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Topics - ams_nanolab

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31
General Questions and Answers / New TB set for black Phosphorous
« on: November 15, 2016, 18:37 »
Hi,
Could you add this recent published tight-binding parameters for black Phosphorous to your database (A. N. Rudenko and M. I. Katsnelson Phys. Rev. B 89, 201408(R))? or maybe just help in conversion to appropriate file format , for the "user defined" SK sets  ;D

https://arxiv.org/pdf/1404.0618.pdf

Final published paper

http://journals.aps.org/prb/abstract/10.1103/PhysRevB.89.201408

32
General Questions and Answers / Eelctron Localization function and electron density
« on: October 25, 2016, 20:59 »
How are the electron localization function and the electron density calculated in ATK fundamentally different? And what more information may be derived from the electrostatic difference potential as compared to the electron difference density?

33
General Questions and Answers / LDOS colormap plots
« on: October 20, 2016, 12:39 »
Is it possible to plot device LDOS like the ones shown in

http://www2.kobe-u.ac.jp/~lerl2/j_research01.html

with ATK? If not could you kindly develop a script for same.

34
General Questions and Answers / Nanotube workfunction
« on: October 19, 2016, 13:43 »
How to simulate workfunction of a CNT using quantumwise?

35
General Questions and Answers / Visualize vdW forces
« on: September 29, 2016, 13:08 »
Is it possible to see the van der waals component of forces between different layers of a stacked structure ?

36
General Questions and Answers / Superpose structures in viewer
« on: September 28, 2016, 13:55 »
Is it possible to superpose to structures in one viewer window? E.g. I have a strained and unstrained MoS2 unit cell and want to show superimposed image? Drag and drop is not working, and just updating the structure to the latest (last one dropped).

37
General Questions and Answers / Cutoff energy and suprecell size
« on: September 1, 2016, 12:59 »
We know a bigger suprecell has higher total energy but from an simulation accuracy point of view how to estimate the correct cutoff energy to simulate large suprecells? What is the correlation between the cut-off energy used in calculations and the size of the suprecell.

38
General Questions and Answers / Error running script
« on: August 30, 2016, 14:42 »
I have some scripts which I have written in VNL -GUI 2016, but while running them in ATK 2015.1 we get the error


+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 2015.1 [Build 5b36b25]                                     |
|                                                                              |
+------------------------------------------------------------------------------+
Traceback (most recent call last):
  File "/root/Desktop/analysis.py", line 127, in <module>
    k_point_sampling=k_point_sampling,
  File "./zipdir/NL/Calculators/GenericParameters/NumericalAccuracyParameters.py", line 99, in __init__
  File "./zipdir/NL/Calculators/GenericParameters/NumericalAccuracyParameters.py", line 276, in setAndCheckKPointSampling
NL.ComputerScienceUtilities.Exceptions.NLValueError: The parameter k_point_sampling, must be a sequence of three positive integers - e.g. (3,2,7)
Traceback (most recent call last):
  File "/root/Desktop/analysis.py", line 127, in <module>
    k_point_sampling=k_point_sampling,
  File "./zipdir/NL/Calculators/GenericParameters/NumericalAccuracyParameters.py", line 99, in __init__
  File "./zipdir/NL/Calculators/GenericParameters/NumericalAccuracyParameters.py", line 276, in setAndCheckKPointSampling
NL.ComputerScienceUtilities.Exceptions.NLValueError: The parameter k_point_sampling, must be a sequence of three positive integers - e.g. (3,2,7)

Timing:                          Total     Per Step        %

--------------------------------------------------------------------------------

Loading Modules + MPI   :       4.84 s       4.84 s      93.95% |=============|
--------------------------------------------------------------------------------
Total                   :       5.15 s

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 6515 RUNNING AT localhost.localdomain
=   EXIT CODE: 1
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================

39
General Questions and Answers / Control over export options
« on: August 26, 2016, 10:48 »
Hello, I want to export a graphene.py file structure into graphene.xyz  but only in the cartesian co-rodinates as the .xyz output file.

original structure in .py
=========================
# Set up lattice
lattice = Hexagonal(2.4612*Angstrom, 6.709*Angstrom)

# Define elements
elements = [Carbon, Carbon]

# Define coordinates
fractional_coordinates = [[ 0.333333333333,  0.166666666667,  0.5           ],
                          [ 0.666666666667,  0.833333333333,  0.5           ]]

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )
-----------------------------

Export as .xyz
==============

2
Bulk
C     6.153000e-01 -3.552436e-01  3.354500e+00    0.33333  0.16667  0.50000
C     1.845900e+00  3.552436e-01  3.354500e+00    0.66667  0.83333  0.50000

----------------------------------------

what I really want is : something like this

2

C     6.153000e-01 -3.552436e-01  3.354500e+00   
C     1.845900e+00  3.552436e-01  3.354500e+00   

===============================

how can it be done? For graphene it's simple to just edit the text but for larger structures doing by hand is difficult.


40
General Questions and Answers / EDD EDP ELF references
« on: August 1, 2016, 14:27 »
Could you give me some references / links to papers regarding electron difference density (EDD) , electrostatic difference potential (EDP), electron localization function (ELF) and how it is calculated in ATK ? The descriptions in

http://www.quantumwise.com/documents/manuals/ATK-2014/ReferenceManual/index.html/ref.electrondifferencedensity.html
https://quantumwise.com/documents/tutorials/latest/GrapheneBloch/index.html/electrondensity.spin.html
and the discussion thread http://quantumwise.com/forum/index.php?topic=2283.0

give some information but I need more details.

41
General Questions and Answers / Multi-core support serial license
« on: July 24, 2016, 09:43 »
If I have a serial license for ATK and try to run on a system with multi-core (say Intel i7) processor, will the serial job be threaded into parallel processes? Or do I must have parallel license?

42
Links to Resources and Publications / QuantumATK hands on
« on: July 22, 2016, 14:25 »
Will it be possible to arrange webcast of ATK events for overseas users specially those in other continents?

43
General Questions and Answers / Surface plots
« on: July 17, 2016, 14:28 »
Will ATK 2016 have 3D surface plots for bandstructures? Like ones used to show the mexican hat in graphene?

44
Future Releases / QMC
« on: July 17, 2016, 14:25 »
Is it possible in future to have Quantum Monte-Carlo implemented in ATK?

45
General Questions and Answers / Supercell energies
« on: July 17, 2016, 14:09 »
I have a basic question, I have two large supercells (same materials, slightly different configuration) showing total energies -97430.8445 and -97430.8925 eV. What does such a large value physically mean?  :o And from this what can I gather about the stability of the two systems?

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