ase graphene sheet with N substitution

-- coding: utf-8 --

3.0

from ase import Atoms from ase.visualize import view import numpy as np import string

np.set_printoptions(precision=3,suppress=True)

def build_sheet(nx, nz=nx): nx=nx+1 basic_cell= Atoms('C4', positions=[[3.11488, 2.50000, 0.71000], [4.34463, 2.50000, 1.42000], [4.34463, 2.50000, 2.84000], [3.11488, 2.50000, 3.55000]], cell=[[2.45951, 0, 0], [0, 1, 0], [0, 0, 4.26]]) atoms=basic_cell.repeat((nx,1,nz)) atoms.pop(basic_cell.get_number_of_atoms()*nz-1) atoms.pop(0) return atoms

def nitrogenate(sheet, position): symbols = atoms.get_chemical_symbols() symbols[position] = 'N' sheet.set_chemical_symbols(symbols)

def print_atoms(atoms): out='' for atom in atoms: atom_str= '{0}\t{1}\t{2}\t{3}\n'.format(atom.symbol, atom.position[0], atom.position[1], atom.position[2]) out=out+atom_str return out

def calc_parameters(filename, method, basis_set, **kwargs): print filename".inp" print string.rjust(! 3), string.rjust(method, 3), string.rjust(basis_set, 3), string.rjust(kwargs, 3)

atoms=build_sheet(1,1) nitrogenate(atoms, 0) print print_atoms(atoms) view(atoms, viewer='avogadro')