[QE-users] NEB : path length is increasing
Tamas Karpati
tkarpati at gmail.com
Mon Oct 26 14:58:24 CET 2020
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 recommend
- make your 2nd image the first,
- make your 6th image the last,
- do use more images (even for a single step reaction,
but your MEP indicates two TS-es meaning a 2 step reaction
which -on more elaboration- may turn out to be an N step one;
only you need more points to see its real E-profile).
- rerun your NEB job.
In fact you should check for imaginary second derivatives by the Phonon code
to ensure about each minima/maxima/TS being what they look in such a MEP.
Of course, it is painfully slow and many just skip this step.
Other ideas:
- check the geometry of your 3 local minima and 2 TS-es
to see if they correspond to chemically rational structures.
- if they look so, decide whether the second minimum is really
your product, and if it is so then this should be your last image
(and not the 6th as I said above) for rerunning your NEB.
- of course, you can model a multistep reaction by a single NEB job,
choose the approach that best serves your postprocessing task.
Hope this helps,
t
On Mon, Oct 26, 2020 at 1:40 PM Antoine Jay <ajay at laas.fr> wrote:
>
> 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 asking if it was enough relaxed.
> Maybe the first exothermic reaction gives enough energy for the second...
> But for sure, when you have such a multi-barriers reaction, a 7 images neb is not enough.
> If you need accurate results, it is better to have 1 neb per barrier, as you have 1 CI per path.
>
> Regards,
>
> Antoine Jay
> LAAS-CNRS
> Toulouse, France
>
> Le Lundi, Octobre 26, 2020 09:10 CET, Omer Mutasim <omermutasim at ymail.com> a écrit:
>
>
>
>
>
> Dear Dr. Jay
> I 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 question goes like : with this oscillated MEP , can i conclude it is barrier-less reaction ? or it is even necessary for barrier-less step to have no oscillation ?
> does changing the adsorption site of the reactant (SO2) to less stable site might solve the issue ?
>
> Regards
> On Monday, October 26, 2020, 11:25:36 AM GMT+4, Antoine Jay <ajay at laas.fr> wrote:
>
>
> 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 simulation box is too small.
>
> Regards,
>
> Antoine Jay
> LAAS-CNRS
> Toulouse, France
>
>
> Le Lundi, Octobre 26, 2020 06:39 CET, Omer Mutasim <omermutasim at ymail.com> a écrit:
>
>
>
>
>
>
> Thanks a lot Dr. Tamas & Dr. Jay. , it is very efficient procedure, it worked for me now for all reaction steps. cheers
>
> However for one elementary step , particularly SO2 dissociation ( SO2 = SO+O ) i got the following activation barrier, (it hasn't finished yet, but expected to remain around these values since it doesn't change much):
>
> ------------------------------ iteration 297 ------------------------------
>
> activation energy (->) = 0.000000 eV
> activation energy (<-) = 0.308512 eV
>
> image energy (eV) error (eV/A) frozen
>
> 1 -92402.4972907 0.036606 T
> 2 -92402.8008646 0.020347 F
> 3 -92402.6789202 0.048720 F
> 4 -92403.2726990 0.102631 F
> 5 -92403.0642888 0.050277 F
> 6 -92403.2377599 0.067121 F
> 7 -92402.8058032 0.029355 T
> activation energy (->) = 0.000000 eV
> activation energy (<-) = 0.308512 eV
>
>
> Attached is the MEP curve. As you see in MEP graph , there is oscillation in energies.
> is it normal to get this oscillated MEP curve for such barrier-less reaction step ? if not, how to get rid of this oscillations ?
> does using "CI" can increase this barrier a bit ?
>
> Thanks in advance
>
> Regards
> On Wednesday, October 21, 2020, 11:04:14 PM GMT+4, Omer Mutasim <omermutasim at ymail.com> wrote:
>
>
> 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
>
>
> On Wednesday, October 21, 2020, 3:06 PM, Tamas Karpati <tkarpati at gmail.com> wrote:
>
> 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 something more reliable result, you can change
> back to the higher basis.
> -- Try leaving opt_scheme at its default value.
> -- For such a reaction (dissociation of such a polarized molecule) you should
> expect a barrier, therefore CI_scheme should be anything except for no-CI.
> -- The best is if you can specify the CI manually in the
> CLIMBING_IMAGES section
> (choose the CI_scheme accordingly).
