Messages

1

General Questions and Answers / Why can not calculate the ElectronDensity of Bulkconfiguration using ATK-SE?

« on: March 25, 2012, 15:39 »

Why can not calculate the ElectronDensity of Bulk configuration using ATK-SE? But I found the ElectronDifferent Density can be calculated. see attachment as following.
What is the meaning of ElectronDifferentDensity if the Electron Density can not be calculated?

2

Scripts, Tutorials and Applications / How to get the value of work function with ATK 10.8.2

« on: December 29, 2010, 09:00 »

The script of work function calculating, getting from the QuantumWise wibsite, can run with ATK and VNL 2008.10 but fails with ATK 10.8.2 . How to calculate the work function with ATK 10.8.2?

3

Scripts, Tutorials and Applications / Re: How to set the K point sampling for DOS calculating(version 10.8)

« on: August 27, 2010, 04:50 »

Thanks for your reply. The calculating detail will be depicted as following：
This is my calculating example which is an armchair graphene nanoribbon (see AGNR.jpg)
The calculator is set to "Extended Huckel" and the K Point Sampling is set to 1X1X15. After running this job, the bandstructure is obtained(see Bandstructure.bmp). The energy gap is found from that plot.
Using the same K points sampling, the DOS plot is shown in DOS(1X1X15).jpg. From this plot, The energy gap can not be found. When the K points sampling increases to 1X1X30 (see DOS(1X1X30).jpg), the energy gap appears.

Why can not observe the right result from DOS plot by setting the same K points sampling as calculator?

4

Scripts, Tutorials and Applications / How to set the K point sampling for DOS calculating(version 10.8)

« on: August 26, 2010, 04:31 »

For ATK10.8, the K point samplings for DOS calculating and caculator setting are segregative. How to set the K point sampling for DOS calculating? Is it the same with the calculator setting? I has calcualted a semiconductor GNR(graphene nanoribbon). From band structure the energy gap is observed. But the energy gap miss when the same K point sampling is set for DOS calculating.

5

Scripts, Tutorials and Applications / How to del the data in nc file

« on: June 7, 2010, 11:41 »

With the ATK SE 2010.02 manual, the commond of 'nlread','nlsave'and 'nlprint' is for operating the relevant ATK files. But the wrong datas or unnecessary data like the trasmission spectrum,Molecular energy spectrum etc. will be deleted for reducing the storage space of nc file or easily dealing with a series of data after finishing ATK running. What can I do for that operation?

6

Scripts, Tutorials and Applications / Re: Function for calculating Projected Density of States

« on: April 27, 2010, 07:06 »

The "lih2li.nc"," projected_density_of_states.py" and "example.py" have been placed in the same directory. And the "example.py" file has been runned on ATK SE2010.02. The error message appears as following.

Code

Traceback (most recent call last):
  File "c:\docume~1\fanghui\locals~1\temp\8573268483295537.py", line 1, in <module>
    from ATK.TwoProbe import *; import numpy 
ImportError: No module named ATK.TwoProbe
NanoLanguageScript execution failure

How to deal with this situation?

7

Scripts, Tutorials and Applications / Re: error with plot the I-V

« on: April 27, 2010, 06:57 »

ATK SE2010.02 of the 2nd bug fix have been installed and tried to drop the nc file to the IV curve analyzer. The error message still exists as following.

Code

Traceback (most recent call last):
  File ".\zipdir\NL\GUI\Core\Runner.py", line 220, in run
  File ".\zipdir\NL\GUI\Tools\CustomAnalyzer\Analyzers\IVCurve.py", line 40, in analyzer
    
  File ".\zipdir\NL\Analysis\TransmissionSpectrum.py", line 357, in current
  File ".\zipdir\NL\IO\NLLogger.py", line 66, in write
IOError: [Errno 9] Bad file descriptor

How to deal with this situation?

8

Scripts, Tutorials and Applications / Re: error with plot the I-V

« on: April 16, 2010, 04:33 »

ATK2010.02 have already been installed but the IV curve analyzer cannot be performed correctly. The error as above description(Reply #2 on: April 1, 2010, 09:32 ) pushes me out of the ATK analyzer and makes me to find out some alternative analysis script. I don't know whether the released 2nd bug fix solves the problem or not.

9

Scripts, Tutorials and Applications / Re: error with plot the I-V

« on: April 14, 2010, 08:29 »

I have checked up the calculating carefully. And the low bias truly applied on the left electrode. For plotting the entire IV curve, the zero bias calculating have been performed after finish transmission calculating of -0.1~-0.5 Volt bias ,notwithstanding redunbance. Moreover, the system used in the simulation example is homogeneous and it is a graphene ribbon twoprobe device(armchaire graphene ribbon with 4 width). The leads and scattering region are set with the same ribbon unit. Is this reversal current normal?

