#1230 merge develop

CHANGELOG.md

@@ -31,6 +31,7 @@
 
 ## Breaking changes
 
+-    The parameters "Positive/Negative particle distribution in x" and "Positive/Negative surface area per unit volume distribution in x" have been deprecated. Instead, users can provide "Positive/Negative particle radius [m]" and "Positive/Negative surface area per unit volume [m-1]" directly as functions of through-cell position (x [m]) ([#1237](https://github.com/pybamm-team/PyBaMM/pull/1237)) 
 
 # [v0.2.4](https://github.com/pybamm-team/PyBaMM/tree/v0.2.4) - 2020-09-07
 

examples/notebooks/compare-ecker-data.ipynb

@@ -103,8 +103,8 @@
     "    var.x_n: int(parameter_values.evaluate(model.param.L_n / 1e-6)),\n",
     "    var.x_s: int(parameter_values.evaluate(model.param.L_s / 1e-6)),\n",
     "    var.x_p: int(parameter_values.evaluate(model.param.L_p / 1e-6)),\n",
-    "    var.r_n: int(parameter_values.evaluate(model.param.R_n / 1e-7)),\n",
-    "    var.r_p: int(parameter_values.evaluate(model.param.R_p / 1e-7)),\n",
+    "    var.r_n: int(parameter_values.evaluate(model.param.R_n_typ / 1e-7)),\n",
+    "    var.r_p: int(parameter_values.evaluate(model.param.R_p_typ / 1e-7)),\n",
     "}"
    ]
   },
@@ -221,13 +221,6 @@
     "\n",
     "[2] Richardson, Giles, et. al. \"Generalised single particle models for high-rate operation of graded lithium-ion electrodes: Systematic derivation and validation.\" Electrochemica Acta 339 (2020): 135862"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

examples/notebooks/models/DFN.ipynb

@@ -71,7 +71,7 @@
     "\n",
     "####  Concentration in the electrode active material:\n",
     "\\begin{gather}\n",
-    "N_{\\text{s,k}}\\big|_{r_{\\text{k}}=0} = 0, \\quad \\text{k} \\in \\text{n, p}, \\quad \\ \\ - \\frac{a_{\\text{k}}\\gamma_{\\text{k}}}{\\mathcal{C}_{\\text{k}}} N_{\\text{s,k}}\\big|_{r_{\\text{k}}=1} = j_{\\text{k}}, \\quad \\text{k} \\in \\text{n, p}.\n",
+    "N_{\\text{s,k}}\\big|_{r_{\\text{k}}=0} = 0, \\quad \\text{k} \\in \\text{n, p}, \\quad \\ \\ - \\frac{a_{R, \\text{k}}\\gamma_{\\text{k}}}{\\mathcal{C}_{\\text{k}}} N_{\\text{s,k}}\\big|_{r_{\\text{k}}=1} = j_{\\text{k}}, \\quad \\text{k} \\in \\text{n, p}.\n",
     "\\end{gather}\n",
     "\n",
     "#### Reference potential:\n",
@@ -203,7 +203,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "b72126bb294743c38f4aa5069787b9b6",
+       "model_id": "eceebcfd564d4b53bf56bda5abf066ff",
        "version_major": 2,
        "version_minor": 0
       },
@@ -240,7 +240,7 @@
     "|$\\mathcal{C}_{\\text{k}}$   | $\\tau_{\\text{k}}^*/\\tau_{\\text{d}}^*$   | Ratio of solid diffusion and discharge timescales |\n",
     "|$\\mathcal{C}_{\\text{e}}$   |$\\tau_{\\text{e}}^*/\\tau_{\\text{d}}^*$    |Ratio of electrolyte transport and discharge timescales|\n",
     "|$\\mathcal{C}_{\\text{r,k}}$ |$\\tau_{\\text{r,k}}^*/\\tau_{\\text{d}}^*$  |Ratio of reaction and discharge timescales|\n",
-    "|$a_{\\text{k}}$             |$a_{\\text{k}}^* R_{\\text{k}}^*$          | Product of particle radius and surface area to volume ratio|\n",
+    "|$a_{R, \\text{k}}$             |$a_{\\text{k}}^* R_{\\text{k}}^*$          | Product of particle radius and surface area to volume ratio|\n",
     "|$\\gamma_{\\text{k}}$        |$c_{\\text{k,max}}^*/c_{\\text{n,max}}^*$  |Ratio of maximum lithium concentrations in solid|\n",
     "|$\\gamma_{\\text{e}}$        |$c_{\\text{e,typ}}^*/c_{\\text{n,max}}^*$  |Ratio of maximum lithium concentration in the negative electrode solid and typical electrolyte concentration|\n",
     "\n",

