(Scientific CSCI596 Computing and Visualization) Assignment 1Molecular Dynamics Due: September 15 (Mon), 2008, at the class The purpose of this assignment is to familiarize yourself with the simple molecular dynamics (MD) program, md.c (and its linked-list cell variant, lmd.c). Note that, later in this course, you will need to be able to modify the programs in various projects such as visualization and parallelization. You will also perform basic performance measurements of the programs. 1. (Scaling) Perform a series of runs of the original md.c, in which the number of atoms is changed systematically. Note that the number of atoms is nAtom = 4 InitUcell[0] InitUcell[1] InitUcell[2]. Try a sequence, InitUcell[] = {3,3,3}, {4,4,4}, {5,5,5}, ..., {10,10,10}, for which nAtom = 108, 256, 500, ..., 4000. (Set StepLimit = 10 and StepAvg = 11, and make sure the constant NMAX in md.h is set larger than nAtom.) Plot the elapsed time per MD step as a function of the number of atoms. Fit the measured elapsed time T to the formula, T = CnAtomp, find and the power p (C is the other fitting parameter). Is your measured scaling, T = O(nAtomp), close to O(nAtom2)? Also perform the same measurement for lmd.c. Is your measured scaling now close to O(nAtom)? 2. (Mflops Performance) Performance of a program is often measured in MFlops (million floating point operations per second). Lets choose InitUcell = {10,10,10} (or nAtom = 4000) and measure the elapsed time of lmd.c. Count the number of floating point operations (+, , *, /) executed (for simplicity, count sqrt() as 1 operation). Divide the resulting number by the elapsed time (in seconds) to obtain the ...