Temperature for alquimia pk

[smolins]

In a nutshell: temperature is not being passed to the alquimia pk.

This issue is described in the user group by Sam, with a simple test example:

https://groups.google.com/g/ats-users/c/KYH5cMQGgLo/m/clwY29amCwAJ

We did not resolve it yet. Creating this issue to track progress.

[swshaheen]

It appears the updated Alquimia PK just requires a temperature key in the xml file within the surface/subsurface chemistry PKs, e.g.;

Without this, temperature is ignored whether it's present in state or not. Eventually it would be good to have a regression test or update the documentation to make this extra clear, but it doesn't appear to be the result of a bug but rather an intentional change in Alquimia_PK.cc requiring a key for temperature.

[smolins]

Does this mean that temperature in the Chemistry PK can be different from the temperature in other PKs, if defined in the other PKs? Sergi

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On Tue, Oct 14, 2025 at 1:31 PM swshaheen ***@***.***> wrote: *swshaheen* left a comment (amanzi/ats#324) <#324 (comment)> It appears the updated Alquimia PK just requires a temperature key in the xml file within the surface/subsurface chemistry PKs, e.g.; Without this, temperature is ignored whether it's present in state or not. Eventually it would be good to have a regression test or update the documentation to make this extra clear, but it doesn't appear to be the result of a bug but rather an intentional change in Alquimia_PK.cc requiring a key for temperature. — Reply to this email directly, view it on GitHub <#324 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADXOTGTXHYXZ4VNVCUBUZDT3XVMQJAVCNFSM6AAAAACGIMECBWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTIMBTGUYTIMRRGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ecoon]

This was discussed a bit in other places, sorry for the delay. Effectively the choice was made to require the user to provide a temp_key_ if the user wanted to pass temperature to chemistry. The concern was that if temperature was always passed to chemistry whenever it existed in ATS at all, there might be cases where that was not appropriate (particularly for Arctic cases, which is our most frequent temperature use case).

I believe at AGU Sam suggested to always provide temp to Alquimia if it existed.

My main question before doing that is:

1. Does PFloTran and Crunch, by default, do temperature-dependent things? Or would a user have to explicitly turn on temperature-dependence?
2. What happens if PFLoTran or Crunch get very cold temperatures (e.g. Arctic temperatures, let's say -10 C)? Will the code do something reasonable? Blow up?

[swshaheen]

I changed my mind-I think the current setup with a key makes the most sense. General aqueous speciation and thermodynamic equilibria would be temperature-dependent by default in the geochemical engines, so there is some risk of Arctic temperatures causing issues. There are also probably use cases where subsurface temperatures are unknown and the user doesn't want to run a full energy balance model but rather prefers to use the geochemical engines' default temperature (25C). So it seems like the key provides the best flexibility.

[smolins]

t makes sense. If not provided the temperature will default to the alquimia engine's temperature, which is what we are doing for other reaction related things, i.e. relying on the engine's input data. We need to document this somewhere.

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On Tue, Jun 2, 2026 at 12:09 PM swshaheen ***@***.***> wrote: *swshaheen* left a comment (amanzi/ats#324) <#324 (comment)> I changed my mind-I think the current setup with a key makes the most sense. General aqueous speciation and thermodynamic equilibria would be temperature-dependent by default in the geochemical engines, so there is some risk of Arctic temperatures causing issues. There are also probably use cases where subsurface temperatures are unknown and the user doesn't want to run a full energy balance model but rather prefers to use the geochemical engines' default temperature (25C). So it seems like the key provides the best flexibility. — Reply to this email directly, view it on GitHub <#324?email_source=notifications&email_token=ADXOTGUOVRZTBPIMMWXKDW3454Q7TA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTINRQGYYTKNBUGI4KM4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L#issuecomment-4606154428>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADXOTGSNF7EMJ3ZF3D2MYJT454Q7TAVCNFSM6AAAAACZXTSB3GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DMMBWGE2TINBSHA> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/ADXOTGWGKIJAA4FH2ZC6T5D454Q7TA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTINRQGYYTKNBUGI4KM4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KUZTPN52GK4S7NFXXG> and Android <https://github.com/notifications/mobile/android/ADXOTGXOHOPS43ETZS7CRID454Q7TA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTINRQGYYTKNBUGI4KM4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2K4ZTPN52GK4S7MFXGI4TPNFSA>. Download it today! You are receiving this because you authored the thread.Message ID: ***@***.***>