<div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">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.<div>The adsorption energy was 17.17 kcal/mol.</div><div>the systems are below</div><div>Complex</div><div><div>&CONTROL</div><div> calculation = "scf"</div><div> forc_conv_thr = 1.00000e-03</div><div> max_seconds = 1.72800e+05</div><div> nstep = 1000</div><div> verbosity='high'</div><div> restart_mode='from_scratch'</div><div> iprint=1</div><div> tprnfor=.true.</div><div> pseudo_dir = '/lfs01/workdirs/val/Test/pseudo', </div><div>outdir='/lfs01/workdirs/val/Test/Out/C',</div><div>/</div><div><br></div><div>&SYSTEM</div><div> a = 7.40525e+00</div><div> c = 9.99906e+00</div><div> ibrav = 4</div><div> nat = 19</div><div> ntyp = 2</div><div> ecutwfc = 45.0 ,</div><div>ecutrho = 450.0 ,</div><div>input_DFT = 'PBE-D2' ,</div><div>occupations = 'smearing' ,</div><div>degauss = 1.0d-4 ,</div><div>vdw_corr = 'Grimme-D2'</div><div>assume_isolated<span style="white-space:pre"> </span>= 'mt'</div><div>smearing = 'marzari-vanderbilt' ,</div><div>/</div><div> </div><div>&ELECTRONS</div><div>conv_thr = 1.0d-7 ,</div><div>electron_maxstep = 1000</div><div>mixing_mode = 'plain' ,</div><div>mixing_beta = 0.3d0 ,</div><div>/</div><div><br></div><div>&IONS</div><div>ion_dynamics='bfgs'</div><div>upscale=20.0</div><div>/</div><div><br></div><div>&CELL</div><div>/</div><div><br></div><div>K_POINTS {automatic}</div><div> 3 3 3 0 0 0</div><div><br></div><div>ATOMIC_SPECIES</div><div>C 12.01070 C.pbe-n-kjpaw_psl.1.0.0.UPF</div><div>H 1.00794 H.pbe-kjpaw_psl.1.0.0.UPF</div><div>ATOMIC_POSITIONS {angstrom}</div><div>C 1.280642168 0.685951341 -0.000431048</div><div>C -1.236653977 3.539880413 -0.001566184</div><div>C -0.000377617 2.903279130 -0.002911997</div><div>C -2.489554615 5.710262290 -0.000852594</div><div>C -1.229721248 4.990709007 -0.000338911</div><div>C 2.449440629 1.438897112 0.002319254</div><div>C 3.702198081 0.707454065 -0.001265064</div><div>C 1.236237242 3.539760579 0.000958837</div><div>C 2.478517989 2.856386275 0.004841971</div><div>C -0.000246038 5.700684987 -0.000997560</div><div>C 1.229347070 4.990770096 -0.000716604</div><div>C 4.955272233 1.438694069 -0.002138838</div><div>C 6.124721243 0.686321393 0.000987763</div><div>C 3.702044434 3.562937903 0.001926384</div><div>C 4.925831271 2.856536000 -0.001755553</div><div>C 2.489209922 5.710445901 -0.000342579</div><div>C 3.702309214 4.976078918 -0.000048704</div><div>H 3.360489134 2.350036356 -3.014528460</div><div>H 2.719672863 2.741584163 -3.037540110</div></div><div><br></div><div><br></div><div>Graphen</div><div><div>&CONTROL</div><div> calculation = "scf"</div><div> forc_conv_thr = 1.00000e-03</div><div> max_seconds = 1.72800e+05</div><div> nstep = 1000</div><div> verbosity='high'</div><div> restart_mode='from_scratch'</div><div> iprint=1</div><div> tprnfor=.true.</div><div> pseudo_dir = '/lfs01/Val/cairo010u1/Test/pseudo', </div><div>outdir='/lfs01/workdirs/Val/Test/Out/G',</div><div>/</div><div><br></div><div>&SYSTEM</div><div> a = 7.40525e+00</div><div> c = 9.99906e+00</div><div> ibrav = 4</div><div> nat = 17</div><div> ntyp = 1</div><div> ecutwfc = 45.0 ,</div><div>ecutrho = 450.0 ,</div><div>input_DFT = 'PBE-D2' ,</div><div>occupations = 'smearing' ,</div><div>degauss = 1.0d-4 ,</div><div>vdw_corr = 'Grimme-D2'</div><div>assume_isolated<span style="white-space:pre"> </span>= 'mt'</div><div>smearing = 'marzari-vanderbilt' ,</div><div>/</div><div> </div><div>&ELECTRONS</div><div>conv_thr = 1.0d-10 ,</div><div>electron_maxstep = 