Merge pull request #73 from kumiori/andres-joss-review

Andres joss review

README.md

@@ -1,61 +1,72 @@
 # Crack Propagation in Brittle Materials
 ## 2024
 
-From little or nothing, to experimental verification of a complex fracture experiment.
-We solve the following (difficult) problem:
+`Irrevolutions` is a computational stability analysis toolkit designed to solve nonlinear and nonconvex evolutionary problems using advanced numerical methods. It provides efficient algorithms for computing solutions constrained minimum problems with application to irreversible evolutions (hence its name). In particular, this framework is relevant in the context of fracture and damage mechanics.
 
-**Evolution of Damage (irreversible)**
+**Irreversible Evolution of Damage**
 
 Let $y=(\alpha, u)$ be an admissible state of a brittle system where $\alpha: \Omega \mapsto [0, 1]$ is a smooth damage field which identifies cracks (where $\alpha =1$) and $u$ is a displacement field. Provided a material model (an energy) $E_\ell$, given a time horizon $T$, let's find a map $t \in [0, T]\mapsto y_t$ such that: damage is non-decreasing and the observed state $y_t$ is energy-minimal, among admissible variations. 
 
+## How to contribute
 
-#### Feature branch workflow
+### Reporting bugs
+If you find a bug in `irrevolutions`, please report it on the GitHub issue tracker.
 
-For each new feature you wish to implement, create a branch named ```{yourname}-{feature}```, 
-as in ```andres-meshes```.
+## Suggesting enhancements
+If you wish to suggest a new feature or an improvement of a current feature, you can submit this on the issue tracker.
 
-https://docs.gitlab.com/ee/gitlab-basics/feature_branch_workflow.html
+## Contributing code (submitting a pull request)
+To contribute code `irrevolutions`, create a pull request. If you want to contribute, but are unsure where to start, get in touch with the authors.
 
- - Create your feature branch:`git checkout -b username-feature`
- - To push your branch: `git push -u origin feature_branch_name`
- - Create a pull request on the main branch for merging. Somebody should approve the pull-request. -
+On opening a pull request, unit tests will run on GitHub Continuous Integration. You can click on these in the pull request to see where (if anywhere) the tests are failing.
 
-### Weekly updates (merge from main)
+For more details on the pull request workflow, check
+https://docs.godotengine.org/en/3.1/community/contributing/pr_workflow.html
+
+
+
+### Installation
+
+Before installing `irrevolutions`, ensure you have `dolfinx` and other dependencies installed. You can install `dolfinx` using one of the following methods:
+
+- Using conda
 ```
-git checkout main
-git pull
-git checkout yourname-branch
-git merge main
+conda create -n fenicsx-env -c conda-forge fenics-dolfinx=0.7.2 mpich pyvista
+conda activate fenicsx-env
 ```
 
-Asymmetrically, feature-work is `rebased`.
+- Using Spack
+see https://github.com/FEniCS/dolfinx/blob/main/README.md#spack
 
-### To run the code (on Docker)
+- Using Apt (ubuntu)
+```
+add-apt-repository ppa:fenics-packages/fenics
+apt update
+apt install fenicsx=1:0.7.3-3~ppa1~lunar1
+```
+
+For detailed instructions, see https://github.com/FEniCS/dolfinx/blob/main/README.md#installation
 
-First, run the container, attaching an interactive session and sharing data space 
-(the current dir) between the host and the container (the syntax is origin:target).
+- Using a Docker container
 
-On an ARM-based machine:
+For an ARM-based machine:
 ```
 docker run --rm -ti -v "$(pwd)":/home/numerix -w /home/numerix kumiori3/numerix:stable
 ```
-On an AMD64 machine:
+For an AMD64 machine:
 ```
 docker run --rm -ti -v "$(pwd)":/home/numerix -w /home/numerix kumiori3/numerix:stable-amd64
 ```
 
-On a windows box:
+For a windows box:
 ```
 docker run --rm -ti -v "C:/...":/home/numerix" -w /home/numerix kumiori3\numerix:stable-amd64
 ```
 
-### Installation
-
-To install the software, run DOLFINx through the aforementioned docker container and install the irrevolutions-package with 
+Finally, to install `irrevolutions` head to the package root directory and run
 
 ```python3 -m pip install .```
 
-from the root of this repository
 
 
 ----
@@ -66,8 +77,11 @@ This code was initially conceived as a support for the teaching course MEC647,
 
 ### Acknowledgements
 
+
 To all the students for their effort, participation, and motivation.
 
+This project contains code from the DOLFINy project (https://github.com/fenics-dolfiny/dolfiny), which is licensed under the LGPLv3 license. We acknowledge and thank the DOLFINy contributors for their work.
+
 See paper.md
 
 ### License
@@ -76,9 +90,7 @@ See `LICENSE` file.
 
 Each file should have at least the "copyright" line and a pointer to where the full notice is found.
 
-    <Irrevolutions is scientific software, it is conceived to compute evolution paths
-    upon a general notion of (unilateral) stability. It applies to fracture and, maybe,
-    not only.>
+    <Irrevolutions is scientific software, it is conceived to compute evolution paths upon a general notion of (unilateral) stability. It applies to fracture and, maybe, not only.>
 
     Copyright or copyLeft (C) <~0>  <ALB/83252>
 
@@ -97,7 +109,7 @@ Each file should have at least the "copyright" line and a pointer to where the f
     book for further abstraction.
 
     You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+    along with `irrevolution`.  If not, see <https://www.gnu.org/licenses/>.
 
 
 

contributed/DIC_CT_35/export_msh.py

@@ -2,9 +2,10 @@
 # coding: utf-8
 
 
-from dolfin import *
 import os
 
+from dolfin import *
+
 filename = "mesh/DIC_running"
 
 
@@ -13,7 +14,7 @@
 os.remove(filename + ".msh")
 # xml to h5 (1-3)
 mesh = Mesh(filename + ".xml")
-#boundaries = MeshFunction("size_t", mesh, "mesh4_facet_region.xml")
+# boundaries = MeshFunction("size_t", mesh, "mesh4_facet_region.xml")
 subdomains = MeshFunction("size_t", mesh, filename + "_physical_region.xml")
 boundaries = MeshFunction("size_t", mesh, filename + "_facet_region.xml")
 
@@ -30,13 +31,13 @@
 os.remove(filename + ".xml")
 
 
-#mesh = Mesh()
-#hdf = HDF5File(mesh.mpi_comm(), filename + ".h5", "r")
-#hdf.read(mesh, "/mesh", False)
-#ndim = mesh.topology().dim()
+# mesh = Mesh()
+# hdf = HDF5File(mesh.mpi_comm(), filename + ".h5", "r")
+# hdf.read(mesh, "/mesh", False)
+# ndim = mesh.topology().dim()
 
-#boundaries = MeshFunction("size_t", mesh,1)
-#hdf.read(boundaries, "/boundaries")
+# boundaries = MeshFunction("size_t", mesh,1)
+# hdf.read(boundaries, "/boundaries")
 
-#subdomains = MeshFunction("size_t", mesh,2)
-#hdf.read(subdomains, "/subdomains")
+# subdomains = MeshFunction("size_t", mesh,2)
+# hdf.read(subdomains, "/subdomains")