openPMD extension for MD

[JunCEEE]

MD extension version 0.0.1 https://github.com/ejcjason/openPMD-standard/blob/EXT_MD/EXT_MD.md

[CFGrote]

Good work. Some comments:

• [ ] Remove references to SIMEX, not relevant
• [ ] Does this also work for other MD codes besides LAMMPS? Should be agnostic to the actual MD code
• [ ] You constantly refer to scope, but only a few items really mention it. Add scope everywhere -[ ] The 2nd example under "edge" is not a cubic box (edges are not of same length) -[ ] Do you want to support storing coordinates in units of box edge vectors or unit cell vectors (primitve cell, conventional cell)? Up to you, just want to bring it up.

[JunCEEE]

• [x] Remove references to SIMEX, not relevant
  • Done
• [x] Does this also work for other MD codes besides LAMMPS? Should be agnostic to the actual MD code
  • Yes. This standard should be agnostic to an actual MD code by design and not limited to LAMMPS. I've deleted the LAMMPS part to avoid the implication.
• [x] You constantly refer to scope, but only a few items really mention it. Add scope everywhere
  • Done.
• [x] The 2nd example under "edge" is not a cubic box (edges are not of same length)
  • Corrected. It is a triclinic box.
• [x] Do you want to support storing coordinates in units of box edge vectors or unit cell vectors (primitve cell, conventional cell)? Up to you, just want to bring it up.
  • Yes, that's a good idea. Actually, I know some people using fractional coordinate quite often. This should be mentioned. Please see the new version: https://github.com/ejcjason/openPMD-standard/blob/EXT_MD/EXT_MD.md