Messages

1

General Questions and Answers / Nedged Elastic Band method

« on: April 5, 2010, 10:03 »

Hi,

I'm asking regarding the NEB method.  I tried modifying the code from the tutorial to apply the NEB method to a bulk material to understand some phase transition issue.  However, I keep getting force=nan error.  I've narrowed it down to the codes in NEB.py when it tried to get the tangent between images which gives a nan value.  As I'm not sure of how to get the tangent, or what it means, so I don't know how to change to code to make it works.

Any suggestions are greatly appreciated.  Thanks in advance.

============
Note: I've modified the code NEB.py and somehow it works.

Change the line:
        utangent=tangent/length(tangent)

To:
        if max(tangent)-0. < 0.01:
          utangent=tangent
        else:
          utangent=tangent/length(tangent)

============

2

General Questions and Answers / Re: Regarding ISOValues [in particular charge density]

« on: November 26, 2009, 03:21 »

I'm thinking more of the LUMO/HOMO (or the conduction band, valance band) for a periodic structure.  That is different from the isoplot for electron density since I can't control the quantum state {band number, k-vector) for that calculation.  I can control the quantum state for wavefunction calculation with is related to the charge density so I was thinking maybe it would be possible to just square the value from wavefunction and plot that as the charge density.

But then again I've got the problem of choosing what isovalue to plot and what information I'm trying to obtain from the plot.

Anyway thanks for the reply.  I'm just thinking aloud on the best way to present the data for some conclusion.

3

General Questions and Answers / Regarding ISOValues [in particular charge density]

« on: November 25, 2009, 11:22 »

Dear all,

Let me refer to a previous post http://quantumwise.com/forum/index.php?topic=126.0
{I'm starting a new one so as not to hijack others' topic}

I would like to know if I can modify the Bloch state [aka wavefunction, phi] calculated {as a function of energy determined by the quantum number, i.e. band number and k-vector} into the charge density {which will also be a function of energy}.

I'm guessing that this would be different from the electron density calculated since that would be summed over all energy and is also dependent on the electron occupancy.  Or can I get the charge density from electron density and occupancy?

Thank you in advance for any info.

4

General Questions and Answers / Re: Visualization of VNL data

« on: November 24, 2009, 08:37 »

Thank you! I'm assuming the CUBE file is for GaussView?

5

General Questions and Answers / Visualization of VNL data

« on: November 23, 2009, 05:48 »

Dear all,

I would like to ask if anyone used other software to visualizing the data (e.g., Electron density) in the VNL files other than VNL?
While the graphics looks great using VNL, I can't seems to maneuver the figures to the correct position.  This is especially difficult when I want to compare the plots of different structures as I can't get to the same viewing angle.

Maybe I'm just a control freak but I would love to be able to control the rotation degrees of the figures.  Any tips on this will be great.

Cheers!

6

General Questions and Answers / Re: Inconsistency in gated two probe method

« on: June 16, 2009, 05:07 »

Thank you.

7

General Questions and Answers / Inconsistency in gated two probe method

« on: June 15, 2009, 12:23 »

Dear Dr. Blom,

I would like to bring your attention to an inconsistency I observed in gated two probe method.  This is regarding the setting of the ‘Initial Density Type’ under TwoProbe Algorithm Parameters.

I’ve set the value to ‘InitialDensityType.NeutralAtom’ but in the gated method, it reverts back to ‘InitialDensityType.EquivalentBulk’.  I’m not sure if it is intentional and the physical significant of this parameters.  I guess it would not matter as the results should converge to a similar value.

I’ve attached my codes (2Probe.py) and the output (2Probe.log) for your investigation.

Rgds,
Kai Tak

8

General Questions and Answers / calculateAtomicForce

« on: April 24, 2009, 16:52 »

Hi,

I would like to ask some question about the force calculated between 2 atoms.

I assume it is the electrostatic force between the 2 atoms and as the distance between them decreases, the forces between them increases.  If the atoms are of similar charge, the force is repulsive and it is attractive if the atoms are of different polarity.

Question 1: When the force is non-zero and of different polarity, does it mean that if I leave the two atoms be, they will move towards each other? (and hence decreasing the distance between them and increasing the attractive force between them).  This would be true even if the force is small (0.05eV/Ang?).

Question 2: Can I interpret the force as such that it is the force required to increase the distance between the atoms?

Any help is greatly appreciated.

