pybamm-team#1330 homogenised notation citations

brosaplanella · Jan 23, 2021 · bcdd19a · bcdd19a
1 parent 810ee79
commit bcdd19a
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Showing 26 changed files with 304 additions and 301 deletions.
diff --git a/pybamm/CITATIONS.txt b/pybamm/CITATIONS.txt
diff --git a/pybamm/citations.py b/pybamm/citations.py
@@ -17,7 +17,7 @@ class Citations:
     Examples
     --------
     >>> import pybamm
-    >>> pybamm.citations.register("sulzer2020python")
+    >>> pybamm.citations.register("Sulzer2020")
     >>> pybamm.print_citations("citations.txt")
     """
 
@@ -30,8 +30,8 @@ def _reset(self):
         # Initialize empty papers to cite
         self._papers_to_cite = set()
         # Register the PyBaMM paper and the numpy paper
-        self.register("sulzer2020python")
-        self.register("harris2020array")
+        self.register("Sulzer2020")
+        self.register("Harris2020")
 
     def read_citations(self):
         "Read the citations text file"

diff --git a/pybamm/models/full_battery_models/lead_acid/full.py b/pybamm/models/full_battery_models/lead_acid/full.py
@@ -50,7 +50,7 @@ def __init__(self, options=None, name="Full model", build=True):
         if build:
             self.build_model()
 
-        pybamm.citations.register("sulzer2019physical")
+        pybamm.citations.register("Sulzer2019physical")
 
     def set_porosity_submodel(self):
         self.submodels["porosity"] = pybamm.porosity.Full(self.param)

diff --git a/pybamm/models/full_battery_models/lead_acid/higher_order.py b/pybamm/models/full_battery_models/lead_acid/higher_order.py
@@ -58,7 +58,7 @@ def __init__(self, options=None, name="Composite model", build=True):
         if build:
             self.build_model()
 
-        pybamm.citations.register("sulzer2019asymptotic")
+        pybamm.citations.register("Sulzer2019asymptotic")
 
     def set_current_collector_submodel(self):
         cc = pybamm.current_collector

diff --git a/pybamm/models/full_battery_models/lead_acid/loqs.py b/pybamm/models/full_battery_models/lead_acid/loqs.py
@@ -52,7 +52,7 @@ def __init__(self, options=None, name="LOQS model", build=True):
         if self.options["dimensionality"] == 0:
             self.use_jacobian = False
 
-        pybamm.citations.register("sulzer2019asymptotic")
+        pybamm.citations.register("Sulzer2019asymptotic")
 
     def set_external_circuit_submodel(self):
         """

diff --git a/pybamm/models/full_battery_models/lithium_ion/basic_dfn.py b/pybamm/models/full_battery_models/lithium_ion/basic_dfn.py
@@ -29,7 +29,7 @@ class BasicDFN(BaseModel):
 
     def __init__(self, name="Doyle-Fuller-Newman model"):
         super().__init__({}, name)
-        pybamm.citations.register("marquis2019asymptotic")
+        pybamm.citations.register("Marquis2019")
         # `param` is a class containing all the relevant parameters and functions for
         # this model. These are purely symbolic at this stage, and will be set by the
         # `ParameterValues` class when the model is processed.

diff --git a/pybamm/models/full_battery_models/lithium_ion/basic_dfn_half_cell.py b/pybamm/models/full_battery_models/lithium_ion/basic_dfn_half_cell.py
@@ -36,7 +36,7 @@ class BasicDFNHalfCell(BaseModel):
 
     def __init__(self, name="Doyle-Fuller-Newman half cell model", options=None):
         super().__init__({}, name)
-        pybamm.citations.register("marquis2019asymptotic")
+        pybamm.citations.register("Marquis2019")
         # `param` is a class containing all the relevant parameters and functions for
         # this model. These are purely symbolic at this stage, and will be set by the
         # `ParameterValues` class when the model is processed.

