pDynamo trajectory

In pDynamo3, trajectories are a set of coordinates discretized frame by frame in a folder with the extension ".ptGeo". The coordinate files inside the folder have naming following the pattern "frameX.pkl", where "X" is the frame number. Each ".pkl" coordinate file is a binary file, and although they also have the same extension as pDynamo's serialization .pkl files, they only contain coordinates.

There are even coordinates generated by two-dimensional energy scans. In this case we have a matrix of X vs Y coordinates, where X and Y are the number of steps adopted for the first and second reaction coordinates respectively. In the same way as for the previously mentioned standard pDynamo trajectories, we have coordinate files generated in a folder with the ".ptGeo" extension, however, the file names follow the "frameX_Y.pkl" pattern.