901
General Questions and Answers / Re: Error with multigrid residual
« on: June 1, 2015, 08:15 »
We will probably need to see the script you are running before we can give you advice on this.
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902
General Questions and Answers / Re: Discrepency in Effective mass calculation
« on: May 29, 2015, 08:29 »
FHI-DZP and OMX tier0 and tier1 basis sets seem to agree pretty well wrt. the curvatures for InAS.
903
General Questions and Answers / Re: Discrepency in Effective mass calculation
« on: May 28, 2015, 16:41 »
Hi,
1) I ran your script and find that both of the methods that you list (effective mass analysis object vs. effective mass from the band structure analysis tool) gives identical effective masses (1.827 and 0.121). Perhaps you did not specify the correct directions in method 2?
2) The values you mention for comparison (0.64 and 0.05) appear to be experimental values. It is very hard for theory to get the X and L valleys correct wrt. to experiments. Even though you fit the TB09LDA c-parameter to experimental Gamma-point band gaps and/or effective mass, the same quantities in the X and L points are not guaranteed to be correct. According to https://engineering.purdue.edu/gekcogrp/publications/pubs_src/DOC119_e125207.pdf, the target theoretical value of the longitudinal effective mass at L is 1.90, which is not much different than the 1.83 you find with ATK.
1) I ran your script and find that both of the methods that you list (effective mass analysis object vs. effective mass from the band structure analysis tool) gives identical effective masses (1.827 and 0.121). Perhaps you did not specify the correct directions in method 2?
2) The values you mention for comparison (0.64 and 0.05) appear to be experimental values. It is very hard for theory to get the X and L valleys correct wrt. to experiments. Even though you fit the TB09LDA c-parameter to experimental Gamma-point band gaps and/or effective mass, the same quantities in the X and L points are not guaranteed to be correct. According to https://engineering.purdue.edu/gekcogrp/publications/pubs_src/DOC119_e125207.pdf, the target theoretical value of the longitudinal effective mass at L is 1.90, which is not much different than the 1.83 you find with ATK.
904
General Questions and Answers / Re: distance optimization/ optimized struct.
« on: May 28, 2015, 11:03 »
Thank you for the script.
To answer your questions:
- 1) There are no options for fixing the graphene interlayer-distance through the Script Generator. However, I think there is no reason to expect that the in-plane lattice constant of graphene will change when constructing the graphene dimer. Therefore, it should suffice to:
a) geometry optimize a single graphene layer (i.e. determine the equilibrium lattice constant of graphene).
b) fix that lattice constant while varying the graphene-graphene distance and determine the minimum-energy distance.
- 2) I have verified that fixing the unit cell Z-component during stress minimization does not work when using the DFT-D2 method. This is a bug and will be taken care of real soon. However, if using the method outlined above, this should really not worry you.
Two further comments:
- You really only need two carbon atoms in a hexagonal unit cell to represent graphene (Builder -> Add --> From database --> Graphene [try also Graphite]). This will reduce the number of carbon atoms from 36 to 4 for your dimer, and significantly speed up your calculations!
- For your information, ATK 2015 will implement the DFT-D3 method, the latest (and probably final) version of the Grimme dispersion corrections. Might be worth a try
To answer your questions:
- 1) There are no options for fixing the graphene interlayer-distance through the Script Generator. However, I think there is no reason to expect that the in-plane lattice constant of graphene will change when constructing the graphene dimer. Therefore, it should suffice to:
a) geometry optimize a single graphene layer (i.e. determine the equilibrium lattice constant of graphene).
b) fix that lattice constant while varying the graphene-graphene distance and determine the minimum-energy distance.
- 2) I have verified that fixing the unit cell Z-component during stress minimization does not work when using the DFT-D2 method. This is a bug and will be taken care of real soon. However, if using the method outlined above, this should really not worry you.
Two further comments:
- You really only need two carbon atoms in a hexagonal unit cell to represent graphene (Builder -> Add --> From database --> Graphene [try also Graphite]). This will reduce the number of carbon atoms from 36 to 4 for your dimer, and significantly speed up your calculations!
