Author Topic: Question about geometry optimization for molecule  (Read 7174 times)

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Offline chp

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Question about geometry optimization for molecule
« on: April 14, 2009, 14:52 »
Hi, everyone!

I have performed a calculation of geometry optimization for a dimer composed of one Bi and one Mn atoms, but the optimized structure cannot be obtained after a large number of optimization steps. (Please see the attached script and out file for details.) However, the same initial structure can be optimized successfuly within a few steps using other DFT-based software with similar parameter settings. I also tried to adjust some parameters, no obvious change has been observed. What is the matter?

Thanks in advance!

Offline Nordland

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Re: Question about geometry optimization for molecule
« Reply #1 on: April 15, 2009, 13:35 »
This was a tough one, but the reason is pretty simple once it was clear.

The element Mn the GGA pseudo-potential requires a little charge added to the basis set generation in order for the orbitals to become
more well-behaved. It is a quite rare and esoteric issue, but it is found from time to time.
If you set the parameter charge=0.05 in the basis set parameters, the basis set function will become more smooth and stable under GGA.

I have attached the updated script and the log for your convience....

Offline chp

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Re: Question about geometry optimization for molecule
« Reply #2 on: April 15, 2009, 16:03 »
Thank you very much for your reply ! But still I have two issues.

1.  You have demonstrated that the question results from the parameter setting of charge for the basis set of Mn, however, in your attached script it can be seen that the parameter charge for both Mn and Bi are set the same value (0.05) although they are defined individually. I want to know since the problem lies in Mn, is it necessary to change the parameter charge of Bi to the same value.

2.  You have said that this issue is quite rare, but how can we find it in time ? In addition, how can we set the parameter charge to an appropriate value ? Is there any simple way to determine a suitable value of charge ?

Thanks again !

Offline Nordland

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Re: Question about geometry optimization for molecule
« Reply #3 on: April 15, 2009, 20:16 »
Thank you very much for your reply ! But still I have two issues.
You are most welcome :)

1.  You have demonstrated that the question results from the parameter setting of charge for the basis set of Mn, however, in your attached script it can be seen that the parameter charge for both Mn and Bi are set the same value (0.05) although they are defined individually. I want to know since the problem lies in Mn, is it necessary to change the parameter charge of Bi to the same value.
It is my error. The value for Bi does need to be changed - so that is an error in my script :)

2.  You have said that this issue is quite rare, but how can we find it in time ? In addition, how can we set the parameter charge to an appropriate value ? Is there any simple way to determine a suitable value of charge ?
How to find it - is quite straight forward - if the element ( in your case Mn ) behaves crazy and is uable to relax a dimer or similar system, then we know we are having this problem.
How much charge? That is a tricky question - I guess there is no easy way to find the proper value, however the influence of this parameter is very small, it simply removes an unwanted unbound state in atomic orbitals. Therefore I would just recommend, a quick trial and error, if you ever encounter this problem again. Try 0.05, if it is not enough, the use 0.10 or see what values makes crazy behavior go away, but choose it as small as possible, and be alert if the charge has to be more than 0.4 or so....

However the problem is very rare, and in my 4 years of extensive usage of ATK I have only encountered the problem once before.....

Offline Anders Blom

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Re: Question about geometry optimization for molecule
« Reply #4 on: April 16, 2009, 23:17 »
I just wanted to offer a few additional comment about the second point, how to
a) know that there is a problem, and
b) how to solve

It is strongly recommended to always start out small, when you approach a new material. If you use house-hold elements like carbon this is less necessary, but even for gold, platinum etc, and especially spin-dependent elements like manganese and more rarely used transition elements, one should make a habit of first investigating the basic properties of the material. That means, look at simple dimers, the bulk band structure, how does the energy scale with the lattice constants, etc.

That is - precisely what you have done (I assume the Mn-Bi molecule dimer is not your real project? :) )

This way you learn which mesh cut-off that is required, if LDA is sufficient or GGA is needed, how many k-points, which basis set to use, etc, etc.

So, what to do if problems are encountered? Well, I must admit that tuning the basis set parameters is not the first thing you would try. It is, however, the place you probably end up if all other things fail :) In this particular case it also helped to plot the Mn basis functions (not a trivial exercise).

And then, once you do end up having to tweak the basis set, the only thing that typically helps is to tune the charge (slightly!); the basis set is not very sensitive to the other parameters, but it does respond nicely to the charge setting.

Now we have informed the community about that! :)

Offline chp

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Re: Question about geometry optimization for molecule
« Reply #5 on: April 18, 2009, 04:40 »
Thank you for your nice tips and comments!

There is one issue that I want to confirm. In Nordland’s reply, he mentioned that “The value for Bi does need to be changed”, however, I think that since the initial problem only lies in Mn, it is not necessary to change the parameter charge of Bi. I have performed test calculations, it can be seen that whether change the charge of Bi or not will not result in different convergence process. So, I think the charge of Bi should not be changed.   Is it right?

Offline Anders Blom

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Re: Question about geometry optimization for molecule
« Reply #6 on: April 19, 2009, 21:33 »
That's right, you don't need to change the charge of Bi from the default, but on the other hand as you noted yourself, changing it or not doesn't really have an impact on the calculation.

The default basis set parameters are common for all elements, but as we've learned in this case, they are not necessarily ideal for all elements. On the other hand, small changes of the basis set parameters often have a relatively small influence on the basis set and the results, and in those cases the exact value of the charge and the other parameters are not extremely important.

Actually, the LDA basis set for Mn is fine, it's only the GGA one which needs the modified charge parameters.

Offline chp

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Re: Question about geometry optimization for molecule
« Reply #7 on: April 22, 2009, 09:26 »
Thanks again !