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Fix Doxygen example structure
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‎example/Numerics/2D_ActiveFluid/main.cpp‎

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@@ -2,9 +2,16 @@
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// Created by Abhinav Singh on 15.03.20.
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//
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/*!
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* \file Two_dim_ActiveFluid/main.cpp
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* \page ActiveFluid Active Fluid
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*
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* \subpage Two_dim_ActiveFluid
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*/
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/*!
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* @file 2D_ActiveFluid/main.cpp
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* @page ActiveFluid ActiveFluid
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* \page Two_dim_ActiveFluid 2D Active Fluid
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*
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* ##A Two Dimensional Active Fluid Solver##
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*
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*/
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/**
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* @page ActiveFluid ActiveFluid
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* \page Two_dim_ActiveFluid 2D Active Fluid
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*
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* ## Including the headers ## {#active_c1_include}
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*
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* These are the header files that we need to include:
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*
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* @snippet example/Numerics/2D_ActiveFluid/main.cpp active1Include
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* @snippet example/Numerics/Two_dim_ActiveFluid/main.cpp active1Include
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*
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*/
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//! @cond [active1Include] @endcond
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//! @cond [active1Include] @endcond
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/**
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* @page ActiveFluid ActiveFluid
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* \page Two_dim_ActiveFluid 2D Active Fluid
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*
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* ## Initialization of the global parameters## {#active_c_init}
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*
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* dist_vector_type as the 2d openfpm distributed vector type
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* dist_vector_type as the 2d openfpm distributed subset vector type
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*
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* @snippet example/Numerics/2D_ActiveFluid/main.cpp Init1active
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* @snippet example/Numerics/Two_dim_ActiveFluid/main.cpp Init1active
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*
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*/
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@@ -109,7 +116,7 @@ typedef vector_dist_ws<2, double,Activegels> vector_type;
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typedef vector_dist_subset<2, double, Activegels> vector_type2;
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//! @cond [Init1active] @endcond
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/**
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* @page ActiveFluid ActiveFluid
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* \page Two_dim_ActiveFluid 2D Active Fluid
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*
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* ## Creating the RHS Functor## {#active_c1_rhs}
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*
@@ -131,7 +138,7 @@ typedef vector_dist_subset<2, double, Activegels> vector_type2;
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* We do our computations as required.
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* Then we copy back the output into the state_type dxdt)
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*
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* @snippet example/Numerics/2D_ActiveFluid/main.cpp RHSActiveFunctor
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* @snippet example/Numerics/Two_dim_ActiveFluid/main.cpp RHSActiveFunctor
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*
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*/
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//! @cond [RHSActiveFunctor] @endcond
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//! @cond [RHSActiveFunctor] @endcond
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/**
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* @page ActiveFluid ActiveFluid
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* \page Two_dim_ActiveFluid 2D Active Fluid
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*
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* ## Creating the Observer Functor## {#ode_c2_obs}
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*
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* We do our computations as required.
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* Then we copy back the output into the state_type dxdt.
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*
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* @snippet example/Numerics/2D_ActiveFluid/main.cpp ActiveObserver2Functor
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* @snippet example/Numerics/Two_dim_ActiveFluid/main.cpp ActiveObserver2Functor
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*
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*/
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//! @cond [ActiveObserver2Functor] @endcond
@@ -581,14 +588,14 @@ struct CalcVelocity
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};
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//! @cond [ActiveObserver2Functor] @endcond
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/**
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* @page ActiveFluid ActiveFluid
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* \page Two_dim_ActiveFluid 2D Active Fluid
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*
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* ## Initializating OpenFPM ## {#Active_c2_initmain}
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*
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* We start with
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* * Initializing OpenFPM
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*
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* @snippet example/Numerics/2D_ActiveFluid/main.cpp ActiveInit
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* @snippet example/Numerics/Two_dim_ActiveFluid/main.cpp ActiveInit
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*
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*/
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//! @cond [ActiveInit] @endcond
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V_err_eps = 5e-4;
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//! @cond [ActiveInit] @endcond
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/**
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* @page ActiveFluid ActiveFluid
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* \page Two_dim_ActiveFluid 2D Active Fluid
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*
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* ## Creating Particles and assigning subsets ## {#odeint_c2_indices}
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*
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* \cos \big(2\pi (\cos\left(\frac{2 x - L_x}{ L_x}\right)-\sin\left(\frac{2 y - L_y}{ L_y}\right)\big)
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* \end{matrix}\right)
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* @f]
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* @snippet example/Numerics/2D_ActiveFluid/main.cpp initActSubset
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* @snippet example/Numerics/Two_dim_ActiveFluid/main.cpp initActSubset
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*
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*/
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//! @cond [initActSubset] @endcond
@@ -672,7 +679,7 @@ int main(int argc, char* argv[])
672679
Particles.ghost_get<POLARIZATION,EXTFORCE,DELMU>(SKIP_LABELLING);
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//! @cond [initActSubset] @endcond
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/**
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* @page ActiveFluid ActiveFluid
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* \page Two_dim_ActiveFluid 2D Active Fluid
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*
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* ## Create the subset, differential operators, steppers and Cast Global Pointers ## {#Active_c2_point}
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*
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*
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* We create DCPSE based operators and alias the particle properties.
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*
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* @snippet example/Numerics/2D_ActiveFluid/main.cpp Pointer2Act
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* @snippet example/Numerics/Two_dim_ActiveFluid/main.cpp Pointer2Act
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*
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*/
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//! @cond [Pointer2Act] @endcond
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double V_err = 1, V_err_old;
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double tim=0;
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/**
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* @page ActiveFluid ActiveFluid
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* \page Two_dim_ActiveFluid 2D Active Fluid
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*
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* ## Calling Odeint ## {#odeint_actc2_1211}
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* We initiliaze the time variable t, step_size dt and final time tf.
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*
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* We finally deallocate the DCPSE operators and finalize the library.
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*
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* @snippet example/Numerics/2D_ActiveFluid/main.cpp ActintTCall
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* @snippet example/Numerics/Two_dim_ActiveFluid/main.cpp ActintTCall
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*
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*/
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////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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}
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/**
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* @page ActiveFluid ActiveFluid
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* \page Two_dim_ActiveFluid 2D Active Fluid
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*
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* ## Full code ## {#actint_c2_full}
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*
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* @include example/Numerics/2D_ActiveFluid/main.cpp
811-
*/
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* @include example/Numerics/Two_dim_ActiveFluid/main.cpp
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*/

