about dimer calculation

Vasp transition state theory tools

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kxshan
Posts: 14
Joined: Fri Oct 19, 2007 8:39 am

about dimer calculation

Post by kxshan »

hi
I am doing the dimer calculation.
My INCAR:
SYSTEM = La4Mo4O18
IBRION=3
POTIM=0.0
ISYM=0
NSW=800
EDIFF=1E-7
EDIFFG=-0.0001
PREC=Norm
LREAL=ON
LWAVE=.FALSE.
LCHARG=.FALSE.

# DIMER PARAMETERS
ICHAIN=2
DdR=0.005
DRotMax=4
DFNMin=0.01
DFNMax=1.0

# OPTIMIZER PARAMETERS
IOPT=2

the DIMCAR is
Step Force Torque Energy Curvature Angle
1 6.45243 16.58549 -232.21228 14.32065 31.86760
1 6.45243 7.48148 -232.21228 3.42504 27.23917
1 6.45243 6.72980 -232.21228 0.92003 20.14422
1 6.45243 6.18008 -232.21228 -0.82054 13.60940
2 5.15889 6.52398 -232.87864 -2.84331 11.48339
2 5.15889 4.96310 -232.87864 -4.30161 11.49395
2 5.15889 4.49564 -232.87864 -5.03130 5.58982
2 5.15889 2.74675 -232.87864 -5.29675 8.22044
3 5.10822 3.58815 -233.53504 -2.60144 7.66682
3 5.10822 3.20952 -233.53504 -2.94692 4.38140
3 5.10822 2.05029 -233.53504 -3.18344 2.96049
3 5.10822 1.82373 -233.53504 -3.21882 2.59884
4 5.22239 3.00591 -234.11719 -2.31679 14.31514
4 5.22239 4.19467 -234.11719 -2.54642 5.34198
4 5.22239 1.59852 -234.11719 -2.94682 3.31584
4 5.22239 1.74065 -234.11719 -3.31059 2.68253
5 5.44404 2.55366 -234.76979 -1.98289 4.85197
5 5.44404 1.93690 -234.76979 -1.91911 2.54446
5 5.44404 1.35792 -234.76979 -2.10491 1.67718
5 5.44404 1.31680 -234.76979 -2.06843 1.79770
6 5.49516 2.86867 -235.47254 -0.82121 15.28834
6 5.49516 4.13655 -235.47254 -0.98614 6.33507
6 5.49516 2.42585 -235.47254 -1.59249 4.53872
6 5.49516 2.55879 -235.47254 -1.62911 4.09464
7 5.30621 3.27433 -236.27056 -2.92077 8.35965
7 5.30621 3.18199 -236.27056 -3.06097 3.62675
7 5.30621 1.49872 -236.27056 -3.31529 2.02372
7 5.30621 1.43309 -236.27056 -3.32484 1.76514
8 4.82355 3.43804 -236.95133 -2.04441 17.33648
8 4.82355 3.93203 -236.95133 -2.35208 5.08543
8 4.82355 1.70923 -236.95133 -2.90746 4.20905
8 4.82355 2.16037 -236.95133 -2.95122 2.48372
9 3.54485 2.34269 -237.60836 -2.94479 7.37546
9 3.54485 2.54274 -237.60836 -2.99572 3.42606
9 3.54485 1.21691 -237.60836 -3.27792 2.22842
9 3.54485 1.17694 -237.60836 -3.21593 1.80387
10 3.43975 3.52297 -238.22371 -2.12801 15.52425
10 3.43975 4.79668 -238.22371 -2.60374 5.88646
10 3.43975 2.03209 -238.22371 -3.23860 3.44767
10 3.43975 2.09231 -238.22371 -3.23072 3.49299
11 4.36685 6.63656 -238.79343 -3.18086 34.11133
11 4.36685 25.52622 -238.79343 -2.25977 72.15130
11 4.36685 31.58076 -238.79343 -65.44083 56.09083
11 4.36685 15.97296 -238.79343 -74.25368 45.66570
12 4.93044 10.77805 -239.18008 11.06188 67.33115
12 4.93044 9.30701 -239.18008 8.84782 62.73806
12 4.93044 6.07717 -239.18008 5.74918 41.15528
12 4.93044 4.06963 -239.18008 2.76853 19.59577
13 6.00562 5.02470 -239.03149 3.72592 14.06730
13 6.00562 4.76090 -239.03149 2.73265 12.02927
13 6.00562 5.42341 -239.03149 1.63984 11.29240
13 6.00562 5.67453 -239.03149 0.77899 10.36874
