QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: zdhlover on June 9, 2016, 10:53

Title: Why I get error optmized structure when I use the ATK optmized method of LBFGS
Post by: zdhlover on June 9, 2016, 10:53

I get error optmized structure  when I use the ATK optmized method of  LBFGS ,maybe also I get the error one when I use the ATK optmized method of  QuasiNewton, which are the hydrogens go away to the error position: or no band with the original of the bonding atoms. I  also have been  meet the phenomenon of atoms  running free，Why？
The structure of the initial and the  0ptimized structur are as the append file.
Thanks a lot.

Title: Re: Why I get error optmized structure when I use the ATK optmized method of LBFGS
Post by: zh on June 10, 2016, 06:43

First, the stick between atoms is the real chemical bond and it is used just to connect two atoms for helping visualization.
If there are no stick between two atoms, it means the bond length of these two atoms exceeding a certain value to show the stick.
The important thing is to check the change of the bond lengths before and after optimization for those atoms you are interested in.

Title: Re: Why I get error optmized structure when I use the ATK optmized method of LBFGS
Post by: Jess Wellendorff on June 10, 2016, 08:36

There is a variable in the VNL Viewer Properties called "fuzz factor", which determines how short the atom-atom distance should be for a bond to be visualized. If you increase the fuzz factor, longer bond lengths are also visualized.

Title: Re: Why I get error optmized structure when I use the ATK optmized method of LBFGS
Post by: zdhlover on June 11, 2016, 05:24

Thanks the reply of the two specialist,I mean what you say . My focus is on why the atoms go away even bonding with other atoms or as an independent  atopms after the optimization, and I met this situation many times.

Title: Re: Why I get error optmized structure when I use the ATK optmized method of LBFGS
Post by: Anders Blom on June 11, 2016, 12:16

See http://quantumwise.com/support/faq/item/846-bonds-between-some-atoms-are-missing

Title: Re: Why I get error optmized structure when I use the ATK optmized method of LBFGS
Post by: zdhlover on June 17, 2016, 08:35

Thank you for your prompt reply, but my point is, when I optimize a structure of the atom I used to go to other places,  and  change to another structure which are not I need. For example: the structure in appeend file of origin2.gif is  my need ,but no matter how do I change the position of the hydrogen atom, it always run to the carbon atoms on the edge of the opposite, and change to the structure in appeend file of optimized2.gif.

And I met the same thing many times,as the other example as the append files.

Title: Re: Why I get error optmized structure when I use the ATK optmized method of LBFGS
Post by: Jess Wellendorff on June 17, 2016, 08:45

2 possible reasons:
1) The initial structure is not the minimum-energy geometry of the molecule. I have no idea if this is so or not.
2) You are not doing the geometry optimization correctly, or are using an insufficiently accurate computational method. I have not seen your ATK Python script, so I cannot say if this is so or not.