[QE-users] Phonon: negative frequencies for adsorbate molecule using "nat-todo" option

[Omer Mutasim]

 Dear all
 I'm doing phonon calculation at Gamma point (q)  in order to estimate the reaction rate constants for a micro-kinetic model.  I have perturbed only the adsorbate molecule with the 3 surface atoms, connected to adsorbate, using "nat-todo" option. However, i got 15 negative frequencies (should be 6 as i know ) ,with high absolute value. 
Can you please help me to know what is wrong with my input files ?
Below are the output & input files:


     Mode symmetry, C_1 (1)     point group:
     freq (  1 -  1) =      -2762.6  [cm-1]   --> A               I+R     freq (  2 -  2) =      -2570.3  [cm-1]   --> A               I+R     freq (  3 -  3) =      -2460.4  [cm-1]   --> A               I+R     freq (  4 -  4) =      -2423.6  [cm-1]   --> A               I+R     freq (  5 -  5) =      -2356.3  [cm-1]   --> A               I+R     freq (  6 -  6) =      -2158.0  [cm-1]   --> A               I+R     freq (  7 -  7) =      -2151.1  [cm-1]   --> A               I+R     freq (  8 -  8) =      -2067.5  [cm-1]   --> A               I+R     freq (  9 -  9) =      -2034.8  [cm-1]   --> A               I+R     freq ( 10 - 10) =      -2025.2  [cm-1]   --> A               I+R     freq ( 11 - 11) =      -1864.3  [cm-1]   --> A               I+R     freq ( 12 - 12) =      -1804.5  [cm-1]   --> A               I+R     freq ( 13 - 13) =      -1099.4  [cm-1]   --> A               I+R     freq ( 14 - 14) =       -947.6  [cm-1]   --> A               I+R     freq ( 15 - 15) =       -912.5  [cm-1]   --> A               I+R     freq (316 -316) =        179.3  [cm-1]   --> A               I+R     freq (317 -317) =        193.0  [cm-1]   --> A               I+R     freq (318 -318) =        215.8  [cm-1]   --> A               I+R     freq (319 -319) =        240.2  [cm-1]   --> A               I+R     freq (320 -320) =        270.4  [cm-1]   --> A               I+R     freq (321 -321) =        317.0  [cm-1]   --> A               I+R     freq (322 -322) =        370.8  [cm-1]   --> A               I+R     freq (323 -323) =        377.3  [cm-1]   --> A               I+R     freq (324 -324) =        398.3  [cm-1]   --> A               I+R     freq (325 -325) =        417.8  [cm-1]   --> A               I+R     freq (326 -326) =        468.2  [cm-1]   --> A               I+R     freq (327 -327) =        659.0  [cm-1]   --> A               I+R     freq (328 -328) =       1096.6  [cm-1]   --> A               I+R     freq (329 -329) =       1795.5  [cm-1]   --> A               I+R     freq (330 -330) =       2199.3  [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)=0.1
 recover=.true  nogg = .true  nat_todo = 5
/0.0 0.0 0.0
1 2 37 46 54


scf input file:

&CONTROL    calculation   = "scf"prefix = 'HS'    outdir = './outdir'    pseudo_dir = '/home/'restart_mode = 'from_scratch'    forc_conv_thr =  1.0e-03etot_conv_thr= 1e-04    nstep         = 999/&SYSTEMibrav =  0    ecutrho                   =  200    ecutwfc                   =  25    nat                       = 110    ntyp                      = 4occupations='smearing',smearing='gaussian',degauss=0.005vdw_corr= 'DFT-D2'     nspin = 2 starting_magnetization(1)=  0.01/&ELECTRONS    conv_thr         = 1e-8    electron_maxstep = 200mixing_mode='local-TF'    mixing_beta      =  0.3/&IONS/K_POINTS {automatic}3 3 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}        11.76538354           0.0000000000         0.0000000000       -5.8826917709        10.189121032         0.0000000000         0.0000000000         0.0000000000        30.993869056ATOMIC_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

regards

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