MDOODZ7.0

MDOODZ mechanical anisotropy module — director-based fabric tracking, anisotropy factors (δ_n, δ_s), viscous transverse isotropy, ViscosityConciseAniso, finite strain evolution, anisotropic rifting methodology, and anisotropy scenario examples.

MDOODZ performance benchmarking — running benchmarks, interpreting perf.csv, grid scaling studies, thread scaling, comparing machines, and the benchmark.sh script.

Build, compile, and run MDOODZ simulations — CMake configuration, make targets (build, build-dev, run, clean), dependency installation (SuiteSparse, HDF5, BLAS/LAPACK), OpenMP parallelisation, env.cmake setup, and common troubleshooting.

Code-to-physics glossary for MDOODZ — variable names, struct fields, function names mapped to physical meaning, equations, SI units, grid naming conventions, creep mechanism abbreviations, and solver process stages.

Debugging a failing MDOODZ model — the three failure families (CHOLMOD non-positive-definite, Powell-Hestenes non-convergence, first-iteration NaN), the error-string lookup table, the eta-contrast reality, the two anisotropy recipes, the single-variable bisection cookbook, and the known MDLIB anisotropy bugs with their fix commits. Use when a run crashes, won't factor, won't converge, NaNs, or stalls mid-production.

MDOODZ logging system — LOG_INFO/WARN/ERR/DBG/TIME macros, .txt configuration parameters (log_dest, log_level, log_timestamp, log_ts_mode, log_metadata), colored console output, ANSI-stripped log files, phase timing instrumentation, and metadata prefixes.

MDOODZ partial melting module — melt model indices, solidus/liquidus parameterizations, melt fraction computation, melt weakening, per-phase melt configuration, kinetic relaxation, and melting scenario examples.

Create and configure MDOODZ simulations — .c callback files, .txt parameter files, SetPhase, SetTemperature, SetGrainSize, SetSurfaceZCoord, boundary conditions, MdoodzSetup, Coordinates, POSITION enum, geometry helpers, and scenario authoring workflow.

Validate MDOODZ .txt parameter files — check scaling ranges, domain/resolution bounds, per-phase material property limits, flow law index consistency, switch compatibility, Courant/CFL constraints, solver tolerances, and anisotropy settings against physical limits.

MDOODZ particle reseeding and recycling — reseeding modes 0/1, particle deactivation (excess culling), recycling mechanism, markers struct fields, min_part_cell threshold, Nb_part_max hard limit, and common failure modes.

MDOODZ governing equations and numerical methods — conservation of momentum (Stokes), energy, and mass, constitutive relations, non-dimensionalisation and scaling, marker-in-cell advection, free surface algorithm, pure shear ALE mode, and theoretical background.

MDOODZ rheological framework — flow laws, viscosity computation, dislocation creep, diffusion creep, Peierls mechanism, grain boundary sliding, elasticity (Maxwell model), plasticity (Drucker-Prager, strain softening), material properties, and the mat_prop structure.

Catalogue of 79 predefined MDOODZ scenarios in SETS/ — grouped by geodynamic application (rifting, subduction, collision, shear zones, anisotropy, necking, viscous flow, thermal, magmatic, phase transitions, topography, benchmarks). Each entry lists the .c file, purpose, and recommended use.

MDOODZ numerical solver architecture — Stokes solver, Newton-Raphson iteration, Picard iteration, convergence criteria, staggered grid, thermal solver, SuiteSparse/CHOLMOD direct solver, time stepping, penalty method, and troubleshooting convergence issues.

Benchmark the MDOODZ Stokes solver on a hard-solve state — build a shear-band checkpoint with a warmup run, restart from the .dat file, and sweep thread counts / interp_mode to measure solve_s under realistic high-viscosity-contrast conditions. Use when the user wants to measure solver cost (not wall time dominated by advection/interp) or compare optimizations (recycled factorization, CHOLMOD threading, Krylov, etc).

Visualising MDOODZ results — HDF5 output structure, Julia/Makie plotting scripts, field names, overlay options (contours, director, velocity vectors, principal stress), multi-panel layouts, marker trajectory analysis, batch PNG/video export.

MDOODZ rheological framework — flow laws, viscosity computation, dislocation creep, diffusion creep, Peierls mechanism, grain boundary sliding, elasticity (Maxwell model), plasticity (Drucker-Prager, strain softening), material properties, and the mat_prop structure.

Visualising MDOODZ results — HDF5 output structure, Julia/Makie plotting scripts, field names, overlay options (contours, director, velocity vectors, principal stress), multi-panel layouts, marker trajectory analysis, batch PNG/video export.