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Commits on Mar 6, 2026

• Major Version Update: 7.00.0 (#1166)

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  Daniel R. Roe

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Commits on Jan 19, 2021

• Major changes to unit cell handling. Fix bugs in GIST, LIE, PairDist actions. Miscellaneous other fixes. (#870)

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Commits on Dec 7, 2020

• Have the 'checkstructure' action respect exclusions (#862)

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Commits on Jan 16, 2018

• DRR - Cpptraj: Properly pass debug level to pair list in StructureCheck

  

  Daniel R. Roe

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Commits on Aug 24, 2017

• Add a few missing algorithm includes for MSVC compatibility

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Commits on Aug 18, 2017

• DRR - Cpptraj: Output mask info in Action_CheckStructure instead of StructureCheck; will suppress non-warning/error setup messages in permutedihedrals.

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• DRR - Cpptraj: Improve help text

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• DRR - Cpptraj: Clean up output, enable silent keyword.

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• DRR - Cpptraj: Make Action_CheckStructure use StructureCheck. Needs lots of validation still.

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• DRR - Cpptraj: Make use of data sets to get 'check' properly working in parallel.

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Commits on Aug 17, 2017

• DRR - Cpptraj: If for some reason a really large cutoff for check is used, adjust the pairlist accordingly.

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• DRR - Cpptraj: Sort bond list. Will help with output, may help locality of reference.

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• DRR - Cpptraj: Use Problem class in place of BondType since they are the same structure.

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• DRR - Cpptraj: Consolidate code for writing out individual problems.

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• DRR - Cpptraj: Use Problem for CheckOverlap. Separate out common write functionality into its own subroutine.

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• DRR - Cpptraj: Use Problem to track long bonds - gets rid of omp critical pragma in the middle of the loop and will eventually allow for consistent output between serial/openmp.

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• DRR - Cpptraj: Make 4.0 the default cutoff for pairlist

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• DRR - Cpptraj: Add ability to change pairlist cutoff

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• DRR - Cpptraj: OpenMP-parallelize

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• DRR - Cpptraj: Version of check using pairlist. So far speedup of ~10x in a 5827 atom system

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Commits on Feb 19, 2016

• DRR - Cpptraj: Add dataset that records number of problems each frame for check

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Commits on Jan 21, 2016

• DRR - Cpptraj: Change '#include "omp.h"' to '#include <omp.h>' since it is a system header.

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• DRR - Cpptraj: Add warnings to check about potential problems with 'skipbadframes' in parallel

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Commits on Dec 10, 2015

• DRR - Cpptraj: Convert Actions

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Commits on Oct 6, 2015

• DRR - Cpptraj: Enable and update areapermol, atommap, atomiccorr, atomicfluct, average, bounds, box, cetner, channel, checkchirality, check, clusterdihedral, contacts, and createreservoir.

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Commits on Sep 12, 2015

• DRR - Cpptraj: Remove TopologyList from Actions.

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Commits on May 22, 2015

• DRR - Cpptraj: Start modifying routines to use CharMask

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Commits on May 14, 2015

• DRR - Cpptraj: Create a separate interface to Action_CheckStructure which can be used outside the ActionList.

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Commits on May 13, 2015

• DRR - Cpptraj: Replace old checkstructure with new code. New code has 'around' functionality and is slightly faster, as well as more memory efficient.

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Commits on Mar 16, 2015

• DRR - Cpptraj: Fix up 'check' and 'dataset' help.

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Commits on Feb 19, 2015

• DRR - Cpptraj: More conversion to CpptrajFile*, add test for grid from bounds command.

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Commits on Jan 23, 2015

• DRR - Cpptraj: Fix some OpenMP-related segfaults.

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Commits on Jan 15, 2015

• Squashed commit of the following:

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Commits on Apr 25, 2014

• DRR - Cpptraj: Use local variable to enable OpenMP compilation with PGI compilers (apparently they cant understand class variables in an openmp pragma...)

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Commits on Apr 4, 2014

• DRR - Cpptraj: Properly clear problem array each frame for openmp check

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