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name: test-build
on:
push:
branches: [ main ]
pull_request:
branches: [ main ]
jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: install dependencies
run: sudo apt-get install emacs
- name: make
run: make -C src/
- name: build docs
run: make -C src/ doc
- name: deploy docs
uses: ./
with:
username: scemama
password: 7da28e533792db220a4811fc4e487b8ba817862f
remote_url: https://github.com/appleboy/gh-pages-action.git
test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: install dependencies
run: sudo apt-get install emacs
- name: Checkout submodules using a PAT
run: |
git config --file .gitmodules --get-regexp url | while read url; do
git config --file=.gitmodules $(echo "$url" | sed -E "s/git@github.com:|https:\/\/github.com\//https:\/\/${{ secrets.CI_PAT }}:${{ secrets.CI_PAT }}@github.com\//")
done
git submodule sync
git submodule update --init --recursive
- name: make
run: make -C src/ test

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[submodule "munit"]
path = munit
url = https://github.com/nemequ/munit/

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BSD 3-Clause License
Copyright (c) 2020, TREX Center of Excellence
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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</head>
<body>
<div id="content">
<h1 class="title">QMCkl source code documentation</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#sec-1">1. Introduction</a>
<ul>
<li><a href="#sec-1-1">1.1. Language used</a></li>
<li><a href="#sec-1-2">1.2. Source code editing</a></li>
<li><a href="#sec-1-3">1.3. Writing in Fortran</a></li>
<li><a href="#sec-1-4">1.4. Coding style</a></li>
</ul>
</li>
<li><a href="#sec-2">2. Design of the library</a>
<ul>
<li><a href="#sec-2-1">2.1. Naming conventions</a></li>
<li><a href="#sec-2-2">2.2. Application programming interface</a></li>
<li><a href="#sec-2-3">2.3. Global state</a></li>
<li><a href="#sec-2-4">2.4. Low-level functions</a></li>
<li><a href="#sec-2-5">2.5. High-level functions</a></li>
<li><a href="#sec-2-6">2.6. Numerical precision</a></li>
</ul>
</li>
<li><a href="#sec-3">3. Algorithms</a></li>
<li><a href="#sec-4">4. Rules for the API</a></li>
<li><a href="#sec-5">5. Documentation</a></li>
<li><a href="#sec-6">6. Acknowledgments</a></li>
</ul>
</div>
</div>
<div id="outline-container-sec-1" class="outline-2">
<h2 id="sec-1"><span class="section-number-2">1</span> Introduction</h2>
<div class="outline-text-2" id="text-1">
<p>
The ultimate goal of QMCkl is to provide a high-performance
implementation of the main kernels of QMC. In this particular
repository, we focus on the definition of the API and the tests,
and on a <i>pedagogical</i> presentation of the algorithms. We expect the
HPC experts to use this repository as a reference for re-writing
optimized libraries.
</p>
<p>
Literate programming is particularly adapted in this context.
Source files are written in <a href="https://karl-voit.at/2017/09/23/orgmode-as-markup-only/">org-mode</a> format, to provide useful
comments and LaTex formulas close to the code. There exists multiple
possibilities to convert org-mode files into different formats such as
HTML or pdf.
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>.
</p>
<p>
The code is extracted from the org files using Emacs as a command-line
tool in the <code>Makefile</code>, and then the produced files are compiled.
</p>
</div>
<div id="outline-container-sec-1-1" class="outline-3">
<h3 id="sec-1-1"><span class="section-number-3">1.1</span> Language used</h3>
<div class="outline-text-3" id="text-1-1">
<p>
Fortran is one of the most common languages used by the community,
and is simple enough to make the algorithms readable. Hence we
propose in this pedagogical implementation of QMCkl to use Fortran
to express the algorithms. For specific internal functions where
the C language is more natural, C is used.
</p>
<p>
As Fortran modules generate compiler-dependent files, the use of
modules is restricted to the internal use of the library, otherwise
the compliance with C is violated.
</p>
<p>
The external dependencies should be kept as small as possible, so
external libraries should be used <i>only</i> if their used is strongly
justified.
</p>
</div>
</div>
<div id="outline-container-sec-1-2" class="outline-3">
<h3 id="sec-1-2"><span class="section-number-3">1.2</span> Source code editing</h3>
<div class="outline-text-3" id="text-1-2">
<p>
Any text editor can be used to edit org-mode files. For a better
user experience Emacs is recommended.
For users hating Emacs, it is good to know that Emacs can behave
like Vim when switched into ``Evil'' mode. There also exists
<a href="https://www.spacemacs.org">Spacemacs</a> which helps the transition for Vim users.
</p>
<p>
For users with a preference for Jupyter notebooks, the following
script can convert jupyter notebooks to org-mode files:
</p>
<div class="org-src-container">
<pre class="src src-"nb_to_org.sh"lang"nb_to_org.sh"switches"nb_to_org.sh"flags">"nb_to_org.sh"body
</pre>
</div>
<p>
And pandoc can convert multiple markdown formats into org-mode.
</p>
</div>
</div>
<div id="outline-container-sec-1-3" class="outline-3">
<h3 id="sec-1-3"><span class="section-number-3">1.3</span> Writing in Fortran</h3>
<div class="outline-text-3" id="text-1-3">
<p>
The Fortran source files should provide a C interface using
<code>iso_c_binding</code>. The name of the Fortran source files should end
with <code>_f.f90</code> to be properly handled by the Makefile.
The names of the functions defined in fortran should be the same as
those exposed in the API suffixed by <code>_f</code>.
Fortran interface files should also be written in a file with a
<code>.fh</code> extension.
</p>
</div>
</div>
<div id="outline-container-sec-1-4" class="outline-3">
<h3 id="sec-1-4"><span class="section-number-3">1.4</span> Coding style</h3>
<div class="outline-text-3" id="text-1-4">
<p>
To improve readability, we maintain a consistent coding style in the library.
</p>
<ul class="org-ul">
<li>For C source files, we will use <span class="underline"><span class="underline">(decide on a coding style)</span></span>
</li>
<li>For Fortran source files, we will use <span class="underline"><span class="underline">(decide on a coding style)</span></span>
</li>
</ul>
<p>
Coding style can be automatically checked with <a href="https://clang.llvm.org/docs/ClangFormat.html">clang-format</a>.
</p>
</div>
</div>
</div>
<div id="outline-container-sec-2" class="outline-2">
<h2 id="sec-2"><span class="section-number-2">2</span> Design of the library</h2>
<div class="outline-text-2" id="text-2">
<p>
The proposed API should allow the library to:
</p>
<ul class="org-ul">
<li>deal with memory transfers between CPU and accelerators
</li>
<li>use different levels of floating-point precision
</li>
</ul>
<p>
We chose a multi-layered design with low-level and high-level
functions (see below).
</p>
</div>
<div id="outline-container-sec-2-1" class="outline-3">
<h3 id="sec-2-1"><span class="section-number-3">2.1</span> Naming conventions</h3>
<div class="outline-text-3" id="text-2-1">
<p>
Use <code>qmckl_</code> as a prefix for all exported functions and variables.
All exported header files should have a filename with the prefix
<code>qmckl_</code>.
</p>
<p>
If the name of the org-mode file is <code>xxx.org</code>, the name of the
produced C files should be <code>xxx.c</code> and <code>xxx.h</code> and the name of the
produced Fortran files should be <code>xxx.f90</code>
</p>
<p>
Arrays are in uppercase and scalars are in lowercase.
</p>
</div>
</div>
<div id="outline-container-sec-2-2" class="outline-3">
<h3 id="sec-2-2"><span class="section-number-3">2.2</span> Application programming interface</h3>
<div class="outline-text-3" id="text-2-2">
<p>
The application programming interface (API) is designed to be
compatible with the C programming language (not C++), to ensure
that the library will be easily usable in any language.
This implies that only the following data types are allowed in the API:
</p>
<ul class="org-ul">
<li>32-bit and 64-bit floats and arrays (<code>real</code> and <code>double</code>)
</li>
<li>32-bit and 64-bit integers and arrays (<code>int32_t</code> and <code>int64_t</code>)
</li>
<li>Pointers should be represented as 64-bit integers (even on
32-bit architectures)
</li>
<li>ASCII strings are represented as a pointers to a character arrays
and terminated by a zero character (C convention).
</li>
</ul>
<p>
To facilitate the use in other languages than C, we provide some
bindings in other languages in other repositories.
</p>
</div>
</div>
<div id="outline-container-sec-2-3" class="outline-3">
<h3 id="sec-2-3"><span class="section-number-3">2.3</span> Global state</h3>
<div class="outline-text-3" id="text-2-3">
<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
<code>context</code> variable, built by the library with the
<code>qmckl_context_create</code> function. The <code>context</code> contains the global
state of the library, and is used as the first argument of many
QMCkl functions.
</p>
<p>
Modifying the state is done by setters and getters, prefixed
by <code>qmckl_context_set_</code> an <code>qmckl_context_get_</code>.
When a context variable is modified by a setter, a copy of the old
data structure is made and updated, and the pointer to the new data
structure is returned, such that the old contexts can still be
accessed.
It is also possible to modify the state in an impure fashion, using
the <code>qmckl_context_update_</code> functions.
The context and its old versions can be destroyed with
<code>qmckl_context_destroy</code>.
</p>
</div>
</div>
<div id="outline-container-sec-2-4" class="outline-3">
<h3 id="sec-2-4"><span class="section-number-3">2.4</span> Low-level functions</h3>
<div class="outline-text-3" id="text-2-4">
<p>
Low-level functions are very simple functions which are leaves of the
function call tree (they don't call any other QMCkl function).
</p>
<p>
This functions are <i>pure</i>, and unaware of the QMCkl <code>context</code>. 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-sec-2-5" class="outline-3">
<h3 id="sec-2-5"><span class="section-number-3">2.5</span> High-level functions</h3>
<div class="outline-text-3" id="text-2-5">
<p>
High-level functions are at the top of the function call tree.
They are able to choose which lower-level function to call
depending on the required precision, and do the corresponding type
conversions.
These functions are also responsible for allocating temporary
storage, to simplify the use of accelerators.
</p>
<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
<code>context</code> variable.
</p>
</div>
</div>
<div id="outline-container-sec-2-6" class="outline-3">
<h3 id="sec-2-6"><span class="section-number-3">2.6</span> Numerical precision</h3>
<div class="outline-text-3" id="text-2-6">
<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
<code>context</code> variable.
</p>
</div>
</div>
</div>
<div id="outline-container-sec-3" class="outline-2">
<h2 id="sec-3"><span class="section-number-2">3</span> Algorithms</h2>
<div class="outline-text-2" id="text-3">
<p>
Reducing the scaling of an algorithm usually implies also reducing
its arithmetic complexity (number of flops per byte). Therefore,
for small sizes \(\mathcal{O}(N^3)\) and \(\mathcal{O}(N^2)\) algorithms
are better adapted than linear scaling algorithms.
As QMCkl is a general purpose library, multiple algorithms should
be implemented adapted to different problem sizes.
</p>
</div>
</div>
<div id="outline-container-sec-4" class="outline-2">
<h2 id="sec-4"><span class="section-number-2">4</span> Rules for the API</h2>
<div class="outline-text-2" id="text-4">
<ul class="org-ul">
<li><code>stdint</code> should be used for integers (<code>int32_t</code>, <code>int64_t</code>)
</li>
<li>integers used for counting should always be <code>int64_t</code>
</li>
<li>floats should be by default <code>double</code>, unless explicitly mentioned
</li>
<li>pointers are converted to <code>int64_t</code> to increase portability
</li>
</ul>
</div>
</div>
<div id="outline-container-sec-5" class="outline-2">
<h2 id="sec-5"><span class="section-number-2">5</span> Documentation</h2>
<div class="outline-text-2" id="text-5">
<ul class="org-ul">
<li><a href="./qmckl.html">Main QMCkl header file</a>
</li>
<li><a href="./qmckl_memory.html">Memory management</a>
</li>
<li><a href="./qmckl_context.html">Context</a>
</li>
<li><a href="./qmckl_distance.html">Distance</a>
</li>
<li><a href="./qmckl_ao.html">Atomic orbitals</a>
</li>
</ul>
</div>
</div>
<div id="outline-container-sec-6" class="outline-2">
<h2 id="sec-6"><span class="section-number-2">6</span> Acknowledgments</h2>
<div class="outline-text-2" id="text-6">
<p>
<img src="https://trex-coe.eu/sites/default/files/inline-images/euflag.jpg" alt="euflag.jpg" />
<a href="https://trex-coe.eu">TREX: Targeting Real Chemical Accuracy at the Exascale</a> project has received funding from the European Union’s Horizon 2020 - Research and Innovation program - under grant agreement no. 952165. The content of this document does not represent the opinion of the European Union, and the European Union is not responsible for any use that might be made of such content.
</p>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="date">Created: 2020-10-28 Wed 23:57</p>
<p class="creator"><a href="http://www.gnu.org/software/emacs/">Emacs</a> 25.2.2 (<a href="http://orgmode.org">Org</a> mode 8.2.10)</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>
</html>

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# QMCkl: Quantum Monte Carlo Kernel Library
![Build Status](https://github.com/TREX-CoE/qmckl/workflows/test-build/badge.svg?branch=main)
The domain of quantum chemistry needs a library in which the main
kernels of Quantum Monte Carlo (QMC) methods are implemented. In the
library proposed in this project, we expose the main algorithms in a
simple language and provide a standard API and tests to enable the
development of high-performance QMCkl implementations taking
advantage of modern hardware.
See the [source code](https://github.com/TREX-CoE/qmckl/tree/main/src)
to read the documentation.
To clone the repository, use:
```
git clone --recursive https://github.com/TREX-CoE/qmckl.git
```
to dowload also the [munit](https://github.com/nemequ/munit) unit testing
framework.
------------------------------
![European flag](https://trex-coe.eu/sites/default/files/inline-images/euflag.jpg)
[TREX: Targeting Real Chemical Accuracy at the Exascale](https://trex-coe.eu) project has received funding from the European Union’s Horizon 2020 - Research and Innovation program - under grant agreement no. 952165. The content of this document does not represent the opinion of the European Union, and the European Union is not responsible for any use that might be made of such content.

