Merge branch 'develop' of github.com:kratman/PyBaMM into feat/useTemp…

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pybamm-team · Sep 29, 2023 · 708f721 · 708f721
2 parents 10c7270 + ad5f51c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -46,6 +46,7 @@
 
 ## Features
 
+- Idaklu solver can be given a list of variables to calculate during the solve ([#3217](https://github.com/pybamm-team/PyBaMM/pull/3217))
 - Enable multithreading in IDAKLU solver ([#2947](https://github.com/pybamm-team/PyBaMM/pull/2947))
 - If a solution contains cycles and steps, the cycle number and step number are now saved when `solution.save_data()` is called ([#2931](https://github.com/pybamm-team/PyBaMM/pull/2931))
 - Experiments can now be given a `start_time` to define when each step should be triggered ([#2616](https://github.com/pybamm-team/PyBaMM/pull/2616))

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -39,8 +39,14 @@ pybind11_add_module(idaklu
   pybamm/solvers/c_solvers/idaklu/casadi_functions.hpp
   pybamm/solvers/c_solvers/idaklu/casadi_solver.cpp
   pybamm/solvers/c_solvers/idaklu/casadi_solver.hpp
-  pybamm/solvers/c_solvers/idaklu/casadi_sundials_functions.hpp
+  pybamm/solvers/c_solvers/idaklu/CasadiSolver.cpp
+  pybamm/solvers/c_solvers/idaklu/CasadiSolver.hpp
+  pybamm/solvers/c_solvers/idaklu/CasadiSolverOpenMP.cpp
+  pybamm/solvers/c_solvers/idaklu/CasadiSolverOpenMP.hpp
+  pybamm/solvers/c_solvers/idaklu/CasadiSolverOpenMP_solvers.cpp
+  pybamm/solvers/c_solvers/idaklu/CasadiSolverOpenMP_solvers.hpp
   pybamm/solvers/c_solvers/idaklu/casadi_sundials_functions.cpp
+  pybamm/solvers/c_solvers/idaklu/casadi_sundials_functions.hpp
   pybamm/solvers/c_solvers/idaklu/common.hpp
   pybamm/solvers/c_solvers/idaklu/python.hpp
   pybamm/solvers/c_solvers/idaklu/python.cpp

diff --git a/docs/source/examples/notebooks/batch_study.ipynb b/docs/source/examples/notebooks/batch_study.ipynb
@@ -31,7 +31,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "\n",
     "# loading up 3 models to compare\n",
@@ -224,7 +224,7 @@
    "source": [
     "# using less number of images in the example\n",
     "# for a smoother GIF use more images\n",
-    "batch_study.create_gif(number_of_images=5, duration=0.2)"
+    "batch_study.create_gif(number_of_images=5, duration=0.2, output_filename=\"batch.gif\")"
    ]
   },
   {

diff --git a/docs/source/examples/notebooks/callbacks.ipynb b/docs/source/examples/notebooks/callbacks.ipynb
@@ -48,7 +48,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q\n",
+    "%pip install \"pybamm[plot,cite]\" -q\n",
     "import pybamm\n",
     "\n",
     "model = pybamm.lithium_ion.DFN()\n",

diff --git a/docs/source/examples/notebooks/change-settings.ipynb b/docs/source/examples/notebooks/change-settings.ipynb
@@ -43,7 +43,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import os\n",

diff --git a/docs/source/examples/notebooks/creating_models/1-an-ode-model.ipynb b/docs/source/examples/notebooks/creating_models/1-an-ode-model.ipynb
@@ -36,7 +36,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt"

diff --git a/docs/source/examples/notebooks/creating_models/2-a-pde-model.ipynb b/docs/source/examples/notebooks/creating_models/2-a-pde-model.ipynb
@@ -41,7 +41,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt"

diff --git a/docs/source/examples/notebooks/creating_models/3-negative-particle-problem.ipynb b/docs/source/examples/notebooks/creating_models/3-negative-particle-problem.ipynb
@@ -58,7 +58,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",

diff --git a/...source/examples/notebooks/creating_models/4-comparing-full-and-reduced-order-models.ipynb b/...source/examples/notebooks/creating_models/4-comparing-full-and-reduced-order-models.ipynb
@@ -62,7 +62,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",

