Squashed 'core/' changes from 7a0c805..f5520ad

f5520ad fix mesh partitioning bug with FF v4.11
b9c7e33 add link to biodeg ui repo in readme
37f42c1 add joss paper to publication list
a1f7abb add joss and license badges to readme

git-subtree-dir: core
git-subtree-split: f5520ad391d376935d9698454bdf72f5f20d1230

README.md

@@ -1,8 +1,11 @@
 # BioDeg, a biodegradation and corrosion simulation code for metallic materials
 
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.04281/status.svg)](https://doi.org/10.21105/joss.04281)
+[![license: GPL v3](https://img.shields.io/badge/license-GPLv3-blue.svg)](LICENSE)
+
 ## About
 
-This repository contains the source code of BioDeg, a code for simulating the  biodegradation and corrosion behavior of metallic materials.
+This repository contains the source code of BioDeg, a code for simulating the  biodegradation and corrosion behavior of metallic materials. A full release of BioDeg, including a graphical user interface (GUI), the computational core (this repository), user manual, theory guide, and preprocessor can be found and downloaded from [this repository](https://github.com/mbarzegary/BioDeg-UI).
 
 <img src="doc/screw_degradation.jpg" width="600" height="auto">
 <p>
@@ -40,6 +43,19 @@ This code has been used in the following publications so far. In scientific work
           doi = {10.1177/10943420211045939},
     }
 
+    @article{Barzegari2022JOSS,
+          author = {Mojtaba Barzegari and Liesbet Geris},
+          title = {BioDeg: A finite element software for the simulation of the corrosion and biodegradation process in metallic biomaterials},
+          journal = {Journal of Open Source Software},
+          year = {2022},
+          publisher = {The Open Journal},
+          volume = {7},
+          number = {74},
+          pages = {4281},
+          doi = {10.21105/joss.04281},
+}
+
+
 ## Getting started
 
 The code is implemented in FreeFEM, a domain-specific language for finite element computing. So, a parallel version of FreeFEM should be installed. A proper MPI runtime is required to run parallel FreeFEM (such as OpenMPI or MPICH). The PETSc module should also be installed and linked to FreeFEM (which is usually the default config for installing/compiling FreeFEM). The installation procedure can be found [here](https://doc.freefem.org/introduction/installation.html) for different platforms.

src/export.idp

@@ -16,7 +16,7 @@ if (exportScaffoldMesh)
     phiTemp = phi;
     phiTemp[] .*= A.D;
 
-    int[int] rst = restrict(SpaceP1, SpaceBackup, n2oGlobal);
+    int[int] rst = restrict(SpaceP1, SpaceBackup, n2oGlob);
 
     phiG = 0;
     for[i, v : rst] phiG[][v] = phiTemp[][i];

src/geometry.idp

@@ -106,8 +106,8 @@ if (mpirank == 0)
   print("Partitioning the mesh...")
 
 int[int] n2oOverlap;
-int[int] n2oGlobal;
-NewMacro MeshN2O() n2oGlobal EndMacro
+int[int] n2oGlob;
+NewMacro MeshN2O() n2oGlob EndMacro
 
 Mat NS, A;
 buildDmesh(Mesh);

src/solver.idp

@@ -29,7 +29,7 @@ if (doRedistance) // if it is configured to redistance distance function
     phiTemp = phi;
     phiTemp[] .*= A.D;
 
-    int[int] rst = restrict(SpaceP1, SpaceBackup, n2oGlobal);
+    int[int] rst = restrict(SpaceP1, SpaceBackup, n2oGlob);
 
     phiG = 0;
     for[i, v : rst] phiG[][v] = phiTemp[][i];