Messages

1

General Questions and Answers / Re: Total energy of Si-doped Tio2 film

« on: January 28, 2016, 09:37 »

Probably your second total energy is from the unoptimized structure. My guess is you did

config = nlread("file.nc", BulkConfiguration)[0]
total_energy = TotalEnergy(config)

where file.nc is the output file from the optimization run. It should be

config = nlread("file.nc", BulkConfiguration)[-1]
total_energy = TotalEnergy(config)

because in that NC file, the first config [ 0 ] is the unoptimized structure, the second one [1] is the optimized one. The notation [-1] mean the LAST object, which is most likely the optimized (if you ran several times the same script, with different settings, you may have more than 2 objects in the file).

Thanks Anders!

FYI, for the second total energy calculation, I sent the optimized geometry (gID001)to the builder and added a new calculator and other analysis. Therefore there is no such 'nlread' command in the script.

Regards

2

General Questions and Answers / Total energy of Si-doped Tio2 film

« on: January 27, 2016, 16:11 »

Hei,

I have built a 2*1*1 TiO2 supercell and substituted a Ti atom with Si. I then add optimizegeometry and total energy together to the calculator to do the geometry optimization and got one value for total energy (TE1=-9287eV). Afterwards I used the optimized Si-doped TiO2 for DFT calculations where band structure, DOS, total energy and others were added. I hereby got another value for total energy(TE2=-8437). My confusion is why TE1 and TE2 are different. I wanted to further calculate the formation energy using E(formation)=E(Si-tio2)-E(tio2)-E(si)+E(Ti), which of the two values (TE1 or TE2) should I use for E(Si-tio2)?

Thanks in advance!
   

3

General Questions and Answers / Re: how to visualize HOMO/LUMO states in a nanotube structure

« on: November 12, 2015, 12:00 »

1& 2. HOMO and LUMO are used to for a molecule or isolated system, not for a periodic system. If your simulated TiO2 nanotube has periodic along the tube axis, you should consider the Bloch states at the valence band maximum and at the conduction band minimum. If your simulated TiO2 nanotube is just a short and isolated nanotube, you may consider the HOMO and LUMO.

3. Each energy level can be occupied by 2 electrons at most. If the molecule contains 8 valence electrons, there will be only 4 occupied states. The unoccupied states aren't related to the number of valence electrons in the system.

Thanks zh! I am still confused about your answer to Q3. I understand that each energy Level can be occupied by 2 Electrons at most. But this only means that a molecule containing 8 valence Electrons has at least 4 occupied states, not necessarily to be exactly 4. In the case of a H2O molecule, H 1s contains only 1 Electron, O 2s contains 2e, O 2p_x contains 2 and O 2p_y 2p_z each contains 1. Among all these occupied energy Levels (if I am correct about this), which are the 4 occupied states you referred to?

4

General Questions and Answers / is there a way to simulate a cluster of quantum dots?

« on: November 10, 2015, 21:16 »

Hi,

I am thinking of using a molecule (Cd₂S₂) to simulate a cluster of CdS Quantum dots, but not sure how to build one. Any comments or suggestions? 

PS: Is there a tutorial teaching how to adsorb a molecule to a nanotube (or any other configuration?)

5

General Questions and Answers / how to visualize HOMO/LUMO states in a nanotube structure

« on: November 10, 2015, 21:05 »

Hi everyone!

I am wondering how to visualize HOMO/LUMO states in a tio2 nanotube structure. I have read the tutorial where the LUMO state of a H2O molecule is visualized. http://quantumwise.com/publications/tutorials/item/108-visualize-the-lumo-state-of-a-water-molecule However, there are still some confusions when applying the same calculation to my structure.
1. Does the configuration have to be changed to a molecule configuration?
2. Does the calculation have to be Applied to the Whole system, or is there a way to calculate only a quadrant (or 1/8) of the tube (considering such a number of atoms in the system)?
3. When it comes to the Quantum number under the Eigenstate Block, it is not so clear where the final number 4 in the tutorial step8 comes from. So my understanding of step8 translates as follows: water has 8 valence Electrons (2*H 1s¹ + O 2s²2p⁴=8), there will be 4 occupied states (which refer to two 1s states from two H atoms and 2s+2p states from O atom?). Therefore set the quantum number to 4 for the LUMO state. (how is this 4 related to the previous 8 valence Electrons and 4 occupied states?)