14 6.23063 6.64452 -238.89053 1.27831 21.37881
14 6.23063 7.91117 -238.89053 -0.38975 12.41223
14 6.23063 5.26422 -238.89053 -1.97029 12.59205
14 6.23063 5.56788 -238.89053 -2.86975 7.92353
15 5.61425 3.92782 -239.45305 -2.94066 10.30059
15 5.61425 3.90593 -239.45305 -3.45763 3.86029
15 5.61425 2.00867 -239.45305 -3.74455 5.50106
15 5.61425 3.13559 -239.45305 -3.90765 2.66900
16 6.07708 3.62423 -240.11174 -4.11598 9.11523
16 6.07708 3.66453 -240.11174 -4.52861 3.52450
16 6.07708 1.80708 -240.11174 -4.87051 3.95297
16 6.07708 2.62123 -240.11174 -4.81904 2.26888
17 4.81899 2.54983 -240.60319 -4.85268 6.64167
17 4.81899 1.99377 -240.60319 -4.73624 3.02078
17 4.81899 1.04000 -240.60319 -4.92684 1.65338
17 4.81899 1.10762 -240.60319 -4.94373 1.27833
18 4.49744 2.38422 -241.31678 -3.11624 9.49899
18 4.49744 2.11541 -241.31678 -3.10916 3.18509
18 4.49744 0.88955 -241.31678 -3.22996 1.84939
19 4.86542 2.88227 -241.82349 -2.89335 9.16691
19 4.86542 3.27031 -241.82349 -3.15394 4.77308
19 4.86542 1.83341 -241.82349 -3.29231 2.68972
19 4.86542 1.78881 -241.82349 -3.33318 2.59334
20 3.38232 3.27448 -242.45330 -1.19767 10.19681
20 3.38232 2.81115 -242.45330 -1.56045 4.96624
20 3.38232 1.58994 -242.45330 -1.72597 2.37475
20 3.38232 1.41707 -242.45330 -1.80229 2.10922
21 4.11239 2.56759 -242.78356 -1.62979 8.59332
21 4.11239 2.55680 -242.78356 -1.66968 4.41373
21 4.11239 1.86860 -242.78356 -1.99373 2.70155
21 4.11239 1.73993 -242.78356 -2.00309 3.16787
22 2.48954 3.39848 -243.20788 -0.71196 10.27643
22 2.48954 3.32557 -243.20788 -0.99758 5.77091
22 2.48954 2.45069 -243.20788 -1.23207 3.49045
22 2.48954 1.88977 -243.20788 -1.31317 3.78594
23 3.57083 3.10989 -243.35788 -0.99014 6.07032
23 3.57083 2.36228 -243.35788 -1.15356 3.56631
23 3.57083 1.55320 -243.35788 -1.26417 2.17066
23 3.57083 1.19237 -243.35788 -1.25591 1.76328
24 2.19827 2.53443 -243.67413 -1.06002 6.18951
24 2.19827 2.31030 -243.67413 -1.24034 4.27137
24 2.19827 1.79680 -243.67413 -1.42297 2.58319
24 2.19827 1.50230 -243.67413 -1.44313 3.32827
25 2.21082 2.95105 -243.77572 -0.44531 6.90821
25 2.21082 2.87500 -243.77572 -0.74714 4.76304
25 2.21082 2.00400 -243.77572 -0.87810 3.68174
25 2.21082 1.98497 -243.77572 -0.88557 3.68203
26 2.00530 2.75723 -243.97738 -1.08977 6.47034
26 2.00530 2.43123 -243.97738 -1.31714 3.77712
26 2.00530 1.74488 -243.97738 -1.45098 2.72199
26 2.00530 1.53326 -243.97738 -1.45662 2.19973
27 2.04762 2.40435 -244.06368 -0.16777 6.61459
27 2.04762 2.48613 -244.06368 -0.22507 4.38709
27 2.04762 2.20156 -244.06368 -0.47509 4.05137
27 2.04762 2.14811 -244.06368 -0.47386 3.57324
28 2.69140 2.01175 -244.17756 -1.00400 4.18668
28 2.69140 1.86998 -244.17756 -0.98757 3.16890

I think the result is wrong. Can you give me some advice?
I want konw how many cycles needed when the dimer convergence?
thanks
graeme
Site Admin
Posts: 2290
Joined: Tue Apr 26, 2005 4:25 am
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Post by graeme »

