Merge remote-tracking branch 'upstream/develop' into develop

CHANGELOG.md

@@ -2,34 +2,42 @@
 
 ## Features
 
+-   Added tab, edge, and surface cooling ([#965](https://github.com/pybamm-team/PyBaMM/pull/965))
 -   Added functionality to solver to automatically discretise a 0D model ([#947](https://github.com/pybamm-team/PyBaMM/pull/947))
 -   Added sensitivity to `CasadiAlgebraicSolver` ([#940](https://github.com/pybamm-team/PyBaMM/pull/940))
 -   Added `ProcessedSymbolicVariable` class, which can handle symbolic variables (i.e. variables for which the inputs are symbolic) ([#940](https://github.com/pybamm-team/PyBaMM/pull/940))
 -   Made `QuickPlot` compatible with Google Colab ([#935](https://github.com/pybamm-team/PyBaMM/pull/935))
 -   Added `BasicFull` model for lead-acid ([#932](https://github.com/pybamm-team/PyBaMM/pull/932))
+-   Added 'arctan' function  ([#973]https://github.com/pybamm-team/PyBaMM/pull/973)
 
 ## Optimizations
 
+-   Changed default solver for DAE models to `CasadiSolver` ([#978](https://github.com/pybamm-team/PyBaMM/pull/978))
+-   Added some extra simplifications to the expression tree ([#971](https://github.com/pybamm-team/PyBaMM/pull/971))
 -   Changed the behaviour of "safe" mode in `CasadiSolver` ([#956](https://github.com/pybamm-team/PyBaMM/pull/956))
 -   Sped up model building ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
 -   Changed default solver for lead-acid to `CasadiSolver` ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
 
 ## Bug fixes
 
--   Fixed `Interpolant` ids to allow processing ([#962](https://github.com/pybamm-team/PyBaMM/pull/962)
+-   Added extra checks when creating a model, for clearer errors ([#971](https://github.com/pybamm-team/PyBaMM/pull/971))
+-   Fixed `Interpolant` ids to allow processing ([#962](https://github.com/pybamm-team/PyBaMM/pull/962))
 -   Fixed a bug in the initial conditions of the potential pair model ([#954](https://github.com/pybamm-team/PyBaMM/pull/954))
--   Changed simulation attributes to assign copies rather than the objects themselves ([#952](https://github.com/pybamm-team/PyBaMM/pull/952)
--   Added default values to base model so that it works with the `Simulation` class ([#952](https://github.com/pybamm-team/PyBaMM/pull/952)
--   Fixed solver to recompute initial conditions when inputs are changed ([#951](https://github.com/pybamm-team/PyBaMM/pull/951)
--   Reformatted thermal submodels ([#938](https://github.com/pybamm-team/PyBaMM/pull/938)
+-   Changed simulation attributes to assign copies rather than the objects themselves ([#952](https://github.com/pybamm-team/PyBaMM/pull/952))
+-   Added default values to base model so that it works with the `Simulation` class ([#952](https://github.com/pybamm-team/PyBaMM/pull/952))
+-   Fixed solver to recompute initial conditions when inputs are changed ([#951](https://github.com/pybamm-team/PyBaMM/pull/951))
+-   Reformatted thermal submodels ([#938](https://github.com/pybamm-team/PyBaMM/pull/938))
 -   Reformatted electrolyte submodels ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
 -   Reformatted convection submodels ([#635](https://github.com/pybamm-team/PyBaMM/pull/635))
 
 ## Breaking changes
 
+-   Renamed "surface area density" to "surface area to volume ratio" ([#975](https://github.com/pybamm-team/PyBaMM/pull/975))
+-   Replaced "reaction rate" with "exchange-current density" ([#975](https://github.com/pybamm-team/PyBaMM/pull/975))
+-   Changed the implementation of reactions in submodels ([#948](https://github.com/pybamm-team/PyBaMM/pull/948))
 -   Removed some inputs like `T_inf`, `R_g` and activation energies to some of the standard function parameters. This is because each of those inputs is specific to a particular function (e.g. the reference temperature at which the function was measured). To change a property such as the activation energy, users should create a new function, specifying the relevant property as a `Parameter` or `InputParameter` ([#942](https://github.com/pybamm-team/PyBaMM/pull/942))
--   The thermal option 'xyz-lumped' has been removed. The option 'thermal current collector' has also been removed ([#938](https://github.com/pybamm-team/PyBaMM/pull/938)
--   The 'C-rate' parameter has been deprecated. Use 'Current function [A]' instead. The cell capacity can be accessed as 'Cell capacity [A.h]', and used to calculate current from C-rate ([#952](https://github.com/pybamm-team/PyBaMM/pull/952)
+-   The thermal option 'xyz-lumped' has been removed. The option 'thermal current collector' has also been removed ([#938](https://github.com/pybamm-team/PyBaMM/pull/938))
+-   The 'C-rate' parameter has been deprecated. Use 'Current function [A]' instead. The cell capacity can be accessed as 'Cell capacity [A.h]', and used to calculate current from C-rate ([#952](https://github.com/pybamm-team/PyBaMM/pull/952))
 
