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3
.gitmodules
vendored
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3
.gitmodules
vendored
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@ -0,0 +1,3 @@
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[submodule "munit"]
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path = munit
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url = https://github.com/nemequ/munit/
|
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29
LICENSE
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29
LICENSE
Normal file
@ -0,0 +1,29 @@
|
||||
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.
|
||||
28
README.md
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28
README.md
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@ -0,0 +1,28 @@
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# QMCkl: Quantum Monte Carlo Kernel Library
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The domain of quantum chemistry needs a library in which the main
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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
|
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development of high-performance QMCkl implementations taking
|
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advantage of modern hardware.
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|
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See the [source code](https://github.com/TREX-CoE/qmckl/tree/main/src)
|
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to read the documentation.
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|
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To clone the repository, use:
|
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```
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git clone --recursive https://github.com/TREX-CoE/qmckl.git
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```
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to dowload also the [munit](https://github.com/nemequ/munit) unit testing
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framework.
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|
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|
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------------------------------
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|
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[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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21
TODO.org
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21
TODO.org
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@ -0,0 +1,21 @@
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* Set up CI on Travis
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* Write tests
|
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|
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* malloc/free : Parameters for accelerators?
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We should define qmckl_malloc and qmckl_free just to give the
|
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possibility of the HPC implementations to define how they allocate the
|
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memory (on CPU or GPU, using alternatives to malloc/free, etc).
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A possibility could be to pass the id of a NUMA domain as a parameter of
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qmckl_malloc, where the domain id is something obtained from the
|
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context.
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|
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|
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* TRANSA, TRANSB
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* Performance info
|
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* Benchmark interpolation of basis functions
|
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* Complex numbers
|
||||
* Adjustable number for derivatives (1,2,3)
|
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|
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* Put pictures
|
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* Make the Makefile part of the documented code ?
|
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* Put the data-flow graph in the code.
|
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0
.gitignore → docs/.gitignore
vendored
0
.gitignore → docs/.gitignore
vendored
1
emacs-htmlize/.gitignore
vendored
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1
emacs-htmlize/.gitignore
vendored
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@ -0,0 +1 @@
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*.elc
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48
emacs-htmlize/NEWS
Normal file
48
emacs-htmlize/NEWS
Normal file
@ -0,0 +1,48 @@
|
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htmlize NEWS -- history of user-visible changes.
|
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|
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* Changes in htmlize 1.51
|
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|
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** `htmlize-face-overrides' can be used to override Emacs's face
|
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definitions.
|
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|
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|
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* Changes in htmlize 1.47
|
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|
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** GNU Emacs 21 is no longer supported.
|
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|
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|
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* Changes in htmlize 1.45
|
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|
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** Correctly handle :inherit specifying a list of faces. (This bug
|
||||
would cause an error in AUX TeX buffers.)
|
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|
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|
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* Changes in htmlize 1.44
|
||||
|
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** Faces specified in the `face' property are now prioritized the same
|
||||
way that Emacs redisplay does it: faces that appear earlier have
|
||||
precedence over those that appear later.
|
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|
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|
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* Changes in htmlize 1.41
|
||||
|
||||
** `before-string' and `after-string' overlay properties are now
|
||||
recognized by htmlize and inserted into the HTML.
|
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|
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** Images specified by `display' property are recognized and inserted
|
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into the HTML as <img src=...>.
|
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|
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*** If the image data comes from a file, the image will be rendered as
|
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a relative URI that would resolve to that file. Images whose data
|
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comes from a string will be rendered inline as data: URIs. The flag
|
||||
`htmlize-force-inline-images' can be used to force inserting *all*
|
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images inline as data: URIs.
|
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|
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** The image's ALT text will be the text that the `display' property is
|
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replacing, if non-empty.
|
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|
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** Arbitrary links can now be added to the generated HTML. If htmlize
|
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encounters buffer text with `htmlize-link' property, it will wrap the
|
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text in <a href="uri">...</a>. If the property value is a string, it
|
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is interpreted as the URI. If it is a list, it should be a property
|
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list whose currently only defined key is :uri.
|
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36
emacs-htmlize/README.md
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36
emacs-htmlize/README.md
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# htmlize --- Convert buffer text and decorations to HTML
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|
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[](https://melpa.org/#/htmlize)
|
||||
|
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This package converts the buffer text and the associated
|
||||
decorations to HTML. Mail to <hniksic@gmail.com> to discuss
|
||||
features and additions. All suggestions are more than welcome.
|
||||
|
||||
To use it, just switch to the buffer you want HTML-ized and type
|
||||
<kbd>M-x htmlize-buffer</kbd>. You will be switched to a new buffer
|
||||
that contains the resulting HTML code. You can edit and inspect this
|
||||
buffer, or you can just save it with <kbd>C-x C-w</kbd>. <kbd>M-x
|
||||
htmlize-file</kbd> will find a file, fontify it, and save the HTML
|
||||
version in `FILE.html`, without any additional intervention. <kbd>M-x
|
||||
htmlize-many-files</kbd> allows you to htmlize any number of files in
|
||||
the same manner. <kbd>M-x htmlize-many-files-dired</kbd> does the
|
||||
same for files marked in a dired buffer.
|
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|
||||
htmlize supports three types of HTML output, selected by setting
|
||||
`htmlize-output-type`: `css`, `inline-css` (optimized for code
|
||||
snippets), and `font` (simpler output, doesn't rely on CSS). See
|
||||
[`htmlize.el.html`][1] for an example of generated HTML.
|
||||
|
||||
You can also use htmlize from your Emacs Lisp code. When called
|
||||
non-interactively, `htmlize-buffer` and `htmlize-region` will
|
||||
return the resulting HTML buffer, but will not change current
|
||||
buffer or move the point. htmlize will do its best to work on
|
||||
non-windowing Emacs sessions but the result will be limited to
|
||||
colors supported by the terminal.
|
||||
|
||||
htmlize aims for compatibility with older Emacs versions. Please
|
||||
let me know if it doesn't work on the version of GNU Emacs that you
|
||||
are using.
|
||||
|
||||
|
||||
[1]: http://htmlpreview.github.io/?https://github.com/hniksic/emacs-htmlize/blob/master/htmlize.el.html
|
||||
1882
emacs-htmlize/htmlize.el
Normal file
1882
emacs-htmlize/htmlize.el
Normal file
File diff suppressed because it is too large
Load Diff
2032
emacs-htmlize/htmlize.el.html
Normal file
2032
emacs-htmlize/htmlize.el.html
Normal file
File diff suppressed because it is too large
Load Diff
11
src/.gitignore
vendored
Normal file
11
src/.gitignore
vendored
Normal file
@ -0,0 +1,11 @@
|
||||
*.o
|
||||
*.c
|
||||
*.f90
|
||||
*.h
|
||||
*.fh
|
||||
*.html
|
||||
*~
|
||||
*.so
|
||||
Makefile.generated
|
||||
test_qmckl
|
||||
merged_qmckl.org
|
||||
63
src/Makefile
Normal file
63
src/Makefile
Normal file
@ -0,0 +1,63 @@
|
||||
COMPILER=GNU
|
||||
#COMPILER=INTEL
|
||||
#COMPILER=LLVM
|
||||
|
||||
ifeq ($(COMPILER),GNU)
|
||||
CC=gcc -g
|
||||
CFLAGS=-fPIC -fexceptions -Wall -Werror -Wpedantic -Wextra
|
||||
|
||||
FC=gfortran -g
|
||||
FFLAGS=-fPIC -fcheck=all -Waliasing -Wampersand -Wconversion -Wsurprising -Wintrinsics-std -Wno-tabs -Wintrinsic-shadow -Wline-truncation -Wreal-q-constant -Wuninitialized -fbacktrace -ffpe-trap=zero,overflow,underflow -finit-real=nan
|
||||
|
||||
LIBS=-lgfortran -lm
|
||||
endif
|
||||
|
||||
ifeq ($(COMPILER),INTEL)
|
||||
CC=icc -xHost
|
||||
CFLAGS=-fPIC -g -O2
|
||||
|
||||
FC=ifort -xHost
|
||||
FFLAGS=-fPIC -g -O2
|
||||
|
||||
LIBS=-lm -lifcore -lirc
|
||||
endif
|
||||
|
||||
#TODO
|
||||
ifeq ($(COMPILER),LLVM)
|
||||
CC=clang
|
||||
CFLAGS=-fPIC -g -O2
|
||||
|
||||
FC=flang
|
||||
FFLAGS=fPIC -g -O2
|
||||
|
||||
LIBS=-lm
|
||||
endif
|
||||
|
||||
|
||||
QMCKL_ROOT=$(shell dirname $(CURDIR))
|
||||
|
||||
export CC CFLAGS FC FFLAGS LIBS QMCKL_ROOT
|
||||
|
||||
ORG_SOURCE_FILES=$(wildcard *.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)
|
||||
$(QMCKL_ROOT)/tools/create_doc.sh
|
||||
|
||||
|
||||
clean:
|
||||
rm -f qmckl.h test_qmckl_* test_qmckl.c test_qmckl qmckl_*.f90 qmckl_*.c qmckl_*.o qmckl_*.h Makefile.generated libqmckl.so *.html *.fh *.mod
|
||||
|
||||
Makefile.generated: Makefile $(QMCKL_ROOT)/tools/create_makefile.sh $(ORG_SOURCE_FILES)
|
||||
$(QMCKL_ROOT)/tools/create_makefile.sh
|
||||
|
||||
246
src/README.org
Normal file
246
src/README.org
Normal file
@ -0,0 +1,246 @@
|
||||
#+TITLE: QMCkl source code documentation
|
||||
#+EXPORT_FILE_NAME: index.html
|
||||
#+PROPERTY: comments org
|
||||
|
||||
#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
|
||||
|
||||
|
||||
* Introduction
|
||||
|
||||
|
||||
The ultimate goal of the QMCkl library is to provide a high-performance
|
||||
implementation of the main kernels of QMC. In this particular
|
||||
implementation of the library, 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
|
||||
|
||||
In a traditional source code, most of the lines of source files of a program
|
||||
are code, scripts, Makefiles, and only a few lines are comments explaining
|
||||
parts of the code that are non-trivial to understand. The documentation of
|
||||
the prorgam is usually written in a separate directory, and is often outdated
|
||||
compared to the code.
|
||||
|
||||
Literate programming is a different approach to programming,
|
||||
where the program is considered as a publishable-quality document. Most of
|
||||
the lines of the source files are text, mathematical formulas, tables,
|
||||
figures, /etc/, and the lines of code are just the translation in a computer
|
||||
language of the ideas and algorithms expressed in the text. More importantly,
|
||||
the "document" is structured like a text document with sections, subsections,
|
||||
a bibliography, a table of contents /etc/, and the place where pieces of code
|
||||
appear are the places where they should belong for the reader to understand
|
||||
the logic of the program, not the places where the compiler expects to find
|
||||
them. Both the publishable-quality document and the binary executable are
|
||||
produced from the same source files.
|
||||
|
||||
Literate programming is particularly well adapted in this context, as the
|
||||
central part of this project is the documentation of an API. The
|
||||
implementation of the algorithms is just an expression of the algorithms in a
|
||||
language that can be compiled, so that the correctness of the algorithms can
|
||||
be tested.
|
||||
|
||||
We have chosen to write the source files in [[https://karl-voit.at/2017/09/23/orgmode-as-markup-only/][org-mode]] format,
|
||||
as any text editor can be used to edit org-mode files. To
|
||||
produce the documentation, there exists multiple possibilities to convert
|
||||
org-mode files into different formats such as HTML or PDF. The source code is
|
||||
easily extracted from the org-mode files invoking the Emacs text editor from
|
||||
the command-line in the =Makefile=, and then the produced files are compiled.
