1
General Questions and Answers / Re: broken bonds in carbon nanotube when optimization
« on: September 16, 2013, 19:21 »
Thanks Dr. Nordland.
Thanks Dr. Blom.
Thanks Dr. Blom.
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2
General Questions and Answers / Re: broken bonds in carbon nanotube when optimization
« on: September 13, 2013, 20:48 »
Dear Dr. Blom,
I have one more question about the C-C bond. As it shows that it can be broken at a certain setup, but I am not sure if the C-C bond reflected the real C-C sp2 bond length? Since it could be very strong to be broken. How did you generate the carbon nanotube, did you take the real strength properties into consideration? Thank you.
Best regards.
I have one more question about the C-C bond. As it shows that it can be broken at a certain setup, but I am not sure if the C-C bond reflected the real C-C sp2 bond length? Since it could be very strong to be broken. How did you generate the carbon nanotube, did you take the real strength properties into consideration? Thank you.
Best regards.
Method used? Input file would help.
3
General Questions and Answers / Re: The thermal considerations of QuantumWise
« on: September 12, 2013, 16:39 »
Thanks Dr. Blom.
Maybe I will switch to other MD software as a backup plan to this kind of research.
thank you so much.
Maybe I will switch to other MD software as a backup plan to this kind of research.
thank you so much.
So in essence you are describing the effect of hot electrons, which usually is very small. In the tutorial I referred to, the main effect is observed when the electrodes is at different temperatures, but also the thermionic effect is larger for larger tunnel distances.
ATK 13.8 can compute phonon frequencies and phonon transport, but electron-phonon interaction is not yet included.
In theory you can do DFT-MD but it's extremely time-consuming, so the sensible choice for mechnical properties is surely classical MD. ATK 13.8 introduces many new functionalities in this area, such as the Tersoff potential, NPT, and a few other things.
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General Questions and Answers / Re: broken bonds in carbon nanotube when optimization
« on: September 12, 2013, 16:37 »
Thanks Mr. Usui.
If you are assuming Cu-C bonds as covalent ones the optimized bond length 2.0 Ang is reasonable.
My idea to relax the initial structure :
The Cu tube radius of your structure is too big, I mean the strain between CNT and Cu are too tight.
Making a smaller radius of Cu tube, you can construct more relaxed structure as the starting point of the optimization.
And also to enlarge the CNT radius is an alternative idea to release the strain in the system.Hi Mr. Usui, thanks for your answer.
I am not sure about the initial distance. I did use 1.5 Angstrom as the initial one, but after relaxation, for device with less copper atoms, it always arrive at the value of around 2 Angstrom.
I am not sure if that's OK for these device results.
I mean, since it will always go through optimization, finally it would arrive at the equilibrium bond length.
Am I understanding it right?
Secondly, what do you mean by "You should make more relaxed structure as the initial configuration for the optimization"?Please check the covalent radius of Cu and C.
Approximate values of them are
Cu = 1.32 Ang.
C = 0.73 Ang (sp2)
by Wiki.
So the initial bond length of the Cu-C for the optimization calculation should be around 1.32 + 0.73 =~ 2.0 Ang.
Looking your initial configuration for the optimization some Cu-C length are too short ( around 1.46 Ang)
and too much forces could be applied to the system and you found the C-C bond breaking.
You should make more relaxed structure as the initial configuration for the optimization.
5
General Questions and Answers / Re: broken bonds in carbon nanotube when optimization
« on: September 12, 2013, 16:37 »
Thanks Dr. Blom.
That's good enough.
That's good enough.
That's a bit too big a question to answer for me, so I will not.
But as a general comment for any study, I would say that unless it's performed with the atoms in the equilibrium position, then one should be able to explain why not. And if the equilibrium positions cannot even be determined since the optimization does not work, well, then it's a bit of a problem for sure. I mean, you can dream up any system, but if it's realistic or relevant is a very different story.