It would be interesting to see a movie of this run. It is not converged, but it may be converging towards the end of the run. At iteration 11, the calculation appears to have taken a turn. This can happen if the dimer is started near a ridge, which turns out not to lead to a saddle. Anways, at iteration 15, it is found a negative mode which remains negative throughout the run. The energy is then dropping, and the force is steady. If the run is near a saddle at this point, convergence will accelerate, and the force will drop fairly rapidly. It has been a while since you posted, so it would be interested to know how it turned out.
kxshan
Posts: 14
Joined: Fri Oct 19, 2007 8:39 am

Post by kxshan »

thank you for your reply
I have stopped the dimer calcualtion for i thought it was wrong. I will restart it and give the result as soon as possible.
I have a question: When i have got a saddle point, how i can trace out the minimum energy path and find the initial and final minimum images?
I cannot understand the scripts interplot.pl .
usage: interpolate.pl (POSCAR 1) (POSCAR 2) (fraction)
output: POSCAR.out file, to STDOUT
here what the POSCAR 1 and POSCAR 2 mean? how to get them?
graeme
Site Admin
Posts: 2290
Joined: Tue Apr 26, 2005 4:25 am
Contact:

Post by graeme »

The interpolate script does exactly what it says: interpolates between two poscar files by the specified fraction. It is up to you to decide which configurations that you want to interpolate between.

There is a dimmins.pl script to generate two positions near a saddle configuration along the lowest curvature direction. If you use this script after the dimer calculation has converged, it will generate two configurations that you can minimize to find the initial and final minima.
kxshan
Posts: 14
Joined: Fri Oct 19, 2007 8:39 am

Post by kxshan »

