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General Questions and Answers / Re: LDOS view problem in Nanoscope
« on: September 12, 2014, 04:33 »
The problem has been solved now!
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General Questions and Answers / LDOS view problem in Nanoscope
« on: September 12, 2014, 04:03 »
Hi，everyone，I have met a problem when I view LDOS in Nanoscope(VNL200810): when I drop the vnl file on Nanoscope, only the atomic structure can be seen, the “insert plot” button only have two submenus: configurationand the coordinate axes. Then I use result browser to open the vnl file, the structure file and LDOS dada can be seen, but when I drop the LDOS data on Nanoscope, the sturcture disappear. How can I get the figure like the lih2li example in the manual?
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General Questions and Answers / Re: the question about viewing LDOS use Nanoscope.
« on: September 12, 2014, 03:58 »An example for calculating the LDOS of Li-H2-Li two-probe system has been demonstrated in the manual of ATK. Please see here:Hi，zh，I met the same problem when I view LDOS in Nanoscope(VNL200810), when I drop vnl file on Nanoscope, only the atomic structure can be seen, the “insert plot” button only have two submanus: configurationand the coordinate axes. Then I use result browser to open the vnl file, the structure file and LDOS dada can be seen, but when I drop the LDOS data on Nanoscope, the sturcture disappear. How can I get the figure like the lih2li example in the manual?
http://www.quantumwise.com/documents/manuals/ATK-2008.10/chap.advtwoprobe.html#sect1.advtwoprobe.dos
For the parameter such as "quantum_number " in calculateLocalDensityOfStates(), it is well explained.QuoteThe quantum numbers depend on whether the system is spin-polarized or not, and should be specified as
* ([k_point], spin) for spin-polarized systems.
* [k_point] for unpolarized systems.
where:
* k_point is a dimensionless two-dimensional list of coordinates representing a k-point in the 2D Brillouin zone of the unit cell transverse to the transport direction. The coordinates must be given in units of the reciprocal lattice vectors.
* spin is the spin σ.
Why are the options such as "Contour plot, Isourface, ..." shown? Maybe, the reason is that in your script file you did not add the atomic configuration into your sample. You could refer to the example mentioned above.
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General Questions and Answers / Re: spin-polarized transport calculation with magnetic electrodes
« on: March 27, 2010, 15:57 »
Hi, Anders, I did some test calculation these days, it seems that use "ElectrodeConstraints.RealSpaceDensity" is the most effective way to avoid this error.
Since the way VNL places them is bad for this method as you said, if I still want to use RealSpaceDensity, how should I arrange the atoms in the electrode unit cell?
Is there any handbook to tell me how to do this? Or I can do it follow the ATK manual?
Since the way VNL places them is bad for this method as you said, if I still want to use RealSpaceDensity, how should I arrange the atoms in the electrode unit cell?
Is there any handbook to tell me how to do this? Or I can do it follow the ATK manual?
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General Questions and Answers / Re: spin-polarized transport calculation with magnetic electrodes
« on: March 25, 2010, 17:17 »
Thank you, nori, your proposal is indeed effective.
I select "ElectrodeConstraints.RealSpaceDensity" and keep other parameters unchanged then re-do the calculation, the error message doesn't appears again.
But, just as Anders Blom said in another post,
"I generally advise against using electrodeConstraints.RealSpaceDensity. It's legacy method that used to be the old default,
but we have discovered a lot of things with it that work less than satisfactorily.",
I wonder whether the results obtained with this option (ElectrodeConstraints.RealSpaceDensity) is reliable? or this option will have any significant effect on the calculated results?
I select "ElectrodeConstraints.RealSpaceDensity" and keep other parameters unchanged then re-do the calculation, the error message doesn't appears again.
But, just as Anders Blom said in another post,
"I generally advise against using electrodeConstraints.RealSpaceDensity. It's legacy method that used to be the old default,
but we have discovered a lot of things with it that work less than satisfactorily.",
I wonder whether the results obtained with this option (ElectrodeConstraints.RealSpaceDensity) is reliable? or this option will have any significant effect on the calculated results?
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General Questions and Answers / Re: spin-polarized transport calculation with magnetic electrodes
« on: March 24, 2010, 15:00 »
Hi, zh, Anders, bad news. In accordance with zh's suggestion, I modified the input file and re-do the calculation on this system. But the error still came out when the equivalentbulk calculation finished and the two-probe calculation starts. Following is the error message.
# sc 50 : Fermi Energy = -0.29203 Ry Etot = -13430.82223 Ry dRho = 2.1265E-05 dEtot = 1.5297E-05 Ry
# sc 51 : Fermi Energy = -0.29203 Ry Etot = -13430.82224 Ry dRho = 1.1465E-04 dEtot = -8.7508E-06 Ry
# ----------------------------------------------------------------
# TwoProbe Calculation
# ----------------------------------------------------------------
# sc 0 : q = 682.01332 e
Traceback (most recent call last):
File "111niben2.py", line 312, in ?
runtime_parameters = runtime_parameters
ATKError: inverse(DZMatrix const &) : Could not LU factorize!
# sc 50 : Fermi Energy = -0.29203 Ry Etot = -13430.82223 Ry dRho = 2.1265E-05 dEtot = 1.5297E-05 Ry
# sc 51 : Fermi Energy = -0.29203 Ry Etot = -13430.82224 Ry dRho = 1.1465E-04 dEtot = -8.7508E-06 Ry
# ----------------------------------------------------------------
# TwoProbe Calculation
# ----------------------------------------------------------------
# sc 0 : q = 682.01332 e
Traceback (most recent call last):
File "111niben2.py", line 312, in ?
runtime_parameters = runtime_parameters
ATKError: inverse(DZMatrix const &) : Could not LU factorize!
