Welcome to Faunus

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.)
• Anisotropic atoms (multipoles, sphero-cylinders)
• Ion titration moves (pKa prediction, Hofmeister effects etc.)
• Highy modular
• Free and open source (GPL)

Detailed information and support:

• Manual: http://faunus.sourceforge.net
• Support: http://github.com/mlund/faunus/issues
• Source code: http://github.com/mlund/faunus

Get the latest revision from GitHub:

$ git clone https://github.com/mlund/faunus.git

Requirements

• C/C++11 compiler (clang3+, gcc4.8+, intel13+, ...)
• CMake 2.8.5+

Optional:

• Doxygen (for code manual)
• Xcode (for neat environment on macos x)
• MPI (for parallelisation)

Developed and tested on Linux and MacOS X.

Compiling

$ cmake . [options]
$ make [help]
$ make test (or use 'ctest -V' for verbose test output)

Build options

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_TWISTER=OFF	Use Mersenne Twister for random numbers
-DENABLE_UNICODE=ON	Use Unicode UTF-16 encoding for pretty output
-ENABLE_POWERSASA=OFF	Enable SASA routines
-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)

Example: Intel's C++ compiler

$ CXX=icpc CC=icc cmake . -DCMAKE_BUILD_TYPE=Release
$ make

Example: Libraries in odd locations

$ LDFLAGS=-L/sw/lib CPPFLAGS=-I/sw/include/openbabel-2.0 cmake . -DENABLE_BABEL=on

Resetting the build system

$ make clean
$ rm -fR CMakeCache.txt CMakeFiles

Contributors

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
 Joao Henriques     Alexei Abrikossov      Giulio Tesei
 Lukas Sukenik

Citing Faunus

• Stenqvist et al. Molecular Simulation 2013, 39:1233 [DOI]

• Lund, M., Persson, B., Trulsson, M. Source Code Biol. Med., 2008, 3:1 [DOI]

 Faunus - A Framework for Molecular Modelling 
 Copyright (C) 2002-2014 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.