[QE-users] convergence problem for a molecule
Dr. K. C. Bhamu
kcbhamu85 at gmail.com
Tue Jan 5 19:29:50 CET 2021
Dear Dr. Giuseppe
Thank you very much for the detailed information.
Yes, I removed 4 H-atoms (two hydrogen molecules) not 2 (-1H2).
I am trying for liberation of different H-atoms and with this particular
configurations the structure didn't converge.
I will check it out with your suggestions.
Thank you very much
Bhamu
On Wed, Jan 6, 2021, 03:18 Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
wrote:
>
> Dear K C Bhamu
> When you simulate molecules having a large amount of rotational
> degrees of freedom, I recommend to use first a tight-binding or
> empirical tool to explore configurations, to avoid high-energy
> structures. The following one is excellent, very easy to use and very
> fast to run.
>
> https://xtb-docs.readthedocs.io/en/latest/contents.html
>
> This said, your starting configuration was trapped in an unfortunate
> structure where two sp2 C atoms (numbers 33 and 35) were twisted
> instead of being planar. You probably removed two H atoms from sp3
> atoms without relaxing them. The following structure, simply optimized
> with a force-field, should not give problems (but I have not run the
> calculation...).
>
> 45
> Energy: 52.7144978
> H 8.48608 10.45663 13.88529
> C 10.12285 10.35161 10.80715
> H 9.75081 9.36965 10.43974
> C 11.49997 10.08512 11.39597
> H 12.30756 9.85722 10.70499
> C 11.75878 10.11652 12.72470
> C 10.64679 10.32692 13.74405
> H 10.74317 9.58583 14.56637
> H 10.73789 11.33550 14.19281
> C 9.24848 10.13193 13.14479
> H 9.07291 9.05796 12.91129
> C 9.14194 10.92818 11.85742
> H 8.10293 10.88215 11.46867
> H 9.38712 11.98966 12.08748
> C 8.94637 11.52201 8.84268
> C 10.25893 11.30287 9.59702
> H 9.13189 12.17491 7.96386
> H 8.19218 12.02297 9.48301
> H 8.54193 10.55155 8.48460
> H 10.65844 12.28636 9.92936
> H 10.98302 10.86213 8.87653
> C 13.17440 9.88279 13.22285
> H 13.11888 9.04537 13.95078
> H 13.83707 9.54798 12.39520
> C 15.69736 11.92481 15.44478
> H 16.74498 11.70891 15.74860
> H 15.07047 11.97162 16.36387
> C 15.58617 13.25420 14.70482
> H 16.14427 13.14997 13.74597
> C 14.09237 13.52300 14.41126
> H 14.03472 14.35009 13.67327
> H 13.54419 13.83190 15.32752
> C 13.36446 12.32498 13.84523
> C 13.87547 11.06693 13.87464
> C 15.21374 10.78810 14.53332
> H 15.14294 9.87981 15.16991
> H 15.94984 10.58575 13.72543
> C 16.23591 15.73576 14.79615
> C 16.23058 14.39236 15.52642
> H 16.75074 16.49369 15.42343
> H 15.20340 16.09456 14.60831
> H 16.77780 15.64679 13.83071
> H 15.70219 14.50766 16.49821
> H 17.28870 14.12285 15.73764
> H 12.40535 12.52093 13.38556
>
> Finally,
>
> > occupations='smearing',
> > smearing='mv',
> > degauss=0.005d0,
>
> This is just a fine way for me to calculate a bunch of unoccupied
> molecular orbitals, but there is no need to use 'mv', which is for
> metals and less stable than 'gaussian', suitable for an "insulator"
> such as your molecule. I would use instead
>
> occupations='smearing', smearing='gaussian', degauss=0.01,
>
> HTH
> Giuseppe
>
>
> Quoting "Dr. K. C. Bhamu" <kcbhamu85 at gmail.com>:
>
> > Dear QE Users
> > I wish you all a very happy new year 2021!
> >
> > I am running a molecule with QE_6.6 but facing a convergence problem.
> > I tried with and without 'local-TF' and both the options are not working.
> >
> > Could someone please have a look and suggest to me any solution?
> >
> >
> > &CONTROL
> > calculation = 'relax'
> > restart_mode = 'from_scratch'
> > outdir = './tmp'
> > pseudo_dir = '/home/kcbhamu/PPs'
> > prefix = 'pwscf'
> > ! disk_io = 'none'
> > verbosity = 'default'
> > etot_conv_thr = 0.0001
> > forc_conv_thr = 0.001
> > nstep = 400
> > tstress = .true.
> > tprnfor = .true.
