Topics

1

General Questions and Answers / select a particular cut-plane of electrostaticdifference

« on: December 10, 2013, 03:08 »

Hi, I would like to find the difference in electrostaticdifference (EDP) of two systems corresponding to different cut-planes. In particular, for system A I need EDP at cut-plane x=x1 (edpA_x1), and for system B at cut-plane x=x2 (edpB_x2)., so I can compute edpA_x1 - edpB_x2..
However,  the following script only computes the difference of the whole systems and so doesn't work for me:

edpA = nlread("systemA.nc", ElectrostaticDifferencePotential)[0] 
edpB = nlread("systemB.nc", ElectrostaticDifferencePotential)[0] 
nlsave("diff.nc", edpA-edpB) 

Any idea on selecting a particular cut-plane?

Also, when I export the EDP data into a CUBE file, the values contained in the file are much smaller as compared with what observed in VNL viewer. This is confusing.. Please advise. Many thanks.

2

General Questions and Answers / bonds broken while optimization

« on: September 9, 2013, 10:25 »

Hi,

I am optimizing the geometry of a small protein molecule (with ~300 atoms) in vacuum. The self-consistent Slater Koster method is used. The optimization converses successfully achieving the requested max forces 0.05 eV/Ang. However, in the optimized geometry, one group of three atoms (O-C-O, they remain connected by themselves) disassociates with the rest of the molecule. This group was originally connected to the rest via a C-C bond. That is, this C-C bond was broken during the optimization process causing the group of three disassociating with the others.

Any suggestions and solutions on the causes of this problem. Many thanks.

 

3

General Questions and Answers / Transmission of graphene ribbon is a pulse instead of spike around Fermi level

« on: June 12, 2013, 14:39 »

Dear ATK users,

I have a issue in using DFT to calculate transmission T(E) of a graphene ribbon. The ribbon is zigzag of ~3nm width, a hole of diameter ~1 nm is created in its center by removing some atoms. Unexpectedly the calculated T(E) around Fermi level looks like a pulse instead of a spike. The calculate energy range is (-2 2) eV with sampling period 0.02 eV. The T(E) has two peaks at two adjacent energy points; having values 2.01 and 2.00 @ E=-0.02 eV and E=0.0 eV respectively. All the default parameters are used in the calculation, including k-point sampling (1, 1, 100) and mesh cutoff 75. The ATK version is 12.8.1. Any ideas on solving this issue? Thanks..

4

General Questions and Answers / Hartree potential contour diagram using SE method

« on: November 9, 2012, 01:42 »

Hi, could anyone help on getting a Hartree potential contour diagram of a graphene nano-ribbon? I can see that using DFT one can get the effective potential (i.e., Hartree potential + EC potential). Is there a way to compute only the Hartree potential and plot it, using a SE method? Thanks a lot.