update in doc

Documentation/intermediate.rst

@@ -2,11 +2,10 @@
 Intermediate usage
 ==================
 
-.. note::
-  This section is still under development.
+.. _mergeJsonStructs:
 
-Pseudo-Four-Dimensional (P4D) Model
-===================================
+Setup a P4D Model using :code:`mergeJsonStructs`
+================================================
 
 Let's build a pseudo-four-dimensional Li-ion battery model and explore more about how to mix-and-match |battmo| parameter definitions!
 
@@ -117,21 +116,23 @@ surface particle concentrations in both electrode at a given time step.
    :target: _images/3dconc.png
 
 
-
-
-
-Direct insertion using :code:`parseBattmoJson`
-==============================================
+File links and insertions with :code:`parseBattmoJson`
+======================================================
 
 There are two mechanisms which can be used to combine JSON input files:
 
-#. Direct insertion using :code:`parseBattmoJson`
 #. Merge function using :code:`mergeJsonStruct`
+#. Direct insertion using :code:`parseBattmoJson`
+
+We have just seen an example of the first mechanism, which can be used within Matlab when we setup the simulation.
 
-The function :battmo:`parseBattmoJson` parses the JSON input to create the corresponding matlab structure, basically
-relying on `jsondecode <https://se.mathworks.com/help/matlab/ref/jsondecode.html>`_. In this process the reserved
-keyword properties :code:`isFile` combined with :code:`filename` are used to fetch and insert in place JSON data located
-in separate files. Here is an example, taken from :battmofile:`lithium_ion_battery_nmc_graphite.json<ParameterData/BatteryCellParameters/LithiumIonBatteryCell/lithium_ion_battery_nmc_graphite.json>` where we have the following lines
+The function :battmo:`parseBattmoJson` is used to parse a JSON input and create the corresponding matlab structure. It
+basically relies on `jsondecode <https://se.mathworks.com/help/matlab/ref/jsondecode.html>`_.
+
+In this process the reserved keyword properties :code:`isFile` combined with :code:`filename` are used to fetch and
+insert in place JSON data located in separate files. Here is an example, taken from
+:battmofile:`lithium_ion_battery_nmc_graphite.json<ParameterData/BatteryCellParameters/LithiumIonBatteryCell/lithium_ion_battery_nmc_graphite.json>`
+where we have the following lines
 
 .. code:: json
           
@@ -176,7 +177,4 @@ the :code:`jsonstruct` that is obtained is equivalent to the one where we would
              "argumentlist" : ["cElectrode", "T", "cmax"]
              }}},          
 
-.. _mergeJsonStructs:
 
-Merge function using :code:`mergeJsonStructs`
----------------------------------------------

Documentation/json.rst

@@ -1,3 +1,4 @@
+
 ========================
 JSON input specification
 ========================
@@ -26,6 +27,8 @@ schemas. Having separate schemas clarify the presentation and corresponds also t
 input. We can easily switch between different geometrical models while keeping the same material properties. For that,
 we use the :battmo:`mergeJsonStructs` function, see the example :ref:`here<mergeJsonStructs>`.
 
+Here, we give an :ref:`Example<jsonexample:Json input example>`
+
 
 Simulation Schema
 =================
@@ -35,8 +38,9 @@ This is the main schema for the input json file. It uses other separate schemas
 .. literalinclude:: ../Utilities/JsonSchemas/Simulation.schema.json
    :language: json
 
-The schemas are available in the directory :battmofile:`JsonSchemas<Utilities/JsonSchemas>`.
-important schemas.
+The schemas are available in the directory
+:battmofile:`JsonSchemas<Utilities/JsonSchemas>`. :ref:`Here<jsonexample:Simulation>` is an example of the main input
+file where the inputs are given in separate files using the :code:`isFile` key.
 
 
 Material Parameters
@@ -64,6 +68,7 @@ It contains references to schemas that are written in separate files
 * Separator
 * Thermal Model
 
+See json :ref:`input example<jsonexample:Battery>`.  
 
