#1100 merge and fix flake8

Author: valentinsulzer

.all-contributorsrc

@@ -272,6 +272,17 @@
         "example",
         "test"
       ]
+    },
+    {
+      "login": "lonnbornj",
+      "name": "lonnbornj",
+      "avatar_url": "https://avatars2.githubusercontent.com/u/35983543?v=4",
+      "profile": "https://github.com/lonnbornj",
+      "contributions": [
+        "code",
+        "test",
+        "example"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/workflows/test_on_push.yml

@@ -47,10 +47,17 @@ jobs:
         sudo apt install gfortran gcc libopenblas-dev graphviz
         sudo apt install python${{ matrix.python-version }}.dev
     
+    # Added fixes to homebrew installs:
+    # rm -f /usr/local/bin/2to3 
+    # (see https://github.com/actions/virtual-environments/issues/2322)
+    # brew unlink gcc@8 gcc@9
+    # (see https://github.com/actions/virtual-environments/issues/2391)
     - name: Install MacOS system dependencies
       if: matrix.os == 'macos-latest'
       run: |
+        rm -f /usr/local/bin/2to3
         brew update
+        brew unlink gcc@8 gcc@9
         brew install graphviz
         brew install openblas
         

CHANGELOG.md

@@ -2,7 +2,15 @@
 
 ## Features
 
+
+-   Updated the way events are handled in `CasadiSolver` for more accurate event location ([#1328](https://github.com/pybamm-team/PyBaMM/pull/1328))
+-   Added error message if initial conditions are outside the bounds of a variable ([#1326](https://github.com/pybamm-team/PyBaMM/pull/1326))
+-   Added temperature dependence to density, heat capacity and thermal conductivity ([#1323](https://github.com/pybamm-team/PyBaMM/pull/1323))
+-   Updated solvers' method `solve()` so it can take a list of inputs dictionaries as the `inputs` keyword argument. In this case the model is solved for each input set in the list, and a list of solutions mapping the set of inputs to the solutions is returned. Note that `solve()` can still take a single dictionary as the `inputs` keyword argument. In this case the behaviour is unchanged compared to previous versions.
+-   Added temperature dependence to the transference number (`t_plus`) ([#1317](https://github.com/pybamm-team/PyBaMM/pull/1317))
 -   Added new functionality for `Interpolant` ([#1312](https://github.com/pybamm-team/PyBaMM/pull/1312))
+-   Added option to express experiments (and extract solutions) in terms of cycles of operating condition ([#1309](https://github.com/pybamm-team/PyBaMM/pull/1309))
+-   The event time and state are now returned as part of `Solution.t` and `Solution.y` so that the event is accurately captured in the returned solution ([#1300](https://github.com/pybamm-team/PyBaMM/pull/1300))
 -   Reformatted the `BasicDFNHalfCell` to be consistent with the other models ([#1282](https://github.com/pybamm-team/PyBaMM/pull/1282))
 -   Added option to make the total interfacial current density a state ([#1280](https://github.com/pybamm-team/PyBaMM/pull/1280))
 -   Added functionality to initialize a model using the solution from another model ([#1278](https://github.com/pybamm-team/PyBaMM/pull/1278))
@@ -11,10 +19,14 @@
 
 ## Optimizations
 
+-   If solver method `solve()` is passed a list of inputs as the `inputs` keyword argument, the resolution of the model for each input set is spread acrosss several Python processes, usually running in parallel on different processors. The default number of processes is the number of processors available. `solve()` takes a new keyword argument `nproc` which can be used to set this number a manually.
+-   Variables are now post-processed using CasADi ([#1316](https://github.com/pybamm-team/PyBaMM/pull/1316))
 -   Operations such as `1*x` and `0+x` now directly return `x` ([#1252](https://github.com/pybamm-team/PyBaMM/pull/1252))
 
 ## Bug fixes
 
+-   Fixed a bug in `CasadiSolver` safe mode which crashed when there were extrapolation events but no termination events ([#1321](https://github.com/pybamm-team/PyBaMM/pull/1321))
+-   When an `Interpolant` is extrapolated an error is raised for `CasadiSolver` (and a warning is raised for the other solvers) ([#1315](https://github.com/pybamm-team/PyBaMM/pull/1315))
 -   Fixed `Simulation` and `model.new_copy` to fix a bug where changes to the model were overwritten ([#1278](https://github.com/pybamm-team/PyBaMM/pull/1278))
 
