From 9d7b0028a603a2f826ee57d23c2317756e6dc383 Mon Sep 17 00:00:00 2001
From: Paul Brinkmeier <hallo@pbrinkmeier.de>
Date: Mon, 5 Feb 2024 13:28:47 +0100
Subject: [PATCH] Add Erics spheroid config for reference

---
 experiments/configs/spheroid/config.json      | 116 ++++++++++++++++++
 .../configs/spheroid/config_filling_1.json    |  44 +++++++
 2 files changed, 160 insertions(+)
 create mode 100644 experiments/configs/spheroid/config.json
 create mode 100644 experiments/configs/spheroid/config_filling_1.json

diff --git a/experiments/configs/spheroid/config.json b/experiments/configs/spheroid/config.json
new file mode 100644
index 0000000..1118fb9
--- /dev/null
+++ b/experiments/configs/spheroid/config.json
@@ -0,0 +1,116 @@
+{
+    "Comments": ["Celltype         Usage", "0                Not Used", "1-5             Solids for blood vessels / ECM", "6               Liquid  ", "7               Apoptotic cell Type ", "8               Basic Non Dividing Cell type (surrounding)", "9               Cancer"],
+    "Application": "Cells",
+    "CellsInSilico": {
+        "ecmdegradation": {
+            "enabled": "false",
+            "steps": 99999,
+            "stochastic": "true",
+            "probability": 0.5
+        },
+        "energyfunctions": ["Volume00", "Surface01", "Motility00", "Adhesion01", "DynamicECM00"],
+        "liquid": 6,
+        "volume": {
+            "default": {
+                "storage": "const",
+                "value": 500
+            },
+            "lambda": [0, 0, 0, 0, 0, 0, 0, 7.5, 7.5, 7.5],
+            "sizechange": [0, 0, 0, 0, 0, 0, 0, -0.05, 0, 0, 0, 0, 0, 0, 0]
+        },
+        "surface": {
+            "default": {
+                "storage": "const",
+                "value": 400
+            },
+            "lambda": [0, 0, 0, 0, 0, 0, 0, 5.625, 5.625, 1],
+            "sizechange": [0, 0, 0, 0, 0, 0, 0, -0.05, 0, 0, 0, 0, 0, 0, 0, 0]
+        },
+        "adhesion": {
+            "matrix": [
+                [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+                [0, 0, 0, 0, 0, 0, 0, 0, 0, 450],
+                [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+                [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+                [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+                [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+                [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+                [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+                [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+                [0, 450, 0, 0, 0, 0, 0, 0, 0, 50]
+            ]
+        },
+        "temperature": 50,
+        "division": {
+            "enabled": "true",
+            "condition": ["", "", "", "", "", "", "", "", "", "( volume >= 0.9 * volume0 )  & ( rnd() <= 0.00001 ) & generation < 1"]
+        },
+        "centerofmass": {
+            "steps": 1
+        },
+        "signaling": {
+            "enabled": false
+        },
+        "orientation": {
+            "enabled": true,
+            "motility": "persistentRandomWalk",
+            "persistenceMagnitude": 0.0,
+            "recalculationtime": 200,
+            "motilityamount": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
+        },
+        "visitor": {
+            "stepwidth": 10,
+            "checkerboard": "01"
+        },
+        "cleaner": {
+            "killDistance": 20
+        },
+        "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
+        }
+    },
+    "Geometry": {
+        "blockcount": [8, 8, 6],
+        "blocksize": [50, 50, 67]
+    },
+    "Settings": {
+        "randomseed": 0,
+        "timesteps": 100
+    },
+    "WriteActions": ["CellInfo"],
+    "Writers": {
+        "CellInfo": {
+            "field": "",
+            "groupsize": 0,
+            "steps": 1,
+            "writer": "CellInfo"
+        },
+        "ParallelVTK_Cells": {
+            "field": "cells",
+            "outputtype": "UInt32",
+            "printhints": false,
+            "steps": 1,
+            "writer": "ParallelVtkImage"
+        },
+        "ParallelVTK_Displacement": {
+            "writer": "ParallelVtkImage",
+            "outputtype": "Float32",
+            "field": "dynamicecm",
+            "components": [0, 1, 2],
+            "steps": 1
+        }
+    },
+    "Include": "config_filling_1.json"
+}
diff --git a/experiments/configs/spheroid/config_filling_1.json b/experiments/configs/spheroid/config_filling_1.json
new file mode 100644
index 0000000..113aece
--- /dev/null
+++ b/experiments/configs/spheroid/config_filling_1.json
@@ -0,0 +1,44 @@
+{
+    "DefineFunctions": [
+        "r_angle()=360*rnd()",
+        "r_size()=400*rnd()"
+    ],
+    "Filling": {
+        "cells": [
+            {
+                "_comment": "This is for the dynamic ECM",
+                "shape": "cube",
+                "box": [
+                  [0, 0, 0],
+                  [399, 399, 401]
+                ],
+                "value": 0,
+                "celltype": 0
+            },
+            {
+                "shape": "sphere",
+                "pattern": "voronoi",
+                "count": 5500,
+                "radius": 75,
+                "center": [
+                    200,
+                    200,
+                    200
+                ],
+                "box": [
+                    [
+                        110,
+                        110,
+                        110
+                    ],
+                    [
+                        290,
+                        290,
+                        290
+                    ]
+                ],
+                "celltype": 9
+            }
+        ]
+    }
+}