Rename "positive electrode diffusivity" to "positive particle diffusivity"

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## Features
 
+- Renamed "electrode diffusivity" to "particle diffusivity" as a non-breaking change with a deprecation warning ([#3624](https://github.com/pybamm-team/PyBaMM/pull/3624))
 - Add support for BPX version 0.4.0 which allows for blended electrodes and user-defined parameters in BPX([#3414](https://github.com/pybamm-team/PyBaMM/pull/3414))
 - Added the ability to specify a custom solver tolerance in `get_initial_stoichiometries` and related functions ([#3714](https://github.com/pybamm-team/PyBaMM/pull/3714))
 

docs/source/examples/notebooks/change-settings.ipynb

@@ -175,7 +175,7 @@
        " 'Negative electrode charge transfer coefficient': 0.5,\n",
        " 'Negative electrode conductivity [S.m-1]': 100.0,\n",
        " 'Negative electrode density [kg.m-3]': 1657.0,\n",
-       " 'Negative electrode diffusivity [m2.s-1]': <function graphite_mcmb2528_diffusivity_Dualfoil1998 at 0x7fb36b2ad040>,\n",
+       " 'Negative particle diffusivity [m2.s-1]': <function graphite_mcmb2528_diffusivity_Dualfoil1998 at 0x7fb36b2ad040>,\n",
        " 'Negative electrode double-layer capacity [F.m-2]': 0.2,\n",
        " 'Negative electrode electrons in reaction': 1.0,\n",
        " 'Negative electrode exchange-current density [A.m-2]': <function graphite_electrolyte_exchange_current_density_Dualfoil1998 at 0x7fb36b2615e0>,\n",
@@ -210,7 +210,7 @@
        " 'Positive electrode charge transfer coefficient': 0.5,\n",
        " 'Positive electrode conductivity [S.m-1]': 10.0,\n",
        " 'Positive electrode density [kg.m-3]': 3262.0,\n",
-       " 'Positive electrode diffusivity [m2.s-1]': <function lico2_diffusivity_Dualfoil1998 at 0x7fb36b2614c0>,\n",
+       " 'Positive particle diffusivity [m2.s-1]': <function lico2_diffusivity_Dualfoil1998 at 0x7fb36b2614c0>,\n",
        " 'Positive electrode double-layer capacity [F.m-2]': 0.2,\n",
        " 'Positive electrode electrons in reaction': 1.0,\n",
        " 'Positive electrode exchange-current density [A.m-2]': <function lico2_electrolyte_exchange_current_density_Dualfoil1998 at 0x7fb36b261310>,\n",
@@ -314,7 +314,7 @@
       "Current function [A]                                                                     0.680616\n",
       "Negative electrode conductivity [S.m-1]                                                     100.0\n",
       "Maximum concentration in negative electrode [mol.m-3]                            24983.2619938437\n",
-      "Negative electrode diffusivity [m2.s-1]                                      <function graphite_mcmb2528_diffusivity_Dualfoil1998 at 0x7fb36b2ad040>\n",
+      "Negative particle diffusivity [m2.s-1]                                      <function graphite_mcmb2528_diffusivity_Dualfoil1998 at 0x7fb36b2ad040>\n",
       "Negative electrode OCP [V]                                                   <function graphite_mcmb2528_ocp_Dualfoil1998 at 0x7fb36b261670>\n",
       "Negative electrode porosity                                                                   0.3\n",
       "Negative electrode active material volume fraction                                            0.6\n",
@@ -332,7 +332,7 @@
       "Negative electrode OCP entropic change [V.K-1]                               <function graphite_entropic_change_Moura2016 at 0x7fb36b261550>\n",
       "Positive electrode conductivity [S.m-1]                                                      10.0\n",
       "Maximum concentration in positive electrode [mol.m-3]                            51217.9257309275\n",
-      "Positive electrode diffusivity [m2.s-1]                                      <function lico2_diffusivity_Dualfoil1998 at 0x7fb36b2614c0>\n",
+      "Positive particle diffusivity [m2.s-1]                                      <function lico2_diffusivity_Dualfoil1998 at 0x7fb36b2614c0>\n",
       "Positive electrode OCP [V]                                                   <function lico2_ocp_Dualfoil1998 at 0x7fb36b2613a0>\n",
       "Positive electrode porosity                                                                   0.3\n",
       "Positive electrode active material volume fraction                                            0.5\n",

docs/source/examples/notebooks/getting_started/tutorial-4-setting-parameter-values.ipynb

