Merge branch 'pgrete/diffusion' into pgrete/next-w-tracer-latest

.devcontainer/devcontainer.json

@@ -0,0 +1,40 @@
+// devcontainer.json
+    {
+      "name": "athenapk-dev",
+      "image": "ghcr.io/parthenon-hpc-lab/cuda11.6-mpi-hdf5-ascent",
+      // disable Dockerfile for now
+      //"build": {
+      //  // Path is relative to the devcontainer.json file.
+      //  "dockerfile": "Dockerfile"
+      //},
+      "hostRequirements": {
+        "cpus": 4
+      },
+      "customizations": {
+        "vscode": {
+          "settings": {},
+          "extensions": [
+            "-ms-vscode.cpptools",
+            "llvm-vs-code-extensions.vscode-clangd",
+            "github.vscode-pull-request-github",
+            "ms-python.python",
+            "ms-toolsai.jupyter",
+            "ms-vscode.live-server",
+            "ms-azuretools.vscode-docker",
+            "swyddfa.esbonio",
+            "tomoki1207.pdf",
+            "ms-vscode.cmake-tools",
+            "ms-vsliveshare.vsliveshare"
+        ]
+        }
+      },
+      "remoteEnv": {
+        "PATH": "${containerEnv:PATH}:/usr/local/hdf5/parallel/bin",
+        "OMPI_MCA_opal_warn_on_missing_libcuda": "0"
+      },
+      //"remoteUser": "ubuntu",
+      // we need to manually checkout the submodules,
+      // but VSCode may try to configure CMake before they are fully checked-out.
+      // workaround TBD
+      "postCreateCommand": "git submodule update --init"
+    }

CHANGELOG.md

@@ -3,20 +3,29 @@
 ## Current develop (i.e., `main` branch)
 
 ### Added (new features/APIs/variables/...)
+- [[PR 89]](https://github.com/parthenon-hpc-lab/athenapk/pull/89) Add viscosity and resistivity
+- [[PR 1]](https://github.com/parthenon-hpc-lab/athenapk/pull/1) Add isotropic thermal conduction and RKL2 supertimestepping
 
 ### Changed (changing behavior/API/variables/...)
+- [[PR 97]](https://github.com/parthenon-hpc-lab/athenapk/pull/97) Fixed Schure cooling curve. Removed SD one. Added description of cooling function conventions.
 - [[PR 84]](https://github.com/parthenon-hpc-lab/athenapk/pull/84) Bump Parthenon to latest develop (2024-02-15)
 
 ### Fixed (not changing behavior/API/variables/...)
 
 ### Infrastructure
+- [[PR 112]](https://github.com/parthenon-hpc-lab/athenapk/pull/112) Add dev container configuration
 - [[PR 109]](https://github.com/parthenon-hpc-lab/athenapk/pull/109) Bump Parthenon to latest develop (2024-05-29)
 - [[PR 105]](https://github.com/parthenon-hpc-lab/athenapk/pull/105) Bump Parthenon to latest develop (2024-03-13)
 - [[PR 84]](https://github.com/parthenon-hpc-lab/athenapk/pull/84) Added `CHANGELOG.md`
 
 ### Removed (removing behavior/API/varaibles/...)
 
 ### Incompatibilities (i.e. breaking changes)
+- [[PR 97]](https://github.com/parthenon-hpc-lab/athenapk/pull/97)
+  - Removes original `schure.cooling` cooling curve as it had unknown origin.
+  - To avoid confusion, only cooling table for a single solar metallicity are supported
+    from now on (i.e., the parameters to specify temperature and lambda columns have been removed).
+  - Added `schure.cooling_#Z` curves (and associated notebook to calculate it from the paper tables).
 - [[PR 109]](https://github.com/parthenon-hpc-lab/athenapk/pull/109) Bump Parthenon to latest develop (2024-05-29)
   - Changed signature of `UserWorkBeforeOutput` to include `SimTime` as last paramter
   - Fixes bitwise idential restarts for AMR simulations (the derefinement counter is now included)

README.md

@@ -14,7 +14,13 @@ Current features include
   - HLLE (hydro and MHD), HLLC (hydro), and HLLD (MHD) Riemann solvers
   - adiabatic equation of state
   - MHD based on hyperbolic divergence cleaning following Dedner+ 2002
-  - anisotropic thermal conduction
+  - diffusion processes
+    - isotropic and anisotropic thermal conduction
+    - viscosity
+    - resistivity
+  - diffusion integrator
+    - unsplit
+    - operator-split, second-order RKL2 supertimestepping
   - optically thin cooling based on tabulated cooling tables with either Townsend 2009 exact integration or operator-split subcycling
 - static and adaptive mesh refinement
 - problem generators for