Adding our customary topology attribute to atom object

[ullaharslan]

Hello Everyone i hope you are doing great. I using LAMMPS for the analysis of my system, I have performed voronoi analysis and saved the dump with voronoi attribute with "atom_style='id type x y z c_voro[1] c_voro[2]',"
is it possible to add voro[1] in data type and then access the atom group with specified attribute ? Here is my code

import MDAnalysis as mda
u=mda.Universe('data_all_1800_1ns','dump_all_1800_1ns', topology_format="data", format="lammpsdump",atom_style='id type x y z c_voro[1] c_voro[2]',timeunit='ps',dt=0.0001)
grp1=u.select_atoms('c_voro[1] 0 ') # i want to group all atoms with topology attribute c_voro =0

any comment suggestoin in this regard will be highly appreciated

[RMeli]

Hello @ullaharslan. From the LAMMPSParser documentation:

This should be a space separated
string indicating the position of the id, type, resid, charge,
x, y and z fields. The resid and charge fields are optional
and any other specified field will be ignored.

Have you tried using the optional resid and charge attribute instead? If you set id type x y z charge resid, then charge should correspond to your data c_voro[1] while resid would correspond to your data c_voro[2] and your selection would the become grp1=u.select_atoms('charge 0 ') instead of grp1=u.select_atoms('c_voro[1] 0 ').

[RMeli]

@ullaharslan thanks for the thumbs up. =) If this solves your issue, please formally accept the answer (so that we can keep track of what is solved and what isn't).

[orbeckst]

@ullaharslan are you able to read the universe? The closed #3504 seems to say that this should work? If so, the data will be in ts.data["c_voro[1]"] and you can write code to find the atoms – maybe it's as simple as

ag = u.atoms[ts.data["c_voro[1]"] == 0]]

There may also be a way to create a new selectable attribute but that may be more involved for a dynamic property.

[ullaharslan]

i am terribly sorry for delay because I was not feeling well. Today I will implement the suggested methodology(That apprantely seems fantastically exact) and will update accordingly. Thank you so much for generous reply. I hope after my checks I will mark it in today date. have a wonderful day.

[ullaharslan]

sorry for late reply guys.
Dear @orbeckst off-course I am able to read the universe, but referred suggestion didn't worked actually. atom group command don't recognise the new voronoi attribute. I believe technically adding an attribute should be possible but not in a simple way.. so we need to do some re work from crash. Suggestion from @RMeli tackle the problem in a smart way.. and I highly appreciate this... so we are using the basic attribute format for our desired ag data.