39 0.95795 2.06972 -246.46431 -2.24400 10.47206
39 0.95795 2.61571 -246.46431 -2.34687 3.21058
39 0.95795 1.09310 -246.46431 -2.59516 1.54195
39 0.95795 1.12670 -246.46431 -2.54713 1.40317
40 0.87977 2.42213 -246.48767 -2.25541 7.05861
40 0.87977 2.61907 -246.48767 -2.16663 3.68902
40 0.87977 1.63281 -246.48767 -2.26632 3.32282
40 0.87977 1.68143 -246.48767 -2.32205 2.26529
41 0.65229 2.33574 -246.49495 -3.08646 8.42323
41 0.65229 2.30344 -246.49495 -3.21242 3.61971
41 0.65229 1.40502 -246.49495 -3.30146 2.43671
41 0.65229 1.21262 -246.49495 -3.35521 1.57978
42 0.36253 2.17433 -246.50058 -2.26232 6.91410
42 0.36253 2.22367 -246.50058 -2.34074 2.75578
42 0.36253 1.07528 -246.50058 -2.51829 1.61914
42 0.36253 1.10429 -246.50058 -2.60702 1.47952
43 0.39801 1.95999 -246.50450 -2.22294 4.78771
43 0.39801 1.80143 -246.50450 -2.21664 2.60699
43 0.39801 1.27756 -246.50450 -2.36796 2.09051
43 0.39801 1.32439 -246.50450 -2.39442 1.66527
44 0.26973 2.18529 -246.50602 -1.29420 5.74693
44 0.26973 1.77634 -246.50602 -1.36653 2.48970
44 0.26973 1.05447 -246.50602 -1.45094 1.90658
44 0.26973 1.18956 -246.50602 -1.44126 1.50958
45 0.29413 2.47049 -246.50707 -2.04418 10.75116
45 0.29413 2.47886 -246.50707 -1.71205 3.54210
45 0.29413 1.24840 -246.50707 -1.88661 1.77077
45 0.29413 1.08776 -246.50707 -1.86544 1.47616
46 0.18018 2.20742 -246.50831 -2.42524 8.47465
46 0.18018 2.36937 -246.50831 -2.54790 2.65168
46 0.18018 0.90181 -246.50831 -2.77457 1.13999
47 0.16094 2.02339 -246.50854 -1.09507 5.98669
47 0.16094 1.84684 -246.50854 -1.14547 2.35185
47 0.16094 0.92811 -246.50854 -1.29633 1.45086
48 0.19722 1.92257 -246.50825 -1.90524 4.76225
48 0.19722 1.57193 -246.50825 -2.00910 2.62006
48 0.19722 1.29673 -246.50825 -2.13050 1.64396
48 0.19722 1.08387 -246.50825 -2.13133 1.43947
49 0.25073 2.55894 -246.50783 -1.38289 5.96843
49 0.25073 1.97480 -246.50783 -1.59855 4.04508
49 0.25073 1.77947 -246.50783 -1.73174 2.47068
49 0.25073 1.24362 -246.50783 -1.78291 1.68840
50 0.22796 2.33451 -246.50841 -1.70773 6.36657
50 0.22796 2.08115 -246.50841 -1.83476 3.25839
50 0.22796 1.34581 -246.50841 -1.97492 1.91847
50 0.22796 1.21990 -246.50841 -1.99977 1.68748
51 0.19628 2.76506 -246.50966 -2.12971 10.67303
51 0.19628 3.18348 -246.50966 -2.11375 4.83709
51 0.19628 1.71151 -246.50966 -2.41008 2.64209
51 0.19628 1.54039 -246.50966 -2.42370 2.53609
52 0.15603 2.61617 -246.51120 -2.14390 6.30778
52 0.15603 2.35503 -246.51120 -2.14355 4.33866
52 0.15603 1.87794 -246.51120 -2.31125 2.66658
52 0.15603 1.37215 -246.51120 -2.41486 2.14059
53 0.14632 2.10548 -246.51184 -2.00656 5.05071
53 0.14632 2.01950 -246.51184 -2.09415 2.55776
53 0.14632 1.14276 -246.51184 -2.26714 1.75221
53 0.14632 1.22673 -246.51184 -2.24698 1.46339
54 0.14857 2.41841 -246.51213 -2.57538 8.45582
54 0.14857 2.40015 -246.51213 -2.53484 3.23772
54 0.14857 1.11494 -246.51213 -2.72926 2.13432
54 0.14857 1.00407 -246.51213 -2.76242 1.25694
55 0.13745 1.44171 -246.51218 -2.82357 3.61732
55 0.13745 1.29496 -246.51218 -2.80056 2.14166
55 0.13745 0.93448 -246.51218 -2.85378 1.26300
56 0.15888 2.07780 -246.51308 -1.74490 5.71426
56 0.15888 1.89955 -246.51308 -1.68292 2.56384
56 0.15888 1.00989 -246.51308 -1.85376 1.64986
56 0.15888 1.07667 -246.51308 -1.83400 1.37613
57 0.09186 1.66245 -246.51353 -2.22656 7.40597
57 0.09186 2.24397 -246.51353 -2.27102 2.54060
57 0.09186 1.11115 -246.51353 -2.45088 1.79064
57 0.09186 1.25491 -246.51353 -2.46357 1.36773
58 0.06669 1.65737 -246.51357 -2.46267 3.72391
58 0.06669 1.56329 -246.51357 -2.55981 2.60771
58 0.06669 1.44961 -246.51357 -2.63452 1.94502
58 0.06669 1.24314 -246.51357 -2.64290 1.60167
59 0.06137 1.54593 -246.51392 -1.83766 4.53373
59 0.06137 1.67276 -246.51392 -1.86005 1.98947
59 0.06137 0.88115 -246.51392 -1.97794 1.17384
60 0.04881 1.30665 -246.51414 -1.99913 3.22103
60 0.04881 1.47902 -246.51414 -2.02195 2.17336
60 0.04881 1.05335 -246.51414 -2.15478 1.43549
60 0.04881 1.02966 -246.51414 -2.15922 1.27348
61 0.04118 1.55342 -246.51424 -1.86365 5.83800
61 0.04118 1.67994 -246.51424 -1.92666 2.11244
61 0.04118 0.72887 -246.51424 -1.98252 1.47788
62 0.03911 1.90027 -246.51415 -2.41781 7.94578
62 0.03911 2.23569 -246.51415 -2.44476 3.13864
