JAMA to EJML migration and dependency retirement

PR #4416 completes the removal of JAMA from production and test calculations. Both pom.xml and pomJava8.xml remove gov.nist.math:jama. No JAMA implementation is vendored, shaded, or used as a fallback. The retired JamaLinearAlgebra backend is removed; select EjmlLinearAlgebra through the existing LinearAlgebraOperations array API.

Phase-envelope numerical correction

The phase-envelope continuation solver stores primitive arrays and solves its linear systems with EJML. Its fugacity equations, material balances, damping, retry limits and convergence tolerances remain unchanged.

The earlier conversion produced a reproducible pure-ethane cricondenbar of 59.0958176754016 bara on Linux and Windows. Restoring JAMA hid the problem; it did not complete the migration. Continuation diagnostics isolate a false accepted state at 277.24989559451365 K and 59.0958176754016 bara: the gas volume implies an EOS pressure of 32.56026344346368 bara, while the liquid volume satisfies the specified pressure. The gas volume iteration has stalled near a spinodal. Distinct positive phase volumes and a small fugacity residual are therefore insufficient to establish pure-component saturation.

Pure-component continuation now also requires both EOS volumes to reproduce the specified pressure within a relative tolerance of 1e-6. Non-finite or inconsistent roots enter the existing step-reduction/retry path. This checks the calculated state; it neither substitutes a critical pressure nor clamps the envelope to a reference value. The original ethane acceptance bounds (42–56 bara and 295–315 K) are retained. Regression coverage checks accepted continuation points directly against the EOS pressure equation. Repeated local calculations with EJML return 48.71999806842542 bara and 305.31999797987163 K.

Film Newton regression fixtures can have condition numbers above 1e20. Their migration checks equation assembly, ownership and damping, plus the normwise linear backward error against a 1e-12 tolerance, rather than requiring backend-specific correction vectors to agree in nearly singular systems. This does not certify those intermediate iterations as converged physical states. The independent Commons Math spectral reference is scaled before decomposition to handle very large finite fluxes; the existing 1e-10 correction comparison tolerance is unchanged.

Public API migration

The complete removal intentionally changes the remaining matrix-specific contracts. This is a source, binary and persisted-solver compatibility boundary, requiring release review under governance and the API lifecycle policy. It must not be advertised as a binary-compatible patch. Existing array APIs remain the preferred interfaces.

Previous JAMA surface	EJML-only replacement
JamaLinearAlgebra	EjmlLinearAlgebra; the former backend is removed.
ChemicalReactionList.calcReacRates(...)	The deprecated method returns an EJML SimpleMatrix column; prefer calcReationRates(...), which returns double[].
FluidBoundaryInterface.getMassTransferCoefficientMatrix()	Returns SimpleMatrix[]; prefer getMassTransferCoefficientArray().
FluidBoundary.massTransferCoefficientMatrix	Transient EJML SimpleMatrix[] views, synchronized with canonical coefficient arrays.
StatisticsBaseClass.checkBounds(...) and displayMatrix(...) matrix overloads	Accept EJML SimpleMatrix; array calls dispatch to those EJML hooks. Rebuild and migrate subclass overrides.
LevenbergMarquardtResult matrix constructor and covariance/correlation getters	Use EJML SimpleMatrix with defensive copies; prefer fromArrays(...) and array getters.
SysNewtonRhapsonPhaseEnvelope persisted working state	Array layout with serialization UID 1001; recreate UID-1000 working solvers from thermodynamic inputs.

For Java and Python/JVM callers, replace JAMA imports and matrix construction with the corresponding EJML type, or migrate to primitive arrays. The EJML accessors do not preserve old JAMA method descriptors. A typed pair of null matrix arguments or the named fromArrays(...) factory avoids constructor overload ambiguity. Previously serialized model graphs containing a UID-1000 phase-envelope solver cannot be restored by adding the old JAR.

Film coefficient access retains lazy allocation, live matrix mutation and replacement, shallow-clone sharing, and synchronization before serialization. EJML stores flat arrays, so synchronization copies values between its matrix views and the canonical row-major coefficient arrays. Array-only callers do not allocate matrix views. Result covariance/correlation accessors return independent copies. Conversion code supports EJML 0.41 for Java 8 as well as the current EJML version.

Validation requirements

• Build and run with JAMA absent from the complete Maven test classpath.
• Retain physical regressions, analytical linear-algebra contracts, ownership, subclass dispatch, coefficient correction order, and serialization tests.
• Reject non-finite EJML results; factorization acceptance alone is insufficient.
• Check the EOS pressure residual as well as fugacity and material balance for pure-component continuation.
• Check both supported POM dependency trees and thin/shaded distributions.
• Run cross-platform CI; a successful local run does not establish identical continuation paths on every runtime or a performance improvement.

The dependency absence regression fails if Jama.Matrix becomes loadable on the Maven test classpath. Independent numerical references use analytical relations or Apache Commons Math; tests never call JAMA.