diff --git a/_sources/publishedExamples/runProtonicMembrane.rst.txt b/_sources/publishedExamples/runProtonicMembrane.rst.txt
index 4a395083..dab90c11 100644
--- a/_sources/publishedExamples/runProtonicMembrane.rst.txt
+++ b/_sources/publishedExamples/runProtonicMembrane.rst.txt
@@ -60,8 +60,8 @@ We setup the initial state using a default setup included in the model
   state0 = model.setupInitialState();
 
 
-Schedule schedule
-=================
+Schedule
+========
 We setup the schedule, which means the timesteps and also the control we want to use. In this case we use current control and the current equal to zero (see here :battmofile:`here<ProtonicMembrane/protonicMembrane.json#86>`).
 We compute the steady-state solution so that the time stepping here is more an artifact to reach the steady-state solution. In particular, it governs the pace at which we increase the non-linearity (not detailed here).
 
diff --git a/advancedtopics.html b/advancedtopics.html
index 13e24083..054c2d48 100644
--- a/advancedtopics.html
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-<li class="toctree-l2"><a class="reference internal" href="publishedExamples/runProtonicMembrane.html#schedule-schedule">Schedule schedule</a></li>
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 <li class="toctree-l2"><a class="reference internal" href="publishedExamples/runProtonicMembrane.html#evolution-of-the-faradic-efficiency">Evolution of the Faradic efficiency</a></li>
diff --git a/architecture.html b/architecture.html
index 0f35e1ee..7827fd2e 100644
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index 1910b42f..ca78ab39 100644
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diff --git a/bibliography.html b/bibliography.html
index b978aedd..55a00dc6 100644
--- a/bibliography.html
+++ b/bibliography.html
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index 322f03f3..9a69ae4d 100644
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index 14cbf01a..a6e6b909 100644
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@@ -355,7 +355,7 @@ <h2>File links and insertions with <code class="code docutils literal notranslat
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index 1583ecf2..3988b7f7 100644
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index 3a41398e..605cb420 100644
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diff --git a/publishedExamples/runProtonicMembrane.html b/publishedExamples/runProtonicMembrane.html
index bf996c71..f3baafd2 100644
--- a/publishedExamples/runProtonicMembrane.html
+++ b/publishedExamples/runProtonicMembrane.html
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-<li class="toctree-l2"><a class="reference internal" href="#schedule-schedule">Schedule schedule</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#schedule">Schedule</a></li>
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@@ -347,8 +347,8 @@ <h2>Initial state setup<a class="headerlink" href="#initial-state-setup" title="
 </pre></div>
 </div>
 </section>
-<section id="schedule-schedule">
-<h2>Schedule schedule<a class="headerlink" href="#schedule-schedule" title="Permalink to this heading"></a></h2>
+<section id="schedule">
+<h2>Schedule<a class="headerlink" href="#schedule" title="Permalink to this heading"></a></h2>
 <p>We setup the schedule, which means the timesteps and also the control we want to use. In this case we use current control and the current equal to zero (see here <a class="reference external" href="https://github.com/BattMoTeam/BattMo/blob/dev/ProtonicMembrane/protonicMembrane.json#L86">here</a>).