@@ -123,7 +123,7 @@
        " 'Negative electrode charge transfer coefficient': 0.5,\n",
        " 'Negative electrode conductivity [S.m-1]': 215.0,\n",
        " 'Negative electrode density [kg.m-3]': 1657.0,\n",
-       " 'Negative electrode diffusivity [m2.s-1]': 3.3e-14,\n",
+       " 'Negative particle diffusivity [m2.s-1]': 3.3e-14,\n",
        " 'Negative electrode double-layer capacity [F.m-2]': 0.2,\n",
        " 'Negative electrode electrons in reaction': 1.0,\n",
        " 'Negative electrode exchange-current density [A.m-2]': <function graphite_LGM50_electrolyte_exchange_current_density_Chen2020 at 0x7fa179f819d0>,\n",
@@ -155,7 +155,7 @@
        " 'Positive electrode charge transfer coefficient': 0.5,\n",
        " 'Positive electrode conductivity [S.m-1]': 0.18,\n",
        " 'Positive electrode density [kg.m-3]': 3262.0,\n",
-       " 'Positive electrode diffusivity [m2.s-1]': 4e-15,\n",
+       " 'Positive particle diffusivity [m2.s-1]': 4e-15,\n",
        " 'Positive electrode double-layer capacity [F.m-2]': 0.2,\n",
        " 'Positive electrode electrons in reaction': 1.0,\n",
        " 'Positive electrode exchange-current density [A.m-2]': <function nmc_LGM50_electrolyte_exchange_current_density_Chen2020 at 0x7fa179f81af0>,\n",

docs/source/examples/notebooks/models/composite_particle.ipynb

@@ -90,8 +90,8 @@
     "    {\n",
     "        \"Primary: Maximum concentration in negative electrode [mol.m-3]\": 28700,\n",
     "        \"Primary: Initial concentration in negative electrode [mol.m-3]\": 23000,\n",
-    "        \"Primary: Negative electrode diffusivity [m2.s-1]\": 5.5e-14,\n",
-    "        \"Secondary: Negative electrode diffusivity [m2.s-1]\": 1.67e-14,\n",
+    "        \"Primary: Negative particle diffusivity [m2.s-1]\": 5.5e-14,\n",
+    "        \"Secondary: Negative particle diffusivity [m2.s-1]\": 1.67e-14,\n",
     "        \"Secondary: Initial concentration in negative electrode [mol.m-3]\": 277000,\n",
     "        \"Secondary: Maximum concentration in negative electrode [mol.m-3]\": 278000,\n",
     "    }\n",

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

@@ -127,8 +127,8 @@
     "param.update(\n",
     "    {\n",
     "        \"Current function [A]\": I_1C * 3,\n",
-    "        \"Negative electrode diffusivity [m2.s-1]\": 3.9 * 10 ** (-14),\n",
-    "        \"Positive electrode diffusivity [m2.s-1]\": 10 ** (-13),\n",
+    "        \"Negative particle diffusivity [m2.s-1]\": 3.9 * 10 ** (-14),\n",
+    "        \"Positive particle diffusivity [m2.s-1]\": 10 ** (-13),\n",
     "        \"Negative current collector surface heat transfer coefficient [W.m-2.K-1]\": 10,\n",
     "        \"Positive current collector surface heat transfer coefficient [W.m-2.K-1]\": 10,\n",
     "        \"Negative tab heat transfer coefficient [W.m-2.K-1]\": 10,\n",