> Bests,
> t
>
> On Tue, Oct 20, 2020 at 6:53 PM Omer Mutasim <omermutasim at ymail.com> wrote:
> >
> > Dear All
> > I'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:
> >
> > BEGIN
> > BEGIN_PATH_INPUT
> > &PATH
> > restart_mode = 'restart'
> > string_method = 'neb',
> > nstep_path = 800,
> > ds = 1.D0,
> > opt_scheme = "broyden",
> > num_of_images = 7,
> > CI_scheme = 'no-CI',
> > path_thr = 0.05D0,
> >
> > /
> > END_PATH_INPUT
> > BEGIN_ENGINE_INPUT
> > &CONTROL
> > calculation = "relax"
> > prefix = 'SO2_neb'
> > outdir = './outdir'
> > pseudo_dir = '/home/yQE-test/pseudo/'
> > restart_mode = 'from_scratch'
> > forc_conv_thr = 1.0e-03
> > etot_conv_thr = 1e-04
> > nstep = 200
> > !tefield = .TRUE
> > !dipfield = .TRUE
> > /
> >
> > &SYSTEM
> > ibrav = 0
> > ecutrho = 270
> > ecutwfc = 45
> > nat = 111
> > ntyp = 4
> > occupations='smearing',smearing='gaussian',degauss=0.005
> > vdw_corr = 'DFT-D2'
> > !edir = 3 , emaxpos = 0.6808, eopreg = 0.08 , eamp = 0.001,
> > nspin = 2
> > starting_magnetization(1)= 0.01
> >
> > /
> > &ELECTRONS
> > conv_thr = 1e-06
> > electron_maxstep = 200
> > mixing_mode ='local-TF'
> > mixing_beta = 0.3
> >
> > /
> >
> > &IONS
> > /
> >
> > K_POINTS {automatic}
> > 3 3 1 0 0 1
> >
> > ATOMIC_SPECIES
> > Ni 58.69340 Ni.pbe-n-rrkjus_psl.0.1.UPF
> > P 30.97376 P.pbe-n-rrkjus_psl.1.0.0.UPF
> > S 32.065 S.pbe-n-rrkjus_psl.1.0.0.UPF
> > O 15.9999 O.pbe-n-rrkjus_psl.1.0.0.UPF
> > CELL_PARAMETERS {angstrom}
> > 11.765383541833 0.0000000000 0.0000000000
> > -5.88269177091652 10.1891210324947 0.0000000000
> > 0.0000000000 0.0000000000 30.9938690567585
> > BEGIN_POSITIONS
> > FIRST_IMAGE
> > ATOMIC_POSITIONS (angstrom)
> > S -1.181561037 6.155418563 12.124345096
> > O -1.100425541 4.672437254 11.356300976
> > O 0.190308001 6.839217965 11.448732238
> > Ni -2.738525121 4.763450297 0.239145520
> > Ni 3.139579474 1.358483744 0.232252034
> > Ni 3.135766403 8.150575392 0.235327906
> > Ni -4.673593720 8.104467836 1.780118367
> > .
> > .
> > .
> > .
> >
> > output file:
> >
> > Program NEB v.6.4.1 starts on 16Oct2020 at 11:35:32
> >
> > This program is part of the open-source Quantum ESPRESSO suite
> > for quantum simulation of materials; please cite
> > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
> > "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
> > URL http://www.quantum-espresso.org",
> > in publications or presentations arising from this work. More details at
> > http://www.quantum-espresso.org/quote
> >
> > Parallel version (MPI), running on 80 processors
> >
> > MPI processes distributed on 5 nodes
> > R & G space division: proc/nbgrp/npool/nimage = 80
> >
> > parsing_file_name: input.in
> > Reading input from pw_1.in
> > Message from routine read_upf::
> >
> >
> > initial path length = 11.3145 bohr
> > initial inter-image distance = 1.8857 bohr
> >
> > string_method = neb
> > restart_mode = from_scratch
> > opt_scheme = broyden
> > num_of_images = 7
> > nstep_path = 800
> > CI_scheme = no-CI
> > first_last_opt = F
> > use_freezing = F
> > ds = 1.0000 a.u.
> > k_max = 0.1000 a.u.
> > k_min = 0.1000 a.u.
> > suggested k_max = 0.6169 a.u.
> > suggested k_min = 0.6169 a.u.
