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gusmaogabriels avatar gusmaogabriels commented on May 24, 2024

HI @paptigshiyf , I have just run the tutorial file (mkm_job.py) without any issues: catmap.__version__ = 0.3.1, Python 3.8.1.
Can you provide additional information on your OS, exact python version, and the .py script in which you create the CatMAP model instance and run it?

Thanks

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paptigshiyf avatar paptigshiyf commented on May 24, 2024

aha! thanks @gusmaogabriels ! Last time I didn't find the tutorial file mkm_job.py in the github repo，and instead I use the code and input on catmap.readthedocs. I just Ctrl+C and Ctrl+V all the code. So the input file energiesWebsite.txt, is like:

surface_name    site_name   species_name    formation_energy    bulk_structure  frequencies other_parameters    reference
None    gas CO2 2.45    None    [1333,2349,667,667] []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
None    gas CO  2.74    None    [2170]  []  "Energy Environ. Sci., 3, 1311-1315 (2010)"
None    gas O2  5.42    None    [1580]  []  "Falsig et al (2012)"
Ru  111 O   -0.07   fcc []  []  "Falsig et al (2012)"
Ni  111 O   0.35    fcc []  []  "Falsig et al (2012)"
Rh  111 O   0.55    fcc []  []  "Falsig et al (2012)"
Cu  111 O   1.07    fcc []  []  "Falsig et al (2012)"
Pd  111 O   1.55    fcc []  []  "Falsig et al (2012)"
Pt  111 O   1.62    fcc []  []  "Falsig et al (2012)"
Ag  111 O   2.05    fcc []  []  "Falsig et al (2012)"
Au  111 O   2.61    fcc []  []  "Falsig et al (2012)"
Ru  111 CO  1.3 fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Rh  111 CO  1.34    fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Pd  111 CO  1.55    fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Ni  111 CO  1.63    fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Pt  111 CO  1.7 fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Cu  111 CO  2.58    fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Ag  111 CO  2.99    fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Au  111 CO  3.04    fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Ru  111 O-CO    2.53    fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Rh  111 O-CO    3.1 fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Ni  111 O-CO    3.25    fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Pt  111 O-CO    4.04    fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Cu  111 O-CO    4.18    fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Pd  111 O-CO    4.2 fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Ag  111 O-CO    5.05    fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Au  111 O-CO    5.74    fcc []  []  "Angew. Chem. Int. Ed., 47, 4835 (2008)"
Ag  111 O-O 5.98    fcc []  []  "Falsig et al (2012)"
Au  111 O-O 7.22    fcc []  []  "Falsig et al (2012)"
Cu  111 O-O 4.74    fcc []  []  "Falsig et al (2012)"
Pt  111 O-O 5.35    fcc []  []  "Falsig et al (2012)"
Rh  111 O-O 3.79    fcc []  []  "Falsig et al (2012)"
Ru  111 O-O 3.34    fcc []  []  "Falsig et al (2012)"
Pd  111 O-O 5.34    fcc []  []  "Falsig et al (2012)"

Thanks for your reminder, I download energies.txt from the repo, and it's like:

surface_name	site_name	species_name	formation_energy	bulk_structure	frequencies	other_parameters	reference
None	gas	CO2	2.45	None	[1333,2349,667,667]	[]	"Angew. Chem. Int. Ed., 47, 4835 (2008)"
None	gas	CO	2.74	None	[2170]	[]	"Energy Environ. Sci., 3, 1311-1315 (2010)"
None	gas	O2	5.42	None	[1580]	[]	Falsig et al (2012)
Re	111	O	-1.15	fcc	[]	[]	Falsig et al (2012)

The minor difference is that the tabs or \t is turned to four space on catmap.readthedocs by HTML5 or the explorer, so when I ran the model last time, table_parser.py of course could not find the \t that should exist in energiesWebsite.txt. Indeed the tutorial file mkm_job.py in repo works well.
Fine, it's done, the sily mistake I made is I haven't seen the tutorial file in the package. Great Thanks!

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gusmaogabriels avatar gusmaogabriels commented on May 24, 2024

No problem! It’s great that you have found the source of the error.

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