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langevin_LJ

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

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DEPENDANCIES, COMPILE & INSTALL

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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 ..

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DOCUMENTATION

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Check the doc directory that contains programming documentation.

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

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LICENSING (all files excepted subdirectory dSFMT)

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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

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NOTE CONCERNING dSFMT

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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

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NOTE CONCERNING OpenMM platform

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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