<html><head></head><body><div class="ydpcfcdaeb4yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:13px;"><div></div>
<div dir="ltr" data-setdir="false"><div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">Dear Dr. Tamas</div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">i tried "nogg", and it does work. However, the frequencies are negative for the perturbed molecule atoms (HS) . I only perturbed the molecule.</div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">Given that the molecule is stable, i.e. not a transition state.</div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">Below are the output & input files:</div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"><br></div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">output:</div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"><br></div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"><div><div> Mode symmetry, C_1 (1) point group:</div><div><br></div><div> freq ( 1 - 1) = -3417.3 [cm-1] --> A I+R</div><div> freq ( 2 - 2) = -2660.2 [cm-1] --> A I+R</div><div> freq ( 3 - 3) = -2139.6 [cm-1] --> A I+R</div><div> freq ( 4 - 4) = -1453.3 [cm-1] --> A I+R</div><div> freq ( 5 - 5) = -1358.9 [cm-1] --> A I+R</div><div> freq ( 6 - 6) = -1036.4 [cm-1] --> A I+R</div><div> freq (325 -325) = 1030.9 [cm-1] --> A I+R</div><div> freq (326 -326) = 1151.4 [cm-1] --> A I+R</div><div> freq (327 -327) = 1295.7 [cm-1] --> A I+R</div><div> freq (328 -328) = 1579.7 [cm-1] --> A I+R</div><div> freq (329 -329) = 2857.6 [cm-1] --> A I+R</div><div> freq (330 -330) = 3310.5 [cm-1] --> A I+R</div></div><br></div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"><br></div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">Ph.x input file:</div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"><br></div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"><div><div>phonon calculation at Gamma point.</div><div>&inputph</div><div> outdir = './outdir'</div><div> prefix = 'HS'</div><div> tr2_ph = 1.0d-09</div><div> epsil = .false.</div><div> amass(1) = 58.69340</div><div> amass(2) = 30.97376</div><div> amass(3) = 1.00784</div><div> amass(4) = 32.065</div><div> fildyn = 'HS.dyn'</div><div>alpha_mix(1)=0.3</div><div> nogg = .true</div><div> nat_todo = 2</div><div><br></div><div>/</div><div>0.0 0.0 0.0</div><div><br></div><div>1 2</div></div><br></div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"><br></div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">scf input file:<br></div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"><br></div><div dir="ltr" data-setdir="false" style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"><div>&CONTROL</div><div> calculation = "scf"</div><div><span style="white-space: pre-wrap;"> </span>prefix = 'HS'</div><div> outdir = './outdir'</div><div> pseudo_dir = '/home/'</div><div><span style="white-space: pre-wrap;"> </span>restart_mode = 'from_scratch'</div><div> forc_conv_thr = 1.0e-03</div><div><span style="white-space: pre-wrap;"> </span>etot_conv_thr<span style="white-space: pre-wrap;"> </span>=<span style="white-space: pre-wrap;"> </span>1e-04</div><div> nstep = 999</div><div>/</div><div>&SYSTEM</div><div><span style="white-space: pre-wrap;"> </span>ibrav <span style="white-space: pre-wrap;"> </span>=<span style="white-space: pre-wrap;"> </span> 0</div><div> ecutrho = 200</div><div> ecutwfc = 25</div><div> nat = 110</div><div> ntyp = 4</div><div><span style="white-space: pre-wrap;"> </span>occupations='smearing',smearing='gaussian',degauss=0.005</div><div><span style="white-space: pre-wrap;"> </span>vdw_corr<span style="white-space: