[QE-users] How to properly restart CI-NEB? convergence issues
Paolo Giannozzi
p.giannozzi at gmail.com
Mon Mar 15 16:29:23 CET 2021
QE version?
P.
On Sun, Mar 14, 2021 at 8:48 PM Oskar Cheong <oskarcheong at gmail.com> wrote:
> Hello QE Team,
> thank you for this nice forum here. I have an issue when restarting with
> CI-NEB.
> 1. Usually I start out with NEB with "no-CI". Then after this calculation
> converges, I restart my calculation with the same input script and switch
> to "auto" and restart my CI-NEB. However, oftentimes convergence is not
> reached.
> I tried to follow the rules here with running "no-CI" then "auto". Can you
> maybe tell me how to properly start my CI-NEB ("auto") when my previous NEB
> calculation without CI has converged?
>
>
> 2. Also, I am not sure whether it is a bug or something, but when I
> manually restart my calculation of NEB, I usually take the structure from
> .crd file and copy and paste it in the input file. When I have only Final
> and Last image, the simulation runs smoothly, but whenever I paste the
> coordinates for intermediate images inside the input file, I get an error
> message:
>
> "xml_AddCharacter: Invalid character in chars"
>
> [image: image.png]
>
> I realised it only happens when I include intermediate images. Please find
> my input file below.
>
> BEGIN
> BEGIN_PATH_INPUT
> &PATH
> restart_mode = 'from_scratch'
> string_method = 'neb',
> nstep_path = 1000,
> ds = 1.D0,
> opt_scheme = "broyden",
> num_of_images = 5,
> CI_scheme = "no-CI",
> path_thr = 0.05D0,
> /
> END_PATH_INPUT
> BEGIN_ENGINE_INPUT
> &CONTROL
> prefix = 'Pt'
> pseudo_dir = './'
> outdir = './'
> etot_conv_thr = 1.0e-4
> forc_conv_thr = 1.0e-3
> disk_io = 'low'
> tstress = .true.
> tprnfor = .true.
> max_seconds = 85000
> /
> &SYSTEM
> ibrav = 0
> nat = 50
> ntyp = 3
> ecutwfc = 50.0
> ecutrho = 200.0
> input_DFT = 'pbe'
> occupations = 'smearing'
> smearing = 'gaussian'
> degauss = 0.02
> nosym = .true.
> /
> &ELECTRONS
> diagonalization = 'david'
> electron_maxstep= 1000
> conv_thr = 1.0e-6
> mixing_beta = 0.3
> /
> &IONS
> /
> ATOMIC_SPECIES
> Pt 195.084 Pt.pbe-n-kjpaw_psl.1.0.0.UPF
> H 1.0 H.pbe-kjpaw_psl.1.0.0.UPF
> C 12.01 C.pbe-n-kjpaw_psl.1.0.0.UPF
> BEGIN_POSITIONS
> FIRST_IMAGE
> ATOMIC_POSITIONS (angstrom)
> Pt 0.0000 0.0000 10.0000 0 0 0
> Pt 5.6286 4.8745 10.0000 0 0 0
> Pt 2.8143 0.0000 10.0000 0 0 0
> Pt 5.6286 0.0000 10.0000 0 0 0
> Pt 4.2214 2.4372 10.0000 0 0 0
> Pt 7.0357 2.4372 10.0000 0 0 0
> Pt 2.8143 4.8745 10.0000 0 0 0
> Pt 1.4071 2.4372 10.0000 0 0 0
> Pt 8.4429 4.8745 10.0000 0 0 0
