Merge pull request #1464 from priyanshuone6/rename_folders

Rename lead-acid and lithium-ion

.gitignore

@@ -104,6 +104,9 @@ KLU_module_deps
 # setup
 setup.log
 
+# test
+test.c
+
 # tox
 .tox/
 

CHANGELOG.md

@@ -12,6 +12,11 @@
 -   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))
 
+## Bug fixes
+
+## Breaking changes
+-   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))
+
 # [v0.4.0](https://github.com/pybamm-team/PyBaMM/tree/v0.4.0) - 2021-03-28
 
 This release introduces:

docs/tutorials/add-parameter-values.rst

@@ -22,7 +22,7 @@ Adding a set of parameters values
 ---------------------------------
 
 Parameter sets are split by material into ``negative_electrodes``, ``separators``, ``positive_electrodes``, ``electrolytes``, ``cells`` (for cell geometries and thermal properties) and ``experiments`` (for initial conditions and charge/discharge rates).
-To add a new parameter set in one of these subcategories, first create a new folder in the appropriate chemistry folder: for example, to add a new negative electrode chemistry for lithium-ion, add a subfolder ``input/parameters/lithium-ion/negative_electrodes/new_negative_electrode_chemistry_AuthorYear``. 
+To add a new parameter set in one of these subcategories, first create a new folder in the appropriate chemistry folder: for example, to add a new negative electrode chemistry for lithium-ion, add a subfolder ``input/parameters/lithium_ion/negative_electrodes/new_negative_electrode_chemistry_AuthorYear``. 
 This subfolder should then contain:
 
 - a csv file ``parameters.csv`` with all the relevant scalar parameters. The expected structure of the csv file is:
@@ -39,7 +39,7 @@ Empty lines, and lines starting with ``#``, will be ignored.
 - python files for any functions, which should be referenced from the ``parameters.csv`` file (see ``Adding a Function`` below)
 - csv files for any data to be interpolated, which should be referenced from the ``parameters.csv`` file (see ``Adding data for interpolation`` below)
 
-The easiest way to start is to copy an existing file (e.g. ````input/parameters/lithium-ion/negative_electrodes/graphite_mcmb2528_Marquis2019``) and replace all entries in all files as appropriate
+The easiest way to start is to copy an existing file (e.g. ````input/parameters/lithium_ion/negative_electrodes/graphite_mcmb2528_Marquis2019``) and replace all entries in all files as appropriate
 
 Adding a function
 -----------------
@@ -110,7 +110,7 @@ If you have added a whole new set of parameters, then you can create a new param
 .. code-block:: python
 
     AuthorYear = {
-        "chemistry": "lithium-ion",
+        "chemistry": "lithium_ion",
         "cell": "new_cell_AuthorYear",
         "negative electrode": "new_negative_electrode_AuthorYear",
         "separator": "new_separator_AuthorYear",
@@ -133,7 +133,7 @@ It's also possible to add parameters for a single material (e.g. negative electr
 
     param = pybamm.ParameterValues(
         chemistry={
-            "chemistry": "lithium-ion",
+            "chemistry": "lithium_ion",
             "cell": "kokam_Marquis2019",
             "negative electrode": "new_negative_electrode_chemistry_AuthorYear",
             "separator": "separator_Marquis2019",