Please help me out and correct me where I am wrong. Thanks 

6

General Questions and Answers / Re: problem optimizing tio2 nanotubes

« on: November 10, 2015, 19:08 »

I doubt that potential is good for TiO2, but you'll have to check the reference. Just because a potential supports nominally the included elements doesn't give any guarantee that it actually works for all possible combinations. Actually, this is a silicate potential that can be used with Ti impurities, if memory serves me right.

Hei, Anders Blom!

Thanks for your answer. I understand that these built-in potential settings may not suitable for my case. So I now am thinking to use ATK-DFT calculator to set up for my structure, but am a little struggled with where to start. It would be great if you can give me some suggestions on a set of parameters I can begin with, for instance exchange correlation type and functional, mech cutoff, and max force and stress. Thanks in advance!

7

General Questions and Answers / problem optimizing tio2 nanotubes

« on: November 9, 2015, 22:24 »

Hi,

I built two different (1 0 1) tio2 nanotubes (tnt) using tube wrapper, tnt(6,0) and tnt (8,0). After Optimizing using the same settings (see attachement 1), I got two different optimized structures (attachement 2&3, before optimization on the left and after optimization on the right). I am expecting structures like optimized tnt(6,0). Can anyone tell me why is something like opt tnt (8,0) happening?

Thanks

8

General Questions and Answers / Re: Problem building a unit cell of bulk tio2

« on: November 5, 2015, 22:15 »

Optimize with DFT-PBE which is the functional you are using to calculate the electronic properties.
It won't take long time.
Yes, you can test the stress tolerance parameters. the value I suggested is a good start.

Also, update to ATK/VNL 2014.3 which is the latest stable version:
http://quantumwise.com/publications/quantumwise-news/item/894
http://quantumwise.com/download/pkgs/archive/

Finally notice that ATK and VNL 2015 has been released. You can consider upgrading to this latest version as well (depending on your license)
http://quantumwise.com/publications/quantumwise-news/item/908-vnl-atk-2015-released.

Hi Umberto

Thanks for your suggestion. The result is finally acceptable.
One more thing that confuses me though. What decides the distance between fermi Level and CB(or VB) in the band structure. It seems that my fermi Level lies almost in the middle of the band gap, while I saw in many Reference papers the fermi Level stays right on top of the valence band.

9

General Questions and Answers / Re: Problem building a unit cell of bulk tio2

« on: November 5, 2015, 10:17 »

When you estimate the impurity concentration, the symmetry nonequivalent atoms in the unit cell should be used.

"And as you mentioned about the size of the cell, I wonder also does it affect the calculated band gap of the bulk material?"
For example, Si, the use of a primitive unit cell (face centered cubic) and a conventional unit cell (simple cubic) would give the same band gap if the k-points used in k-point sampling are symmetry equivalent.

Thanks

10

General Questions and Answers / Re: Problem building a unit cell of bulk tio2

« on: November 5, 2015, 10:14 »

Thanks for your answer, Jess! Yet I have gotten another problem and hope that you can share your opinion on it.
I have used the unit cell to calculate the band structure of the bulk tio2 and the resulting band gap is only 1.807eV. I have referred to many literatures using the same settings (GGA+PBE) and almost all claim the calculated band gap in the range of 2.1-2.2eV. Can you suggest what the problem could be? (The mesh cut off energy of 75Hartree and k-sampling of 5*5*5 are used after convergence test.) I have also tried to do the calculation in a 2*2*1 supercell and the result is slightly different 1.862 vs. 1.807eV)

Thanks in advance!

did you optimize the lattice parameters?
Uncheck "constrain cell" in Optimize Geometry and set a stress tolerance to something like 0.002/0.001 eV/A^3

Hi Umberto,

I did optimize the structure, but only with the quick optimizer with the max force 0.01eV/Å right after building the model. I will try with the optimize geometry right now and let you know how it works. But which potential settings I should choose (I don't see the Tersoff potential in my version 2014.0 as is used in one of your tutorials)? And the value of the stress tolerance you suggested, should I do the convergence test and make adjustment too?