docs/source/examples/notebooks/models/using-submodels.ipynb

@@ -278,7 +278,7 @@
        "{Variable(0x3825da4a5fc4eb0b, Discharge capacity [A.h], children=[], domains={}): Multiplication(0x7678edd47e530eec, *, children=['0.0002777777777777778', 'Current function [A]'], domains={}),\n",
        " Variable(-0x7fb8d0e6e9632372, Throughput capacity [A.h], children=[], domains={}): Multiplication(-0x7c65e8600b424661, *, children=['0.0002777777777777778', 'abs(Current function [A])'], domains={}),\n",
        " Variable(0x69f725db1a464db8, Average negative particle concentration [mol.m-3], children=[], domains={'primary': ['current collector']}): MatrixMultiplication(0xf98a766c86b2483, @, children=['mass(Average negative particle concentration [mol.m-3])', '-3.0 * Current function [A] / (Number of electrodes connected in parallel to make a cell * Electrode width [m] * Electrode height [m]) / Negative electrode thickness [m] / x-average(3.0 * Negative electrode active material volume fraction / Negative particle radius [m]) / Faraday constant [C.mol-1] / x-average(Negative particle radius [m])'], domains={'primary': ['current collector']}),\n",
-       " Variable(0x48143b39c7603013, X-averaged positive particle concentration [mol.m-3], children=[], domains={'primary': ['positive particle'], 'secondary': ['current collector']}): Divergence(0x17c75a81711ad510, div, children=['Positive electrode diffusivity [m2.s-1] * grad(X-averaged positive particle concentration [mol.m-3])'], domains={'primary': ['positive particle'], 'secondary': ['current collector']})}"
+       " Variable(0x48143b39c7603013, X-averaged positive particle concentration [mol.m-3], children=[], domains={'primary': ['positive particle'], 'secondary': ['current collector']}): Divergence(0x17c75a81711ad510, div, children=['Positive particle diffusivity [m2.s-1] * grad(X-averaged positive particle concentration [mol.m-3])'], domains={'primary': ['positive particle'], 'secondary': ['current collector']})}"
       ]
      },
      "execution_count": 9,

examples/scripts/emperical_hysteresis.py → examples/scripts/empirical_hysteresis.py

@@ -122,9 +122,9 @@ def exchange_current_density_average(sto):
         "": exchange_current_density_lithiation,
         "Negative electrode delithiation exchange-current density [A.m-2]"
         "": exchange_current_density_delithiation,
-        "Negative electrode diffusivity [m2.s-1]": 3.3e-14,
-        "Negative electrode lithiation diffusivity [m2.s-1]": 4e-14,
-        "Negative electrode delithiation diffusivity [m2.s-1]": 2.6e-14,
+        "Negative particle diffusivity [m2.s-1]": 3.3e-14,
+        "Negative particle lithiation diffusivity [m2.s-1]": 4e-14,
+        "Negative particle delithiation diffusivity [m2.s-1]": 2.6e-14,
     },
     check_already_exists=False,
 )

examples/scripts/minimal_example_of_lookup_tables.py

@@ -22,7 +22,7 @@ def process_2D(name, data):
 parameter_values = pybamm.ParameterValues(pybamm.parameter_sets.Chen2020)
 
 # overwrite the diffusion coefficient with a 2D lookup table
-D_s_n = parameter_values["Negative electrode diffusivity [m2.s-1]"]
+D_s_n = parameter_values["Negative particle diffusivity [m2.s-1]"]
 df = pd.DataFrame(
     {
         "T": [0, 0, 25, 25, 45, 45],
@@ -31,15 +31,15 @@ def process_2D(name, data):
     }
 )
 df["T"] = df["T"] + 273.15
-D_s_n_data = process_2D("Negative electrode diffusivity [m2.s-1]", df)
+D_s_n_data = process_2D("Negative particle diffusivity [m2.s-1]", df)
 
 
 def D_s_n(sto, T):
     name, (x, y) = D_s_n_data
     return pybamm.Interpolant(x, y, [T, sto], name)
 
