Merge branch 'issue-923-reformat-electrolyte' into issue-546-convection

CHANGELOG.md

@@ -1,4 +1,18 @@
-# [Unreleased](https://github.com/pybamm-team/PyBaMM)
+# [Unreleased](https://github.com/pybamm-team/PyBaMM/)
+
+## Optimizations
+
+-   Made `QuickPlot` compatible with Google Colab ([#935](https://github.com/pybamm-team/PyBaMM/pull/935))
+-   Sped up model building ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
+-   Changed default solver for lead-acid to `CasadiSolver` ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
+
+## Bug fixes
+
+-   Reformatted electrolyte submodels ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
+
+# [v0.2.1](https://github.com/pybamm-team/PyBaMM/tree/v0.2.1) - 2020-03-31
+
+New expression tree node types, models, parameter sets and solvers, as well as general bug fixes and new examples.
 
 ## Features
 
@@ -9,9 +23,6 @@
 -   Added functionality to broadcast to edges ([#891](https://github.com/pybamm-team/PyBaMM/pull/891))
 -   Reformatted and cleaned up `QuickPlot` ([#886](https://github.com/pybamm-team/PyBaMM/pull/886))
 -   Added thermal effects to lead-acid models ([#885](https://github.com/pybamm-team/PyBaMM/pull/885))
--   Add new symbols `VariableDot`, representing the derivative of a variable wrt time,
-    and `StateVectorDot`, representing the derivative of a state vector wrt time
-    ([#858](https://github.com/pybamm-team/PyBaMM/issues/858))
 -   Added a helper function for info on function parameters ([#881](https://github.com/pybamm-team/PyBaMM/pull/881))
 -   Added additional notebooks showing how to create and compare models ([#877](https://github.com/pybamm-team/PyBaMM/pull/877))
 -   Added `Minimum`, `Maximum` and `Sign` operators
@@ -24,14 +35,9 @@
     and `StateVectorDot`, representing the derivative of a state vector wrt time
     ([#858](https://github.com/pybamm-team/PyBaMM/issues/858))
 
-## Optimizations
-
--   Sped up model building ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
--   Changed default solver for lead-acid to `CasadiSolver` ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
-
 ## Bug fixes
 
--   Reformatted electrolyte submodels ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
+-   Fixed tight layout for QuickPlot in jupyter notebooks ([#930](https://github.com/pybamm-team/PyBaMM/pull/930))
 -   Fixed bug raised if function returns a scalar ([#919](https://github.com/pybamm-team/PyBaMM/pull/919))
 -   Fixed event handling in `ScipySolver` ([#905](https://github.com/pybamm-team/PyBaMM/pull/905))
 -   Made input handling clearer in solvers ([#905](https://github.com/pybamm-team/PyBaMM/pull/905))

docs/conf.py

@@ -28,7 +28,7 @@
 # The short X.Y version
 version = "0.2"
 # The full version, including alpha/beta/rc tags
-release = "0.2.0"
+release = "0.2.1"
 
 
 # -- General configuration ---------------------------------------------------

docs/source/models/submodels/electrolyte_conductivity/surface_form/index.rst

@@ -3,5 +3,5 @@ Surface Form
 
 .. toctree::
 
-  full_surface_form_stefan_maxwell_conductivity
-  leading_surface_form_stefan_maxwell_conductivity
+  full_surface_form_conductivity
+  leading_surface_form_conductivity

examples/scripts/compare_lead_acid.py

@@ -17,15 +17,15 @@
 
 # load models
 models = [
-    # pybamm.lead_acid.LOQS(),
-    # # pybamm.lead_acid.FOQS(),
-    # pybamm.lead_acid.Composite(),
+    pybamm.lead_acid.LOQS(),
+    pybamm.lead_acid.FOQS(),
+    pybamm.lead_acid.CompositeExtended(),
     pybamm.lead_acid.Full(),
 ]
 
