PyLith v3.0.0beta2

• Through-going faults work!
• Fix for h5py/six for Linux binary.

PyLith v3.0.0beta1

Tagged v3.0.0beta1

PyLith v2.2.1

• Added new examples.

  • examples/3d/subduction: New suite of examples for a 3-D subduction zone. This intermediate level suite of examples illustrates a wide range of PyLith features for quasi-static simulations.

  • examples/2d/subduction: Added quasi-static spontaneous rupture earthquake cycle examples (Steps 5 and 6) for slip-weakening and rate- and state-friction.

  • These new examples make use of ParaView Python scripts to facilitate using ParaView with PyLith.

• Improved the PyLith manual

  • Added diagram to guide users on which installation method best meets their needs.

  • Added instructions for how to use the Windows Subsystem for Linux to install the PyLith Linux binary on systems running Windows 10.

• Fixed bug in generating Xdmf files for 2-D vector output. Converted Xdmf generator from C++ to Python for more robust generation of Xdmf files from Python scripts.

• Updated spatialdata to v1.9.10. Improved error messages when reading SimpleDB and SimpleGridDB files.

• Updated PyLith parameter viewer to v1.1.0. Application and documentation are now available on line at https://geodynamics.github.io/pylith_parameters. Small fix to insure hierarchy path listed matches the one for PyLith.

• Updated PETSc to v3.7.6. See the PETSc documentation for a summary of all of the changes.

• Switched to using CentOS 6.9 for Linux binary builds to insure compatibility with glibc 2.12 and later.

PyLith v2.2.1rc1

Release Candidate 1

• Added new examples.

  • examples/3d/subduction: New suite of examples for a 3-D subduction zone.

  • examples/2d/subduction: Added spontaneous rupture examples for slip-weakening and rate- and state-friction.

• Fixed bug in generating Xdmf files for 2-D vector output.

• Updated PETSc to v3.7.6.

PyLith v2.2.0

• Added a browser-based parameter viewer for interactive viewing of all PyLith parameters and version information. See Section 4.10 PyLith Parameter Viewer of the PyLith user manual.

• Adjusted packaging of the binary distributions so that they can be used to extend PyLith and/or integrate other code with PyLith.

• Converted the user manual from Lyx to LaTeX and added syntax highlighting of parameter and spatial database files. Fixed several typos.

• Fixed bug that sometimes resulted in an inconsistent fault orientation when running in parallel. The bug appears to have been introduced in v2.0.

• Fixed two bugs in output of solution at points that sometimes happened in parallel simulations. The errors include:

  • The order of the station names does not match the order of the points. The point data is written in parallel by process order, so the points for process 0 are written first, then those for process 1, etc. This often results in reordering of the points. The station names were written in the original order.

  • The output values for some points are incorrect. The wrong cells were being used in the interpolation.

• Updated PETSc to v3.7.5.

PyLith v2.1.4

• Added --version command line argument to display version information for PyLith and its dependencies.
• Improved information displayed with the --help command line argument.
• Added --include-citations command line argument to display publications to cite when publishing results from computations using PyLith. General PyLith references are also displayed with the --version command line argument.
• Allow use of NetCDF versions greater than 4.1.3. Switch from using C++ API to C API.
• Fixed bug in Pythia associated with validation of parameters being done before help could be displayed.
• Fixed typos in manual for gravity and point forces.
• Added integration with Travis for automated testing.

PyLith v2.1.3

Release Notes v2.1.3

• Add generate_statedb.py and postseismic.pvsm files missing from examples/2d/gravity.
• Update handling of fault intersection when creating boundary condition nodesets in examples/meshing/surface_nurbs/subduction.
• Fixes to Darwin binary package.
  • Fix linking of netCDF4 Python module.
  • Fix linking and executable mode permissions for Python scripts in binary by using nemesis so relative links are valid.

PyLith v2.1.2

Release Notes

• Bugfixes for finite-strain formulation.
  • Added output of the Cauchy stresses (cauchy_stress). The second Pioloa-Kirchoff stresses are output via the stress field.
  • Material properties and state variables were not retrieved properly when updating state variables.
• Bugfixes for setting initial stress and state variables for viscoelastic materials. The deviatoric stress state is carried forward using the state variables, so the initial deviatoric stress should not be considered when computing the stresses.
• Created new examples showing how to use gravity, initial stress, and finite-strain in 2-D (examples/2d/gravity).
• Reintroduced check (that had been inadvertently removed in v2.x) for ambiguous description of fault surface based on groups of vertices defining faces of cells.
• Flush the output of the progress monitor so progress reports are updated promptly.
• Updates to the user manual.
  • Added section on the debugging examples covered in recent tutorials.
  • Added tables describing the spatial database values for each material.
  • Included a more complete discussion of the finite-strain formulation.
• PETSc
  • Updated to PETSc v3.7.2 (knepley/pylith branch).
  • Fixed Trilinos/ML configuration and code so that it can be built without a Fortran compiler.

