Split expressions into static and dynamic #2303
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## develop #2303 +/- ##
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+ Coverage 77.72% 77.83% +0.10%
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Files 321 321
Lines 20601 20678 +77
Branches 1436 1440 +4
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+ Hits 16013 16095 +82
+ Misses 4585 4580 -5
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Currently, parameters that are targets of initial assignments don't show up as parameters or expressions in the amici model. This is rather not what most users would expect. Therefore, treat all SBML parameters that are initial assignment targets and whose initial assignment does not evaluate to a number (for those that do, see AMICI-dev#2304) as amici expressions. Those static expressions will be handled more efficiently after AMICI-dev#2303. Related to AMICI-dev#2150.
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Currently, parameters that are targets of initial assignments don't show up as parameters or expressions in the amici model. This is rather not what most users would expect. Therefore, treat all SBML parameters that are initial assignment targets and whose initial assignment does not evaluate to a number (for those that do, see AMICI-dev#2304) as amici expressions. Those static expressions will be handled more efficiently after AMICI-dev#2303. Related to AMICI-dev#2150.
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On second thought, I'll directly include dwd* here as well. |
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| return self._static_indices[name] | ||
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| if name in ("dwdw", "dwdx", "dwdp"): | ||
| static_indices_w = set(self.static_indices("w")) |
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how computationally intensive are those computations? Is caching worthwhile?
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Currently they are cached, but I didn't profile it yet.
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| # dynamic expressions | ||
| if len(dynamic_idxs := self.model.dynamic_indices(function)): | ||
| tmp_symbols = sp.Matrix( |
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partial duplication of code above
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True. But currently I don't think that moving those lines to some separate function will make it clearer or more maintainable, rather the opposite.
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Resolved. Was related to other changes. |
Split expressions in `w` into dynamic (explicitly or implicitly time-dependent) and static ones. Evaluate static ones only when needed, i.e. after (re)initializing x_rdata or parameters. See AMICI-dev#1269
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For a model with nw: 227, nx: 67, ndwdx: 759, ndwdw: 471:
Looks like some further profiling/optimization is required... |
Okay, for that model, I am now down to EDIT: I removed the derivative-based check for dwd* elements. With just checking for whether the expressions contain dynamic symbols, we have minimal overhead (<1s) and probably don't lose much. |
…2305) Currently, parameters that are targets of initial assignments don't show up as parameters or expressions in the amici model. This is rather not what most users would expect. Therefore, treat all SBML parameters that are initial assignment targets and whose initial assignment does not evaluate to a number (for those that do, see #2304) as amici expressions. Those static expressions will be handled more efficiently after #2303. Related to #2150. See also #2304.
Split expressions in
wand its derivatives into dynamic (explicitly or implicitly time-dependent) and static ones.Evaluate static ones only when needed, i.e. after (re)initializing x_rdata or parameters.
See #1269