|
||||
Moreover, within the Emacs text editor the source code blocks can be executed
|
||||
interactively, in the same spirit as Jupyter notebooks.
|
||||
|
||||
|
||||
** Source code editing
|
||||
|
||||
For a tutorial on literate programming with org-mode, follow [[http://www.howardism.org/Technical/Emacs/literate-programming-tutorial.html][this link]].
|
||||
|
||||
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.
|
||||
|
||||
In the =tools/init.el= file, we provide a minimal Emacs configuration
|
||||
file for vim users. This file should be copied into =.emacs.d/init.el=.
|
||||
|
||||
For users with a preference for Jupyter notebooks, we also provide the
|
||||
=tools/nb_to_org.sh= script can convert jupyter notebooks into org-mode
|
||||
files.
|
||||
|
||||
Note that pandoc can be used to convert multiple markdown formats into
|
||||
org-mode.
|
||||
|
||||
|
||||
** Choice of the programming language
|
||||
|
||||
Most of the codes of the TREX CoE are written in Fortran with some scripts in
|
||||
Bash and Python. Outside of the CoE, Fortran is also important (Casino, Amolqc),
|
||||
and other important languages used by the community are C and C++ (QMCPack,
|
||||
QWalk), and Julia is gaining in popularity. The library we design should be
|
||||
compatible with all of these languages. The QMCkl API has to be compatible
|
||||
with the C language since libraries with a C-compatible API can be used in
|
||||
every other language.
|
||||
|
||||
High-performance versions of the QMCkl, with the same API, will be rewritten by
|
||||
the experts in HPC. These optimized libraries will be tuned for specific
|
||||
architectures, among which we can cite x86 based processors, and GPU
|
||||
accelerators. Nowadays, the most efficient software tools to take advantage of
|
||||
low-level features of the processor (intrinsics) and of GPUs are for C++
|
||||
developers. It is highly probable that the optimized implementations will be
|
||||
written in C++, and this is agreement with our choice to make the API
|
||||
C-compatible.
|
||||
|
||||
Fortran is one of the most common languages used by the community, and is simple
|
||||
enough to make the algorithms readable both by experts in QMC, and experts in
|
||||
HPC. Hence we propose in this pedagogical implementation of QMCkl to use Fortran
|
||||
to express the QMC algorithms. As the main languages of the library is C, this
|
||||
implies that the exposed C functions call the Fortran routine. However, for
|
||||
internal functions related to system programming, the C language is more natural
|
||||
than Fortran.
|
||||
|
||||
The Fortran source files should provide a C interface using the
|
||||
~iso_c_binding~ module. 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 interfaces should also be written in the =qmckl_f.f90= file.
|
||||
|
||||
For more guidelines on using Fortran to generate a C interface, see
|
||||
[[http://fortranwiki.org/fortran/show/Generating+C+Interfaces][this link]].
|
||||
|
||||
|
||||
# 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, and to use different levels of floating-point
|
||||
precision. We chose a multi-layered design with low-level and high-level
|
||||
functions (see below).
|
||||
|
||||
*** Naming conventions
|
||||
|
||||
To avoid namespace collisions, we use =qmckl_= as a prefix for all exported
|
||||
functions and variables. All exported header files should have a file name
|
||||
prefixed with =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 file should be =xxx.f90=.
|
||||
|
||||
Arrays are in uppercase and scalars are in lowercase.
|
||||
|
||||
In the names of the variables and functions, only the singular
|
||||
form is allowed.
|
||||
|
||||
*** Application programming interface
|
||||
|
||||
In the C language, the number of bits used by the integer types can change
|
||||
from one architecture to another one. To circumvent this problem, we choose to
|
||||
use the integer types defined in ~<stdint.h>~ where the number of bits used for
|
||||
the integers are fixed.
|
||||
|
||||
To ensure that the library will be easily usable in /any/ other language
|
||||
than C, we restrict the data types in the interfaces to the following:
|
||||
- 32-bit and 64-bit integers, scalars and and arrays (~int32_t~ and ~int64_t~)
|
||||
- 32-bit and 64-bit floats, scalars and and arrays (~float~ and ~double~)
|
||||
- Pointers are always casted into 64-bit integers, even on legacy 32-bit architectures
|
||||
- ASCII strings are represented as a pointers to character arrays
|
||||
and terminated by a ~'\0'~ character (C convention).
|
||||
- Complex numbers can be represented by an array of 2 floats.
|
||||
- Boolean variables are stored as integers, ~1~ for ~true~ and ~0~ for ~false~
|
||||
- Floating point variables should be by default
|
||||
- ~double~ unless explicitly mentioned
|
||||
- integers used for counting should always be ~int64_t~
|
||||
|
||||
To facilitate the use in other languages than C, we will provide some
|
||||
bindings in other languages in other repositories.
|
||||
|
||||
# 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.
|
||||
|
||||
The internal structure of the context is not specified, to give a
|
||||
maximum of freedom to the different implementations. 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).
|
||||
|
||||
These 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
|
||||
|
||||
# The .org files will be appended here in the order specified in the
|
||||
# table_of_contents file
|
||||
|
||||
36
src/qmckl.org
Normal file
36
src/qmckl.org
Normal file
@ -0,0 +1,36 @@
|
||||
|
||||
** =qmckl.h= header file
|
||||
|
||||
The =qmckl.h= header file has to be included in <<<C>>> codes when
|
||||
QMCkl functions are used:
|
||||
#+BEGIN_SRC C :tangle none
|
||||
#include "qmckl.h"
|
||||
#+END_SRC f90
|
||||
|
||||
|
||||
In <<<Fortran>>> programs, the =qmckl_f.f90= interface file should be
|
||||
included in the source code using the library, and the Fortran codes
|
||||
should use the ~qmckl~ module as
|
||||
#+BEGIN_SRC f90 :tangle none
|
||||
use qmckl
|
||||
#+END_SRC f90
|
||||
|
||||
*** Top of header files :noexport:
|
||||
|
||||
#+BEGIN_SRC C :tangle qmckl.h :noweb yes
|
||||
#ifndef QMCKL_H
|
||||
#define QMCKL_H
|
||||
#include <stdlib.h>
|
||||
#include <stdint.h>
|
||||
|
||||
<<type-exit-code>>
|
||||
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC f90 :tangle qmckl_f.f90
|
||||
module qmckl
|
||||
use, intrinsic :: iso_c_binding
|
||||
#+END_SRC
|
||||
|
||||
The bottoms of the files are located in the [[qmckl_footer.org]] file.
|
||||
|
||||
751
src/qmckl_ao.org
Normal file
751
src/qmckl_ao.org
Normal file
@ -0,0 +1,751 @@
|
||||
** Atomic Orbitals
|
||||
:PROPERTIES:
|
||||
:f: qmckl_ao.f90
|
||||
:c_test: test_qmckl_ao.c
|
||||
:fh: qmckl_f.f90
|
||||
:h: qmckl.h
|
||||
:f_test: test_qmckl_ao_f.f90
|
||||
:END:
|
||||
|
||||
|
||||
This files contains all the routines for the computation of the
|
||||
values, gradients and Laplacian of the atomic basis functions.
|
||||
|
||||
3 files are produced:
|
||||
- a source file : =qmckl_ao.f90=
|
||||
- a C test file : =test_qmckl_ao.c=
|
||||
- a Fortran test file : =test_qmckl_ao_f.f90=
|
||||
|
||||
*** Test :noexport:
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c_test" t)
|
||||
#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_power~
|
||||
|
||||
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 :tangle (org-entry-get nil "h" t)
|
||||
qmckl_exit_code qmckl_ao_power(const qmckl_context context,
|
||||
const int64_t n,
|
||||
const double *X, const int32_t *LMAX,
|
||||
const double *P, const int64_t LDP);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "f" t)
|
||||
integer function qmckl_ao_power_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_power_f
|
||||
#+END_SRC
|
||||
|
||||
***** C interface :noexport:
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "f" t)
|
||||
integer(c_int32_t) function qmckl_ao_power(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_power_f
|
||||
info = qmckl_ao_power_f(context, n, X, LMAX, P, ldp)
|
||||
end function qmckl_ao_power
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer(c_int32_t) function qmckl_ao_power(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_power
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** Test :noexport:
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "f_test" t)
|
||||
integer(c_int32_t) function test_qmckl_ao_power(context) bind(C)
|
||||
use qmckl
|
||||
implicit none
|
||||
|
||||
integer(c_int64_t), intent(in), value :: context
|
||||
|
||||
integer*8 :: n, LDP
|
||||
integer, allocatable :: LMAX(:)
|
||||
double precision, allocatable :: X(:), P(:,:)
|
||||
integer*8 :: i,j
|
||||
double precision :: epsilon
|
||||
|
||||
epsilon = qmckl_context_get_epsilon(context)
|
||||
|
||||
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, 5),4)
|
||||
end do
|
||||
|
||||
test_qmckl_ao_power = qmckl_ao_power(context, n, X, LMAX, P, LDP)
|
||||
if (test_qmckl_ao_power /= 0) return
|
||||
|
||||
test_qmckl_ao_power = -1
|
||||
|
||||
do j=1,n
|
||||
do i=1,LMAX(j)
|
||||
if ( X(j)**i == 0.d0 ) then
|
||||
if ( P(i,j) /= 0.d0) return
|
||||
else
|
||||
if ( dabs(1.d0 - P(i,j) / (X(j)**i)) > epsilon ) return
|
||||
end if
|
||||
end do
|
||||
end do
|
||||
|
||||
test_qmckl_ao_power = 0
|
||||
deallocate(X,P,LMAX)
|
||||
end function test_qmckl_ao_power
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c_test" t)
|
||||
int test_qmckl_ao_power(qmckl_context context);
|
||||
munit_assert_int(0, ==, test_qmckl_ao_power(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
|
||||
- ~lmax~ >= 0
|
||||
- ~ldl~ >= 3
|
||||
- ~ldv~ >= 5
|
||||
- ~X~ is allocated with at least $3 \times 8$ bytes
|
||||
- ~R~ is allocated with at least $3 \times 8$ bytes
|
||||
- ~n~ >= ~(lmax+1)(lmax+2)(lmax+3)/6~
|
||||
- ~L~ is allocated with at least $3 \times n \times 4$ bytes
|
||||
- ~VGL~ is allocated with at least $5 \times n \times 8$ bytes
|
||||
- On output, ~n~ should be equal to ~(lmax+1)(lmax+2)(lmax+3)/6~
|
||||
- On output, the powers are given in the following order (l=a+b+c):
|
||||
- Increase values of ~l~
|
||||
- Within a given value of ~l~, alphabetical order of the
|
||||
string made by a*"x" + b*"y" + c*"z" (in Python notation).
