TAMkin reports an error when loading a molecule from a CP2K computation

[Wei Chen]

Dear all,

I am new to TAMkin. To get started, I use the example “021_water_formation” to learn TAMkin.  I have modified the script “formation.py” at  loading molecule part  so that TAMkin could load  molecules from CP2K computations.

The following error was reported.

Traceback (most recent call last):
  File "formation.py", line 42, in <module>
    mol_oxygen = load_molecule_cp2k("O2-Energy.out","O2_Freq.out",is_periodic=False)
  File "/python3.10/site-packages/tamkin/io/cp2k.py", line 164, in load_molecule_cp2k
    hessian[free_indices[i2 + i1], free_indices[j]] = \
IndexError: index 3 is out of bounds for axis 0 with size 3

I am using Python 3.10, TAMkin-1.2.6 and CP2k 9.1,  I have attached all input files.

I would be very grateful if anyone could give me some advice.

Best wishes,

Wei

[Wei Chen]

Dear all,

It is me again.

I used CP2K 5.1 to produce the input data for TAMkin,  everything went well. While, when I chose CP2K 9.1 with the same in file, TAMkin reported the error.  It seems that CP2K has somehow changed the structure of its output file.

Best wishes,

Wei

[Herbert Fruchtl]

Dear Wei (and others),

Your post is almost two years old, so this probably comes too late, but others may be interested. I have fixed two problems in cp2k.py that broke the code for outputs from CP2K versions >= 9. If interested, I'm happy to share this (obviously also with the developers).

  Herbert