examples/notebooks/models/SPMe.ipynb

@@ -33,7 +33,7 @@
     "\\mathcal{C}_{\\text{k}} \\frac{\\partial c_{\\text{s,k}}}{\\partial t} &= -\\frac{1}{r_{\\text{k}}^2} \\frac{\\partial}{\\partial r_{\\text{k}}} \\left(r_{\\text{k}}^2 N_{\\text{s,k}}\\right), \\\\\n",
     "N_{\\text{s,k}} &= -D_{\\text{s,k}}(c_{\\text{s,k}}) \\frac{\\partial c_{\\text{s,k}}}{\\partial r_{\\text{k}}}, \\quad \\text{k} \\in \\text{n, p}, \\end{align}\n",
     "$$\n",
-    "N_{\\text{s,k}}\\big|_{r_{\\text{k}}=0} = 0, \\quad \\text{k} \\in \\text{n, p}, \\quad \\ \\ - \\frac{a_{\\text{k}}\\gamma_{\\text{k}}}{\\mathcal{C}_{\\text{k}}} N_{\\text{s,k}}\\big|_{r_{\\text{k}}=1} = \n",
+    "N_{\\text{s,k}}\\big|_{r_{\\text{k}}=0} = 0, \\quad \\text{k} \\in \\text{n, p}, \\quad \\ \\ - \\frac{a_{R, \\text{k}}\\gamma_{\\text{k}}}{\\mathcal{C}_{\\text{k}}} N_{\\text{s,k}}\\big|_{r_{\\text{k}}=1} = \n",
     "\\begin{cases}\n",
     "\t\t  \\frac{I}{L_{\\text{n}}}, \\quad &\\text{k}=\\text{n}, \\\\ \n",
     "\t\t  -\\frac{I}{L_{\\text{p}}}, \\quad &\\text{k}=\\text{p}, \n",
@@ -155,7 +155,7 @@
     {
      "data": {
       "text/plain": [
-       "<pybamm.solvers.solution.Solution at 0x7f69f08dd2e8>"
+       "<pybamm.solvers.solution.Solution at 0x7f5cd829b4a8>"
       ]
      },
      "execution_count": 3,
@@ -183,7 +183,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "47ee8d1901bd4bdd87fba1d347da16ec",
+       "model_id": "5f19fdea006d4f22ae77a584c87d5eb3",
        "version_major": 2,
        "version_minor": 0
       },
@@ -218,7 +218,7 @@
     "|$\\mathcal{C}_{\\text{k}}$   | $\\tau_{\\text{k}}^*/\\tau_{\\text{d}}^*$   | Ratio of solid diffusion and discharge timescales |\n",
     "|$\\mathcal{C}_{\\text{e}}$   |$\\tau_{\\text{e}}^*/\\tau_{\\text{d}}^*$    |Ratio of electrolyte transport and discharge timescales|\n",
     "|$\\mathcal{C}_{\\text{r,k}}$ |$\\tau_{\\text{r,k}}^*/\\tau_{\\text{d}}^*$  |Ratio of reaction and discharge timescales|\n",
-    "|$a_{\\text{k}}$             |$a_{\\text{k}}^* R_{\\text{k}}^*$          | Product of particle radius and surface area to volume ratio|\n",
+    "|$a_{R, \\text{k}}$             |$a_{\\text{k}}^* R_{\\text{k}}^*$          | Product of particle radius and surface area to volume ratio|\n",
     "|$\\gamma_{\\text{k}}$        |$c_{\\text{k,max}}^*/c_{\\text{n,max}}^*$  |Ratio of maximum lithium concentrations in solid|\n",
     "|$\\gamma_{\\text{e}}$        |$c_{\\text{e,typ}}^*/c_{\\text{n,max}}^*$  |Ratio of maximum lithium concentration in the negative electrode solid and typical electrolyte concentration|\n",
     "\n",

