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
<[email protected]> wrote:
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 images, so the
smallest that is possible.
A CI (=auto or suggested by the user) also increases the velocity of the
convergeance and the precision.
To be even faster (10times) and accurate (10times), you can use ARTn that has
been coupled with QE this year and have shown formidable efficiencies (DOI:
10.1021/acs.jctc.0c00541)
Regards,
Antoine Jay
LAAS CNRS
Toulouse, France
Le Mercredi, Octobre 21, 2020 21:04 CEST, Omer Mutasim <[email protected]>
a écrit:
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 <[email protected]>
wrote:
Dear Omar, Hope it helps, just some ideas:- I could tell more if you would
attach the whole input file (ie. thestructures).- Without knowing the
structures only I can give some hints: -- Try using smaller PW basis and lower
ecutwfc, ecutrho to speed upyour simulation. -- When you obtain something more
reliable result, you can changeback 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 theCLIMBING_IMAGES section (choose the CI_scheme
accordingly).Bests, t On Tue, Oct 20, 2020 at 6:53 PM Omer Mutasim
<[email protected]> 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>>>>>
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