added toctrees

Author: piotrkluba

docs/02.simulation-setup/01.flow-conditions/README.md

@@ -18,4 +18,11 @@
 
 ### **[Farfield](./02.farfield.md)**
 
-*Settings governing the farfield generation or identification.*
+*Settings governing the farfield generation or identification.*
+
+```{toctree}
+:hidden:
+:maxdepth: 3
+./01.operating-condition.md
+./02.farfield.md
+```

docs/02.simulation-setup/02.mesh/03.refinements/README.md

@@ -143,4 +143,16 @@ meshing=MeshingParams(
     ]
 )
 ```
-</details> 
+</details> 
+
+
+```{toctree}
+:hidden:
+:maxdepth: 3
+./01.surface-edge-refinement.md
+./02.surface-refinement.md
+./03.boundary-layer-refinement.md
+./04.passive-spacing.md
+./05.uniform-refinement.md
+./06.axisymmetric-refinement.md
+```

docs/02.simulation-setup/02.mesh/README.md

@@ -31,4 +31,12 @@ A section for defining the meshing settings.
 - **[Boundary Layer Refinement](./03.refinements/03.boundary-layer-refinement.md)** - Creates prismatic layers near walls
 - **[Passive Spacing](./03.refinements/04.passive-spacing.md)** - Controls mesh behavior without direct refinement
 - **[Uniform Refinement](./03.refinements/05.uniform-refinement.md)** - Creates uniform mesh spacing in a region
-- **[Axisymmetric Refinement](./03.refinements/06.axisymmetric-refinement.md)** - Creates structured-like mesh with cylindrical bias
+- **[Axisymmetric Refinement](./03.refinements/06.axisymmetric-refinement.md)** - Creates structured-like mesh with cylindrical bias
+
+```{toctree}
+:hidden:
+:maxdepth: 3
+./01.mesh.md
+./02.rotation-regions.md
+./03.refinements/README.md
+```

docs/02.simulation-setup/03.flow-solver/01.boundary-conditions/README.md

@@ -18,4 +18,17 @@ Boundary conditions specify how the fluid behaves at the boundaries of the simul
 
 Additionally, [Turbulence Quantities](./08.turbulence-quantities.md) are used to specify turbulence parameters at all types of boundaries, such as Turbulence Intensity, Eddy Viscosity Ratio, Length Scale, etc.
 
-Click on each boundary condition type to see detailed documentation including available parameters, descriptions, usage tips, and example configurations. 
+Click on each boundary condition type to see detailed documentation including available parameters, descriptions, usage tips, and example configurations.
+
+```{toctree}
+:hidden:
+:maxdepth: 3
+./01.wall.md
+./02.freestream.md
+./03.inflow.md
+./04.outflow.md
+./05.periodic.md
+./06.symmetry.md
+./07.slip-wall.md
+./08.turbulence-quantities.md
+``` 

docs/02.simulation-setup/03.flow-solver/03.physics/01.fluid/README.md

@@ -59,4 +59,14 @@ The Fluid model is used in virtually all Flow360 simulations, including:
 - For most aerospace applications, the Spalart-Allmaras turbulence model provides a good balance of accuracy and efficiency
 - Consider enabling the transition model for flows at moderate Reynolds numbers where transition location significantly impacts results
 - For challenging simulations, start with more robust settings (lower CFL, higher gradient limiters) and then relax these constraints as the solution develops
-- Remember that fluid properties (viscosity, etc.) must be specified in the Operating Condition section, not in the Fluid model 
+- Remember that fluid properties (viscosity, etc.) must be specified in the Operating Condition section, not in the Fluid model
+
+```{toctree}
+:hidden:
+:maxdepth: 3
+./01.navier-stokes-solver.md
+./02.turbulence-model.md
+./03.transition-model.md
+./04.initial-condition.md
+``` 
+

docs/02.simulation-setup/03.flow-solver/03.physics/02.solid/README.md

@@ -53,4 +53,12 @@ The Solid model is used in conjugate heat transfer simulations, including:
 - Ensure all material properties are specified in consistent units.
