#2376, added bpx conversions and some defaults, remove events in simu…

…lation, still problems with diffusivity

pybamm/parameters/bpx.py

@@ -1,8 +1,10 @@
 from bpx import BPX, Function, InterpolatedTable
-import numbers
 import pybamm
 import math
 from dataclasses import dataclass
+import numpy as np
+from pybamm import constants
+from pybamm import exp
 
 
 @dataclass
@@ -18,6 +20,7 @@ class Domain:
                  short_pre_name='Positive ')
 electrolyte = Domain(name='electrolyte', pre_name='Electrolyte ', short_pre_name='')
 separator = Domain(name='separator', pre_name='Separator ', short_pre_name='')
+experiment = Domain(name='experiment', pre_name='', short_pre_name='')
 
 
 def bpx_to_param_dict(bpx: BPX) -> dict:
@@ -32,14 +35,41 @@ def bpx_to_param_dict(bpx: BPX) -> dict:
         bpx.parameterisation.cathode, pybamm_dict, cathode
     )
     pybamm_dict = _bpx_to_param_dict(
-        bpx.parameterisation.cathode, pybamm_dict, electrolyte
+        bpx.parameterisation.electrolyte, pybamm_dict, electrolyte
     )
+    print(pybamm_dict, bpx)
     pybamm_dict = _bpx_to_param_dict(
         bpx.parameterisation.separator, pybamm_dict, separator
     )
+    pybamm_dict = _bpx_to_param_dict(
+        bpx.parameterisation.separator, pybamm_dict, experiment
+    )
+
+    # set a default current function
+    pybamm_dict['Current function [A]'] = 1
+
+    # Ambient temp
+    pybamm_dict['Ambient temperature [K]'] = pybamm_dict['Reference temperature [K]']
+
+    for domain in [anode, cathode]:
+        pybamm_dict[domain.pre_name + 'electrons in reaction'] = 1.0
+
+    # typical electrolyte concentration
+    pybamm_dict['Typical electrolyte concentration [mol.m-3]'] = pybamm_dict[
+        'Initial concentration in electrolyte [mol.m-3]'
+    ]
+
+    for domain in [anode, cathode]:
+        pybamm_dict[domain.pre_name + 'OCP entropic change [V.K-1]'] = 0.0
+
+    for domain in [anode, separator, cathode]:
+        pybamm_dict[domain.pre_name + 'Bruggeman coefficient (electrolyte)'] = 1.5
+        pybamm_dict[domain.pre_name + 'Bruggeman coefficient (electrode)'] = 1.5
+
+    pybamm_dict['Number of cells connected in series to make a battery'] = 1
 
     # electrode area
-    equal_len_width = math.sqrt(pybamm_dict['Electrode area [m]'])
+    equal_len_width = math.sqrt(pybamm_dict['Electrode area [m2]'])
     pybamm_dict['Electrode width [m]'] = equal_len_width
     pybamm_dict['Electrode height [m]'] = equal_len_width
 
@@ -51,7 +81,8 @@ def bpx_to_param_dict(bpx: BPX) -> dict:
     ]:
         for domain in [anode, cathode, separator]:
             pybamm_name = domain.pre_name + name[:1].lower() + name[1:]
-            pybamm_dict[pybamm_name] = pybamm_dict[name]
+            if name in pybamm_dict:
+                pybamm_dict[pybamm_name] = pybamm_dict[name]
 
     # BET surface area
     for domain in [anode, cathode]:
@@ -83,7 +114,8 @@ def bpx_to_param_dict(bpx: BPX) -> dict:
         k_norm = pybamm_dict[
             domain.pre_name + 'reaction rate [mol.m-2.s-1]'
         ]
-        k = k_norm * F / (c_n_max * c_e ** 0.5)
+        F = 96485
+        k = k_norm * F / (c_max * c_e ** 0.5)
         def exchange_current_density(c_e, c_s_surf, c_s_max, T):
             k_ref = k  # (A/m2)(mol/m3)**1.5 - includes ref concentrations
             E_r = 53400
@@ -96,37 +128,8 @@ def exchange_current_density(c_e, c_s_surf, c_s_max, T):
             exchange_current_density
         )
 