examples/notebooks/parameter-management.ipynb

@@ -19,7 +19,7 @@
     "The `input/parameters` directory is organised as follows:\n",
     "```\n",
     "input/parameters\n",
-    "  lithium-ion/ # chemistry\n",
+    "  lithium_ion/ # chemistry\n",
     "    negative_electrodes/ # Component\n",
     "      graphite_Chen2020/ # parameter set\n",
     "        parameters.csv\n",
@@ -34,7 +34,7 @@
     "    seis/\n",
     "    separators/\n",
     "    experiments/\n",
-    "  lead-acid/\n",
+    "  lead_acid/\n",
     "    ...\n",
     "```"
    ]
@@ -63,9 +63,9 @@
     {
      "data": {
       "text/plain": [
-       "['/home/ferranbrosa/PyBaMM',\n",
-       " '/home/ferranbrosa/PyBaMM/examples/notebooks',\n",
-       " '/home/ferranbrosa/PyBaMM/pybamm/input/parameters']"
+       "['/home/priyanshu/work/PyBaMM',\n",
+       " '/home/priyanshu/work/notebooks',\n",
+       " '/home/priyanshu/work/PyBaMM/pybamm/input/parameters']"
       ]
      },
      "execution_count": 1,
@@ -109,14 +109,14 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Directory lithium-ion does not exist.\n"
+      "Directory lithium_ion does not exist.\n"
      ]
     }
    ],
    "source": [
     "%%bash\n",
-    "if [[ ! -d \"lithium-ion\" ]]; then\n",
-    "echo \"Directory lithium-ion does not exist.\"\n",
+    "if [[ ! -d \"lithium_ion\" ]]; then\n",
+    "echo \"Directory lithium_ion does not exist.\"\n",
     "fi"
    ]
   },
@@ -127,14 +127,14 @@
    "outputs": [],
    "source": [
     "%%bash\n",
-    "pybamm_edit_parameter lithium-ion"
+    "pybamm_edit_parameter lithium_ion"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The above commands will create a `lithium-ion` directory in the current directory, populated with copies of the default parameters, for editing:"
+    "The above commands will create a `lithium_ion` directory in the current directory, populated with copies of the default parameters, for editing:"
    ]
   },
   {
@@ -149,23 +149,24 @@
       "cells\n",
       "electrolytes\n",
       "experiments\n",
+      "lithium_platings\n",
       "negative_electrodes\n",
       "positive_electrodes\n",
-      "SEIs\n",
+      "seis\n",
       "separators\n"
      ]
     }
    ],
    "source": [
     "%%bash\n",
-    "ls lithium-ion"
+    "ls lithium_ion"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "As an example, let's create a new parameter file for the `cell` component, for the `lithium-ion` chemistry. We first create a new directory `my_new_param_set`:"
+    "As an example, let's create a new parameter file for the `cell` component, for the `lithium_ion` chemistry. We first create a new directory `my_new_param_set`:"
    ]
   },
   {
@@ -175,7 +176,7 @@
    "outputs": [],
    "source": [
     "%%bash\n",
-    "mkdir lithium-ion/cells/my_new_param_set"
+    "mkdir lithium_ion/cells/my_new_param_set"
    ]
   },
   {
@@ -192,7 +193,7 @@
    "outputs": [],
    "source": [
     "# Create example parameter file\n",
-    "f = open(\"lithium-ion/cells/my_new_param_set/param_file.csv\", \"w+\")\n",
+    "f = open(\"lithium_ion/cells/my_new_param_set/param_file.csv\", \"w+\")\n",
     "f.write(\n",
     "\"\"\"\n",
     "Name [units],Value\n",
@@ -221,10 +222,10 @@
     {
      "data": {
       "text/plain": [
-       "['lithium-ion/cells/my_new_param_set',\n",
-       " '/home/ferranbrosa/PyBaMM',\n",
-       " '/home/ferranbrosa/PyBaMM/examples/notebooks',\n",
-       " '/home/ferranbrosa/PyBaMM/pybamm/input/parameters']"
+       "['lithium_ion/cells/my_new_param_set',\n",
+       " '/home/priyanshu/work/PyBaMM',\n",
+       " '/home/priyanshu/work/notebooks',\n",
+       " '/home/priyanshu/work/PyBaMM/pybamm/input/parameters']"
       ]
      },
      "execution_count": 7,
@@ -233,7 +234,7 @@
     }
    ],
    "source": [
-    "pybamm.PARAMETER_PATH.insert(0, \"lithium-ion/cells/my_new_param_set\")\n",
+    "pybamm.PARAMETER_PATH.insert(0, \"lithium_ion/cells/my_new_param_set\")\n",
     "pybamm.PARAMETER_PATH"
    ]
   },
@@ -293,7 +294,7 @@
    "source": [
     "%%bash\n",
     "# pybamm_add_parameter <dir> <chemistry> <component>\n",
-    "pybamm_add_parameter lithium-ion/cells/my_new_param_set lithium-ion cells"
+    "pybamm_add_parameter lithium_ion/cells/my_new_param_set lithium_ion cells"
    ]
   },
   {
@@ -311,9 +312,9 @@
     {
      "data": {
       "text/plain": [
-       "['/home/ferranbrosa/PyBaMM',\n",
-       " '/home/ferranbrosa/PyBaMM/examples/notebooks',\n",
-       " '/home/ferranbrosa/PyBaMM/pybamm/input/parameters']"
+       "['/home/priyanshu/work/PyBaMM',\n",
+       " '/home/priyanshu/work/notebooks',\n",
+       " '/home/priyanshu/work/PyBaMM/pybamm/input/parameters']"
       ]
      },
      "execution_count": 10,
@@ -322,7 +323,7 @@
     }
    ],
    "source": [
-    "pybamm.PARAMETER_PATH.remove(\"lithium-ion/cells/my_new_param_set\")\n",
+    "pybamm.PARAMETER_PATH.remove(\"lithium_ion/cells/my_new_param_set\")\n",
     "pybamm.PARAMETER_PATH"
    ]
   },
@@ -345,7 +346,7 @@
     }
    ],
    "source": [
-    "pybamm.ParameterValues(\"lithium-ion/cells/my_new_param_set/param_file.csv\")"
+    "pybamm.ParameterValues(\"lithium_ion/cells/my_new_param_set/param_file.csv\")"
    ]
   },
   {
@@ -362,14 +363,14 @@
    "outputs": [],
    "source": [
     "%%bash\n",
-    "pybamm_rm_parameter -f lithium-ion/cells/my_new_param_set lithium-ion cells"
+    "pybamm_rm_parameter -f lithium_ion/cells/my_new_param_set lithium_ion cells"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Let's remove the local lithium-ion directory to leave this directory as we found it"
+    "Let's remove the local lithium_ion directory to leave this directory as we found it"
    ]
   },
   {
@@ -379,7 +380,7 @@
    "outputs": [],
    "source": [
     "%%bash\n",
-    "rm -rf lithium-ion"
+    "rm -rf lithium_ion"
    ]
   },
   {
@@ -413,9 +414,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "PyBaMM development (env)",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "pybamm-dev"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -427,7 +428,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.8"
   }
  },
  "nbformat": 4,

