Merge pull request #2268 from pybamm-team/develop

Make release v22.8

.github/workflows/work_precision_sets.yml

@@ -0,0 +1,37 @@
+name: Generate work precision sets
+
+on:
+  release:
+   types: [created]
+  workflow_dispatch: 
+
+jobs:
+
+  benchmarks_on_release:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Setup python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+    - name: Get current date
+      run: echo "VERSION=$(date +'%y.%-m')" >> $GITHUB_ENV
+    - name: Install PyBaMM
+      run: python -m pip install pybamm==${{ env.VERSION }}
+    - name: Run time_vs_* benchmarks for PyBaMM v${{ env.VERSION }}
+      run: |
+        python benchmarks/work_precision_sets/time_vs_dt_max.py
+        python benchmarks/work_precision_sets/time_vs_mesh_size.py
+        python benchmarks/work_precision_sets/time_vs_no_of_states.py
+        python benchmarks/work_precision_sets/time_vs_reltols.py
+        python benchmarks/work_precision_sets/time_vs_abstols.py
+    - name: Create Pull Request
+      uses: peter-evans/create-pull-request@v3
+      with:
+        delete-branch: true
+        branch-suffix: short-commit-hash
+        commit-message: Work precision sets for PyBaMM version ${{ env.VERSION }}
+        title: Work precision sets for PyBaMM version ${{ env.VERSION }}
+        body: |
+            Update work precision sets for PyBaMM version ${{ env.VERSION }} in `release_work_precision_sets.md`

.gitignore

@@ -13,6 +13,7 @@
 !CMakeLists.txt
 !pybamm/CITATIONS.txt
 !pybamm/input/**/*.csv
+!benchmarks/benchmark_images/*.png
 
 # running files
 *.pyc

CHANGELOG.md

@@ -1,5 +1,31 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+# [v22.8](https://github.com/pybamm-team/PyBaMM/tree/v22.8) - 2022-08-31
+
+## Features
+
+-   Added `CurrentSigmoidOpenCircuitPotential` model to model voltage hysteresis for charge/discharge ([#2256](https://github.com/pybamm-team/PyBaMM/pull/2256))
+-   Added "Chen2020_composite" parameter set for a composite graphite/silicon electrode. ([#2256](https://github.com/pybamm-team/PyBaMM/pull/2256))
+-   Added new cumulative variables `Throughput capacity [A.h]` and `Throughput energy [W.h]` to standard variables and summary variables, to assist with degradation studies. Throughput variables are only calculated if `calculate discharge energy` is set to `true`. `Time [s]` and `Time [h]` also added to summary variables. ([#2249](https://github.com/pybamm-team/PyBaMM/pull/2249))
+-   Added `lipf6_OKane2022` electrolyte to `OKane2022` parameter set ([#2249](https://github.com/pybamm-team/PyBaMM/pull/2249))
+-   Reformated submodel structure to allow composite electrodes. Composite positive electrode is now also possible. With current implementation, electrodes can have at most two phases. ([#2248](https://github.com/pybamm-team/PyBaMM/pull/2248))
+
+## Bug fixes
+
+-   Added new parameter `Ratio of lithium moles to SEI moles` (short name z_sei) to fix a bug where this number was incorrectly hardcoded to 1. ([#2222](https://github.com/pybamm-team/PyBaMM/pull/2222))
+-   Changed short name of parameter `Inner SEI reaction proportion` from alpha_SEI to inner_sei_proportion, to avoid confusion with transfer coefficients. ([#2222](https://github.com/pybamm-team/PyBaMM/pull/2222))
+-   Deleted legacy parameters with short names beta_sei and beta_plating. ([#2222](https://github.com/pybamm-team/PyBaMM/pull/2222))
+-   Corrected initial SEI thickness for OKane2022 parameter set. ([#2218](https://github.com/pybamm-team/PyBaMM/pull/2218))
+
+## Optimizations
+
+-   Simplified scaling for the exchange-current density. The dimensionless parameter `C_r` is kept, but no longer used anywhere ([#2238](https://github.com/pybamm-team/PyBaMM/pull/2238))
+-   Added limits for variables in some functions to avoid division by zero, sqrt(negative number), etc ([#2213](https://github.com/pybamm-team/PyBaMM/pull/2213))
+
+## Breaking changes
+
+-   Parameters specific to a (primary/secondary) phase in a domain are doubly nested. e.g. `param.c_n_max` is now `param.n.prim.c_max` ([#2248](https://github.com/pybamm-team/PyBaMM/pull/2248))
+
 # [v22.7](https://github.com/pybamm-team/PyBaMM/tree/v22.7) - 2022-07-31
 
