451
General Questions and Answers / Re: Geometry Optimization
« on: February 27, 2014, 13:38 »
can you provide your python input script?
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452
General Questions and Answers / Re: Boundary conditions -reg
« on: February 27, 2014, 11:22 »
device: use FFT2D unless you have spatial regions, then Multigrid.
bulk: FFT unless it is charged. In that case you will need Multigrid
molecule: Multigrid, multipole
then there are some special cases that you may consider, see for example the slab calculations in this tutorial: Tuning the work function of silver by deposition of ultrathin oxide layers
bulk: FFT unless it is charged. In that case you will need Multigrid
molecule: Multigrid, multipole
then there are some special cases that you may consider, see for example the slab calculations in this tutorial: Tuning the work function of silver by deposition of ultrathin oxide layers
453
General Questions and Answers / Re: k point sampling-reg
« on: February 27, 2014, 09:07 »
150 to save some computational time.
454
General Questions and Answers / Re: optimization-reg
« on: February 27, 2014, 09:05 »
Very very shortly, in a MD you simulate the motion of the atoms in time at a finite temperature.
In a geometry optimization you will use the forces to minimize the total energy of your configuration and find the equilibrium geometry.
Please, take a look to any solid state book.
About the parameters, you can find all the available parameters for the two methods here:
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.optimizegeometry.html
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.moleculardynamics.html
About the Poisson solver the short answer is:
device: use FFT2D unless you have spatial regions, then Multigrid.
bulk: FFT unless it is charged. In that case you will need Multigrid
molecule: Multigrid, multipole
then there are some special cases that you may consider, see for example the slab calculations in this tutorial: Tuning the work function of silver by deposition of ultrathin oxide layers
In a geometry optimization you will use the forces to minimize the total energy of your configuration and find the equilibrium geometry.
Please, take a look to any solid state book.
About the parameters, you can find all the available parameters for the two methods here:
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.optimizegeometry.html
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.moleculardynamics.html
About the Poisson solver the short answer is:
device: use FFT2D unless you have spatial regions, then Multigrid.
bulk: FFT unless it is charged. In that case you will need Multigrid
molecule: Multigrid, multipole
then there are some special cases that you may consider, see for example the slab calculations in this tutorial: Tuning the work function of silver by deposition of ultrathin oxide layers
455
General Questions and Answers / Re: Boundary conditions of FFT2D Poisson solver
« on: February 26, 2014, 09:38 »
You are right, in a device configuration the Dirichlet boundary conditions are set for the C direction.
The boundary conditions that are printed in the script are the ones for the left and right electrodes and are set to periodic in all three directions.
Select "show default" in the Script detail window when you save the script and all the parameters, including the default ones, will be printed in the script.
including the Poisson solver for the device:
The boundary conditions that are printed in the script are the ones for the left and right electrodes and are set to periodic in all three directions.
Select "show default" in the Script detail window when you save the script and all the parameters, including the default ones, will be printed in the script.
including the Poisson solver for the device:
Code
device_poisson_solver = FastFourier2DSolver(
boundary_conditions=[[PeriodicBoundaryCondition,PeriodicBoundaryCondition],
[PeriodicBoundaryCondition,PeriodicBoundaryCondition],
[DirichletBoundaryCondition,DirichletBoundaryCondition]],
order=2
)456
General Questions and Answers / Re: Grid like metal structure
« on: February 25, 2014, 09:36 »
I see. I definitely did not get your question 
- you can import the conventional bulk structure (cubic) and repeat the structure nxnxn times.
Just enough to form a single repetition unit of your grid, not the whole structure.
- Select the atoms to delete by using the Select>By Expression tool and write something like "z>5 and z<15 and y>5 and y<15" to have channels perpendicular to the yz plane for example.
Also selecting the atoms with the mouse works well.
- delete those atoms.
