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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Dear Prof. Stefano,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thank you. So, is this a special feature of VASP? <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Regards,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Rolly<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> pw_forum-bounces@pwscf.org [mailto:pw_forum-bounces@pwscf.org] <b>On Behalf Of </b>Stefano de Gironcoli<br><b>Sent:</b> Wednesday, August 17, 2016 12:14 PM<br><b>To:</b> PWSCF Forum<br><b>Subject:</b> Re: [Pw_forum] Total energy of adsorbed molecule in a full system<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-bottom:12.0pt'><br>On 17 Aug 2016, at 10:40, Rolly Ng <<a href="mailto:rollyng@gmail.com">rollyng@gmail.com</a>> wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p>Dear QE experts,<o:p></o:p></p><p>I read about molecule deformation energy in the following article, I believe it was computed with VASP.<o:p></o:p></p><p class=MsoNormal>DFT studies of the bonding mechanism of 8-hydroxyquinoline and derivatives on the (111) aluminum surface.<br>DOI:10.1039/C5CP03095A<br><br>The molecule deformation energy was defined as as, E(deform mol) = E(mol/ads) - E(mol/vac).<br>where E(mol/vac) is the total energy of the free molecule in vacuum, and E(mol/ads) is the total energy of the isolated molecule at the geometry after adsorption.<br><br>My question is how to get E(mol/ads) of the molecule from the full system? <o:p></o:p></p></div></blockquote><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>You can't.<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Stefano <o:p></o:p></p></div><div><p class=MsoNormal><br><br><o:p></o:p></p><div><p class=MsoNormal>I have searched the .out file for "energy" but I canto find energy of individual atoms in the full system so I cannot do any summation like sumpdos.x?<br><br>Can anyone help?<br><br>Thank you,<br>Rolly Ng<br><br><o:p></o:p></p><pre>-- <o:p></o:p></pre><pre>PhD. Research Fellow,<o:p></o:p></pre><pre>Dept. of Physics & Materials Science,<o:p></o:p></pre><pre>City University of Hong Kong<o:p></o:p></pre><pre>Tel: +852 3442 4000<o:p></o:p></pre><pre>Fax: +852 3442 0538<o:p></o:p></pre></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>_______________________________________________<br>Pw_forum mailing list<br><a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br><a href="http://pwscf.org/mailman/listinfo/pw_forum">http://pwscf.org/mailman/listinfo/pw_forum</a><o:p></o:p></p></div></blockquote></div></div></div></body></html>