Merge pull request #1490 from pybamm-team/issue-1405-xaverage

Issue 1405 xaverage
pybamm-team · May 24, 2021 · 7d8ec5c · 7d8ec5c
2 parents 8445c27 + 6835652
commit 7d8ec5c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,8 @@
 
 ## Features
 
+-   Added a new "reaction-driven" model for LAM from Reniers et al (2019) ([#1490](https://github.com/pybamm-team/PyBaMM/pull/1490))
+-   Some features ("loss of active material" and "particle mechanics") can now be specified separately for the negative electrode and positive electrode by passing a 2-tuple ([#1490](https://github.com/pybamm-team/PyBaMM/pull/1490))
 -   `plot` and `plot2D` now take and return a matplotlib Axis to allow for easier customization ([#1472](https://github.com/pybamm-team/PyBaMM/pull/1472))
 -   `ParameterValues.evaluate` can now return arrays to allow function parameters to be easily evaluated ([#1472](https://github.com/pybamm-team/PyBaMM/pull/1472))
 -   Added Batch Study class ([#1455](https://github.com/pybamm-team/PyBaMM/pull/1455))
@@ -10,6 +12,7 @@
 
 ## Optimizations
 
+-   Models that mostly use x-averaged quantities (SPM and SPMe) now use x-averaged degradation models ([#1490](https://github.com/pybamm-team/PyBaMM/pull/1490))
 -   Improved how the CasADi solver's "safe" mode finds events ([#1450](https://github.com/pybamm-team/PyBaMM/pull/1450))
 -   Perform more automatic simplifications of the expression tree ([#1449](https://github.com/pybamm-team/PyBaMM/pull/1449))
 -   Reduce time taken to hash a sparse `Matrix` object ([#1449](https://github.com/pybamm-team/PyBaMM/pull/1449))
@@ -20,6 +23,7 @@
 
 ## Breaking changes
 
+-   Changed how options are specified for the "loss of active material" and "particle cracking" submodels. "loss of active material" can now be one of "none", "stress-driven", or "reaction-driven", or a 2-tuple for different options in negative and positive electrode. Similarly "particle cracking" (now called "particle mechanics") can now be "none", "swelling only", "swelling and cracking", or a 2-tuple ([#1490](https://github.com/pybamm-team/PyBaMM/pull/1490))
 -   Changed the variable in the full diffusion model from "Electrolyte concentration" to "Porosity times concentration" ([#1476](https://github.com/pybamm-team/PyBaMM/pull/1476))
 -   Renamed `lithium-ion` folder to `lithium_ion` and `lead-acid` folder to `lead_acid` in parameters ([#1464](https://github.com/pybamm-team/PyBaMM/pull/1464))
 
@@ -94,11 +98,11 @@ This release introduces:
 
 # [v0.3.0](https://github.com/pybamm-team/PyBaMM/tree/v0.3.0) - 2020-12-01
 
-This release introduces a new aging model for particle swelling and cracking, a new reduced-order model (TSPMe), and a parameter set for A123 LFP cells. Additionally, there have been several backend optimizations to speed up model creation and solving, and other minor features and bug fixes.
+This release introduces a new aging model for particle mechanics, a new reduced-order model (TSPMe), and a parameter set for A123 LFP cells. Additionally, there have been several backend optimizations to speed up model creation and solving, and other minor features and bug fixes.
 
 ## Features
 
--   Added a submodel for particle swelling and cracking ([#1232](https://github.com/pybamm-team/PyBaMM/pull/1232))
+-   Added a submodel for particle mechanics ([#1232](https://github.com/pybamm-team/PyBaMM/pull/1232))
 -   Added a notebook on how to speed up the solver and handle instabilities ([#1223](https://github.com/pybamm-team/PyBaMM/pull/1223))
 -   Improve string printing of `BinaryOperator`, `Function`, and `Concatenation` objects ([#1223](https://github.com/pybamm-team/PyBaMM/pull/1223))
 -   Added `Solution.integration_time`, which is the time taken just by the integration subroutine, without extra setups ([#1223](https://github.com/pybamm-team/PyBaMM/pull/1223))

diff --git a/docs/source/models/base_models/base_battery_model.rst b/docs/source/models/base_models/base_battery_model.rst
@@ -4,5 +4,5 @@ Base Battery Model
 .. autoclass:: pybamm.BaseBatteryModel
     :members:
 
