If the geometry of 4-ZGNR is optimized until all residual forces on each atom are smaller than 0.05 eV/angstrom , what is the physical meaning for 0.05 eV/angstrom , and What is the corresponding energy convergence per atom? The configuration of 4-ZGNR is obtained using following manuscript. I have carefully read ATK manual, but I cannot find corresponding information for this question. Who can help me?
armchair = False # False -> zigzag
width = 8 # ribbon width across, number of layers (must be even for zigzag)
repetitions = 1 # repetitions of the minimal unit along the ribbon
PAC = True # False -> molecule
# C-C and C-H and unit cell padding distances (all in Angstrom)
aCC = 1.42086
aCH = 1.101
cell_pad = 30.
'''===========================================================================
Nothing needs to be modified below this line!
==========================================================================='''
from ATK.KohnSham import *
from numpy import array, fromfunction
import math
# -------------------------------------------------------------------------------------------
# Positions are in units of aCC until the very end!
# -------------------------------------------------------------------------------------------
def unit_cell_C_atoms (zigzag,layers):
zpos = []
xpos = []
zigzag_zpos = [0.0,0.5,0.5,0.0]
zigzag_xpos = [0.0,0.5,1.5,2.0]
for x in range(0,layers):
if zigzag:
zpos += [zigzag_zpos[x%4] * math.sqrt(3.)]
xpos += [zigzag_xpos[x%4] + 3.*(x//4)]
else:
zpos += [0.5+1.5*(x%2), 1.5-1.5*(x%2)]
xpos += [x*math.sqrt(3.)/2.,]*2
return (xpos,zpos)
def unit_cell_H_atoms (zigzag,layers,xpos,zpos,xCH,zCH):
if zigzag:
hydrogen_z = [0., 0.5*math.sqrt(3.)*((width/2)%2)]
hydrogen_x = [xpos[0]-xCH, xpos[-1]+xCH]
else:
hydrogen_z = [zpos[0]-zCH, zpos[1]+zCH, zpos[-2]-zCH, zpos[-1]+zCH]
hydrogen_x = [xpos[0]-xCH, xpos[0]-xCH, xpos[-1]+xCH, xpos[-1]+xCH]
return (hydrogen_x,hydrogen_z)
# -----------------------------------------------------------------------
zigzag = not armchair
if (zigzag and (width%2==1)):
raise ValueError, "Width must be an even number for zigzag"
pad = cell_pad/aCC
# For zigzag, the unit cell in Z is sqrt(3)*aCC, for armchair 3*aCC
if zigzag:
atoms_per_cell = width + 2
period_z = math.sqrt(3.)
xCH = aCH/aCC
zCH = 0.
elements = ([Carbon,]*width+[Hydrogen,]*2)*repetitions
else:
atoms_per_cell = width*2 + 4
period_z = 3.
xCH = aCH/aCC*math.sqrt(3.)/2.
zCH = aCH/aCC/2.
elements = ([Carbon,]*2*width+[Hydrogen,]*4)*repetitions
# -----------------------------------------------------------------------
# Set up the unit cell along the ribbon
(xpos,zpos) = unit_cell_C_atoms (zigzag,width)
(h_xpos,h_zpos) = unit_cell_H_atoms (zigzag,width,xpos,zpos,xCH,zCH)
# Merge C and H, and repeat desired times along ribbon length (Z)
xpos = array((xpos + h_xpos)*repetitions)
zpos = array((zpos + h_zpos)*repetitions)
# The coordinates in zpos must still be shifted along z by N*unit cell width where N=0,1,2,3,...,repetitions-1
# This part is not needed if we would do all repetitions in VNL
shift = fromfunction( lambda i,j : j//atoms_per_cell, (1,atoms_per_cell*repetitions) )
zpos = zpos + shift[0] * period_z
# Unit cell
# In x, add the desired padding the the distance between the outermost atoms
# In y, use the desired padding
# In z, the period is given by period_z, we just need to scale it properly
unit_x = (max(xpos)-min(xpos)) + pad
unit_y = pad
unit_z = period_z * repetitions
unit_cell = array([ [unit_x, 0., 0. ],
[0., unit_y, 0. ],
[0., 0., unit_z ] ])
# Center the atoms in the unit cell
# For x, first adjust for position of H atom, then shift by half the padding
xpos += xCH + pad/2.
# z shift is half
if zigzag:
zpos += period_z / 4.
else:
zpos += period_z / 6.
# And finally y
ypos = array([0.] * repetitions * atoms_per_cell) + pad/2.
# Merge coordinates to xyz
pos = array([xpos,ypos,zpos]).transpose()
# Apply final scaling by aCC * Angstrom
# Note: If PACs can be dropped on Molecular Builder, we can do PAC=True permanently
if PAC:
graphene_ribbon = PeriodicAtomConfiguration (unit_cell*aCC*Ang, elements, pos*aCC*Ang)
else:
graphene_ribbon_as_molecule = MoleculeConfiguration (elements,pos*aCC*Ang)