 
-parameter_values["Negative electrode diffusivity [m2.s-1]"] = D_s_n
+parameter_values["Negative particle diffusivity [m2.s-1]"] = D_s_n
 
 k_n = parameter_values["Negative electrode exchange-current density [A.m-2]"]
 

pybamm/input/parameters/lithium_ion/Ai2020.py

@@ -582,7 +582,7 @@ def get_parameter_values():
         # negative electrode
         "Negative electrode conductivity [S.m-1]": 100.0,
         "Maximum concentration in negative electrode [mol.m-3]": 28700.0,
-        "Negative electrode diffusivity [m2.s-1]": graphite_diffusivity_Dualfoil1998,
+        "Negative particle diffusivity [m2.s-1]": graphite_diffusivity_Dualfoil1998,
         "Negative electrode OCP [V]": graphite_ocp_Enertech_Ai2020,
         "Negative electrode porosity": 0.33,
         "Negative electrode active material volume fraction": 0.61,
@@ -617,7 +617,7 @@ def get_parameter_values():
         # positive electrode
         "Positive electrode conductivity [S.m-1]": 10.0,
         "Maximum concentration in positive electrode [mol.m-3]": 49943.0,
-        "Positive electrode diffusivity [m2.s-1]": lico2_diffusivity_Dualfoil1998,
+        "Positive particle diffusivity [m2.s-1]": lico2_diffusivity_Dualfoil1998,
         "Positive electrode OCP [V]": lico2_ocp_Ai2020,
         "Positive electrode porosity": 0.32,
         "Positive electrode active material volume fraction": 0.62,

pybamm/input/parameters/lithium_ion/Chen2020.py

@@ -273,7 +273,7 @@ def get_parameter_values():
         # negative electrode
         "Negative electrode conductivity [S.m-1]": 215.0,
         "Maximum concentration in negative electrode [mol.m-3]": 33133.0,
-        "Negative electrode diffusivity [m2.s-1]": 3.3e-14,
+        "Negative particle diffusivity [m2.s-1]": 3.3e-14,
         "Negative electrode OCP [V]": graphite_LGM50_ocp_Chen2020,
         "Negative electrode porosity": 0.25,
         "Negative electrode active material volume fraction": 0.75,
@@ -291,7 +291,7 @@ def get_parameter_values():
         # positive electrode
         "Positive electrode conductivity [S.m-1]": 0.18,
         "Maximum concentration in positive electrode [mol.m-3]": 63104.0,
-        "Positive electrode diffusivity [m2.s-1]": 4e-15,
+        "Positive particle diffusivity [m2.s-1]": 4e-15,
         "Positive electrode OCP [V]": nmc_LGM50_ocp_Chen2020,
         "Positive electrode porosity": 0.335,
         "Positive electrode active material volume fraction": 0.665,

pybamm/input/parameters/lithium_ion/Chen2020_composite.py

@@ -394,7 +394,7 @@ def get_parameter_values():
         "Negative electrode conductivity [S.m-1]": 215.0,
         "Primary: Maximum concentration in negative electrode [mol.m-3]": 28700.0,
         "Primary: Initial concentration in negative electrode [mol.m-3]": 27700.0,
-        "Primary: Negative electrode diffusivity [m2.s-1]": 5.5e-14,
+        "Primary: Negative particle diffusivity [m2.s-1]": 5.5e-14,
         "Primary: Negative electrode OCP [V]": graphite_ocp_Enertech_Ai2020,
         "Negative electrode porosity": 0.25,
         "Primary: Negative electrode active material volume fraction": 0.735,
@@ -411,7 +411,7 @@ def get_parameter_values():
         "Primary: Negative electrode OCP entropic change [V.K-1]": 0.0,
         "Secondary: Maximum concentration in negative electrode [mol.m-3]": 278000.0,
         "Secondary: Initial concentration in negative electrode [mol.m-3]": 276610.0,
-        "Secondary: Negative electrode diffusivity [m2.s-1]": 1.67e-14,
+        "Secondary: Negative particle diffusivity [m2.s-1]": 1.67e-14,
         "Secondary: Negative electrode lithiation OCP [V]"
         "": silicon_ocp_lithiation_Mark2016,
         "Secondary: Negative electrode delithiation OCP [V]"
@@ -425,7 +425,7 @@ def get_parameter_values():
         # positive electrode
         "Positive electrode conductivity [S.m-1]": 0.18,
         "Maximum concentration in positive electrode [mol.m-3]": 63104.0,
-        "Positive electrode diffusivity [m2.s-1]": 4e-15,
+        "Positive particle diffusivity [m2.s-1]": 4e-15,
         "Positive electrode OCP [V]": nmc_LGM50_ocp_Chen2020,
         "Positive electrode porosity": 0.335,
         "Positive electrode active material volume fraction": 0.665,

