Messages

466

General Questions and Answers / Re: Geometry optimization 3AGNR repeated 9 times in the z direction

« on: January 31, 2014, 16:56 »

Of course Nanna is right.
Although for a single SW defects in the center of a 10times long nanoribbon both solutions are fine (optimize bulk conf. and create device - create device and optimize device conf.)

Note that in the electrode extension regions of a device configuration the positions of the atoms are kept fixed and they match the atom positions of the electrodes.
http://www.quantumwise.com/documents/tutorials/latest/ATKTutorialDevice/index.html/chap.input.html#sect1.input.device

In this respect, if you break the periodicity in a region close to the walls of the cell during the optimization of the bulk configuration, the "Device from Bulk" plugin will not recognize the periodicity that you need to create the electrodes.
Hence, you will have to do it manually.
(Actually, it may recognize the periodicity of a "distorted" structure.)
So, "If you optimize the ribbon as a bulk system, you MAY HAVE to insure this manually" always applies.
This should answer to your second question.

About the first question the answer is: no, if the plugin managed to do it automatically.

It is hard to give general and universal answers, you may need to adapt from case to case.
But I hope everything is more clear now, is it?

467

General Questions and Answers / Re: Geometry optimization 3AGNR repeated 9 times in the z direction

« on: January 31, 2014, 10:18 »

You can release the constrain only along z at step (1). Along x and y directions you have a vacuum region meaning no stress along these directions.

At step (2) you have the same structure which is already optimized.

at step (3) you may have stress along z if your nanoribbon is too short as the SW defect will influence the geometry of the surrounding.
However, you should have a nanoribbon which is long enough such that you defect is isolated (if this is what you want).
Therefore you do not need to release the z constrain here.

468

General Questions and Answers / Re: III-V nanowire

« on: January 27, 2014, 08:59 »

A simple model would be to create a InAs nanowire and substitute 47% of the In atoms with Ga atoms following some pattern.
As Nordland pointed out, this arrangement of atoms is the main issue.

You may want to study the In0.5Ga0.5As stoichiometry first (smaller cell as you have to substitute exactly half of the In atoms) to test different atoms arrangement.

469

General Questions and Answers / Re: Minimizing molecules on Si(100)

« on: January 21, 2014, 13:00 »

Indeed, it looks like you managed to reproduce the structure in your Ref.
Although, you need to increase the vacuum region around your structure (increase the lattice parameters with Bulk Tools>Lattice Parameters and center the configuration by Coordinate Tools>Center) or even better, convert to a MoleculeConfiguration.
You can easily do that clicking on the icon on the left side of the Builder.

In both cases you do not need k-points, (1,1,1)

The reason is that you are using a cluster approach to simulate a surface.
Common and good approximation in 2004. Now you can properly simulate a surface with a periodic approach if you wish.
See for example http://quantumwise.com/publications/tutorials/mini-tutorials/190

470

General Questions and Answers / Re: How to optimize the molecule in device.

« on: January 20, 2014, 14:42 »

Sorry about the late reply!

1. You may try to optimize the cell along the Z direction (c vector) by unchecking the z box in the Constrain cell option in your OptimizeGeometry object.

2. Using a gold (2x2) unit cell, as you do, gives you a distance between the repeated molecules along XY of about 3.2Å which is comparable with the Pb-S distance of you molecule  (2.7Å).This means that you cannot really say that your molecule is isolated and you may instead create a periodic "2D like" configuration (which you actually get after optimization).
Try with a larger cell, (3x3).

3. I will also speculate. Might be that the Au-molecule interaction is so strong that your molecule will dissociate when placed on a Au surface. Not much to do with that.

471

General Questions and Answers / Re: Seebeck Coeff. :SWCNT

« on: January 17, 2014, 12:17 »

Exactly as it is reported here http://quantumwise.com/documents/tutorials/latest/Phonon/index.html/chap.thermoelectric.html#sect2.thermoelectric.analyze
namely, Peltier coefficient/T

But you are right, it is not really clear. We will highlight this point.

472

News and Announcements / New mini-tutorial: Isotope impurity effect on a single-wall carbon nanotube!

« on: January 16, 2014, 16:23 »

In this mini-tutorial you will study the effect a ring of ¹⁴C atoms embedded in a "regular" carbon nanotube on the thermal transport properties.
You will use the graphical user interface to set the structure and calculation up, but the part that makes this work requires Python scripting.
This tutorial really demonstrates some of the power that comes with having a direct programming interface to the core calculation engine.