> Pt 9.8500 4.0621 12.2979 0 0 0
> Pt 5.6286 6.4993 12.2979 0 0 0
> Pt 8.4429 1.6248 12.2979 0 0 0
> Pt 11.2571 6.4993 12.2979 0 0 0
> Pt 5.6286 1.6248 12.2979 0 0 0
> Pt 8.4429 6.4993 12.2979 0 0 0
> Pt 2.8143 1.6248 12.2979 0 0 0
> Pt 4.2214 4.0621 12.2979 0 0 0
> Pt 7.0357 4.0621 12.2979 0 0 0
> Pt 8.4424 3.2667 14.5822
> Pt 7.0409 0.8263 14.5649
> Pt 9.8552 5.7001 14.5651
> Pt 7.0411 5.6948 14.5830
> Pt 5.6399 3.2666 14.5824
> Pt 1.4165 0.8282 14.5828
> Pt 4.2229 0.8285 14.5835
> Pt 2.8202 3.2588 14.5832
> Pt 4.2271 5.7002 14.5650
> Pt 7.0467 2.4820 16.8783
> Pt 2.8256 0.0388 16.8723
> Pt 9.8689 2.4600 16.8700
> Pt 4.2233 2.4598 16.8727
> Pt 11.2686 4.9020 16.8360
> Pt 8.4525 0.0273 16.8355
> Pt 8.4391 4.8946 16.8781
> Pt 5.6404 0.0271 16.8358
> Pt 5.6542 4.8941 16.8779
> Pt 5.6349 6.5377 19.1512
> Pt 8.4521 1.6570 19.1532
> Pt 4.2344 4.1074 19.1533
> Pt 8.4664 6.5378 19.1528
> Pt 9.8694 4.1084 19.1508
> Pt 2.8266 1.6633 19.2737
> Pt 5.6474 1.6560 19.1529
> Pt 7.0514 4.1010 19.3651
> Pt 11.2724 6.5376 19.1503
> C 7.0593 4.1235 21.4390
> H 6.6870 3.1544 21.7906
> H 6.4055 4.9377 21.7729
> H 8.0899 4.2906 21.7738
> H 2.8009 1.6863 20.8320
> INTERMEDIATE_IMAGE
> ATOMIC_POSITIONS (angstrom)
> Pt 0.0000 0.0000 10.0000 0 0 0
> Pt 5.6286 4.8745 10.0000 0 0 0
> Pt 2.8143 0.0000 10.0000 0 0 0
> Pt 5.6286 0.0000 10.0000 0 0 0
> Pt 4.2214 2.4372 10.0000 0 0 0
> Pt 7.0357 2.4372 10.0000 0 0 0
> Pt 2.8143 4.8745 10.0000 0 0 0
> Pt 1.4071 2.4372 10.0000 0 0 0
> Pt 8.4429 4.8745 10.0000 0 0 0
> Pt 9.8500 4.0621 12.2979 0 0 0
> Pt 5.6286 6.4993 12.2979 0 0 0
> Pt 8.4429 1.6248 12.2979 0 0 0
> Pt 11.2571 6.4993 12.2979 0 0 0
> Pt 5.6286 1.6248 12.2979 0 0 0
> Pt 8.4429 6.4993 12.2979 0 0 0
> Pt 2.8143 1.6248 12.2979 0 0 0
> Pt 4.2214 4.0621 12.2979 0 0 0
> Pt 7.0357 4.0621 12.2979 0 0 0
> Pt 8.4141 3.2483 14.5861
> Pt 7.0133 0.8085 14.5661
> Pt 9.8251 5.6857 14.5588
> Pt 7.0148 5.6788 14.5815
> Pt 5.6076 3.2535 14.5982
> Pt 1.3842 0.8086 14.5708
> Pt 4.1985 0.8056 14.5643
> Pt 2.7930 3.2473 14.5781
> Pt 4.1987 5.6808 14.5769
> Pt 6.9773 2.4386 16.8820
> Pt 2.7560 -0.0205 16.8413
> Pt 9.7939 2.4225 16.8466
> Pt 4.1652 2.4279 16.8563
> Pt 11.2060 4.8590 16.8503
> Pt 8.3853 -0.0149 16.8380
> Pt 8.3659 4.8515 16.8725
> Pt 5.5726 -0.0186 16.8319
> Pt 5.5641 4.8410 16.9151
> Pt 5.5255 6.4711 19.1482
> Pt 8.3481 1.5834 19.1454
> Pt 4.0918 4.0054 19.2558
> Pt 8.3500 6.4687 19.1465
> Pt 9.7381 4.0371 19.1386
> Pt 2.7095 1.5688 19.1462
> Pt 5.5319 1.5725 19.1376
> Pt 6.9307 4.0270 19.3367
> Pt 11.1608 6.4682 19.1422
> C 6.8583 3.9836 21.4053
