1246
General Questions and Answers / Re: problem with plotting bandstructure
« on: September 24, 2016, 21:31 »
Could you describe your problem in more detail?
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1247
General Questions and Answers / Re: Simulation of Photovoltaic Cell | Quantum Dots
« on: September 24, 2016, 21:24 »
It really depends on what you mean by saying "simulate the cell". What kind of PV cells are you working on? How large is the corresponding device structure of your interest? Do you want to simulate a part of the device or the entire device?
1248
General Questions and Answers / Re: How to analyze a Optical Spectrum graph?
« on: September 24, 2016, 21:06 »
What exactly do you mean by saying "how to analyze ..."? The ATK optical spectrum analysis gives you the dielectric function on the graph enclosed. It is up to you to decide on what is to be done with this function, and how to interpret the results. I guess it depends on the goal of your research study.
1249
General Questions and Answers / Re: orbital resolved band structure calculation
« on: September 5, 2016, 10:12 »
You can calculate density-of-states, and then plot it for each orbital type as discussed in the Additional analysis section in the tutorial on the band structure calculation, see http://docs.quantumwise.com/tutorials/intro_vnl_atk1/intro_vnl_atk1.html?highlight=density%20states .
1250
General Questions and Answers / Re: Opening a band gap in silicene in C direction
« on: September 5, 2016, 09:18 »
You have to swap axes to make your transport C-direction in-plane, see the following tutorial http://docs.quantumwise.com/tutorials/transmission_gr_mos2/transmission_gr_mos2.html?highlight=graphene.
1251
General Questions and Answers / Re: non magnetic device in LSDA
« on: September 2, 2016, 20:48 »
There are several things that I would suggest to modify in your script.
- The extensions of your device structure appear to be small and need to be enlarged, especially for the left electrode. I enclose an image showing what the structure should look like in a decent setup. In general, there must be a sufficient amount of buffer layers between the actual semi-infinite left (right) electrode and the central region, see http://docs.quantumwise.com/tutorials/atk_transport_calculations/atk_transport_calculations.html?highlight=atk%20transport.
- In the present script, you have the k-point mesh (6,6,10) and (6,6,1) for the left and right electrode, respectively. The k-point mesh should be consistent for the left and right Pd electrodes, e.g., set it to k_point_sampling=(6, 6, 101). You need a lot of k-points in the transport direction to properly match the Fermi level in the electrodes and central region, see http://docs.quantumwise.com/tutorials/transport_kpoints/transport_kpoints.html?highlight=why%20point .
- The electron temperature might need to be increased to something like 1200 K (which corresponds to broadening of ~0.1 eV) since the system is metallic, see http://docs.quantumwise.com/tutorials/fe_mgo_fe/fe_mgo_fe.html?highlight=initial%20state
In addition, I would suggest first doing geometry optimization for the corresponding slab structure, allowing Co and some neighboring Pd atoms/layers to relax and setting constraints for all the other atoms, e.g., see the tutotial http://docs.quantumwise.com/tutorials/geometry_optimization/geometry_optimization.html?highlight=geometry%20optimization on rigid and fixed constraint options. This will also allow you optimizing the separation distance between the electrodes.
You will then have a good initial structure for device calculation, and perhaps not even need to do geometry optimization for the device configuration afterwards. But you may do it indeed, if needed. To optimize the structure, you may just do it with LDA, this will save you the computational time.
- The extensions of your device structure appear to be small and need to be enlarged, especially for the left electrode. I enclose an image showing what the structure should look like in a decent setup. In general, there must be a sufficient amount of buffer layers between the actual semi-infinite left (right) electrode and the central region, see http://docs.quantumwise.com/tutorials/atk_transport_calculations/atk_transport_calculations.html?highlight=atk%20transport.
- In the present script, you have the k-point mesh (6,6,10) and (6,6,1) for the left and right electrode, respectively. The k-point mesh should be consistent for the left and right Pd electrodes, e.g., set it to k_point_sampling=(6, 6, 101). You need a lot of k-points in the transport direction to properly match the Fermi level in the electrodes and central region, see http://docs.quantumwise.com/tutorials/transport_kpoints/transport_kpoints.html?highlight=why%20point .
- The electron temperature might need to be increased to something like 1200 K (which corresponds to broadening of ~0.1 eV) since the system is metallic, see http://docs.quantumwise.com/tutorials/fe_mgo_fe/fe_mgo_fe.html?highlight=initial%20state
In addition, I would suggest first doing geometry optimization for the corresponding slab structure, allowing Co and some neighboring Pd atoms/layers to relax and setting constraints for all the other atoms, e.g., see the tutotial http://docs.quantumwise.com/tutorials/geometry_optimization/geometry_optimization.html?highlight=geometry%20optimization on rigid and fixed constraint options. This will also allow you optimizing the separation distance between the electrodes.
