Messages

1

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

« on: December 11, 2013, 00:51 »

This helps a lot, thanks. One thing is that I have problem in viewing the vDiff.
Is there anyway to show vDiff in VNL, for example, by saving it into a .nc file then use VNL's Results Viewer to visualize and plot it? I tried nlsave("diff.nc", vDiff) but it didn't work..

2

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.

3

General Questions and Answers / Re: bonds broken while optimization

« on: September 24, 2013, 03:05 »

Thanks for advices. I'll have a go..

4

General Questions and Answers / Re: bonds broken while optimization

« on: September 19, 2013, 05:14 »

Hi Anders, The other basis set available in ATK is CP2K non-selfconsistent; seems the DFT has to be used, which would take too long to converge for the ~300 atoms system..Thanks.. 

5

General Questions and Answers / Re: bonds broken while optimization

« on: September 10, 2013, 11:14 »

Hi Anders, I am using the DFTB (CP2K, selfconsistent) basis set. Thanks..

6

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.

 

7

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

« on: June 16, 2013, 03:53 »

Hi Anders and Nori, I take your advices, much appreciated! Regards, Wanzhi.

8

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..

9

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

« on: November 14, 2012, 11:48 »

Hi Anders, I calculated the ElectostaticDfferencePotential using DFT, and the result is still different from the Hartree potential plot I was expecting. Probably something is wrong with my expectation. Many thanks.

10

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

« on: November 12, 2012, 01:24 »

Hi Anders, thanks very much for your help. I tried to use the ExternalPotential as advised to calculate the Hartree potential of a graphene ribbon with zero bias voltage using the DFTB method, the resulted plot is just a plane with uniform color (ie one value). This is very different from Hartree potential figures published in the literature that have may varying values across the ribbon. Any further advice? Thanks and regards, wanzhi.

11

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.