diff --git a/experiments/configs/medium.json b/experiments/configs/medium.json new file mode 100644 index 0000000..f7d93d2 --- /dev/null +++ b/experiments/configs/medium.json @@ -0,0 +1,109 @@ +{ + "#Testing": { + "description": "Cellular Potts Model with dynamic ECM" + }, + "Application": "Cells", + "Geometry": { + "blocksize": [90, 90, 60], + "blockcount": [2, 2, 3] + }, + "Settings": { + "timesteps": 100, + "randomseed": 42 + }, + "Filling": { + "cells": [ + { + "_comment": "This is for the dynamic ECM", + "shape": "cube", + "box": [ + [0, 0, 0], + [179, 179, 179] + ], + "value": 0, + "celltype": 0 + }, + { + "shape": "cube", + "pattern": "voronoi", + "box": [ + [20, 20, 20], + [159, 159, 159] + ], + "count": 1500, + "celltype": [0, 0, 750, 750] + } + ] + }, + "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": { + "storage": "const", + "value": 2000 + }, + "lambda": { + "storage": "const", + "value": 10 + } + }, + "surface": { + "default": { + "storage": "const", + "value": 800 + }, + "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 + } + }, + "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"] +}