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FESADev/PROGRESS.md
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NINI 59dcc77a24 refactor: add phase1 module scaffold
2026-05-05 00:35:31 +09:00

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PROGRESS

Purpose

PROGRESS.md is the shared chronological status log for FESA agents.

Every new agent session must read this file together with PLAN.md before planning or editing. Keep this file factual: what changed, what was verified, what is blocked, and what remains risky.

How To Use

  • Add a new entry whenever a meaningful planning, documentation, implementation, verification, or review task is completed.
  • Include date, agent or author when known, changed files, verification performed, and follow-up items.
  • Record blockers explicitly.
  • Do not use this file as a future task list. Put future tasks in PLAN.md.
  • Do not remove history unless the user explicitly asks for archival cleanup.

Current Status

Phase 1 has a completed rebaseline execution path in phases/1-linear-static-mitc4-rebaseline. Steps 0 through 15 are complete, and P1R-15 recorded a pass-with-documented-gaps evaluator closeout. The follow-up architecture refactor phase in phases/1-structure-alignment-refactor is underway because the current production implementation is concentrated in include/fesa/fesa.hpp instead of the module directories documented in docs/ARCHITECTURE.md; P1A-00 and P1A-01 are complete, so the next step is P1A-02 Core/Util extraction. quad_02_phase1.inp is the normalized Phase 1-compatible input path for the stored quad_02 S4 reference pair, while the original quad_02.inp remains preserved unsupported provenance. Core numeric aliases, DOF mapping, validation harness, model diagnostic context, the Phase 1 parser/domain subset, validation/singular diagnostics, DofManager/reaction foundation, minimum result model metadata, displacement CSV comparator foundation, MITC4 geometry/director scaffolding, MITC4 displacement/strain/tying row scaffolding, MITC4 material/transform/integration scaffolding, MITC4 stiffness/drilling/internal-force scaffolding, MITC4 patch/locking-sensitivity tests, full-space assembly, reduced projection, sparse-pattern scaffold, solver adapter injection, full-vector internal/reaction force state, active AnalysisModel construction, input-to-AnalysisState-to-U/RF result workflow, and the first stored Abaqus displacement regression have been revalidated. Full PRD Phase 1 completion still depends on the open architecture/reference gaps R-014, R-010, and R-013. The old phases/1-linear-static-mitc4 path is historical and superseded after the MITC4 formulation reset.

Completed Work

2026-05-05 - P1A-01 module scaffold and facade completed

Author: Codex

Changed files:

  • CMakeLists.txt
  • include/fesa/ModuleInfo.hpp
  • include/fesa/Analysis/Analysis.hpp
  • include/fesa/Assembly/Assembly.hpp
  • include/fesa/Boundary/Boundary.hpp
  • include/fesa/Core/Core.hpp
  • include/fesa/Element/Element.hpp
  • include/fesa/IO/IO.hpp
  • include/fesa/Load/Load.hpp
  • include/fesa/Math/Math.hpp
  • include/fesa/Material/Material.hpp
  • include/fesa/Property/Property.hpp
  • include/fesa/Results/Results.hpp
  • include/fesa/Util/Util.hpp
  • include/fesa/fesa.hpp
  • src/Analysis/Analysis.cpp
  • src/Assembly/Assembly.cpp
  • src/Boundary/Boundary.cpp
  • src/Core/Core.cpp
  • src/Element/Element.cpp
  • src/IO/IO.cpp
  • src/Load/Load.cpp
  • src/Math/Math.cpp
  • src/Material/Material.cpp
  • src/Property/Property.cpp
  • src/Results/Results.cpp
  • src/Util/Util.cpp
  • tests/test_main.cpp
  • phases/1-structure-alignment-refactor/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added architecture module scaffold headers and matching source directories for Analysis, Assembly, Boundary, Core, Element, IO, Load, Math, Material, Property, Results, and Util.
  • Added include/fesa/ModuleInfo.hpp to record the module list and stable umbrella facade header policy without changing solver behavior, and exposed it through the existing fesa/fesa.hpp umbrella.
  • Updated CMake to discover current and future src/**/*.cpp files under the module directories.
  • Added an include compatibility smoke test that includes all module headers before fesa/fesa.hpp and checks the module list plus existing DOF mapping still works.
  • No production symbols were moved from include/fesa/fesa.hpp in this step.

Verification:

  • First ran python scripts/validate_workspace.py after adding the smoke test; it failed as expected because fesa/Analysis/Analysis.hpp did not exist yet.
  • After adding the scaffold and CMake wiring, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1A-02 Core/Util extraction while preserving all public symbols and behavior.
  • Keep R-014 open until P1A-09 independently accepts the final architecture alignment.

2026-05-05 - P1A-00 architecture drift audit completed

Author: Codex

Changed files:

  • phases/1-structure-alignment-refactor/step0-architecture-map.md
  • phases/1-structure-alignment-refactor/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Confirmed the Phase 1 architecture drift: production code is concentrated in include/fesa/fesa.hpp, src/fesa.cpp only holds static assertions, and tests/test_main.cpp holds all Phase 1 tests.
  • Added a module-by-module migration map assigning current Phase 1 production symbol groups to Analysis, Assembly, Boundary, Core, Element, IO, Load, Math, Material, Property, Results, and Util.
  • Recorded behavior locks for the refactor: no parser-scope changes, no MITC4 formula changes, no numerical convention changes, no reference tolerance changes, no reduced-vector RF recovery, no Abaqus execution requirement, and no MKL/TBB/HDF5 dependency introduction.
  • Identified contract refinements that later steps should resolve carefully: AnalysisState belongs to Core in docs/ARCHITECTURE.md, the basic Material domain record is needed before IO extraction, and Node/Element record ownership should avoid a Core to element-kernel dependency cycle.
  • Marked P1A-00 completed and moved the active objective to P1A-01.

Verification:

  • Before writing the audit artifact, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.
  • After writing the audit artifact and status updates, phases/index.json and phases/1-structure-alignment-refactor/index.json parsed successfully, git diff --check passed, and python scripts/validate_workspace.py passed again.

Follow-up:

  • Continue with P1A-01 module scaffold and umbrella facade.
  • Keep R-014 open until the full structure-alignment refactor passes P1A-09.
  • Keep R-010 and R-013 visible; P1A-00 does not solve missing Abaqus reaction CSV or the three-reference PRD target.

