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Recognize Drude particles, improve handling of lone pairs #1099

Merged
merged 28 commits into from
Aug 29, 2024
Merged

Recognize Drude particles, improve handling of lone pairs #1099

merged 28 commits into from
Aug 29, 2024

Commits on Aug 27, 2024

  1. Start reading lone pairs

    @drroe
    drroe committed Aug 27, 2024
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  2. Add check for zero total mass when using mass weighting for distance

    @drroe
    drroe committed Aug 27, 2024
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  3. Check for zero mass in masks for angle/dihedral calcs

    @drroe
    drroe committed Aug 27, 2024
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  4. Read and store lone pairs

    @drroe
    drroe committed Aug 27, 2024
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  5. Read the lone pair atoms

    @drroe
    drroe committed Aug 27, 2024
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  6. Add bonds from lone pair info

    @drroe
    drroe committed Aug 27, 2024
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  7. Prefer https, more portable

    @drroe
    drroe committed Aug 27, 2024
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  8. Check for zero mass last to preserve backwards compat. as much as pos… 

    …sible.
    @drroe
    drroe committed Aug 27, 2024
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  9. Add Drude element. Add support for detecting Drude particles from cha… 

    …rmm PSF
    @drroe
    drroe committed Aug 27, 2024
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  10. Add geom keyword to vector, check for zero mass in masks

    @drroe
    drroe committed Aug 27, 2024
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  11. Hide some debug info

    @drroe
    drroe committed Aug 27, 2024
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  12. Version 6.29.0. Minor version bump for recognition of Drude particles… 

    … and checks for zero mass in distance/angle/dihedral/vector
    @drroe
    drroe committed Aug 27, 2024
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Commits on Aug 28, 2024

  1. Add bondparminfo command

    @drroe
    drroe committed Aug 28, 2024
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  2. Add angle

    @drroe
    drroe committed Aug 28, 2024
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  3. If adding a duplicate bond, if the existing bond has no parameter but… 

    … there is a parameter being passed in, use the passed in parameter.
    @drroe
    drroe committed Aug 28, 2024
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  4. Add some defaults for lone pair bonds

    @drroe
    drroe committed Aug 28, 2024
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  5. Save dihedrals. Not sure if saving torsion in phase is ok for lone pa… 

    …irs...
    @drroe
    drroe committed Aug 28, 2024
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Commits on Aug 29, 2024

  1. Add 'debye' keyword to report 'vector dipole' units as Debye

    @drroe
    drroe committed Aug 29, 2024
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  2. Add drude versions of ala3

    @drroe
    drroe committed Aug 29, 2024
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  3. Add Drude PSF read test

    @drroe
    drroe committed Aug 29, 2024
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  4. Fix help

    @drroe
    drroe committed Aug 29, 2024
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  5. Document bondparminfo

    @drroe
    drroe committed Aug 29, 2024
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  6. Document vector geom and debye

    @drroe
    drroe committed Aug 29, 2024
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  7. Add old Atom constructor back for pytraj

    @drroe
    drroe committed Aug 29, 2024
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  8. Increase tag size by 1 for storing null for sscanf("%10s")

    @drroe
    drroe committed Aug 29, 2024
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  9. Add PDF versions of the manual and dev guide.

    @drroe
    drroe committed Aug 29, 2024
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  10. Disable automatic build of the manual until lyx on Jenkins is updated.

    @drroe
    drroe committed Aug 29, 2024
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  11. Change documentation URLs to GitHub for now until Jenkins is updated.

    @drroe
    drroe committed Aug 29, 2024
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