. Algorithms</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org8732f54" class="outline-2">
<h2 id="org8732f54"><span class="section-number-2">1</span> Using QMCkl</h2>
<div id="outline-container-orgd1006c4" class="outline-2">
<h2 id="orgd1006c4"><span class="section-number-2">1</span> Using QMCkl</h2>
<div class="outline-text-2" id="text-1">
<p>
The <code>qmckl.h</code> header file installed in the <code>${prefix}/include</code> directory
@ -385,12 +385,12 @@ Both files are located in the <code>include/</code> directory.
</div>
</div>
<div id="outline-container-org72375bf" class="outline-2">
<h2 id="org72375bf"><span class="section-number-2">2</span> Developing in QMCkl</h2>
<div id="outline-container-orga0b07a9" class="outline-2">
<h2 id="orga0b07a9"><span class="section-number-2">2</span> Developing in QMCkl</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org2fd5baf" class="outline-3">
<h3 id="org2fd5baf"><span class="section-number-3">2.1</span> Literate programming</h3>
<div id="outline-container-orgf235310" class="outline-3">
<h3 id="orgf235310"><span class="section-number-3">2.1</span> Literate programming</h3>
<div class="outline-text-3" id="text-2-1">
<p>
In a traditional source code, most of the lines of source files of a program
@ -435,8 +435,8 @@ interactively, in the same spirit as Jupyter notebooks.
</div>
</div>
<div id="outline-container-orgeca8f61" class="outline-3">
<h3 id="orgeca8f61"><span class="section-number-3">2.2</span> Source code editing</h3>
<div id="outline-container-org2efd276" class="outline-3">
<h3 id="org2efd276"><span class="section-number-3">2.2</span> Source code editing</h3>
<div class="outline-text-3" id="text-2-2">
<p>
For a tutorial on literate programming with org-mode, follow <a href="http://www.howardism.org/Technical/Emacs/literate-programming-tutorial.html">this link</a>.
@ -467,8 +467,8 @@ org-mode.
</div>
</div>
<div id="outline-container-org6344806" class="outline-3">
<h3 id="org6344806"><span class="section-number-3">2.3</span> Choice of the programming language</h3>
<div id="outline-container-org91a43fd" class="outline-3">
<h3 id="org91a43fd"><span class="section-number-3">2.3</span> Choice of the programming language</h3>
<div class="outline-text-3" id="text-2-3">
<p>
Most of the codes of the <a href="https://trex-coe.eu">TREX CoE</a> are written in Fortran with some scripts in
@ -516,8 +516,8 @@ For more guidelines on using Fortran to generate a C interface, see
</div>
</div>
<div id="outline-container-org18c6ca4" class="outline-3">
<h3 id="org18c6ca4"><span class="section-number-3">2.4</span> Coding rules</h3>
<div id="outline-container-org0bb366f" class="outline-3">
<h3 id="org0bb366f"><span class="section-number-3">2.4</span> Coding rules</h3>
<div class="outline-text-3" id="text-2-4">
<p>
The authors should follow the recommendations of the C99
@ -535,8 +535,8 @@ Compliance can be checked with <code>cppcheck</code> as:
</div>
</div>
<div id="outline-container-org7c2077d" class="outline-3">
<h3 id="org7c2077d"><span class="section-number-3">2.5</span> Design of the library</h3>
<div id="outline-container-orgd5dd075" class="outline-3">
<h3 id="orgd5dd075"><span class="section-number-3">2.5</span> Design of the library</h3>
<div class="outline-text-3" id="text-2-5">
<p>
The proposed API should allow the library to: deal with memory transfers
@ -547,8 +547,8 @@ functions (see below).
</div>
</div>
<div id="outline-container-org05b95f0" class="outline-3">
<h3 id="org05b95f0"><span class="section-number-3">2.6</span> Naming conventions</h3>
<div id="outline-container-org7092a15" class="outline-3">
<h3 id="org7092a15"><span class="section-number-3">2.6</span> Naming conventions</h3>
<div class="outline-text-3" id="text-2-6">
<p>
To avoid namespace collisions, we use <code>qmckl_</code> as a prefix for all exported
@ -573,8 +573,8 @@ form is allowed.
</div>
</div>
<div id="outline-container-org8da24c9" class="outline-3">
<h3 id="org8da24c9"><span class="section-number-3">2.7</span> Application programming interface</h3>
<div id="outline-container-org0811a18" class="outline-3">
<h3 id="org0811a18"><span class="section-number-3">2.7</span> Application programming interface</h3>
<div class="outline-text-3" id="text-2-7">
<p>
In the C language, the number of bits used by the integer types can change
@ -606,15 +606,15 @@ bindings in other languages in other repositories.
</div>
</div>
<div id="outline-container-org0b94751" class="outline-3">
<h3 id="org0b94751"><span class="section-number-3">2.8</span> Global state</h3>
<div id="outline-container-orgd4e885b" class="outline-3">
<h3 id="orgd4e885b"><span class="section-number-3">2.8</span> Global state</h3>
<div class="outline-text-3" id="text-2-8">
<p>
Global variables should be avoided in the library, because it is
possible that one single program needs to use multiple instances
of the library. To solve this problem we propose to use a pointer
to a <a href="./qmckl_context.html"><code>context</code></a> variable, built by the library with the
<code>qmckl_context_create</code> function. The <a id="orge351a7b">=context=</a> contains the global
<code>qmckl_context_create</code> function. The <a id="org6c95d82">=context=</a> contains the global
state of the library, and is used as the first argument of many
QMCkl functions.
</p>
@ -628,8 +628,8 @@ the state is done by setters and getters, prefixed by
</div>
</div>
<div id="outline-container-org3e8524f" class="outline-3">
<h3 id="org3e8524f"><span class="section-number-3">2.9</span> Headers</h3>
<div id="outline-container-orgd9d3690" class="outline-3">
<h3 id="orgd9d3690"><span class="section-number-3">2.9</span> Headers</h3>
<div class="outline-text-3" id="text-2-9">
<p>
A single <code>qmckl.h</code> header to be distributed by the library
@ -717,8 +717,8 @@ and the types definitions should be written in the <code>*_f_type.f90</code> fil
</div>
</div>
<div id="outline-container-org6a0c67f" class="outline-3">
<h3 id="org6a0c67f"><span class="section-number-3">2.10</span> Low-level functions</h3>
<div id="outline-container-org19e4e9e" class="outline-3">
<h3 id="org19e4e9e"><span class="section-number-3">2.10</span> Low-level functions</h3>
<div class="outline-text-3" id="text-2-10">
<p>
Low-level functions are very simple functions which are leaves of
@ -727,14 +727,14 @@ the function call tree (they don't call any other QMCkl function).
<p>
These functions are <i>pure</i>, and unaware of the QMCkl
<a href="#orge351a7b"><code>context</code></a>. They are not allowed to allocate/deallocate memory, and
<a href="#org6c95d82"><code>context</code></a>. They are not allowed to allocate/deallocate memory, and
if they need temporary memory it should be provided in input.
</p>
</div>
</div>
<div id="outline-container-org5ef4513" class="outline-3">
<h3 id="org5ef4513"><span class="section-number-3">2.11</span> High-level functions</h3>
<div id="outline-container-org64e0a70" class="outline-3">
<h3 id="org64e0a70"><span class="section-number-3">2.11</span> High-level functions</h3>
<div class="outline-text-3" id="text-2-11">
<p>
High-level functions are at the top of the function call tree.
@ -747,27 +747,27 @@ temporary storage, to simplify the use of accelerators.
<p>
The high-level functions should be pure, unless the introduction
of non-purity is justified. All the side effects should be made in
the <a href="#orge351a7b"><code>context</code></a> variable.
the <a href="#org6c95d82"><code>context</code></a> variable.
</p>
</div>
</div>
<div id="outline-container-orgaca373f" class="outline-3">
<h3 id="orgaca373f"><span class="section-number-3">2.12</span> Numerical precision</h3>
<div id="outline-container-org96f36d7" class="outline-3">
<h3 id="org96f36d7"><span class="section-number-3">2.12</span> Numerical precision</h3>
<div class="outline-text-3" id="text-2-12">
<p>
The number of bits of precision required for a function should be
given as an input of low-level computational functions. This input
will be used to define the values of the different thresholds that
might be used to avoid computing unnecessary noise. High-level
functions will use the precision specified in the <a href="#orge351a7b"><code>context</code></a>
functions will use the precision specified in the <a href="#org6c95d82"><code>context</code></a>
variable.
</p>
</div>
</div>
<div id="outline-container-orgd9442d3" class="outline-3">
<h3 id="orgd9442d3"><span class="section-number-3">2.13</span> Algorithms</h3>
<div id="outline-container-org9785916" class="outline-3">
<h3 id="org9785916"><span class="section-number-3">2.13</span> Algorithms</h3>
<div class="outline-text-3" id="text-2-13">
<p>
Reducing the scaling of an algorithm usually implies also reducing
@ -783,7 +783,7 @@ implemented adapted to different problem sizes.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX CoE</p>
<p class="date">Created: 2021-05-18 Tue 10:33</p>
<p class="date">Created: 2021-05-18 Tue 23:32</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

158
qmckl_ao.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-05-18 Tue 10:33 -->
<!-- 2021-05-18 Tue 23:32 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Atomic Orbitals</title>
@ -333,52 +333,52 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org863b0d4">1. Context</a>
<li><a href="#orge566884">1. Context</a>
<ul>
<li><a href="#org3dd1c32">1.1. Data structure</a></li>
<li><a href="#org9d91b4a">1.2. Access functions</a></li>
<li><a href="#org4607a3d">1.3. Initialization functions</a></li>
<li><a href="#org70b0e20">1.4. <span class="todo TODO">TODO</span> Fortran interfaces</a></li>
<li><a href="#org2c49619">1.1. Data structure</a></li>
<li><a href="#org97c8b5c">1.2. Access functions</a></li>
<li><a href="#org28fd348">1.3. Initialization functions</a></li>
<li><a href="#orga0917a7">1.4. <span class="todo TODO">TODO</span> Fortran interfaces</a></li>
</ul>
</li>
<li><a href="#orgf5f4b46">2. Polynomial part</a>
<li><a href="#orga732f29">2. Polynomial part</a>
<ul>
<li><a href="#orge5c06eb">2.1. Powers of \(x-X_i\)</a>
<li><a href="#org0689079">2.1. Powers of \(x-X_i\)</a>
<ul>
<li><a href="#org9087143">2.1.1. Requirements</a></li>
<li><a href="#orge43dd13">2.1.2. C Header</a></li>
<li><a href="#orgf7c150c">2.1.3. Source</a></li>
<li><a href="#org69a0758">2.1.4. C interface</a></li>
<li><a href="#org7b89bd3">2.1.5. Fortran interface</a></li>
<li><a href="#org6bc139e">2.1.6. Test</a></li>
<li><a href="#org5f8e212">2.1.1. Requirements</a></li>
<li><a href="#orgdd6b0af">2.1.2. C Header</a></li>
<li><a href="#org3a10081">2.1.3. Source</a></li>
<li><a href="#orgf57b5e6">2.1.4. C interface</a></li>
<li><a href="#org898f254">2.1.5. Fortran interface</a></li>
<li><a href="#orgb4ff218">2.1.6. Test</a></li>
</ul>
</li>
<li><a href="#org0caea4a">2.2. Value, Gradient and Laplacian of a polynomial</a>
<li><a href="#org9aa3e7c">2.2. Value, Gradient and Laplacian of a polynomial</a>
<ul>
<li><a href="#org73fe6fb">2.2.1. Requirements</a></li>
<li><a href="#org4ec074f">2.2.2. C Header</a></li>
<li><a href="#orgd7ade7f">2.2.3. Source</a></li>
<li><a href="#org3a56acc">2.2.4. C interface</a></li>
<li><a href="#org6227e9d">2.2.5. Fortran interface</a></li>
<li><a href="#org8c26478">2.2.6. Test</a></li>
<li><a href="#org05f71d2">2.2.1. Requirements</a></li>
<li><a href="#org1527e1b">2.2.2. C Header</a></li>
<li><a href="#orgc927910">2.2.3. Source</a></li>
<li><a href="#org172b6f2">2.2.4. C interface</a></li>
<li><a href="#org2d4b852">2.2.5. Fortran interface</a></li>
<li><a href="#org6fd7e9b">2.2.6. Test</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgc8ad16a">3. Radial part</a>
<li><a href="#org42e061e">3. Radial part</a>
<ul>
<li><a href="#org8a338ee">3.1. Gaussian basis functions</a></li>
<li><a href="#org320ff80">3.2. <span class="todo TODO">TODO</span> Slater basis functions</a></li>
<li><a href="#org2309ef2">3.3. <span class="todo TODO">TODO</span> Radial functions on a grid</a></li>
<li><a href="#org9c9f595">3.1. Gaussian basis functions</a></li>
<li><a href="#org1a9549b">3.2. <span class="todo TODO">TODO</span> Slater basis functions</a></li>
<li><a href="#org70b226c">3.3. <span class="todo TODO">TODO</span> Radial functions on a grid</a></li>
</ul>
</li>
<li><a href="#orgdbf8f98">4. Combining radial and polynomial parts</a></li>
<li><a href="#orgaca3955">4. Combining radial and polynomial parts</a></li>
</ul>
</div>
</div>
<div id="outline-container-org863b0d4" class="outline-2">
<h2 id="org863b0d4"><span class="section-number-2">1</span> Context</h2>
<div id="outline-container-orge566884" class="outline-2">
<h2 id="orge566884"><span class="section-number-2">1</span> Context</h2>
<div class="outline-text-2" id="text-1">
<p>
The following arrays are stored in the context:
@ -503,8 +503,8 @@ coefficient = [ 0.006068, 0.045308, 0.202822, 0.503903, 0.383421,
</pre>
</div>
<div id="outline-container-org3dd1c32" class="outline-3">
<h3 id="org3dd1c32"><span class="section-number-3">1.1</span> Data structure</h3>
<div id="outline-container-org2c49619" class="outline-3">
<h3 id="org2c49619"><span class="section-number-3">1.1</span> Data structure</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> <span style="color: #228b22;">qmckl_ao_basis_struct</span> {
@ -533,8 +533,8 @@ struct is then initialized and <code>provided == true</code>.
