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.

Sunday, 23rd November 08, 0100 hrs

Work done till date:
Indentation done for a 20x20x10 Cr (bcc) system with 3 layer Carbon indenter (tetragonal). 2-body Morse potentials used.
L-D Graph obtained but shows multiple maxima.

Porgrams run: (awaiting results)
30x30x20 system with a 10 layer indenter and complete L-D curve (including indenter retreival)
20x20x20 system for surface stability

Issues:
C-Cr potential still dubious.
Imploding surface (a theory which can solve this, but still some pain in tummy)
Indenter size is limited by segmentation error.
Universal Linked List should be applied for the system. Unfortunately SEGFAULT.
System size must be increased. Present system size is about 16 nm long. Conventional systems are 2x10^7 nm atleast. Parallelization critical.

Pending work:
Linked list to be extended to indenter as well. (done today)
Atomic data and initial conditions to be input from a file. (AP)
Program to be parallelized using SMP and threads. (AG)
Genuine Randomization of initial velocities. (AG)

Future Work:
Carbon potentials, Tetragonal shape & 2 body potential
Embedded Atom Method to applied for Chromium system. (AP)

(Requirements) Aquaguard installed outside lab. Graphics Card on one system.