Thin out trajectry file

ASE
1

I have a a big trajectry file, which occupy my strage.
I do not wan to remove the file and make re-run becuase calculation time is very long.

Are there any methods that can thin out the trajectry file to compress data it self, and save the file again?
Best regards

2

Hi,

  • You can try a strong zip algorithm like 7z
  • You can drop some of the frames in the trajectory file if you don’t need all of them
  • Depending on what atoms objects you have inside the file, maybe they contain arrays that are less important (e.g., tags). You can use ase info -v <filename> to write something.
  • You can attempt to establish a trajectory file using float32 rather than the default float64, but that requires non-trivial coding

Best regards
Ask

3

Thanks for the reply

You can drop some of the frames in the trajectory file if you don’t need all of them

I’d like to follow this, how should I do it?

4

You can either use ase.io.iread() to iterate over them and then save, or the command-line. Something like ase convert myfile.traj@::20 myotherfile.traj. See ase convert --help.

It’s wise to independently verify, e.g. using a script, that all your required data is stored correctly before deleting the old file.

1 Like
5

Thanks for the additional comments,
It was solved! best regards!