> > path_thr = 0.0500 eV / A
> >
> > ------------------------------ iteration 1 ------------------------------
> >
> > tcpu = 6.2 self-consistency for image 1
> > tcpu = 3675.5 self-consistency for image 2
> > tcpu = 7662.5 self-consistency for image 3
> > tcpu = 11422.7 self-consistency for image 4
> > tcpu = 15346.3 self-consistency for image 5
> > tcpu = 19108.7 self-consistency for image 6
> > tcpu = 22571.1 self-consistency for image 7
> >
> > activation energy (->) = 70.216194 eV
> > activation energy (<-) = 71.022062 eV
> >
> > image energy (eV) error (eV/A) frozen
> >
> > 1 -92476.9473351 0.023792 T
> > 2 -92468.8536637 23.505267 F
> > 3 -92442.9691259 150.213122 F
> > 4 -92406.7311409 330.353055 F
> > 5 -92431.0052901 207.333777 F
> > 6 -92469.0661237 51.663167 F
> > 7 -92477.7532028 0.024858 T
> >
> > path length = 11.314 bohr
> > inter-image distance = 1.886 bohr
> >
> > ------------------------------ iteration 2 ------------------------------
> >
> > tcpu = 26119.7 self-consistency for image 2
> > tcpu = 28731.5 self-consistency for image 3
> > tcpu = 31027.4 self-consistency for image 4
> > tcpu = 34094.2 self-consistency for image 5
> > tcpu = 36988.0 self-consistency for image 6
> >
> > activation energy (->) = 22.531451 eV
> > activation energy (<-) = 23.337319 eV
> >
> > image energy (eV) error (eV/A) frozen
> >
> > 1 -92476.9473351 0.023792 T
> > 2 -92469.5101428 22.300995 F
> > 3 -92454.4158842 70.627594 F
> > 4 -92461.1206812 34.307062 F
> > 5 -92464.4669859 46.783708 F
> > 6 -92471.4896125 37.765708 F
> > 7 -92477.7532028 0.024858 T
> >
> > path length = 11.384 bohr
> > inter-image distance = 1.897 bohr
> >
> > ------------------------------ iteration 3 ------------------------------
> >
> > tcpu = 39172.0 self-consistency for image 2
> > tcpu = 41888.0 self-consistency for image 3
> > tcpu = 44777.8 self-consistency for image 4
> > tcpu = 47642.0 self-consistency for image 5
> > tcpu = 50615.2 self-consistency for image 6
> >
> > activation energy (->) = 13.435341 eV
> > activation energy (<-) = 14.241209 eV
> >
> > image energy (eV) error (eV/A) frozen
> >
> > 1 -92476.9473351 0.023792 T
> > 2 -92471.6434742 16.119604 F
> > 3 -92463.5119937 28.367753 F
> > 4 -92468.1466546 16.740841 F
> > 5 -92472.7705146 11.019872 F
> > 6 -92475.3040517 10.662908 F
> > 7 -92477.7532028 0.024858 T
> >
> > path length = 11.502 bohr
> > inter-image distance = 1.917 bohr
> >
> > ------------------------------ iteration 4 ------------------------------
> >
> > tcpu = 53323.8 self-consistency for image 2
> > tcpu = 56077.9 self-consistency for image 3
> > tcpu = 59014.9 self-consistency for image 4
> > tcpu = 61990.6 self-consistency for image 5
> > tcpu = 64608.8 self-consistency for image 6
> >
> > activation energy (->) = 6.530687 eV
> > activation energy (<-) = 7.336554 eV
> >
> > image energy (eV) error (eV/A) frozen
> >
> > 1 -92476.9473351 0.023792 T
> > 2 -92474.0378392 7.910468 F
> > 3 -92470.4166483 13.061889 F
> > 4 -92471.2528453 9.923078 F
> > 5 -92474.2165523 4.209611 F
> > 6 -92476.2787664 3.450159 F
> > 7 -92477.7532028 0.024858 T
> >
> > path length = 11.724 bohr
> > inter-image distance = 1.954 bohr
> >
> > ------------------------------ iteration 5 ------------------------------
> >
> > tcpu = 67273.9 self-consistency for image 2
