Calibrator: Reuse residual from solver

[mrp089]

Problem

We currently reimplement the residual in the calibrator, e.g., for the BloodVessel block:

svZeroDSolver/src/model/BloodVessel.cpp

Lines 126 to 130 in 32b46d7

	residual(global_eqn_ids[0]) =
	y0 - (resistance + stenosis_resistance) * y1 - y2 - inductance * dy3;
	residual(global_eqn_ids[1]) =
	y1 - y3 - capacitance * dy0 +
	capacitance * (resistance + 2.0 * stenosis_resistance) * dy1;

However, the residual is the same as in the solver. Compare equations (2.18) and (2.24) in this paper. Only the Jacobian is different and needs to be implemented separately for the solver and calibrator.

Solution

Automatically reuse the solver's residual in the calibrator for all blocks.

Additional context

No response

Code of Conduct

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[mrp089]

As a first step towards that, I cleaned up the calibrator a bit: https://github.com/mrp089/svZeroDSolver/tree/restructure_calibrator_153

I removed (now unused) untested legacy options set_capacitance_to_zero (always false) and calibrate_stenosis_coefficient (always true). I moved the creation of the Model to Parameters (which I renamed from SimulationParameters) which now contains SimulationParameters and CalibrationParameters. I also simplified the calibration model setup by reusing functions from the simulation setup to create vessels and junctions. Calibration tests still pass.

[mrp089]

The next step will be to give the calibrator a SparseSystem that's similar to the solver's to enable easy calculation of the calibrator residual. Also, calibrate.cppstill contains a lot of code that is specific only to BloodVessel and BloodVesselJunction. This should apply to any block. Ideally, each block will get a list of calibration_parameters where the user can specify which parameters should be calibrated. The ones not calibrated will maintain their constant value from the calibration input file.