Merge pull request #821 from baagaard-usgs/feature-meshio-hdf5

Add support for specifying surfaces (BCs, faults) using faces and reading meshes in PETSc HDF5 format

Author: baagaard-usgs

.vscode/c_cpp_properties.json

@@ -12,14 +12,13 @@
                 "${env:MPI_INCDIR}",
                 "${env:HDF5_INCDIR}",
                 "${env:PROJ_INCDIR}",
-                "${env:CPPUNIT_INCDIR}",
                 "${env:CATCH2_INCDIR}",
                 "${env:PETSC_DIR}/include",
                 "${env:PETSC_DIR}/${env:PETSC_ARCH}/include"
             ],
             "defines": [],
             "macFrameworkPath": [
-                "/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/System/Library/Frameworks"
+                "/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks"
             ],
             "cStandard": "c11",
             "cppStandard": "c++14",
@@ -37,7 +36,6 @@
                 "${env:MPI_INCDIR}",
                 "${env:HDF5_INCDIR}",
                 "${env:PROJ_INCDIR}",
-                "${env:CPPUNIT_INCDIR}",
                 "${env:CATCH2_INCDIR}",
                 "${env:PETSC_DIR}/include",
                 "${env:PETSC_DIR}/${env:PETSC_ARCH}/include"

CHANGES.md

@@ -8,11 +8,20 @@ The version numbers are in the form `MAJOR.MINOR.PATCH`, where major releases in
 ## Version 5.0.0
 
 * **Changed**
+  * ASCII mesh format
+    * Changed `group` to `vertex-group`; remove `group` `type`.
   * Use the VTU (XML) format for VTK files instead of the legacy ASCII format.
+  * Renamed `VertexGroup` to `BoundaryGroup` in `meshio.gmsh_utils` and changed default behavior to not be recursive (generate "face" groups, not "vertex" groups).
+  * Material `description` property is no longer used; a deprecation warning is printed to stdout if it is specified. This feature will be removed in v6.0.
+  * Internal labels for meshes and fields are now derived from the Pyre component name and identifier.
   * Update PETSc to 3.22.3
 * **Added**
   * Improve documentation for pylith_eqinfo and illustrate its use in examples.
-
+  * Add 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).
+    * `Gmsh`: Create physical groups only at the dimension of the boundary.
+  
 ## Version 4.2.0
 
 * **Changed**

Makefile.am

@@ -36,7 +36,8 @@ dist_noinst_PYTHON = \
 	applications/pylith_genxdmf \
 	applications/pylith_runner \
 	applications/pylith_viz \
-	applications/pylith_powerlaw_gendb
+	applications/pylith_powerlaw_gendb \
+	applications/pylith_convertmesh
 
 
 EXTRA_DIST = \

applications/pylith_convertmesh

@@ -0,0 +1,12 @@
+#!/usr/bin/env nemesis
+"""Application for converting mesh files from one format to another.
+"""
+
+
+if __name__ == "__main__":
+    from pylith.apps.ConvertMeshApp import ConvertMeshApp
+    from pythia.pyre.applications import start
+    start(applicationClass=ConvertMeshApp)
+
+
+# End of file

configure.ac

@@ -10,7 +10,7 @@ dnl ============================================================================
 dnl Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.59)
-AC_INIT([PyLith], [4.2.0], [https://geodynamics.org/resources/pylith])
+AC_INIT([PyLith], [5.0.0dev], [https://geodynamics.org/resources/pylith])
 AC_CONFIG_AUX_DIR([./aux-config])
 AC_CONFIG_HEADER([portinfo])
 AC_CONFIG_MACRO_DIR([m4])
@@ -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([3.22.3])
+CIT_PATH_PETSC([3.23.1])
 CIT_HEADER_PETSC
 CIT_CHECK_LIB_PETSC
 

docs/conf.py

@@ -17,12 +17,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'PyLith'
-copyright = '2010-2025, University of California, Davis'
-author = 'Brad T. Aagaard, Matthew G. Knepley, Charles A. Williams'
+project = "PyLith"
+copyright = "2010-2025, University of California, Davis"
+author = "Brad T. Aagaard, Matthew G. Knepley, Charles A. Williams"
 