> > /
> >
> > &SYSTEM
> > ibrav=1,
> > celldm(1)=47.2431531141d0,
> > nat=45,
> > ntyp=2,
> > ecutwfc=65,
> > ecutrho=650,
> > occupations='smearing',
> > smearing='mv',
> > degauss=0.005d0,
> > vdw_corr = 'DFT-D3'
> > assume_isolated='mt'
> > /
> >
> > &ELECTRONS
> > electron_maxstep=999
> > conv_thr=1d-06,
> > mixing_beta=0.2,
> > mixing_mode='local-TF'
> >
> > /
> > &IONS
> > ion_dynamics = 'bfgs'
> > /
> >
> > ATOMIC_SPECIES
> > C 12.0107000000 C.pbe-n-rrkjus_psl.1.0.0.UPF
> > H 1.0079000000 H.pbe-rrkjus_psl.1.0.0.UPF
> >
> >
> > ATOMIC_POSITIONS {crystal}
> > H 0.3386670148d0 0.4101931225d0 0.5567254731d0
> > C 0.4036222773d0 0.4149138472d0 0.4333448459d0
> > H 0.3896346255d0 0.3765041141d0 0.4161167921d0
> > C 0.4581434036d0 0.4058061800d0 0.4574431361d0
> > H 0.4912475090d0 0.4017946150d0 0.4290030859d0
> > C 0.4691277774d0 0.4031817060d0 0.5099401207d0
> > C 0.4253264110d0 0.4071145213d0 0.5513729998d0
> > H 0.4327529164d0 0.3774401630d0 0.5831675023d0
> > H 0.4276381009d0 0.4464313224d0 0.5714430496d0
> > C 0.3695729050d0 0.3993621172d0 0.5273547231d0
> > H 0.3636345597d0 0.3567170026d0 0.5178739313d0
> > C 0.3632663685d0 0.4323236400d0 0.4762330101d0
> > H 0.3222111650d0 0.4290965819d0 0.4608472936d0
> > H 0.3700270318d0 0.4749720278d0 0.4855397879d0
> > C 0.3550607872d0 0.4623307485d0 0.3556503474d0
> > C 0.4072533598d0 0.4549686753d0 0.3866434814d0
> > H 0.3606425820d0 0.4892876373d0 0.3214193048d0
> > H 0.3233410756d0 0.4794322728d0 0.3807732671d0
> > H 0.3403880199d0 0.4238800875d0 0.3400782741d0
> > H 0.4209431037d0 0.4937648655d0 0.4025522295d0
> > H 0.4387880407d0 0.4413449118d0 0.3590270889d0
> > C 0.5253811195d0 0.3963553146d0 0.5303629030d0
> > H 0.5275121376d0 0.3597814346d0 0.5550954410d0
> > H 0.5527498198d0 0.3902494747d0 0.4963382387d0
> > C 0.6241002137d0 0.4781543529d0 0.6196978697d0
> > H 0.6647510385d0 0.4689076884d0 0.6339462788d0
> > H 0.5991190333d0 0.4830564471d0 0.6558173241d0
> > C 0.6245138950d0 0.5312336801d0 0.5887880064d0
> > H 0.6519223460d0 0.5264394769d0 0.5543229817d0
> > C 0.5684449407d0 0.5426728657d0 0.5664333374d0
> > H 0.5687315910d0 0.5794127480d0 0.5422455469d0
> > H 0.5411292134d0 0.5502889434d0 0.6003493599d0
> > C 0.5467291274d0 0.4961698023d0 0.5329872592d0
> > H 0.5063039439d0 0.5054115901d0 0.5182523433d0
> > C 0.5462494021d0 0.4434602904d0 0.5642948220d0
> > C 0.6023141698d0 0.4317080266d0 0.5862549648d0
> > H 0.6016470576d0 0.3946830496d0 0.6101287345d0
> > H 0.6295099445d0 0.4241153738d0 0.5522682608d0
> > C 0.6550325759d0 0.6297412310d0 0.5941577656d0
> > C 0.6461033707d0 0.5769127641d0 0.6236837684d0
> > H 0.6727321964d0 0.6599556430d0 0.6206848621d0
> > H 0.6175101186d0 0.6464185973d0 0.5785534114d0
> > H 0.6823409744d0 0.6243625417d0 0.5600843513d0
> > H 0.6183422352d0 0.5832463756d0 0.6574159578d0
> > H 0.6841825362d0 0.5638719462d0 0.6416905666d0
> >
> > K_POINTS (gamma)
> >
> >
> >
> > Thank you very much
> > K C Bhamu
> > University of Ulsan
> > ROK
>
>
>
> GIUSEPPE MATTIOLI
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> Via Salaria Km 29,300 - C.P. 10
> I-00015 - Monterotondo Scalo (RM)
> Mob (*preferred*) +39 373 7305625
> Tel + 39 06 90672342 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
>
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