New: failed analytics

.gitignore

@@ -18,3 +18,4 @@ env/
 *.toc
 *.out
 *.egg-info
+.ipynb_checkpoints/

playground/training-models.ipynb

@@ -39,17 +39,25 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "86b8162b-ed07-4c65-9c31-3f18daafc915",
+   "id": "3bc80bca-03ce-416e-be2f-ab7ae2af95fa",
    "metadata": {},
    "outputs": [],
    "source": [
-    "df_keys = [ key for key in df.keys() ]"
+    "df_numeric = df[[\n",
+    "    col for col in df.columns \n",
+    "        if not isinstance(df[col][0], str) \n",
+    "            and not isinstance(df[col][0], numpy.bool_)\n",
+    "            and not isinstance(df[col][0], dict)\n",
+    "            and not isinstance(df[col][0], list)\n",
+    "            and not df[col][0] is None\n",
+    "            and not col[-3: ] == \"_id\"\n",
+    "]]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 5,
-   "id": "3bc80bca-03ce-416e-be2f-ab7ae2af95fa",
+   "id": "eab92bcc-8f1f-4490-8dc6-8ebf191d6cf2",
    "metadata": {},
    "outputs": [
     {
@@ -58,7 +66,7 @@
        "<AxesSubplot:>"
       ]
      },
-     "execution_count": 18,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     },
@@ -74,21 +82,190 @@
     }
    ],
    "source": [
-    "df_numeric = df[[\n",
-    "    col for col in df.columns \n",
-    "        if not isinstance(df[col][0], str) \n",
-    "            and not isinstance(df[col][0], numpy.bool_)\n",
-    "            and not isinstance(df[col][0], dict)\n",
-    "            and not col[-3: ] == \"_id\"\n",
-    "]]\n",
     "seaborn.set(rc = { \"figure.figsize\": (30, 20) })\n",
     "seaborn.heatmap(df_numeric.corr(), annot = True)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "7611c892-1e13-404e-849e-3cfa15d8dfca",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "x = df_numeric[[\"theta\", \"r0\", \"L\", \"radius\"]] #.drop(columns = [\"flowRate\"])\n",
+    "y = df_numeric[\"flowRate\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "1a38aaa0-89fb-40f7-abce-e500ab696349",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from sklearn.model_selection import train_test_split\n",
+    "xtr, xte, ytr, yte = train_test_split(x, y, test_size = 0.2, random_state = 100)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "1b7e9f62-35a9-4a1a-9ffa-a2a6e757ff46",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from sklearn import preprocessing\n",
+    "scaler = preprocessing.MinMaxScaler()\n",
+    "x_scaled = scaler.fit_transform(xtr)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "19bd2f52-a5bf-404c-93f7-0626bc35a915",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "DecisionTreeRegressor(random_state=500)"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from sklearn.tree import DecisionTreeRegressor\n",
+    "neigh = DecisionTreeRegressor(random_state = 500)\n",
+    "neigh.fit(x_scaled, ytr)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "d063265f-2f06-4290-811e-b6b1753bcac9",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "2.664398739090909e-15"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from sklearn.metrics import mean_absolute_error\n",
+    "xte_scaled = scaler.transform(xte)\n",
+    "y_pred = neigh.predict(xte_scaled)\n",
+    "mean_absolute_error(yte, y_pred)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "762af50c-371a-4ba5-b5ab-763970ef2a37",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#df_numeric[[\"theta\", \"r0\", \"L\", \"radius\", \"flowRate\", \"volumeCell\", \"volume\"]]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "7a951647-efa1-4231-b96d-f67bc0ed6c33",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>theta</th>\n",
+       "      <th>r0</th>\n",
+       "      <th>L</th>\n",
+       "      <th>radius</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>0.29</td>\n",
+       "      <td>1.0</td>\n",
+       "      <td>2.0</td>\n",
+       "      <td>1.408451</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "   theta   r0    L    radius\n",
+       "0   0.29  1.0  2.0  1.408451"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "test_df = DataFrame([{\n",
+    "    \"theta\": 0.29,\n",
+    "    \"r0\": 1.,\n",
+    "    \"L\": 2.,\n",
+    "    \"radius\": 1. / (1. - 0.29)\n",
+    "}]); test_df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "bc9204db-bde4-4032-b4f5-313e99e25ab5",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "array([4.53058768e-15])"
+      ]
+     },
+     "execution_count": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "neigh.predict(scaler.transform(test_df))"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1fda6819-a8da-4751-be3d-d62320b799ae",
+   "id": "4b95277f-c49e-42b9-8d5f-3334d5ca7729",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -96,15 +273,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f19311bb-e992-4592-83b2-0b003a6b78ae",
+   "id": "c56035b1-18d5-4c88-94b6-da4d7eccac9a",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7f06bc5b-80ba-4763-8fec-121c0623ccf2",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -112,7 +281,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -126,7 +295,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.9.6"
   }
  },
  "nbformat": 4,

