Issue 685 casadi interpolation

CHANGELOG.md

@@ -3,30 +3,31 @@
 ## Features
 
 -   Added Simulation class ([#693](https://github.com/pybamm-team/PyBaMM/pull/693))
--   Add interface to CasADi solver ([#687](https://github.com/pybamm-team/PyBaMM/pull/687))
--   Add option to use CasADi's Algorithmic Differentiation framework to calculate Jacobians ([#687](https://github.com/pybamm-team/PyBaMM/pull/687))
--   Add method to evaluate parameters more easily ([#669](https://github.com/pybamm-team/PyBaMM/pull/669))
--   Add `Jacobian` class to reuse known Jacobians of expressions ([#665](https://github.com/pybamm-team/PyBaMM/pull/670))
--   Add `Interpolant` class to interpolate experimental data (e.g. OCP curves) ([#661](https://github.com/pybamm-team/PyBaMM/pull/661))
+-   Added interface to CasADi solver ([#687](https://github.com/pybamm-team/PyBaMM/pull/687), [#691](https://github.com/pybamm-team/PyBaMM/pull/691), [#714](https://github.com/pybamm-team/PyBaMM/pull/714)). This makes the SUNDIALS DAE solvers (Scikits and KLU) truly optional (though IDA KLU is recommended for solving the DFN).
+-   Added option to use CasADi's Algorithmic Differentiation framework to calculate Jacobians ([#687](https://github.com/pybamm-team/PyBaMM/pull/687))
+-   Added method to evaluate parameters more easily ([#669](https://github.com/pybamm-team/PyBaMM/pull/669))
+-   Added `Jacobian` class to reuse known Jacobians of expressions ([#665](https://github.com/pybamm-team/PyBaMM/pull/670))
+-   Added `Interpolant` class to interpolate experimental data (e.g. OCP curves) ([#661](https://github.com/pybamm-team/PyBaMM/pull/661))
 -   Added interface (via pybind11) to sundials with the IDA KLU sparse linear solver ([#657](https://github.com/pybamm-team/PyBaMM/pull/657))
--   Allow parameters to be set by material or by specifying a particular paper ([#647](https://github.com/pybamm-team/PyBaMM/pull/647))
+-   Allowed parameters to be set by material or by specifying a particular paper ([#647](https://github.com/pybamm-team/PyBaMM/pull/647))
 -   Set relative and absolute tolerances independently in solvers ([#645](https://github.com/pybamm-team/PyBaMM/pull/645))
--   Add basic method to allow (a part of) the State Vector to be updated with results obtained from another solution or package ([#624](https://github.com/pybamm-team/PyBaMM/pull/624))
--   Add some non-uniform meshes in 1D and 2D ([#617](https://github.com/pybamm-team/PyBaMM/pull/617))
+-   Added basic method to allow (a part of) the State Vector to be updated with results obtained from another solution or package ([#624](https://github.com/pybamm-team/PyBaMM/pull/624))
+-   Added some non-uniform meshes in 1D and 2D ([#617](https://github.com/pybamm-team/PyBaMM/pull/617))
 
 ## Optimizations
 
+-   Use CasADi's automatic differentation algorithms by default when solving a model ([#714](https://github.com/pybamm-team/PyBaMM/pull/714))
 -   Avoid re-checking size when making a copy of an `Index` object ([#656](https://github.com/pybamm-team/PyBaMM/pull/656))
 -   Avoid recalculating `_evaluation_array` when making a copy of a `StateVector` object ([#653](https://github.com/pybamm-team/PyBaMM/pull/653))
 
