Add first incarnation of parallel analysis, Hausdorff distance calculation#664

Merged

drroe merged 32 commits intoAmber-MD:masterfrom

drroe:parallel_analysis

Feb 1, 2019

Commits on Apr 13, 2018

DRR - Cpptraj: Initial incarnation of parallel analysis action.
Daniel R. Roe
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DRR - Cpptraj: Finish initial incarnation of parallel analysis.
Daniel R. Roe
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Commits on Apr 16, 2018

DRR - Cpptraj: Add a parallel version of master data file write
Daniel R. Roe
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Commits on Apr 23, 2018

DRR - Cpptraj: Initial incarnation of the Hausdorff distance calculation.
Daniel R. Roe
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DRR - Cpptraj: Add some output options
Daniel R. Roe
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DRR - Cpptraj: Start implementing a sync option for parallel analysis
Daniel R. Roe
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DRR - Cpptraj: Simple data set sync after analysis to master. Only works for float matrices so far.
Daniel R. Roe
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DRR - Cpptraj: Add some timing data.
Daniel R. Roe
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Commits on May 11, 2018

Merge branch 'master' into parallel_analysis
Daniel R. Roe
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Commits on Dec 21, 2018

Merge branch 'master' into parallel_analysis
Daniel R. Roe
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Commits on Jan 2, 2019

Commits on Feb 1, 2019

Merge branch 'master' into parallel_analysis
Daniel R. Roe
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DRR - Cpptraj: Fix up Hausdorff distance calc. Was previously only doing a single directed Hausdorff distance. Now doing both and the symmetric distance as well.
Daniel R. Roe
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DRR - Cpptraj: Pass distance matrix in as const ref. Add help text and clean up info.
Daniel R. Roe
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DRR - Cpptraj: Add output data sets for directed Hausdorff
Daniel R. Roe
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DRR - Cpptraj: Add keywords for redirecting directed Hausdorff output
Daniel R. Roe
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DRR - Cpptraj: Simple Hausdorff distance test.
Daniel R. Roe
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DRR - Cpptraj: More complex test with 2d rms
Daniel R. Roe
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DRR - Cpptraj: Check for 2D sets in setup
Daniel R. Roe
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DRR - Cpptraj: Hide debug info
Daniel R. Roe
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DRR - Cpptraj: Fix output for real triangular matrix
Daniel R. Roe
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DRR - Cpptraj: Add title keyword for gnuplot output
Daniel R. Roe
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DRR - Cpptraj: Add full matrix output, ensure A->B and B->A matrices are populated.
Daniel R. Roe
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DRR - Cpptraj: Fix up info output
Daniel R. Roe
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DRR - Cpptraj: Add full matrix output test.
Daniel R. Roe
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DRR - Cpptraj: Fix clean rule.
Daniel R. Roe
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DRR - Cpptraj: Enable test.
Daniel R. Roe
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DRR - Cpptraj: Add parallel version of the test.
Daniel R. Roe
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DRR - Cpptraj: Fix up help text and info output, hide some debug info.
Daniel R. Roe
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DRR - Cpptraj: Revision bump for adding Hausdorff, parallel analysis, gnuplot 'title'
Daniel R. Roe
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DRR - Cpptraj: Add some missing includes.
Daniel R. Roe
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