2026-05-05 - Phase 1 structure-alignment refactor phase planned

Author: Codex

Changed files:

  • phases/index.json
  • phases/1-structure-alignment-refactor/index.json
  • phases/1-structure-alignment-refactor/step0.md
  • phases/1-structure-alignment-refactor/step1.md
  • phases/1-structure-alignment-refactor/step2.md
  • phases/1-structure-alignment-refactor/step3.md
  • phases/1-structure-alignment-refactor/step4.md
  • phases/1-structure-alignment-refactor/step5.md
  • phases/1-structure-alignment-refactor/step6.md
  • phases/1-structure-alignment-refactor/step7.md
  • phases/1-structure-alignment-refactor/step8.md
  • phases/1-structure-alignment-refactor/step9.md
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added a dedicated Phase 1 structure-alignment refactor phase to correct the architecture drift where production code is concentrated in include/fesa/fesa.hpp.
  • Decomposed the refactor into 10 Harness steps: audit, scaffold/facade, Core/Util plus Boundary/Load/Property extraction, Math/Solver extraction, IO parser extraction, Results/reference extraction, MITC4 geometry/strain extraction, MITC4 material/stiffness extraction, Assembly/Analysis extraction, and independent evaluator closeout.
  • Updated PLAN.md with R-014 and P1A-00 through P1A-09 so new agents can execute the refactor without private context.

Verification:

  • Parsed phases/index.json and phases/1-structure-alignment-refactor/index.json with PowerShell ConvertFrom-Json.
  • Verified all 10 structure-alignment step files contain the required sprint contract sections from docs/HARNESS_ENGINEERING.md.
  • python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Start with P1A-00 architecture drift audit.
  • Keep R-010 and R-013 visible; the structure refactor does not solve missing reaction CSV or the three-reference PRD target.

2026-05-04 - P1R-15 evaluator closeout completed

Author: Codex

Changed files:

  • phases/1-linear-static-mitc4-rebaseline/step15-evaluator-report.md
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • phases/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Performed the independent closeout review for the 1-linear-static-mitc4-rebaseline phase.
  • Recorded a PASS verdict for the rebaseline sprint sequence, with product-level Phase 1 reference gaps explicitly documented instead of silently approved.
  • Marked P1R-15 complete and marked the rebaseline phase complete in the phase registry.
  • Updated PLAN.md so the next work is closing R-010 and R-013 before claiming full PRD Phase 1 completion.

Verification:

  • python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • R-010 remains open: add Abaqus reaction-force CSV artifacts, preferably *_reactions.csv, or explicitly adopt internal equilibrium tests as the Phase 1 RF verification basis until Abaqus RF output is available.
  • R-013 remains open: add enough additional small Abaqus S4 reference cases for the PRD target of three stored references: one single-element case, one simple multi-element plate/shell case, and one curved shell benchmark.

2026-05-04 - P1R-14 stored reference regression completed

Author: Codex

Changed files:

  • tests/test_main.cpp
  • docs/VERIFICATION_PLAN.md
  • references/quad_02_notes.md
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added a fixture discovery test that keeps references/quad_02.inp as unsupported Abaqus/CAE provenance while verifying references/quad_02_phase1.inp is the accepted executable Phase 1 derivative.
  • Added the first automated stored Abaqus displacement regression: run quad_02_phase1.inp, extract FESA /results/steps/Step-1/frames/0/fieldOutputs/U, and compare against references/quad_02_displacements.csv by node id.
  • Used the documented tolerance for this reference pair: abs_tol = 1.0e-12, rel_tol = 1.0e-5, reference_scale = 1.0.
  • Updated verification/reference notes so quad_02_phase1 is no longer a future regression target; it is now active test coverage.

Verification:

  • python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.
  • Stored reference result: quad_02_phase1.inp displacement regression passed against quad_02_displacements.csv using the tolerance above.

Follow-up:

  • Continue with P1R-15 independent evaluator closeout.
  • R-013 remains open: Phase 1 still needs enough additional stored Abaqus S4 reference cases for the PRD target of three stored references: one single-element case, one simple multi-element plate/shell case, and one curved shell benchmark.
  • R-010 remains open: no quad_02_reactions.csv or other Abaqus reaction CSV exists yet, so RF remains verified by internal full-vector equilibrium.

2026-05-04 - P1R-13 linear static workflow completed

Author: Codex

Changed files:

  • include/fesa/fesa.hpp
  • tests/test_main.cpp
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added an explicit AnalysisModel value object for the active Phase 1 linear static step, including active element ids, boundary/load indices, shell section indices, and material keys.
  • Added buildLinearStaticAnalysisModel() and routed LinearStaticAnalysis through it before DOF mapping, assembly, solve, state update, and result writing.
  • Preserved the one-step Phase 1 execution boundary with a diagnostic for multiple parsed steps instead of silently executing them.
  • Added runLinearStaticInputString() so parser diagnostics, domain validation diagnostics, active model construction, solve, AnalysisState, and U/RF result writing are exercised as one workflow.
  • Extended the in-memory result model with element type metadata and ensured result writing uses the active model step name.
  • Added tests for active model activation without mutating Domain, multiple-step rejection, input-to-result U/RF schema readiness, full-vector reaction balance, and parse/validation error propagation through the workflow.

Verification:

  • First ran python scripts/validate_workspace.py after adding Step 13 tests; it failed as expected because AnalysisModel and input-string workflow APIs did not exist yet.
  • After implementation, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1R-14 stored-reference displacement regression using references/quad_02_phase1.inp and references/quad_02_displacements.csv.
  • Step 13 intentionally did not add nonlinear, dynamic, pressure, thermal, HDF5, multi-step execution, or stored Abaqus CSV regression behavior.

2026-05-04 - P1R-12 assembly sparse solver path completed

Author: Codex

Changed files:

  • include/fesa/fesa.hpp
  • tests/test_main.cpp
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added deterministic reduced sparse-pattern scaffolding from DofManager element equation connectivity, preserving int64 equation and nonzero counts for the future sparse/MKL path.
  • Added projectToReducedSystem() so constrained/free projection is a named assembly boundary instead of being embedded directly inside LinearStaticAnalysis.
  • Extended AssemblyResult to carry full-space stiffness, full external load, reduced sparse pattern, and diagnostics.
  • Reworked assembly to call the rebuilt MITC4 stiffness result path directly and preserve full-space K_full/F_full for reaction recovery.
  • Added solver injection to LinearStaticAnalysis so the deterministic Gaussian solver remains the default test adapter while future MKL-backed solvers stay behind the LinearSolver interface.
  • Added AnalysisState::f_internal_full and verified RF = Fint_full - Fext_full = K_full * U_full - F_full.
  • Added tests for deterministic sparse pattern ordering, reduced projection with known displacement, full-space assembly/load preservation, reduced residual satisfaction, solver adapter injection, and singular solver diagnostic propagation.