-.. autoclass:: pybamm.Options
+.. autoclass:: pybamm.BatteryModelOptions
     :members:
diff --git a/docs/source/models/submodels/active_material/base_active_material.rst b/docs/source/models/submodels/active_material/base_active_material.rst
@@ -0,0 +1,6 @@
+Base Model
+===========
+
+.. autoclass:: pybamm.active_material.BaseModel
+    :members:
+
diff --git a/docs/source/models/submodels/active_material/constant_active_material.rst b/docs/source/models/submodels/active_material/constant_active_material.rst
@@ -0,0 +1,7 @@
+Constant Active Material
+========================
+
+.. autoclass:: pybamm.active_material.Constant
+    :members:
+
+
diff --git a/docs/source/models/submodels/active_material/index.rst b/docs/source/models/submodels/active_material/index.rst
@@ -0,0 +1,13 @@
+Active Material
+===============
+
+Submodels for (loss of) active material
+
+.. toctree::
+  :maxdepth: 1
+
+  base_active_material
+  constant_active_material
+  reaction_driven_active_material
+  stress_driven_active_material
+
diff --git a/docs/source/models/submodels/active_material/reaction_driven_active_material.rst b/docs/source/models/submodels/active_material/reaction_driven_active_material.rst
@@ -0,0 +1,8 @@
+Reaction-driven Loss of Active Material
+=======================================
+
+.. autoclass:: pybamm.active_material.ReactionDriven
+    :members:
+
+
+
diff --git a/docs/source/models/submodels/active_material/stress_driven_active_material.rst b/docs/source/models/submodels/active_material/stress_driven_active_material.rst
@@ -0,0 +1,8 @@
+Stress-driven Loss of Active Material 
+=====================================
+
+.. autoclass:: pybamm.active_material.StressDriven
+    :members:
+
+
+
diff --git a/docs/source/models/submodels/index.rst b/docs/source/models/submodels/index.rst
@@ -5,6 +5,7 @@ Submodels
     :maxdepth: 1
 
     base_submodel
+    active_material/index
     current_collector/index
     convection/index
     electrode/index

diff --git a/docs/source/models/submodels/particle_cracking/index.rst b/docs/source/models/submodels/particle_cracking/index.rst
@@ -6,4 +6,4 @@ Particle Cracking
 
   base_cracking
   crack_propagation
-  no_cracking
+  swelling_only
diff --git a/docs/source/models/submodels/particle_cracking/no_cracking.rst b/docs/source/models/submodels/particle_cracking/no_cracking.rst
diff --git a/docs/source/models/submodels/particle_cracking/swelling_only.rst b/docs/source/models/submodels/particle_cracking/swelling_only.rst
@@ -0,0 +1,5 @@
+Swelling Only Model
+===================
+
+.. autoclass:: pybamm.particle_cracking.SwellingOnly
+    :members:
diff --git a/docs/source/models/submodels/porosity/full_reaction_driven_porosity.rst b/docs/source/models/submodels/porosity/full_reaction_driven_porosity.rst
diff --git a/docs/source/models/submodels/porosity/index.rst b/docs/source/models/submodels/porosity/index.rst
@@ -6,6 +6,5 @@ Porosity
 
   base_porosity
   constant_porosity
-  leading_reaction_driven_porosity
-  full_reaction_driven_porosity
+  reaction_driven_porosity
 
