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paul
2024-03-08 17:04:58 +01:00
parent 4661646b4f
commit b36d8a748d
6 changed files with 575 additions and 0 deletions
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experiments/configs/julian-animation.json
+330
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@@ -0,0 +1,330 @@
{
"Comments": [
"Celltype Usage",
"0 Dynamic ECM",
"1-5 Not Used",
"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,
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0
],
[
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],
[
0,
0,
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],
[
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],
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],
[
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],
[
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": [
2,
4,
4
],
"blocksize": [
200,
100,
100
]
},
"Settings": {
"randomseed": 0,
"timesteps": 5000,
"statusoutput": 1
},
"WriteActions": ["ParallelVTK_Cells", "ParallelVTK_Displacement"],
"Writers": {
"CellInfo": {
"field": "",
"groupsize": 0,
"steps": 1,
"writer": "CellInfo"
},
"ParallelVTK_Cells": {
"field": "cells",
"outputtype": "UInt32",
"printhints": false,
"steps": 100,
"writer": "ParallelVtkImage"
},
"ParallelVTK_Displacement": {
"writer": "ParallelVtkImage",
"outputtype": "Float32",
"field": "dynamicecm",
"components": [
0,
1,
2
],
"steps": 100
}
},
"Include": "measurements/strong/config_filling_1.json"
}