pybamm/parameters/parameter_sets.py

@@ -92,7 +92,7 @@
 #
 
 NCA_Kim2011 = {
-    "chemistry": "lithium-ion",
+    "chemistry": "lithium_ion",
     "cell": "Kim2011",
     "negative electrode": "graphite_Kim2011",
     "separator": "separator_Kim2011",
@@ -104,7 +104,7 @@
 }
 
 Ecker2015 = {
-    "chemistry": "lithium-ion",
+    "chemistry": "lithium_ion",
     "cell": "kokam_Ecker2015",
     "negative electrode": "graphite_Ecker2015",
     "separator": "separator_Ecker2015",
@@ -116,7 +116,7 @@
 }
 
 Yang2017 = {
-    "chemistry": "lithium-ion",
+    "chemistry": "lithium_ion",
     "cell": "Yang2017",
     "negative electrode": "graphite_Yang2017",
     "separator": "separator_Yang2017",
@@ -130,7 +130,7 @@
 
 
 Marquis2019 = {
-    "chemistry": "lithium-ion",
+    "chemistry": "lithium_ion",
     "cell": "kokam_Marquis2019",
     "negative electrode": "graphite_mcmb2528_Marquis2019",
     "separator": "separator_Marquis2019",
@@ -142,7 +142,7 @@
 }
 
 Chen2020 = {
-    "chemistry": "lithium-ion",
+    "chemistry": "lithium_ion",
     "cell": "LGM50_Chen2020",
     "negative electrode": "graphite_Chen2020",
     "separator": "separator_Chen2020",
@@ -154,7 +154,7 @@
 }
 
 Chen2020_plating = {
-    "chemistry": "lithium-ion",
+    "chemistry": "lithium_ion",
     "cell": "LGM50_Chen2020",
     "negative electrode": "graphite_Chen2020_plating",
     "separator": "separator_Chen2020",
@@ -167,7 +167,7 @@
 }
 
 Mohtat2020 = {
-    "chemistry": "lithium-ion",
+    "chemistry": "lithium_ion",
     "cell": "UMBL_Mohtat2020",
     "negative electrode": "graphite_UMBL_Mohtat2020",
     "separator": "separator_Mohtat2020",
@@ -179,7 +179,7 @@
 }
 
 Ramadass2004 = {
-    "chemistry": "lithium-ion",
+    "chemistry": "lithium_ion",
     "cell": "sony_Ramadass2004",
     "negative electrode": "graphite_Ramadass2004",
     "separator": "separator_Ecker2015",  # no values found, relevance?
@@ -191,7 +191,7 @@
 }
 
 Prada2013 = {
-    "chemistry": "lithium-ion",
+    "chemistry": "lithium_ion",
     "cell": "A123_Lain2019",
     "negative electrode": "graphite_Chen2020",
     "separator": "separator_Chen2020",
@@ -202,7 +202,7 @@
 }
 
 Ai2020 = {
-    "chemistry": "lithium-ion",
+    "chemistry": "lithium_ion",
     "cell": "Enertech_Ai2020",
     "negative electrode": "graphite_Ai2020",
     "separator": "separator_Ai2020",
@@ -218,7 +218,7 @@
 #
 
 Sulzer2019 = {
-    "chemistry": "lead-acid",
+    "chemistry": "lead_acid",
     "cell": "BBOXX_Sulzer2019",
     "negative electrode": "lead_Sulzer2019",
     "separator": "agm_Sulzer2019",

pybamm/parameters/parameter_values.py

@@ -45,7 +45,7 @@ class ParameterValues:
     >>> param = pybamm.ParameterValues(values)
     >>> param["some parameter"]
     1
-    >>> file = "input/parameters/lithium-ion/cells/kokam_Marquis2019/parameters.csv"
+    >>> file = "input/parameters/lithium_ion/cells/kokam_Marquis2019/parameters.csv"
     >>> values_path = pybamm.get_parameters_filepath(file)
     >>> param = pybamm.ParameterValues(values=values_path)
     >>> param["Negative current collector thickness [m]"]

pybamm/parameters/update_parameter_sets_doc.py

@@ -51,7 +51,7 @@ def generate_ps_doc(parameter_set_dict):
     for ps_chemistry in sorted(parameter_set_dict.keys()):
         output_list.append("")
         ps_citations = parameter_set_dict[ps_chemistry]
-        chem_name = ps_chemistry.capitalize() + " " + "parameter sets"
+        chem_name = ps_chemistry.capitalize().replace("_", "-") + " " + "parameter sets"
         output_list.append(chem_name)
         dashes = "-" * len(ps_chemistry) + "-" * 15
         output_list.append(dashes)