please consult the PHonon documentation on how to select perturbed atoms
On Tue, Oct 27, 2020 at 3:13 PM Omer Mutasim wrote:
>
> Great idea.
> but how to fix atoms in lowermost layer(s) in phonon calculation?
> my supercell is large (110 atoms ) , i have fixed lowermost layers by
> setting "
Sorry for confusing.
Single q is OK, k point I don't know but probably also OK
(this one I would check; first use just Gamma here, too).
With the isolated molecule use the same cell size as with
slab and slab+mol for consistency.
Atom fixing: fix only the lowermost layer(s) far from reaction
Omer,
Congrats!
What do you mean by Gamma point vibs. (k points or q points)?
For a single molecule (no slab at all) and large-enough cell i think
both are OK.
For rxn-on-slab I would calibrate but guess it's a good approximation.
Again, fixing the surf. atoms kills chemistry off... try to keep
Dear Antoine,
Thanks for pointing out 1. I guess it's like global minimum search
(more complex, though), thus one need to either heuristically
(by chemical intuition) track some paths or make metadynamics/MC...
As for 2, with good luck (chem. int.) one may need just a few attempts,
albeit second
you saved my life, thanks a bunch Dr. Tamas
I'm only interested in dissociation reaction (SO2 to SO & O) , so i should only
consider image 1 & 2 only, based on AXSF file , for running NEB , right ? what
are these two steps you have seen ?
i'm doing micro-kinetic modeling for reaction
Dear Omer, dear all,
I would like to remind that there is absolutly no reason that the path
returned by the NEB is the real MEP.
The relaxed mep totaly depends on the initial guess of the MEP, which is most
of the time a linear interpolation between the initial and final states, except
if
As i see in the attached axsf file, the dissociation reaction occurs at image
2 , and there is no transition state between image 1 & 2 , does it mean it is
barrier-less reaction ?
On Monday, October 26, 2020, 06:31:22 PM GMT+4, Tamas Karpati
wrote:
please note that in case your
Dear Dr. Tamas your ideas are very helpful. Your are right.i have just noticed
that it is a surface reaction + diffusion of dissociated products (SO & O) to
most stable sites ( one reaction + 2 diffusion step). Dissociation occurs in
image 2 immediately , image 3,4,5 shows diffusion of SO
Dear Dr. Michal I have relaxed both initial and final structure with
forc_conv_thr = 1.0e-03 , and after convergence , each structure has a total
force that is less than 0.004.but after running NEB , it increased to the
above-mentioned values (0.02 & 0.03).However, i will try a tighter
yes, there is a barrier for the reverse reaction.i have check the initial &
final structure again , it was relaxed until force is less than 0.003.I do also
agree with you that i should use 1 neb with barrier, and this is what i'm
doing exactly.but for this dissociation reaction step (SO2 =
Dear Omer,
You have shown a figure of a MEP. Most probably image 4 is either R (reactant)
or P (product). In one case im2=R, im3=TS, im4=P (and im6 is the diffused P),
the other possibility is that im2=diffused R and im4=R then im6=P (im5=TS).
Try to judge which is which, then use R and P to
Dear Omer, dear prof. Kokalj and the QE developer team,
Thank you for the AXSF hint, the format and developing/sharing
XCrySDen and QE for so long!
Each is invaluable.
Best regards,
t
On Mon, Oct 26, 2020 at 6:13 PM Tone Kokalj wrote:
>
> On Mon, 2020-10-26 at 14:38 +, Omer Mutasim
On Mon, 2020-10-26 at 14:38 +, Omer Mutasim wrote:
> Dear Dr. Michal
> I have relaxed both initial and final structure with forc_conv_thr =
> 1.0e-03 ,
> but after running NEB , it increased to the above-mentioned values
> (0.02 & 0.03).
Which is OK, because the unit of force in pw.x is
Dear Omer,
1, SO (being "locally" linear) is not really rotating (just nomenclature)
and such movements are unimportant in this case, I think
2, as for the NEB: as I said, choose the beginning and end images
of what you consider eg. step 1 and run a NEB like before,
except for
please note that in case your preoptimized first and/or last structures
are not the direct reactant and product structures but a R+diffusion
or P+diffusion step results, your MEP would (and it does) look
as if you have modelled a two (or even more) steps "reaction" even if
just one of them is
Dear Omer,
I'd like to underline what Antoine has said and suggest that
both your first and last structures are saddle points (of order K and L,
respectively), rather than minima. Also I agree that your reaction
is not barrierless -in accordance with chemical intuition.
To make it simple, I
Dear Omar,
This:
imageenergy (eV)error (eV/A)frozen
1 -92402.49729070.036606T
2 -92402.80086460.020347F
3 -92402.67892020.048720F
4 -92403.2726990
There is an energy barrier:
the one between your intermediate minima and your final state.
There is no barrier between initial and intermediate minima.
You should wonder why you have an intermediate minima that is lower in energy
(<0.4eV) than the final inserted molecule, this is why I was
Dear Dr. JayI have relaxed the initial and final structures before neb.
Regarding simulation box, i'm using sqrt(3)*sqrt(3) supercell, the other five
reaction steps converged well.However, i have seen in the literature that
similar catalyst resulted in such barrier-less dissociation.So my
Dear Omer,
I think your initial and final minima have not been well relaxed.
When you fix the initial and final structures in a neb you must have relaxed
them before, otherwise, you will have negative energy barriers.
Moreover, you may have rotation of molecules that return local minima if your
Thanks a lot Dr. Antoine Jay for your help.
I've went through your paper, r-ART is by far more faster & precise than NEB, i
will try it.
On Wednesday, October 21, 2020, 11:48:33 PM GMT+4, Antoine Jay
wrote:
Dear Omar,
After your pre-converged step, you can copy all the intermediate
Very helpful ideas.But after pre-converging with inexpensive parameters, i will
get first & last image that are different than my actual images with higher
parameters ( k-pointss, cutoff,..)So then how i can use this pre-converged path
for my actual settings?
Sent from Yahoo Mail for iPhone
Dear Omar,
After your pre-converged step, you can copy all the intermediate images from
the .crd file.
This is a very standard procedure for heavy systems.
Do not worry about the size of the path: it can only increase because the
initial path is the linear interpolation between first and last
Dear Omar,
Hope it helps, just some ideas:
- I could tell more if you would attach the whole input file (ie. the
structures).
- Without knowing the structures only I can give some hints:
-- Try using smaller PW basis and lower ecutwfc, ecutrho to speed up
your simulation.
-- When you obtain
Dear AllI'm doning NEB for dissociation reaction of SO2 to SO +O. But it is not
converging for more than a week, and the path length is increasing. Please tell
me what is wrong in my input file:
below is the input & output files:
Input file:
BEGINBEGIN_PATH_INPUT restart_mode = 'restart'
25 matches
Mail list logo