|
||||
For example, with a=0, b=2 and c=1 the string is "yyz"
|
||||
|
||||
***** Error codes
|
||||
|
||||
| -1 | Null context |
|
||||
| -2 | Inconsistent ~ldl~ |
|
||||
| -3 | Inconsistent ~ldv~ |
|
||||
| -4 | Inconsistent ~lmax~ |
|
||||
|
||||
***** Header
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "h" t)
|
||||
qmckl_exit_code qmckl_ao_polynomial_vgl(const qmckl_context context,
|
||||
const double *X, const double *R,
|
||||
const int32_t lmax, const int64_t *n,
|
||||
const int32_t *L, const int64_t ldl,
|
||||
const double *VGL, const int64_t ldv);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "f" t)
|
||||
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_power_f
|
||||
double precision :: xy, yz, xz
|
||||
double precision :: da, db, dc, dd
|
||||
|
||||
info = 0
|
||||
|
||||
if (context == 0_8) then
|
||||
info = -1
|
||||
return
|
||||
endif
|
||||
|
||||
if (ldl < 3) then
|
||||
info = -2
|
||||
return
|
||||
endif
|
||||
|
||||
if (ldv < 5) then
|
||||
info = -3
|
||||
return
|
||||
endif
|
||||
|
||||
if (lmax <= 0) then
|
||||
info = -4
|
||||
return
|
||||
endif
|
||||
|
||||
|
||||
do i=1,3
|
||||
Y(i) = X(i) - R(i)
|
||||
end do
|
||||
|
||||
lmax_array(1:3) = lmax
|
||||
if (lmax == 0) then
|
||||
VGL(1,1) = 1.d0
|
||||
vgL(2:5,1) = 0.d0
|
||||
l(1:3,1) = 0
|
||||
n=1
|
||||
else if (lmax > 0) then
|
||||
pows(-2:0,1:3) = 1.d0
|
||||
do i=1,lmax
|
||||
pows(i,1) = pows(i-1,1) * Y(1)
|
||||
pows(i,2) = pows(i-1,2) * Y(2)
|
||||
pows(i,3) = pows(i-1,3) * Y(3)
|
||||
end do
|
||||
|
||||
VGL(1:5,1:4) = 0.d0
|
||||
l(1:3,1:4) = 0
|
||||
|
||||
VGL(1,1) = 1.d0
|
||||
vgl(1:5,2:4) = 0.d0
|
||||
|
||||
l(1,2) = 1
|
||||
vgl(1,2) = pows(1,1)
|
||||
vgL(2,2) = 1.d0
|
||||
|
||||
l(2,3) = 1
|
||||
vgl(1,3) = pows(1,2)
|
||||
vgL(3,3) = 1.d0
|
||||
|
||||
l(3,4) = 1
|
||||
vgl(1,4) = pows(1,3)
|
||||
vgL(4,4) = 1.d0
|
||||
|
||||
n=4
|
||||
endif
|
||||
|
||||
! l>=2
|
||||
dd = 2.d0
|
||||
do d=2,lmax
|
||||
da = dd
|
||||
do a=d,0,-1
|
||||
db = dd-da
|
||||
do b=d-a,0,-1
|
||||
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
|
||||
|
||||
info = 0
|
||||
|
||||
end function qmckl_ao_polynomial_vgl_f
|
||||
#+END_SRC
|
||||
|
||||
***** C interface :noexport:
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "f" t)
|
||||
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
|
||||
|
||||
***** Fortran interface :noexport:
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
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 :tangle (org-entry-get nil "f_test" t)
|
||||
integer(c_int32_t) function test_qmckl_ao_polynomial_vgl(context) bind(C)
|
||||
use qmckl
|
||||
implicit none
|
||||
|
||||
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
|
||||
double precision :: epsilon
|
||||
|
||||
epsilon = qmckl_context_get_epsilon(context)
|
||||
|
||||
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,d), VGL(ldv,d))
|
||||
|
||||
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
|
||||
test_qmckl_ao_polynomial_vgl = -11
|
||||
do i=1,3
|
||||
if (L(i,j) < 0) return
|
||||
end do
|
||||
test_qmckl_ao_polynomial_vgl = -12
|
||||
if (dabs(1.d0 - VGL(1,j) / (&
|
||||
Y(1)**L(1,j) * Y(2)**L(2,j) * Y(3)**L(3,j) &
|
||||
)) > epsilon ) return
|
||||
|
||||
test_qmckl_ao_polynomial_vgl = -13
|
||||
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) &
|
||||
)) > epsilon ) return
|
||||
end if
|
||||
|
||||
test_qmckl_ao_polynomial_vgl = -14
|
||||
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) &
|
||||
)) > epsilon ) return
|
||||
end if
|
||||
|
||||
test_qmckl_ao_polynomial_vgl = -15
|
||||
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) &
|
||||
)) > epsilon ) return
|
||||
end if
|
||||
|
||||
test_qmckl_ao_polynomial_vgl = -16
|
||||
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) > epsilon ) return
|
||||
end do
|
||||
|
||||
test_qmckl_ao_polynomial_vgl = 0
|
||||
|
||||
deallocate(L,VGL)
|
||||
end function test_qmckl_ao_polynomial_vgl
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c_test" t)
|
||||
int test_qmckl_ao_polynomial_vgl(qmckl_context context);
|
||||
munit_assert_int(0, ==, test_qmckl_ao_polynomial_vgl(context));
|
||||
#+END_SRC
|
||||
|
||||
*** Gaussian basis functions
|
||||
|
||||
**** ~qmckl_ao_gaussian_vgl~
|
||||
|
||||
Computes the values, gradients and Laplacians at a given point of
|
||||
~n~ Gaussian functions centered at the same point:
|
||||
|
||||
\[ v_i = \exp(-a_i |X-R|^2) \]
|
||||
\[ \nabla_x v_i = -2 a_i (X_x - R_x) v_i \]
|
||||
\[ \nabla_y v_i = -2 a_i (X_y - R_y) v_i \]
|
||||
\[ \nabla_z v_i = -2 a_i (X_z - R_z) v_i \]
|
||||
\[ \Delta v_i = a_i (4 |X-R|^2 a_i - 6) v_i \]
|
||||
|
||||
***** 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 |
|
||||
| ~n~ | input | Number of computed gaussians |
|
||||
| ~A(n)~ | input | Exponents of the Gaussians |
|
||||
| ~VGL(ldv,5)~ | output | Value, gradients and Laplacian of the Gaussians |
|
||||
| ~ldv~ | input | Leading dimension of array ~VGL~ |
|
||||
|
||||
***** Requirements
|
||||
|
||||
- ~context~ is not 0
|
||||
- ~n~ > 0
|
||||
- ~ldv~ >= 5
|
||||
- ~A(i)~ > 0 for all ~i~
|
||||
- ~X~ is allocated with at least $3 \times 8$ bytes
|
||||
- ~R~ is allocated with at least $3 \times 8$ bytes
|
||||
- ~A~ is allocated with at least $n \times 8$ bytes
|
||||
- ~VGL~ is allocated with at least $n \times 5 \times 8$ bytes
|
||||
|
||||
***** Header
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "h" t)
|
||||
qmckl_exit_code qmckl_ao_gaussian_vgl(const qmckl_context context,
|
||||
const double *X, const double *R,
|
||||
const int64_t *n, const int64_t *A,
|
||||
const double *VGL, const int64_t ldv);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "f" t)
|
||||
integer function qmckl_ao_gaussian_vgl_f(context, X, R, n, A, VGL, ldv) result(info)
|
||||
implicit none
|
||||
integer*8 , intent(in) :: context
|
||||
real*8 , intent(in) :: X(3), R(3)
|
||||
integer*8 , intent(in) :: n
|
||||
real*8 , intent(in) :: A(n)
|
||||
real*8 , intent(out) :: VGL(ldv,5)
|
||||
integer*8 , intent(in) :: ldv
|
||||
|
||||
integer*8 :: i,j
|
||||
real*8 :: Y(3), r2, t, u, v
|
||||
|
||||
info = 0
|
||||
|
||||
if (context == 0_8) then
|
||||
info = -1
|
||||
return
|
||||
endif
|
||||
|
||||
if (n <= 0) then
|
||||
info = -2
|
||||
return
|
||||
endif
|
||||
|
||||
if (ldv < n) then
|
||||
info = -3
|
||||
return
|
||||
endif
|
||||
|
||||
|
||||
do i=1,3
|
||||
Y(i) = X(i) - R(i)
|
||||
end do
|
||||
r2 = Y(1)*Y(1) + Y(2)*Y(2) + Y(3)*Y(3)
|
||||
|
||||
do i=1,n
|
||||
VGL(i,1) = dexp(-A(i) * r2)
|
||||
end do
|
||||
|
||||
do i=1,n
|
||||
VGL(i,5) = A(i) * VGL(i,1)
|
||||
end do
|
||||
|
||||
t = -2.d0 * ( X(1) - R(1) )
|
||||
u = -2.d0 * ( X(2) - R(2) )
|
||||
v = -2.d0 * ( X(3) - R(3) )
|
||||
|
||||
do i=1,n
|
||||
VGL(i,2) = t * VGL(i,5)
|
||||
VGL(i,3) = u * VGL(i,5)
|
||||
VGL(i,4) = v * VGL(i,5)
|
||||
end do
|
||||
|
||||
t = 4.d0 * r2
|
||||
do i=1,n
|
||||
VGL(i,5) = (t * A(i) - 6.d0) * VGL(i,5)
|
||||
end do
|
||||
|
||||
end function qmckl_ao_gaussian_vgl_f
|
||||
#+END_SRC
|
||||
|
||||
***** C interface :noexport:
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "f" t)
|
||||
integer(c_int32_t) function qmckl_ao_gaussian_vgl(context, X, R, n, A, 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_int64_t) , intent(in) , value :: n
|
||||
real (c_double) , intent(in) :: A(n)
|
||||
real (c_double) , intent(out) :: VGL(ldv,5)
|
||||
integer (c_int64_t) , intent(in) , value :: ldv
|
||||
|
||||
integer, external :: qmckl_ao_gaussian_vgl_f
|
||||
info = qmckl_ao_gaussian_vgl_f(context, X, R, n, A, VGL, ldv)
|
||||
end function qmckl_ao_gaussian_vgl
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer(c_int32_t) function qmckl_ao_gaussian_vgl(context, X, R, n, A, VGL, ldv) &
|
||||
bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t) , intent(in) , value :: context
|
||||
integer (c_int64_t) , intent(in) , value :: ldv
|
||||
integer (c_int64_t) , intent(in) , value :: n
|
||||
real (c_double) , intent(in) :: X(3), R(3), A(n)
|
||||
real (c_double) , intent(out) :: VGL(ldv,5)
|
||||
end function qmckl_ao_gaussian_vgl
|
||||
end interface
|
||||
#+END_SRC
|
||||
***** Test :noexport:
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "f_test" t)
|
||||
integer(c_int32_t) function test_qmckl_ao_gaussian_vgl(context) bind(C)
|
||||
use qmckl
|
||||
implicit none
|
||||
|
||||
integer(c_int64_t), intent(in), value :: context
|
||||
|
||||
integer*8 :: n, ldv, j, i
|
||||
double precision :: X(3), R(3), Y(3), r2
|
||||
double precision, allocatable :: VGL(:,:), A(:)
|
||||
double precision :: epsilon
|
||||
|
||||
epsilon = qmckl_context_get_epsilon(context)
|
||||
|
||||
X = (/ 1.1 , 2.2 , 3.3 /)
|
||||
R = (/ 0.1 , 1.2 , -2.3 /)
|
||||
Y(:) = X(:) - R(:)
|
||||
r2 = Y(1)**2 + Y(2)**2 + Y(3)**2
|
||||
|
||||
n = 10;
|
||||
ldv = 100;
|
||||
|
||||
allocate (A(n), VGL(ldv,5))
|
||||
do i=1,n
|
||||
A(i) = 0.0013 * dble(ishft(1,i))
|
||||
end do
|
||||
|
||||
|
||||
test_qmckl_ao_gaussian_vgl = &
|
||||
qmckl_ao_gaussian_vgl(context, X, R, n, A, VGL, ldv)
|
||||
if (test_qmckl_ao_gaussian_vgl /= 0) return
|
||||
|
||||
test_qmckl_ao_gaussian_vgl = -1
|
||||
|
||||
do i=1,n
|
||||
test_qmckl_ao_gaussian_vgl = -11
|
||||
if (dabs(1.d0 - VGL(i,1) / (&
|
||||
dexp(-A(i) * r2) &
|
||||
)) > epsilon ) return
|
||||
|
||||
test_qmckl_ao_gaussian_vgl = -12
|
||||
if (dabs(1.d0 - VGL(i,2) / (&
|
||||
-2.d0 * A(i) * Y(1) * dexp(-A(i) * r2) &
|
||||
)) > epsilon ) return
|
||||
|
||||
test_qmckl_ao_gaussian_vgl = -13
|
||||
if (dabs(1.d0 - VGL(i,3) / (&
|
||||
-2.d0 * A(i) * Y(2) * dexp(-A(i) * r2) &
|
||||
)) > epsilon ) return
|
||||
|
||||
test_qmckl_ao_gaussian_vgl = -14
|
||||
if (dabs(1.d0 - VGL(i,4) / (&
|
||||
-2.d0 * A(i) * Y(3) * dexp(-A(i) * r2) &
|
||||
)) > epsilon ) return
|
||||
|
||||
test_qmckl_ao_gaussian_vgl = -15
|
||||
if (dabs(1.d0 - VGL(i,5) / (&
|
||||
A(i) * (4.d0*r2*A(i) - 6.d0) * dexp(-A(i) * r2) &
|
||||
)) > epsilon ) return
|
||||
end do
|
||||
|
||||
test_qmckl_ao_gaussian_vgl = 0
|
||||
|
||||
deallocate(VGL)
|
||||
end function test_qmckl_ao_gaussian_vgl
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c_test" t)
|
||||
int test_qmckl_ao_gaussian_vgl(qmckl_context context);
|
||||
munit_assert_int(0, ==, test_qmckl_ao_gaussian_vgl(context));
|
||||
#+END_SRC
|
||||
|
||||
|
||||
*** TODO Slater basis functions
|
||||
|
||||
*** End of files :noexport:
|
||||
|
||||
***** Test
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c_test" t)
|
||||
if (qmckl_context_destroy(context) != QMCKL_SUCCESS)
|
||||
return QMCKL_FAILURE;
|
||||
return MUNIT_OK;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
|
||||
# -*- mode: org -*-
|
||||
# vim: syntax=c
|
||||
|
||||
922
src/qmckl_context.org
Normal file
922
src/qmckl_context.org
Normal file
@ -0,0 +1,922 @@
|
||||
** Context
|
||||
:PROPERTIES:
|
||||
:c: qmckl_context.c
|
||||
:c_test: test_qmckl_context.c
|
||||
:fh: qmckl_f.f90
|
||||
:h: qmckl.h
|
||||
:END:
|
||||
|
||||
This file is written in C because it is more natural to express the
|
||||
context in C than in Fortran.
