[Epic] Crystallization digital-twin demonstrator

[andres9403]

Goal

Deliver a crystallization digital-twin demonstrator: a calibration-ready
mechanistic model with PAT-relevant measurement prediction, an estimation and
uncertainty workflow, and a reproducible case study.

Status: scope provisional

A full-time crystallizer developer is starting. The exact deliverable scope is
open to redefinition, so this epic tracks the outcome and its dependencies
rather than a fixed task list.

Dependency: this stream overlaps the refactor

Unlike the bioreactor stream (#152), this work touches the same modules that
MultiPhaseVesselRefactor rewrites - Crystallizers.py, Phases.py,
Kinetics.py, ThermoModule.py. Two consequences:

1. Merge order must be declared. Default until decided: [Epic] Integrate the MultiPhaseVessel architecture #148 merges first,
   this stream reconciles. The newer, smaller, better-tested stream should pay
   the reconciliation cost.
2. The demonstrator sits on defective foundations today. There are 11 open
   area:crystallizers and 8 area:kinetics defects, including the only open
   severity:critical issue (Critical: [Crystallizers] Energy balances crash in adiabatic/jacket modes and mix enthalpy bases #68). A demonstrator built before those close
   cannot claim trustworthy results.

How the overlap is handled - parallel-and-reconcile, sequence behind the
refactor, or re-scope away from the shared modules - is a stakeholder decision.
Deadline: end of Month 2.

Acceptance criteria

• Mechanistic crystallization model with documented kinetics, assumptions, and units
• PAT-relevant measurement prediction tied to observable quantities
• Calibration on public or openly shareable data
• Uncertainty reporting for estimated parameters
• Model-based design of experiments (conditional - verify tooling maintenance before committing)
• Reproducible notebook, data templates, tests, documentation page
• Blocking crystallizer defects closed or explicitly disclosed as limitations

Dependencies

• [Epic] Integrate the MultiPhaseVessel architecture #148 MultiPhaseVessel integration (merge order)
• Critical: [Crystallizers] Energy balances crash in adiabatic/jacket modes and mix enthalpy bases #68 critical crystallizer energy-balance defect
• High: [Crystallizers] Concentration Jacobian diagonal has wrong sign for crystallization sink #26, High: [Kinetics] Activation-energy derivative is wrong for non-reformulated crystallization kinetics #35, Medium: [Kinetics] deriv_cryst ignores sup_sat_type and hardcodes relative supersaturation #43, High: [Crystallizers] MSMPR concentration balance uses solid density in the liquid transfer term #46, High: [Crystallizers] Mass-fraction conversion is dead code in Batch/Semibatch crystal balances #47 crystallizer/kinetics correctness
• [Scoping] Crystallizer model extensions (agglomeration, breakage, polymorphism, 2-D PBE) #15 crystallizer model extensions (split before scheduling)
• Integration contract for parallel development workflows #150 integration contract, before the first commit