diff --git a/CHANGES.md b/CHANGES.md index 9a68031ef4..28633c2783 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -5,6 +5,12 @@ Starting with v3.0.0, we strictly follow the [semantic versioning guidelines](ht The version numbers are in the form `MAJOR.MINOR.PATCH`, where major releases indicate changes to the public API (parameters), minor releases indicate new functionality that is backward compatible, and patch releases indicate backward compatible bug fixes. ::: +## Version 4.1.1 (2024/06/09) + +* **Fixed** + * Improved setup of variable block Jacobian preconditioner used for elasticity with faults to reduce runtime. + * Fix several typos and update a few diagrams in the documentation. + ## Version 4.1.0 (2024/06/05) * **Changed** @@ -16,7 +22,7 @@ The version numbers are in the form `MAJOR.MINOR.PATCH`, where major releases in * New 2D and 3D crustal strike-slip faults examples based on the 2019 Ridgecrest earthquake. * New 2D subduction zone outer-rise faulting example examining poroelastic response to bending stresses. * New `pylith_viz` utility for plotting PyLith results. - * Updated `examples/strikeslip-2d` and `examples/reverse-2d` to demonstrate use of uniform refinement and higher ordder discretizations to improve resolution of solution. + * Updated `examples/strikeslip-2d` and `examples/reverse-2d` to demonstrate use of uniform refinement and higher order discretizations to improve resolution of solution. * Documentation * Developer Guide: Added description of the process for adding event logging and evaluating performance, including performance logging. * Developer Guide: Added checklist for what is needed when contributing examples. diff --git a/CITATION.cff b/CITATION.cff index 3988660abf..5039c4857a 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -22,7 +22,7 @@ authors: orcid: "https://orcid.org/0000-0001-7435-9196" identifiers: - type: doi - value: 10.5281/zenodo.11479383 + value: 10.5281/zenodo.11534872 repository-code: "https://github.com/geodynamics/pylith" url: "https://geodynamics.org/resources/pylith" keywords: @@ -31,7 +31,7 @@ keywords: - earthquake - finite element license: MIT -version: 4.1.0 +version: 4.1.1 date-released: "2024-06-05" preferred-citation: type: article diff --git a/README.md b/README.md index f9591b4d7d..3d73c9993f 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # PyLith -[![DOI](https://www.zenodo.org/badge/DOI/10.5281/zenodo.11479383.svg)](https://doi.org/10.5281/zenodo.11479383) +[![DOI](https://www.zenodo.org/badge/DOI/10.5281/zenodo.11534872.svg)](https://doi.org/10.5281/zenodo.11534872) [![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/geodynamics/pylith/blob/main/LICENSE.md) [![Build Status](https://dev.azure.com/baagaard-usgs/pylith/_apis/build/status/geodynamics.pylith?branchName=main)](https://dev.azure.com/baagaard-usgs/pylith/_build/latest?definitionId=2&branchName=main) [![codecov](https://codecov.io/gh/geodynamics/pylith/branch/master/graph/badge.svg?token=JiwLVB64EF)](https://codecov.io/gh/geodynamics/pylith) diff --git a/configure.ac b/configure.ac index ebc6376b50..76cf34a13b 100644 --- a/configure.ac +++ b/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], [4.1.0], [https://geodynamics.org/resources/pylith]) +AC_INIT([PyLith], [4.1.1], [https://geodynamics.org/resources/pylith]) AC_CONFIG_AUX_DIR([./aux-config]) AC_CONFIG_HEADER([portinfo]) AC_CONFIG_MACRO_DIR([m4]) @@ -173,7 +173,7 @@ CIT_FUNCTIONSTRING dnl VERSION CIG_PKG_GIT(PYLITH) AC_DEFINE_UNQUOTED([PYLITH_VERSION], ["$PACKAGE_VERSION"], [Define PyLith version]) -AC_DEFINE_UNQUOTED([PYLITH_DOI], ["10.5281/zenodo.11479383"], [Define PyLith doi]) +AC_DEFINE_UNQUOTED([PYLITH_DOI], ["10.5281/zenodo.11534872"], [Define PyLith doi]) dnl ENDIANNESS AC_C_BIGENDIAN diff --git a/developer/pdf_to_svg.py b/developer/pdf_to_svg.py new file mode 100755 index 0000000000..f55da6ccdc --- /dev/null +++ b/developer/pdf_to_svg.py @@ -0,0 +1,16 @@ +#!