 ## Bug fixes
 
--   Correct a sign error in Dirichlet boundary conditions in the Finite Element Method ([#706](https://github.com/pybamm-team/PyBaMM/pull/706))
--   Pass the correct dimensional temperature to open circuit potential ([#702](https://github.com/pybamm-team/PyBaMM/pull/702))
--   Adds missing temperature dependence in electrolyte and interface submodels ([#698](https://github.com/pybamm-team/PyBaMM/pull/698))
--   Fix differentiation of functions that have more than one argument ([#687](https://github.com/pybamm-team/PyBaMM/pull/687))
--   Add warning if `ProcessedVariable` is called outside its interpolation range ([#681](https://github.com/pybamm-team/PyBaMM/pull/681))
--   Improve the way `ProcessedVariable` objects are created in higher dimensions ([#581](https://github.com/pybamm-team/PyBaMM/pull/581))
+-   Corrected a sign error in Dirichlet boundary conditions in the Finite Element Method ([#706](https://github.com/pybamm-team/PyBaMM/pull/706))
+-   Passed the correct dimensional temperature to open circuit potential ([#702](https://github.com/pybamm-team/PyBaMM/pull/702))
+-   Added missing temperature dependence in electrolyte and interface submodels ([#698](https://github.com/pybamm-team/PyBaMM/pull/698))
+-   Fixed differentiation of functions that have more than one argument ([#687](https://github.com/pybamm-team/PyBaMM/pull/687))
+-   Added warning if `ProcessedVariable` is called outside its interpolation range ([#681](https://github.com/pybamm-team/PyBaMM/pull/681))
+-   Improved the way `ProcessedVariable` objects are created in higher dimensions ([#581](https://github.com/pybamm-team/PyBaMM/pull/581))
 
 # [v0.1.0](https://github.com/pybamm-team/PyBaMM/tree/v0.1.0) - 2019-10-08
 

INSTALL-LINUX.md

@@ -94,25 +94,25 @@ Before installing scikits.odes, you need to have installed:
 - Fortran compiler (e.g. gfortran)
 - BLAS/LAPACK install (OpenBLAS is recommended by the scikits.odes developers)
 - CMake (for building Sundials)
-- Sundials 3.1.1
+- Sundials 4.1.0
 
 You can install these on Ubuntu or Debian using apt-get:
 
 ```bash
 sudo apt-get install python3-dev gfortran gcc cmake libopenblas-dev
 ```
 
-To install Sundials 3.1.1, on the command-line type:
+To install Sundials 4.1.0, on the command-line type:
 
 ```bash
 INSTALL_DIR=`pwd`/sundials
-wget https://computation.llnl.gov/projects/sundials/download/sundials-3.1.1.tar.gz
-tar -xvf sundials-3.1.1.tar.gz
-mkdir build-sundials-3.1.1
-cd build-sundials-3.1.1/
-cmake -DLAPACK_ENABLE=ON -DSUNDIALS_INDEX_TYPE=int32_t -DBUILD_ARKODE:BOOL=OFF -DEXAMPLES_ENABLE:BOOL=OFF -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR ../sundials-3.1.1/
+wget https://computation.llnl.gov/projects/sundials/download/sundials-4.1.0.tar.gz
+tar -xvf sundials-4.1.0.tar.gz
+mkdir build-sundials-4.1.0
+cd build-sundials-4.1.0/
+cmake -DLAPACK_ENABLE=ON -DSUNDIALS_INDEX_TYPE=int32_t -DBUILD_ARKODE:BOOL=OFF -DEXAMPLES_ENABLE:BOOL=OFF -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR ../sundials-4.1.0/
 make install
-rm -r ../sundials-3.1.1
+rm -r ../sundials-4.1.0
 ```
 
 Then install [scikits.odes](https://github.com/bmcage/odes), letting it know the sundials install location:

