diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6ee541bdac..c6f57ddeb8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,15 @@
+# Unreleased
+
+## Features
+
+## Optimizations
+
+## Bug fixes
+
+- 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
+
# [v0.2.2](https://github.com/pybamm-team/PyBaMM/tree/v0.2.2) - 2020-06-01
New SEI models, simplification of submodel structure, as well as optimisations and general bug fixes.
diff --git a/pybamm/__init__.py b/pybamm/__init__.py
index 066e6ef8d3..9c16b3b551 100644
--- a/pybamm/__init__.py
+++ b/pybamm/__init__.py
@@ -52,8 +52,12 @@ def version(formatted=False):
script_path = os.path.abspath(__file__)
from .util import root_dir
+
ABSOLUTE_PATH = root_dir()
-PARAMETER_PATH = [os.getcwd(), os.path.join(root_dir(), "pybamm", "input", "parameters")]
+PARAMETER_PATH = [
+ os.getcwd(),
+ os.path.join(root_dir(), "pybamm", "input", "parameters"),
+]
#
# Utility classes and methods
@@ -217,7 +221,7 @@ def version(formatted=False):
#
# Plotting
#
-from .plotting.quick_plot import QuickPlot
+from .plotting.quick_plot import QuickPlot, close_plots
from .plotting.plot import plot
from .plotting.plot2D import plot2D
from .plotting.dynamic_plot import dynamic_plot
diff --git a/pybamm/plotting/quick_plot.py b/pybamm/plotting/quick_plot.py
index a14b8d435b..ed5649dd42 100644
--- a/pybamm/plotting/quick_plot.py
+++ b/pybamm/plotting/quick_plot.py
@@ -44,6 +44,13 @@ def split_long_string(title, max_words=4):
return first_line + "\n" + second_line
+def close_plots():
+ "Close all open figures"
+ import matplotlib.pyplot as plt
+
+ plt.close("all")
+
+
class QuickPlot(object):
"""
Generates a quick plot of a subset of key outputs of the model so that the model
@@ -265,6 +272,7 @@ def set_output_variables(self, output_variables, solutions):
self.first_spatial_scale = {}
self.second_spatial_scale = {}
self.is_x_r = {}
+ self.is_y_z = {}
# Calculate subplot positions based on number of variables supplied
self.subplot_positions = {}
@@ -354,8 +362,15 @@ def set_output_variables(self, output_variables, solutions):
)
if first_spatial_var_name == "r" and second_spatial_var_name == "x":
self.is_x_r[variable_tuple] = True
+ self.is_y_z[variable_tuple] = False
+ elif (
+ first_spatial_var_name == "y" and second_spatial_var_name == "z"
+ ):
+ self.is_x_r[variable_tuple] = False
+ self.is_y_z[variable_tuple] = True
else:
self.is_x_r[variable_tuple] = False
+ self.is_y_z[variable_tuple] = False
# Store variables and subplot position
self.variables[variable_tuple] = variables
@@ -585,7 +600,11 @@ def plot(self, t):
y_name = list(spatial_vars.keys())[1][0]
x = self.first_dimensional_spatial_variable[key]
y = self.second_dimensional_spatial_variable[key]
- var = variable(t_in_seconds, **spatial_vars, warn=False).T
+ # need to transpose if domain is x-z
+ if self.is_y_z[key] is True:
+ var = variable(t_in_seconds, **spatial_vars, warn=False)
+ else:
+ var = variable(t_in_seconds, **spatial_vars, warn=False).T
ax.set_xlabel(
"{} [{}]".format(x_name, self.spatial_unit), fontsize=fontsize
)
@@ -593,9 +612,12 @@ def plot(self, t):
"{} [{}]".format(y_name, self.spatial_unit), fontsize=fontsize
)
vmin, vmax = self.variable_limits[key]
- ax.contourf(
+ # store the plot and the var data (for testing) as cant access
+ # z data from QuadContourSet object
+ self.plots[key][0][0] = ax.contourf(
x, y, var, levels=100, vmin=vmin, vmax=vmax, cmap="coolwarm"
)
+ self.plots[key][0][1] = var
if vmin is None and vmax is None:
vmin = ax_min(var)
vmax = ax_max(var)
@@ -717,10 +739,17 @@ def slider_update(self, t):
else:
x = self.first_dimensional_spatial_variable[key]
