Delegate reactor implementation to user-provided Python classes #1003
Commits on Dec 31, 2021
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Revise behavior of "after" delegates that return a value
For 'after' delegates, if the return code from the wrapped function is non-zero, then the delegate's return value will be the sum of the values from the base and wrapped functions.
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[Python] Prefix replacement delegate methods with 'replace_'
Avoids name clashes with existing Python names that may have different method signatures, e.g. Reactor.get_state.
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[Reactor] Introduce simpler function for reactor ODE function
The function for evaluating dy/dt no longer needs the vector of sensitivity parameters, and should not operate directly on the state vector (which should be processed by updateState).
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Added RHS and LHS user variables to Reactor class
Implemented LHS/RHS notation in eval functions of Reactor classes
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Created new setDelegate method for void(double, double*, double*) type
Required for LHS/RHS arguments Added name to authors list
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Whitespace deletions, unnecessary comment removal, Doxygen string formatting
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Fix custom2.py to use RHS/LHS eval function
Co-authored-by: Ray Speth <speth@mit.edu>
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[Kinetics] Make "declared-species" option work for surfaces
When adding reactions, the check for whether or not surface sites are conserved needs to occur after the check for whether all species in the reaction exist, since the number of sites isn't known for an undefined species.
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[Reactor] Modify signature of evalSurfaces
This signature makes it possible to write delegates for this function that change the gas phase species production rates
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[Python/Reactor] Sync state when accessing ReactorSurface.kinetics
This is analogous to the automatic synchronization done when accessing Reactor.thermo.
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[Delegator] Hold delegate references in Python instead of C++
This prevents the creation of circular references that aren't traversable by the Python garbage collector and therefore can never be reclaimed.
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