Revert some changes from testing

RangamaniLabUCSD · Apr 1, 2024 · 4e49086 · 4e49086
1 parent 317c87a
commit 4e49086
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Showing 3 changed files with 6 additions and 42 deletions.
diff --git a/examples/example3/example3.ipynb b/examples/example3/example3.ipynb
@@ -297,7 +297,7 @@
     "Atot = Parameter(\"Atot\", 1.0, vol_unit)\n",
     "# Phosphorylation of Adephos at the PM\n",
     "kkin = Parameter(\"kkin\", 50.0, 1/sec)\n",
-    "curRadius = 2  # first radius value to test\n",
+    "curRadius = 1  # first radius value to test\n",
     "# vol to surface area ratio of the cell (overwritten for each cell size)\n",
     "VolSA = Parameter(\"VolSA\", curRadius/3, um)\n",
     "r1 = Reaction(\"r1\", [], [\"Aphos\"], param_map={\"kon\": \"kkin\", \"Atot\": \"Atot\", \"VolSA\": \"VolSA\"},\n",
@@ -366,18 +366,8 @@
    "source": [
     "# Base mesh\n",
     "# 0 in second argument corresponds to no inner sphere\n",
-    "xSize, ySize, zSize = 20.0, 20.0, 2.0\n",
-    "domain = d.BoxMesh(d.Point(0.0, 0.0, 0.0), d.Point(xSize, ySize, zSize), 10, 10, 2)\n",
-    "cell_markers = d.MeshFunction(\"size_t\", domain, 3, 1)\n",
-    "facet_markers = d.MeshFunction(\"size_t\", domain, 2, 0)\n",
-    "for f in d.facets(domain):\n",
-    "    x, y, z = f.midpoint()[:]\n",
-    "    if np.isclose(z, 0.) or np.isclose(z, zSize):\n",
-    "            # or np.isclose(y, 0.) or np.isclose(y, ySize)\\\n",
-    "            # or np.isclose(z, 0.) or np.isclose(z, zSize):\n",
-    "        facet_markers[f] = 10\n",
-    "# domain, facet_markers, cell_markers = mesh_tools.create_spheres(curRadius, 0, hEdge=0.05, hInnerEdge=0.05)\n",
-    "# visualization.plot_dolfin_mesh(domain, cell_markers, facet_markers)"
+    "domain, facet_markers, cell_markers = mesh_tools.create_spheres(curRadius, 0, hEdge=0.05, hInnerEdge=0.05)\n",
+    "visualization.plot_dolfin_mesh(domain, cell_markers, facet_markers)"
    ]
   },
   {
@@ -526,7 +516,7 @@
     "    # End if we've passed the final time\n",
     "    if model_cur.t >= model_cur.final_t:\n",
     "        break\n",
-    "# visualization.plot(model_cur.sc['Aphos'].u['u'])"
+    "visualization.plot(model_cur.sc['Aphos'].u['u'])"
    ]
   },
   {
@@ -580,27 +570,6 @@
     "print(f\"Current L2 norm is {L2norm}\")"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "993c1b6a",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "xvec = d.SpatialCoordinate(cc[\"Cyto\"].dolfin_mesh)\n",
-    "k_kin = kkin.value*VolSA.value\n",
-    "k_p = kp.value\n",
-    "cT = Atot.value\n",
-    "D = Aphos.D\n",
-    "zFactor = zSize / np.sqrt(D/k_p)\n",
-    "Az = (k_kin*zSize/(2*D))*np.exp(zFactor) / ((zFactor/2)*(np.exp(zFactor)-1) + (k_kin*zSize/(2*D))*(1+np.exp(zFactor)))\n",
-    "Bz = (k_kin*zSize/(2*D)) / ((zFactor/2)*(np.exp(zFactor)-1) + (k_kin*zSize/(2*D))*(1+np.exp(zFactor)))\n",
-    "expFactor = np.sqrt(k_p/(D))\n",
-    "sol = cT * ((Az*d.exp(-expFactor*xvec[2]) + Bz*d.exp(expFactor*xvec[2])))\n",
-    "L2norm = d.assemble_mixed((sol-model_cur.sc[\"Aphos\"].u[\"u\"])**2 *dx)\n",
-    "print(f\"Current L2 norm is {L2norm}\")"
-   ]
-  },
   {
    "attachments": {},
    "cell_type": "markdown",

diff --git a/examples/example3/example3_withaxisymm.ipynb b/examples/example3/example3_withaxisymm.ipynb
@@ -211,7 +211,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Aphos = Species(\"Aphos\", 0.1, vol_unit, 0.1, D_unit, \"Cyto\")"
+    "Aphos = Species(\"Aphos\", 0.1, vol_unit, 10.0, D_unit, \"Cyto\")"
    ]
   },
   {
@@ -367,7 +367,7 @@
    "outputs": [],
    "source": [
     "# Base mesh\n",
-    "domain, facet_markers, cell_markers = mesh_tools.create_2Dcell(outerExpr=f\"r**2 + (z-({curRadius}+1))**2 - {curRadius}**2\", innerExpr=\"\", hEdge=0.2)\n",
+    "domain, facet_markers, cell_markers = mesh_tools.create_2Dcell(outerExpr=f\"r**2 + (z-({curRadius}+1))**2 - {curRadius}**2\", innerExpr=\"\", hEdge=0.1)\n",
     "visualization.plot_dolfin_mesh(domain, cell_markers)"
    ]
   },

diff --git a/smart/model_assembly.py b/smart/model_assembly.py
@@ -1785,11 +1785,6 @@ def sbmodel_from_locals(local_values):
     species = [x for x in local_values if isinstance(x, Species)]
     compartments = [x for x in local_values if isinstance(x, Compartment)]
     reactions = [x for x in local_values if isinstance(x, Reaction)]
-    # we just reverse the list so that the order is the same as how they were defined
-    # parameters.reverse()
-    # species.reverse()
-    # compartments.reverse()
-    # reactions.reverse()
     pc.add(parameters)
     sc.add(species)
     cc.add(compartments)