From 2342453f3991f8179d375764476f36dfb28cdbb2 Mon Sep 17 00:00:00 2001
From: jstark <jstark@mpi-cbg.de>
Date: Fri, 20 Aug 2021 15:39:58 +0200
Subject: [PATCH] Renamed circle -> disk.
---
.../example_sussman_circle/Makefile | 24 -
.../example_sussman_circle/config.cfg | 2 -
.../example_sussman_circle/main.cpp | 436 ------------------
3 files changed, 462 deletions(-)
delete mode 100644 example/Numerics/Sussman_redistancing/example_sussman_circle/Makefile
delete mode 100644 example/Numerics/Sussman_redistancing/example_sussman_circle/config.cfg
delete mode 100644 example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp
diff --git a/example/Numerics/Sussman_redistancing/example_sussman_circle/Makefile b/example/Numerics/Sussman_redistancing/example_sussman_circle/Makefile
deleted file mode 100644
index 78f653991..000000000
--- a/example/Numerics/Sussman_redistancing/example_sussman_circle/Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-include ../../../example.mk
-
-CC=mpic++
-
-LDIR =
-
-OBJ = main.o
-
-%.o: %.cpp
- $(CC) -O3 -c --std=c++14 -o $@ $< $(INCLUDE_PATH)
-
-example_sussman_circle: $(OBJ)
- $(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
-
-all: example_sussman_circle
-
-run: all
- mpirun --oversubscribe -np 2 ./example_sussman_circle
-
-.PHONY: clean all run
-
-clean:
- rm -f *.o *~ core example_sussman_circle
-
diff --git a/example/Numerics/Sussman_redistancing/example_sussman_circle/config.cfg b/example/Numerics/Sussman_redistancing/example_sussman_circle/config.cfg
deleted file mode 100644
index 1eecbac35..000000000
--- a/example/Numerics/Sussman_redistancing/example_sussman_circle/config.cfg
+++ /dev/null
@@ -1,2 +0,0 @@
-[pack]
-files = main.cpp Makefile
diff --git a/example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp b/example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp
deleted file mode 100644
index f9687785f..000000000
--- a/example/Numerics/Sussman_redistancing/example_sussman_circle/main.cpp
+++ /dev/null
@@ -1,436 +0,0 @@
-//
-// Created by jstark on 2020-05-18.
-//
-/**
- * @file example_sussman_disk/main.cpp
- * @page Examples_SussmanRedistancing Examples Sussman Redistancing
- *
- * @subpage example_sussman_disk
- * @subpage example_sussman_sphere
- * @subpage example_sussman_images_2D
- * @subpage example_sussman_images_3D
- *
- * In each of these examples, we either create a geometrical object on a grid or load a binary image / volume onto
- * the grid. The geometrical objects are initially defined by the following indicator function
- *
- * @f[ \phi_{\text{indicator}} = \begin{cases}
- * +1 & \text{point lies inside the object} \\
- * -1 & \text{point lies outside the object} \\
- * \end{cases} @f]
-
- * This indicator function is already some form of a level-set-function.
- * In order to convert Phi_indicator into a signed-distance function (SDF), where @f[|\nabla\phi| = 1@f] we
- * will perform Sussman redistancing (see: <a href="https://www.researchgate
- * .net/publication/2642502_An_Efficient_Interface_Preserving_Level_Set_Re
- * -Distancing_Algorithm_And_Its_Application_To_Interfacial_Incompressible_Fluid_Flow.html">M. Sussman and E. Fatemi,
- * “Efficient, interface-preserving level set redistancing algorithm and its application to interfacial
- * incompressible fluid flow†(1999)</a>, Appendix A).
- *
- * In the Sussman-redistancing, a level-set-function, which can be as simple as a step-function but requires a switch
- * of sign accross the surface of the object, is reinitialized to a SDF by finding the steady-state solution of the
- * following PDE:
- * @f[ \phi_{t} + sgn(\phi_{0})(|\nabla\phi| - 1) = 0 @f]
- *
- * For improved numerical stability and faster convergence, the sign function is replaced by:
- * @f[ sgn_{\epsilon}(\phi) = \frac{\phi}{ \sqrt{\phi^2 + |\nabla\phi|^2 \Delta x^2} }@f]
- *
- * where the \a φ is the approximation of the SDF from the last iteration (see: <a href="https://www.math.uci
- * .edu/~zhao/publication/mypapers/ps/local_levelset.ps">Peng \a et \a al. "A PDE-Based Fast Local
- * Level Set Method"</a>, equation (36)).