</div>
</div>
<div id="outline-container-org9d91b4a" class="outline-3">
<h3 id="org9d91b4a"><span class="section-number-3">1.2</span> Access functions</h3>
<div id="outline-container-org97c8b5c" class="outline-3">
<h3 id="org97c8b5c"><span class="section-number-3">1.2</span> Access functions</h3>
<div class="outline-text-3" id="text-1-2">
<p>
When all the data for the AOs have been provided, the following
@ -548,8 +548,8 @@ function returns <code>true</code>.
</div>
</div>
<div id="outline-container-org4607a3d" class="outline-3">
<h3 id="org4607a3d"><span class="section-number-3">1.3</span> Initialization functions</h3>
<div id="outline-container-org28fd348" class="outline-3">
<h3 id="org28fd348"><span class="section-number-3">1.3</span> Initialization functions</h3>
<div class="outline-text-3" id="text-1-3">
<p>
To set the basis set, all the following functions need to be
@ -572,17 +572,17 @@ called. When
</div>
</div>
<div id="outline-container-org70b0e20" class="outline-3">
<h3 id="org70b0e20"><span class="section-number-3">1.4</span> <span class="todo TODO">TODO</span> Fortran interfaces</h3>
<div id="outline-container-orga0917a7" class="outline-3">
<h3 id="orga0917a7"><span class="section-number-3">1.4</span> <span class="todo TODO">TODO</span> Fortran interfaces</h3>
</div>
</div>
<div id="outline-container-orgf5f4b46" class="outline-2">
<h2 id="orgf5f4b46"><span class="section-number-2">2</span> Polynomial part</h2>
<div id="outline-container-orga732f29" class="outline-2">
<h2 id="orga732f29"><span class="section-number-2">2</span> Polynomial part</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orge5c06eb" class="outline-3">
<h3 id="orge5c06eb"><span class="section-number-3">2.1</span> Powers of \(x-X_i\)</h3>
<div id="outline-container-org0689079" class="outline-3">
<h3 id="org0689079"><span class="section-number-3">2.1</span> Powers of \(x-X_i\)</h3>
<div class="outline-text-3" id="text-2-1">
<p>
The <code>qmckl_ao_power</code> function computes all the powers of the <code>n</code>
@ -594,7 +594,7 @@ the \(n\) points:
\[ P_{ik} = X_i^k \]
</p>
<table id="orga189a72" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6373930" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -652,8 +652,8 @@ the \(n\) points:
</table>
</div>
<div id="outline-container-org9087143" class="outline-4">
<h4 id="org9087143"><span class="section-number-4">2.1.1</span> Requirements</h4>
<div id="outline-container-org5f8e212" class="outline-4">
<h4 id="org5f8e212"><span class="section-number-4">2.1.1</span> Requirements</h4>
<div class="outline-text-4" id="text-2-1-1">
<ul class="org-ul">
<li><code>context</code> is not <code>QMCKL_NULL_CONTEXT</code></li>
@ -666,8 +666,8 @@ the \(n\) points:
</div>
</div>
<div id="outline-container-orge43dd13" class="outline-4">
<h4 id="orge43dd13"><span class="section-number-4">2.1.2</span> C Header</h4>
<div id="outline-container-orgdd6b0af" class="outline-4">
<h4 id="orgdd6b0af"><span class="section-number-4">2.1.2</span> C Header</h4>
<div class="outline-text-4" id="text-2-1-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_ao_power</span> (
@ -682,8 +682,8 @@ the \(n\) points:
</div>
</div>
<div id="outline-container-orgf7c150c" class="outline-4">
<h4 id="orgf7c150c"><span class="section-number-4">2.1.3</span> Source</h4>
<div id="outline-container-org3a10081" class="outline-4">
<h4 id="org3a10081"><span class="section-number-4">2.1.3</span> Source</h4>
<div class="outline-text-4" id="text-2-1-3">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer </span><span style="color: #a020f0;">function</span><span style="color: #a0522d;"> </span><span style="color: #0000ff;">qmckl_ao_power_f</span><span style="color: #000000; background-color: #ffffff;">(context, n, X, LMAX, P, ldp) result(info)</span>
@ -734,15 +734,15 @@ the \(n\) points:
</div>
</div>
<div id="outline-container-org69a0758" class="outline-4">
<h4 id="org69a0758"><span class="section-number-4">2.1.4</span> C interface</h4>
<div id="outline-container-orgf57b5e6" class="outline-4">
<h4 id="orgf57b5e6"><span class="section-number-4">2.1.4</span> C interface</h4>
</div>
<div id="outline-container-org7b89bd3" class="outline-4">
<h4 id="org7b89bd3"><span class="section-number-4">2.1.5</span> Fortran interface</h4>
<div id="outline-container-org898f254" class="outline-4">
<h4 id="org898f254"><span class="section-number-4">2.1.5</span> Fortran interface</h4>
</div>
<div id="outline-container-org6bc139e" class="outline-4">
<h4 id="org6bc139e"><span class="section-number-4">2.1.6</span> Test</h4>
<div id="outline-container-orgb4ff218" class="outline-4">
<h4 id="orgb4ff218"><span class="section-number-4">2.1.6</span> Test</h4>
<div class="outline-text-4" id="text-2-1-6">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer</span>(<span style="color: #008b8b;">c_int32_t</span>) <span style="color: #a020f0;">function</span> <span style="color: #0000ff;">test_qmckl_ao_power</span>(context) <span style="color: #a020f0;">bind</span>(C)
@ -793,8 +793,8 @@ the \(n\) points:
</div>
</div>
<div id="outline-container-org0caea4a" class="outline-3">
<h3 id="org0caea4a"><span class="section-number-3">2.2</span> Value, Gradient and Laplacian of a polynomial</h3>
<div id="outline-container-org9aa3e7c" class="outline-3">
<h3 id="org9aa3e7c"><span class="section-number-3">2.2</span> Value, Gradient and Laplacian of a polynomial</h3>
<div class="outline-text-3" id="text-2-2">
<p>
A polynomial is centered on a nucleus \(\mathbf{R}_i\)
@ -839,7 +839,7 @@ Laplacians at a given point in space, of all polynomials with an
angular momentum up to <code>lmax</code>.
</p>
<table id="org79789d9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge94f30d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -918,8 +918,8 @@ angular momentum up to <code>lmax</code>.
</table>
</div>
<div id="outline-container-org73fe6fb" class="outline-4">
<h4 id="org73fe6fb"><span class="section-number-4">2.2.1</span> Requirements</h4>
<div id="outline-container-org05f71d2" class="outline-4">
<h4 id="org05f71d2"><span class="section-number-4">2.2.1</span> Requirements</h4>
<div class="outline-text-4" id="text-2-2-1">
<ul class="org-ul">
<li><code>context</code> is not <code>QMCKL_NULL_CONTEXT</code></li>
@ -944,8 +944,8 @@ For example, with a=0, b=2 and c=1 the string is "yyz"</li>
</div>
</div>
<div id="outline-container-org4ec074f" class="outline-4">
<h4 id="org4ec074f"><span class="section-number-4">2.2.2</span> C Header</h4>
<div id="outline-container-org1527e1b" class="outline-4">
<h4 id="org1527e1b"><span class="section-number-4">2.2.2</span> C Header</h4>
<div class="outline-text-4" id="text-2-2-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_ao_polynomial_vgl</span> (
@ -963,8 +963,8 @@ For example, with a=0, b=2 and c=1 the string is "yyz"</li>
</div>
</div>
<div id="outline-container-orgd7ade7f" class="outline-4">
<h4 id="orgd7ade7f"><span class="section-number-4">2.2.3</span> Source</h4>
<div id="outline-container-orgc927910" class="outline-4">
<h4 id="orgc927910"><span class="section-number-4">2.2.3</span> Source</h4>
<div class="outline-text-4" id="text-2-2-3">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer </span><span style="color: #a020f0;">function</span><span style="color: #a0522d;"> </span><span style="color: #0000ff;">qmckl_ao_polynomial_vgl_f</span><span style="color: #000000; background-color: #ffffff;">(context, X, R, lmax, n, L, ldl, VGL, ldv) result(info)</span>
@ -1099,16 +1099,16 @@ For example, with a=0, b=2 and c=1 the string is "yyz"</li>
</div>
</div>
<div id="outline-container-org3a56acc" class="outline-4">
<h4 id="org3a56acc"><span class="section-number-4">2.2.4</span> C interface</h4>
<div id="outline-container-org172b6f2" class="outline-4">
<h4 id="org172b6f2"><span class="section-number-4">2.2.4</span> C interface</h4>
</div>
<div id="outline-container-org6227e9d" class="outline-4">
<h4 id="org6227e9d"><span class="section-number-4">2.2.5</span> Fortran interface</h4>
<div id="outline-container-org2d4b852" class="outline-4">
<h4 id="org2d4b852"><span class="section-number-4">2.2.5</span> Fortran interface</h4>
</div>
<div id="outline-container-org8c26478" class="outline-4">
<h4 id="org8c26478"><span class="section-number-4">2.2.6</span> Test</h4>
<div id="outline-container-org6fd7e9b" class="outline-4">
<h4 id="org6fd7e9b"><span class="section-number-4">2.2.6</span> Test</h4>
<div class="outline-text-4" id="text-2-2-6">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer</span>(<span style="color: #008b8b;">c_int32_t</span>) <span style="color: #a020f0;">function</span> <span style="color: #0000ff;">test_qmckl_ao_polynomial_vgl</span>(context) <span style="color: #a020f0;">bind</span>(C)
@ -1213,12 +1213,12 @@ assert(0 == test_qmckl_ao_polynomial_vgl(context));
</div>
</div>
<div id="outline-container-orgc8ad16a" class="outline-2">
<h2 id="orgc8ad16a"><span class="section-number-2">3</span> Radial part</h2>
<div id="outline-container-org42e061e" class="outline-2">
<h2 id="org42e061e"><span class="section-number-2">3</span> Radial part</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org8a338ee" class="outline-3">
<h3 id="org8a338ee"><span class="section-number-3">3.1</span> Gaussian basis functions</h3>
<div id="outline-container-org9c9f595" class="outline-3">
<h3 id="org9c9f595"><span class="section-number-3">3.1</span> Gaussian basis functions</h3>
<div class="outline-text-3" id="text-3-1">
<p>
<code>qmckl_ao_gaussian_vgl</code> computes the values, gradients and
@ -1450,21 +1450,21 @@ Requirements
</div>
</div>
<div id="outline-container-org320ff80" class="outline-3">
<h3 id="org320ff80"><span class="section-number-3">3.2</span> <span class="todo TODO">TODO</span> Slater basis functions</h3>
<div id="outline-container-org1a9549b" class="outline-3">
<h3 id="org1a9549b"><span class="section-number-3">3.2</span> <span class="todo TODO">TODO</span> Slater basis functions</h3>
</div>
<div id="outline-container-org2309ef2" class="outline-3">
<h3 id="org2309ef2"><span class="section-number-3">3.3</span> <span class="todo TODO">TODO</span> Radial functions on a grid</h3>
<div id="outline-container-org70b226c" class="outline-3">
<h3 id="org70b226c"><span class="section-number-3">3.3</span> <span class="todo TODO">TODO</span> Radial functions on a grid</h3>
</div>
</div>
<div id="outline-container-orgdbf8f98" class="outline-2">
<h2 id="orgdbf8f98"><span class="section-number-2">4</span> Combining radial and polynomial parts</h2>
<div id="outline-container-orgaca3955" class="outline-2">