> > tcpu = 70152.2 self-consistency for image 3
> > tcpu = 73153.1 self-consistency for image 4
> > tcpu = 76203.5 self-consistency for image 5
> > tcpu = 78824.8 self-consistency for image 6
> >
> > activation energy (->) = 3.710859 eV
> > activation energy (<-) = 4.516727 eV
> >
> > image energy (eV) error (eV/A) frozen
> >
> > 1 -92476.9473351 0.023792 T
> > 2 -92475.5387437 3.615458 F
> > 3 -92473.5622985 4.695416 F
> > 4 -92473.2364760 5.734324 F
> > 5 -92474.4833513 2.877608 F
> > 6 -92476.4425910 2.876700 F
> > 7 -92477.7532028 0.024858 T
> >
> > path length = 12.038 bohr
> > inter-image distance = 2.006 bohr
> >
> > ------------------------------ iteration 6 ------------------------------
> >
> > tcpu = 81355.0 self-consistency for image 2
> > tcpu = 84402.5 self-consistency for image 3
> > tcpu = 87564.5 self-consistency for image 4
> > tcpu = 90568.2 self-consistency for image 5
> > tcpu = 93110.5 self-consistency for image 6
> >
> > activation energy (->) = 2.560838 eV
> > activation energy (<-) = 3.366706 eV
> >
> > image energy (eV) error (eV/A) frozen
> >
> > 1 -92476.9473351 0.023792 T
> > 2 -92476.0900010 1.040106 F
> > 3 -92474.7832671 2.988289 F
> > 4 -92474.3864972 2.085630 F
> > 5 -92474.8266397 1.998808 F
> > 6 -92476.6377600 0.667994 F
> > 7 -92477.7532028 0.024858 T
> >
> > path length = 12.364 bohr
> > inter-image distance = 2.061 bohr
> >
> > ------------------------------ iteration 7 ------------------------------
> >
> > tcpu = 95248.7 self-consistency for image 2
> > tcpu = 98189.3 self-consistency for image 3
> > tcpu = 101337.9 self-consistency for image 4
> > tcpu = 104423.7 self-consistency for image 5
> > tcpu = 107076.7 self-consistency for image 6
> >
> > activation energy (->) = 2.125802 eV
> > activation energy (<-) = 2.931670 eV
> >
> > image energy (eV) error (eV/A) frozen
> >
> > 1 -92476.9473351 0.023792 T
> > 2 -92476.0736630 1.319140 F
> > 3 -92475.4151167 1.955048 F
> > 4 -92474.8215329 1.921925 F
> > 5 -92475.0627346 2.135695 F
> > 6 -92476.7117640 0.696381 F
> > 7 -92477.7532028 0.024858 T
> >
> > path length = 12.868 bohr
> > inter-image distance = 2.145 bohr
> >
> > ------------------------------ iteration 8 ------------------------------
> >
> > tcpu = 108885.3 self-consistency for image 2
> > tcpu = 111194.4 self-consistency for image 3
> > tcpu = 113961.2 self-consistency for image 4
> > tcpu = 116506.3 self-consistency for image 5
> > tcpu = 118361.2 self-consistency for image 6
> >
> > activation energy (->) = 2.073805 eV
> > activation energy (<-) = 2.879673 eV
> >
> > image energy (eV) error (eV/A) frozen
> >
> > 1 -92476.9473351 0.023792 T
> > 2 -92476.1622863 0.861666 F
> > 3 -92475.4162307 2.192183 F
> > 4 -92474.8735300 1.631538 F
> > 5 -92475.0684015 1.824977 F
> > 6 -92476.7113576 0.606060 F
> > 7 -92477.7532028 0.024858 T
> >
> > path length = 12.633 bohr
> > inter-image distance = 2.105 bohr
> >
> >
> > .
> > .
> > .
> > .
> > .
> > .
> > reading file 'SO2_neb.path'
> >
> >
> > string_method = neb
> > restart_mode = restart
> > opt_scheme = broyden
> > num_of_images = 7
> > nstep_path = 800
> > CI_scheme = no-CI
> > first_last_opt = F
> > use_freezing = F
> > ds = 1.0000 a.u.
> > k_max = 0.1000 a.u.
> > k_min = 0.1000 a.u.
> > suggested k_max = 0.6169 a.u.
> > suggested k_min = 0.6169 a.u.
