Re: [Pw_forum] bfgs optimization not going anywhere
Found the culprit! When I turned off the dipole correction, the system converged. Digging deeper, I found the underlying problem. I had been reckless and used the 'emaxpos' value unchanged from a different set of calculation, inadvertently setting it to too close to the edge of the vacuum. A change from 0.70 to 0.50 solved the problem. Thanks for the all contributions! As for the dispersion correction, the discussion is still open :-) Matej -Original Message- From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf Of Ilya Ryabinkin Sent: Tuesday, November 24, 2015 8:03 PM To: PWSCF Forum Subject: Re: [Pw_forum] bfgs optimization not going anywhere Colleagues, to summarize: what would be 'the best' DFT correction on to of *existing* functionals, e.g. PBE for molecule-metal-interaction? As far as I understood, vdw-DF must be used with the corresponding pseudopotential (BTW, where one can get them?). -- I. On Tue, Nov 24, 2015 at 8:30 AM, Giuseppe Mattioli wrote: > > Dear Matej (and all) > >> As for DFT-D2, I admit I am a bit in the dark here. How 'wrong' is >> it? Or to put differently, is it more wrong that not using dispersion >> correction at all? > > Regarding the dispersion correction(s) this is the Stephan Grimme's > paper which indicates that DFT-D2 doubles the DFT-D3 interaction energy > between molecules and metal surfaces: > > J. Chem. Phys. (2010) 132, 154104 > > In my experience of phthalocyanine/metal interactions (but if I > remember well Ari has also performed calculations on > porphyrin/phthalocyanine molecules adsorbed on metal surfaces and he > can add his own knowledge), adsorption geometries and energies are > very different, so that the results are also quite different. See for > example this paper (Cu phthalocyanine interacting with Ag (100) with > DFT-D2) > > PRL 105, 115702 (2010) > > And my paper (TiO phthalocyanine interacting with Ag (100) with > vdW-DF) > > J. Phys. Chem. C 2014, 118, 5255 > > And, yes, of course: if you use no dispersion correction you badly > underestimate the interaction between the molecule and the surface... > > 2 more hints: > > 1) In the case of molecule/metal systems, ab initio functionals > modeling long distance correlation between electrons should be (in my > opinion) preferred to semiempirical functional with add pairwise > forces based on tabulations (or partial calculations) of C6 > coefficients. There is a nice perspective written by J. L. Bredas > which addresses the issue > > Nature Nanotechnology > 8, > 230–231 > (2013) > > 2) Regarding lattice parameters, Ari is right in the case of vdwdf. > But I've tried to simulate gold (bulk and) surfaces in contact with > molecules by using the reparametrized vdwdf-c09 functional: lattice parameter > of gold is ok, and also molecule-surface interactions are expected to be > improved with respect to vdwdf! > >> Also, if I change/switch off the dispersion correction, then I will >> have to re-optimize all already converged structures (metal, isolated >> molecules, adsorbed intermediates), right? Looks rather tedious > > Yes, you should recalculate everything...:-( > > HTH > Giuseppe > > On Tuesday, November 24, 2015 11:37:45 AM Matej Huš wrote: >> Thanks for very useful comments. >> >> Yes, vacuum region is indeed too low in this example (whoops, seems >> like I've attached an old input file). I also ran a calculation with >> 10 A of vacuum without any improvement. Open shell is unnecessary as >> it quickly converges to a closed shell solution. I've just wasted >> some CPU time with that. >> >> Ectuwfc, ecutrhc are large enough (converged). I believe K points >> should also not be the source of a problem. >> >> As for DFT-D2, I admit I am a bit in the dark here. How 'wrong' is >> it? Or to put differently, is it more wrong that not using dispersion >> correction at all? How about vdw-DF, how do I turn it on and does it >> perform better? Where can I find more important about that? >> >> Also, if I change/switch off the dispersion correction, then I will >> have to re-optimize all already converged structures (metal, isolated >> molecules, adsorbed intermediates), right? Looks rather tedious >> >> >> Matej >> >> >> >> -Original Message- >> From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] >> On Behalf Of Ari P Seitsonen >> Sent: Tuesday, November 24, 2015 11:22 AM >> To: PWSCF Forum >> Subject: Re: [Pw_forum] bfgs optimization not going anywhere >> >> >> Dear Matej Hus, >> >>Adding to the previous comments (I think that it is ok to use the >> k points, even though you might gain some CPU time by first indeed >> using Gamma-only and then increasing, as your cell is quite large), >> have you checked the length of your vacuum/lattice vector along the surface >> normal? >> If I see correctly, you have only about six Ångströms, which is >> already very >> (too) little, plus the DFT-