 ## Breaking changes
@@ -59,7 +71,7 @@ This release introduces a new aging model for particle swelling and cracking, a
 
 ## Breaking changes
 
--    The parameters "Positive/Negative particle distribution in x" and "Positive/Negative surface area to volume ratio distribution in x" have been deprecated. Instead, users can provide "Positive/Negative particle radius [m]" and "Positive/Negative surface area to volume ratio [m-1]" directly as functions of through-cell position (x [m]) ([#1237](https://github.com/pybamm-team/PyBaMM/pull/1237)) 
+-    The parameters "Positive/Negative particle distribution in x" and "Positive/Negative surface area to volume ratio distribution in x" have been deprecated. Instead, users can provide "Positive/Negative particle radius [m]" and "Positive/Negative surface area to volume ratio [m-1]" directly as functions of through-cell position (x [m]) ([#1237](https://github.com/pybamm-team/PyBaMM/pull/1237))
 
 # [v0.2.4](https://github.com/pybamm-team/PyBaMM/tree/v0.2.4) - 2020-09-07
 
@@ -91,17 +103,12 @@ This release adds new operators for more complex models, some basic sensitivity
 
 ## Breaking changes
 
-<<<<<<< HEAD
 -   Changed sensitivity API. Removed `ProcessedSymbolicVariable`, all sensitivity now handled within the solvers and `ProcessedVariable` ()
--  The modules containing standard parameters are now classes so they can take options
-(e.g. `standard_parameters_lithium_ion` is now `LithiumIonParameters`) ([#1120])(https://github.com/pybamm-team/PyBaMM/pull/1120)
 -  Renamed `quick_plot_vars` to `output_variables` in `Simulation` to be consistent with `QuickPlot`. Passing `quick_plot_vars` to `Simulation.plot()` has been deprecated and `output_variables` should be passed instead ([#1099](https://github.com/pybamm-team/PyBaMM/pull/1099))
-=======
 -   The "fast diffusion" particle option has been renamed "uniform profile" ([#1130](https://github.com/pybamm-team/PyBaMM/pull/1130))
 -   The modules containing standard parameters are now classes so they can take options
 (e.g. `standard_parameters_lithium_ion` is now `LithiumIonParameters`) ([#1120](https://github.com/pybamm-team/PyBaMM/pull/1120))
 -   Renamed `quick_plot_vars` to `output_variables` in `Simulation` to be consistent with `QuickPlot`. Passing `quick_plot_vars` to `Simulation.plot()` has been deprecated and `output_variables` should be passed instead ([#1099](https://github.com/pybamm-team/PyBaMM/pull/1099))
->>>>>>> develop
 
 # [v0.2.3](https://github.com/pybamm-team/PyBaMM/tree/v0.2.3) - 2020-07-01
 

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2018-2020, the PyBaMM team.
+Copyright (c) 2018-2021, the PyBaMM team.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -6,7 +6,7 @@
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pybamm-team/PyBaMM/blob/master/)
 [![black_code_style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-22-orange.svg?style=flat-square)](#contributors-)
+[![All Contributors](https://img.shields.io/badge/all_contributors-23-orange.svg?style=flat-square)](#contributors-)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 PyBaMM (Python Battery Mathematical Modelling) solves physics-based electrochemical DAE models by using state-of-the-art automatic differentiation and numerical solvers. The Doyle-Fuller-Newman model can be solved in under 0.1 seconds, while the reduced-order Single Particle Model and Single Particle Model with electrolyte can be solved in just a few milliseconds. Additional physics can easily be included such as thermal effects, fast particle diffusion, 3D effects, and more. All models are implemented in a flexible manner, and a wide range of models and parameter sets (NCA, NMC, LiCoO2, ...) are available. There is also functionality to simulate any set of experimental instructions, such as CCCV or GITT, or specify drive cycles.
@@ -142,6 +142,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
   </tr>
   <tr>
     <td align="center"><a href="https://github.com/weilongai"><img src="https://avatars1.githubusercontent.com/u/41424174?v=4" width="100px;" alt=""/><br /><sub><b>WEILONG AI</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=weilongai" title="Code">💻</a> <a href="#example-weilongai" title="Examples">💡</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=weilongai" title="Tests">⚠️</a></td>
+    <td align="center"><a href="https://github.com/lonnbornj"><img src="https://avatars2.githubusercontent.com/u/35983543?v=4" width="100px;" alt=""/><br /><sub><b>lonnbornj</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=lonnbornj" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=lonnbornj" title="Tests">⚠️</a> <a href="#example-lonnbornj" title="Examples">💡</a></td>
   </tr>
 </table>
 

