<div>Hi, Tom</div><div><br></div><div>Here is an example for phonons at Gamma</div><div>phonons at Gamma<br> &inputph<br> tr2_ph=1.0d-14,<br> prefix='sym',<br> alpha_mix=0.1,<br> fildyn='phG.dyn',<br> amass(3)=107.8682,<br> amass(1)=15.999,<br> amass(2)=1.0079,<br> outdir='./'<br> nat_todo=5,<br> /<br>0.0 0.0 0.0<br>1 2 3 4 5</div><div><br></div><div><hr align="left" style="margin: 0 0 10px 0;border: 0;border-bottom:1px solid #E4E5E6;height:0;line-height:0;font-size:0;padding: 20px 0 0 0;width: 50px;"></div><div><div style="font-size:14px;font-family:Verdana;color:#000;"><div><i><font color="#0000ff" face="Times New Roman" size="2"><b>Dr. Jibiao Li, </b></font></i></div><div><i><font color="#0000ff" face="Times New Roman" size="2"><b>Department of Material Science and Engineering</b></font></i></div><div><i><font color="#0000ff" face="Times New Roman" size="2"><b>Yangtze Normal University</b></font></i></div><div><i><font face="Times New Roman"><font size="2"><font color="#0000ff"><b><span style="text-align: left; text-transform: none; line-height: 21px; text-indent: 0px; letter-spacing: normal; font-variant: normal; text-decoration: none; word-spacing: 0px; display: inline !important; white-space: normal; orphans: 2; float: none; -webkit-text-stroke-width: 0px; background-color: transparent;">Juxian Dadao 16#,</span> Fuling, Chongqing, China</b></font></font></font></i></div><div><i><font color="#0000ff" face="Times New Roman" size="2"><b>Email: jibiaoli@yznu.edu.cn, jibiaoli@foxmail.com, jibiao.li@hotmail.com</b></font></i></div><div><i><font color="#0000ff" face="Times New Roman" size="2"><b>Homepage: https://www.researchgate.net/profile/Jibiao_Li</b></font></i></div>
</div></div><div><br></div><div> </div><div><div><br></div><div><br></div><div style="font-size: 12px;font-family: Arial Narrow;padding:2px 0 2px 0;">------------------ Original ------------------</div><div style="font-size: 12px;background:#efefef;padding:8px;"><div><b>From:</b> "thorgalg"<thorgalg@poczta.onet.pl>;</div><div><b>Date:</b> Sat, Oct 19, 2019 11:25 PM</div><div><b>To:</b> "Quantum ESPRESSO users Forum"<users@lists.quantum-espresso.org>;<wbr></div><div></div><div><b>Subject:</b> Re: [QE-users] zero-point energy (ZPE) correction</div></div><div><br></div><div>Dear All,</div>
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<div>thank you for the help. I tried to find an example how to calculate the vibrational modes of the adsorbate</div>
<div>using the ph.x code but I didn't. Does anyone give me a link to such calculations?</div>
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<div>Best,</div>
<div>Tom</div>
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<div>W dniu 2019-10-18 18:02:19 użytkownik Weitzner, Stephen Eric <weitzner1@llnl.gov> napisał:</div>
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<p>Hi Tom,</p>
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<p>This can be done using the phonon code. Take a look at the documentation for the ph.x code (<a href="https://www.quantum-espresso.org/Doc/INPUT_PH.html#idm292" target="_blank">https://www.quantum-espresso.org/Doc/INPUT_PH.html#idm292</a>). This will explain not only how to compute phonons / vibrational modes, but also how to restrict the calculation to deal only with adsorbates on surfaces. From there, you can follow one of the numerous tutorials available online for how to use the phonon code and its associated tools to diagonalize the dynamical matrix to obtain the vibrational modes of the adsorbate. Alternatively, you can use a finite displacement method. For this you could write a simple code yourself in python or use an existing tool such as phonopy (<a href="https://atztogo.github.io/phonopy/reference.html" target="_blank">https://atztogo.github.io/phonopy/reference.html</a>).</p>
<p> </p>
<p>Hope that helps.</p>
<p>Steve</p>
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<p>-- </p>
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<p>Stephen Weitzner, PhD</p>
<p>Postdoctoral Research Scientist</p>
<p>Quantum Simulations Group</p>
<p>Lawrence Livermore National Laboratory</p>
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<p><strong><span style="font-size: 12.0pt; color: black;">From: </span></strong><span style="font-size: 12.0pt; color: black;">users <users-bounces@lists.quantum-espresso.org> on behalf of thorgalg <thorgalg@poczta.onet.pl><br> <strong>Reply-To: </strong>Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br> <strong>Date: </strong>Friday, October 18, 2019 at 7:03 AM<br> <strong>To: </strong>"users@lists.quantum-espresso.org" <users@lists.quantum-espresso.org><br> <strong>Subject: </strong>[QE-users] zero-point energy (ZPE) correction</span></p>
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<p><span style="font-size: 13.5pt; font-family: 'Arial',sans-serif;">Dear All</span><br> <span style="font-size: 13.5pt; font-family: 'Arial',sans-serif;"> </span></p>
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<p><span style="font-size: 13.5pt; font-family: 'Arial',sans-serif;"> </span></p>
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<p><span style="font-size: 13.5pt; font-family: 'Arial',sans-serif;">I'm going to simulate a catalytic process including transition state calculations.</span><br> <span style="font-size: 13.5pt; font-family: 'Arial',sans-serif;">Furthermore, I want to calculate the zero-point energy (ZPE) correction to get the </span><br> <span style="font-size: 13.5pt; font-family: 'Arial',sans-serif;">Gibbs free energy. Therefore, I would like to ask you how to calculate vibrational </span><br> <span style="font-size: 13.5pt; font-family: 'Arial',sans-serif;">modes only for the adsorbate using the QE packages?</span><br> <span style="font-size: 13.5pt; font-family: 'Arial',sans-serif;"> </span><br> <span style="font-size: 13.5pt; font-family: 'Arial',sans-serif;">Best,</span><br> <span style="font-size: 13.5pt; font-family: 'Arial',sans-serif;">Tom</span></p>
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