- repeat the structure to form your grid.
about the interfacing, you should create an oxide slab with similar dimensions of your metal grid in the xy plane and then you can use the interface plugin.
if you do not need to adapt the two cells but only "deposit" the grid on an oxide layer then you can create an oxide layer which is bigger (in the xy plane) then the metal grid and simply drag and drop the metal grid from the Stash to the oxide layer configuration. Then translate it wherever you wish.
- you can import the conventional bulk structure (cubic) and repeat the structure nxnxn times.
Just enough to form a single repetition unit of your grid, not the whole structure.
- Select the atoms to delete by using the Select>By Expression tool and write something like "z>5 and z<15 and y>5 and y<15" to have channels perpendicular to the yz plane for example.
Also selecting the atoms with the mouse works well.
- delete those atoms.
- repeat the structure to form your grid.
about the interfacing, you should create an oxide slab with similar dimensions of your metal grid in the xy plane and then you can use the interface plugin.
if you do not need to adapt the two cells but only "deposit" the grid on an oxide layer then you can create an oxide layer which is bigger (in the xy plane) then the metal grid and simply drag and drop the metal grid from the Stash to the oxide layer configuration. Then translate it wherever you wish.
457
General Questions and Answers / Re: Grid like metal structure
« on: February 24, 2014, 09:14 »
1- yes, you can easily build a Ag/Au multilayer structure with the interface plugin, for example, with Ag or Au electrodes. (if this is what you mean with grid like structure)
2- when you build the structure you can define the interface distance. Select a good starting value, you can also check in the literature about that.
Check also the best match in terms of relative position along the xy- plane.
Finally, in a DeviceConfiguration geometry optimization uncheck the constrain cell along z to optimize the C vector and hence the interface distance.
2- when you build the structure you can define the interface distance. Select a good starting value, you can also check in the literature about that.
Check also the best match in terms of relative position along the xy- plane.
Finally, in a DeviceConfiguration geometry optimization uncheck the constrain cell along z to optimize the C vector and hence the interface distance.
458
General Questions and Answers / Re: armchair mos2 nanoribbon
« on: February 20, 2014, 09:27 »hi,
please explain how to change unit cell of mos2 to build armchair mos2 nanoribbon.
Follow this tutorial until point 5 to have a MoS2 monolayer:
http://quantumwise.com/support/tutorials/item/100-mos2-nanotubes
6. Open Bulk Tools>Repeat. repeat in A by N times to have the N-wide armchair nanoribbon.
7. increase the size of your cell along the A axis bi about 15-20 Å and center the coordinate Coordinate Tools>Center
8. "Bulk Tools>Swap Axes", click BC then YZ
9. have fun.
459
General Questions and Answers / Re: "PeriodicAtomConfiguration" error
« on: February 20, 2014, 09:05 »In the VNL 13.8, Is it still necessary to set these following parameters when I use a "New Calculator"?
type = DoubleZetaPolarized,
radial_sampling_dr = 0.001*Bohr,
energy_shift = 0.01*Rydberg,
delta_rinn = 0.8,
v0 = 40.0*Rydberg,
charge = 0.0,
split_norm = 0.15
They are the "basis set" parameters in VNL2008. I am not sure whether they are still the same default value in VNL13.8.
You can see all the available parameters and the default values used in the new version in the new Manual.
In particular, check:
http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.lcaocalculator.html
http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.basisset.html
and the specific links therein.
460
General Questions and Answers / Re: "PeriodicAtomConfiguration" error
« on: February 19, 2014, 09:36 »
You can import old scripts form VNL 2008 if you include these two lines at the beginning of your script (the new version will check for these two lines and recognize the file format):
Drag and Drop your file directly from the Project Files list to the Builder or Viewer.
You will see that it still not properly imported due to some particular keywords that are present in your script.
Still, you are able extract the three regions (device+electrodes) from the builder using the Split device tool, play around a bit and reconstruct your device.
Please, check the attachment.
Another solution is to simply open you old script and adapt your old TwoProbeConfiguration to the new DeviceConfiguration class following the Manual
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.deviceconfiguration.html
Code
from ATK.KohnSham import *
from ATK.TwoProbe import *Drag and Drop your file directly from the Project Files list to the Builder or Viewer.
