polymer1
commented
10 years ago Hey Dave, I've just committed the changes I've been working on and I pushed to my repository. I manually tested it but I still need to write some unit tests for the getNeighbors function as well as fix some of the existing tests because the grid size is too small. There was an existing SpCell::getNeighbors function that was largely copied from ddMd::Cell::getNeighbors and I replaced it. There was a comment inside the old getNeighbors function about not adding cells where the cell id was greater than this->id_ in order to avoid double counting of the pairs. I didn't quite understand that so my implementation just adds all the atoms from all 27 cells with the atoms in this cell being added first. I'm going to keep working on those unit tests and there's a little bit of clean up left to do but now you can take a look at it and let me know if you have suggestions.
Cheers! -Mark
On Thu, Jul 10, 2014 at 7:47 PM, David Morse notifications@github.com wrote:
Merged #27 https://github.com/dmorse/simpatico/pull/27.
— Reply to this email directly or view it on GitHub https://github.com/dmorse/simpatico/pull/27#event-140455070.
Restructured code so the (Atom|Group)(Distributor|Collector) objects are now members of the (Atom|Group)Storage classes instead of the configIo class. This required doing the associating/initializing/allocating of these objects only once inside the simulation class. As a result of this, specifying the parameters (atom|bond|angle|dihedral)CacheCapacity inside the parameter file will no longer do anything. These parameters have all been hardcoded to 100.