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* Set up CI on Travis
* Write tests
* malloc/free : Parameters for accelerators?
We should define qmckl_malloc and qmckl_free just to give the
possibility of the HPC implementations to define how they allocate the
memory (on CPU or GPU, using alternatives to malloc/free, etc).
A possibility could be to pass the id of a NUMA domain as a parameter of
qmckl_malloc, where the domain id is something obtained from the
context.
* TRANSA, TRANSB
* Performance info
* Benchmark interpolation of basis functions
* Complex numbers
* Adjustable number for derivatives (1,2,3)

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Subproject commit fbbdf1467eb0d04a6ee465def2e529e4c87f2118

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<h1 class="title">QMCkl C header</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#sec-1">1. Constants</a>
<ul>
<li><a href="#sec-1-1">1.1. Success/failure</a></li>
<li><a href="#sec-1-2">1.2. Precision-related constants</a></li>
</ul>
</li>
<li><a href="#sec-2">2. Header files</a></li>
<li><a href="#sec-3">3. End of header</a></li>
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<p>
This file produces the <code>qmckl.h</code> header file, which is included in all
other C header files. It is the main entry point to the library.
</p>
<div class="org-src-container">
<pre class="src src-C">#ifndef QMCKL_H
#define QMCKL_H
#include &lt;stdlib.h&gt;
#include &lt;stdint.h&gt;
</pre>
</div>
<div id="outline-container-sec-1" class="outline-2">
<h2 id="sec-1"><span class="section-number-2">1</span> Constants</h2>
<div class="outline-text-2" id="text-1">
</div><div id="outline-container-sec-1-1" class="outline-3">
<h3 id="sec-1-1"><span class="section-number-3">1.1</span> Success/failure</h3>
<div class="outline-text-3" id="text-1-1">
<p>
These are the codes returned by the functions to indicate success
or failure. All such functions should have as a return type <code>qmckl_exit_code</code>.
</p>
<div class="org-src-container">
<pre class="src src-C">#define QMCKL_SUCCESS 0
#define QMCKL_FAILURE 1
typedef int32_t qmckl_exit_code;
typedef int64_t qmckl_context ;
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-1-2" class="outline-3">
<h3 id="sec-1-2"><span class="section-number-3">1.2</span> Precision-related constants</h3>
<div class="outline-text-3" id="text-1-2">
<p>
Controlling numerical precision enables optimizations. Here, the
default parameters determining the target numerical precision and
range are defined.
</p>
<div class="org-src-container">
<pre class="src src-C">#define QMCKL_DEFAULT_PRECISION 53
#define QMCKL_DEFAULT_RANGE 11
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-2" class="outline-2">
<h2 id="sec-2"><span class="section-number-2">2</span> Header files</h2>
<div class="outline-text-2" id="text-2">
<p>
All the functions expoed in the API are defined in the following
header files.
</p>
<div class="org-src-container">
<pre class="src src-C">#include "qmckl_memory.h"
#include "qmckl_context.h"
#include "qmckl_distance.h"
#include "qmckl_ao.h"
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-3" class="outline-2">
<h2 id="sec-3"><span class="section-number-2">3</span> End of header</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-C">#endif
</pre>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="date">Created: 2020-10-28 Wed 23:57</p>
<p class="creator"><a href="http://www.gnu.org/software/emacs/">Emacs</a> 25.2.2 (<a href="http://orgmode.org">Org</a> mode 8.2.10)</p>
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<head>
<title>Atomic Orbitals</title>
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<h1 class="title">Atomic Orbitals</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#sec-1">1. Polynomials</a>
<ul>
<li><a href="#sec-1-1">1.1. <code>qmckl_ao_powers</code></a>
<ul>
<li><a href="#sec-1-1-1">1.1.1. Arguments</a></li>
<li><a href="#sec-1-1-2">1.1.2. Requirements</a></li>
<li><a href="#sec-1-1-3">1.1.3. Header</a></li>
<li><a href="#sec-1-1-4">1.1.4. Source</a></li>
</ul>
</li>
<li><a href="#sec-1-2">1.2. <code>qmckl_ao_polynomial_vgl</code></a>
<ul>
<li><a href="#sec-1-2-1">1.2.1. Arguments</a></li>
<li><a href="#sec-1-2-2">1.2.2. Requirements</a></li>
<li><a href="#sec-1-2-3">1.2.3. Header</a></li>
<li><a href="#sec-1-2-4">1.2.4. Source</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#sec-2">2. <span class="todo TODO">TODO</span> Gaussian basis functions</a></li>
<li><a href="#sec-3">3. <span class="todo TODO">TODO</span> Slater basis functions</a></li>
</ul>
</div>
</div>
<p>
This files contains all the routines for the computation of the
values, gradients and Laplacian of the atomic basis functions.
</p>
<p>
4 files are produced:
</p>
<ul class="org-ul">
<li>a header file : <code>qmckl_ao.h</code>
</li>
<li>a source file : <code>qmckl_ao.f90</code>
</li>
<li>a C test file : <code>test_qmckl_ao.c</code>
</li>
<li>a Fortran test file : <code>test_qmckl_ao_f.f90</code>
</li>
</ul>
<div id="outline-container-sec-1" class="outline-2">
<h2 id="sec-1"><span class="section-number-2">1</span> Polynomials</h2>
<div class="outline-text-2" id="text-1">
<p>
\[
P_l(\mathbf{r},\mathbf{R}_i) = (x-X_i)^a (y-Y_i)^b (z-Z_i)^c
\]
</p>
\begin{eqnarray*}
\frac{\partial }{\partial x} P_l\left(\mathbf{r},\mathbf{R}_i \right) & = & a (x-X_i)^{a-1} (y-Y_i)^b (z-Z_i)^c \\
\frac{\partial }{\partial y} P_l\left(\mathbf{r},\mathbf{R}_i \right) & = & b (x-X_i)^a (y-Y_i)^{b-1} (z-Z_i)^c \\
\frac{\partial }{\partial z} P_l\left(\mathbf{r},\mathbf{R}_i \right) & = & c (x-X_i)^a (y-Y_i)^b (z-Z_i)^{c-1} \\
\end{eqnarray*}
\begin{eqnarray*}
\left( \frac{\partial }{\partial x^2} +
\frac{\partial }{\partial y^2} +
\frac{\partial }{\partial z^2} \right) P_l
\left(\mathbf{r},\mathbf{R}_i \right) & = &
a(a-1) (x-X_i)^{a-2} (y-Y_i)^b (z-Z_i)^c + \\
&& b(b-1) (x-X_i)^a (y-Y_i)^{b-1} (z-Z_i)^c + \\
&& c(c-1) (x-X_i)^a (y-Y_i)^b (z-Z_i)^{c-1}
\end{eqnarray*}
</div>
<div id="outline-container-sec-1-1" class="outline-3">
<h3 id="sec-1-1"><span class="section-number-3">1.1</span> <code>qmckl_ao_powers</code></h3>
<div class="outline-text-3" id="text-1-1">
<p>
Computes all the powers of the <code>n</code> input data up to the given
maximum value given in input for each of the \(n\) points:
</p>
<p>
\[ P_{ij} = X_j^i \]
</p>
</div>
<div id="outline-container-sec-1-1-1" class="outline-4">
<h4 id="sec-1-1-1"><span class="section-number-4">1.1.1</span> Arguments</h4>
<div class="outline-text-4" id="text-1-1-1">
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="left" />
<col class="left" />
<col class="left" />
</colgroup>
<tbody>
<tr>
<td class="left"><code>context</code></td>
<td class="left">input</td>
<td class="left">Global state</td>
</tr>
<tr>
<td class="left"><code>n</code></td>
<td class="left">input</td>
<td class="left">Number of values</td>
</tr>
<tr>
<td class="left"><code>X(n)</code></td>
<td class="left">input</td>
<td class="left">Array containing the input values</td>
</tr>
<tr>
<td class="left"><code>LMAX(n)</code></td>
<td class="left">input</td>
<td class="left">Array containing the maximum power for each value</td>
</tr>
<tr>
<td class="left"><code>P(LDP,n)</code></td>
<td class="left">output</td>
<td class="left">Array containing all the powers of <code>X</code></td>
</tr>
<tr>
<td class="left"><code>LDP</code></td>
<td class="left">input</td>
<td class="left">Leading dimension of array <code>P</code></td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-sec-1-1-2" class="outline-4">
<h4 id="sec-1-1-2"><span class="section-number-4">1.1.2</span> Requirements</h4>
<div class="outline-text-4" id="text-1-1-2">
<ul class="org-ul">
<li><code>context</code> is not 0
</li>
<li><code>n</code> &gt; 0
</li>
<li><code>X</code> is allocated with at least \(n \times 8\) bytes
</li>
<li><code>LMAX</code> is allocated with at least \(n \times 4\) bytes
</li>
<li><code>P</code> is allocated with at least \(n \times \max_i \text{LMAX}_i \times 8\) bytes
</li>
<li><code>LDP</code> &gt;= \(\max_i\) <code>LMAX[i]</code>
</li>
</ul>
</div>
</div>
<div id="outline-container-sec-1-1-3" class="outline-4">
<h4 id="sec-1-1-3"><span class="section-number-4">1.1.3</span> Header</h4>
<div class="outline-text-4" id="text-1-1-3">
<div class="org-src-container">
<pre class="src src-C">qmckl_exit_code qmckl_ao_powers(qmckl_context context,
int64_t n,
double *X, int32_t *LMAX,
double *P, int64_t LDP);
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-1-1-4" class="outline-4">
<h4 id="sec-1-1-4"><span class="section-number-4">1.1.4</span> Source</h4>
<div class="outline-text-4" id="text-1-1-4">
<div class="org-src-container">
<pre class="src src-f90">integer function qmckl_ao_powers_f(context, n, X, LMAX, P, ldp) result(info)
implicit none
integer*8 , intent(in) :: context
integer*8 , intent(in) :: n
real*8 , intent(in) :: X(n)
integer , intent(in) :: LMAX(n)
real*8 , intent(out) :: P(ldp,n)
integer*8 , intent(in) :: ldp
integer*8 :: i,j
info = 0
if (context == 0_8) then
info = -1
return
endif
if (LDP &lt; MAXVAL(LMAX)) then
info = -2
return
endif
do j=1,n
P(1,j) = X(j)
do i=2,LMAX(j)
P(i,j) = P(i-1,j) * X(j)
end do
end do
end function qmckl_ao_powers_f
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-1-2" class="outline-3">
<h3 id="sec-1-2"><span class="section-number-3">1.2</span> <code>qmckl_ao_polynomial_vgl</code></h3>
<div class="outline-text-3" id="text-1-2">
<p>
Computes the values, gradients and Laplacians at a given point of
all polynomials with an angular momentum up to <code>lmax</code>.
</p>
</div>
<div id="outline-container-sec-1-2-1" class="outline-4">
<h4 id="sec-1-2-1"><span class="section-number-4">1.2.1</span> Arguments</h4>
<div class="outline-text-4" id="text-1-2-1">
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="left" />
<col class="left" />
<col class="left" />
</colgroup>
<tbody>
<tr>
<td class="left"><code>context</code></td>
<td class="left">input</td>
<td class="left">Global state</td>
</tr>
<tr>
<td class="left"><code>X(3)</code></td>
<td class="left">input</td>
<td class="left">Array containing the coordinates of the points</td>
</tr>
<tr>
<td class="left"><code>R(3)</code></td>
<td class="left">input</td>
<td class="left">Array containing the x,y,z coordinates of the center</td>
</tr>
<tr>
<td class="left"><code>lmax</code></td>
<td class="left">input</td>
<td class="left">Maximum angular momentum</td>
</tr>
<tr>
<td class="left"><code>n</code></td>
<td class="left">output</td>
<td class="left">Number of computed polynomials</td>
</tr>
<tr>
<td class="left"><code>L(ldl,n)</code></td>
<td class="left">output</td>
<td class="left">Contains a,b,c for all <code>n</code> results</td>
</tr>
<tr>
<td class="left"><code>ldl</code></td>
<td class="left">input</td>
<td class="left">Leading dimension of <code>L</code></td>
</tr>
<tr>
<td class="left"><code>VGL(ldv,n)</code></td>
<td class="left">output</td>
<td class="left">Value, gradients and Laplacian of the polynomials</td>
</tr>
<tr>
<td class="left"><code>ldv</code></td>
<td class="left">input</td>
<td class="left">Leading dimension of array <code>VGL</code></td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-sec-1-2-2" class="outline-4">
<h4 id="sec-1-2-2"><span class="section-number-4">1.2.2</span> Requirements</h4>
<div class="outline-text-4" id="text-1-2-2">
<ul class="org-ul">
<li><code>context</code> is not 0
</li>
<li><code>n</code> &gt; 0
</li>
<li><code>X</code> is allocated with at least \(3 \times 8\) bytes
</li>
<li><code>R</code> is allocated with at least \(3 \times 8\) bytes
</li>
<li><code>lmax</code> &gt;= 0
</li>
<li>On output, <code>n</code> should be equal to (=lmax=+1)(=lmax=+2)(=lmax=+3)/6
</li>
<li><code>L</code> is allocated with at least \(3 \times n \times 4\) bytes
</li>
<li><code>ldl</code> &gt;= 3
</li>
<li><code>VGL</code> is allocated with at least \(5 \times n \times 8\) bytes
</li>
<li><code>ldv</code> &gt;= 5
</li>
</ul>
</div>
</div>
<div id="outline-container-sec-1-2-3" class="outline-4">
<h4 id="sec-1-2-3"><span class="section-number-4">1.2.3</span> Header</h4>
<div class="outline-text-4" id="text-1-2-3">
<div class="org-src-container">
<pre class="src src-C">qmckl_exit_code qmckl_ao_polynomial_vgl(qmckl_context context,
double *X, double *R,
int32_t lmax, int64_t *n,
int32_t *L, int64_t ldl,
double *VGL, int64_t ldv);
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-1-2-4" class="outline-4">
<h4 id="sec-1-2-4"><span class="section-number-4">1.2.4</span> Source</h4>
<div class="outline-text-4" id="text-1-2-4">
<div class="org-src-container">
<pre class="src src-f90">integer function qmckl_ao_polynomial_vgl_f(context, X, R, lmax, n, L, ldl, VGL, ldv) result(info)
implicit none
integer*8 , intent(in) :: context
real*8 , intent(in) :: X(3), R(3)
integer , intent(in) :: lmax
integer*8 , intent(out) :: n
integer , intent(out) :: L(ldl,(lmax+1)*(lmax+2)*(lmax+3)/6)
integer*8 , intent(in) :: ldl
real*8 , intent(out) :: VGL(ldv,(lmax+1)*(lmax+2)*(lmax+3)/6)
integer*8 , intent(in) :: ldv
integer*8 :: i,j
integer :: a,b,c,d
real*8 :: Y(3)
integer :: lmax_array(3)
real*8 :: pows(-2:lmax,3)
integer, external :: qmckl_ao_powers_f
double precision :: xy, yz, xz
double precision :: da, db, dc, dd
info = 0
if (context == 0_8) then
info = -1
return
endif
n = (lmax+1)*(lmax+2)*(lmax+3)/6
if (ldl &lt; 3) then
info = -2
return
endif
if (ldv &lt; 5) then
info = -3
return
endif
do i=1,3
Y(i) = X(i) - R(i)
end do
pows(-2:-1,1:3) = 0.d0
pows(0,1:3) = 1.d0
lmax_array(1:3) = lmax
info = qmckl_ao_powers_f(context, 1_8, Y(1), (/lmax/), pows(1,1), size(pows,1,kind=8))
if (info /= 0) return
info = qmckl_ao_powers_f(context, 1_8, Y(2), (/lmax/), pows(1,2), size(pows,1,kind=8))
if (info /= 0) return
info = qmckl_ao_powers_f(context, 1_8, Y(3), (/lmax/), pows(1,3), size(pows,1,kind=8))
if (info /= 0) return
n=1
vgl(1:5,1:n) = 0.d0
l(1:3,n) = 0
vgl(1,n) = 1.d0
dd = 1.d0
do d=1,lmax
da = 0.d0
do a=0,d
db = 0.d0
do b=0,d-a
c = d - a - b
dc = dd - da - db
n = n+1
l(1,n) = a
l(2,n) = b
l(3,n) = c
xy = pows(a,1) * pows(b,2)
yz = pows(b,2) * pows(c,3)
xz = pows(a,1) * pows(c,3)
vgl(1,n) = xy * pows(c,3)
xy = dc * xy
xz = db * xz
yz = da * yz
vgl(2,n) = pows(a-1,1) * yz
vgl(3,n) = pows(b-1,2) * xz
vgl(4,n) = pows(c-1,3) * xy
vgl(5,n) = &amp;
(da-1.d0) * pows(a-2,1) * yz + &amp;
(db-1.d0) * pows(b-2,2) * xz + &amp;
(dc-1.d0) * pows(c-2,3) * xy
db = db + 1.d0
end do
da = da + 1.d0
end do
dd = dd + 1.d0
end do
end function qmckl_ao_polynomial_vgl_f
</pre>
</div>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-2" class="outline-2">
<h2 id="sec-2"><span class="section-number-2">2</span> <span class="todo TODO">TODO</span> Gaussian basis functions</h2>
</div>
<div id="outline-container-sec-3" class="outline-2">
<h2 id="sec-3"><span class="section-number-2">3</span> <span class="todo TODO">TODO</span> Slater basis functions</h2>
</div>
</div>
<div id="postamble" class="status">
<p class="date">Created: 2020-10-28 Wed 23:57</p>
<p class="creator"><a href="http://www.gnu.org/software/emacs/">Emacs</a> 25.2.2 (<a href="http://orgmode.org">Org</a> mode 8.2.10)</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<body>
<div id="content">
<h1 class="title">Context</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#sec-1">1. Context</a>
<ul>
<li>
<ul>
<li><a href="#sec-1-0-1">1.0.1. Source</a></li>
</ul>
</li>
<li><a href="#sec-1-1">1.1. <code>qmckl_context_check</code></a>
<ul>
<li><a href="#sec-1-1-1">1.1.1. Header</a></li>
<li><a href="#sec-1-1-2">1.1.2. Source</a></li>
</ul>
</li>
<li><a href="#sec-1-2">1.2. <code>qmckl_context_create</code></a>
<ul>
<li><a href="#sec-1-2-1">1.2.1. Header</a></li>
<li><a href="#sec-1-2-2">1.2.2. Source</a></li>
</ul>
</li>
<li><a href="#sec-1-3">1.3. <code>qmckl_context_copy</code></a>
<ul>
<li><a href="#sec-1-3-1">1.3.1. Header</a></li>
<li><a href="#sec-1-3-2">1.3.2. Source</a></li>
</ul>
</li>
<li><a href="#sec-1-4">1.4. <code>qmckl_context_previous</code></a>
<ul>
<li><a href="#sec-1-4-1">1.4.1. Header</a></li>
<li><a href="#sec-1-4-2">1.4.2. Source</a></li>
</ul>
</li>
<li><a href="#sec-1-5">1.5. <code>qmckl_context_destroy</code></a>
<ul>
<li><a href="#sec-1-5-1">1.5.1. Header</a></li>
<li><a href="#sec-1-5-2">1.5.2. Source</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#sec-2">2. Precision</a>
<ul>
<li><a href="#sec-2-1">2.1. <code>qmckl_context_update_precision</code></a>
<ul>
<li><a href="#sec-2-1-1">2.1.1. Source</a></li>
</ul>
</li>
<li><a href="#sec-2-2">2.2. <code>qmckl_context_update_range</code></a>
<ul>
<li><a href="#sec-2-2-1">2.2.1. Source</a></li>
</ul>
</li>
<li><a href="#sec-2-3">2.3. <code>qmckl_context_set_precision</code></a>
<ul>
<li><a href="#sec-2-3-1">2.3.1. Source</a></li>
</ul>
</li>
<li><a href="#sec-2-4">2.4. <code>qmckl_context_set_range</code></a>
<ul>
<li><a href="#sec-2-4-1">2.4.1. Source</a></li>
</ul>
</li>
<li><a href="#sec-2-5">2.5. <code>qmckl_context_get_precision</code></a>
<ul>
<li><a href="#sec-2-5-1">2.5.1. Source</a></li>
</ul>
</li>
<li><a href="#sec-2-6">2.6. <code>qmckl_context_get_range</code></a>
<ul>
<li><a href="#sec-2-6-1">2.6.1. Source</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
</div>
<p>
This file is written in C because it is more natural to express the context in
C than in Fortran.
</p>
<p>
3 files are produced:
</p>
<ul class="org-ul">
<li>a header file : <code>qmckl_context.h</code>
</li>
<li>a source file : <code>qmckl_context.c</code>
</li>
<li>a test file : <code>test_qmckl_context.c</code>
</li>
</ul>
<div id="outline-container-sec-1" class="outline-2">
<h2 id="sec-1"><span class="section-number-2">1</span> Context</h2>
<div class="outline-text-2" id="text-1">
<p>
The context variable is a handle for the state of the library, and
is stored in the following data structure, which can't be seen
outside of the library. To simplify compatibility with other
languages, the pointer to the internal data structure is converted
into a 64-bit signed integer, defined in the <code>qmckl_context</code> type.
A value of 0 for the context is equivalent to a <code>NULL</code> pointer.
</p>
</div>
<div id="outline-container-sec-1-0-1" class="outline-4">
<h4 id="sec-1-0-1"><span class="section-number-4">1.0.1</span> Source</h4>
<div class="outline-text-4" id="text-1-0-1">
<div class="org-src-container">
<pre class="src src-C">typedef struct qmckl_context_struct {
struct qmckl_context_struct * prev;
uint32_t tag;
int32_t precision;
int32_t range;
} qmckl_context_struct;
#define VALID_TAG 0xBEEFFACE
#define INVALID_TAG 0xDEADBEEF
</pre>
</div>
<p>
The tag is used internally to check if the memory domain pointed by
a pointer is a valid context.
</p>
</div>
</div>
<div id="outline-container-sec-1-1" class="outline-3">
<h3 id="sec-1-1"><span class="section-number-3">1.1</span> <code>qmckl_context_check</code></h3>
<div class="outline-text-3" id="text-1-1">
<p>
Checks if the domain pointed by the pointer is a valid context.
Returns the input <code>qmckl_context</code> if the context is valid, 0 otherwise.
</p>
</div>
<div id="outline-container-sec-1-1-1" class="outline-4">
<h4 id="sec-1-1-1"><span class="section-number-4">1.1.1</span> Header</h4>
<div class="outline-text-4" id="text-1-1-1">
<div class="org-src-container">
<pre class="src src-C">qmckl_context qmckl_context_check(const qmckl_context context) ;
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-1-1-2" class="outline-4">
<h4 id="sec-1-1-2"><span class="section-number-4">1.1.2</span> Source</h4>
<div class="outline-text-4" id="text-1-1-2">
<div class="org-src-container">
<pre class="src src-C">qmckl_context qmckl_context_check(const qmckl_context context) {