diff --git a/docs/source/examples/notebooks/creating_models/5-half-cell-model.ipynb b/docs/source/examples/notebooks/creating_models/5-half-cell-model.ipynb
@@ -71,7 +71,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "\n",

diff --git a/docs/source/examples/notebooks/creating_models/6-a-simple-SEI-model.ipynb b/docs/source/examples/notebooks/creating_models/6-a-simple-SEI-model.ipynb
@@ -123,7 +123,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import os\n",

diff --git a/docs/source/examples/notebooks/experiments-start-time.ipynb b/docs/source/examples/notebooks/experiments-start-time.ipynb
@@ -36,7 +36,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "from datetime import datetime"
    ]

diff --git a/docs/source/examples/notebooks/expression_tree/broadcasts.ipynb b/docs/source/examples/notebooks/expression_tree/broadcasts.ipynb
@@ -24,7 +24,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np"
    ]

diff --git a/docs/source/examples/notebooks/expression_tree/expression-tree.ipynb b/docs/source/examples/notebooks/expression_tree/expression-tree.ipynb
@@ -35,7 +35,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "\n",

diff --git a/docs/source/examples/notebooks/getting_started/tutorial-1-how-to-run-a-model.ipynb b/docs/source/examples/notebooks/getting_started/tutorial-1-how-to-run-a-model.ipynb
@@ -34,7 +34,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm"
    ]
   },

diff --git a/docs/source/examples/notebooks/getting_started/tutorial-10-creating-a-model.ipynb b/docs/source/examples/notebooks/getting_started/tutorial-10-creating-a-model.ipynb
@@ -40,7 +40,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm"
    ]
   },

diff --git a/docs/source/examples/notebooks/getting_started/tutorial-11-creating-a-submodel.ipynb b/docs/source/examples/notebooks/getting_started/tutorial-11-creating-a-submodel.ipynb
@@ -32,7 +32,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm"
    ]
   },

diff --git a/docs/source/examples/notebooks/getting_started/tutorial-2-compare-models.ipynb b/docs/source/examples/notebooks/getting_started/tutorial-2-compare-models.ipynb
@@ -32,7 +32,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm"
    ]
   },

diff --git a/docs/source/examples/notebooks/getting_started/tutorial-3-basic-plotting.ipynb b/docs/source/examples/notebooks/getting_started/tutorial-3-basic-plotting.ipynb
@@ -40,7 +40,7 @@
         }
       ],
       "source": [
-        "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+        "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
         "import pybamm\n",
         "import matplotlib.pyplot as plt\n",
         "\n",

diff --git a/docs/source/examples/notebooks/getting_started/tutorial-4-setting-parameter-values.ipynb b/docs/source/examples/notebooks/getting_started/tutorial-4-setting-parameter-values.ipynb
@@ -32,7 +32,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import os\n",
     "os.chdir(pybamm.__path__[0]+'/..')"

diff --git a/docs/source/examples/notebooks/getting_started/tutorial-5-run-experiments.ipynb b/docs/source/examples/notebooks/getting_started/tutorial-5-run-experiments.ipynb
@@ -33,7 +33,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np"
    ]

diff --git a/docs/source/examples/notebooks/getting_started/tutorial-6-managing-simulation-outputs.ipynb b/docs/source/examples/notebooks/getting_started/tutorial-6-managing-simulation-outputs.ipynb
@@ -42,7 +42,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "model = pybamm.lithium_ion.SPMe()\n",
     "sim = pybamm.Simulation(model)\n",

diff --git a/docs/source/examples/notebooks/getting_started/tutorial-7-model-options.ipynb b/docs/source/examples/notebooks/getting_started/tutorial-7-model-options.ipynb
@@ -24,7 +24,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm"
    ]
   },

diff --git a/docs/source/examples/notebooks/getting_started/tutorial-8-solver-options.ipynb b/docs/source/examples/notebooks/getting_started/tutorial-8-solver-options.ipynb
@@ -28,7 +28,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm"
    ]
   },

diff --git a/docs/source/examples/notebooks/getting_started/tutorial-9-changing-the-mesh.ipynb b/docs/source/examples/notebooks/getting_started/tutorial-9-changing-the-mesh.ipynb
@@ -28,7 +28,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm"
    ]
   },

