#609 reformat particle models

docs/source/models/submodels/particle/fast_many_particles.rst

@@ -0,0 +1,5 @@
+Fast Many Particles
+===================
+
+.. autoclass:: pybamm.particle.FastManyParticles
+    :members:

docs/source/models/submodels/particle/fast_single_particle.rst

@@ -0,0 +1,5 @@
+Fast Single Particle
+====================
+
+.. autoclass:: pybamm.particle.FastSingleParticle
+    :members:

docs/source/models/submodels/particle/fickian_many_particles.rst

@@ -0,0 +1,7 @@
+Fickian Many Particles
+======================
+
+.. autoclass:: pybamm.particle.FickianManyParticles
+    :members:
+
+

docs/source/models/submodels/particle/fickian_single_particle.rst

@@ -0,0 +1,6 @@
+Fickian Single Particle
+=======================
+
+.. autoclass:: pybamm.particle.FickianSingleParticle
+    :members:
+

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

@@ -5,5 +5,7 @@ Particle
   :maxdepth: 1
 
   base_particle
-  fickian/index
-  fast/index
+  fickian_single_particle
+  fickian_many_particles
+  fast_single_particle
+  fast_many_particles

examples/notebooks/using-submodels.ipynb

@@ -113,7 +113,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model.submodels[\"negative particle\"] = pybamm.particle.fast.SingleParticle(model.param, \"Negative\")"
+    "model.submodels[\"negative particle\"] = pybamm.particle.FastSingleParticle(model.param, \"Negative\")"
    ]
   },
   {
@@ -370,10 +370,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model.submodels[\"negative particle\"] = pybamm.particle.fast.SingleParticle(\n",
+    "model.submodels[\"negative particle\"] = pybamm.particle.FastSingleParticle(\n",
     "    model.param, \"Negative\"\n",
     ")\n",
-    "model.submodels[\"positive particle\"] = pybamm.particle.fast.SingleParticle(\n",
+    "model.submodels[\"positive particle\"] = pybamm.particle.FastSingleParticle(\n",
     "    model.param, \"Positive\"\n",
     ")"
    ]

examples/scripts/custom_model.py

@@ -22,10 +22,10 @@
 model.submodels["positive electrode"] = pybamm.electrode.ohm.LeadingOrder(
     model.param, "Positive"
 )
-model.submodels["negative particle"] = pybamm.particle.fast.SingleParticle(
+model.submodels["negative particle"] = pybamm.particle.FastSingleParticle(
     model.param, "Negative"
 )
-model.submodels["positive particle"] = pybamm.particle.fast.SingleParticle(
+model.submodels["positive particle"] = pybamm.particle.FastSingleParticle(
     model.param, "Positive"
 )
 model.submodels["negative interface"] = pybamm.interface.InverseButlerVolmer(

pybamm/models/full_battery_models/lithium_ion/dfn.py

@@ -70,17 +70,17 @@ def set_interfacial_submodel(self):
     def set_particle_submodel(self):
 
         if self.options["particle"] == "Fickian diffusion":
-            self.submodels["negative particle"] = pybamm.particle.fickian.ManyParticles(
+            self.submodels["negative particle"] = pybamm.particle.FickianManyParticles(
                 self.param, "Negative"
             )
-            self.submodels["positive particle"] = pybamm.particle.fickian.ManyParticles(
+            self.submodels["positive particle"] = pybamm.particle.FickianManyParticles(
                 self.param, "Positive"
             )
         elif self.options["particle"] == "fast diffusion":
-            self.submodels["negative particle"] = pybamm.particle.fast.ManyParticles(
+            self.submodels["negative particle"] = pybamm.particle.FastManyParticles(
                 self.param, "Negative"
             )
-            self.submodels["positive particle"] = pybamm.particle.fast.ManyParticles(
+            self.submodels["positive particle"] = pybamm.particle.FastManyParticles(
                 self.param, "Positive"
             )
 

pybamm/models/full_battery_models/lithium_ion/spm.py

@@ -79,17 +79,17 @@ def set_interfacial_submodel(self):
     def set_particle_submodel(self):
 