Link: Isotope impurity effect on a single-wall carbon nanotube

473

General Questions and Answers / Re: Checking for Correct Optimized Structure

« on: January 15, 2014, 22:36 »

Click on the 3D view (Jmol applet) before saving the file.
Here the two files.

474

General Questions and Answers / Re: Checking for Correct Optimized Structure

« on: January 15, 2014, 09:39 »

I did not use any extra parameters.

The .MOL file that you download from chemspider.com has already the H atoms included

475

General Questions and Answers / Re: construct Au electrode with 2 × 2 layers in x and y directions

« on: January 15, 2014, 09:34 »

yes, the process is reasonable.
Indeed you may have too few layers. Please check again the two links above for some more information.

A faster and easier way could be to use the Builder->Interface plugin using the structure you used to create your last figure 1 twice.
With the tool Shift Surfaces inside this plugin you can increase the Z separation.
Finally simply use Add/Remove Layer to get exactly what you want.

476

General Questions and Answers / Re: construct Au electrode with 2 × 2 layers in x and y directions

« on: January 13, 2014, 21:28 »

The steps you follow above are correct and are done in order to optimize the Au bulk structure.
Just use a mesh of k-points like (n,n,n) because the unit cell is cubic (around 20x20x20 should be more then fine)

The second step is to build the device configuration as you report in your picture.
Sorry if my last reply was not complete but I may misunderstood your initial question.

1- take the optimized bulk structure and send it to the Builder.
2- here, with the Builder>Surface(cleave) plugin cut a (100) or a (111) surface according to your wish.
From your figure it looks like the plane perpendicular to the transport direction is the (100)..
Here, you can also define the unit cell (you mentioned 2x2)
Always with this plugin, choose the number of layers you want.
3-  Once the structure is created, transform you bulk configuration in a DeviceConfiguration using the Device Tools>Device from Bulk plugin.

In step 2 and 3 choose carefully the number of layers that will constitute the central region and the electrodes.
here some relevant informations:
http://www.quantumwise.com/documents/tutorials/latest/ATKTutorialDevice/index.html/chap.input.html#sect2.input.devicefrombulk
http://quantumwise.com/publications/tutorials/mini-tutorials/99

477

General Questions and Answers / Re: Checking for Correct Optimized Structure

« on: January 13, 2014, 10:25 »

Looks like there is something wrong with the initial structure. Not completely (atomic units?)
The structure you can find here http://www.chemspider.com/Chemical-Structure.112728.html looks fine.
Attached you can find the .xyz format converted with openbabel.

You can optimize the structure in a molecular configuration meaning also that you do not need k-points (1,1,1)

478

General Questions and Answers / Re: construct Au electrode with 2 × 2 layers in x and y directions

« on: January 13, 2014, 09:42 »

How do you optimize the structure?

You should first optimize the Au bulk structure (optimize the lattice parameter) and only after this step you create the 2x2 Au surface with 8 layers.
Add the structure form the Database.
You can then optimize the lattice parameter by removing the "constrain cell" option in the OptimizeGeometry block.
Remember to check the convergence with respect to k-points sampling.

479

General Questions and Answers / Re: Fcc NaCl including 8 atoms

« on: January 7, 2014, 13:14 »

Correct. Also, notice that the primitive NaCl cell contains only two atoms in 0,0,0 and 0.5,  0.5,  0.5.
You will get this configuration after following the instruction of Shinji.

If you want to use the conventional (non-primitive) unit cell with 8 atoms instead, your script should look like:

Code

# Set up lattice
vector_a = [5.64056, 0.0, 0.0]*Angstrom
vector_b = [0.0, 5.64056, 0.0]*Angstrom
vector_c = [0.0, 0.0, 5.64056]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Sodium, Chlorine, Sodium, Chlorine, Sodium, Chlorine, Sodium,
            Chlorine]

# Define coordinates
fractional_coordinates = [[ 0. ,  0. ,  0. ],
                          [ 0.5,  0.5,  0.5],
                          [ 0.5,  0.5,  0. ],
                          [ 0. ,  0. ,  0.5],
                          [ 0.5,  0. ,  0.5],
                          [ 0. ,  0.5,  0. ],
                          [ 0. ,  0.5,  0.5],
                          [ 0.5,  0. ,  0. ]]

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )