[gmx-developers] Domain decomposition and consistency of state and state_global

Vedran Miletić vedran at miletic.net
Wed Mar 21 20:10:27 CET 2018


I'm developing the conditional stop feature (proposal at [1], a somewhat
working (but not yet mergeable) code dump at [2]; it's using 2016, but
will be rebased to 2018 and master when done). Non-DD code is rather
easy to get up and running, but I'm struggling with understanding how am
I supposed to use state and state_global with DD.

I figured out how ga2la_get() is intended to be used, but the local atom
coordinates I get (relevant part of the log file is in [3]) are
consistent with global atom coordinates in 0 (modulo 8x8x8 box PBC,
which is taken into account when computing distances), but not in step 1000.

I assume that new coordinates have not been communicated yet and that
I'm placing the code somewhere wrongly. Aside from the placement in [4],
I tried placing it in both places after dd_collect_state() in the main
while loop, but it did not help.

Ideas are welcome.


[1] https://redmine.gromacs.org/issues/2224

Vedran Miletić

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