 - When using patterns in entities, verify all matched volumes are intended for heat transfer simulation.
 - Consider mesh resolution near areas with high temperature gradients.
-- For conjugate heat transfer, ensure proper interface matching with fluid regions. 
+- For conjugate heat transfer, ensure proper interface matching with fluid regions.
+
+```{toctree}
+:hidden:
+:maxdepth: 3
+./01.heat-equation-solver.md
+./02.material.md
+./03.initial-condition.md
+``` 

docs/02.simulation-setup/03.flow-solver/03.physics/README.md

@@ -13,7 +13,7 @@
 | **[Actuator disk](./05.actuator-disk.md)** | Simplified model for propellers and rotors | Thrust coefficient, Swirl distribution |
 | **[Porous medium](./06.porous-medium.md)** | Model for flow through porous regions | Darcy coefficient, Forchheimer coefficient |
 
-Click on each model to see detailed documentation including available parameters, descriptions, usage tips, and example configurations. 
+Click on each model to see detailed documentation including available parameters, descriptions, usage tips, and example configurations.
 
 ---
 
@@ -72,3 +72,13 @@ Click on each model to see detailed documentation including available parameters
 
 *Advanced modeling of flow through porous regions including filters, heat exchangers, and porous materials. Implements Darcy-Forchheimer theory with comprehensive coefficient specification for accurate pressure drop and flow distribution prediction.*
 
+```{toctree}
+:hidden:
+:maxdepth: 3
+./01.fluid/README.md
+./02.solid/README.md
+./03.rotation.md
+./04.bet-disk.md
+./05.actuator-disk.md
+./06.porous-medium.md
+``` 

docs/02.simulation-setup/03.flow-solver/README.md

@@ -49,3 +49,11 @@ A section for setting the solver numerics and domain boundary conditions.
 *Advanced capability for implementing custom time-dependent motion of simulation components. Enables complex trajectories, rotations, and dynamic interactions between aerodynamic forces and component movement. Currently optimized for Python API implementation with enhanced debugging and flexibility for sophisticated dynamic scenarios.*
 
 
+```{toctree}
+:hidden:
+:maxdepth: 3
+./01.boundary-conditions/README.md
+./02.time.md
+./03.physics/README.md
+./04.user-defined-dynamics.md
+```

docs/02.simulation-setup/04.output/02.outputs-list/README.md

@@ -159,3 +159,21 @@ User defined expressions with dimensions. By default, the following expressions
 
 ---
 
+```{toctree}
+:hidden:
+:maxdepth: 3
+./01.volume-output.md
+./02.time-averaging-volume-output.md
+./03.surface-output.md
+./04.time-averaging-surface-output.md
+./05.slice-output.md
+./06.time-averaging-slice-output.md
+./07.probe-outputs.md
+./08.Time-averaging-probe-outputs.md
+./09.surface-probe-outputs.md
+./10.surface-slice-output.md
+./11.isosurface-output.md
+./12.time-averaging-isosurface-output.md
+./13.aeroacoustic-output.md
+./15.streamline-output.md
+```

docs/02.simulation-setup/04.output/README.md

@@ -36,4 +36,12 @@
 - **[Time-averaging Isosurface Output](./02.outputs-list/12.time-averaging-isosurface-output.md)** - Time-averaged flow field data on surfaces of constant variable value
 - **[Aeroacoustic Output](./02.outputs-list/13.aeroacoustic-output.md)** - Data for aeroacoustic analysis at observer positions
 - **[Output Formats](./02.outputs-list/14.output-formats.md)** - File format specifications for output data
-- **[Streamline Output](./02.outputs-list/15.streamline-output.md)** - Visualization of 3D flow structures 
+- **[Streamline Output](./02.outputs-list/15.streamline-output.md)** - Visualization of 3D flow structures
+
+```{toctree}
+:hidden:
+:maxdepth: 3
+./01.reference-dimensions.md
+./02.outputs-list/README.md
+``` 
+