[Pw_forum] The value of Larange multipliers when doing constrained ab initio molecular dynamics
Dear pw_forum, I am trying to do a series of constrained ab initio molecular dynamics to obtain the the free energy profie from one intermediate to the next. In order to obtain the free energy of constrained molecular dynamics, I have to obtain the values of Lagrange multipliers for the constraint technique. Can someone tell me where the values of Lagrange multipilers are printed when the constrained ab initio MD is running? Thank you very much. Below is a sample of my input file, I try to constrain the three O-H distance of a hydronium ion in liquid water. There should be a serial of Lagrande multipliers related to the constraint, right? How should I obtain the values of Lagrande multipliers when doing the calculation? --&CONTROL calculation='cp', dt=3.0D0, prefix='test', restart_mode='from_scratch', nstep=99000, iprint=1, isave=50, ndr=91, ndw=92, outdir='/home/temp', pseudo_dir="/home", tprnfor=.TRUE., tstress=.FALSE., disk_io='default', verbosity='default', max_seconds=86D+3/&SYSTEM ibrav=1, celldm(1)=24.802, nat=193, ntyp=2, nspin=1, ecutwfc=30.D0, ecutrho=240.D0, nr1b=28, nr2b=28, nr3b=28, tot_charge=0.0 vdw_corr='DFT-D', london_s6=0.75 london_rcut=200 ! degauss=0.002 ! occupations='smearing' ! smearing='mp'/&ELECTRONS electron_dynamics='verlet', ! electron_temperature='nose', ! ekincw=0.035d0, ! fnosee=200.d0 emass=400.d0, emass_cutoff=2.5d0, ortho_max=400,/ &IONS ion_dynamics='verlet', ion_radius(1)=1.0ion_radius(2)=1.0 ion_temperature='nose', tempw=300.0, fnosep=40.0, nhptyp=2, nhpcl=4,/ATOMIC_SPECIES H 1.000 H.pbe-van_bm.UPF O 16.000 O.pbe-van_bm.UPFATOMIC_POSITIONS angstrom193generated 0.00H 10.0154 5.9257 7.6968O 1.3610 5.7350 7.5670H 0.7690 5.2550 8.2140H 1.1890 5.3950 6.6430O 11.0980 4.3090 3.2760H 10.5150 3.9560 4.0060H 10.5570 4.4260 2.4430O 9.1760 6.1450 8.1060H 8.4380 6.7670 7.8460H 8.9630 5.7250 8.9880O 4.0590 11.0180 5.7560H 4.5850 10.9720 6.6050H 3.8910 11.9750 5.5200O 4.2620 6.3560 7.1420H 3.3990 6.3890 7.6460H 4.0740 6.3280 6.1600O 8.0830 1.2070 3.5110H 7.6000 1.5430 2.7030H 8.8620 0.6480 3.2260O 4.4710 3.6790 4.2970H 3.8940 3.4070 3.5260H 4.4660 2.9570 4.9880O 12.1370 1.4190 12.1310H 12.4300 0.4900 11.9000H 11.2650 1.6140 11.6830O 6.7530 10.4470 10.6850H 7.6260 10.7580 11.0620H 6.0020 10.8870 11.1770O 4.5670 1.7530 6.3570H 4.5730 1.7960 7.3560H 5.4070 1.3140 6.0370O 2.6960 0.9500 11.1090H 2.1290 1.3620 10.3950H 2.6150 1.4850 11.9500O 9.0360 12.2130 7.4380H 9.2020 11.9490 8.3880H 9.2660 11.4490 6.8350O 9.1710 9.9580 5.6590H 8.2800 9.6800 6.0190H 9.0400 10.5900 4.8960O 0.3290 2.3180 2.3960H -0.2660 3.0080 2.8090H 0.0890 2.2050 1.4320O 0.8050 8.4680 4.5200H 1.0010 9.2390 5.1260H -0.1820 8.4060 4.3670O 4.7880 10.2540 1.4240H 5.7450 9.9650 1.3980H 4.3370 9.8430 2.2160O 9.1290 3.2360 4.7200H 8.3060 3.7730 4.9060H 8.8810 2.4070 4.2200O 0.2220 7.4780 11.5880H 0.9800 7.8360 11.0410H 0.4170 7.6170 12.5590O 2.8060 4.5670 12.3120H 1.8550 4.2850 12.1880H 3.2320 4.7050 11.4180O 7.0040 5.0180 4.3520H 6.8100 5.9840 4.5200H 6.1580 4.4900 4.4290O 9.7160 8.0730 11.9000H 10.6530 8.0320 11.5550H 9.0760 7.9070 11.1490O 5.0130 0.6990 3.2560H 5.4990 -0.1600 3.4170H 4.0890 0.5030 2.9270O 7.9480 5.1020 1.3710H 8.8180 4.8270 0.9620H 7.9820 4.9550 2.3590O 9.1970 11.6630 10.5210H 10.1280 11.2980 10.5540H 9.2130 12.6370 10.7480O 0.5590 10.4940 1.2100H 1.0660 9.6460 1.3640H -0.4110 10.3410 1.3970O 4.6840 11.9510 11.8510H 4.5340 11.3000 12.5950H 3.8060 12.3230 11.5500O 3.5460 9.2240 3.8870H 2.8180 8.6630 4.2810H 3.7040 10.0220 4.4680O 6.1300 2.9030 2.1740H 5.5590 2.1400 2.4760H 5.9940 3.6830 2.7850O 8.4120 5.2620 