<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" target="_blank" rel="nofollow" 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>