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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.
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
SOC 職業分類に基づく
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.
| name | skill-scenario-gallery |
| description | 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. |
Every simulation is defined by a .c / .txt file pair in SETS/.
The .c file contains setup callbacks; the .txt file contains model parameters.
| File | Description | Key features |
|---|---|---|
RiftingBasic.c | Lithosphere-scale extension with crustal and mantle layers | Weak seed zone for strain localisation |
RiftingChenin.c | Rheologically controlled rifting | Imposed topography perturbation, multi-layer lithosphere |
RiftingRoman.c | Rifting with mantle diapirism | Perturbed Moho geometry, noise filtering |
RiftingMelting.c | Extension with partial melting | Lower-crust and decompression mantle melting |
RiftingAnisotropy.c | Rifting with crystal anisotropy | Olivine/OPX fabric evolution during extension |
RiftingCheninAniso.c | Combined topography perturbation + anisotropy | Full aniso rifting workflow |
RiftingCombinedYield.c | Rifting with combined mode-I/mode-II yield + melting | plast=2, 9 phases, VEP + melt weakening (Popov 2025) |
RiftingComprehensive.c | All-physics rifting for benchmarking | Combined yield + melting + anisotropy + GSE, 9 phases, 4 resolution tiers (lowres/default/medres/highres) |
When to use: Start with RiftingBasic for a first lithospheric extension run. Use RiftingChenin for multi-layer setups. Add RiftingAnisotropy or RiftingCheninAniso to study fabric effects on rifting. Use RiftingCombinedYield for combined tensile+shear failure with melting. Use RiftingComprehensive for performance benchmarking — it exercises all subsystems (thermal, advection, melting, anisotropy, GSE) and has pre-defined resolution tiers.
| File | Description | Key features |
|---|---|---|
AnneloreSubduction.c | Plunging lithospheric slab | Crustal/mantle structure, thermal evolution |
DoubleSubduction.c | Two-sided subduction | Dual oceanic plates, polar/Cartesian geometry |
SubductionMelting.c | Subduction with fluid-released melting | Slab-edge rheological weakening |
SubductionBenchmarkCase2.c | Benchmark subduction | Comparison with analytical solutions |
ThanushikaSubduction.c | Simplified subduction | Solver performance testing |
OceanicCooling.c | Plate cooling away from ridge | Thermal half-space model |
ThermalStructureSubduction.c | Thermal tracking of slab | Mantle/crust temperature transitions |
When to use: SubductionBenchmarkCase2 for validation. AnneloreSubduction for realistic slab geometry. SubductionMelting when fluid/melt coupling matters.
| File | Description | Key features |
|---|---|---|
CollisionZone.c | Symmetric continental collision | Two cratons + oceanic basin |
CollisionIra.c | Asymmetric collision | West-central-east lithosphere configuration |
CollisionPolarCartesian.c | Collision in polar coordinates | Curved Earth-like geometry |
CollisionPolarCartesianAniso.c | Polar collision + anisotropy | Fabric tracking in curved geometry |
CollisionAnisotropy.c | Shortening with crystal anisotropy | Mountain building + fabric evolution |
When to use: CollisionZone for basic orogenesis. Add CollisionAnisotropy for fabric-controlled deformation during convergence.
| File | Description | Key features |
|---|---|---|
ShearTemplate.c | Simple shear with circular inclusion | Viscosity contrast testing |
ShearTemplateAniso.c | Simple shear + anisotropic viscosity | Director evolution in shear |
ShearBoxLaeti.c | Shear box with pre-stress | Weak inclusion, loading conditions |
SimpleShearAnisoHomo.c | Homogeneous simple shear | Anisotropic deformation law testing |
ShearInclusionAniso.c | Weak ellipse in shear flow | Anisotropy development around inclusion |
ShearHeatingDuretz14.c | Shear heating benchmark | Viscous dissipation (Duretz et al. 2014) |
CrustalShearBandingAnisotropy.c | Crustal shear zone with mica layers | Elliptical weak inclusions promoting strain bands |
StrainLocalization_SH_GSE.c | Shear heating + grain size evolution | Coupled localisation mechanisms |
When to use: ShearTemplate as a starting point for shear experiments. ShearHeatingDuretz14 for thermal-mechanical coupling. CrustalShearBandingAnisotropy for crustal fabric studies.
| File | Description | Key features |
|---|---|---|
AnisotropyDabrowski.c | Analytical benchmark: flow around inclusion | Dani Schmid solution, pure/simple shear |
AnisotropyLayer.c | Layered anisotropic material | Fabric tracking verification |
AnisoHomoVEVP.c | Homogeneous VEVP + anisotropy | Full rheology coupling test |
AnisoVEVP.c | VEVP deformation + anisotropy | Parallel variant |
AnisoViscTest_Ellipses.c | 299 elliptical weak inclusions | Stress/strain field testing |
AnisoViscTest_HomoRandomAngle.c | Random director orientation field | Statistical anisotropy |
AnisoViscTest_evolv.c | Anisotropy evolution in pure shear | Time-dependent fabric growth |
AnisoViscTest_MWE.c | Minimal working example (46 ellipses) | Quick debugging/verification |
AnisoViscTest_Debug.c | Debug configuration | Solver diagnostics |
TestAnisotropy.c | General test suite (269 elements) | Comprehensive aniso testing |
WedgeAnisotropy.c | Subduction wedge + anisotropy | Mica-dominated fabric |
When to use: AnisotropyDabrowski for code validation against analytics. AnisoViscTest_MWE for fast debugging. AnisoViscTest_evolv for fabric evolution studies. WedgeAnisotropy for subduction-related fabric.