|
||||
|
||||
2 files are produced:
|
||||
- a source file : =qmckl_context.c=
|
||||
- a test file : =test_qmckl_context.c=
|
||||
|
||||
*** Headers :noexport:
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
#include "qmckl.h"
|
||||
#include <math.h>
|
||||
#include <string.h>
|
||||
#include <assert.h>
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c_test" t)
|
||||
#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.
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle qmckl.h
|
||||
typedef int64_t qmckl_context ;
|
||||
#+END_SRC
|
||||
|
||||
**** Data for error handling
|
||||
|
||||
We define here the the data structure containing the strings
|
||||
necessary for error handling.
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle qmckl.h
|
||||
#define QMCKL_MAX_FUN_LEN 256
|
||||
#define QMCKL_MAX_MSG_LEN 1024
|
||||
|
||||
typedef struct qmckl_error_struct {
|
||||
|
||||
qmckl_exit_code exit_code;
|
||||
char function[QMCKL_MAX_FUN_LEN];
|
||||
char message [QMCKL_MAX_MSG_LEN];
|
||||
|
||||
} qmckl_error_struct;
|
||||
#+END_SRC
|
||||
|
||||
|
||||
**** Basis set data structure
|
||||
|
||||
Data structure for the info related to the atomic orbitals
|
||||
basis set.
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
typedef struct qmckl_ao_basis_struct {
|
||||
|
||||
int64_t shell_num;
|
||||
int64_t prim_num;
|
||||
int64_t * shell_center;
|
||||
int32_t * shell_ang_mom;
|
||||
double * shell_factor;
|
||||
double * exponent ;
|
||||
double * coefficient ;
|
||||
int64_t * shell_prim_num;
|
||||
char type;
|
||||
|
||||
} qmckl_ao_basis_struct;
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
|
||||
The tag is used internally to check if the memory domain pointed
|
||||
by a pointer is a valid context.
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
typedef struct qmckl_context_struct {
|
||||
|
||||
struct qmckl_context_struct * prev;
|
||||
|
||||
/* Molecular system */
|
||||
// struct qmckl_nucleus_struct * nucleus;
|
||||
// struct qmckl_electron_struct * electron;
|
||||
struct qmckl_ao_basis_struct * ao_basis;
|
||||
// struct qmckl_mo_struct * mo;
|
||||
// struct qmckl_determinant_struct * det;
|
||||
|
||||
/* Numerical precision */
|
||||
uint32_t tag;
|
||||
int32_t precision;
|
||||
int32_t range;
|
||||
|
||||
/* Error handling */
|
||||
struct qmckl_error_struct * error;
|
||||
|
||||
} qmckl_context_struct;
|
||||
|
||||
#define VALID_TAG 0xBEEFFACE
|
||||
#define INVALID_TAG 0xDEADBEEF
|
||||
#+END_SRC
|
||||
|
||||
**** ~qmckl_context_update_error~
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
qmckl_exit_code
|
||||
qmckl_context_update_error(qmckl_context context, const qmckl_exit_code exit_code, const char* function, const char* message);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
qmckl_exit_code
|
||||
qmckl_context_update_error(qmckl_context context, const qmckl_exit_code exit_code, const char* function, const char* message)
|
||||
{
|
||||
assert (context != 0);
|
||||
assert (function != NULL);
|
||||
assert (message != NULL);
|
||||
assert (exit_code > 0);
|
||||
assert (exit_code < QMCKL_INVALID_EXIT_CODE);
|
||||
|
||||
qmckl_context_struct* ctx = (qmckl_context_struct*) context;
|
||||
if (ctx == NULL) return QMCKL_FAILURE;
|
||||
|
||||
if (ctx->error != NULL) {
|
||||
free(ctx->error);
|
||||
ctx->error = NULL;
|
||||
}
|
||||
|
||||
qmckl_error_struct* error = (qmckl_error_struct*) qmckl_malloc (context, sizeof(qmckl_error_struct));
|
||||
error->exit_code = exit_code;
|
||||
strcpy(error->function, function);
|
||||
strcpy(error->message, message);
|
||||
|
||||
ctx->error = error;
|
||||
|
||||
return QMCKL_SUCCESS;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** TODO Test
|
||||
|
||||
**** ~qmckl_context_set_error~
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
qmckl_context
|
||||
qmckl_context_set_error(qmckl_context context, const qmckl_exit_code exit_code, const char* function, const char* message);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
qmckl_context
|
||||
qmckl_context_set_error(qmckl_context context, const qmckl_exit_code exit_code, const char* function, const char* message)
|
||||
{
|
||||
assert (context != 0);
|
||||
assert (function != NULL);
|
||||
assert (message != NULL);
|
||||
assert (exit_code > 0);
|
||||
assert (exit_code < QMCKL_INVALID_EXIT_CODE);
|
||||
|
||||
qmckl_context new_context = qmckl_context_copy(context);
|
||||
if (new_context == 0) return context;
|
||||
|
||||
if (qmckl_context_update_error(new_context, exit_code,
|
||||
function, message) != QMCKL_SUCCESS) {
|
||||
return context;
|
||||
}
|
||||
|
||||
return new_context;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** TODO Test
|
||||
|
||||
***** Test :noexport:
|
||||
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c_test" t)
|
||||
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.
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
qmckl_context qmckl_context_check(const qmckl_context context) ;
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
qmckl_context qmckl_context_check(const qmckl_context context) {
|
||||
|
||||
if (context == (qmckl_context) 0) return (qmckl_context) 0;
|
||||
|
||||
const qmckl_context_struct * 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
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
qmckl_context qmckl_context_create();
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
qmckl_context qmckl_context_create() {
|
||||
|
||||
qmckl_context_struct* context =
|
||||
(qmckl_context_struct*) qmckl_malloc ((qmckl_context) 0, sizeof(qmckl_context_struct));
|
||||
if (context == NULL) {
|
||||
return (qmckl_context) 0;
|
||||
}
|
||||
|
||||
context->prev = NULL;
|
||||
context->ao_basis = NULL;
|
||||
context->precision = QMCKL_DEFAULT_PRECISION;
|
||||
context->range = QMCKL_DEFAULT_RANGE;
|
||||
context->tag = VALID_TAG;
|
||||
context->error = NULL;
|
||||
|
||||
return (qmckl_context) context;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** Fortran interface
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer (c_int64_t) function qmckl_context_create() bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
end function qmckl_context_create
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** Test :noexport:
|
||||
#+BEGIN_SRC C :comments link :tangle (org-entry-get nil "c_test" t)
|
||||
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
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
qmckl_context qmckl_context_copy(const qmckl_context context);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
qmckl_context qmckl_context_copy(const qmckl_context context) {
|
||||
|
||||
const qmckl_context checked_context = qmckl_context_check(context);
|
||||
|
||||
if (checked_context == (qmckl_context) 0) {
|
||||
return (qmckl_context) 0;
|
||||
}
|
||||
|
||||
qmckl_context_struct* old_context = (qmckl_context_struct*) checked_context;
|
||||
|
||||
qmckl_context_struct* new_context =
|
||||
(qmckl_context_struct*) qmckl_malloc (context, sizeof(qmckl_context_struct));
|
||||
if (new_context == NULL) {
|
||||
return (qmckl_context) 0;
|
||||
}
|
||||
|
||||
new_context->prev = old_context;
|
||||
new_context->ao_basis = old_context->ao_basis;
|
||||
new_context->precision = old_context->precision;
|
||||
new_context->range = old_context->range;
|
||||
new_context->tag = VALID_TAG;
|
||||
new_context->error = old_context->error;
|
||||
|
||||
return (qmckl_context) new_context;
|
||||
}
|
||||
|
||||
#+END_SRC
|
||||
|
||||
***** Fortran interface
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer (c_int64_t) function qmckl_context_copy(context) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
end function qmckl_context_copy
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** Test :noexport:
|
||||
#+BEGIN_SRC C :comments link :tangle (org-entry-get nil "c_test" t)
|
||||
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
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
qmckl_context qmckl_context_previous(const qmckl_context context);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
qmckl_context qmckl_context_previous(const qmckl_context context) {
|
||||
|
||||
const qmckl_context checked_context = qmckl_context_check(context);
|
||||
if (checked_context == (qmckl_context) 0) {
|
||||
return (qmckl_context) 0;
|
||||
}
|
||||
|
||||
const qmckl_context_struct* ctx = (qmckl_context_struct*) checked_context;
|
||||
return qmckl_context_check((qmckl_context) ctx->prev);
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** Fortran interface
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer (c_int64_t) function qmckl_context_previous(context) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
end function qmckl_context_previous
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** Test :noexport:
|
||||
#+BEGIN_SRC C :comments link :tangle (org-entry-get nil "c_test" t)
|
||||
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
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
qmckl_exit_code qmckl_context_destroy(qmckl_context context);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
qmckl_exit_code qmckl_context_destroy(const qmckl_context context) {
|
||||
|
||||
const qmckl_context checked_context = qmckl_context_check(context);
|
||||
if (checked_context == (qmckl_context) 0) return QMCKL_FAILURE;
|
||||
|
||||
qmckl_context_struct* ctx = (qmckl_context_struct*) context;
|
||||
if (ctx == NULL) return QMCKL_FAILURE;
|
||||
|
||||
ctx->tag = INVALID_TAG;
|
||||
return qmckl_free(context,ctx);
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** Fortran interface
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer (c_int32_t) function qmckl_context_destroy(context) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
end function qmckl_context_destroy
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** Test :noexport:
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c_test" t)
|
||||
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
|
||||
|
||||
**** Basis set
|
||||
|
||||
For H_2 with the following basis set,
|
||||
|
||||
#+BEGIN_EXAMPLE
|
||||
HYDROGEN
|
||||
S 5
|
||||
1 3.387000E+01 6.068000E-03
|
||||
2 5.095000E+00 4.530800E-02
|
||||
3 1.159000E+00 2.028220E-01
|
||||
4 3.258000E-01 5.039030E-01
|
||||
5 1.027000E-01 3.834210E-01
|
||||
S 1
|
||||
1 3.258000E-01 1.000000E+00
|
||||
S 1
|
||||
1 1.027000E-01 1.000000E+00
|
||||
P 1
|
||||
1 1.407000E+00 1.000000E+00
|
||||
P 1
|
||||
1 3.880000E-01 1.000000E+00
|
||||
D 1
|
||||
1 1.057000E+00 1.0000000
|
||||
#+END_EXAMPLE
|
||||
|
||||
we have:
|
||||
|
||||
#+BEGIN_EXAMPLE
|
||||
type = 'G'
|
||||
shell_num = 12
|
||||
prim_num = 20
|
||||
SHELL_CENTER = [1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2]
|
||||
SHELL_ANG_MOM = ['S', 'S', 'S', 'P', 'P', 'D', 'S', 'S', 'S', 'P', 'P', 'D']
|
||||
SHELL_PRIM_NUM = [5, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1]
|
||||
prim_index = [1, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20]
|
||||
EXPONENT = [ 33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027,
|
||||
1.407, 0.388, 1.057, 33.87, 5.095, 1.159, 0.3258, 0.1027,
|
||||
0.3258, 0.1027, 1.407, 0.388, 1.057]
|
||||
COEFFICIENT = [ 0.006068, 0.045308, 0.202822, 0.503903, 0.383421,
|
||||
1.0, 1.0, 1.0, 1.0, 1.0, 0.006068, 0.045308, 0.202822,
|
||||
0.503903, 0.383421, 1.0, 1.0, 1.0, 1.0, 1.0]
|
||||
#+END_EXAMPLE
|
||||
|
||||
**** ~qmckl_context_update_ao_basis~
|
||||
|
||||
Updates the data describing the AO basis set into the context.
