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Add MPI parallelism and rotatable grids to GIST #1055
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use GridMover instead.
determine voxels for all other grids
…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.
of the grid for any translation calc
in MPI since it occurs outside the print function. Make entropy timers relative to total for same reason.
addition of 'rmsfit' keyword to GIST, addition of imaging to GIST order calculation (and pairlist for speedup), and addition of fast 'ndiff' functionality to cpptraj.
The PGI build in Jenkins failed. |
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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.
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).Other improvements:
--ndiff
flag to cpptraj to mimic thendiff
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 cpptrajndiff
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.