Merge pull request #846 from baagaard-usgs/fix-boundary-integration-overlap-all

Fix boundary integration overlap, parallel output of refined mesh, and a few other small fixes

Author: baagaard-usgs

configure.ac

@@ -114,7 +114,7 @@ AC_CHECK_HEADER([mpi.h], [], [AC_MSG_ERROR([header 'mpi.h' not found])])
 
 dnl PETSC
 AC_LANG(C)
-CIT_PATH_PETSC([3.23.2])
+CIT_PATH_PETSC([3.23.4])
 CIT_HEADER_PETSC
 CIT_CHECK_LIB_PETSC
 

docs/user/components/materials/Elasticity.md

@@ -31,7 +31,7 @@ Implements `Material`.
 * `description`=\<str\>: Descriptive label for material (deprecated in v5.0; will be removed in v6.0).
   - **default value**: ''
   - **current value**: '', from {default}
-  - **validator**: <function validateDescription at 0x10608f2e0>
+  - **validator**: <function validateDescription at 0x10480b2e0>
 * `label`=\<str\>: Name of label for material. Currently only 'material-id' is allowed.
   - **default value**: 'material-id'
   - **current value**: 'material-id', from {default}
@@ -50,7 +50,6 @@ Example of setting `Elasticity` Pyre properties and facilities in a parameter fi
 :::{code-block} cfg
 [pylithapp.problem.materials.mat_elastic]
 label_value = 4
-description = Upper crust elastic material
 use_body_force = False
 bulk_rheology = pylith.materials.IsotropicLinearElasticity
 

docs/user/components/materials/IncompressibleElasticity.md

@@ -31,7 +31,7 @@ Implements `Material`.
 * `description`=\<str\>: Descriptive label for material (deprecated in v5.0; will be removed in v6.0).
   - **default value**: ''
   - **current value**: '', from {default}
-  - **validator**: <function validateDescription at 0x10608f2e0>
+  - **validator**: <function validateDescription at 0x10480b2e0>
 * `label`=\<str\>: Name of label for material. Currently only 'material-id' is allowed.
   - **default value**: 'material-id'
   - **current value**: 'material-id', from {default}
@@ -49,7 +49,6 @@ Example of setting `IncompressibleElasticity` Pyre properties and facilities in
 
 :::{code-block} cfg
 [pylithapp.problem.materials.mat_incompelastic]
-description = Upper crust incompressible elastic material
 label_value = 3
 use_body_force = True
 bulk_rheology = pylith.materials.IsotropicLinearIncompElasticity

docs/user/components/materials/Poroelasticity.md

@@ -31,7 +31,7 @@ Implements `Material`.
 * `description`=\<str\>: Descriptive label for material (deprecated in v5.0; will be removed in v6.0).
   - **default value**: ''
   - **current value**: '', from {default}
-  - **validator**: <function validateDescription at 0x10608f2e0>
+  - **validator**: <function validateDescription at 0x10480b2e0>
 * `label`=\<str\>: Name of label for material. Currently only 'material-id' is allowed.
   - **default value**: 'material-id'
   - **current value**: 'material-id', from {default}
@@ -55,7 +55,6 @@ Example of setting `Poroelasticity` Pyre properties and facilities in a paramete
 
 :::{code-block} cfg
 [pylithapp.problem.materials.mat_poroelastic]
-description = Upper crust poroelastic material
 label_value = 3
 use_body_force = True
 use_source_density = False

docs/user/components/meshio/MeshIOPetsc.md

@@ -24,7 +24,7 @@ Implements `MeshIOObj`.
 * `filename`=\<str\>: Name of mesh file for reading with PETSc.
   - **default value**: ''
   - **current value**: '', from {default}
-* `gmsh_mark_vertices`=\<bool\>: Gmsh file marks faces, edges, and vertices rather than just faces.
+* `gmsh_mark_recursive`=\<bool\>: Gmsh file marks faces, edges, and vertices rather than just faces (3D) or edges (2D).
   - **default value**: False
   - **current value**: False, from {default}
 * `options_prefix`=\<str\>: Name of PETSc options prefix for this mesh.

docs/user/components/meshio/OutputPhysics.md

@@ -45,8 +45,8 @@ Example of setting `OutputPhysics` Pyre properties and facilities in a parameter
 :::{code-block} cfg
 [observer]
 # Skip two time steps between output.
-output_trigger = pylith.meshio.OutputTriggerStep
-output_trigger.num_skip = 2
+trigger = pylith.meshio.OutputTriggerStep
+trigger.num_skip = 2
 
 # Write output to HDF5 file with name `boundary_xpos.h5`.
 writer = pylith.meshio.DataWriterHDF5

docs/user/components/meshio/OutputSolnBoundary.md

@@ -29,7 +29,7 @@ Implements `OutputSoln`.
 * `label`=\<str\>: Name of label identifier for external boundary.
   - **default value**: ''
   - **current value**: '', from {default}
-  - **validator**: <function validateLabel at 0x10816d800>
+  - **validator**: <function validateLabel at 0x104835e40>
 * `label_value`=\<int\>: Value of label identifier for external boundary (tag of physical group in Gmsh files).
   - **default value**: 1
   - **current value**: 1, from {default}
@@ -53,8 +53,8 @@ data_fields = [displacement]
 label = boundary_xpos
 
 # Skip two time steps between output.
-output_trigger = pylith.meshio.OutputTriggerStep
-output_trigger.num_skip = 2
+trigger = pylith.meshio.OutputTriggerStep
+trigger.num_skip = 2
 
 # Write output to HDF5 file with name `boundary_xpos.h5`.
 writer = pylith.meshio.DataWriterHDF5

docs/user/components/meshio/OutputSolnDomain.md

@@ -44,8 +44,8 @@ Example of setting `OutputSolnDomain` Pyre properties and facilities in a parame
 data_fields = [displacement]
 
 # Skip two time steps between output.
-output_trigger = pylith.meshio.OutputTriggerStep
-output_trigger.num_skip = 2
+trigger = pylith.meshio.OutputTriggerStep
+trigger.num_skip = 2
 
 # Write output to HDF5 file with name `domain.h5`.
 writer = pylith.meshio.DataWriterHDF5

docs/user/components/meshio/OutputSolnPoints.md

@@ -55,8 +55,8 @@ reader = pylith.meshio.PointsList
 reader.filename = stations.txt
 
 # Skip two time steps between output.
-output_trigger = pylith.meshio.OutputTriggerStep
-output_trigger.num_skip = 2
+trigger = pylith.meshio.OutputTriggerStep
+trigger.num_skip = 2
 
 # Write output to HDF5 file with name `domain.h5`.
 writer = pylith.meshio.DataWriterHDF5

docs/user/components/topology/MeshImporter.md

@@ -13,7 +13,7 @@ Implements `MeshGenerator`.
 * `distributor`: Distributes mesh among processes.
   - **current value**: 'mesh_distributor', from {default}
   - **configurable as**: mesh_distributor, distributor
-* `reader`: Reader for mesh files.
+* `reader`: Reader for mesh file.
   - **current value**: 'meshioascii', from {default}
   - **configurable as**: meshioascii, reader
 * `refiner`: Performs uniform global mesh refinement after distribution among processes (default is no refinement).