/usr/bin/env nemesis + +import sys +import pymupdf + +if len(sys.argv) != 2: + print("usage: pdf_to_svg.py FILENAME") + sys.exit(1) + +filename_pdf = sys.argv[1] +doc = pymupdf.open(filename_pdf) # open a document +page = doc[0] + +filename_svg = filename_pdf.replace(".pdf", ".svg") +with open(filename_svg, "w", encoding="utf-8") as svg_out: + svg_out.write(page.get_svg_image()) diff --git a/docs/conf.py b/docs/conf.py index b10a8ca114..839005c589 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -22,7 +22,7 @@ author = 'Brad T. Aagaard, Matthew G. Knepley, Charles A. Williams' # The full version, including alpha/beta/rc tags -release = '4.1.0' +release = '4.1.1' # -- General configuration --------------------------------------------------- diff --git a/docs/intro/preface.md b/docs/intro/preface.md index 73c0d25407..bf594d1451 100644 --- a/docs/intro/preface.md +++ b/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 (2024a), *PyLith v4.1.0.* Davis, CA: Computational Infrastructure of Geodynamics. DOI: 10.5281/zenodo.11479383. +- Aagaard, B., M. Knepley, C. Williams (2024a), *PyLith v4.1.1.* Davis, CA: Computational Infrastructure of Geodynamics. DOI: 10.5281/zenodo.11534872. -- Aagaard, B., M. Knepley, C. Williams (2024b), *PyLith Manual, Version 4.1.0.* Davis, CA: Computational Infrastructure of Geodynamics. https://pylith.readthedocs.io/en/v4.1.0 +- Aagaard, B., M. Knepley, C. Williams (2024b), *PyLith Manual, Version 4.1.1.* Davis, CA: Computational Infrastructure of Geodynamics. https://pylith.readthedocs.io/en/v4.1.1 ## Publishing Models @@ -43,7 +43,7 @@ Common output files include the solution fields and state variables as `.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 4.1.0 (Aagaard et al., 2013; Aagaard et al., 2023a; Aagaard et al., 2023b) 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.11479383). +PyLith version 4.1.1 (Aagaard et al., 2013; Aagaard et al., 2023a; Aagaard et al., 2023b) 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.11479383). The project is being actively developed on GitHub and can be accessed via https://github.com/geodynamics/pylith. ## Support diff --git a/docs/user/examples/magma-2d/step02-inflation-statevars.md b/docs/user/examples/magma-2d/step02-inflation-statevars.md index 542dc88b39..04286d8e52 100644 --- a/docs/user/examples/magma-2d/step02-inflation-statevars.md +++ b/docs/user/examples/magma-2d/step02-inflation-statevars.md @@ -93,7 +93,7 @@ ksp_divtol = 1.0e+5 --- caption: Run Step 2 simulation --- -$ pylith step02_inflation.cfg +$ pylith step02_inflation_statevars.cfg # The output should look something like the following. >> /software/unix/py3.12-venv/pylith-opt/lib/python3.12/site-packages/pylith/apps/PyLithApp.py:77:main diff --git a/docs/user/install/index.md b/docs/user/install/index.md index 7700c04abd..114c3eaa53 100644 --- a/docs/user/install/index.md +++ b/docs/user/install/index.md @@ -49,10 +49,10 @@ On macOS systems you can check the operating system version by clicking on the A 3. Unpack the tarball. ```{code-block} bash # Linux 64-bit - $ tar -xzf pylith-4.1.0-linux-x86_64.tar.gz + $ tar -xzf pylith-4.1.1-linux-x86_64.tar.gz # macOS - $ tar -xzf pylith-4.1.0-macOS-10.15-x86_64.tar.gz + $ tar -xzf pylith-4.1.1-macOS-10.15-x86_64.tar.gz ``` 4. Set environment variables. The provided `setup.sh` script only works if you are using bash shell. @@ -66,20 +66,20 @@ Ready to run PyLith. To bypass macOS quarantine restrictions, simply use command line program `curl` to download the