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ImplicitSpecies.n can be space and time dependent #886

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merged 8 commits into from
Jan 14, 2025
Merged

ImplicitSpecies.n can be space and time dependent #886

merged 8 commits into from
Jan 14, 2025

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RemDelaporteMathurin
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@RemDelaporteMathurin RemDelaporteMathurin commented Oct 2, 2024 •
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Proposed changes

This fixes #644 by allowing the n attribute of ImplicitSpecies to be a function of x and t.

Pinging @kaelyndunnell

Usage:

density_func= lambda x: 10 - 10 * x[0]

empty = F.ImplicitSpecies(n=density_func, name="empty", others=[trapped_H])

Step function:

density_func= lambda x: ufl.conditional(ufl.gt(x[0], 0.5), 10, 0.0)

empty = F.ImplicitSpecies(n=density_func, name="empty", others=[trapped_H])

Types of changes

What types of changes does your code introduce to FESTIM?

  • Bugfix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • Code refactoring
  • Documentation Update (if none of the other choices apply)
  • New tests

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  • Unit tests pass locally with my changes
  • I have added tests that prove my fix is effective or that my feature works
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@RemDelaporteMathurin RemDelaporteMathurin linked an issue Oct 2, 2024 that may be closed by this pull request
Trap density varies in space and time #644
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@RemDelaporteMathurin RemDelaporteMathurin removed the request for review from jhdark October 2, 2024 21:23
@RemDelaporteMathurin RemDelaporteMathurin marked this pull request as draft October 2, 2024 21:23
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codecov bot commented Oct 3, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.84%. Comparing base (8c5a965) to head (ad0ff2a).
Report is 35 commits behind head on fenicsx.

Additional details and impacted files 
@@             Coverage Diff             @@
##           fenicsx     #886      +/-   ##
===========================================
+ Coverage    97.80%   97.84%   +0.04%     
===========================================
  Files           44       44              
  Lines         2142     2182      +40     
===========================================
+ Hits          2095     2135      +40     
  Misses          47       47

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@RemDelaporteMathurin RemDelaporteMathurin marked this pull request as ready for review October 3, 2024 12:49
@RemDelaporteMathurin RemDelaporteMathurin mentioned this pull request Oct 4, 2024
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@RemDelaporteMathurin RemDelaporteMathurin mentioned this pull request Nov 1, 2024
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@RemDelaporteMathurin RemDelaporteMathurin requested review from jhdark and removed request for jhdark November 3, 2024 00:42
@RemDelaporteMathurin RemDelaporteMathurin mentioned this pull request Nov 5, 2024
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@RemDelaporteMathurin RemDelaporteMathurin added enhancement New feature or request fenicsx Issue that is related to the fenicsx support labels Nov 5, 2024
@RemDelaporteMathurin RemDelaporteMathurin requested review from jhdark and removed request for jhdark November 9, 2024 18:30
@RemDelaporteMathurin RemDelaporteMathurin requested review from jhdark and removed request for jhdark December 8, 2024 18:43
@RemDelaporteMathurin
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@jhdark would you mind giving this a look?

jhdark
jhdark reviewed Jan 13, 2025
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Should an implicit species not also be able to be temperature dependent?

@RemDelaporteMathurin
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Should an implicit species not also be able to be temperature dependent?

What does this mean exactly?

@RemDelaporteMathurin
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Should an implicit species not also be able to be temperature dependent?

So we discussed this internally and James' question was about having an annealing term (temperature dependent) affecting the empty trap concentration: this is now doable directly with Reaction and shouldn't be related to ImplicitSpecies

@RemDelaporteMathurin RemDelaporteMathurin merged commit 819379a into festim-dev:fenicsx Jan 14, 2025
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Trap density varies in space and time
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