ls1-MarDyn is a massively parallel Molecular Dynamics (MD) code for large systems. Its main target is the simulation of thermodynamics and nanofluidics. ls1-MarDyn is designed with a focus on performance and easy extensibility.

The current doxygen documentation can be found here: https://www5.in.tum.de/mardyn/doxygen_doc/html/

• a C++11 compiler (GCC, Clang, Intel, PGI, Cray, NEC SX, IBM XL, ...)
• a working MPI installation compatible with the MPI 3.0 specification or later (Open MPI, MPICH, MVAPICH, Intel MPI, Cray MPI, NEC MPI, IBM Platform MPI, ...)

• FFTW3: http://www.fftw.org
• VTK: http://www.vtk.org
• QuickSched: https://arxiv.org/abs/1601.05384

ls1-MarDyn is build from source code using GNU make.

A default build using the GNU compiler and a MPI library providing the mpicxx compiler wrapper is done with

  cd src
  make

To get an overview of options to control the build process, e.g. to use another compiler, disable MPI, ... run

  make help

To see a list of all supported target platforms and compilers call

  make cfg_list

and run then make with the desired configuration:

  make CFG=<config name>

To display further information about the available suboptions for a configuration use

  make CFG=<cfg name> cfg_help

The basic command to run ls1-mardyn is as follows:

MarDyn [options] <inputfile>

where MarDyn is the executable build in the INSTALLATION section, [options] are any "--"-prefixed options as listed by MarDyn --help and <inputfile> is a input file.

Detailed help can be obtained by running

MarDyn --help

ls1-MarDyn comes with a set of examples, which can be found in the examples folder.

cd examples/EOX/305K_liq
mpirun -np 2 ../../../src/MarDyn config.xml  --steps 10

optional: to make the simulation aware of time limits like on a compute node, which should stop the simulation even if the desired amount of steps is not reached use loop-abort-time in (s) in XML or CLI:

mpirun -np 2 ../../../src/MarDyn config.xml  --steps 10 --loop-abort-time 3600

ls1-MarDyn is documented using doxygen. To build the documentation run

doxygen Doxyfile

It includes information about the following topics

• \ref ls1MarDynInputFiles Mardyn Input Files
• \ref unitTests Unit tests
• \ref visualisation Graphical Simulation Output

as well as the documentation of the source code.

• http://www.ls1-mardyn.de : the official ls1-MarDyn web page.
• mailto:[email protected] : can be used for general questions around ls1-MarDyn.
• mailto:[email protected] : can be used to reach the developers of ls1-MarDyn.