<div dir="ltr">Hi Jaap,<div><br></div><div>Thanks for your response. I fixed all the other atoms and it worked but the problem now is that CP2K doesn't print the imaginary frequency. I'm sure the structure I input should at least have one but CP2K apparently is only printing the positive ones. I thought putting the RANGE keyword will take care of this but it didn't. I have pasted the relevant sections of my input and output files below.</div><div><br></div><div>Thanks,</div><div>Mohammad<br></div><div><br></div><div><b>Input:</b></div><div><div><font color="#666666">&GLOBAL</font></div><div><font color="#666666"> PROJECT test</font></div><div><font color="#666666"> RUN_TYPE NORMAL_MODES</font></div><div><font color="#666666"> PRINT_LEVEL MEDIUM</font></div><div><font color="#666666">&END GLOBAL</font></div><div><font color="#666666"><br></font></div><div><font color="#666666">&MOTION</font></div><div><font color="#666666"> &CONSTRAINT</font></div><div><font color="#666666"> &FIXED_ATOMS</font></div><div><font color="#666666"> COMPONENTS_TO_FIX XYZ</font></div><div><font color="#666666"> LIST 1..7</font></div><div><font color="#666666"> LIST 9..515</font></div><div><font color="#666666"> LIST 517..521</font></div><div><font color="#666666"> LIST 523..539</font></div><div><font color="#666666"> LIST 541..545</font></div><div><font color="#666666"> LIST 547..553</font></div><div><font color="#666666"> &END FIXED_ATOMS</font></div><div><font color="#666666"> &END CONSTRAINT</font></div><div><font color="#666666">&END MOTION</font></div><div><font color="#666666"><br></font></div><div><font color="#666666">&VIBRATIONAL_ANALYSIS</font></div><div><font color="#666666"> NPROC_REP 24</font></div><div><font color="#666666"> &MODE_SELECTIVE</font></div><div><font color="#666666"> ATOMS 8 516 522 540 546 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576</font></div><div><font color="#666666"> FREQUENCY -500</font></div><div><font color="#666666"> RANGE -500 100</font></div><div><font color="#666666"> &INVOLVED_ATOMS </font></div><div><font color="#666666"> INVOLVED_ATOMS 8 516 522 540 546 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576</font></div><div><font color="#666666"> RANGE -500 100</font></div><div><font color="#666666"> &END INVOLVED_ATOMS</font></div><div><font color="#666666"> &END MODE_SELECTIVE</font></div><div><font color="#666666"> &PRINT</font></div><div><font color="#666666"> &MOLDEN_VIB</font></div><div><font color="#666666"> FILENAME test</font></div><div><font color="#666666"> &END MOLDEN_VIB</font></div><div><font color="#666666"> &END PRINT</font></div><div><font color="#666666">&END VIBRATIONAL_ANALYSIS</font></div></div><div><br></div><div><b>Output:</b></div><div><div><font color="#666666"> REPLICA| layout of the replica grid, number of groups 1</font></div><div><font color="#666666"> REPLICA| layout of the replica grid, size of each group 16</font></div><div><font color="#666666"> REPLICA| MPI process to grid (group,rank) correspondence:</font></div><div><font color="#666666"> ( 0 : 0, 0) ( 1 : 0, 1) ( 2 : 0, 2) ( 3 : 0, 3)</font></div><div><font color="#666666"> ( 4 : 0, 4) ( 5 : 0, 5) ( 6 : 0, 6) ( 7 : 0, 7)</font></div><div><font color="#666666"> ( 8 : 0, 8) ( 9 : 0, 9) ( 10 : 0, 10) ( 11 : 0, 11)</font></div><div><font color="#666666"> ( 12 : 0, 12) ( 13 : 0, 13) ( 14 : 0, 14) ( 15 : 0, 15)</font></div><div><font color="#666666"> MS| ITERATION STEP 1</font></div><div><font color="#666666"> MS| TRACKED MODE 1067.402517cm-1 NOT CONVERGED</font></div><div><font color="#666666"> MS| ITERATION STEP 2</font></div><div><font color="#666666"> MS| TRACKED MODE 629.589298cm-1 NOT CONVERGED</font></div><div><font color="#666666"> MS| ITERATION STEP 3</font></div><div><font color="#666666"> MS| TRACKED MODE 516.249401cm-1 NOT CONVERGED</font></div><div><font color="#666666"> MS| ITERATION STEP 4</font></div><div><font color="#666666"> MS| TRACKED