Merge pull request #850 from baagaard-usgs/add-test-poroelasticity-fault

Add full-scale test for poroelasticity and prescribed fault slip

Author: baagaard-usgs

CHANGES.md

@@ -17,16 +17,18 @@ The version numbers are in the form `MAJOR.MINOR.PATCH`, where major releases in
   * Update PETSc to 3.23.1
 * **Added**
   * Improved documentation for `pylith_eqinfo` and illustrate use in `examples/strikdslip-2d`, `examples/crustal-strikeslip-2d`, and `examples/crustal-strikeslip-3d`.
-  * Add `pylith_convertmesh` for converting Cubit and Gmsh files to the PETSc HDF5 mesh format.
-  * Add support for specifying boundary conditions using marked boundaries rather than vertices.
+  * Added `pylith_convertmesh` for converting Cubit and Gmsh files to the PETSc HDF5 mesh format.
+  * Added support for specifying boundary conditions using marked boundaries rather than vertices.
     * `MeshIOAscii`: Use `face-group` for specifying boundary conditions via cell and `face` vertices.
     * `MeshIOCubit`: Read sidesets from ExodusII files (generated by Cubit).
     * `MeshIOPetsc`
       * `Gmsh`: Create physical groups only at the dimension of the boundary.
-      * Add compatibility for reading PETSc HDF5 format
+      * Added compatibility for reading PETSc HDF5 format
+  * Improved the organization of the governing equations section and added documentation for poroelasticity with prescribed fault slip, including governing equations and default PETSc solver settings. Also added a full-scale test.
 * **Fixed**
   * Account for processes without cells in initial condition patch when verifying configuration.
   * Avoid divide by zero for `KinSrcRamp` when final slip is zero.
+  * Remove `solid_bulk_modulus` as a spatial database field for poroelasticity; compute it from the other fields.
   * Fix pythia import in `pylith_eqinfo`.
 
 ## Version 4.2.0 (2025-01-15)

configure.ac

@@ -266,6 +266,7 @@ AC_CONFIG_FILES([Makefile
 		tests/fullscale/viscoelasticity/nofaults-2d/Makefile
 		tests/fullscale/viscoelasticity/nofaults-3d/Makefile
 		tests/fullscale/poroelasticity/Makefile
+		tests/fullscale/poroelasticity/faults-2d/Makefile
 		tests/fullscale/poroelasticity/terzaghi/Makefile
 		tests/fullscale/poroelasticity/mandel/Makefile
 		tests/fullscale/poroelasticity/cryer/Makefile

docs/Makefile.am

@@ -594,28 +594,38 @@ dist_noinst_DATA = \
 	user/file-formats/meshio-ascii.md \
 	user/file-formats/points-list.md \
 	user/glossary/index.md \
-	user/governingeqns/elasticity-derivation.md \
-	user/governingeqns/elasticity-infstrain-prescribedslip/dynamic.md \
-	user/governingeqns/elasticity-infstrain-prescribedslip/index.md \
-	user/governingeqns/elasticity-infstrain-prescribedslip/quasistatic.md \
-	user/governingeqns/elasticity-infstrain/dynamic.md \
-	user/governingeqns/elasticity-infstrain/index.md \
-	user/governingeqns/elasticity-infstrain/quasistatic.md \
-	user/governingeqns/elasticity-infstrain/bulk-rheologies/index.md \
-	user/governingeqns/elasticity-infstrain/bulk-rheologies/elasticity-constitutive.md \
-	user/governingeqns/elasticity-infstrain/bulk-rheologies/effective-stress.md \
-	user/governingeqns/elasticity-infstrain/bulk-rheologies/linear-elastic.md \
-	user/governingeqns/elasticity-infstrain/bulk-rheologies/linear-genmaxwell.md \
-	user/governingeqns/elasticity-infstrain/bulk-rheologies/linear-maxwell.md \
-	user/governingeqns/elasticity-infstrain/bulk-rheologies/powerlaw.md \
-	user/governingeqns/elasticity-infstrain/bulk-rheologies/figs/viscoelastic-schematic.pdf \
-	user/governingeqns/elasticity-infstrain/bulk-rheologies/figs/viscoelastic-schematic.svg \
-	user/governingeqns/incompressible-elasticity.md \
 	user/governingeqns/index.md \
 	user/governingeqns/petsc-formulation.md \
-	user/governingeqns/poroelasticity/dynamic.md \
+	user/governingeqns/elasticity/index.md \
+	user/governingeqns/elasticity/derivation.md \
+	user/governingeqns/elasticity/infinitesimal-strain.md \
+	user/governingeqns/elasticity/infinitesimal-strain-quasistatic.md \
+	user/governingeqns/elasticity/infinitesimal-strain-dynamic.md \
+	user/governingeqns/elasticity/prescribed-slip.md \
+	user/governingeqns/elasticity/prescribed-slip-quasistatic.md \
+	user/governingeqns/elasticity/prescribed-slip-dynamic.md \
+	user/governingeqns/elasticity/bulk-rheologies/index.md \
+	user/governingeqns/elasticity/bulk-rheologies/elasticity-constitutive.md \
+	user/governingeqns/elasticity/bulk-rheologies/effective-stress.md \
+	user/governingeqns/elasticity/bulk-rheologies/linear-elastic.md \
+	user/governingeqns/elasticity/bulk-rheologies/linear-genmaxwell.md \
+	user/governingeqns/elasticity/bulk-rheologies/linear-maxwell.md \
+	user/governingeqns/elasticity/bulk-rheologies/powerlaw.md \
+	user/governingeqns/elasticity/bulk-rheologies/figs/viscoelastic-schematic.pdf \
+	user/governingeqns/elasticity/bulk-rheologies/figs/viscoelastic-schematic.svg \
+	user/governingeqns/incompressible-elasticity/index.md \
+	user/governingeqns/incompressible-elasticity/infinitesimal-strain.md \
+	user/governingeqns/incompressible-elasticity/infinitesimal-strain-quasistatic.md \
+	user/governingeqns/incompressible-elasticity/bulk-rheologies/index.md \
+	user/governingeqns/incompressible-elasticity/bulk-rheologies/linear-elastic.md \
 	user/governingeqns/poroelasticity/index.md \
-	user/governingeqns/poroelasticity/quasistatic.md \
+	user/governingeqns/poroelasticity/infinitesimal-strain.md \
+	user/governingeqns/poroelasticity/infinitesimal-strain-quasistatic.md \
+	user/governingeqns/poroelasticity/infinitesimal-strain-dynamic.md \
+	user/governingeqns/poroelasticity/prescribed-slip.md \
+	user/governingeqns/poroelasticity/prescribed-slip-quasistatic.md \
+	user/governingeqns/poroelasticity/bulk-rheologies/index.md \
+	user/governingeqns/poroelasticity/bulk-rheologies/linear-elastic.md \
 	user/index.md \
 	user/install/figs/install_choices.pdf \
 	user/install/figs/install_choices.svg \

docs/developer/ides/vs-code.md

@@ -20,6 +20,9 @@ If you are working in VS Code with local source code, then we recommend setting
 | `PROJ_INCDIR`        | Directory containing Proj header files [^vscode]        |
 | `CATCH_INCDIR`       | Directory containing Catch2 header files [^vscode]      |
 
+[^vscode]: Used in VS Code tasks.
+
+
 ## Starting VS Code
 
 If you have PyLith source code on your local machine, then it is best to start VS Code from a terminal in which you have activated the PyLith virtual environment.