added documentation for gas layer

BattMoTeam · Dec 18, 2024 · 097e713 · 097e713
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diff --git a/Documentation/publishedExamples/runGasSupply.png b/Documentation/publishedExamples/runGasSupply.png
diff --git a/Documentation/publishedExamples/runGasSupply.rst b/Documentation/publishedExamples/runGasSupply.rst
@@ -0,0 +1,202 @@
+.. _runGasSupply:
+
+
+================
+Gas Supply Layer
+================
+*Generated from runGasSupply.m*
+
+
+Single gas supply layer where a mixture of two gases (here H2O and O2) is injected at the bottom and flows to the top (See illustration below).
+
+json input data
+===============
+We load the input data that is given by json structures. The physical properties of the supply gas layer is given in the json file :battmofile:`gas-supply.json <ProtonicMembrane/jsonfiles/gas-supply.json>`
+
+.. code-block:: matlab
+
+  filename = fullfile(battmoDir(), 'ProtonicMembrane', 'jsonfiles', 'gas-supply.json');
+  jsonstruct_material = parseBattmoJson(filename);
+
+The geometry input is loaded from :battmofile:`2d-gas-layer-geometry.json <ProtonicMembrane/jsonfiles/2d-gas-layer-geometry.json>`
+
+.. code-block:: matlab
+
+  filename = fullfile(battmoDir(), 'ProtonicMembrane', 'jsonfiles', '2d-gas-layer-geometry.json');
+  jsonstruct_geometry = parseBattmoJson(filename);
+
+The input for the initial state is loaded from :battmofile:`gas-supply-initialization.json <ProtonicMembrane/jsonfiles/gas-supply-initialization.json>`
+
+.. code-block:: matlab
+
+  filename = fullfile(battmoDir(), 'ProtonicMembrane', 'jsonfiles', 'gas-supply-initialization.json');
+  jsonstruct_initialization = parseBattmoJson(filename);
+  
+  jsonstruct = mergeJsonStructs({jsonstruct_material, ...
+                                 jsonstruct_geometry, ...
+                                 jsonstruct_initialization});
+
+
+Input parameter setup
+=====================
+We setup the input parameter structure which will we be used to instantiate the model
+
+.. code-block:: matlab
+
+  inputparams = ProtonicMembraneGasSupplyInputParams(jsonstruct);
+
+We setup the grid, which is done by calling the function :battmo:`setupProtonicMembraneGasLayerGrid`
+
+.. code-block:: matlab
+
+  [inputparams, gridGenerator] = setupProtonicMembraneGasLayerGrid(inputparams, jsonstruct);
+
+
+Model setup
+===========
+We instantiate the model for the gas supply layer
+
+.. code-block:: matlab
+
+  model = ProtonicMembraneGasSupply(inputparams);
+
+The model is equipped for simulation using the following command (this step may become unnecessary in future versions)
+
+.. code-block:: matlab
+
+  model = model.setupForSimulation();
+
+
+Model Plot
+==========
+We plot the simulation grid
+
+.. code-block:: matlab
+
+  G = model.grid;
+  
+  plotGrid(G);
+
+.. figure:: runGasSupply_01.png
+  :figwidth: 100%
+
+The boundary conditions have been given by the input json file, see :battmofile:`gas-supply.json <ProtonicMembrane/jsonfiles/gas-supply.json#16>`. In this case we have rate control at the inlet at the bottom, and pressure control at the outlet at the top.
+The index of the faces for the inlet and outlet are stored in a :code:`couplingTerm` structure (see :battmo:`here <couplingTerm>` for the base class). Those have been assigned when the grid is setup (for this example we have used :battmo:`GasSupplyGridGenerator2D`).
+We plot the inlet faces.
+
+.. code-block:: matlab
+
+  coupTerm = model.couplingTerms{1};
+  plotFaces(G, coupTerm.couplingfaces, 'edgecolor', 'blue', 'linewidth', 3)
+
+.. figure:: runGasSupply_02.png
+  :figwidth: 100%
+
+We plot the outlet faces.
+
+.. code-block:: matlab
+
+  coupTerm = model.couplingTerms{2};
+  plotFaces(G, coupTerm.couplingfaces, 'edgecolor', 'red', 'linewidth', 3)
+
+.. figure:: runGasSupply_03.png
+  :figwidth: 100%
+
+
+Setup initial state
+===================
+The model provides us with a default initialization
+
+.. code-block:: matlab
+
+  initstate = model.setupInitialState(jsonstruct);
+
+
+Schedule setup
+==============
+The schedule structure constains two fields :code:`step`, :code:`control`, which gives respectively the time steps and the control to be applied.