<h2 id="orgaca3955"><span class="section-number-2">4</span> Combining radial and polynomial parts</h2>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX CoE</p>
<p class="date">Created: 2021-05-18 Tue 10:33</p>
<p class="date">Created: 2021-05-18 Tue 23:32</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

44
qmckl_context.html
View File

@ -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>
<!-- 2021-05-18 Tue 10:33 -->
<!-- 2021-05-18 Tue 23:32 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Context</title>
@ -311,21 +311,21 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orge0b125a">1. Context handling</a>
<li><a href="#org6298d6e">1. Context handling</a>
<ul>
<li><a href="#orgb7b6401">1.1. Data structure</a></li>
<li><a href="#orgb3f6bbf">1.2. Creation</a></li>
<li><a href="#orgd4a2ce0">1.3. Locking</a></li>
<li><a href="#orgae5a1bf">1.4. <span class="todo TODO">TODO</span> Copy</a></li>
<li><a href="#orgce1aa9b">1.5. Destroy</a></li>
<li><a href="#org5b6c069">1.1. Data structure</a></li>
<li><a href="#orgcd54caa">1.2. Creation</a></li>
<li><a href="#org68f7f9f">1.3. Locking</a></li>
<li><a href="#orgb6b1ac9">1.4. <span class="todo TODO">TODO</span> Copy</a></li>
<li><a href="#orge80cdd5">1.5. Destroy</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orge0b125a" class="outline-2">
<h2 id="orge0b125a"><span class="section-number-2">1</span> Context handling</h2>
<div id="outline-container-org6298d6e" class="outline-2">
<h2 id="org6298d6e"><span class="section-number-2">1</span> Context handling</h2>
<div class="outline-text-2" id="text-1">
<p>
The context variable is a handle for the state of the library,
@ -338,7 +338,7 @@ A value of <code>QMCKL_NULL_CONTEXT</code> for the context is equivalent to a
</p>
<div class="org-src-container">
<pre class="src src-c" id="orgb60c4d2"><span style="color: #a020f0;">typedef</span> <span style="color: #228b22;">int64_t</span> <span style="color: #228b22;">qmckl_context</span> ;
<pre class="src src-c" id="org51ef2cd"><span style="color: #a020f0;">typedef</span> <span style="color: #228b22;">int64_t</span> <span style="color: #228b22;">qmckl_context</span> ;
<span style="color: #483d8b;">#define</span> <span style="color: #a0522d;">QMCKL_NULL_CONTEXT</span> (qmckl_context) 0
</pre>
</div>
@ -356,8 +356,8 @@ and <code>ctx</code> is a <code>qmckl_context_struct*</code> pointer.
</p>
</div>
<div id="outline-container-orgb7b6401" class="outline-3">
<h3 id="orgb7b6401"><span class="section-number-3">1.1</span> Data structure</h3>
<div id="outline-container-org5b6c069" class="outline-3">
<h3 id="org5b6c069"><span class="section-number-3">1.1</span> Data structure</h3>
<div class="outline-text-3" id="text-1-1">
<p>
The context keeps a ``date'' that allows to check which data needs
@ -367,7 +367,7 @@ coordinates are updated.
<p>
When a new element is added to the context, the functions
<a href="#orgb3f6bbf">qmckl<sub>context</sub><sub>create</sub></a>, <a href="#orgce1aa9b">qmckl<sub>context</sub><sub>destroy</sub></a> and <a href="#orgae5a1bf">qmckl<sub>context</sub><sub>copy</sub></a>
<a href="#orgcd54caa">qmckl<sub>context</sub><sub>create</sub></a>, <a href="#orge80cdd5">qmckl<sub>context</sub><sub>destroy</sub></a> and <a href="#orgb6b1ac9">qmckl<sub>context</sub><sub>copy</sub></a>
should be updated inorder to make deep copies.
</p>
@ -416,8 +416,8 @@ if the context is valid, <code>QMCKL_NULL_CONTEXT</code> otherwise.
</div>
</div>
<div id="outline-container-orgb3f6bbf" class="outline-3">
<h3 id="orgb3f6bbf"><span class="section-number-3">1.2</span> Creation</h3>
<div id="outline-container-orgcd54caa" class="outline-3">
<h3 id="orgcd54caa"><span class="section-number-3">1.2</span> Creation</h3>
<div class="outline-text-3" id="text-1-2">
<p>
To create a new context, <code>qmckl_context_create()</code> should be used.
@ -492,8 +492,8 @@ To create a new context, <code>qmckl_context_create()</code> should be used.
</div>
</div>
</div>
<div id="outline-container-orgd4a2ce0" class="outline-3">
<h3 id="orgd4a2ce0"><span class="section-number-3">1.3</span> Locking</h3>
<div id="outline-container-org68f7f9f" class="outline-3">
<h3 id="org68f7f9f"><span class="section-number-3">1.3</span> Locking</h3>
<div class="outline-text-3" id="text-1-3">
<p>
For thread safety, the context may be locked/unlocked. The lock is
@ -538,8 +538,8 @@ number of times the thread has locked it is saved in the
</div>
</div>
<div id="outline-container-orgae5a1bf" class="outline-3">
<h3 id="orgae5a1bf"><span class="section-number-3">1.4</span> <span class="todo TODO">TODO</span> Copy</h3>
<div id="outline-container-orgb6b1ac9" class="outline-3">
<h3 id="orgb6b1ac9"><span class="section-number-3">1.4</span> <span class="todo TODO">TODO</span> Copy</h3>
<div class="outline-text-3" id="text-1-4">
<p>
<code>qmckl_context_copy</code> makes a deep copy of a context. It returns
@ -587,8 +587,8 @@ number of times the thread has locked it is saved in the
</div>
</div>
</div>
<div id="outline-container-orgce1aa9b" class="outline-3">
<h3 id="orgce1aa9b"><span class="section-number-3">1.5</span> Destroy</h3>
<div id="outline-container-orge80cdd5" class="outline-3">
<h3 id="orge80cdd5"><span class="section-number-3">1.5</span> Destroy</h3>
<div class="outline-text-3" id="text-1-5">
<p>
The context is destroyed with <code>qmckl_context_destroy</code>, leaving the ancestors untouched.
@ -642,7 +642,7 @@ It frees the context, and returns the previous context.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX CoE</p>
<p class="date">Created: 2021-05-18 Tue 10:33</p>
<p class="date">Created: 2021-05-18 Tue 23:32</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

90
qmckl_distance.html
View File

@ -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>
<!-- 2021-05-18 Tue 10:33 -->
<!-- 2021-05-18 Tue 23:33 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Inter-particle distances</title>
@ -333,26 +333,26 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org86817a7">1. Squared distance</a>
<li><a href="#orgfd597cc">1. Squared distance</a>
<ul>
<li><a href="#org5e174ce">1.1. <code>qmckl_distance_sq</code></a>
<li><a href="#orgf842b40">1.1. <code>qmckl_distance_sq</code></a>
<ul>
<li><a href="#orga7edc85">1.1.1. Requirements</a></li>
<li><a href="#orgf21fa6c">1.1.2. C header</a></li>
<li><a href="#org73e82f5">1.1.3. Source</a></li>
<li><a href="#orgee238a2">1.1.4. Performance</a></li>
<li><a href="#orgca18732">1.1.1. Requirements</a></li>
<li><a href="#org6b79fc4">1.1.2. C header</a></li>
<li><a href="#orgd7230eb">1.1.3. Source</a></li>
<li><a href="#orgbe9540c">1.1.4. Performance</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgeffa0f3">2. Distance</a>
<li><a href="#org7b49a08">2. Distance</a>
<ul>
<li><a href="#org810dd4b">2.1. <code>qmckl_distance</code></a>
<li><a href="#orgc93a75f">2.1. <code>qmckl_distance</code></a>
<ul>
<li><a href="#orgd606c7b">2.1.1. Requirements</a></li>
<li><a href="#orgd0757bc">2.1.2. C header</a></li>
<li><a href="#org9a6fd22">2.1.3. Source</a></li>
<li><a href="#orgb5a07d0">2.1.4. Performance</a></li>
<li><a href="#org8a65fdd">2.1.1. Requirements</a></li>
<li><a href="#org3a6aa2c">2.1.2. C header</a></li>
<li><a href="#orgfc61a7b">2.1.3. Source</a></li>
<li><a href="#orgf5df4ab">2.1.4. Performance</a></li>
</ul>
</li>
</ul>
@ -361,12 +361,12 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org86817a7" class="outline-2">
<h2 id="org86817a7"><span class="section-number-2">1</span> Squared distance</h2>
<div id="outline-container-orgfd597cc" class="outline-2">
<h2 id="orgfd597cc"><span class="section-number-2">1</span> Squared distance</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org5e174ce" class="outline-3">
<h3 id="org5e174ce"><span class="section-number-3">1.1</span> <code>qmckl_distance_sq</code></h3>
<div id="outline-container-orgf842b40" class="outline-3">
<h3 id="orgf842b40"><span class="section-number-3">1.1</span> <code>qmckl_distance_sq</code></h3>
<div class="outline-text-3" id="text-1-1">
<p>
<code>qmckl_distance_sq</code> computes the matrix of the squared distances
@ -379,7 +379,7 @@ between all pairs of points in two sets, one point within each set:
\]
</p>
<table id="orgfc17b71" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdbc0c13" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -472,8 +472,8 @@ between all pairs of points in two sets, one point within each set:
</table>
</div>
<div id="outline-container-orga7edc85" class="outline-4">
<h4 id="orga7edc85"><span class="section-number-4">1.1.1</span> Requirements</h4>
<div id="outline-container-orgca18732" class="outline-4">
<h4 id="orgca18732"><span class="section-number-4">1.1.1</span> Requirements</h4>
<div class="outline-text-4" id="text-1-1-1">
<ul class="org-ul">
<li><code>context</code> is not <code>QMCKL_NULL_CONTEXT</code></li>
@ -491,8 +491,8 @@ between all pairs of points in two sets, one point within each set:
</div>
</div>
<div id="outline-container-orgf21fa6c" class="outline-4">
<h4 id="orgf21fa6c"><span class="section-number-4">1.1.2</span> C header</h4>
<div id="outline-container-org6b79fc4" class="outline-4">
<h4 id="org6b79fc4"><span class="section-number-4">1.1.2</span> C header</h4>
<div class="outline-text-4" id="text-1-1-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_distance</span> (
@ -512,8 +512,8 @@ between all pairs of points in two sets, one point within each set:
</div>
</div>
<div id="outline-container-org73e82f5" class="outline-4">
<h4 id="org73e82f5"><span class="section-number-4">1.1.3</span> Source</h4>
<div id="outline-container-orgd7230eb" class="outline-4">
<h4 id="orgd7230eb"><span class="section-number-4">1.1.3</span> Source</h4>
<div class="outline-text-4" id="text-1-1-3">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer</span><span style="color: #a0522d;"> function qmckl_distance_sq_f(context, transa, transb, m, n, </span><span style="color: #a020f0;">&amp;</span>
@ -648,23 +648,23 @@ between all pairs of points in two sets, one point within each set:
</div>
</div>
<div id="outline-container-orgee238a2" class="outline-4">
<h4 id="orgee238a2"><span class="section-number-4">1.1.4</span> Performance</h4>
<div id="outline-container-orgbe9540c" class="outline-4">
<h4 id="orgbe9540c"><span class="section-number-4">1.1.4</span> Performance</h4>
<div class="outline-text-4" id="text-1-1-4">
<p>
This function might be more efficient when <code>A</code> and <code>B</code> are
This function is more efficient when <code>A</code> and <code>B</code> are
transposed.