pre-wrap;"> </span>=<span style="white-space: pre-wrap;"> </span>'DFT-D2'</div><div> <span style="white-space: pre-wrap;"> </span> nspin = 2</div><div><span style="white-space: pre-wrap;"> </span> starting_magnetization(1)= 0.01</div><div>/</div><div>&ELECTRONS</div><div> conv_thr =<span style="white-space: pre-wrap;"> </span>1e-8</div><div> electron_maxstep = 200</div><div><span style="white-space: pre-wrap;"> </span>mixing_mode<span style="white-space: pre-wrap;"> </span>='local-TF'</div><div> mixing_beta = 0.3</div><div>/</div><div>&IONS</div><div>/</div><div>K_POINTS {automatic}</div><div>1<span style="white-space: pre-wrap;"> </span>1<span style="white-space: pre-wrap;"> </span>1<span style="white-space: pre-wrap;"> </span>0<span style="white-space: pre-wrap;"> </span>0<span style="white-space: pre-wrap;"> </span>0</div><div>ATOMIC_SPECIES</div><div>Ni<span style="white-space: pre-wrap;"> </span>58.69340<span style="white-space: pre-wrap;"> </span>Ni.pbe-n-rrkjus_psl.0.1.UPF</div><div>P<span style="white-space: pre-wrap;"> </span>30.97376<span style="white-space: pre-wrap;"> </span>P.pbe-n-rrkjus_psl.1.0.0.UPF</div><div>H<span style="white-space: pre-wrap;"> </span>1.00784<span style="white-space: pre-wrap;"> </span>H.pbe-rrkjus_psl.0.1.UPF</div><div>S <span style="white-space: pre-wrap;"> </span>32.065 S.pbe-n-rrkjus_psl.1.0.0.UPF </div><div>CELL_PARAMETERS {angstrom}</div><div> 11.765383541833 0.0000000000 0.0000000000</div><div> -5.88269177091652 10.1891210324947 0.0000000000</div><div> 0.0000000000 0.0000000000 30.9938690567585</div><div>ATOMIC_POSITIONS (angstrom)</div><div>H 0.879694621 3.392266427 10.708999692</div><div>S 2.266698845 3.396363162 10.560733430</div><div>Ni -2.744571590 4.755054131 0.244939179</div><div>Ni 3.134031329 1.363792691 0.248008546</div><div>.</div><div>.</div><div>.</div><div>P -1.060403962 1.841094610 1.604930623</div><div>P -3.921453199 6.792156181 0.000000000 0 0 0</div><div>P 1.960697149 3.396027080 0.000000000 0 0 0</div><div>P 7.842906399 0.000000000 0.000000000 0 0 0</div><div><br></div></div></div><br></div><div><br></div>
</div><div id="yahoo_quoted_4467896184" class="yahoo_quoted">
<div style="font-family:'Helvetica Neue', Helvetica, Arial, sans-serif;font-size:13px;color:#26282a;">
<div>
On Thursday, October 29, 2020, 02:20:23 PM GMT+4, Tamas Karpati <tkarpati@gmail.com> wrote:
</div>
<div><br></div>
<div><br></div>
<div><div dir="ltr">did you try nogg=.true. ?<br clear="none">if not, i suggest you to apply the minimum necessary amount of<br clear="none">parameters in your input file.<br clear="none"><br clear="none">On Wed, Oct 28, 2020 at 3:14 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">> I just tried but i got the following error message:<br clear="none">><br clear="none">> "<br clear="none">> Error in routine phq_readin (1):<br clear="none">> gamma_gamma tricks with nat_todo not available. Use nogg=.true.<br clear="none">><br clear="none">> "<br clear="none">> i'm doing single q phonon calculation<br clear="none">> any help ?<br clear="none">> On Wednesday, October 28, 2020, 05:45:15 PM GMT+4, Tamas Karpati <<a shape="rect" ymailto="mailto:tkarpati@gmail.com" href="mailto:tkarpati@gmail.com">tkarpati@gmail.com</a>> wrote:<br clear="none">><br clear="none">><br clear="none">> 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">><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<br clear="none">><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="yqt7604644607" id="yqtfd08708"><br clear="none">><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><br clear="none"></div></div></div>
</div>
</div></body></html>