MODE 297.969319cm-1 NOT CONVERGED</font></div><div><font color="#666666"> MS| ITERATION STEP 5</font></div><div><font color="#666666"> MS| TRACKED MODE 274.303122cm-1 NOT CONVERGED</font></div><div><font color="#666666"> MS| ITERATION STEP 6</font></div><div><font color="#666666"> MS| TRACKED MODE 197.889363cm-1 NOT CONVERGED</font></div><div><font color="#666666"> MS| ITERATION STEP 7</font></div><div><font color="#666666"> MS| TRACKED MODE 177.282435cm-1 NOT CONVERGED</font></div><div><font color="#666666"> MS| ITERATION STEP 8</font></div><div><font color="#666666"> MS| TRACKED MODE 150.074885cm-1 NOT CONVERGED</font></div><div><font color="#666666"> MS| ITERATION STEP 9</font></div><div><font color="#666666"> MS| TRACKED MODE 125.450225cm-1 NOT CONVERGED</font></div><div><font color="#666666"> MS| ITERATION STEP 10</font></div><div><font color="#666666"> MS| TRACKED MODE 98.399232cm-1 NOT CONVERGED</font></div><div><font color="#666666"> MS| ITERATION STEP 11</font></div><div><font color="#666666"> MS| TRACKED MODE 81.644671cm-1 NOT CONVERGED</font></div><div><font color="#666666"> MS| DAVIDSON ALGORITHM CONVERGED</font></div><div><font color="#666666"> MS| TRACKED FREQUENCY (1) IS: 11.618812 cm-1</font></div><div><font color="#666666"> -------------------------------------------------------------------------------</font></div><div><font color="#666666"> FREQUENCY AND CONVERGENCE LIST</font></div><div><font color="#666666"> FREQUENCY MAXVAL CRITERIA NORM CRITERIA CONVERGENCE</font></div><div><font color="#666666"> VIB| 451.221 0.127135E-05 0.451E-05 NO</font></div><div><font color="#666666"> VIB| 826.941 0.177668E-05 0.712E-05 NO</font></div><div><font color="#666666"> VIB| 1192.902 0.287789E-05 0.102E-04 NO</font></div><div><font color="#666666"> VIB| 1405.678 0.172961E-05 0.694E-05 NO</font></div><div><font color="#666666"> VIB| 1585.591 0.153388E-05 0.545E-05 NO</font></div><div><font color="#666666"> VIB| 3001.268 0.126841E-05 0.450E-05 NO</font></div><div><font color="#666666"> VIB| 3082.088 0.826133E-06 0.293E-05 NO</font></div><div><font color="#666666"> VIB| 3131.784 0.131471E-05 0.467E-05 NO</font></div><div><font color="#666666"> VIB| 3553.575 0.370080E-07 0.148E-06 YES</font></div><div><font color="#666666"> VIB| 3706.396 0.161133E-07 0.646E-07 YES</font></div><div><font color="#666666"> VIB| 3776.399 0.240125E-07 0.963E-07 YES</font></div><div><font color="#666666"><br></font></div><div><font color="#666666"> -------------------------------------------------------------------------------</font></div><div><font color="#666666"> - -</font></div><div><font color="#666666"> - DBCSR STATISTICS -</font></div><div><font color="#666666"> - -</font></div><div><font color="#666666"> -------------------------------------------------------------------------------</font></div></div><div><br></div><div><br></div><div><br>On Monday, 29 October 2018 02:47:42 UTC-7, Jaap Louwen wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hi Mohammad,<div><br></div><div>I have no experience with mode selective calculations, but if you just want to compute a partial Hessian over atoms directly involved in the TS, fixing all other atoms will work for you.</div><div>Your vibrational analysis namelist will just read something like:</div><div><br></div><div><div>&VIBRATIONAL_ANALYSIS</div><div> NPROC_REP 28</div><div> FULLY_PERIODIC</div><div>&END VIBRATIONAL_ANALYSIS</div></div><div><br></div><div>while within the &Motion namelist you include a constraint section like:</div><div><div> &CONSTRAINT</div><div> &FIXED_ATOMS</div><div> COMPONENTS_TO_FIX XYZ</div><div> LIST 1..12</div><div> LIST 14..24</div><div> LIST 26..65</div><div> LIST 67..144</div><div> &END FIXED_ATOMS</div><div> &END CONSTRAINT</div></div><div><br></div><div>CP2K will simply skip the fixed atoms.