sjklipp
commented
3 weeks ago Luna,
I am not immediately bothered by that idea. And as you say, we could add some flag to avoid the resorting.
What I would not like to have happen is to have the forward/reverse direction of the reaction changed. For example, for good reason it is often preferable to write a reaction in the exothermic direction. Arbitrarily changing that would mess that up. But I don't think you are planning to do that anyways.
Stephen
From: Luna Pratali Maffei @.> Sent: Tuesday, August 20, 2024 5:53 PM To: Auto-Mech/mechanalyzer @.> Cc: Klippenstein, Stephen J. @.>; Assign @.> Subject: [Auto-Mech/mechanalyzer] new rxn name ordering => more robust pes/subpes/channel assignment (Issue #295)
Every time we read a mechanism, we assign (from mechdriver by default, or when sorting for e. g. , generating prompt reactions) a pes. subpes. chnl sorting. if the comments are written in the form "# pes. subpes. channel", then no resorting is made. ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization.
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Every time we read a mechanism, we assign (from mechdriver by default, or when sorting for e.g., generating prompt reactions) a pes.subpes.chnl sorting. if the comments are written in the form "# pes.subpes.channel", then no resorting is made. In any case, the pes are ordered by formula https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/parser/_util.py#L140https://urldefense.us/v3/__https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/parser/_util.py*L140__;Iw!!G_uCfscf7eWS!ZD8Ivst6MrdI51jU089Oeqm36C-_5bPScy1bs1rYwR9be1EuEgjdIVIPs16c9XD4Q1nnSP-Cy5nYNnZ47OT0$ while the reactions within a pes and a subpes (i.e., the ubpes and channels) are only reordered by "reaction name" https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/builder/sort_fct.py#L198https://urldefense.us/v3/__https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/builder/sort_fct.py*L198__;Iw!!G_uCfscf7eWS!ZD8Ivst6MrdI51jU089Oeqm36C-_5bPScy1bs1rYwR9be1EuEgjdIVIPs16c9XD4Q1nnSP-Cy5nYNo08smtn$ this means that the value of the subpes and channels will depend on how the reaction is written (A+B=C, B+A=C will be ordered differently).
So what I would like to do is to try and make the subpes/channel sorting independent on how the reaction is written in the mechanism and order reactants and products according to this function, already used in the sorter for other purposes: https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/builder/sort_fct.py#L258https://urldefense.us/v3/__https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/builder/sort_fct.py*L258__;Iw!!G_uCfscf7eWS!ZD8Ivst6MrdI51jU089Oeqm36C-_5bPScy1bs1rYwR9be1EuEgjdIVIPs16c9XD4Q1nnSP-Cy5nYNkVey7eo$ https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/parser/_util.py#L16https://urldefense.us/v3/__https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/parser/_util.py*L16__;Iw!!G_uCfscf7eWS!ZD8Ivst6MrdI51jU089Oeqm36C-_5bPScy1bs1rYwR9be1EuEgjdIVIPs16c9XD4Q1nnSP-Cy5nYNlAIn0Qh$ where names of bimol reactions are arranged according to the formulas, and only then according to e.g., alphabetical order. so I would rewrite reaction strings and keys according to this classification. And I should also edit the criterion used within this function to make it consistent with the count_atoms used for the pes instead of the total atom counting that is currently done (https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/parser/_util.py#L34https://urldefense.us/v3/__https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/parser/_util.py*L34__;Iw!!G_uCfscf7eWS!ZD8Ivst6MrdI51jU089Oeqm36C-_5bPScy1bs1rYwR9be1EuEgjdIVIPs16c9XD4Q1nnSP-Cy5nYNnDi95Bi$)
Hopefully this would reduce the number of entries in the dataframe of the sorter, make it a bit simpler, and increase consistency/robustness. However, this would imply that the reaction lines might be re-written differently from what the user has in the input of mechanism.dat, which is instead debatable. One could probably use the "# pes.subpes.channel" also to avoid the resorting of reaction names. Or alternatively, I could implement consistent re-ordering for subpes/channel assignment but without changes to the reaction names so that they are consistent with the input by the user.
what do you think about this?
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lpratalimaffei
avcopan
Every time we read a mechanism, we assign (from mechdriver by default, or when sorting for e.g., generating prompt reactions) a pes.subpes.chnl sorting. if the comments are written in the form "# pes.subpes.channel", then no resorting is made. In any case, the pes are ordered by formula https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/parser/_util.py#L140 while the reactions within a pes and a subpes (i.e., the ubpes and channels) are only reordered by "reaction name" https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/builder/sort_fct.py#L198 this means that the value of the subpes and channels will depend on how the reaction is written (A+B=C, B+A=C will be ordered differently).
So what I would like to do is to try and make the subpes/channel sorting independent on how the reaction is written in the mechanism and order reactants and products according to this function, already used in the sorter for other purposes: https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/builder/sort_fct.py#L258 https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/parser/_util.py#L16 where names of bimol reactions are arranged according to the formulas, and only then according to e.g., alphabetical order. so I would rewrite reaction strings and keys according to this classification. And I should also edit the criterion used within this function to make it consistent with the count_atoms used for the pes instead of the total atom counting that is currently done (https://github.com/Auto-Mech/mechanalyzer/blob/777991b8330d0e85bd544b9cec55b75949f6d192/mechanalyzer/parser/_util.py#L34)
Hopefully this would reduce the number of entries in the dataframe of the sorter, make it a bit simpler, and increase consistency/robustness. However, this would imply that the reaction lines might be re-written differently from what the user has in the input of mechanism.dat, which is instead debatable. One could probably use the "# pes.subpes.channel" also to avoid the resorting of reaction names. Or alternatively, I could implement consistent re-ordering for subpes/channel assignment but without changes to the reaction names so that they are consistent with the input by the user.
what do you think about this?