<div><div>Dear all,</div><div> I want to do phonon calculation on an adsorption system with symmetry. So Idid some test calculations.</div><div>I did a test calculation on a system, say an molecule is adsorbed on a surface. I just want to calculate the vibrational frequencies of the molecule. I set "nat_todo" in the input file of ph.x, and set the list of indices of atoms of the molecule. But in the result file there is not phonons. I don't know what's wrong with it, and how to set parameter in the input file of ph.x. Please help me! Thank you!</div><div><br></div></div><div><b><span class="Apple-style-span" style="font-size: large;">This is the output that I have set "nat_todo" in the input file,from output file we can't find the phonon data at the end of file:</span></b></div><div><div> Representation # 12 mode # 12</div><div><br></div><div> Self-consistent Calculation</div><div><br></div><div> iter # 1 total cpu time : 77.3 secs av.it.: 4.0</div><div> thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.128E-07</div><div><br></div><div> iter # 2 total cpu time : 78.3 secs av.it.: 9.0</div><div> thresh= 0.113E-04 alpha_mix = 0.700 |ddv_scf|^2 = 0.274E-08</div><div><br></div><div> iter # 3 total cpu time : 79.5 secs av.it.: 9.0</div><div> thresh= 0.524E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.182E-10</div><div><br></div><div> iter # 4 total cpu time : 80.6 secs av.it.: 9.0</div><div> thresh= 0.426E-06 alpha_mix = 0.700 |ddv_scf|^2 = 0.678E-11</div><div><br></div><div> iter # 5 total cpu time : 81.6 secs av.it.: 8.0</div><div> thresh= 0.260E-06 alpha_mix = 0.700 |ddv_scf|^2 = 0.270E-13</div><div><br></div><div> iter # 6 total cpu time : 82.7 secs av.it.: 9.0</div><div> thresh= 0.164E-07 alpha_mix = 0.700 |ddv_scf|^2 = 0.140E-14</div><div><br></div><div> iter # 7 total cpu time : 83.7 secs av.it.: 8.0</div><div> thresh= 0.374E-08 alpha_mix = 0.700 |ddv_scf|^2 = 0.344E-16</div><div><br></div><div> End of self-consistent calculation</div><div><br></div><div> Convergence has been achieved </div><div><br></div><div> Stopping because representation 3 is not done</div><div><br></div><div> PHONON : 1m12.13s CPU time, 1m24.02s WALL time</div><div><br></div><div> INITIALIZATION: </div><div> phq_setup : 0.04s CPU 0.04s WALL ( 1 calls)</div><div> phq_init : 4.69s CPU 5.19s WALL ( 1 calls)</div><div><br></div><div> phq_init : 4.69s CPU 5.19s WALL ( 1 calls)</div><div> init_vloc : 0.02s CPU 0.02s WALL ( 1 calls)</div><div> init_us_1 : 0.15s CPU 0.17s WALL ( 1 calls)</div><div> newd : 0.11s CPU 0.13s WALL ( 1 calls)</div><div> dvanqq : 1.90s CPU 2.11s WALL ( 1 calls)</div><div> drho : 1.59s CPU 1.82s WALL ( 1 calls)</div><div><br></div><div> DYNAMICAL MATRIX:</div><div> dynmat0 : 0.17s CPU 0.18s WALL ( 1 calls)</div></div><div>…………………………</div><div><br></div><div><br></div><div><b><span class="Apple-style-span" style="font-size: large;">and below is the normal output that I have not set "nat_todo" in the inputfile, from which we can see the phonon data at the end of file:</span></b></div><div><div> Representation # 12 mode # 12</div><div><br></div><div> Self-consistent Calculation</div><div><br></div><div> iter # 1 total cpu time : 1155.5 secs av.it.: 5.0</div><div> thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.319E-07</div><div><br></div><div> iter # 2 total cpu time : 1164.9 secs av.it.: 12.0</div><div> thresh= 0.179E-04 alpha_mix = 0.700 |ddv_scf|^2 = 0.161E-08</div><div><br></div><div> iter # 3 total cpu time : 1174.6 secs av.it.: 12.0</div><div> thresh= 0.401E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.157E-09</div><div><br></div><div> iter # 4 total cpu time : 1184.7 secs av.it.: 13.0</div><div> thresh= 0.125E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.126E-10</div><div><br></div><div> iter # 5 total cpu time : 1194.7 secs av.it.: 13.0</div><div> thresh= 0.355E-06 alpha_mix = 0.700 |ddv_scf|^2 = 0.184E-11</div><div><br></div><div> iter # 6 total cpu time : 1204.7 secs av.it.: 13.0</div><div> thresh= 0.136E-06 alpha_mix = 0.700 |ddv_scf|^2 = 0.701E-12</div><div><br></div><div> iter # 7 total cpu time : 1214.2 secs av.it.: 12.0</div><div> thresh= 0.837E-07 alpha_mix = 0.700 |ddv_scf|^2 = 0.131E-12</div><div><br></div><div> iter # 8 total cpu time : 1223.8 secs av.it.: 12.0</div><div> thresh= 0.361E-07 alpha_mix = 0.700 |ddv_scf|^2 = 0.149E-15</div><div><br></div><div> iter # 9 total cpu time : 1233.4 secs av.it.: 13.0</div><div> thresh= 0.122E-08 alpha_mix = 0.700 |ddv_scf|^2 = 0.157E-16</div><div><br></div><div> End of self-consistent calculation</div><div><br></div><div> Convergence has been achieved </div><div><br></div><div> Number of q in the star = 1</div><div> List of q in the star:</div><div> 1 0.000000000 0.000000000 0.000000000</div><div><br></div><div> Dielectric constant in cartesian axis </div><div><br></div><div> ( 1.031610391 -0.000228657 -0.003149580 )</div><div> ( -0.000228341 1.027755025 -0.000009279 )</div><div> ( -0.003149520 -0.000009203 1.019026580 )</div><div><br></div><div> Polarizability (a.u.)^3 Polarizability (A^3)</div><div> 23.14 -0.17 -2.33 3.4285 -0.0250 -0.3452</div><div> -0.17 20.34 -0.01 -0.0251 3.0141 -0.0010</div><div> -2.33 -0.01 13.98 -0.3452 -0.0010 2.0722</div><div><br></div><div> Effective charges (d Force / dE) in cartesian axis</div><div><br></div><div> atom 1 C </div><div> Ex ( 1.02010 -0.00463 -0.20246 )</div><div> Ey ( 0.00824 0.87800 -0.00178 )</div><div> Ez ( -0.20024 -0.00018 0.24077 )</div><div> atom 2 O </div><div> Ex ( -0.71604 0.00033 0.12390 )</div><div> Ey ( -0.00376 -0.27604 0.00052 )</div><div> Ez ( 0.12315 -0.00045 -0.22813 )</div><div> atom 3 H </div><div> Ex ( -0.03234 -0.13357 0.03345 )</div><div> Ey ( -0.09805 -0.18872 0.02571 )</div><div> Ez ( 0.03330 0.03431 0.09234 )</div><div> atom 4 H </div><div> Ex ( -0.03402 0.13935 0.03451 )</div><div> Ey ( 0.09420 -0.17340 -0.02427 )</div><div> Ez ( 0.03316 -0.03389 0.09281 )</div><div><br></div><div> Effective charges (d P / du) in cartesian axis </div><div><br></div><div> atom 1 C </div><div> Px ( 0.78251 0.00752 -0.18968 )</div><div> Py ( -0.00610 0.63820 0.00003 )</div><div> Pz ( -0.19199 -0.00193 0.04292 )</div><div> atom 2 O </div><div> Px ( -0.71616 -0.00367 0.12322 )</div><div> Py ( 0.00032 -0.27610 -0.00045 )</div><div> Pz ( 0.12395 0.00050 -0.22806 )</div><div> atom 3 H </div><div> Px ( -0.03233 -0.09805 0.03330 )</div><div> Py ( -0.13358 -0.18873 0.03431 )</div><div> Pz ( 0.03349 0.02571 0.09233 )</div><div> atom 4 H </div><div> Px ( -0.03402 0.09420 0.03316 )</div><div> Py ( 0.13936 -0.17336 -0.03389 )</div><div> Pz ( 0.03455 -0.02427 0.09280 )</div><div><br></div><div> Diagonalizing the dynamical matrix</div><div><br></div><div> q = ( 0.000000000 0.000000000 0.000000000 ) </div><div><br></div><div> **************************************************************************</div><div> omega( 1) = -4.939872 [THz] = -164.777486 [cm-1]</div><div> omega( 2) = -0.211017 [THz] = -7.038823 [cm-1]</div><div> omega( 3) = -0.078881 [THz] = -2.631210 [cm-1]</div><div> omega( 4) = -0.004765 [THz] = -0.158929 [cm-1]</div><div> omega( 5) = 3.572645 [THz] = 119.171410 [cm-1]</div><div> omega( 6) = 4.364949 [THz] = 145.600002 [cm-1]</div><div> omega( 7) = 33.896117 [THz] = 1130.660267 [cm-1]</div><div> omega( 8) = 35.856463 [THz] = 1196.050798 [cm-1]</div><div> omega( 9) = 43.444675 [THz] = 1449.167993 [cm-1]</div><div> omega(10) = 51.275820 [THz] = 1710.388618 [cm-1]</div><div> omega(11) = 84.045119 [THz] = 2803.462049 [cm-1]</div><div> omega(12) = 85.673216 [THz] = 2857.769859 [cm-1]</div><div> **************************************************************************</div><div><br></div><div> Mode symmetry, C_1 (1) point group:</div><div><br></div><div> omega( 7 - 7) = 1130.7 [cm-1] --> A I+R</div><div> omega( 8 - 8) = 1196.1 [cm-1] --> A I+R</div><div> omega( 9 - 9) = 1449.2 [cm-1] --> A I+R</div><div> omega( 10 - 10) = 1710.4 [cm-1] --> A I+R</div><div> omega( 11 - 11) = 2803.5 [cm-1] --> A I+R</div><div> omega( 12 - 12) = 2857.8 [cm-1] --> A I+R</div><div><br></div><div> **************************************************************************</div><div><br></div><div> PHONON : 19m24.01s CPU time, 20m34.88s WALL time</div><div><br></div><div> INITIALIZATION: </div><div> phq_setup : 0.36s CPU 0.39s WALL ( 1 calls)</div><div> phq_init : 95.50s CPU 97.48s WALL ( 1 calls)</div><div><br></div><div> phq_init : 95.50s CPU 97.48s WALL ( 1 calls)</div><div> init_vloc : 12.90s CPU 12.95s WALL ( 1 calls)</div><div> init_us_1 : 1.16s CPU 1.21s WALL ( 1 calls)</div><div> newd : 2.21s CPU 2.45s WALL ( 1 calls)</div><div> dvanqq : 38.14s CPU 38.66s WALL ( 1 calls)</div><div> drho : 28.73s CPU 30.10s WALL ( 1 calls)</div><div> cmpt_qdipol : 0.00s CPU 0.00s WALL ( 1 calls)</div><div><br></div><div> DIELECTRIC CONSTANT AND EFFECTIVE CHARGES:</div><div> solve_e : 269.98s CPU 302.42s WALL ( 1 calls)</div><div> dielec : 0.01s CPU 0.05s WALL ( 1 calls)</div><div> zstar_eu : 13.30s CPU 16.84s WALL ( 1 calls)</div><div><br></div><div> DYNAMICAL MATRIX:</div><div> dynmat0 : 1.56s CPU 1.57s WALL ( 1 calls)</div></div><div><br></div><div>The attachment is the output file of input that I have set "nat_todo=2", the molecule is HCHO, just for test.</div><div>Here is the input file:</div><div><div>vibrations of hcho</div><div> &inputph</div><div> nat_todo=2, </div><div> tr2_ph=4.0d-17,</div><div> prefix='HCHO',</div><div> outdir='/home/jerry/tmp',</div><div> amass(1)=12.d0,</div><div> amass(2)=16.d0,</div><div> amass(3)=1.d0,</div><div> fildyn='hcho.dyn',</div><div> iverbosity=1,</div><div> trans=.true.,</div><div> nogg=.true.</div><div>/</div><div>0.0 0.0 0.0</div><div>1 3 </div></div><div>But in the result file there is not any vibration modes data.</div><br><br><span title="neteasefooter"/><hr/>
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