tarball from within a terminal rather than using a web browser. ``` -curl -L -O https://github.com/geodynamics/pylith/releases/download/v4.1.0/pylith-4.1.0-macOS-10.15-x86_64.tar.gz +curl -L -O https://github.com/geodynamics/pylith/releases/download/v4.1.1/pylith-4.1.1-macOS-10.15-x86_64.tar.gz ``` Alternatively, if you do download the tarball using a web browser, after you unpack the tarball you can remove the macOS quarantine flags using the following commands (requires Administrator access): ``` # Show extended attributes -xattr ./pylith-4.1.0-macOS-10.15-x86_64 +xattr ./pylith-4.1.1-macOS-10.15-x86_64 # Output should be com.apple.quarantine # Remove quarantine attributes -sudo xattr -r -d com.apple.quarantine ./pylith-4.1.0-macOS-10.15-x86_64 +sudo xattr -r -d com.apple.quarantine ./pylith-4.1.1-macOS-10.15-x86_64 ``` ::: @@ -142,7 +142,7 @@ For each package this utility downloads the source code, configures it, builds i ## Verifying PyLith is Installed Correctly The easiest way to verify that PyLith has been installed correctly is to run one or more of the examples supplied with the binary and source code. -In the binary distribution, the examples are located in `src/pylith-4.1.0/examples` while in the source distribution, they are located in `pylith-4.1.0/examples`. +In the binary distribution, the examples are located in `src/pylith-4.1.1/examples` while in the source distribution, they are located in `pylith-4.1.1/examples`. {ref}`sec-examples` discusses how to run and visualize the results for the examples. To run the example discussed in Section {ref}`sec-examples-box-2d`: diff --git a/docs/user/intro/figs/workflow.pdf b/docs/user/intro/figs/workflow.pdf index d64982c73d..6ce96d02ce 100644 Binary files a/docs/user/intro/figs/workflow.pdf and b/docs/user/intro/figs/workflow.pdf differ diff --git a/docs/user/intro/figs/workflow.svg b/docs/user/intro/figs/workflow.svg index e741971a70..485116542b 100644 --- a/docs/user/intro/figs/workflow.svg +++ b/docs/user/intro/figs/workflow.svg @@ -1,5568 +1,611 @@ - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/user/intro/figs/workflow.tex b/docs/user/intro/figs/workflow.tex index edb851b322..9a58253768 100644 --- a/docs/user/intro/figs/workflow.tex +++ b/docs/user/intro/figs/workflow.tex @@ -61,7 +61,8 @@ \node (abaqus) [commercial, below=of relax] {Abaqus}; % Visualization - \node (paraview) [open, below=of viz] {ParaView}; + \node (pylith-viz) [open, below=of viz] {pylith\_viz (PyVista)}; + \node (paraview) [open, below=of pylith-viz] {ParaView}; \node (visit) [open, below=of paraview] {Visit}; \node (matplotlib) [open, below=of visit] {Matplotlib}; \node (matlab) [commercial, below=of matplotlib] {Matlab}; @@ -78,6 +79,7 @@ \path (cubit.east) edge[available] (pylith.west); \path (cubit.east) edge[available] (abaqus.west); + \path (pylith.east) edge[available] (pylith-viz.west); \path (pylith.east) edge[available] (paraview.west); \path (pylith.east) edge[available] (visit.west); \path (pylith.east) edge[available] (matlab.west); diff --git a/docs/user/intro/new.md b/docs/user/intro/new.md index d24f1eadf3..4d2af863a2 100644 --- a/docs/user/intro/new.md +++ b/docs/user/intro/new.md @@ -1,4 +1,23 @@ -# New in PyLith Version 3.0.0 +# Significant Recent Changes + +## PyLith Version 4.1 + +* Improved runtime performance, including better preconditioners for elasticity with faults and poroelasticity +* 2D and 3D crustal strike-slip faults examples based on the 2019 Ridgecrest earthquake. +* 2D subduction zone outer-rise faulting example examining poroelastic response to bending stresses. +* `pylith_viz` utility for plotting PyLith results. +* Updated `examples/strikeslip-2d` and `examples/reverse-2d` to demonstrate use