1. ReMoDy Reactive Molecular Dynamics for Surface Chemistry Simulations
A.Smirnov and R.A.Carreno-Chavez

2. Objectives
A Molecular dynamics model with reactive interactions and the possibility of bond formation.
Efficient processing of large ensembles of molecules

3. Link to ab-initio QM calculations
Provision for molecular bonding by retrieving electron configuration energy from the fast-access database. This database is continuously updated from the results of atomistic simulations. The missing data not covered by atomistic simulations can be replaced with those taken from experiments or other sources.

4. Classical Dynamics
In simulations of a gaseous phase and gas- solid interactions, each molecule is advanced as a material point following the conservation of its linear momentum. In addition to this each molecule is characterized by rotational and vibrational degrees of freedom.

5. Probabilistic Interactions
A bonding probability is introduced, which determines the transition event for the two species to form a molecular bond. Each molecule of a compound specie is treated as a rigid body subjected to Newton's laws of motion.

6. Stochastic Energy Distribution
Energy distribution among the molecules calculated in a statistical sense, with distribution probabilities determined by molecule's inertia tensor and relative bonding strengths between it's atoms. The data on these characteristics are provided by atomistic simulations.

7. Advantages
The small time scale of molecular vibrations and rotations can be avoided.
The quantum mechanical effects can be incorporated.
Effects of bonding can be introduced in a probabilistic sense.

8. Code Prototyping C++, OOP implementation
Single/multiple processor modes
A simple OpenGL viewer from the earlier work was developed.
The essential classes include: Atom: to represent species, and Molecule: to represent chemical compounds.

9. Interaction Acceleration
Space segmentation
scheme
Enables to achieve near linear dependence of execution time on the number of molecules.

10. Sample Simulations
Validation on Maxwell-Boltzman ensemble

11. Performance CPU *0.001s No of Molecules Simple Segmented 1000 80 3
10000
2800 34

12. Conclusions
The approach promisses to provide the possibility of simulating 105 molecules on a workstation.
Probabilistic interaction scheme will enable to relate to QM and describe bond fomation.
First prototype validation completed.