 # [v0.2.1](https://github.com/pybamm-team/PyBaMM/tree/v0.2.1) - 2020-03-31
 

INSTALL-LINUX-MAC.md

@@ -66,6 +66,10 @@ On Ubuntu/debian
 ```
 sudo apt install libopenblas-dev
 ```
+and on Mac OS
+```
+brew install openblas
+```
 After installing PyBaMM, the following command can be used to automatically install `scikits.odes`
 and its dependencies
 ```
@@ -155,5 +159,5 @@ might say:
 ```
 
 If this is the case, on a Debian or Ubuntu system you can install OpenBLAS using `sudo
-apt-get install libopenblas-dev` and then re-install sundials using the instructions
+apt-get install libopenblas-dev` (or `brew install openblas` for Mac OS) and then re-install sundials using the instructions
 above.

MANIFEST.in

@@ -35,20 +35,20 @@ include pybamm/input/parameters/lead-acid/electrolytes/sulfuric_acid_Sulzer2019/
 include pybamm/input/parameters/lead-acid/electrolytes/sulfuric_acid_Sulzer2019/darken_thermodynamic_factor_Chapman1968.py
 include pybamm/input/parameters/lead-acid/electrolytes/sulfuric_acid_Sulzer2019/viscosity_Chapman1968.py
 include pybamm/input/parameters/lithium-ion/anodes/graphite_Chen2020/graphite_LGM50_diffusivity_Chen2020.py
-include pybamm/input/parameters/lithium-ion/anodes/graphite_Chen2020/graphite_LGM50_electrolyte_reaction_rate_Chen2020.py
+include pybamm/input/parameters/lithium-ion/anodes/graphite_Chen2020/graphite_LGM50_electrolyte_exchange_current_density_Chen2020.py
 include pybamm/input/parameters/lithium-ion/anodes/graphite_mcmb2528_Marquis2019/graphite_mcmb2528_ocp_Dualfoil1998.py
-include pybamm/input/parameters/lithium-ion/anodes/graphite_mcmb2528_Marquis2019/graphite_electrolyte_reaction_rate_Dualfoil1998.py
+include pybamm/input/parameters/lithium-ion/anodes/graphite_mcmb2528_Marquis2019/graphite_electrolyte_exchange_current_density_Dualfoil1998.py
 include pybamm/input/parameters/lithium-ion/anodes/graphite_mcmb2528_Marquis2019/graphite_entropic_change_Moura2016.py
 include pybamm/input/parameters/lithium-ion/anodes/graphite_mcmb2528_Marquis2019/graphite_mcmb2528_diffusivity_Dualfoil1998.py
-include pybamm/input/parameters/lithium-ion/anodes/graphite_Kim2011/graphite_electrolyte_reaction_rate_Kim2011.py
+include pybamm/input/parameters/lithium-ion/anodes/graphite_Kim2011/graphite_electrolyte_exchange_current_density_Kim2011.py
 include pybamm/input/parameters/lithium-ion/anodes/graphite_Kim2011/graphite_ocp_Kim2011.py
 include pybamm/input/parameters/lithium-ion/anodes/graphite_Kim2011/graphite_diffusivity_Kim2011.py
 include pybamm/input/parameters/lithium-ion/cathodes/nca_Kim2011/nca_ocp_Kim2011_function.py
 include pybamm/input/parameters/lithium-ion/cathodes/nca_Kim2011/nca_diffusivity_Kim2011.py
-include pybamm/input/parameters/lithium-ion/cathodes/nca_Kim2011/nca_electrolyte_reaction_rate_Kim2011.py
+include pybamm/input/parameters/lithium-ion/cathodes/nca_Kim2011/nca_electrolyte_exchange_current_density_Kim2011.py
 include pybamm/input/parameters/lithium-ion/cathodes/nmc_Chen2020/nmc_LGM50_diffusivity_Chen2020.py
-include pybamm/input/parameters/lithium-ion/cathodes/nmc_Chen2020/nmc_LGM50_electrolyte_reaction_rate_Chen2020.py
-include pybamm/input/parameters/lithium-ion/cathodes/lico2_Marquis2019/lico2_electrolyte_reaction_rate_Dualfoil1998.py
+include pybamm/input/parameters/lithium-ion/cathodes/nmc_Chen2020/nmc_LGM50_electrolyte_exchange_current_density_Chen2020.py
+include pybamm/input/parameters/lithium-ion/cathodes/lico2_Marquis2019/lico2_electrolyte_exchange_current_density_Dualfoil1998.py
 include pybamm/input/parameters/lithium-ion/cathodes/lico2_Marquis2019/lico2_ocp_Dualfoil1998.py
 include pybamm/input/parameters/lithium-ion/cathodes/lico2_Marquis2019/lico2_entropic_change_Moura2016.py
 include pybamm/input/parameters/lithium-ion/cathodes/lico2_Marquis2019/lico2_diffusivity_Dualfoil1998.py

