Issue 1221 convert to casadi

CHANGELOG.md

@@ -13,6 +13,7 @@
 
 ## Optimizations
 
+-   Variables are now post-processed using CasADi ([#1316](https://github.com/pybamm-team/PyBaMM/pull/1316))
 -   Operations such as `1*x` and `0+x` now directly return `x` ([#1252](https://github.com/pybamm-team/PyBaMM/pull/1252))
 
 ## Bug fixes

examples/notebooks/Getting Started/Tutorial 6 - Managing simulation outputs.ipynb

@@ -22,23 +22,23 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "stream",
      "name": "stdout",
+     "output_type": "stream",
      "text": [
-      "\u001b[33mWARNING: You are using pip version 20.2.1; however, version 20.2.4 is available.\n",
+      "\u001b[33mWARNING: You are using pip version 20.2.4; however, version 20.3.3 is available.\n",
       "You should consider upgrading via the '/Users/vsulzer/Documents/Energy_storage/PyBaMM/.tox/dev/bin/python -m pip install --upgrade pip' command.\u001b[0m\n",
       "Note: you may need to restart the kernel to use updated packages.\n"
      ]
     },
     {
-     "output_type": "execute_result",
      "data": {
       "text/plain": [
-       "<pybamm.solvers.solution.Solution at 0x1467c6820>"
+       "<pybamm.solvers.solution.Solution at 0x1479dff10>"
       ]
      },
+     "execution_count": 1,
      "metadata": {},
-     "execution_count": 1
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -102,33 +102,33 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "execute_result",
      "data": {
       "text/plain": [
-       "array([3.77047806, 3.75305163, 3.74567013, 3.74038819, 3.73581198,\n",
-       "       3.73153388, 3.72742394, 3.72343938, 3.71956644, 3.71580196,\n",
-       "       3.71214617, 3.70860034, 3.70516557, 3.70184247, 3.69863116,\n",
-       "       3.69553115, 3.69254136, 3.6896602 , 3.68688564, 3.68421527,\n",
+       "array([3.77047806, 3.75305182, 3.74567027, 3.74038822, 3.73581196,\n",
+       "       3.73153391, 3.72742393, 3.72343929, 3.71956623, 3.71580184,\n",
+       "       3.71214621, 3.7086004 , 3.70516561, 3.70184253, 3.69863121,\n",
+       "       3.69553118, 3.69254137, 3.68966018, 3.68688562, 3.68421526,\n",
        "       3.68164637, 3.67917591, 3.6768006 , 3.67451688, 3.67232094,\n",
-       "       3.6702087 , 3.66817572, 3.66621717, 3.66432763, 3.66250091,\n",
-       "       3.66072975, 3.65900537, 3.65731692, 3.65565067, 3.65398896,\n",
-       "       3.65230898, 3.65058136, 3.6487688 , 3.64682545, 3.64469796,\n",
-       "       3.64232964, 3.63966968, 3.63668791, 3.63339298, 3.62984705,\n",
-       "       3.62616685, 3.62250444, 3.61901236, 3.61580864, 3.61295718,\n",
-       "       3.61046845, 3.60831404, 3.60644483, 3.60480596, 3.60334607,\n",
+       "       3.67020869, 3.66817572, 3.66621717, 3.66432762, 3.6625009 ,\n",
+       "       3.66072974, 3.65900536, 3.65731692, 3.65565066, 3.65398895,\n",
+       "       3.65230898, 3.65058135, 3.6487688 , 3.64682546, 3.64469798,\n",
+       "       3.64232968, 3.63966973, 3.63668796, 3.63339303, 3.62984711,\n",
+       "       3.62616692, 3.6225045 , 3.61901241, 3.61580868, 3.6129572 ,\n",
+       "       3.61046847, 3.60831405, 3.60644483, 3.60480596, 3.60334607,\n",
        "       3.60202167, 3.60079822, 3.5996495 , 3.59855637, 3.59750531,\n",
        "       3.59648723, 3.59549638, 3.59452954, 3.59358541, 3.59266405,\n",
        "       3.59176646, 3.59089417, 3.59004885, 3.58923192, 3.58844407,\n",
        "       3.58768477, 3.58695179, 3.58624057, 3.58554372, 3.58485045,\n",
        "       3.58414611, 3.58341187, 3.58262441, 3.58175587, 3.58077378,\n",
        "       3.57964098, 3.57831538, 3.5767492 , 3.57488745, 3.57266504,\n",
-       "       3.5700019 , 3.56679523, 3.56290767, 3.5581495 , 3.55225276,\n",
