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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