diff --git a/pybamm/models/full_battery_models/lithium_ion/basic_spm.py b/pybamm/models/full_battery_models/lithium_ion/basic_spm.py
@@ -29,7 +29,7 @@ class BasicSPM(BaseModel):
 
     def __init__(self, name="Single Particle Model"):
         super().__init__({}, name)
-        pybamm.citations.register("marquis2019asymptotic")
+        pybamm.citations.register("Marquis2019")
         # `param` is a class containing all the relevant parameters and functions for
         # this model. These are purely symbolic at this stage, and will be set by the
         # `ParameterValues` class when the model is processed.

diff --git a/pybamm/models/full_battery_models/lithium_ion/dfn.py b/pybamm/models/full_battery_models/lithium_ion/dfn.py
@@ -51,7 +51,7 @@ def __init__(self, options=None, name="Doyle-Fuller-Newman model", build=True):
         if build:
             self.build_model()
 
-        pybamm.citations.register("doyle1993modeling")
+        pybamm.citations.register("Doyle1993")
 
     def set_porosity_submodel(self):
 

diff --git a/pybamm/models/full_battery_models/lithium_ion/spm.py b/pybamm/models/full_battery_models/lithium_ion/spm.py
@@ -52,7 +52,7 @@ def __init__(self, options=None, name="Single Particle Model", build=True):
         if build:
             self.build_model()
 
-        pybamm.citations.register("marquis2019asymptotic")
+        pybamm.citations.register("Marquis2019")
 
     def set_porosity_submodel(self):
 

diff --git a/pybamm/models/full_battery_models/lithium_ion/spme.py b/pybamm/models/full_battery_models/lithium_ion/spme.py
@@ -54,7 +54,7 @@ def __init__(
         if build:
             self.build_model()
 
-        pybamm.citations.register("marquis2019asymptotic")
+        pybamm.citations.register("Marquis2019")
 
     def set_porosity_submodel(self):
 

diff --git a/pybamm/models/submodels/current_collector/effective_resistance_current_collector.py b/pybamm/models/submodels/current_collector/effective_resistance_current_collector.py
@@ -51,7 +51,7 @@ def __init__(
         self.set_boundary_conditions(self.variables)
         self.set_initial_conditions(self.variables)
 
-        pybamm.citations.register("timms2020")
+        pybamm.citations.register("Timms2020")
 
     def get_fundamental_variables(self):
         # Get necessary parameters
@@ -399,7 +399,7 @@ def __init__(self):
             {"y": var.y, "y [m]": var.y * L_y, "z": var.z, "z [m]": var.z * L_z}
         )
 
-        pybamm.citations.register("timms2020")
+        pybamm.citations.register("Timms2020")
 
     def post_process(self, solution, param_values, V_av, I_av):
         """

diff --git a/pybamm/models/submodels/current_collector/potential_pair.py b/pybamm/models/submodels/current_collector/potential_pair.py
@@ -28,7 +28,7 @@ class BasePotentialPair(BaseModel):
     def __init__(self, param):
         super().__init__(param)
 
-        pybamm.citations.register("timms2020")
+        pybamm.citations.register("Timms2020")
 
     def get_fundamental_variables(self):
 

diff --git a/pybamm/models/submodels/electrolyte_conductivity/integrated_conductivity.py b/pybamm/models/submodels/electrolyte_conductivity/integrated_conductivity.py
@@ -30,7 +30,7 @@ class Integrated(BaseElectrolyteConductivity):
     """
 
     def __init__(self, param, domain=None):
-        pybamm.citations.register("brosaplanella2020TSPMe")
+        pybamm.citations.register("BrosaPlanella2020")
         super().__init__(param, domain)
 
     def _higher_order_macinnes_function(self, x):

diff --git a/pybamm/models/submodels/particle/polynomial_many_particles.py b/pybamm/models/submodels/particle/polynomial_many_particles.py
@@ -34,7 +34,7 @@ def __init__(self, param, domain, name):
         super().__init__(param, domain)
         self.name = name
 