         if self.options["particle"] == "Fickian diffusion":
-            self.submodels[
-                "negative particle"
-            ] = pybamm.particle.fickian.SingleParticle(self.param, "Negative")
-            self.submodels[
-                "positive particle"
-            ] = pybamm.particle.fickian.SingleParticle(self.param, "Positive")
+            self.submodels["negative particle"] = pybamm.particle.FickianSingleParticle(
+                self.param, "Negative"
+            )
+            self.submodels["positive particle"] = pybamm.particle.FickianSingleParticle(
+                self.param, "Positive"
+            )
         elif self.options["particle"] == "fast diffusion":
-            self.submodels["negative particle"] = pybamm.particle.fast.SingleParticle(
+            self.submodels["negative particle"] = pybamm.particle.FastSingleParticle(
                 self.param, "Negative"
             )
-            self.submodels["positive particle"] = pybamm.particle.fast.SingleParticle(
+            self.submodels["positive particle"] = pybamm.particle.FastSingleParticle(
                 self.param, "Positive"
             )
 

pybamm/models/full_battery_models/lithium_ion/spme.py

@@ -81,17 +81,17 @@ def set_interfacial_submodel(self):
     def set_particle_submodel(self):
 
         if self.options["particle"] == "Fickian diffusion":
-            self.submodels[
-                "negative particle"
-            ] = pybamm.particle.fickian.SingleParticle(self.param, "Negative")
-            self.submodels[
-                "positive particle"
-            ] = pybamm.particle.fickian.SingleParticle(self.param, "Positive")
+            self.submodels["negative particle"] = pybamm.particle.FickianSingleParticle(
+                self.param, "Negative"
+            )
+            self.submodels["positive particle"] = pybamm.particle.FickianSingleParticle(
+                self.param, "Positive"
+            )
         elif self.options["particle"] == "fast diffusion":
-            self.submodels["negative particle"] = pybamm.particle.fast.SingleParticle(
+            self.submodels["negative particle"] = pybamm.particle.FastSingleParticle(
                 self.param, "Negative"
             )
-            self.submodels["positive particle"] = pybamm.particle.fast.SingleParticle(
+            self.submodels["positive particle"] = pybamm.particle.FastSingleParticle(
                 self.param, "Positive"
             )
 

pybamm/models/submodels/particle/__init__.py

@@ -1,3 +1,5 @@
 from .base_particle import BaseParticle
-from . import fickian
-from . import fast
+from .fickian_many_particles import FickianManyParticles
+from .fickian_single_particle import FickianSingleParticle
+from .fast_many_particles import FastManyParticles
+from .fast_single_particle import FastSingleParticle

pybamm/models/submodels/particle/fast/fast_many_particles.py → pybamm/models/submodels/particle/fast_many_particles.py

@@ -4,10 +4,10 @@
 #
 import pybamm
 
-from .base_fast_particle import BaseModel
+from .base_particle import BaseParticle
 
 
-class ManyParticles(BaseModel):
+class FastManyParticles(BaseParticle):
     """Base class for molar conservation in many particles with
     uniform concentration in r (i.e. infinitely fast diffusion within particles).
 
@@ -19,7 +19,7 @@ class ManyParticles(BaseModel):
         The domain of the model either 'Negative' or 'Positive'
 
 
-    **Extends:** :class:`pybamm.particle.fast.BaseModel`
+    **Extends:** :class:`pybamm.particle.BaseParticle`
     """
 
     def __init__(self, param, domain):
@@ -63,16 +63,17 @@ def get_fundamental_variables(self):
 
         return variables
 
-    def _unpack(self, variables):
+    def set_rhs(self, variables):
         c_s_surf = variables[self.domain + " particle surface concentration"]
-        N_s = variables[self.domain + " particle flux"]
         j = variables[self.domain + " electrode interfacial current density"]
+        if self.domain == "Negative":
+            self.rhs = {c_s_surf: -3 * j / self.param.a_n}
 
-        return c_s_surf, N_s, j
+        elif self.domain == "Positive":
+            self.rhs = {c_s_surf: -3 * j / self.param.a_p / self.param.gamma_p}
 
     def set_initial_conditions(self, variables):
-        c, _, _ = self._unpack(variables)
-
+        c_s_surf = variables[self.domain + " particle surface concentration"]
         if self.domain == "Negative":
             x_n = pybamm.standard_spatial_vars.x_n
             c_init = self.param.c_n_init(x_n)
@@ -81,4 +82,4 @@ def set_initial_conditions(self, variables):
             x_p = pybamm.standard_spatial_vars.x_p
             c_init = self.param.c_p_init(x_p)
 