diff --git a/docs/source/models/submodels/porosity/leading_reaction_driven_porosity.rst b/docs/source/models/submodels/porosity/leading_reaction_driven_porosity.rst
diff --git a/docs/source/models/submodels/porosity/reaction_driven_porosity.rst b/docs/source/models/submodels/porosity/reaction_driven_porosity.rst
@@ -0,0 +1,8 @@
+Reaction-driven Model 
+=====================
+
+.. autoclass:: pybamm.porosity.ReactionDriven
+    :members:
+
+
+
diff --git a/examples/notebooks/Validating_mechanical_models_Enertech_DFN.ipynb b/examples/notebooks/Validating_mechanical_models_Enertech_DFN.ipynb
diff --git a/examples/notebooks/submodel_cracking_DFN_or_SPM,.ipynb b/examples/notebooks/submodel_cracking_DFN_or_SPM,.ipynb
@@ -17,6 +17,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "\u001b[33mWARNING: You are using pip version 21.0.1; however, version 21.1.1 is available.\n",
+      "You should consider upgrading via the '/Users/vsulzer/Documents/Energy_storage/PyBaMM/.tox/dev/bin/python -m pip install --upgrade pip' command.\u001b[0m\n",
       "Note: you may need to restart the kernel to use updated packages.\n"
      ]
     }
@@ -48,10 +50,7 @@
     "# model = pybamm.lithium_ion.SPMe(\n",
     "# model = pybamm.lithium_ion.SPM(\n",
     "model = pybamm.lithium_ion.DFN(\n",
-    "    options = {\n",
-    "        \"particle\": \"Fickian diffusion\",  \n",
-    "        \"particle cracking\": \"both\", # other options are \"positive\", \"negative\" or \"none\"\n",
-    "    }\n",
+    "    options = {\"particle mechanics\": \"swelling and cracking\"}\n",
     ")"
    ]
   },
@@ -90,7 +89,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "cefb37faadae47bcb1ddbeb5ea034ad8",
+       "model_id": "c3b1f934d8e34942a66d8771c0d09d17",
        "version_major": 2,
        "version_minor": 0
       },
@@ -129,7 +128,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "8e09d0af090a45a78fe27f6595821aa9",
+       "model_id": "232ab4b5fb4b49d6832cc709518ad61a",
        "version_major": 2,
        "version_minor": 0
       },
@@ -196,7 +195,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "4df7bf436fbd4067aee4b16a61793577",
+       "model_id": "f42ca205ce824664917d70d8ff35bebf",
        "version_major": 2,
        "version_minor": 0
       },
@@ -269,9 +268,22 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.8"
+  },
+  "toc": {
+   "base_numbering": 1,
+   "nav_menu": {},
+   "number_sections": true,
+   "sideBar": true,
+   "skip_h1_title": false,
+   "title_cell": "Table of Contents",
+   "title_sidebar": "Contents",
+   "toc_cell": false,
+   "toc_position": {},
+   "toc_section_display": true,
+   "toc_window_display": true
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
diff --git a/examples/notebooks/submodel_loss_of_active_materials.ipynb b/examples/notebooks/submodel_loss_of_active_materials.ipynb
diff --git a/examples/scripts/cycling_ageing_yang.py b/examples/scripts/cycling_ageing_yang.py
@@ -42,7 +42,7 @@
     ]
 )
 sim = pb.Simulation(model, experiment=experiment)
-sim.solve(solver=pb.CasadiSolver(mode="safe"))
+sim.solve(solver=pb.CasadiSolver(mode="fast with events"))
 sim.plot(
     [
         "Current [A]",

diff --git a/pybamm/__init__.py b/pybamm/__init__.py
@@ -120,7 +120,10 @@ def version(formatted=False):
 from .models.event import EventType
 
 # Battery models
-from .models.full_battery_models.base_battery_model import BaseBatteryModel, Options
+from .models.full_battery_models.base_battery_model import (
+    BaseBatteryModel,
+    BatteryModelOptions,
+)
 from .models.full_battery_models import lead_acid
 from .models.full_battery_models import lithium_ion
 

diff --git a/pybamm/input/parameters/lithium_ion/seis/example/parameters.csv b/pybamm/input/parameters/lithium_ion/seis/example/parameters.csv
@@ -21,4 +21,8 @@ EC initial concentration in electrolyte [mol.m-3], 4.541E3, Safari paper,
 EC diffusivity [m2.s-1], 2E-18, adjusted parameter in Yang paper,
 SEI kinetic rate constant [m.s-1], 1e-12, adjusted parameter in Yang paper,
 SEI open-circuit potential [V], 0.4, Safari paper,
+,,,
+# Reaction-driven LAM example,,,
+Negative electrode reaction-driven LAM factor [m3.mol-1],0,,
+Positive electrode reaction-driven LAM factor [m3.mol-1],0,,
 
diff --git a/pybamm/models/base_model.py b/pybamm/models/base_model.py
@@ -86,7 +86,7 @@ class BaseModel(object):
 
     def __init__(self, name="Unnamed model"):
         self.name = name
-        self.options = {}
+        self._options = {}
 
         # Initialise empty model
         self._rhs = {}