Merge pull request #796 from pybamm-team/issue-790-param-not-recognized

Issue 790 param not recognized
pybamm-team · Jan 28, 2020 · d1344e3 · d1344e3
2 parents 29683da + 1d10e77
commit d1344e3
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diff --git a/.requirements-docs.txt b/.requirements-docs.txt
@@ -8,3 +8,4 @@ scikit-fem>=0.2.0
 casadi>=3.5.0
 guzzle-sphinx-theme
 sphinx>=1.5
+python-Levenshtein>=0.12.0
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,8 @@
 
 ## Features
 
+-   Added fuzzy string matching for parameters and variables ([#796](https://github.com/pybamm-team/PyBaMM/pull/796))
+-   Changed ParameterValues to raise an error when a parameter that wasn't previously defined is updated ([#796](https://github.com/pybamm-team/PyBaMM/pull/796))
 -   Added some basic models (BasicSPM and BasicDFN) in order to clearly demonstrate the PyBaMM model structure for battery models ([#795](https://github.com/pybamm-team/PyBaMM/pull/795))
 -   Added the harmonic mean to the Finite Volume method, which is now used when computing fluxes ([#783](https://github.com/pybamm-team/PyBaMM/pull/783))
 -   Refactored `Solution` to make it a dictionary that contains all of the solution variables. This automatically creates `ProcessedVariable` objects when required, so that the solution can be obtained much more easily. ([#781](https://github.com/pybamm-team/PyBaMM/pull/781))