</p>
</div>
</div>
</div>
</div>
<div id="outline-container-orgeffa0f3" class="outline-2">
<h2 id="orgeffa0f3"><span class="section-number-2">2</span> Distance</h2>
<div id="outline-container-org7b49a08" class="outline-2">
<h2 id="org7b49a08"><span class="section-number-2">2</span> Distance</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org810dd4b" class="outline-3">
<h3 id="org810dd4b"><span class="section-number-3">2.1</span> <code>qmckl_distance</code></h3>
<div id="outline-container-orgc93a75f" class="outline-3">
<h3 id="orgc93a75f"><span class="section-number-3">2.1</span> <code>qmckl_distance</code></h3>
<div class="outline-text-3" id="text-2-1">
<p>
<code>qmckl_distance</code> computes the matrix of the distances between all
@ -677,7 +677,12 @@ pairs of points in two sets, one point within each set:
\]
</p>
<table id="orgbd71683" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<p>
If the input array is normal (<code>'N'</code>), the xyz coordinates are in
the leading dimension: <code>[n][3]</code> in C and <code>(3,n)</code> in Fortran.
</p>
<table id="orge4c6738" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -770,8 +775,8 @@ pairs of points in two sets, one point within each set:
</table>
</div>
<div id="outline-container-orgd606c7b" class="outline-4">
<h4 id="orgd606c7b"><span class="section-number-4">2.1.1</span> Requirements</h4>
<div id="outline-container-org8a65fdd" class="outline-4">
<h4 id="org8a65fdd"><span class="section-number-4">2.1.1</span> Requirements</h4>
<div class="outline-text-4" id="text-2-1-1">
<ul class="org-ul">
<li><code>context</code> is not <code>QMCKL_NULL_CONTEXT</code></li>
@ -789,8 +794,8 @@ pairs of points in two sets, one point within each set:
</div>
</div>
<div id="outline-container-orgd0757bc" class="outline-4">
<h4 id="orgd0757bc"><span class="section-number-4">2.1.2</span> C header</h4>
<div id="outline-container-org3a6aa2c" class="outline-4">
<h4 id="org3a6aa2c"><span class="section-number-4">2.1.2</span> C header</h4>
<div class="outline-text-4" id="text-2-1-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_distance</span> (
@ -810,8 +815,8 @@ pairs of points in two sets, one point within each set:
</div>
</div>
<div id="outline-container-org9a6fd22" class="outline-4">
<h4 id="org9a6fd22"><span class="section-number-4">2.1.3</span> Source</h4>
<div id="outline-container-orgfc61a7b" class="outline-4">
<h4 id="orgfc61a7b"><span class="section-number-4">2.1.3</span> Source</h4>
<div class="outline-text-4" id="text-2-1-3">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer</span><span style="color: #a0522d;"> function qmckl_distance_f(context, transa, transb, m, n, </span><span style="color: #a020f0;">&amp;</span>
@ -950,12 +955,11 @@ pairs of points in two sets, one point within each set:
</div>
</div>
<div id="outline-container-orgb5a07d0" class="outline-4">
<h4 id="orgb5a07d0"><span class="section-number-4">2.1.4</span> Performance</h4>
<div id="outline-container-orgf5df4ab" class="outline-4">
<h4 id="orgf5df4ab"><span class="section-number-4">2.1.4</span> Performance</h4>
<div class="outline-text-4" id="text-2-1-4">
<p>
This function might be more efficient when <code>A</code> and <code>B</code> are
transposed.
This function is more efficient when <code>A</code> and <code>B</code> are transposed.
</p>
</div>
</div>
@ -964,7 +968,7 @@ transposed.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX CoE</p>
<p class="date">Created: 2021-05-18 Tue 10:33</p>
<p class="date">Created: 2021-05-18 Tue 23:33</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

221
qmckl_electron.html
View File

@ -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>
<!-- 2021-05-18 Tue 10:33 -->
<!-- 2021-05-18 Tue 23:32 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Electrons</title>
@ -311,34 +311,34 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org4ae82b8">1. Context</a>
<li><a href="#orgc550db7">1. Context</a>
<ul>
<li><a href="#org44d0cf1">1.1. Data structure</a></li>
<li><a href="#org32db4b3">1.2. Access functions</a>
<li><a href="#org21908af">1.1. Data structure</a></li>
<li><a href="#orgc205ade">1.2. Access functions</a>
<ul>
<li><a href="#orgb0e5c5d">1.2.1. Number of electrons</a></li>
<li><a href="#org802b79e">1.2.2. Number of walkers</a></li>
<li><a href="#orgce8cd5d">1.2.3. Electron coordinates</a></li>
<li><a href="#orgc4b796a">1.2.1. Number of electrons</a></li>
<li><a href="#org09c0ebc">1.2.2. Number of walkers</a></li>
<li><a href="#org926985c">1.2.3. Electron coordinates</a></li>
</ul>
</li>
<li><a href="#orgb9b087f">1.3. Initialization functions</a></li>
<li><a href="#org1642b98">1.4. Test</a></li>
<li><a href="#org0af01cc">1.3. Initialization functions</a></li>
<li><a href="#orge550a96">1.4. Test</a></li>
</ul>
</li>
<li><a href="#org3ed5156">2. Computation</a>
<li><a href="#orgd481931">2. Computation</a>
<ul>
<li><a href="#org538bfe6">2.1. Electron-electron distances</a>
<li><a href="#org3b53198">2.1. Electron-electron distances</a>
<ul>
<li><a href="#orge753cbc">2.1.1. Get</a></li>
<li><a href="#org89cae6c">2.1.2. Compute</a></li>
<li><a href="#orga2b618b">2.1.3. Test</a></li>
<li><a href="#org59b0f4a">2.1.1. Get</a></li>
<li><a href="#org0352ed3">2.1.2. Compute</a></li>
<li><a href="#org9ec7f5a">2.1.3. Test</a></li>
</ul>
</li>
<li><a href="#org9d0036f">2.2. Electron-nucleus distances</a>
<li><a href="#org15a922e">2.2. Electron-nucleus distances</a>
<ul>
<li><a href="#org5e73d24">2.2.1. Get</a></li>
<li><a href="#org8bd0535">2.2.2. Compute</a></li>
<li><a href="#org95d9b34">2.2.3. Test</a></li>
<li><a href="#org6d804db">2.2.1. Get</a></li>
<li><a href="#org7e27cb4">2.2.2. Compute</a></li>
<li><a href="#orgd04408e">2.2.3. Test</a></li>
</ul>
</li>
</ul>
@ -347,8 +347,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org4ae82b8" class="outline-2">
<h2 id="org4ae82b8"><span class="section-number-2">1</span> Context</h2>
<div id="outline-container-orgc550db7" class="outline-2">
<h2 id="orgc550db7"><span class="section-number-2">1</span> Context</h2>
<div class="outline-text-2" id="text-1">
<p>
The following data stored in the context:
@ -446,8 +446,8 @@ The following data stored in the context:
</table>
</div>
<div id="outline-container-org44d0cf1" class="outline-3">
<h3 id="org44d0cf1"><span class="section-number-3">1.1</span> Data structure</h3>
<div id="outline-container-org21908af" class="outline-3">
<h3 id="org21908af"><span class="section-number-3">1.1</span> Data structure</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> <span style="color: #228b22;">qmckl_electron_struct</span> {
@ -487,8 +487,8 @@ following function returns <code>true</code>.
</div>
</div>
<div id="outline-container-org32db4b3" class="outline-3">
<h3 id="org32db4b3"><span class="section-number-3">1.2</span> Access functions</h3>
<div id="outline-container-orgc205ade" class="outline-3">
<h3 id="orgc205ade"><span class="section-number-3">1.2</span> Access functions</h3>
<div class="outline-text-3" id="text-1-2">
<p>
Access functions return <code>QMCKL_SUCCESS</code> when the data has been
@ -500,12 +500,12 @@ contains the requested data. Otherwise, this variable is untouched.
</p>
</div>
<div id="outline-container-orgb0e5c5d" class="outline-4">
<h4 id="orgb0e5c5d"><span class="section-number-4">1.2.1</span> Number of electrons</h4>
<div id="outline-container-orgc4b796a" class="outline-4">
<h4 id="orgc4b796a"><span class="section-number-4">1.2.1</span> Number of electrons</h4>
</div>
<div id="outline-container-org802b79e" class="outline-4">
<h4 id="org802b79e"><span class="section-number-4">1.2.2</span> Number of walkers</h4>
<div id="outline-container-org09c0ebc" class="outline-4">
<h4 id="org09c0ebc"><span class="section-number-4">1.2.2</span> Number of walkers</h4>
<div class="outline-text-4" id="text-1-2-2">
<p>
A walker is a set of electron coordinates that are arguments of
@ -514,8 +514,8 @@ the wave function. <code>walk_num</code> is the number of walkers.
</div>
</div>
<div id="outline-container-orgce8cd5d" class="outline-4">
<h4 id="orgce8cd5d"><span class="section-number-4">1.2.3</span> Electron coordinates</h4>
<div id="outline-container-org926985c" class="outline-4">
<h4 id="org926985c"><span class="section-number-4">1.2.3</span> Electron coordinates</h4>
<div class="outline-text-4" id="text-1-2-3">
<p>
Returns the current electron coordinates. The pointer is assumed
@ -527,8 +527,8 @@ Fortran it is <code>(elec_num,3,walk_num)</code>.
</div>
</div>
<div id="outline-container-orgb9b087f" class="outline-3">
<h3 id="orgb9b087f"><span class="section-number-3">1.3</span> Initialization functions</h3>
<div id="outline-container-org0af01cc" class="outline-3">
<h3 id="org0af01cc"><span class="section-number-3">1.3</span> Initialization functions</h3>
<div class="outline-text-3" id="text-1-3">
<p>
To set the data relative to the electrons in the context, the
@ -559,28 +559,32 @@ electrons have been set.