Verification:

  • First ran python scripts/validate_workspace.py after adding Step 12 tests; it failed as expected because reduced sparse pattern, projection, solver injection, and f_internal_full did not exist yet.
  • After implementation, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1R-13 linear static workflow revalidation from Phase 1 input through U and RF result fields.
  • Step 12 intentionally did not add MKL/TBB APIs, stored Abaqus reference comparison, pressure loads, or a production sparse matrix storage backend.

2026-05-04 - P1R-11 MITC4 patch and benchmark tests completed

Author: Codex

Changed files:

  • tests/test_main.cpp
  • docs/VERIFICATION_PLAN.md
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added reusable MITC4 test helpers for analytic displacement/rotation fields, local strain sampling through the tied strain-row path, and a one-element cantilever smoke model.
  • Added constant membrane patch tests that verify uniform local [eps11, eps22, gamma12] at all 2 x 2 x 2 samples and positive physical energy.
  • Added pure bending, pure transverse shear, and pure twist patch tests to exercise through-thickness bending behavior, MITC transverse shear tying, and bilinear twist/shear interpolation.
  • Added a drilling-sensitivity negative check proving membrane patch energy is not hidden by the artificial drilling scale when no drilling DOF participates.
  • Added a thin one-element cantilever strip test that verifies tip displacement grows materially as thickness decreases, providing early shear-locking sensitivity coverage before stored Abaqus reference regression.
  • Documented the Step 11 analytic patch layer and kept Scordelis-Lo as a deferred benchmark scaffold until pressure-load support and a stored curved-shell reference artifact are defined.

Verification:

  • python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1R-12 assembly, solver-adapter boundary, constrained solve, and full-vector RF recovery revalidation.
  • Step 11 intentionally did not execute Abaqus, add pressure loads, add stored CSV reference regression, or tune benchmark tolerances against Abaqus artifacts.

2026-05-04 - P1R-10 MITC4 stiffness and drilling completed

Author: Codex

Changed files:

  • include/fesa/fesa.hpp
  • tests/test_main.cpp
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added tests and implementation for MITC4 element stiffness accumulation using tied strain rows, transformed material matrices, and 2 x 2 x 2 integration samples.
  • Added a stiffness result API that exposes local physical stiffness, local drilling-stabilized stiffness, global stiffness, integration-point count, drilling reference diagonal, and drilling stiffness metadata.
  • Replaced the old default drilling scale with the documented drilling_stiffness_scale = 1.0e-3 and applied it to the minimum positive physical local stiffness diagonal before global transformation.
  • Added diagnostics for invalid drilling scale and missing positive drilling reference diagonal.
  • Added tests for stiffness symmetry, drilling scale sensitivity, rigid translation zero energy, documented drilling-only energy, and f_int_e = K_e u_e consistency.
  • Routed MITC4ElementKernel::stiffness through the rebuilt formulation path so later assembly uses the Step 7 through Step 10 MITC4 helpers.

Verification:

  • First ran python scripts/validate_workspace.py after adding Step 10 tests; it failed as expected because the MITC4 stiffness/drilling/internal-force APIs did not exist yet.
  • After implementation, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1R-11 MITC4 patch, locking-sensitivity, and benchmark tests.
  • Step 10 intentionally did not tune the drilling scale to a reference case, add stress/resultant output, introduce reduced integration/hourglass logic, or rebuild sparse/global assembly beyond routing the existing kernel to the new element formulation.

2026-05-04 - P1R-09 MITC4 material integration scaffolding completed

Author: Codex

Changed files:

  • include/fesa/fesa.hpp
  • tests/test_main.cpp
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added tests and implementation for the documented isotropic local plane-stress shell material matrix in strain order [eps11, eps22, eps33, gamma23, gamma13, gamma12], with sigma_33 = 0 and transverse shear correction kappa = 5/6.
  • Added material diagnostics for invalid elastic modulus, Poisson ratio, and shear correction factor.
  • Added 2 x 2 x 2 Gauss integration point infrastructure with unit weights and total natural-domain weight 8.
  • Added covariant-to-local strain transformation and D_convected = T^T D_hat T, including identity and flat-element energy-equivalence tests.
  • Added MITC4 material integration sample scaffolding that carries integration basis, tied strain rows, local material, strain transform, and convected material for the later stiffness rebuild.

Verification:

  • First ran python scripts/validate_workspace.py after adding Step 9 tests; it failed as expected because the MITC4 material/integration APIs did not exist yet.
  • After implementation, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1R-10 MITC4 stiffness/internal force rebuild, six-DOF local-to-global transform, and drilling stabilization.
  • The legacy MITC4ElementKernel::stiffness path still needs to be rebuilt against the Step 7 through Step 9 formulation helpers; Step 9 intentionally did not add reduced integration, hourglass logic, stress/result output recovery, or the final drilling stiffness policy.

2026-05-04 - P1R-08 MITC4 covariant strain tying completed

Author: Codex

Changed files:

  • include/fesa/fesa.hpp
  • tests/test_main.cpp
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added MITC4 tests for global rotation to local alpha, beta, gamma mapping and verified drilling gamma does not enter the physical director increment.
  • Added degenerated-continuum displacement interpolation tests at the midsurface and through-thickness points, including rotation-driven q_k = -V2_k alpha_k + V1_k beta_k behavior.
  • Added direct covariant strain-row finite-difference tests in the documented order [eps11, eps22, eps33, gamma23, gamma13, gamma12].
  • Added MITC tying tests proving FESA A/C signs for gamma13 and B/D signs for gamma23, and proving Gauss-point shear rows are interpolated from tying rows rather than using direct Gauss-point transverse shear.
  • Implemented reusable MITC4 displacement derivative, direct strain evaluation, direct strain-row, tied strain-row, and row-evaluation helpers for later material/integration and stiffness steps.

Verification:

  • First ran python scripts/validate_workspace.py after adding Step 8 tests; it failed as expected because the MITC4 displacement/strain/tying APIs did not exist yet.
  • After implementation, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1R-09 material matrix, transform, and 2 x 2 x 2 integration scaffolding.
  • The existing stiffness kernel still needs to be rebuilt against the new row APIs in steps 9 and 10; Step 8 intentionally did not integrate stiffness, add material transforms, or add S4R behavior.

