change step offset to 1e-9

Author: valentinsulzer

CHANGELOG.md

@@ -18,7 +18,7 @@
 
 ## Breaking changes
 
-- When using `solver.step()`, the first time point in the step is shifted by `pybamm.settings.step_start_offset` (default 1 us) to avoid having duplicate times in the solution steps from the end of one step and the start of the next. ([#2773](https://github.com/pybamm-team/PyBaMM/pull/2773))
+- When using `solver.step()`, the first time point in the step is shifted by `pybamm.settings.step_start_offset` (default 1 ns) to avoid having duplicate times in the solution steps from the end of one step and the start of the next. ([#2773](https://github.com/pybamm-team/PyBaMM/pull/2773))
 - Renamed "Measured open circuit voltage [V]" to "Surface open-circuit voltage [V]". This variable was calculated from surface particle concentrations, and hence "hid" the overpotential from particle gradients. The new variable "Open-circuit voltage [V]" is calculated from bulk particle concentrations instead. ([#2740](https://github.com/pybamm-team/PyBaMM/pull/2740))
 - Renamed all references to "open circuit" to be "open-circuit" instead. ([#2740](https://github.com/pybamm-team/PyBaMM/pull/2740))
 - Renamed parameter "1 + dlnf/dlnc" to "Thermodynamic factor". ([#2727](https://github.com/pybamm-team/PyBaMM/pull/2727))

pybamm/settings.py

@@ -12,7 +12,7 @@ class Settings(object):
     _abs_smoothing = "exact"
     max_words_in_line = 4
     max_y_value = 1e5
-    step_start_offset = 1e-6
+    step_start_offset = 1e-9
     tolerances = {
         "D_e__c_e": 10,  # dimensional
         "kappa_e__c_e": 10,  # dimensional

pybamm/solvers/base_solver.py

@@ -1100,7 +1100,7 @@ def step(
         if t_start == 0:
             t_start_shifted = t_start
         else:
-            # offset t_start by t_start_offset (default 1 us)
+            # offset t_start by t_start_offset (default 1 ns)
             # to avoid repeated times in the solution
             # from having the same time at the end of the previous step and
             # the start of the next step

tests/integration/test_experiments.py

@@ -23,7 +23,7 @@ def test_discharge_rest_charge(self):
         sim.solve()
         np.testing.assert_array_almost_equal(
             sim._solution["Time [h]"].entries,
-            np.array([0, 0.5, 1, 1 + 1e-6, 1.5, 2, 2 + 1e-6, 2.5, 3]),
+            np.array([0, 0.5, 1, 1 + 1e-9, 1.5, 2, 2 + 1e-9, 2.5, 3]),
         )
         cap = model.default_parameter_values["Nominal cell capacity [A.h]"]
         np.testing.assert_array_almost_equal(

tests/unit/test_simulation.py

@@ -155,19 +155,19 @@ def test_step(self):
         sim.step(dt)  # automatically append the next step
         self.assertEqual(sim.solution.y.full()[0, :].size, 4)
         np.testing.assert_array_almost_equal(
-            sim.solution.t, np.array([0, dt, dt + 1e-6, 2 * dt])
+            sim.solution.t, np.array([0, dt, dt + 1e-9, 2 * dt])
         )
 
         sim.step(dt, save=False)  # now only store the two end step points
         self.assertEqual(sim.solution.y.full()[0, :].size, 2)
         np.testing.assert_array_almost_equal(
-            sim.solution.t, np.array([2 * dt + 1e-6, 3 * dt])
+            sim.solution.t, np.array([2 * dt + 1e-9, 3 * dt])
         )
         # Start from saved solution
         sim.step(dt, starting_solution=saved_sol)
         self.assertEqual(sim.solution.y.full()[0, :].size, 4)
         np.testing.assert_array_almost_equal(
-            sim.solution.t, np.array([0, dt, dt + 1e-6, 2 * dt])
+            sim.solution.t, np.array([0, dt, dt + 1e-9, 2 * dt])
         )
 