</div>
</div>
<div id="outline-container-org1642b98" class="outline-3">
<h3 id="org1642b98"><span class="section-number-3">1.4</span> Test</h3>
<div id="outline-container-orge550a96" class="outline-3">
<h3 id="orge550a96"><span class="section-number-3">1.4</span> Test</h3>
<div class="outline-text-3" id="text-1-4">
<div class="org-src-container">
<pre class="src src-c">/* <span style="color: #b22222;">Reference input data </span>*/
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">walk_num</span> = chbrclf_walk_num;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">elec_num</span> = chbrclf_elec_num;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">elec_up_num</span> = chbrclf_elec_up_num;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">elec_dn_num</span> = chbrclf_elec_dn_num;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>*** <span style="color: #a0522d;">elec_coord</span> = chbrclf_elec_coord;
<span style="color: #483d8b;">#define</span> <span style="color: #a0522d;">up_num</span> ((<span style="color: #228b22;">int64_t</span>) 3)
<span style="color: #483d8b;">#define</span> <span style="color: #a0522d;">down_num</span> ((<span style="color: #228b22;">int64_t</span>) 2)
<span style="color: #483d8b;">#define</span> <span style="color: #a0522d;">walk_num</span> ((<span style="color: #228b22;">int64_t</span>) 2)
<span style="color: #483d8b;">#define</span> <span style="color: #a0522d;">num</span> (up_num+down_num)
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">nucl_num</span> = chbrclf_nucl_num;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">charge</span> = chbrclf_charge;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>** <span style="color: #a0522d;">nucl_coord</span> = chbrclf_nucl_coord;
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">coord</span>[walk_num*3*num] =
{ 7.303633091022677881e+00, 1.375868694453235719e+01, 1.167371490471771217e-01,
4.547755371567960836e+00, 3.245907105524011182e+00, 2.410764357550297110e-01,
5.932816068137344523e+00, 1.491671465549257469e+01, 3.825374039119375236e-01,
7.347336142660052083e+00, 1.341946976062362129e+00, 1.648917914228352322e+00,
5.735221530102248444e+00, 1.064667491680036271e+01, 4.227201772236627297e-01,
8.099550978782254163e+00, 6.861498941099086757e+00, 4.015884841159429036e-02,
1.014757367558326173e+01, 5.219335322173662917e+00, 5.037004126899931322e-02,
1.484094322159507051e+01, 9.777903829455864226e+00, 5.243007994024882767e-02,
9.081723054990456845e+00, 5.499568496038920173e+00, 2.910446438899221347e-02,
2.583154239492383653e+00, 1.442282811294904432e+00, 6.387191629878670451e-02 };
<span style="color: #228b22;">double</span>* <span style="color: #a0522d;">coord</span> = (<span style="color: #228b22;">double</span>*) <span style="color: #0000ff;">malloc</span>(<span style="color: #228b22;">walk_num</span>*<span style="color: #0000ff;">num</span>*3*<span style="color: #a020f0;">sizeof</span>(<span style="color: #228b22;">double</span>));
<span style="color: #228b22;">double</span>* <span style="color: #a0522d;">x</span> = coord;
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">int</span> <span style="color: #a0522d;">i</span>=0 ; i&lt;walk_num ; ++i) {
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">int</span> <span style="color: #a0522d;">k</span>=0 ; k&lt;3 ; ++k) {
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">int</span> <span style="color: #a0522d;">j</span>=0 ; j&lt;num ; ++j) {
*x = coord_in[i][j][k];
x += 1;
}
}
}
/* <span style="color: #b22222;">--- </span>*/
@ -647,8 +651,8 @@ rc = qmckl_get_electron_coord (context, coord2);
</div>
</div>
<div id="outline-container-org3ed5156" class="outline-2">
<h2 id="org3ed5156"><span class="section-number-2">2</span> Computation</h2>
<div id="outline-container-orgd481931" class="outline-2">
<h2 id="orgd481931"><span class="section-number-2">2</span> Computation</h2>
<div class="outline-text-2" id="text-2">
<p>
The computed data is stored in the context so that it can be reused
@ -661,12 +665,12 @@ current date is stored.
</p>
</div>
<div id="outline-container-org538bfe6" class="outline-3">
<h3 id="org538bfe6"><span class="section-number-3">2.1</span> Electron-electron distances</h3>
<div id="outline-container-org3b53198" class="outline-3">
<h3 id="org3b53198"><span class="section-number-3">2.1</span> Electron-electron distances</h3>
<div class="outline-text-3" id="text-2-1">
</div>
<div id="outline-container-orge753cbc" class="outline-4">
<h4 id="orge753cbc"><span class="section-number-4">2.1.1</span> Get</h4>
<div id="outline-container-org59b0f4a" class="outline-4">
<h4 id="org59b0f4a"><span class="section-number-4">2.1.1</span> Get</h4>
<div class="outline-text-4" id="text-2-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_get_electron_ee_distance</span>(<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">distance</span>);
@ -675,10 +679,10 @@ current date is stored.
</div>
</div>
<div id="outline-container-org89cae6c" class="outline-4">
<h4 id="org89cae6c"><span class="section-number-4">2.1.2</span> Compute</h4>
<div id="outline-container-org0352ed3" class="outline-4">
<h4 id="org0352ed3"><span class="section-number-4">2.1.2</span> Compute</h4>
<div class="outline-text-4" id="text-2-1-2">
<table id="orgb590c45" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org310b126" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -758,16 +762,15 @@ current date is stored.
<span style="color: #a020f0;">return</span>
<span style="color: #a020f0;">endif</span>
!<span style="color: #b22222;">$OMP PARALLEL DO DEFAULT(NONE) &amp;</span>
!<span style="color: #b22222;">$OMP SHARED(elec_num, walk_num, coord, ee_distance)</span>
!<span style="color: #b22222;">$OMP PRIVATE(k)</span>
<span style="color: #a020f0;">do</span> k=1,walk_num
info = qmckl_distance(context, <span style="color: #8b2252;">'T'</span>, <span style="color: #8b2252;">'T'</span>, elec_num, elec_num, <span style="color: #a020f0;">&amp;</span>
coord(1,1,k), elec_num, <span style="color: #a020f0;">&amp;</span>
coord(1,1,k), elec_num, <span style="color: #a020f0;">&amp;</span>
ee_distance(1,1,k), elec_num)
<span style="color: #a020f0;">if</span> (info /= QMCKL_SUCCESS) <span style="color: #a020f0;">then</span>
<span style="color: #a020f0;">exit</span>
<span style="color: #a020f0;">endif</span>
<span style="color: #a020f0;">end do</span>
!<span style="color: #b22222;">$OMP END PARALLEL DO</span>
<span style="color: #a020f0;">end function</span> <span style="color: #0000ff;">qmckl_compute_ee_distance_f</span>
</pre>
@ -775,19 +778,33 @@ current date is stored.
</div>
</div>
<div id="outline-container-orga2b618b" class="outline-4">
<h4 id="orga2b618b"><span class="section-number-4">2.1.3</span> Test</h4>
<div id="outline-container-org9ec7f5a" class="outline-4">
<h4 id="org9ec7f5a"><span class="section-number-4">2.1.3</span> Test</h4>
<div class="outline-text-4" id="text-2-1-3">
<div class="org-src-container">
<pre class="src src-c">/* <span style="color: #b22222;">Reference input data </span>*/
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">qmckl_electron_provided</span>(<span style="color: #a0522d;">context</span>));
<pre class="src src-c"><span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">qmckl_electron_provided</span>(<span style="color: #a0522d;">context</span>));
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">ee_distance</span>[walk_num*num*num];
rc = qmckl_get_electron_ee_distance(context, ee_distance);
// <span style="color: #b22222;">(e1,e2,w)</span>
// <span style="color: #b22222;">(0,0,0) == 0.</span>
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">ee_distance</span>[0] == 0.);
// <span style="color: #b22222;">(1,0,0) == (0,1,0)</span>
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">ee_distance</span>[1] == ee_distance[num]);
<span style="color: #0000ff;">assert</span>(fabs(<span style="color: #228b22;">ee_distance</span>[1]-8.6114953086801) &lt; 1.e-12);
// <span style="color: #b22222;">value of (1,0,0)</span>
<span style="color: #0000ff;">assert</span>(fabs(<span style="color: #228b22;">ee_distance</span>[1]-7.152322512964209) &lt; 1.e-12);
// <span style="color: #b22222;">(0,0,1) == 0.</span>
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">ee_distance</span>[num*num] == 0.);
// <span style="color: #b22222;">(1,0,1) == (0,1,1)</span>
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">ee_distance</span>[num*num+1] == ee_distance[num*num+num]);
// <span style="color: #b22222;">value of (1,0,1)</span>
<span style="color: #0000ff;">assert</span>(fabs(<span style="color: #228b22;">ee_distance</span>[num*num+1]-6.5517646321055665) &lt; 1.e-12);
</pre>
</div>
@ -795,12 +812,12 @@ rc = qmckl_get_electron_ee_distance(context, ee_distance);
</div>
</div>
<div id="outline-container-org9d0036f" class="outline-3">
<h3 id="org9d0036f"><span class="section-number-3">2.2</span> Electron-nucleus distances</h3>
<div id="outline-container-org15a922e" class="outline-3">
<h3 id="org15a922e"><span class="section-number-3">2.2</span> Electron-nucleus distances</h3>
<div class="outline-text-3" id="text-2-2">
</div>
<div id="outline-container-org5e73d24" class="outline-4">
<h4 id="org5e73d24"><span class="section-number-4">2.2.1</span> Get</h4>
<div id="outline-container-org6d804db" class="outline-4">
<h4 id="org6d804db"><span class="section-number-4">2.2.1</span> Get</h4>
<div class="outline-text-4" id="text-2-2-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_get_electron_en_distance</span>(<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">distance</span>);
@ -809,10 +826,10 @@ rc = qmckl_get_electron_ee_distance(context, ee_distance);
</div>
</div>
<div id="outline-container-org8bd0535" class="outline-4">
<h4 id="org8bd0535"><span class="section-number-4">2.2.2</span> Compute</h4>
<div id="outline-container-org7e27cb4" class="outline-4">
<h4 id="org7e27cb4"><span class="section-number-4">2.2.2</span> Compute</h4>
<div class="outline-text-4" id="text-2-2-2">
<table id="org9abca0e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge984116" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -862,7 +879,7 @@ rc = qmckl_get_electron_ee_distance(context, ee_distance);
<tr>
<td class="org-left">double</td>
<td class="org-left">nucl<sub>coord</sub>[walk<sub>num</sub>][3][elec<sub>num</sub>]</td>
<td class="org-left">nucl<sub>coord</sub>[3][elec<sub>num</sub>]</td>
<td class="org-left">in</td>
<td class="org-left">Nuclear coordinates</td>
</tr>
@ -886,7 +903,7 @@ rc = qmckl_get_electron_ee_distance(context, ee_distance);
<span style="color: #228b22;">integer</span>*8 , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> nucl_num</span>
<span style="color: #228b22;">integer</span>*8 , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> walk_num</span>
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> elec_coord(elec_num,3,walk_num)</span>
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> nucl_coord(nucl_num,3,walk_num)</span>
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> nucl_coord(nucl_num,3)</span>
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(out) ::<span style="color: #a0522d;"> en_distance(elec_num,nucl_num,walk_num)</span>
<span style="color: #228b22;">integer</span>*8 ::<span style="color: #a0522d;"> k</span>
@ -913,16 +930,15 @@ rc = qmckl_get_electron_ee_distance(context, ee_distance);
<span style="color: #a020f0;">return</span>
<span style="color: #a020f0;">endif</span>
!<span style="color: #b22222;">$OMP PARALLEL DO DEFAULT(NONE) &amp;</span>
!<span style="color: #b22222;">$OMP SHARED(elec_num, nucl_num, walk_num, elec_coord, nucl_coord, en_distance)</span>
!<span style="color: #b22222;">$OMP PRIVATE(k)</span>
<span style="color: #a020f0;">do</span> k=1,walk_num
info = qmckl_distance(context, <span style="color: #8b2252;">'T'</span>, <span style="color: #8b2252;">'T'</span>, elec_num, nucl_num, <span style="color: #a020f0;">&amp;</span>
elec_coord(1,1,k), elec_num, <span style="color: #a020f0;">&amp;</span>
nucl_coord, nucl_num, <span style="color: #a020f0;">&amp;</span>
en_distance(1,1,k), elec_num)
<span style="color: #a020f0;">if</span> (info /= QMCKL_SUCCESS) <span style="color: #a020f0;">then</span>
<span style="color: #a020f0;">exit</span>
<span style="color: #a020f0;">endif</span>
<span style="color: #a020f0;">end do</span>
!<span style="color: #b22222;">$OMP END PARALLEL DO</span>
<span style="color: #a020f0;">end function</span> <span style="color: #0000ff;">qmckl_compute_en_distance_f</span>
</pre>
@ -930,17 +946,44 @@ rc = qmckl_get_electron_ee_distance(context, ee_distance);
</div>
</div>
<div id="outline-container-org95d9b34" class="outline-4">
<h4 id="org95d9b34"><span class="section-number-4">2.2.3</span> Test</h4>
<div id="outline-container-orgd04408e" class="outline-4">
<h4 id="orgd04408e"><span class="section-number-4">2.2.3</span> Test</h4>
<div class="outline-text-4" id="text-2-2-3">
<div class="org-src-container">
<pre class="src src-c">/* <span style="color: #b22222;">Reference input data </span>*/
<pre class="src src-c">assert(!qmckl_nucleus_provided(context));
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">qmckl_electron_provided</span>(<span style="color: #a0522d;">context</span>));
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">en_distance</span>[walk_num*num*num];
rc = qmckl_get_electron_en_distance(context, en_distance);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_NOT_PROVIDED);
rc = qmckl_set_nucleus_num (context, nucl_num);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
rc = qmckl_set_nucleus_charge (context, charge);
<span style="color: #0000ff;">assert</span> (rc == QMCKL_SUCCESS);
rc = qmckl_set_nucleus_coord (context, &amp;(nucl_coord[0]));
<span style="color: #0000ff;">assert</span> (rc == QMCKL_SUCCESS);
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">qmckl_nucleus_provided</span>(<span style="color: #a0522d;">context</span>));
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">en_distance</span>[walk_num][nucl_num][num];
rc = qmckl_get_electron_en_distance(context, &amp;(en_distance[0][0][0]));
<span style="color: #0000ff;">assert</span> (rc == QMCKL_SUCCESS);
// <span style="color: #b22222;">(e,n,w) in Fortran notation</span>
// <span style="color: #b22222;">(1,1,1)</span>
<span style="color: #0000ff;">assert</span>(fabs(<span style="color: #228b22;">en_distance</span>[0][0][0] - 6.855624268793153) &lt; 1.e-12);
// <span style="color: #b22222;">(2,1,1)</span>
<span style="color: #0000ff;">assert</span>(fabs(<span style="color: #228b22;">en_distance</span>[0][0][1] - 3.698922010513608) &lt; 1.e-12);
// <span style="color: #b22222;">(1,2,1)</span>
<span style="color: #0000ff;">assert</span>(fabs(<span style="color: #228b22;">en_distance</span>[0][1][0] - 8.143800105434433) &lt; 1.e-12);
// <span style="color: #b22222;">(2,2,1)</span>
<span style="color: #0000ff;">assert</span>(fabs(<span style="color: #228b22;">en_distance</span>[0][1][1] - 5.16360835635664) &lt; 1.e-12);
// <span style="color: #b22222;">(4,3,2)</span>
<span style="color: #0000ff;">assert</span>(fabs(<span style="color: #228b22;">en_distance</span>[1][2][3] - 12.599138999960012) &lt; 1.e-12);
</pre>
</div>
@ -951,7 +994,7 @@ rc = qmckl_get_electron_en_distance(context, en_distance);
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX CoE</p>
<p class="date">Created: 2021-05-18 Tue 10:33</p>
<p class="date">Created: 2021-05-18 Tue 23:32</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

28
qmckl_error.html
View File

@ -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>
<!-- 2021-05-18 Tue 10:33 -->
<!-- 2021-05-18 Tue 23:32 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Error handling</title>
@ -311,16 +311,16 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org8d2fb10">1. Decoding errors</a></li>
<li><a href="#org1d1e45a">2. Data structure in context</a></li>
<li><a href="#orgfc4aca2">3. Updating errors in the context</a></li>
<li><a href="#org6d69812">4. Failing</a></li>
<li><a href="#org20768f0">1. Decoding errors</a></li>
<li><a href="#org3674e93">2. Data structure in context</a></li>
<li><a href="#org8db481f">3. Updating errors in the context</a></li>
<li><a href="#orga79f7e7">4. Failing</a></li>
</ul>
</div>
</div>
<div id="outline-container-org8d2fb10" class="outline-2">
<h2 id="org8d2fb10"><span class="section-number-2">1</span> Decoding errors</h2>
<div id="outline-container-org20768f0" class="outline-2">
<h2 id="org20768f0"><span class="section-number-2">1</span> Decoding errors</h2>
<div class="outline-text-2" id="text-1">
<p>
To decode the error messages, <code>qmckl_string_of_error</code> converts an
@ -417,8 +417,8 @@ The text strings are extracted from the previous table.
