Merge branch 'develop' into issue-849-parallel-processing

Add "initial_conditions" kwarg to BaseSolve.solve following #1278

.gitignore

@@ -107,3 +107,5 @@ setup.log
 # tox
 .tox/
 
+# julia
+Manifest.toml

CHANGELOG.md

@@ -2,6 +2,8 @@
 
 ## Features
 
+-   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))
 -   Added submodels for active material ([#1262](https://github.com/pybamm-team/PyBaMM/pull/1262))
 -   Added composite surface form electrolyte models: `CompositeDifferential` and `CompositeAlgebraic` ([#1207](https://github.com/pybamm-team/PyBaMM/issues/1207))
 
@@ -11,8 +13,10 @@
 
 ## Bug fixes
 
+-   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
 
+-   Boolean model options ('sei porosity change', 'convection') must now be given in string format ('true' or 'false' instead of True or False) ([#1280](https://github.com/pybamm-team/PyBaMM/pull/1280))
 -   Operations such as `1*x` and `0+x` now directly return `x`. This can be bypassed by explicitly creating the binary operators, e.g. `pybamm.Multiplication(1, x)` ([#1252](https://github.com/pybamm-team/PyBaMM/pull/1252))
 
 # [v0.3.0](https://github.com/pybamm-team/PyBaMM) - 2020-11-22

CODE-OF-CONDUCT.md

@@ -34,7 +34,7 @@ This Code of Conduct applies both within project spaces and in public spaces whe
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at [email protected]. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at [email protected]. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
 
 Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
 
@@ -43,4 +43,4 @@ Project maintainers who do not follow or enforce the Code of Conduct in good fai
 This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
 
 [homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/
+[version]: http://contributor-covenant.org/version/1/4/

docs/source/models/submodels/external_circuit/index.rst

@@ -13,4 +13,3 @@ variable to be constant.
 
   current_control_external_circuit
   function_control_external_circuit
-  experiment_events

examples/notebooks/initialize-model-with-solution.ipynb

@@ -0,0 +1,316 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Initializing a model"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Example showing how to initialize a model with another model"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[33mWARNING: You are using pip version 20.2.4; however, version 20.3 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"
+     ]
+    }
+   ],
+   "source": [
+    "%pip install pybamm -q\n",
+    "\n",
+    "import pybamm\n",
+    "import pandas as pd\n",
+    "import os\n",
+    "\n",
+    "os.chdir(pybamm.__path__[0]+'/..')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Solve a model with a drive cycle"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Load model"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model = pybamm.lithium_ion.DFN()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Set up drive cycle"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# import drive cycle from file\n",
+    "drive_cycle = pd.read_csv(\n",
+    "    \"pybamm/input/drive_cycles/US06.csv\", comment=\"#\", header=None\n",
+    ").to_numpy()\n",
+    "# create interpolant\n",
+    "param = model.default_parameter_values\n",
+    "timescale = param.evaluate(model.timescale)\n",
+    "current_interpolant = pybamm.Interpolant(drive_cycle, timescale * pybamm.t)\n",
+    "# set drive cycle\n",
+    "param[\"Current function [A]\"] = current_interpolant"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Create and run simulation using the CasadiSolver in \"fast\" mode, remembering to pass in the updated parameters"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sim_US06_1 = pybamm.Simulation(\n",
+    "    model, parameter_values=param, solver=pybamm.CasadiSolver(mode=\"fast\")\n",
+    ")\n",
+    "sol_US06_1 = sim_US06_1.solve()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Update initial conditions based on a solution and solve again"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Now pre-charge with CCCV, update the initial conditions, and solve again with the US06 drive cycle"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "experiment = pybamm.Experiment(\n",
+    "    [\"Charge at 1 A until 4.1 V\", \"Hold at 4.1 V until 50 mA\"]\n",
+    ")\n",
+    "sim_cccv = pybamm.Simulation(model, experiment=experiment)\n",
+    "sol_cccv = sim_cccv.solve()\n",
+    "\n",
+    "# MODEL RE-INITIALIZATION: #############################################################\n",
+    "# Now initialize the model with the solution of the charge, and then discharge with\n",
+    "# the US06 drive cycle\n",
+    "# We could also do this inplace by setting inplace to True, which modifies the original\n",
+    "# model in place\n",
+    "new_model = model.set_initial_conditions_from(sol_cccv, inplace=False)\n",
+    "########################################################################################\n",
+    "\n",
+    "sim_US06_2 = pybamm.Simulation(\n",
+    "    new_model, parameter_values=param, solver=pybamm.CasadiSolver(mode=\"fast\")\n",
+    ")\n",
+    "sol_US06_2 = sim_US06_2.solve()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Plot both solutions, we can clearly see the difference now that initial conditions have been updated"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "1e429e6661e24d43bb04d9e4e43f7732",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "interactive(children=(FloatSlider(value=0.0, description='t', max=600.0, step=6.0), Output()), _dom_classes=('…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x13eb1c0d0>"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pybamm.dynamic_plot(\n",
+    "    [sol_US06_1, sol_US06_2], labels=[\"Default initial conditions\", \"Fully charged\"]\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Initialize using a different model"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We can also initialize the model using the solution of a different model"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "spm = pybamm.lithium_ion.SPM()\n",
+    "sim_spm_cccv = pybamm.Simulation(spm, experiment=experiment)\n",
+    "sol_spm_cccv = sim_spm_cccv.solve()\n",
+    "\n",
+    "# MODEL RE-INITIALIZATION: #############################################################\n",
+    "# Now initialize the model with the solution of the charge, and then discharge with\n",
+    "# the US06 drive cycle\n",
+    "# We could also do this inplace by setting inplace to True, which modifies the original\n",
+    "# model in place\n",
+    "new_dfn = model.set_initial_conditions_from(sol_spm_cccv, inplace=False)\n",
+    "########################################################################################\n",
+    "\n",
+    "sim_US06_3 = pybamm.Simulation(\n",
+    "    new_dfn, parameter_values=param, solver=pybamm.CasadiSolver(mode=\"fast\")\n",
+    ")\n",
+    "sol_US06_3 = sim_US06_3.solve()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Now the model initialized by the DFN and the model initialized by the SPM give the same solution"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "d33aa8dd8ac54446968d608c46eb24b9",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "interactive(children=(FloatSlider(value=0.0, description='t', max=600.0, step=6.0), Output()), _dom_classes=('…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x1407ae940>"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pybamm.dynamic_plot(\n",
+    "    [sol_US06_1, sol_US06_2, sol_US06_3], \n",
+    "    labels=[\"Default initial conditions\", \"Fully charged (from DFN)\", \"Fully charged (from SPM)\"]\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "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,
+ "nbformat_minor": 4
+}

examples/scripts/cycling_ageing_yang.py

@@ -1,7 +1,7 @@
 import pybamm as pb
 
 pb.set_logging_level("INFO")
-options = {"sei": "ec reaction limited", "sei porosity change": True}
+options = {"sei": "ec reaction limited", "sei porosity change": "true"}
 param = pb.ParameterValues(chemistry=pb.parameter_sets.Ramadass2004)
 model = pb.lithium_ion.DFN(options)
 experiment = pb.Experiment(

pybamm/__init__.py

@@ -116,6 +116,7 @@ def version(formatted=False):
 from .expression_tree.operations.jacobian import Jacobian
 from .expression_tree.operations.convert_to_casadi import CasadiConverter
 from .expression_tree.operations.unpack_symbols import SymbolUnpacker
+from .expression_tree.operations.replace_symbols import SymbolReplacer
 
 #
 # Model classes