Topics

16

General Questions and Answers / error in transmission spectra run at a specific vibrational modes

« on: February 16, 2017, 13:02 »

I attach herewith the input and output of a transmission spectra run at a specific vibrational modes. But it did not run, kindly opine how to correct the input file.

with regards,

Sabyasachi Sen

17

General Questions and Answers / Generation of es states and MPSH states during IETS run

« on: December 24, 2016, 12:54 »

The .nc file obatined with my IETS run is showing error while trying to get es states needed for MPSH states calculations. However, with elastic scatterings (usual one) it works well. Kindly suggest, how to do it with IETS case.

18

General Questions and Answers / Restarting a IETS run

« on: August 6, 2016, 11:11 »

Dear Sir

Let me know the command for restarting a IETS job. In our machine similar programme has been running for few days, .nc file was developed but job terminated afterwords due to power failure. Now, please suggest, how to restart the job from the said .nc file, which already keeps dynamical matrix,  vibrational modes and only the transmission job is left with.

Kindly reply,

Sabyasachi Sen

19

General Questions and Answers / numerical data such as intensity of vibration/vibational amplitude in IETS run

« on: July 16, 2016, 13:56 »

I furnish below part of the result obtained with a IETS run;

------------------------------------------------------------------------------+
| Vibrational Mode Report |
| ---------------------------------------------------------------------------- |
| K-point = [0.000000, 0.000000, 0.000000] (fractional) |
+------------------------------------------------------------------------------+
Mode index Energy Wavenumber
+------------------------------------------------------------------------------+
Mode 0: -3928.83 meV -31688.14 cm^-1 (eigenmode available)
Mode 1: -3478.62 meV -28056.95 cm^-1 (eigenmode available)
Mode 2: -3084.02 meV -24874.30 cm^-1 (eigenmode available)
Mode 3: -2952.32 meV -23812.08 cm^-1 (eigenmode available)
Mode 4: -2084.22 meV -16810.40 cm^-1 (eigenmode available)


The problem is there are altogether 82 modes available. Energies are probably phonon energy. In the output it is written 'eigenmode available'; but which vibartional mode is important would be understood if numerical data such as intensity of vibration/vibational amplitude is known.  Kindly, inform me how to get the intensity of various vibrational mode so that we can make transmission spectrum calculation only on those significant modes.

20

General Questions and Answers / eigenvalue of vibrational modes in IETS run

« on: July 9, 2016, 12:02 »

Kindly highlight me how to get eigenvalue of vibrational modes form Vibrational Mode Report  in IETS run using a twoprobe  relaxed geometry.

21

General Questions and Answers / unequal occupation in 2 spin channels of AFM arrangement

« on: October 25, 2015, 08:18 »

TMR caln using magentic electrode, insulating tunnel barrier shows unequal occupation in 2 different spin channels in AFM arrangement as per .es file. This is ambiguous as unequal occupation implies net spin even with AFM arrangement. Kindly explain.

22

General Questions and Answers / Blue and Green lines of transmission path-not known

« on: July 1, 2015, 12:35 »

Kindly help me in identifying the meaning of Blue and Green lines of transmission path attached as .jpeg file with this query. Please also note in the output only spin up data is presented (see output and .py file) for spinpolarized calculation. Please help me in getting data of both spin up and down. Also illustrate the meaning of various terms in the outpt file.

23

General Questions and Answers / how to extract spin dependent transmission pathways from the related .nc file

« on: June 13, 2015, 10:49 »

Let me know how to extract spin dependent transmission pathways from the related .nc file.
Its very urgent.

24

General Questions and Answers / the job suddenly stopped running without showing any error

« on: May 9, 2015, 09:11 »

In an ATK two-probe transmission spectrum analyses over a voltage loop, the job running suddenly stopped after zero bias data. Shows no error, no progress over past three days (first run is at 0.1 V and zero bias data obtained after 1 day). This is astonishing and when we have give 'top' command in our linux machine each time it shows atk jobs are running. But no progress any where over 3 days. Kindly help.