1000</div><div>mixing_mode = 'plain' ,</div><div>mixing_beta = 0.3d0 ,</div><div>/</div><div><br></div><div>&IONS</div><div>ion_dynamics='bfgs'</div><div>upscale=20.0</div><div>/</div><div><br></div><div>&CELL</div><div>/</div><div><br></div><div>K_POINTS {automatic}</div><div> 3 3 3 0 0 0</div><div><br></div><div>ATOMIC_SPECIES</div><div>C 12.01070 C.pbe-n-kjpaw_psl.1.0.0.UPF</div><div><br></div><div>ATOMIC_POSITIONS {angstrom}</div><div>C 1.280642168 0.685951341 -0.000431048</div><div>C -1.236653977 3.539880413 -0.001566184</div><div>C -0.000377617 2.903279130 -0.002911997</div><div>C -2.489554615 5.710262290 -0.000852594</div><div>C -1.229721248 4.990709007 -0.000338911</div><div>C 2.449440629 1.438897112 0.002319254</div><div>C 3.702198081 0.707454065 -0.001265064</div><div>C 1.236237242 3.539760579 0.000958837</div><div>C 2.478517989 2.856386275 0.004841971</div><div>C -0.000246038 5.700684987 -0.000997560</div><div>C 1.229347070 4.990770096 -0.000716604</div><div>C 4.955272233 1.438694069 -0.002138838</div><div>C 6.124721243 0.686321393 0.000987763</div><div>C 3.702044434 3.562937903 0.001926384</div><div>C 4.925831271 2.856536000 -0.001755553</div><div>C 2.489209922 5.710445901 -0.000342579</div><div>C 3.702309214 4.976078918 -0.000048704</div><div><br></div><div><br></div><div><br></div><div>Hydrogen</div></div><div><div>&CONTROL</div><div> calculation = "scf"</div><div> forc_conv_thr = 1.00000e-03</div><div> max_seconds = 1.72800e+05</div><div> nstep = 1000</div><div> verbosity='high'</div><div> restart_mode='from_scratch'</div><div> iprint=1</div><div> tprnfor=.true.</div><div> pseudo_dir = '/lfs01/workdirs/Val/Test/pseudo', </div><div>outdir='/lfs01/workdirs/Val/Test/Out/HY',</div><div>/</div><div><br></div><div>&SYSTEM</div><div> a = 7.40525e+00</div><div> c = 9.99906e+00</div><div> ibrav = 4</div><div> nat = 2</div><div> ntyp = 1</div><div> ecutwfc = 45.0 ,</div><div>ecutrho = 450.0 ,</div><div>input_DFT = 'PBE-D2' ,</div><div>occupations = 'smearing' ,</div><div>degauss = 1.0d-4 ,</div><div>vdw_corr = 'Grimme-D2'</div><div>assume_isolated<span style="white-space:pre"> </span>= 'mt'</div><div>smearing = 'marzari-vanderbilt' ,</div><div><br></div><div>/</div><div> </div><div>&ELECTRONS</div><div>conv_thr = 1.0d-7 ,</div><div>electron_maxstep = 1000</div><div>mixing_mode = 'plain' ,</div><div>mixing_beta = 0.3d0 ,</div><div>/</div><div><br></div><div>&IONS</div><div>ion_dynamics='bfgs'</div><div>upscale=20.0</div><div>/</div><div><br></div><div>&CELL</div><div>/</div><div><br></div><div>K_POINTS {automatic}</div><div> 3 3 3 0 0 0</div><div><br></div><div>ATOMIC_SPECIES</div><div>H 1.00794 H.pbe-kjpaw_psl.1.0.0.UPF</div><div>ATOMIC_POSITIONS {angstrom}</div><div>H 3.360489134 2.350036356 -3.014528460</div><div>H 2.719672863 2.741584163 -3.037540110</div><div><br></div></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, 5 Dec 2018 at 21:09, Stefano Baroni <<a href="mailto:baroni@sissa.it" target="_blank">baroni@sissa.it</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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?<br>
Regards, Stefano B<br>
<br>
___<br>
Stefano Baroni, Trieste -- <a href="http://stefano.baroni.me" rel="noreferrer" target="_blank">http://stefano.baroni.me</a><br>
<br>
> On 5 Dec 2018, at 18:45, Mohamed Safy <<a href="mailto:msafy505@gmail.com" target="_blank">msafy505@gmail.com</a>> wrote:<br>
> <br>
> Dear QE users<br>
> 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.<br>
> Thanks in advance<br>
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