|
||||
|
||||
| ~type~ | Gaussian or Slater |
|
||||
| ~shell_num~ | Number of shells |
|
||||
| ~prim_num~ | Total number of primitives |
|
||||
| ~SHELL_CENTER(shell_num)~ | Id of the nucleus on which the shell is centered |
|
||||
| ~SHELL_ANG_MOM(shell_num)~ | Id of the nucleus on which the shell is centered |
|
||||
| ~SHELL_FACTOR(shell_num)~ | Normalization factor for the shell |
|
||||
| ~SHELL_PRIM_NUM(shell_num)~ | Number of primitives in the shell |
|
||||
| ~SHELL_PRIM_INDEX(shell_num)~ | Address of the first primitive of the shelll in the ~EXPONENT~ array |
|
||||
| ~EXPONENT(prim_num)~ | Array of exponents |
|
||||
| ~COEFFICIENT(prim_num)~ | Array of coefficients |
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
qmckl_exit_code
|
||||
qmckl_context_update_ao_basis(qmckl_context context , const char type,
|
||||
const int64_t shell_num , const int64_t prim_num,
|
||||
const int64_t * SHELL_CENTER, const int32_t * SHELL_ANG_MOM,
|
||||
const double * SHELL_FACTOR, const int64_t * SHELL_PRIM_NUM,
|
||||
const int64_t * SHELL_PRIM_INDEX,
|
||||
const double * EXPONENT , const double * COEFFICIENT);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
qmckl_exit_code
|
||||
qmckl_context_update_ao_basis(qmckl_context context , const char type,
|
||||
const int64_t shell_num , const int64_t prim_num,
|
||||
const int64_t * SHELL_CENTER, const int32_t * SHELL_ANG_MOM,
|
||||
const double * SHELL_FACTOR, const int64_t * SHELL_PRIM_NUM,
|
||||
const int64_t * SHELL_PRIM_INDEX,
|
||||
const double * EXPONENT , const double * COEFFICIENT)
|
||||
{
|
||||
|
||||
int64_t i;
|
||||
|
||||
/* Check input */
|
||||
|
||||
if (type != 'G' && type != 'S') return QMCKL_FAILURE;
|
||||
if (shell_num <= 0) return QMCKL_FAILURE;
|
||||
if (prim_num <= 0) return QMCKL_FAILURE;
|
||||
if (prim_num < shell_num) return QMCKL_FAILURE;
|
||||
|
||||
for (i=0 ; i<shell_num ; i++) {
|
||||
if (SHELL_CENTER[i] <= 0) return QMCKL_FAILURE;
|
||||
if (SHELL_PRIM_NUM[i] <= 0) return QMCKL_FAILURE;
|
||||
if (SHELL_ANG_MOM[i] < 0) return QMCKL_FAILURE;
|
||||
if (SHELL_PRIM_INDEX[i] < 0) return QMCKL_FAILURE;
|
||||
}
|
||||
|
||||
for (i=0 ; i<prim_num ; i++) {
|
||||
if (EXPONENT[i] <= 0) return QMCKL_FAILURE;
|
||||
}
|
||||
|
||||
qmckl_context_struct* ctx = (qmckl_context_struct*) context;
|
||||
if (ctx == NULL) return QMCKL_FAILURE;
|
||||
|
||||
qmckl_ao_basis_struct* basis = (qmckl_ao_basis_struct*) malloc (sizeof(qmckl_ao_basis_struct));
|
||||
if (basis == NULL) return QMCKL_FAILURE;
|
||||
|
||||
|
||||
/* Memory allocations */
|
||||
|
||||
basis->shell_center = (int64_t*) malloc (shell_num * sizeof(int64_t));
|
||||
if (basis->shell_center == NULL) {
|
||||
qmckl_free(context, basis);
|
||||
return QMCKL_FAILURE;
|
||||
}
|
||||
|
||||
basis->shell_ang_mom = (int32_t*) malloc (shell_num * sizeof(int32_t));
|
||||
if (basis->shell_ang_mom == NULL) {
|
||||
qmckl_free(context, basis->shell_center);
|
||||
qmckl_free(context, basis);
|
||||
return QMCKL_FAILURE;
|
||||
}
|
||||
|
||||
basis->shell_prim_num= (int64_t*) malloc (shell_num * sizeof(int64_t));
|
||||
if (basis->shell_prim_num == NULL) {
|
||||
qmckl_free(context, basis->shell_ang_mom);
|
||||
qmckl_free(context, basis->shell_center);
|
||||
qmckl_free(context, basis);
|
||||
return QMCKL_FAILURE;
|
||||
}
|
||||
|
||||
basis->shell_factor = (double *) malloc (shell_num * sizeof(double ));
|
||||
if (basis->shell_factor == NULL) {
|
||||
qmckl_free(context, basis->shell_prim_num);
|
||||
qmckl_free(context, basis->shell_ang_mom);
|
||||
qmckl_free(context, basis->shell_center);
|
||||
qmckl_free(context, basis);
|
||||
return QMCKL_FAILURE;
|
||||
}
|
||||
|
||||
basis->exponent = (double *) malloc (prim_num * sizeof(double ));
|
||||
if (basis->exponent == NULL) {
|
||||
qmckl_free(context, basis->shell_factor);
|
||||
qmckl_free(context, basis->shell_prim_num);
|
||||
qmckl_free(context, basis->shell_ang_mom);
|
||||
qmckl_free(context, basis->shell_center);
|
||||
qmckl_free(context, basis);
|
||||
return QMCKL_FAILURE;
|
||||
}
|
||||
|
||||
basis->coefficient = (double *) malloc (prim_num * sizeof(double ));
|
||||
if (basis->coefficient == NULL) {
|
||||
qmckl_free(context, basis->exponent);
|
||||
qmckl_free(context, basis->shell_factor);
|
||||
qmckl_free(context, basis->shell_prim_num);
|
||||
qmckl_free(context, basis->shell_ang_mom);
|
||||
qmckl_free(context, basis->shell_center);
|
||||
qmckl_free(context, basis);
|
||||
return QMCKL_FAILURE;
|
||||
}
|
||||
|
||||
|
||||
/* Assign data */
|
||||
|
||||
basis->type = type;
|
||||
basis->shell_num = shell_num;
|
||||
basis->prim_num = prim_num;
|
||||
|
||||
for (i=0 ; i<shell_num ; i++) {
|
||||
basis->shell_center [i] = SHELL_CENTER [i];
|
||||
basis->shell_ang_mom [i] = SHELL_ANG_MOM [i];
|
||||
basis->shell_prim_num[i] = SHELL_PRIM_NUM[i];
|
||||
basis->shell_factor [i] = SHELL_FACTOR [i];
|
||||
}
|
||||
|
||||
for (i=0 ; i<prim_num ; i++) {
|
||||
basis->exponent [i] = EXPONENT[i];
|
||||
basis->coefficient[i] = COEFFICIENT[i];
|
||||
}
|
||||
|
||||
ctx->ao_basis = basis;
|
||||
return QMCKL_SUCCESS;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** Fortran interface
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer (c_int32_t) function qmckl_context_update_ao_basis(context, &
|
||||
typ, shell_num, prim_num, SHELL_CENTER, SHELL_ANG_MOM, SHELL_FACTOR, &
|
||||
SHELL_PRIM_NUM, SHELL_PRIM_INDEX, EXPONENT, COEFFICIENT) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
character(c_char) , intent(in), value :: typ
|
||||
integer (c_int64_t), intent(in), value :: shell_num
|
||||
integer (c_int64_t), intent(in), value :: prim_num
|
||||
integer (c_int64_t), intent(in) :: SHELL_CENTER(shell_num)
|
||||
integer (c_int32_t), intent(in) :: SHELL_ANG_MOM(shell_num)
|
||||
double precision , intent(in) :: SHELL_FACTOR(shell_num)
|
||||
integer (c_int64_t), intent(in) :: SHELL_PRIM_NUM(shell_num)
|
||||
integer (c_int64_t), intent(in) :: SHELL_PRIM_INDEX(shell_num)
|
||||
double precision , intent(in) :: EXPONENT(prim_num)
|
||||
double precision , intent(in) :: COEFFICIENT(prim_num)
|
||||
end function qmckl_context_update_ao_basis
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** TODO Test
|
||||
|
||||
**** ~qmckl_context_set_ao_basis~
|
||||
|
||||
Sets the data describing the AO basis set into the context.
