QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: ams_nanolab on August 26, 2016, 10:48
-
Hello, I want to export a graphene.py file structure into graphene.xyz but only in the cartesian co-rodinates as the .xyz output file.
original structure in .py
=========================
# Set up lattice
lattice = Hexagonal(2.4612*Angstrom, 6.709*Angstrom)
# Define elements
elements = [Carbon, Carbon]
# Define coordinates
fractional_coordinates = [[ 0.333333333333, 0.166666666667, 0.5 ],
[ 0.666666666667, 0.833333333333, 0.5 ]]
# Set up configuration
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)
-----------------------------
Export as .xyz
==============
2
Bulk
C 6.153000e-01 -3.552436e-01 3.354500e+00 0.33333 0.16667 0.50000
C 1.845900e+00 3.552436e-01 3.354500e+00 0.66667 0.83333 0.50000
----------------------------------------
what I really want is : something like this
2
C 6.153000e-01 -3.552436e-01 3.354500e+00
C 1.845900e+00 3.552436e-01 3.354500e+00
===============================
how can it be done? For graphene it's simple to just edit the text but for larger structures doing by hand is difficult.
-
You can erase the fractional coordinates in a 'filename.xyz' with the script enclosed.
$ python convert.py filename.xyz > filename_new.xyz
or
$ atkpython convert.py filename.xyz > filename_new.xyz
The new file contains the atomic coordinates in Cartesian only.
-
Thanks :)