Reading quaternions

Hello all

I am using LAMMPS version 31 March, 2017. Can you suggest me how to merge two simulations data into one? We can do this by read dump and read data commands but can we read quaternions or orientations of ellipsoids using these? As I go through the LAMMPS mailing list, there was a solution of using other tools like pizza.py, topotools and moltemplate.sh to merge two simulations data. But I wonder that can they also read quaternions or orientations of ellipsoids? Or what would be the good approach to merge two simulations data into one in case of ellipsoids?

Hello all

I am using LAMMPS version 31 March, 2017. Can you suggest me how to merge two simulations data into one? We can do this by read dump and read data commands but can we read quaternions or orientations of ellipsoids using these? As I go through the LAMMPS mailing list, there was a solution of using other tools like pizza.py, topotools and moltemplate.sh to merge two simulations data. But I wonder that can they also read quaternions or orientations of ellipsoids? Or what would be the good approach to merge two simulations data into one in case of ellipsoids?

i have four suggestions for you:

  • your best bet is probably to use read_dump multiple times. however, this requires some care and particularly a careful study of the documentation.
  • use the latest LAMMPS version (currently 16 August 2018), as the feature to use read_dump multiple times is somewhat new, and there are still bugs found and fixed for corner cases, and your scenario is definitely not common.
  • make tests with small inputs (handwritten, just a few atoms), so you can compare the result of the merge with reading through a data file generated by write_data.
  • always visualize your inputs and results and be very careful and paranoid. you are using a feature, that is complicated and even if you get all the syntax right, it may still not produce the result you expect. there are no guarantees.

axel.