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Localize kinetic reaction rates.#1232

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1uc merged 6 commits into
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1uc/kinetic_local_variables
Apr 9, 2024
Merged

Localize kinetic reaction rates.#1232
1uc merged 6 commits into
masterfrom
1uc/kinetic_local_variables

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@1uc

@1uc 1uc commented Apr 4, 2024 •
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If assignments and reaction equations are interspersed the ODE might use incorrect reaction rates. Example:

rate = 42.0
~ a <-> b (1.0*rate, 2.0*rate)
rate = 43.0
~ c <-> d (3.0*rate, 4.0*rate)

was equivalent to:

rate = 42.0
rate = 43.0
~ a <-> b (1.0*rate, 2.0*rate)
~ c <-> d (3.0*rate, 4.0*rate)

This PR solves the issue by localizing the rates, i.e. it'll produce:

LOCAL kf0_, kb0_, kf1_, kb1_
rate = 42.0
kf0_ = 1.0*rate
kb0_ = 2.0*rate
~ a <-> b (kf0_, kb0_)
rate = 43.0
kf1_ = 3.0*rate
kb1_ = 4.0*rate
~ c <-> d (kf1_, kb1_)

Which can then be safely shuffled into:

LOCAL kf0_, kb0_, kf1_, kb1_
rate = 42.0
kf0_ = 1.0*rate
kb0_ = 2.0*rate

rate = 43.0
kf1_ = 3.0*rate
kb1_ = 4.0*rate

~ a <-> b (kf0_, kb0_)
~ c <-> d (kf1_, kb1_)

and from there transformed as usual.

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codecov-commenter commented Apr 5, 2024 •
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Codecov Report

Attention: Patch coverage is 96.20253% with 3 lines in your changes are missing coverage. Please review.

Project coverage is 86.65%. Comparing base (98e6df2) to head (8483416).
Report is 1 commits behind head on master.

❗ Current head 8483416 differs from pull request most recent head b8ebe7f. Consider uploading reports for the commit b8ebe7f to get more accurate results

Files Patch % Lines
src/visitors/kinetic_block_visitor.cpp 96.20% 3 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##           master    #1232      +/-   ##
==========================================
+ Coverage   86.59%   86.65%   +0.05%     
==========================================
  Files         176      176              
  Lines       13053    13132      +79     
==========================================
+ Hits        11303    11379      +76     
- Misses       1750     1753       +3

☔ View full report in Codecov by Sentry.
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@1uc 1uc force-pushed the 1uc/kinetic_local_variables branch from 30727b1 to 8bd19d9 Compare April 5, 2024 08:59
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@1uc 1uc marked this pull request as ready for review April 5, 2024 12:38
@1uc 1uc force-pushed the 1uc/kinetic_local_variables branch from 8bd19d9 to 8483416 Compare April 5, 2024 12:39
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pramodk
pramodk reviewed Apr 5, 2024
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Two minor suggestions. It's done nicely! With the tests, it quite clear! 👌

Comment thread src/visitors/kinetic_block_visitor.cpp
Comment thread src/visitors/kinetic_block_visitor.cpp
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Logfiles from GitLab pipeline #203899 (:white_check_mark:) have been uploaded here!

Status and direct links:

@1uc 1uc mentioned this pull request Apr 8, 2024
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pramodk
pramodk approved these changes Apr 9, 2024
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Comment thread test/unit/visitor/kinetic_block.cpp
Comment thread src/visitors/kinetic_block_visitor.cpp
@1uc 1uc merged commit 868ce13 into master Apr 9, 2024
@1uc 1uc deleted the 1uc/kinetic_local_variables branch April 9, 2024 15:10
JCGoran pushed a commit to neuronsimulator/nrn that referenced this pull request Mar 12, 2025
@1uc
Localize kinetic reaction rates. (BlueBrain/nmodl#1232)
da6f3fb 
Store the forward and reverse rates in local variables, e.g.:
```
rate = 42.0
~ a <-> b (1.0*rate, 2.0*rate)
```
is converted to:
```
LOCAL kf0_, kb0_
rate = 42.0
kf0_ = 1.0*rate
kb0_ = 2.0*rate
~ a <-> b (kf0_, kb0_)
```

This solves a bug that assigning to `rate` between two reaction equation statements would mean the first line sees the value meant for the second line.

NMODL Repo SHA: BlueBrain/nmodl@868ce13
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