[CP2K:10076] Re: CP2K reads and writes the correct atomic coordinates

[Tiziano Müller]

Dear Davide

There seems to be a bit an inconsistency in the files you provided:

The coordinate section can't be in an XYZ file (CP2K will fail while 
parsing it).

Now, when I enter the coordinates you mention into an XYZ file, CP2K 
gives me:

   Atom  Kind  Element       X           Y           Z          Z(eff) 
     Mass

        1     1 Co  27    3.108670    4.979180    4.103000     17.00 
  58.9332
        2     2 C    6    5.012420    5.338520    4.024640      4.00 
  12.0107
        3     3 O    8    6.120010    5.547740    3.979040      6.00 
  15.9994
        4     2 C    6    3.039780    4.921110    2.166350      4.00 
  12.0107
        5     3 O    8    2.999670    4.887060    1.039490      6.00 
  15.9994
        6     2 C    6    3.177500    5.036160    6.039690      4.00 
  12.0107
        7     3 O    8    3.217530    5.069060    7.166590      6.00 
  15.9994
        8     4 H    1    1.543250    4.684900    4.167410      1.00 
   1.0079

which looks correct.

Also, when I put the &COORD section you provided in the provided input 
file instead of the &TOPOLOGY, I get:

        1     1 Co  27    3.108670    4.979180    4.103000     17.00 
  58.9332
        2     2 C    6    5.012420    5.338520    4.024640      4.00 
  12.0107
        3     3 O    8    6.120010    5.547740    3.979040      6.00 
  15.9994
        4     2 C    6    3.039780    4.921110    2.166350      4.00 
  12.0107
        5     3 O    8    2.999670    4.887060    1.039490      6.00 
  15.9994
        6     2 C    6    3.177500    5.036160    6.039690      4.00 
  12.0107
        7     3 O    8    3.217530    5.069060    7.166590      6.00 
  15.9994
        8     4 H    1    1.543250    4.684900    4.167410      1.00 
   1.0079

Which also seems ok.

Best regards,
Tiziano

On 09.03.2018 13:44, David T wrote:
> Dear Mat
> 
> thanks for answering. I attached the full input.
> 
> Best Regards
> Davide
> 
> On Friday, 9 March 2018 12:32:56 UTC, Matt W wrote:
> 
>     Full input deck please.
> 
>     On Friday, March 9, 2018 at 12:10:00 PM UTC, David T wrote:
> 
>         Dear all
> 
>         I am experiencing some very strange problem using CP2k v5.1
> 
>         This is the xyz I put in the input:
> 
>              &COORD
>                  Co         3.10867        4.97918        4.10300
>                  C          5.01242        5.33852        4.02464
>                  O          6.12001        5.54774        3.97904
>                  C          3.03978        4.92111        2.16635
>                  O          2.99967        4.88706        1.03949
>                  C          3.17750        5.03616        6.03969
>                  O          3.21753        5.06906        7.16659
>                  H          1.54325        4.68490        4.16741
>              &END
> 
>         This is what CP2K reads and writes in the output:
> 
>           Co         0.0160950570       11.2078020944        4.0719885297
>            C         3.4670167381        5.1560899034        4.0134146454
>            O         6.1012882958        5.4441242537        4.0661997577
>            C         1.2629748230        8.4349412628        2.0423121577
>            O        -0.9667191619       19.0654343689        0.5979795609
>            C         2.4935029798        5.7739885277        6.2317402018
>            O         1.8313194493        5.1044335466        9.6405816871
>            H        -1.4880140591        4.6452140486        4.2099725360
> 
> 
>         What is going on?
> 
>         I am honestly lost. To me it seems some bug but I am sure it
>         cannot be since it hasn't been reported yet.
> 
>         Thanks for helping
>         Davide
> 
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-- 
Tiziano Müller
University of Zurich
Department of Chemistry
Winterthurerstrasse 190
CH-8057 Zürich

Tel: +41 44 63 54234
www.chem.uzh.ch
tiziano... at chem.uzh.ch