Messages

106

General Questions and Answers / Re: Counterpoise correction

« on: August 4, 2017, 10:42 »

Hi,

by "initial self-consistent field calculation", do you mean the geometry optimization?

You can check this tutorial for a detailed explanation of how the counterpoise correction works in ATK:

http://docs.quantumwise.com/tutorials/dispersion_corrections_and_bsse/dispersion_corrections_and_bsse.html

Regards,
Daniele,

107

General Questions and Answers / Re: Grephene and Mos2 Phonon vibration mode

« on: August 3, 2017, 12:17 »

As Jess Wellendorf mentioned in other forum posts, we would certainly like to help you in reproducing that paper, but truth is we don not have the scripts you ask for. I suggest you contact the correpsonding author on the paper, Tue Gunst (tue.gunst@nanotech.dtu.dk)

Regards,

Daniele.

108

General Questions and Answers / Re: Grain Boundaries

« on: August 1, 2017, 16:00 »

Dear Eric,

the interface builder does not take into account the atomistic details of the interface, but work by matching the two surface cells by rotating and straining them. In this sense, the interface cell for a Sigma3 boundary is the same as that for the pristine materials, since the cells of both surfaces are not strained and are rotated by a multiple of 60 degrees.
The only way to create a Sigma3 boundary with the interface builder would be to create two surfaces which are one the mirror image of the other, and then match them together. You can use the 'Mirror' plugin for that: Coordinate Tools -> Mirror.
To remove overlapping atom, you can use the 'Close Neighbors' plugin: Selectron Tools -> Close Neighbors

Regarding the second question, what do you mean by "a portion of the GB"? If you want to move only selected atoms, this can be done during the setup of the phonon calculation.

Regards,
Daniele.

109

General Questions and Answers / Re: Grephene and Mos2 Phonon vibration mode

« on: August 1, 2017, 09:19 »

Hi,

I think your calculations are correct. In the case of graphene, the two modes you visualize are linear combinations of the LO and TO normal modes. These two modes can form linear combinations since they are iso-energetic at the Gamma-point.

To obtain the "conventional" normal modes, shown in PRB 93, 035414 (2016), you simply have to modify the atomic positions of the graphene atoms as shown in the attached script. Calculating the phonons with this geometry will result in normal modes which are similar to those show in Fig. 4(c) and Fig. 4(d) of the paper.

Regards,
Daniele. 

110

General Questions and Answers / Re: question on validation

« on: July 20, 2017, 09:45 »

I think this is more a scientific discussion rather than a discussion on ATK and its usage, so this might not be the appropriate forum to ask.

What I read from the sentence above, is that the question on whether the approximation is valid or not depends on the length of the CNT system. The approximation should be valid for frequencies up to 1 eV for CNT systems up 1 micrometer.

111

General Questions and Answers / Re: difference in current value of IV plot and Transmission Analyzer

« on: July 20, 2017, 09:01 »

Hi,

We will be happy to help, but I guess that also the answer is still the same: "please provide an ATK script that reproduces the problem. Thanks!"

Regards,
Daniele.

112

General Questions and Answers / Re: Are there any questions in this py files?

« on: July 19, 2017, 14:58 »

It is just that in Python one can choose to read a list from the beginning, or from the end 

('BN-AP-0.3.nc', DeviceConfiguration)[0] : if you have N DeviceConfiguration objects, it takes the first one (with index = 0)
('BN-AP-0.3.nc', DeviceConfiguration)[-1] : if you have N DeviceConfiguration objects, it takes the last one (with index = N-1)

113

General Questions and Answers / Re: question on validation

« on: July 19, 2017, 14:39 »

Hi Rose,

As mentioned in the paper from which the model is taken (PRB 81, 115448 (2010)):

"Here, “low-frequency” means that omega is much smaller than an inverse of dwell time d−1 that an electron stays inside the central device region of a
SWNT. For example, such a low-frequency regime is estimated as omega<1 THz for 1-microm-length metallic SWNTs."

