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Fix remaining GeometryEngine issues #51

Merged
merged 57 commits into from
Dec 8, 2015
Merged

Fix remaining GeometryEngine issues #51

merged 57 commits into from
Dec 8, 2015

Commits on Dec 1, 2015

  1. replace rejection sampling with selection from precomputed values

    pgrinaway committed Dec 1, 2015
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  2. fixing probability calculations

    pgrinaway committed Dec 1, 2015
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  3. moved old geometry engine to the attic

    pgrinaway committed Dec 1, 2015
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  4. add 1/2 prefactor

    pgrinaway committed Dec 1, 2015
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  5. calculate logZ separately

    pgrinaway committed Dec 1, 2015
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Commits on Dec 2, 2015

  1. fixed bond and angle proposals

    pgrinaway committed Dec 2, 2015
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  2. make sure beta is in the right units

    pgrinaway committed Dec 2, 2015
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  3. fixed angle thing

    pgrinaway committed Dec 2, 2015
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  4. removed unused method

    pgrinaway committed Dec 2, 2015
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  5. calculate reverse torsion_logp

    pgrinaway committed Dec 2, 2015
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  6. removed unnecessary imports

    pgrinaway committed Dec 2, 2015
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  7. fixed some unit stuff

    pgrinaway committed Dec 2, 2015
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  8. remove loop

    pgrinaway committed Dec 2, 2015
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  9. remove another loop

    pgrinaway committed Dec 2, 2015
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  10. make jacobian optional again

    pgrinaway committed Dec 2, 2015
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  11. prevent integer division

    pgrinaway committed Dec 2, 2015
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  12. make some fixes

    pgrinaway committed Dec 2, 2015
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  13. rename

    pgrinaway committed Dec 2, 2015
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  14. cleaning up additional errors

    pgrinaway committed Dec 2, 2015
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  15. added some explicit units

    pgrinaway committed Dec 2, 2015
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  16. subtracted max from logq

    pgrinaway committed Dec 2, 2015
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  17. fix denominator

    pgrinaway committed Dec 2, 2015
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  18. fix units

    pgrinaway committed Dec 2, 2015
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Commits on Dec 3, 2015

  1. create functions to assign units properly

    pgrinaway committed Dec 3, 2015
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  2. continue fixing unit errors

    pgrinaway committed Dec 3, 2015
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  3. fix more units...

    pgrinaway committed Dec 3, 2015
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  4. removed superfluous units

    pgrinaway committed Dec 3, 2015
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  5. still more units...

    pgrinaway committed Dec 3, 2015
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  6. don't add another set of units...

    pgrinaway committed Dec 3, 2015
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  7. corrected sign

    pgrinaway committed Dec 3, 2015
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  8. changed sum

    pgrinaway committed Dec 3, 2015
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  9. fix unit mistake

    pgrinaway committed Dec 3, 2015
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  10. another unit mistake.

    pgrinaway committed Dec 3, 2015
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  11. bond units

    pgrinaway committed Dec 3, 2015
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  12. fixed torsion units

    pgrinaway committed Dec 3, 2015
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  13. stop casting beta

    pgrinaway committed Dec 3, 2015
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  14. fix some unit stuff

    pgrinaway committed Dec 3, 2015
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  15. fix force constants

    pgrinaway committed Dec 3, 2015
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  16. replace -inf with exception

    pgrinaway committed Dec 3, 2015
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  17. change logp calculation

    pgrinaway committed Dec 3, 2015
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  18. fixed torsion units

    pgrinaway committed Dec 3, 2015
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  19. fix torsion selection

    pgrinaway committed Dec 3, 2015
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  20. fix typo

    pgrinaway committed Dec 3, 2015
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  21. make unit-ing idempotent

    pgrinaway committed Dec 3, 2015
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Commits on Dec 4, 2015

  1. replace linspace with arange

    pgrinaway committed Dec 4, 2015
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  2. fixed arange

    pgrinaway committed Dec 4, 2015
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  3. use more numerically stable cartesian to internal coordinate conversion

    pgrinaway committed Dec 4, 2015
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Commits on Dec 6, 2015

  1. add coordinate conversion with units

    pgrinaway committed Dec 6, 2015
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  2. change parmtop input

    pgrinaway committed Dec 6, 2015
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Commits on Dec 7, 2015

  1. fixes

    pgrinaway committed Dec 7, 2015
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Commits on Dec 8, 2015

  1. fix angles

    pgrinaway committed Dec 8, 2015
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  2. test angle computation

    pgrinaway committed Dec 8, 2015
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  3. remove plotting

    pgrinaway committed Dec 8, 2015
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  4. temprorary unit fix

    pgrinaway committed Dec 8, 2015
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  5. change name of test to make run

    pgrinaway committed Dec 8, 2015
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  6. calculate determinant of jacobian

    pgrinaway committed Dec 8, 2015
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  7. fix unit

    pgrinaway committed Dec 8, 2015
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