 Electrolyte
 -----------
@@ -85,6 +90,8 @@ concentration and temperature, see examples :battmofile:`here<ParameterData/Mate
 .. literalinclude:: ../Utilities/JsonSchemas/Electrolyte.schema.json
    :language: json
 
+See json :ref:`input example<jsonexample:Electrolyte>`.
+
 Electrode
 ---------
 
@@ -93,6 +100,8 @@ The electrode input data contains essentially the input data for the coating and
 .. literalinclude:: ../Utilities/JsonSchemas/Electrode.schema.json
    :language: json
 
+See json :ref:`input example<jsonexample:Negative Electrode>` and also :ref:`here<jsonexample:Positive Electrode>`.
+
 Coating
 -------
 
@@ -103,6 +112,8 @@ provide the data for the two active materials (:code:`ActiveMaterial1` and :code
 .. literalinclude:: ../Utilities/JsonSchemas/Coating.schema.json
    :language: json
 
+See json :ref:`input example<jsonexample:Coating>`
+
 Active Material
 ---------------
 
@@ -120,7 +131,9 @@ property :code:`diffusionModelType` is used to choose between the different diff
 
 .. literalinclude::  ../Utilities/JsonSchemas/ActiveMaterial.schema.json
    :language: json
-
+
+See json :ref:`input example<jsonexample:Active Material>`
+
 Interface
 ---------
 
@@ -132,6 +145,8 @@ functions.
 .. literalinclude:: ../Utilities/JsonSchemas/Interface.schema.json
    :language: json
 
+See json :ref:`input example<jsonexample:Interface>`
+
 Solid Diffusion
 ---------------
 
@@ -142,6 +157,8 @@ full diffusion model, we can provide a diffusion coefficient that depends on the
 .. literalinclude:: ../Utilities/JsonSchemas/SolidDiffusionModel.schema.json
    :language: json
 
+See json :ref:`input example<jsonexample:Solid Diffusion>`
+
 Full Solid Diffusion
 --------------------
 
@@ -157,16 +174,20 @@ the guest stoichiometries and the saturation concentration.
 
 
 .. literalinclude:: ../Utilities/JsonSchemas/FullSolidDiffusionModel.schema.json
-   :language: json              
-
+   :language: json
+
+See json :ref:`input example<jsonexample:Solid Diffusion>`
+
 Binder
 ------
 
 The conductivity of the binder and conductiving additive are used to compute the overall conductivity of the coating.
 
 .. literalinclude::  ../Utilities/JsonSchemas/Binder.schema.json
    :language: json
-
+
+See json :ref:`input example<jsonexample:Binder>`
+
 Conducting Additive
 -------------------
 
@@ -175,12 +196,15 @@ The conductivity of the binder and conductiving additive are used to compute the
 .. literalinclude::  ../Utilities/JsonSchemas/ConductingAdditive.schema.json
    :language: json
 
+See json :ref:`input example<jsonexample:Conducting Additive>`
+
 Current Collector
 -----------------
 
 .. literalinclude:: ../Utilities/JsonSchemas/CurrentCollector.schema.json
    :language: json
 
+See json :ref:`input example<jsonexample:Current Collector>`
 
 Separator
 ---------
@@ -190,6 +214,8 @@ The porosity of the separator gives the volume fraction of the electrolyte in th
 .. literalinclude:: ../Utilities/JsonSchemas/Separator.schema.json
    :language: json
 
+See json :ref:`input example<jsonexample:Separator>`
+
 
 Thermal Model
 -------------
@@ -199,7 +225,8 @@ The thermal parameters are essentially the thermal conductivity and heat capacit
 .. literalinclude:: ../Utilities/JsonSchemas/ThermalComponent.schema.json
    :language: json
 
-
+See json :ref:`input example<jsonexample:Thermal Model>`
+
 .. _geometryschema:                 
 
 Geometry Setup
@@ -214,6 +241,9 @@ For each design, the parameters are described in the schema.
 