- For your information, ATK 2015 will implement the DFT-D3 method, the latest (and probably final) version of the Grimme dispersion corrections. Might be worth a try
905
General Questions and Answers / Re: optimisation taking alot of time
« on: May 28, 2015, 08:52 »
Hi.
In general, it is impossible to say exactly how long time a geometry optimization will take, especially for large structures with many degrees of freedom. But you can look at the calculation output to see if the optimization is proceeding as expected (forces get smaller) and to estimate how many more optimization steps are needed. Simply look for the string "Forces step" in the ATK output.
In general, it is impossible to say exactly how long time a geometry optimization will take, especially for large structures with many degrees of freedom. But you can look at the calculation output to see if the optimization is proceeding as expected (forces get smaller) and to estimate how many more optimization steps are needed. Simply look for the string "Forces step" in the ATK output.
906
General Questions and Answers / Re: spin-dependent Seeback coefficients
« on: May 27, 2015, 15:55 »
Q1
OK, I agree that the script I made does not quite cut it.
So I had a closer look at the theory of calculating the Seebeck coefficient (http://arxiv.org/pdf/1107.5687.pdf, page 3, top part of left column), and realized I had made an error
This should be fixed in the attached script. My output from the carbon chain transmission spectrum is:
**********
spin=1 : Seebeck coefficient = -1.530e-06 V/K
spin=2 : Seebeck coefficient = +7.274e-10 V/K
total Seebeck coefficient = -1.529e-06 V/K
**********
The sum of the two spin contributions ("total") now matches the VNL result from the Thermoelectric Coefficients plugin.
Q2
For the IV curve plotting, I recommend you use the "IV-Generator" and "IV-Plot..." plugins (available in the right-hand panel next to LabFloor) instead of the Custom Analyzers.
Recipe:
Best,
Jess
OK, I agree that the script I made does not quite cut it.
So I had a closer look at the theory of calculating the Seebeck coefficient (http://arxiv.org/pdf/1107.5687.pdf, page 3, top part of left column), and realized I had made an error
This should be fixed in the attached script. My output from the carbon chain transmission spectrum is:
**********
spin=1 : Seebeck coefficient = -1.530e-06 V/K
spin=2 : Seebeck coefficient = +7.274e-10 V/K
total Seebeck coefficient = -1.529e-06 V/K
**********
The sum of the two spin contributions ("total") now matches the VNL result from the Thermoelectric Coefficients plugin.
Q2
For the IV curve plotting, I recommend you use the "IV-Generator" and "IV-Plot..." plugins (available in the right-hand panel next to LabFloor) instead of the Custom Analyzers.
Recipe:
- Highlight all your transmission spectra and use the IV-Generator to generate a single iv_curve.nc file.
- That file contains the I(V) object, which you can plot using the IV-Plot plugin.
- You can select which spin channels to see in the IV-Plot (Sum, Up, Down).
Best,
Jess
907
General Questions and Answers / Re: Optoelectronic device
« on: May 27, 2015, 09:24 »
Hi!
Yes, ATK can certainly be used for calculating optical properties of materials, particularly semiconductors. See for example our tutorial on calculating optical properties of silicon (http://quantumwise.com/documents/tutorials/latest/SiliconOptical/index.html/index.html). The tutorial shows how to use the OpticalSpectrum analysis object to calculate the real and imaginary parts of the dielectric constant, absorption coefficient, refractive index, etc.
Yes, ATK can certainly be used for calculating optical properties of materials, particularly semiconductors. See for example our tutorial on calculating optical properties of silicon (http://quantumwise.com/documents/tutorials/latest/SiliconOptical/index.html/index.html). The tutorial shows how to use the OpticalSpectrum analysis object to calculate the real and imaginary parts of the dielectric constant, absorption coefficient, refractive index, etc.
908
General Questions and Answers / Re: distance optimization/ optimized struct.