qmckl_context_struct * ctx;
if (context == (qmckl_context) 0) return (qmckl_context) 0;
ctx = (qmckl_context_struct*) context;
if (ctx-&gt;tag != VALID_TAG) return (qmckl_context) 0;
return context;
}
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-1-2" class="outline-3">
<h3 id="sec-1-2"><span class="section-number-3">1.2</span> <code>qmckl_context_create</code></h3>
<div class="outline-text-3" id="text-1-2">
<p>
To create a new context, use <code>qmckl_context_create()</code>.
</p>
<ul class="org-ul">
<li>On success, returns a pointer to a context using the <code>qmckl_context</code> type
</li>
<li>Returns 0 upon failure to allocate the internal data structure
</li>
</ul>
</div>
<div id="outline-container-sec-1-2-1" class="outline-4">
<h4 id="sec-1-2-1"><span class="section-number-4">1.2.1</span> Header</h4>
<div class="outline-text-4" id="text-1-2-1">
<div class="org-src-container">
<pre class="src src-C">qmckl_context qmckl_context_create();
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-1-2-2" class="outline-4">
<h4 id="sec-1-2-2"><span class="section-number-4">1.2.2</span> Source</h4>
<div class="outline-text-4" id="text-1-2-2">
<div class="org-src-container">
<pre class="src src-C">qmckl_context qmckl_context_create() {
qmckl_context_struct* context;
context = (qmckl_context_struct*) qmckl_malloc ((qmckl_context) 0, sizeof(qmckl_context_struct));
if (context == NULL) {
return (qmckl_context) 0;
}
context-&gt;prev = NULL;
context-&gt;precision = QMCKL_DEFAULT_PRECISION;
context-&gt;range = QMCKL_DEFAULT_RANGE;
context-&gt;tag = VALID_TAG;
return (qmckl_context) context;
}
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-1-3" class="outline-3">
<h3 id="sec-1-3"><span class="section-number-3">1.3</span> <code>qmckl_context_copy</code></h3>
<div class="outline-text-3" id="text-1-3">
<p>
This function makes a shallow copy of the current context.
</p>
<ul class="org-ul">
<li>Copying the 0-valued context returns 0
</li>
<li>On success, returns a pointer to the new context using the <code>qmckl_context</code> type
</li>
<li>Returns 0 upon failure to allocate the internal data structure
for the new context
</li>
</ul>
</div>
<div id="outline-container-sec-1-3-1" class="outline-4">
<h4 id="sec-1-3-1"><span class="section-number-4">1.3.1</span> Header</h4>
<div class="outline-text-4" id="text-1-3-1">
<div class="org-src-container">
<pre class="src src-C">qmckl_context qmckl_context_copy(const qmckl_context context);
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-1-3-2" class="outline-4">
<h4 id="sec-1-3-2"><span class="section-number-4">1.3.2</span> Source</h4>
<div class="outline-text-4" id="text-1-3-2">
<div class="org-src-container">
<pre class="src src-C">qmckl_context qmckl_context_copy(const qmckl_context context) {
qmckl_context_struct* old_context;
qmckl_context_struct* new_context;
qmckl_context checked_context;
checked_context = qmckl_context_check(context);
if (checked_context == (qmckl_context) 0) {
return (qmckl_context) 0;
}
new_context = (qmckl_context_struct*) qmckl_malloc (context, sizeof(qmckl_context_struct));
if (new_context == NULL) {
return (qmckl_context) 0;
}
old_context = (qmckl_context_struct*) checked_context;
new_context-&gt;prev = old_context;
new_context-&gt;precision = old_context-&gt;precision;
new_context-&gt;range = old_context-&gt;range;
new_context-&gt;tag = VALID_TAG;
return (qmckl_context) new_context;
}
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-1-4" class="outline-3">
<h3 id="sec-1-4"><span class="section-number-3">1.4</span> <code>qmckl_context_previous</code></h3>
<div class="outline-text-3" id="text-1-4">
<p>
Returns the previous context
</p>
<ul class="org-ul">
<li>On success, returns the ancestor of the current context
</li>
<li>Returns 0 for the initial context
</li>
<li>Returns 0 for the 0-valued context
</li>
</ul>
</div>
<div id="outline-container-sec-1-4-1" class="outline-4">
<h4 id="sec-1-4-1"><span class="section-number-4">1.4.1</span> Header</h4>
<div class="outline-text-4" id="text-1-4-1">
<div class="org-src-container">
<pre class="src src-C">qmckl_context qmckl_context_previous(const qmckl_context context);
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-1-4-2" class="outline-4">
<h4 id="sec-1-4-2"><span class="section-number-4">1.4.2</span> Source</h4>
<div class="outline-text-4" id="text-1-4-2">
<div class="org-src-container">
<pre class="src src-C">qmckl_context qmckl_context_previous(const qmckl_context context) {
qmckl_context checked_context;
qmckl_context_struct* ctx;
checked_context = qmckl_context_check(context);
if (checked_context == (qmckl_context) 0) {
return (qmckl_context) 0;
}
ctx = (qmckl_context_struct*) checked_context;
return qmckl_context_check((qmckl_context) ctx-&gt;prev);
}
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-1-5" class="outline-3">
<h3 id="sec-1-5"><span class="section-number-3">1.5</span> <code>qmckl_context_destroy</code></h3>
<div class="outline-text-3" id="text-1-5">
<p>
Destroys the current context, leaving the ancestors untouched.
</p>
<ul class="org-ul">
<li>Succeeds if the current context is properly destroyed
</li>
<li>Fails otherwise
</li>
<li>Fails if the 0-valued context is given in argument
</li>
<li>Fails if the the pointer is not a valid context
</li>
</ul>
</div>
<div id="outline-container-sec-1-5-1" class="outline-4">
<h4 id="sec-1-5-1"><span class="section-number-4">1.5.1</span> Header</h4>
<div class="outline-text-4" id="text-1-5-1">
<div class="org-src-container">
<pre class="src src-C">qmckl_exit_code qmckl_context_destroy(qmckl_context context);
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-1-5-2" class="outline-4">
<h4 id="sec-1-5-2"><span class="section-number-4">1.5.2</span> Source</h4>
<div class="outline-text-4" id="text-1-5-2">
<div class="org-src-container">
<pre class="src src-C">qmckl_exit_code qmckl_context_destroy(qmckl_context context) {
qmckl_context_struct* ctx;
qmckl_context checked_context;
checked_context = qmckl_context_check(context);
if (checked_context == (qmckl_context) 0) return QMCKL_FAILURE;
ctx = (qmckl_context_struct*) context;
if (ctx == NULL) return QMCKL_FAILURE;
ctx-&gt;tag = INVALID_TAG;
qmckl_free(ctx);
return QMCKL_SUCCESS;
}
</pre>
</div>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-2" class="outline-2">
<h2 id="sec-2"><span class="section-number-2">2</span> Precision</h2>
<div class="outline-text-2" id="text-2">
<p>
The following functions set and get the expected required precision
and range. <code>precision</code> should be an integer between 2 and 53, and
<code>range</code> should be an integer between 2 and 11.
</p>
<p>
The setter functions functions return a new context as a 64-bit integer.
The getter functions return the value, as a 32-bit integer.
The update functions return <code>QMCKL_SUCCESS</code> or <code>QMCKL_FAILURE</code>.
</p>
</div>
<div id="outline-container-sec-2-1" class="outline-3">
<h3 id="sec-2-1"><span class="section-number-3">2.1</span> <code>qmckl_context_update_precision</code></h3>
<div class="outline-text-3" id="text-2-1">
</div><div id="outline-container-sec-2-1-1" class="outline-4">
<h4 id="sec-2-1-1"><span class="section-number-4">2.1.1</span> Source</h4>
<div class="outline-text-4" id="text-2-1-1">
<div class="org-src-container">
<pre class="src src-C">qmckl_exit_code qmckl_context_update_precision(const qmckl_context context, const int precision);
</pre>
</div>
<div class="org-src-container">
<pre class="src src-C">qmckl_exit_code qmckl_context_update_precision(const qmckl_context context, const int precision) {
qmckl_context_struct* ctx;
if (precision &lt; 2) return QMCKL_FAILURE;
if (precision &gt; 53) return QMCKL_FAILURE;
ctx = (qmckl_context_struct*) context;
if (ctx == NULL) return QMCKL_FAILURE;
ctx-&gt;precision = precision;
return QMCKL_SUCCESS;
}
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-2-2" class="outline-3">
<h3 id="sec-2-2"><span class="section-number-3">2.2</span> <code>qmckl_context_update_range</code></h3>
<div class="outline-text-3" id="text-2-2">
</div><div id="outline-container-sec-2-2-1" class="outline-4">
<h4 id="sec-2-2-1"><span class="section-number-4">2.2.1</span> Source</h4>
<div class="outline-text-4" id="text-2-2-1">
<div class="org-src-container">
<pre class="src src-C">qmckl_exit_code qmckl_context_update_range(const qmckl_context context, const int range);
</pre>
</div>
<div class="org-src-container">
<pre class="src src-C">qmckl_exit_code qmckl_context_update_range(const qmckl_context context, const int range) {
qmckl_context_struct* ctx;
if (range &lt; 2) return QMCKL_FAILURE;
if (range &gt; 11) return QMCKL_FAILURE;
ctx = (qmckl_context_struct*) context;
if (ctx == NULL) return QMCKL_FAILURE;
ctx-&gt;range = range;
return QMCKL_SUCCESS;
}
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-2-3" class="outline-3">
<h3 id="sec-2-3"><span class="section-number-3">2.3</span> <code>qmckl_context_set_precision</code></h3>
<div class="outline-text-3" id="text-2-3">
</div><div id="outline-container-sec-2-3-1" class="outline-4">
<h4 id="sec-2-3-1"><span class="section-number-4">2.3.1</span> Source</h4>
<div class="outline-text-4" id="text-2-3-1">
<div class="org-src-container">
<pre class="src src-C">qmckl_context qmckl_context_set_precision(const qmckl_context context, const int precision);
</pre>
</div>
<div class="org-src-container">
<pre class="src src-C">qmckl_context qmckl_context_set_precision(const qmckl_context context, const int precision) {
qmckl_context new_context;
new_context = qmckl_context_copy(context);
if (new_context == 0) return 0;
if (qmckl_context_update_precision(context, precision) == QMCKL_FAILURE) return 0;
return new_context;
}
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-2-4" class="outline-3">
<h3 id="sec-2-4"><span class="section-number-3">2.4</span> <code>qmckl_context_set_range</code></h3>
<div class="outline-text-3" id="text-2-4">
</div><div id="outline-container-sec-2-4-1" class="outline-4">
<h4 id="sec-2-4-1"><span class="section-number-4">2.4.1</span> Source</h4>
<div class="outline-text-4" id="text-2-4-1">
<div class="org-src-container">
<pre class="src src-C">qmckl_context qmckl_context_set_range(const qmckl_context context, const int range);
</pre>
</div>
<div class="org-src-container">
<pre class="src src-C">qmckl_context qmckl_context_set_range(const qmckl_context context, const int range) {
qmckl_context new_context;
new_context = qmckl_context_copy(context);
if (new_context == 0) return 0;
if (qmckl_context_update_range(context, range) == QMCKL_FAILURE) return 0;
return new_context;
}
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-2-5" class="outline-3">
<h3 id="sec-2-5"><span class="section-number-3">2.5</span> <code>qmckl_context_get_precision</code></h3>
<div class="outline-text-3" id="text-2-5">
</div><div id="outline-container-sec-2-5-1" class="outline-4">
<h4 id="sec-2-5-1"><span class="section-number-4">2.5.1</span> Source</h4>
<div class="outline-text-4" id="text-2-5-1">
<div class="org-src-container">
<pre class="src src-C">int qmckl_context_get_precision(const qmckl_context context);
</pre>
</div>
<div class="org-src-container">
<pre class="src src-C">int qmckl_context_get_precision(const qmckl_context context) {
qmckl_context_struct* ctx;
ctx = (qmckl_context_struct*) context;
return ctx-&gt;precision;
}
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-2-6" class="outline-3">
<h3 id="sec-2-6"><span class="section-number-3">2.6</span> <code>qmckl_context_get_range</code></h3>
<div class="outline-text-3" id="text-2-6">
</div><div id="outline-container-sec-2-6-1" class="outline-4">
<h4 id="sec-2-6-1"><span class="section-number-4">2.6.1</span> Source</h4>
<div class="outline-text-4" id="text-2-6-1">
<div class="org-src-container">
<pre class="src src-C">int qmckl_context_get_range(const qmckl_context context);
</pre>
</div>
<div class="org-src-container">
<pre class="src src-C">int qmckl_context_get_range(const qmckl_context context) {
qmckl_context_struct* ctx;
ctx = (qmckl_context_struct*) context;
return ctx-&gt;range;
}
</pre>
</div>
</div>
</div>
</div>
</div>
</div>
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<div id="content">
<h1 class="title">Computation of distances</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#sec-1">1. Squared distance</a>
<ul>
<li><a href="#sec-1-1">1.1. <code>qmckl_distance_sq</code></a>
<ul>
<li><a href="#sec-1-1-1">1.1.1. Arguments</a></li>
<li><a href="#sec-1-1-2">1.1.2. Requirements</a></li>
<li><a href="#sec-1-1-3">1.1.3. Performance</a></li>
<li><a href="#sec-1-1-4">1.1.4. Header</a></li>
<li><a href="#sec-1-1-5">1.1.5. Source</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
</div>
<p>
Function for the computation of distances between particles.
</p>
<p>
3 files are produced:
</p>
<ul class="org-ul">
<li>a header file : <code>qmckl_distance.h</code>
</li>
<li>a source file : <code>qmckl_distance.f90</code>
</li>
<li>a C test file : <code>test_qmckl_distance.c</code>
</li>
<li>a Fortran test file : <code>test_qmckl_distance_f.f90</code>
</li>
</ul>
<div id="outline-container-sec-1" class="outline-2">
<h2 id="sec-1"><span class="section-number-2">1</span> Squared distance</h2>
<div class="outline-text-2" id="text-1">
</div><div id="outline-container-sec-1-1" class="outline-3">
<h3 id="sec-1-1"><span class="section-number-3">1.1</span> <code>qmckl_distance_sq</code></h3>
<div class="outline-text-3" id="text-1-1">
<p>
Computes the matrix of the squared distances between all pairs of
points in two sets, one point within each set:
\[
C_{ij} = \sum_{k=1}^3 (A_{k,i}-B_{k,j})^2
\]
</p>
</div>
<div id="outline-container-sec-1-1-1" class="outline-4">
<h4 id="sec-1-1-1"><span class="section-number-4">1.1.1</span> Arguments</h4>
<div class="outline-text-4" id="text-1-1-1">
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="left" />
<col class="left" />
<col class="left" />
</colgroup>
<tbody>
<tr>
<td class="left"><code>context</code></td>
<td class="left">input</td>
<td class="left">Global state</td>
</tr>
<tr>
<td class="left"><code>transa</code></td>
<td class="left">input</td>
<td class="left">Array <code>A</code> is <code>N</code>: Normal, <code>T</code>: Transposed</td>
</tr>
<tr>
<td class="left"><code>transb</code></td>
<td class="left">input</td>
<td class="left">Array <code>B</code> is <code>N</code>: Normal, <code>T</code>: Transposed</td>
</tr>
<tr>
<td class="left"><code>m</code></td>
<td class="left">input</td>
<td class="left">Number of points in the first set</td>
</tr>
<tr>
<td class="left"><code>n</code></td>
<td class="left">input</td>
<td class="left">Number of points in the second set</td>
</tr>
<tr>
<td class="left"><code>A(lda,3)</code></td>
<td class="left">input</td>
<td class="left">Array containing the \(m \times 3\) matrix \(A\)</td>
</tr>
<tr>
<td class="left"><code>lda</code></td>
<td class="left">input</td>
<td class="left">Leading dimension of array <code>A</code></td>
</tr>
<tr>
<td class="left"><code>B(ldb,3)</code></td>
<td class="left">input</td>
<td class="left">Array containing the \(n \times 3\) matrix \(B\)</td>
</tr>
<tr>
<td class="left"><code>ldb</code></td>
<td class="left">input</td>
<td class="left">Leading dimension of array <code>B</code></td>
</tr>
<tr>
<td class="left"><code>C(ldc,n)</code></td>
<td class="left">output</td>
<td class="left">Array containing the \(m \times n\) matrix \(C\)</td>
</tr>
<tr>
<td class="left"><code>ldc</code></td>
<td class="left">input</td>
<td class="left">Leading dimension of array <code>C</code></td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-sec-1-1-2" class="outline-4">
<h4 id="sec-1-1-2"><span class="section-number-4">1.1.2</span> Requirements</h4>
<div class="outline-text-4" id="text-1-1-2">
<ul class="org-ul">
<li><code>context</code> is not 0
</li>
<li><code>m</code> &gt; 0
</li>
<li><code>n</code> &gt; 0
</li>
<li><code>lda</code> &gt;= 3 if <code>transa</code> is <code>N</code>
</li>
<li><code>lda</code> &gt;= m if <code>transa</code> is <code>T</code>
</li>
<li><code>ldb</code> &gt;= 3 if <code>transb</code> is <code>N</code>
</li>
<li><code>ldb</code> &gt;= n if <code>transb</code> is <code>T</code>
</li>
<li><code>ldc</code> &gt;= m if <code>transa</code> is =
</li>
<li><code>A</code> is allocated with at least \(3 \times m \times 8\) bytes
</li>
<li><code>B</code> is allocated with at least \(3 \times n \times 8\) bytes
</li>
<li><code>C</code> is allocated with at least \(m \times n \times 8\) bytes
</li>
</ul>
</div>
</div>
<div id="outline-container-sec-1-1-3" class="outline-4">
<h4 id="sec-1-1-3"><span class="section-number-4">1.1.3</span> Performance</h4>
<div class="outline-text-4" id="text-1-1-3">
<p>
This function might be more efficient when <code>A</code> and <code>B</code> are
transposed.
</p>
</div>
</div>
<div id="outline-container-sec-1-1-4" class="outline-4">
<h4 id="sec-1-1-4"><span class="section-number-4">1.1.4</span> Header</h4>
<div class="outline-text-4" id="text-1-1-4">
<div class="org-src-container">
<pre class="src src-C">qmckl_exit_code qmckl_distance_sq(qmckl_context context,
char transa, char transb,
int64_t m, int64_t n,
double *A, int64_t lda,
double *B, int64_t ldb,
double *C, int64_t ldc);
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-1-1-5" class="outline-4">
<h4 id="sec-1-1-5"><span class="section-number-4">1.1.5</span> Source</h4>
<div class="outline-text-4" id="text-1-1-5">
<div class="org-src-container">
<pre class="src src-f90">integer function qmckl_distance_sq_f(context, transa, transb, m, n, A, LDA, B, LDB, C, LDC) result(info)
implicit none
integer*8 , intent(in) :: context
character , intent(in) :: transa, transb
integer*8 , intent(in) :: m, n
integer*8 , intent(in) :: lda
real*8 , intent(in) :: A(lda,*)
integer*8 , intent(in) :: ldb
real*8 , intent(in) :: B(ldb,*)
integer*8 , intent(in) :: ldc
real*8 , intent(out) :: C(ldc,*)
integer*8 :: i,j
real*8 :: x, y, z
integer :: transab
info = 0
if (context == 0_8) then
info = -1
return
endif
if (m &lt;= 0_8) then
info = -2
return
endif
if (n &lt;= 0_8) then
info = -3
return
endif
if (transa == 'N' .or. transa == 'n') then
transab = 0
else if (transa == 'T' .or. transa == 't') then
transab = 1
else
transab = -100
endif
if (transb == 'N' .or. transb == 'n') then
continue
else if (transa == 'T' .or. transa == 't') then
transab = transab + 2
else
transab = -100
endif
if (transab &lt; 0) then
info = -4
return
endif
if (iand(transab,1) == 0 .and. LDA &lt; 3) then
info = -5
return
endif
if (iand(transab,1) == 1 .and. LDA &lt; m) then
info = -6
return
endif
if (iand(transab,2) == 0 .and. LDA &lt; 3) then
info = -6
return
endif
if (iand(transab,2) == 2 .and. LDA &lt; m) then
info = -7
return
endif
select case (transab)
case(0)
do j=1,n
do i=1,m
x = A(1,i) - B(1,j)
y = A(2,i) - B(2,j)
z = A(3,i) - B(3,j)
C(i,j) = x*x + y*y + z*z
end do
end do
case(1)
do j=1,n
do i=1,m
x = A(i,1) - B(1,j)
y = A(i,2) - B(2,j)
z = A(i,3) - B(3,j)
C(i,j) = x*x + y*y + z*z
end do
end do
case(2)
do j=1,n
do i=1,m
x = A(1,i) - B(j,1)
y = A(2,i) - B(j,2)
z = A(3,i) - B(j,3)
C(i,j) = x*x + y*y + z*z
end do
end do
case(3)
do j=1,n
do i=1,m
x = A(i,1) - B(j,1)
y = A(i,2) - B(j,2)
z = A(i,3) - B(j,3)
C(i,j) = x*x + y*y + z*z
end do
end do
end select
end function qmckl_distance_sq_f
</pre>
</div>
</div>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="date">Created: 2020-10-28 Wed 23:57</p>
<p class="creator"><a href="http://www.gnu.org/software/emacs/">Emacs</a> 25.2.2 (<a href="http://orgmode.org">Org</a> mode 8.2.10)</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>
</html>

