[QE-users] How to properly restart CI-NEB? convergence issues
Oskar Cheong
oskarcheong at gmail.com
Mon Mar 15 17:13:02 CET 2021
Hello Paolo,
its version 6.4. The newer versions I have not compiled yet, but once I do
that I will let you know asap.
Towards the first question I asked:
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?
Do I do something wrong here by using the .crd file? I read somewhere in
the threads that for CI-NEB calculation ("auto") I should not restart my
converged NEB ("no-CI"). Is that correct? What is the correct procedure
here?
Kind regards,
Oskar
On Mon, Mar 15, 2021 at 4:32 PM Paolo Giannozzi <p.giannozzi at gmail.com>
wrote:
> Ah, it's visible in the picture: 6.4. What happens with newer versions?
>
> Paolo
>
> On Mon, Mar 15, 2021 at 4:29 PM Paolo Giannozzi <p.giannozzi at gmail.com>
> wrote:
>
>> 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
>>>
>>> _______________________________________________
>>> 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
>>
>>
>>
>> --
>> 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
>>
>>
>
> --
> 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
>
> _______________________________________________
> 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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