Trajectory output Atom Types

[shrmiao]

Describe the feature / issue
Accumulated trajectory files can be very useful for post-dissolve analysis and it is a good way to make sure various analysis are performed over the same geometry/energy landscape. Currently, the output trajectory file only contains 4 columns: Element, X-coord, Y-coord, Z-coord.

I think it would be more useful to output: Atom Type, X-coord, Y-coord, Z-coord; so that sites can be differentiated among functional groups (i.e. hydroxyl hydrogen and alkyl hydrogen).

If possible, I think it would be even better if the output could include 6 columns: Element, Atom Type, Atom Index (within the species), X, Y, Z

As an example (2 water molecules per frame):

6 (total number of atoms in 1 frame)
blah blah (box name)
H Hw 1 X Y Z
H Hw 2 X Y Z
O Ow 3 X Y Z
H Hw 1 X Y Z
H Hw 2 X Y Z
O Ow 3 X Y Z
6
blah blah
...

[rprospero]

@shrmiao @trisyoungs Would it be acceptible to have the columns be

1. Element
2. X
3. Y
4. Z
5. Atom Type
6. Atom Index

I mostly ask because this would keep the first four columns in their original order in the case where users already have scripts for analysing these files?

[shrmiao]

I actually wrote codes based on the first 4 columns too so keeping them the same would be a good idea :)