README

Developers and contact:
This benchmark was developed by Nikhil Jain as part of PPL's effort
to develop miniapplications that demonstrate utility of Charm++. It
mimics the short-ranged force computation (due to Lennard Jones potential)
in NAMD. It is roughly based on mol3d, developed by Edgar Solomonik and
Abhinav Bhatele, which is a benchmark based on NAMD. Phil Miller's guidance
was crucial in writing the SDAG routines. Later on Esteban Meneses and Xiang Ni
added fault tolerance to it. It has been used in many publications related
to Charm++. Contact nikhil.jain@acm.org for any bug report or comments.

TO COMPILE-
Do a make in this folder

TO RUN-
Either provide no arguments or provide all
./charmrun +p<Procs> ./leanmd <dimX,dimY,dimZ,steps,firstLBstep,LBPeriod>
Example - ./charmrun +p8 ./leanmd 2 2 2 1001 20 20
Example - ./charmrun +p8 ./leanmd 2 2 2 1001 20 20 +balancer RefineLB
Here is an example on how to use MetaBalancer
Example - ./charmrun +p8 ./leanmd 2 2 2 1001 10 5 +balancer RefineLB +MetaLB
Here is an example showing how to enable checkpoint and restart
Example - ./charmrun +p8 ./leanmd 2 2 2 1001 20 20 25 +wp6
Here is an example showing how to enable checkpoint application states, the applications states are stored in directory log
Example - ./charmrun +p8 ./leanmd 2 2 2 1001 20 20 25 log

READ ORDER
leanmd.ci - contains the most important aspects of the program, look for run()
function for each chare which is called right after constructor call for each
chare. It contains most of the parallel flow and control flow information.

Cell.* - contains the implementation of important functions attached with
Cell; focus on sendPositions() and updateProperties()

Compute.* - contains the implementation for Compute; the interact() function
is important as it does the force computation.

Main.* - contains the constructor for Main chare; also the starting point
of the application; main chare passes control to run() of Main chare and
constructors of Cell.

physics.h - contains physics equation implementation for force computation; also
contains the contribute for reduction of forces.

defs.h - #define for constant values and some class declaration