Adding some unique information in the log seems to be crucial.

Just realized the urge of unique meaningful id in the each of the log files. It looks messy without it now, I'm kind of lost among couple of dozens of run logs.

Decide to add run time stamp along with name of config used:

## current setup: running at Friday, April 13, 2007, 10:11:40 AM HST,
config used: config_O3_2000.xml

Fixed parameters setUp in the code.

Finally get to organize parameter passing through the code. All parameters are standardized now by fixed constants set and there will be no mess anymore. Also fixed all broken tests.
Cost? 6 hours:

Evolution differences between grain population with and w/o bury, 10E5

I've found that three main species, H2O, CO and CO2 evolve differently in the cases when bury is switched on and off.

ESPECIALLY CO, somehow, without bury, CO stays almost constant, while with bury, it looks like it freezes in ice and gains abundance.

New plot, separated D and H species.

Cascade does exactly the thing it suppose to do

The plot shows the evolution of ozone on the grain surface along with ozone evolution within the ice, buried population.


Cascade does exactly the thing it suppose to do, i.e.:
DO3 + O2 -> OD + ...
OD + CO -> D + ...
D + O3 -> OD + ...
OD + H2 -> H + ...
H + O3 -> HO + ...
OH + CO -> H ...
proof done by the log (should i post it here???):
accretion event: 9999999 got OD as the product of DO3_O2, grain popSize: 6699852
accretion event: 9999999 got D as the product of OD_CO, grain popSize: 6699852
accretion event: 9999999 got OD as the product of DO3_O2, grain popSize: 6699852
accretion event: 9999999 got H as the product of OD_H2, grain popSize: 6699853
accretion event: 9999999 got OH as the product of HO3_O2, grain popSize: 6699853
accretion event: 9999999 got H as the product of OH_CO, grain popSize: 6699853

BUT:
I little concern about timing, it is interesting, how much does it takes for this little cascade to happen at first, and second is: I THINK that there suppose to be some accretion events to happen during this time, that would obviously alter this cascade thing...

The voodoo-voodoo magic!

Again, after a lot of effort to clean up the code and reveal the bug, I didn't succeed. Plots are pretty the same. :-(((( Maybe it is a feature?

Some improvement done

Some improvement done. I think there was some bug in the code. So, first of all, cleaned up PopulationWithBury class to make all the names more "comprehendable" and clean. Went over chemistry cycle to see potential bottlenecks, fixed some stuff in logging, and scheduled some runs again to check. They are running now. Will get plots tonight.