Regards,
Daniele.

114

General Questions and Answers / Re: Extract data from Optical spectrum Analyzer

« on: July 17, 2017, 17:17 »

http://docs.quantumwise.com/tutorials/optical/optical.html

115

General Questions and Answers / Re: Are there any questions in this py files?

« on: July 13, 2017, 16:33 »

I do not think it is necessary to set again the initial spin, unless you want to change both the initial spin and the voltage at the same time (which is something I strongly discourage).

If your target is to restart a calculation from a previously converged DeviceConfiguration and change the bias voltage, the script can be as simple as:

bias = 0.5*Volt
device_configuration = nlread('BN-AP-0.3.nc', DeviceConfiguration)[-1]
calculator = device_configuration.calculator()
calculator=calculator(electrode_voltages=(bias/2, -bias/2))
device_configuration.setCalculator(
      calculator(),
      initial_state=device_configuration)
device_configuration.update()
nlsave('output.nc', device_configuration)

116

General Questions and Answers / Re: Young's Modulus of a bulk material

« on: July 13, 2017, 12:51 »

Here are some relevant reference on the calculation of stress and related quantities:

O. H. Nielsen and Richard M. Martin "First-Principles Calculation of Stress" Phys. Rev. Lett. 50, 697
O. H. Nielsen and Richard M. Martin "Quantum-mechanical theory of stress and force" Phys. Rev. B 32, 3780

http://docs.quantumwise.com/tutorials/elastic_constants/elastic_constants.html

117

General Questions and Answers / Re: electron-phonon interaction in two probe system

« on: June 27, 2017, 09:02 »

Hello,

- the IETS should be symmetric, so the modes at negative bias are the same as those at positive bias. Notice that the IETS is the normalized second derivative of the transmission spectrum, hence it is not required to have values between 0 and 1.

- The fact that you get an asymmetric IETS could indicate that the system is not converged, however, I cannot say anything more, without looking at the actual scripts.

- I suggest you to read the papers about the underlying methodology to the IETS calculations, which will help you in understand how the spectra should be understood and analysed:
https://journals.aps.org/prb/abstract/10.1103/PhysRevB.75.205413

- Regarding the thermoelectric transport properties, if I understood your question correctly, T should be the temperature which enters the the formula of the thermoelectric figure of merit: http://docs.quantumwise.com/tutorials/phonon_calcs/phonon_calcs.html

Regards,
Daniele.

118

General Questions and Answers / Re: something wrong with the "viewer" plug-in？

« on: June 19, 2017, 13:13 »

Hi,

I can reproduce it, the bug appears only in the Windows version. I will post a bug about it.

Regards,
Daniele

119

General Questions and Answers / Re: On Fermi Level

« on: June 19, 2017, 09:53 »

Hi Rose,

for semiconductors such as MoS2, the exact position of the chemical potential inside the gap is heavily dependent on the k-points sampling. If the Brillouin zone is undersampled, there will be an error in the position of the chemical potential, and  the system will appear as doped, even if the system is still charge neutral.

Regarding the doping method, the main difference between the two methods is that in the "Explicit charge" method the extra charge redistributes over the entire unit cell, whereas the "Atomic compensation charges" method allows to localize the extra charge in some specific region of your simulation cell. 

If you plan to study a transistor-like geometry of the type metal-semiconductor-metal, then the "Atomic compensation charges" is the method of choice, because it will allow you to dope the semiconductor without doping the metal, see for example: https://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.155302

If you just want to add an intrinsic doping to a bulk material, then I would use the "Explicit charge" method.

Regards,
Daniele.

120

General Questions and Answers / Re: something wrong with the "viewer" plug-in？

« on: June 16, 2017, 14:41 »

We have found that this should actually be a bug in the viewer, and a bug has been filed.
However, there should be a workaround for that: you should first change the fuzz factor, and then modify all the other quantities.