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Commit 05dc7fbe authored by Pietro Incardona's avatar Pietro Incardona
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Merge branch 'develop' of git.mpi-cbg.de:openfpm/openfpm_pdata into develop

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example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp
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......@@ -2,10 +2,10 @@
// Created by jstark on 2020-05-18.
//
/**
* @file example_sussman_circle/main.cpp
* @file example_sussman_disk/main.cpp
* @page Examples_SussmanRedistancing Examples Sussman Redistancing
*
* @subpage example_sussman_circle
* @subpage example_sussman_disk
* @subpage example_sussman_sphere
* @subpage example_sussman_images_2D
* @subpage example_sussman_images_3D
......@@ -44,19 +44,19 @@
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Circle 2D
*
* # Get the signed distance function for a 2D circle via Sussman Redistancing #
* # Get the signed distance function for a 2D disk via Sussman Redistancing #
*
* In this example, we perform Sussman redistancing on a filled 2D circle. Here, the circle is constructed via
* In this example, we perform Sussman redistancing on a 2D disk. Here, the disk is constructed via
* equation. For image based reconstruction and redistancing see @ref example_sussman_images_2D.
*
* A filled circle with center a, b can be constructed by the following equation:
* A disk with center a, b can be constructed by the following equation:
*
*
* @f[ (x-a)^2 + (y-b)^2 <= r^2 @f]
*
* We will create a filled circle on a 2D grid, where the circle is represented by a -1/+1 step function
* We will create a disk on a 2D grid, where the disk is represented by a -1/+1 step function
* (indicator function) as:
*
* @f[ \phi_{\text{indicator}} = \begin{cases}
......@@ -75,14 +75,14 @@
*
* Once we have received the Phi_SDF from the redistancing, particles can be placed on narrow band around the interface.
*
* * Creates filled 2D circle with -1/+1 indicator function
* * Creates 2D disk with -1/+1 indicator function
* * Runs Sussman redistancing (see @ref RedistancingSussman.hpp)
* * Places particles on narrow band around interface
*
* Output:
* print on promt : Iteration, Change, Residual (see: #DistFromSol::change, #DistFromSol::residual)
* writes vtk and hdf5 files of:
* 1.) 2D grid with circle pre-redistancing and post-redistancing (Phi_0 and Phi_SDF, respectively)
* 1.) 2D grid with disk pre-redistancing and post-redistancing (Phi_0 and Phi_SDF, respectively)
* 2.) particles on narrow band around interface
*
* ## Visualization of example output in Paraview ##
......@@ -92,13 +92,13 @@
*/
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Circle 2D
*
* ## Include ## {#e2d_c_include}
*
* These are the header files that we need to include:
*
* @snippet example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp Include
* @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Include
*
*/
//! @cond [Include] @endcond
......@@ -107,11 +107,11 @@
#include "util/PathsAndFiles.hpp"
#include "level_set/redistancing_Sussman/RedistancingSussman.hpp"
#include "level_set/redistancing_Sussman/NarrowBand.hpp"
#include "Draw/DrawCircle.hpp"
#include "Draw/DrawDisk.hpp"
//! @cond [Include] @endcond
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Circle 2D
*
* ## Initialization and output folder ## {#e2d_c_init}
*
......@@ -119,7 +119,7 @@
* * Initializing OpenFPM
* * Setting the output path and creating an output folder
*
* @snippet example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp Initialization and output folder
* @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Initialization and output folder
*
*/
//! @cond [Initialization and output folder] @endcond
......@@ -130,13 +130,13 @@ int main(int argc, char* argv[])
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// Set current working directory, define output paths and create folders where output will be saved
std::string cwd = get_cwd();
const std::string path_output = cwd + "/output_circle";
const std::string path_output = cwd + "/output_disk";
create_directory_if_not_exist(path_output);
//! @cond [Initialization and output folder] @endcond
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Circle 2D
*
* ## Indices for the grid ## {#e2d_c_indices}
*
......@@ -145,7 +145,7 @@ int main(int argc, char* argv[])
* * \p y: Second dimension
* * \p Phi_0_grid: Index of property that stores the initial level-set-function
* * \p Phi_SDF_grid: Index of property where the redistancing result should be written to
* @snippet example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp Indices grid
* @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Indices grid
*
*/
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
......@@ -161,7 +161,7 @@ int main(int argc, char* argv[])
//! @cond [Indices grid] @endcond
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Circle 2D
*
* ## Create the grid ## {#e2d_c_grid}
*
......@@ -173,7 +173,7 @@ int main(int argc, char* argv[])
* the post-redistancing Phi_SDF should be written to.