-       "       3.54483362, 3.53533853, 3.52296795, 3.50656968, 3.48449277,\n",
-       "       3.45439366, 3.41299183, 3.35578872, 3.27680073, 3.16842637])"
+       "       3.5700019 , 3.56679523, 3.56290766, 3.5581495 , 3.55225276,\n",
+       "       3.54483361, 3.53533853, 3.52296795, 3.50656968, 3.48449277,\n",
+       "       3.45439366, 3.41299182, 3.35578871, 3.27680072, 3.16842636])"
       ]
      },
+     "execution_count": 4,
      "metadata": {},
-     "execution_count": 4
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -148,7 +148,6 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "execute_result",
      "data": {
       "text/plain": [
        "array([   0.        ,   36.36363636,   72.72727273,  109.09090909,\n",
@@ -178,8 +177,9 @@
        "       3490.90909091, 3527.27272727, 3563.63636364, 3600.        ])"
       ]
      },
+     "execution_count": 5,
      "metadata": {},
-     "execution_count": 5
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -199,14 +199,14 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "execute_result",
      "data": {
       "text/plain": [
-       "array([3.72947891, 3.70860034, 3.67810702, 3.65400558])"
+       "array([3.72947892, 3.7086004 , 3.67810702, 3.65400557])"
       ]
      },
+     "execution_count": 6,
      "metadata": {},
-     "execution_count": 6
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -265,16 +265,18 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "display_data",
      "data": {
-      "text/plain": "interactive(children=(FloatSlider(value=0.0, description='t', max=1.0, step=0.01), Output()), _dom_classes=('w…",
       "application/vnd.jupyter.widget-view+json": {
+       "model_id": "8ceaea70446149079f0194450d7828dc",
        "version_major": 2,
-       "version_minor": 0,
-       "model_id": "0b4ebac3fdd947218f9444b2b381cf04"
-      }
+       "version_minor": 0
+      },
+      "text/plain": [
+       "interactive(children=(FloatSlider(value=0.0, description='t', max=1.0, step=0.01), Output()), _dom_classes=('w…"
+      ]
      },
-     "metadata": {}
+     "metadata": {},
+     "output_type": "display_data"
     }
    ],
    "source": [
@@ -311,26 +313,28 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "display_data",
      "data": {
-      "text/plain": "interactive(children=(FloatSlider(value=0.0, description='t', max=1.0, step=0.01), Output()), _dom_classes=('w…",
       "application/vnd.jupyter.widget-view+json": {
+       "model_id": "9c9e516a7aef46688f03aaea77505636",
        "version_major": 2,
-       "version_minor": 0,
-       "model_id": "f4a1b65b2bf945099197135c5598084b"
-      }
+       "version_minor": 0
+      },
+      "text/plain": [
+       "interactive(children=(FloatSlider(value=0.0, description='t', max=1.0, step=0.01), Output()), _dom_classes=('w…"
+      ]
      },
-     "metadata": {}
+     "metadata": {},
+     "output_type": "display_data"
     },
     {
-     "output_type": "execute_result",
      "data": {
       "text/plain": [
-       "<pybamm.plotting.quick_plot.QuickPlot at 0x14be13b80>"
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x149685400>"
       ]
      },
+     "execution_count": 11,
      "metadata": {},
-     "execution_count": 11
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -425,9 +429,22 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5-final"
+   "version": "3.8.6"
+  },
+  "toc": {
+   "base_numbering": 1,
+   "nav_menu": {},
+   "number_sections": true,
+   "sideBar": true,
+   "skip_h1_title": false,
+   "title_cell": "Table of Contents",
+   "title_sidebar": "Contents",
+   "toc_cell": false,
+   "toc_position": {},
+   "toc_section_display": true,
+   "toc_window_display": true
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}

