Reflecting boundaries

[amartyads]

Description

Added "native" support for reflecting and outflow boundaries in ls1.

The actual communication code was left untouched, and the boundary effects were manages with these two steps:

• Manually deleting halo particles after they're populated after balanceAndExchange
• Using a region iterator over the regions one cutoff away from global walls, and reflecting/deleting molecules as required.

The communication code was not changed, because I did not want to mess up the inter-subdomain communication for internal molecules.

How Has This Been Tested?

Since this adds more checks for default (periodic) behaviour, I ran a test on the AMD minicluster to make sure that default behaviour is not slower.

configForBoundary.txt

jobForBoundary.txt

50000 steps, 485150 particles

I ran each run 5 times, took time values from the output files, averaged them, and here are the results (in seconds):

Container	Run Type	Wall time	Boundary Effects Time	Force Computation Time	Total Computation Time	Communication Time
AP	master	746.116	0.000000	548.0748	582.2928	132.6998
	periodic	744.350	0.090808	544.4254	578.4000	134.4734
	reflecting	737.930	15.541120	542.4348	586.7612	124.2872
LC	master	1413.200	0.000000	735.0464	885.0394	282.4636
	periodic	1404.534	0.149090	737.6524	880.9132	276.3130
	reflecting	1486.748	147.659200	713.3886	887.7828	267.289

So compared to master, running periodic boundaries on this branch seems to have negligible overhead, hence performance should not be massively affected overall.

Otherwise, this has been more or less extensively tested, both with and without MaMiCo, so everything should be fine.

[amartyads]

@HomesGH Do you want to take a look at the comments Fabio left in the files that were part of #336 ?

[HomesGH]

@HomesGH Do you want to take a look at the comments Fabio left in the files that were part of #336 ?

I went through the comments in the files Domain.* and ResultWriter.* and resolved them.
However, I have no idea about the following section

double _universalProfiledComponentMass;  // set from outside
double _universalLambda;  // set from outside
float _globalDecisiveDensity;  // set from outside

[amartyads]

@HomesGH Do you want to take a look at the comments Fabio left in the files that were part of #336 ?

I went through the comments in the files Domain.* and ResultWriter.* and resolved them. However, I have no idea about the following section

double _universalProfiledComponentMass;  // set from outside
double _universalLambda;  // set from outside
float _globalDecisiveDensity;  // set from outside

I have no idea either, unfortunately

Checking git history, seems like those lines have existed unchanged since 2012 (commit 9b1e251)

[amartyads]

After all these changes I redid the performance test, and the results don't seem impacted at all (I didn't rerun master):

Container	Run Type	Wall time	Boundary Effects Time	Force Computation Time	Total Computation Time	Communication Time
AP	master	746.116	0.000000	548.0748	582.2928	132.6998
	periodic	740.762	0.164010	543.6474	578.2006	131.9316
	reflecting	739.328	0.106152	541.3684	576.2200	132.5192
LC	master	1413.200	0.000000	735.0464	885.0394	282.4636
	periodic	1403.222	0.292358	722.1366	866.5802	282.3060
	reflecting	1404.236	0.178882	731.8196	874.3370	280.8740

LC (base ls1) seems less consistent somehow, maybe last time's runs got skewed by one bad run (possible because I'm testing on the minicluster).

But in either case, no slowdowns from all the corrections.

[amartyads]

After fixing the implementation so that it actually works now, I reran the speed tests just for completeness's sake. Not much changed, so that's good.

Container	Run Type	Walltime	Boundary Effects Time	Force Computation Time	Total Computation Time	Communication Time
AP	master	746.116	0.000000	548.0748	582.2928	132.6998
	periodic	750.502	0.108154	551.0130	585.5592	133.6746
	reflecting	735.690	15.147920	537.2156	581.5974	127.1540
LC	master	1413.200	0.000000	735.0464	885.0394	282.4636
	periodic	1405.444	0.175187	728.6756	875.6406	276.0900
	reflecting	1324.986	34.878960	651.8310	823.5968	265.7218