Topics

1

General Questions and Answers / A question about LDOS parameters

« on: July 1, 2010, 21:41 »

Hello,

I am trying to calculate LDOS for a two probe system and I had a question about the parameters.  For 'quantum numbers'  if I do not expect there to be a difference in the spin up/down DOS is there some way that I can just say something like spin.both or should I just calculate it twice for spin up and down?  Also what is the best way to pick the k point for a nanotube?

Thanks very much.

2

General Questions and Answers / The scale of energies for DOS?

« on: April 15, 2010, 20:07 »

I am looking at the density of states for a CNT in a two probe system. All the calculations are going fine, but I was wondering what range of energies to look at.  I just looked at +/- 7eV around the zero energy level. Is there some range that is generally considered to be adequate ?

Thanks.

3

General Questions and Answers / 'Too many values to unpack'

« on: April 1, 2010, 07:08 »

Hi

I get the following error 'Too many values to unpack' from the line in my script where I specify the Brillouin zone integration parameters in the arguments for calculating density of states.
 
I looked up this to see if it was a Python error and I found that you get it if you do something like the following.
a,b,c = [1,2,3,4]

Now I have specified the the Brillouin zone integration parameters like normal, and I would think if there was some issue with how I was specifying them the error would first appear when I plug them into the electrode parameters.

Any idea what might be causing this?  Thanks a lot.

4

General Questions and Answers / Trouble Restarting from a checkpoint file

« on: February 18, 2010, 20:44 »

I am trying to restart an aborted calculation using a checkpoint file. It is my understanding that executeSelfConsistentCalculation() will take a restoreSelfConsistentCalculation object as an argument.  I tried this and got the following error:

Traceback (most recent call last):
  File "<string>", line 11, in ?
KeyError: 'Electrode'


My code basically looks like this.

from ATK.KohnSham import *
from ATK.MPI import*

sc_calc = restoreSelfConsistentCalculation('/filepath/filename.nc')

scf = executeSelfConsistentCalculation(
self_consitent_calculation = sc_calc
)


if processIsMaster():
        print calculateTotalEnergy(scf)

I'd like to salvage this calculation if possible and I would really appreciate the help.
Thanks,

BT

5

General Questions and Answers / A strange error

« on: February 4, 2010, 20:18 »

I killed a run today, presuming I had a convergence issue that was unresolved when I discovered the following error:

# ----------------------------------------------------------------
# Equivalent Bulk Calculation (Initial Density for TwoProbe)
# ----------------------------------------------------------------
/home/local/bin/atk-64: line 3: 16373 Killed                  LD_LIBRARY_PATH=$EXEC_DIR/../lib $EXEC_DIR/atk_exec $*
/home/local/bin/atk-64: line 3: 16923 Killed                  LD_LIBRARY_PATH=$EXEC_DIR/../lib $EXEC_DIR/atk_exec $*
Traceback (most recent call last):
  File "<string>", line 414, in ?
ATKError: St9bad_alloc
Traceback (most recent call last):
  File "<string>", line 414, in ?
ATKError: St9bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
  what():  St9bad_alloc
/home/local/bin/atk-64: line 3: 15631 Aborted                 LD_LIBRARY_PATH=$EXEC_DIR/../lib $EXEC_DIR/atk_exec $*
terminate called after throwing an instance of 'std::bad_alloc'
  what():  St9bad_alloc
/home/local/bin/atk-64: line 3: 16988 Aborted                 LD_LIBRARY_PATH=$EXEC_DIR/../lib $EXEC_DIR/atk_exec $*
mpiexec: Warning: tasks 0,6 exited with status 134.
mpiexec: Warning: tasks 2,5 exited with status 137.

Now I don't doubt that some of what is up there may be particular to our cluster/our installation of Linux, but can is there anything up there that can otherwise be made sense of ?

I'm not sure if I have made it clear before, but I really appreciate how responsive and helpful everyone is here in the forum. It makes everything much easier.

Thanks again,
BT

6

General Questions and Answers / Electron temperature and convergence problems

« on: January 22, 2010, 21:12 »

So I have read on the forums and on the tutorial for convergence that electron temperature can have an effect on convergence.  Right now I am trying to run a simulation that includes fcc copper and a metallic CNT. 