| File | Description | Key features |
|---|---|---|
NeckingRoman.c | Lithospheric necking | Perturbation-driven localisation |
NeckingReview.c | Systematic necking study | High-resolution strain rate tracking |
PinchSwellGSE.c | Pinch-and-swell instability | Grain size evolution |
FaultSmearing.c | Fault initiation and smearing | Plastic strain accumulation |
Shrinking.c | Shrinking viscous inclusion | Negative buoyancy test |
Shrinking_New.c | Updated shrinking inclusion | Revised parameters |
When to use: NeckingRoman for rift necking studies. PinchSwellGSE when grain size evolution controls folding.
| File | Description | Key features |
|---|---|---|
ViscousInclusion.c | Weak circular inclusion in matrix | Analytical benchmark |
ViscousInclusionTestSuite.c | Extended inclusion tests | Multiple configurations |
ViscousSinker.c | Buoyant sphere / Stokes sinker | Convection benchmark |
MLPS_Ellipses.c | Multilayer passive sink ellipses | Multilayer particle structure |
Multilayers.c | Passive multilayer contrasts | No anisotropy |
Anais2Shrink.c | Layered anisotropic + shrinking | Combined test |
Anais2Shrink_preload.c | Pre-loaded aniso shrinking | Pre-stress variant |
AnaisReference.c | Reference anisotropic layers | Baseline comparison |
When to use: ViscousInclusion and ViscousSinker for fundamental Stokes solver validation.
| File | Description | Key features |
|---|---|---|
ThermalDiffusion.c | Pure heat diffusion | Homogeneous medium |
ThermoElastic.c | Thermo-elastic coupling | Temperature-dependent stiffness |
CoolingChamber.c | Lithospheric cooling chamber | Magma chamber analogue |
TCMagmaticSystem.c | Thermo-chemical magmatic evolution | Multi-process, plast=2, melting, dike injection |
MeltingOverpressure.c | Melting-induced overpressure | Magma chamber pressurisation |
BlankenBench.c | Blankenbach Case 1a convection | Ra=10⁴, isoviscous, free-slip, thermal benchmark |
When to use: ThermalDiffusion to verify thermal solver. BlankenBench for thermal convection benchmark (Boussinesq coupling). TCMagmaticSystem for coupled magmatic studies.
| File | Description | Key features |
|---|---|---|
PressurizedMagmaChamber.c | Pressurised circular chamber | Deformation around intrusion, plast=2, T_st |
ChristmasTree.c | Complex dike geometry | Multi-branch intrusion |
ChemicalDiffusion.c | Chemical element transport | Diffusion-driven |
ChemicalProduction.c | In-situ phase production | Metamorphic reaction tracking |
When to use: PressurizedMagmaChamber for studying deformation driven by magmatic overpressure.
| File | Description | Key features |
|---|---|---|
QuartzCoesite.c | Quartz → coesite transition | Phase diagram coupling |
QuartzCoesite_Simple.c | Simplified variant | Reduced complexity |
QuartzCoesite_paper.c | Paper variant | Resolutions: 100, 150, 200 |
CrystallisationStuewe1995.c | Crystallisation kinetics | Stüwe (1995) framework |
When to use: QuartzCoesite to test phase transition coupling. CrystallisationStuewe1995 for metamorphic reaction kinetics.
| File | Description | Key features |
|---|---|---|
FreeSurfaceBenchmarkFEM.c | Free surface evolution benchmark | Initial perturbation decay |
TopoBenchCase1.c | Topographic benchmark | Cosine perturbation |
ElasticFlexureLineLoad.c | Elastic plate flexure | Line load on plate |
StressBC_FreeSurf.c | Free surface + stress BCs | Combined boundary types |
When to use: TopoBenchCase1 for free surface validation. ElasticFlexureLineLoad for flexure studies.
| File | Description | Key features |
|---|---|---|
VEP_Duretz18.c | Visco-elasto-plastic benchmark | Duretz et al. (2018) |
Popov2025_Pureshear_VEVP.c | Pure shear VEVP test | Combined mode-I/mode-II yield benchmark (plast=2) |
Popov2025_Tensile_VEVP.c | Tensile/necking VEVP test | Tensile failure with plast=2, T_st |
PlasticityLayers.c | Plasticity in layered systems | Layer-controlled localisation |
StressBC_ShearTemplate.c | Shear with stress BCs | Non-velocity-driven loading |
When to use: VEP_Duretz18 for standard VEP benchmarking. Popov2025_Pureshear_VEVP and Popov2025_Tensile_VEVP for testing/validating the combined mode-I/mode-II yield function (plast=2).
| File | Description | Key features |
|---|---|---|
RiverTom.c | Large-scale lithospheric model | Regional study |
RiverTomLowerCrust.c | Lower crustal rheology variant | Focus on deep crust |
| Goal | Start with |
|---|---|
| First simulation ever | ViscousInclusion.c (simple, has analytical solution) |
| Basic rifting | RiftingBasic.c |
| Anisotropy introduction | AnisoViscTest_MWE.c (fast) or AnisotropyDabrowski.c (validated) |
| Full-featured rifting | RiftingCheninAniso.c |
| Subduction | SubductionBenchmarkCase2.c |
| Solver verification | ViscousSinker.c or TopoBenchCase1.c |
| Thermal solver only | ThermalDiffusion.c |
| Thermal convection benchmark | BlankenBench.c |
| VEP rheology testing | VEP_Duretz18.c |
| Combined yield (plast=2) | Popov2025_Pureshear_VEVP.c or Popov2025_Tensile_VEVP.c |
| Rifting + melting + combined yield | RiftingCombinedYield.c |
| Melting + melt weakening | RiftingMelting.c |