|
||||
|
||||
| ~type~ | Gaussian or Slater |
|
||||
| ~shell_num~ | Number of shells |
|
||||
| ~prim_num~ | Total number of primitives |
|
||||
| ~SHELL_CENTER(shell_num)~ | Id of the nucleus on which the shell is centered |
|
||||
| ~SHELL_ANG_MOM(shell_num)~ | Id of the nucleus on which the shell is centered |
|
||||
| ~SHELL_FACTOR(shell_num)~ | Normalization factor for the shell |
|
||||
| ~SHELL_PRIM_NUM(shell_num)~ | Number of primitives in the shell |
|
||||
| ~SHELL_PRIM_INDEX(shell_num)~ | Address of the first primitive of the shelll in the ~EXPONENT~ array |
|
||||
| ~EXPONENT(prim_num)~ | Array of exponents |
|
||||
| ~COEFFICIENT(prim_num)~ | Array of coefficients |
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
qmckl_context
|
||||
qmckl_context_set_ao_basis(const qmckl_context context , const char type,
|
||||
const int64_t shell_num , const int64_t prim_num,
|
||||
const int64_t * SHELL_CENTER, const int32_t * SHELL_ANG_MOM,
|
||||
const double * SHELL_FACTOR, const int64_t * SHELL_PRIM_NUM,
|
||||
const int64_t * SHELL_PRIM_INDEX,
|
||||
const double * EXPONENT , const double * COEFFICIENT);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
qmckl_context
|
||||
qmckl_context_set_ao_basis(const qmckl_context context , const char type,
|
||||
const int64_t shell_num , const int64_t prim_num,
|
||||
const int64_t * SHELL_CENTER, const int32_t * SHELL_ANG_MOM,
|
||||
const double * SHELL_FACTOR, const int64_t * SHELL_PRIM_NUM,
|
||||
const int64_t * SHELL_PRIM_INDEX,
|
||||
const double * EXPONENT , const double * COEFFICIENT)
|
||||
{
|
||||
|
||||
qmckl_context new_context = qmckl_context_copy(context);
|
||||
if (new_context == 0) return 0;
|
||||
|
||||
if (qmckl_context_update_ao_basis(new_context, type, shell_num, prim_num,
|
||||
SHELL_CENTER, SHELL_ANG_MOM, SHELL_FACTOR,
|
||||
SHELL_PRIM_NUM, SHELL_PRIM_INDEX, EXPONENT,
|
||||
COEFFICIENT
|
||||
) == QMCKL_FAILURE)
|
||||
return 0;
|
||||
|
||||
return new_context;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** Fortran interface
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer (c_int64_t) function qmckl_context_set_ao_basis(context, &
|
||||
typ, shell_num, prim_num, SHELL_CENTER, SHELL_ANG_MOM, SHELL_FACTOR, &
|
||||
SHELL_PRIM_NUM, SHELL_PRIM_INDEX, EXPONENT, COEFFICIENT) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
character(c_char) , intent(in), value :: typ
|
||||
integer (c_int64_t), intent(in), value :: shell_num
|
||||
integer (c_int64_t), intent(in), value :: prim_num
|
||||
integer (c_int64_t), intent(in) :: SHELL_CENTER(shell_num)
|
||||
integer (c_int32_t), intent(in) :: SHELL_ANG_MOM(shell_num)
|
||||
double precision , intent(in) :: SHELL_FACTOR(shell_num)
|
||||
integer (c_int64_t), intent(in) :: SHELL_PRIM_NUM(shell_num)
|
||||
integer (c_int64_t), intent(in) :: SHELL_PRIM_INDEX(shell_num)
|
||||
double precision , intent(in) :: EXPONENT(prim_num)
|
||||
double precision , intent(in) :: COEFFICIENT(prim_num)
|
||||
end function qmckl_context_set_ao_basis
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** TODO Test
|
||||
|
||||
**** 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~
|
||||
Modifies the parameter for the numerical precision in a given context.
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
qmckl_exit_code qmckl_context_update_precision(const qmckl_context context, const int precision);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
qmckl_exit_code qmckl_context_update_precision(const qmckl_context context, const int precision) {
|
||||
|
||||
if (precision < 2) return QMCKL_FAILURE;
|
||||
if (precision > 53) return QMCKL_FAILURE;
|
||||
|
||||
qmckl_context_struct* ctx = (qmckl_context_struct*) context;
|
||||
if (ctx == NULL) return QMCKL_FAILURE;
|
||||
|
||||
ctx->precision = precision;
|
||||
return QMCKL_SUCCESS;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** Fortran interface
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer (c_int32_t) function qmckl_context_update_precision(context, precision) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
integer (c_int32_t), intent(in), value :: precision
|
||||
end function qmckl_context_update_precision
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** TODO Tests :noexport:
|
||||
**** ~qmckl_context_update_range~
|
||||
Modifies the parameter for the numerical range in a given context.
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
qmckl_exit_code qmckl_context_update_range(const qmckl_context context, const int range);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
qmckl_exit_code qmckl_context_update_range(const qmckl_context context, const int range) {
|
||||
|
||||
if (range < 2) return QMCKL_FAILURE;
|
||||
if (range > 11) return QMCKL_FAILURE;
|
||||
|
||||
qmckl_context_struct* ctx = (qmckl_context_struct*) context;
|
||||
if (ctx == NULL) return QMCKL_FAILURE;
|
||||
|
||||
ctx->range = range;
|
||||
return QMCKL_SUCCESS;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** Fortran interface
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer (c_int32_t) function qmckl_context_update_range(context, range) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
integer (c_int32_t), intent(in), value :: range
|
||||
end function qmckl_context_update_range
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** TODO Tests :noexport:
|
||||
**** ~qmckl_context_set_precision~
|
||||
Returns a copy of the context with a different precision parameter.
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
qmckl_context qmckl_context_set_precision(const qmckl_context context, const int precision);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
qmckl_context qmckl_context_set_precision(const qmckl_context context, const int precision) {
|
||||
qmckl_context new_context = qmckl_context_copy(context);
|
||||
if (new_context == 0) return 0;
|
||||
|
||||
if (qmckl_context_update_precision(new_context, precision) == QMCKL_FAILURE) return 0;
|
||||
|
||||
return new_context;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** Fortran interface
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer (c_int64_t) function qmckl_context_set_precision(context, precision) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
integer (c_int32_t), intent(in), value :: precision
|
||||
end function qmckl_context_set_precision
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** TODO Tests :noexport:
|
||||
**** ~qmckl_context_set_range~
|
||||
Returns a copy of the context with a different precision parameter.
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
qmckl_context qmckl_context_set_range(const qmckl_context context, const int range);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
qmckl_context qmckl_context_set_range(const qmckl_context context, const int range) {
|
||||
qmckl_context new_context = qmckl_context_copy(context);
|
||||
if (new_context == 0) return 0;
|
||||
|
||||
if (qmckl_context_update_range(new_context, range) == QMCKL_FAILURE) return 0;
|
||||
|
||||
return new_context;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** Fortran interface
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer (c_int64_t) function qmckl_context_set_range(context, range) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
integer (c_int32_t), intent(in), value :: range
|
||||
end function qmckl_context_set_range
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** TODO Tests :noexport:
|
||||
|
||||
**** ~qmckl_context_get_precision~
|
||||
Returns the value of the numerical precision in the context
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
int32_t qmckl_context_get_precision(const qmckl_context context);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
int qmckl_context_get_precision(const qmckl_context context) {
|
||||
const qmckl_context_struct* ctx = (qmckl_context_struct*) context;
|
||||
return ctx->precision;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** Fortran interface
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer (c_int32_t) function qmckl_context_get_precision(context) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
end function qmckl_context_get_precision
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** TODO Tests :noexport:
|
||||
**** ~qmckl_context_get_range~
|
||||
Returns the value of the numerical range in the context
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
int32_t qmckl_context_get_range(const qmckl_context context);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
int qmckl_context_get_range(const qmckl_context context) {
|
||||
const qmckl_context_struct* ctx = (qmckl_context_struct*) context;
|
||||
return ctx->range;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** Fortran interface
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
integer (c_int32_t) function qmckl_context_get_range(context) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
end function qmckl_context_get_range
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** TODO Tests :noexport:
|
||||
|
||||
**** ~qmckl_context_get_epsilon~
|
||||
Returns $\epsilon = 2^{1-n}$ where ~n~ is the precision
|
||||
#+BEGIN_SRC C :comments org :tangle (org-entry-get nil "h" t)
|
||||
double qmckl_context_get_epsilon(const qmckl_context context);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
double qmckl_context_get_epsilon(const qmckl_context context) {
|
||||
const qmckl_context_struct* ctx = (qmckl_context_struct*) context;
|
||||
return pow(2.0,(double) 1-ctx->precision);
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
***** Fortran interface
|
||||
#+BEGIN_SRC f90 :tangle (org-entry-get nil "fh" t)
|
||||
interface
|
||||
real (c_double) function qmckl_context_get_epsilon(context) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
end function qmckl_context_get_epsilon
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
***** TODO Tests :noexport:
|
||||
|
||||
|
||||
|
||||
*** End of files :noexport:
|
||||
|
||||
***** Test
|
||||
#+BEGIN_SRC C :comments link :tangle (org-entry-get nil "c_test" t)
|
||||
return MUNIT_OK;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
|
||||
|
||||
# -*- mode: org -*-
|
||||
# vim: syntax=c
|
||||
356
src/qmckl_distance.org
Normal file
356
src/qmckl_distance.org
Normal file
@ -0,0 +1,356 @@
|
||||
** Computation of distances
|
||||
|
||||
Function for the computation of distances between particles.
|
||||
|
||||
3 files are produced:
|
||||
- a source file : =qmckl_distance.f90=
|
||||
- a C test file : =test_qmckl_distance.c=
|
||||
- a Fortran test file : =test_qmckl_distance_f.f90=
|
||||
|
||||
**** Headers :noexport:
|
||||
#+BEGIN_SRC C :comments link :tangle test_qmckl_distance.c
|
||||
#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
|
||||
- ~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.
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle qmckl.h
|
||||
qmckl_exit_code qmckl_distance_sq(const qmckl_context context,
|
||||
const char transa, const char transb,
|
||||
const int64_t m, const int64_t n,
|
||||
const double *A, const int64_t lda,
|
||||
const double *B, const int64_t ldb,
|
||||
const double *C, const int64_t ldc);
|
||||
#+END_SRC
|
||||
|
||||
***** Source
|
||||
#+BEGIN_SRC f90 :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 :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 :tangle qmckl_f.f90
|
||||
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 :tangle test_qmckl_distance_f.f90
|
||||
integer(c_int32_t) function test_qmckl_distance_sq(context) bind(C)
|
||||
use qmckl
|
||||
implicit none
|
||||
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:
|
||||
|
||||
#+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
|
||||
|
||||
|
||||
# -*- mode: org -*-
|
||||
# vim: syntax=c
|
||||
193
src/qmckl_error.org
Normal file
193
src/qmckl_error.org
Normal file
@ -0,0 +1,193 @@
|
||||
# This file is part of the qmckl.h file
|
||||
** Error handling
|
||||
:PROPERTIES:
|
||||
:c: qmckl_error.c
|
||||
:c_test: test_qmckl_error.c
|
||||
:fh: qmckl_f.f90
|
||||
:h: qmckl.h
|
||||
:END:
|
||||
|
||||
This file is written in C because it is more natural to express the
|
||||
error handling in C than in Fortran.