</div>
</div>
<div id="outline-container-org1d1e45a" class="outline-2">
<h2 id="org1d1e45a"><span class="section-number-2">2</span> Data structure in context</h2>
<div id="outline-container-org3674e93" class="outline-2">
<h2 id="org3674e93"><span class="section-number-2">2</span> Data structure in context</h2>
<div class="outline-text-2" id="text-2">
<p>
The strings are declared with a maximum fixed size to avoid
@ -441,8 +441,8 @@ dynamic memory allocation.
</div>
</div>
<div id="outline-container-orgfc4aca2" class="outline-2">
<h2 id="orgfc4aca2"><span class="section-number-2">3</span> Updating errors in the context</h2>
<div id="outline-container-org8db481f" class="outline-2">
<h2 id="org8db481f"><span class="section-number-2">3</span> Updating errors in the context</h2>
<div class="outline-text-2" id="text-3">
<p>
The error is updated in the context using <code>qmckl_set_error</code>.
@ -488,8 +488,8 @@ explaining the error. The exit code can't be <code>QMCKL_SUCCESS</code>.
</div>
</div>
<div id="outline-container-org6d69812" class="outline-2">
<h2 id="org6d69812"><span class="section-number-2">4</span> Failing</h2>
<div id="outline-container-orga79f7e7" class="outline-2">
<h2 id="orga79f7e7"><span class="section-number-2">4</span> Failing</h2>
<div class="outline-text-2" id="text-4">
<p>
To make a function fail, the <code>qmckl_failwith</code> function should be
@ -552,7 +552,7 @@ For example, this function can be used as
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX CoE</p>
<p class="date">Created: 2021-05-18 Tue 10:33</p>
<p class="date">Created: 2021-05-18 Tue 23:32</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

22
qmckl_memory.html
View File

@ -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>
<!-- 2021-05-18 Tue 10:33 -->
<!-- 2021-05-18 Tue 23:32 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Memory management</title>
@ -311,15 +311,15 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org956e18f">1. Memory data structure for the context</a></li>
<li><a href="#org1434687">2. Passing info to allocation routines</a></li>
<li><a href="#orga14a108">3. Allocation/deallocation functions</a></li>
<li><a href="#org939aa30">1. Memory data structure for the context</a></li>
<li><a href="#org532191c">2. Passing info to allocation routines</a></li>
<li><a href="#org40c01f6">3. Allocation/deallocation functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org956e18f" class="outline-2">
<h2 id="org956e18f"><span class="section-number-2">1</span> Memory data structure for the context</h2>
<div id="outline-container-org939aa30" class="outline-2">
<h2 id="org939aa30"><span class="section-number-2">1</span> Memory data structure for the context</h2>
<div class="outline-text-2" id="text-1">
<p>
Every time a new block of memory is allocated, the information
@ -361,8 +361,8 @@ array, and the number of allocated blocks.
</div>
</div>
<div id="outline-container-org1434687" class="outline-2">
<h2 id="org1434687"><span class="section-number-2">2</span> Passing info to allocation routines</h2>
<div id="outline-container-org532191c" class="outline-2">
<h2 id="org532191c"><span class="section-number-2">2</span> Passing info to allocation routines</h2>
<div class="outline-text-2" id="text-2">
<p>
Passing information to the allocation routine should be done by
@ -371,8 +371,8 @@ passing an instance of a <code>qmckl_memory_info_struct</code>.
</div>
</div>
<div id="outline-container-orga14a108" class="outline-2">
<h2 id="orga14a108"><span class="section-number-2">3</span> Allocation/deallocation functions</h2>
<div id="outline-container-org40c01f6" class="outline-2">
<h2 id="org40c01f6"><span class="section-number-2">3</span> Allocation/deallocation functions</h2>
<div class="outline-text-2" id="text-3">
<p>
Memory allocation inside the library should be done with
@ -535,7 +535,7 @@ allocation and needs to be updated.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX CoE</p>
<p class="date">Created: 2021-05-18 Tue 10:33</p>
<p class="date">Created: 2021-05-18 Tue 23:32</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

262
qmckl_nucleus.html
View File

@ -3,11 +3,12 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-05-18 Tue 10:33 -->
<!-- 2021-05-18 Tue 23:33 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>&lrm;</title>
<title>Nucleus</title>
<meta name="generator" content="Org mode" />
<meta name="author" content="TREX CoE" />
<style type="text/css">
<!--/*--><![CDATA[/*><!--*/
.title { text-align: center;
@ -179,6 +180,79 @@
.org-svg { width: 90%; }
/*]]>*/-->
</style>
<link rel="stylesheet" title="Standard" href="qmckl.css" type="text/css" />
<script type="text/javascript" src="org-info.js">
/**
*
* @source: org-info.js
*
* @licstart The following is the entire license notice for the
* JavaScript code in org-info.js.
*
* Copyright (C) 2012-2019 Free Software Foundation, Inc.
*
*
* The JavaScript code in this tag is free software: you can
* redistribute it and/or modify it under the terms of the GNU
* General Public License (GNU GPL) as published by the Free Software
* Foundation, either version 3 of the License, or (at your option)
* any later version. The code is distributed WITHOUT ANY WARRANTY;
* without even the implied warranty of MERCHANTABILITY or FITNESS
* FOR A PARTICULAR PURPOSE. See the GNU GPL for more details.
*
* As additional permission under GNU GPL version 3 section 7, you
* may distribute non-source (e.g., minimized or compacted) forms of
* that code without the copy of the GNU GPL normally required by
* section 4, provided you include this license notice and a URL
* through which recipients can access the Corresponding Source.
*
* @licend The above is the entire license notice
* for the JavaScript code in org-info.js.
*
*/
</script>
<script type="text/javascript">
/*
@licstart The following is the entire license notice for the
JavaScript code in this tag.
Copyright (C) 2012-2019 Free Software Foundation, Inc.
The JavaScript code in this tag is free software: you can
redistribute it and/or modify it under the terms of the GNU
General Public License (GNU GPL) as published by the Free Software
Foundation, either version 3 of the License, or (at your option)
any later version. The code is distributed WITHOUT ANY WARRANTY;
without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU GPL for more details.
As additional permission under GNU GPL version 3 section 7, you
may distribute non-source (e.g., minimized or compacted) forms of
that code without the copy of the GNU GPL normally required by
section 4, provided you include this license notice and a URL
through which recipients can access the Corresponding Source.
@licend The above is the entire license notice
for the JavaScript code in this tag.
*/
<!--/*--><![CDATA[/*><!--*/
org_html_manager.set("TOC_DEPTH", "4");
org_html_manager.set("LINK_HOME", "index.html");
org_html_manager.set("LINK_UP", "");
org_html_manager.set("LOCAL_TOC", "1");
org_html_manager.set("VIEW_BUTTONS", "0");
org_html_manager.set("MOUSE_HINT", "underline");
org_html_manager.set("FIXED_TOC", "0");
org_html_manager.set("TOC", "1");
org_html_manager.set("VIEW", "info");
org_html_manager.setup(); // activate after the parameters are set
/*]]>*///-->
</script>
<script type="text/javascript">
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@ -249,33 +323,38 @@ for the JavaScript code in this tag.
src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS_HTML"></script>
</head>
<body>
<div id="content">
<div id="org-div-home-and-up">
<a accesskey="h" href=""> UP </a>
|
<a accesskey="H" href="index.html"> HOME </a>
</div><div id="content">
<h1 class="title">Nucleus</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org2379e3e">1. Context</a>
<li><a href="#org9f37522">1. Context</a>
<ul>
<li><a href="#org8b955ad">1.1. Data structure</a></li>
<li><a href="#org0fbaa5e">1.2. Access functions</a></li>
<li><a href="#org3f2250b">1.3. Initialization functions</a></li>
<li><a href="#org4bb7623">1.4. Test</a></li>
<li><a href="#orgab0aa73">1.1. Data structure</a></li>
<li><a href="#org0153f10">1.2. Access functions</a></li>
<li><a href="#org24b49e6">1.3. Initialization functions</a></li>
<li><a href="#org14a850d">1.4. Test</a></li>
</ul>
</li>
<li><a href="#orgead9976">2. Computation</a>
<li><a href="#org009476a">2. Computation</a>
<ul>
<li><a href="#orgd58caca">2.1. Nucleus-nucleus distances</a>
<li><a href="#org501b136">2.1. Nucleus-nucleus distances</a>
<ul>
<li><a href="#org4abfc83">2.1.1. Get</a></li>
<li><a href="#orga1f1505">2.1.2. Compute</a></li>
<li><a href="#orgb3e4a24">2.1.3. Test</a></li>
<li><a href="#org67c0e6f">2.1.1. Get</a></li>
<li><a href="#orgd6729f5">2.1.2. Compute</a></li>
<li><a href="#orgcf4c735">2.1.3. Test</a></li>
</ul>
</li>
<li><a href="#orgda6dc52">2.2. Nuclear repulsion energy</a>
<li><a href="#org4bd7b85">2.2. Nuclear repulsion energy</a>
<ul>
<li><a href="#org7483570">2.2.1. Get</a></li>
<li><a href="#orgecb367a">2.2.2. Compute</a></li>
<li><a href="#orgcf592cd">2.2.3. Test</a></li>
<li><a href="#org254299a">2.2.1. Get</a></li>
<li><a href="#org8a90dc0">2.2.2. Compute</a></li>
<li><a href="#org1c127a4">2.2.3. Test</a></li>
</ul>
</li>
</ul>
@ -283,16 +362,9 @@ for the JavaScript code in this tag.
