1
General Questions and Answers / DFT-D3
« on: August 11, 2015, 03:51 »
Whether ATK 2015.b1 version have implemented the DFT-D3 method, the latest version of the Grimme dispersion corrections?
Show Posts
This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.
Pages: [1] 2
2
General Questions and Answers / How to solve the odd and unbelievable currents trouble?
« on: February 22, 2011, 10:33 »
Hi,everyone!
Recently I read a paper “Conductance through short DNA molecules”, published in J. Phys. Chem. C used ATK 2008.10. I am calculating one system very similar to their model(attached): four base pairs are inserted two Au electrodes, and the DNA molecule is situated at about 3.5 Å parallel to each Au surface. My applied version is ATK 2008.02. The author obtained very ideal I-V curve. But for the similar geometry, I obtained very odd results, as following:
#I-V Bias (Volt) Current (Ampere)
#I-V 0.0 0.0000
#I-V 0.1 1.60e-10
#I-V 0.2 9.02e-9
#I-V 0.3 5.72e-8
#I-V 0.4 1.73e-9
I feel these results are very unbelievable. The calculated I-V curve is abnormal. And I think this is absolutely not the negative differential resistance effect.
I also consulted the author for more calculate details. He told me the basis set functions in ATK should be changed for this weak interacted system. But I not dare to change this parameter due to not be familiar with the ATK computation algorithms. I try my best for a long time but the results still are unbelievable. I almost despaired.
I hope someone can help me to solve this trouble. Thanks a lot in advance.
The geometry model and my calculated details are attached.
Recently I read a paper “Conductance through short DNA molecules”, published in J. Phys. Chem. C used ATK 2008.10. I am calculating one system very similar to their model(attached): four base pairs are inserted two Au electrodes, and the DNA molecule is situated at about 3.5 Å parallel to each Au surface. My applied version is ATK 2008.02. The author obtained very ideal I-V curve. But for the similar geometry, I obtained very odd results, as following:
#I-V Bias (Volt) Current (Ampere)
#I-V 0.0 0.0000
#I-V 0.1 1.60e-10
#I-V 0.2 9.02e-9
#I-V 0.3 5.72e-8
#I-V 0.4 1.73e-9
I feel these results are very unbelievable. The calculated I-V curve is abnormal. And I think this is absolutely not the negative differential resistance effect.
I also consulted the author for more calculate details. He told me the basis set functions in ATK should be changed for this weak interacted system. But I not dare to change this parameter due to not be familiar with the ATK computation algorithms. I try my best for a long time but the results still are unbelievable. I almost despaired.
I hope someone can help me to solve this trouble. Thanks a lot in advance.
The geometry model and my calculated details are attached.
3
General Questions and Answers / Re: How to calculate the differential conductance?
« on: September 8, 2010, 14:46 »
Thank you for your help!!
4
General Questions and Answers / Re: How to calculate the differential conductance?
« on: August 26, 2010, 16:10 »
Hope someone can give me a helpful suggestion!!!
5
General Questions and Answers / How to calculate the differential conductance?
« on: August 26, 2010, 08:59 »
Hello, everyone!
I ofen see the differential conductance was calculated as a property of electron transport in many papers. I search through the ATK manual and the forum, but do not know how to calculate it ? I now only know the method to calculate the conductance at zero bias. I hope someone can give me a detailed input file.
Thank you very much!
I ofen see the differential conductance was calculated as a property of electron transport in many papers. I search through the ATK manual and the forum, but do not know how to calculate it ? I now only know the method to calculate the conductance at zero bias. I hope someone can give me a detailed input file.
Thank you very much!
6
General Questions and Answers / Re: Can the ATK2009.12 handle with the charged system for DeviceConfigurations?
« on: January 30, 2010, 10:23 »
Thank you for your kindly replies!
A redox-avtive molecule is one important candidate for molecular switch. Its charge can be controled by electrochemistry gate,for example:J. Am. Chem. Soc., 2008, 130 (37), pp 12204–12205;. Am. Chem. Soc., 2008, 130 (28), pp 9013–9018.
Now, I am confused with the difference between the ATK's gate and the electrochemistry gate. I feel their effects maybe different.
