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@drroe drroe commented Feb 1, 2019

This PR adds support for performing Analyses in parallel with cpptraj. Adds this command:

parallelanalysis [sync]

This command requests that all currently set up analyses be split up and run over currently available MPI processes. If sync is specified all data sets are synced back to the master thread for e.g. subsequent analysis.

The parallelanalysis command was added largely to support rapid calculation of multiple 2drms analyses for use in creating a larger Hausdorff distance matrix, which introduces the new Hausdorff analysis command:

[help hausdorff]
	<set arg0> [<set arg1> ...]
	[outtype {basic|trimatrix nrows <#>|fullmatrix nrows <#> [ncols <#>]}]
	[name <output set name>] [out <file>] [outab <file>] [outba <file>]

Currently this command expects one or more 2D matrices which contain the distances between two sets; the Hausdorff distance is determined from this. The Hausdorff distance H is determined from:

H = max{dH(A,B), dH(B,A)]

Where dH(A,B) is the directed Hausdorff distance between sets A and B, etc. Colloquially speaking, the directed Hausdorff distance between A and B is determined as follows:

  1. What is the closest approach (distance) of each point in A to any point in B?
  2. Choose the largest distance from among those distances.

If desired, the output can be formed into a matrix, which can be useful e.g. when doing multiple 2D rms calculations on different regions of a trajectory.

This PR also adds a new keyword to gnuplot output, title, for changing the plot title.

Adds a few test cases for hausdorff and one for parallelanalysis + hausdorff.

Daniel R. Roe and others added 30 commits April 13, 2018 15:11
…ing a single directed Hausdorff distance. Now doing both and the symmetric distance as well.
@drroe drroe self-assigned this Feb 1, 2019
@hainm
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hainm commented Mar 17, 2019

Should this issue labeled as new analysis too? pytraj missed it. :D

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2 participants