What would be a good electron temperature to help these respective systems converge ? What would be a good temperature for a system that includes both ?  So far I have been using the default 300K for all my simulations. 

I have been having convergence issues.  I tried reducing the basis set size to no avail.  Soon I will try adding more scattering layers and beefing up the k-point sampling.  If a different electron temperature will help I'd like to try that too.

Thanks for your time.

7

General Questions and Answers / Appropriate runtimes and convergence

« on: December 8, 2009, 18:59 »

Hello,

I currently have a script running that has been going for a little over 7 days.  It is running in parallel on 8 64-bit processors.

This seems a bit much to me.  Now its the biggest two-probe system I have ever tried to simulate.  There are 171 atoms in the central region.  Are these calculation times appropriate or should I assume that something is amiss?

Could there be some convergence issue?  If so how could I fix it?

Thanks much for your help,

BT

8

General Questions and Answers / "Spatial Sizes," two probe systems and super cell vectors

« on: October 30, 2009, 19:44 »

Hello,

Today I received the following error:

NLValueError: The resulting electrode cells for the electrodes have different spatial size in the A direction

So I'm guessing this has something to do with the super cell vectors.  A guess only.  Something about propagating the system about with the super cell vectors to do some Fourier business ?

I'm working with heterogeneous electrodes by the way, a (4,4) CNT on one side and a copper surface on the other.  If that were not the case I would just make both sets of super cell vectors the same, but since that is the case I am not sure how to change the vectors, assuming that is the issue.

Any help would be much appreciated,

BT

9

General Questions and Answers / An error with the Monkhorst Pack Parameters

« on: October 13, 2009, 22:41 »

Hello,

I have a question about an error I received.

"NLValueError: the monkhorst_pack_parameters set in ElectrodeParameters must be the same in the (kx,ky) plane.

From what I could find the Monkhorst Pack Parameters has to do with the Brillouin Zone Integration parameters and the sampling of k-points.

Could the problem stem from having two different kinds of electrodes ? I specified to different sets of brillouin zone integration parameters, one for each electrode.  Is that allowed?

10

General Questions and Answers / A question of indices

« on: April 10, 2009, 20:42 »

Sorry for the pile of posts, but this question just occurred to me as well.

So there are multiple parts of VNL/ATK that take the indices of atoms as arguments.  The geometrical optimization command and the equivalent atoms argument in the two probe set up come to mind.

Are the indices as simple as their position in the list ?  So if you read down the list of some atoms, the 8th one you count has an index of 7, because, I assume you start at 0.

Also, is it safe to assume that the the nth atom of a list of atoms corresponds to the nth set of coordinates in a list of the atomic coordinates ?

Thanks,

BT

11

General Questions and Answers / A sequence of elements

« on: April 10, 2009, 20:10 »

Hi again,

Here is my question:

I have a script that is failing in the line that has the 'electrode repetitions' argument for the Two Probe configuration. The error message says that the argument must be a 'sequence of elements.'  As far as I know I have specified it as such, creating Periodic Atom Configurations for my two electrodes that appears to otherwise be valid.

Particular error message:

Traceback (most recent call last):
    File "blahblahblah.py", line 199 in ?
        electrode_repetitions= [(1,1),(5,5)]
NLTypeError: Error in TwoProbeConfiguration setup : The 'elements' must be a sequence of elements.

Not sure what the issue is but I would love your input.

BT

12

General Questions and Answers / Convenient ways to generate nanotube segments ?

« on: February 27, 2009, 20:20 »

Howdy folks,

My question is this:

Suppose I make a (4,4) nanotube in the Nanotube Grower.  It is in the bulk configuration.  Is there anyway I can, say, make six unit cells out of it and make it a molecule configuration ?

My real goal here is just to be able to generate coordinates for any given length I might be interested in, that I can then drop in the script editor where all the magic happens.

Thanks in advance,

BT

13

General Questions and Answers / Geometrical optimization of a TwoProbe system

« on: February 13, 2009, 22:27 »

First post here.

I have a bit of a question. I am trying to optimize a two probe system.  The manual says you must indicate the indices for those that will not move.  What are these indices ? 

If I have to define them, what is the best way to do so if I have a big bunch of atoms of the same type, like in a nanotube, but only wish to optimize a few of them? To be clear, I am referring to the atoms in the scattering region.

Thanks in advance,

BT