Messages

1261

General Questions and Answers / Re: Optimize Geometry

« on: August 15, 2016, 12:22 »

You should specify an extension for the trajectory file, meaning that the file name '3optianatasetraj' in the '3opti.py' script (or directly in the Scripter) needs to be replaced with '3optianatasetraj.nc'.

In the '3opit.log' file, you may see that there exists an error message on this issue: NL.ComputerScienceUtilities.Exceptions.NLValueError: The file name, 3optianatasetraj, must have the extension .nc or .py. So, it is always a good idea to take a look at the log file in case something is going not as it should.

1262

Scripts, Tutorials and Applications / Re: Incorrect Si band structure

« on: August 12, 2016, 09:19 »

The attachment is missing in your post. Could you please post the picture and python script of your calculation?

1263

General Questions and Answers / Re: Creating ions using Builder

« on: August 8, 2016, 10:04 »

You can export the structure as a POSCAR file of VASP, see the tutorial http://docs.quantumwise.com/tutorials/vnl_io_export/vnl_io_export.html?highlight=export. You may also use the VASP scripter to setup a VASP calculation (input files) directly from VNL, see http://docs.quantumwise.com/tutorials/vasp_scripter_addon/vasp_scripter_addon.html?highlight=vasp%20addon.

To construct a structure of interest, you may import it to the Builder from the Database or from Plugin: Add -> Database, or Add -> from Plugin. The latter has many options .

1264

General Questions and Answers / Re: wrong results got by Surface Model in 2016.0

« on: July 25, 2016, 17:40 »

According to the tutorial on SurfaceConfiguration calculation, see http://docs.quantumwise.com/tutorials/gf_surface.html?highlight=surface%20configuration, one should, "in the Poisson solver settings, change the boundary condition on the right-hand C-face to Neumann".

It seems that you have not changed that setting for the boundary condition as it follows from your python script. 

1265

General Questions and Answers / Re: Hydrogen Passivation

« on: July 11, 2016, 01:03 »

The CONTCAR file looks pretty normal, and I have been able to do hydrogen passivation for the corresponding structure, using the 2016.b1 version of VNL.

You may try restarting VNL and adding the structure to Stash from this CONTCAR file once again, and then use Custom Passivator as usual.

1266

General Questions and Answers / Re: Conductance as a function of gate potential .py sample

« on: July 11, 2016, 00:41 »

I have checked the script. It works for me. What version of VNL-ATK are you using?

1267

General Questions and Answers / Re: unit cell and scattering region

« on: July 10, 2016, 17:33 »

The number of unit cells in an electrode structure is the total number of atoms in the electrode divided by the number of atoms in the unit cell. It then depends on how you have defined the unit cell and electrode structure for CrO2.

It is not clear what exactly you mean by "to calculate the scattering region". You may have a look at the following tutorial, http://docs.quantumwise.com/tutorials/atk_transport_calculations.html?highlight=transport, to get an idea of how the scattering problem is formulated and solved in relation to the electron transport problem that I guess you are interested in.

1268

General Questions and Answers / Re: Thermoelectric properties for bulk fcc

« on: July 10, 2016, 13:15 »

I guess you may want calculating the thermoelectric properties for a particular crystallographic direction(s). If you go through the following tutorial, http://docs.quantumwise.com/tutorials/ag_au_interface.html?highlight=device, you will then be able to build any device of your interest for bulk fcc-BN, including BN-based devices with metal electrodes.

To study the properties of pure bulk BN, one may just use BN for the right and left electrode, meaning that you study an imaginary BN-BN "interface" instead of a real interface such as the Ag-Au interface discussed in the tutorial.

Note that you do not need to follow the tutorial straightforwardly as you may build this kind device in the Builder by adding bulk fcc-BN from the Database to Stash, and then use Builders -> Surface (Cleave) (choose the desired crystallographic direction) ->  Define surface lattice (keep it as it is) -> Finalize output configuration (set thickness to what you need to have two BN electrodes and central region of BN) -> Finish, and then use Device from Bulk as discussed in the Ag-Au tutorial.

1269

General Questions and Answers / Re: DOS and PDOS

« on: July 4, 2016, 17:29 »

DOS and PDOS stand for the 'density of states' and 'projected density of states', respectively.

You may have a look, for example, at this introductory tutorial, http://docs.quantumwise.com/tutorials/intro_vnl_atk1.html, to find out how it can be calculated and analyzed.

1270

General Questions and Answers / Re: how to plot graphene phonon band structure having 18 atoms in unit cell

« on: July 4, 2016, 16:27 »

To see the change of phonon frequencies of graphene, you may first do a supercell calculation for a single graphene sheet on the metal surface of your interest at the actual equilibrium separation distance between the graphene sheet and metal surface.

You then increase the separation distance to a larger value to significantly reduce the interaction between the graphene sheet and metal surface, and do a supercell calculation once again. This should give you an idea on how the phonon frequencies change upon decoupling graphene from the metal surface, i.e., upon increasing the separation distance.

For the sake of comparison, you may also want doing two additional supercell calculations for a free-standing graphene sheet and a bare metal surface without graphene. For both calculations, one should adopt the same supercell as that in the graphene-metal system.

All that information should allow you making some conclusions on the effect of the metal substrate on the phonon frequencies of supported graphene.       

1271

General Questions and Answers / Re: Refractive Index Script

« on: July 3, 2016, 13:51 »

You may export the data for n and alpha (as a function of wavelength, l) to file by adding the following lines to the python script given in the tutorial.

f = open('alpha.dat','w')
for i in range(len(l)):
   temp = str(l[ i ]) + '    ' + str(alpha[ i ]) + ' \n'
   f.write(temp)
f.close()

f = open('n.dat','w')
for i in range(len(l)):
   temp = str(l[ i ]) + '    ' + str(n[ i ]) + ' \n'
   f.write(temp)
f.close()

The data for refraction index (n) and absorption coefficient (alpha) are then saved to the 'n.dat' and 'alpha.dat' file, respectively. Note that the data are given in xy-format (x->wavelength l value and y->n or alpha value), and the files are just text files.

1272

General Questions and Answers / Re: Simulating a Graphene Based Transistor

« on: July 2, 2016, 11:16 »

You may read the section 'Building a bilayer graphene structure' in the following tutorial, http://docs.quantumwise.com/tutorials/opening_a_band_gap.html?highlight=graphene, to build a multilayered graphene structure, i.e., with 4 monolayers.

For learning how to build a graphene  transistor, you may then take a look at this tutorial http://docs.quantumwise.com/tutorials/vnl_graphene_transistor.html?highlight=graphene.

1273

General Questions and Answers / Re: Volume

« on: May 19, 2016, 17:12 »

Your question is not really clear. For primitive cell, unit cell or supercell calculations, the volume of the corresponding periodic structure is defined as the volume of the finite primitive cell, unit cell and supercell, respectively. The volume of the entire periodic structure is infinite since it contains an infinite number of the cells, or in other words it corresponds to an infinitely large supercell.   

1274

General Questions and Answers / Re: k points for bulk

« on: May 19, 2016, 17:03 »

Total energy is not variational with respect to the number of k-points used to sample the Brillouin zone, i.e., it just converges to some value upon increasing the k-grid density. The convergence may also be rather non-monotonic, e.g., even and odd k-grids often provide a different convergence speed.

Your second question is not clear. What frequency are you talking about?

1275

General Questions and Answers / Re: Current segregation and whether higher T(E) guarantee higher current?

« on: May 18, 2016, 08:58 »

Higher T(E) is somewhat poorly defined for a function. Is the T(E) function higher for the entire energy range?