GitLab

Fix the handling and units of box lengths in CHARMM files

boxVectors, so they should be a property computed from the vectors). Also make
sure that any attempts to change the boxVectors correspondingly deletes the
cached copies of the box lengths so they are recomputed if necessary.

Small tweak to fix parsing of par_all36_carb.prm

different from _all_ of the others.

Rewrite Amber inpcrd file parsers

Added TIP3P-FB and TIP4P-FB water models

Fix for static linking

element.

fix the remaining CI issues.

Also make sure .ncrst files are copied over in the test directory.

Seed default RNG from /dev/urandom

and angles makes numbers exactly 0 that _should_ be zero (but aren't due to
precision and round-off issues).

Now the box vector code in the prmtop file is fully general for every type of
box that Amber supports.

Again, this will need to be done in the future anyway for general triclinic
support.

    - existence of velocities and box vectors is auto-detected, so
      loadVelocities and loadBoxVectors are unnecessary
    - recognizes NetCDF-format Amber restart files (which can be written by
      tleap, sander, pmemd, and cpptraj).
    - Restart files coordinate/velocity/box fields have a hard width of 12
      characters and does not ensure that fields are whitespace delimited. This
      commit will correctly parse (valid) Amber restart files in which a
      particular coordinate is <= -100 A or >= 1000 A (not uncommon for restart
      files from sander/pmemd).
    - File format (ASCII vs. NetCDF) is auto-detected.

I deprecated the loadVelocities and loadBoxVectors arguments, since the behavior
does not change (and is correct) whether these variables are set or not. A
DeprecationWarning is emitted if users specify these variables.

Fixed incorrect units in AmoebaStretchBendForce.getStretchBendParameters()

Implemented AMOEBA 2013 force field

Fixed typo in modeller docstring.