Wednesday, 17th December 08, 1900 hrs

Apparently the trip to SERC, IISc has been fruitful. Even though the field of parallel processing maybe intensely convoluted and even after facing the atrocities of Linux, I have managed to retain my nerves. It was evident that programming using threads and MPIs are two completely different approaches to PP but the problem at hand requires extensive knowledge of both.

We shall be using multiple clusters each having multiple cores which makes the job interesting, if not frightening. I was exposed to graph partitioning and realised that METIS made my job a LOT easier. All i had to do was to generate the graph containing a list of expected interactions every atom would be having, which was a piece of cake considering the program structure. Incorporating the pmetis code into my existing program took a lot of time: linking it to its libraries was a major bottleneck, eventually circumvented by running my original code itself from the metis test folder. I also learnt gcc and g++ are disturbingly different, and had to change my .cpp to a .c as the metis code was written in C.

After writing (copying :D ) a program to compute the value of pi, I got a clearer idea of POSIX threads. Now all I have to do, is to implement POSIX threads on my MD code, which is going to be a helluva job. And wait! I haven't even begun on cluster programming and MPI, so till then i wont be using METIS.

Thursday, 11th December 08, 2315 hrs

Much, much better shape stability observed with the EAM model. A 10x10x10 cube was simulated and allowed to stabilize. Even after shrinking and edge rounding, the basic shape of the cube was maintained. Thank god.

Strictly as per Joe's instructions, we have decided to simulate a larger cube and observe system energies. I am hoping to get constant total energy after stabilization. We might even run a simulation or 10 days or more.

Wednesday, 10th December 08, 1321 hrs

At last the long awaited EAM has finally been programmed for a Chromium system. For the last 10 days, the program was displaying "nan" as the embedding energy and modified energy values. Tried almost everything to get rid of the error, (i) shifted the entire dimension base from amu(A)2/(fs)2 to eV, but with no avail, (ii) knight.abhi suggested that there's a 0/0 computation somewhere, but accounting for that also proved to be of no avail. Guess what the ridiculous error was: too large a timestep (t=10 fs) which was finally reduced to (t=1 fs) to get the program running correctly.

Another code was run for 20x20x20 system for stability, keeping five boundaries fixed and the top surface open so that the surface shrinks. With this setup the average distance between nearest atoms were found out by considering the 8 closest atoms to each atom, after all the closest atoms were selected using a (r<1.5*r0) criterion and sorted. The average distance after 200.000 fs was computed to be 2.65289503 A, whereas the initial bcc lattice was constructed using r0 = 2.754. So, the system shrinkage is accounted for.