* * Set some property names (optionally. These names show up when opening the grid vtk in Paraview.)
*
* @snippet example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp Grid creation
* @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Grid creation
*
*/
//! @cond [Grid creation] @endcond
......@@ -191,13 +191,13 @@ int main(int argc, char* argv[])
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Circle 2D
*
* ## Get filled circle on the grid ## {#e2d_c_getcircle}
* ## Get disk on the grid ## {#e2d_c_getdisk}
*
*
* On the grid that we have just created, we can now initialize Phi_0 as a filled circle of defined radius.
* The center of the circle is passed as x_center and y_center (see @ref Circle.hpp). Phi_0 will then be:
* On the grid that we have just created, we can now initialize Phi_0 as a disk of defined radius.
* The center of the disk is passed as x_center and y_center (see @ref Circle.hpp). Phi_0 will then be:
*
* @f[ \phi_{\text{indicator}} = \begin{cases}
* +1 & \text{point lies inside the object} \\
......@@ -206,49 +206,49 @@ int main(int argc, char* argv[])
* \end{cases} @f]
*
* Optionally, we can save this initial grid as a vtk file, if we want to visualize and check it in Paraview.
* @snippet example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp Get circle
* @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Get disk
*/
//! @cond [Get circle] @endcond
// Now we initialize the grid with a filled circle. Outside the circle, the value of Phi_0 will be -1, inside +1.
double radius = 1.0; // Radius of the circle
init_grid_with_circle<Phi_0_grid>(g_dist, radius, 2.5, 2.5); // Initialize circle onto grid, centered at (2.5, 2.5)
//! @cond [Get disk] @endcond
// Now we initialize the grid with a disk. Outside the disk, the value of Phi_0 will be -1, inside +1.
double radius = 1.0; // Radius of the disk
init_grid_with_disk<Phi_0_grid>(g_dist, radius, 2.5, 2.5); // Initialize disk onto grid, centered at (2.5, 2.5)
g_dist.write(path_output + "/grid_circle_preRedistancing_radius" + std::to_string((int)radius) , FORMAT_BINARY); // Save the circle as vtk file
//! @cond [Get circle] @endcond
g_dist.write(path_output + "/grid_disk_preRedistancing_radius" + std::to_string((int)radius) , FORMAT_BINARY); // Save the disk as vtk file
//! @cond [Get disk] @endcond
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Disk 2D
*
* ## Set the redistancing options ## {#e2d_c_redistoptions}
*
* For the redistancing, we can choose some options. These options will then be passed bundled as a structure to
* the redistancing function. Setting these options is optional, since they all have a Default value as well. In
* particular the following options can be set by the user:
* * \p min_iter: Minimum number of iterations before steady state in narrow band will be checked (Default: 100).
* * \p min_iter: Minimum number of iterations before steady state in narrow band will be checked (Default: 1e5).
* * \p max_iter: Maximum number of iterations you want to run the redistancing, even if steady state might not yet
* have been reached (Default: 1e6).
* * \p convTolChange.value: Convolution tolerance for the normalized total change of Phi in the narrow band between
* two consecutive iterations (Default: 1e-6).
* * \p convTolChange.check: Set true, if you want to use the normalized total change between two iterations as
* have been reached (Default: 1e12).
* * \p convTolChange.value: Convergence tolerance for the maximal change of Phi within the narrow band between
* two consecutive iterations (Default: 1e-15).
