Messages

1

General Questions and Answers / Re: A question about LDOS parameters

« on: July 10, 2010, 22:38 »

I see.  I will just loop it in python.  Thanks again

2

General Questions and Answers / Re: A question about LDOS parameters

« on: July 7, 2010, 20:56 »

Thanks for your previously reply.  I missed the part in the manual where you have the option to not include the spin as a parameter.  One more question and perhaps this is a silly one: but why do you supply only one energy for Local Density of States instead of a list of energies like Density of States ?

Thanks again.

3

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.

4

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

« on: April 22, 2010, 19:45 »

Excellent, thank you.

5

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.

6

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

« on: April 2, 2010, 21:10 »

I figured it out. For calculateDensityOfStates(), Brillouin Zone Integration parameters requires only two arguments instead of three.  This fixes my Python 'Too many values to unpack' error. 

My new question is why does Brillouin zone integration parameters require only two arguments in calculateDensityOfStates() and three arguments in ElectrodeParameters ?  I am just curious.

Thanks.

7

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.

8

General Questions and Answers / Re: Trouble Restarting from a checkpoint file

« on: February 22, 2010, 18:17 »

Well I am using Neutral Atom density because I have heterogeneous electrodes.  I don't know if that makes any difference.

I think I will first try running my initial script with 'initial_calculation = sc_calc" and if that does not work I will just restart the whole thing from scratch.

Thanks for the help.

9

General Questions and Answers / Re: Trouble Restarting from a checkpoint file

« on: February 21, 2010, 04:23 »

I made the switch, but I receive the same error.  I also tried importing KhonSham and TwoProbe, but received the same output.

10

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

11

General Questions and Answers / Re: A strange error

« on: February 8, 2010, 19:00 »

Excellent.

I will likely reduce the mesh cutoff, but I do have a question about the two probe algorithm.  Are there any consequences to using the 'Neutral Atom Density' other than increased convergence time ?  That is are the results in general, the same ?

Thanks again,

BT

12

General Questions and Answers / Re: A strange error

« on: February 5, 2010, 17:56 »

No kidding ?  What kind of measure could I take to remedy this ?

Thanks again.

13

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

14

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.

15

General Questions and Answers / Re: Appropriate runtimes and convergence

« on: December 15, 2009, 12:35 »

Well the iteration control parameters and iteration mixing parameters are both at default.

Could it be that one of the electrode (the CNT one in my case) has the basis set being double zeta polarized?

Maybe I should be more clear.  I have a CNT electrode and a copper one.  All copper atoms I set to use single zeta, all carbon atoms I set to use double zeta polarized.

I of course have the scattering layers in correctly, I think.