 We compute the steady-state solution so that the time stepping here is more an artifact to reach the steady-state solution. In particular, it governs the pace at which we increase the non-linearity (not detailed here).</p>
 <div class="highlight-matlab notranslate"><div class="highlight"><pre><span></span><span class="n">schedule</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="n">model</span><span class="p">.</span><span class="n">Control</span><span class="p">.</span><span class="n">setupSchedule</span><span class="p">(</span><span class="n">inputparams</span><span class="p">.</span><span class="n">jsonstruct</span><span class="p">);</span>
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and Implementation": [[5, "graph-setup-and-implementation"]], "Control models": [[6, "control-models"]], "Json input control interface": [[6, "json-input-control-interface"]], "Control model description": [[6, "control-model-description"]], "Battery Geometries": [[7, "battery-geometries"]], "BatteryGeneratorP2D": [[7, "batterygeneratorp2d"]], "Parameters with values used in plot above": [[7, "id2"], [7, "id3"], [7, "id4"]], "BatteryGeneratorP3D": [[7, "batterygeneratorp3d"]], "BatteryGeneratorP4D": [[7, "batterygeneratorp4d"]], "SpiralBatteryGenerator": [[7, "spiralbatterygenerator"]], "Thickness and discretization number (N) are passed through the dictionaries widthDict and nrDict, with values used in plot above.": [[7, "id5"]], "Other parameters, with values used in plot above.": [[7, "id6"]], "CoinCellBatteryGenerator": [[7, "coincellbatterygenerator"]], "Parameters for each component : thickness, diameter, number of cell layers (Nl), with the values used in the plot above (a CR 2016 coin cell)": [[7, "id7"]], "Other parameters, with values used in plot above": [[7, "id8"], [7, "id10"]], "BatteryGeneratorMultilayerPouch": [[7, "batterygeneratormultilayerpouch"]], "Parameters for each component : thickness and number of cell (Nl) for a layer, with the values used in the plot above": [[7, "id9"]], "BattMo App": [[8, "battmo-app"]], "Calculations": [[9, "calculations"]], "Features": [[10, "features"]], "Use default materials": [[10, "use-default-materials"]], "Define your own materials": [[10, "define-your-own-materials"]], "Visualize your geometry": [[10, "visualize-your-geometry"]], "Download your input data": [[10, "download-your-input-data"]], "Visualize and download your results": [[10, "visualize-and-download-your-results"]], "Troubleshooting": [[11, "troubleshooting"]], "Unnatural artifacts in your results": [[11, "unnatural-artifacts-in-your-results"]], "Welcome": [[12, "welcome"]], "Acknowledgements": [[12, "acknowledgements"]], "Installation and First Steps": [[13, "installation-and-first-steps"]], "Intermediate usage": [[14, "intermediate-usage"]], "Setup a P4D Model using mergeJsonStructs": [[14, "setup-a-p4d-model-using-mergejsonstructs"]], "Visualize Results": [[14, "visualize-results"]], "File links and insertions with parseBattmoJson": [[14, "file-links-and-insertions-with-parsebattmojson"]], "JSON input specification": [[15, "json-input-specification"]], "Simulation Schema": [[15, "simulation-schema"]], "Material Parameters": [[15, "material-parameters"]], "Electrolyte": [[15, "electrolyte"], [16, "electrolyte"]], "Electrode": [[15, "electrode"]], "Coating": [[15, "coating"], [16, "coating"]], "Active Material": [[15, "active-material"], [16, "active-material"]], "Interface": [[15, "interface"], [16, "interface"]], "Solid Diffusion": [[15, "solid-diffusion"], [16, "solid-diffusion"]], "Full Solid Diffusion": [[15, "full-solid-diffusion"]], "Binder": [[15, "binder"], [16, "binder"]], "Conducting Additive": [[15, 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solver": [[24, "setup-the-properties-of-the-nonlinear-solver"], [36, "setup-the-properties-of-the-nonlinear-solver"]], "Process output and recover the output voltage and current from