build_manylinux_wheels/Dockerfile

@@ -1,7 +1,8 @@
-FROM quay.io/pypa/manylinux2010_x86_64:2020-05-29-c06f15c
+FROM quay.io/pypa/manylinux2014_x86_64:2020-11-11-bc8ce45
 
-ENV PLAT manylinux2010_x86_64
+ENV PLAT manylinux2014_x86_64
 
+RUN yum -y update
 RUN yum -y remove cmake
 RUN yum -y install wget openblas-devel
 RUN /opt/python/cp37-cp37m/bin/pip install --upgrade pip cmake

docs/source/solvers/solution.rst

@@ -1,8 +1,5 @@
 Solutions
 =========
 
-.. autoclass:: pybamm._BaseSolution
-  :members:
-
 .. autoclass:: pybamm.Solution
   :members:

examples/notebooks/Getting Started/Tutorial 5 - Run experiments.ipynb

@@ -47,11 +47,11 @@
    "source": [
     "experiment = pybamm.Experiment(\n",
     "    [\n",
-    "        \"Discharge at C/10 for 10 hours or until 3.3 V\",\n",
+    "        (\"Discharge at C/10 for 10 hours or until 3.3 V\",\n",
     "        \"Rest for 1 hour\",\n",
     "        \"Charge at 1 A until 4.1 V\",\n",
     "        \"Hold at 4.1 V until 50 mA\",\n",
-    "        \"Rest for 1 hour\",\n",
+    "        \"Rest for 1 hour\"),\n",
     "    ] * 3\n",
     ")"
    ]
@@ -60,7 +60,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In this case, the experiment consists of a cycle of constant current C/10 discahrge, a one hour rest, a constant current (1 A) constant voltage (4.1 V) and another one hour rest, all of it repeated three times (notice the `* 3`).\n",
+    "A cycle is defined by a tuple of operating instructions. In this case, the experiment consists of a cycle of constant current C/10 discharge, a one hour rest, a constant current (1 A) constant voltage (4.1 V) and another one hour rest, all of it repeated three times (notice the * 3).\n",
     "\n",
     "Then we can choose our model"
    ]
@@ -146,33 +146,30 @@
     "\n",
     "Optionally, each instruction can contain at the end the expression \"(x minute period)\" in which the period at which to record the simulation outputs during that instruction. To change the period for the whole experiment we can pass it as a keyword argument in the experiment.\n",
     "\n",
-    "Additionally, we can use the operators `+` and `*` to combine and repeat lists:"
+    "Additionally, we can use the operators `+` and `*` on lists in order to combine and repeat cycles:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
+     "output_type": "execute_result",
      "data": {
       "text/plain": [
-       "['Discharge at 1C for 0.5 hours',\n",
-       " 'Discharge at C/20 for 0.5 hours',\n",
-       " 'Discharge at 1C for 0.5 hours',\n",
-       " 'Discharge at C/20 for 0.5 hours',\n",
-       " 'Discharge at 1C for 0.5 hours',\n",
-       " 'Discharge at C/20 for 0.5 hours',\n",
-       " 'Charge at 0.5 C for 45 minutes']"
+       "[('Discharge at 1C for 0.5 hours', 'Discharge at C/20 for 0.5 hours'),\n",
+       " ('Discharge at 1C for 0.5 hours', 'Discharge at C/20 for 0.5 hours'),\n",
+       " ('Discharge at 1C for 0.5 hours', 'Discharge at C/20 for 0.5 hours'),\n",
+       " ('Charge at 0.5 C for 45 minutes',)]"
       ]
      },
-     "execution_count": 6,
      "metadata": {},
-     "output_type": "execute_result"
+     "execution_count": 4
     }
    ],
    "source": [
-    "[\"Discharge at 1C for 0.5 hours\", \"Discharge at C/20 for 0.5 hours\"] * 3 + [\"Charge at 0.5 C for 45 minutes\"]"
+    "[(\"Discharge at 1C for 0.5 hours\", \"Discharge at C/20 for 0.5 hours\")] * 3 + [(\"Charge at 0.5 C for 45 minutes\",)]"
    ]
   },
   {
@@ -206,9 +203,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.8"
+   "version": "3.8.2-final"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}