 # load parameter values and process models and geometry
 param = models[0].default_parameter_values
-param.update({"Current function [A]": 10, "Initial State of Charge": 1})
+param.update({"Current function [A]": 85, "Initial State of Charge": 1})
 for model in models:
     param.process_model(model)
 

examples/scripts/drive_cycle.py

@@ -13,7 +13,7 @@
 # create and run simulation using the CasadiSolver in "fast" mode, remembering to
 # pass in the updated parameters
 sim = pybamm.Simulation(
-    model, parameter_values=param, solver=pybamm.CasadiSolver(mode="fast"),
+    model, parameter_values=param, solver=pybamm.CasadiSolver(mode="fast")
 )
 sim.solve()
 sim.plot(

examples/scripts/experimental_protocols/cccv.py

@@ -13,7 +13,7 @@
         "Hold at 4.1 V until 50 mA",
         "Rest for 1 hour",
     ]
-    * 3,
+    * 3
 )
 model = pybamm.lithium_ion.DFN()
 sim = pybamm.Simulation(model, experiment=experiment, solver=pybamm.CasadiSolver())

examples/scripts/experimental_protocols/gitt.py

@@ -4,9 +4,7 @@
 import pybamm
 
 pybamm.set_logging_level("INFO")
-experiment = pybamm.Experiment(
-    ["Discharge at C/20 for 1 hour", "Rest for 1 hour"] * 20,
-)
+experiment = pybamm.Experiment(["Discharge at C/20 for 1 hour", "Rest for 1 hour"] * 20)
 model = pybamm.lithium_ion.DFN()
 sim = pybamm.Simulation(model, experiment=experiment, solver=pybamm.CasadiSolver())
 sim.solve()

pybamm/CITATIONS.txt

@@ -72,6 +72,14 @@ year={2019},
 publisher={The Electrochemical Society}
 }
 
+@article{Mohtat2020,
+author = {Mohtat, Peyman and Siegel, Jason B and Stefanopoulou, Anna G},
+title = {{High C-rate Differential Expansion and Voltage Model for Li-ion Batteries}},
+journal = {Submitted for publication},
+year = {2019},
+publisher={ECSarXiv}
+}
+
 @article{scikits-odes,
   year  = {2018},
   month = {feb},

pybamm/__init__.py

@@ -220,7 +220,7 @@ def version(formatted=False):
 # other
 #
 from .processed_variable import ProcessedVariable
-from .quick_plot import QuickPlot, ax_min, ax_max
+from .quick_plot import QuickPlot, dynamic_plot, ax_min, ax_max
 
 from .simulation import Simulation, load_sim, is_notebook
 

pybamm/expression_tree/broadcasts.py

@@ -252,8 +252,8 @@ class FullBroadcast(Broadcast):
     "A class for full broadcasts"
 
     def __init__(self, child, broadcast_domain, auxiliary_domains, name=None):
-        if auxiliary_domains == "current collector":
-            auxiliary_domains = {"secondary": "current collector"}
+        if isinstance(auxiliary_domains, str):
+            auxiliary_domains = {"secondary": auxiliary_domains}
         super().__init__(
             child,
             broadcast_domain,

pybamm/expression_tree/state_vector.py

@@ -45,8 +45,9 @@ def __init__(
             if y_slices[0].start is None:
                 name = base_name + "[:{:d}]".format(y_slice.stop)
             else:
-                name = base_name + \
-                    "[{:d}:{:d}".format(y_slices[0].start, y_slices[0].stop)
+                name = base_name + "[{:d}:{:d}".format(
+                    y_slices[0].start, y_slices[0].stop
+                )
             if len(y_slices) > 1:
                 name += ",{:d}:{:d}".format(y_slices[1].start, y_slices[1].stop)
                 if len(y_slices) > 2:
@@ -222,10 +223,14 @@ def __init__(
         auxiliary_domains=None,
         evaluation_array=None,
     ):
-        super().__init__(*y_slices,
-                         base_name="y", name=name, domain=domain,
-                         auxiliary_domains=auxiliary_domains,
-                         evaluation_array=evaluation_array)
+        super().__init__(
+            *y_slices,
+            base_name="y",
+            name=name,
+            domain=domain,
+            auxiliary_domains=auxiliary_domains,
+            evaluation_array=evaluation_array,
+        )
 
     def _base_evaluate(self, t=None, y=None, y_dot=None, inputs=None):
         """ See :meth:`pybamm.Symbol._base_evaluate()`. """
@@ -245,10 +250,13 @@ def diff(self, variable):
         if variable.id == self.id:
             return pybamm.Scalar(1)
         if variable.id == pybamm.t.id:
-            return StateVectorDot(*self._y_slices, name=self.name + "'",
-                                  domain=self.domain,
-                                  auxiliary_domains=self.auxiliary_domains,
-                                  evaluation_array=self.evaluation_array)
+            return StateVectorDot(
+                *self._y_slices,
+                name=self.name + "'",
+                domain=self.domain,
+                auxiliary_domains=self.auxiliary_domains,
+                evaluation_array=self.evaluation_array,
+            )
         else:
             return pybamm.Scalar(0)
 
