Dear Giuseppe I took your advice but the E[cation+anion] system was very difficult to be converged. I tried to reduce the mixing_beta and conv_thr with no results. Thanks
On Sun, 9 Dec 2018 at 14:37, Mohamed Safy <[email protected]> wrote: > Dear Giuseppe > Many thanks for your response. > I will try with your advice and give you the response > Thanks > > On Thu, 6 Dec 2018 at 12:24, Giuseppe Mattioli < > [email protected]> wrote: > >> >> Dear Mohamed >> >> charged ions are tricky in DFT for multiple reasons. The excess and >> well localized charge can suffer a very strong delocalization error >> which may lead to unbound electronic states. Moreover, charged ions >> are generally not stable in gas phase. They often require a polar >> solvent to exist. Finally, in periodic boundary conditions a >> distribution of charge (aka "jellium") is required to compensate the >> positive/negative charge in a supercell, and the reference potential >> is affected by the insertion of such charge, so that for example you >> cannot calculate the ionization energy of a molecule as >> E[q=+1]-E[q=0], as you do when you use GTO codes. >> >> This said, it is not impossible to calculate the adsorption energy of >> charged ions on a given substrate, provided that: >> >> 1) You use a hybrid EXX-GGA functional. This is not mandatory, but it >> is recommended because it generally avoids the accommodation of excess >> electrons in unbound states. >> >> 2) You embed your system in an implicit dielectric medium (maybe >> "water", in your case). In QE this is easily provided by the >> QUANTUM-ENVIRON plug-in. >> >> Then you can calculate the adsorption energy in two ways: >> >> A) you can start from the interacting configuration of your system and >> progressively remove the ion in several snapshots (or a few snapshot, >> depending on the computational resources you can afford). Then you >> build an interaction potential curve and yiu try to estimate its >> asymptotic value. It requires also a large supercell, of course. >> >> B) you can use a little trick (which however requires 1 and 2 above). >> Put a cation in a part of your supercell where the interaction energy >> with you polymer+anion system is negligible. Then calculate the energy >> of your cation+anion system in a neutral supercell where their charge >> is exactly compensated. The energy difference between three neutral >> supercells E[polymer+anion+cation]-E[polymer]-E[cation+anion] should >> be a sensible estimate of the anion adsorption energy >> >> HTH >> Giuseppe >> >> Mohamed Safy <[email protected]> ha scritto: >> >> > Thanks for your valuable information but I have experimental results >> which >> > indicate the presence of adsorption. is this can be considered a >> > conflict?. I tried to validate the method using a smaller system. I >> > studied the adsorption of H2 on Graphene. >> > The adsorption energy was 17.17 kcal/mol. >> > the systems are below >> > Complex >> > &CONTROL >> > calculation = "scf" >> > forc_conv_thr = 1.00000e-03 >> > max_seconds = 1.72800e+05 >> > nstep = 1000 >> > verbosity='high' >> > restart_mode='from_scratch' >> > iprint=1 >> > tprnfor=.true. >> > pseudo_dir = '/lfs01/workdirs/val/Test/pseudo', >> > outdir='/lfs01/workdirs/val/Test/Out/C', >> > / >> > >> > &SYSTEM >> > a = 7.40525e+00 >> > c = 9.99906e+00 >> > ibrav = 4 >> > nat = 19 >> > ntyp = 2 >> > ecutwfc = 45.0 , >> > ecutrho = 450.0 , >> > input_DFT = 'PBE-D2' , >> > occupations = 'smearing' , >> > degauss = 1.0d-4 , >> > vdw_corr = 'Grimme-D2' >> > assume_isolated = 'mt' >> > smearing = 'marzari-vanderbilt' , >> > / >> > >> > &ELECTRONS >> > conv_thr = 1.0d-7 , >> > electron_maxstep = 1000 >> > mixing_mode = 'plain' , >> > mixing_beta = 0.3d0 , >> > / >> > >> > &IONS >> > ion_dynamics='bfgs' >> > upscale=20.0 >> > / >> > >> > &CELL >> > / >> > >> > K_POINTS {automatic} >> > 3 3 3 0 0 0 >> > >> > ATOMIC_SPECIES >> > C 12.01070 C.pbe-n-kjpaw_psl.1.0.0.UPF >> > H 1.00794 H.pbe-kjpaw_psl.1.0.0.UPF >> > ATOMIC_POSITIONS {angstrom} >> > C 1.280642168 0.685951341 -0.000431048 >> > C -1.236653977 3.539880413 -0.001566184 >> > C -0.000377617 2.903279130 -0.002911997 >> > C -2.489554615 5.710262290 -0.000852594 >> > C -1.229721248 4.990709007 -0.000338911 >> > C 2.449440629 1.438897112 0.002319254 >> > C 3.702198081 0.707454065 -0.001265064 >> > C 1.236237242 3.539760579 0.000958837 >> > C 2.478517989 2.856386275 0.004841971 >> > C -0.000246038 5.700684987 -0.000997560 >> > C 1.229347070 4.990770096 -0.000716604 >> > C 4.955272233 1.438694069 -0.002138838 >> > C 6.124721243 0.686321393 0.000987763 >> > C 3.702044434 3.562937903 0.001926384 >> > C 4.925831271 2.856536000 -0.001755553 >> > C 