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

@@ -356,7 +356,8 @@
     "comsol_solution = pybamm.Solution(solutions[\"1+1D DFN\"].t, solutions[\"1+1D DFN\"].y)\n",
     "comsol_model.timescale = simulations[\"1+1D DFN\"].model.timescale\n",
     "comsol_model.length_scales = simulations[\"1+1D DFN\"].model.length_scales\n",
-    "comsol_solution.model = comsol_model"
+    "comsol_solution.model = comsol_model\n",
+    "comsol_solution.inputs = {}"
    ]
   },
   {

examples/scripts/DFN.py

@@ -30,7 +30,7 @@
 
 # solve model
 t_eval = np.linspace(0, 3600, 100)
-solver = pybamm.CasadiSolver(mode="fast", atol=1e-6, rtol=1e-3)
+solver = pybamm.CasadiSolver(mode="safe", atol=1e-6, rtol=1e-3)
 solution = solver.solve(model, t_eval)
 
 # plot

pybamm/__init__.py

@@ -56,6 +56,7 @@ def version(formatted=False):
 
 ABSOLUTE_PATH = root_dir()
 PARAMETER_PATH = [
+    root_dir(),
     os.getcwd(),
     os.path.join(root_dir(), "pybamm", "input", "parameters"),
 ]

pybamm/models/base_model.py

@@ -109,6 +109,7 @@ def __init__(self, name="Unnamed model"):
         self.external_variables = []
         self._parameters = None
         self._input_parameters = None
+        self._variables_casadi = {}
 
         # Default behaviour is to use the jacobian and simplify
         self.use_jacobian = True
@@ -117,6 +118,7 @@ def __init__(self, name="Unnamed model"):
 
         # Model is not initially discretised
         self.is_discretised = False
+        self.y_slices = None
 
         # Default timescale is 1 second
         self.timescale = pybamm.Scalar(1)
@@ -327,6 +329,14 @@ def new_empty_copy(self):
         new_model.convert_to_format = self.convert_to_format
         new_model.timescale = self.timescale
         new_model.length_scales = self.length_scales
+
+        # Variables from discretisation
+        new_model.is_discretised = self.is_discretised
+        new_model.y_slices = self.y_slices
+        new_model.concatenated_rhs = self.concatenated_rhs
+        new_model.concatenated_algebraic = self.concatenated_algebraic
+        new_model.concatenated_initial_conditions = self.concatenated_initial_conditions
+
         return new_model
 
     def new_copy(self):
@@ -412,6 +422,31 @@ def set_initial_conditions_from(self, solution, inplace=True):
                     "Variable must have type 'Variable' or 'Concatenation'"
                 )
 
+        # Also update the concatenated initial conditions if the model is already
+        # discretised
+        if model.is_discretised:
+            # Unpack slices for sorting
+            y_slices = {var.id: slce for var, slce in model.y_slices.items()}
+            slices = []
+            for symbol in model.initial_conditions.keys():
+                if isinstance(symbol, pybamm.Concatenation):
+                    # must append the slice for the whole concatenation, so that
+                    # equations get sorted correctly
+                    slices.append(
+                        slice(
+                            y_slices[symbol.children[0].id][0].start,
+                            y_slices[symbol.children[-1].id][0].stop,
+                        )
+                    )
+                else:
+                    slices.append(y_slices[symbol.id][0])
+            equations = list(model.initial_conditions.values())
+            # sort equations according to slices
+            sorted_equations = [eq for _, eq in sorted(zip(slices, equations))]
+            model.concatenated_initial_conditions = pybamm.NumpyConcatenation(
+                *sorted_equations
+            )
+
         return model
 
