Experiment state

2023-12-15 15:12:14 +01:00
parent c7d4a50a85
commit 409ec8b4c2
10 changed files with 199 additions and 4 deletions
@@ -0,0 +1,99 @@
+{
+  "#Testing": {
+    "description": "Cellular Potts Model with dynamic ECM"
+  },
+  "Application": "Cells",
+  "Geometry": {
+    "blocksize": [30, 30, 40],
+    "blockcount": [4, 4, 3]
+  },
+  "Settings": {
+    "timesteps": 500,
+    "randomseed": 42
+  },
+  "Filling": {
+    "cells": [
+      {
+        "_comment": "This is for the dynamic ECM",
+        "shape": "cube",
+        "box": [
+          [0, 0, 0],
+          [119, 119, 119]
+        ],
+        "value": 0,
+        "celltype": 0
+      }
+    ]
+  },
+  "CellsInSilico": {
+    "liquid": 1,
+    "adhesion": {
+      "matrix": [
+        [ 0, 0,  0, 10],
+        [ 0, 0,  0, 10],
+        [10, 0, 40,  5],
+        [10, 0,  5, 40]
+      ]
+    },
+    "temperature": 15,
+    "volume": {
+      "default": {
+        "storage": "const",
+        "value": 5000
+      },
+      "lambda": {
+        "storage": "const",
+        "value": 10
+      }
+    },
+    "surface": {
+      "default": {
+        "storage": "const",
+        "value": 1000
+      },
+      "lambda": {
+        "storage": "const",
+        "value": 10
+      }
+    },
+    "cleaner": {
+      "killdistance": 100
+    },
+    "checkerboard": "00",
+    "energyfunctions": ["Volume00", "Surface00", "Adhesion00", "DynamicECM00"],
+    "centerofmass": {
+      "steps": 10
+    },
+    "dynamicecm": {
+      "enabled": true,
+      "stepsPerMcs": 200,
+      "pushSteps": 10,
+      "pushWeight": 2,
+      "ecmCellID": 0,
+      "deltat": 0.1,
+      "eta": 0.25,
+      "k0": 0.1,
+      "k1": 0.1,
+      "c": 4,
+      "alpha": 2,
+      "d": 0.3,
+      "phi": 1
+    }
+  },
+  "Writers": {
+    "ParallelVTK_Cells": {
+      "writer": "ParallelVtkImage",
+      "outputtype": "UInt32",
+      "field": "cells",
+      "steps": 5
+    },
+    "ParallelVTK_Displacement": {
+      "writer": "ParallelVtkImage",
+      "outputtype": "Float32",
+      "field": "dynamicecm",
+      "components": [0, 1, 2],
+      "steps": 5
+    }
+  },
+  "WriteActions": ["ParallelVTK_Cells", "ParallelVTK_Displacement"]
+}