</ul>
</div>
</div>
<p>
#i+TITLE: Nucleus
</p>
<p>
A ll the data relative to the molecular geometry is described here.
</p>
<div id="outline-container-org2379e3e" class="outline-2">
<h2 id="org2379e3e"><span class="section-number-2">1</span> Context</h2>
<div id="outline-container-org9f37522" class="outline-2">
<h2 id="org9f37522"><span class="section-number-2">1</span> Context</h2>
<div class="outline-text-2" id="text-1">
<p>
The following data stored in the context:
@ -336,7 +408,7 @@ The following data stored in the context:
<tr>
<td class="org-left"><code>coord</code></td>
<td class="org-left">double[3][num]</td>
<td class="org-left">Nuclear coordinates</td>
<td class="org-left">Nuclear coordinates, in transposed format</td>
</tr>
<tr>
@ -366,8 +438,8 @@ The following data stored in the context:
</table>
</div>
<div id="outline-container-org8b955ad" class="outline-3">
<h3 id="org8b955ad"><span class="section-number-3">1.1</span> Data structure</h3>
<div id="outline-container-orgab0aa73" class="outline-3">
<h3 id="orgab0aa73"><span class="section-number-3">1.1</span> Data structure</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> <span style="color: #228b22;">qmckl_nucleus_struct</span> {
@ -393,8 +465,8 @@ struct is then initialized and <code>provided == true</code>.
</div>
</div>
<div id="outline-container-org0fbaa5e" class="outline-3">
<h3 id="org0fbaa5e"><span class="section-number-3">1.2</span> Access functions</h3>
<div id="outline-container-org0153f10" class="outline-3">
<h3 id="org0153f10"><span class="section-number-3">1.2</span> Access functions</h3>
<div class="outline-text-3" id="text-1-2">
<p>
When all the data relative to nuclei have been set, the following
@ -408,8 +480,8 @@ function returns <code>true</code>.
</div>
</div>
<div id="outline-container-org3f2250b" class="outline-3">
<h3 id="org3f2250b"><span class="section-number-3">1.3</span> Initialization functions</h3>
<div id="outline-container-org24b49e6" class="outline-3">
<h3 id="org24b49e6"><span class="section-number-3">1.3</span> Initialization functions</h3>
<div class="outline-text-3" id="text-1-3">
<p>
To set the data relative to the nuclei in the context, the
@ -419,7 +491,7 @@ following functions need to be called.
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_set_nucleus_num</span> (<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">num</span>);
<span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_set_nucleus_charge</span> (<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">charge</span>);
<span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_set_nucleus_coord</span> (<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">coord</span>);
<span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_set_nucleus_coord</span> (<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span> <span style="color: #a0522d;">transp</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">coord</span>);
</pre>
</div>
@ -428,7 +500,7 @@ To set the number of nuclei, use
</p>
<p>
The following function sets the nuclear charges of all the atoms.
The following function sets the nuclear charges of all the atoms.
</p>
<p>
@ -438,26 +510,13 @@ atoms. The coordinates should be given in atomic units.
</div>
</div>
<div id="outline-container-org4bb7623" class="outline-3">
<h3 id="org4bb7623"><span class="section-number-3">1.4</span> Test</h3>
<div id="outline-container-org14a850d" class="outline-3">
<h3 id="org14a850d"><span class="section-number-3">1.4</span> Test</h3>
<div class="outline-text-3" id="text-1-4">
<div class="org-src-container">
<pre class="src src-c">/* <span style="color: #b22222;">Reference input data </span>*/
<span style="color: #483d8b;">#define</span> <span style="color: #a0522d;">num</span> ((<span style="color: #228b22;">int64_t</span>) 9)
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">charge</span>[num] = { 6., 6., 6., 7., 7., 1., 1., 1., 1. };
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">coord</span>[3*num] =
{ 4.166279566732572e-01, -1.526183863767697e+00, 1.041604719335635e+00,
-1.903457631371503e+00, 2.242154435363994e+00, 6.550163404813796e-01,
-3.575005445908036e+00, -3.063638942318878e+00, 2.086739409279095e+00,
2.060062599100338e+00, -1.623431626827498e+00, -1.930074272670425e+00,
9.491495662916423e-01, 3.808343139803397e-01, 4.077482772289367e+00,
1.841031662652821e+00, -2.945591662994877e+00, -3.670011011125464e+00,
0.000000000000000e+00, 0.000000000000000e+00, 0.000000000000000e+00,
0.000000000000000e+00, 0.000000000000000e+00, 0.000000000000000e+00,
0.000000000000000e+00, 0.000000000000000e+00, 0.000000000000000e+00};
<pre class="src src-c"><span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">nucl_num</span> = chbrclf_nucl_num;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">nucl_charge</span> = chbrclf_charge;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">nucl_coord</span> = &amp;(chbrclf_nucl_coord[0][0]);
/* <span style="color: #b22222;">--- </span>*/
@ -470,42 +529,50 @@ rc = qmckl_get_nucleus_num (context, &amp;n);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_NOT_PROVIDED);
rc = qmckl_set_nucleus_num (context, num);
rc = qmckl_set_nucleus_num (context, nucl_num);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
assert(!qmckl_nucleus_provided(context));
rc = qmckl_get_nucleus_num (context, &amp;n);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
<span style="color: #0000ff;">assert</span>(n == num);
<span style="color: #0000ff;">assert</span>(n == nucl_num);
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">coord2</span>[3*num];
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">nucl_coord2</span>[3*nucl_num];
rc = qmckl_get_nucleus_coord (context, coord2);
rc = qmckl_get_nucleus_coord (context, <span style="color: #8b2252;">'T'</span>, nucl_coord2);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_NOT_PROVIDED);
rc = qmckl_set_nucleus_coord (context, coord);
rc = qmckl_set_nucleus_coord (context, <span style="color: #8b2252;">'T'</span>, &amp;(nucl_coord[0]));
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
rc = qmckl_get_nucleus_coord (context, coord2);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">i</span>=0 ; i&lt;3*num ; ++i) {
assert( coord[i] == coord2[i] );
}
assert(!qmckl_nucleus_provided(context));
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">charge2</span>[num];
rc = qmckl_get_nucleus_coord (context, <span style="color: #8b2252;">'N'</span>, nucl_coord2);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">k</span>=0 ; k&lt;3 ; ++k) {
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">i</span>=0 ; i&lt;nucl_num ; ++i) {
assert( nucl_coord[nucl_num*k+i] == nucl_coord2[3*i+k] );
}
}
rc = qmckl_get_nucleus_charge(context, charge2);
rc = qmckl_get_nucleus_coord (context, <span style="color: #8b2252;">'T'</span>, nucl_coord2);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">i</span>=0 ; i&lt;3*nucl_num ; ++i) {
assert( nucl_coord[i] == nucl_coord2[i] );
}
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">nucl_charge2</span>[nucl_num];
rc = qmckl_get_nucleus_charge(context, nucl_charge2);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_NOT_PROVIDED);
rc = qmckl_set_nucleus_charge(context, charge);
rc = qmckl_set_nucleus_charge(context, nucl_charge);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
rc = qmckl_get_nucleus_charge(context, charge2);
rc = qmckl_get_nucleus_charge(context, nucl_charge2);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">i</span>=0 ; i&lt;num ; ++i) {
assert( charge[i] == charge2[i] );
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">i</span>=0 ; i&lt;nucl_num ; ++i) {
assert( nucl_charge[i] == nucl_charge2[i] );
}
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">qmckl_nucleus_provided</span>(<span style="color: #a0522d;">context</span>));
</pre>
@ -514,8 +581,8 @@ rc = qmckl_get_nucleus_charge(context, charge2);
</div>
</div>
<div id="outline-container-orgead9976" class="outline-2">
<h2 id="orgead9976"><span class="section-number-2">2</span> Computation</h2>
<div id="outline-container-org009476a" class="outline-2">
<h2 id="org009476a"><span class="section-number-2">2</span> Computation</h2>
<div class="outline-text-2" id="text-2">
<p>
The computed data is stored in the context so that it can be reused
@ -528,12 +595,12 @@ current date is stored.
</p>
</div>
<div id="outline-container-orgd58caca" class="outline-3">
<h3 id="orgd58caca"><span class="section-number-3">2.1</span> Nucleus-nucleus distances</h3>
<div id="outline-container-org501b136" class="outline-3">
<h3 id="org501b136"><span class="section-number-3">2.1</span> Nucleus-nucleus distances</h3>
<div class="outline-text-3" id="text-2-1">
</div>
<div id="outline-container-org4abfc83" class="outline-4">
<h4 id="org4abfc83"><span class="section-number-4">2.1.1</span> Get</h4>
<div id="outline-container-org67c0e6f" class="outline-4">
<h4 id="org67c0e6f"><span class="section-number-4">2.1.1</span> Get</h4>
<div class="outline-text-4" id="text-2-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_get_nucleus_nn_distance</span>(<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">distance</span>);
@ -542,10 +609,10 @@ current date is stored.
</div>
</div>
<div id="outline-container-orga1f1505" class="outline-4">
<h4 id="orga1f1505"><span class="section-number-4">2.1.2</span> Compute</h4>
<div id="outline-container-orgd6729f5" class="outline-4">
<h4 id="orgd6729f5"><span class="section-number-4">2.1.2</span> Compute</h4>
<div class="outline-text-4" id="text-2-1-2">
<table id="orgc1b87f5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfa4dfe4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -623,20 +690,19 @@ current date is stored.
