<html><head></head><body><div class="yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:13px;"><div><br></div><div dir="ltr" data-setdir="false"><div><div style="color: rgb(0, 0, 0); font-family: Arial;"><font size="3">Dear all</font></div><div style="color: rgb(0, 0, 0); font-family: Arial;"><font size="3"><br></font></div><div style="color: rgb(0, 0, 0); font-family: Arial;" dir="ltr" data-setdir="false"><font size="3"> I need to calculate the the virbrational frequencies of adsorbate molecule on surface using <span><span style="color: rgb(5, 5, 5); font-family: "Segoe UI Historic", "Segoe UI", Helvetica, Arial, sans-serif; white-space: pre-wrap;">phonon single q calculation</span></span> , in order to estimate the partition function (for entropy ,reaction rate constants). so my questions go like:</font></div><div style="color: rgb(0, 0, 0); font-family: Arial;"><font size="3"><br></font></div><div style="" dir="ltr" data-setdir="false"><font size="3"><font face="Arial"> I have a large supercell (110 atoms) which means a high </font><span style="color: rgb(0, 0, 0); font-family: Arial;"><span style="color: rgb(0, 0, 0); font-family: Arial;">degrees of freedom (330 DOF)</span></span><font face="Arial"> , so i want to decrease this DOF , by perturbing only </font><span style="color: rgb(0, 0, 0); font-family: Arial;"><span style="color: rgb(5, 5, 5); font-family: "Segoe UI Historic", "Segoe UI", Helvetica, Arial, sans-serif; white-space: pre-wrap;">adsorbate molecule and the the two uppermost layers</span></span></font></div><div style="" dir="ltr" data-setdir="false"><font color="#050505" face="Segoe UI Historic, Segoe UI, Helvetica, Arial, sans-serif" size="3"><span style="white-space: pre-wrap;"><br></span></font><div style="color: rgb(0, 0, 0); font-family: Arial;"><div style="font-family: "Segoe UI Historic", "Segoe UI", Helvetica, Arial, sans-serif; color: rgb(5, 5, 5); white-space: pre-wrap;"><font size="3">how to select the perturbed atoms in quantum espresso ?</font></div><div style="font-family: "Segoe UI Historic", "Segoe UI", Helvetica, Arial, sans-serif; color: rgb(5, 5, 5); white-space: pre-wrap;" dir="ltr" data-setdir="false"><font size="3">I have heard that it can be done by finite difference method, which wasn't employed in QE. </font></div></div><div style="" dir="ltr" data-setdir="false"><font color="#050505" face="Segoe UI Historic, Segoe UI, Helvetica, Arial, sans-serif" size="3"><span style="white-space: pre-wrap;">However, i have seen a post where Dr. <span>Paolo Giannozzi</span> said: " it can be performed by two finite-difference calculations with opposite displacements "</span></font></div><div style="" dir="ltr" data-setdir="false"><font color="#050505" face="Segoe UI Historic, Segoe UI, Helvetica, Arial, sans-serif" size="3"><span style="white-space: pre-wrap;">So , can you please tell me, what are the steps involved in doing this <span><span style="color: rgb(5, 5, 5); font-family: "Segoe UI Historic", "Segoe UI", Helvetica, Arial, sans-serif; white-space: pre-wrap;">finite-difference method </span></span>mentioned by Dr. Paolo ? or any other procedure that can be do the same ?</span></font></div><font face="Arial" size="3"> </font></div><div style="color: rgb(0, 0, 0); font-family: Arial;" dir="ltr" data-setdir="false"><br></div><div style="color: rgb(0, 0, 0); font-family: Arial;"><font size="3"> Thanks in advance</font></div></div><font size="3"><br></font></div><div dir="ltr" data-setdir="false"><font size="3"><br></font></div><div dir="ltr" data-setdir="false"><font size="3"><br></font></div><div dir="ltr" data-setdir="false"><font size="3"><br></font></div><div dir="ltr" data-setdir="false"><font size="3">Omer Elmutasim </font></div><div dir="ltr" data-setdir="false"><font size="3">Research Assistant</font></div><div dir="ltr" data-setdir="false"><font size="3">Chemical Engineering Department</font></div><div dir="ltr" data-setdir="false"><font size="3">Khalifa university- UAE</font></div></div></body></html>