252
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<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<head>
<title>Memory management</title>
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#postamble p, #preamble p { font-size: 90%; margin: .2em; }
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border: 1px solid #ccc;
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pre.src {
position: relative;
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padding-top: 1.2em;
}
pre.src:before {
display: none;
position: absolute;
background-color: white;
top: -10px;
right: 10px;
padding: 3px;
border: 1px solid black;
}
pre.src:hover:before { display: inline;}
pre.src-sh:before { content: 'sh'; }
pre.src-bash:before { content: 'sh'; }
pre.src-emacs-lisp:before { content: 'Emacs Lisp'; }
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th.right { text-align: center; }
th.left { text-align: center; }
th.center { text-align: center; }
td.right { text-align: right; }
td.left { text-align: left; }
td.center { text-align: center; }
dt { font-weight: bold; }
.footpara:nth-child(2) { display: inline; }
.footpara { display: block; }
.footdef { margin-bottom: 1em; }
.figure { padding: 1em; }
.figure p { text-align: center; }
.inlinetask {
padding: 10px;
border: 2px solid gray;
margin: 10px;
background: #ffffcc;
}
#org-div-home-and-up
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textarea { overflow-x: auto; }
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</head>
<body>
<div id="content">
<h1 class="title">Memory management</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#sec-1">1. <code>qmckl_malloc</code></a>
<ul>
<li><a href="#sec-1-1">1.1. Header</a></li>
<li><a href="#sec-1-2">1.2. Source</a></li>
</ul>
</li>
<li><a href="#sec-2">2. <code>qmckl_free</code></a>
<ul>
<li><a href="#sec-2-1">2.1. Header</a></li>
<li><a href="#sec-2-2">2.2. Source</a></li>
</ul>
</li>
</ul>
</div>
</div>
<p>
We override the allocation functions to enable the possibility of
optimized libraries to fine-tune the memory allocation.
</p>
<p>
3 files are produced:
</p>
<ul class="org-ul">
<li>a header file : <code>qmckl_memory.h</code>
</li>
<li>a source file : <code>qmckl_memory.c</code>
</li>
<li>a test file : <code>test_qmckl_memory.c</code>
</li>
</ul>
<div id="outline-container-sec-1" class="outline-2">
<h2 id="sec-1"><span class="section-number-2">1</span> <code>qmckl_malloc</code></h2>
<div class="outline-text-2" id="text-1">
<p>
Analogous of <code>malloc, but passing a context and a signed 64-bit integers as argument.</code>
</p>
</div>
<div id="outline-container-sec-1-1" class="outline-3">
<h3 id="sec-1-1"><span class="section-number-3">1.1</span> Header</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-C">void* qmckl_malloc(const qmckl_context ctx, const size_t size);
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-1-2" class="outline-3">
<h3 id="sec-1-2"><span class="section-number-3">1.2</span> Source</h3>
<div class="outline-text-3" id="text-1-2">
<div class="org-src-container">
<pre class="src src-C">void* qmckl_malloc(const qmckl_context ctx, const size_t size) {
if (ctx == (qmckl_context) 0) {
/* Avoids unused parameter error */
return malloc( (size_t) size );
}
return malloc( (size_t) size );
}
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-2" class="outline-2">
<h2 id="sec-2"><span class="section-number-2">2</span> <code>qmckl_free</code></h2>
<div class="outline-text-2" id="text-2">
</div><div id="outline-container-sec-2-1" class="outline-3">
<h3 id="sec-2-1"><span class="section-number-3">2.1</span> Header</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-C">void qmckl_free(void *ptr);
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-2-2" class="outline-3">
<h3 id="sec-2-2"><span class="section-number-3">2.2</span> Source</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-C">void qmckl_free(void *ptr) {
free(ptr);
}
</pre>
</div>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="date">Created: 2020-10-28 Wed 23:57</p>
<p class="creator"><a href="http://www.gnu.org/software/emacs/">Emacs</a> 25.2.2 (<a href="http://orgmode.org">Org</a> mode 8.2.10)</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>
</html>

9
src/.gitignore vendored
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@ -1,9 +0,0 @@
*.o
*.c
*.f90
*.h
*.html
*~
*.so
Makefile.generated
test_qmckl

40
src/Makefile
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@ -1,40 +0,0 @@
CC=gcc
CFLAGS=-fPIC -fexceptions -Wall -Werror -Wpedantic -Wextra -g
FC=gfortran
FFLAGS=-fPIC -g -fcheck=all -Waliasing -Wampersand -Wconversion -Wsurprising -Wintrinsics-std -Wno-tabs -Wintrinsic-shadow -Wline-truncation -Wreal-q-constant -Wuninitialized -fbacktrace -ffpe-trap=zero,overflow,underflow -finit-real=nan
LIBS=-lgfortran -lm
#CC=icc
#CFLAGS=-fPIC -g
#
#FC=ifort
#FFLAGS=-fPIC -g
#
#LIBS=-lm -lifcore -lirc
export CC CFLAGS FC FFLAGS LIBS
ORG_SOURCE_FILES=$(wildcard qmckl*.org) test_qmckl.org
OBJECT_FILES=$(filter-out $(EXCLUDED_OBJECTS), $(patsubst %.org,%.o,$(ORG_SOURCE_FILES)))
.PHONY: clean
.SECONDARY: # Needed to keep the produced C and Fortran files
libqmckl.so: Makefile.generated
$(MAKE) -f Makefile.generated
test: Makefile.generated
$(MAKE) -f Makefile.generated test
doc:$(ORG_SOURCE_FILES)
./create_doc.sh README.org $(ORG_SOURCE_FILES)
clean:
rm -f qmckl.h test_qmckl_* test_qmckl.c qmckl_*.f90 qmckl_*.c qmckl_*.o qmckl_*.h Makefile.generated libqmckl.so *.html *.fh
Makefile.generated: $(ORG_SOURCE_FILES) Makefile create_makefile.sh
./create_makefile.sh $(ORG_SOURCE_FILES)