y = self.second_dimensional_spatial_variable[key]
- var = variable(time_in_seconds, **spatial_vars, warn=False).T
- ax.contourf(
+ # need to transpose if domain is x-z
+ if self.is_y_z[key] is True:
+ var = variable(time_in_seconds, **spatial_vars, warn=False)
+ else:
+ var = variable(time_in_seconds, **spatial_vars, warn=False).T
+ # store the plot and the updated var data (for testing) as cant
+ # access z data from QuadContourSet object
+ self.plots[key][0][0] = ax.contourf(
x, y, var, levels=100, vmin=vmin, vmax=vmax, cmap="coolwarm"
)
+ self.plots[key][0][1] = var
if (vmin, vmax) == (None, None):
vmin = ax_min(var)
vmax = ax_max(var)
diff --git a/tests/unit/test_quick_plot.py b/tests/unit/test_quick_plot.py
index a5dee5379f..dfda895664 100644
--- a/tests/unit/test_quick_plot.py
+++ b/tests/unit/test_quick_plot.py
@@ -269,6 +269,8 @@ def test_simple_ode_model(self):
):
pybamm.QuickPlot(solution, ["NaN variable"])
+ pybamm.close_plots()
+
def test_spm_simulation(self):
# SPM
model = pybamm.lithium_ion.SPM()
@@ -282,26 +284,51 @@ def test_spm_simulation(self):
quick_plot = pybamm.QuickPlot([sim, sim.solution])
quick_plot.plot(0)
- def test_loqs_spm_base(self):
+ pybamm.close_plots()
+
+ def test_loqs_spme(self):
t_eval = np.linspace(0, 10, 2)
- # SPM
- for model in [pybamm.lithium_ion.SPM(), pybamm.lead_acid.LOQS()]:
+ for model in [pybamm.lithium_ion.SPMe(), pybamm.lead_acid.LOQS()]:
geometry = model.default_geometry
param = model.default_parameter_values
param.process_model(model)
param.process_geometry(geometry)
- mesh = pybamm.Mesh(
- geometry, model.default_submesh_types, model.default_var_pts
- )
+ var = pybamm.standard_spatial_vars
+ var_pts = {var.x_n: 5, var.x_s: 5, var.x_p: 5, var.r_n: 5, var.r_p: 5}
+ mesh = pybamm.Mesh(geometry, model.default_submesh_types, var_pts)
disc = pybamm.Discretisation(mesh, model.default_spatial_methods)
disc.process_model(model)
solver = model.default_solver
solution = solver.solve(model, t_eval)
pybamm.QuickPlot(solution)
- # test quick plot of particle for spm
- if model.name == "Single Particle Model":
+ # check 1D (space) variables update properly for different time units
+ c_e = solution["Electrolyte concentration [mol.m-3]"].entries
+
+ for unit, scale in zip(["seconds", "minutes", "hours"], [1, 60, 3600]):
+ quick_plot = pybamm.QuickPlot(
+ solution, ["Electrolyte concentration [mol.m-3]"], time_unit=unit
+ )
+ quick_plot.plot(0)
+ # take off extrapolated points
+ qp_data = (
+ quick_plot.plots[("Electrolyte concentration [mol.m-3]",)][0][
+ 0
+ ].get_ydata()[1:-1],
+ )[0]
+ np.testing.assert_array_almost_equal(qp_data, c_e[:, 0])
+ quick_plot.slider_update(t_eval[-1] / scale)
+ # take off extrapolated points
+ qp_data = (
+ quick_plot.plots[("Electrolyte concentration [mol.m-3]",)][0][
+ 0
+ ].get_ydata()[1:-1],
+ )[0][:, 0]
+ np.testing.assert_array_almost_equal(qp_data, c_e[:, 1])
+
+ # test quick plot of particle for spme
+ if model.name == "Single Particle Model with electrolyte":
output_variables = [
"X-averaged negative particle concentration [mol.m-3]",
"X-averaged positive particle concentration [mol.m-3]",
@@ -310,6 +337,61 @@ def test_loqs_spm_base(self):
]
pybamm.QuickPlot(solution, output_variables)
+ # check 2D (space) variables update properly for different time units
+ c_n = solution["Negative particle concentration [mol.m-3]"].entries
+
+ for unit, scale in zip(["seconds", "minutes", "hours"], [1, 60, 3600]):
+ quick_plot = pybamm.QuickPlot(
+ solution,
+ ["Negative particle concentration [mol.m-3]"],
+ time_unit=unit,
+ )
+ quick_plot.plot(0)
+ qp_data = quick_plot.plots[
+ ("Negative particle concentration [mol.m-3]",)