2026-05-04 - P1R-07 MITC4 geometry and directors completed

Author: Codex

Changed files:

  • include/fesa/fesa.hpp
  • tests/test_main.cpp
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added MITC4 tests for shape-function derivatives, FESA/Abaqus S4 natural-coordinate node order, tying point labels A, B, C, and D, and edge-node mapping.
  • Added Phase 1 MITC4 geometry structures for natural points, tying points, center midsurface derivatives, center-normal director policy, nodal director frames, and integration-point local Cartesian bases.
  • Implemented the documented center director policy Vn = normalize(G1_c x G2_c), nodal V1 = normalize(EY x Vn) with deterministic fallback axes, and right-handed V2 = Vn x V1.
  • Added integration-basis construction from degenerated-continuum covariant basis vectors and diagnostics for invalid thickness, singular center normal, singular basis, and near-zero Jacobian.
  • Replaced the legacy computeLocalBasis() internals with the new center-director geometry policy while leaving stiffness/strain/drilling reimplementation to later steps.

Verification:

  • First ran python scripts/validate_workspace.py after adding Step 7 tests; it failed as expected because the MITC4 geometry/director API did not exist yet.
  • After implementation, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1R-08 degenerated-continuum displacement, covariant strain rows, and MITC shear tying.
  • The existing stiffness kernel still needs to be rebuilt against the new formulation in steps 8 through 10; Step 7 intentionally did not add stiffness, stress, strain, or S4R behavior.

2026-05-04 - P1R-06 results model and displacement CSV comparator completed

Author: Codex

Changed files:

  • include/fesa/fesa.hpp
  • tests/test_main.cpp
  • docs/RESULTS_SCHEMA.md
  • docs/VERIFICATION_PLAN.md
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added result model tests for Phase 1 root metadata, frame 0 metadata, and mandatory U/RF field labels, positions, entity type, and global basis.
  • Extended the in-memory result model with solver/schema metadata, linear-static frame metadata, nodal field metadata, and mandatory U/RF descriptions while keeping S, E, and SF optional.
  • Added string/stream-based Abaqus displacement CSV loading so tests can cover required headers, duplicate node labels, missing/non-numeric node labels, and nonnumeric component values without temporary files.
  • Strengthened displacement comparison so it matches by node id, verifies exact FESA U component labels and nodal/global metadata, rejects duplicate actual node ids, reports missing FESA nodes, and uses combined absolute/relative tolerances.

Verification:

  • First ran python scripts/validate_workspace.py after adding Step 6 tests; it failed as expected because the result metadata fields and string CSV loader did not exist yet.
  • After implementation, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1R-07 MITC4 geometry, node order, tying points, directors, and local bases.
  • Keep RF reference CSV availability open; current RF verification remains internal full-vector equilibrium until a stored *_reactions.csv artifact is provided.

2026-05-04 - P1R-05 DofManager and reaction foundation completed

Author: Codex

Changed files:

  • include/fesa/fesa.hpp
  • tests/test_main.cpp
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added DofManager tests for six-DOF global ordering, noncontiguous node-id stability, constrained/free partitioning, equation numbering, full-vector reduction/reconstruction, element sparse-connectivity inputs, and a full-system reaction recovery formula.
  • Extended DofManager with full DOF addresses, constrained full-index lists, full-vector reduction, element full-index connectivity, and element equation-id connectivity while keeping equation ids outside Node and Element.
  • Added recoverFullReaction(K_full, U_full, F_full) and routed LinearStaticAnalysis through it so reaction recovery remains a full-vector operation rather than a reduced-vector shortcut.
  • Updated assembly to consume element full DOF indices from DofManager, preserving DofManager ownership of sparse-pattern inputs.

Verification:

  • First ran python scripts/validate_workspace.py after adding tests; it failed as expected because the new DofManager/reaction APIs did not exist yet.
  • After implementing the DofManager and reaction-foundation APIs, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1R-06 results model and displacement CSV comparator foundation.
  • Keep RF reference CSV availability open; current RF verification remains internal full-vector equilibrium until a stored *_reactions.csv artifact is provided.

2026-05-04 - P1R-04 validation and singular diagnostics completed

Author: Codex

Changed files:

  • include/fesa/fesa.hpp
  • tests/test_main.cpp
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added negative validation tests for missing node/property/material references, missing shell-section/boundary/load sets, missing set members, non-positive shell thickness, invalid boundary/load DOFs, no active elements, no free DOFs, isolated free DOFs, and weak drilling DOF smoke coverage.
  • Strengthened validateDomain so it reports missing Nset node members, missing Elset element members, non-positive or non-finite shell thickness, invalid Abaqus DOF ranges, no-free-DOF states, free DOFs untouched by active element connectivity, and free drilling DOF weak-stabilization warnings.
  • Kept mesh quality diagnostics out of Phase 1; no aspect ratio, skew, warpage, or distortion diagnostics were added.
  • Added keyword context to solver size, solver singularity, and fallback no-free-DOF diagnostics.

Verification:

  • First ran python scripts/validate_workspace.py after adding tests; it failed as expected on the missing new diagnostics.
  • After implementing the validation diagnostics, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1R-05 DofManager and reaction-foundation revalidation.
  • Keep RF reference CSV availability open; current Phase 1 RF validation remains internal full-vector equilibrium until a stored *_reactions.csv artifact is provided.

2026-05-04 - P1R-03 parser/domain subset completed

Author: Codex

Changed files:

  • include/fesa/fesa.hpp
  • tests/test_main.cpp
  • docs/ABAQUS_INPUT_SUBSET.md
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added parser acceptance coverage for repeated explicit sets, generated *Nset and *Elset, D exponent numeric input, keyword-line continuation, and every Phase 1 structural input keyword.
  • Expanded unsupported-feature coverage for S4R, Part, Assembly, Instance, *Include, *Density, and NLGEOM=YES.
  • Added negative coverage for unsupported parameters and flags on otherwise supported keywords, unsupported shell-section data modes, malformed numeric fields, and invalid DOF fields with file, line, and keyword diagnostics.
  • Tightened the parser so supported keywords reject unknown parameters/flags, fixed-width data rows reject extra non-empty fields, generated sets require exactly first,last,increment, and keyword continuation lines are assembled before keyword parsing.
  • Clarified docs/ABAQUS_INPUT_SUBSET.md so the strict parameter and fixed-width data-row rules are explicit.

Verification:

  • First ran python scripts/validate_workspace.py after adding unsupported-parameter tests; it failed as expected because the parser still accepted supported keywords with unknown controls.
  • After implementing strict keyword-control rejection, validation passed.
  • Added keyword-continuation tests and first observed the expected failure; after implementing continuation handling, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1R-04 validation and singular diagnostic coverage.
  • Keep Part/Assembly/Instance, S4R, *Density, and NLGEOM=YES outside the Phase 1 parser until an ADR and parser contract intentionally broaden the subset.