+
+.. code-block:: matlab
+
+  T  = 1e-2*second;
+  N  = 10;
+  
+  dt = rampupTimesteps(T, T/N, 1);
+  
+  step.val = dt;
+  step.control = ones(numel(step.val), 1);
+  
+  control.src = []; % The control is taking care of by a dedicated submobel. Hence, the empty field here.
+  
+  schedule = struct('control', control, 'step', step);
+
+
+Simulation
+==========
+We start the simulation
+
+.. code-block:: matlab
+
+  [~, states, report] = simulateScheduleAD(initstate, model, schedule);
+
+
+Result plots
+============
+To analyse the result, we can use the interactive :code:`plotToolbar` command (see :mrstfile:`here <visualization/mrst-gui/plotToolbar.m>`)
+
+.. code-block:: matlab
+
+  figure
+  plotToolbar(model.grid, states);
+  %
+  %
+
+.. figure:: runGasSupply_04.png
+  :figwidth: 100%
+
+We plot the pressure at the final step.
+
+.. code-block:: matlab
+
+  set(0, 'defaultlinelinewidth', 3);
+  set(0, 'defaultaxesfontsize', 15);
+  
+  state = states{end};
+  
+  G = model.grid;
+  
+  figure
+  plotCellData(G, state.pressure/barsa);
+  colorbar
+  title('Pressure / bar');
+
+.. figure:: runGasSupply_05.png
+  :figwidth: 100%
+
+We plot the water mass fractions at three different time step
+
+.. code-block:: matlab
+
+  inds = [1; 5; 10];
+  ninds = numel(inds);
+  for i = 1 : ninds
+      figure
+      state = states{inds(i)};
+      plotCellData(G, state.massfractions{1}, 'edgecolor', 'none');
+      clim([0.2, 0.4]);
+      title(sprintf('H2O mass fraction\n(timestep:%d)', inds(i)));
+      colorbar
+  end
+
+.. figure:: runGasSupply_06.png
+  :figwidth: 100%
+
+.. figure:: runGasSupply_07.png
+  :figwidth: 100%
+
+.. figure:: runGasSupply_08.png
+  :figwidth: 100%
+
+
+
+complete source code can be found :ref:`here<runGasSupply_source>`
diff --git a/Documentation/publishedExamples/runGasSupply_01.png b/Documentation/publishedExamples/runGasSupply_01.png
diff --git a/Documentation/publishedExamples/runGasSupply_02.png b/Documentation/publishedExamples/runGasSupply_02.png
diff --git a/Documentation/publishedExamples/runGasSupply_03.png b/Documentation/publishedExamples/runGasSupply_03.png
diff --git a/Documentation/publishedExamples/runGasSupply_04.png b/Documentation/publishedExamples/runGasSupply_04.png
diff --git a/Documentation/publishedExamples/runGasSupply_05.png b/Documentation/publishedExamples/runGasSupply_05.png
diff --git a/Documentation/publishedExamples/runGasSupply_06.png b/Documentation/publishedExamples/runGasSupply_06.png
diff --git a/Documentation/publishedExamples/runGasSupply_07.png b/Documentation/publishedExamples/runGasSupply_07.png
diff --git a/Documentation/publishedExamples/runGasSupply_08.png b/Documentation/publishedExamples/runGasSupply_08.png
diff --git a/Documentation/publishedExamples/runGasSupply_source.rst b/Documentation/publishedExamples/runGasSupply_source.rst
@@ -0,0 +1,158 @@
+:orphan:
+
+.. _runGasSupply_source:
+
+Source code for runGasSupply
+----------------------------
+
+.. code:: matlab
+
+
+  %% Gas Supply Layer
+  %
+  % Single gas supply layer where a mixture of two gases (here H2O and O2) is injected at the bottom and flows to the top
+  % (See illustration below).
+  %
+  
+  %% json input data
+  %
+  % We load the input data that is given by json structures. The physical properties of the supply gas layer is given in the json file :battmofile:`gas-supply.json <ProtonicMembrane/jsonfiles/gas-supply.json>` 
+  %
+  
+  filename = fullfile(battmoDir(), 'ProtonicMembrane', 'jsonfiles', 'gas-supply.json');
+  jsonstruct_material = parseBattmoJson(filename);
+  
+  %%
+  % The geometry input is loaded from :battmofile:`2d-gas-layer-geometry.json <ProtonicMembrane/jsonfiles/2d-gas-layer-geometry.json>`
+  %
+  filename = fullfile(battmoDir(), 'ProtonicMembrane', 'jsonfiles', '2d-gas-layer-geometry.json');
+  jsonstruct_geometry = parseBattmoJson(filename);
+  
+  %%
+  % The input for the initial state is loaded from :battmofile:`gas-supply-initialization.json <ProtonicMembrane/jsonfiles/gas-supply-initialization.json>`
+  %
+  
+  filename = fullfile(battmoDir(), 'ProtonicMembrane', 'jsonfiles', 'gas-supply-initialization.json');
+  jsonstruct_initialization = parseBattmoJson(filename);
+  
+  jsonstruct = mergeJsonStructs({jsonstruct_material, ...