* * \p convTolChange.check: Set true, if you want to use the maximal change of Phi between two iterations as
* measure of how close you are to the steady state solution. Redistancing will then stop
* if convTolChange.value is reached or if the current iteration is bigger than max_iter.
* * \p convTolResidual.value: Convolution tolerance for the residual, that is abs(magnitude gradient of phi - 1) of
* Phi in the narrow band (Default 1e-1).
* * \p convTolResidual.value: Convergence tolerance for the residual, that is max{abs(magnitude gradient of phi -
* 1)} of Phi in the narrow band (Default 1e-3).
* * \p convTolResidual.check: Set true, if you want to use the residual of the current iteration as measure of how
* close you are to the steady state solution. Redistancing will then stop if
* convTolResidual.value is reached or if the current iteration is bigger than max_iter.
* * \p interval_check_convergence: Interval of #iterations at which convergence to steady state is checked
* (Default: 100).
* * \p width_NB_in_grid_points: Width of narrow band in number of grid points. Must be at least 4, in order to
* have at least 2 grid points on each side of the interface. Is automatically set
* * \p width_NB_in_grid_points: Width of narrow band in number of grid points. Must be at least 4, in order to
* have at least 2 grid points on each side of the interface. Is automatically set
* to 4, if a value smaller than 4 is chosen (Default: 4).
* * \p print_current_iterChangeResidual: If true, the number of the current iteration, the corresponding change
* w.r.t the previous iteration and the residual is printed (Default: false).
* * \p print_steadyState_iter: If true, the number of the steady-state-iteration, the corresponding change
* w.r.t the previous iteration and the residual is printed (Default: false).
*
* @snippet example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp Redistancing options
* @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Redistancing options
*/
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//! @cond [Redistancing options] @endcond
......@@ -270,7 +270,7 @@ int main(int argc, char* argv[])
//! @cond [Redistancing options] @endcond
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Disk 2D
*
* ## Run the redistancing ## {#e2d_c_runredist}
*
......@@ -287,7 +287,7 @@ int main(int argc, char* argv[])
* containing the signed distance function in Prop. 2. The vtk-file can be opened in Paraview. If we want, we can
* further save the result as hdf5 file that can be reloaded onto an openFPM grid.
*
* @snippet example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp Run redistancing
* @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Run redistancing
*/
//! @cond [Run redistancing] @endcond
RedistancingSussman<grid_in_type> redist_obj(g_dist, redist_options); // Instantiation of Sussman-redistancing class
......@@ -296,13 +296,13 @@ int main(int argc, char* argv[])
// where the resulting SDF should be written to.
redist_obj.run_redistancing<Phi_0_grid, Phi_SDF_grid>();
g_dist.write(path_output + "/grid_circle_postRedistancing", FORMAT_BINARY); // Save the result as vtk file
g_dist.save(path_output + "/grid_circle_postRedistancing" + ".bin"); // Save the result as hdf5 file that can be
g_dist.write(path_output + "/grid_disk_postRedistancing", FORMAT_BINARY); // Save the result as vtk file
g_dist.save(path_output + "/grid_disk_postRedistancing" + ".bin"); // Save the result as hdf5 file that can be
// reloaded onto an openFPM grid
//! @cond [Run redistancing] @endcond
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Disk 2D
*
* ## Initialize empty vector for narrow band particles ## {#e2d_c_initnbvector}
*
......@@ -313,7 +313,7 @@ int main(int argc, char* argv[])
* one, but you can have particles with arbitrary many properties, depending on what you want to use them for
* later on. Here, we exemplarily define 3 properties.
