#1066 add numpy function sqrt, sin, cos and exp to convert_to_casadi

CHANGELOG.md

@@ -10,6 +10,8 @@
 
 ## Bug fixes
 
+-   Allowed for pybamm functions exp, sin, cos, sqrt to be used in expression trees that 
+    are converted to casadi format ([#1067](https://github.com/pybamm-team/PyBaMM/pull/1067)
 -   Fix a bug where variables that depend on y and z were transposed in `QuickPlot` ([#1055](https://github.com/pybamm-team/PyBaMM/pull/1055))
 
 ## Breaking changes

examples/scripts/compare_lithium_ion.py

@@ -3,7 +3,7 @@
 #
 import pybamm
 
-pybamm.set_logging_level("INFO")
+# pybamm.set_logging_level("INFO")
 
 # load models
 models = [

pybamm/expression_tree/array.py

@@ -74,7 +74,7 @@ def entries_string(self, value):
             if issparse(entries):
                 self._entries_string = str(entries.__dict__)
             else:
-                self._entries_string = entries.tostring()
+                self._entries_string = entries.tobytes()
 
     def set_id(self):
         """ See :meth:`pybamm.Symbol.set_id()`. """

pybamm/expression_tree/interpolant.py

@@ -86,7 +86,7 @@ def entries_string(self, value):
             self._entries_string = value
         else:
             entries = self.data
-            self._entries_string = entries.tostring()
+            self._entries_string = entries.tobytes()
 
     def set_id(self):
         """ See :meth:`pybamm.Symbol.set_id()`. """

pybamm/expression_tree/operations/convert_to_casadi.py

@@ -101,6 +101,28 @@ def _convert(self, symbol, t, y, y_dot, inputs):
                 return casadi.mmax(*converted_children)
             elif symbol.function == np.abs:
                 return casadi.fabs(*converted_children)
+            elif symbol.function == np.sqrt:
+                return casadi.sqrt(*converted_children)
+            elif symbol.function == np.sin:
+                return casadi.sin(*converted_children)
+            elif symbol.function == np.arcsinh:
+                return casadi.arcsinh(*converted_children)
+            elif symbol.function == np.arccosh:
+                return casadi.arccosh(*converted_children)
+            elif symbol.function == np.tanh:
+                return casadi.tanh(*converted_children)
+            elif symbol.function == np.cosh:
+                return casadi.cosh(*converted_children)
+            elif symbol.function == np.sinh:
+                return casadi.sinh(*converted_children)
+            elif symbol.function == np.cos:
+                return casadi.cos(*converted_children)
+            elif symbol.function == np.exp:
+                return casadi.exp(*converted_children)
+            elif symbol.function == np.log:
+                return casadi.log(*converted_children)
+            elif symbol.function == np.sign:
+                return casadi.sign(*converted_children)
             elif isinstance(symbol.function, (PchipInterpolator, CubicSpline)):
                 return casadi.interpolant("LUT", "bspline", [symbol.x], symbol.y)(
                     *converted_children

pybamm/expression_tree/symbol.py

@@ -740,7 +740,7 @@ def shape(self):
         # Default behaviour is to try to evaluate the object directly
         # Try with some large y, to avoid having to unpack (slow)
         try:
-            y = np.linspace(0.1, 0.9, int(1e4))
+            y = np.nan * np.ones((1000, 1))
             evaluated_self = self.evaluate(0, y, y, inputs="shape test")
         # If that fails, fall back to calculating how big y should really be
         except ValueError:
@@ -753,7 +753,7 @@ def shape(self):
                     len(x._evaluation_array) for x in state_vectors_in_node
                 )
                 # Pick a y that won't cause RuntimeWarnings
-                y = np.linspace(0.1, 0.9, min_y_size)
+                y = np.nan * np.ones((min_y_size, 1))
             evaluated_self = self.evaluate(0, y, y, inputs="shape test")
 
         # Return shape of evaluated object

tests/unit/test_expression_tree/test_operations/test_convert_to_casadi.py

@@ -30,11 +30,11 @@ def test_convert_scalar_symbols(self):
         self.assertEqual(abs(c).to_casadi(), casadi.MX(1))
 
         # function
-        def sin(x):
-            return np.sin(x)
+        def square_plus_one(x):
+            return x ** 2 + 1
 
-        f = pybamm.Function(sin, b)
-        self.assertEqual(f.to_casadi(), casadi.MX(np.sin(1)))
+        f = pybamm.Function(square_plus_one, b)
+        self.assertEqual(f.to_casadi(), 2)
 
         def myfunction(x, y):
             return x + y
@@ -95,6 +95,12 @@ def test_special_functions(self):
         self.assert_casadi_equal(
             pybamm.Function(np.abs, c).to_casadi(), casadi.MX(3), evalf=True
         )
+        for np_fun in [np.sqrt, np.tanh, np.cosh, np.sinh,
+                       np.exp, np.log, np.sign, np.sin, np.cos,
+                       np.arccosh, np.arcsinh]:
+            self.assert_casadi_equal(
+                pybamm.Function(np_fun, c).to_casadi(), casadi.MX(np_fun(3)), evalf=True
+            )
 
     def test_interpolation(self):
         x = np.linspace(0, 1)[:, np.newaxis]