Description

A small library to provide algebraic operations on vectors in 3D space. The package defines only 3 template classes:

algebra3d::Vector3 <fpType> - for vectors in 3D space; to represent positions in 3D and also rotations (Cayley vectors);
algebra3d::Matrix3 <fpType> - 3 by 3 matrices to represent rotations;
algebra3d::Quaternion <fpType> - to represent rotations; added for efficiency

Each of the template types is specialized only for double and float, i.e. only the following types can be used (these are typedefs for abbreviation):

algebra3d::Vector3D (equiv. to algebra3d::Vector3 <double>)
algebra3d::Vector3F (equiv. to algebra3d::Vector3 <float>);
algebra3d::Matrix3D (equiv. to algebra3d::Matrix3 <double>)
algebra3d::Matrix3F (equiv. to algebra3d::Matrix3 <float>);
algebra3d::QuaternionD (equiv. to algebra3d::Quaternion <double>)
algebra3d::QuaternionF (equiv. to algebra3d::Quaternion <float>).

In addition some helper functions are defined in global.h. Some of those are fully defined in the header to make it possible for the compiler to inline them.

Download

The library can be obtained either by cloning the static Mercurial 2.8.1 repository:

hg clone http://lcvmwww.epfl.ch/software/algebra3d/repo algebra3d

or downloading a ZIP archive.

Building

The library has no extra dependencies. Any extra compilation settings should be set in Makefile.config. Provided all compilation setting are set appropriately the code can be build simply by running

$ make

which creates the following files:

./lib/libalgebra3d.a – a static library
./lib/libalgebra3d.so – a dynamic library

Note

On MacOS if you want to move the dynamic library to another location remember that dynamic libraries on Mac have their path stored internally. To see the current information use

$ otool -L /path/to/where/it/is/lib/libalgebra3d.so

To modify the install path use

$ install_name_tool -id /new/location/libalgebra3d.so /new/location/libalgebra3d.so

If you want just to rename the file to libalgebra3d.dylib (to use the MacOS convention) you would also need to do the above. To save yourself trouble you can also just use the static library.

The software has been tested on:

Gentoo Linux Kernel 3.18.12, g++ 4.8.4
Mac OS X 10.7.5, Darwin Kernel Version 11.4.2, g++ 4.2

Tests

The library has a set of unit tests based on CppUnit 1.12.1. To build the tests you need to have CppUnit available in your include path and library path. If it is not in your default paths add what is necessary to Makefile.config.

To build the tests use

$ make all_test

In addition to the results of products of the default build rule this will create test binaries:

./bin/TesterD – double precision version of tests for dynamic library
./bin/TesterF – single precision version of tests for dynamic library
./bin/TesterStaicD – double precision version of tests for static library
./bin/TesterStaticF – single precision version of tests for static library

The static and dynamic versions are exactly the same, they are both built to test static and dynamic linking. The pertinent rules in the Makefile might be of interest.

Timing

A simple program for running performance tests is available in src/timing.cpp. This is not compiled by the default make rule, but can be built by:

$ make timing

which builds two binaries:

./bin/timingD – a binary for timing double precision computations
./bin/timingF – a binary for timing single precision computations

How to cite

If you find this code useful please cite:

Jonathan S. Mitchell, Jaroslaw Glowacki, Alexandre E. Grandchamp, Robert S. Manning and John H. Maddocks,
Sequence-dependent persistence lengths of DNA
submitted.

DOI: ?

Copyright: Copyright 2015 Jaroslaw Glowacki
jarek (dot) glowacki (at) gmail (dot) com

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

algebra3d is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with algebra3d. If not, see http://www.gnu.org/licenses/.