Molecular Dynamics Simulation Achieved speedup: 37x-60x.



1.  Physical background
Explosives containing C, H, N, O produce mixture of N2, H20, C02 at high temperatures(1000-5000K) and high pressures(1-500GPa).  In [1], it was predicted that under such extreme condition N2/H20 mixture mixture might exhibit phase separation behind detonation waves. This prediction was investigated by Prof. Koshi, M. and  Matsui, H. who confirmed that under certain conditions on the temperature and density  the phase separation indeed occurs.  This investigation has been done using molecular dynamics program NVT3, originally written by Prof. Koshi in FORTRAN 77. The size of the system was N=256 molecules (128 H20 + 128 N2) and the temperature T=2000 K.


2.  Description of NVT3 molecular dynamics program
NVT3 program computes molecular dynamics for the binary mixture for NVT or NVE ensembles.  The force/energy computation uses modified Buckingham (exp-6) potential.  The motion integration is done using leap-frog method. During simulation run program outputs temperature, pressure, total energy of the system plus some additional parameters. To analyze the structure of the binary mixture,  program also outputs pair correlation function data.


3.  Acceleration of MD program NVT3
We converted NVT3 program, kindly provided to us by Prof. Koshi, first to C and then to CUDA.  Then, to observe real-time molecular dynamics simulation we added particle rendering capability and disabled computation of some system parameters not necessary for the MD computation.  As a result, we observed 37x to 60x acceleration of MD simulation compared to all-CPU version of this program.   


4.  Results.
Below are the actual images of the equimolar binary system at the near-initial state (step 10, t=10 femtoseconds) and at the phase separated state (step 10400, t=10.4 picoseconds).  The number of molecules in this simulation is N = 13500, the temperature is T=2500K and the density is ρ = 2.3867 g / cm3. This simulation was run for 20000 time-steps, which corresponds to 20 picoseconds.  On Intel (R) Core(TM) i7 machine with GeForce GT480 GPU, the computational time of the entire simulation was 12 minutes.  


frame_1.gif
Figure 1: Near-initial state (10ps) of the H20/N2 system. 
No phase separation can be observed.


md_simulation_movie.gif
Figure 2: Step 10400 (10.4 ps): Phase separation occurred: one can clearly see the clustering of the water molecules (blue) and the nitrogen molecules (white).

Download movie of the entire simulation, WM9 compressed:
High Quality (60MB)  Medium Quality (30MB)  Low Quality (5MB)


5. Possible applications
The program can be used to perform  MD simulations of the binary molecular mixtures interacting by exp-6 potential.  The size of the system can be large, of the order of tens of thousands. 

It is also possible to modify the program to compute molecular dynamics of 3 or more components, interacting by either exp-6 or by some other potential.


6. References
[1] F.H. Ree,
  ”Supercritical fluid phase separations: Implications for detonation properties of condensed explosives” ,
  J. Chem. Phys.,84, 5845 (1986)

[2] Koshi, M., Matsui, H., “Molecular Dynamics Study of High Temperature
  Phase-Separation in H2O/N2 mixture with exp-6 interactions”, Molecular Simulation,
  1994, Vol. 12(3-6), pp. 227-239.


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