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SUNCAT-Center / catmap

Catalyst Micro-kinetic Analysis Package for automated creation of micro-kinetic models used in catalyst screening
GNU General Public License v3.0
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Type error #130

Open Lillejanur opened 3 years ago

Lillejanur commented 3 years ago

When I run catmap on either linux or Mac I get a type error. The program expects a float and gets an array. It seems as though the problem is in enthalpy_entropy.py in the function get_frequency_cutoff. It returns an array with one element while e.g. the function call in harmonic_adsorbate suggests that a float is wanted. Picking the first element of get_frequency_cutoff and returning it allows the program to run seemingly without error.

gusmaogabriels commented 3 years ago

@Lillejanur, can you provide the inputs to reproduce the error?

Lillejanur commented 3 years ago

Yes, of course. Please find attached the files. inputs.zip

gusmaogabriels commented 3 years ago

@Lillejanur, I have just run your MKM on a linux machine without any issues.

rootfinding_iteration_4: fail - stagnated or diverging (residual = 2501228228.5012946)
minresid_iteration_0: fail - [623.15,-1.00] using coverages from [623.15,-1.00]; initial residual was 1298433859320.3535 (residual = 2501228228.5012946)
rootfinding_iteration_6: fail - stagnated or diverging (residual = 89808.91426886935)
minresid_iteration_1: fail - [623.15,-1.00] using coverages from [623.15,-1.00]; initial residual was 12571182661550.072 (residual = 89808.91426886935)
minresid_iteration_2: success - [623.15,-1.00] using coverages from [623.15,-1.00]
minresid_iteration_0: success - [598.15,-1.00] using coverages from [598.15,-1.00]
minresid_iteration_0: success - [573.15,-1.00] using coverages from [573.15,-1.00]
minresid_iteration_0: success - [548.15,-1.00] using coverages from [548.15,-1.00]
minresid_iteration_0: success - [523.15,-1.00] using coverages from [523.15,-1.00]
minresid_iteration_0: success - [498.15,-1.00] using coverages from [498.15,-1.00]
minresid_iteration_0: success - [473.15,-1.00] using coverages from [473.15,-1.00]
minresid_iteration_0: success - [448.15,-1.00] using coverages from [448.15,-1.00]
minresid_iteration_0: success - [423.15,-1.00] using coverages from [423.15,-1.00]
mapper_iteration_1: status - 0 points do not have valid solution.
descriptors [623.15, -1.0]
intermediates ('CH_f', 'COH_f', 'C_f', 'H_h', 'CH2O_s', 'CH2_s', 'CH3O_s', 'CH3_s', 'CHO_s', 'COOH_s', 'CO_s', 'H2COOH_s', 'H2O_s', 'HCOOH_s', 'HCOO_s', 'OH_s', 'O_s')
coverages [4.829315367489012e-15, 2.812481121488104e-19, 8.965626971970323e-13, 0.3223503173748633, 9.661292367592998e-21, 4.658942635078617e-17, 2.0278570697150554e-21, 1.1657375678668861e-17, 2.525346443019582e-16, 2.850113056570854e-12, 8.626063346795594e-08, 8.53219163801225e-23, 6.578914416583461e-14, 2.225613580532355e-15, 1.0507053826550442e-05, 2.662248142153112e-05, 1.9829322574838473e-05]
('g', 's', 'f', 'h')

Could you list the versions of the main CatMAP dependencies you have installed?

Dependencies python 3.7.5 numpy 1.17.0 scipy 1.3.1 mpamath 1.0.0

Lillejanur commented 3 years ago

Hello Gabriel,

I just installed Catmap on two computer clusters, and the type error appeared on one of them and not the other at first, so I thought I had something new to bring to the discussion. I saw on GitHub that you asked which dependencies I used, while the question did not appear in the email . Sorry that I didn't perceive the continued inquiry.

I believe that the problem lies with scipy, with 1.4 working and 1.5 giving type errors.

I have as follows:

Cluster 1 (the one I used in February): numpy 1.18.5 scipy 1.5 mpmath 1.1.0 python 3.8.3 Type error occurs as described

Cluster 2: numpy 1.20.2 scipy 1.6.2 mpmath 1.2.1 python 3.9.1 Type error occurs as described

Cluster 3: numpy 1.18.3 scipy 1.4.1 mpmath 1.1.0 python 3.8.2 No type error occurs. First time 'get_frequency_cutoff' is called, 'nu_cutoff' has type with no dimension, but seems to be correctly interpreted as a float further on.

Cluster 3, with newer dependencies: numpy 1.19.4 scipy 1.5.4 mpmath 1.10 python 3.8.6 Type error occurs as described

Best regards,

Mikael

Den sön 7 feb. 2021 kl 05:59 skrev Gabriel S. Gusmão < @.***>:

@Lillejanur https://github.com/Lillejanur, I have just run your MKM on a linux machine without any issues.

rootfinding_iteration_4: fail - stagnated or diverging (residual = 2501228228.5012946) minresid_iteration_0: fail - [623.15,-1.00] using coverages from [623.15,-1.00]; initial residual was 1298433859320.3535 (residual = 2501228228.5012946) rootfinding_iteration_6: fail - stagnated or diverging (residual = 89808.91426886935) minresid_iteration_1: fail - [623.15,-1.00] using coverages from [623.15,-1.00]; initial residual was 12571182661550.072 (residual = 89808.91426886935) minresid_iteration_2: success - [623.15,-1.00] using coverages from [623.15,-1.00] minresid_iteration_0: success - [598.15,-1.00] using coverages from [598.15,-1.00] minresid_iteration_0: success - [573.15,-1.00] using coverages from [573.15,-1.00] minresid_iteration_0: success - [548.15,-1.00] using coverages from [548.15,-1.00] minresid_iteration_0: success - [523.15,-1.00] using coverages from [523.15,-1.00] minresid_iteration_0: success - [498.15,-1.00] using coverages from [498.15,-1.00] minresid_iteration_0: success - [473.15,-1.00] using coverages from [473.15,-1.00] minresid_iteration_0: success - [448.15,-1.00] using coverages from [448.15,-1.00] minresid_iteration_0: success - [423.15,-1.00] using coverages from [423.15,-1.00] mapper_iteration_1: status - 0 points do not have valid solution. descriptors [623.15, -1.0] intermediates ('CH_f', 'COH_f', 'C_f', 'H_h', 'CH2O_s', 'CH2_s', 'CH3O_s', 'CH3_s', 'CHO_s', 'COOH_s', 'CO_s', 'H2COOH_s', 'H2O_s', 'HCOOH_s', 'HCOO_s', 'OH_s', 'O_s') coverages [4.829315367489012e-15, 2.812481121488104e-19, 8.965626971970323e-13, 0.3223503173748633, 9.661292367592998e-21, 4.658942635078617e-17, 2.0278570697150554e-21, 1.1657375678668861e-17, 2.525346443019582e-16, 2.850113056570854e-12, 8.626063346795594e-08, 8.53219163801225e-23, 6.578914416583461e-14, 2.225613580532355e-15, 1.0507053826550442e-05, 2.662248142153112e-05, 1.9829322574838473e-05] ('g', 's', 'f', 'h')

Dependencies python 3.7.5 numpy 1.17.0 scipy 1.3.1 mpamath 1.0.0

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