2026-05-04 - P1R-02 core harness guardrails completed

Author: Codex

Changed files:

  • include/fesa/fesa.hpp
  • tests/test_main.cpp
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Strengthened C++ guardrail tests for centralized numeric aliases: Real, GlobalId, LocalIndex, EquationId, and SparseIndex.
  • Expanded DOF mapping coverage to prove all six shell DOFs round-trip with Abaqus DOF numbers 1..6, labels, and invalid DOF rejection.
  • Added compile-time type checks so the core aliases remain double and signed std::int64_t.
  • Added model-validation diagnostic context through a shared makeDiagnostic helper and populated source keywords for element, shell section, boundary, cload, analysis model, and missing target diagnostics.
  • Kept the existing CMake/CTest validation path as the real repository validation command.

Verification:

  • First ran python scripts/validate_workspace.py after adding tests; it failed as expected because model diagnostics did not yet populate source keywords.
  • After implementing the diagnostic guardrail, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1R-03 parser/domain subset revalidation.
  • Leave MITC4 stiffness and parser feature expansion to later dedicated steps.

2026-05-04 - P1R-01 quad_02 reference onboarding completed

Author: Codex

Changed files:

  • references/quad_02_phase1.inp
  • references/quad_02_notes.md
  • references/README.md
  • docs/ABAQUS_INPUT_SUBSET.md
  • docs/VERIFICATION_PLAN.md
  • tests/test_main.cpp
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Preserved references/quad_02.inp and references/quad_02_displacements.csv unchanged as the original Abaqus/CAE S4 reference provenance.
  • Added references/quad_02_phase1.inp, a normalized Phase 1-compatible derivative input that removes Part/Assembly/Instance, *Density, restart/output requests, and unsupported step metadata while preserving ids, connectivity, material, shell thickness, fixed boundary nodes, load node, and load magnitude.
  • Added references/quad_02_notes.md with provenance, compatibility, unit-system, result mapping, tolerance, and RF limitation notes.
  • Added tests proving the original quad_02.inp remains unsupported provenance, the normalized input parses into 121 nodes and 100 S4 elements, and quad_02_displacements.csv loads 121 node rows.
  • Updated reference and parser documentation so the normalized file is the accepted quad_02 path for future Phase 1 stored-reference regression.

Verification:

  • First ran python scripts/validate_workspace.py after adding tests; it failed as expected because quad_02_phase1.inp did not exist yet.
  • After adding the normalized input and documentation, python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Continue with P1R-02 core harness guardrails.
  • Keep RF verified by internal full-vector equilibrium until a *_reactions.csv artifact is provided.

2026-05-04 - P1R-00 rebaseline audit completed

Author: Codex

Changed files:

  • phases/1-linear-static-mitc4-rebaseline/step0-audit.md
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • PLAN.md
  • PROGRESS.md

Summary:

  • Audited the existing C++ Phase 1 implementation against the revised paper-based docs/MITC4_FORMULATION.md without changing production solver behavior.
  • Classified reusable scaffolding for revalidation: CMake/CTest validation, core aliases, DOF mapping, diagnostics, parser/domain skeleton, in-memory U/RF results, displacement CSV comparator, full-vector reaction recovery, and the linear static workflow.
  • Identified MITC4 conflicts requiring rebuild: averaged-edge local basis, 2D projected Jacobian, direct Cartesian-like shear row construction, membrane/bending/shear pre-integration, midsurface-only 2 x 2 integration, and old 1.0e-6 drilling stabilization.
  • Preserved the compatibility decision that quad_02.inp is an S4 reference artifact but still contains Part/Assembly/Instance and *Density, so Step 1 must choose a normalized-input or explicit parser-compatibility path.

Verification:

  • Inspected include/fesa/fesa.hpp, tests/test_main.cpp, current reference files, and active rebaseline phase contracts.
  • python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.

Follow-up:

  • Continue with P1R-01 reference onboarding.
  • Revalidate retained scaffolding in its assigned steps before treating it as Phase 1 evidence.

2026-05-04 - Phase 1 rebaseline steps redefined

Author: Codex

Changed files:

  • phases/index.json
  • phases/1-linear-static-mitc4-rebaseline/index.json
  • phases/1-linear-static-mitc4-rebaseline/step0.md
  • phases/1-linear-static-mitc4-rebaseline/step1.md
  • phases/1-linear-static-mitc4-rebaseline/step2.md
  • phases/1-linear-static-mitc4-rebaseline/step3.md
  • phases/1-linear-static-mitc4-rebaseline/step4.md
  • phases/1-linear-static-mitc4-rebaseline/step5.md
  • phases/1-linear-static-mitc4-rebaseline/step6.md
  • phases/1-linear-static-mitc4-rebaseline/step7.md
  • phases/1-linear-static-mitc4-rebaseline/step8.md
  • phases/1-linear-static-mitc4-rebaseline/step9.md
  • phases/1-linear-static-mitc4-rebaseline/step10.md
  • phases/1-linear-static-mitc4-rebaseline/step11.md
  • phases/1-linear-static-mitc4-rebaseline/step12.md
  • phases/1-linear-static-mitc4-rebaseline/step13.md
  • phases/1-linear-static-mitc4-rebaseline/step14.md
  • phases/1-linear-static-mitc4-rebaseline/step15.md
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added a new 16-step Phase 1 rebaseline phase that supersedes the old Phase 1 execution path while preserving the old phase as historical record.
  • Split the redo into audit, reference onboarding, core guardrails, parser/domain, validation diagnostics, DOF/reaction foundation, results/comparator, MITC4 geometry, MITC4 covariant strain tying, material/integration, stiffness/drilling, patch benchmarks, assembly, linear static workflow, stored-reference regression, and evaluator closeout.
  • Updated PLAN.md so new agents execute phases/1-linear-static-mitc4-rebaseline and treat the old 1-linear-static-mitc4 phase as blocked/superseded.
  • Kept unresolved decisions visible: quad_02 normalization versus explicit parser compatibility sprint, RF CSV availability, and the PRD target of three stored Phase 1 reference cases.

Verification:

  • Parsed phases/index.json and phases/1-linear-static-mitc4-rebaseline/index.json with PowerShell ConvertFrom-Json.
  • Verified all 16 rebaseline step files contain the required sprint contract sections from docs/HARNESS_ENGINEERING.md.
  • python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Start with python scripts/execute.py 1-linear-static-mitc4-rebaseline when ready.
  • Step 1 must resolve how to use quad_02 without silently expanding parser support.

