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Add two nastja configs

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This commit is contained in:
Paul Brinkmeier 2023-12-09 17:49:19 +01:00
parent d68f8b9cd9
commit 7f747be334
2 changed files with 167 additions and 22 deletions
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79
experiments/configs/genesis.json
View File

@ -4,51 +4,74 @@
},
"Application": "Cells",
"Geometry": {
"blocksize": [80, 40, 20],
"blockcount": [1, 2, 4]
"blocksize": [20, 40, 40],
"blockcount": [4, 2, 2]
},
"Settings": {
"timesteps": 100,
"timesteps": 250,
"randomseed": 42
},
"Filling": {
"cells": [
{
"_comment": "This is for the dynamic ECM",
"shape": "cube",
"box": [
[21, 35, 10],
[25, 39, 15]
[0, 0, 0],
[79, 79, 79]
],
"value": 0,
"celltype": 0
},
{
"shape": "cube",
"box": [
[15, 15, 14],
[22, 22, 20]
[41, 35, 10],
[45, 39, 15]
],
"celltype": 0
"celltype": 2
},
{
"shape": "cube",
"box": [
[40, 15, 14],
[47, 22, 20]
],
"celltype": 2
},
{
"shape": "cube",
"box": [
[40, 20, 20],
[47, 27, 26]
],
"celltype": 3
},
{
"shape": "cube",
"box": [
[38, 20, 60],
[45, 27, 66]
],
"celltype": 3
}
]
},
"CellsInSilico": {
"liquid": 1,
"adhesion": {
"matrix": [
[0, 0, 0, 0],
[0, 20, 5, 5],
[0, 5, 10, 5],
[0, 5, 5, 5]
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 10, 5],
[0, 0, 5, 5]
]
},
"potential": {
"direction": [1, 1, 0],
"coupling": [0, 150, 100, 50]
},
"temperature": 15,
"volume": {
"default": {
"storage": "const",
"value": 300
"value": 2000
},
"lambda": {
"storage": "const",
@ -58,7 +81,7 @@
"surface": {
"default": {
"storage": "const",
"value": 400
"value": 800
},
"lambda": {
"storage": "const",
@ -69,13 +92,24 @@
"killdistance": 100
},
"checkerboard": "00",
"energyfunctions": ["Volume00", "Surface00", "Adhesion00", "Potential00"],
"energyfunctions": ["Volume00", "Surface00", "Adhesion00", "DynamicECM00"],
"centerofmass": {
"steps": 10
},
"dynamicecm": {
"enabled": true,
"deltat": 0.1
"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": {
@ -83,12 +117,13 @@
"writer": "ParallelVtkImage",
"outputtype": "UInt32",
"field": "cells",
"steps": 5
"steps": 1
},
"ParallelVTK_Displacement": {
"writer": "ParallelVtkImage",
"outputtype": "Float32",
"field": "dynamicecm_displacement",
"field": "dynamicecm",
"components": [0, 1, 2],
"steps": 1
}
},

110
experiments/configs/mini.json Normal file
View File

@ -0,0 +1,110 @@
{
"#Testing": {
"description": "Cellular Potts Model with dynamic ECM, small experiment"
},
"Application": "Cells",
"Geometry": {
"blocksize": [20, 20, 20],
"blockcount": [2, 1, 1]
},
"Settings": {
"timesteps": 500,
"randomseed": 42
},
"Filling": {
"cells": [
{
"_comment": "This is for the dynamic ECM",
"shape": "cube",
"box": [
[10, 0, 0],
[39, 19, 19]
],
"value": 0,
"celltype": 0
},
{
"shape": "cube",
"box": [
[2, 8, 8],
[9, 13, 13]
],
"celltype": 2
},
{
"shape": "cube",
"box": [
[30, 8, 8],
[37, 13, 13]
],
"celltype": 3
}
]
},
"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, 7000, 1000],
"lambda": {
"storage": "const",
"value": 10
}
},
"surface": {
"default": [0, 0, 2500, 1000],
"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,
"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"]
}