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Fixes and improvements related to random number generation. Improvements for data set filtering. #887

Merged
merged 81 commits into from
Mar 15, 2021
Merged

Fixes and improvements related to random number generation. Improvements for data set filtering. #887

merged 81 commits into from
Mar 15, 2021

Commits on Feb 27, 2021

  1. Avoid modulo bias by using bit shifting

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    drroe committed Feb 27, 2021
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  2. Fix Makefile; source changed to cpp

    @drroe
    drroe committed Feb 27, 2021
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  3. Change function name, results can include max

    @drroe
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  4. Override Number_UpTo for Marsaglia since it natively returns between … 

    …0 and 1
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  5. Use Number_UpTo() for interval functions

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  6. Use rn_num_interval instead of rn_gen

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  7. Set RNG to Marsaglia to recover earlier test results.

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  8. Try generating numbers between 0 and 1 using method of Doornik

    @drroe
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Commits on Feb 28, 2021

  1. Use the shuffle from Random_Number. Set Marsaglia for Kmeans random t… 

    …est.
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  2. Use rn_num_interval for cluster sieve. Set Marsaglia gen for test.

    @drroe
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  3. Try to avoid range and modulo bias

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Commits on Mar 4, 2021

  1. Change number of bits reported to dieharder based on RNG. Does not 

    change results.
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  2. Merge branch 'master' into update.rng

    @drroe
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  3. Merge remote-tracking branch 'origin/update.rng' into update.rng

    @drroe
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  4. Merge branch 'master' into update.rng

    @drroe
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Commits on Mar 6, 2021

  1. Merge branch 'master' into update.rng

    @drroe
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Commits on Mar 8, 2021

  1. use rng_gen() times two PI instead of integer values for angle

    @drroe
    drroe committed Mar 8, 2021
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  2. Try a simpler random algorithm.

    @drroe
    drroe committed Mar 8, 2021
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  3. Use new simpler algorithm unless back-tracking is specified

    @drroe
    drroe committed Mar 8, 2021
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  4. Allow other names besides RunTest.sh (more flexible)

    @drroe
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  5. Add test for new method, update test for old method

    @drroe
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  6. Increase the residue cutoff for the new method.

    @drroe
    drroe committed Mar 8, 2021
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  7. Add code docs

    @drroe
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Commits on Mar 9, 2021

  1. Only set up CheckResidue() stuff if needed (not needed for new routin… 

    …e). Make max_factor_ a double, and make the default 10.
    @drroe
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  2. Get rid of duplicate check

    @drroe
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  3. Only need to convert to degrees for debug

    @drroe
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  4. Change max factor default back to 2. In new random rotate routine, have 

    max rotations be on a per-dihedral basis. Make rotation counts unsigned
in old routine. Fix printf formatting.
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  5. Hide some debug info. Fix cleanup

    @drroe
    drroe committed Mar 9, 2021
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  6. Set default RNG to Marsaglia for tests

    @drroe
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  7. Set marsaglia for test

    @drroe
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  8. Add some new versions of the randomizeions algorithm, one that does no 

    distance checking, one that only checks for around.
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  9. Enable algorithm 3

    @drroe
    drroe committed Mar 9, 2021
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Commits on Mar 10, 2021

  1. Split around select around function

    @drroe
    drroe committed Mar 10, 2021
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  2. Version that respects around and overlap

    @drroe
    drroe committed Mar 10, 2021
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  3. Start adding separate DataFilter class

    @drroe
    drroe committed Mar 10, 2021
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  4. Start adding init

    @drroe
    drroe committed Mar 10, 2021
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  5. Add support for 'filterset' arg

    @drroe
    drroe committed Mar 10, 2021
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  6. Start implementing filterindex

    @drroe
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  7. Add set to be filtered stuff

    @drroe
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  8. Add support for filtering 2d sets

    @drroe
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  9. Add support for 3d sets and a check

    @drroe
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  10. Enable version 4

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  11. Rename functions to better describe how they work

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  12. Move regular index selection into its own function

    @drroe
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  13. Make separate placement with no overlap function

    @drroe
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  14. use swapIons_NoOverlap()

    @drroe
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  15. Add function for only respecting overlap

    @drroe
    drroe committed Mar 10, 2021
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  16. Move towards using the new algorithms automatically

    @drroe
    drroe committed Mar 10, 2021
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  17. Add 'originalalgorithm' keyword.

    @drroe
    drroe committed Mar 10, 2021
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  18. Update help

    @drroe
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  19. Add test for new algorithms.

    @drroe
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Commits on Mar 11, 2021

  1. Fix 0 to 1 RNG for stdlib generator

    @drroe
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  2. Fix code docs

    @drroe
    drroe committed Mar 11, 2021
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  3. Add 'gauss' mode to random.

    @drroe
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  4. Update manual with gauss keyword for random command.

    @drroe
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  5. Add function determining the minimum number of elements among all input 

    data sets.
    @drroe
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  6. Save pointer to master dsl

    @drroe
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  7. Add Finalize() routine.

    @drroe
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  8. Add functions for returning npassed and nfiltered

    @drroe
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  9. Add printout

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Commits on Mar 12, 2021

  1. Use DataFilter in FilterByData action

    @drroe
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Commits on Mar 13, 2021

  1. Use DataFilter for exec filter command. Fix infinite loop in DataFilter.

    @drroe
    drroe committed Mar 13, 2021
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Commits on Mar 15, 2021

  1. Remove old code

    @drroe
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  2. Remove old code.

    @drroe
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  3. Clean up keyword help functions

    @drroe
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  4. Fix up help

    @drroe
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  5. Add count sets and countout keyword

    @drroe
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  6. Add 2d matrix filter and count test.

    @drroe
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  7. Hide debug info.

    @drroe
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  8. Move final printout to individual functions; ensure it only happens when 

    !multi
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  9. Fix up filter action and datafilter command entries

    @drroe
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  10. Add link to Emmett Leddin's cpptraj vim syntax file

    @drroe
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  11. DRR - Go back to Marsaglia for now. New generators still need more 

    testing.
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  12. Minor version bump for RNG improvements, data filter improvements, ra… 

    …ndomizeions improvements, and permutedihedrals improvements.
    @drroe
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  13. Fix up and improve randomizeions manual entry.

    @drroe
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  14. Fix up help for permutedihedrals

    @drroe
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  15. maxfactor option was listed twice

    @drroe
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  16. Hail mary to fix github actions...

    @drroe
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  17. Merge branch 'master' into update.rng

    @drroe
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  18. Try to fix GitHub Actions by putting update and install in the same 

    command instance
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  19. Well that was a bust. Try removing the update command...

    @drroe
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