examples/notebooks/Getting Started/Tutorial 2 - Setting Parameter Values.ipynb

@@ -296,9 +296,9 @@
        "    'Negative electrode double-layer capacity [F.m-2]': 0.2,\n",
        "    'Negative electrode electrons in reaction': 1.0,\n",
        "    'Negative electrode porosity': 0.3,\n",
-       "    'Negative electrode reaction rate': <function graphite_electrolyte_reaction_rate_Dualfoil1998 at 0x7f42bfb4a7a0>,\n",
+       "    'Negative electrode exchange-current density [A.m-2]': <function graphite_electrolyte_exchange_current_density_Dualfoil1998 at 0x7f42bfb4a7a0>,\n",
        "    'Negative electrode specific heat capacity [J.kg-1.K-1]': 700.0,\n",
-       "    'Negative electrode surface area density [m-1]': 180000.0,\n",
+       "    'Negative electrode surface area to volume ratio [m-1]': 180000.0,\n",
        "    'Negative electrode thermal conductivity [W.m-1.K-1]': 1.7,\n",
        "    'Negative electrode thickness [m]': 0.0001,\n",
        "    'Negative particle distribution in x': 1.0,\n",
@@ -328,9 +328,9 @@
        "    'Positive electrode double-layer capacity [F.m-2]': 0.2,\n",
        "    'Positive electrode electrons in reaction': 1.0,\n",
        "    'Positive electrode porosity': 0.3,\n",
-       "    'Positive electrode reaction rate': <function lico2_electrolyte_reaction_rate_Dualfoil1998 at 0x7f42bfb36710>,\n",
+       "    'Positive electrode exchange-current density [A.m-2]': <function lico2_electrolyte_exchange_current_density_Dualfoil1998 at 0x7f42bfb36710>,\n",
        "    'Positive electrode specific heat capacity [J.kg-1.K-1]': 700.0,\n",
-       "    'Positive electrode surface area density [m-1]': 150000.0,\n",
+       "    'Positive electrode surface area to volume ratio [m-1]': 150000.0,\n",
        "    'Positive electrode thermal conductivity [W.m-1.K-1]': 2.1,\n",
        "    'Positive electrode thickness [m]': 0.0001,\n",
        "    'Positive particle distribution in x': 1.0,\n",

examples/notebooks/change-settings.ipynb

@@ -170,7 +170,7 @@
       "Negative electrode active material volume fraction                                            0.7\n",
       "Negative particle radius [m]                                                                1e-05\n",
       "Negative particle distribution in x                                                           1.0\n",
-      "Negative electrode surface area density [m-1]                                            180000.0\n",
+      "Negative electrode surface area to volume ratio [m-1]                                            180000.0\n",
       "Negative electrode Bruggeman coefficient (electrolyte)                                        1.5\n",
       "Negative electrode Bruggeman coefficient (electrode)                                          1.5\n",
       "Negative electrode cation signed stoichiometry                                               -1.0\n",
@@ -183,7 +183,7 @@
       "Negative electrode thermal conductivity [W.m-1.K-1]                                           1.7\n",
       "Negative electrode OCP entropic change [V.K-1]                               <function graphite_entropic_change_Moura2016 at 0x13020a0d0>\n",
       "Reference temperature [K]                                                                  298.15\n",
-      "Negative electrode reaction rate                                             <function graphite_electrolyte_reaction_rate_Dualfoil1998 at 0x13020a158>\n",
+      "Negative electrode exchange-current density [A.m-2]                                             <function graphite_electrolyte_exchange_current_density_Dualfoil1998 at 0x13020a158>\n",
       "Negative reaction rate activation energy [J.mol-1]                                        37480.0\n",
       "Negative solid diffusion activation energy [J.mol-1]                                      42770.0\n",
       "Positive electrode conductivity [S.m-1]                                                      10.0\n",
@@ -194,7 +194,7 @@
       "Positive electrode active material volume fraction                                            0.7\n",
       "Positive particle radius [m]                                                                1e-05\n",
       "Positive particle distribution in x                                                           1.0\n",
-      "Positive electrode surface area density [m-1]                                            150000.0\n",
+      "Positive electrode surface area to volume ratio [m-1]                                            150000.0\n",
       "Positive electrode Bruggeman coefficient (electrolyte)                                        1.5\n",
       "Positive electrode Bruggeman coefficient (electrode)                                          1.5\n",
       "Positive electrode cation signed stoichiometry                                               -1.0\n",
@@ -206,7 +206,7 @@
       "Positive electrode specific heat capacity [J.kg-1.K-1]                                      700.0\n",
       "Positive electrode thermal conductivity [W.m-1.K-1]                                           2.1\n",
       "Positive electrode OCP entropic change [V.K-1]                               <function lico2_entropic_change_Moura2016 at 0x13020a2f0>\n",
-      "Positive electrode reaction rate                                             <function lico2_electrolyte_reaction_rate_Dualfoil1998 at 0x13020a378>\n",
+      "Positive electrode exchange-current density [A.m-2]                                             <function lico2_electrolyte_exchange_current_density_Dualfoil1998 at 0x13020a378>\n",
       "Positive reaction rate activation energy [J.mol-1]                                        39570.0\n",
       "Positive solid diffusion activation energy [J.mol-1]                                      18550.0\n",
       "Separator porosity                                                                            1.0\n",

