Analysis.py provides clearly incorrect destruction rates, they never seem to overtake the production, so the "derivative" never becomes smaller than 0. See the files below. Above plot shows the abundances for a static model like in the test runs, the bottom plots show the following three lines:
The sign of the first order forward difference of the abundance (terrible approximation, but the sign should be correct)
The derivative retrieved with get_odes (directly from UCLCHEM wrap), this has the correct sign but a much different magnitude than analysis.
The deriatives obtained by subtracting the destruction from production from analysis.py
This is done for three species, the deriatives for non abundant species are more terrible (fluctuate around zero), so I didnt even bother with those. Plots below are on UCLCHEM v3.2.0 release candidate.
Below a snippet of the text output of analysis.py in UCLCHEM v3.1.0
Analysis.py provides clearly incorrect destruction rates, they never seem to overtake the production, so the "derivative" never becomes smaller than 0. See the files below. Above plot shows the abundances for a static model like in the test runs, the bottom plots show the following three lines:
get_odes
(directly from UCLCHEM wrap), this has the correct sign but a much different magnitude than analysis.This is done for three species, the deriatives for non abundant species are more terrible (fluctuate around zero), so I didnt even bother with those. Plots below are on UCLCHEM v3.2.0 release candidate.
Below a snippet of the text output of analysis.py in UCLCHEM v3.1.0