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NOTE: C++11 required!!!

While most of the code still uses the C++98 standard, in order to compile it a C++11 compiler is required. Due to problems with the boost/functional/factory library when compiling on Mac OS X (OS X High Sierra and later) SAMoS no longer uses that library. Instead a light-weight class factory was implemented using the C++11 standard (it relies on variadic templates).

Soft Active Matter on Surfaces (SAMoS)

1. OS

The code has been developed and tested under Linux and Mac OS X. In principle it should be possible to build and run the code on a Windows machine. However, this would require modifying the CMake build scripts. This has not been tested.

2. TUTORIALS

A detailed tutorial on how to set up a simulation in SAMoS can be found in /path/to/SAMoS_install/doc/tutorial/tutorial.html

here /path/to/SAMoS_install/ is the directory where SAMoS is installed (see section 5 below).

3. REQUIREMENTS

SAMoS code is written in C++. Data analysis and initial configuration building tools are written in Python 2.7 and require NumPy to run.

  • Modern C++ compiler supporting the C++11 standard
  • Boost libraries (1.48 or newer, in particular Spirit parser)
  • GNU Scientific Library (GSL) - version 1.13 or newer
  • CMake (2.8 or newer) - it is recommended to install ccmake GUI
  • Doxygen - optional but recommended (LaTeX support for building the PDF reference manual
  • VTK library (version 5 or 6)
  • CGAL library (version 4.3 or newer). NOTE: Code will fail to compile with CGAL 4.2 or older

NOTE: On Mac OS X, it is suggested to use Mac Ports to install all necessary libraries.

NOTE: SAMoS is able to generate VTP files as its output. We suggest installing and using ParaView to visualise the results.

4. COMPILING

a) Clone the code from the GitHub repository using

git clone https://github.com/sknepneklab/SAMoS.git

b) cd SAMoS (or the name of the directory you chose to download the code into)
c) mkdir build
d) cd build
e) ccmake ../
f) Use the CMake's GUI to chose appropriate settings
g) Press 'c' key several times to configure
h) If all libraries have been found, CMake will allow you to create a Makefile. If not, please exit CMake GUI and install missing libraries.
i) Press 'g' to create Make files. This will terminate CMake's GUI is return you to the shell.
j) Type 'make -j 8' (-j option tells make how many parallel threads to use to compile; on a 4-core machine one can typically use 8 threads).
k) If the compilation is successful, an executable 'samos' should appear in the build directory.

NOTE: Some Linux distributions with newer C++ compilers may have problems with running 8 parallel threads and can cause the machine to crash. If this happens, use '-j 2', which is likely not to cause any problems on most modern computers.

NOTE: SAMoS uses many templated libraries in Boost. Compiling it may take several minutes even on a very fast machine.

NOTE: Depending on the compiler, you may get a number of warning messages. Those are harmless and you may safely ignore them.

NOTE: SAMoS will only compile using c++11 (or newer) standard.

WARNING: Some Mac users have reported problems with compiling SAMoS on Sierra and High Sierra using packages installed with 'brew'. Switching to the 'MacPorts' seems to solve the problem.

5. INSTALLING SAMoS

After build has been successfully completed you can install SAMoS by typing

make install

in the build directory. This will install SAMoS package into $HOME/samos directory, where $HOME is the environment variable containing full path to your home directory.

  • SAMoS binary (samos) will be placed in $HOME/samos/bin
  • Examples will be in $HOME/samos/examples
  • Analysis scripts will be placed in $HOME/samos/analysis
  • Basic tutorial files will be placed in $HOME/samos/doc/tutorial

Please make sure to add $HOME/samos/analysis to your PYTHONPATH shell variable and $HOME/samos/bin to the PATH variable.

NOTE: You can change the default installation directory by setting CMAKE_INSTALL_PREFIX variable in step 4.

6. RUNNING SAMoS

The code requires two files to run:

  1. conf file containing simulation parameters, force field, integrator type, etc.
  2. data file containing initial position of particles (see configurations directory for a number of examples)

NOTE: Format of the configuration and data files can be found in the 'configurations' directory.

code is executed with

./samos conf_file.conf

7. SOURCE DIRECTORY STRUCTURE

samos 
   /FormerAnalysis   - some earlier versions of scripts for data analysis
   /analysis         - current set of tools for analysing simulation results 
   /build            - build directory (contains the executable)
   /configurations   - contains set of directories with examples of different systems that can be studies with SAMoS. Some directories 
                       contain Python scripts for generating initial configurations. 
   /doc              - Doxygen files for generating documentation
   /utils            - Several additional utilities for building initial configuration 
   /src              - Source code 
      \aligner       - Implementations of different alignment interactions that control particle orientation 
         \pair       - Pairwise aligners (alignments between pairs of particles)
         \external   - Single particle aligners (such as alignment to the extrenal field)
      /constraints   - Implementations of constraints to different curved surfaces 
      /dump          - Handles output of the simulation data (it supports several standard formats, plain text, VTP, mol2, dcd, etc.)
      /integrators   - Implements several integrators of the equations of motion
      /log           - Handles logging of the simulation state (e.g., current time step, total energy, etc.)
      /messenger     - Handles info, warning and error messages produced by the code, as well as generating metadata (JSON of XML format)
      /parser        - Set of Boost Spirit parsers for parsing configuration files
      /population    - Handles 'population' control (e.g., cell division and death, particle type change, particle removal and addition, etc.)
      /potential     - Implements various interactions (some of them may not be actual potential)
         /angle      - Angle potentials for filament simulations
         /bond       - Bond potentials for filament simulations 
         /external   - Potentials (and forces) acting on a single particle (such as external field)
         /pair       - Pair (or multibody) forces acting as the result of interparticle interactions (e.g., Lennard-Jones)
      /system        - Definition of the base classes that define the system (particles, simulation box, mesh, etc.)
      /utils         - Several utility functions (e.g., random number generator classes)

8. CREDITS

Lead developer:

Rastko Sknepnek (University of Dundee, UK)

Major contributors to the code:

Silke Henkes (University of Aberdeen, UK) - many tools for building inital configurations and analysis tools
Daniel Barton (University of Dundee, UK) - tools for building and analysing tissue mechanics simulations
Amit Das (National Institute for Biological Sciences, India) - tools for building and analysing actomyosin simulations