25

General Questions and Answers / increased number steps-does not work to overcome convergence proble

« on: May 9, 2015, 09:00 »

I have used following commands to overcome convergence problems,
"
#----------------------------------------
# Iteration Control Settings
#----------------------------------------
left_electrode_iteration_control_parameters = IterationControlParameters(
    damping_factor=0.5,
    max_steps=120,
    tolerance=0.001,
    number_of_history_steps=25,
    )

right_electrode_iteration_control_parameters = IterationControlParameters(
    damping_factor=0.5,
    max_steps=120,
    tolerance=0.001,
    number_of_history_steps=25,
    )

device_iteration_control_parameters = IterationControlParameters(
    damping_factor=0.5,
    max_steps=120,
    tolerance=0.001,
    number_of_history_steps=25,
    )
   
"

However, it shows convergence error with following commands,

------------------------------------------------------------------------------+
|  99 E = -360.947 dE =  1.548518e-03 dH =  4.940824e-03                       |
+------------------------------------------------------------------------------+
################################################################################
#                                                                              #
# Warning: The calculation did not converge to the requested tolerance!        #
#                                                                              #
################################################################################
+------------------------------------------------------------------------------+
|                                                                              |
Therefore, increase of number of steps not all has any impact to improve to sort out the convergence problem. This problems are more at a higher bias in loop run of I-V calculation.

Kindly help me.

26

General Questions and Answers / difining an atom in triplet and confrimation through outpt or nc

« on: January 23, 2015, 10:15 »

Kindly inform me, how do I define spin state of a particular atom using vnl e.g Hf in triplet state. Please also tell me how  to check that system was actually in triplet state form the results presented in output or .nc file.

27

General Questions and Answers / commands to get spin polarized current from I-V curve run

« on: October 18, 2014, 09:24 »

Kindly inform me how do I get current for separate spin channels from the .nc file of a spin polarized two-probe calculations with commands written for I-V curve calculations. Presently, with vnl I could only get net spin current in the spin polarized run.

28

General Questions and Answers / MKL ERROR: Parameter 7 was incorrect on entry to ZHSEQR info=-7

« on: September 20, 2014, 06:58 »

I am getting following error in my two-probe run, Transmission spectrum does not appear at all. The input  file is attached

MKL ERROR: Parameter 7 was incorrect on entry to ZHSEQR
info=-7

MKL ERROR: Parameter 7 was incorrect on entry to ZHSEQR
info=-7
+------------------------------------------------------------------------------+
|                                                                              |
| Device DFT Calculation  [Finished Fri Sep 19 03:42:56 2014]                  |
|                                                                              |
+------------------------------------------------------------------------------+

MKL ERROR: Parameter 7 was incorrect on entry to ZHSEQR
info=-7

MKL ERROR: Parameter 7 was incorrect on entry to ZHSEQR
info=-7

MKL ERROR: Parameter 7 was incorrect on entry to ZHSEQR
info=-7

MKL ERROR: Parameter 7 was incorrect on entry to ZHSEQR
info=-7

Kindly help me.

29

General Questions and Answers / sfc-convergence-error remains-even after lowering convergence criterion-iteratio

« on: July 31, 2014, 13:06 »

Please find the attached .py file and related .out file for which is showing error in scf convergence as follows:
+------------------------------------------------------------------------------+
|  99 E = -695.443 dE =  6.250511e-04 dH =  1.643567e-03                       |
+------------------------------------------------------------------------------+
################################################################################
#                                                                              #
# Warning: The calculation did not converge to the requested tolerance!        #
#                                                                              #
####################################


Even after using higher damping, higher tolerance, higher history cycle, the error remains (see the attached .py and .out file). The error remains even with larger no. of iterations (100 to 120). I doubt the impact of increasing cycles or reducing other criterion does not become effective in the final output. Kindly see the attached .py file and suggest me the remedy,
(i) how do I understand that their effect is actually influencing the final output.
(ii) Kindly suggest me a way out to get rid of the said convergence problem.

Sabyasachi Sen

30

General Questions and Answers / calculation did not converged-even-after chaning the tolerance-two-probe-job

« on: July 12, 2014, 11:45 »

I am performing two-probe run on a system having 7x7 Au eletrodes with SZ basis and molecule consisting of C, H, N, Mn; with DZP basis. Large molecule needed large electrode for better connectivity.
However, in the outpt, an error appers just befor transmission spectrum analysis, the error is repoted as

+------------------------------------------------------------------------------+
|  99 E = -313.274 dE =  7.651696e-04 dH =  3.574468e-02                       |
+------------------------------------------------------------------------------+
################################################################################
#                                                                              #
# Warning: The calculation did not converge to the requested tolerance!        #


Looking at this I have given rerun of the job with higher tolerance given as,

left_electrode_iteration_control_parameters = IterationControlParameters(
    tolerance=0.1,
    )

right_electrode_iteration_control_parameters = IterationControlParameters(
    tolerance=0.1,
    )

device_iteration_control_parameters = IterationControlParameters(
    tolerance=0.1,
    )

However, the output shows similar covergence problem.

Kindly, suggest me how to overcome this problem.