111 lines
2.1 KiB
JSON
111 lines
2.1 KiB
JSON
{
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"#Testing": {
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"description": "Cellular Potts Model with dynamic ECM, small experiment"
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},
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"Application": "Cells",
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"Geometry": {
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"blocksize": [20, 20, 20],
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"blockcount": [2, 1, 1]
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},
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"Settings": {
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"timesteps": 500,
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"randomseed": 42
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},
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"Filling": {
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"cells": [
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{
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"_comment": "This is for the dynamic ECM",
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"shape": "cube",
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"box": [
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[10, 0, 0],
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[39, 19, 19]
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],
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"value": 0,
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"celltype": 0
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},
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{
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"shape": "cube",
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"box": [
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[2, 8, 8],
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[9, 13, 13]
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],
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"celltype": 2
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},
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{
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"shape": "cube",
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"box": [
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[30, 8, 8],
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[37, 13, 13]
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],
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"celltype": 3
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}
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]
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},
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"CellsInSilico": {
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"liquid": 1,
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"adhesion": {
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"matrix": [
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[0, 0, 0, 0],
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[0, 0, 0, 0],
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[0, 0, 10, 5],
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[0, 0, 5, 5]
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]
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},
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"temperature": 15,
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"volume": {
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"default": [0, 0, 7000, 1000],
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"lambda": {
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"storage": "const",
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"value": 10
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}
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},
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"surface": {
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"default": [0, 0, 2500, 1000],
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"lambda": {
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"storage": "const",
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"value": 10
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}
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},
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"cleaner": {
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"killdistance": 100
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},
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"checkerboard": "00",
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"energyfunctions": ["Volume00", "Surface00", "Adhesion00", "DynamicECM00"],
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"centerofmass": {
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"steps": 10
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},
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"dynamicecm": {
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"enabled": true,
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"stepsPerMcs": 100,
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"pushSteps": 10,
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"pushWeight": 2,
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"ecmCellID": 0,
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"deltat": 0.1,
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"eta": 0.25,
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"k0": 0.1,
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"k1": 0.1,
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"c": 4,
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"alpha": 2,
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"d": 0.3,
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"phi": 1,
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"lambda": 50
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}
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},
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"Writers": {
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"ParallelVTK_Cells": {
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"writer": "ParallelVtkImage",
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"outputtype": "UInt32",
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"field": "cells",
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"steps": 1
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},
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"ParallelVTK_Displacement": {
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"writer": "ParallelVtkImage",
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"outputtype": "Float32",
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"field": "dynamicecm",
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"components": [0, 1, 2],
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"steps": 1
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}
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},
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"WriteActions": ["ParallelVTK_Cells", "ParallelVTK_Displacement"]
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}
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