Regards

11

General Questions and Answers / Re: Problem building a unit cell of bulk tio2

« on: November 4, 2015, 22:31 »

If you understand the periodic boundary of unit cell, your problem will be easily gotten answer.

1). Some atoms in (a) are equivalent. For example, the atoms in the vertexal points of the cell; the atoms in the middle of a and b lattice vectors.

2). The size of two cells are different, even you make the same numbers of atom in two cells.

Thank you for your answer zh! I can see the equivalence of some atoms, and they are not shown in my model compared to (a). But my question is should we count them when doing calculation Let me put it this way so that you can understand my confusion better: If I substitute one atom with an impurity atom in the unit cell, is the concentration of the impurity 1/12 or?

And as you mentioned about the size of the cell, I wonder also does it affect the calculated band gap of the bulk material?

Thanks

12

General Questions and Answers / Re: Problem building a unit cell of bulk tio2

« on: November 4, 2015, 22:13 »

Dear zhySarah. The image from the article is cheating you a bit, and it is important that you understand why: The key concept is that of the "repeted cell" for calculations on bulk structures. You should always try to do calculations for the smallest unit cell possible and account for periodicity by using k-point sampling - this is simply most efficient in terms of CPU hours. The structure you have built is the minimal cell: If you repeat it along all directions, you see that it really does form anatase TiO2.

The authors of the article have tried to make it easy to interpret the image and recognize the TiO2 bulk by repeating the cell and cutting away the atoms outside the unit cell. This is perfectly fine for illustrations, but in their calculations they have certainly used the minimal cell. You should do so too.

Thanks for your answer, Jess! Yet I have gotten another problem and hope that you can share your opinion on it.
I have used the unit cell to calculate the band structure of the bulk tio2 and the resulting band gap is only 1.807eV. I have referred to many literatures using the same settings (GGA+PBE) and almost all claim the calculated band gap in the range of 2.1-2.2eV. Can you suggest what the problem could be? (The mesh cut off energy of 75Hartree and k-sampling of 5*5*5 are used after convergence test.) I have also tried to do the calculation in a 2*2*1 supercell and the result is slightly different 1.862 vs. 1.807eV)

Thanks in advance!

13

General Questions and Answers / Re: Problem building a unit cell of bulk tio2

« on: November 2, 2015, 12:59 »

Yes, the structure looks exactly the same.
You can use Bulk Tools->Repeat to repeat your structure one more time along the A or B directions to bale the structure reported in (b).

Thanks for your reply Umberto! That is to say that in my unit cell there are as well 4 Ti atoms and 8 O atoms as in reported structure (a)?   Or it is only the atoms shown in the cell that counts for the total number of atoms in the unit cell? It matters because I need to know the impurity concentration in the (b) like structure.

PS: what if I repeat my structure in all three dimensions first and then delete all the atoms outside the unit cell to make a structure exactly like the one in (a). What difference it will make compared to the one I have now.

14

General Questions and Answers / Problem building a unit cell of bulk tio2

« on: October 31, 2015, 00:17 »

Hi,

I am trying to build a unit cell of bulk TiO₂ anatase as is shown in the first attachment (a). However I am only able to build one as shown in the second attachment. I am wondering if these two are equivalent when doing calculations? If not, how can I build the other model?

Thanks in advance!

15

General Questions and Answers / Difference between k-sampling under numerical accuracy parameter/basic and DOS

« on: October 30, 2015, 23:53 »

I am new to ATK and wondering if I should keep the k-samplings under these two tabs the same?

Thanks