 ## Features 
@@ -34,7 +60,7 @@
 ## Breaking changes
 
 -   Exchange-current density functions (and some other functions) now take an additional argument, the maximum particle concentration for that phase ([#2134](https://github.com/pybamm-team/PyBaMM/pull/2134))
--   Loss of lithium to SEI on cracks is now a degradation variable, so setting a particle mechanics submodel is now compulsory (NoMechanics will suffice)
+-   Loss of lithium to SEI on cracks is now a degradation variable, so setting a particle mechanics submodel is now compulsory (NoMechanics will suffice) ([#2104](https://github.com/pybamm-team/PyBaMM/pull/2104))
 
 # [v22.6](https://github.com/pybamm-team/PyBaMM/tree/v22.6) - 2022-06-30
 
@@ -56,6 +82,7 @@
 
 ## Features
 
+-   Added a casadi version of the IDKLU solver, which is used for `model.convert_to_format = "casadi"` ([#2002](https://github.com/pybamm-team/PyBaMM/pull/2002))
 -   Added functionality to generate Julia expressions from a model. See [PyBaMM.jl](https://github.com/tinosulzer/PyBaMM.jl) for how to use these ([#1942](https://github.com/pybamm-team/PyBaMM/pull/1942)))
 -   Added basic callbacks to the Simulation class, and a LoggingCallback ([#1880](https://github.com/pybamm-team/PyBaMM/pull/1880)))
 
@@ -65,7 +92,7 @@
 
 ## Breaking changes
 
--   Changed domain-specific parameter names to a nested attribute, e.g. `param.c_n_max` is now `param.n.c_max` ([#2063](https://github.com/pybamm-team/PyBaMM/pull/2063))
+-   Changed domain-specific parameter names to a nested attribute. `param.n.l_n` is now `param.n.l` ([#2063](https://github.com/pybamm-team/PyBaMM/pull/2063))
 
 # [v22.4](https://github.com/pybamm-team/PyBaMM/tree/v22.4) - 2022-04-30
 

CITATION.cff

@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "22.7"
+version: "22.8"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"

benchmarks/release-work-precision-sets.md

@@ -0,0 +1,15 @@
+# PyBaMM 22.7
+## Solve Time vs Abstols
+<img src='./benchmark_images/time_vs_abstols_22.7.png'>
+
+## Solve Time vs Reltols
+<img src='./benchmark_images/time_vs_reltols_22.7.png'>
+
+## Solve Time vs Mesh size
+<img src='./benchmark_images/time_vs_mesh_size_22.7.png'>
+
+## Solve Time vs dt_max
+<img src='./benchmark_images/time_vs_dt_max_22.7.png'>
+
+## Solve Time vs Number of states
+<img src='./benchmark_images/time_vs_no_of_states_22.7.png'>

benchmarks/work_precision_sets/time_vs_abstols.py

@@ -0,0 +1,108 @@
+import pybamm
+import numpy as np
+import matplotlib.pyplot as plt
+import itertools
+
+
+parameters = ["Marquis2019", "Ecker2015", "Ramadass2004", "Chen2020"]
+
+models = {"SPM": pybamm.lithium_ion.SPM(), "DFN": pybamm.lithium_ion.DFN()}
+
+abstols = [
+    0.0001,
+    1.0e-5,
+    1.0e-6,
+    1.0e-7,
+    1.0e-8,
+    1.0e-9,
+    1.0e-10,
+    1.0e-11,
+    1.0e-12,
+    1.0e-13,
+]
+
+solvers = {
+    "IDAKLUSolver": pybamm.IDAKLUSolver(),
+    "Casadi - safe": pybamm.CasadiSolver(),
+    "Casadi - fast": pybamm.CasadiSolver(mode="fast"),
+}
+
+
+fig, axs = plt.subplots(len(solvers), len(models), figsize=(8, 10))
+
+for ax, i, j in zip(
+    axs.ravel(),
+    itertools.product(solvers.values(), models.values()),
+    itertools.product(solvers, models),
+):
+
+    for params in parameters:
+
+        time_points = []
+        solver = i[0]
+
+        model = i[1].new_copy()
+        c_rate = 1
+        tmax = 3500 / c_rate
+        nb_points = 500
+        t_eval = np.linspace(0, tmax, nb_points)
+        geometry = model.default_geometry
+
+        # load parameter values and process model and geometry
+        param = pybamm.ParameterValues(params)
+        param.process_model(model)
+        param.process_geometry(geometry)
+
+        # set mesh
+        var_pts = {
+            "x_n": 20,
+            "x_s": 20,
+            "x_p": 20,
+            "r_n": 30,
+            "r_p": 30,
+            "y": 10,
+            "z": 10,
+        }
+        mesh = pybamm.Mesh(geometry, model.default_submesh_types, var_pts)
+
+        # discretise model
+        disc = pybamm.Discretisation(mesh, model.default_spatial_methods)
+        disc.process_model(model)
+
+        for tol in abstols:
+
+            solver.atol = tol
+            solver.solve(model, t_eval=t_eval)
+            time = 0
+            runs = 20
+            for k in range(0, runs):
+
+                solution = solver.solve(model, t_eval=t_eval)
+                time += solution.solve_time.value
+            time = time / runs
+
+            time_points.append(time)
+
+        ax.set_xscale("log")
+        ax.set_yscale("log")
+        ax.set_xlabel("abstols")
+        ax.set_ylabel("time(s)")
+        ax.set_title(f"{j[1]} with {j[0]}")
+        ax.plot(abstols, time_points)
+
+plt.tight_layout()
+plt.gca().legend(
+    parameters,
+    loc="lower right",
+)
+
+
+plt.savefig(f"benchmarks/benchmark_images/time_vs_abstols_{pybamm.__version__}.png")
+
+
+content = f"# PyBaMM {pybamm.__version__}\n## Solve Time vs Abstols\n<img src='./benchmark_images/time_vs_abstols_{pybamm.__version__}.png'>\n"  # noqa
+
+with open("./benchmarks/release_work_precision_sets.md", "r") as original:
+    data = original.read()
+with open("./benchmarks/release_work_precision_sets.md", "w") as modified:
+    modified.write(f"{content}\n{data}")

