Unknown Element kind

[bharat poudel]

I got this error while running a md simulation with cp2k:

Unknown element for KIND <C       13.203000       15.816000       13.931000>. This *
 *  \___/       problem can be fixed specifying properly elements in PDB or    *
 *    |       specifying a KIND section or getting in touch with one of  the   *
 *  O/|                                 developers!

This is the first few lines of of the structure I used.

        C        13.203000        15.816000        13.931000
        C        16.157000        16.336000        11.615000
        C        17.399000        18.490000        11.117000
        C        19.605000        18.928000        12.016000
        C        10.364000        12.516000        12.740000
        C        10.574000        11.787000        13.918000
        C        10.884000        10.426000        13.860000
        C        10.779000        10.503000        11.447000
        C        8.740000        14.386000        12.806000
        C        7.644000        13.325000        12.827000

The error is associated with the element kind C and I believe I have correctly mentioned it.

Here is the KIND part of cp2k input:

&COORD
      @include 'final_system.xyz'
    &END COORD
    &TOPOLOGY
      &CENTER_COORDINATES
     &END
    &END TOPOLOGY
    &KIND H
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE
    &END KIND
    &KIND N
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE
    &END KIND
    &KIND C
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE
    &END KIND
    &KIND O
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE
    &END KIND

The version of CP2K that I am using is 7.1.

I think I have missed something (some silly mistake) that I could not figure out. Any helps/suggestions will be appreciated.

[rashe...@gmail.com]

Hi,

I get the same error on 9.1! I am sure it is not related to the input file because a user ran my file and it was fine. I hope someone point to the possible reason for this error.

eftrsd

[Frederick Stein]

Dear all,

My guess is that some of the spaces are actually tabulators/tabs. This may happen if you copy/paste something between operating systems and/or editors and/or different encodings. On bash, you may try something along the lines of `sed -i "s/\t/ /g" <you input file>`. This replaces tabs with ordinary spaces. CP2K accepts only spaces as separators, not tabs. If my suggestion does not help, I need the actual files.

Best,

Frederick