You will see that it still not properly imported due to some particular keywords that are present in your script.
Still, you are able extract the three regions (device+electrodes) from the builder using the Split device tool, play around a bit and reconstruct your device.
Please, check the attachment.
Another solution is to simply open you old script and adapt your old TwoProbeConfiguration to the new DeviceConfiguration class following the Manual
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.deviceconfiguration.html
461
General Questions and Answers / Re: warning devide by zero
« on: February 18, 2014, 10:41 »
Indeed you get the warning message above. The warning is due to the fact that your first element in the energies array is 0 and you use it in the equation:
However, it is just a warning and you do get some results in the plot you posted at the beginning.
You are just plotting the data in the "wrong" range which is defined by the two lines in the refrac.py script (which was used to study the properties of Silicon):
you can comment the lines or choose to plot in a different range, for example:
Code
l = (speed_of_light*planck_constant/energies).inUnitsOf(nanoMeter)However, it is just a warning and you do get some results in the plot you posted at the beginning.
You are just plotting the data in the "wrong" range which is defined by the two lines in the refrac.py script (which was used to study the properties of Silicon):
Code
ax.axis([180,1000,2.2,6.4])
ax.axis([180,1000,0,0.24])you can comment the lines or choose to plot in a different range, for example:
Code
ax.axis([0,4000, 0.6,1.6])
ax.axis([0,4000, 0.,0.01])462
General Questions and Answers / Re: z-shaped capped junction device
« on: February 17, 2014, 16:33 »
cool system
First of all you have 1336 atoms overlapping. You can check if you have atoms that overlap from the Builder by clicking on Select>Close Neighbors and choose a very small threshold. Click on select and you will see them. Simply delete them, you may have mixed configurations while creating the junction.
Second, it looks like you have already performed some king of geometry optimization to ALL your atoms.
In doing that you have lost any periodicity close to the electrode regions. This is the reason the "device from bulk" plugin does not suggest you any electrode length.
You may want to perform the optimization only on a central region or build the device before.
First of all you have 1336 atoms overlapping. You can check if you have atoms that overlap from the Builder by clicking on Select>Close Neighbors and choose a very small threshold. Click on select and you will see them. Simply delete them, you may have mixed configurations while creating the junction.
Second, it looks like you have already performed some king of geometry optimization to ALL your atoms.
In doing that you have lost any periodicity close to the electrode regions. This is the reason the "device from bulk" plugin does not suggest you any electrode length.
You may want to perform the optimization only on a central region or build the device before.
463
News and Announcements / New mini-tutorial: tuning the work function of a metal surface...
« on: February 11, 2014, 18:16 »Check how you can easily build an oxide-metal interface with VNL
and calculate with ATK the work function change induced on the metal surface by the deposition of an ultra-thin oxide film:
Tuning the work function of silver by deposition of ultrathin oxide layers
464
General Questions and Answers / Re: doubt in relaxing the geometry
« on: February 6, 2014, 21:59 »Quote
In two probe system, when i tried to make Au electrode supercell from fcc structure, i got minima at 2.88 A.
Indeed the Au-Au distance from Au fcc imported from the database (I assume you imported from there) is 2.88Å.
You are not really clear about what you mean with "make Au electrode supercell".
Quote
When i use the electrode with 2.88 inter atomic distance, at the end of relaxation, i get Au-Au distance between 2.68 to 2.80.
Again, what is exactly your "electrode"? please provide more info, for example the script you use for the optimization.
Quote
Au-Au distance is not same for atoms. Is it possible or i m doing some mistakes in taking parameters to make the geometry??? How we can check feasibility of my system???
It could be that you are doing some mistake. Again, you should provide more info.
Although, it could also be that you have a surface and hence different Au-Au bond length.
465
General Questions and Answers / Re: Geometry optimization 3AGNR repeated 9 times in the z direction
« on: February 4, 2014, 15:34 »
Correct, as long as you do not chance the dimension of your device along the C direction you can keep the same k-points sampling in your project.