examples/notebooks/change-input-current.ipynb

@@ -22,7 +22,7 @@
     "\n",
     "In this notebook we will use the SPM as the example model, and change the input current from the default option. If you are not familiar with running a model in PyBaMM, please see [this](./models/SPM.ipynb) notebook for more details.\n",
     "\n",
-    "In PyBaMM, the current function is set using the parameter \"Current function\". By default this is set to be a constant current provided by the class [`pybamm.GetConstantCurrent`](https://pybamm.readthedocs.io/en/latest/source/parameters/standard_current_functions/get_constant_current.html).  This class takes a single optional argument \"current\" which is the size of the current in Amperes. If no argument is passed, the value of the current is set by the parameter \"Typical current [A]\" (see [this](parameter-values.ipynb) notebook for more information about parameters).\n",
+    "In PyBaMM, the current function is set using the parameter \"Current function\". By default this is set to be a constant current provided by the class [`pybamm.ConstantCurrent`](https://pybamm.readthedocs.io/en/latest/source/parameters/standard_current_functions/get_constant_current.html).  This class takes a single optional argument \"current\" which is the size of the current in Amperes. If no argument is passed, the value of the current is set by the parameter \"Typical current [A]\" (see [this](parameter-values.ipynb) notebook for more information about parameters).\n",
     "\n",
     "In general it is recommended to change the size of a constant current input by changing the parameter \"Typical current [A]\", since this value is used to non-dimensionlise the model. Below we load the SPM with the default parameters, and then change the the typical current 16A. We then explicilty set the current function to be a constant current."
    ]
@@ -49,14 +49,14 @@
     "\n",
     "# change the typical current and set a constant discharge using the typical current value\n",
     "param[\"Typical current [A]\"] = 16\n",
-    "param[\"Current function\"] = pybamm.GetConstantCurrent()\n"
+    "param[\"Current function\"] = pybamm.ConstantCurrent()\n"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "However, you may wish to change the value of the constant current without altering the typical current value used for non-dimensionlidation. For instance, the current function could be change to draw a current of 8A by updating the current function and passing the optional argument \"current\" to the class `GetConstantCurrent`"
+    "However, you may wish to change the value of the constant current without altering the typical current value used for non-dimensionlidation. For instance, the current function could be change to draw a current of 8A by updating the current function and passing the optional argument \"current\" to the class `ConstantCurrent`"
    ]
   },
   {
@@ -66,7 +66,7 @@
    "outputs": [],
    "source": [
     "# update the value of the current profile *without* changing the typical current used for non-dimensionlisation\n",
-    "param[\"Current function\"] = pybamm.GetConstantCurrent(current=pybamm.Scalar(8))"
+    "param[\"Current function\"] = pybamm.ConstantCurrent(current=pybamm.Scalar(8))"
    ]
   },
   {
@@ -84,7 +84,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "fc997d14787542f69f2cba123ce0b994",
+       "model_id": "b900a39a72704c88927058510b7913b2",
        "version_major": 2,
        "version_minor": 0
       },
@@ -127,11 +127,7 @@
    "source": [
     "## Loading in current data <a name=\"data\"></a>\n",
     "\n",
-    "Data can be loaded in from a csv file using the class [`pybamm.GetCurrentData`](https://pybamm.readthedocs.io/en/latest/source/parameters/standard_current_functions/get_current_data). Data should be given as a function of time (in seconds) and may be dimensional (in Amperes) or non-diemsnional (e.g. C-rate). Optionally, voltage data (in Volts) may be loaded in for convinient plotting and comparison. \n",
-    "\n",
-    "The input csv files should be stored in PyBaMM/input/drive_cycles and have the headings: \"time [s]\"; either \"current [A]\" for dimensional data, or \"current []\" for dimensionless data; and, optionally, \"voltage [V]\". \n",
-    "\n",
-    "To load in dimensional data we simply provide the filename and set the units to \"[A]\", e.g."
+    "Data can be loaded in from a csv file by specifying the path to that file and using the prefix \"[current data]\"."
    ]
   },
   {
@@ -140,54 +136,30 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "param[\"Current function\"] = pybamm.GetCurrentData(\"US06.csv\", units=\"[A]\")"
+    "param[\"Current function\"] = \"[current data]US06\""
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "For non dimensional data, you also need to provide a current scale. For instance, if the data were C-rate then you would set the current scale to the 1C discharge current. If the 1C discharge current were 24 A and we had some C-rate data in the file car_current.csv, this would be loaded in as"
