Update small.json for CUDA testing

.gitignore

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

experiments/configs/small.json

@@ -1,21 +1,40 @@
 {
   "#Testing": {
-    "description": "Cellular Potts Model with dynamic ECM"
+    "description": "Minimal config for debugging CUDA code"
   },
   "Application": "Cells",
   "Geometry": {
-    "blocksize": [15, 15, 15],
+    "blocksize": [5, 5, 5],
     "blockcount": [1, 1, 1]
   },
   "Settings": {
-    "timesteps": 100,
+    "timesteps": 1,
     "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],
@@ -53,12 +72,15 @@
       "killdistance": 100
     },
     "checkerboard": "00",
-    "energyfunctions": ["Volume00", "Surface00", "Adhesion00", "Potential00"],
+    "energyfunctions": ["Volume00", "Surface00", "Adhesion00", "Potential00", "DynamicECM00"],
     "centerofmass": {
       "steps": 10
     },
     "dynamicecm": {
       "enabled": true,
+      "ecmCellID": 0,
+      "stepsPerMcs": 1,
+      "pushSteps": 1,
       "deltat": 0.1,
       "eta": 0.5
     }
@@ -67,7 +89,7 @@
     "ParallelVTK_Displacement": {
       "writer": "ParallelVtkImage",
       "outputtype": "Float32",
-      "field": "dynamicecm_displacement",
+      "field": "dynamicecm",
       "steps": 1
     }
   },

experiments/requirements.txt

@@ -1,98 +1 @@
-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
+click==8.1.7