Hi all,
I want to add the word “atom” before the x,y, and z coordinates for each element for an input generator. I know this can be done manually in the text editor but I would like to automate the process and incorporate this into the python code. I am only a beginner in python, but how should I modify the output:
output += ‘$$coords:xyz_S$$’
in order to add a string “atom” before the coordinates?
The $$coords$$ options will format a whole block, so that won’t quite work for you.
I’d take a look at the dalton.py script. Dalton requires sorting atoms by element type, so it’s not quite what you want, but something like this might help:
coords3d = cjson['atoms']['coords']['3d']
for z in cjson['atoms']['elements']['number']:
coords = coords3d[start:start + 3]
coordfile += 'atom %15.5f%15.5f%15.5f %s\n' % (
coords[0], coords[1], coords[2], symbols[z])
start += 3
Happy to help - always looking for more generator scripts. 
Thank you so much for your help!. This is exactly what I needed.
Let me know when you finish the script - we’re working on a system to distribute new plugins.
By the way, what program are you using? (e.g., what’s the program for the input generator?)
I was creating an input generator for the FHI-aims package. I finished the script, and have uploaded it on GitHub. It produces the required “geometry.in” input file.
https://github.com/frda058/ColumbiaMRSEC/blob/a659b508b02d3ea9c2347b62deb5a8738ffb04bd/aimsinput.py
Do you need the unit cell information / fractional coordinates? I should have asked earlier. For cases with a unit cell, you can get lattice vectors and coordinates in fractional unit cell coords too.
Dear Francesca
Did you finish the FHI-aims input generator? I saw your Github, but there were no plugins there! I’ll be happy to help.