pybamm/input/parameters/lithium_ion/Ecker2015.py

@@ -462,7 +462,7 @@ def get_parameter_values():
         # negative electrode
         "Negative electrode conductivity [S.m-1]": 14.0,
         "Maximum concentration in negative electrode [mol.m-3]": 31920.0,
-        "Negative electrode diffusivity [m2.s-1]": graphite_diffusivity_Ecker2015,
+        "Negative particle diffusivity [m2.s-1]": graphite_diffusivity_Ecker2015,
         "Negative electrode OCP [V]": graphite_ocp_Ecker2015,
         "Negative electrode porosity": 0.329,
         "Negative electrode active material volume fraction": 0.372403,
@@ -478,7 +478,7 @@ def get_parameter_values():
         # positive electrode
         "Positive electrode conductivity [S.m-1]": 68.1,
         "Maximum concentration in positive electrode [mol.m-3]": 48580.0,
-        "Positive electrode diffusivity [m2.s-1]": nco_diffusivity_Ecker2015,
+        "Positive particle diffusivity [m2.s-1]": nco_diffusivity_Ecker2015,
         "Positive electrode OCP [V]": nco_ocp_Ecker2015,
         "Positive electrode porosity": 0.296,
         "Positive electrode active material volume fraction": 0.40832,

pybamm/input/parameters/lithium_ion/Ecker2015_graphite_halfcell.py

@@ -386,7 +386,7 @@ def get_parameter_values():
         # positive electrode
         "Positive electrode conductivity [S.m-1]": 14.0,
         "Maximum concentration in positive electrode [mol.m-3]": 31920.0,
-        "Positive electrode diffusivity [m2.s-1]": graphite_diffusivity_Ecker2015,
+        "Positive particle diffusivity [m2.s-1]": graphite_diffusivity_Ecker2015,
         "Positive electrode OCP [V]": graphite_ocp_Ecker2015,
         "Positive electrode porosity": 0.329,
         "Positive electrode active material volume fraction": 0.372403,

pybamm/input/parameters/lithium_ion/MSMR_example_set.py

@@ -136,7 +136,7 @@ def get_parameter_values():
         "j0_ref_n_5": 2.7,
         "Negative electrode conductivity [S.m-1]": 215.0,
         "Maximum concentration in negative electrode [mol.m-3]": 33133.0,
-        "Negative electrode diffusivity [m2.s-1]": 3.3e-14,
+        "Negative particle diffusivity [m2.s-1]": 3.3e-14,
         "Negative electrode porosity": 0.25,
         "Negative electrode active material volume fraction": 0.75,
         "Negative particle radius [m]": 5.86e-06,
@@ -167,7 +167,7 @@ def get_parameter_values():
         "j0_ref_p_3": 1e6,
         "Positive electrode conductivity [S.m-1]": 0.18,
         "Maximum concentration in positive electrode [mol.m-3]": 63104.0,
-        "Positive electrode diffusivity [m2.s-1]": 4e-15,
+        "Positive particle diffusivity [m2.s-1]": 4e-15,
         "Positive electrode porosity": 0.335,
         "Positive electrode active material volume fraction": 0.665,
         "Positive particle radius [m]": 5.22e-06,

