C++ Classical Molecular Modeling Code for Pedagogical Purposes

Copyright (C) 2011-2012, Li Ding dingmaotu at 126.com Licenced under GPL v3

This is a molecular modeling code I wrote when I entered the Institute of Geology and Geophysics, CAS. I was a newbie of molecular modeling though I had taken several related classes in the CAS graduate school. My supervisor suggested that I start a simple modeling code, with the purpose of learning inner workings of a real package. It is extremely helpful to really write the code, which involves searching the internet and reading a lot of related books. I found it illuminating to know the inner working of molecular dynamics, so I want to share the experience with others who also want to really understand how a modeling is performed.

Acctually, this code currently only do classical molecular dynamics with only one type of atom, and it has only one force field: Lenard Jones 12-6 potential for Ar atoms. This system is the most studied one, however, and you can learn a lot from it.

This is the very first working version, and the code is a bit nasty. I put it on github to make a conscience effort to improve it. I want to improve it like this:

1. Make a clear OO design to show the inner workings of a simulation program
2. Make it easy to add new functionalities and to play with
3. Perform most common types of molecular dynamics and Monte Carlo simulations
4. If possible, show how MPI is used to leverage clusters
5. Last but not least, a collection of easy to understand documentation

Performance is NOT critical to LDMM since its purpose is education.

You need to compile the source distribution. It is very simple: you just type make or make release to build a release version (optimised and without debugging symbols). Optionally you can make debug to build a debug version. The binary executable is in the root directory of the distribution, and all intermidiate object files are in the build directory. Type make clean to clean up all binaries.

Intel C++ or g++ is supported. Default C++ compiler is used if not specified. You can specify your C++ compiler in the make commmand (for example, make CXX=icpc release).

To use LDMM, type ldmm [your config file]. There is a sample config file called ar.config and associated ar.gro in the root directory.

This is a very important part for LDMM but now it is not written. However, basic documentation will be added soon.

• Minor update to 0.4
  1. Reorganized the layout of the project, and updated the Makefile. SCons is removed.
• Version 0.4
  1. Added OpenMP support to parallelize the computation. This slightly speeds up the program.
• Version 0.3
  1. Added Batch Mode, which can do a series of NVT simulations by varying the temperature.
  2. Automatically average of T and P (after BatchCollect steps)
• Version 0.2
  1. Changed the brute-force LJ12-6 computation to a neighber-list based algorithm, and added cut-off controls.
  2. Implemented a Berendson heat bath to perform NVT simulations.
  3. Output common instant properties of the system: T, P, Potential, Kinetic, and Total Energy.
  4. Access of configuration files from the exe directory.
• Version 0.1
  1. NVE LJ12-6 Atomic Fluid Simulation (No cut-off)