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@drroe drroe commented Nov 17, 2023

Version 6.22.0.

This PR is mainly a big enhancement to the GIST code (@fwaibl @tkurtzman @EricChen521), with a few other fixes/improvements thrown in.

  • Addition of MPI parallelism to GIST. GIST now benefits from across-trajectory parallelism (benefits the solvation energy calculation). The post-trajectory-processing entropy calculation is also MPI-parallelized to prevent it from becoming too much of a bottleneck for long trajectories.
  • Adds a new keyword to GIST, rmsfit, which allows the grid itself to be centered/rotated around a group of atoms of interest (rather than having to rms-fit the whole system to a grid).
  • The order calculation in GIST now respects imaging. To prevent this from becoming too slow, a pairlist is used. The final speed is comparable to the old non-imaged order calculation.

Other improvements:

  • Fixed the variable type when summing in MPI for double precision grids (was previously float by mistake). Shouldn't have affected anything previously since I think nothing MPI was using double precision grids (only single).
  • Add --ndiff flag to cpptraj to mimic the ndiff awk script used for numerical comparisons of tests. The awk script was getting too slow for large files (such as those output by GIST). The cpptraj ndiff is orders of magnitude faster. @dacase if there are any places in the Amber test suite where you think this could be useful let me know.

drroe and others added 30 commits August 8, 2022 16:09
…f water is in a 1.5 Ang region around the grid, create a "border" grid that extends 1.5 Ang in each dimension; makes it easier to check if waters are near the grid if the grid has been rotated.
works if grid is x-aligned orthogonal); just use the already-calculated voxel indices.
@drroe drroe added enhancement New keywords New keywords for existing commands. labels Nov 17, 2023
@drroe drroe self-assigned this Nov 17, 2023
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The PGI build in Jenkins failed.

@drroe drroe merged commit bc47e44 into Amber-MD:master Nov 17, 2023
@drroe drroe deleted the gist.rotate branch November 17, 2023 19:27
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