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Rename "positive electrode diffusivity" to "positive particle diffusi…
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…vity" (#3624)

* merge_conflicts

* merge_conflicts_

* update_pr_number

* rename_empirical_hysteresis

* style: pre-commit fixes

* style: pre-commit fixes

* update changelog

* fix bpx

* style: pre-commit fixes

* update changelog

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Ferran Brosa Planella <[email protected]>
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1 change: 1 addition & 0 deletions CHANGELOG.md
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## 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))

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8 changes: 4 additions & 4 deletions docs/source/examples/notebooks/change-settings.ipynb
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Expand Up @@ -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",
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" '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",
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"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",
Expand All @@ -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",
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Expand Up @@ -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",
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" '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",
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Expand Up @@ -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",
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20 changes: 10 additions & 10 deletions docs/source/examples/notebooks/models/latexify.ipynb

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4 changes: 2 additions & 2 deletions docs/source/examples/notebooks/models/pouch-cell-model.ipynb
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Expand Up @@ -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",
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Expand Up @@ -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,
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Expand Up @@ -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,
)
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6 changes: 3 additions & 3 deletions examples/scripts/minimal_example_of_lookup_tables.py
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Expand Up @@ -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],
Expand All @@ -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]"]

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4 changes: 2 additions & 2 deletions pybamm/input/parameters/lithium_ion/Ai2020.py
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Expand Up @@ -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,
Expand Down Expand Up @@ -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,
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4 changes: 2 additions & 2 deletions pybamm/input/parameters/lithium_ion/Chen2020.py
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Expand Up @@ -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,
Expand All @@ -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,
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6 changes: 3 additions & 3 deletions pybamm/input/parameters/lithium_ion/Chen2020_composite.py
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Expand Up @@ -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,
Expand All @@ -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]"
Expand All @@ -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,
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4 changes: 2 additions & 2 deletions pybamm/input/parameters/lithium_ion/Ecker2015.py
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Expand Up @@ -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,
Expand All @@ -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,
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Expand Up @@ -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,
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4 changes: 2 additions & 2 deletions pybamm/input/parameters/lithium_ion/MSMR_example_set.py
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Expand Up @@ -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,
Expand Down Expand Up @@ -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,
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4 changes: 2 additions & 2 deletions pybamm/input/parameters/lithium_ion/Marquis2019.py
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Expand Up @@ -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,
Expand All @@ -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,
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4 changes: 2 additions & 2 deletions pybamm/input/parameters/lithium_ion/Mohtat2020.py
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Expand Up @@ -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,
Expand All @@ -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,
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4 changes: 2 additions & 2 deletions pybamm/input/parameters/lithium_ion/NCA_Kim2011.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand All @@ -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,
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