PyLith v2.1.0

This release provides a few new small features and bugfixes.

Migrating from v2.0 to v2.1

The points file for OutputSolnPoints must now contain station names as
the first column.

Release Notes

• Station names are required for output at arbitrary points
  (OutputSolnPoints) and are included in a /stations dataset in HDF5
  files.
• A progress monitor will update a text file with the progress of a
  simulation (time in the time stepping loop or the number of impulses
  completed) and given an estimate of when the simulation will be
  completed.
• Bug fixes
  • A few bugs related to creating cohesive cells for fault
    intersections have been fixed. Faults can now meet at T
    intersections provided the buried edges of the faults are
    clamped. In other words, the fault ending at the T intersection
    has a clamped edge along the intersection. The fault ending at the
    intersection must also come AFTER the through-going fault in the
    list of fault interfaces.
  • There have been two major bug fixes for Drucker-Prager plasticity,
    for both DruckerPrager3D and DruckerPragerPlaneStrain. The first fix
    was a missing initial pressure term for the plastic multiplier
    in the Drucker-Prager formulation. This affects plasticity
    calculations when initial stresses are used. The error has been
    corrected in the code, the manual, and the unit tests. The second
    bug was an incorrect test for tensile yield that could cause
    PyLith to exit with an error when plastic yield had not actually
    occurred. The error would only occur when the allow_tensile_yield
    flag was set to False. This bug has been fixed in the code, and the
    new test is also described in the manual. This should prevent
    problems that previously existed when allow_tensile_yield was set
    to False (as it should be for most quasi-static problems).
  • Fixed bug in DataWriterHDF5Ext associated with multiple processes
    writing information to the HDF5 file. With external datasets the
    HDF5 file is limited to metadata and is maintained by process 0.
  • A two-dimensional gravity example has been added, based on the
    tutorial from the June, 2014 workshop at Stanford University.
    The tutorial itself is in examples/2d/gravity, and a new section
    has also been added to the manual describing the example.
  • Fixed inconsistent fault orientation when running in parallel
    for 2-D domains.

PyLith v2.0.3

This release provides several small updates for (1) improved CUBIT/Trelis compatibility, (2) building with recent versions of automake, and (3) additional examples from the 2014 Crustal Deformation Modeling Workshop tutorials.

No changes are needed in .cfg files to switch from v2.0.0 to v2.0.3.

Binaries are available from the links below. Detailed installation instructions for the binary packages are in the User Manual.

Migrating from version 1.9 to 2.0

Changes to various C++ objects permitted simplifying the specification of a number of components. The map below indicates the name changes.

  CellFilterAvgMesh -> CellFilterAvg
  DataWriterVTKMesh -> DataWriterVTK
  DataWriterVTKSubMesh -> DataWriterVTK
  DataWriterVTKSubSubMesh -> DataWriterVTK
  DataWriterHDF5Mesh -> DataWriterHDF5
  DataWriterHDF5SubMesh -> DataWriterHDF5
  DataWriterHDF5SubSubMesh -> DataWriterHDF5
  DataWriterHDF5ExtMesh -> DataWriterHDF5Ext
  DataWriterHDF5ExtSubMesh -> DataWriterHDF5Ext
  DataWriterHDF5ExtSubSubMesh -> DataWriterHDF5Ext

Running the script:

bash $PYLITH_DIR/doc/developer/update_1.9to2.0.sh

will update all .cfg files in the current directory and all subdirectories with the new names (you will need to replace $PYLITH_DIR with the directory containing the PyLith source code).

PyLith allows use of the Chaco and ParMetis/Metis partitioners. The name of the ParMetis/Metis partitioner was changed from "parmetis" to "metis".

  [pylithapp.mesh_generator]
  distributor.partitioner = metis

Buried edges of faults are handled differently in v2.0. A separate nodeset/pset should be created and contain the vertices on the buried edges of the fault. See the Section 6.4.2 of the PyLith manual for more information.

Release Notes

Version 2.0.3

• Bug fixes
  • Updated autotools files (Makefile.am, configure.ac) for
    compatibility with recent versions of automake (up to and including
    v1.14.1).

Version 2.0.2

• Bug fixes
  • Fixed linking issue in Darwin binary distribution, primarily
    affecting systems with OS X 10.7 and 10.8.
  • Improved example journal files for CUBIT/Trelis to improve
    compability (examples/meshing/surface_nurbs/dem).
  • Updated more journal in examples so that APREPRO lines have a
    leading '$' instead of a '#' to differentiate from comments.
  • Added examples/debugging files from Crustal Deformation Modeling
    workshop debugging tutorial.

Version 2.0.1

• Bug fixes
  • Improved example journal files for CUBIT/Trelis to improve
    compability. All journal files should work with CUBIT 14.1 and
    Trelis 15.0.
  • Created examples of IDless journal files in examples/2d/greensfns.
    These files should work with all recent versions of CUBIT and
    Trelis.
  • Switched journal APREPRO lines to have leading '$' instead of '#'
    to differentiate from comments.