-    return pybamm_dict
-
-
-def positive_electrode_exchange_current_density(c_e, c_s_surf, c_s_max, T):
-    """
-    Exchange-current density for Butler-Volmer reactions.
-    Parameters
-    ----------
-    c_e : :class:`pybamm.Symbol`
-        Electrolyte concentration [mol.m-3]
-    c_s_surf : :class:`pybamm.Symbol`
-        Particle concentration [mol.m-3]
-    c_s_max : :class:`pybamm.Symbol`
-        Maximum particle concentration [mol.m-3]
-    T : :class:`pybamm.Symbol`
-        Temperature [K]
-    Returns
-    -------
-    :class:`pybamm.Symbol`
-        Exchange-current density [A.m-2]
-    """
-
-    k_ref = 1.3499500722289229e-06  # (A/m2)(mol/m3)**1.5 - includes ref concentrations
-    E_r = 27010
-    arrhenius = exp(E_r / constants.R * (1 / 298.15 - 1 / T))
-
-    return (
-        k_ref * arrhenius * c_e ** 0.5 * c_s_surf ** 0.5 * (c_s_max - c_s_surf) ** 0.5
-    )
 
-    pybamm_dict[] = k_norm * F / (c_max * c_e ** 0.5)
+    return pybamm_dict
 
 
 preamble = (
@@ -143,11 +146,11 @@ def _bpx_to_param_dict(instance: BPX, pybamm_dict: dict, domain: Domain) -> dict
             value = value.to_python_function(preamble=preamble)
         elif isinstance(value, InterpolatedTable):
             timescale = 1
-            x = value.x
-            y = value.y
+            x = np.array(value.x)
+            y = np.array(value.y)
             interpolator = 'linear'
             value = pybamm.Interpolant(
-                x, y, pybamm.t * timescale,
+                [x], y, pybamm.t * timescale,
                 name=name, interpolator=interpolator
             )
 
@@ -160,12 +163,17 @@ def _bpx_to_param_dict(instance: BPX, pybamm_dict: dict, domain: Domain) -> dict
             init_len = len("Initial concentration ")
             pybamm_name = (
                 pybamm_name[:init_len] +
+                'in ' +
                 domain.pre_name.lower() +
                 pybamm_name[init_len:]
             )
         elif pybamm_name.startswith("Particle radius"):
             pybamm_name = domain.short_pre_name + pybamm_name_lower
-        else:
+        elif pybamm_name.startswith('OCP'):
+            pybamm_name = domain.pre_name + pybamm_name
+        elif pybamm_name.startswith('Cation transference number'):
+            pybamm_name = pybamm_name
+        elif domain.pre_name != '':
             pybamm_name = domain.pre_name + pybamm_name_lower
 
         pybamm_dict[pybamm_name] = value

tests/unit/test_parameters/test_parameter_values.py

@@ -13,6 +13,8 @@
 import pandas as pd
 
 import pybamm
+import tests
+print(tests.__file__)
 import tests.shared as shared
 from pybamm.input.parameters.lithium_ion.Marquis2019 import (
     lico2_ocp_Dualfoil1998,
@@ -1034,6 +1036,7 @@ def test_bpx(self):
                 "Cell": {
                     "Initial temperature [K]": 299.0,
                     "Reference temperature [K]": 299.0,
+                    "Nominal cell capacity [A.h]": 5.0,
                     "Electrode area [m2]": 2.0,
                     "Number of electrodes connected in parallel to make a cell": 1,
                 },
@@ -1083,7 +1086,7 @@ def test_bpx(self):
         import tempfile
         filename = 'tmp.json'
         with tempfile.NamedTemporaryFile(
-            suffix=filename, delete=False
+            suffix=filename, delete=False, mode='w'
         ) as tmp:
             # write to a tempory file so we can
             # get the source later on using inspect.getsource
@@ -1092,7 +1095,14 @@ def test_bpx(self):
             tmp.flush()
 
             pv = pybamm.ParameterValues.create_from_bpx(tmp.name)
-            print('got pv', pv)
+
+            model = pybamm.lithium_ion.DFN()
+            model.events = []
+            experiment = pybamm.Experiment([
+                "Discharge at C/5 for 1 hour",
+            ])
+            sim = pybamm.Simulation(model, parameter_values=pv, experiment=experiment)
+            sim.solve(calc_esoh=False)
 
 
 if __name__ == "__main__":