> H 6.5185 2.9866 21.7101
> H 6.1451 4.7483 21.7328
> H 7.8653 4.1902 21.7836
> H 3.6773 3.6911 20.7378
> INTERMEDIATE_IMAGE
> ATOMIC_POSITIONS (angstrom)
> Pt 0.0000 0.0000 10.0000 0 0 0
> Pt 5.6286 4.8745 10.0000 0 0 0
> Pt 2.8143 0.0000 10.0000 0 0 0
> Pt 5.6286 0.0000 10.0000 0 0 0
> Pt 4.2214 2.4372 10.0000 0 0 0
> Pt 7.0357 2.4372 10.0000 0 0 0
> Pt 2.8143 4.8745 10.0000 0 0 0
> Pt 1.4071 2.4372 10.0000 0 0 0
> Pt 8.4429 4.8745 10.0000 0 0 0
> Pt 9.8500 4.0621 12.2979 0 0 0
> Pt 5.6286 6.4993 12.2979 0 0 0
> Pt 8.4429 1.6248 12.2979 0 0 0
> Pt 11.2571 6.4993 12.2979 0 0 0
> Pt 5.6286 1.6248 12.2979 0 0 0
> Pt 8.4429 6.4993 12.2979 0 0 0
> Pt 2.8143 1.6248 12.2979 0 0 0
> Pt 4.2214 4.0621 12.2979 0 0 0
> Pt 7.0357 4.0621 12.2979 0 0 0
> Pt 8.4102 3.2602 14.6085
> Pt 7.0106 0.8187 14.5759
> Pt 9.8225 5.6907 14.5789
> Pt 7.0109 5.6872 14.6128
> Pt 5.6064 3.2578 14.6093
> Pt 1.3842 0.8170 14.5906
> Pt 4.1992 0.8165 14.5753
> Pt 2.7894 3.2548 14.5904
> Pt 4.1955 5.6933 14.5844
> Pt 6.9707 2.4663 16.9214
> Pt 2.7473 0.0084 16.8889
> Pt 9.7841 2.4485 16.8785
> Pt 4.1589 2.4561 16.8841
> Pt 11.1926 4.8823 16.8725
> Pt 8.3829 0.0066 16.8737
> Pt 8.3528 4.8704 16.9403
> Pt 5.5612 0.0067 16.8507
> Pt 5.5777 4.8796 16.9353
> Pt 5.5502 6.5265 19.2549
> Pt 8.3390 1.6382 19.1927
> Pt 4.1071 4.0748 19.2476
> Pt 8.3399 6.5025 19.1953
> Pt 9.7346 4.0696 19.2030
> Pt 2.7113 1.6442 19.1905
> Pt 5.5200 1.6151 19.1754
> Pt 6.9054 4.0190 19.5666
> Pt 11.1242 6.5227 19.1640
> C 6.5607 3.7858 21.6460
> H 6.2171 2.7608 21.8439
> H 5.8173 4.4829 22.0581
> H 7.5293 3.9692 22.1189
> H 4.8384 5.3756 20.3119
> INTERMEDIATE_IMAGE
> ATOMIC_POSITIONS (angstrom)
> Pt 0.0000 0.0000 10.0000 0 0 0
> Pt 5.6286 4.8745 10.0000 0 0 0
> Pt 2.8143 0.0000 10.0000 0 0 0
> Pt 5.6286 0.0000 10.0000 0 0 0
> Pt 4.2214 2.4372 10.0000 0 0 0
> Pt 7.0357 2.4372 10.0000 0 0 0
> Pt 2.8143 4.8745 10.0000 0 0 0
> Pt 1.4071 2.4372 10.0000 0 0 0
> Pt 8.4429 4.8745 10.0000 0 0 0
> Pt 9.8500 4.0621 12.2979 0 0 0
> Pt 5.6286 6.4993 12.2979 0 0 0
> Pt 8.4429 1.6248 12.2979 0 0 0
> Pt 11.2571 6.4993 12.2979 0 0 0
> Pt 5.6286 1.6248 12.2979 0 0 0
> Pt 8.4429 6.4993 12.2979 0 0 0
> Pt 2.8143 1.6248 12.2979 0 0 0
> Pt 4.2214 4.0621 12.2979 0 0 0
> Pt 7.0357 4.0621 12.2979 0 0 0
> Pt 8.4305 3.2508 14.5722
> Pt 7.0230 0.8148 14.5726
> Pt 9.8366 5.6879 14.5742
> Pt 7.0227 5.6893 14.5706
> Pt 5.6151 3.2512 14.5706
> Pt 1.3944 0.8146 14.5741
> Pt 4.2078 0.8144 14.5730
> Pt 2.8009 3.2509 14.5733
> Pt 4.2078 5.6892 14.5707
> Pt 7.0068 2.4400 16.8435
> Pt 2.7869 0.0036 16.8479
> Pt 9.8213 2.4413 16.8508
