diff --git a/experiments/configs/comp.json b/experiments/configs/comp.json new file mode 100644 index 0000000..57fea4c --- /dev/null +++ b/experiments/configs/comp.json @@ -0,0 +1,102 @@ +{ + "#Testing": { + "description": "Small experiment for comparing CPU and GPU implementations" + }, + "Application": "Cells", + "Geometry": { + "blocksize": [10, 10, 10], + "blockcount": [1, 1, 1] + }, + "Settings": { + "timesteps": 4, + "randomseed": 42 + }, + "Filling": { + "cells": [ + { + "_comment": "This is for the dynamic ECM", + "shape": "cube", + "box": [ + [0, 0, 0], + [9, 9, 9] + ], + "value": 0, + "celltype": 0 + }, + { + "shape": "cube", + "box": [ + [4, 4, 4], + [7, 7, 7] + ], + "celltype": 2 + } + ] + }, + "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, 64, 64], + "lambda": { + "storage": "const", + "value": 10 + } + }, + "surface": { + "default": [0, 0, 80, 80], + "lambda": { + "storage": "const", + "value": 10 + } + }, + "cleaner": { + "killdistance": 100 + }, + "checkerboard": "00", + "energyfunctions": ["Volume00", "Surface00", "Adhesion00", "DynamicECM00"], + "centerofmass": { + "steps": 10 + }, + "dynamicecm": { + "enabled": true, + "stepsPerMcs": 10, + "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"] +} diff --git a/experiments/configs/mini.json b/experiments/configs/mini.json index dd741da..fdd9bb4 100644 --- a/experiments/configs/mini.json +++ b/experiments/configs/mini.json @@ -4,11 +4,11 @@ }, "Application": "Cells", "Geometry": { - "blocksize": [20, 20, 20], - "blockcount": [2, 1, 1] + "blocksize": [40, 20, 20], + "blockcount": [1, 1, 1] }, "Settings": { - "timesteps": 500, + "timesteps": 200, "randomseed": 42 }, "Filling": { @@ -76,7 +76,7 @@ }, "dynamicecm": { "enabled": true, - "stepsPerMcs": 100, + "stepsPerMcs": 10, "pushSteps": 10, "pushWeight": 2, "ecmCellID": 0, diff --git a/experiments/configs/small.json b/experiments/configs/small.json index 30720d9..d890bec 100644 --- a/experiments/configs/small.json +++ b/experiments/configs/small.json @@ -8,7 +8,7 @@ "blockcount": [1, 1, 1] }, "Settings": { - "timesteps": 1, + "timesteps": 3, "randomseed": 42 }, "Filling": {