Topics

16

General Questions and Answers / DOS values

« on: September 9, 2010, 00:35 »

Code

trans = nlread('ATsupergap.nc',TransmissionSpectrum,object_id="gID015")[0]
dos = nlread('ATsupergap.nc',DeviceDensityOfStates,object_id="gID016")[0]

e=dos.energies()
t=trans.transmission()

to get the transmission values i use the .transmission(), for DOS would i use .DensityOfStates() ?

17

General Questions and Answers / Example Script???

« on: September 1, 2010, 19:24 »

Can someone, write an example script of how to take a converge electronic *.nc file and begin to optimize the geometry with constraints on some atoms?

Code

device_configuration = nlread("CGsupergap05.nc", object_id="gID000")[0]

device_configuration = OptimizeGeometry(
        device_configuration,
        maximum_forces=0.05*eV/Ang,
        constraints=[0,1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,178,179,180,181,185,186,187,188,194,195,204,205,206,207,211,212,213,214,215,216,218,219,222,223,224,225,230,231,232,233,234,235,238,239,241,242,243,244,246,247,249,250,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404],
        trajectory_filename=None,
    )
nlsave('CGsupergap05.nc', device_configuration)
nlprint(device_configuration)

Another question: Between each optimization step is there an electronic convergence and if so, how are the criterion implemented.

18

General Questions and Answers / Help error

« on: August 30, 2010, 00:04 »

I am trying to relax under bias and i get this error.

Code

Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(773)................: MPI_Allreduce(sbuf=0x2aab03087830, rbuf=0x2aab61adfe10, count=258, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Allreduce(385)...............:
MPIDI_CH3U_Receive_data_found(129): Message from rank 5 and tag 14 truncated; 2000 bytes received but buffer size is 1024
Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(773)..................: MPI_Allreduce(sbuf=0x2aab2e8fcd50, rbuf=0x2aaacfa7de10, count=258, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Allreduce(385).................:
MPIC_Sendrecv(155)..................:
MPIDI_CH3U_Request_unpack_uebuf(600): Message truncated; 2000 bytes received but buffer size is 512
Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(773)................: MPI_Allreduce(sbuf=0x2aab03d80420, rbuf=0x2aab455a3fe0, count=258, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Allreduce(385)...............:
MPIDI_CH3U_Receive_data_found(129): Message from rank 6 and tag 14 truncated; 2000 bytes received but buffer size is 1040

19

General Questions and Answers / Current

« on: August 25, 2010, 01:41 »

What type of numerical integral is used to compute the current?

20

General Questions and Answers / Vnl 10.8

« on: August 12, 2010, 02:30 »

How does one get the labels/names to show on the new atk?

Thanks
Jacob

21

General Questions and Answers / convergence

« on: July 26, 2010, 09:06 »

I m having trouble converging a system at -0.3 volts, however I had no trouble converging at -0.8 volts. any ideas?

Jacob

22

General Questions and Answers / Device DOS

« on: July 15, 2010, 04:40 »

Two questions:


1. Angular momenta: what numbers correspond to what orbitals.

Code

[dos.evaluate(projection_list = ProjectionList([....], angular_momenta=[2]))]

I used numbers like 0,1,2, thinking they correspond to  s,p,d respectively but my values do not add up in the end to the regular pdos. What is my mistake here?

2. Contributions: could some explain more on this argument what it means to be left, right and all? I tried to find more information but I kept find information on LDOS

23

General Questions and Answers / restart a job

« on: July 14, 2010, 22:36 »

Is it possible to restart a job in the case where a job was interrupted for atk 10.8?

24

General Questions and Answers / NC file

« on: July 12, 2010, 22:56 »

How does one get rid of information in a nc file?

25

General Questions and Answers / Confused on DOS

« on: July 9, 2010, 19:33 »

I was wondering is the DOS normalized by the volume of the unit cell?

also could some one explain more on the comment from the manual

The atoms in the central region which have equivalent electrode atoms (the so called surface atoms, which are the first left_electrode_number_atoms and the last right_electrode_number_atoms ), are not included in the DOS.

26

General Questions and Answers / initialize a job

« on: July 8, 2010, 08:17 »

I had trouble initializing for a bias calculation. I get this error

Contour Integration Error  : 0.018386

from this code

Code

###############################################################
# Initial State
###############################################################
device_configuration = nlread('analysis.nc', object_id="gID0")[0]

###############################################################
# Calculator
###############################################################
#----------------------------------------
# Numerical Accuracy Settings
#----------------------------------------
left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=(1, 1, 100),
    )

right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=(1, 1, 100),
    )

device_numerical_accuracy_parameters = NumericalAccuracyParameters(
    grid_mesh_cutoff=100.0*Rydberg,
    )

#----------------------------------------
# Electrode Calculators
#----------------------------------------
left_electrode_calculator = LCAOCalculator(
    numerical_accuracy_parameters=left_electrode_numerical_accuracy_parameters,
    )

right_electrode_calculator = LCAOCalculator(
    numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters,
    )

#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
    numerical_accuracy_parameters=device_numerical_accuracy_parameters,
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    electrode_voltages=( 0.1*Volt, 0.0*Volt)
    )

device_configuration.setCalculator(calculator,
    initial_state=device_configuration,
)

device_configuration.update()
nlsave('analysis1.nc', device_configuration)
nlprint(device_configuration)

27

General Questions and Answers / voltage Drop atk 10.8

« on: July 6, 2010, 03:52 »

Does anyone know how to go about obtaining the voltage drop for ATK 2010.8?


Jacob

28

General Questions and Answers / errors

« on: July 5, 2010, 22:03 »

I get this error

Code

** Back Engine Exception 21 : incompatible size of electrode and central region density in A direction
** Location : twoprobeutils.cpp:502

I assume it means my system is not configured properly, however it seems my bulk converged nicely.

Also I calculated the DOS for a bulk device and which i was quite pleased with except for the dips i see just above 0 eV and below 0.5 eV. Also there seem to be a little dip just before the peak above zero eV. I attache the picture. Does anyone have any suggestions?

29

General Questions and Answers / extended huckel

« on: July 5, 2010, 06:06 »

Hello,

I try to run the extended huckel and i get this error;

Code

+ -------------------------------------------------------------
| NanoLanguageScript execution started
+ -------------------------------------------------------------
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 10.8.b1                                                    |
|                                                                              |
+------------------------------------------------------------------------------+
LM-X Error: (Internal: 470 Feature: ATKSEMaster)

[NETWORK] [email protected] - (Err: 9) Feature not found
[NETWORK] [email protected] - (Err: 9) Feature not found

For further information go to http://www.x-formation.com

NanoLanguageScript execution failure
+ -------------------------------------------------------------
| NanoLanguageScript execution finished
+ -------------------------------------------------------------

however DFT works fine

30

General Questions and Answers / ATK 2010.8

« on: June 29, 2010, 03:05 »

I am having trouble with the new ATK I cant send anything to the job manager, or viewer, the window opens and it is just blank. also the scripter looks different than in the tutorials, I have attached a file of what my scripter looks like. Im runing vista on 3gb of memoey, and i unistalled the old version of vnl.

Jacob