.gitignore

@@ -1,4 +1,2 @@
 *.swp
 outdir
-venv
-dump

experiments/configs/small.json

@@ -1,40 +1,21 @@
 {
   "#Testing": {
-    "description": "Minimal config for debugging CUDA code"
+    "description": "Cellular Potts Model with dynamic ECM"
   },
   "Application": "Cells",
   "Geometry": {
-    "blocksize": [5, 5, 5],
+    "blocksize": [15, 15, 15],
     "blockcount": [1, 1, 1]
   },
   "Settings": {
-    "timesteps": 1,
+    "timesteps": 100,
     "randomseed": 42
   },
   "Filling": {
     "cells": [
-      {
-        "_comment": "This is for the dynamic ECM",
-        "shape": "cube",
-        "box": [
-          [0, 0, 0],
-          [4, 2, 4]
-        ],
-        "value": 0,
-        "celltype": 0
-      },
-      {
-        "shape": "cube",
-        "box": [
-          [1, 1, 1],
-          [3, 3, 3]
-        ],
-        "celltype": 2
-      }
     ]
   },
   "CellsInSilico": {
-    "liquid": 1,
     "adhesion": {
       "matrix": [
         [0, 0, 0, 0],
@@ -72,15 +53,12 @@
       "killdistance": 100
     },
     "checkerboard": "00",
-    "energyfunctions": ["Volume00", "Surface00", "Adhesion00", "Potential00", "DynamicECM00"],
+    "energyfunctions": ["Volume00", "Surface00", "Adhesion00", "Potential00"],
     "centerofmass": {
       "steps": 10
     },
     "dynamicecm": {
       "enabled": true,
-      "ecmCellID": 0,
-      "stepsPerMcs": 1,
-      "pushSteps": 1,
       "deltat": 0.1,
       "eta": 0.5
     }
@@ -89,7 +67,7 @@
     "ParallelVTK_Displacement": {
       "writer": "ParallelVtkImage",
       "outputtype": "Float32",
-      "field": "dynamicecm",
+      "field": "dynamicecm_displacement",
       "steps": 1
     }
   },

experiments/requirements.txt

@@ -1 +1,98 @@
-click==8.1.7
+anyio==3.7.0
+argon2-cffi==21.3.0
+argon2-cffi-bindings==21.2.0
+arrow==1.2.3
+asttokens==2.2.1
+async-lru==2.0.2
+attrs==23.1.0
+Babel==2.12.1
+backcall==0.2.0
+beautifulsoup4==4.12.2
+bleach==6.0.0
+certifi==2023.5.7
+cffi==1.15.1
+charset-normalizer==3.1.0
+comm==0.1.3
+contourpy==1.1.0
+cycler==0.11.0
+debugpy==1.6.7
+decorator==5.1.1
+defusedxml==0.7.1
+exceptiongroup==1.1.1
+executing==1.2.0
+fastjsonschema==2.17.1
+fonttools==4.40.0
+fqdn==1.5.1
+idna==3.4
+ipykernel==6.23.2
+ipython==8.14.0
+ipywidgets==8.0.6
+isoduration==20.11.0
+jedi==0.18.2
+Jinja2==3.1.2
+json5==0.9.14
+jsonpointer==2.3
+jsonschema==4.17.3
+jupyter-events==0.6.3
+jupyter-lsp==2.2.0
+jupyter_client==8.2.0
+jupyter_core==5.3.1
+jupyter_server==2.6.0
+jupyter_server_terminals==0.4.4
+jupyterlab==4.0.2
+jupyterlab-pygments==0.2.2
+jupyterlab-widgets==3.0.7
+jupyterlab_server==2.23.0
+kiwisolver==1.4.4
+MarkupSafe==2.1.3
+matplotlib==3.7.1
+matplotlib-inline==0.1.6
+mistune==2.0.5
+nbclient==0.8.0
+nbconvert==7.5.0
+nbformat==5.9.0
+nest-asyncio==1.5.6
+notebook_shim==0.2.3
+numpy==1.24.3
+overrides==7.3.1
+packaging==23.1
+pandocfilters==1.5.0
+parso==0.8.3
+pexpect==4.8.0
+pickleshare==0.7.5
+Pillow==9.5.0
+platformdirs==3.5.3
+prometheus-client==0.17.0
+prompt-toolkit==3.0.38
+psutil==5.9.5
+ptyprocess==0.7.0
+pure-eval==0.2.2
+pycparser==2.21
+Pygments==2.15.1
+pyparsing==3.0.9
+pyrsistent==0.19.3
+python-dateutil==2.8.2
+python-json-logger==2.0.7
+PyYAML==6.0
+pyzmq==25.1.0
+requests==2.31.0
+rfc3339-validator==0.1.4
+rfc3986-validator==0.1.1
+Send2Trash==1.8.2
+six==1.16.0
+sniffio==1.3.0
+soupsieve==2.4.1
+stack-data==0.6.2
+terminado==0.17.1
+tinycss2==1.2.1
+tomli==2.0.1
+tornado==6.3.2
+traitlets==5.9.0
+typing_extensions==4.6.3
+uri-template==1.2.0
+urllib3==2.0.3
+wcwidth==0.2.6
+webcolors==1.13
+webencodings==0.5.1
+websocket-client==1.5.3
+widgetsnbextension==4.0.7