Messages

1

General Questions and Answers / Zig-zag graphene nanoribbon bandgap

« on: April 1, 2016, 06:50 »

Dear Quantumwise staff

In recent research, it appears the zigzag graphene nanoribbon has a band gap.
How can I correctly reproduce the result?

2

General Questions and Answers / Re: Use ATK DFT to calculate the hydrogen atom energy levels

« on: October 8, 2014, 03:25 »

This is actually surprisingly "difficult" in DFT
I had a script somewhere that gives 13.57 or something, I don't remember now, I can look for it, but the key is to turn on spin-polarization and use GGA. You might also need to increase the accuracy by using a large basis set and high mesh cut-off. See what that gives you, and I'll keep looking for my old script...

Thanks a lot for the answer.

I've tried with SGGA.PBE with DZDP basis set, the mesh cut off set for 75H,300H,1200H. The molecular ground state energy does not change as I increase the mesh cut off setting. The Spin Up is about -7.30eV and the spin down energy level is about 2.59eV.  I also used other functional to calculated and get the similar results around -7.eV and 2.5eV. Change of Density mesh cut off seems do not change the final result significantly.

I'm a bit confuse about this problem. Why is this happening? Since calculate the Hydrogen atom will need so much effort, how can we assure other more complex molecule are right? What mechanism underline ATK makes calculation of Hydrogen so "difficult" while other more complex molecules becomes easy?

3

General Questions and Answers / Use ATK DFT to calculate the hydrogen atom energy levels

« on: October 7, 2014, 01:35 »

I might ask a dumb question.
I was trying to use ATK DFT method to calculate the isolated hydrogen atom energy level.
But I just couldn't get it right. The calculated ground state energy level is always around -5.77eV using DFT method (-6.34eV for SK method).
I already knew that the Hydrogen atom energy level should have a ground state energy -13.6eV.
Where did I get it wrong?
(BTW, the Extend Huckel works pretty well, as I expect.)

Code

# -------------------------------------------------------------
# Molecule configuration
# -------------------------------------------------------------

# Define elements
elements = [Hydrogen]

# Define coordinates
cartesian_coordinates = [[ 0.,  0.,  0.]]*Angstrom

# Set up configuration
molecule_configuration = MoleculeConfiguration(
    elements=elements,
    cartesian_coordinates=cartesian_coordinates
    )

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
calculator = LCAOCalculator()

molecule_configuration.setCalculator(calculator)
nlprint(molecule_configuration)
molecule_configuration.update()
nlsave('C:/ATK/ATKstudy/Hydrogen_MO_1.nc', molecule_configuration)

# -------------------------------------------------------------
# Molecular energy spectrum
# -------------------------------------------------------------
molecular_energy_spectrum = MolecularEnergySpectrum(
    configuration=molecule_configuration,
    energy_zero_parameter=AbsoluteEnergy,
    projection_list=ProjectionList(elements=[Hydrogen], angular_momenta=[0, 1, 2, 3])
    )
nlsave('C:/ATK/ATKstudy/Hydrogen_MO_1.nc', molecular_energy_spectrum)
nlprint(molecular_energy_spectrum)

4

Installation and License Questions / Version confilict 12.2&12.8

« on: April 3, 2014, 01:46 »

Got some problems of using different versions of ATK.
I use both desktop and server to do calculation.
The atk installed on my desktop is 12.8 and 13.8 and the atk on the server is 12.2,12.8 and 13.8.
Usually I use command "atkpython *** " to set up calculation on server.
However, the server will defaultly use 12.2 atkpython to calculate which causes some problem.

