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        <div dir="ltr" data-setdir="false">i have perturbed the molecule with the 3 surface atoms. Also i tried 9 surface atoms connected to it (currently running), however i got the same negative frequencies. Does the frequencies, shown below, have the same order of perturbed atoms ? i.e. the <span> (  1 -  1) correspond to the first atom, <span> (  2 -  2) for the second atom ,.. ?</span></span></div><div dir="ltr" data-setdir="false"><span><span>what does " <span> I+R " & " A" means ?</span></span></span></div><div dir="ltr" data-setdir="false"><span><span><span>could the higher frequencies ( > 600 ), at the end, correspond to the molecule ? </span></span></span><br></div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">below are the results for molecule + 3 surface atoms:</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false"><div>     freq (  1 -  1) =      -2644.2  [cm-1]   --> A               I+R<br>     freq (  2 -  2) =      -2633.2  [cm-1]   --> A               I+R<br>     freq (  3 -  3) =      -2304.5  [cm-1]   --> A               I+R<br>     freq (  4 -  4) =      -2238.8  [cm-1]   --> A               I+R<br>     freq (  5 -  5) =      -2164.5  [cm-1]   --> A               I+R<br>     freq (  6 -  6) =      -2121.2  [cm-1]   --> A               I+R<br>     freq (  7 -  7) =      -2104.9  [cm-1]   --> A               I+R<br>     freq (  8 -  8) =      -2080.8  [cm-1]   --> A               I+R<br>     freq (  9 -  9) =      -2061.5  [cm-1]   --> A               I+R<br>     freq ( 10 - 10) =      -1925.4  [cm-1]   --> A               I+R<br>     freq ( 11 - 11) =      -1897.1  [cm-1]   --> A               I+R<br>     freq ( 12 - 12) =      -1397.0  [cm-1]   --> A               I+R<br>     freq ( 13 - 13) =      -1234.0  [cm-1]   --> A               I+R<br>     freq ( 14 - 14) =      -1161.7  [cm-1]   --> A               I+R<br>     freq ( 15 - 15) =      -1015.3  [cm-1]   --> A               I+R<br>     freq (316 -316) =        138.5  [cm-1]   --> A               I+R<br>     freq (317 -317) =        145.4  [cm-1]   --> A               I+R<br>     freq (318 -318) =        206.2  [cm-1]   --> A               I+R<br>     freq (319 -319) =        216.9  [cm-1]   --> A               I+R<br>     freq (320 -320) =        263.8  [cm-1]   --> A               I+R<br>     freq (321 -321) =        291.9  [cm-1]   --> A               I+R<br>     freq (322 -322) =        295.8  [cm-1]   --> A               I+R<br>     freq (323 -323) =        384.0  [cm-1]   --> A               I+R<br>     freq (324 -324) =        459.1  [cm-1]   --> A               I+R<br>     freq (325 -325) =        529.7  [cm-1]   --> A               I+R<br>     freq (326 -326) =        621.1  [cm-1]   --> A               I+R<br>     freq (327 -327) =        640.1  [cm-1]   --> A               I+R<br>     freq (328 -328) =       1190.8  [cm-1]   --> A               I+R<br>     freq (329 -329) =       1568.2  [cm-1]   --> A               I+R<br>     freq (330 -330) =       1851.0  [cm-1]   --> A               I+R<br><br></div><div><br></div></div><div><br></div>
        
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                    On Thursday, October 29, 2020, 3:52:29 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">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="yqt0076132923" id="yqtfd79823"><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></div>
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