-        self.initial_conditions = {c: c_init}
+        self.initial_conditions = {c_s_surf: c_init}

pybamm/models/submodels/particle/fast/fast_single_particle.py → pybamm/models/submodels/particle/fast_single_particle.py

@@ -4,10 +4,10 @@
 #
 import pybamm
 
-from .base_fast_particle import BaseModel
+from .base_particle import BaseParticle
 
 
-class SingleParticle(BaseModel):
+class FastSingleParticle(BaseParticle):
     """Base class for molar conservation in a single x-averaged particle with
     uniform concentration in r (i.e. infinitely fast diffusion within particles).
 
@@ -19,7 +19,7 @@ class SingleParticle(BaseModel):
         The domain of the model either 'Negative' or 'Positive'
 
 
-    **Extends:** :class:`pybamm.particle.fast.BaseModel`
+    **Extends:** :class:`pybamm.particle.BaseParticle`
     """
 
     def __init__(self, param, domain):
@@ -35,61 +35,67 @@ def get_fundamental_variables(self):
             c_s_xav = pybamm.PrimaryBroadcast(c_s_surf_xav, ["negative particle"])
             c_s = pybamm.SecondaryBroadcast(c_s_xav, ["negative electrode"])
 
-            N_s = pybamm.FullBroadcast(
+            N_s = pybamm.FullBroadcastToEdges(
                 0,
                 ["negative particle"],
                 auxiliary_domains={
                     "secondary": "negative electrode",
                     "tertiary": "current collector",
                 },
             )
-            N_s_xav = pybamm.x_average(N_s)
+            N_s_xav = pybamm.FullBroadcast(0, "negative electrode", "current collector")
 
         elif self.domain == "Positive":
             c_s_surf_xav = pybamm.standard_variables.c_s_p_surf_xav
             c_s_xav = pybamm.PrimaryBroadcast(c_s_surf_xav, ["positive particle"])
             c_s = pybamm.SecondaryBroadcast(c_s_xav, ["positive electrode"])
 
-            N_s = pybamm.FullBroadcast(
+            N_s = pybamm.FullBroadcastToEdges(
                 0,
                 ["positive particle"],
                 auxiliary_domains={
                     "secondary": "positive electrode",
                     "tertiary": "current collector",
                 },
             )
-            N_s_xav = pybamm.x_average(N_s)
+            N_s_xav = pybamm.FullBroadcast(0, "positive electrode", "current collector")
 
         variables = self._get_standard_concentration_variables(c_s, c_s_xav)
         variables.update(self._get_standard_flux_variables(N_s, N_s_xav))
 
         return variables
 
-    def _unpack(self, variables):
+    def set_rhs(self, variables):
+
         c_s_surf_xav = variables[
             "X-averaged " + self.domain.lower() + " particle surface concentration"
         ]
-        N_s_xav = variables["X-averaged " + self.domain.lower() + " particle flux"]
-        j_av = variables[
+        j_xav = variables[
             "X-averaged "
             + self.domain.lower()
             + " electrode interfacial current density"
         ]
 
-        return c_s_surf_xav, N_s_xav, j_av
+        if self.domain == "Negative":
+            self.rhs = {c_s_surf_xav: -3 * j_xav / self.param.a_n}
+
+        elif self.domain == "Positive":
+            self.rhs = {c_s_surf_xav: -3 * j_xav / self.param.a_p / self.param.gamma_p}
 
     def set_initial_conditions(self, variables):
         """
         For single particle models, initial conditions can't depend on x so we
         arbitrarily evaluate them at x=0 in the negative electrode and x=1 in the
         positive electrode (they will usually be constant)
         """
-        c, _, _ = self._unpack(variables)
+        c_s_surf_xav = variables[
+            "X-averaged " + self.domain.lower() + " particle surface concentration"
+        ]
 
         if self.domain == "Negative":
             c_init = self.param.c_n_init(0)
 
         elif self.domain == "Positive":
             c_init = self.param.c_p_init(1)
 
-        self.initial_conditions = {c: c_init}
+        self.initial_conditions = {c_s_surf_xav: c_init}