*
* @snippet example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp Initialize narrow band
* @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Initialize narrow band
*/
//! @cond [Initialize narrow band] @endcond
// Get narrow band: Place particles on interface (narrow band width e.g. 2 grid points on each side of the interface)
......@@ -322,7 +322,7 @@ int main(int argc, char* argv[])
// Minimum is 1 property, to which the Phi_SDF can be written
// In this example we chose 3 properties. The 1st for the Phi_SDF, the 2nd for the gradient of phi and the 3rd for
// the magnitude of the gradient
typedef aggregate<double, Point<grid_dim, double>, double> props_nb;
typedef aggregate<double, double[grid_dim], double> props_nb;
typedef vector_dist<grid_dim, double, props_nb> vd_type;
Ghost<grid_dim, double> ghost_vd(0);
vd_type vd_narrow_band(0, box, bc, ghost_vd);
......@@ -330,7 +330,7 @@ int main(int argc, char* argv[])
//! @cond [Initialize narrow band] @endcond
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Disk 2D
*
* ## Instantiate narrow band ## {#e2d_c_instnarrowband}
*
......@@ -345,7 +345,7 @@ int main(int argc, char* argv[])
* grid points (size_t), physical width (double) or extension of narrow band as physical width inside of object
* and outside the object (double, double).
*
* @snippet example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp Instantiate narrow band
* @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Instantiate narrow band
*/
//! @cond [Instantiate narrow band] @endcond
size_t thickness_of_narrowBand_in_grid_points = 6;
......@@ -353,14 +353,14 @@ int main(int argc, char* argv[])
//! @cond [Instantiate narrow band] @endcond
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Disk 2D
*
* ## Indices for the narrow band vector ## {#e2d_c_indices}
*
* Again, we can define some indices for better code readability. This is just an example, you may want to choose
* different names and have a different number of properties thus different number of indices.
*
* @snippet example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp Indices narrow band
* @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Indices narrow band
*
*/
//////////////////////////////////////////////////////////////////////////////////////////////
......@@ -372,7 +372,7 @@ int main(int argc, char* argv[])
//! @cond [Indices narrow band] @endcond
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Disk 2D
*
* ## Fill the vector with particles placed within a narrow band around the interface ## {#e2d_c_getnarrowband}
*
......@@ -391,7 +391,7 @@ int main(int argc, char* argv[])
*
* We save the particles in a vtk file (open in Paraview) and as hdf5 file (can be loaded back on particles).
*
* @snippet example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp Get narrow band
* @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Get narrow band
*/
// Get the narrow band. You can decide, if you only want the Phi_SDF saved to your particles or
// if you also want the gradients or gradients and magnitude of gradient.
......@@ -403,18 +403,18 @@ int main(int argc, char* argv[])
//! @cond [Get narrow band] @endcond
narrowBand.get_narrow_band<Phi_SDF_grid, Phi_SDF_vd, Phi_grad_vd, Phi_magnOfGrad_vd>(g_dist, vd_narrow_band);
vd_narrow_band.write(path_output + "/vd_narrow_band_circle", FORMAT_BINARY); // Save particles as vtk file
vd_narrow_band.save(path_output + "/vd_narrow_band_circle.bin"); // Save particles as hdf5 file -> can be reloaded as particles
vd_narrow_band.write(path_output + "/vd_narrow_band_disk", FORMAT_BINARY); // Save particles as vtk file
vd_narrow_band.save(path_output + "/vd_narrow_band_disk.bin"); // Save particles as hdf5 file -> can be reloaded as particles
//! @cond [Get narrow band] @endcond
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Disk 2D
*
* ## Terminate ## {#e2d_c_terminate}
*
* We end with terminating OpenFPM
*
* @snippet example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp Terminate
* @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Terminate
*/
//! @cond [Terminate] @endcond
openfpm_finalize(); // Finalize openFPM library
......@@ -423,11 +423,11 @@ int main(int argc, char* argv[])
//! @cond [Terminate] @endcond
/**
* @page example_sussman_circle Circle 2D
* @page example_sussman_disk Disk 2D
*
* ## Full code ## {#e2d_c_full}
*
* @include example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp
* @include example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp
*/
......
openfpm_io @ 41fcad3e
Subproject commit 48e5e8912314b9eff58711cea88ce5c3d78fe5f6
Subproject commit 41fcad3e6ca84084663fbf2898c2af2b84643c98
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