     def test_solve_with_initial_soc(self):
@@ -233,7 +233,7 @@ def test_step_with_inputs(self):
         )  # automatically append the next step
         self.assertEqual(sim.solution.y.full()[0, :].size, 4)
         np.testing.assert_array_almost_equal(
-            sim.solution.t, np.array([0, dt, dt + 1e-6, 2 * dt])
+            sim.solution.t, np.array([0, dt, dt + 1e-9, 2 * dt])
         )
         np.testing.assert_array_equal(
             sim.solution.all_inputs[1]["Current function [A]"], 2

tests/unit/test_solvers/test_casadi_solver.py

@@ -292,7 +292,7 @@ def test_model_step(self):
         # Step again (return 5 points)
         step_sol_2 = solver.step(step_sol, model, dt, npts=5)
         np.testing.assert_array_equal(
-            step_sol_2.t, np.array([0, 1, 1 + 1e-6, 1.25, 1.5, 1.75, 2])
+            step_sol_2.t, np.array([0, 1, 1 + 1e-9, 1.25, 1.5, 1.75, 2])
         )
         np.testing.assert_array_almost_equal(
             step_sol_2.y.full()[0], np.exp(0.1 * step_sol_2.t)
@@ -324,7 +324,7 @@ def test_model_step_with_input(self):
         step_sol_2 = solver.step(step_sol, model, dt, npts=5, inputs={"a": -1})
         np.testing.assert_array_almost_equal(
             step_sol_2.t,
-            np.array([0, 0.025, 0.05, 0.075, 0.1, 0.1 + 1e-6, 0.125, 0.15, 0.175, 0.2]),
+            np.array([0, 0.025, 0.05, 0.075, 0.1, 0.1 + 1e-9, 0.125, 0.15, 0.175, 0.2]),
         )
         np.testing.assert_array_equal(
             step_sol_2["a"].entries,

tests/unit/test_solvers/test_scikits_solvers.py

@@ -532,7 +532,7 @@ def test_model_step_ode_python(self):
         # Step again (return 5 points)
         step_sol_2 = solver.step(step_sol, model, dt, npts=5)
         np.testing.assert_array_equal(
-            step_sol_2.t, np.array([0, 1, 1 + 1e-6, 1.25, 1.5, 1.75, 2])
+            step_sol_2.t, np.array([0, 1, 1 + 1e-9, 1.25, 1.5, 1.75, 2])
         )
         np.testing.assert_allclose(step_sol_2.y[0], np.exp(-0.1 * step_sol_2.t))
 
@@ -566,7 +566,7 @@ def test_model_step_dae_python(self):
         # Step again (return 5 points)
         step_sol_2 = solver.step(step_sol, model, dt, npts=5)
         np.testing.assert_array_equal(
-            step_sol_2.t, np.array([0, 1, 1 + 1e-6, 1.25, 1.5, 1.75, 2])
+            step_sol_2.t, np.array([0, 1, 1 + 1e-9, 1.25, 1.5, 1.75, 2])
         )
         np.testing.assert_allclose(step_sol_2.y[0, :], np.exp(0.1 * step_sol_2.t))
         np.testing.assert_allclose(step_sol_2.y[-1, :], 2 * np.exp(0.1 * step_sol_2.t))
@@ -598,7 +598,7 @@ def test_model_solver_ode_events_casadi(self):
         solution = solver.solve(model, t_eval)
         np.testing.assert_allclose(solution.y[0], np.exp(0.1 * solution.t))
         np.testing.assert_array_less(solution.y[0:, -1], 1.5)
-        np.testing.assert_array_less(solution.y[0:, -1], 1.25 + 1e-6)
+        np.testing.assert_array_less(solution.y[0:, -1], 1.25 + 1e-9)
         np.testing.assert_equal(solution.t_event[0], solution.t[-1])
         np.testing.assert_array_equal(solution.y_event[:, 0], solution.y[:, -1])
 

tests/unit/test_solvers/test_scipy_solver.py

@@ -180,7 +180,7 @@ def test_model_step_python(self):
         # Step again (return 5 points)
         step_sol_2 = solver.step(step_sol, model, dt, npts=5)
         np.testing.assert_array_equal(
-            step_sol_2.t, np.array([0, 1, 1 + 1e-6, 1.25, 1.5, 1.75, 2])
+            step_sol_2.t, np.array([0, 1, 1 + 1e-9, 1.25, 1.5, 1.75, 2])
         )
         np.testing.assert_array_almost_equal(
             step_sol_2.y[0], np.exp(0.1 * step_sol_2.t)