Faunus is a C++ framework for Metropolis Monte Carlo simulations of molecular systems. Below is a brief overview of features:
- Canonical, Grand Canonical, Isobaric-Isothermal statistical mechanical ensembles
- General hamiltonian parallel tempering (temperature, screening length, bonds etc.)
- 4D simulations on hyperspheres
- Anisotropic atoms (multipoles, sphero-cylinders)
- Ion titration moves (pKa prediction, Hofmeister effects etc.)
- Highly expandable!
- Free and open source (GPL)
Detailed information and support:
- Website: http://github.com/mlund/faunus
- Documentation: http://faunus.sourceforge.net/doxyhtml
- Support: http://github.com/mlund/faunus/issues
Get the latest resivions from GitHub:
$ git clone https://github.com/mlund/faunus.git
- C/C++11 compiler (clang3+, gcc4.6+, intel13+, ...)
- CMake 2.8+
Optional:
- SWIG 2.0+ (for python, ruby, ... modules)
- OpenBabel 2 (numerous molecular formats)
- Doxygen and Graphviz (for code manual)
- Xcode (for neat environment on macos x)
Developed and tested on Linux and MacOS X.
$ cmake . [options]
$ make [help]
$ make test (or use 'ctest -V' for verbose test output)
| Option | Description |
|---|---|
-DENABLE_BABEL=OFF |
Use OpenBabel for file I/O |
-DENABLE_MPI=OFF |
Build MPI programs (parallel tempering etc.) |
-DENABLE_OPENMP=OFF |
Enable OpenMP support |
-DENABLE_STATIC=OFF |
Static linkage of faunus as opposed to default dynamic linkage |
-DENABLE_SWIG=OFF |
Build python, ruby, tcl etc. modules |
-DENABLE_TWISTER=OFF |
Use Mersenne Twister for random numbers |
-DENABLE_UNICODE=ON |
Use Unicode UTF-16 encoding for pretty output |
-DCMAKE_BUILD_TYPE=RelWithDebInfo |
Alternatives: Debug or Release (faster) |
-DCMAKE_CXX_FLAGS_RELEASE="..." |
Compiler options for Release mode |
-DCMAKE_CXX_FLAGS_DEBUG="..." |
Compiler options for Debug mode |
-DMYPLAYGROUND="..." |
Add additional source directory (use absolute path) |
$ CXX=icpc CC=icc cmake . -DENABLE_OPENMP=on -DCMAKE_BUILD_TYPE=Release
$ make
$ LDFLAGS=-L/sw/lib CPPFLAGS=-I/sw/include/openbabel-2.0 cmake . -DENABLE_BABEL=on
$ make clean
$ rm CMakeCache.txt
In chronological order:
Mikael Lund Bjorn Persson Martin Trulsson
Ondrej Marsalek Christophe Labbez Andre Teixeira
Anil Kurut Chris Evers Magnus Ullner
Robert Vacha Axel Thuresson Bjorn Stenqvist
- Lund, M., Persson, B., Trulsson, M. Source Code Biol. Med., 2008, 3:1 [DOI]
Faunus - A Framework for Molecular Modelling
Copyright (C) 2002-2013 Mikael Lund
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 2 of the License, or
(at your option) any later version.
This program 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 this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.