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Improved TauHybrid with single SSA step #829

Merged
merged 58 commits into from
Jul 20, 2022
Merged

Improved TauHybrid with single SSA step #829

merged 58 commits into from
Jul 20, 2022

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briandrawert
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Closes #826

@briandrawert briandrawert added this to the 1.6.10 milestone Jun 13, 2022
@briandrawert briandrawert linked an issue Jun 13, 2022 that may be closed by this pull request
Loop over integrate error in TauHybridSolver and TauHybridCSolver need to be clarified #826
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@briandrawert briandrawert marked this pull request as draft June 13, 2022 18:08
@briandrawert briandrawert linked an issue Jun 13, 2022 that may be closed by this pull request
TauHybridCSolver fails consistently on create_toggle_switch example model #830
Closed
briandrawert and others added 19 commits June 16, 2022 12:37
@briandrawert
for single SSA step: r must be set, not decrimented, relaxed non-neg …
1a37711 
…check to allow for positive r values
@briandrawert
Changing the TauHybrid algorithm, no loop over integrate instead take…
3ed5ebd 
… a single SSA step. C++ converson begun.
@jtcooper10
get_reaction_state() helper method
c8ffeac
@briandrawert
Code complete, compile errors
5a91a27
@briandrawert
fixed compile errors
376571f
@briandrawert
saving debug output
8a8aa12
@briandrawert
removing debugging
d66bf10
@briandrawert
fixing the post-step assignment for discrete/continious
b06f784
@briandrawert
merged
8230a2f
@briandrawert
removed dead code
1366d6a
@briandrawert
Merge pull request #838 from StochSS/improved_tau_hybrid_ssa_step--no…
78a0b5a 
…debug

Improved tau hybrid ssa step  nodebug
@briandrawert
New adendum to algorithm: if estimated single ssa tau is less thatn 1…
58fe95f 
…e-10 (min integration time), fire said reaction at current time and re-attempt step at current time
@briandrawert
Merged
614365e
@briandrawert
fixed stoch-det reactions
22622f7
@briandrawert
merge
c5131a0
@briandrawert
Merge pull request #839 from StochSS/improved_tau_hybrid_ssa_step--no…
89918e1 
…debug

Improved tau hybrid ssa step  nodebug
@briandrawert
restoring defaults
fce00ea
@briandrawert
Experiment to show that Poisson approximation to the Erwin-Hall disti…
b1c61fa 
…rbution works
@briandrawert
The Poisson approximation to the sum of N URN (Irwin-Hall)
9a18d9d
@briandrawert briandrawert marked this pull request as ready for review June 21, 2022 23:12
@briandrawert briandrawert requested a review from seanebum June 21, 2022 23:12
BryanRumsey
BryanRumsey requested changes Jul 1, 2022
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Testing notebook crashed due to excessive output

@briandrawert briandrawert linked an issue Jul 6, 2022 that may be closed by this pull request
Michaelis-Menten model not accurate in TauHybridSolver #843
Closed
@briandrawert briandrawert requested a review from BryanRumsey July 6, 2022 02:40
@seanebum seanebum self-requested a review July 13, 2022 14:42
seanebum
seanebum requested changes Jul 13, 2022
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Currently, it looks like species explicitly declared as 'continuous' are not being updated. See photosynthesis notebook using python hybrid solver.

@briandrawert briandrawert merged commit 3be327b into develop Jul 20, 2022
@briandrawert briandrawert deleted the improved_tau_hybrid_ssa_step branch July 20, 2022 17:29
@BryanRumsey BryanRumsey mentioned this pull request Aug 10, 2022
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@BryanRumsey BryanRumsey BryanRumsey approved these changes

@seanebum seanebum seanebum approved these changes

@jtcooper10 jtcooper10 Awaiting requested review from jtcooper10

@kevinsanft kevinsanft Awaiting requested review from kevinsanft

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