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#+TITLE: QMCkl source code documentation
#+EXPORT_FILE_NAME: index.html
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
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#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
* Introduction
The ultimate goal of QMCkl is to provide a high-performance
implementation of the main kernels of QMC. In this particular
repository, we focus on the definition of the API and the tests,
and on a /pedagogical/ presentation of the algorithms. We expect the
HPC experts to use this repository as a reference for re-writing
optimized libraries.
Literate programming is particularly adapted in this context.
Source files are written in [[https://karl-voit.at/2017/09/23/orgmode-as-markup-only/][org-mode]] format, to provide useful
comments and LaTex formulas close to the code. There exists multiple
possibilities to convert org-mode files into different formats such as
HTML or pdf.
For a tutorial on literate programming with org-mode, follow
[[http://www.howardism.org/Technical/Emacs/literate-programming-tutorial.html][this link]].
The code is extracted from the org files using Emacs as a command-line
tool in the =Makefile=, and then the produced files are compiled.
** Language used
Fortran is one of the most common languages used by the community,
and is simple enough to make the algorithms readable. Hence we
propose in this pedagogical implementation of QMCkl to use Fortran
to express the algorithms. For specific internal functions where
the C language is more natural, C is used.
As Fortran modules generate compiler-dependent files, the use of
modules is restricted to the internal use of the library, otherwise
the compliance with C is violated.
The external dependencies should be kept as small as possible, so
external libraries should be used /only/ if their used is strongly
justified.
** Source code editing
Any text editor can be used to edit org-mode files. For a better
user experience Emacs is recommended.
For users hating Emacs, it is good to know that Emacs can behave
like Vim when switched into ``Evil'' mode. There also exists
[[https://www.spacemacs.org][Spacemacs]] which helps the transition for Vim users.
For users with a preference for Jupyter notebooks, the following
script can convert jupyter notebooks to org-mode files:
#+BEGIN_SRC sh tangle: nb_to_org.sh
#!/bin/bash
# $ nb_to_org.sh notebook.ipynb
# produces the org-mode file notebook.org
set -e
nb=$(basename $1 .ipynb)
jupyter nbconvert --to markdown ${nb}.ipynb --output ${nb}.md
pandoc ${nb}.md -o ${nb}.org
rm ${nb}.md
#+END_SRC
And pandoc can convert multiple markdown formats into org-mode.
** Writing in Fortran
The Fortran source files should provide a C interface using
=iso_c_binding=. The name of the Fortran source files should end
with =_f.f90= to be properly handled by the Makefile.
The names of the functions defined in fortran should be the same as
those exposed in the API suffixed by =_f=.
Fortran interface files should also be written in a file with a
=.fh= extension.
** Coding style
# TODO: decide on a coding style
To improve readability, we maintain a consistent coding style in the library.
- For C source files, we will use __(decide on a coding style)__
- For Fortran source files, we will use __(decide on a coding style)__
Coding style can be automatically checked with [[https://clang.llvm.org/docs/ClangFormat.html][clang-format]].
* Design of the library
The proposed API should allow the library to:
- deal with memory transfers between CPU and accelerators
- use different levels of floating-point precision
We chose a multi-layered design with low-level and high-level
functions (see below).
** Naming conventions
Use =qmckl_= as a prefix for all exported functions and variables.
All exported header files should have a filename with the prefix
=qmckl_=.
If the name of the org-mode file is =xxx.org=, the name of the
produced C files should be =xxx.c= and =xxx.h= and the name of the
produced Fortran files should be =xxx.f90=
Arrays are in uppercase and scalars are in lowercase.
** Application programming interface
The application programming interface (API) is designed to be
compatible with the C programming language (not C++), to ensure
that the library will be easily usable in any language.
This implies that only the following data types are allowed in the API:
- 32-bit and 64-bit floats and arrays (=real= and =double=)
- 32-bit and 64-bit integers and arrays (=int32_t= and =int64_t=)
- Pointers should be represented as 64-bit integers (even on
32-bit architectures)
- ASCII strings are represented as a pointers to a character arrays
and terminated by a zero character (C convention).
# TODO : Link to repositories for bindings
To facilitate the use in other languages than C, we provide some
bindings in other languages in other repositories.
** Global state
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
=context= variable, built by the library with the
=qmckl_context_create= function. The =context= contains the global
state of the library, and is used as the first argument of many
QMCkl functions.
Modifying the state is done by setters and getters, prefixed
by =qmckl_context_set_= an =qmckl_context_get_=.
When a context variable is modified by a setter, a copy of the old
data structure is made and updated, and the pointer to the new data
structure is returned, such that the old contexts can still be
accessed.
It is also possible to modify the state in an impure fashion, using
the =qmckl_context_update_= functions.
The context and its old versions can be destroyed with
=qmckl_context_destroy=.
** Low-level functions
Low-level functions are very simple functions which are leaves of the
function call tree (they don't call any other QMCkl function).
This functions are /pure/, and unaware of the QMCkl =context=. They are
not allowed to allocate/deallocate memory, and if they need
temporary memory it should be provided in input.
** High-level functions
High-level functions are at the top of the function call tree.
They are able to choose which lower-level function to call
depending on the required precision, and do the corresponding type
conversions.
These functions are also responsible for allocating temporary
storage, to simplify the use of accelerators.
The high-level functions should be pure, unless the introduction of
non-purity is justified. All the side effects should be made in the
=context= variable.
# TODO : We need an identifier for impure functions
** Numerical precision
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
=context= variable.
* Algorithms
Reducing the scaling of an algorithm usually implies also reducing
its arithmetic complexity (number of flops per byte). Therefore,
for small sizes \(\mathcal{O}(N^3)\) and \(\mathcal{O}(N^2)\) algorithms
are better adapted than linear scaling algorithms.
As QMCkl is a general purpose library, multiple algorithms should
be implemented adapted to different problem sizes.
* Rules for the API
- =stdint= should be used for integers (=int32_t=, =int64_t=)
- integers used for counting should always be =int64_t=
- floats should be by default =double=, unless explicitly mentioned
- pointers are converted to =int64_t= to increase portability
* Documentation
- [[./qmckl.org][Main QMCkl header file]]
- [[./qmckl_memory.org][Memory management]]
- [[./qmckl_context.org][Context]]
- [[./qmckl_distance.org][Distance]]
- [[./qmckl_ao.org][Atomic orbitals]]
* Acknowledgments
[[https://trex-coe.eu/sites/default/files/inline-images/euflag.jpg]]
[[https://trex-coe.eu][TREX: Targeting Real Chemical Accuracy at the Exascale]] project has received funding from the European Union’s Horizon 2020 - Research and Innovation program - under grant agreement no. 952165. The content of this document does not represent the opinion of the European Union, and the European Union is not responsible for any use that might be made of such content.

87
src/config.el
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@ -1,87 +0,0 @@
(require 'org)
(require 'font-lock)
(require 'subr-x) ;; for `when-let'
(unless (boundp 'maximal-integer)
(defconst maximal-integer (lsh -1 -1)
"Maximal integer value representable natively in emacs lisp."))
(defun face-spec-default (spec)
"Get list containing at most the default entry of face SPEC.
Return nil if SPEC has no default entry."
(let* ((first (car-safe spec))
(display (car-safe first)))
(when (eq display 'default)
(list (car-safe spec)))))
(defun face-spec-min-color (display-atts)
"Get min-color entry of DISPLAY-ATTS pair from face spec."
(let* ((display (car-safe display-atts)))
(or (car-safe (cdr (assoc 'min-colors display)))
maximal-integer)))
(defun face-spec-highest-color (spec)
"Search face SPEC for highest color.
That means the DISPLAY entry of SPEC
with class 'color and highest min-color value."
(let ((color-list (cl-remove-if-not
(lambda (display-atts)
(when-let ((display (car-safe display-atts))
(class (and (listp display)
(assoc 'class display)))
(background (assoc 'background display)))
(and (member 'light (cdr background))
(member 'color (cdr class)))))
spec)))
(cl-reduce (lambda (display-atts1 display-atts2)
(if (> (face-spec-min-color display-atts1)
(face-spec-min-color display-atts2))
display-atts1
display-atts2))
(cdr color-list)
:initial-value (car color-list))))
(defun face-spec-t (spec)
"Search face SPEC for fall back."
(cl-find-if (lambda (display-atts)
(eq (car-safe display-atts) t))
spec))
(defun my-face-attribute (face attribute &optional frame inherit)
"Get FACE ATTRIBUTE from `face-user-default-spec' and not from `face-attribute'."
(let* ((face-spec (face-user-default-spec face))
(display-attr (or (face-spec-highest-color face-spec)
(face-spec-t face-spec)))
(attr (cdr display-attr))
(val (or (plist-get attr attribute) (car-safe (cdr (assoc attribute attr))))))
;; (message "attribute: %S" attribute) ;; for debugging
(when (and (null (eq attribute :inherit))
(null val))
(let ((inherited-face (my-face-attribute face :inherit)))
(when (and inherited-face
(null (eq inherited-face 'unspecified)))
(setq val (my-face-attribute inherited-face attribute)))))
;; (message "face: %S attribute: %S display-attr: %S, val: %S" face attribute display-attr val) ;; for debugging
(or val 'unspecified)))
(advice-add 'face-attribute :override #'my-face-attribute)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Debugging:
(defmacro print-args-and-ret (fun)
"Prepare FUN for printing args and return value."
`(advice-add (quote ,fun) :around
(lambda (oldfun &rest args)
(let ((ret (apply oldfun args)))
(message ,(concat "Calling " (symbol-name fun) " with args %S returns %S.") args ret)
ret))
'((name "print-args-and-ret"))))
; (print-args-and-ret htmlize-faces-in-buffer)
; (print-args-and-ret htmlize-get-override-fstruct)
; (print-args-and-ret htmlize-face-to-fstruct)
; (print-args-and-ret htmlize-attrlist-to-fstruct)
; (print-args-and-ret face-foreground)
; (print-args-and-ret face-background)
; (print-args-and-ret face-attribute)

23
src/create_doc.sh
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@ -1,23 +0,0 @@
#!/bin/bash
# Tangle org files
emacsclient -a "" \
--socket-name=org_to_code \
--eval "(load-file \"config.el\")"
for INPUT in $@ ; do
echo $INPUT
emacsclient \
--no-wait \
--socket-name=org_to_code \
--eval "(find-file \"$INPUT\")" \
--eval "(org-html-export-to-html)"
done
mv *.html ../docs
emacsclient \
--no-wait \
--socket-name=org_to_code \
--eval '(kill-emacs)'

105
src/create_makefile.sh
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@ -1,105 +0,0 @@
#!/bin/bash
OUTPUT=Makefile.generated
# Tangle org files
emacsclient -a "" \
--socket-name=org_to_code \
--eval "(require 'org)"
for INPUT in $@ ; do
emacsclient \
--no-wait \
--socket-name=org_to_code \
--eval "(org-babel-tangle-file \"$INPUT\")"
done
emacsclient \
--no-wait \
--socket-name=org_to_code \
--eval '(kill-emacs)'
# Create the list of *.o files to be created
OBJECTS=""
for i in $(ls qmckl_*.c) ; do
FILE=${i%.c}
OBJECTS="${OBJECTS} ${FILE}.o"
done >> $OUTPUT
for i in $(ls qmckl_*.f90) ; do
FILE=${i%.f90}
OBJECTS="${OBJECTS} ${FILE}.o"
done >> $OUTPUT
TESTS=""
for i in $(ls test_qmckl_*.c) ; do
FILE=${i%.c}.o
TESTS="${TESTS} ${FILE}"
done >> $OUTPUT
TESTS_F=""
for i in $(ls test_qmckl_*.f90) ; do
FILE=${i%.f90}.o
TESTS_F="${TESTS_F} ${FILE}"
done >> $OUTPUT
# Write the Makefile
cat << EOF > $OUTPUT
CC=$CC
CFLAGS=$CFLAGS -I../munit/
FC=$FC
FFLAGS=$FFLAGS
OBJECT_FILES=$OBJECTS
TESTS=$TESTS
TESTS_F=$TESTS_F
LIBS=$LIBS
libqmckl.so: \$(OBJECT_FILES)
\$(CC) -shared \$(OBJECT_FILES) -o libqmckl.so
%.o: %.c
\$(CC) \$(CFLAGS) -c \$*.c -o \$*.o
%.o: %.f90
\$(FC) \$(FFLAGS) -c \$*.f90 -o \$*.o
test_qmckl: test_qmckl.c libqmckl.so \$(TESTS) \$(TESTS_F)
\$(CC) \$(CFLAGS) -Wl,-rpath,$PWD -L. \
../munit/munit.c \$(TESTS) \$(TESTS_F) -lqmckl \$(LIBS) test_qmckl.c -o test_qmckl
test: test_qmckl
./test_qmckl
.PHONY: test
EOF
for i in $(ls qmckl_*.c) ; do
FILE=${i%.c}
echo "${FILE}.o: ${FILE}.c " *.h
done >> $OUTPUT
for i in $(ls qmckl_*.f90) ; do
FILE=${i%.f90}
echo "${FILE}.o: ${FILE}.f90"
done >> $OUTPUT
for i in $(ls test_qmckl_*.c) ; do
FILE=${i%.c}
echo "${FILE}.o: ${FILE}.c qmckl.h"
done >> $OUTPUT
for i in $(ls test_qmckl*.f90) ; do
FILE=${i%.f90}
echo "${FILE}.o: ${FILE}.f90"
done >> $OUTPUT

70
src/qmckl.org
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@ -1,70 +0,0 @@
# -*- mode: org -*-
# vim: syntax=c
#+TITLE: QMCkl C header
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
#+HTML_HEAD: <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
#+HTML_HEAD: <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/lib/js/jquery.stickytableheaders.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
This file produces the =qmckl.h= header file, which is included in all
other C header files. It is the main entry point to the library.
#+BEGIN_SRC C :tangle qmckl.h
#ifndef QMCKL_H
#define QMCKL_H
#include <stdlib.h>
#include <stdint.h>
#+END_SRC
* Constants
** Success/failure
These are the codes returned by the functions to indicate success
or failure. All such functions should have as a return type =qmckl_exit_code=.
#+BEGIN_SRC C :tangle qmckl.h
#define QMCKL_SUCCESS 0
#define QMCKL_FAILURE 1
typedef int32_t qmckl_exit_code;
typedef int64_t qmckl_context ;
#+END_SRC
** Precision-related constants
Controlling numerical precision enables optimizations. Here, the
default parameters determining the target numerical precision and
range are defined.
#+BEGIN_SRC C :tangle qmckl.h
#define QMCKL_DEFAULT_PRECISION 53
#define QMCKL_DEFAULT_RANGE 11
#+END_SRC
* Header files
All the functions expoed in the API are defined in the following
header files.
#+BEGIN_SRC C :tangle qmckl.h
#include "qmckl_memory.h"
#include "qmckl_context.h"
#include "qmckl_distance.h"
#include "qmckl_ao.h"
#+END_SRC
* End of header
#+BEGIN_SRC C :tangle qmckl.h
#endif
#+END_SRC