2.489209922 5.710445901 -0.000342579 >> > C 3.702309214 4.976078918 -0.000048704 >> > H 3.360489134 2.350036356 -3.014528460 >> > H 2.719672863 2.741584163 -3.037540110 >> > >> > >> > Graphen >> > &CONTROL >> > calculation = "scf" >> > forc_conv_thr = 1.00000e-03 >> > max_seconds = 1.72800e+05 >> > nstep = 1000 >> > verbosity='high' >> > restart_mode='from_scratch' >> > iprint=1 >> > tprnfor=.true. >> > pseudo_dir = '/lfs01/Val/cairo010u1/Test/pseudo', >> > outdir='/lfs01/workdirs/Val/Test/Out/G', >> > / >> > >> > &SYSTEM >> > a = 7.40525e+00 >> > c = 9.99906e+00 >> > ibrav = 4 >> > nat = 17 >> > ntyp = 1 >> > ecutwfc = 45.0 , >> > ecutrho = 450.0 , >> > input_DFT = 'PBE-D2' , >> > occupations = 'smearing' , >> > degauss = 1.0d-4 , >> > vdw_corr = 'Grimme-D2' >> > assume_isolated = 'mt' >> > smearing = 'marzari-vanderbilt' , >> > / >> > >> > &ELECTRONS >> > conv_thr = 1.0d-10 , >> > electron_maxstep = 1000 >> > mixing_mode = 'plain' , >> > mixing_beta = 0.3d0 , >> > / >> > >> > &IONS >> > ion_dynamics='bfgs' >> > upscale=20.0 >> > / >> > >> > &CELL >> > / >> > >> > K_POINTS {automatic} >> > 3 3 3 0 0 0 >> > >> > ATOMIC_SPECIES >> > C 12.01070 C.pbe-n-kjpaw_psl.1.0.0.UPF >> > >> > ATOMIC_POSITIONS {angstrom} >> > C 1.280642168 0.685951341 -0.000431048 >> > C -1.236653977 3.539880413 -0.001566184 >> > C -0.000377617 2.903279130 -0.002911997 >> > C -2.489554615 5.710262290 -0.000852594 >> > C -1.229721248 4.990709007 -0.000338911 >> > C 2.449440629 1.438897112 0.002319254 >> > C 3.702198081 0.707454065 -0.001265064 >> > C 1.236237242 3.539760579 0.000958837 >> > C 2.478517989 2.856386275 0.004841971 >> > C -0.000246038 5.700684987 -0.000997560 >> > C 1.229347070 4.990770096 -0.000716604 >> > C 4.955272233 1.438694069 -0.002138838 >> > C 6.124721243 0.686321393 0.000987763 >> > C 3.702044434 3.562937903 0.001926384 >> > C 4.925831271 2.856536000 -0.001755553 >> > C 2.489209922 5.710445901 -0.000342579 >> > C 3.702309214 4.976078918 -0.000048704 >> > >> > >> > >> > Hydrogen >> > &CONTROL >> > calculation = "scf" >> > forc_conv_thr = 1.00000e-03 >> > max_seconds = 1.72800e+05 >> > nstep = 1000 >> > verbosity='high' >> > restart_mode='from_scratch' >> > iprint=1 >> > tprnfor=.true. >> > pseudo_dir = '/lfs01/workdirs/Val/Test/pseudo', >> > outdir='/lfs01/workdirs/Val/Test/Out/HY', >> > / >> > >> > &SYSTEM >> > a = 7.40525e+00 >> > c = 9.99906e+00 >> > ibrav = 4 >> > nat = 2 >> > ntyp = 1 >> > ecutwfc = 45.0 , >> > ecutrho = 450.0 , >> > input_DFT = 'PBE-D2' , >> > occupations = 'smearing' , >> > degauss = 1.0d-4 , >> > vdw_corr = 'Grimme-D2' >> > assume_isolated = 'mt' >> > smearing = 'marzari-vanderbilt' , >> > >> > / >> > >> > &ELECTRONS >> > conv_thr = 1.0d-7 , >> > electron_maxstep = 1000 >> > mixing_mode = 'plain' , >> > mixing_beta = 0.3d0 , >> > / >> > >> > &IONS >> > ion_dynamics='bfgs' >> > upscale=20.0 >> > / >> > >> > &CELL >> > / >> > >> > K_POINTS {automatic} >> > 3 3 3 0 0 0 >> > >> > ATOMIC_SPECIES >> > H 1.00794 H.pbe-kjpaw_psl.1.0.0.UPF >> > ATOMIC_POSITIONS {angstrom} >> > H 3.360489134 2.350036356 -3.014528460 >> > H 2.719672863 2.741584163 -3.037540110 >> > >> > >> > On Wed, 5 Dec 2018 at 21:09, Stefano Baroni <[email protected]> wrote: >> > >> >> I know nothing about your system, but what you report simply seem the >> >> evidence of an endothermal adsorption, stabilized by a energy barrier. >> >> Have you got strong reasons to believe that this cannot be the case? >> >> Regards, Stefano B >> >> >> >> ___ >> >> Stefano Baroni, Trieste -- http://stefano.baroni.me >> >> >> >> > On 5 Dec 2018, at 18:45, Mohamed Safy <[email protected]> wrote: >> >> > >> >> > Dear QE users >> >> > I am trying to study the adsorption of a negatively charged molecule >> on >> >> a core of polymer. The relaxed cell showed the formation of four >> hydrogen >> >> bonds (with O...H distance range between 1.7 and 1.95 angstrom). But, >> when >> >> I calculated the adsorption energy I found it a positive value (44 >> >> kcal/mol). any advice or suggestion please. >> >> > Thanks in advance >> >> > _______________________________________________ >> >> > users mailing list >> >> > [email protected] >> >> > https://lists.quantum-espresso.org/mailman/listinfo/users >> >> >> >> _______________________________________________ >> >> users mailing list >> >> [email protected] >> >> https://lists.quantum-espresso.org/mailman/listinfo/users >> >> >> >> >> >> 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: <[email protected]> >> >> _______________________________________________ >> users mailing list >> [email protected] >> https://lists.quantum-espresso.org/mailman/listinfo/users >> >
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