#49 VASP format output

closed
File Types (14)
5
2012-10-23
2011-11-10
Jiri Klimes
No

Added support to write VASP structure files (POSCAR) and read "Selectivedynamics" information from input structure.
This info is stored in PairData, seems to be working right.
The output is ordered by default according to atomic number, command line flag -xw keeps the ordering.

Discussion

  • Jiri Klimes

    Jiri Klimes - 2011-11-10
     
  • David Lonie

    David Lonie - 2011-11-10

    Hi Jiri, thanks for the contribution. I'll take a look at this patch tomorrow and, if all is well, merge it in.

    Dave

     
  • David Lonie

    David Lonie - 2011-11-11

    I've pushed this to master as part of r4667. I made a few modifications for style, and changed how the atoms were sorted (I'm not sure if modifying the input OBMol is allowed in a format reader, but it seemed like a bad idea ;-) ).

    I tested this on a few files with selective dynamics, and it roundtrips without issue. If my modifications broke any of your intended functionality, please do not hesistate to let me know.

    Thanks again for the contribution!

     
  • Jiri Klimes

    Jiri Klimes - 2011-11-12

    Thanks, that looks good (and cleaner codewise).

    I was only thinking that maybe reordering the atoms by default might not be the best thing from user point of view.
    For example, when I'm converting some .pdb of an organic molecule then I'd definitely like to reorder the atoms
    but in case that I load a POSCAR with Avogadro, do something and then save it, it'd be better to keep the order.
    And in a case that I want to order them I can run obabel separately again.
    Any strong opinions? Sorry for the confusion.

     
  • David Lonie

    David Lonie - 2011-11-14

    That makes sense -- I changed the behavior of -xw so that order is preserved by default (r4668).

     


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