> Pt 4.1928 2.4402 16.8458
> Pt 11.2279 4.8799 16.8461
> Pt 8.4120 0.0034 16.8465
> Pt 8.4151 4.8796 16.8450
> Pt 5.6003 0.0026 16.8462
> Pt 5.5990 4.8798 16.8401
> Pt 5.5828 6.5149 19.1386
> Pt 8.3984 1.6290 19.1485
> Pt 4.1672 4.0682 19.1352
> Pt 8.3990 6.5087 19.1505
> Pt 9.8071 4.0690 19.1506
> Pt 2.7688 1.6308 19.1515
> Pt 5.5826 1.6261 19.1406
> Pt 7.0016 4.0676 19.1287
> Pt 11.2110 6.5069 19.1534
> C 5.9976 3.9723 22.2288
> H 5.8501 2.8885 22.2957
> H 5.7225 4.4577 23.1708
> H 7.0530 4.1843 22.0080
> H 5.3524 4.3885 21.4312
> LAST_IMAGE
> ATOMIC_POSITIONS (angstrom)
> Pt 0.0000 0.0000 10.0000 0 0 0
> Pt 5.6286 4.8745 10.0000 0 0 0
> Pt 2.8143 0.0000 10.0000 0 0 0
> Pt 5.6286 0.0000 10.0000 0 0 0
> Pt 4.2214 2.4372 10.0000 0 0 0
> Pt 7.0357 2.4372 10.0000 0 0 0
> Pt 2.8143 4.8745 10.0000 0 0 0
> Pt 1.4071 2.4372 10.0000 0 0 0
> Pt 8.4429 4.8745 10.0000 0 0 0
> Pt 9.8500 4.0621 12.2979 0 0 0
> Pt 5.6286 6.4993 12.2979 0 0 0
> Pt 8.4429 1.6248 12.2979 0 0 0
> Pt 11.2571 6.4993 12.2979 0 0 0
> Pt 5.6286 1.6248 12.2979 0 0 0
> Pt 8.4429 6.4993 12.2979 0 0 0
> Pt 2.8143 1.6248 12.2979 0 0 0
> Pt 4.2214 4.0621 12.2979 0 0 0
> Pt 7.0357 4.0621 12.2979 0 0 0
> Pt 8.4390 3.2543 14.5731
> Pt 7.0340 0.8180 14.5743
> Pt 9.8480 5.6929 14.5760
> Pt 7.0318 5.6924 14.5729
> Pt 5.6258 3.2563 14.5732
> Pt 1.4047 0.8174 14.5738
> Pt 4.2180 0.8184 14.5750
> Pt 2.8131 3.2544 14.5737
> Pt 4.2201 5.6924 14.5733
> Pt 7.0293 2.4476 16.8501
> Pt 2.8088 0.0096 16.8500
> Pt 9.8450 2.4476 16.8501
> Pt 4.2177 2.4477 16.8515
> Pt 11.2526 4.8845 16.8496
> Pt 8.4380 0.0097 16.8503
> Pt 8.4375 4.8843 16.8482
> Pt 5.6236 0.0107 16.8517
> Pt 5.6234 4.8842 16.8531
> Pt 5.6212 6.5127 19.1603
> Pt 8.4346 1.6377 19.1600
> Pt 4.2147 4.0756 19.1648
> Pt 8.4353 6.5124 19.1601
> Pt 9.8424 4.0765 19.1600
> Pt 2.8077 1.6374 19.1611
> Pt 5.6214 1.6401 19.1611
> Pt 7.0275 4.0754 19.1641
> Pt 11.2500 6.5125 19.1618
> C 5.5680 4.0330 23.0743
> H 5.1554 3.0796 22.7232
> H 5.4764 4.0926 24.1657
> H 6.6254 4.1001 22.7906
> H 5.0131 4.8607 22.6148
> END_POSITIONS
>
> CELL_PARAMETERS angstrom
> 8.44285496736738 0.00000000000000 0.00000000000000
> 4.22142748368369 7.31172688220779 0.00000000000000
> 0.00000000000000 0.00000000000000 29.19141628549884
>
> K_POINTS (automatic)
> 4 4 1 0 0 0
> END_ENGINE_INPUT
> END
>
>
>
>
> Thank you for your help.
>
>
> Kind regards,
>
> Oskar
>
> _______________________________________________
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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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