</div>
</div>
<div id="outline-container-orgb3e4a24" class="outline-4">
<h4 id="orgb3e4a24"><span class="section-number-4">2.1.3</span> Test</h4>
<div id="outline-container-orgcf4c735" class="outline-4">
<h4 id="orgcf4c735"><span class="section-number-4">2.1.3</span> Test</h4>
<div class="outline-text-4" id="text-2-1-3">
<div class="org-src-container">
<pre class="src src-c">/* <span style="color: #b22222;">Reference input data </span>*/
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">qmckl_nucleus_provided</span>(<span style="color: #a0522d;">context</span>));
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">distance</span>[num*num];
rc = qmckl_get_nucleus_nn_distance(context, distance);
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">distance</span>[nucl_num*nucl_num];
rc = qmckl_get_nucleus_nn_distance(context, distance);
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">distance</span>[0] == 0.);
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">distance</span>[1] == distance[num]);
<span style="color: #0000ff;">assert</span>(fabs(<span style="color: #228b22;">distance</span>[1]-4.164450441785663) &lt; 1.e-12);
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">distance</span>[1] == distance[nucl_num]);
<span style="color: #0000ff;">assert</span>(fabs(<span style="color: #228b22;">distance</span>[1]-2.070304721365169) &lt; 1.e-12);
</pre>
</div>
@ -644,8 +710,8 @@ rc = qmckl_get_nucleus_nn_distance(context, distance);
</div>
</div>
<div id="outline-container-orgda6dc52" class="outline-3">
<h3 id="orgda6dc52"><span class="section-number-3">2.2</span> Nuclear repulsion energy</h3>
<div id="outline-container-org4bd7b85" class="outline-3">
<h3 id="org4bd7b85"><span class="section-number-3">2.2</span> Nuclear repulsion energy</h3>
<div class="outline-text-3" id="text-2-2">
<p>
\[
@ -654,8 +720,8 @@ rc = qmckl_get_nucleus_nn_distance(context, distance);
</p>
</div>
<div id="outline-container-org7483570" class="outline-4">
<h4 id="org7483570"><span class="section-number-4">2.2.1</span> Get</h4>
<div id="outline-container-org254299a" class="outline-4">
<h4 id="org254299a"><span class="section-number-4">2.2.1</span> Get</h4>
<div class="outline-text-4" id="text-2-2-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_get_nucleus_repulsion</span>(<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">energy</span>);
@ -664,10 +730,10 @@ rc = qmckl_get_nucleus_nn_distance(context, distance);
</div>
</div>
<div id="outline-container-orgecb367a" class="outline-4">
<h4 id="orgecb367a"><span class="section-number-4">2.2.2</span> Compute</h4>
<div id="outline-container-org8a90dc0" class="outline-4">
<h4 id="org8a90dc0"><span class="section-number-4">2.2.2</span> Compute</h4>
<div class="outline-text-4" id="text-2-2-2">
<table id="org8040774" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgde71515" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -745,10 +811,9 @@ rc = qmckl_get_nucleus_nn_distance(context, distance);
energy = 0.d0
<span style="color: #a020f0;">do</span> j=2, nucl_num
<span style="color: #a020f0;">do</span> i=1, j-1
energy = energy + charge(i) * charge(j) / nn_distance(i,j)
energy = energy + charge(i) * charge(j) / nn_distance(i,j)
<span style="color: #a020f0;">end do</span>
<span style="color: #a020f0;">end do</span>
<span style="color: #a020f0;">print</span> *, energy
<span style="color: #a020f0;">end function</span> <span style="color: #0000ff;">qmckl_compute_nucleus_repulsion_f</span>
</pre>
@ -756,8 +821,8 @@ rc = qmckl_get_nucleus_nn_distance(context, distance);
</div>
</div>
<div id="outline-container-orgcf592cd" class="outline-4">
<h4 id="orgcf592cd"><span class="section-number-4">2.2.3</span> Test</h4>
<div id="outline-container-org1c127a4" class="outline-4">
<h4 id="org1c127a4"><span class="section-number-4">2.2.3</span> Test</h4>
<div class="outline-text-4" id="text-2-2-3">
<div class="org-src-container">
<pre class="src src-c">/* <span style="color: #b22222;">Reference input data </span>*/
@ -766,7 +831,7 @@ rc = qmckl_get_nucleus_nn_distance(context, distance);
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">rep</span>;
rc = qmckl_get_nucleus_repulsion(context, &amp;rep);
<span style="color: #0000ff;">assert</span>(rep - 163.50434957121263 &lt; 1.e-10);
<span style="color: #0000ff;">assert</span>(rep - 318.2309879436158 &lt; 1.e-10);
</pre>
</div>
@ -776,7 +841,8 @@ rc = qmckl_get_nucleus_repulsion(context, &amp;rep);
</div>
</div>
<div id="postamble" class="status">
<p class="date">Created: 2021-05-18 Tue 10:33</p>
<p class="author">Author: TREX CoE</p>
<p class="date">Created: 2021-05-18 Tue 23:33</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

30
qmckl_numprec.html
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@ -3,7 +3,7 @@
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<head>
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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>Numerical precision</title>
@ -333,16 +333,16 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9a58ae1">1. Control of the numerical precision</a></li>
<li><a href="#org83e0e2f">2. Precision</a></li>
<li><a href="#org4543f2a">3. Range</a></li>
<li><a href="#org8bdcd43">4. Helper functions</a></li>
<li><a href="#org7e3cfa0">1. Control of the numerical precision</a></li>
<li><a href="#org8a69568">2. Precision</a></li>
<li><a href="#org9dfff30">3. Range</a></li>
<li><a href="#org6f82e86">4. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org9a58ae1" class="outline-2">
<h2 id="org9a58ae1"><span class="section-number-2">1</span> Control of the numerical precision</h2>
<div id="outline-container-org7e3cfa0" class="outline-2">
<h2 id="org7e3cfa0"><span class="section-number-2">1</span> Control of the numerical precision</h2>
<div class="outline-text-2" id="text-1">
<p>
Controlling numerical precision enables optimizations. Here, the
@ -353,7 +353,7 @@ Arithmetic (IEEE 754),
refers to the number of exponent bits.
</p>
<table id="org86a282c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdf94399" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -397,8 +397,8 @@ integer. The update functions return <code>QMCKL_SUCCESS</code> or
</div>
</div>
<div id="outline-container-org83e0e2f" class="outline-2">
<h2 id="org83e0e2f"><span class="section-number-2">2</span> Precision</h2>
<div id="outline-container-org8a69568" class="outline-2">
<h2 id="org8a69568"><span class="section-number-2">2</span> Precision</h2>
<div class="outline-text-2" id="text-2">
<p>
<code>qmckl_context_set_numprec_precision</code> modifies the parameter for the
@ -485,8 +485,8 @@ numerical precision in the context.
</div>
</div>
<div id="outline-container-org4543f2a" class="outline-2">
<h2 id="org4543f2a"><span class="section-number-2">3</span> Range</h2>
<div id="outline-container-org9dfff30" class="outline-2">
<h2 id="org9dfff30"><span class="section-number-2">3</span> Range</h2>
<div class="outline-text-2" id="text-3">
<p>
<code>qmckl_set_numprec_range</code> modifies the parameter for the numerical
@ -561,8 +561,8 @@ range in a given context.
</div>
</div>
</div>
<div id="outline-container-org8bdcd43" class="outline-2">
<h2 id="org8bdcd43"><span class="section-number-2">4</span> Helper functions</h2>
<div id="outline-container-org6f82e86" class="outline-2">
<h2 id="org6f82e86"><span class="section-number-2">4</span> Helper functions</h2>
<div class="outline-text-2" id="text-4">
<p>
<code>qmckl_get_numprec_epsilon</code> returns \(\epsilon = 2^{1-n}\) where <code>n</code> is the precision.
@ -581,7 +581,7 @@ We need to remove the sign bit from the precision.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX CoE</p>
<p class="date">Created: 2021-05-18 Tue 10:33</p>
<p class="date">Created: 2021-05-18 Tue 23:32</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<h1 class="title">Utility functions</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org09f8af3">1. Matrix operations</a>
<ul>
<li><a href="#orgd2b51a9">1.1. <code>qmckl_transpose</code></a>
<ul>
<li><a href="#org8ccd87e">1.1.1. Requirements</a></li>
<li><a href="#org4f2e36a">1.1.2. C header</a></li>
<li><a href="#orgf5f7428">1.1.3. Source</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org09f8af3" class="outline-2">
<h2 id="org09f8af3"><span class="section-number-2">1</span> Matrix operations</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orgd2b51a9" class="outline-3">
<h3 id="orgd2b51a9"><span class="section-number-3">1.1</span> <code>qmckl_transpose</code></h3>
<div class="outline-text-3" id="text-1-1">
<p>
Transposes a matrix: \(B_{ji} = A_{ij}\)
</p>
<table id="org55a674c" 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>
<tbody>
<tr>
<td class="org-left">qmckl<sub>context</sub></td>
<td class="org-left">context</td>
<td class="org-left">in</td>
<td class="org-left">Global state</td>
</tr>
<tr>
<td class="org-left">int64<sub>t</sub></td>
<td class="org-left">m</td>
<td class="org-left">in</td>
<td class="org-left">Number of rows of the input matrix</td>
</tr>
<tr>
<td class="org-left">int64<sub>t</sub></td>
<td class="org-left">n</td>
<td class="org-left">in</td>
<td class="org-left">Number of columns of the input matrix</td>
</tr>
<tr>
<td class="org-left">double</td>
<td class="org-left">A[][lda]</td>
<td class="org-left">in</td>
<td class="org-left">Array containing the \(m \times n\) matrix \(A\)</td>
</tr>
<tr>
<td class="org-left">int64<sub>t</sub></td>
<td class="org-left">lda</td>
<td class="org-left">in</td>
<td class="org-left">Leading dimension of array <code>A</code></td>
</tr>
<tr>
<td class="org-left">double</td>
<td class="org-left">B[][ldb]</td>
<td class="org-left">out</td>
<td class="org-left">Array containing the \(n \times m\) matrix \(B\)</td>
</tr>
<tr>
<td class="org-left">int64<sub>t</sub></td>
<td class="org-left">ldb</td>
<td class="org-left">in</td>
<td class="org-left">Leading dimension of array <code>B</code></td>
</tr>
</tbody>
</table>
</div>
<div id="outline-container-org8ccd87e" class="outline-4">
<h4 id="org8ccd87e"><span class="section-number-4">1.1.1</span> Requirements</h4>
<div class="outline-text-4" id="text-1-1-1">
<ul class="org-ul">
<li><code>context</code> is not <code>QMCKL_NULL_CONTEXT</code></li>
<li><code>m &gt; 0</code></li>
<li><code>n &gt; 0</code></li>
<li><code>lda &gt;= m</code></li>
<li><code>ldb &gt;= n</code></li>
<li><code>A</code> is allocated with at least \(m \times n \times 8\) bytes</li>
<li><code>B</code> is allocated with at least \(n \times m \times 8\) bytes</li>
</ul>
</div>
</div>
<div id="outline-container-org4f2e36a" class="outline-4">
<h4 id="org4f2e36a"><span class="section-number-4">1.1.2</span> C header</h4>
<div class="outline-text-4" id="text-1-1-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_transpose</span> (
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">m</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">n</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">A</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">lda</span>,
<span style="color: #228b22;">double</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">B</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">ldb</span> );
</pre>
</div>
</div>
</div>
<div id="outline-container-orgf5f7428" class="outline-4">
<h4 id="orgf5f7428"><span class="section-number-4">1.1.3</span> Source</h4>
<div class="outline-text-4" id="text-1-1-3">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer </span><span style="color: #a020f0;">function</span><span style="color: #a0522d;"> </span><span style="color: #0000ff;">qmckl_transpose_f</span><span style="color: #000000; background-color: #ffffff;">(context, m, n, A, LDA, B, LDB)</span><span style="color: #a0522d;"> </span><span style="color: #a020f0;">&amp;</span>
<span style="color: #a020f0;">result</span>(info)
<span style="color: #a020f0;">use</span> <span style="color: #0000ff;">qmckl</span>
<span style="color: #a020f0;">implicit</span> <span style="color: #228b22;">none</span>
<span style="color: #228b22;">integer</span>(qmckl_context) , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> context</span>
<span style="color: #228b22;">integer</span>*8 , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> m, n</span>
<span style="color: #228b22;">integer</span>*8 , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> lda</span>
<span style="color: #228b22;">real</span>*8 , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> A(lda,*)</span>
<span style="color: #228b22;">integer</span>*8 , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> ldb</span>
<span style="color: #228b22;">real</span>*8 , <span style="color: #a020f0;">intent</span>(out) ::<span style="color: #a0522d;"> B(ldb,*)</span>
<span style="color: #228b22;">integer</span>*8 ::<span style="color: #a0522d;"> i,j</span>
info = QMCKL_SUCCESS
<span style="color: #a020f0;">if</span> (context == QMCKL_NULL_CONTEXT) <span style="color: #a020f0;">then</span>
info = QMCKL_INVALID_CONTEXT
<span style="color: #a020f0;">return</span>
<span style="color: #a020f0;">endif</span>
<span style="color: #a020f0;">if</span> (m &lt;= 0_8) <span style="color: #a020f0;">then</span>
info = QMCKL_INVALID_ARG_2
<span style="color: #a020f0;">return</span>
<span style="color: #a020f0;">endif</span>
<span style="color: #a020f0;">if</span> (n &lt;= 0_8) <span style="color: #a020f0;">then</span>
info = QMCKL_INVALID_ARG_3
<span style="color: #a020f0;">return</span>
<span style="color: #a020f0;">endif</span>
<span style="color: #a020f0;">if</span> (LDA &lt; m) <span style="color: #a020f0;">then</span>
info = QMCKL_INVALID_ARG_5
<span style="color: #a020f0;">return</span>
<span style="color: #a020f0;">endif</span>
<span style="color: #a020f0;">if</span> (LDB &lt; n) <span style="color: #a020f0;">then</span>
info = QMCKL_INVALID_ARG_7
<span style="color: #a020f0;">return</span>
<span style="color: #a020f0;">endif</span>
<span style="color: #a020f0;">do</span> j=1,m
<span style="color: #a020f0;">do</span> i=1,n
B(i,j) = A(j,i)
<span style="color: #a020f0;">end do</span>
<span style="color: #a020f0;">end do</span>
<span style="color: #a020f0;">end function</span> <span style="color: #0000ff;">qmckl_transpose_f</span>
</pre>
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<div id="postamble" class="status">
<p class="author">Author: TREX CoE</p>
<p class="date">Created: 2021-05-18 Tue 23:32</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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