of uniform refinement and higher order discretizations to improve resolution of solution. + +## PyLith Version 4.0 + +* Changed name of fault Lagrange multiplier field for solution component in Python from `lagrange_fault` to `lagrange_multiplier_fault` to match name of solution field in C++. +* Removed support for importing meshes from LaGriT. +* Change in fault tractions are now included in the fault `data_fields` for prescribed slip. +* Fault and boundary orientation directions are now included in the `info_fields` for simulation output. +* State variables are now included in the default `data_fields` for simulation output. +* The default solver settings use the PETSc proper orthogonal decomposition (POD) methodology for initial guess of solutions to improve convergence. + +## PyLith Version 3.0 * Major rewrite of the finite-element implementation to support higher order discretizations and flexible specification of the governing equations. * Use of pointwise functions to implement governing equations; diff --git a/docs/user/run-pylith/figs/pylith_simulation.pdf b/docs/user/run-pylith/figs/pylith_simulation.pdf index 4842cb5e8d..c811d087c6 100644 Binary files a/docs/user/run-pylith/figs/pylith_simulation.pdf and b/docs/user/run-pylith/figs/pylith_simulation.pdf differ diff --git a/docs/user/run-pylith/figs/pylith_simulation.svg b/docs/user/run-pylith/figs/pylith_simulation.svg index 99d5da7eed..68800d5357 100644 --- a/docs/user/run-pylith/figs/pylith_simulation.svg +++ b/docs/user/run-pylith/figs/pylith_simulation.svg @@ -1,4139 +1,733 @@ - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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\node (viz) [visualize, below= of pylith, text height=15em, minimum width=20em] {Visualization}; - \node (postprocess) [postprocess, right=of viz, text height=8em, xshift=5em] {Post-processing}; + \node (viz) [visualize, below= of pylith, text height=15em, minimum width=28em] {Visualization}; + \node (postprocess) [postprocess, right=of viz, text height=8em, xshift=2em] {Post-processing}; \end{pgfonlayer} @@ -82,8 +82,9 @@ \node (vtk) [output, xshift=-5.5em, yshift=+2em] at (viz) {VTK File(s) [.vtk]}; \node (hdf5) [output, right=of vtk, text width=8em] {HDF5 File(s) [.h5] \par Xdmf File(s) [.xmf]}; - \node (paraview) [app, below=of vtk, yshift=-2em] {ParaView}; + \node (paraview) [app, below=of vtk, xshift=-3.0em, yshift=-2em] {ParaView}; \node (visit) [app, right=of paraview] {Visit}; + \node (pylith-viz) [app, right=of visit] {pylith\_viz (PyVista)}; % Post-processing @@ -115,6 +116,7 @@ \path (vtk.south) edge[arrowto_minor] (visit.north); \path (hdf5.south) edge[arrowto_minor] (paraview.north); \path (hdf5.south) edge[arrowto_minor] (visit.north); + \path (hdf5.south) edge[arrowto_minor] (pylith-viz.north); \end{tikzpicture} diff --git a/docs/user/run-pylith/overview.md b/docs/user/run-pylith/overview.md index 8c39517582..2664b9bacd 100644 --- a/docs/user/run-pylith/overview.md +++ b/docs/user/run-pylith/overview.md @@ -203,13 +203,14 @@ The user supplies: PyLith writes solution information, such as solution fields and state variables, to either VTK files or HDF5/Xdmf files using the observer components. ParaView and Visit as well as several other visualization tools can read both types of files. +PyLith includes {ref}`sec-user-run-pylith-viz` for visualizing PyLith HDF files using PyVista. Post-processing of output is generally performed using HDF5 files accessed via a Python script and the h5py package or a Matlab script. :::{figure-md} fig:pylith:simulation Diagram of a PyLith simulation PyLith requires a finite-element mesh (three different mechanisms for generating a mesh are currently supported), simulation parameters, and