-        pybamm.citations.register("subramanian2005")
+        pybamm.citations.register("Subramanian2005")
 
     def get_fundamental_variables(self):
         variables = {}

diff --git a/pybamm/models/submodels/particle/polynomial_single_particle.py b/pybamm/models/submodels/particle/polynomial_single_particle.py
@@ -34,7 +34,7 @@ def __init__(self, param, domain, name):
         super().__init__(param, domain)
         self.name = name
 
-        pybamm.citations.register("subramanian2005")
+        pybamm.citations.register("Subramanian2005")
 
     def get_fundamental_variables(self):
         # For all orders we solve an equation for the average concentration

diff --git a/pybamm/models/submodels/particle_cracking/base_cracking.py b/pybamm/models/submodels/particle_cracking/base_cracking.py
@@ -32,8 +32,8 @@ def __init__(self, param, domain):
         self.domain = domain
         super().__init__(param)
 
-        pybamm.citations.register("Ai_2019")
-        pybamm.citations.register("deshpande2012battery")
+        pybamm.citations.register("Ai2019")
+        pybamm.citations.register("Deshpande2012")
 
     def _get_standard_variables(self, l_cr):
         domain = self.domain.lower() + " particle"

diff --git a/pybamm/parameters/parameter_sets.py b/pybamm/parameters/parameter_sets.py
@@ -74,7 +74,7 @@
     "electrolyte": "lipf6_Kim2011",
     "experiment": "1C_discharge_from_full_Kim2011",
     "sei": "example",
-    "citation": "kim2011multi",
+    "citation": "Kim2011",
 }
 
 Ecker2015 = {
@@ -86,7 +86,7 @@
     "electrolyte": "lipf6_Ecker2015",
     "experiment": "1C_discharge_from_full_Ecker2015",
     "sei": "example",
-    "citation": ["ecker2015i", "ecker2015ii", "richardson2020"],
+    "citation": ["Ecker2015i", "Ecker2015ii", "Richardson2020"],
 }
 
 Marquis2019 = {
@@ -98,7 +98,7 @@
     "electrolyte": "lipf6_Marquis2019",
     "experiment": "1C_discharge_from_full_Marquis2019",
     "sei": "example",
-    "citation": "marquis2019asymptotic",
+    "citation": "Marquis2019",
 }
 
 Chen2020 = {
@@ -122,7 +122,7 @@
     "electrolyte": "LiPF6_Mohtat2020",
     "experiment": "1C_charge_from_empty_Mohtat2020",
     "sei": "example",
-    "citation": "mohtat2020differential",
+    "citation": "Mohtat2020",
 }
 
 Ramadass2004 = {
@@ -134,7 +134,7 @@
     "electrolyte": "lipf6_Ramadass2004",
     "experiment": "1C_discharge_from_full_Ramadass2004",
     "sei": "ramadass2004",
-    "citation": "marquis2019asymptotic",
+    "citation": "Marquis2019",
 }
 
 Prada2013 = {
@@ -145,7 +145,7 @@
     "cathode": "LFP_Prada2013",
     "electrolyte": "lipf6_Nyman2008",
     "experiment": "4C_discharge_from_full_Prada2013",
-    "citation": ["Chen2020", "lain2019design", "prada2013simplified"],
+    "citation": ["Chen2020", "Lain2019", "Prada2013"],
 }
 
 Ai2020 = {
@@ -157,7 +157,7 @@
     "electrolyte": "lipf6_Enertech_Ai2020",
     "experiment": "1C_discharge_from_full_Ai2020",
     "sei": "example",
-    "citation": "Ai2020JES",
+    "citation": "Ai2019",
 }
 