the output states.": [[24, "process-output-and-recover-the-output-voltage-and-current-from-the-output-states"]], "Source code for runBatteryP2D": [[25, "source-code-for-runbatteryp2d"]], "Alkaline Membrane Electrolyser": [[26, "alkaline-membrane-electrolyser"]], "Setup input": [[26, "setup-input"]], "Setup model": [[26, "setup-model"]], "Setup the initial condition": [[26, "setup-the-initial-condition"]], "Setup the schedule with the time discretization": [[26, "setup-the-schedule-with-the-time-discretization"]], "Setup the non-linear solver": [[26, "setup-the-non-linear-solver"]], "Visualize the results": [[26, "visualize-the-results"]], "pH distribution plot": [[26, "ph-distribution-plot"]], "Source code for runElectrolyser": [[28, "source-code-for-runelectrolyser"]], "BattMo example Json input": [[29, 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{}})
\ No newline at end of file
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31, "given": 31, "evolut": 31, "farad": 31, "effici": 31, "runprotonicmembran": 33, "particl": 34, "sei": 34, "growth": 34, "runseiactivemateri": 35, "silicon": 36, "graphit": 36, "shortcut": 36, "instanti": 36, "discharg": 36, "perio": 36, "visualis": 36, "runsilicongraphitebatteri": 37, "runthermalmodel": 38, "see": 39, "also": 39, "factori": 39, "fair": 39, "curat": 42, "unit": 43, "convert": 43}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinxcontrib.bibtex": 9, "sphinx.ext.intersphinx": 1, "sphinx": 57}, "alltitles": {"Advanced Usage": [[0, "advanced-usage"]], "BattMo Model Architecture": [[1, "battmo-model-architecture"]], "Basic Usage": [[2, "basic-usage"]], "A First BattMo Model": [[2, "a-first-battmo-model"]], "Define Parameters": 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and Implementation": [[5, "graph-setup-and-implementation"]], "Control models": [[6, "control-models"]], "Json input control interface": [[6, "json-input-control-interface"]], "Control model description": [[6, "control-model-description"]], "Battery Geometries": [[7, "battery-geometries"]], "BatteryGeneratorP2D": [[7, "batterygeneratorp2d"]], "Parameters with values used in plot above": [[7, "id2"], [7, "id3"], [7, "id4"]], "BatteryGeneratorP3D": [[7, "batterygeneratorp3d"]], "BatteryGeneratorP4D": [[7, "batterygeneratorp4d"]], "SpiralBatteryGenerator": [[7, "spiralbatterygenerator"]], "Thickness and discretization number (N) are passed through the dictionaries widthDict and nrDict, with values used in plot above.": [[7, "id5"]], "Other parameters, with values used in plot above.": [[7, "id6"]], "CoinCellBatteryGenerator": [[7, "coincellbatterygenerator"]], "Parameters for each component : thickness, diameter, number of cell layers (Nl), with the values used in the plot above (a CR 2016 coin cell)": [[7, "id7"]], "Other parameters, with values used in plot above": [[7, "id8"], [7, "id10"]], "BatteryGeneratorMultilayerPouch": [[7, "batterygeneratormultilayerpouch"]], "Parameters for each component : thickness and number of cell (Nl) for a layer, with the values used in the plot above": [[7, "id9"]], "BattMo App": [[8, "battmo-app"]], "Calculations": [[9, "calculations"]], "Features": [[10, "features"]], "Use default materials": [[10, "use-default-materials"]], "Define your own materials": [[10, "define-your-own-materials"]], "Visualize your geometry": [[10, "visualize-your-geometry"]], "Download your input data": [[10, "download-your-input-data"]], "Visualize and download your results": [[10, "visualize-and-download-your-results"]], "Troubleshooting": [[11, "troubleshooting"]], "Unnatural artifacts in your results": [[11, "unnatural-artifacts-in-your-results"]], "Welcome": [[12, "welcome"]], "Acknowledgements": [[12, "acknowledgements"]], "Installation and First Steps": [[13, "installation-and-first-steps"]], "Intermediate usage": [[14, "intermediate-usage"]], "Setup a P4D Model using mergeJsonStructs": [[14, "setup-a-p4d-model-using-mergejsonstructs"]], "Visualize