2026-05-04 - MITC4 formulation reset from local papers

Author: Codex

Changed files:

  • docs/Paper/
  • docs/MITC4_FORMULATION.md
  • docs/ADR.md
  • docs/NUMERICAL_CONVENTIONS.md
  • docs/README.md
  • docs/ABAQUS_INPUT_SUBSET.md
  • docs/VERIFICATION_PLAN.md
  • references/quad_02.inp
  • references/quad_02_displacements.csv
  • PLAN.md
  • PROGRESS.md

Summary:

  • Read the local MITC4 paper set under docs/Paper/ and rewrote docs/MITC4_FORMULATION.md as the new Phase 1 formulation contract.
  • Replaced the earlier simplified baseline with degenerated-continuum geometry, convected covariant strain components, FESA/Abaqus S4 tying-point convention, MITC transverse shear interpolation, local/global six-DOF rotation transformation, 2 x 2 x 2 Gauss integration, and thesis-backed drilling stabilization using drilling_stiffness_scale = 1.0e-3.
  • Updated ADR-018, numerical conventions, and documentation readiness notes so the old 1.0e-6 averaged-edge baseline is no longer the active rule.
  • Recorded quad_02 as the new stored S4 reference pair while keeping its Part/Assembly/Instance and *Density features outside automatic Phase 1 parser acceptance.
  • Updated PLAN.md so the next work is a Phase 1 redo/rebaseline, not continuation of the old P1-15/P1-16 path.

Verification:

  • python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed.

Follow-up:

  • Draft new Phase 1 redo sprint contracts against the revised MITC4 formulation before modifying solver code.
  • Decide whether quad_02.inp should be normalized into the current parser subset or used to justify a dedicated Abaqus/CAE Part/Assembly/Instance parser sprint.
  • Decide whether Phase 1 RF gets Abaqus *_reactions.csv artifacts or remains verified by full-vector equilibrium tests.

2026-05-01 - P1-01 through P1-14 implementation pass

Author: Codex

Changed files:

  • CMakeLists.txt
  • include/fesa/fesa.hpp
  • src/fesa.cpp
  • tests/test_main.cpp
  • scripts/validate_workspace.py
  • README.md
  • docs/ADR.md
  • docs/MITC4_FORMULATION.md
  • PLAN.md
  • PROGRESS.md
  • phases/index.json
  • phases/1-linear-static-mitc4/index.json

Summary:

  • Added a CMake/CTest C++17 build and test harness, and updated scripts/validate_workspace.py to run CMake configure, build, and CTest directly.
  • Added core numeric aliases, DOF mapping, diagnostics, Domain entities, Abaqus Phase 1 parser, Domain validation, DofManager, dense test matrix, deterministic Gaussian solver, in-memory result model, displacement CSV loader/comparator, MITC4 baseline stiffness kernel, full-system assembly, and LinearStaticAnalysis.
  • Closed the Phase 1 MITC4 baseline decisions in docs/MITC4_FORMULATION.md: midside shear tying interpolation, averaged-edge local basis, 2x2 integration, drilling_stiffness_scale = 1.0e-6, and mandatory U/RF output scope.
  • Added ADR-017 for the CMake/CTest build harness and ADR-018 for the Phase 1 MITC4 baseline closure.
  • Added tests for parser acceptance/rejection, quad_01 unsupported provenance, validation diagnostics, DOF reconstruction, singular solve diagnostics, result fields, CSV loading/comparison, MITC4 shape/stiffness behavior, and end-to-end linear static RF recovery.
  • Marked phase steps P1-01 through P1-14 completed in phases/1-linear-static-mitc4/index.json.
  • Marked P1-15 blocked because no Phase 1-compatible Abaqus S4 reference case exists yet; P1-16 remains pending behind that blocker.

Verification:

  • python scripts/validate_workspace.py configured CMake, built fesa_core and fesa_tests, and ran CTest successfully.
  • CTest result: 1 test executable passed, covering 12 named in-repo test cases.

Follow-up:

  • Add at least one Phase 1-compatible Abaqus TYPE=S4 linear static input and matching *_displacements.csv.
  • Add or explicitly defer *_reactions.csv; current RF validation is by internal full-vector equilibrium/reaction tests.
  • After reference artifacts are added, unblock P1-15 and run stored-reference regression, then complete P1-16 evaluator closeout.

2026-05-01 - P1-00 Phase 1 sprint contracts generated

Author: Codex

Changed files:

  • phases/index.json
  • phases/1-linear-static-mitc4/index.json
  • phases/1-linear-static-mitc4/step0.md
  • phases/1-linear-static-mitc4/step1.md
  • phases/1-linear-static-mitc4/step2.md
  • phases/1-linear-static-mitc4/step3.md
  • phases/1-linear-static-mitc4/step4.md
  • phases/1-linear-static-mitc4/step5.md
  • phases/1-linear-static-mitc4/step6.md
  • phases/1-linear-static-mitc4/step7.md
  • phases/1-linear-static-mitc4/step8.md
  • phases/1-linear-static-mitc4/step9.md
  • phases/1-linear-static-mitc4/step10.md
  • phases/1-linear-static-mitc4/step11.md
  • phases/1-linear-static-mitc4/step12.md
  • phases/1-linear-static-mitc4/step13.md
  • phases/1-linear-static-mitc4/step14.md
  • phases/1-linear-static-mitc4/step15.md
  • PLAN.md
  • PROGRESS.md

Summary:

  • Converted Phase 1 milestones P1-01 through P1-16 into executable Harness step files under phases/1-linear-static-mitc4.
  • Added top-level and phase-level JSON indices using the zero-based scripts/execute.py convention.
  • Embedded sprint contracts in every step with objective, required reading, scope, allowed files, explicit non-goals, tests to write first, reference-artifact policy, acceptance command, evaluator checklist, and handoff requirements.
  • Kept readiness blockers visible, especially MITC4 formulation decisions, build-system selection, reference comparator tolerance, missing reaction CSV, and the need for Phase 1-compatible TYPE=S4 references.
  • Updated PLAN.md so new agents can find and execute the active phase files.

Verification:

  • Parsed phases/index.json and phases/1-linear-static-mitc4/index.json with PowerShell ConvertFrom-Json.
  • Verified the phase registry points to 1-linear-static-mitc4, all 16 steps are pending, step names are kebab-case, and every stepN.md file exists.
  • Verified every step file includes the required sprint contract sections from docs/HARNESS_ENGINEERING.md.
  • python scripts/validate_workspace.py exited successfully, but still reported no configured validation commands.

Follow-up:

  • Begin Phase 1 execution with python scripts/execute.py 1-linear-static-mitc4 after confirming readiness blockers are accepted, resolved, or intentionally deferred.