spatial databases (defining the spatial variation of various parameters). -PyLith writes the solution output to either VTK or HDF5/Xdmf files, which can be visualized with ParaView or Visit. Post-processing is generally done using the HDF5 files with Python or Matlab scripts. +PyLith writes the solution output to either VTK or HDF5/Xdmf files, which can be visualized with ParaView or Visit. PyLith includes {ref}`sec-user-run-pylith-viz` for visualizing PyLith HDF files using PyVista. Post-processing is generally done using the HDF5 files with Python or Matlab scripts. ::: ## Nondimensionalization diff --git a/examples/reverse-2d/generate_gmsh.py b/examples/reverse-2d/generate_gmsh.py index d39bd31edf..0a350048c4 100755 --- a/examples/reverse-2d/generate_gmsh.py +++ b/examples/reverse-2d/generate_gmsh.py @@ -101,7 +101,7 @@ def create_geometry(self): # Create curves. We store the curve tag as a data member # so that we can refer to them later. # We traverse the curves in a counter clock-wise direction. - # If the curve is in the opporite direction, we use the negative tag. + # If the curve is in the opposite direction, we use the negative tag. self.c_yneg = gmsh.model.geo.add_line(p1, p2) self.c_xpos = gmsh.model.geo.add_line(p2, p3) self.c_ypos_fw = gmsh.model.geo.add_line(p3, p7) diff --git a/examples/strikeslip-2d/generate_gmsh.py b/examples/strikeslip-2d/generate_gmsh.py index 4e548097e7..dcbb7814f8 100755 --- a/examples/strikeslip-2d/generate_gmsh.py +++ b/examples/strikeslip-2d/generate_gmsh.py @@ -95,7 +95,7 @@ def create_geometry(self): # Create curve loops and surfaces from the curves. # We traverse the curves in a counter clock-wise direction. - # If the curve is in the opporite direction, we use the negative tag. + # If the curve is in the opposite direction, we use the negative tag. c0 = gmsh.model.geo.add_curve_loop([self.c_yneg1, self.c_fault, self.c_ypos1, self.c_xneg]) self.s_xneg = gmsh.model.geo.add_plane_surface([c0]) c1 = gmsh.model.geo.add_curve_loop([self.c_yneg2, self.c_xpos, self.c_ypos2, -self.c_fault]) diff --git a/release-notes/Makefile.am b/release-notes/Makefile.am index fa17ee6f6e..46a5a17d07 100644 --- a/release-notes/Makefile.am +++ b/release-notes/Makefile.am @@ -43,7 +43,8 @@ EXTRA_DIST = \ announce_v3.0.2.md \ announce_v3.0.3.md \ announce_v4.0.0.md \ - announce_v4.1.0.md + announce_v4.1.0.md \ + announce_v4.1.1.md # End of file diff --git a/release-notes/announce_v4.1.0.md b/release-notes/announce_v4.1.0.md index 7b33eea364..de34f8ed1a 100644 --- a/release-notes/announce_v4.1.0.md +++ b/release-notes/announce_v4.1.0.md @@ -19,7 +19,7 @@ Documentation * New 2D and 3D crustal strike-slip faults examples based on the 2019 Ridgecrest earthquake. * New 2D subduction zone outer-rise faulting example examining poroelastic response to bending stresses. * New `pylith_viz` utility for plotting PyLith results. - * Updated `examples/strikeslip-2d` and `examples/reverse-2d` to demonstrate use of uniform refinement and higher ordder discretizations to improve resolution of solution. + * Updated `examples/strikeslip-2d` and `examples/reverse-2d` to demonstrate use of uniform refinement and higher order discretizations to improve resolution of solution. * Documentation * Developer Guide: Added description of the process for adding event logging and evaluating performance, including performance logging. * Developer Guide: Added checklist for what is needed when contributing examples. diff --git a/release-notes/announce_v4.1.1.md b/release-notes/announce_v4.1.1.md new file mode 100644 index 0000000000..6f55b48e52 --- /dev/null +++ b/release-notes/announce_v4.1.1.md @@ -0,0 +1,50 @@ +# PyLith v4.1.1 now available + +I am pleased to announce the