You will then have a good initial structure for device calculation, and perhaps not even need to do geometry optimization for the device configuration afterwards. But you may do it indeed, if needed. To optimize the structure, you may just do it with LDA, this will save you the computational time.
1252
General Questions and Answers / Re: non magnetic device in LSDA
« on: September 2, 2016, 14:12 »
Seeing the actual script and log-file would be of help in understanding the issue.
1253
General Questions and Answers / Re: non magnetic device in LSDA
« on: September 2, 2016, 09:57 »
What kind of system are you studying? It is possible to have local magnetization in non-magnetic materials with defects or some other kind of spacial inhomogeneity. But one should keep in mind that this might also be an artifact of the particular density functional chosen for the DFT calculation.
Could you supply your python script and output log-file?
Could you supply your python script and output log-file?
1254
General Questions and Answers / Re: spin density + atomic structure
« on: August 31, 2016, 15:50 »
You can do it in the Viewer. You may open the spin density in the Viewer first, and then drag-and-drop your atomic structure (gID000) from the LabFloor onto the Viewer.
1255
General Questions and Answers / Re: mos2 FET
« on: August 30, 2016, 09:43 »
Please go through the second example on MoS2 in the tutorial http://docs.quantumwise.com/tutorials/transmission_gr_mos2/transmission_gr_mos2.html?highlight=mos2. You may adopt the bulk MoS2 structure from the Database, and then modify it in the Builder.
- Locate molybdenite in the crystal database and add it to the stash.
- Remove one layer, leaving only 3 atoms in the unit cell.
- Then perform the same transformation to the orthorhombic structure as for graphene above.
- As an additional step, open Coordinate Tools>Center and center the atoms in all directions.
- Locate molybdenite in the crystal database and add it to the stash.
- Remove one layer, leaving only 3 atoms in the unit cell.
- Then perform the same transformation to the orthorhombic structure as for graphene above.
- As an additional step, open Coordinate Tools>Center and center the atoms in all directions.
1256
General Questions and Answers / Re: Control over export options
« on: August 26, 2016, 16:13 »
You can erase the fractional coordinates in a 'filename.xyz' with the script enclosed.
$ python convert.py filename.xyz > filename_new.xyz
or
$ atkpython convert.py filename.xyz > filename_new.xyz
The new file contains the atomic coordinates in Cartesian only.
$ python convert.py filename.xyz > filename_new.xyz
or
$ atkpython convert.py filename.xyz > filename_new.xyz
The new file contains the atomic coordinates in Cartesian only.
1257
General Questions and Answers / Re: mos2 FET
« on: August 26, 2016, 15:04 »
You may take a look at the following two tutorials, http://docs.quantumwise.com/tutorials/vnl_graphene_transistor/vnl_graphene_transistor.html?highlight=transistor
http://docs.quantumwise.com/tutorials/transmission_gr_mos2/transmission_gr_mos2.html?highlight=mos2.
http://docs.quantumwise.com/tutorials/transmission_gr_mos2/transmission_gr_mos2.html?highlight=mos2.
1258
General Questions and Answers / Re: E_in-plane
« on: August 16, 2016, 15:04 »what did you mean by saying " take into account the contribution of atomic relaxation to the stress on the strained cell" ?!!
How it is different from the case... where I opt for the "Optimization=None" (I'm talking about the 2nd round of optimization) ??
Applying general stress to a solid deforms the shape and volume of its unit cell. Consequently, the atoms in the deformed unit cell may or may not be at their equilibrium positions anymore, even so they were at equilibrium positions in the original unit cell before stress application. So, the atoms are to be allowed to relax to their equilibrium positions in the deformed unit cell. This is why one has to do a second geometry optimization for atoms only, keeping the shape and volume of the deformed unit cell fixed indeed.
1259
General Questions and Answers / Re: SRH recomb.
« on: August 16, 2016, 10:48 »
The SRH recombination is trap-assisted recombination, so that there will be no SRH recombination in layered semiconductor materials if there are no defect levels in the mid-gap of the semiconductor. So, you first need to identify what is the recombination mechanism in your system to figure out the actual 'entity' that might be calculated from ground state DFT to be then used for the recombination problem.
1260
General Questions and Answers / Re: Optimize Geometry
« on: August 16, 2016, 01:07 »
I guess the structural relaxation is relatively minor for your system of study to see atom displacements clearly in the Viewer or Movie Tool for the corresponding trajectory, '4opti.nc'. You may look through the '4optimizecalculationanatase.log' file to see how the structure evolves during geometry optimization, or use Text Representation for two objects of '4optimizecalculationanatase.nc' on the Lab Floor. The objects with gID000 and gID001 should contain the initial (before relaxation) and final (after relaxation) structures, respectively.