|
||||
|
||||
2 files are produced:
|
||||
- a source file : =qmckl_error.c=
|
||||
- a test file : =test_qmckl_error.c=
|
||||
|
||||
*** Headers :noexport:
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c" t)
|
||||
#include "qmckl.h"
|
||||
#include <math.h>
|
||||
#include <string.h>
|
||||
#include <errno.h>
|
||||
#include <assert.h>
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC C :tangle (org-entry-get nil "c_test" t)
|
||||
#include "qmckl.h"
|
||||
#include "munit.h"
|
||||
MunitResult test_qmckl_error() {
|
||||
#+END_SRC
|
||||
|
||||
*** Error handling
|
||||
|
||||
The library should never make the calling programs abort, nor
|
||||
perform any input/output operations. This decision has to be taken
|
||||
by the developer of the code calling the library.
|
||||
|
||||
All the functions return with an <<<exit code>>>, defined as
|
||||
#+NAME: type-exit-code
|
||||
#+BEGIN_SRC C :comments org :tangle qmckl.h
|
||||
typedef int32_t qmckl_exit_code;
|
||||
#+END_SRC
|
||||
|
||||
The exit code returns the completion status of the function to the
|
||||
calling program. When a function call completed successfully, the
|
||||
~QMCKL_SUCCESS~ exit code is returned. If one of the functions of
|
||||
the library fails to complete the requested task, an appropriate
|
||||
error code is returned to the program.
|
||||
|
||||
Here is the complete list of exit codes.
|
||||
|
||||
#+NAME: table-exit-codes
|
||||
| ~QMCKL_SUCCESS~ | 0 |
|
||||
| ~QMCKL_INVALID_ARG_1~ | 1 |
|
||||
| ~QMCKL_INVALID_ARG_2~ | 2 |
|
||||
| ~QMCKL_INVALID_ARG_3~ | 3 |
|
||||
| ~QMCKL_INVALID_ARG_4~ | 4 |
|
||||
| ~QMCKL_INVALID_ARG_5~ | 5 |
|
||||
| ~QMCKL_INVALID_ARG_6~ | 6 |
|
||||
| ~QMCKL_INVALID_ARG_7~ | 7 |
|
||||
| ~QMCKL_INVALID_ARG_8~ | 8 |
|
||||
| ~QMCKL_INVALID_ARG_9~ | 9 |
|
||||
| ~QMCKL_INVALID_ARG_10~ | 10 |
|
||||
| ~QMCKL_NULL_CONTEXT~ | 101 |
|
||||
| ~QMCKL_FAILURE~ | 102 |
|
||||
| ~QMCKL_ERRNO~ | 103 |
|
||||
| ~QMCKL_INVALID_EXIT_CODE~ | 104 |
|
||||
|
||||
# We need to force Emacs not to indent the Python code:
|
||||
# -*- org-src-preserve-indentation: t
|
||||
#+BEGIN_SRC python :var table=table-exit-codes :results drawer :exports result
|
||||
""" This script generates the C and Fortran constants for the error
|
||||
codes from the org-mode table.
|
||||
"""
|
||||
|
||||
result = [ "#+BEGIN_SRC C :comments org :tangle qmckl.h" ]
|
||||
for (text, code) in table:
|
||||
text=text.replace("~","")
|
||||
result += [ f"#define {text:30s} {code:d}" ]
|
||||
result += [ "#+END_SRC" ]
|
||||
|
||||
result += [ "" ]
|
||||
|
||||
result += [ "#+BEGIN_SRC f90 :comments org :tangle qmckl_f.f90" ]
|
||||
for (text, code) in table:
|
||||
text=text.replace("~","")
|
||||
result += [ f" integer, parameter :: {text:30s} = {code:d}" ]
|
||||
result += [ "#+END_SRC" ]
|
||||
|
||||
return '\n'.join(result)
|
||||
|
||||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:results:
|
||||
#+BEGIN_SRC C :comments org :tangle qmckl.h
|
||||
#define QMCKL_SUCCESS 0
|
||||
#define QMCKL_INVALID_ARG_1 1
|
||||
#define QMCKL_INVALID_ARG_2 2
|
||||
#define QMCKL_INVALID_ARG_3 3
|
||||
#define QMCKL_INVALID_ARG_4 4
|
||||
#define QMCKL_INVALID_ARG_5 5
|
||||
#define QMCKL_INVALID_ARG_6 6
|
||||
#define QMCKL_INVALID_ARG_7 7
|
||||
#define QMCKL_INVALID_ARG_8 8
|
||||
#define QMCKL_INVALID_ARG_9 9
|
||||
#define QMCKL_INVALID_ARG_10 10
|
||||
#define QMCKL_NULL_CONTEXT 101
|
||||
#define QMCKL_FAILURE 102
|
||||
#define QMCKL_ERRNO 103
|
||||
#define QMCKL_INVALID_EXIT_CODE 104
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC f90 :comments org :tangle qmckl_f.f90
|
||||
integer, parameter :: QMCKL_SUCCESS = 0
|
||||
integer, parameter :: QMCKL_INVALID_ARG_1 = 1
|
||||
integer, parameter :: QMCKL_INVALID_ARG_2 = 2
|
||||
integer, parameter :: QMCKL_INVALID_ARG_3 = 3
|
||||
integer, parameter :: QMCKL_INVALID_ARG_4 = 4
|
||||
integer, parameter :: QMCKL_INVALID_ARG_5 = 5
|
||||
integer, parameter :: QMCKL_INVALID_ARG_6 = 6
|
||||
integer, parameter :: QMCKL_INVALID_ARG_7 = 7
|
||||
integer, parameter :: QMCKL_INVALID_ARG_8 = 8
|
||||
integer, parameter :: QMCKL_INVALID_ARG_9 = 9
|
||||
integer, parameter :: QMCKL_INVALID_ARG_10 = 10
|
||||
integer, parameter :: QMCKL_NULL_CONTEXT = 101
|
||||
integer, parameter :: QMCKL_FAILURE = 102
|
||||
integer, parameter :: QMCKL_ERRNO = 103
|
||||
integer, parameter :: QMCKL_INVALID_EXIT_CODE = 104
|
||||
#+END_SRC
|
||||
:end:
|
||||
|
||||
To make a function fail, the <<<~qmckl_failwith~>>> function should be
|
||||
called, such that information about the failure is stored in
|
||||
the context. The desired exit code is given as an argument, as
|
||||
well as the name of the function and an error message. The return
|
||||
code of the function is the desired return code.
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle qmckl.h
|
||||
qmckl_exit_code qmckl_failwith(qmckl_context context,
|
||||
const qmckl_exit_code exit_code,
|
||||
const char* function,
|
||||
const char* message) ;
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle qmckl_error.c
|
||||
qmckl_exit_code qmckl_failwith(qmckl_context context,
|
||||
const qmckl_exit_code exit_code,
|
||||
const char* function,
|
||||
const char* message) {
|
||||
if (context == 0) return QMCKL_NULL_CONTEXT;
|
||||
assert (exit_code > 0);
|
||||
assert (exit_code < QMCKL_INVALID_EXIT_CODE);
|
||||
assert (function != NULL);
|
||||
assert (message != NULL);
|
||||
assert (strlen(function) < QMCKL_MAX_FUN_LEN);
|
||||
assert (strlen(message) < QMCKL_MAX_MSG_LEN);
|
||||
|
||||
context = qmckl_context_set_error(context, exit_code, function, message);
|
||||
return exit_code;
|
||||
}
|
||||
|
||||
#+END_SRC
|
||||
|
||||
For example, this function can be used as
|
||||
#+BEGIN_SRC C :tangle no
|
||||
if (x < 0) {
|
||||
return qmckl_failwith(context,
|
||||
QMCKL_INVALID_ARG_2,
|
||||
"qmckl_function",
|
||||
"Expected x >= 0");
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
|
||||
# To decode the error messages, the <<<~qmckl_strerror~>>> converts an
|
||||
# error code into a string.
|
||||
|
||||
*** End of files :noexport:
|
||||
|
||||
***** Test
|
||||
#+BEGIN_SRC C :comments link :tangle (org-entry-get nil "c_test" t)
|
||||
return MUNIT_OK;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
|
||||
|
||||
# -*- mode: org -*-
|
||||
# vim: syntax=c
|
||||
|
||||
# -*- mode: org -*-
|
||||
# vim: syntax=c
|
||||
18
src/qmckl_footer.org
Normal file
18
src/qmckl_footer.org
Normal file
@ -0,0 +1,18 @@
|
||||
* 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.
|
||||
|
||||
* End of header files :noexport:
|
||||
|
||||
#+BEGIN_SRC C :tangle qmckl.h
|
||||
#endif
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC f90 :tangle qmckl_f.f90
|
||||
end module qmckl
|
||||
#+END_SRC
|
||||
|
||||
|
||||
# -*- mode: org -*-
|
||||
|
||||
117
src/qmckl_memory.org
Normal file
117
src/qmckl_memory.org
Normal file
@ -0,0 +1,117 @@
|
||||
** Memory management
|
||||
|
||||
We override the allocation functions to enable the possibility of
|
||||
optimized libraries to fine-tune the memory allocation.
|
||||
|
||||
2 files are produced:
|
||||
- a source file : =qmckl_memory.c=
|
||||
- a test file : =test_qmckl_memory.c=
|
||||
|
||||
*** Headers :noexport:
|
||||
#+BEGIN_SRC C :tangle qmckl_memory.c
|
||||
#include "qmckl.h"
|
||||
#include <assert.h>
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC C :tangle test_qmckl_memory.c
|
||||
#include "qmckl.h"
|
||||
#include "munit.h"
|
||||
MunitResult test_qmckl_memory() {
|
||||
#+END_SRC
|
||||
|
||||
*** ~qmckl_malloc~
|
||||
|
||||
Memory allocation function, letting the library choose how the
|
||||
memory will be allocated, and a pointer is returned to the user.
|
||||
The context is passed to let the library store data related to the
|
||||
allocation inside the context.
|
||||
|
||||
#+BEGIN_SRC C :tangle qmckl.h
|
||||
void* qmckl_malloc(const qmckl_context ctx, const size_t size);
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC f90 :tangle qmckl_f.f90
|
||||
interface
|
||||
type (c_ptr) function qmckl_malloc (context, size) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
integer (c_int64_t), intent(in), value :: size
|
||||
end function qmckl_malloc
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
**** Source
|
||||
#+BEGIN_SRC C :tangle qmckl_memory.c
|
||||
void* qmckl_malloc(const qmckl_context ctx, const size_t size) {
|
||||
if (ctx == (qmckl_context) 0) {}; /* Avoid unused argument warning */
|
||||
void * result = malloc( (size_t) size );
|
||||
assert (result != NULL) ;
|
||||
return result;
|
||||
}
|
||||
|
||||
#+END_SRC
|
||||
|
||||
**** Test :noexport:
|
||||
#+BEGIN_SRC C :tangle test_qmckl_memory.c
|
||||
int *a = NULL;
|
||||
munit_assert(a == NULL);
|
||||
a = (int*) qmckl_malloc( (qmckl_context) 1, 3*sizeof(int));
|
||||
munit_assert(a != NULL);
|
||||
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~
|
||||
|
||||
The context is passed, in case some important information has been
|
||||
stored related to memory allocation and needs to be updated.