6
General Questions and Answers / Re: broken bonds in carbon nanotube when optimization
« on: September 11, 2013, 17:48 »
Thanks Dr. Blom.
Since the initial structure is not physical realistic, how could I justify it? From the result?
I did some research based the same initial distance yielding results, would that mean my research was not correct?
Since the initial structure is not physical realistic, how could I justify it? From the result?
I did some research based the same initial distance yielding results, would that mean my research was not correct?
I don't see any principal problem with the calculation. Most likely it's simply not a physical situation to have the Cu atoms that close to each other inside the nanotube. The trajectory clearly shows that in the very first steps the Cu atoms experience very large forces, as I interpret it due to the repulsion between Cu-Cu, and so they move outwards which in turn creates large forces on the C atoms, and then it all breaks. So Shinji is correct, the initial structure is the problem, it's not realistic.
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General Questions and Answers / Re: The thermal considerations of QuantumWise
« on: September 11, 2013, 17:44 »
Thanks Dr. Blom.
I used DFT and that's the way I felt a little bit unproper.
About how I did it, I just set the temperature of each calculations at different values, and then calculate the corresponding result.
On the other hand, if you suggest MD, does QuantumWise considered phonons?
And if I want to do research not only on the thermal properties, but also on the mechanical properties, which method is the suitable way?
Thanks very much.
I used DFT and that's the way I felt a little bit unproper.
About how I did it, I just set the temperature of each calculations at different values, and then calculate the corresponding result.
On the other hand, if you suggest MD, does QuantumWise considered phonons?
And if I want to do research not only on the thermal properties, but also on the mechanical properties, which method is the suitable way?
Thanks very much.
Not enough information available. Method used, DFT?
It's probably not really a suitable way to study the temperature effect as the temperature-dependent of the conductance is more due to the interaction of phonons and electrons than the difference in conductance due to some random fluctuation of the atom position with temperature. One could do an MD simulation and take snapshots at different times, do statistics, and the compare the average at different temperatures, but it seems that's not how you do it. In fact, I'm not sure I understand how you take the temperature into account at all in the optimization (are you doing MD?), hence the question about method etc.
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General Questions and Answers / Re: broken bonds in carbon nanotube when optimization
« on: September 11, 2013, 17:39 »
Hi Mr. Usui, thanks for your answer.
I am not sure about the initial distance. I did use 1.5 Angstrom as the initial one, but after relaxation, for device with less copper atoms, it always arrive at the value of around 2 Angstrom.
I am not sure if that's OK for these device results.
I mean, since it will always go through optimization, finally it would arrive at the equilibrium bond length.
Am I understanding it right?
Secondly, what do you mean by "You should make more relaxed structure as the initial configuration for the optimization"?
I am not sure about the initial distance. I did use 1.5 Angstrom as the initial one, but after relaxation, for device with less copper atoms, it always arrive at the value of around 2 Angstrom.
I am not sure if that's OK for these device results.
I mean, since it will always go through optimization, finally it would arrive at the equilibrium bond length.
Am I understanding it right?
Secondly, what do you mean by "You should make more relaxed structure as the initial configuration for the optimization"?
Please check the covalent radius of Cu and C.
Approximate values of them are
Cu = 1.32 Ang.
C = 0.73 Ang (sp2)
by Wiki.
So the initial bond length of the Cu-C for the optimization calculation should be around 1.32 + 0.73 =~ 2.0 Ang.
Looking your initial configuration for the optimization some Cu-C length are too short ( around 1.46 Ang)
and too much forces could be applied to the system and you found the C-C bond breaking.
You should make more relaxed structure as the initial configuration for the optimization.
9
General Questions and Answers / Re: broken bonds in carbon nanotube when optimization
« on: September 11, 2013, 17:33 »
Dr. Blom,
I used DFT. And the input file is attatched.
I used DFT. And the input file is attatched.
Method used? Input file would help.