Results": [[14, "visualize-results"]], "File links and insertions with parseBattmoJson": [[14, "file-links-and-insertions-with-parsebattmojson"]], "JSON input specification": [[15, "json-input-specification"]], "Simulation Schema": [[15, "simulation-schema"]], "Material Parameters": [[15, "material-parameters"]], "Electrolyte": [[15, "electrolyte"], [16, "electrolyte"]], "Electrode": [[15, "electrode"]], "Coating": [[15, "coating"], [16, "coating"]], "Active Material": [[15, "active-material"], [16, "active-material"]], "Interface": [[15, "interface"], [16, "interface"]], "Solid Diffusion": [[15, "solid-diffusion"], [16, "solid-diffusion"]], "Full Solid Diffusion": [[15, "full-solid-diffusion"]], "Binder": [[15, "binder"], [16, "binder"]], "Conducting Additive": [[15, "conducting-additive"], [16, "conducting-additive"]], "Current Collector": [[15, "current-collector"], [16, "current-collector"]], "Separator": [[15, "separator"], [16, "separator"]], "Thermal Model": [[15, "thermal-model"], [16, "thermal-model"]], "Geometry Setup": [[15, "geometry-setup"]], "Simulation Control Parameters": [[15, "simulation-control-parameters"]], "Time Stepping Parameters": [[15, "time-stepping-parameters"]], "Solver Parameters": [[15, "solver-parameters"]], "Output Parameters": [[15, "output-parameters"]], "Json input example": [[16, "json-input-example"]], "Simulation": [[16, "simulation"], [31, "simulation"]], "Battery": [[16, "battery"]], "Negative Electrode": [[16, "negative-electrode"]], "Positive Electrode": [[16, "positive-electrode"]], "Geometry": [[16, "geometry"], [29, "geometry"]], "Model Specification": [[16, "model-specification"]], "Control": [[16, "control"], [29, "control"]], "Time Stepping": [[16, "time-stepping"]], "State Initialization": [[16, 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"optimization-example"]], "Parameter sets": [[21, "parameter-sets"], [21, "id4"]], "BattMo Tutorial": [[22, "battmo-tutorial"]], "Setting up the environment": [[22, "setting-up-the-environment"], [29, "setting-up-the-environment"]], "Specifying the physical model": [[22, "specifying-the-physical-model"]], "Setting up the geometry": [[22, "setting-up-the-geometry"]], "Initialising the battery model object": [[22, "initialising-the-battery-model-object"]], "Plotting the OCP curves against state of charge": [[22, "plotting-the-ocp-curves-against-state-of-charge"]], "Controlling the simulation": [[22, "controlling-the-simulation"]], "Setting the initial state of the battery": [[22, "setting-the-initial-state-of-the-battery"]], "Running the simulation": [[22, "running-the-simulation"]], "Plotting the results": [[22, "plotting-the-results"]], "Source code for battMoTutorial": [[23, "source-code-for-battmotutorial"]], "Pseudo-Two-Dimensional (P2D) Lithium-Ion Battery Model": [[24, "pseudo-two-dimensional-p2d-lithium-ion-battery-model"]], "Import the required modules from MRST": [[24, "import-the-required-modules-from-mrst"], [34, "import-the-required-modules-from-mrst"], [36, "import-the-required-modules-from-mrst"]], "Setup the properties of Li-ion battery materials and cell design": [[24, "setup-the-properties-of-li-ion-battery-materials-and-cell-design"], [34, "setup-the-properties-of-li-ion-battery-materials-and-cell-design"]], "Setup the geometry and computational grid": [[24, "setup-the-geometry-and-computational-grid"]], "Initialize the battery model.": [[24, "initialize-the-battery-model"]], "Compute the nominal cell capacity and choose a C-Rate": [[24, "compute-the-nominal-cell-capacity-and-choose-a-c-rate"]], "Setup the time step schedule": [[24, "setup-the-time-step-schedule"]], "Setup the initial state of the model": [[24, "setup-the-initial-state-of-the-model"], [36, "setup-the-initial-state-of-the-model"]], "Setup the properties of the nonlinear solver": [[24, "setup-the-properties-of-the-nonlinear-solver"], [36, "setup-the-properties-of-the-nonlinear-solver"]], "Process