examples/notebooks/models/DFN.ipynb

@@ -232,7 +232,7 @@
     "|$\\mathcal{C}_{\\text{k}}$   | $\\tau_{\\text{k}}^*/\\tau_{\\text{d}}^*$   | 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 density|\n",
+    "|$a_{\\text{k}}$             |$a_{\\text{k}}^* R_{\\text{k}}^*$          | 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/SPM.ipynb

@@ -866,7 +866,7 @@
     "| $L_{\\text{k}}$            | $L_{\\text{k}}^*/L^*$                    | Ratio of region thickness to cell thickness|\n",
     "|$\\mathcal{C}_{\\text{k}}$   | $\\tau_{\\text{k}}^*/\\tau_{\\text{d}}^*$   | Ratio of solid diffusion 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 density|\n",
+    "|$a_{\\text{k}}$             |$a_{\\text{k}}^* R_{\\text{k}}^*$          | 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|"
    ]
   },

examples/notebooks/models/SPMe.ipynb

@@ -231,7 +231,7 @@
     "|$\\mathcal{C}_{\\text{k}}$   | $\\tau_{\\text{k}}^*/\\tau_{\\text{d}}^*$   | 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 density|\n",
+    "|$a_{\\text{k}}$             |$a_{\\text{k}}^* R_{\\text{k}}^*$          | 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/using-model-options_thermal-example.ipynb

@@ -65,7 +65,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We choose to use the parameters from [1]. We then update the heat transfer coefficient to be 0.1 [W/m^2/K] (see the [Parameter Values notebook](./parameter-values.ipynb) for more details)"
+    "We choose to use the parameters from [1]. We then update the heat transfer coefficients (see the [Parameter Values notebook](./parameter-values.ipynb) for more details)"
    ]
   },
   {
@@ -75,7 +75,17 @@
    "outputs": [],
    "source": [
     "param = pybamm.ParameterValues(chemistry=pybamm.parameter_sets.Marquis2019)\n",
-    "param.update({\"Heat transfer coefficient [W.m-2.K-1]\": 0.1})"
+    "param.update(\n",
+    "    {\n",
+    "        \"Negative current collector\"\n",
+    "        + \" surface heat transfer coefficient [W.m-2.K-1]\": 5,\n",
+    "        \"Positive current collector\"\n",
+    "        + \" surface heat transfer coefficient [W.m-2.K-1]\": 5,\n",
+    "        \"Negative tab heat transfer coefficient [W.m-2.K-1]\": 0,\n",
+    "        \"Positive tab heat transfer coefficient [W.m-2.K-1]\": 0,\n",
+    "        \"Edge heat transfer coefficient [W.m-2.K-1]\": 0,\n",
+    "    }\n",
+    ")"
    ]
   },
   {
@@ -121,7 +131,7 @@
    "source": [
     "# solve model\n",
     "solver = model.default_solver\n",
-    "t_eval = np.linspace(0, 1, 250)\n",
+    "t_eval = np.linspace(0, 3600, 250)\n",
     "solution = solver.solve(model, t_eval)"
    ]
   },
@@ -140,12 +150,12 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "c3d04dd597c24caf83c370bd01fe6131",
+       "model_id": "115696cc7c7e4297bb6d85a9f8220a82",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "interactive(children=(FloatSlider(value=0.0, description='t', max=1.0, step=0.01), Output()), _dom_classes=('w…"
+       "interactive(children=(FloatSlider(value=0.0, description='t', max=3599.9999999999995, step=35.99999999999999),…"
       ]
      },
      "metadata": {},
@@ -202,9 +212,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.5"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}