‎example/Numerics/Closest_point/0_sphere_redistancing/main.cpp‎

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}
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/**
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* @page example_closest_point ClosestPoint Redistancing
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* @page example_closest_point_sphere Redistancing a sphere given as indicator function
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*
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* ## Full code ## {#e2d_c_full}
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*

‎example/Numerics/PS-CMA-ES/main.cpp‎

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*
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* \page Numerics Numerics
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* \subpage PS_CMA_ES
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* \subpage Vortex_in_cell_petsc
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* \subpage Vortex_in_cell
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* \subpage Odeint
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* \subpage Stokes_flow
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* \subpage Examples_ClosestPoint
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* \subpage Examples_SussmanRedistancing
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* \subpage ActiveFluid
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*
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* \page PS_CMA_ES Particle swarm CMA-ES Evolution strategy
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}
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#endif
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‎example/Numerics/Vortex_in_cell/main_vic_petsc.cpp‎

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/**
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* @file Vortex_in_cell/main_vic_petsc.cpp
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* @page Vortex_in_cell Vortex in cell
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*
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* @subpage Vortex_in_cell_petsc
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* @subpage Vortex_in_cell_petsc_opt
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*
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*
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*/
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/*! \page Vortex_in_cell_petsc Vortex in Cell 3D
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*
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* # Vortex in Cell 3D ring with ringlets # {#vic_ringlets}

‎example/SparseGrid/10_heat_conduction_reticulate_porous_ceramics/main.cu‎

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//
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/*!
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*
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* \page 10_heat_conduction_RPC Heat conduction in reticulate porous ceramics using sparse grids on GPU
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* \page heat_conduction_RPC Heat conduction in reticulate porous ceramics using sparse grids on GPU
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*
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* [TOC]
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*
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* # Solving heat conduction in the image-based geometry of reticulate porous ceramics # {#e10_heat_conduction_RPC_gpu}
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* # Solving heat conduction in the image-based geometry of reticulate porous ceramics # {#eheat_conduction_RPC_gpu}
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*
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* In this example, we simulate heat conduction in the solid phase of reticulate porous ceramics with heat dissipation at the surface. For the complete image-based simulation pipeline and performance of this simulation, we refer to
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* <a href="https://doi.org/10.1016/j.jocs.2023.102118">J. Stark, I. F. Sbalzarini "An open-source pipeline for solving continuous reaction-diffusion models in image-based geometries of porous media", Journal of Computational Science (2023).</a>

‎example/SparseGrid/1_gray_scott_3d_sparse/main.cpp‎

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* \subpage Grid_3_gs_3D_sparse_gpu_opt
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* \subpage Grid_3_gs_3D_sparse_cs
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* \subpage Grid_3_gs_3D_sparse_gpu_cs
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* \subpage Grid_3_gs_3D_sparse_gpu_cs_opt
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* \subpage Grid_3_gs_3D_sparse_gpu_cs_exp
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* \subpage inhomogeneous_diffusion_porous_catalyst_CaCO3
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* \subpage heat_conduction_RPC
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*
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*/
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/*!
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*
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* \page Grid_3_gs_3D_sparse Gray Scott in\subpage Grid_3_gs_3D_sparse_opt 3D using sparse grids
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* \page Grid_3_gs_3D_sparse Gray Scott in 3D using sparse grids on CPU
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*
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* [TOC]
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*
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//! \cond [time stepping] \endcond
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/*!
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* \page Grid_3_gs_3D_sparse Gray Scott in 3D
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* \page Grid_3_gs_3D_sparse Gray Scott in 3D using sparse grids on CPU
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*
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* ## Finalize ##
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*
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//! \cond [finalize] \endcond
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/*!
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* \page Grid_3_gs_3D_sparse Gray Scott in 3D
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* \page Grid_3_gs_3D_sparse Gray Scott in 3D using sparse grids on CPU
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*
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* # Full code # {#code}
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*

