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mushroomfire / mdapy

A simple and fast python library to handle the data generated from molecular dynamics simulations
https://mdapy.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
53 stars 5 forks source link

About the trajectory analysis #6

Open Sacho2020 opened 2 weeks ago

Sacho2020 commented 2 weeks ago

Hi,

I would like to know whether the current version supports the analysis of multiple atomic configurations in the trajectory?

I found that it is unable to load all atomic configurations of a trajectory, and only recognizes the box information of first atomic configuration, including xyz and dump files., and it also shows the error "found more fields than defined in 'Schema'" for the loading of trajectory data in xyz format.

Sacho

mushroomfire commented 2 weeks ago

Hi, @Sacho2020 . Mdapy is mainly designed for analyzing single frame. While you can split the trajectory by mp.split_xyz() into separate frames, and then you can read them by mp.System or mp.MultiSystem, and do what you want to do.