62 0.03911 1.15042 -246.51415 -2.56143 2.15482
62 0.03911 1.22396 -246.51415 -2.49860 1.73757
63 0.02721 1.67014 -246.51404 -2.67963 4.96894
63 0.02721 1.72162 -246.51404 -2.71896 2.29612
63 0.02721 1.14324 -246.51404 -2.78239 1.64244
63 0.02721 1.02912 -246.51404 -2.75317 1.31461
64 0.03282 1.41493 -246.51404 -2.60155 6.09994
64 0.03282 2.05618 -246.51404 -2.48828 2.35973
64 0.03282 0.96774 -246.51404 -2.64374 1.75123
65 0.04127 1.88346 -246.51375 -1.74006 3.99659
65 0.04127 1.57102 -246.51375 -1.75596 2.47549
65 0.04127 1.10826 -246.51375 -1.86837 1.64108
65 0.04127 1.00005 -246.51375 -1.87794 1.23023
66 0.03712 1.95893 -246.51388 -2.25519 5.76559
66 0.03712 1.42541 -246.51388 -2.28779 2.45053
66 0.03712 1.34795 -246.51388 -2.48185 1.93839
66 0.03712 1.25073 -246.51388 -2.51672 1.94107
67 0.05397 2.11785 -246.51376 -2.23669 5.88486
67 0.05397 2.09583 -246.51376 -2.27724 2.94942
67 0.05397 1.26848 -246.51376 -2.45909 2.13969
67 0.05397 1.45078 -246.51376 -2.39432 2.39748
68 0.06604 1.47764 -246.51360 -1.98117 3.88958
68 0.06604 1.68595 -246.51360 -2.03900 2.78116
68 0.06604 1.29898 -246.51360 -2.16843 1.78759
68 0.06604 1.12846 -246.51360 -2.18549 1.34828
69 0.04991 1.90968 -246.51280 -1.98214 6.39940
69 0.04991 2.28142 -246.51280 -1.98607 3.28078
69 0.04991 1.43461 -246.51280 -2.10070 2.23465
69 0.04991 1.21763 -246.51280 -2.12942 1.55331
70 0.04438 1.98710 -246.51294 -1.58714 5.36721
70 0.04438 1.78828 -246.51294 -1.53386 2.75892
70 0.04438 1.18155 -246.51294 -1.71296 1.73777
70 0.04438 1.06317 -246.51294 -1.72857 1.37869
71 0.03805 1.27506 -246.51280 -1.62044 3.06375
71 0.03805 1.15487 -246.51280 -1.62965 2.27432
71 0.03805 0.94535 -246.51280 -1.67387 1.46422
72 0.04049 1.78452 -246.51313 -2.00287 7.63974
72 0.04049 2.01375 -246.51313 -2.12309 2.94023
72 0.04049 1.02387 -246.51313 -2.20310 1.52474
72 0.04049 0.99079 -246.51313 -2.15637 1.28876
73 0.03557 2.37158 -246.51336 -2.76468 8.77774
73 0.03557 2.07758 -246.51336 -2.82761 3.10453
73 0.03557 1.27084 -246.51336 -2.96983 1.93489
73 0.03557 1.26527 -246.51336 -2.94013 1.56362
74 0.03258 1.87865 -246.51333 -2.84295 5.14071
74 0.03258 2.05493 -246.51333 -2.75525 2.97501
74 0.03258 1.36815 -246.51333 -2.93690 2.07654
74 0.03258 1.37367 -246.51333 -2.92610 1.63638
75 0.03252 2.08622 -246.51343 -3.10485 5.12528
75 0.03252 1.63916 -246.51343 -3.27664 4.24929
75 0.03252 1.60500 -246.51343 -3.39688 1.94712
75 0.03252 0.89716 -246.51343 -3.47687 1.18820
76 0.03091 1.94333 -246.51344 -3.56470 5.98210
76 0.03091 1.83530 -246.51344 -3.51094 2.07493
76 0.03091 0.84334 -246.51344 -3.70855 1.10948
77 0.03287 2.26544 -246.51322 -3.40092 4.68319
77 0.03287 1.68136 -246.51322 -3.53969 2.95063
77 0.03287 1.30735 -246.51322 -3.69843 1.59206
77 0.03287 0.97944 -246.51322 -3.70512 1.20207
78 0.06087 1.89493 -246.51254 -2.86292 4.97053
78 0.06087 1.32163 -246.51254 -2.85587 2.31467
78 0.06087 1.18926 -246.51254 -2.90727 3.16783
78 0.06087 1.39888 -246.51254 -2.94648 1.62489
79 0.09542 1.56215 -246.51190 -2.60049 5.80152
79 0.09542 1.54352 -246.51190 -2.71210 2.30711
the force decrease but it seems not converge.
graeme
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Post by graeme »

It looks to me as if it is converging, but a bit slowly. It also looks like there might be some noise in the force because it keeps rotating a bit, and the torque is not dropping to zero. This may be due to LREAL, but that's a bit of a guess. I expect that the force will eventually drop below 0.01, but it's unlikely to get to your specified 0.0001 eV/Ang, and that your saddle point energy will be close to what you have now.
kxshan
Posts: 14
Joined: Fri Oct 19, 2007 8:39 am

Post by kxshan »

May i can increase the number of rotating to find the precision direction of iterative?
graeme
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Post by graeme »

You could, but these rotations also take time, so as long as the force is steadily dropping, it might be faster to keep going as it is. If it were not for the last two iterations (78 and 79) things would be looking great. And it may be converging just fine, as long as these last two iterations are a blip rather than a trend.
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