I don't know whether the charge of this kind molecules flows or not in real two-probe system. In my calculations, I meet many molecules,which geomtry and electronic properties can change with the charge state. I alwayes want to compare their conductive properties with the neutral ones. But I don't know for two-probe system in ATK how to distinguish them.
A redox-avtive molecule is one important candidate for molecular switch. Its charge can be controled by electrochemistry gate,for example:J. Am. Chem. Soc., 2008, 130 (37), pp 12204–12205;. Am. Chem. Soc., 2008, 130 (28), pp 9013–9018.
Now, I am confused with the difference between the ATK's gate and the electrochemistry gate. I feel their effects maybe different.
I don't know whether the charge of this kind molecules flows or not in real two-probe system. In my calculations, I meet many molecules,which geomtry and electronic properties can change with the charge state. I alwayes want to compare their conductive properties with the neutral ones. But I don't know for two-probe system in ATK how to distinguish them.
7
General Questions and Answers / Re: Can the ATK2009.12 handle with the charged system for DeviceConfigurations?
« on: January 27, 2010, 11:45 »
Yes，your reply is right,indeed.
However, I find many charged system may have very interesting conductive properties. Compared them with the nuetral systems, it can have high on-off retio in current. May be this can not realize in fact ? But there are many related reports.
Thank you very much!
However, I find many charged system may have very interesting conductive properties. Compared them with the nuetral systems, it can have high on-off retio in current. May be this can not realize in fact ? But there are many related reports.
Thank you very much!
8
General Questions and Answers / Can the ATK2009.12 handle with the charged system for DeviceConfigurations?
« on: January 27, 2010, 10:15 »
For the recently released ATK2009.12,one difference is it can allow to calculate charged system. But after reading through the manual, I find the charged system is limited to MoleculeConfiguration and BulkCondiguration. Is it really that the ATK2009.12 cannot handle with the charged system for DeviceConfigurations yet?
9
General Questions and Answers / Re: the question about viewing LDOS use Nanoscope.
« on: November 14, 2009, 08:50 »
Thank you vergy much,Zh!!
You are right,it's well done. I only used the output manuscript by NanolanguageScripter and not change. But for "quantum number" I maybe need to read some related books to understand deeply.
You are right,it's well done. I only used the output manuscript by NanolanguageScripter and not change. But for "quantum number" I maybe need to read some related books to understand deeply.
10
General Questions and Answers / the question about viewing LDOS use Nanoscope.
« on: November 13, 2009, 09:10 »
Dear everyone:
Now I meet a problem when I try to view LDOS in Nanoscope: after runing the py file, the cooresponding VNL file has changed from about 6K to 5MB. And when droping the vnl file to Result Browser, the message is “Grid data - Preview not available. Drop the Sample on the Nanoscope to view this property”. Then I droped the vnlfile to Nanoscope, the “insert plot” button only have two submanus: configurationand the coordinate axes. There were not other three submanus: Contour plot, Isosurface, Volume plot. The parameter of “quantum_number” in LDOS is set as (0.5,0.5). I searched for this parameter in this forum, one post says the range is -0.5 to 0.5. And I change this parameter to (0.0,0.0),or (0.0,0.5) etc, the error is same. In addition, my system is a two-probe system(3 dimension).
The py file is attached.
I will appreciate if someone can help me!
Now I meet a problem when I try to view LDOS in Nanoscope: after runing the py file, the cooresponding VNL file has changed from about 6K to 5MB. And when droping the vnl file to Result Browser, the message is “Grid data - Preview not available. Drop the Sample on the Nanoscope to view this property”. Then I droped the vnlfile to Nanoscope, the “insert plot” button only have two submanus: configurationand the coordinate axes. There were not other three submanus: Contour plot, Isosurface, Volume plot. The parameter of “quantum_number” in LDOS is set as (0.5,0.5). I searched for this parameter in this forum, one post says the range is -0.5 to 0.5. And I change this parameter to (0.0,0.0),or (0.0,0.5) etc, the error is same. In addition, my system is a two-probe system(3 dimension).
The py file is attached.