2026-05-01 - Phase 1 implementation master plan added

Author: Codex

Changed files:

  • PLAN.md
  • PROGRESS.md

Summary:

  • Expanded PLAN.md from a short implementation sequence into a Phase 1 master implementation plan.
  • Added Phase 1 Definition of Done, execution gates, milestone backlog P1-00 through P1-16, sprint contract rules, verification strategy, reference plan, and risk controls.
  • Kept implementation blocked behind readiness decisions for MITC4 formulation, build system, reference comparator, reaction verification, and Phase 1-compatible reference input.
  • Aligned the plan with the Planner -> Generator -> Evaluator harness in docs/HARNESS_ENGINEERING.md.

Verification:

  • Reviewed the plan against docs/PRD.md, docs/ARCHITECTURE.md, docs/HARNESS_ENGINEERING.md, docs/NUMERICAL_CONVENTIONS.md, docs/ABAQUS_INPUT_SUBSET.md, docs/VERIFICATION_PLAN.md, docs/RESULTS_SCHEMA.md, and docs/MITC4_FORMULATION.md.
  • python scripts/validate_workspace.py ran, but reported no configured validation commands.

Follow-up:

  • Convert P1 milestones into phases/ step files with sprint contract sections when the user asks for executable phase planning.

2026-05-01 - Planner/Generator/Evaluator harness structure added

Author: Codex

Changed files:

  • AGENTS.md
  • PLAN.md
  • PROGRESS.md
  • README.md
  • docs/README.md
  • docs/HARNESS_ENGINEERING.md
  • docs/MULTI_AGENT_RESEARCH_PLAN.md
  • .codex/agents/harness-sprint-planner.toml
  • .codex/agents/implementation-generator.toml
  • .codex/agents/harness-sprint-evaluator.toml
  • .codex/agents/phase-planner.toml
  • .codex/agents/harness-reviewer.toml
  • .codex/agents/test-strategy-reviewer.toml
  • .codex/skills/fesa-phase-planning/SKILL.md
  • .codex/skills/fesa-review/SKILL.md
  • .codex/skills/fesa-cpp-tdd/SKILL.md
  • plugins/fesa-commands/commands/phase-draft.md

Summary:

  • Added docs/HARNESS_ENGINEERING.md as the durable Planner -> Generator -> Evaluator contract for long-running FESA work.
  • Updated AGENTS.md so nontrivial solver, parser, result schema, reference comparator, MITC4, and phase execution work requires a sprint contract before implementation.
  • Added custom agents for sprint contract planning, contract-bound implementation, and independent sprint evaluation.
  • Updated existing planner/reviewer/test strategy guidance to enforce contract compliance, evaluator pass/fail review, TDD, and PLAN/PROGRESS handoff.

Verification:

  • .codex/agents/*.toml parsed successfully with Python tomllib.
  • Codex skill and plugin command frontmatter checks passed.
  • python scripts/validate_workspace.py ran, but reported no configured validation commands.

Follow-up:

  • When implementation planning begins, generate phase steps with sprint contract sections before assigning Generator work.

2026-05-01 - Abaqus reference CSV contract adopted

Author: Codex

Changed files:

  • AGENTS.md
  • README.md
  • PLAN.md
  • PROGRESS.md
  • docs/README.md
  • docs/PRD.md
  • docs/ARCHITECTURE.md
  • docs/ADR.md
  • docs/NUMERICAL_CONVENTIONS.md
  • docs/ABAQUS_INPUT_SUBSET.md
  • docs/VERIFICATION_PLAN.md
  • docs/RESULTS_SCHEMA.md
  • docs/MITC4_FORMULATION.md
  • docs/MULTI_AGENT_RESEARCH_PLAN.md
  • references/README.md
  • .codex/agents/*.toml
  • .codex/skills/*.md
  • plugins/fesa-commands/commands/*.md

Summary:

  • Accepted references/ as the project reference artifact root.
  • Documented the initial artifact pair references/quad_01.inp and references/quad_01_displacements.csv.
  • Adopted Abaqus-exported *_displacements.csv as the first automated displacement comparison format.
  • Mapped CSV columns Node Label, U-U1, U-U2, U-U3, UR-UR1, UR-UR2, UR-UR3 to FESA U components UX, UY, UZ, RX, RY, RZ.
  • Documented that quad_01.inp includes S4R, Part/Assembly/Instance, *Density, and NLGEOM=YES; it is stored reference provenance and a future compatibility target, not a Phase 1 parser acceptance expansion.

Verification:

  • Inspected quad_01_displacements.csv: 121 data rows and the required Abaqus displacement/rotation columns.
  • Parsed documentation and Codex extension metadata checks.
  • python scripts/validate_workspace.py ran, but reported no configured validation commands.

Follow-up:

  • Add or define reaction-force reference artifacts, preferably *_reactions.csv, or verify RF by equilibrium tests until Abaqus RF CSV is available.
  • Add at least one Phase 1-compatible TYPE=S4 reference input for the first MITC4 linear static implementation path.

2026-05-01 - FESA commands converted to repo plugin

Author: Codex

Changed files:

  • plugins/fesa-commands/.codex-plugin/plugin.json
  • plugins/fesa-commands/commands/*.md
  • .agents/plugins/marketplace.json
  • .codex/commands/*.md
  • .codex/hooks/pre_edit_policy.py
  • .codex/hooks/post_tool_use_policy.py
  • PLAN.md
  • PROGRESS.md

Summary:

  • Created the repo-local fesa-commands plugin and registered it in .agents/plugins/marketplace.json.
  • Moved the FESA command prompts from .codex/commands/ into plugins/fesa-commands/commands/.
  • Removed the old .codex/commands/*.md files so plugin commands are the single maintained location.
  • Updated hook policy scripts to watch plugin manifests, plugin commands, and marketplace registration files.
  • Resolved the prior .codex/commands discovery concern by converting the commands to plugin form.

Verification:

  • Parsed plugin manifests and .agents/plugins/marketplace.json with Python json.
  • Checked plugin command Markdown frontmatter.
  • Parsed .codex/config.toml and .codex/agents/*.toml with Python tomllib.
  • Parsed .codex/hooks.json with Python json.
  • python scripts/validate_workspace.py ran, but reported no configured validation commands.

Follow-up:

  • Confirm that the fesa-commands plugin appears in the active Codex plugin/command surface.

2026-05-01 - Project-local Codex extension pack added

Author: Codex

Changed files:

  • .codex/config.toml
  • .codex/hooks.json
  • .codex/agents/*.toml
  • .codex/commands/*.md
  • .codex/skills/*/SKILL.md
  • .codex/hooks/*.py
  • PLAN.md
  • PROGRESS.md

Summary:

  • Added focused project agents for reference artifact curation, numerical convention review, solver architecture, sparse solver design, HDF5 results schema, DOF/boundary conditions, C++ build planning, MITC4 implementation review, test strategy, and PLAN/PROGRESS auditing.
  • Added project command prompts for status, readiness, plan sync, reference checks, documentation guards, phase drafting, ADR work, benchmark onboarding, extension verification, and handoff.
  • Added project-local FESA skills and registered them through .codex/config.toml.
  • Added hooks for session startup context, pre-edit coordination reminders, post-edit validation reminders, and expanded destructive shell command blocking.