10.5220H 8.3510 6.2060 10.8460H 7.6680 4.7250 10.9200O 2.9560 3.0680 2.2970H 2.9150 3.8150 1.6330H 2.0300 2.7420 2.4890O 1.2320 10.6220 6.2540H 2.2230 10.7580 6.2290H 1.0200 9.8230 6.8170O 7.3500 7.7510 10.4780H 7.2760 8.7420 10.3740H 6.6780 7.4350 11.1470O 0.4990 8.5380 7.7490H -0.4910 8.4110 7.8020H 0.9230 7.7080 7.3860O 6.2320 7.9070 4.3870H 5.3260 8.0760 3.9990H 6.3820 8.5200 5.1630O 0.8910 7.8290 1.8590H 1.7870 7.3860 1.9040H 0.6080 8.1010 2.7780O 10.1370 9.4020 1.8420H 10.1350 8.9860 0.9330H 10.3340 8.7020 2.5290O 3.5210 6.6410 1.6150H 3.0830 5.9930 0.9910H 4.3940 6.9380 1.2280O 11.9420 4.4990 8.9590H 11.6670 3.5910 8.6440H 11.2730 5.1760 8.6530O 1.3570 1.3190 8.5430H 1.6370 1.8290 7.7300H 0.4010 1.0420 8.4500O 1.7160 9.4610 10.1300H 2.5010 8.8780 10.3380H 1.2920 9.1570 9.2760O 6.6930 9.4320 6.4250H 6.3310 10.1370 7.0350H 6.7180
Re: [Pw_forum] i-v characteristics
Yes, pwcond would be ideal for this. But is it possible to simulate electron transport in doped graphene (or doped materials in general) using pwcond? To include the dopant atoms explicitly, would require very large unit cells I believe. Is there a better way to do it in pwcond? Thanks, Sridhar Purdue University On Wed, Nov 25, 2015 at 3:29 AM, Karim Elgammal wrote: > I believe that pwcond code in espresso, can do the job. > I myself, wants to do the same for graphene properly as well. > you can check the documentation here, it is based on Landauer-Buttiker > formula: http://iramis.cea.fr/Pisp/alexander.smogunov/PWCOND/pwcond.html > and here is the input file parameters: > http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PWCOND.html > > Karim Elgammal > PhD student > Materials- and Nanophysics > KTH > Sweden > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Query during Fermi surface calculation
Dear QE users and Developers, I am trying to calculate the fermi surface for my system by following the steps mentioned in example 8. I am using esspresso 5.0.2. First I have done scf calculation, then generates the k-points by kvecs_FS.x for preparing input file for nscf calculation and then run the nscf calculation by preparing Sysname.fs_sp.in as below: mpirun -np 4 pw.x -in sysname.fs_sp.in> sysname.fs_sp.out run is going to complete after approximately 20-24 hours. I am not getting any error but output file sysname.fs_sp.out does not provide band calculation for all the k-points and it stops. it does not provide any band energies and occupation number. last part of the output file is given below. Starting wfc are 24 randomized atomic wfcs total cpu time spent up to now is 7.1 secs per-process dynamical memory: 40.0 Mb Band Structure Calculation Davidson diagonalization with overlap Computing kpt #: 1 total cpu time spent up to now is 8.3 secs Computing kpt #: 2 total cpu time spent up to now is 9.9 secs Computing kpt #: 3 For your reference input file is given below: &control calculation='nscf' restart_mode='from_scratch', tstress = .true. tprnfor = .true. verbosity= 'high' prefix='Sys_name', wf_collect=.true., pseudo_dir = '/usr/share/espresso/pseudo/', outdir='/tmp/' / &system ibrav= 2, celldm(1)= 10.5615, nat=4,ntyp=2, ecutwfc =80, ecutrho= 800, nbnd=29 occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01 nspin=2, starting_magnetization(1)=0.3, starting_magnetization(2)=0.1 / &electrons conv_thr = 1.0d-5 mixing_beta = 0.1 / ATOMIC_SPECIES atom 1 55.845 Fe.pbe-nd-rrkjus.UPF atom 2 58.6934 Ni.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS atom 1 0.00 0.00 0.00 atom 1 0.25 0.25 0.25 atom 1 0.50 0.50 0.50 atom 2 0.75 0.75 0.75 K_POINTS 4913 kindly provide your suggestions or corrections for the same. Your help will be highly appreciated. Thanking you, Nirav Pandya, Ph.D. Student India ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] i-v characteristics
I believe that pwcond code in espresso, can do the job. I myself, wants to do the same for graphene properly as well. you can check the documentation here, it is based on Landauer-Buttiker formula: http://iramis.cea.fr/Pisp/alexander.smogunov/PWCOND/pwcond.html and here is the input file parameters: http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PWCOND.html Karim Elgammal PhD student Materials- and Nanophysics KTH Sweden ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
