Topics

1

General Questions and Answers / Structural optimization with ATK-SE

« on: January 28, 2013, 21:55 »

Dear QuantumWise Staff,

I am trying to use the ATK-SE package, but there are two questions which are not clear to me. Would you please give me some advice?

1.   I am going to perform structural optimization within the framework of ATK-SE: Slater-Koster, however, there is a choice of “No SCF iteration” in the settings of Slter-Koster Basis set. What’s the difference of optimization with and without “No SCF iteration”?

2.   In general, the ATK-SE method can run for a larger system than DFT method. Taking an example, if I run a two-dimensional system consisting of Boron Nitride and graphene in parallel (for example, with 8 CPUs), what’s the upper limit of the numbers of atoms in the system?

Thanks for the help.

2

General Questions and Answers / The effect of bias on transport property?

« on: November 1, 2011, 15:55 »

    Recently, I performed some test calculations bout the effects of the applied bias on the transport properties of graphenen nanoribbons. The attached figure shows the results of two kinds of armchair nanoribbons. It can be seen that in both of cases, with the increase of bias, the transport spectra move further away from the Fermi level as well as the suppressed amplitude for a wide range of energies. At higher bias voltage, there are nonzero transmission values near the Fermi level in the original band gap, the transmission values of which are dependent on the bias voltage. Where do the nonzero transmission values in the original band gap come from? How to understand these phenomena?

    Thanks in advance!

3

General Questions and Answers / About the current of semiconductor nanotube

« on: October 28, 2011, 10:30 »

Hi:

Recently, I have performed some test calculations on the I-V characteristics of semiconductor SiC nanobube. It is shown that the SiC nanotube has a band gap of 1.55 eV. However, it need about 3.5 V bias to inject a current in the nanotube? (Please see the attached python script and the pictures) Why? Is there any mistake?

Thanks in advance!

4

General Questions and Answers / About the transmission spectrum of zigzag graphene nanoribbon under bias

« on: June 14, 2011, 14:43 »

Hi:

     I performed some test calculations on zigzag graphene nanoribbon. The transmission spectrum, density of states (DOS), and projected density of states (PDOS) of the nanoribbon without bias can give a reasonable result. However, the transmission spectrum obtained under bias has an energy gap, conflicting with the corresponding results of DOS and PDOS (please see the attached picture, which gives the examples of zero bias and at the bias voltage of 0.5V, respectively). I cannot understand it. I doubt if I set any inappropriately parameter (please see the attached file). 

Thanks in advance.

5

General Questions and Answers / About the transmission spectrum of carbon nanotube

« on: May 28, 2011, 12:24 »

Hi:

    I performed some test calculations on pristine (4,4) carbon nanotube. It is recognized that the (4,4) tube is metallic, but in the obtained transmission spectrum there is a deep trench at the Fermi level (please see the attach picture), which is different from other theoretical results. Moreover, the transmission coefficients (0.00815129) is not consistent with the transmission eigenvalues (1.00005082 , 0.99371959) at the energy of 0.0*electronVolt. I doubt if I set any inappropriately parameters (please see the attached file).
 
    Thanks in advance.

6

General Questions and Answers / About structural optimization of atomic cluster

« on: July 13, 2009, 12:12 »

Recently I have written a small python script based on ATK for structural optimization of randomly generated atomic clusters. It works well for small molecular, however, when it is used for medium-sized cluster, it cannot converge after thousands of steps. I have tried to adjust some parameters, but no obvious improvement has been observed.

Please see the following script for structural optimization, an randomly generated cluster compose of 34 oxygen atoms and 34 zinc atoms, and output file.

What is the matter ? How to deal with it? Thanks everyone !!!

7

General Questions and Answers / Question about geometry optimization for molecule

« on: April 14, 2009, 14:52 »

Hi, everyone!

I have performed a calculation of geometry optimization for a dimer composed of one Bi and one Mn atoms, but the optimized structure cannot be obtained after a large number of optimization steps. (Please see the attached script and out file for details.) However, the same initial structure can be optimized successfuly within a few steps using other DFT-based software with similar parameter settings. I also tried to adjust some parameters, no obvious change has been observed. What is the matter?

Thanks in advance!

8

General Questions and Answers / Questions about conductance of nanowire

« on: March 26, 2009, 06:24 »

Recently I have performed calculations for conductance of Au nanowire ( see the following script and output ), however, the obtained value (1.368 G0) is much smaller than other experimental and theoretical results ( about 3 G0 ). This situation is more notable in other thicker nanowires. I have tried to adjust some parameters such as basis set size, mesh cut-off, exchange-correlation function, and k-points, no obvious change has been observed. What is the matter ?

I appreciate any reply.  Thanks a lot !

9

General Questions and Answers / Cannot run script in parallel

« on: March 26, 2009, 04:18 »

Recently I have writen a small python script based on ATK, it can work correctly when I run it with the command “ mpiexec  -machinefile  mpd.hosts  -n  1  $ATK_BIN_DIR/atk  $WORK_DIR/script.py”.  However, when I run it in parallel with the command “mpiexec  -machinefile  mpd.hosts  -n  8  $ATK_BIN_DIR/atk  $WORK_DIR/script.py”, it cannot work with the following hints:

[ch@console ~]$mpiexec  -machinefile  mpd.hosts  -n  8  $ATK_BIN_DIR/atk  $WORK_DIR/script.py
5: [cli_5]: aborting job:
rank 5 in job 133  console_45778   caused collective abort of all ranks
  exit status of rank 5: return code 1
5: Fatal error in MPI_Allreduce: Message truncated, error stack:
5: MPI_Allreduce(707).....................: MPI_Allreduce(sbuf=0x57136008, rbuf=0x5763d008, count=658560, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD) failed
5: MPIR_Allreduce(385)....................:
5: MPIDI_CH3U_Post_data_receive_found(163): Message from rank 4 and tag 14 truncated; 2814240 bytes received but buffer size is 2634240
[ch@console ~]$

I think it must have something to do with the “buffer size” of mpich2-1.0.5p4.
How to deal with it?  Thanks everyone !!!