« on: May 26, 2015, 16:38 »
Dear Dipankar,
could you provide a python script with an example of what you are trying to achieve? I do not know what "the two layers" are...
could you provide a python script with an example of what you are trying to achieve? I do not know what "the two layers" are...
909
General Questions and Answers / Re: spin-dependent Seeback coefficients
« on: May 26, 2015, 10:55 »
Q1) The Thermoelectric Coefficients plugin gives you the average Seebeck coefficient (averaged over both spin channels). You therefore have the relation S = (S1+S2)/2.
Q2) To get the temperature dependence, the VNL plugin offers you the option of setting the temperature (300 K is default). You can do the same with the script: 300 K is default, but you can set the temperature like this:
*******
from NL.CommonConcepts.PhysicalQuantity import Kelvin
T = 400*Kelvin
S = evaluateThermoelectricTransportCoefficients(transmission_spectrum, spin, temperature=T)
*******
Q2) To get the temperature dependence, the VNL plugin offers you the option of setting the temperature (300 K is default). You can do the same with the script: 300 K is default, but you can set the temperature like this:
*******
from NL.CommonConcepts.PhysicalQuantity import Kelvin
T = 400*Kelvin
S = evaluateThermoelectricTransportCoefficients(transmission_spectrum, spin, temperature=T)
*******
910
General Questions and Answers / Re: Why a delocalized spin-up HOMO can not give rise to a strong spin-up transmisson
« on: May 26, 2015, 10:16 »
Where does the spin-down electron "go" in order to facilitate transmission? Perhaps the spin-up HOMO electron have nowhere to "go"?
911
General Questions and Answers / Re: spin-dependent Seeback coefficients
« on: May 25, 2015, 12:25 »
The attached script shows how one should be able to calculate the Seebeck coefficient for each spin channel. You'll need an nc-file containing the electronic TransmissionSpectrum. The script has been only moderately tested, but I think it should work.
912
General Questions and Answers / Re: Electron Density...
« on: May 22, 2015, 10:43 »
The plot shows that average electron density (in units of 1/Angstrom^3) projected along the C axis. Yes, the plot does not show a straight line, so the electron density is (of course) inhomogeneous when you "walk around" in the unit cell. A particular electron may or may not be regarded a "carrier", depends on whether it is far below the valence band or not in a band structure calculation...
913
General Questions and Answers / Re: How to get Contact Resistance in ATK
« on: May 21, 2015, 14:22 »
In order to get anywhere with this question, you should probably first define what you mean by "trans conductance", and then be very specific in your question. Makes it easier to help.
914
General Questions and Answers / Re: Vasp DOS in VNL
« on: May 21, 2015, 14:15 »
Hi Fernando,
unfortunately, it is currently not possible to shift the VASP DOS plot such that the Fermi energy is at 0 eV. But we will consider it a user request
What you can do is to export the DOS from the VNL 2D plot window (right click and choose export). This will give you a text file with energies in column 1 and DOS in column 2. The Fermi level is written at the end of the file, just below "# Constant line number 0". Then it should be easy to manually plot the shifted DOS.
unfortunately, it is currently not possible to shift the VASP DOS plot such that the Fermi energy is at 0 eV. But we will consider it a user request
What you can do is to export the DOS from the VNL 2D plot window (right click and choose export). This will give you a text file with energies in column 1 and DOS in column 2. The Fermi level is written at the end of the file, just below "# Constant line number 0". Then it should be easy to manually plot the shifted DOS.
915
General Questions and Answers / Re: convergence problem
« on: May 21, 2015, 10:02 »
ok, so you have increased the maximum number of SCF steps to 120. That's not really a big increase from 100.
I suggest you try lower the damping factor and increase the max_steps:
left_electrode_iteration_control_parameters = IterationControlParameters(
damping_factor=0.05,
max_steps=500,
)
I suggest you try lower the damping factor and increase the max_steps:
left_electrode_iteration_control_parameters = IterationControlParameters(
damping_factor=0.05,
max_steps=500,
)