I used my desktop to calculate Dos and Transmission Spectra with atk 12.8.
Then I want to use the calculated .nc file to calculate the IV curve.
It seems atk 12.2 can not read the 12.8 nc file properly.
--------------------------------------------------------------------------------------------------------------------
First error message:
I use command "atkpython **.py" to setup calculation, the server returns the error message
*******************************************************************************************
psTraceback (most recent call last):
  File "EH-IV-setup.py", line 2, in <module>
    device_configuration = nlread("/storage2/beta/users/lmj/ATK/EH-DosTs.nc",DeviceConfiguration)[0]
  File "./zipdir/NL/IO/NLSaveUtilities.py", line 256, in nlread
NL.ComputerScienceUtilities.Exceptions.NLValueError: This version has no support for reading netcdf files from ATK 12.8.0
*******************************************************************************************

So I try the method to read and rewrite the nc file by atk 12.2

Code

objects = nlread("EH-DosTs.nc")  
for x in objects:  
    nlsave("EH-DosTs(new).nc", x)  

It turns out the ATK 12.2 can't read the nc file created by 12.8
*******************************************************************************************
Traceback (most recent call last):
  File "SavenewNC.py", line 1, in <module>
    objects = nlread("EH-DosTs.nc")
  File "./zipdir/NL/IO/NLSaveUtilities.py", line 256, in nlread
NL.ComputerScienceUtilities.Exceptions.NLValueError: This version has no support for reading netcdf files from ATK 12.8.0
*******************************************************************************************

So I use the 12.8 "atkpython" to execute the calculation by "/usr/local/QuantumWise/atk-12.8.2/atkpython/bin/atkpython **.py"
However, it still returns some problems after calculate for sometimes(error returns in about 0.5hr~1hr after calculation started)
*******************************************************************************************
/usr/local/QuantumWise/atk-12.8.2/atkpython/bin/atkpython: line 7: 73174 Segmentation fault      (core dumped) $EXEC_DIR/atkpython_exec $*
[1]    Exit 139     
*******************************************************************************************

How should I fix the problem?
If you need the future information, let me know.

5

Scripts, Tutorials and Applications / Re: Error in open Transmission spectrum results

« on: March 5, 2014, 04:21 »

We would need to investigate the file. It's possible it was computed with an older version of ATK that is no longer compatible (and by that I would mean very old). Or, it could have been produced with a beta-version of some recent ATK version, in which case the file may not be readable.

Thanks for the reply. I checked the ATK version on the server. It is very old, like 12.2.1. So I have to switch back to the 12.8.2. It seems this problem doesn't happen in 12.8.2.

6

Scripts, Tutorials and Applications / Error in open Transmission spectrum results

« on: March 4, 2014, 02:13 »

Problem: VNL can not open transmission spectrum
Detail: The transmission spectrum is calculated on a server and then copied to the laptop to do analysis.
At first, the transmission spectrum can be opened. But problem occurs after some operation such as use transmission spectrum to generate the I/V.
After the operation, when click the Transmission Spectrum, an error dialog will pop out and referring:
"An error occurred
The following error was generated during execution of the program:
'energy_zero_parameter'
If the message is not clear or the error is caused by VNL itself, please report the issue to QuantumWise, and make sure to include the traceback (click "Show Details...") and the script.''
How do I fix this?
Let me know if you need any further information.
(PS: 1. The problem only occurs on the calculation results copied from server. No errors for the local calculated results.
       2. No issues in the calculation process.
       3. Both the calculations (server and desktop) use the same script to calculate transmission spectrum.)
======================================================================================================
Traceback (most recent call last):
  File ".\zipdir\NL\GUI\MainWindow\LabFloor\LabFloorModel.py", line 201, in load
  File "C:\Program Files (x86)\QuantumWise\atk-13.8.1\vnl\Lib\site-packages\AddOns\ATKNCImporter\ATKNCImporter.py", line 138, in load
    return nlread(filename, object_id=object_id, read_state=False)[0]
  File ".\zipdir\NL\IO\NLSaveUtilities.py", line 358, in nlread
  File ".\zipdir\NL\ComputerScienceUtilities\Timer.py", line 45, in __call__
  File ".\zipdir\NL\IO\NLSaveUtilities.py", line 358, in <lambda>
  File ".\zipdir\NL\Analysis\TransmissionSpectrum.py", line 810, in nlreadTransmissionSpectrum
KeyError: 'energy_zero_parameter'