495
src/qmckl_ao.org
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@ -1,495 +0,0 @@
# -*- mode: org -*-
# vim: syntax=c
#+TITLE: Atomic Orbitals
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
#+HTML_HEAD: <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
#+HTML_HEAD: <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/lib/js/jquery.stickytableheaders.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
This files contains all the routines for the computation of the
values, gradients and Laplacian of the atomic basis functions.
4 files are produced:
- a header file : =qmckl_ao.h=
- a source file : =qmckl_ao.f90=
- a C test file : =test_qmckl_ao.c=
- a Fortran test file : =test_qmckl_ao_f.f90=
*** Header :noexport:
#+BEGIN_SRC C :comments link :tangle qmckl_ao.h
#ifndef QMCKL_AO_H
#define QMCKL_AO_H
#include "qmckl_context.h"
#include "qmckl_distance.h"
#+END_SRC
*** Test :noexport:
#+BEGIN_SRC C :comments link :tangle test_qmckl_ao.c
#include <math.h>
#include "qmckl.h"
#include "munit.h"
MunitResult test_qmckl_ao() {
qmckl_context context;
context = qmckl_context_create();
#+END_SRC
* Polynomials
\[
P_l(\mathbf{r},\mathbf{R}_i) = (x-X_i)^a (y-Y_i)^b (z-Z_i)^c
\]
\begin{eqnarray*}
\frac{\partial }{\partial x} P_l\left(\mathbf{r},\mathbf{R}_i \right) & = & a (x-X_i)^{a-1} (y-Y_i)^b (z-Z_i)^c \\
\frac{\partial }{\partial y} P_l\left(\mathbf{r},\mathbf{R}_i \right) & = & b (x-X_i)^a (y-Y_i)^{b-1} (z-Z_i)^c \\
\frac{\partial }{\partial z} P_l\left(\mathbf{r},\mathbf{R}_i \right) & = & c (x-X_i)^a (y-Y_i)^b (z-Z_i)^{c-1} \\
\end{eqnarray*}
\begin{eqnarray*}
\left( \frac{\partial }{\partial x^2} +
\frac{\partial }{\partial y^2} +
\frac{\partial }{\partial z^2} \right) P_l
\left(\mathbf{r},\mathbf{R}_i \right) & = &
a(a-1) (x-X_i)^{a-2} (y-Y_i)^b (z-Z_i)^c + \\
&& b(b-1) (x-X_i)^a (y-Y_i)^{b-1} (z-Z_i)^c + \\
&& c(c-1) (x-X_i)^a (y-Y_i)^b (z-Z_i)^{c-1}
\end{eqnarray*}
** =qmckl_ao_powers=
Computes all the powers of the =n= input data up to the given
maximum value given in input for each of the $n$ points:
\[ P_{ij} = X_j^i \]
*** Arguments
| =context= | input | Global state |
| =n= | input | Number of values |
| =X(n)= | input | Array containing the input values |
| =LMAX(n)= | input | Array containing the maximum power for each value |
| =P(LDP,n)= | output | Array containing all the powers of =X= |
| =LDP= | input | Leading dimension of array =P= |
*** Requirements
- =context= is not 0
- =n= > 0
- =X= is allocated with at least $n \times 8$ bytes
- =LMAX= is allocated with at least $n \times 4$ bytes
- =P= is allocated with at least $n \times \max_i \text{LMAX}_i \times 8$ bytes
- =LDP= >= $\max_i$ =LMAX[i]=
*** Header
#+BEGIN_SRC C :comments link :tangle qmckl_ao.h
qmckl_exit_code qmckl_ao_powers(qmckl_context context,
int64_t n,
double *X, int32_t *LMAX,
double *P, int64_t LDP);
#+END_SRC
*** Source
#+BEGIN_SRC f90 :comments link :tangle qmckl_ao.f90
integer function qmckl_ao_powers_f(context, n, X, LMAX, P, ldp) result(info)
implicit none
integer*8 , intent(in) :: context
integer*8 , intent(in) :: n
real*8 , intent(in) :: X(n)
integer , intent(in) :: LMAX(n)
real*8 , intent(out) :: P(ldp,n)
integer*8 , intent(in) :: ldp
integer*8 :: i,j
info = 0
if (context == 0_8) then
info = -1
return
endif
if (LDP < MAXVAL(LMAX)) then
info = -2
return
endif
do j=1,n
P(1,j) = X(j)
do i=2,LMAX(j)
P(i,j) = P(i-1,j) * X(j)
end do
end do
end function qmckl_ao_powers_f
#+END_SRC
*** C interface :noexport:
#+BEGIN_SRC f90 :comments link :tangle qmckl_ao.f90
integer(c_int32_t) function qmckl_ao_powers(context, n, X, LMAX, P, ldp) &
bind(C) result(info)
use, intrinsic :: iso_c_binding
implicit none
integer (c_int64_t) , intent(in) , value :: context
integer (c_int64_t) , intent(in) , value :: n
real (c_double) , intent(in) :: X(n)
integer (c_int32_t) , intent(in) :: LMAX(n)
real (c_double) , intent(out) :: P(ldp,n)
integer (c_int64_t) , intent(in) , value :: ldp
integer, external :: qmckl_ao_powers_f
info = qmckl_ao_powers_f(context, n, X, LMAX, P, ldp)
end function qmckl_ao_powers
#+END_SRC
#+BEGIN_SRC f90 :comments link :tangle qmckl_ao.fh
interface
integer(c_int32_t) function qmckl_ao_powers(context, n, X, LMAX, P, ldp) bind(C)
use, intrinsic :: iso_c_binding
integer (c_int64_t) , intent(in) , value :: context
integer (c_int64_t) , intent(in) , value :: n
integer (c_int64_t) , intent(in) , value :: ldp
real (c_double) , intent(in) :: X(n)
integer (c_int32_t) , intent(in) :: LMAX(n)
real (c_double) , intent(out) :: P(ldp,n)
end function qmckl_ao_powers
end interface
#+END_SRC
*** Test :noexport:
#+BEGIN_SRC f90 :comments link :tangle test_qmckl_ao_f.f90
integer(c_int32_t) function test_qmckl_ao_powers(context) bind(C)
use, intrinsic :: iso_c_binding
implicit none
include 'qmckl_ao.fh'
integer(c_int64_t), intent(in), value :: context
integer*8 :: n, LDP
integer, allocatable :: LMAX(:)
double precision, allocatable :: X(:), P(:,:)
integer*8 :: i,j
n = 100;
LDP = 10;
allocate(X(n), P(LDP,n), LMAX(n))
do j=1,n
X(j) = -5.d0 + 0.1d0 * dble(j)
LMAX(j) = 1 + int(mod(j, 9),4)
end do
test_qmckl_ao_powers = qmckl_ao_powers(context, n, X, LMAX, P, LDP)
if (test_qmckl_ao_powers /= 0) return
test_qmckl_ao_powers = -1
do j=1,n
do i=1,LMAX(j)
if ( dabs(1.d0 - P(i,j) / (X(j)**i)) > 1.d-14 ) return
end do
end do
test_qmckl_ao_powers = 0
deallocate(X,P,LMAX)
end function test_qmckl_ao_powers
#+END_SRC
#+BEGIN_SRC C :comments link :tangle test_qmckl_ao.c
int test_qmckl_ao_powers(qmckl_context context);
munit_assert_int(0, ==, test_qmckl_ao_powers(context));
#+END_SRC
** =qmckl_ao_polynomial_vgl=
Computes the values, gradients and Laplacians at a given point of
all polynomials with an angular momentum up to =lmax=.
*** Arguments
| =context= | input | Global state |
| =X(3)= | input | Array containing the coordinates of the points |
| =R(3)= | input | Array containing the x,y,z coordinates of the center |
| =lmax= | input | Maximum angular momentum |
| =n= | output | Number of computed polynomials |
| =L(ldl,n)= | output | Contains a,b,c for all =n= results |
| =ldl= | input | Leading dimension of =L= |
| =VGL(ldv,n)= | output | Value, gradients and Laplacian of the polynomials |
| =ldv= | input | Leading dimension of array =VGL= |
*** Requirements
- =context= is not 0
- =n= > 0
- =X= is allocated with at least $3 \times 8$ bytes
- =R= is allocated with at least $3 \times 8$ bytes
- =lmax= >= 0
- On output, =n= should be equal to (=lmax=+1)(=lmax=+2)(=lmax=+3)/6
- =L= is allocated with at least $3 \times n \times 4$ bytes
- =ldl= >= 3
- =VGL= is allocated with at least $5 \times n \times 8$ bytes
- =ldv= >= 5
*** Header
#+BEGIN_SRC C :comments link :tangle qmckl_ao.h
qmckl_exit_code qmckl_ao_polynomial_vgl(qmckl_context context,
double *X, double *R,
int32_t lmax, int64_t *n,
int32_t *L, int64_t ldl,
double *VGL, int64_t ldv);
#+END_SRC
*** Source
#+BEGIN_SRC f90 :comments link :tangle qmckl_ao.f90
integer function qmckl_ao_polynomial_vgl_f(context, X, R, lmax, n, L, ldl, VGL, ldv) result(info)
implicit none
integer*8 , intent(in) :: context
real*8 , intent(in) :: X(3), R(3)
integer , intent(in) :: lmax
integer*8 , intent(out) :: n
integer , intent(out) :: L(ldl,(lmax+1)*(lmax+2)*(lmax+3)/6)
integer*8 , intent(in) :: ldl
real*8 , intent(out) :: VGL(ldv,(lmax+1)*(lmax+2)*(lmax+3)/6)
integer*8 , intent(in) :: ldv
integer*8 :: i,j
integer :: a,b,c,d
real*8 :: Y(3)
integer :: lmax_array(3)
real*8 :: pows(-2:lmax,3)
integer, external :: qmckl_ao_powers_f
double precision :: xy, yz, xz
double precision :: da, db, dc, dd
info = 0
if (context == 0_8) then
info = -1
return
endif
n = (lmax+1)*(lmax+2)*(lmax+3)/6
if (ldl < 3) then
info = -2
return
endif
if (ldv < 5) then
info = -3
return
endif
do i=1,3
Y(i) = X(i) - R(i)
end do
pows(-2:-1,1:3) = 0.d0
pows(0,1:3) = 1.d0
lmax_array(1:3) = lmax
info = qmckl_ao_powers_f(context, 1_8, Y(1), (/lmax/), pows(1,1), size(pows,1,kind=8))
if (info /= 0) return
info = qmckl_ao_powers_f(context, 1_8, Y(2), (/lmax/), pows(1,2), size(pows,1,kind=8))
if (info /= 0) return
info = qmckl_ao_powers_f(context, 1_8, Y(3), (/lmax/), pows(1,3), size(pows,1,kind=8))
if (info /= 0) return
n=1
vgl(1:5,1:n) = 0.d0
l(1:3,n) = 0
vgl(1,n) = 1.d0
dd = 1.d0
do d=1,lmax
da = 0.d0
do a=0,d
db = 0.d0
do b=0,d-a
c = d - a - b
dc = dd - da - db
n = n+1
l(1,n) = a
l(2,n) = b
l(3,n) = c
xy = pows(a,1) * pows(b,2)
yz = pows(b,2) * pows(c,3)
xz = pows(a,1) * pows(c,3)
vgl(1,n) = xy * pows(c,3)
xy = dc * xy
xz = db * xz
yz = da * yz
vgl(2,n) = pows(a-1,1) * yz
vgl(3,n) = pows(b-1,2) * xz
vgl(4,n) = pows(c-1,3) * xy
vgl(5,n) = &
(da-1.d0) * pows(a-2,1) * yz + &
(db-1.d0) * pows(b-2,2) * xz + &
(dc-1.d0) * pows(c-2,3) * xy
db = db + 1.d0
end do
da = da + 1.d0
end do
dd = dd + 1.d0
end do
end function qmckl_ao_polynomial_vgl_f
#+END_SRC
*** C interface :noexport:
#+BEGIN_SRC f90 :comments link :tangle qmckl_ao.f90
integer(c_int32_t) function qmckl_ao_polynomial_vgl(context, X, R, lmax, n, L, ldl, VGL, ldv) &
bind(C) result(info)
use, intrinsic :: iso_c_binding
implicit none
integer (c_int64_t) , intent(in) , value :: context
real (c_double) , intent(in) :: X(3), R(3)
integer (c_int32_t) , intent(in) , value :: lmax
integer (c_int64_t) , intent(out) :: n
integer (c_int32_t) , intent(out) :: L(ldl,(lmax+1)*(lmax+2)*(lmax+3)/6)
integer (c_int64_t) , intent(in) , value :: ldl
real (c_double) , intent(out) :: VGL(ldv,(lmax+1)*(lmax+2)*(lmax+3)/6)
integer (c_int64_t) , intent(in) , value :: ldv
integer, external :: qmckl_ao_polynomial_vgl_f
info = qmckl_ao_polynomial_vgl_f(context, X, R, lmax, n, L, ldl, VGL, ldv)
end function qmckl_ao_polynomial_vgl
#+END_SRC
#+BEGIN_SRC f90 :comments link :tangle qmckl_ao.fh
interface
integer(c_int32_t) function qmckl_ao_polynomial_vgl(context, X, R, lmax, n, L, ldl, VGL, ldv) &
bind(C)
use, intrinsic :: iso_c_binding
integer (c_int64_t) , intent(in) , value :: context
integer (c_int32_t) , intent(in) , value :: lmax
integer (c_int64_t) , intent(in) , value :: ldl
integer (c_int64_t) , intent(in) , value :: ldv
real (c_double) , intent(in) :: X(3), R(3)
integer (c_int64_t) , intent(out) :: n
integer (c_int32_t) , intent(out) :: L(ldl,(lmax+1)*(lmax+2)*(lmax+3)/6)
real (c_double) , intent(out) :: VGL(ldv,(lmax+1)*(lmax+2)*(lmax+3)/6)
end function qmckl_ao_polynomial_vgl
end interface
#+END_SRC
*** Test :noexport:
#+BEGIN_SRC f90 :comments link :tangle test_qmckl_ao_f.f90
integer(c_int32_t) function test_qmckl_ao_polynomial_vgl(context) bind(C)
use, intrinsic :: iso_c_binding
implicit none
include 'qmckl_ao.fh'
integer(c_int64_t), intent(in), value :: context
integer :: lmax, d, i
integer, allocatable :: L(:,:)
integer*8 :: n, ldl, ldv, j
double precision :: X(3), R(3), Y(3)
double precision, allocatable :: VGL(:,:)
double precision :: w
X = (/ 1.1 , 2.2 , 3.3 /)
R = (/ 0.1 , 1.2 , -2.3 /)
Y(:) = X(:) - R(:)
lmax = 4;
n = 0;
ldl = 3;
ldv = 100;
d = (lmax+1)*(lmax+2)*(lmax+3)/6
allocate (L(ldl,100), VGL(ldv,100))
test_qmckl_ao_polynomial_vgl = &
qmckl_ao_polynomial_vgl(context, X, R, lmax, n, L, ldl, VGL, ldv)
if (test_qmckl_ao_polynomial_vgl /= 0) return
test_qmckl_ao_polynomial_vgl = -1
if (n /= d) return
do j=1,n
do i=1,3
if (L(i,j) < 0) return
end do
if (dabs(1.d0 - VGL(1,j) / (&
Y(1)**L(1,j) * Y(2)**L(2,j) * Y(3)**L(3,j) &
)) > 1.d-14 ) return
if (L(1,j) < 1) then
if (VGL(2,j) /= 0.d0) return
else
if (dabs(1.d0 - VGL(2,j) / (&
L(1,j) * Y(1)**(L(1,j)-1) * Y(2)**L(2,j) * Y(3)**L(3,j) &
)) > 1.d-14 ) return
end if
if (L(2,j) < 1) then
if (VGL(3,j) /= 0.d0) return
else
if (dabs(1.d0 - VGL(3,j) / (&
L(2,j) * Y(1)**L(1,j) * Y(2)**(L(2,j)-1) * Y(3)**L(3,j) &
)) > 1.d-14 ) return
end if
if (L(3,j) < 1) then
if (VGL(4,j) /= 0.d0) return
else
if (dabs(1.d0 - VGL(4,j) / (&
L(3,j) * Y(1)**L(1,j) * Y(2)**L(2,j) * Y(3)**(L(3,j)-1) &
)) > 1.d-14 ) return
end if
w = 0.d0
if (L(1,j) > 1) then
w = w + L(1,j) * (L(1,j)-1) * Y(1)**(L(1,j)-2) * Y(2)**L(2,j) * Y(3)**L(3,j)
end if
if (L(2,j) > 1) then
w = w + L(2,j) * (L(2,j)-1) * Y(1)**L(1,j) * Y(2)**(L(2,j)-2) * Y(3)**L(3,j)
end if
if (L(3,j) > 1) then
w = w + L(3,j) * (L(3,j)-1) * Y(1)**L(1,j) * Y(2)**L(2,j) * Y(3)**(L(3,j)-2)
end if
if (dabs(1.d0 - VGL(5,j) / w) > 1.d-14 ) return
end do
test_qmckl_ao_polynomial_vgl = 0
deallocate(L,VGL)
end function test_qmckl_ao_polynomial_vgl
#+END_SRC
#+BEGIN_SRC C :comments link :tangle test_qmckl_ao.c
int test_qmckl_ao_polynomial_vgl(qmckl_context context);
munit_assert_int(0, ==, test_qmckl_ao_polynomial_vgl(context));
#+END_SRC
#+END_SRC
* TODO Gaussian basis functions
* TODO Slater basis functions
* End of files :noexport:
*** Header
#+BEGIN_SRC C :comments link :tangle qmckl_ao.h
#endif
#+END_SRC
*** Test
#+BEGIN_SRC C :comments link :tangle test_qmckl_ao.c
if (qmckl_context_destroy(context) != QMCKL_SUCCESS)
return QMCKL_FAILURE;
return MUNIT_OK;
}
#+END_SRC