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General Questions and Answers / Re: spin-polarized transport calculation with magnetic electrodes
« on: March 23, 2010, 16:57 »
Hi,zh, I checked the xyz files, it seems that some Nickel atoms of the right surface is missing. My input file is all generated by VNL. I have just checked it again and didn't find significant structural errors, moreover, the calculation can complete correctly for exactly the same system without spin, so I guess the error should not due to the geometry structure.
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General Questions and Answers / Re: spin-polarized transport calculation with magnetic electrodes
« on: March 23, 2010, 16:03 »
Thanks for your advice, zh.
For the electron temperature, the value I previously used was the default value (300K), after I came across this error, I change it to 1000K and then 4K under the advise of Anders Blom, but the error still not been eliminated.
Your advice for spin-polarized calculation is very important and valuable, I will follow it in my future calculation.
In anther topic "Error about runtime_parameters" of the forum, I have already talk about this error with Anders Blom and Nordland. Actually, I had already do a bulk calculation for the spin-polarized Ni (follow the instruction of the atk manual on spin polarized iron), the obtained spin polarization is about 0.33(I made a mistake in previous post). I have also tried many different initial spin for Ni, but the error still always unavoidable.
For the electron temperature, the value I previously used was the default value (300K), after I came across this error, I change it to 1000K and then 4K under the advise of Anders Blom, but the error still not been eliminated.
Your advice for spin-polarized calculation is very important and valuable, I will follow it in my future calculation.
In anther topic "Error about runtime_parameters" of the forum, I have already talk about this error with Anders Blom and Nordland. Actually, I had already do a bulk calculation for the spin-polarized Ni (follow the instruction of the atk manual on spin polarized iron), the obtained spin polarization is about 0.33(I made a mistake in previous post). I have also tried many different initial spin for Ni, but the error still always unavoidable.
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General Questions and Answers / Re: Error about runtime_parameters
« on: March 23, 2010, 09:07 »
Ok, Anders, I will try, Thank you!
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General Questions and Answers / Re: Error about runtime_parameters
« on: March 23, 2010, 08:15 »
Hi,Anders, the calculation can indeed complete correctly for exactly the same system without spin. The error will come out when I give an initial spin to Nickel.
I'm sorry but I'm not quite understand "the atoms in the central region are not ordered in Z.", do you mean that I should try to enlarge the distance between atomic layer of the surface region in Z direction? or I can increase the number of screening layers?
I'm sorry but I'm not quite understand "the atoms in the central region are not ordered in Z.", do you mean that I should try to enlarge the distance between atomic layer of the surface region in Z direction? or I can increase the number of screening layers?
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General Questions and Answers / Re: spin-polarized transport calculation with magnetic electrodes
« on: March 23, 2010, 07:47 »
Hi, Nordland, thanks for your reply!
I did another test calculation with a simplest molecule, that is , a benzenedithion between two Nickel 4*4(111) surface, the initial spin of the Nickel is set to 0.1 while others set to 0. The error also occurs. It seems a really trickey problem. The input and output files are both enclosed.
I did another test calculation with a simplest molecule, that is , a benzenedithion between two Nickel 4*4(111) surface, the initial spin of the Nickel is set to 0.1 while others set to 0. The error also occurs. It seems a really trickey problem. The input and output files are both enclosed.
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General Questions and Answers / spin-polarized transport calculation with magnetic electrodes
« on: March 21, 2010, 11:20 »
Dear all:
Does anyone has ever successfuly did spin-polarized transport calculation using Nickel or other magnetic metal as electrodes? I did some test calculation these days and I find that if I use spin-polarized Nickel or iron as electrodes, then no matter what kind of molecule I choose and what kinds of calculation parameters I used, this error will always appear. It seems that this is a bug of the program. This error bothers me a lot and I don’t know how to avoid this error right now. Can anyone help me?a
Does anyone has ever successfuly did spin-polarized transport calculation using Nickel or other magnetic metal as electrodes? I did some test calculation these days and I find that if I use spin-polarized Nickel or iron as electrodes, then no matter what kind of molecule I choose and what kinds of calculation parameters I used, this error will always appear. It seems that this is a bug of the program. This error bothers me a lot and I don’t know how to avoid this error right now. Can anyone help me?a
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General Questions and Answers / Re: Error about runtime_parameters
« on: March 20, 2010, 08:50 »
Thank you, Anders Blom! Really very tricky problem, I have also trid to running it with NeutralAtoms as initial density or change the type of XC function, but the error will continue to appear all the same…… 
I guess is it possible that there are some problem with the basis of Nickel atom?
I guess is it possible that there are some problem with the basis of Nickel atom?
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Future Releases / Re: What is your Linux distribution?
« on: March 19, 2010, 20:05 »
CentOS release 4.4 (Final)
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General Questions and Answers / Re: Error about runtime_parameters
« on: March 19, 2010, 19:42 »
Thanks for you reply, Anders Bolm. Actually, I had already do a bulk calculation for the spin-polarized Ni (follow the instruction of the atk manual on spin polarized iron), the obtained spin polarization is about 0.13. I have also tried many different initial spin for Ni, but the error still always unavoidable
.
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