From 7f747be334557f001fce48ba95db84d91521fd44 Mon Sep 17 00:00:00 2001
From: Paul Brinkmeier <hallo@pbrinkmeier.de>
Date: Sat, 9 Dec 2023 17:49:19 +0100
Subject: [PATCH] Add two nastja configs

---
 experiments/configs/genesis.json |  79 +++++++++++++++-------
 experiments/configs/mini.json    | 110 +++++++++++++++++++++++++++++++
 2 files changed, 167 insertions(+), 22 deletions(-)
 create mode 100644 experiments/configs/mini.json

diff --git a/experiments/configs/genesis.json b/experiments/configs/genesis.json
index a7d2442..d4c92e6 100644
--- a/experiments/configs/genesis.json
+++ b/experiments/configs/genesis.json
@@ -4,51 +4,74 @@
   },
   "Application": "Cells",
   "Geometry": {
-    "blocksize": [80, 40, 20],
-    "blockcount": [1, 2, 4]
+    "blocksize": [20, 40, 40],
+    "blockcount": [4, 2, 2]
   },
   "Settings": {
-    "timesteps": 100,
+    "timesteps": 250,
     "randomseed": 42
   },
   "Filling": {
     "cells": [
       {
+        "_comment": "This is for the dynamic ECM",
         "shape": "cube",
         "box": [
-          [21, 35, 10],
-          [25, 39, 15]
+          [0, 0, 0],
+          [79, 79, 79]
         ],
+        "value": 0,
         "celltype": 0
       },
       {
         "shape": "cube",
         "box": [
-          [15, 15, 14],
-          [22, 22, 20]
+          [41, 35, 10],
+          [45, 39, 15]
         ],
-        "celltype": 0
+        "celltype": 2
+      },
+      {
+        "shape": "cube",
+        "box": [
+          [40, 15, 14],
+          [47, 22, 20]
+        ],
+        "celltype": 2
+      },
+      {
+        "shape": "cube",
+        "box": [
+          [40, 20, 20],
+          [47, 27, 26]
+        ],
+        "celltype": 3
+      },
+      {
+        "shape": "cube",
+        "box": [
+          [38, 20, 60],
+          [45, 27, 66]
+        ],
+        "celltype": 3
       }
     ]
   },
   "CellsInSilico": {
+    "liquid": 1,
     "adhesion": {
       "matrix": [
-        [0, 0, 0, 0],
-        [0, 20, 5, 5],
-        [0, 5, 10, 5],
-        [0, 5, 5, 5]
+        [0, 0,  0, 0],
+        [0, 0,  0, 0],
+        [0, 0, 10, 5],
+        [0, 0,  5, 5]
       ]
     },
-    "potential": {
-      "direction": [1, 1, 0],
-      "coupling": [0, 150, 100, 50]
-    },
     "temperature": 15,
     "volume": {
       "default": {
         "storage": "const",
-        "value": 300
+        "value": 2000
       },
       "lambda": {
         "storage": "const",
@@ -58,7 +81,7 @@
     "surface": {
       "default": {
         "storage": "const",
-        "value": 400
+        "value": 800
       },
       "lambda": {
         "storage": "const",
@@ -69,13 +92,24 @@
       "killdistance": 100
     },
     "checkerboard": "00",
-    "energyfunctions": ["Volume00", "Surface00", "Adhesion00", "Potential00"],
+    "energyfunctions": ["Volume00", "Surface00", "Adhesion00", "DynamicECM00"],
     "centerofmass": {
       "steps": 10
     },
     "dynamicecm": {
       "enabled": true,
-      "deltat": 0.1
+      "stepsPerMcs": 100,
+      "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": {
@@ -83,12 +117,13 @@
       "writer": "ParallelVtkImage",
       "outputtype": "UInt32",
       "field": "cells",
-      "steps": 5
+      "steps": 1
     },
     "ParallelVTK_Displacement": {
       "writer": "ParallelVtkImage",
       "outputtype": "Float32",
-      "field": "dynamicecm_displacement",
+      "field": "dynamicecm",
+      "components": [0, 1, 2],
       "steps": 1
     }
   },
diff --git a/experiments/configs/mini.json b/experiments/configs/mini.json
new file mode 100644
index 0000000..dd741da
--- /dev/null
+++ b/experiments/configs/mini.json
@@ -0,0 +1,110 @@
+{
+  "#Testing": {
+    "description": "Cellular Potts Model with dynamic ECM, small experiment"
+  },
+  "Application": "Cells",
+  "Geometry": {
+    "blocksize": [20, 20, 20],
+    "blockcount": [2, 1, 1]
+  },
+  "Settings": {
+    "timesteps": 500,
+    "randomseed": 42
+  },
+  "Filling": {
+    "cells": [
+      {
+        "_comment": "This is for the dynamic ECM",
+        "shape": "cube",
+        "box": [
+          [10, 0, 0],
+          [39, 19, 19]
+        ],
+        "value": 0,
+        "celltype": 0
+      },
+      {
+        "shape": "cube",
+        "box": [
+          [2, 8, 8],
+          [9, 13, 13]
+        ],
+        "celltype": 2
+      },
+      {
+        "shape": "cube",
+        "box": [
+          [30, 8, 8],
+          [37, 13, 13]
+        ],
+        "celltype": 3
+      }
+    ]
+  },
+  "CellsInSilico": {
+    "liquid": 1,
+    "adhesion": {
+      "matrix": [
+        [0, 0,  0, 0],
+        [0, 0,  0, 0],
+        [0, 0, 10, 5],
+        [0, 0,  5, 5]
+      ]
+    },
+    "temperature": 15,
+    "volume": {
+      "default": [0, 0, 7000, 1000],
+      "lambda": {
+        "storage": "const",
+        "value": 10
+      }
+    },
+    "surface": {
+      "default": [0, 0, 2500, 1000],
+      "lambda": {
+        "storage": "const",
+        "value": 10
+      }
+    },
+    "cleaner": {
+      "killdistance": 100
+    },
+    "checkerboard": "00",
+    "energyfunctions": ["Volume00", "Surface00", "Adhesion00", "DynamicECM00"],
+    "centerofmass": {
+      "steps": 10
+    },
+    "dynamicecm": {
+      "enabled": true,
+      "stepsPerMcs": 100,
+      "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,
+      "lambda": 50
+    }
+  },
+  "Writers": {
+    "ParallelVTK_Cells": {
+      "writer": "ParallelVtkImage",
+      "outputtype": "UInt32",
+      "field": "cells",
+      "steps": 1
+    },
+    "ParallelVTK_Displacement": {
+      "writer": "ParallelVtkImage",
+      "outputtype": "Float32",
+      "field": "dynamicecm",
+      "components": [0, 1, 2],
+      "steps": 1
+    }
+  },
+  "WriteActions": ["ParallelVTK_Cells", "ParallelVTK_Displacement"]
+}