Idea proposed #1

[rezabma]

Hi,
I use flos with siesta to find transition state of chemical reaction by NEB method. I worked with some other codes (such as FHI-aims and OPENMX) to use them for NEB calculation. I will write my ideas for neb calculation by flos/siesta, and propose some idea for its performance. This is the first part (#1):

1- As a chemist user (which are the main user of NEB), I don't need detailed information on forces, such as tangent, perpendicular, spring, ... . Only one parameter (i.e., maximum force on images) is more clear for the neb iteration step. So, I need to know that in each NEB iteration, what is the maximum force, and does the path goes to the minimize the force or not. By seeing fluctuations in maximum force (and also their images) I decided to continue the job or kill it. It is very important. Because, we (chemists) could easily find from the images of a NEB iteration that if the path is good for NEB or not.

2- I am not sure, and didn't investigate their detail codes, but I think ASE approach in FHI-aims has less force fluctuation. I have tested the same job with FHI-aims and flos/siesta.

3- We need that for each NEB iteration to see the proposed path and its maximum force. Jmol program can easily show the path, but need that all images be in one file. We need jmol or other similar open source code to see the path. So, for each iteration it is better that the code save all images in one file. Now, the code writes all iterations of an image in a file which is not useful for investigating the NEB path for each iteration step.

4- Maybe saving jmol xyz file in a directory with the name of iterationXXX is better.

5- It is better that the code gets initial and final optimized structure in the fdf file and generate the images authomatically. it is more user-friendly work.

6- All NEB parameters (such as number of images, the maximum force criteria, needing climbing or not, spring force constant, initial and final image, ....) should be readable from one fdf input file. It is more user-friendly work.

Siesta code is very fast. using more user-friendly flos with it, could be convert it to the most usable code for NEB.

Thanks
Reza

[zerothi]

Thanks for all your suggestions! They are highly welcoming!

I am a bit busy at the moment, but I will have all your suggestions in mind when I return for this.

Let me note your mark 2. With Siesta you may need to ensure a very high cutoff to stabilize forces. The egg-box effect will play tricks on you. Alternatively you can use GridCellSampling to damp the fluctuations.

[zerothi]

5. has just been implemented, now one can either supply images manually or let the NEB class do linear interpolation.

[rezabma]

thanks

[zerothi]

I'll reopen since there are other issues that I need to take care of! :)
Again, thanks.

[rezabma]

Hi,
Recently, an automated version of NEB has been proposed by the NEB developer teams:

1- https://aip.scitation.org/doi/abs/10.1063/1.4961868
J. Chem. Phys. 145, 094107 (2016); https://doi.org/10.1063/1.4961868

2- https://aip.scitation.org/doi/abs/10.1063/1.5021153
J. Chem. Phys. 148, 029903 (2018); https://doi.org/10.1063/1.5021153

It needs less iteration numbers with better estimated TS for complex chemical reactions. It is highly requested to be included in flos NEB.

[zerothi]

Thanks for your information!
I'll leave open in case other people wish to take on this!

[rezabma]

I'm not sure, but I think ASE developers used this approach for their NEB version:
https://wiki.fysik.dtu.dk/ase/ase/neb.html#