playground/woPrismaticLayer-2/anisotropy.toml

@@ -0,0 +1,281 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
+[logger]
+name = "anisotropy"
+format = "[ %(levelname)s ] %(message)s"
+
+[base]
+simple = true 
+bodyCentered = true 
+faceCentered = true 
+
+[[structures]]
+    [structures.structure]
+    type = "simple"
+    # auto # from theta: list # theta: float
+    theta = [0.01, 0.28, 0.01]  # [min, max, step]
+    # auto # from directions:list # direction: list
+    directions = [  
+        [1, 0, 0],
+        [0, 0, 1],
+        [1, 1, 1]
+    ]
+
+    # r0 = 
+    # L = 
+    # radius = 
+
+    filletsEnabled = true
+    # auto # fillets: float
+
+    [structures.mesh]
+    maxSize = 0.5
+    minSize = 0.05
+
+    fineness = 5
+    growthRate = 0.5
+    nbSegPerEdge = 2
+    nbSegPerRadius = 1
+    
+    chordalErrorEnabled = true
+    chordalError = 0.25
+    
+    secondOrder = false
+    optimize = true
+    quadAllowed = false
+    useSurfaceCurvature = true
+    fuseEdges = true
+    checkChartBoundary = false
+
+    viscousLayers = false
+    thickness = [0.01, 0.005]   # [min, max] # step is controlled by theta count
+    numberOfLayers = 1
+    stretchFactor = 1
+    isFacesToIgnore = true 
+    facesToIgnore = ["inlet", "outlet"]
+    # auto # faces: list
+    extrusionMethod = "SURF_OFFSET_SMOOTH"
+
+    [[structures.submesh]]
+    name = "strips"
+    maxSize = 0.5
+    minSize = 0.05
+
+    fineness = 5
+    growthRate = 0.2
+    nbSegPerEdge = 2
+    nbSegPerRadius = 3
+    
+    chordalErrorEnabled = true
+    chordalError = 0.25
+    
+    secondOrder = false
+    optimize = true
+    quadAllowed = false
+    useSurfaceCurvature = true
+    fuseEdges = true
+    checkChartBoundary = false
+
+    [structures.flowapproximation]
+    transportProperties.nu = 1e-6
+
+    pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
+    pressure.boundaryField.outlet = { type = "fixedValue", value = 0.0 }
+
+    # multiplication velocity value with flow direction vector
+    velocity.boundaryField.inlet = { type = "fixedValue", value = 6e-5 }
+    velocity.boundaryField.outlet = { type = "zeroGradient", value = "None" }
+
+    [structures.flow]
+    scale = [ 1e-5, 1e-5, 1e-5 ]
+
+    transportProperties.nu = 1e-6
+
+    pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
+    pressure.boundaryField.outlet = { type = "fixedValue", value = 0.0 }
+
+    velocity.boundaryField.inlet = { type = "pressureInletVelocity", value = 0.0 }
+    velocity.boundaryField.outlet = { type = "zeroGradient", value = "None" }
+
+
+[[structures]]
+    [structures.structure]
+    type = "bodyCentered"
+    # auto # from theta: list # theta: float
+    theta = [0.01, 0.17, 0.01]  # [min, max, step]
+    # auto # from directions:list # direction: list
+    directions = [  
+        [1, 0, 0],
+        [0, 0, 1],
+        [1, 1, 1]
+    ]
+
+    # r0 = 
+    # L = 
+    # radius = 
+
+    filletsEnabled = true
+    # auto # fillets: float
+
+    [structures.mesh]
+    maxSize = 0.5
+    minSize = 0.05
+
+    fineness = 5
+    growthRate = 0.5
+    nbSegPerEdge = 2
+    nbSegPerRadius = 1
+    
+    chordalErrorEnabled = true
+    chordalError = 0.25
+    
+    secondOrder = false
+    optimize = true
+    quadAllowed = false
+    useSurfaceCurvature = true
+    fuseEdges = true
+    checkChartBoundary = false
+
+    viscousLayers = false
+    thickness = [0.005, 0.0005]   # [min, max] # step is controlled by theta count
+    numberOfLayers = 1
+    stretchFactor = 1
+    isFacesToIgnore = true 
+    facesToIgnore = ["inlet", "outlet"]
