Messages

1

General Questions and Answers / Re: fixed spin

« on: June 2, 2009, 17:57 »

While optimizing atomic coordinates of a magnetic system, I noticed that magnetic moment per cell changes with lattice constant. For this reason I want to fix moment at first, then make optimization calculations for different lattice constants. Repeating this procedure for different moments, I obtain different magnetic branches of the structure. The branch with minimum energy configuration will be ground state, I assume.

2

General Questions and Answers / fixed spin

« on: June 2, 2009, 13:59 »

Is there any way to utilize the fixed spin tag for periodic calculations?

3

General Questions and Answers / Re: Small Transmission Coefficients and Low Current

« on: April 13, 2009, 22:06 »

Due to periodic boundary conditions does the first atom of the left electrode overlaps with the last atom of the right electrode in the geometry created by 2probe_configuration2.py? If this is the problem how can I make the right electrode to start 1.267 Ang far from the central region?

4

General Questions and Answers / Re: Small Transmission Coefficients and Low Current

« on: April 13, 2009, 20:15 »

At first I optimized the central region atoms (in periodic atom configuration) then I used the optimized geometry as central region. The scripts for setting up the geometry and zero-bias calculation are attached. Structures built by 2probe_configuration.py runs without any problem, but device-right electrode distance is not 1.267 Ang. as I wanted. 2probe_configuration2.py fixes this problem (I cannot see any overlapping atoms in VNL) but its two-probe calculation gives "fail to diagonalize matrix" error

5

General Questions and Answers / Re: Small Transmission Coefficients and Low Current

« on: April 13, 2009, 16:03 »

Cr's

6

General Questions and Answers / Re: Small Transmission Coefficients and Low Current

« on: April 13, 2009, 14:11 »

Carbon linear chains are used as electrodes. I tried to increase the electrode by 50% as you said but I got the following message:
ATKError: inverse(DZMatrix const &) : Could not LU factorize!
So I increased the electrode by 25% (without getting any error messages). Unfortunately there is no improvement, actually I got the same zero bias transmission spectrum. The plot for comparision is attached, the zero bias trans. spectrum can be seen. When I inspected the the structure with VNL I noticed that the distance between right electrode and the central region is different from what I wanted. While building the two-probe geometry I was using the same configuration for both electrodes.  By taking the mirror image of the left electrode  configuration for right electrode, I've solved this problem. Now both contact distances are symmetric. But this time I got the following message for zero bias calculation:

ATKError: solveSymmetricGeneralizedEigenProblem : Failed to diagonalize matrix!

Is there any other way to say the ATK to put the electrodes at a specific distance away from the central region?
 
Another thing in my mind is electrode repetition. I am using the default value but I am including more than one atoms in electrode unit cell. Could it be the reason?

7

General Questions and Answers / Re: Small Transmission Coefficients and Low Current

« on: April 10, 2009, 15:10 »

plot#2,3&4

8

General Questions and Answers / Small Transmission Coefficients and Low Current

« on: April 10, 2009, 15:09 »

Hi all,
I am calculating  a 1D structure and seeing small transmission coeffients such that the resulting current values are at microAmpere range at finite biases. I first checked charge but there is no charge missing. There are approximately 51.60272 spin-up charges and 52.72461 spin-down charges in the central region at 1V (# sc 47 : q =  104.32771 e  Etot = -397.37066 Ry  dRho =  9.6462E-04  dEtot =  3.2366E-04 Ry). Then I tought that it might depend on number of buffer layers, so I repeated the calculation with 10-10, 20-20 and 40-40 buffer layers. Unfortunately this caused another problem. I saw that transmission properties of the device changes depending on the number of buffer layers. This is unphysical. At last I've checked the voltage drop (by choosing electrode constraint as Density Matrix) and saw no abrupt change in the potential. Then I conclude that the scattering of the electrons from the contact cannot be the cause of this small transmission coefficients.
Any new ideas? 

ps. Plots of the voltage drop for the spin-up and spin-down electrons and transmission spectrums at 1V are attached successively (due to size limitations I attached them seperately).

9

General Questions and Answers / Re: MPI error: killed by signal 9

« on: February 19, 2009, 10:39 »

upps! sorry i copied the wrong line..
yes MPICH2 version is 1.0.5. We have two core 2 quad xeon processors running under open suse 11.
mpiexec -n 4 /usr/local/btk/bin/atk test-mpi.py command prints
# Master node
# Slave node
# Slave node
# Slave node
On the other hand i have a large unitcell (10x10x110 Ang.^3) with 85 atoms

10

General Questions and Answers / Re: MPI error: killed by signal 9

« on: February 18, 2009, 08:25 »

I started to get the same error.  At first i thought it s a kind of parallelization problem and tried different k-points while changing number of nodes to run the calculation.
Several tries consisting of (1,1,1) k-points on 4-nodes, (1,1,3) k-points on 2-nodes, (1,1,3) k-points on 4-nodes gives the following error,
rank 2 in job 46  DualQuad_19430   caused collective abort of all ranks
  exit status of rank 2: killed by signal 9

But somehow i had managed to run the calculations with (1,1,5)  k-points on 3 nodes and they converged without error until yesterday. Yesterday when i started another calculation with  (1,1,5)  k-points on 3 nodes and this morning got the same error. Do you know why?

ps. I am using ATK 2008.10.0 on a Linux-x86_64 machine. My mpich2 version is ATK 2008.10.0 Linux-x86_64

11

General Questions and Answers / Re: How to initialize an optimization calculation using elec.dens. of another calc.?

« on: February 17, 2009, 12:47 »

thanks a lot..

12

General Questions and Answers / Re: How to initialize an optimization calculation using elec.dens. of another calc.?

« on: February 17, 2009, 08:47 »

i tried to use the code given above but i got confused about how to define electron density in the method. when i dont define ant initial electron density in the method it becomes spin unpolarized by default and i got "The two system has different spin dimensions"  error since the initial calculation is spin polarized. On the other hand i dont want to define any initial electron density because i want to start the calculation from previous calculation's density. So what do you suggest?

13

General Questions and Answers / How to initialize an optimization calculation using elec.dens. of another calc.?

« on: February 12, 2009, 15:35 »

I want to  use relaxed atomic positions and electron density of a previously converged calculation as an initial guess to an optimization calculation. However, 'initial_calculation' argument is only avaible for executeSelfConsistentCalculation not for calculateOptimizedAtomicGeometry. Is there another way?