Messages

1231

General Questions and Answers / Re: script to calculates the absorption coefficient and refractive index from diele

« on: October 13, 2016, 08:27 »

What is .pf  file? I guess you need a python script. The script text is enclosed to the tutorial mentioned by Daniele in the section 'Optical spectrum'. You have to copy and paste the text in any text editor, and save it as filename.py. 

1232

General Questions and Answers / Re: electrical conductivity of metal-DNA for single nanowires?

« on: October 12, 2016, 09:44 »

Have a look at the tutorial, http://docs.quantumwise.com/tutorials/device_relaxation/device_relaxation.html, where the geometry optimization for a device configuration is discussed.

1233

General Questions and Answers / Re: Absorption Coeff.

« on: October 12, 2016, 08:17 »

To plot absorption coefficient vs energy, one should first calculate it, and this is what OpticalSpectrum analizer essentially does by calculating the imaginary part of the dielectric function related to the absorption coefficient, see http://docs.quantumwise.com/tutorials/optical/optical.html.

1234

General Questions and Answers / Re: xyz input and output files with VNL

« on: October 11, 2016, 14:22 »

When you import a XYZ file into VNL, you import it as a molecule configuration, i.e., there is not periodic box (periodic boundary conditions) assigned to it.

What you can do is to transform this "molecule" structure to bulk structure (i.e., you assign periodic boundary conditions to the structure with some default lattice parameters), using molecule to bulk plugin in the Builder, see 'Convert to bulk' at http://docs.quantumwise.com/tutorials/builder_manual/builder_plugins/builder_plugins.html.

Using Bulk Tools, you can then change the default lattice type and lattice parameters to the actual lattice type and lattice parameters of your bulk structure.   

After that, you must be able to use the Builder Tools, e.g., to repeat the structure.

1235

General Questions and Answers / Re: Optical Spectrum, Oscillator strength and Transition states.

« on: October 11, 2016, 13:40 »

Regarding #1, the oscillator strength is defined for an optical transition between two particular electronic states, see https://en.wikipedia.org/wiki/Oscillator_strength. The standard ATK output for the Optical Spectrum is the susceptibilty and dielectric tensor, given by the Kubo-Greenwood formula, see Notes in the reference manual   http://docs.quantumwise.com/manuals/Types/OpticalSpectrum/OpticalSpectrum.html?highlight=optical%20spectrum#NL.Analysis.OpticalSpectrum.OpticalSpectrum. The oscillator strength between state n and m is essentially given by the dipole matrix elements (pi_nm) in the Kubo-Greenwood formula.
 
Regarding #2, I would say it usually works other way. One first defines the transition of interest, i.e., state n and m, and then calculate the corresponding oscillator strength for that transition between these states. If the oscillator strength is zero, the optical transition is forbidden.  If you have a full dipole matrix, you may then identify those transitions (states) that are optically active, i.e., have non-zero oscillator strength. 
 
Regarding #3, HOMO and LUMO are just two states, and one may calculate the oscillator strength between HOMO and LUMO states, i.e., n=LUMO and m=HOMO.
 
The dipole matrix elements (oscillator strength) are not a part of basic output for Optical Spectrum analysis.

1236

General Questions and Answers / Re: Molecular orbital diagram

« on: October 11, 2016, 12:26 »

As a tip, I may say that according to this article https://en.wikipedia.org/wiki/Molecular_orbital_diagram, the MO diagram analysis is qualitative and mainly suited for very small structures/molecules.  Having 325 electrons seems to refer to a relatively large system.

1237

General Questions and Answers / Re: Intensity calculation

« on: October 11, 2016, 12:13 »

Do you want to calculate the Raman intensity (spectrum)?

1238

General Questions and Answers / Re: atomic relaxation problem

« on: October 6, 2016, 18:36 »

You may first try relaxing the structure without spin-polarization included, i.e., using GGA instead of SGGA, and then do geometry optimization with SGGA to refine the structure.

1239

General Questions and Answers / Re: Spin transmission spectrum messed up

« on: October 5, 2016, 19:07 »

What do you mean by "fake"? You have an individual transmission spectrum for each of the two spin channels. 

If your transmission spectrum depends on the tolerance parameter, it means that your calculation of the transmission curves is not converged yet. You have to decrease the tolerance parameter to the values for which this dependence virtually vanishes.

1240

General Questions and Answers / Re: K-poit selection

« on: October 5, 2016, 17:13 »

The vacuum separation layer can be increased by setting the lateral lattice parameters of the nanowire supercell to a larger value. Note that you should then keep atomic coordinates in Cartesian (not fractional) coordinates to avoid a change of atomic positions in the nanowire structure.   

1241

General Questions and Answers / Re: K-poit selection

« on: October 3, 2016, 09:12 »

The Cu2O nanowire is modeled with too little vacuum separation layer between the image cells. Before doing the k-point convergence test, I would do the convergence test for the separation distance  (it is now of 4.7 Angs only) as also suggested by Anders. Assuming a given number of k-points (e.g., 1x1x40), I would set the separation distance to 10 and 15 Angs to see if it makes any difference to the results.

As proposed by Daniele, this kind of tests can first be done for a non-spin-polarized system. 

1242

General Questions and Answers / Re: How to optimize AFM and FM materials?

« on: September 29, 2016, 09:49 »

As a general recommendation, it is not a bad idea of first doing non-spin polarized calculation for a spin-polarized system, and then use it for further spin-polarized calculations.

1243

General Questions and Answers / Re: harmonic and cubic force constants

« on: September 27, 2016, 10:01 »

In principle,  anharmonic interatomic force constants can be extracted from molecular dynamics (MD) simulations, e.g., take a look at the following papers http://iopscience.iop.org.globalproxy.cvt.dk/article/10.1088/0953-8984/26/22/225402/meta and http://journals.aps.org/prb/pdf/10.1103/PhysRevB.77.144112.

This extraction is not automatic in the VNL-ATK. You should first do DFT or classical MD calculations in ATK for the system of interest, and then follow the extraction procedure described in the references enclosed. For classical MD, you have to make sure that the classical potential you have adopted for MD accounts for anharmonic effects.

1244

Installation and License Questions / Re: Anyone having Gallium Nitride CIF file???Plz send me...

« on: September 26, 2016, 09:34 »

You can find it in the Database that is a part of VNL-ATK. In the Builder, click on Add -> From Database, search for GaN, double-click on GaN (hexagonal, wurtzite) in the search list to add it to Stash in the Builder.

To save it in the CIF format, you may right-click on the structure item in the Stash and export it as a CIF file.

1245

General Questions and Answers / Re: Simulation of Photovoltaic Cell | Quantum Dots

« on: September 26, 2016, 08:17 »

If you want to simulate the entire device of 2 microns, you need to use TCAD tools that are designed to study devices at the macroscopic level in the continuum approximation. VNL-ATK is meant for atomistic modeling of devices at the microscopic level. 

VNL-ATK can, however, be used to extract microscopic, material-specific parameters for TCAD models that adopt this kind of parameters as input. You may also construct and visualize a nanoscaled device in VNL-ATK, e.g., a quantum dot attached to electrodes, and then calculate IV characteristics or other properties of this kind of nanodevices.