 .. literalinclude:: ../Utilities/JsonSchemas/Geometry.schema.json
    :language: json
+
+See json :ref:`input example<jsonexample:Geometry>`
+
 
 Simulation Control Parameters
 =============================
@@ -224,6 +254,8 @@ various control models can be read from the schema.
 .. literalinclude:: ../Utilities/JsonSchemas/ControlModel.schema.json
    :language: json
 
+See json :ref:`input example<jsonexample:Control>`
+
 
 Time Stepping Parameters
 ========================
@@ -233,7 +265,8 @@ The description of the time stepping parameters can be read from the schema. Def
 .. literalinclude:: ../Utilities/JsonSchemas/TimeStepping.schema.json
    :language: json
 
-
+See json :ref:`input example<jsonexample:Time Stepping>`
+
 Solver Parameters
 =================
 

Documentation/jsonexample.rst

@@ -1,11 +1,136 @@
-remove stack.json from repo
+:orphan:
+
+==================
+Json input example
+==================
 
-comment on volumeFraction entry in interface.json
+In this page, we present an example of a json input
 
-change density from interface to active material
 
-fix nominal concentration
+TODO
+====
 
-fix thermal property in electrolyte
+* comment on volumeFraction entry in interface.json
+* change density from interface to active material
+* fix nominal concentration
+* fix thermal property in electrolyte
+* remove thermal model.
 
-remove thermal model.
+Simulation
+==========
+
+.. literalinclude:: scripts/jsonfiles/Example/simulation.json
+   :language: json
+
+Battery
+=======
+
+.. literalinclude:: scripts/jsonfiles/Example/battery.json
+   :language: json
+
+Negative Electrode
+==================
+
+.. literalinclude:: scripts/jsonfiles/Example/negativeElectrode.json
+   :language: json
+
+Coating
+=======
+
+.. literalinclude:: scripts/jsonfiles/Example/coating.json
+   :language: json
+
+Active Material
+===============
+
+.. literalinclude:: scripts/jsonfiles/Example/activeMaterial.json
+   :language: json
+
+Interface
+=========
+
+.. literalinclude:: scripts/jsonfiles/Example/interface.json
+   :language: json
+
+Solid Diffusion
+===============
+
+.. literalinclude:: scripts/jsonfiles/Example/solidDiffusion.json
+   :language: json
+
+Binder
+======
+
+.. literalinclude:: scripts/jsonfiles/Example/binder.json
+   :language: json
+
+Conducting Additive
+===================
+
+.. literalinclude:: scripts/jsonfiles/Example/conductingAdditive.json
+   :language: json
+
+Current Collector
+=================
+
+.. literalinclude:: scripts/jsonfiles/Example/currentCollector.json
+   :language: json
+
+Positive Electrode
+==================
+
+Here, we provide all the parameter in a single json structure without linking to other files.
+
+.. literalinclude:: scripts/jsonfiles/Example/positiveElectrode.json
+   :language: json
+
+Electrolyte
+===========
+
+.. literalinclude:: scripts/jsonfiles/Example/electrolyte.json
+   :language: json
+
+Separator
+=========
+
+.. literalinclude:: scripts/jsonfiles/Example/electrolyte.json
+   :language: json
+
+Thermal Model
+=============
+
+.. literalinclude:: scripts/jsonfiles/Example/thermalComponent.json
+   :language: json
+
+Geometry
+========
+
+We consider the 3D demo model, see :ref:`here<3dgeometry>`
+
+.. literalinclude:: scripts/jsonfiles/Example/geometry.json
+   :language: json
+
+Model Specification
+===================
+
+.. literalinclude:: scripts/jsonfiles/Example/modelSpecification.json
+   :language: json
+
+Control
+=======
+
+.. literalinclude:: scripts/jsonfiles/Example/control.json
+   :language: json              
+
+Time Stepping
+=============
+
+.. literalinclude:: scripts/jsonfiles/Example/timeStepping.json
+   :language: json
+
+State Initialization
+====================
+
+.. literalinclude:: scripts/jsonfiles/Example/stateInitialization.json
+   :language: json                            
+

Documentation/scripts/jsonfiles/Example/simulation.json

@@ -1,9 +1,9 @@
 {
   "isFile" : true,
-  "filenames": ["modelSpecification.json",
-                "battery.json",
-                "control.json",
+  "filenames": ["battery.json",
                 "geometry.json",
+                "modelSpecification.json",
+                "control.json",
                 "timeStepping.json",
                 "stateInitialization.json"]
 }