Rgds
Dick

9

General Questions and Answers / Re: Transmission spectrum for GatedTwoProbeMethod

« on: March 17, 2009, 10:22 »

Oh... So the transmission should change (but not just a simple shift) and the gate bias is only applied at the Hamiltonian (something like G=inv(E-H-Vg)) but not at the source and drain Fermi-Dirac distributions (f1,f2).  I had the impressions that Vg was applied at the (f1,f2) in the earlier versions of ATK and just want to be sure about the implementation and the results I got.

10

General Questions and Answers / Re: Transmission spectrum for GatedTwoProbeMethod

« on: March 14, 2009, 06:02 »

Thank you Dr. Blom.  However, I still have some questions that I would like to clear about this issue.  Parden me if my understanding of NEGF is incorrect and appreciate you will point me to the correct path.

1)  Transmission under different gate biases.
If the transmission does not change under different gate biases, and if the chemical different between the two probe remains the same, how can the current be different?  I'm guessing that the chemical potential at the source and drain and also changed by the gate biases (in addition to the change in the device Hamiltonian) but I'm not sure how to varify that.

2) Screening length and gate biases.
I did a little experiment with Prof. Datta's codes in Quantum Transport and implemented the Vg similar to ATK (according to what I understand).  I found out that if my screening length is not sufficient, the transmission will be changed (not shifted, just some anormalies) if different gate biases are applied.  And this screening length requirement increases with larger biases (which make sense intuitively but I've yet to understand why).  Hence can I safely assumes that if and when I found anormalies in the transmission spectrum from ATK under gate biases, the first thing I should do is to increase the screen region? (I would actually want to try simulate this but my structure is already too big and the time taken to varify would be too long).

It would be great to have ATK implement the gate bias self-consistently.  However, I'm just wondering should I expect the transmission to shift by the same amount of the gate bias if it is implemented 'correctly' or maybe my understanding of transmission spectrum under gate bias is totally wrong?

11

General Questions and Answers / Transmission spectrum for GatedTwoProbeMethod

« on: March 13, 2009, 10:14 »

Hi,

I'm having some problem understanding the transmission spectrum for GatedTwoProbe calculations.
I was expecting the transmission to be shifted along the energy axis by the same amount of bias that is applied but that doesn't seem to be the case.  Does defining the screening atoms have any effect on the transmission spectrum?

Rgds,
Dick

12

General Questions and Answers / Re: Issue with parallel two probe calculations

« on: January 28, 2009, 11:51 »

A big thank you to both Dr. Blom and Nordland.  I'll try with the upgrade once the current calculations end and do a comparison on the speed and results to the same system.

13

General Questions and Answers / Re: Issue with parallel two probe calculations

« on: January 28, 2009, 11:22 »

Yes the MPI setup is correct and ATK can run in parallel using the test_mpi.py script.  I've also verified that the types of license (master and slaves) are correctly checked out.  When I check for parallelism, basically I just see the load of my machines.  I have a job with 4 processors. While I can see that there are 4 instances of ATK running, only one of them is active when the program is running the SCF for Fermi energy of scattering region.  Otherwise, all 4 of them are active.  I'm looking at the output file to determine which part of the calculation the program is running (runlevel 6).  This is more prominent as my scattering region is over 1200 atoms.
Serial calculation at:

Code

Equivalent Bulk Calculation (Initial Density for TwoProbe)

My system is installed with MPICH2 1.0.7.  I have the job scheduler/load balancing software Torque/Maui install (with the appropriate mpiexec script) but I don't think that is the cause of the issue since I observe the same issue when I'm not using the job scheduler.  The OS is Fedora 7 and ATK version is 2008.02.1.

I'm tempted to run without the initial bulk SCF loop.  But as the job has already been running for 200+ hrs I'm not inclined to stop it and try again.  I've tried to do that once before but found out that although there is a .nc file, it can be used to restart/continue the calculation.

14

General Questions and Answers / Issue with parallel two probe calculations

« on: January 28, 2009, 04:26 »

Hi all,

I would like to know if anyone observed that during the calculation of parallel two probe calculation, the SCF loop for the scattering region (The one right after the calculation of Fermi energy of electrodes and before the calculation of charge of the system) runs on a single processor?

I'm just wondering if there is anyway to make that part of the calculation run on the multi-processor to speed things up.

Any suggestions will be much appreciated.

Cheers!
Dick LAM