examples/notebooks/Getting Started/Tutorial 9 - Changing the mesh.ipynb

@@ -22,6 +22,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "\u001b[33mWARNING: You are using pip version 20.2.4; however, version 20.3.3 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"
      ]
     }
@@ -64,13 +66,13 @@
     {
      "data": {
       "text/plain": [
-       "{SpatialVariable(0x62eb5d16885394c9, x_n, children=[], domain=['negative electrode'], auxiliary_domains={'secondary': \"['current collector']\"}): 20,\n",
-       " SpatialVariable(-0x14459c29151bda45, x_s, children=[], domain=['separator'], auxiliary_domains={'secondary': \"['current collector']\"}): 20,\n",
-       " SpatialVariable(-0x4a38fdaaecee173f, x_p, children=[], domain=['positive electrode'], auxiliary_domains={'secondary': \"['current collector']\"}): 20,\n",
-       " SpatialVariable(-0xf387938c410c357, r_n, children=[], domain=['negative particle'], auxiliary_domains={'secondary': \"['negative electrode']\", 'tertiary': \"['current collector']\"}): 30,\n",
-       " SpatialVariable(0x2f93da3e03d4dcbe, r_p, children=[], domain=['positive particle'], auxiliary_domains={'secondary': \"['positive electrode']\", 'tertiary': \"['current collector']\"}): 30,\n",
-       " SpatialVariable(0x14b0200ccfc1f5cc, y, children=[], domain=['current collector'], auxiliary_domains={}): 10,\n",
-       " SpatialVariable(-0x4938b510c47f7708, z, children=[], domain=['current collector'], auxiliary_domains={}): 10}"
+       "{SpatialVariable(0x3452d5d06e5d6beb, x_n, children=[], domain=['negative electrode'], auxiliary_domains={'secondary': \"['current collector']\"}): 20,\n",
+       " SpatialVariable(-0x561e00d7cc14367b, x_s, children=[], domain=['separator'], auxiliary_domains={'secondary': \"['current collector']\"}): 20,\n",
+       " SpatialVariable(-0x71763e2ccac3ade7, x_p, children=[], domain=['positive electrode'], auxiliary_domains={'secondary': \"['current collector']\"}): 20,\n",
+       " SpatialVariable(-0x19c83c2dfa4ac578, r_n, children=[], domain=['negative particle'], auxiliary_domains={'secondary': \"['negative electrode']\", 'tertiary': \"['current collector']\"}): 30,\n",
+       " SpatialVariable(0x5c2de4f3839b67be, r_p, children=[], domain=['positive particle'], auxiliary_domains={'secondary': \"['positive electrode']\", 'tertiary': \"['current collector']\"}): 30,\n",
+       " SpatialVariable(-0x5746d0678b95cd9a, y, children=[], domain=['current collector'], auxiliary_domains={}): 10,\n",
+       " SpatialVariable(-0x7e1ee8ded1c165e8, z, children=[], domain=['current collector'], auxiliary_domains={}): 10}"
       ]
      },
      "execution_count": 3,
@@ -123,7 +125,7 @@
     {
      "data": {
       "text/plain": [
-       "<pybamm.solvers.solution.Solution at 0x7f8beed56e80>"
+       "<pybamm.solvers.solution.Solution at 0x1453f6880>"
       ]
      },
      "execution_count": 5,
@@ -151,7 +153,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "0613bdd52da440c9925d1dcb26558e71",
+       "model_id": "fbd0fd9401444435940b9933716cb07d",
        "version_major": 2,
        "version_minor": 0
       },
@@ -238,7 +240,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "99cad0a3137b4ee1ba353ae02b02b43f",
+       "model_id": "1ef54c1f3c1941f988d9ce0459149078",
        "version_major": 2,
        "version_minor": 0
       },
@@ -252,7 +254,7 @@
     {
      "data": {
       "text/plain": [
-       "<pybamm.plotting.quick_plot.QuickPlot at 0x7f8beb334e80>"
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x146458400>"
       ]
      },
      "execution_count": 9,
@@ -288,7 +290,20 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.8"
+   "version": "3.8.6"
+  },
+  "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,

