Merge branch 'main' into pierluigi-review

.github/workflows/workflow.yaml

@@ -0,0 +1,28 @@
+name: Run Tests in Docker Container
+run-name: We are testing irrevolutions
+
+on:
+  push:
+    branches:
+      - "**"
+
+jobs:
+  set-up-computing-environment:
+    runs-on: ubuntu-latest
+    container: kumiori3/numerix:stable-amd64
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: python3 -m pip install .
+
+      - name: Test import
+        run: python3 -c "import irrevolutions"
+
+      - name: Run 1d test
+        run: pytest -v test/test_1d.py
+
+      - name: Run tests
+        run: cd test && pytest -v .

.github/workflows/workflow_dolfinx_container.yaml

@@ -0,0 +1,28 @@
+name: Run Tests in Dolfinx Container
+run-name: We are testing irrevolutions
+
+on:
+  push:
+    branches:
+      - "**"
+
+jobs:
+  set-up-computing-environment:
+    runs-on: ubuntu-latest
+    container: ghcr.io/fenics/dolfinx/dolfinx:v0.7.2
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: python3 -m pip install .
+
+      - name: Test import
+        run: python3 -c "import irrevolutions"
+
+      - name: Run 1d test
+        run: pytest -v test/test_1d.py
+
+      - name: Run tests
+        run: cd test && pytest -v .

.gitignore

@@ -51,4 +51,5 @@ docs/build/
 test_*/
 src/irrevolutions/test/output/*
 **/output/**
-**egg-info**
+**egg-info**
+.venv/**

MANIFEST.in

@@ -0,0 +1 @@
+include irrevolutions/models/default_parameters.yml

README.md

@@ -35,20 +35,33 @@ Asymmetrically, feature-work is `rebased`.
 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).
 
-On a Mac:
+On an ARM-based machine:
 ```
-docker run --rm -ti -v "$(pwd)":/home/numerix -w /home/numerix kumiori3/numerix:latest
+docker run --rm -ti -v "$(pwd)":/home/numerix -w /home/numerix kumiori3/numerix:stable
+```
+On an AMD64 machine:
+```
+docker run --rm -ti -v "$(pwd)":/home/numerix -w /home/numerix kumiori3/numerix:stable-amd64
 ```
 
