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Very insightful ideas , i will try it , then i will let you know the results <br><br><br><a href="https://overview.mail.yahoo.com/?.src=iOS">Sent from Yahoo Mail for iPhone</a><br><br><p class="yahoo-quoted-begin" style="font-size: 15px; color: #715FFA; padding-top: 15px; margin-top: 0">On Thursday, October 29, 2020, 3:52 PM, Tamas Karpati <tkarpati@gmail.com> wrote:</p><blockquote class="iosymail"><div dir="ltr">Dear Omer,<br clear="none"><br clear="none">Very well, your simulation completes successfully.<br clear="none">Negative (ie. imaginary) eigenvalues indicate for all-atom<br clear="none">perturbations that your system is not in a local minimum conformation.<br clear="none">In such an overlimited situation, however, these numbers are probably<br clear="none">meaningless. To see what is behind, try to add more and more<br clear="none">atoms to the perturbation pool. The followings might show you<br clear="none">how much of the reactant environment is necessary to account for:<br clear="none"> - first add the metal atoms that connect to S or O<br clear="none"> - then add metal atoms directly connected to the above metals<br clear="none"> - extend further (2 then more metal bond environments).<br clear="none">In principle the all-atom phonon sim. would give you 6 pcs.<br clear="none">of near zero "frequencies" if your structure is a real local minimum.<br clear="none">If not, the no. of imaginary freqs. (also called nimag) informs you<br clear="none">about the dimensions of the E-hypersurface that you need to climb more.<br clear="none">Note: R and P need zero, TS needs exactly one for nimag.<br clear="none"><br clear="none">One more point: your molecule was SO2 which decomposed so that<br clear="none">you left out the other O from your simulation (for just 2). It would<br clear="none">be more correct<br clear="none">to do the above steps including all S + 2 O and their direct/indirect<br clear="none">chemical environments... I'm curious what others would say to this.<br clear="none"><br clear="none">Good luck,<br clear="none"> t<br clear="none"><br clear="none"><br clear="none"><br clear="none"><br clear="none"><div class="yqt2538346425" id="yqtfd37313"><br clear="none">On Thu, Oct 29, 2020 at 11:55 AM 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">> Dear Dr. Tamas<br clear="none">> i tried "nogg", and it does work. However, the frequencies are negative for the perturbed molecule atoms (HS) . I only perturbed the molecule.<br clear="none">> Given that the molecule is stable, i.e. not a transition state.<br clear="none">> Below are the output & input files:<br clear="none">><br clear="none">> output:<br clear="none">><br clear="none">> Mode symmetry, C_1 (1) point group:<br clear="none">><br clear="none">> freq ( 1 - 1) = -3417.3 [cm-1] --> A I+R<br clear="none">> freq ( 2 - 2) = -2660.2 [cm-1] --> A I+R<br clear="none">> freq ( 3 - 3) = -2139.6 [cm-1] --> A I+R<br clear="none">> freq ( 4 - 4) = -1453.3 [cm-1] --> A I+R<br clear="none">> freq ( 5 - 5) = -1358.9 [cm-1] --> A I+R<br clear="none">> freq ( 6 - 6) = -1036.4 [cm-1] --> A I+R<br clear="none">> freq (325 -325) = 1030.9 [cm-1] --> A I+R<br clear="none">> freq (326 -326) = 1151.4 [cm-1] --> A I+R<br clear="none">> freq (327 -327) = 1295.7 [cm-1] --> A I+R<br clear="none">> freq (328 -328) = 1579.7 [cm-1] --> A I+R<br clear="none">> freq (329 -329) = 2857.6 [cm-1] --> A I+R<br clear="none">> freq (330 -330) = 3310.5 [cm-1] --> A I+R<br clear="none">><br clear="none">><br clear="none">> Ph.x input file:<br clear="none">><br clear="none">> phonon calculation at Gamma point.<br clear="none">> &inputph<br clear="none">> outdir = './outdir'<br clear="none">> prefix = 'HS'<br clear="none">> tr2_ph = 1.0d-09<br clear="none">> epsil = .false.<br clear="none">> amass(1) = 58.69340<br clear="none">> amass(2) = 30.97376<br clear="none">> amass(3) = 1.00784<br clear="none">> amass(4) = 32.065<br clear="none">> fildyn = 'HS.dyn'<br clear="none">> alpha_mix(1)=0.3<br clear="none">> nogg = .true<br clear="none">> nat_todo = 2<br clear="none">><br clear="none">> /<br clear="none">> 0.0 0.0 0.0<br clear="none">><br clear="none">> 1 2<br clear="none">><br clear="none">><br clear="none">> scf input file:<br clear="none">><br clear="none">> &CONTROL<br clear="none">> calculation = "scf"<br clear="none">> prefix = 'HS'<br clear="none">> outdir = './outdir'<br clear="none">> pseudo_dir = '/home/'<br clear="none">> restart_mode = 'from_scratch'<br clear="none">> forc_conv_thr = 1.0e-03<br clear="none">> etot_conv_thr = 1e-04<br clear="none">> nstep = 999<br clear="none">> /<br clear="none">> &SYSTEM<br clear="none">> ibrav = 0<br clear="none">> ecutrho = 200<br clear="none">> ecutwfc = 25<br clear="none">> nat = 110<br clear="none">> ntyp = 4<br clear="none">> occupations='smearing',smearing='gaussian',degauss=0.005<br clear="none">> vdw_corr = 'DFT-D2'<br clear="none">> nspin = 2<br clear="none">> starting_magnetization(1)= 0.01<br clear="none">> /<br clear="none">> &ELECTRONS<br clear="none">> conv_thr = 1e-8<br clear="none">> electron_maxstep = 200<br clear="none">> mixing_mode ='local-TF'<br clear="none">> mixing_beta = 0.3<br clear="none">> /<br clear="none">> &IONS<br clear="none">> /<br clear="none">> K_POINTS {automatic}<br clear="none">> 1 1 1 0 0 0<br clear="none">> ATOMIC_SPECIES<br clear="none">> Ni 58.69340 Ni.pbe-n-rrkjus_psl.0.1.UPF<br clear="none">> P 30.97376 P.pbe-n-rrkjus_psl.1.0.0.UPF<br clear="none">> H 1.00784 H.pbe-rrkjus_psl.0.1.UPF<br clear="none">> S 32.065 S.pbe-n-rrkjus_psl.1.0.0.UPF<br clear="none">> CELL_PARAMETERS {angstrom}<br clear="none">> 11.765383541833 0.0000000000 0.0000000000<br clear="none">> -5.88269177091652 10.1891210324947 0.0000000000<br clear="none">> 0.0000000000 0.0000000000 30.9938690567585<br clear="none">> ATOMIC_POSITIONS (angstrom)<br clear="none">> H 0.879694621 3.392266427 10.708999692<br clear="none">> S 2.266698845 3.396363162 10.560733430<br clear="none">> Ni -2.744571590 4.755054131 0.244939179<br clear="none">> Ni 3.134031329 1.363792691 0.248008546<br clear="none">> .<br clear="none">> .<br clear="none">> .<br clear="none">> P -1.060403962 1.841094610 1.604930623<br clear="none">> P -3.921453199 6.792156181 0.000000000 0 0 0<br clear="none">> P 1.960697149 3.396027080 0.000000000 0 0 0<br clear="none">> P 7.842906399 0.000000000 0.000000000 0 0 0<br clear="none">><br clear="none">><br clear="none">><br clear="none">> On Thursday, October 29, 2020, 02:20:23 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">> 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><br clear="none">><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><blockquote></blockquote></blockquote>
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