examples/notebooks/models/pouch-cell-model.ipynb

@@ -91,7 +91,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/user/Documents/PyBaMM/pybamm/models/full_battery_models/base_battery_model.py:361: UserWarning: 1+1D Thermal models are only valid if both tabs are placed at the top of the cell.\n",
+      "/home/user/Documents/PyBaMM/pybamm/models/full_battery_models/base_battery_model.py:375: UserWarning: 1+1D Thermal models are only valid if both tabs are placed at the top of the cell.\n",
       "  \"1+1D Thermal models are only valid if both tabs are \"\n"
      ]
     }
@@ -339,7 +339,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We then add the solution object from the 1+1D model. This is just so that PyBaMM uses the same times behind the scenes when dealing with COMSOL model and the reduced-order models: the variables in `comsol_model.variables` are functions of time only that return the (interpolated in space) COMSOL solution."
+    "We then add the solution object from the 1+1D model. This is just so that PyBaMM uses the same (dimensionless) times behind the scenes when dealing with COMSOL model and the reduced-order models: the variables in `comsol_model.variables` are functions of time only that return the (interpolated in space) COMSOL solution. We also need to update the time and length scales for the COMSOL model so that any dimensionless variables are scaled correctly. "
    ]
   },
   {

examples/scripts/compare_comsol/compare_comsol_DFN.py

@@ -141,8 +141,8 @@ def myinterp(t):
 # Make new solution with same t and y
 comsol_solution = pybamm.Solution(pybamm_solution.t, pybamm_solution.y)
 # Update solution scales to match the pybamm model
-comsol_solution.timescale_eval = pybamm_model.timescale_eval
-comsol_solution.length_scales_eval = pybamm_model.length_scales_eval
+comsol_model.timescale_eval = pybamm_model.timescale_eval
+comsol_model.length_scales_eval = pybamm_model.length_scales_eval
 comsol_solution.model = comsol_model
 
 # plot

examples/scripts/compare_lithium_ion_particle_distribution.py

@@ -16,17 +16,22 @@
 params = [models[0].default_parameter_values, models[1].default_parameter_values]
 
 
-def negative_distribution(x):
-    return 1 + 2 * x / models[1].param.l_n
+def negative_radius(x):
+    "Negative particle radius as a function of through-cell position (x_n [m])"
+    R_n_0 = params[0]["Negative particle radius [m]"]
+    grading = 1 + 2 * x / models[1].param.L_n
+    return grading * R_n_0
 
 
-def positive_distribution(x):
-    return 1 + 2 * (1 - x) / models[1].param.l_p
+def positive_radius(x):
+    "Positive particle radius as a function of through-cell position (x_p [m])"
+    R_p_0 = params[0]["Positive particle radius [m]"]
+    grading = 1 + 2 * (models[1].param.L_x - x) / models[1].param.L_p
+    return grading * R_p_0
 
 
-params[1]["Negative particle distribution in x"] = negative_distribution
-params[1]["Positive particle distribution in x"] = positive_distribution
-
+params[1]["Negative particle radius [m]"] = negative_radius
+params[1]["Positive particle radius [m]"] = positive_radius
 
 # set up and solve simulations
 t_eval = np.linspace(0, 3600, 100)
@@ -45,8 +50,8 @@ def positive_distribution(x):
     "Electrolyte potential [V]",
     "Positive electrode potential [V]",
     "Terminal voltage [V]",
-    "Negative particle distribution in x",
-    "Positive particle distribution in x",
+    "Negative particle radius",
+    "Positive particle radius",
 ]
 
 # plot

examples/scripts/compare_particle_shape.py

@@ -27,8 +27,6 @@
             {
                 "Negative electrode surface area to volume ratio [m-1]": 170000,
                 "Positive electrode surface area to volume ratio [m-1]": 200000,
-                "Negative surface area per unit volume distribution in x": 1,
-                "Positive surface area per unit volume distribution in x": 1,
             },
             check_already_exists=False,
         )

pybamm/__init__.py

@@ -111,6 +111,7 @@ def version(formatted=False):
 
 if system() != "Windows":
     from .expression_tree.operations.evaluate import EvaluatorJax
+    from .expression_tree.operations.evaluate import JaxCooMatrix
 
 from .expression_tree.operations.jacobian import Jacobian
 from .expression_tree.operations.convert_to_casadi import CasadiConverter