Add some recent stuff

experiments/ELM_Debug.ipynb

@@ -248,7 +248,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.10.11"
   }
  },
  "nbformat": 4,

experiments/collatz.py

@@ -0,0 +1,31 @@
+import time
+
+def collatz(x):
+    seq = [x]
+    while x != 1:
+        if x % 2 == 0:
+            x //= 2
+        else:
+            x = 3 * x + 1
+        seq.append(x)
+    return seq
+
+if __name__ == "__main__":
+    best = None
+    try:
+        i = 1
+        start = time.time()
+        while True:
+            pair = (i, collatz(i))
+
+            if (not best or len(pair[1]) > len(best[1])) and not any(c >= 2**31 for c in pair[1]):
+                best = pair
+
+            if i % 10000 == 0:
+                now = time.time()
+                print(f"{i:>10}   best: {best[0]:>10} {len(best[1]):>5} {(now - start) * 1000 / i:5.2}ns/seq")
+            i += 1
+    except KeyboardInterrupt:
+        pass
+    
+    print(best)

experiments/configs/genesis.json

@@ -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"]
+}

experiments/configs/small.json

@@ -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"]
+}