Fixed polygon_mesh reader so that it works with user-generated .ma files, not just autogenerated ones

find_stacks routine moved to segmentmodel_from_lists using only coordinates and transforms; generate stacks automatically if None

kept old find_stacks routine in segmentmodel_from_pdb as find_stacks_mdanalysis

1) Passthrough of mrdna.segmentmodel arguments
2) Improved input validation
3) Stacks are removed unless stack[bp[stack]] == stack
4) Cleaner code for assigning ends of terminally-connected "segments"

Eliminated numpy log(0) error message when writing bond potentials, which is caught anyway by .isnan

Prepared code structure in potential section so that dsDNA and ssDNA are treated using separate defs

Reduced timestep of high resolution simulations from 50 to 40 fs because of instability in some systems

Fixed issue affecting systems with long polymers where update_splines previously used float16 to obtain unique beads; now rounding to nearest 1/10th nt

Improved orientation potentials at junctions when local_twist is enabled; now dihedrals are more local and work in more situations