Parallel Computing & Air Pollution Study

[Image courtsey: Brian M. Wong, MIT]

Until now, chemistry researchers lacked an accurate model to calculate some important chemical properties such as the equilibrium and reaction rates, at varying temperatures. But recently researchers at MIT’s Department of Chemistry applied a new innovative method for performing complex computation for the thermochemical properties of hydrocarbons from petrol combustion. Their molecular models could eventually help scientists reduce air pollution.

The MIT scientists, Bryan M. Wong and Sumathy Raman, did not use approximations and so the data files and molecular models were so huge that they could only be processed using parallel methods. Using Interactive Supercomputing’s Star-P software the scientists could perform parallel computing while still working within their application of choice – Matlab. The software also allowed them to quickly interact with the data. 'Star-P' (as described in our past posting) lets scientists continue to work with their preferred tools, shielding them from the programming complexities of parallel systems. It can automatically connect MATLAB to the server and parallelises the application code.

Reference:
Bryan M. Wong and Sumathy Raman,
"Thermodynamic Calculations for Molecules with Asymmetric Internal Rotors - Application to 1,3-Butadiene", The Journal of Computational Chemistry, 28, 759 - 766 (2007).

AceGen & AceFEM (Mathematica Packages)

AceGen and AceFEM are third-party Mathematica packages developed by Jože Korelc, a professor at the University of Ljubljana’s (Slovenia) faculty of civil and geodetic engineering. Both are steadily gaining more popularity among users of 'Mathematica' (mathematical software from Wolfram, Inc.).

Acegen is basically a code-generator and is used for automatically deriving numerical procedures formulae. A number of different techniques are combined to shorten the evolution route and the results can be exported as compiled FORTRAN or C code with automated interfacing. The AceGen package provides also a collection of prearranged modules for the automatic creation of the interface between the automatically generated code and the numerical environment where the code would be executed.

AceFEM is a finite element methods package offering parallel options for either manual exploration of behavior or high speed black box computation of results. It has two components. The main part handles procedures that are not numerically intensive (e.g. processing of user-input data, mesh generation, control of the solution procedures, graphic post-processing of results, etc). The second part is a specialized numerical module that handles numerically intensive operations such as evaluating and assembling finite element (FE) quantities (including tangent matrix, residual, sensitivity vectors, etc.), solving linear systems of equations, and performing contact search procedures. The AceFEM package comes with a large library of finite elements (solid, thermal, contact, 2D, 3D, etc.), including full symbolic input for all elements.

AceGen is set up to talk with other numerical environments, including its sibling AceFEM. Each package combines use of Mathematica’s facilities with external handling of intensive computation by compiled modules.

Here is Prof. Korelc's website for these two packages: www.fgg.uni-lj.si/Symech/