<html><head></head><body><div class="yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:13px;"><div dir="ltr" data-setdir="false"><div><div style="color: rgb(0, 0, 0); font-family: Arial; font-size: 13.3333px;"> Dear all</div><div style="color: rgb(0, 0, 0); font-family: Arial; font-size: 13.3333px;"><br></div><div style=""><div dir="ltr" style="" data-setdir="false"><font face="Arial"><span style="font-size: 13.3333px;"> I'm doing <span>phonon calculation at Gamma point (q) <span><span style="color: rgb(0, 0, 0); font-family: Arial; font-size: 13.3333px;"> in order to estimate the reaction rate constants for a micro-kinetic model</span></span>. <span><span style="color: rgb(0, 0, 0); font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;"> I have perturbed only the adsorbate molecule with the 3 surface atoms, connected to adsorbate, using "nat-todo" option. </span></span></span></span></font><span style="font-size: 13.3333px; font-family: Arial;">However, i got 15 negative frequencies (should be 6 as i know ) ,with high absolute value. </span></div><div dir="ltr" style="color: rgb(0, 0, 0); font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;"><span style="font-family: Arial; font-size: 13.3333px;"><br></span></div><div dir="ltr" style="color: rgb(0, 0, 0); font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;"><span style="font-family: Arial; font-size: 13.3333px;">Can you please help me to know what is wrong with my input files ?</span></div><div dir="ltr" style="color: rgb(0, 0, 0); font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;"><br></div><div dir="ltr" style="color: rgb(0, 0, 0); font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;">Below are the output & input files:</div><div dir="ltr" style="color: rgb(0, 0, 0); font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;"><br></div><div dir="ltr" style="color: rgb(0, 0, 0); font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;"><br></div></div><div style="color: rgb(0, 0, 0); font-family: Arial; font-size: 13.3333px;"><div dir="ltr" style="color: rgb(29, 34, 40); font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;"><br clear="none"></div><div dir="ltr" style="color: rgb(29, 34, 40); font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;" data-setdir="false"><div><div> Mode symmetry, C_1 (1) point group:</div><div><br></div><div> freq ( 1 - 1) = -2762.6 [cm-1] --> A I+R</div><div> freq ( 2 - 2) = -2570.3 [cm-1] --> A I+R</div><div> freq ( 3 - 3) = -2460.4 [cm-1] --> A I+R</div><div> freq ( 4 - 4) = -2423.6 [cm-1] --> A I+R</div><div> freq ( 5 - 5) = -2356.3 [cm-1] --> A I+R</div><div> freq ( 6 - 6) = -2158.0 [cm-1] --> A I+R</div><div> freq ( 7 - 7) = -2151.1 [cm-1] --> A I+R</div><div> freq ( 8 - 8) = -2067.5 [cm-1] --> A I+R</div><div> freq ( 9 - 9) = -2034.8 [cm-1] --> A I+R</div><div> freq ( 10 - 10) = -2025.2 [cm-1] --> A I+R</div><div> freq ( 11 - 11) = -1864.3 [cm-1] --> A I+R</div><div> freq ( 12 - 12) = -1804.5 [cm-1] --> A I+R</div><div> freq ( 13 - 13) = -1099.4 [cm-1] --> A I+R</div><div> freq ( 14 - 14) = -947.6 [cm-1] --> A I+R</div><div> freq ( 15 - 15) = -912.5 [cm-1] --> A I+R</div><div> freq (316 -316) = 179.3 [cm-1] --> A I+R</div><div> freq (317 -317) = 193.0 [cm-1] --> A I+R</div><div> freq (318 -318) = 215.8 [cm-1] --> A I+R</div><div> freq (319 -319) = 240.2 [cm-1] --> A I+R</div><div> freq (320 -320) = 270.4 [cm-1] --> A I+R</div><div> freq (321 -321) = 317.0 [cm-1] --> A I+R</div><div> freq (322 -322) = 370.8 [cm-1] --> A I+R</div><div> freq (323 -323) = 377.3 [cm-1] --> A I+R</div><div> freq (324 -324) = 398.3 [cm-1] --> A I+R</div><div> freq (325 -325) = 417.8 [cm-1] --> A I+R</div><div> freq (326 -326) = 468.2 [cm-1] --> A I+R</div><div> freq (327 -327) = 659.0 [cm-1] --> A I+R</div><div> freq (328 -328) = 1096.6 [cm-1] --> A I+R</div><div> freq (329 -329) = 1795.5 [cm-1] --> A I+R</div><div> freq (330 -330) = 2199.3 [cm-1] --> A I+R</div></div><br></div></div><div style="color: rgb(0, 0, 0); font-family: Arial; font-size: 13.3333px;"><span style="font-size: 10pt;"><b><br></b></span></div><div style="color: rgb(0, 0, 0); font-family: Arial; font-size: 13.3333px;"><div dir="ltr" style="font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;"><b>ph.x input file:</b></div><div dir="ltr" style="font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;"><br clear="none"></div><div dir="ltr" style="font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;"><div dir="ltr" data-setdir="false"><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><br></div><div>alpha_mix(1)=0.1</div><div><br></div><div> recover=.true</div><div> nogg = .true</div><div> nat_todo = 5</div><div><br></div><div>/</div><div>0.0 0.0 0.0</div><div><br></div><div>1 2 37 46 54</div></div><br></div><br clear="none"></div><div dir="ltr" style="font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;"><br clear="none"></div><div dir="ltr" style="font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;"><b>scf input file:</b><br clear="none"></div><div dir="ltr" style="font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;"><br clear="none"></div><div dir="ltr" style="font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px;"><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'<b>,smearing='gaussian'</b>,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>3 3 1 0 0 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> 11.76538354 0.0000000000 0.0000000000</div><div> -5.8826917709 10.189121032 0.0000000000 </div><div> 0.0000000000 0.0000000000 30.993869056</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></div><div style="color: rgb(0, 0, 0); font-family: Arial; font-size: 13.3333px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Arial; font-size: 13.3333px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Arial; font-size: 13.3333px;">regards</div><div style="color: rgb(0, 0, 0); font-family: Arial; font-size: 13.3333px;"><br></div></div><br></div></div></body></html>