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

@@ -353,11 +353,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "comsol_solution = pybamm.Solution(solutions[\"1+1D DFN\"].t, solutions[\"1+1D DFN\"].y)\n",
     "comsol_model.timescale = simulations[\"1+1D DFN\"].model.timescale\n",
     "comsol_model.length_scales = simulations[\"1+1D DFN\"].model.length_scales\n",
-    "comsol_solution.model = comsol_model\n",
-    "comsol_solution.inputs = {}"
+    "comsol_solution = pybamm.Solution(solutions[\"1+1D DFN\"].t, solutions[\"1+1D DFN\"].y, comsol_model, {})"
    ]
   },
   {

examples/scripts/compare_comsol/compare_comsol_DFN.py

@@ -123,11 +123,12 @@ def get_interp_fun(variable_name, domain):
 }
 
 # Make new solution with same t and y
-comsol_solution = pybamm.Solution(pybamm_solution.t, pybamm_solution.y)
 # Update solution scales to match the pybamm model
 comsol_model.timescale_eval = pybamm_model.timescale_eval
 comsol_model.length_scales_eval = pybamm_model.length_scales_eval
-comsol_solution.model = comsol_model
+comsol_solution = pybamm.Solution(
+    pybamm_solution.t, pybamm_solution.y, comsol_model, {}
+)
 
 # plot
 output_variables = [

examples/scripts/experimental_protocols/cccv.py

@@ -7,11 +7,13 @@
 pybamm.set_logging_level("INFO")
 experiment = pybamm.Experiment(
     [
-        "Discharge at C/10 for 10 hours or until 3.3 V",
-        "Rest for 1 hour",
-        "Charge at 1 A until 4.1 V",
-        "Hold at 4.1 V until 50 mA",
-        "Rest for 1 hour",
+        (
+            "Discharge at C/5 for 10 hours or until 3.3 V",
+            "Rest for 1 hour",
+            "Charge at 1 A until 4.1 V",
+            "Hold at 4.1 V until 50 mA",
+            "Rest for 1 hour",
+        ),
     ]
     * 3
 )
@@ -23,16 +25,16 @@
 fig, ax = plt.subplots()
 for i in range(3):
     # Extract sub solutions
-    sol = sim.solution.sub_solutions[i * 5]
+    sol = sim.solution.cycles[i]
     # Extract variables
     t = sol["Time [h]"].entries
     V = sol["Terminal voltage [V]"].entries
     # Plot
     ax.plot(t - t[0], V, label="Discharge {}".format(i + 1))
     ax.set_xlabel("Time [h]")
     ax.set_ylabel("Voltage [V]")
-    ax.set_xlim([0, 13])
-ax.legend()
+    ax.set_xlim([0, 10])
+ax.legend(loc="lower left")
 
 # Save time, voltage, current, discharge capacity, temperature, and electrolyte
 # concentration to csv and matlab formats

examples/scripts/experimental_protocols/gitt.py

@@ -4,7 +4,9 @@
 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/__init__.py

@@ -214,7 +214,7 @@ def version(formatted=False):
 #
 # Solver classes
 #
-from .solvers.solution import Solution, _BaseSolution
+from .solvers.solution import Solution
 from .solvers.processed_variable import ProcessedVariable
 from .solvers.base_solver import BaseSolver
 from .solvers.dummy_solver import DummySolver