Verification:

  • Parsed .codex/config.toml and .codex/agents/*.toml with Python tomllib.
  • Parsed .codex/hooks.json with Python json.
  • Checked .codex/skills/*/SKILL.md and .codex/commands/*.md frontmatter.
  • Smoke-tested the new hook scripts with representative JSON payloads.
  • python scripts/validate_workspace.py ran, but reported no configured validation commands.

Follow-up:

  • Resolved later by converting .codex/commands/*.md into the fesa-commands repo plugin.
  • Confirm hook behavior in the actual Codex runtime on native Windows.

2026-05-01 - PLAN/PROGRESS coordination files added

Author: Codex

Changed files:

  • PLAN.md
  • PROGRESS.md
  • AGENTS.md
  • docs/README.md
  • docs/MULTI_AGENT_RESEARCH_PLAN.md
  • .codex/agents/phase-planner.toml
  • .codex/agents/harness-reviewer.toml

Summary:

  • Added PLAN.md as the shared forward-looking work plan for multi-agent coordination.
  • Added PROGRESS.md as the shared chronological progress, verification, blocker, and risk log.
  • Updated AGENTS.md so every new work session must read PROGRESS.md and PLAN.md before planning or editing.
  • Updated documentation index and Codex agent instructions so planning/review agents enforce PLAN/PROGRESS usage.

Verification:

  • .codex/agents/*.toml parsed successfully with Python tomllib.
  • python scripts/validate_workspace.py ran, but reported no configured validation commands.

2026-05-01 - Documentation coordination and multi-agent planning state

Author: Codex

Changed files:

  • AGENTS.md
  • README.md
  • docs/README.md
  • docs/PRD.md
  • docs/ARCHITECTURE.md
  • docs/ADR.md
  • docs/NUMERICAL_CONVENTIONS.md
  • docs/ABAQUS_INPUT_SUBSET.md
  • docs/VERIFICATION_PLAN.md
  • docs/RESULTS_SCHEMA.md
  • docs/MITC4_FORMULATION.md
  • docs/MULTI_AGENT_RESEARCH_PLAN.md
  • .codex/agents/*.toml

Summary:

  • Added docs/README.md as documentation index and implementation readiness gate.
  • Reinforced Phase 1 invariants across project docs.
  • Added readiness gates for numerical conventions, parser acceptance, reference onboarding, mandatory result outputs, and MITC4 pre-implementation decisions.
  • Updated Codex agent definitions so delegated agents read the current documentation set.
  • Root README.md now points to the FESA documentation entry point.

Verification:

  • .codex/agents/*.toml parsed successfully with Python tomllib.
  • python scripts/validate_workspace.py ran, but reported no configured validation commands.

Follow-up:

  • Keep PLAN.md and PROGRESS.md current for multi-agent coordination.

2026-04-22 - Technical dossier documents added

Author: Codex

Changed files:

  • docs/NUMERICAL_CONVENTIONS.md
  • docs/ABAQUS_INPUT_SUBSET.md
  • docs/VERIFICATION_PLAN.md
  • docs/RESULTS_SCHEMA.md
  • docs/MITC4_FORMULATION.md
  • AGENTS.md
  • docs/PRD.md
  • docs/ARCHITECTURE.md
  • docs/ADR.md
  • docs/MULTI_AGENT_RESEARCH_PLAN.md
  • .codex/agents/*.toml

Summary:

  • Captured user decisions: 6 DOF shell nodes, artificial drilling stiffness, Abaqus-style units and signs, constrained DOF elimination, full-vector reaction recovery, no Phase 1 mesh quality diagnostics, singular diagnostics required, double, int64 indexing, S4-to-MITC4 mapping, S4R deferral.
  • Added technical dossier documents for numerical conventions, Abaqus subset, verification, results schema, and MITC4 formulation.
  • Added ADRs for numerical baseline, boundary/reaction policy, drilling stabilization, S4/S4R policy, singular diagnostics, and technical dossier contracts.

Verification:

  • .codex/agents/*.toml parsed successfully with Python tomllib.
  • python scripts/validate_workspace.py ran, but reported no configured validation commands.

2026-04-21 - Initial architecture and agent setup

Author: Codex

Changed files:

  • docs/PRD.md
  • docs/ARCHITECTURE.md
  • docs/ADR.md
  • AGENTS.md
  • docs/MULTI_AGENT_RESEARCH_PLAN.md
  • .codex/agents/fem-literature-researcher.toml
  • .codex/agents/verification-benchmark-researcher.toml
  • .codex/agents/mitc4-formulation-researcher.toml
  • .codex/agents/abaqus-compatibility-researcher.toml

Summary:

  • Established solver architecture direction: runtime polymorphism, Strategy + Template Method, Factory + Registry, adapter boundaries, immutable Domain, mutable AnalysisState, DofManager ownership, step/frame/history results.
  • Created first research agents for FEM literature, verification benchmarks, MITC4 formulation, and Abaqus compatibility.

Verification:

  • .codex/agents/*.toml parsed successfully with Python tomllib.
  • python scripts/validate_workspace.py ran, but reported no configured validation commands.

Known Blockers

  • Phase 1 architecture is not yet accepted: production code is concentrated in include/fesa/fesa.hpp instead of the src/ module layout documented in docs/ARCHITECTURE.md.
  • No reaction-force reference artifact exists yet under references/.
  • The PRD target of three stored Phase 1 reference cases is not yet satisfied; only quad_02_phase1 is an active stored displacement regression.
  • The current initial quad_01.inp reference contains S4R, Part/Assembly/Instance, *Density, and NLGEOM=YES, so it is not a Phase 1 parser acceptance case as-is.

Current Risks

  • Implementation could start from the quad_01 reference input without accounting for its unsupported Abaqus features.
  • Implementation could treat the old MITC4 kernel as authoritative even though it conflicts with the revised formulation contract.
  • Future work could accidentally parse the original quad_02.inp instead of the normalized quad_02_phase1.inp before parser compatibility is explicitly expanded.
  • Reaction output may be wrong if full-space stiffness/load data is not preserved or reconstructed.
  • Large-model support may be weakened if any module narrows ids or sparse indices below int64.
  • The structure-alignment refactor could accidentally change solver behavior unless each step preserves characterization tests and quad_02_phase1 regression coverage.
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