406
src/qmckl_context.org
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@ -1,406 +0,0 @@
# -*- mode: org -*-
# vim: syntax=c
#+TITLE: Context
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
#+HTML_HEAD: <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
#+HTML_HEAD: <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/lib/js/jquery.stickytableheaders.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
This file is written in C because it is more natural to express the context in
C than in Fortran.
3 files are produced:
- a header file : =qmckl_context.h=
- a source file : =qmckl_context.c=
- a test file : =test_qmckl_context.c=
*** Header :noexport:
#+BEGIN_SRC C :comments link :tangle qmckl_context.h
#ifndef QMCKL_CONTEXT_H
#define QMCKL_CONTEXT_H
#include "qmckl.h"
#+END_SRC
*** Source :noexport:
#+BEGIN_SRC C :comments link :tangle qmckl_context.c
#include "qmckl.h"
#+END_SRC
*** Test :noexport:
#+BEGIN_SRC C :comments link :tangle test_qmckl_context.c
#include "qmckl.h"
#include "munit.h"
MunitResult test_qmckl_context() {
#+END_SRC
* Context
The context variable is a handle for the state of the library, and
is stored in the following data structure, which can't be seen
outside of the library. To simplify compatibility with other
languages, the pointer to the internal data structure is converted
into a 64-bit signed integer, defined in the =qmckl_context= type.
A value of 0 for the context is equivalent to a =NULL= pointer.
*** Source
#+BEGIN_SRC C :comments link :tangle qmckl_context.c
typedef struct qmckl_context_struct {
struct qmckl_context_struct * prev;
uint32_t tag;
int32_t precision;
int32_t range;
} qmckl_context_struct;
#define VALID_TAG 0xBEEFFACE
#define INVALID_TAG 0xDEADBEEF
#+END_SRC
The tag is used internally to check if the memory domain pointed by
a pointer is a valid context.
*** Test :noexport:
We declare here the variables used in the tests.
#+BEGIN_SRC C :comments link :tangle test_qmckl_context.c
qmckl_context context;
qmckl_context new_context;
#+END_SRC
** =qmckl_context_check=
Checks if the domain pointed by the pointer is a valid context.
Returns the input =qmckl_context= if the context is valid, 0 otherwise.
*** Header
#+BEGIN_SRC C :comments link :tangle qmckl_context.h
qmckl_context qmckl_context_check(const qmckl_context context) ;
#+END_SRC
*** Source
#+BEGIN_SRC C :comments link :tangle qmckl_context.c
qmckl_context qmckl_context_check(const qmckl_context context) {
qmckl_context_struct * ctx;
if (context == (qmckl_context) 0) return (qmckl_context) 0;
ctx = (qmckl_context_struct*) context;
if (ctx->tag != VALID_TAG) return (qmckl_context) 0;
return context;
}
#+END_SRC
** =qmckl_context_create=
To create a new context, use =qmckl_context_create()=.
- On success, returns a pointer to a context using the =qmckl_context= type
- Returns 0 upon failure to allocate the internal data structure
*** Header
#+BEGIN_SRC C :comments link :tangle qmckl_context.h
qmckl_context qmckl_context_create();
#+END_SRC
*** Source
#+BEGIN_SRC C :comments link :tangle qmckl_context.c
qmckl_context qmckl_context_create() {
qmckl_context_struct* context;
context = (qmckl_context_struct*) qmckl_malloc ((qmckl_context) 0, sizeof(qmckl_context_struct));
if (context == NULL) {
return (qmckl_context) 0;
}
context->prev = NULL;
context->precision = QMCKL_DEFAULT_PRECISION;
context->range = QMCKL_DEFAULT_RANGE;
context->tag = VALID_TAG;
return (qmckl_context) context;
}
#+END_SRC
*** Test :noexport:
#+BEGIN_SRC C :comments link :tangle test_qmckl_context.c
context = qmckl_context_create();
munit_assert_int64( context, !=, (qmckl_context) 0);
munit_assert_int64( qmckl_context_check(context), ==, context);
#+END_SRC
** =qmckl_context_copy=
This function makes a shallow copy of the current context.
- Copying the 0-valued context returns 0
- On success, returns a pointer to the new context using the =qmckl_context= type
- Returns 0 upon failure to allocate the internal data structure
for the new context
*** Header
#+BEGIN_SRC C :comments link :tangle qmckl_context.h
qmckl_context qmckl_context_copy(const qmckl_context context);
#+END_SRC
*** Source
#+BEGIN_SRC C :comments link :tangle qmckl_context.c
qmckl_context qmckl_context_copy(const qmckl_context context) {
qmckl_context_struct* old_context;
qmckl_context_struct* new_context;
qmckl_context checked_context;
checked_context = qmckl_context_check(context);
if (checked_context == (qmckl_context) 0) {
return (qmckl_context) 0;
}
new_context = (qmckl_context_struct*) qmckl_malloc (context, sizeof(qmckl_context_struct));
if (new_context == NULL) {
return (qmckl_context) 0;
}
old_context = (qmckl_context_struct*) checked_context;
new_context->prev = old_context;
new_context->precision = old_context->precision;
new_context->range = old_context->range;
new_context->tag = VALID_TAG;
return (qmckl_context) new_context;
}
#+END_SRC
*** Test :noexport:
#+BEGIN_SRC C :comments link :tangle test_qmckl_context.c
new_context = qmckl_context_copy(context);
munit_assert_int64(new_context, !=, (qmckl_context) 0);
munit_assert_int64(new_context, !=, context);
munit_assert_int64(qmckl_context_check(new_context), ==, new_context);
#+END_SRC
** =qmckl_context_previous=
Returns the previous context
- On success, returns the ancestor of the current context
- Returns 0 for the initial context
- Returns 0 for the 0-valued context
*** Header
#+BEGIN_SRC C :comments link :tangle qmckl_context.h
qmckl_context qmckl_context_previous(const qmckl_context context);
#+END_SRC
*** Source
#+BEGIN_SRC C :comments link :tangle qmckl_context.c
qmckl_context qmckl_context_previous(const qmckl_context context) {
qmckl_context checked_context;
qmckl_context_struct* ctx;
checked_context = qmckl_context_check(context);
if (checked_context == (qmckl_context) 0) {
return (qmckl_context) 0;
}
ctx = (qmckl_context_struct*) checked_context;
return qmckl_context_check((qmckl_context) ctx->prev);
}
#+END_SRC
*** Test :noexport:
#+BEGIN_SRC C :comments link :tangle test_qmckl_context.c
munit_assert_int64(qmckl_context_previous(new_context), !=, (qmckl_context) 0);
munit_assert_int64(qmckl_context_previous(new_context), ==, context);
munit_assert_int64(qmckl_context_previous(context), ==, (qmckl_context) 0);
munit_assert_int64(qmckl_context_previous((qmckl_context) 0), ==, (qmckl_context) 0);
#+END_SRC
** =qmckl_context_destroy=
Destroys the current context, leaving the ancestors untouched.
- Succeeds if the current context is properly destroyed
- Fails otherwise
- Fails if the 0-valued context is given in argument
- Fails if the the pointer is not a valid context
*** Header
#+BEGIN_SRC C :comments link :tangle qmckl_context.h
qmckl_exit_code qmckl_context_destroy(qmckl_context context);
#+END_SRC
*** Source
#+BEGIN_SRC C :comments link :tangle qmckl_context.c
qmckl_exit_code qmckl_context_destroy(qmckl_context context) {
qmckl_context_struct* ctx;
qmckl_context checked_context;
checked_context = qmckl_context_check(context);
if (checked_context == (qmckl_context) 0) return QMCKL_FAILURE;
ctx = (qmckl_context_struct*) context;
if (ctx == NULL) return QMCKL_FAILURE;
ctx->tag = INVALID_TAG;
qmckl_free(ctx);
return QMCKL_SUCCESS;
}
#+END_SRC
*** Test :noexport:
#+BEGIN_SRC C :comments link :tangle test_qmckl_context.c
munit_assert_int64(qmckl_context_check(new_context), ==, new_context);
munit_assert_int64(new_context, !=, (qmckl_context) 0);
munit_assert_int32(qmckl_context_destroy(new_context), ==, QMCKL_SUCCESS);
munit_assert_int64(qmckl_context_check(new_context), !=, new_context);
munit_assert_int64(qmckl_context_check(new_context), ==, (qmckl_context) 0);
munit_assert_int64(qmckl_context_destroy((qmckl_context) 0), ==, QMCKL_FAILURE);
#+END_SRC
* Precision
The following functions set and get the expected required precision
and range. =precision= should be an integer between 2 and 53, and
=range= should be an integer between 2 and 11.
The setter functions functions return a new context as a 64-bit integer.
The getter functions return the value, as a 32-bit integer.
The update functions return =QMCKL_SUCCESS= or =QMCKL_FAILURE=.
** =qmckl_context_update_precision=
*** Source
#+BEGIN_SRC C :comments link :tangle qmckl_context.h
qmckl_exit_code qmckl_context_update_precision(const qmckl_context context, const int precision);
#+END_SRC
#+BEGIN_SRC C :comments link :tangle qmckl_context.c
qmckl_exit_code qmckl_context_update_precision(const qmckl_context context, const int precision) {
qmckl_context_struct* ctx;
if (precision < 2) return QMCKL_FAILURE;
if (precision > 53) return QMCKL_FAILURE;
ctx = (qmckl_context_struct*) context;
if (ctx == NULL) return QMCKL_FAILURE;
ctx->precision = precision;
return QMCKL_SUCCESS;
}
#+END_SRC
*** TODO Tests :noexport:
** =qmckl_context_update_range=
*** Source
#+BEGIN_SRC C :comments link :tangle qmckl_context.h
qmckl_exit_code qmckl_context_update_range(const qmckl_context context, const int range);
#+END_SRC
#+BEGIN_SRC C :comments link :tangle qmckl_context.c
qmckl_exit_code qmckl_context_update_range(const qmckl_context context, const int range) {
qmckl_context_struct* ctx;
if (range < 2) return QMCKL_FAILURE;
if (range > 11) return QMCKL_FAILURE;
ctx = (qmckl_context_struct*) context;
if (ctx == NULL) return QMCKL_FAILURE;
ctx->range = range;
return QMCKL_SUCCESS;
}
#+END_SRC
*** TODO Tests :noexport:
** =qmckl_context_set_precision=
*** Source
#+BEGIN_SRC C :comments link :tangle qmckl_context.h
qmckl_context qmckl_context_set_precision(const qmckl_context context, const int precision);
#+END_SRC
#+BEGIN_SRC C :comments link :tangle qmckl_context.c
qmckl_context qmckl_context_set_precision(const qmckl_context context, const int precision) {
qmckl_context new_context;
new_context = qmckl_context_copy(context);
if (new_context == 0) return 0;
if (qmckl_context_update_precision(context, precision) == QMCKL_FAILURE) return 0;
return new_context;
}
#+END_SRC
*** TODO Tests :noexport:
** =qmckl_context_set_range=
*** Source
#+BEGIN_SRC C :comments link :tangle qmckl_context.h
qmckl_context qmckl_context_set_range(const qmckl_context context, const int range);
#+END_SRC
#+BEGIN_SRC C :comments link :tangle qmckl_context.c
qmckl_context qmckl_context_set_range(const qmckl_context context, const int range) {
qmckl_context new_context;
new_context = qmckl_context_copy(context);
if (new_context == 0) return 0;
if (qmckl_context_update_range(context, range) == QMCKL_FAILURE) return 0;
return new_context;
}
#+END_SRC
*** TODO Tests :noexport:
** =qmckl_context_get_precision=
*** Source
#+BEGIN_SRC C :comments link :tangle qmckl_context.h
int qmckl_context_get_precision(const qmckl_context context);
#+END_SRC
#+BEGIN_SRC C :comments link :tangle qmckl_context.c
int qmckl_context_get_precision(const qmckl_context context) {
qmckl_context_struct* ctx;
ctx = (qmckl_context_struct*) context;
return ctx->precision;
}
#+END_SRC
*** TODO Tests :noexport:
** =qmckl_context_get_range=
*** Source
#+BEGIN_SRC C :comments link :tangle qmckl_context.h
int qmckl_context_get_range(const qmckl_context context);
#+END_SRC
#+BEGIN_SRC C :comments link :tangle qmckl_context.c
int qmckl_context_get_range(const qmckl_context context) {
qmckl_context_struct* ctx;
ctx = (qmckl_context_struct*) context;
return ctx->range;
}
#+END_SRC
*** TODO Tests :noexport:
* End of files :noexport:
*** Header
#+BEGIN_SRC C :comments link :tangle qmckl_context.h
#endif
#+END_SRC
*** Test
#+BEGIN_SRC C :comments link :tangle test_qmckl_context.c
return MUNIT_OK;
}
#+END_SRC