</div><div><br></div><div>Regards, Jaap</div><div><br></div><div><br><br>Op zaterdag 27 oktober 2018 19:59:25 UTC+2 schreef Mohammad Momeni Taheri:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi, I have problems in computing normal modes for a structure that I got from NEB calculations. My smallest system has 476 atoms and therefore I cannot perform a full numerical frequency calculations. However, when I use the inout below it seems that CP2K still tries to diagonalize the entire hessian matrix (the job fails after 48hrs; output file is attached). Is my input correct if not could you please provide a sample input file for these calculations?<div><br></div><div>Thanks in advance,</div><div>Mohammad</div><div><br></div><div><br></div><div>Below is my input file:</div><div><br></div><div><div><font color="#666666">&GLOBAL</font></div><div><font color="#666666"> PROJECT test</font></div><div><font color="#666666"> RUN_TYPE NORMAL_MODES</font></div><div><font color="#666666"> PRINT_LEVEL MEDIUM</font></div><div><font color="#666666">&END GLOBAL</font></div><div><font color="#666666"><br></font></div><div><font color="#666666">&VIBRATIONAL_ANALYSIS</font></div><div><font color="#666666"><span style="white-space:pre"> </span>NPROC_REP 28</font></div><div><font color="#666666"><span style="white-space:pre"> </span>FULLY_PERIODIC TRUE</font></div><div><font color="#666666"><span style="white-space:pre"> </span>&MODE_SELECTIVE</font></div><div><font color="#666666"><span style="white-space:pre"> </span>ATOMS 450 451 452 446 468 434 445 413 398 99 447 448 449 457 453 454 455 456 458 459 460 461 462 463 464 465 466 467</font></div><div><font color="#666666"><span style="white-space:pre"> </span>LOWEST_FREQUENCY -500</font></div><div><font color="#666666"><span style="white-space:pre"> </span>RANGE -500 100</font></div><div><font color="#666666"><span style="white-space:pre"> </span>&INVOLVED_ATOMS </font></div><div><font color="#666666"><span style="white-space:pre"> </span>INVOLVED_ATOMS 450 451 452 446 468 434 445 413 398 99 447 448 449 457 453 454 455 456 458 459 460 461 462 463 464 465 466 467</font></div><div><font color="#666666"><span style="white-space:pre"> </span>RANGE -500 100</font></div><div><font color="#666666"><span style="white-space:pre"> </span>&END INVOLVED_ATOMS</font></div><div><font color="#666666"><span style="white-space:pre"> </span>&END MODE_SELECTIVE</font></div><div><font color="#666666">&END VIBRATIONAL_ANALYSIS</font></div><div><font color="#666666"><br></font></div><div><font color="#666666">&FORCE_EVAL</font></div><div><font color="#666666"> METHOD Quickstep</font></div><div><font color="#666666"> &SUBSYS</font></div><div><font color="#666666"> &KIND Zr</font></div><div><font color="#666666"> ELEMENT Zr</font></div><div><font color="#666666"> BASIS_SET DZVP-MOLOPT-SR-GTH</font></div><div><font color="#666666"> POTENTIAL GTH-PBE-q12</font></div><div><font color="#666666"> &END</font></div><div><font color="#666666"> &KIND C</font></div><div><font color="#666666"> ELEMENT C</font></div><div><font color="#666666"> BASIS_SET DZVP-MOLOPT-GTH</font></div><div><font color="#666666"> POTENTIAL GTH-PBE-q4</font></div><div><font color="#666666"> &END </font></div><div><font color="#666666"> &KIND O</font></div><div><font color="#666666"> ELEMENT O</font></div><div><font color="#666666"> BASIS_SET DZVP-MOLOPT-GTH</font></div><div><font color="#666666"> POTENTIAL GTH-PBE-q6</font></div><div><font color="#666666"> &END </font></div><div><font color="#666666"> &KIND H</font></div><div><font color="#666666"> ELEMENT H</font></div><div><font color="#666666"> BASIS_SET DZVP-MOLOPT-GTH</font></div><div><font color="#666666"> POTENTIAL GTH-PBE-q1</font></div><div><font color="#666666"> &END </font></div><div><font color="#666666"> &KIND F</font></div><div><font color="#666666"> ELEMENT F</font></div><div><font color="#666666"> BASIS_SET DZVP-MOLOPT-GTH</font></div><div><font color="#666666"> POTENTIAL GTH-PBE-q7</font></div><div><font color="#666666"> &END