instanton rate with fix_atoms active

[Dominik Primožič]

Hello,

I've been playing around with instanton rate calculations and I started using fix_atoms to maintain the system I am intersted in. This introduces reduced degrees of freedom that the engine itself easily computes. 

The trouble comes from analysis as I' ve noticed there is no filter option for TS or instanton case in the ipi.utils.tools.instanton_postproc.py script. I did implement a filter that cleans out removed dof from all arrays but now I come to a standstill.

1) Should I reduce the system completely, natoms, beads.q, m, beads.m3 (which in clean_hessian function says is supposed to be vector with degrees of freedom) because then I dont know if sprint_hessian, B_N and spring_pot are computed correctly. 

2) I read the references and the code and I can't seem to place all the terms so I am not too confident about rewriting too much 

for instanton rate Q_vib its 

logQvib= (-np.sum( np.log(betaP * hbar * np.sqrt(np.absolute(np.delete(d, [1])))))) + nzeros * np.log(nbeads)+ np.log(nbeads)
and I don't know where the secong logN comes from

Thank you very much if anyone is more familiar with this 

[Mariana Rossi]

Hi there, sorry for the slow reply! I will try to activate Yair Litman who wrote the post-processing tool.

The cleanest way is to work on a "masked" space, where you only see the degrees of freedom that you are interested in, so you reduce the dimension of all arrays to the reduced ndof -- I think that is what you are trying to implement, yes?

From a mathematical point of view, all quantities you quote should live in this lower-dimensional space, but one needs to be a bit careful to ensure you have no spurious negative eigenvalues and so on. 

I am not sure I understand your second question, I think it is simply a manipulation of the original expression. Check, e.g., https://pure.mpg.de/view/item_3246769  

Cheers,

Mariana

[yairl...@gmail.com]

Hi,

Have you tried using the filter option in the script?


 python3 instanton_postproc.py -h
[...]
 -f FILTER, --filter FILTER
                        List of atoms indexes to filter (i.e. eliminate its componentes in the position,mass and hessian arrays. It is 0 based.

[...]


Best,
Yair