pybamm/input/parameters/lithium_ion/Marquis2019.py

@@ -399,7 +399,7 @@ def get_parameter_values():
         # negative electrode
         "Negative electrode conductivity [S.m-1]": 100.0,
         "Maximum concentration in negative electrode [mol.m-3]": 24983.2619938437,
-        "Negative electrode diffusivity [m2.s-1]"
+        "Negative particle diffusivity [m2.s-1]"
         "": graphite_mcmb2528_diffusivity_Dualfoil1998,
         "Negative electrode OCP [V]": graphite_mcmb2528_ocp_Dualfoil1998,
         "Negative electrode porosity": 0.3,
@@ -419,7 +419,7 @@ def get_parameter_values():
         # positive electrode
         "Positive electrode conductivity [S.m-1]": 10.0,
         "Maximum concentration in positive electrode [mol.m-3]": 51217.9257309275,
-        "Positive electrode diffusivity [m2.s-1]": lico2_diffusivity_Dualfoil1998,
+        "Positive particle diffusivity [m2.s-1]": lico2_diffusivity_Dualfoil1998,
         "Positive electrode OCP [V]": lico2_ocp_Dualfoil1998,
         "Positive electrode porosity": 0.3,
         "Positive electrode active material volume fraction": 0.5,

pybamm/input/parameters/lithium_ion/Mohtat2020.py

@@ -389,7 +389,7 @@ def get_parameter_values():
         # negative electrode
         "Negative electrode conductivity [S.m-1]": 100.0,
         "Maximum concentration in negative electrode [mol.m-3]": 28746.0,
-        "Negative electrode diffusivity [m2.s-1]": graphite_diffusivity_PeymanMPM,
+        "Negative particle diffusivity [m2.s-1]": graphite_diffusivity_PeymanMPM,
         "Negative electrode OCP [V]": graphite_ocp_PeymanMPM,
         "Negative electrode porosity": 0.3,
         "Negative electrode active material volume fraction": 0.61,
@@ -411,7 +411,7 @@ def get_parameter_values():
         # positive electrode
         "Positive electrode conductivity [S.m-1]": 100.0,
         "Maximum concentration in positive electrode [mol.m-3]": 35380.0,
-        "Positive electrode diffusivity [m2.s-1]": NMC_diffusivity_PeymanMPM,
+        "Positive particle diffusivity [m2.s-1]": NMC_diffusivity_PeymanMPM,
         "Positive electrode OCP [V]": NMC_ocp_PeymanMPM,
         "Positive electrode porosity": 0.3,
         "Positive electrode active material volume fraction": 0.445,

pybamm/input/parameters/lithium_ion/NCA_Kim2011.py

@@ -362,7 +362,7 @@ def get_parameter_values():
         # negative electrode
         "Negative electrode conductivity [S.m-1]": 100.0,
         "Maximum concentration in negative electrode [mol.m-3]": 28700.0,
-        "Negative electrode diffusivity [m2.s-1]": graphite_diffusivity_Kim2011,
+        "Negative particle diffusivity [m2.s-1]": graphite_diffusivity_Kim2011,
         "Negative electrode OCP [V]": graphite_ocp_Kim2011,
         "Negative electrode porosity": 0.4,
         "Negative electrode active material volume fraction": 0.51,
@@ -380,7 +380,7 @@ def get_parameter_values():
         # positive electrode
         "Positive electrode conductivity [S.m-1]": 10.0,
         "Maximum concentration in positive electrode [mol.m-3]": 49000.0,
-        "Positive electrode diffusivity [m2.s-1]": nca_diffusivity_Kim2011,
+        "Positive particle diffusivity [m2.s-1]": nca_diffusivity_Kim2011,
         "Positive electrode OCP [V]": nca_ocp_Kim2011,
         "Positive electrode porosity": 0.4,
         "Positive electrode active material volume fraction": 0.41,