KIND</font></div><div><font color="#666666"> &KIND P</font></div><div><font color="#666666"> ELEMENT P</font></div><div><font color="#666666"> BASIS_SET DZVP-MOLOPT-GTH</font></div><div><font color="#666666"> POTENTIAL GTH-PBE-q5</font></div><div><font color="#666666"> &END KIND</font></div><div><font color="#666666"> &CELL</font></div><div><font color="#666666"> A [angstrom] 23.34964320 0.00000000 0.00000000</font></div><div><font color="#666666"> B [angstrom] -11.67970624 20.19999013 0.00000000</font></div><div><font color="#666666"> C [angstrom] -0.24143113 0.14997040 51.67634031</font></div><div><font color="#666666"> PERIODIC XYZ</font></div><div><font color="#666666"> &END CELL</font></div><div><font color="#666666"><br></font></div><div><font color="#666666">&TOPOLOGY ! Section used to center the atomic coordinates in the given box. Useful for big molecules</font></div><div><font color="#666666">&CENTER_COORDINATES</font></div><div><font color="#666666">&END</font></div><div><font color="#666666">COORD_FILE_FORMAT xyz</font></div><div><font color="#666666">COORD_FILE_NAME ./<a href="http://test.xyz" rel="nofollow" target="_blank" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ftest.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG1uRc_UOU1zJAVL3FsD95f2euxRQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ftest.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG1uRc_UOU1zJAVL3FsD95f2euxRQ';return true;">test.xyz</a></font></div><div><font color="#666666">&END</font></div><div><font color="#666666"><br></font></div><div><font color="#666666"> &END SUBSYS</font></div><div><font color="#666666"> &DFT</font></div><div><font color="#666666"> BASIS_SET_FILE_NAME /opt/packages/CP2K/cp2k-5.1/<wbr>data/BASIS_MOLOPT</font></div><div><font color="#666666"> POTENTIAL_FILE_NAME /opt/packages/CP2K/cp2k-5.1/<wbr>data/POTENTIAL</font></div><div><font color="#666666"><br></font></div><div><font color="#666666"> &POISSON</font></div><div><font color="#666666"> PERIODIC XYZ</font></div><div><font color="#666666"> &END POISSON</font></div><div><font color="#666666"> </font></div><div><font color="#666666"> &QS</font></div><div><font color="#666666"> EPS_DEFAULT 1.0E-12</font></div><div><font color="#666666"> &END QS</font></div><div><font color="#666666"> &XC</font></div><div><font color="#666666"> &XC_FUNCTIONAL PBE</font></div><div><font color="#666666"> &END XC_FUNCTIONAL</font></div><div><font color="#666666"> &vdW_POTENTIAL</font></div><div><font color="#666666"> DISPERSION_FUNCTIONAL PAIR_POTENTIAL</font></div><div><font color="#666666"> &PAIR_POTENTIAL</font></div><div><font color="#666666"> TYPE DFTD3(BJ)</font></div><div><font color="#666666"> CALCULATE_C9_TERM .TRUE.</font></div><div><font color="#666666"> REFERENCE_C9_TERM .TRUE.</font></div><div><font color="#666666"> LONG_RANGE_CORRECTION .TRUE.</font></div><div><font color="#666666"> PARAMETER_FILE_NAME ./dftd3.dat</font></div><div><font color="#666666"> REFERENCE_FUNCTIONAL PBE</font></div><div><font color="#666666"> R_CUTOFF 15</font></div><div><font color="#666666"> &END PAIR_POTENTIAL </font></div><div><font color="#666666"> &END vdW_POTENTIAL</font></div><div><font color="#666666"> &END XC</font></div><div><font color="#666666"> &SCF</font></div><div><font color="#666666"> SCF_GUESS ATOMIC</font></div><div><font color="#666666"> EPS_SCF 1.0E-6</font></div><div><font color="#666666"> MAX_SCF 500</font></div><div><font color="#666666"> &OT</font></div><div><font color="#666666"> MINIMIZER CG</font></div><div><font color="#666666"> PRECONDITIONER FULL_ALL</font></div><div><font color="#666666"> ENERGY_GAP 0.001</font></div><div><font color="#666666"> &END OT</font></div><div><font color="#666666"> &END SCF</font></div><div><font color="#666666"> &END DFT</font></div><div><font color="#666666"> &END</font></div></div><div><br></div></div></blockquote></div></div></blockquote></div></div>