+                                 jsonstruct_geometry, ...
+                                 jsonstruct_initialization});
+  
+  %% Input parameter setup
+  %
+  % We setup the input parameter structure which will we be used to instantiate the model
+  %
+  
+  inputparams = ProtonicMembraneGasSupplyInputParams(jsonstruct);
+  
+  %%
+  % We setup the grid, which is done by calling the function :battmo:`setupProtonicMembraneGasLayerGrid`
+  [inputparams, gridGenerator] = setupProtonicMembraneGasLayerGrid(inputparams, jsonstruct);
+  
+  %% Model setup
+  %
+  % We instantiate the model for the gas supply layer
+  %
+  
+  model = ProtonicMembraneGasSupply(inputparams);
+  
+  %%
+  % The model is equipped for simulation using the following command (this step may become unnecessary in future versions)
+  
+  model = model.setupForSimulation();
+  
+  %% Model Plot
+  %
+  % We plot the simulation grid
+  %
+  G = model.grid;
+  
+  plotGrid(G);
+  
+  %%
+  % The boundary conditions have been given by the input json file, see :battmofile:`gas-supply.json
+  % <ProtonicMembrane/jsonfiles/gas-supply.json#16>`. In this case we have rate control at the inlet at the bottom, and
+  % pressure control at the outlet at the top.
+  %
+  % The index of the faces for the inlet and outlet are stored in a :code:`couplingTerm` structure (see :battmo:`here
+  % <couplingTerm>` for the base class). Those have been assigned when the grid is setup (for this example we have used
+  % :battmo:`GasSupplyGridGenerator2D`).
+  %
+  % We plot the inlet faces.
+  coupTerm = model.couplingTerms{1};
+  plotFaces(G, coupTerm.couplingfaces, 'edgecolor', 'blue', 'linewidth', 3)
+  
+  %%
+  % We plot the outlet faces.
+  coupTerm = model.couplingTerms{2};
+  plotFaces(G, coupTerm.couplingfaces, 'edgecolor', 'red', 'linewidth', 3)
+  
+  %% Setup initial state
+  %
+  % The model provides us with a default initialization
+  
+  initstate = model.setupInitialState(jsonstruct);
+  
+  %% Schedule setup
+  %
+  % The schedule structure constains two fields :code:`step`, :code:`control`, which gives respectively the time steps and
+  % the control to be applied.
+  
+  T  = 1e-2*second;
+  N  = 10;
+  
+  dt = rampupTimesteps(T, T/N, 1);
+  
+  step.val = dt;
+  step.control = ones(numel(step.val), 1);
+  
+  control.src = []; % The control is taking care of by a dedicated submobel. Hence, the empty field here.
+  
+  schedule = struct('control', control, 'step', step);
+  
+  %% Simulation
+  %
+  % We start the simulation
+  [~, states, report] = simulateScheduleAD(initstate, model, schedule);
+  
+  %% Result plots
+  % 
+  % To analyse the result, we can use the interactive :code:`plotToolbar` command (see :mrstfile:`here <visualization/mrst-gui/plotToolbar.m>`)
+  %
+  figure
+  plotToolbar(model.grid, states);
+  %
+  %
+  
+  %%
+  % We plot the pressure at the final step.
+  %
+  
+  set(0, 'defaultlinelinewidth', 3);
+  set(0, 'defaultaxesfontsize', 15);
+  
+  state = states{end};
+  
+  G = model.grid;
+  
+  figure
+  plotCellData(G, state.pressure/barsa);
+  colorbar
+  title('Pressure / bar');
+  
+  %%
+  % We plot the water mass fractions at three different time step
+  
+  inds = [1; 5; 10];
+  ninds = numel(inds);
+  for i = 1 : ninds
+      figure
+      state = states{inds(i)};
+      plotCellData(G, state.massfractions{1}, 'edgecolor', 'none');
+      clim([0.2, 0.4]);
+      title(sprintf('H2O mass fraction\n(timestep:%d)', inds(i)));
+      colorbar
+  end
+  
+