@@ -289,10 +297,14 @@ def __init__(
         auxiliary_domains=None,
         evaluation_array=None,
     ):
-        super().__init__(*y_slices,
-                         base_name="y_dot", name=name, domain=domain,
-                         auxiliary_domains=auxiliary_domains,
-                         evaluation_array=evaluation_array)
+        super().__init__(
+            *y_slices,
+            base_name="y_dot",
+            name=name,
+            domain=domain,
+            auxiliary_domains=auxiliary_domains,
+            evaluation_array=evaluation_array,
+        )
 
     def _base_evaluate(self, t=None, y=None, y_dot=None, inputs=None):
         """ See :meth:`pybamm.Symbol._base_evaluate()`. """

pybamm/input/parameters/lithium-ion/anodes/graphite_UMBL_Mohtat2020/graphite_diffusivity_PeymanMPM.py

@@ -0,0 +1,38 @@
+import pybamm
+
+
+def graphite_diffusivity_PeymanMPM(sto, T, T_inf, E_D_s, R_g):
+    """
+    Graphite diffusivity as a function of stochiometry, in this case the
+    diffusivity is taken to be a constant. The value is taken from Peyman MPM.
+
+    References
+    ----------
+    .. [1] http://www.cchem.berkeley.edu/jsngrp/fortran.html
+
+    Parameters
+    ----------
+    sto: :class: `numpy.Array`
+        Electrode stochiometry
+    T: :class: `numpy.Array`
+        Dimensional temperature
+    T_inf: double
+        Reference temperature
+    E_D_s: double
+        Solid diffusion activation energy
+    R_g: double
+        The ideal gas constant
+
+    Returns
+    -------
+    : double
+        Solid diffusivity
+   """
+
+    D_ref = 5.0 * 10 ** (-15)
+    arrhenius = pybamm.exp(E_D_s / R_g * (1 / T_inf - 1 / T))
+
+    # Removing the fudge factor 0 * sto requires different handling of either
+    # either simplifications or how sto is passed into this function.
+    # See #547
+    return D_ref * arrhenius + 0 * sto

pybamm/input/parameters/lithium-ion/anodes/graphite_UMBL_Mohtat2020/graphite_electrolyte_reaction_rate_PeymanMPM.py

@@ -0,0 +1,32 @@
+import pybamm
+
+
+def graphite_electrolyte_reaction_rate_PeymanMPM(T, T_inf, E_r, R_g):
+    """
+    Reaction rate for Butler-Volmer reactions between graphite and LiPF6 in EC:DMC.
+    Check the unit of Reaction rate constant k0 is from Peyman MPM.
+
+    References
+    ----------
+    .. [2] http://www.cchem.berkeley.edu/jsngrp/fortran.html
+
+    Parameters
+    ----------
+    T: :class: `numpy.Array`
+        Dimensional temperature
+    T_inf: double
+        Reference temperature
+    E_r: double
+        Reaction activation energy
+    R_g: double
+        The ideal gas constant
+
+    Returns
+    -------
+    :`numpy.Array`
+        Reaction rate
+    """
+    m_ref = 1.061 * 10 ** (-6)  # unit has been converted
+    arrhenius = pybamm.exp(E_r / R_g * (1 / T_inf - 1 / T))
+
+    return m_ref * arrhenius

pybamm/input/parameters/lithium-ion/anodes/graphite_UMBL_Mohtat2020/graphite_entropic_change_PeymanMPM.py

@@ -0,0 +1,28 @@
+def graphite_entropic_change_PeymanMPM(sto, c_n_max):
+    """
+        Graphite entropic change in open circuit potential (OCP) at a temperature of
+        298.15K as a function of the stochiometry taken from [1]
+
+        References
+        ----------
+        .. [1] K.E. Thomas, J. Newman, "Heats of mixing and entropy in porous insertion
+               electrode", J. of Power Sources 119 (2003) 844-849
+
+          Parameters
+          ----------
+          sto: double
+               Stochiometry of material (li-fraction)
+
+    """
+
+    du_dT = 10 ** (-3) * (
+        0.28
+        - 1.56 * sto
+        - 8.92 * sto ** (2)
+        + 57.21 * sto ** (3)
+        - 110.7 * sto ** (4)
+        + 90.71 * sto ** (5)
+        - 27.14 * sto ** (6)
+    )
+
+    return du_dT

pybamm/input/parameters/lithium-ion/anodes/graphite_UMBL_Mohtat2020/graphite_ocp_PeymanMPM.py