378
src/qmckl_distance.org
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@ -1,378 +0,0 @@
# -*- mode: org -*-
# vim: syntax=c
#+TITLE: Computation of distances
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
#+HTML_HEAD: <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
#+HTML_HEAD: <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/lib/js/jquery.stickytableheaders.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
Function for the computation of distances between particles.
3 files are produced:
- a header file : =qmckl_distance.h=
- a source file : =qmckl_distance.f90=
- a C test file : =test_qmckl_distance.c=
- a Fortran test file : =test_qmckl_distance_f.f90=
*** Header :noexport:
#+BEGIN_SRC C :comments link :tangle qmckl_distance.h
#ifndef QMCKL_DISTANCE_H
#define QMCKL_DISTANCE_H
#include "qmckl_context.h"
#+END_SRC
*** Test :noexport:
#+BEGIN_SRC C :comments link :tangle test_qmckl_distance.c
#include <math.h>
#include "qmckl.h"
#include "munit.h"
MunitResult test_qmckl_distance() {
qmckl_context context;
context = qmckl_context_create();
#+END_SRC
* Squared distance
** =qmckl_distance_sq=
Computes the matrix of the squared distances between all pairs of
points in two sets, one point within each set:
\[
C_{ij} = \sum_{k=1}^3 (A_{k,i}-B_{k,j})^2
\]
*** Arguments
| =context= | input | Global state |
| =transa= | input | Array =A= is =N=: Normal, =T=: Transposed |
| =transb= | input | Array =B= is =N=: Normal, =T=: Transposed |
| =m= | input | Number of points in the first set |
| =n= | input | Number of points in the second set |
| =A(lda,3)= | input | Array containing the $m \times 3$ matrix $A$ |
| =lda= | input | Leading dimension of array =A= |
| =B(ldb,3)= | input | Array containing the $n \times 3$ matrix $B$ |
| =ldb= | input | Leading dimension of array =B= |
| =C(ldc,n)= | output | Array containing the $m \times n$ matrix $C$ |
| =ldc= | input | Leading dimension of array =C= |
*** Requirements
- =context= is not 0
- =m= > 0
- =n= > 0
- =lda= >= 3 if =transa= is =N=
- =lda= >= m if =transa= is =T=
- =ldb= >= 3 if =transb= is =N=
- =ldb= >= n if =transb= is =T=
- =ldc= >= m if =transa= is =
- =A= is allocated with at least $3 \times m \times 8$ bytes
- =B= is allocated with at least $3 \times n \times 8$ bytes
- =C= is allocated with at least $m \times n \times 8$ bytes
*** Performance
This function might be more efficient when =A= and =B= are
transposed.
*** Header
#+BEGIN_SRC C :comments link :tangle qmckl_distance.h
qmckl_exit_code qmckl_distance_sq(qmckl_context context,
char transa, char transb,
int64_t m, int64_t n,
double *A, int64_t lda,
double *B, int64_t ldb,
double *C, int64_t ldc);
#+END_SRC
*** Source
#+BEGIN_SRC f90 :comments link :tangle qmckl_distance.f90
integer function qmckl_distance_sq_f(context, transa, transb, m, n, A, LDA, B, LDB, C, LDC) result(info)
implicit none
integer*8 , intent(in) :: context
character , intent(in) :: transa, transb
integer*8 , intent(in) :: m, n
integer*8 , intent(in) :: lda
real*8 , intent(in) :: A(lda,*)
integer*8 , intent(in) :: ldb
real*8 , intent(in) :: B(ldb,*)
integer*8 , intent(in) :: ldc
real*8 , intent(out) :: C(ldc,*)
integer*8 :: i,j
real*8 :: x, y, z
integer :: transab
info = 0
if (context == 0_8) then
info = -1
return
endif
if (m <= 0_8) then
info = -2
return
endif
if (n <= 0_8) then
info = -3
return
endif
if (transa == 'N' .or. transa == 'n') then
transab = 0
else if (transa == 'T' .or. transa == 't') then
transab = 1
else
transab = -100
endif
if (transb == 'N' .or. transb == 'n') then
continue
else if (transa == 'T' .or. transa == 't') then
transab = transab + 2
else
transab = -100
endif
if (transab < 0) then
info = -4
return
endif
if (iand(transab,1) == 0 .and. LDA < 3) then
info = -5
return
endif
if (iand(transab,1) == 1 .and. LDA < m) then
info = -6
return
endif
if (iand(transab,2) == 0 .and. LDA < 3) then
info = -6
return
endif
if (iand(transab,2) == 2 .and. LDA < m) then
info = -7
return
endif
select case (transab)
case(0)
do j=1,n
do i=1,m
x = A(1,i) - B(1,j)
y = A(2,i) - B(2,j)
z = A(3,i) - B(3,j)
C(i,j) = x*x + y*y + z*z
end do
end do
case(1)
do j=1,n
do i=1,m
x = A(i,1) - B(1,j)
y = A(i,2) - B(2,j)
z = A(i,3) - B(3,j)
C(i,j) = x*x + y*y + z*z
end do
end do
case(2)
do j=1,n
do i=1,m
x = A(1,i) - B(j,1)
y = A(2,i) - B(j,2)
z = A(3,i) - B(j,3)
C(i,j) = x*x + y*y + z*z
end do
end do
case(3)
do j=1,n
do i=1,m
x = A(i,1) - B(j,1)
y = A(i,2) - B(j,2)
z = A(i,3) - B(j,3)
C(i,j) = x*x + y*y + z*z
end do
end do
end select
end function qmckl_distance_sq_f
#+END_SRC
*** C interface :noexport:
#+BEGIN_SRC f90 :comments link :tangle qmckl_distance.f90
integer(c_int32_t) function qmckl_distance_sq(context, transa, transb, m, n, A, LDA, B, LDB, C, LDC) &
bind(C) result(info)
use, intrinsic :: iso_c_binding
implicit none
integer (c_int64_t) , intent(in) , value :: context
character (c_char) , intent(in) , value :: transa, transb
integer (c_int64_t) , intent(in) , value :: m, n
integer (c_int64_t) , intent(in) , value :: lda
real (c_double) , intent(in) :: A(lda,3)
integer (c_int64_t) , intent(in) , value :: ldb
real (c_double) , intent(in) :: B(ldb,3)
integer (c_int64_t) , intent(in) , value :: ldc
real (c_double) , intent(out) :: C(ldc,n)
integer, external :: qmckl_distance_sq_f
info = qmckl_distance_sq_f(context, transa, transb, m, n, A, LDA, B, LDB, C, LDC)
end function qmckl_distance_sq
#+END_SRC
#+BEGIN_SRC f90 :comments link :tangle qmckl_distance.fh
interface
integer(c_int32_t) function qmckl_distance_sq(context, transa, transb, m, n, A, LDA, B, LDB, C, LDC) &
bind(C)
use, intrinsic :: iso_c_binding
implicit none
integer (c_int64_t) , intent(in) , value :: context
character (c_char) , intent(in) , value :: transa, transb
integer (c_int64_t) , intent(in) , value :: m, n
integer (c_int64_t) , intent(in) , value :: lda
integer (c_int64_t) , intent(in) , value :: ldb
integer (c_int64_t) , intent(in) , value :: ldc
real (c_double) , intent(in) :: A(lda,3)
real (c_double) , intent(in) :: B(ldb,3)
real (c_double) , intent(out) :: C(ldc,n)
end function qmckl_distance_sq
end interface
#+END_SRC
*** Test :noexport:
#+BEGIN_SRC f90 :comments link :tangle test_qmckl_distance_f.f90
integer(c_int32_t) function test_qmckl_distance_sq(context) bind(C)
use, intrinsic :: iso_c_binding
implicit none
include 'qmckl_distance.fh'
integer(c_int64_t), intent(in), value :: context
double precision, allocatable :: A(:,:), B(:,:), C(:,:)
integer*8 :: m, n, LDA, LDB, LDC
double precision :: x
integer*8 :: i,j
m = 5
n = 6
LDA = m
LDB = n
LDC = 5
allocate( A(LDA,m), B(LDB,n), C(LDC,n) )
do j=1,m
do i=1,m
A(i,j) = -10.d0 + dble(i+j)
end do
end do
do j=1,n
do i=1,n
B(i,j) = -1.d0 + dble(i*j)
end do
end do
test_qmckl_distance_sq = qmckl_distance_sq(context, 'X', 't', m, n, A, LDA, B, LDB, C, LDC)
if (test_qmckl_distance_sq == 0) return
test_qmckl_distance_sq = qmckl_distance_sq(context, 't', 'X', m, n, A, LDA, B, LDB, C, LDC)
if (test_qmckl_distance_sq == 0) return
test_qmckl_distance_sq = qmckl_distance_sq(context, 'T', 't', m, n, A, LDA, B, LDB, C, LDC)
if (test_qmckl_distance_sq /= 0) return
test_qmckl_distance_sq = -1
do j=1,n
do i=1,m
x = (A(i,1)-B(j,1))**2 + &
(A(i,2)-B(j,2))**2 + &
(A(i,3)-B(j,3))**2
if ( dabs(1.d0 - C(i,j)/x) > 1.d-14 ) return
end do
end do
test_qmckl_distance_sq = qmckl_distance_sq(context, 'n', 'T', m, n, A, LDA, B, LDB, C, LDC)
if (test_qmckl_distance_sq /= 0) return
test_qmckl_distance_sq = -1
do j=1,n
do i=1,m
x = (A(1,i)-B(j,1))**2 + &
(A(2,i)-B(j,2))**2 + &
(A(3,i)-B(j,3))**2
if ( dabs(1.d0 - C(i,j)/x) > 1.d-14 ) return
end do
end do
test_qmckl_distance_sq = qmckl_distance_sq(context, 'T', 'n', m, n, A, LDA, B, LDB, C, LDC)
if (test_qmckl_distance_sq /= 0) return
test_qmckl_distance_sq = -1
do j=1,n
do i=1,m
x = (A(i,1)-B(1,j))**2 + &
(A(i,2)-B(2,j))**2 + &
(A(i,3)-B(3,j))**2
if ( dabs(1.d0 - C(i,j)/x) > 1.d-14 ) return
end do
end do
test_qmckl_distance_sq = qmckl_distance_sq(context, 'n', 'N', m, n, A, LDA, B, LDB, C, LDC)
if (test_qmckl_distance_sq /= 0) return
test_qmckl_distance_sq = -1
do j=1,n
do i=1,m
x = (A(1,i)-B(1,j))**2 + &
(A(2,i)-B(2,j))**2 + &
(A(3,i)-B(3,j))**2
if ( dabs(1.d0 - C(i,j)/x) > 1.d-14 ) return
end do
end do
test_qmckl_distance_sq = 0
deallocate(A,B,C)
end function test_qmckl_distance_sq
#+END_SRC
#+BEGIN_SRC C :comments link :tangle test_qmckl_distance.c
int test_qmckl_distance_sq(qmckl_context context);
munit_assert_int(0, ==, test_qmckl_distance_sq(context));
#+END_SRC
* End of files :noexport:
*** Header
#+BEGIN_SRC C :comments link :tangle qmckl_distance.h
#endif
#+END_SRC
*** Test
#+BEGIN_SRC C :comments link :tangle test_qmckl_distance.c
if (qmckl_context_destroy(context) != QMCKL_SUCCESS)
return QMCKL_FAILURE;
return MUNIT_OK;
}
#+END_SRC

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# -*- mode: org -*-
# vim: syntax=c
#+TITLE: Memory management
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
#+HTML_HEAD: <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
#+HTML_HEAD: <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/lib/js/jquery.stickytableheaders.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
We override the allocation functions to enable the possibility of
optimized libraries to fine-tune the memory allocation.
3 files are produced:
- a header file : =qmckl_memory.h=
- a source file : =qmckl_memory.c=
- a test file : =test_qmckl_memory.c=
** Header :noexport:
#+BEGIN_SRC C :comments link :tangle qmckl_memory.h
#ifndef QMCKL_MEMORY_H
#define QMCKL_MEMORY_H
#include "qmckl.h"
#+END_SRC
** Source :noexport:
#+BEGIN_SRC C :comments link :tangle qmckl_memory.c
#include <stdlib.h>
#include "qmckl_memory.h"
#+END_SRC
** Test :noexport:
#+BEGIN_SRC C :comments link :tangle test_qmckl_memory.c
#include "qmckl.h"
#include "munit.h"
MunitResult test_qmckl_memory() {
#+END_SRC
* =qmckl_malloc=
Analogous of =malloc, but passing a context and a signed 64-bit integers as argument.=
** Header
#+BEGIN_SRC C :comments link :tangle qmckl_memory.h
void* qmckl_malloc(const qmckl_context ctx, const size_t size);
#+END_SRC
** Source
#+BEGIN_SRC C :comments link :tangle qmckl_memory.c
void* qmckl_malloc(const qmckl_context ctx, const size_t size) {
if (ctx == (qmckl_context) 0) {
/* Avoids unused parameter error */
return malloc( (size_t) size );
}
return malloc( (size_t) size );
}
#+END_SRC
** Test :noexport:
#+BEGIN_SRC C :comments link :tangle test_qmckl_memory.c
int *a;
a = (int*) qmckl_malloc( (qmckl_context) 1, 3*sizeof(int));
a[0] = 1;
a[1] = 2;
a[2] = 3;
munit_assert_int(a[0], ==, 1);
munit_assert_int(a[1], ==, 2);
munit_assert_int(a[2], ==, 3);
#+END_SRC
* =qmckl_free=
** Header
#+BEGIN_SRC C :comments link :tangle qmckl_memory.h
void qmckl_free(void *ptr);
#+END_SRC
** Source
#+BEGIN_SRC C :comments link :tangle qmckl_memory.c
void qmckl_free(void *ptr) {
free(ptr);
}
#+END_SRC
** Test :noexport:
#+BEGIN_SRC C :comments link :tangle test_qmckl_memory.c
qmckl_free(a);
#+END_SRC
* End of files :noexport:
** Header
#+BEGIN_SRC C :comments link :tangle qmckl_memory.h
#endif
#+END_SRC
** Test
#+BEGIN_SRC C :comments link :tangle test_qmckl_memory.c
return MUNIT_OK;
}
#+END_SRC

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#+TITLE: QMCkl test
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
#+HTML_HEAD: <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
#+HTML_HEAD: <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/lib/js/jquery.stickytableheaders.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
This file is the main program of the unit tests. The tests rely on the
$\mu$unit framework, which is provided as a git submodule.
First, we use a script to find the list of all the produced test files:
#+NAME: test-files
#+BEGIN_SRC sh :exports none :results value
grep BEGIN_SRC *.org | \
grep test_qmckl_ | \
rev | \
cut -d ' ' -f 1 | \
rev | \
sort | \
uniq
#+END_SRC
#+RESULTS: test-files
| test_qmckl_ao.c |
| test_qmckl_context.c |
| test_qmckl_distance.c |
| test_qmckl_memory.c |
We generate the function headers
#+BEGIN_SRC sh :var files=test-files :exports output :results raw
echo "#+NAME: headers"
echo "#+BEGIN_SRC C :tangle no"
for file in $files
do
routine=${file%.c}
echo "MunitResult ${routine}();"
done
echo "#+END_SRC"
#+END_SRC
#+RESULTS:
#+NAME: headers
#+BEGIN_SRC C :tangle no
MunitResult test_qmckl_ao();
MunitResult test_qmckl_context();
MunitResult test_qmckl_distance();
MunitResult test_qmckl_memory();
#+END_SRC
and the required function calls:
#+BEGIN_SRC sh :var files=test-files :exports output :results raw
echo "#+NAME: calls"
echo "#+BEGIN_SRC C :tangle no"
for file in $files
do
routine=${file%.c}
echo " { (char*) \"${routine}\", ${routine}, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},"
done
echo "#+END_SRC"
#+END_SRC
#+RESULTS:
#+NAME: calls
#+BEGIN_SRC C :tangle no
{ (char*) "test_qmckl_ao", test_qmckl_ao, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},
{ (char*) "test_qmckl_context", test_qmckl_context, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},
{ (char*) "test_qmckl_distance", test_qmckl_distance, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},
{ (char*) "test_qmckl_memory", test_qmckl_memory, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},
#+END_SRC
#+BEGIN_SRC C :comments link :noweb yes :tangle test_qmckl.c
#include "qmckl.h"
#include "munit.h"
<<headers>>
int main(int argc, char* argv[MUNIT_ARRAY_PARAM(argc + 1)]) {
static MunitTest test_suite_tests[] =
{
<<calls>>
{ NULL, NULL, NULL, NULL, MUNIT_TEST_OPTION_NONE, NULL }
};
static const MunitSuite test_suite =
{
(char*) "", test_suite_tests, NULL, 1, MUNIT_SUITE_OPTION_NONE
};
return munit_suite_main(&test_suite, (void*) "µnit", argc, argv);
}
#+END_SRC

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<h1 class="title">QMCkl test</h1>
<p>
This file is the main program of the unit tests. The tests rely on the
$&mu;$unit framework, which is provided as a git submodule.
</p>
<p>
First, we use a script to find the list of all the produced test files:
We generate the function headers
</p>
<div class="org-src-container">
<pre class="src src-sh">echo "#+NAME: headers"
echo "#+BEGIN_SRC C :tangle no"
for file in $files
do
routine=${file%.c}
echo "MunitResult ${routine}();"
done
echo "#+END_SRC"
</pre>
</div>
<div class="org-src-container">
<pre class="src src-C" id="headers">MunitResult test_qmckl_ao();
MunitResult test_qmckl_context();
MunitResult test_qmckl_distance();
MunitResult test_qmckl_memory();
</pre>
</div>
<p>
and the required function calls:
</p>
<div class="org-src-container">
<pre class="src src-sh">echo "#+NAME: calls"
echo "#+BEGIN_SRC C :tangle no"
for file in $files
do
routine=${file%.c}
echo " { (char*) \"${routine}\", ${routine}, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},"
done
echo "#+END_SRC"
</pre>
</div>
<div class="org-src-container">
<pre class="src src-C" id="calls">{ (char*) "test_qmckl_ao", test_qmckl_ao, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},
{ (char*) "test_qmckl_context", test_qmckl_context, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},
{ (char*) "test_qmckl_distance", test_qmckl_distance, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},
{ (char*) "test_qmckl_memory", test_qmckl_memory, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},
</pre>
</div>
<div class="org-src-container">
<pre class="src src-C">#include "qmckl.h"
#include "munit.h"
MunitResult test_qmckl_ao();
MunitResult test_qmckl_context();
MunitResult test_qmckl_distance();
MunitResult test_qmckl_memory();
int main(int argc, char* argv[MUNIT_ARRAY_PARAM(argc + 1)]) {
static MunitTest test_suite_tests[] =
{
{ (char*) "test_qmckl_ao", test_qmckl_ao, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},
{ (char*) "test_qmckl_context", test_qmckl_context, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},
{ (char*) "test_qmckl_distance", test_qmckl_distance, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},
{ (char*) "test_qmckl_memory", test_qmckl_memory, NULL,NULL,MUNIT_TEST_OPTION_NONE,NULL},
{ NULL, NULL, NULL, NULL, MUNIT_TEST_OPTION_NONE, NULL }
};
static const MunitSuite test_suite =
{
(char*) "", test_suite_tests, NULL, 1, MUNIT_SUITE_OPTION_NONE
};
return munit_suite_main(&amp;test_suite, (void*) "µnit", argc, argv);
}
</pre>
</div>
</div>
<div id="postamble" class="status">
<p class="date">Created: 2020-10-28 Wed 23:57</p>
<p class="creator"><a href="http://www.gnu.org/software/emacs/">Emacs</a> 25.2.2 (<a href="http://orgmode.org">Org</a> mode 8.2.10)</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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