> > path_thr = 0.0500 eV / A
> >
> > ------------------------------ iteration 26 ------------------------------
> >
> > tcpu = 6.2 self-consistency for image 2
> > tcpu = 3713.3 self-consistency for image 3
> > tcpu = 7137.5 self-consistency for image 4
> > tcpu = 10796.2 self-consistency for image 5
> > tcpu = 14447.3 self-consistency for image 6
> >
> > activation energy (->) = 0.640765 eV
> > activation energy (<-) = 1.446632 eV
> >
> > image energy (eV) error (eV/A) frozen
> >
> > 1 -92476.9473351 0.023792 T
> > 2 -92476.3065704 0.250516 F
> > 3 -92477.0673165 0.278078 F
> > 4 -92476.7787332 0.431860 F
> > 5 -92476.4800774 0.453182 F
> > 6 -92476.5576488 0.296200 F
> > 7 -92477.7532028 0.024858 T
> >
> > path length = 17.545 bohr
> > inter-image distance = 2.924 bohr
> >
> > ------------------------------ iteration 27 ------------------------------
> >
> > tcpu = 18237.5 self-consistency for image 2
> > tcpu = 20736.0 self-consistency for image 3
> > tcpu = 23008.1 self-consistency for image 4
> > tcpu = 25721.8 self-consistency for image 5
> > tcpu = 28310.3 self-consistency for image 6
> >
> > activation energy (->) = 0.643277 eV
> > activation energy (<-) = 1.449145 eV
> >
> > image energy (eV) error (eV/A) frozen
> >
> > 1 -92476.9473351 0.023792 T
> > 2 -92476.3040583 0.235899 F
> > 3 -92477.0080434 0.474599 F
> > 4 -92476.8143156 0.678632 F
> > 5 -92476.4592005 0.597470 F
> > 6 -92476.4827638 0.224064 F
> > 7 -92477.7532028 0.024858 T
> >
> > path length = 18.367 bohr
> > inter-image distance = 3.061 bohr
> >
> > ------------------------------ iteration 28 ------------------------------
> >
> > tcpu = 30382.0 self-consistency for image 2
> > tcpu = 32498.8 self-consistency for image 3
> > tcpu = 34597.5 self-consistency for image 4
> > tcpu = 37250.7 self-consistency for image 5
> > tcpu = 39649.7 self-consistency for image 6
> >
> > activation energy (->) = 0.651733 eV
> > activation energy (<-) = 1.457601 eV
> >
> > image energy (eV) error (eV/A) frozen
> >
> > 1 -92476.9473351 0.023792 T
> > 2 -92476.2956021 0.236096 F
> > 3 -92476.9388664 0.680956 F
> > 4 -92476.8025379 0.874373 F
> > 5 -92476.3933083 0.734403 F
> > 6 -92476.4272820 0.239132 F
> > 7 -92477.7532028 0.024858 T
> >
> > path length = 19.115 bohr
> > inter-image distance = 3.186 bohr
> >
> > ------------------------------ iteration 29 ------------------------------
> >
> > tcpu = 41622.7 self-consistency for image 2
> > tcpu = 43787.2 self-consistency for image 3
> > tcpu = 45892.1 self-consistency for image 4
> > tcpu = 48482.6 self-consistency for image 5
> > tcpu = 50617.1 self-consistency for image 6
> >
> > activation energy (->) = 0.661553 eV
> > activation energy (<-) = 1.467420 eV
> >
> > image energy (eV) error (eV/A) frozen
> >
> > 1 -92476.9473351 0.023792 T
> > 2 -92476.2857825 0.249692 F
> > 3 -92476.8823826 0.778237 F
> > 4 -92476.7843580 1.002202 F
> > 5 -92476.3323697 0.748960 F
> > 6 -92476.3885082 0.238984 F
> > 7 -92477.7532028 0.024858 T
> >
> > path length = 19.742 bohr
> > inter-image distance = 3.290 bohr
> >
> > ------------------------------ iteration 30 ------------------------------
> >
> > tcpu = 52474.3 self-consistency for image 2
> > tcpu = 54679.9 self-consistency for image 3
> > tcpu = 57012.5 self-consistency for image 4
> > tcpu = 59877.3 self-consistency for image 5
> > tcpu = 62490.2 self-consistency for image 6
> >
> > activation energy (->) = 0.704760 eV
> > activation energy (<-) = 1.510628 eV
> >
> > image energy (eV) error (eV/A) frozen
> >
> > 1 -92476.9473351 0.023792 T
> > 2 -92476.2668397 0.342411 F
> > 3 -92476.7810889 0.907920 F
> > 4 -92476.7414553 1.153276 F
> > 5 -92476.2425749 0.898295 F
> > 6 -92476.3370447 0.341313 F
> > 7 -92477.7532028 0.024858 T
> >
> > path length = 20.745 bohr
> > inter-image distance = 3.457 bohr
> >
> > ------------------------------ iteration 31 ------------------------------
> >
> > tcpu = 64431.3 self-consistency for image 2
> > tcpu = 66430.0 self-consistency for image 3
> > tcpu = 68491.4 self-consistency for image 4
> > tcpu = 70987.8 self-consistency for image 5
> >
> >
> >
> >
> > _______________________________________________
> > Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> > users mailing list users at lists.quantum-espresso.org
> > https://lists.quantum-espresso.org/mailman/listinfo/users
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
>
>
>
>
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
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