 #
@@ -171,5 +171,5 @@
     "cathode": "lead_dioxide_Sulzer2019",
     "electrolyte": "sulfuric_acid_Sulzer2019",
     "experiment": "1C_discharge_from_full",
-    "citation": "sulzer2019physical",
+    "citation": "Sulzer2019physical",
 }
diff --git a/pybamm/solvers/algebraic_solver.py b/pybamm/solvers/algebraic_solver.py
@@ -36,7 +36,7 @@ def __init__(self, method="lm", tol=1e-6, extra_options=None):
         self.extra_options = extra_options or {}
         self.name = "Algebraic solver ({})".format(method)
         self.algebraic_solver = True
-        pybamm.citations.register("virtanen2020scipy")
+        pybamm.citations.register("Virtanen2020")
 
     @property
     def tol(self):

diff --git a/pybamm/solvers/idaklu_solver.py b/pybamm/solvers/idaklu_solver.py
@@ -58,8 +58,8 @@ def __init__(
         )
         self.name = "IDA KLU solver"
 
-        pybamm.citations.register("hindmarsh2000pvode")
-        pybamm.citations.register("hindmarsh2005sundials")
+        pybamm.citations.register("Hindmarsh2000")
+        pybamm.citations.register("Hindmarsh2005")
 
     def set_atol_by_variable(self, variables_with_tols, model):
         """

diff --git a/pybamm/solvers/jax_solver.py b/pybamm/solvers/jax_solver.py
@@ -70,7 +70,7 @@ def __init__(
         self.extra_options = extra_options or {}
         self.name = "JAX solver ({})".format(method)
         self._cached_solves = dict()
-        pybamm.citations.register("jax2018github")
+        pybamm.citations.register("jax2018")
 
     def get_solve(self, model, t_eval):
         """

diff --git a/pybamm/solvers/scikits_dae_solver.py b/pybamm/solvers/scikits_dae_solver.py
@@ -68,9 +68,9 @@ def __init__(
 
         self.extra_options = extra_options or {}
 
-        pybamm.citations.register("scikits-odes")
-        pybamm.citations.register("hindmarsh2000pvode")
-        pybamm.citations.register("hindmarsh2005sundials")
+        pybamm.citations.register("Malengier2018")
+        pybamm.citations.register("Hindmarsh2000")
+        pybamm.citations.register("Hindmarsh2005")
 
     def _integrate(self, model, t_eval, inputs_dict=None):
         """

diff --git a/pybamm/solvers/scikits_ode_solver.py b/pybamm/solvers/scikits_ode_solver.py
@@ -65,9 +65,9 @@ def __init__(
         self.ode_solver = True
         self.name = "Scikits ODE solver ({})".format(method)
 
-        pybamm.citations.register("scikits-odes")
-        pybamm.citations.register("hindmarsh2000pvode")
-        pybamm.citations.register("hindmarsh2005sundials")
+        pybamm.citations.register("Malengier2018")
+        pybamm.citations.register("Hindmarsh2000")
+        pybamm.citations.register("Hindmarsh2005")
 
     def _integrate(self, model, t_eval, inputs_dict=None):
         """

diff --git a/pybamm/solvers/scipy_solver.py b/pybamm/solvers/scipy_solver.py
@@ -34,7 +34,7 @@ def __init__(
         self.ode_solver = True
         self.extra_options = extra_options or {}
         self.name = "Scipy solver ({})".format(method)
-        pybamm.citations.register("virtanen2020scipy")
+        pybamm.citations.register("Virtanen2020")
 
     def _integrate(self, model, t_eval, inputs_dict=None):
         """

diff --git a/pybamm/spatial_methods/scikit_finite_element.py b/pybamm/spatial_methods/scikit_finite_element.py
@@ -29,7 +29,7 @@ class ScikitFiniteElement(pybamm.SpatialMethod):
 
     def __init__(self, options=None):
         super().__init__(options)
-        pybamm.citations.register("scikit-fem")
+        pybamm.citations.register("Gustafsson2020")
 
     def build(self, mesh):
         super().build(mesh)