10

Scripts, Tutorials and Applications / Re: error with plot the I-V

« on: April 11, 2010, 07:46 »

For this calculating example, the lower bias is always applied on the left electrode. And all the bias is negative value showing above. Under such condition, the current is negative value when bias is -0.4 Volt. But the current changes to the positive value applying -0.6~-1.0 Volt. Why can I get the opposite current when the left electrode is always lower bias?

11

Scripts, Tutorials and Applications / Re: error with plot the I-V

« on: April 10, 2010, 07:47 »

Thanks for your help. I have solved this calculating error follow your suggestion. But I met a strange problem. That is the negative value of current. The results of my IV calculation as following.

Code

 Voltage (V)	Current(nA)
===============================
-0.1 	-1.87583990988e-06
-0.2 	-7.38462057173e-06
-0.3 	-3.48761791403e-05
-0.4 	-0.000168109047444
-0.5 	-9.75295926357e-05
0.0 	0.0
-0.6 	2.02511109092e-05
-0.7 	0.000175293199431
-0.8 	0.000297218070319
-0.9 	0.000474492254908
-1.0 	0.000221309940839

What is the explanation of negative current showing above?

12

Scripts, Tutorials and Applications / Re: error with plot the I-V

« on: April 7, 2010, 04:45 »

The above script fails running on job manager windows. The message is showed as following.

Code

+ -------------------------------------------------------------
| NanoLanguageScript execution started
+ -------------------------------------------------------------
Traceback (most recent call last):
  File "c:\users\hfang\appdata\local\temp\0817546369726710.py", line 2, in <module>
    left_temperature = 100*Kelvin
NameError: name 'Kelvin' is not defined
NanoLanguageScript execution failure
+ -------------------------------------------------------------
| NanoLanguageScript execution finished
+ -------------------------------------------------------------

How to deal with this error?

13

Scripts, Tutorials and Applications / calculating the PDOS with ATK2010.02

« on: April 2, 2010, 04:26 »

Pay attention to the changing syntax of ATK2010.02, I think the scripts of calculating Projected Density of States  should have corresponding changes. How to modify the script of PDOS in ATK2008?

Admin modification: Changed the subject from POS to PDOS to make searching for this easier

14

Scripts, Tutorials and Applications / Re: error with plot the I-V

« on: April 1, 2010, 09:32 »

I dragged the .py file to job manager following the operation of ATK2010.02 manual. The code of .py file is the same with the manual as follow

Code

from NanoLanguage import *

#read in the old configuration
device_configuration = nlread("LiH2.nc",DeviceConfiguration)[0]
calculator = device_configuration.calculator()

# Define sample biases
voltage_list = numpy.linspace(0.1,1.0,10)

for voltage in voltage_list:

    # Set the calculator and use the old scf state as starting input.
    device_configuration.setCalculator(
        calculator(electrode_voltages=(-0.5*voltage,0.5*voltage)*Volt ), 
        initial_state=device_configuration 
        )

    #Analysis
    filename = 'lih2li.nc'
    electrostatic_potential = ElectrostaticDifferencePotential(device_configuration)
    nlsave(filename, electrostatic_potential, object_id='pot'+str(voltage))

    transmission_spectrum = TransmissionSpectrum(
        configuration=device_configuration,
        energies=numpy.linspace(-5,5,200)*eV,
        )

    nlsave(filename, transmission_spectrum,object_id='trans'+str(voltage))
    
    molecular_energy_spectrum = MolecularEnergySpectrum(
        configuration=device_configuration,
        energy_zero_parameter=FermiLevel,
        projection_list=ProjectionList([Hydrogen])
        )
    nlsave(filename, molecular_energy_spectrum,object_id='mpsh'+str(voltage) )

In the above code, I just changed the nc filename. After completion of calculation I  had dropped the file lih2li.nc onto the NC file drop zone of the VNL Custom Analyzer tool. Then the following error appeared in the log window.

Code

Traceback (most recent call last):
  File ".\zipdir\NL\GUI\Core\Runner.py", line 220, in run
  File ".\zipdir\NL\GUI\Tools\CustomAnalyzer\Analyzers\IVCurve.py", line 40, in analyzer
    
  File ".\zipdir\NL\Analysis\TransmissionSpectrum.py", line 341, in current
  File ".\zipdir\NL\IO\NLLogger.py", line 66, in write
IOError: [Errno 9] Bad file descriptor

 
I also wants to know why this error occurred like zhangfuchun and how to get the correct plot of IV curve.

15

General Questions and Answers / How to optimize the structure with VNL2010.02?

« on: March 29, 2010, 10:45 »

With VNL2010.02 , I didn't find out the item of optimizing structure which I can easily see in older edition of VNL for example VNL2008.02. When I carefully read the tutorials of VNL2010.02, I also can not find out the related method of optimizing structure.