release of PyLith 4.1.1, a finite-element code designed to solve dynamic elastic problems and quasi-static viscoelastic problems in tectonic deformation. + +You can download the source code and binaries from + + +Documentation + + +## Release Notes + +* **Fixed** + * Improved setup of variable block Jacobian preconditioner used for elasticity with faults to reduce runtime. + * Fix several typos and update a few diagrams in the documentation. + +### Version 4.1.0 + +* **Changed** + * Improved the default preconditioners for poroelasticity for improved scalability. + * Improved the default preconditioners for elasticity with faults for improved scalability. + * Replaced use of Cubit journal files with Cubit Python scripts for several examples, and use the skeleton sizing function to increase cell size with distance from the fault. + * Removed ParaView Python scripts (replaced by `pylith_viz`) +* **Added** + * New 2D and 3D crustal strike-slip faults examples based on the 2019 Ridgecrest earthquake. + * New 2D subduction zone outer-rise faulting example examining poroelastic response to bending stresses. + * New `pylith_viz` utility for plotting PyLith results. + * Updated `examples/strikeslip-2d` and `examples/reverse-2d` to demonstrate use of uniform refinement and higher order discretizations to improve resolution of solution. + * Documentation + * Developer Guide: Added description of the process for adding event logging and evaluating performance, including performance logging. + * Developer Guide: Added checklist for what is needed when contributing examples. +* **Fixed** + * Updated `examples/subduction-3d` Steps 6, 7, and 8 to work with PyLith v3+. + * Fix performance bottleneck when reading Gmsh files. + * Remove extra (wrong) kernels for poroelasticity when using state variables. + * Update Python unit tests setup for compatibility with the current unittest API (use `load_tests()`). + +### Known issues + +* The new default preconditioner for simulations using elasticity and faults can cause convergence issues when running in parallel in which fault faces lie on the boundaries between processors. The workaround is to use the previous preconditioner provided in `share/settings/solver_fault_fieldsplit.cfg`. +* The default PETSc options provide a computationally expensive preconditioner when solving incompressible elasticity problems. We expect to have a more optimal preconditioner in the next release. + +## Contributors + +* Brad Aagaard ![ORCID iD](/_static/images/ORCIDiD_icon32x32.png){w=16px}[0000-0002-8795-9833](https://orcid.org/0000-0002-8795-9833) +* Matthew Knepley ![ORCID iD](/_static/images/ORCIDiD_icon32x32.png){w=16px}[0000-0002-2292-0735](https://orcid.org/0000-0002-2292-0735) +* Charles Williams ![ORCID iD](/_static/images/ORCIDiD_icon32x32.png){w=16px}[0000-0001-7435-9196](https://orcid.org/0000-0001-7435-9196) +* Daniel Douglas ![ORCID iD](/_static/images/ORCIDiD_icon32x32.png){w=16px}[0000-0002-7871-018X](https://orcid.org/0000-0002-7871-018X) +* Evan Marschall ![ORCID iD](/_static/images/ORCIDiD_icon32x32.png){w=16px}[0009-0003-0916-6656](https://orcid.org/0009-0003-0916-6656) +* Zechao Zhuo ![ORCID iD](/_static/images/ORCIDiD_icon32x32.png){w=16px}[0000-0002-8163-5731](https://orcid.org/0000-0002-8163-5731) diff --git a/setup.cfg b/setup.cfg index e8e4ebb283..d62805fc7d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -4,7 +4,7 @@ tag_date = 0 [metadata] name = pylith -version = 4.1.0 +version = 4.1.1 author = Brad Aagaard, Matthew Knepley, Charles Williams author_email = baagaard@usgs.gov, knepley@buffalo.edu, c.williams@gns.cri.nz description = Finite-element software for modeling crustal deformation with an emphasis on earthquake faulting.