I will appreciate if someone can help me!
11
General Questions and Answers / Re: Can ATK be used to study the weak connected molecule?
« on: November 11, 2009, 15:38 »
Thank you for your kindly helps.
My system is one dimer binded by two hydrogen bonds, similar to the H-bond in base pair. I remember some papers about base pair in DNA were calculated by ATK or Siesta.
And sorry, I cant understand " What the referee asks, is how do you know that your system is not weakly coupled." your mean is I can think my system is weakly coupled system?
Thanks a lot!
My system is one dimer binded by two hydrogen bonds, similar to the H-bond in base pair. I remember some papers about base pair in DNA were calculated by ATK or Siesta.
And sorry, I cant understand " What the referee asks, is how do you know that your system is not weakly coupled." your mean is I can think my system is weakly coupled system?
Thanks a lot!
12
General Questions and Answers / Re: Can ATK be used to study the weak connected molecule?
« on: November 11, 2009, 12:42 »
Dear all:
Why there is no reply to this question? Does it really mean ATK cannot be applied to weak bonded system?
Why there is no reply to this question? Does it really mean ATK cannot be applied to weak bonded system?
13
General Questions and Answers / Can ATK be used to study the weak connected molecule?
« on: November 7, 2009, 10:48 »
Hello, everyone!
Now I receive the comments of one reviewee to my paper, one of which is : “The ATK program is based on the first-principles calculations and treated the current calculation self-consistently. However, it treats only the electron transfer with the scattering mechanism. It can not predict the transportation of hopping and other mechanisms. In the present study, the authors used a pair of molecules linked with hydrogen bonds. How can they evaluate the reliability of the methodology. Can they rule out other mechanisms? I worry about the weak connection might change the scattering electron transfer mechanism. ” Because I can’t deeply understand the basis theory of ATK, I don’t know how to answer him.
I will appreciate your help if someone can answer this question!!
Now I receive the comments of one reviewee to my paper, one of which is : “The ATK program is based on the first-principles calculations and treated the current calculation self-consistently. However, it treats only the electron transfer with the scattering mechanism. It can not predict the transportation of hopping and other mechanisms. In the present study, the authors used a pair of molecules linked with hydrogen bonds. How can they evaluate the reliability of the methodology. Can they rule out other mechanisms? I worry about the weak connection might change the scattering electron transfer mechanism. ” Because I can’t deeply understand the basis theory of ATK, I don’t know how to answer him.
I will appreciate your help if someone can answer this question!!
14
General Questions and Answers / Re: How to calculate the projected density of each MPSH state?
« on: October 22, 2009, 15:47 »
Thank you, Anders Blom !
I searched through many papers to study PDOS. In one papaer I found a formula of PDOS very similar the difination of LDOS in our ATK manual.
If I set the energy in LDOS as the specific value of the calculated MPSH eigenvalue, can the LDOS represent the mean of the referee?
I searched through many papers to study PDOS. In one papaer I found a formula of PDOS very similar the difination of LDOS in our ATK manual.
If I set the energy in LDOS as the specific value of the calculated MPSH eigenvalue, can the LDOS represent the mean of the referee?
15
General Questions and Answers / How to calculate the projected density of each MPSH state?
« on: October 21, 2009, 04:05 »
Hello, everyone! Now I meet a problem: one review suggestion to my submitted paper is: "Eigenvalues and functions of the MPSH states are calculated for analysis of the conductance. However, the MPSH energies are not sufficient to analyze conductance channel. The coupling strength of MPSH states with electrodes is also important factor. Simply, authors can calculate the projected density of each MPSH state."
To my knowledge, ATK manual only mentioned DOS and LDOS,but the two all are not the asked results. And I searched this forum the "PDOS" that can calculated in ATK is projected DOS on some atoms.
How to solve the reviewee's suggestion about PDOS on some state?
Thanks!!!!
To my knowledge, ATK manual only mentioned DOS and LDOS,but the two all are not the asked results. And I searched this forum the "PDOS" that can calculated in ATK is projected DOS on some atoms.
How to solve the reviewee's suggestion about PDOS on some state?
Thanks!!!!
Pages: [1] 2