 # The full version, including alpha/beta/rc tags
-release = '4.2.0'
+release = "5.0.0dev"
 
 
 # -- General configuration ---------------------------------------------------
@@ -46,7 +46,7 @@
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -61,7 +61,7 @@
 # a list of builtin themes.
 #
 html_logo = "_static/images/cig_short_pylith.png"
-html_theme = 'pydata_sphinx_theme'
+html_theme = "pydata_sphinx_theme"
 html_context = {
     "default_mode": "light",
     "github_user": "geodynamics",
@@ -94,8 +94,8 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 html_css_files = [
-    'css/custom.css',
+    "css/custom.css",
 ]
 html_last_updated_fmt = ""

docs/developer/testing/performance-tools.md

@@ -1,9 +1,7 @@
 (developer-performance-tools)=
 # Performance Tools
 
-:::{note}
-New in v4.1.0
-:::
+*New in v4.1.0.*
 
 ## Overview
 

docs/intro/conventions.md

@@ -14,7 +14,7 @@ This is a tip, helpful hint, or suggestion.
 
 For features recently added to PyLith, we show the version number when they
 were added.
-*New in v3.0.0*
+*New in v3.0.0.*
 
 ## Command Line Arguments
 

docs/intro/development-plan.md

@@ -24,21 +24,21 @@ Because we strictly follow the [semantic versioning guidelines](https://semver.o
 This can happen if realize that we should modify the parameters to improve maintainability or prepare for future changes.
 :::
 
-## Version 5.0 (April 2025)
+## Version 5.0 (May 2025)
 
 This version will include a few very minor changes to the public API.
 
-* Specify boundary conditions using faces instead of vertices ![expert](images/intermediate.png) [75%]
-* Parallel mesh loading ![expert](images/expert.png) [85%]
+* Parallel mesh loading ![expert](images/expert.png) [90%]
+* Specify boundary conditions using faces instead of vertices ![expert](images/intermediate.png) [100%]
 * Update VTK output to use `vtu` files rather than legacy `vtk` files ![easy](images/easy.png) [100%]
 
-## Version 5.1 (June 2025)
+## Version 5.1 (August 2025)
 
 * Dynamic prescribed slip with diagonal Jacobian for explicit part of IMEX formulation ![expert](images/expert.png) [80%]
 * Add `examples/barwaves-2d` ![expert](images/expert.png) [25%]
 * Better preconditioner for incompressible elasticity ![expert](images/expert.png) [80%]
 
-## Version 5.2 (October 2025)
+## Version 5.2 (December 2025)
 
 * Spontaneous rupture for quasistatic and dynamic simulations ![expert](images/expert.png) [30%]
 

docs/intro/preface.md

@@ -17,9 +17,9 @@ The following peer-reviewed paper discusses the development of PyLith:
 
 To cite the software and manual, use:
 
-- Aagaard, B., M. Knepley, C. Williams (2025a), *PyLith v4.2.0.* Davis, CA: Computational Infrastructure of Geodynamics. DOI: 10.5281/zenodo.14635926.
+- Aagaard, B., M. Knepley, C. Williams (2025a), *PyLith v5.0.0.* Davis, CA: Computational Infrastructure of Geodynamics. DOI: 10.5281/zenodo.14635926.
 
-- Aagaard, B., M. Knepley, C. Williams (2025b), *PyLith Manual, Version 4.2.0.* Davis, CA: Computational Infrastructure of Geodynamics. https://pylith.readthedocs.io/en/v4.2.0
+- Aagaard, B., M. Knepley, C. Williams (2025b), *PyLith Manual, Version 5.0.0.* Davis, CA: Computational Infrastructure of Geodynamics. https://pylith.readthedocs.io/en/v5.0.0
 
 ## Publishing Models
 
@@ -41,7 +41,7 @@ Common output files include the solution fields and state variables in `.h5`, `.
 
 The configuration files, parameters of the simulation, and solution field for the models in this study are available at DOI (Authors X, Y, Z) under CC BY-NC-SA 4.0.
 
-PyLith version 4.2.0 (Aagaard et al., 2013; Aagaard et al., 2025a; Aagaard et al., 2025b) used in these models is freely available under the MIT license for download through its software landing page https://geodynamics.org/resources/pylith or Zenodo (10.5281/zenodo.14635926).
+PyLith version 5.0.0 (Aagaard et al., 2013; Aagaard et al., 2025a; Aagaard et al., 2025b) used in these models is freely available under the MIT license for download through its software landing page https://geodynamics.org/resources/pylith or Zenodo (10.5281/zenodo.14635926).
 The project is being actively developed on GitHub and can be accessed via https://github.com/geodynamics/pylith.
 
 ## Support