‎example/SparseGrid/2_gray_scott_3d_sparse_opt/main.cpp‎

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/*!
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*
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* \page Grid_3_gs_3D_sparse_opt Gray Scott in 3D using sparse grids optimized on CPU
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* \page Grid_3_gs_3D_sparse_opt Gray Scott in 3D using sparse grids on CPU (Optimized)
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*
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* [TOC]
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*
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* # Solving a gray scott-system in 3D using sparse grids optimized on CPU # {#e3_gs_gray_scott_opt}
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* # Solving a gray scott-system in 3D using sparse grids on CPU (Optimized) # {#e3_gs_gray_scott_opt}
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*
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* This example show how to solve a Gray-Scott system in 3D using sparse grids in an optimized way
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*
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//! \cond [time stepping] \endcond
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/*!
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* \page Grid_3_gs_3D_sparse_opt Gray Scott in 3D using sparse grids optimized on CPU
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* \page Grid_3_gs_3D_sparse_opt Gray Scott in 3D using sparse grids on CPU (Optimized)
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*
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* ## Finalize ##
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*
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//! \cond [finalize] \endcond
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/*!
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* \page Grid_3_gs_3D_sparse_opt Gray Scott in 3D using sparse grids optimized on CPU
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* \page Grid_3_gs_3D_sparse_opt Gray Scott in 3D using sparse grids on CPU (Optimized)
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*
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* # Full code # {#code}
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*

‎example/SparseGrid/3_gray_scott_3d_sparse_gpu_cs/main.cu‎

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/*!
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*
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* \page Grid_3_gs_3D_sparse_gpu_cs Gray Scott in 3D using sparse grids on gpu in complex geometry
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* \page Grid_3_gs_3D_sparse_gpu_cs Gray Scott in 3D using sparse grids on GPU in complex geometry
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*
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* [TOC]
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*
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//! \cond [time stepping] \endcond
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/*!
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* \page Grid_3_gs_3D_sparse_gpu_cs Gray Scott in 3D using sparse grids on gpu in complex geometry
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* \page Grid_3_gs_3D_sparse_gpu_cs Gray Scott in 3D using sparse grids on GPU in complex geometry
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*
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* ## Finalize ##
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*
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//! \cond [finalize] \endcond
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/*!
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* \page Grid_3_gs_3D_sparse_gpu_cs Gray Scott in 3D using sparse grids on gpu in complex geometry
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* \page Grid_3_gs_3D_sparse_gpu_cs Gray Scott in 3D using sparse grids on GPU in complex geometry
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*
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* # Full code # {#code}
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*

‎example/SparseGrid/3_gray_scott_3d_sparse_gpu_cs_opt/main.cu‎

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/*!
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*
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* \page Grid_3_gs_3D_sparse_gpu_cs_opt Gray Scott in 3D using sparse grids on gpu in complex geometry
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* \page Grid_3_gs_3D_sparse_gpu_cs_opt Gray Scott in 3D using sparse grids on GPU in complex geometry (Optimized)
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*
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* [TOC]
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*
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//! \cond [time stepping] \endcond
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/*!
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* \page Grid_3_gs_3D_sparse_gpu_cs Gray Scott in 3D using sparse grids on gpu in complex geometry
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* \page Grid_3_gs_3D_sparse_gpu_cs_opt Gray Scott in 3D using sparse grids on GPU in complex geometry (Optimized)
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*
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* ## Finalize ##
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*
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//! \cond [finalize] \endcond
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/*!
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* \page Grid_3_gs_3D_sparse_gpu_cs Gray Scott in 3D using sparse grids on gpu in complex geometry
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* \page Grid_3_gs_3D_sparse_gpu_cs_opt Gray Scott in 3D using sparse grids on GPU in complex geometry (Optimized)
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*
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* # Full code # {#code}
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*

‎example/SparseGrid/7_gray_scott_3d_sparse_gpu_sphere_expanding/main.cu‎

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/*!
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*
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* \page Grid_3_gs_3D_sparse_gpu_cs Gray Scott in 3D using sparse grids on gpu in complex geometry
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* \page Grid_3_gs_3D_sparse_gpu_cs_exp Gray Scott in 3D using sparse grids on GPU in expanding complex geometry
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*
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* [TOC]
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*
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//! \cond [time stepping] \endcond
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/*!
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* \page Grid_3_gs_3D_sparse_gpu_cs Gray Scott in 3D using sparse grids on gpu in complex geometry
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* \page Grid_3_gs_3D_sparse_gpu_cs_exp Gray Scott in 3D using sparse grids on GPU in expanding complex geometry
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*
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* ## Finalize ##
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*
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//! \cond [finalize] \endcond
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/*!
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* \page Grid_3_gs_3D_sparse_gpu_cs Gray Scott in 3D using sparse grids on gpu in complex geometry
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* \page Grid_3_gs_3D_sparse_gpu_cs_exp Gray Scott in 3D using sparse grids on GPU in expanding complex geometry
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*
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* # Full code # {#code}
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*

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