benchmarks/work_precision_sets/time_vs_dt_max.py

@@ -0,0 +1,111 @@
+import pybamm
+import numpy as np
+import matplotlib.pyplot as plt
+
+
+parameters = [
+    "Marquis2019",
+    "Prada2013",
+    "Ramadass2004",
+    "Chen2020",
+]
+
+models = {"SPM": pybamm.lithium_ion.SPM(), "DFN": pybamm.lithium_ion.DFN()}
+
+dt_max = [
+    10,
+    20,
+    50,
+    80,
+    100,
+    150,
+    250,
+    400,
+    600,
+    900,
+    1200,
+    1600,
+    2100,
+    2600,
+    3000,
+    3600,
+]
+
+
+fig, axs = plt.subplots(1, len(models), figsize=(8, 3))
+
+for ax, model_, model_name in zip(
+    axs.ravel(),
+    models.values(),
+    models,
+):
+
+    for params in parameters:
+
+        time_points = []
+        # solver = pybamm.CasadiSolver()
+
+        model = model_.new_copy()
+        c_rate = 10
+        tmax = 3600 / c_rate
+        nb_points = 500
+        t_eval = np.linspace(0, tmax, nb_points)
+        geometry = model.default_geometry
+
+        # load parameter values and process model and geometry
+        param = pybamm.ParameterValues(params)
+        param.process_model(model)
+        param.process_geometry(geometry)
+
+        # set mesh
+        var_pts = {
+            "x_n": 20,
+            "x_s": 20,
+            "x_p": 20,
+            "r_n": 30,
+            "r_p": 30,
+            "y": 10,
+            "z": 10,
+        }
+        mesh = pybamm.Mesh(geometry, model.default_submesh_types, var_pts)
+
+        # discretise model
+        disc = pybamm.Discretisation(mesh, model.default_spatial_methods)
+        disc.process_model(model)
+
+        for t in dt_max:
+
+            solver = pybamm.CasadiSolver(dt_max=t)
+
+            solver.solve(model, t_eval=t_eval)
+            time = 0
+            runs = 20
+            for k in range(0, runs):
+
+                solution = solver.solve(model, t_eval=t_eval)
+                time += solution.solve_time.value
+            time = time / runs
+
+            time_points.append(time)
+
+        ax.set_xscale("log")
+        ax.set_yscale("log")
+        ax.set_xlabel("dt_max")
+        ax.set_ylabel("time(s)")
+        ax.set_title(f"{model_name}")
+        ax.plot(dt_max, time_points)
+
+plt.tight_layout()
+plt.gca().legend(
+    parameters,
+    loc="upper right",
+)
+plt.savefig(f"benchmarks/benchmark_images/time_vs_dt_max_{pybamm.__version__}.png")
+
+
+content = f"## Solve Time vs dt_max\n<img src='./benchmark_images/time_vs_dt_max_{pybamm.__version__}.png'>\n"  # noqa
+
+with open("./benchmarks/release_work_precision_sets.md", "r") as original:
+    data = original.read()
+with open("./benchmarks/release_work_precision_sets.md", "w") as modified:
+    modified.write(f"{content}\n{data}")