|
||||
|
||||
#+BEGIN_SRC C :tangle qmckl.h
|
||||
qmckl_exit_code qmckl_free(qmckl_context context, void *ptr);
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC f90 :tangle qmckl_f.f90
|
||||
interface
|
||||
integer (c_int32_t) function qmckl_free (context, ptr) bind(C)
|
||||
use, intrinsic :: iso_c_binding
|
||||
integer (c_int64_t), intent(in), value :: context
|
||||
type (c_ptr), intent(in), value :: ptr
|
||||
end function qmckl_free
|
||||
end interface
|
||||
#+END_SRC
|
||||
|
||||
**** Source
|
||||
#+BEGIN_SRC C :tangle qmckl_memory.c
|
||||
qmckl_exit_code qmckl_free(qmckl_context context, void *ptr) {
|
||||
if (context == 0) return QMCKL_INVALID_ARG_1;
|
||||
if (ptr == NULL) return QMCKL_INVALID_ARG_2;
|
||||
free(ptr);
|
||||
return QMCKL_SUCCESS;
|
||||
}
|
||||
#+END_SRC
|
||||
|
||||
**** Test :noexport:
|
||||
#+BEGIN_SRC C :tangle test_qmckl_memory.c
|
||||
munit_assert(a != NULL);
|
||||
qmckl_exit_code rc;
|
||||
rc = qmckl_free( (qmckl_context) 1, a);
|
||||
munit_assert(rc == QMCKL_SUCCESS);
|
||||
|
||||
#+END_SRC
|
||||
|
||||
*** End of files :noexport:
|
||||
|
||||
**** Test
|
||||
#+BEGIN_SRC C :comments org :tangle test_qmckl_memory.c
|
||||
return MUNIT_OK;
|
||||
}
|
||||
|
||||
#+END_SRC
|
||||
|
||||
|
||||
# -*- mode: org -*-
|
||||
# vim: syntax=c
|
||||
21
src/qmckl_precision.org
Normal file
21
src/qmckl_precision.org
Normal file
@ -0,0 +1,21 @@
|
||||
# This file is part of the qmckl.h file
|
||||
|
||||
*** Multi-precision related constants
|
||||
|
||||
Controlling numerical precision enables optimizations. Here, the
|
||||
default parameters determining the target numerical precision and
|
||||
range are defined.
|
||||
|
||||
#+BEGIN_SRC C :comments org :tangle qmckl.h
|
||||
#define QMCKL_DEFAULT_PRECISION 53
|
||||
#define QMCKL_DEFAULT_RANGE 11
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC f90 :comments org :tangle qmckl_f.f90
|
||||
integer, parameter :: QMCKL_DEFAULT_PRECISION = 53
|
||||
integer, parameter :: QMCKL_DEFAULT_RANGE = 11
|
||||
#+END_SRC
|
||||
|
||||
|
||||
# -*- mode: org -*-
|
||||
# vim: syntax=c
|
||||
9
src/table_of_contents
Normal file
9
src/table_of_contents
Normal file
@ -0,0 +1,9 @@
|
||||
qmckl.org
|
||||
qmckl_context.org
|
||||
qmckl_error.org
|
||||
qmckl_precision.org
|
||||
qmckl_memory.org
|
||||
qmckl_distance.org
|
||||
qmckl_ao.org
|
||||
test_qmckl.org
|
||||
qmckl_footer.org
|
||||
85
src/test_qmckl.org
Normal file
85
src/test_qmckl.org
Normal file
@ -0,0 +1,85 @@
|
||||
* QMCkl test :noexport:
|
||||
|
||||
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
|
||||
0
to_be_processed/.gitignore
vendored
Normal file
0
to_be_processed/.gitignore
vendored
Normal file
47
tools/create_doc.sh
Executable file
47
tools/create_doc.sh
Executable file
@ -0,0 +1,47 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -x
|
||||
|
||||
INPUT=merged.org
|
||||
if [[ -z $QMCKL_ROOT ]]
|
||||
then
|
||||
print "QMCKL_ROOT is not defined"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
|
||||
# Install htmlize if needed
|
||||
[[ -f ${QMCKL_ROOT}/docs/htmlize.el ]] || (
|
||||
cd ${QMCKL_ROOT}/docs/
|
||||
git clone https://github.com/hniksic/emacs-htmlize
|
||||
cp emacs-htmlize/htmlize.el .
|
||||
rm -rf emacs-htmlize
|
||||
cd -
|
||||
)
|
||||
|
||||
[[ -f ${QMCKL_ROOT}/docs/htmlize.el ]] || exit 1
|
||||
|
||||
|
||||
# Switch to TMPDIR for easy cleanup
|
||||
TMPDIR=$(mktemp -d)
|
||||
${QMCKL_ROOT}/tools/merge_org.sh $TMPDIR/$INPUT
|
||||
cd $TMPDIR
|
||||
|
||||
|
||||
# Create documentation
|
||||
emacs --batch \
|
||||
--load ${QMCKL_ROOT}/docs/htmlize.el \
|
||||
--load ${QMCKL_ROOT}/docs/config.el \
|
||||
$INPUT -f org-html-export-to-html
|
||||
|
||||
if [[ $? -eq 0 ]]
|
||||
then
|
||||
mv index.html ${QMCKL_ROOT}/docs/
|
||||
rm -rf $TMPDIR
|
||||
exit 0
|
||||
else
|
||||
rm -rf $TMPDIR
|
||||
exit 2
|
||||
fi
|
||||
|
||||
|
||||
98
tools/create_makefile.sh
Executable file
98
tools/create_makefile.sh
Executable file
@ -0,0 +1,98 @@
|
||||
#!/bin/bash
|
||||
|
||||
MERGED=merged.org
|
||||
${QMCKL_ROOT}/tools/merge_org.sh $MERGED
|
||||
|
||||
OUTPUT=Makefile.generated
|
||||
|
||||
# Tangle org files
|
||||
emacs \
|
||||
$MERGED \
|
||||
--batch \
|
||||
-f org-babel-tangle \
|
||||
--kill
|
||||
|
||||
rm $MERGED
|
||||
|
||||
|
||||
# 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=$LIBS
|
||||
|
||||
libqmckl.so: \$(OBJECT_FILES)
|
||||
\$(CC) -shared \$(OBJECT_FILES) -o libqmckl.so
|
||||
|
||||
%.o: %.c
|
||||
\$(CC) \$(CFLAGS) -c \$*.c -o \$*.o
|
||||
|
||||
%.o: %.f90 qmckl_f.o
|
||||
\$(FC) \$(FFLAGS) -c \$*.f90 -o \$*.o
|
||||
|
||||
test_qmckl: test_qmckl.c libqmckl.so \$(TESTS) \$(TESTS_F)
|
||||
\$(CC) \$(CFLAGS) -Wl,-rpath,$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
|
||||
|
||||
|
||||
80
tools/init.el
Normal file
80
tools/init.el
Normal file
@ -0,0 +1,80 @@
|
||||
(package-initialize)
|
||||
(add-to-list 'package-archives
|
||||
'("gnu" . "https://elpa.gnu.org/packages/"))
|
||||
(add-to-list 'package-archives
|
||||
'("melpa-stable" . "https://stable.melpa.org/packages/"))
|
||||
(add-to-list 'package-archives
|
||||
'("melpa" . "https://melpa.org/packages/"))
|
||||
(setq package-archive-priorities '(("melpa-stable" . 100)
|
||||
("melpa" . 50)
|
||||
("gnu" . 10)))
|
||||
|
||||
(require 'cl)
|
||||
(let* ((required-packages
|
||||
'(htmlize
|
||||
evil
|
||||
org-evil
|
||||
org-bullets
|
||||
))
|
||||
(missing-packages (remove-if #'package-installed-p required-packages)))
|
||||
(when missing-packages
|
||||
(message "Missing packages: %s" missing-packages)
|
||||
(package-refresh-contents)
|
||||
(dolist (pkg missing-packages)
|
||||
(package-install pkg)
|
||||
(message "Package %s has been installed" pkg))))
|
||||
|
||||
(setq backup-directory-alist
|
||||
`(("." . ,(concat user-emacs-directory "backups"))))
|
||||
(setq backup-by-copying t)
|
||||
|
||||
(require 'org)
|
||||
(setq org-format-latex-options (plist-put org-format-latex-options :scale 1.6))
|
||||
|
||||
(setq org-hide-leading-stars t)
|
||||
(setq org-alphabetical-lists t)
|
||||
(setq org-src-fontify-natively t)
|
||||
(setq org-src-tab-acts-natively t)
|
||||
(setq org-src-preserve-indentation t)
|
||||
(setq org-hide-emphasis-markers nil)
|
||||
(setq org-pretty-entities nil)
|
||||
(setq org-confirm-babel-evaluate nil) ;; Do not ask for confirmation all the time!!
|
||||
|
||||
(org-babel-do-load-languages
|
||||
'org-babel-load-languages
|
||||
'(
|
||||
(emacs-lisp . t)
|
||||
(shell . t)
|
||||
(python . t)
|
||||
(C . t)
|
||||
(org . t)
|
||||
(makefile . t)
|
||||
))
|
||||
|
||||
(add-hook 'org-babel-after-execute-hook 'org-display-inline-images)
|
||||
'(indent-tabs-mode nil)
|
||||
|
||||
(require 'evil)
|
||||
(setq evil-want-C-i-jump nil)
|
||||
(evil-mode 1)
|
||||
(global-font-lock-mode t)
|
||||
(global-superword-mode 1)
|
||||
|
||||
(setq line-number-mode 1)
|
||||
(setq column-number-mode 1)
|
||||
|
||||
(evil-select-search-module 'evil-search-module 'evil-search)
|
||||
|
||||
(global-set-key (kbd "C-+") 'text-scale-increase)
|
||||
(global-set-key (kbd "C--") 'text-scale-decrease)
|
||||
|
||||
|
||||
(custom-set-variables
|
||||
;; custom-set-variables was added by Custom.
|
||||
;; If you edit it by hand, you could mess it up, so be careful.
|
||||
;; Your init file should contain only one such instance.
|
||||
;; If there is more than one, they won't work right.
|
||||
'(ansi-color-faces-vector
|
||||
[default default default italic underline success warning error])
|
||||
'(custom-enabled-themes (quote (leuven)))
|
||||
)
|
||||
8
tools/merge_org.sh
Executable file
8
tools/merge_org.sh
Executable file
@ -0,0 +1,8 @@
|
||||
#!/bin/bash
|
||||
|
||||
OUTPUT=$1
|
||||
|
||||
for i in README.org $(cat $QMCKL_ROOT/src/table_of_contents)
|
||||
do
|
||||
cat $i >> $1
|
||||
done
|
||||
11
tools/nb_to_org.sh
Executable file
11
tools/nb_to_org.sh
Executable file
@ -0,0 +1,11 @@
|
||||
#!/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
|
||||
|
||||
44
tools/rename.py
Executable file
44
tools/rename.py
Executable file
@ -0,0 +1,44 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
"""
|
||||
Changes the name of a function into all the org files.
|
||||
This script should be run in the src directory.
|
||||
"""
|
||||
|
||||
import sys
|
||||
import os
|
||||
|
||||
|
||||
def help():
|
||||
print("Syntax : {0} OLD_FUNC_NAME NEW_FUNC_NAME".format(sys.argv[0]))
|
||||
|
||||
|
||||
|
||||
def replace_in_file(filename, old_func_name, new_func_name):
|
||||
with open(filename,'r') as f:
|
||||
text = f.read()
|
||||
|
||||
new_text = text.replace(old_func_name, new_func_name)
|
||||
|
||||
with open(filename,'w') as f:
|
||||
f.write(new_text)
|
||||
|
||||
|
||||
def main():
|
||||
if len(sys.argv) != 3:
|
||||
help()
|
||||
sys.exit(-1)
|
||||
old_func_name = sys.argv[1]
|
||||
new_func_name = sys.argv[2]
|
||||
|
||||
for filename in os.listdir(os.getcwd()):
|
||||
if filename.endswith(".org"):
|
||||
replace_in_file(filename, old_func_name, new_func_name)
|
||||
|
||||
print("Done. run git diff to check what has been changed.")
|
||||
|
||||
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
Loading…
Reference in New Issue
Block a user