diff --git a/examples/notebooks/change-settings.ipynb b/examples/notebooks/change-settings.ipynb
@@ -123,6 +123,26 @@
    "cell_type": "code",
    "execution_count": 3,
    "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<bound method ParameterValues.items of <pybamm.parameters.parameter_values.ParameterValues object at 0x1113519e8>>"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "model.default_parameter_values.items"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -155,8 +175,8 @@
       "Typical current [A]                                                                      0.680616\n",
       "Negative electrode conductivity [S.m-1]                                                     100.0\n",
       "Maximum concentration in negative electrode [mol.m-3]                            24983.2619938437\n",
-      "Negative electrode diffusivity [m2.s-1]                                      <function graphite_mcmb2528_diffusivity_Dualfoil1998 at 0x13e6f9840>\n",
-      "Negative electrode OCP [V]                                                   <function graphite_mcmb2528_ocp_Dualfoil1998 at 0x13e6f96a8>\n",
+      "Negative electrode diffusivity [m2.s-1]                                      <function graphite_mcmb2528_diffusivity_Dualfoil1998 at 0x13dad4400>\n",
+      "Negative electrode OCP [V]                                                   <function graphite_mcmb2528_ocp_Dualfoil1998 at 0x13dad4598>\n",
       "Negative electrode porosity                                                                   0.3\n",
       "Negative electrode active material volume fraction                                            0.7\n",
       "Negative particle radius [m]                                                                1e-05\n",
@@ -173,15 +193,15 @@
       "Negative electrode density [kg.m-3]                                                        1657.0\n",
       "Negative electrode specific heat capacity [J.kg-1.K-1]                                      700.0\n",
       "Negative electrode thermal conductivity [W.m-1.K-1]                                           1.7\n",
-      "Negative electrode OCP entropic change [V.K-1]                               <function graphite_entropic_change_Moura2016 at 0x13e6f9730>\n",
+      "Negative electrode OCP entropic change [V.K-1]                               <function graphite_entropic_change_Moura2016 at 0x13dad4488>\n",
       "Reference temperature [K]                                                                  298.15\n",
-      "Negative electrode reaction rate                                             <function graphite_electrolyte_reaction_rate_Dualfoil1998 at 0x13e6f98c8>\n",
+      "Negative electrode reaction rate                                             <function graphite_electrolyte_reaction_rate_Dualfoil1998 at 0x13dad4620>\n",
       "Negative reaction rate activation energy [J.mol-1]                                        37480.0\n",
       "Negative solid diffusion activation energy [J.mol-1]                                      42770.0\n",
       "Positive electrode conductivity [S.m-1]                                                      10.0\n",
       "Maximum concentration in positive electrode [mol.m-3]                            51217.9257309275\n",
-      "Positive electrode diffusivity [m2.s-1]                                      <function lico2_diffusivity_Dualfoil1998 at 0x13e6f97b8>\n",
-      "Positive electrode OCP [V]                                                   <function lico2_ocp_Dualfoil1998 at 0x13e6f9950>\n",
+      "Positive electrode diffusivity [m2.s-1]                                      <function lico2_diffusivity_Dualfoil1998 at 0x13dad4510>\n",
+      "Positive electrode OCP [V]                                                   <function lico2_ocp_Dualfoil1998 at 0x13dad46a8>\n",
       "Positive electrode porosity                                                                   0.3\n",
       "Positive electrode active material volume fraction                                            0.7\n",
       "Positive particle radius [m]                                                                1e-05\n",
@@ -198,8 +218,8 @@
       "Positive electrode density [kg.m-3]                                                        3262.0\n",
       "Positive electrode specific heat capacity [J.kg-1.K-1]                                      700.0\n",
       "Positive electrode thermal conductivity [W.m-1.K-1]                                           2.1\n",
-      "Positive electrode OCP entropic change [V.K-1]                               <function lico2_entropic_change_Moura2016 at 0x13e6f9a60>\n",
-      "Positive electrode reaction rate                                             <function lico2_electrolyte_reaction_rate_Dualfoil1998 at 0x13e6f9ae8>\n",
+      "Positive electrode OCP entropic change [V.K-1]                               <function lico2_entropic_change_Moura2016 at 0x13dad47b8>\n",
+      "Positive electrode reaction rate                                             <function lico2_electrolyte_reaction_rate_Dualfoil1998 at 0x13dad4840>\n",
       "Positive reaction rate activation energy [J.mol-1]                                        39570.0\n",
       "Positive solid diffusion activation energy [J.mol-1]                                      18550.0\n",
       "Separator porosity                                                                            1.0\n",
@@ -210,8 +230,8 @@
       "Separator thermal conductivity [W.m-1.K-1]                                                   0.16\n",
       "Typical electrolyte concentration [mol.m-3]                                                1000.0\n",
       "Cation transference number                                                                    0.4\n",
-      "Electrolyte diffusivity [m2.s-1]                                             <function electrolyte_diffusivity_Capiglia1999 at 0x13e6f9c80>\n",
-      "Electrolyte conductivity [S.m-1]                                             <function electrolyte_conductivity_Capiglia1999 at 0x13e6f99d8>\n",
+      "Electrolyte diffusivity [m2.s-1]                                             <function electrolyte_diffusivity_Capiglia1999 at 0x13dad49d8>\n",
+      "Electrolyte conductivity [S.m-1]                                             <function electrolyte_conductivity_Capiglia1999 at 0x13dad4730>\n",
       "Electrolyte diffusion activation energy [J.mol-1]                                         37040.0\n",
       "Electrolyte conductivity activation energy [J.mol-1]                                      34700.0\n",
       "Heat transfer coefficient [W.m-2.K-1]                                                        10.0\n",
@@ -250,7 +270,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -282,7 +302,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -298,7 +318,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -314,7 +334,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -352,7 +372,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -384,7 +404,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -408,7 +428,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
@@ -453,7 +473,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -477,7 +497,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {

diff --git a/examples/notebooks/parameter-values.ipynb b/examples/notebooks/parameter-values.ipynb
@@ -47,7 +47,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "parameter values are {'a': 1, 'b': 2, 'c': 3}\n"
+      "parameter values are <pybamm.parameters.parameter_values.ParameterValues object at 0x13dd5e0f0>\n"
      ]
     }
    ],
@@ -73,7 +73,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "parameter values are {'a': 4, 'b': 5, 'c': 6}\n"
+      "parameter values are <pybamm.parameters.parameter_values.ParameterValues object at 0x13dd5e860>\n"
      ]
     }
    ],
@@ -126,7 +126,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can input functions into the parameter values, either directly"
+    "We can input functions into the parameter values, either directly (note we bypass the check that the parameter already exists)"
    ]
   },
   {
@@ -138,14 +138,14 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "parameter values are {'a': 4, 'b': 5, 'c': 6, 'cube function': <function cubed at 0x136260a60>}\n"
+      "parameter values are <pybamm.parameters.parameter_values.ParameterValues object at 0x13dd5e860>\n"
      ]
     }
    ],
    "source": [
     "def cubed(x):\n",
     "    return x ** 3\n",
-    "parameter_values.update({\"cube function\": cubed})\n",
+    "parameter_values.update({\"cube function\": cubed}, check_already_exists=False)\n",
     "print(\"parameter values are {}\".format(parameter_values))"
    ]
   },
@@ -165,7 +165,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "parameter values are {'a': 4, 'b': 5, 'c': 6, 'cube function': <function cubed at 0x136260a60>, 'square function': <function squared at 0x136260ae8>}\n"
+      "parameter values are <pybamm.parameters.parameter_values.ParameterValues object at 0x13dd5e860>\n"
      ]
     }
    ],
@@ -178,7 +178,7 @@
     "\"\"\"\n",
     ")\n",
     "f.close()\n",
-    "parameter_values.update({\"square function\": pybamm.load_function(\"squared.py\")})\n",
+    "parameter_values.update({\"square function\": pybamm.load_function(\"squared.py\")}, check_already_exists=False)\n",
     "print(\"parameter values are {}\".format(parameter_values))"
    ]
   },
@@ -405,7 +405,7 @@
     {
      "data": {
       "text/plain": [
-       "{Variable(-0x53753a8d5f6f95de, u, children=[], domain=[], auxiliary_domains={}): Multiplication(0x3e1bde14593f44cc, *, children=['-a', 'y[0:1]'], domain=[], auxiliary_domains={})}"
+       "{Variable(0x1b4aef6f668c631, u, children=[], domain=[], auxiliary_domains={}): Multiplication(-0x36caade7fdf02dac, *, children=['-a', 'y[0:1]'], domain=[], auxiliary_domains={})}"
       ]
      },
      "execution_count": 12,

diff --git a/examples/scripts/DFN.py b/examples/scripts/DFN.py
@@ -15,7 +15,7 @@
 
 # load parameter values and process model and geometry
 param = model.default_parameter_values
-param["Voltage function [V]"] = 4.1
+param.update({"Voltage function [V]": 4.1}, check_already_exists=False)
 param.process_model(model)
 param.process_geometry(geometry)
 

diff --git a/examples/scripts/compare_lead_acid_3D.py b/examples/scripts/compare_lead_acid_3D.py
@@ -46,7 +46,6 @@
 param.update(
     {
         "Current function [A]": 1,
-        "Bruggeman  coefficient": 0.001,
         "Initial State of Charge": 1,
         "Typical electrolyte concentration [mol.m-3]": 5600,
         "Negative electrode reference exchange-current density [A.m-2]": 0.08,

diff --git a/pybamm/__init__.py b/pybamm/__init__.py
@@ -55,7 +55,7 @@ def version(formatted=False):
 #
 # Utility classes and methods
 #
-from .util import Timer
+from .util import Timer, FuzzyDict
 from .util import root_dir, load_function, rmse, get_infinite_nested_dict, load
 from .logger import logger, set_logging_level
 from .settings import settings

diff --git a/pybamm/models/base_model.py b/pybamm/models/base_model.py
@@ -104,7 +104,7 @@ def __init__(self, name="Unnamed model"):
         self._algebraic = {}
         self._initial_conditions = {}
         self._boundary_conditions = {}
-        self._variables = {}
+        self._variables = pybamm.FuzzyDict()
         self._events = {}
         self._concatenated_rhs = None
         self._concatenated_algebraic = None
@@ -208,7 +208,7 @@ def variables(self):
 
     @variables.setter
     def variables(self, variables):
-        self._variables = variables
+        self._variables = pybamm.FuzzyDict(variables)
 
     def variable_names(self):
         return list(self._variables.keys())