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<div dir="ltr" data-setdir="false">Dear Dr. Tamas</div><div dir="ltr" data-setdir="false">I have just checked it, it is what i'm looking to exactly.</div><div dir="ltr" data-setdir="false">what is the syntax for <span><span style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">nat_todo ? it is not clear from ph.x documentation </span></span></div><div dir="ltr" data-setdir="false"><span><span style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">Can you please clarify it ?</span></span></div><div dir="ltr" data-setdir="false"><span><span style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"><br></span></span></div><div dir="ltr" data-setdir="false"><div><table style="font-family: arial, helvetica, sans-serif; border-color: rgb(80, 80, 135); border-style: solid; border-width: 0px; margin-bottom: 10px; table-layout: auto; width: 702px;"><tbody><tr><td><h3 style="font-size: 16px;">Syntax:</h3><blockquote><i><a href="https://www.quantum-espresso.org/Doc/INPUT_PH.html#idm346" rel="nofollow" target="_blank" class="enhancr_card_4720738668">atom(1) atom(2) ... atom(nat_todo) </a></i><div><br></div><div id="ydpaa009dcbenhancr_card_4720738668" class="ydpaa009dcbyahoo-link-enhancr-card ydpaa009dcbyahoo-link-enhancr-not-allow-cover ydpaa009dcbymail-preserve-class ydpaa009dcbymail-preserve-style" style="max-width:400px;font-family:YahooSans, Helvetica Neue, Segoe UI, Helvetica, Arial, sans-serif" data-url="https://www.quantum-espresso.org/Doc/INPUT_PH.html#idm346" data-type="YENHANCER" data-size="MEDIUM" contenteditable="false"><a href="https://www.quantum-espresso.org/Doc/INPUT_PH.html#idm346" style="text-decoration:none !important;color:#000 !important" class="ydpaa009dcbyahoo-enhancr-cardlink" rel="nofollow" target="_blank"><table border="0" class="ydpaa009dcbcard-wrapper ydpaa009dcbyahoo-ignore-table" cellpadding="0" cellspacing="0" style="max-width:400px"><tbody><tr><td width="400"><table border="0" class="ydpaa009dcbcard ydpaa009dcbyahoo-ignore-table" cellpadding="0" cellspacing="0" width="100%" style="max-width:400px;border-width:1px;border-style:solid;border-color:rgb(224, 228, 233);border-radius:2px"><tbody><tr><td><table border="0" class="ydpaa009dcbcard-info ydpaa009dcbyahoo-ignore-table" cellpadding="0" cellspacing="0" style="background:#fff;position:relative;z-index:2;width:100%;max-width:400px;border-radius:0 0 2px 2px;border-top:1px solid rgb(224, 228, 233)"><tbody><tr><td style="background-color:#ffffff;padding:16px 0 16px 12px;vertical-align:top;border-radius:0 0 0 2px"></td><td style="vertical-align:middle;padding:12px 24px 16px 12px;width:99%;font-family:YahooSans, Helvetica Neue, Segoe UI, Helvetica, Arial, sans-serif;border-radius:0 0 2px 0"><h2 class="ydpaa009dcbcard-title" style="font-size: 14px; line-height: 19px; margin: 0px 0px 6px; font-family: YahooSans, Helvetica Neue, Segoe UI, Helvetica, Arial, sans-serif; color: rgb(38, 40, 42); max-width: 314px;">ph.x: input description</h2><p class="ydpaa009dcbcard-description" style="font-size: 12px; line-height: 16px; margin: 0px; color: rgb(151, 155, 167);"></p></td></tr></tbody></table></td></tr></tbody></table></td></tr></tbody></table></a></div><div><br></div><div><br></div> </blockquote></td></tr></tbody></table></div><br></div><div><br></div>
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On Wednesday, October 28, 2020, 05:45:15 PM GMT+4, Tamas Karpati <tkarpati@gmail.com> wrote:
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<div><div dir="ltr">Dear Omer,<br clear="none"><br clear="none">Did you try to use the nat_todo option in your PH.x input file?<br clear="none">(Do not forget to list the perturbed atom indices on the last line.)<br clear="none"><br clear="none">ASE can use QE as "calculator" and I think it can do what you want.<br clear="none">If not, use Phonopy.<br clear="none"><br clear="none">HTH,<br clear="none"> t<br clear="none"><div class="yqt3727004091" id="yqtfd81320"><br clear="none">On Wed, Oct 28, 2020 at 1:28 PM Omer Mutasim <<a shape="rect" ymailto="mailto:omermutasim@ymail.com" href="mailto:omermutasim@ymail.com">omermutasim@ymail.com</a>> wrote:<br clear="none">><br clear="none">><br clear="none">> Dear all<br clear="none">><br clear="none">> I need to calculate the the virbrational frequencies of adsorbate molecule on surface using phonon single q calculation , in order to estimate the partition function (for entropy ,reaction rate constants). so my questions go like:<br clear="none">><br clear="none">> I have a large supercell (110 atoms) which means a high degrees of freedom (330 DOF) , so i want to decrease this DOF , by perturbing only adsorbate molecule and the the two uppermost layers<br clear="none">><br clear="none">> how to select the perturbed atoms in quantum espresso ?<br clear="none">> I have heard that it can be done by finite difference method, which wasn't employed in QE.<br clear="none">> However, i have seen a post where Dr. Paolo Giannozzi said: " it can be performed by two finite-difference calculations with opposite displacements "<br clear="none">> So , can you please tell me, what are the steps involved in doing this finite-difference method mentioned by Dr. Paolo ? or any other procedure that can be do the same ?<br clear="none">><br clear="none">><br clear="none">> Thanks in advance<br clear="none">><br clear="none">><br clear="none">><br clear="none">><br clear="none">> Omer Elmutasim<br clear="none">> Research Assistant<br clear="none">> Chemical Engineering Department<br clear="none">> Khalifa university- UAE</div><br clear="none">> _______________________________________________<br clear="none">> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)<br clear="none">> users mailing list <a shape="rect" ymailto="mailto:users@lists.quantum-espresso.org" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br clear="none">> <a shape="rect" href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br clear="none">_______________________________________________<br clear="none">Quantum ESPRESSO is supported by MaX (www.max-centre.eu)<br clear="none">users mailing list <a shape="rect" ymailto="mailto:users@lists.quantum-espresso.org" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br clear="none"><a shape="rect" href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><div class="yqt3727004091" id="yqtfd99702"><br clear="none"></div></div></div>
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