+ ][0][1]
+ np.testing.assert_array_almost_equal(qp_data, c_n[:, :, 0])
+ quick_plot.slider_update(t_eval[-1] / scale)
+ qp_data = quick_plot.plots[
+ ("Negative particle concentration [mol.m-3]",)
+ ][0][1]
+ np.testing.assert_array_almost_equal(qp_data, c_n[:, :, 1])
+
+ pybamm.close_plots()
+
+ def test_plot_1plus1D_spme(self):
+ spm = pybamm.lithium_ion.SPMe(
+ {"current collector": "potential pair", "dimensionality": 1}
+ )
+ geometry = spm.default_geometry
+ param = spm.default_parameter_values
+ param.process_model(spm)
+ param.process_geometry(geometry)
+ var = pybamm.standard_spatial_vars
+ var_pts = {var.x_n: 5, var.x_s: 5, var.x_p: 5, var.r_n: 5, var.r_p: 5, var.z: 5}
+ mesh = pybamm.Mesh(geometry, spm.default_submesh_types, var_pts)
+ disc_spm = pybamm.Discretisation(mesh, spm.default_spatial_methods)
+ disc_spm.process_model(spm)
+ t_eval = np.linspace(0, 100, 10)
+ solution = spm.default_solver.solve(spm, t_eval)
+
+ # check 2D (x,z space) variables update properly for different time units
+ # Note: these should be the transpose of the entries in the processed variable
+ c_e = solution["Electrolyte concentration [mol.m-3]"].entries
+
+ for unit, scale in zip(["seconds", "minutes", "hours"], [1, 60, 3600]):
+ quick_plot = pybamm.QuickPlot(
+ solution, ["Electrolyte concentration [mol.m-3]"], time_unit=unit
+ )
+ quick_plot.plot(0)
+ qp_data = quick_plot.plots[("Electrolyte concentration [mol.m-3]",)][0][1]
+ np.testing.assert_array_almost_equal(qp_data.T, c_e[:, :, 0])
+ quick_plot.slider_update(t_eval[-1] / scale)
+ qp_data = quick_plot.plots[("Electrolyte concentration [mol.m-3]",)][0][1]
+ np.testing.assert_array_almost_equal(qp_data.T, c_e[:, :, -1])
+
+ pybamm.close_plots()
+
def test_plot_2plus1D_spm(self):
spm = pybamm.lithium_ion.SPM(
{"current collector": "potential pair", "dimensionality": 2}
@@ -331,11 +413,11 @@ def test_plot_2plus1D_spm(self):
mesh = pybamm.Mesh(geometry, spm.default_submesh_types, var_pts)
disc_spm = pybamm.Discretisation(mesh, spm.default_spatial_methods)
disc_spm.process_model(spm)
- t_eval = np.linspace(0, 3600, 100)
- solution_spm = spm.default_solver.solve(spm, t_eval)
+ t_eval = np.linspace(0, 100, 10)
+ solution = spm.default_solver.solve(spm, t_eval)
quick_plot = pybamm.QuickPlot(
- solution_spm,
+ solution,
[
"Negative current collector potential [V]",
"Positive current collector potential [V]",
@@ -345,10 +427,28 @@ def test_plot_2plus1D_spm(self):
quick_plot.dynamic_plot(testing=True)
quick_plot.slider_update(1)
- with self.assertRaisesRegex(NotImplementedError, "Shape not recognized for"):
- pybamm.QuickPlot(
- solution_spm, ["Negative particle concentration [mol.m-3]"]
+ # check 2D (y,z space) variables update properly for different time units
+ phi_n = solution["Negative current collector potential [V]"].entries
+
+ for unit, scale in zip(["seconds", "minutes", "hours"], [1, 60, 3600]):
+ quick_plot = pybamm.QuickPlot(
+ solution, ["Negative current collector potential [V]"], time_unit=unit
)
+ quick_plot.plot(0)
+ qp_data = quick_plot.plots[("Negative current collector potential [V]",)][
+ 0
+ ][1]
+ np.testing.assert_array_almost_equal(qp_data, phi_n[:, :, 0])
+ quick_plot.slider_update(t_eval[-1] / scale)
+ qp_data = quick_plot.plots[("Negative current collector potential [V]",)][
+ 0
+ ][1]
+ np.testing.assert_array_almost_equal(qp_data, phi_n[:, :, -1])
+
+ with self.assertRaisesRegex(NotImplementedError, "Shape not recognized for"):
+ pybamm.QuickPlot(solution, ["Negative particle concentration [mol.m-3]"])
+
+ pybamm.close_plots()
def test_failure(self):
with self.assertRaisesRegex(TypeError, "solutions must be"):