diff --git a/docs/source/examples/notebooks/initialize-model-with-solution.ipynb b/docs/source/examples/notebooks/initialize-model-with-solution.ipynb
@@ -23,14 +23,14 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "\u001b[33mWARNING: You are using pip version 21.0.1; however, version 21.1 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",
+      "\u001B[33mWARNING: You are using pip version 21.0.1; however, version 21.1 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"
      ]
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "\n",
     "import pybamm\n",
     "import pandas as pd\n",

diff --git a/docs/source/examples/notebooks/models/DFN-with-particle-size-distributions.ipynb b/docs/source/examples/notebooks/models/DFN-with-particle-size-distributions.ipynb
@@ -42,7 +42,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import matplotlib.pyplot as plt"
    ]

diff --git a/docs/source/examples/notebooks/models/DFN.ipynb b/docs/source/examples/notebooks/models/DFN.ipynb
@@ -128,7 +128,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np"
    ]

diff --git a/docs/source/examples/notebooks/models/MPM.ipynb b/docs/source/examples/notebooks/models/MPM.ipynb
@@ -103,7 +103,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import matplotlib.pyplot as plt"
    ]

diff --git a/docs/source/examples/notebooks/models/MSMR.ipynb b/docs/source/examples/notebooks/models/MSMR.ipynb
@@ -23,7 +23,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import matplotlib.pyplot as plt"
    ]

diff --git a/docs/source/examples/notebooks/models/SEI-on-cracks.ipynb b/docs/source/examples/notebooks/models/SEI-on-cracks.ipynb
@@ -21,14 +21,14 @@
      "output_type": "stream",
      "text": [
       "\n",
-      "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip available: \u001b[0m\u001b[31;49m22.3.1\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m23.0.1\u001b[0m\n",
-      "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n",
+      "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m A new release of pip available: \u001B[0m\u001B[31;49m22.3.1\u001B[0m\u001B[39;49m -> \u001B[0m\u001B[32;49m23.0.1\u001B[0m\n",
+      "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m To update, run: \u001B[0m\u001B[32;49mpip install --upgrade pip\u001B[0m\n",
       "Note: you may need to restart the kernel to use updated packages.\n"
      ]
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import matplotlib.pyplot as plt"
    ]

diff --git a/docs/source/examples/notebooks/models/SPM.ipynb b/docs/source/examples/notebooks/models/SPM.ipynb
@@ -73,7 +73,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import os\n",

diff --git a/docs/source/examples/notebooks/models/SPMe.ipynb b/docs/source/examples/notebooks/models/SPMe.ipynb
@@ -126,7 +126,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm"
    ]
   },

diff --git a/docs/source/examples/notebooks/models/Validating_mechanical_models_Enertech_DFN.ipynb b/docs/source/examples/notebooks/models/Validating_mechanical_models_Enertech_DFN.ipynb
@@ -23,7 +23,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import os\n",
     "import matplotlib.pyplot as plt\n",

diff --git a/docs/source/examples/notebooks/models/compare-comsol-discharge-curve.ipynb b/docs/source/examples/notebooks/models/compare-comsol-discharge-curve.ipynb
@@ -32,7 +32,7 @@
    },
    "outputs": [],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import os\n",

diff --git a/docs/source/examples/notebooks/models/compare-ecker-data.ipynb b/docs/source/examples/notebooks/models/compare-ecker-data.ipynb
@@ -32,7 +32,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import os\n",
     "import pandas as pd\n",

diff --git a/docs/source/examples/notebooks/models/compare-lithium-ion.ipynb b/docs/source/examples/notebooks/models/compare-lithium-ion.ipynb
@@ -48,7 +48,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import os\n",
     "os.chdir(pybamm.__path__[0]+'/..')\n",

diff --git a/docs/source/examples/notebooks/models/compare-particle-diffusion-models.ipynb b/docs/source/examples/notebooks/models/compare-particle-diffusion-models.ipynb
@@ -35,7 +35,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import os\n",
     "import numpy as np\n",

diff --git a/docs/source/examples/notebooks/models/composite_particle.ipynb b/docs/source/examples/notebooks/models/composite_particle.ipynb
@@ -36,7 +36,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "#%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import os\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",

diff --git a/docs/source/examples/notebooks/models/coupled-degradation.ipynb b/docs/source/examples/notebooks/models/coupled-degradation.ipynb
@@ -29,7 +29,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm[plot,cite] -q    # install PyBaMM if it is not installed\n",
+    "%pip install \"pybamm[plot,cite]\" -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import matplotlib.pyplot as plt"
    ]