 On a windows box:
 ```
-docker run --rm -ti -v "C:/...":/home/numerix" -w /home/numerix kumiori3\numerix:latest
+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 
+
+```python3 -m pip install .```
+
+from the root of this repository
+
+
+----
+
 This code was initially conceived as a support for the teaching course MEC647, 
-(Complex) Crack Propagation in Brittle Materials, delivered to the students of the international
-master programme, joint between École Polytechnique and ENSTA-Paristech throughout 2020-2022. 
-Hence the cryptic repository name.
+(Complex) Crack Propagation in Brittle Materials, delivered to the students of the international master programme, joint between École Polytechnique and ENSTA-Paristech throughout 2020-2022. 
 
 
 ### Acknowledgements

paper/paper.bib

@@ -1,9 +1,6 @@
 %% This BibTeX bibliography file was created using BibDesk.
 %% http://bibdesk.sourceforge.net/
 
-%% Created for pierluigi at 2024-08-16 14:54:57 +0900 
-
-
 %% Saved with string encoding Unicode (UTF-8) 
 
 
@@ -26,8 +23,6 @@ @article{SICSIC
 @article{bazant,
 	abstract = {We consider a wide class of gradient damage models which are characterized by two constitutive functions after a normalization of the scalar damage parameter. The evolution problem is formulated following a variational approach based on the principles of irreversibility, stability and energy balance. Applied to a monotonically increasing traction test of a one-dimensional bar, we consider the homogeneous response where both the strain and the damage fields are uniform in space. In the case of a softening behavior, we show that the homogeneous state of the bar at a given time is stable provided that the length of the bar is less than a state dependent critical value and unstable otherwise. However, we also show that bifurcations can appear even if the homogeneous state is stable. All these results are obtained in a closed form. Finally, we propose a practical method to identify the two constitutive functions. This method is based on the measure of the homogeneous response in a situation where this response is stable without possibility of bifurcation, and on a procedure which gives the opportunity to detect its loss of stability. All the theoretical analyses are illustrated by examples.},
 	author = {Zden\v{e}k P. Ba\v{z}ant},
-	date-added = {2024-08-02 17:17:28 +0900},
-	date-modified = {2024-08-16 14:54:04 +0900},
 	doi = {10.1061/(ASCE)0733-9399(1988)114:12(2013)},
 	journal = {Journal of Engineering Mechanics},
 	title = {{Stable States and Paths of Stmuctures with Plasticity or Damage}},
@@ -105,13 +100,13 @@ @unpublished{camilla
 	date-modified = {2024-08-02 16:58:32 +0900},
 	journal = {preprint, \url{https://hal.sorbonne-universite.fr/hal-04552309}},
 	title = {Stability and crack nucleation in variational phase-field models of fracture: effects of length-scales and stress multi-axiality}}
+	year = {}}
 
 @article{Pham2013aa,
 	abstract = {Considering a family of gradient-enhanced damage models and taking advantage of its variational formulation, we study the stability of homogeneous states in a full three-dimensional context. We show that gradient terms have a stabilizing effect, but also how those terms induce structural effects. We emphasize the great importance of the type of boundary conditions, the size and the shape of the body on the stability properties of such states.},
 	author = {Pham, K. and Marigo, J. -J.},
 	date = {2013/01/01},
 	date-added = {2024-08-02 14:24:09 +0900},
-	date-modified = {2024-08-16 14:54:24 +0900},
 	doi = {10.1007/s10659-012-9382-5},
 	id = {Pham2013},
 	isbn = {1573-2681},
@@ -175,7 +170,6 @@ @article{FRANCFORT
 @article{dalcinpazklercosimo2011,
 	author = {Lisandro D. Dalcin and Rodrigo R. Paz and Pablo A. Kler and Alejandro Cosimo},
 	date-added = {2024-08-02 11:42:21 +0900},
-	date-modified = {2024-08-16 14:54:55 +0900},
 	doi = {10.1016/j.advwatres.2011.04.013},
 	issn = {0309-1708},
 	journal = {Advances in Water Resources},
@@ -190,13 +184,14 @@ @article{dalcinpazklercosimo2011
 @article{moreau:hal-01867187,
 	author = {Moreau, Jean Jacques},
 	date-added = {2024-07-31 15:03:36 +0900},
-	date-modified = {2024-08-16 14:51:56 +0900},
 	hal_id = {hal-01867187},
 	hal_version = {v1},
 	journal = {{Comptes rendus hebdomadaires des s{\'e}ances de l'Acad{\'e}mie des sciences}},
 	pages = {238-240},
 	publisher = {{Gauthier-Villars}},
 	title = {{D{\'e}composition orthogonale d'un espace hilbertien selon deux c{\^o}nes mutuellement polaires}},
+	pdf = {https://hal.science/hal-01867187/file/D%C3%A9composition_orthogonale_espace_hilbertien_Moreau_CRAS_1962.pdf},
+	url = {https://hal.science/hal-01867187},
 	volume = {255},
 	year = {1962},
 	bdsk-url-1 = {https://hal.science/hal-01867187}}
@@ -205,7 +200,6 @@ @article{pham:2011-the-issues
 	abstract = {We consider a wide class of gradient damage models which are characterized by two constitutive functions after a normalization of the scalar damage parameter. The evolution problem is formulated following a variational approach based on the principles of irreversibility, stability and energy balance. Applied to a monotonically increasing traction test of a one-dimensional bar, we consider the homogeneous response where both the strain and the damage fields are uniform in space. In the case of a softening behavior, we show that the homogeneous state of the bar at a given time is stable provided that the length of the bar is less than a state dependent critical value and unstable otherwise. However, we also show that bifurcations can appear even if the homogeneous state is stable. All these results are obtained in a closed form. Finally, we propose a practical method to identify the two constitutive functions. This method is based on the measure of the homogeneous response in a situation where this response is stable without possibility of bifurcation, and on a procedure which gives the opportunity to detect its loss of stability. All the theoretical analyses are illustrated by examples.},
 	author = {Kim Pham and Jean-Jacques Marigo and Corrado Maurini},
 	date-added = {2024-07-31 14:57:29 +0900},
-	date-modified = {2024-08-16 14:52:13 +0900},
 	doi = {10.1016/j.jmps.2011.03.010},
 	issn = {0022-5096},
 	journal = {Journal of the Mechanics and Physics of Solids},