     def check_and_combine_dict(self, dict1, dict2):
@@ -888,10 +923,7 @@ def default_spatial_methods(self):
     @property
     def default_solver(self):
         "Return default solver based on whether model is ODE model or DAE model"
-        if len(self.algebraic) == 0:
-            return pybamm.ScipySolver()
-        else:
-            return pybamm.CasadiSolver(mode="safe")
+        return pybamm.CasadiSolver(mode="safe")
 
 
 # helper functions for finding symbols

pybamm/simulation.py

@@ -517,35 +517,6 @@ def step(self, dt, solver=None, npts=2, save=True, **kwargs):
 
         return self.solution
 
-    def get_variable_array(self, *variables):
-        """
-        A helper function to easily obtain a dictionary of arrays of values
-        for a list of variables at the latest timestep.
-
-        Parameters
-        ----------
-        variable: str
-            The name of the variable/variables you wish to obtain the arrays for.
-
-        Returns
-        -------
-        variable_arrays: dict
-            A dictionary of the variable names and their corresponding
-            arrays.
-        """
-
-        variable_arrays = [
-            self.built_model.variables[var].evaluate(
-                self.solution.t[-1], self.solution.y[:, -1]
-            )
-            for var in variables
-        ]
-
-        if len(variable_arrays) == 1:
-            return variable_arrays[0]
-        else:
-            return tuple(variable_arrays)
-
     def plot(self, output_variables=None, quick_plot_vars=None, **kwargs):
         """
         A method to quickly plot the outputs of the simulation. Creates a
@@ -695,6 +666,8 @@ def save(self, filename):
             and self._solver.integrator_specs != {}
         ):
             self._solver.integrator_specs = {}
+        if self.solution is not None:
+            self.solution.clear_casadi_attributes()
         with open(filename, "wb") as f:
             pickle.dump(self, f, pickle.HIGHEST_PROTOCOL)
 

pybamm/solvers/base_solver.py

@@ -956,7 +956,6 @@ def __init__(self, function, name, model):
         self.timescale = self.model.timescale_eval
 
     def __call__(self, t, y, inputs):
-        y = y.reshape(-1, 1)
         if self.name in ["RHS", "algebraic", "residuals"]:
             pybamm.logger.debug(
                 "Evaluating {} for {} at t={}".format(

pybamm/solvers/casadi_solver.py

@@ -133,8 +133,6 @@ def _integrate(self, model, t_eval, inputs=None):
             return solution
         elif self.mode in ["safe", "safe without grid"]:
             y0 = model.y0
-            if isinstance(y0, casadi.DM):
-                y0 = y0.full().flatten()
             # Step-and-check
             t = t_eval[0]
             t_f = t_eval[-1]
@@ -151,7 +149,7 @@ def _integrate(self, model, t_eval, inputs=None):
                 # to avoid having to create several times
                 self.create_integrator(model, inputs)
                 # Initialize solution
-                solution = pybamm.Solution(np.array([t]), y0[:, np.newaxis])
+                solution = pybamm.Solution(np.array([t]), y0)
                 solution.solve_time = 0
                 solution.integration_time = 0
             else:
@@ -402,7 +400,7 @@ def _run_integrator(self, model, y0, inputs, t_eval):
                     x0=y0_diff, z0=y0_alg, p=inputs, **self.extra_options_call
                 )
                 integration_time = timer.time()
-                y_sol = np.concatenate([sol["xf"].full(), sol["zf"].full()])
+                y_sol = casadi.vertcat(sol["xf"], sol["zf"])
                 sol = pybamm.Solution(t_eval, y_sol)
                 sol.integration_time = integration_time
                 return sol