Dear Dr. Tamasi tried "nogg", and it does work. However, the frequencies are negative for the perturbed molecule atoms (HS) . I only perturbed the molecule.Given that the molecule is stable, i.e. not a transition state.Below are the output & input files: output: Mode symmetry, C_1 (1) point group: freq ( 1 - 1) = -3417.3 [cm-1] --> A I+R freq ( 2 - 2) = -2660.2 [cm-1] --> A I+R freq ( 3 - 3) = -2139.6 [cm-1] --> A I+R freq ( 4 - 4) = -1453.3 [cm-1] --> A I+R freq ( 5 - 5) = -1358.9 [cm-1] --> A I+R freq ( 6 - 6) = -1036.4 [cm-1] --> A I+R freq (325 -325) = 1030.9 [cm-1] --> A I+R freq (326 -326) = 1151.4 [cm-1] --> A I+R freq (327 -327) = 1295.7 [cm-1] --> A I+R freq (328 -328) = 1579.7 [cm-1] --> A I+R freq (329 -329) = 2857.6 [cm-1] --> A I+R freq (330 -330) = 3310.5 [cm-1] --> A I+R
Ph.x input file: phonon calculation at Gamma point.&inputph outdir = './outdir' prefix = 'HS' tr2_ph = 1.0d-09 epsil = .false. amass(1) = 58.69340 amass(2) = 30.97376 amass(3) = 1.00784 amass(4) = 32.065 fildyn = 'HS.dyn'alpha_mix(1)=0.3 nogg = .true nat_todo = 2 /0.0 0.0 0.0 1 2 scf input file: &CONTROL calculation = "scf" prefix = 'HS' outdir = './outdir' pseudo_dir = '/home/' restart_mode = 'from_scratch' forc_conv_thr = 1.0e-03 etot_conv_thr = 1e-04 nstep = 999/&SYSTEM ibrav = 0 ecutrho = 200 ecutwfc = 25 nat = 110 ntyp = 4 occupations='smearing',smearing='gaussian',degauss=0.005 vdw_corr = 'DFT-D2' nspin = 2 starting_magnetization(1)= 0.01/&ELECTRONS conv_thr = 1e-8 electron_maxstep = 200 mixing_mode ='local-TF' mixing_beta = 0.3/&IONS/K_POINTS {automatic}1 1 1 0 0 0ATOMIC_SPECIESNi 58.69340 Ni.pbe-n-rrkjus_psl.0.1.UPFP 30.97376 P.pbe-n-rrkjus_psl.1.0.0.UPFH 1.00784 H.pbe-rrkjus_psl.0.1.UPFS 32.065 S.pbe-n-rrkjus_psl.1.0.0.UPF CELL_PARAMETERS {angstrom} 11.765383541833 0.0000000000 0.0000000000 -5.88269177091652 10.1891210324947 0.0000000000 0.0000000000 0.0000000000 30.9938690567585ATOMIC_POSITIONS (angstrom)H 0.879694621 3.392266427 10.708999692S 2.266698845 3.396363162 10.560733430Ni -2.744571590 4.755054131 0.244939179Ni 3.134031329 1.363792691 0.248008546...P -1.060403962 1.841094610 1.604930623P -3.921453199 6.792156181 0.000000000 0 0 0P 1.960697149 3.396027080 0.000000000 0 0 0P 7.842906399 0.000000000 0.000000000 0 0 0 On Thursday, October 29, 2020, 02:20:23 PM GMT+4, Tamas Karpati <tkarp...@gmail.com> wrote: did you try nogg=.true. ? if not, i suggest you to apply the minimum necessary amount of parameters in your input file. On Wed, Oct 28, 2020 at 3:14 PM Omer Mutasim <omermuta...@ymail.com> wrote: > > I just tried but i got the following error message: > > " > Error in routine phq_readin (1): > gamma_gamma tricks with nat_todo not available. Use nogg=.true. > > " > i'm doing single q phonon calculation > any help ? > On Wednesday, October 28, 2020, 05:45:15 PM GMT+4, Tamas Karpati > <tkarp...@gmail.com> wrote: > > > Dear Omer, > > Did you try to use the nat_todo option in your PH.x input file? > (Do not forget to list the perturbed atom indices on the last line.) > > ASE can use QE as "calculator" and I think it can do what you want. > If not, use Phonopy. > > HTH, > t > > On Wed, Oct 28, 2020 at 1:28 PM Omer Mutasim <omermuta...@ymail.com> wrote: > > > > > > Dear all > > > > 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: > > > > 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 > > > > how to select the perturbed atoms in quantum espresso ? > > I have heard that it can be done by finite difference method, which wasn't > > employed in QE. > > However, i have seen a post where Dr. Paolo Giannozzi said: " it can be > > performed by two finite-difference calculations with opposite displacements > > " > > 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 ? > > > > > > Thanks in advance > > > > > > > > > > Omer Elmutasim > > Research Assistant > > Chemical Engineering Department > > Khalifa university- UAE > > > _______________________________________________ > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > > users mailing list users@lists.quantum-espresso.org > > https://lists.quantum-espresso.org/mailman/listinfo/users > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users _______________________________________________ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
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