output and recover the output voltage and current from the output states.": [[24, "process-output-and-recover-the-output-voltage-and-current-from-the-output-states"]], "Source code for runBatteryP2D": [[25, "source-code-for-runbatteryp2d"]], "Alkaline Membrane Electrolyser": [[26, "alkaline-membrane-electrolyser"]], "Setup input": [[26, "setup-input"]], "Setup model": [[26, "setup-model"]], "Setup the initial condition": [[26, "setup-the-initial-condition"]], "Setup the schedule with the time discretization": [[26, "setup-the-schedule-with-the-time-discretization"]], "Setup the non-linear solver": [[26, "setup-the-non-linear-solver"]], "Visualize the results": [[26, "visualize-the-results"]], "pH distribution plot": [[26, "ph-distribution-plot"]], "Source code for runElectrolyser": [[28, "source-code-for-runelectrolyser"]], "BattMo example Json input": [[29, "battmo-example-json-input"]], "We load the json files": [[29, "we-load-the-json-files"]], "Material properties": [[29, "material-properties"]], "Simulation parameters": [[29, "simulation-parameters"]], "Ouput specificiations": [[29, "ouput-specificiations"]], "We start the simulation": [[29, "we-start-the-simulation"]], "Plotting": [[29, "plotting"], [31, "plotting"], [34, "plotting"]], "Source code for runJsonScript": [[30, "source-code-for-runjsonscript"]], "Protonic Membrane model": [[31, "protonic-membrane-model"]], "Model overview": [[31, "model-overview"], [32, "model-overview"]], "Governing equations": [[31, "governing-equations"], [32, "governing-equations"]], "Boundary conditions": [[31, "boundary-conditions"], [32, "boundary-conditions"]], "Load and parse input from given json files": [[31, "load-and-parse-input-from-given-json-files"]], "Input structure setup": [[31, "input-structure-setup"]], "Model setup": [[31, "model-setup"]], "Initial state setup": [[31, "initial-state-setup"]], "Schedule": [[31, "schedule"]], "Evolution of the Faradic efficiency": [[31, "evolution-of-the-faradic-efficiency"]], "Source code for runProtonicMembrane": [[33, "source-code-for-runprotonicmembrane"]], "Particle simulation with SEI layer growth": [[34, "particle-simulation-with-sei-layer-growth"]], "Setup the model": [[34, "setup-the-model"]], "Setup initial state": [[34, "setup-initial-state"]], "Setup schedule": [[34, "setup-schedule"]], "Setup non-linear solver": [[34, "setup-non-linear-solver"]], "Run simulation": [[34, "run-simulation"]], "Source code for runSEIActiveMaterial": [[35, "source-code-for-runseiactivematerial"]], "Composite Silicon Graphite electrode": [[36, "composite-silicon-graphite-electrode"]], "Shortcuts": [[36, "shortcuts"]], "Setup the properties of the battery": [[36, "setup-the-properties-of-the-battery"]], "Model Instantiation": [[36, "model-instantiation"]], "Setup schedule (control and time stepping)": [[36, "setup-schedule-control-and-time-stepping"]], "Run the simulation for the discharge": [[36, "run-the-simulation-for-the-discharge"]], "Setup charge schedule": [[36, "setup-charge-schedule"]], "Run the simulation for the charge perios": [[36, "run-the-simulation-for-the-charge-perios"]], "Visualisation": [[36, "visualisation"]], "Source code for runSiliconGraphiteBattery": [[37, "source-code-for-runsilicongraphitebattery"]], "runThermalModel": [[38, "runthermalmodel"]], "See Also": [[39, "see-also"]], "MRST": [[39, "mrst"]], "Visualization Tutorial": [[39, "visualization"]], "Grid Factory Tutorial": [[39, "id2"]], "FAIR Data": [[39, "fair-data"]], "Solid Diffusion Models": [[40, "solid-diffusion-models"]], "Thermal Simulation": [[41, "thermal-simulation"]], "List of curated examples": [[42, "list-of-curated-examples"]], "Units": [[43, "units"]], "Converting units in BattMo": [[43, "converting-units-in-battmo"]], "Units and JSON input": [[43, "units-and-json-input"]]}, "indexentries": 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