+    # auto # faces: list
+    extrusionMethod = "SURF_OFFSET_SMOOTH"
+
+    [[structures.submesh]]
+    name = "strips"
+    maxSize = 0.5
+    minSize = 0.05
+
+    fineness = 5
+    growthRate = 0.2
+    nbSegPerEdge = 2
+    nbSegPerRadius = 3
+    
+    chordalErrorEnabled = true
+    chordalError = 0.25
+    
+    secondOrder = false
+    optimize = true
+    quadAllowed = false
+    useSurfaceCurvature = true
+    fuseEdges = true
+    checkChartBoundary = false
+
+    [structures.flowapproximation]
+    transportProperties.nu = 1e-6
+
+    pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
+    pressure.boundaryField.outlet = { type = "fixedValue", value = 0.0 }
+
+    # multiplication velocity value with direction vector
+    velocity.boundaryField.inlet = { type = "fixedValue", value = 6e-5 }
+    velocity.boundaryField.outlet = { type = "zeroGradient", value = "None" }
+
+    [structures.flow]
+    scale = [ 1e-5, 1e-5, 1e-5 ]
+
+    transportProperties.nu = 1e-6
+
+    pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
+    pressure.boundaryField.outlet = { type = "fixedValue", value = 0.0 }
+
+    velocity.boundaryField.inlet = { type = "pressureInletVelocity", value = 0.0 }
+    velocity.boundaryField.outlet = { type = "zeroGradient", value = "None" }
+
+
+[[structures]]
+    [structures.structure]
+    type = "faceCentered"
+    # auto # from theta: list # theta: float
+    theta = [0.01, 0.12, 0.01]  # [min, max, step]
+    # auto # from directions:list # direction: list
+    directions = [  
+        [1, 0, 0],
+        [0, 0, 1],
+        [1, 1, 1]
+    ]
+
+    # r0 = 
+    # L = 
+    # radius = 
+
+    filletsEnabled = true
+    # auto # fillets: float
+
+    [structures.mesh]
+    maxSize = 0.5
+    minSize = 0.05
+
+    fineness = 5
+    growthRate = 0.5
+    nbSegPerEdge = 2
+    nbSegPerRadius = 1
+    
+    chordalErrorEnabled = true
+    chordalError = 0.25
+    
+    secondOrder = false
+    optimize = true
+    quadAllowed = false
+    useSurfaceCurvature = true
+    fuseEdges = true
+    checkChartBoundary = false
+
+    viscousLayers = false
+    thickness = [0.001, 0.0005]   # [min, max] # step is controlled by theta count
+    numberOfLayers = 1
+    stretchFactor = 1
+    isFacesToIgnore = true 
+    facesToIgnore = ["inlet", "outlet"]
+    # auto # faces: list
+    extrusionMethod = "SURF_OFFSET_SMOOTH"
+
+    [[structures.submesh]]
+    name = "strips"
+    maxSize = 0.5
+    minSize = 0.05
+
+    fineness = 5
+    growthRate = 0.2
+    nbSegPerEdge = 2
+    nbSegPerRadius = 3
+    
+    chordalErrorEnabled = true
+    chordalError = 0.25
+    
+    secondOrder = false
+    optimize = true
+    quadAllowed = false
+    useSurfaceCurvature = true
+    fuseEdges = true
+    checkChartBoundary = false
+
+    [structures.flowapproximation]
+    transportProperties.nu = 1e-6
+
+    pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
+    pressure.boundaryField.outlet = { type = "fixedValue", value = 0.0 }
+
+    # multiplication velocity value with direction vector
+    velocity.boundaryField.inlet = { type = "fixedValue", value = 6e-5 }
+    velocity.boundaryField.outlet = { type = "zeroGradient", value = "None" }
+
+    [structures.flow]
+    scale = [ 1e-5, 1e-5, 1e-5 ]
+
+    transportProperties.nu = 1e-6
+    
+    pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
+    pressure.boundaryField.outlet = { type = "fixedValue", value = 0.0 }
+
+    velocity.boundaryField.inlet = { type = "pressureInletVelocity", value = 0.0 }
+    velocity.boundaryField.outlet = { type = "zeroGradient", value = "None" }
+
+
+