10
General Questions and Answers / The thermal considerations of QuantumWise
« on: September 10, 2013, 17:38 »
Dear everyone,
I am working on a case that CNT-Bi's conductance properties VS temperature. We optimized the same structure at different temperatures and then calculate their transmission spectrum. However, the structure after the optimization looks ridiculous as the metal atoms go far away from the carbon nanotube. And the transmission coefficient has no particular trend, as it goes down from 300K to 403K, but goes up from 403K to 423K.
I am not sure if the QuantumWise software considered the temperature effect on properties, and to which extent? Maybe it's not a proper way to try to pry the temperature effect on this software?
On the other side, my device may have problem and any picky advice is very welcomed.
Thanks very much!
I am working on a case that CNT-Bi's conductance properties VS temperature. We optimized the same structure at different temperatures and then calculate their transmission spectrum. However, the structure after the optimization looks ridiculous as the metal atoms go far away from the carbon nanotube. And the transmission coefficient has no particular trend, as it goes down from 300K to 403K, but goes up from 403K to 423K.
I am not sure if the QuantumWise software considered the temperature effect on properties, and to which extent? Maybe it's not a proper way to try to pry the temperature effect on this software?
On the other side, my device may have problem and any picky advice is very welcomed.
Thanks very much!
11
General Questions and Answers / broken bonds in carbon nanotube when optimization
« on: September 10, 2013, 17:12 »
Hi all!
I am optimizing a carbon nanotube clamped with 20 copper atoms in it. However, in the process of the optimization, the carbon nanotube has been broken and copper has been embedded into the carbon nanotube.
I am not sure this situation is reasonable, since the carbon-carbon sp2 bond is said to be stronger than that of diamond, so why the copper atoms can break the c-c bond? Is the carbon nanotube generated in this software give consideration of the physical properties of real carbon nanotube? If so,what mechanism is underlying? Hope anyone could clarify that for me. Discussion is also welcome.
The relaxation trajectory is attatched. Thanks.
I am optimizing a carbon nanotube clamped with 20 copper atoms in it. However, in the process of the optimization, the carbon nanotube has been broken and copper has been embedded into the carbon nanotube.
I am not sure this situation is reasonable, since the carbon-carbon sp2 bond is said to be stronger than that of diamond, so why the copper atoms can break the c-c bond? Is the carbon nanotube generated in this software give consideration of the physical properties of real carbon nanotube? If so,what mechanism is underlying? Hope anyone could clarify that for me. Discussion is also welcome.
The relaxation trajectory is attatched. Thanks.
12
General Questions and Answers / Re: Question on Van der Waals potential in DFT-NEGF
« on: July 2, 2013, 16:40 »
I have the same question here:
Does the current version include the van der waals interaction? Thanks.
Does the current version include the van der waals interaction? Thanks.
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Scripts, Tutorials and Applications / Re: script for calculating Seebeck coeffient, thermal conductance, and ZT
« on: March 25, 2013, 20:56 »
Dear Everyone,
I am just wondering if it's capable for ATK to calculate the thermal conductance for system with phonon transport now? Then it should be more realistic.
I am just wondering if it's capable for ATK to calculate the thermal conductance for system with phonon transport now? Then it should be more realistic.
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General Questions and Answers / Re: VNL error
« on: March 14, 2013, 17:05 »
Dear Dr. Blom,
I didn't save the trajectory file in the same name as the relaxation file. It's just 1100kB but it already exceeds the maximum limit. I've already sent it to you via the link you mentioned.
The relaxation file is also attatched.
Thank you for your patience. BR.
I didn't save the trajectory file in the same name as the relaxation file. It's just 1100kB but it already exceeds the maximum limit. I've already sent it to you via the link you mentioned.
The relaxation file is also attatched.Thank you for your patience. BR.
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General Questions and Answers / Re: VNL error
« on: March 13, 2013, 19:00 »
Dear Dr. Blom,
The attatched is the input script, please check it out.
The trajectory nc file is too large to upload, though.
Thank you.
Best regards.
The attatched is the input script, please check it out.
The trajectory nc file is too large to upload, though.
Thank you.
Best regards.