+    "As an example, we show how to solve the SPM using the US06 drive cycle"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 5,
    "metadata": {},
-   "outputs": [],
-   "source": [
-    "param[\"Current function\"] = pybamm.GetCurrentData(\"car_current.csv\", units=\"[]\", current_scale=24)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "As an example, we how to solve the SPM using the US06 drive cycle"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 6,
-   "metadata": {},
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/user/Documents/PyBaMM/pybamm/parameters/standard_current_functions/get_current_data.py:88: ModelWarning: Requested time (2387.404004088835) is outside of the data range [0, 600]\n",
-      "  pybamm.ModelWarning,\n"
-     ]
-    },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "3f4c99601ab8417ba2186987cb532600",
+       "model_id": "26e7b28104b34991b3ebac266dab4934",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "interactive(children=(FloatSlider(value=0.0, description='t', max=0.03900922998674932, step=0.001), Output()),…"
+       "interactive(children=(FloatSlider(value=0.0, description='t', max=0.026526276390989537, step=0.001), Output())…"
       ]
      },
      "metadata": {},
@@ -202,7 +174,7 @@
     "\n",
     "# load parameter values and process model and geometry\n",
     "param = model.default_parameter_values\n",
-    "param[\"Current function\"] = pybamm.GetCurrentData(\"US06.csv\", units=\"[A]\")\n",
+    "param[\"Current function\"] = \"[current data]US06\"\n",
     "param.process_model(model)\n",
     "param.process_geometry(geometry)\n",
     "\n",
@@ -240,14 +212,14 @@
    "source": [
     "## Adding your own current function <a name=\"function\"></a>\n",
     "\n",
-    "A user defined current function can be passed to any model using the class [`pybamm.GetUserCurrent`](https://pybamm.readthedocs.io/en/latest/source/parameters/standard_current_functions/get_user_current). The class takes in a method, which returns the current as a function of time, followed by any keyword arguments required by the method.  \n",
+    "A user defined current function can be passed to any model using the class [`pybamm.UserCurrent`](https://pybamm.readthedocs.io/en/latest/source/parameters/standard_current_functions/get_user_current). The class takes in a method, which returns the current as a function of time, followed by any keyword arguments required by the method.  \n",
     "\n",
     "For example, you may want to simulate a sinusoidal current with amplitude A and freqency omega. In order to do so you must first define the method"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -262,12 +234,12 @@
    "source": [
     "Note that time *must* me the first arguemnt of the function. The parameters may either be provided as floats, or may be one of the standard parameters provided in PyBaMM (see [here](https://pybamm.readthedocs.io/en/latest/source/parameters)). \n",
     "\n",
-    "The the model may be loaded and the \"Current function\" parameter updated to be a `GetUserCurrent` class which calls `my_fun`"
+    "The the model may be loaded and the \"Current function\" parameter updated to be a `UserCurrent` class which calls `my_fun`"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -282,7 +254,7 @@
     "# set user defined current function\n",
     "A = pybamm.electrical_parameters.I_typ\n",
     "omega = 0.1\n",
-    "param[\"Current function\"] = pybamm.GetUserCurrent(my_fun, A=A, omega=omega)\n",
+    "param[\"Current function\"] = pybamm.UserCurrent(my_fun, A=A, omega=omega)\n",
     "\n",
     "# process model and geometry\n",
     "param.process_model(model)\n",
@@ -293,31 +265,23 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note that the parameters in `my_fun` were passed as keyword arguments to the `GetUserCurrent` class. The model may then be solved in the usual way"
+    "Note that the parameters in `my_fun` were passed as keyword arguments to the `UserCurrent` class. The model may then be solved in the usual way"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/user/Documents/PyBaMM/venv/lib/python3.6/site-packages/ipykernel_launcher.py:12: DeprecationWarning: object of type <class 'float'> cannot be safely interpreted as an integer.\n",
-      "  if sys.path[0] == '':\n"
-     ]
-    },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "913efe4e3e9e4b37bad2ded9c71b975e",
+       "model_id": "629672e99152464dad01e57ff152347a",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "interactive(children=(FloatSlider(value=0.0, description='t', max=0.0019504614993374662, step=9.75230749668733…"
+       "interactive(children=(FloatSlider(value=0.0, description='t', max=0.0013263138195494769, step=6.63156909774738…"
       ]
      },
      "metadata": {},
@@ -372,7 +336,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.4"
   }
  },
  "nbformat": 4,