@@ -0,0 +1,36 @@
+import pybamm
+
+
+def graphite_ocp_PeymanMPM(sto):
+    """
+       Graphite Open Circuit Potential (OCP) as a function of the
+       stochiometry. The fit is taken from Peyman MPM [1].
+
+       References
+       ----------
+       .. [1] Peyman Mohtat et al, MPM (to be submitted)
+       """
+
+    u_eq = (
+        0.063
+        + 0.8 * pybamm.exp(-75 * (sto + 0.007))
+        - 0.0120 * pybamm.tanh((sto - 0.127) / 0.016)
+        - 0.0118 * pybamm.tanh((sto - 0.155) / 0.016)
+        - 0.0035 * pybamm.tanh((sto - 0.220) / 0.020)
+        - 0.0095 * pybamm.tanh((sto - 0.190) / 0.013)
+        - 0.0145 * pybamm.tanh((sto - 0.490) / 0.020)
+        - 0.0800 * pybamm.tanh((sto - 1.030) / 0.055)
+    )
+
+    # u_eq = 1.0 + (0 * sto)
+
+    return u_eq
+
+
+# if __name__ == "__main__": # pragma: no cover
+#     import matplotlib.pyplot as plt
+#     import numpy as np
+
+#     x = np.linspace(0, 1)
+#     plt.plot(x, graphite_ocp_PeymanMPM(x))
+#     plt.show()

pybamm/input/parameters/lithium-ion/anodes/graphite_UMBL_Mohtat2020/parameters.csv

@@ -0,0 +1,41 @@
+Name [units],Value,Reference,Notes
+# Empty rows and rows starting with ‘#’ will be ignored,,,
+,,,
+# Electrode properties,,,
+Negative electrode conductivity [S.m-1],100,Scott Moura FastDFN,no info from Peyman MPM 
+Maximum concentration in negative electrode [mol.m-3],28746,Peyman MPM,
+Negative electrode diffusion coefficient [m2.s-1],5.0E-15,Peyman MPM,
+Negative electrode diffusivity [m2.s-1],[function]graphite_diffusivity_PeymanMPM,,
+Negative electrode OCP [V],[function]graphite_ocp_PeymanMPM,Peyman MPM,
+,,,
+# Microstructure,,,
+Negative electrode porosity,0.3,Peyman MPM, 
+Negative electrode active material volume fraction,0.61,Peyman MPM,rest is binder
+Negative particle radius [m],2.5E-06,Peyman MPM,
+Negative particle distribution in x,1,,
+Negative electrode surface area density [m-1],732000,Peyman MPM,Eq. (48)
+Negative electrode Bruggeman coefficient (electrode),1.5,Peyman MPM,
+Negative electrode Bruggeman coefficient (electrolyte),1.5,Peyman MPM,
+Negative electrode tortuosity, 0.16,
+,,,
+# Interfacial reactions,,,
+Negative electrode cation signed stoichiometry,-1,,no info from Peyman MPM
+Negative electrode electrons in reaction,1,,no info from Peyman MPM
+Negative electrode reference exchange-current density [A.m-2(m3.mol)1.5],1.061E-6,Peyman MPM,convert unit
+Reference OCP vs SHE in the negative electrode [V],,,
+Negative electrode charge transfer coefficient,0.5,Peyman MPM,
+Negative electrode double-layer capacity [F.m-2],0.2,,no info from Peyman MPM
+,,,
+# Density,,,
+Negative electrode density [kg.m-3],3100,Peyman MPM, cell lumped value 
+,,,
+# Thermal parameters,,,
+Negative electrode specific heat capacity [J.kg-1.K-1],1100,Peyman MPM,cell lumped value
+Negative electrode thermal conductivity [W.m-1.K-1],1.7,,no info from Peyman MPM
+Negative electrode OCP entropic change [V.K-1],[function]graphite_entropic_change_PeymanMPM,,
+,,,
+# Activation energies,,,
+Reference temperature [K],298.15,25C,
+Negative electrode reaction rate,[function]graphite_electrolyte_reaction_rate_PeymanMPM,,
+Negative reaction rate activation energy [J.mol-1],37480,,no info from Peyman MPM
+Negative solid diffusion activation energy [J.mol-1],42770,,no info from Peyman MPM