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langevin_LJ

C program for Langevin MD simulations applied to Lennard Jones clusters only.

DEPENDANCIES, COMPILE & INSTALL

A C compiler compatible with the C11 standard is required.

You will need to Download or Compile the OpenMM library, a required dependancy : see https://simtk.org/home/openmm and/or https://github.com/pandegroup/openmm

Be sure to have CMAKE installed (http://www.cmake.org/), available on most repositories.

Tested compilers (ubuntu 15.10 and 16.04):

  • gcc 4.8.5 - 4.9.3 - 5.2.1 -5.4.0
  • clang 3.4.2 - 3.6.2
  • icc 16.0.0

Create a build directory and move to that directory:

  • mkdir build && cd build

For buildind a debug or release (default) version :

  • cmake -DCMAKE_BUILD_TYPE=Debug ..
  • cmake -DCMAKE_BUILD_TYPE=Release ..

Debug builds are slower but useful when debugging with gdb or valgrind.

Then, once cmake built a Makefile, just execute :

  • make

For a verbose make, use :

  • make VERBOSE=1

Please never edit this autogenerated Makefile, edit the CMakeLists.txt instead.

For specifying another compiler on linux (for example clang or Intel icc):

  • CC=clang cmake ..
  • CC=icc cmake ..

DOCUMENTATION

Check the doc directory that contains programming documentation.

For generating the documentation, run doxygen in the current directory (http://www.doxygen.org)

LICENSING (all files excepted subdirectory dSFMT)

Copyright (c) 2016-2017, Florent Hédin, Tony Lelièvre, and École des Ponts - ParisTech All rights reserved.

The 3-clause BSD license is applied to this software.

See LICENSE.txt

NOTE CONCERNING dSFMT

This project uses as random numbers generator the dSFMT code : http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/

All files in the subdirectory dSFMT are licensed with a 3-clause BSD license and copyrighted as following : Copyright (C) 2007,2008 Mutsuo Saito, Makoto Matsumoto and Hiroshima University. All rights reserved.

See dSFMT/LICENSE_dSFMT.txt

NOTE CONCERNING OpenMM platform

The software should automatically detect the fastest OpenMM Platform available on your computer (i.e. CUDA, OpenCL, ...) If not it will run with the slow Reference platform : it is most probably because the OpenMM directory with the 'plugins' library is not found. You may need to export the following OPENMM_PLUGIN_DIR environment variable to solve the problem :

For example for a custom installation in /home/$USER/bin/openmm.

  • export OPENMM_PLUGIN_DIR=$HOME/bin/openmm/lib/plugins