76
General Questions and Answers / Re: Visualize vdW forces
« on: September 30, 2016, 09:45 »
Is it possible to at least plot the nature of the potential between two groups (layers) of atoms in a multi-layered structure?
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77
General Questions and Answers / Re: Visualize vdW forces
« on: September 29, 2016, 15:09 »
Yes, DFT-D2 for example.
78
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 ?
79
General Questions and Answers / Re: Superpose structures in viewer
« on: September 28, 2016, 15:29 »
Thanks, its a nice workaround. 
80
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).
81
General Questions and Answers / Re: Cutoff energy and suprecell size
« on: September 1, 2016, 14:22 »
Yes it was the mesch cutoff energy, thanks.
82
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.
83
General Questions and Answers / Re: Error running script
« on: August 31, 2016, 10:30 »
Okay, I thought so. Thanks for the tip.
84
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
===================================================================================
+------------------------------------------------------------------------------+
| |
| 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
===================================================================================
85
General Questions and Answers / Re: Control over export options
« on: August 30, 2016, 14:37 »
Thanks
86
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.
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.
87
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.
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.
88
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?
89
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?
90
General Questions and Answers / Re: Surface plots
« on: July 22, 2016, 14:15 »
Something like this.