Add some recent stuff

2023-09-04 16:46:22 +02:00
parent 0aa9986ada
commit d68f8b9cd9
32 changed files with 2665 additions and 3949 deletions
@@ -0,0 +1,96 @@
+{
+  "#Testing": {
+    "description": "Cellular Potts Model with dynamic ECM"
+  },
+  "Application": "Cells",
+  "Geometry": {
+    "blocksize": [80, 40, 20],
+    "blockcount": [1, 2, 4]
+  },
+  "Settings": {
+    "timesteps": 100,
+    "randomseed": 42
+  },
+  "Filling": {
+    "cells": [
+      {
+        "shape": "cube",
+        "box": [
+          [21, 35, 10],
+          [25, 39, 15]
+        ],
+        "celltype": 0
+      },
+      {
+        "shape": "cube",
+        "box": [
+          [15, 15, 14],
+          [22, 22, 20]
+        ],
+        "celltype": 0
+      }
+    ]
+  },
+  "CellsInSilico": {
+    "adhesion": {
+      "matrix": [
+        [0, 0, 0, 0],
+        [0, 20, 5, 5],
+        [0, 5, 10, 5],
+        [0, 5, 5, 5]
+      ]
+    },
+    "potential": {
+      "direction": [1, 1, 0],
+      "coupling": [0, 150, 100, 50]
+    },
+    "temperature": 15,
+    "volume": {
+      "default": {
+        "storage": "const",
+        "value": 300
+      },
+      "lambda": {
+        "storage": "const",
+        "value": 10
+      }
+    },
+    "surface": {
+      "default": {
+        "storage": "const",
+        "value": 400
+      },
+      "lambda": {
+        "storage": "const",
+        "value": 10
+      }
+    },
+    "cleaner": {
+      "killdistance": 100
+    },
+    "checkerboard": "00",
+    "energyfunctions": ["Volume00", "Surface00", "Adhesion00", "Potential00"],
+    "centerofmass": {
+      "steps": 10
+    },
+    "dynamicecm": {
+      "enabled": true,
+      "deltat": 0.1
+    }
+  },
+  "Writers": {
+    "ParallelVTK_Cells": {
+      "writer": "ParallelVtkImage",
+      "outputtype": "UInt32",
+      "field": "cells",
+      "steps": 5
+    },
+    "ParallelVTK_Displacement": {
+      "writer": "ParallelVtkImage",
+      "outputtype": "Float32",
+      "field": "dynamicecm_displacement",
+      "steps": 1
+    }
+  },
+  "WriteActions": ["ParallelVTK_Cells", "ParallelVTK_Displacement"]
+}
@@ -0,0 +1,75 @@
+{
+  "#Testing": {
+    "description": "Cellular Potts Model with dynamic ECM"
+  },
+  "Application": "Cells",
+  "Geometry": {
+    "blocksize": [15, 15, 15],
+    "blockcount": [1, 1, 1]
+  },
+  "Settings": {
+    "timesteps": 100,
+    "randomseed": 42
+  },
+  "Filling": {
+    "cells": [
+    ]
+  },
+  "CellsInSilico": {
+    "adhesion": {
+      "matrix": [
+        [0, 0, 0, 0],
+        [0, 20, 5, 5],
+        [0, 5, 10, 5],
+        [0, 5, 5, 5]
+      ]
+    },
+    "temperature": 15,
+    "volume": {
+      "default": {
+        "storage": "const",
+        "value": 300
+      },
+      "lambda": {
+        "storage": "const",
+        "value": 10
+      }
+    },
+    "potential": {
+      "direction": [1, 1, 0],
+      "coupling": [0, 150, 100, 50]
+    },
+    "surface": {
+      "default": {
+        "storage": "const",
+        "value": 400
+      },
+      "lambda": {
+        "storage": "const",
+        "value": 10
+      }
+    },
+    "cleaner": {
+      "killdistance": 100
+    },
+    "checkerboard": "00",
+    "energyfunctions": ["Volume00", "Surface00", "Adhesion00", "Potential00"],
+    "centerofmass": {
+      "steps": 10
+    },
+    "dynamicecm": {
+      "enabled": true,
+      "deltat": 0.1,
+      "eta": 0.5
+    }
+  },
+  "Writers": {
+    "ParallelVTK_Displacement": {
+      "writer": "ParallelVtkImage",
+      "outputtype": "Float32",
+      "field": "dynamicecm_displacement",
+      "steps": 1
+    }
+  },
+  "WriteActions": ["ParallelVTK_Displacement"]
+}