- */
-
-
-
-
-
-/**
- * @page example_sussman_disk Circle 2D
- *
- * # Get the signed distance function for a 2D disk via Sussman Redistancing #
- *
- * 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 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 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}
- * +1 & \text{point lies inside the object} \\
- * 0 & \text{object surface} \\
- * -1 & \text{point lies outside the object} \\
- * \end{cases} @f]
- *
- * By Sussman redistancing, this indicator function is transformed into a signed distance function:
- *
- * @f[ \phi_{\text{SDF}} = \begin{cases}
- * +d & \text{orthogonal distance to the closest surface of a point lying inside the object} \\
- * 0 & \text{object surface} \\
- * -d & \text{orthogonal distance to the closest surface of a point lying outside the object} \\
- * \end{cases} @f]
- *
- * Once we have received the Phi_SDF from the redistancing, particles can be placed on narrow band around the interface.
- *
- * * 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 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 ##
- * @htmlonly
- * <img src="http://openfpm.mpi-cbg.de/web/images/examples/sussman_redistancing/example_sussman_circle_paraview.png" width="1024px"/>
- * @endhtmlonly
- */
-
-/**
- * @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_disk/main.cpp Include
- *
- */
-//! @cond [Include] @endcond
-
-// Include Redistancing header files
-#include "util/PathsAndFiles.hpp"
-#include "level_set/redistancing_Sussman/RedistancingSussman.hpp"
-#include "level_set/redistancing_Sussman/NarrowBand.hpp"
-#include "Draw/DrawDisk.hpp"
-//! @cond [Include] @endcond
-
-/**
- * @page example_sussman_disk Circle 2D
- *
- * ## Initialization and output folder ## {#e2d_c_init}
- *
- * We start with
- * * Initializing OpenFPM
- * * Setting the output path and creating an output folder
- *
- * @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Initialization and output folder
- *
- */
-//! @cond [Initialization and output folder] @endcond
-int main(int argc, char* argv[])
-{
- // initialize library
- openfpm_init(&argc, &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_disk";
-
- create_directory_if_not_exist(path_output);
- //! @cond [Initialization and output folder] @endcond
-
- /**
- * @page example_sussman_disk Circle 2D
- *
- * ## Indices for the grid ## {#e2d_c_indices}
- *
- * Optionally, we can define the grid dimensionality and some indices for better code readability later on.
- * * \p x: First dimension
- * * \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_disk/main.cpp Indices grid
- *
- */
- ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
- //! @cond [Indices grid] @endcond
- // Grid dimension
- const unsigned int grid_dim = 2;
- // Some indices for the grid / grid properties
- const size_t x = 0;
- const size_t y = 1;
-
- const size_t Phi_0_grid = 0;
- const size_t Phi_SDF_grid = 1;
- //! @cond [Indices grid] @endcond
- ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
- /**
- * @page example_sussman_disk Circle 2D
- *
- * ## Create the grid ## {#e2d_c_grid}
- *
- * In order to get a grid, we
- * * Define the grid size in terms of number of grid points per dimension
- * * Create a Box that defines our domain
- * * Create a Ghost object that will define the extension of the ghost part
- * * Create a 2D grid with two properties of type double, one for the pre-redistancing Phi_initial and one, where
- * 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_disk/main.cpp Grid creation
- *
- */
- //! @cond [Grid creation] @endcond
- // Here we create a 2D grid that stores 2 properties:
- // Prop1: store the initial Phi;
- // Prop2: here the re-initialized Phi (signed distance function) will be written to in the re-distancing step
- size_t sz[grid_dim] = {128, 128}; // Grid size in terms of number of grid points per dimension
- Box<grid_dim, double> box({0.0, 0.0}, {5.0, 5.0}); // 2D
- Ghost<grid_dim, long int> ghost(0);
- typedef aggregate<double, double> props;
- typedef grid_dist_id<grid_dim, double, props > grid_in_type;
- grid_in_type g_dist(sz, box, ghost);
- g_dist.setPropNames({"Phi_0", "Phi_SDF"});
- //! @cond [Grid creation] @endcond
-
-
- /**
- * @page example_sussman_disk Circle 2D
- *
- * ## Get disk on the grid ## {#e2d_c_getdisk}
- *
- *
- * 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} \\
- * 0 & \text{object surface} \\
- * -1 & \text{point lies outside the object} \\
- * \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_disk/main.cpp Get disk
- */
- //! @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_disk_preRedistancing_radius" + std::to_string((int)radius) , FORMAT_BINARY); // Save the disk as vtk file
- //! @cond [Get disk] @endcond
-
-
- /**
- * @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: 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: 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: 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
- * 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_disk/main.cpp Redistancing options
- */
- ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
- //! @cond [Redistancing options] @endcond
- // Now we want to convert the initial Phi into a signed distance function (SDF) with magnitude of gradient = 1.
- // For the initial re-distancing we use the Sussman method. First of all, we can set some redistancing options.
- Redist_options redist_options;
- redist_options.min_iter = 100;
- redist_options.max_iter = 10000;
-
- redist_options.convTolChange.value = 1e-6;
- redist_options.convTolChange.check = true;
- redist_options.convTolResidual.value = 1e-6;
- redist_options.convTolResidual.check = false;
-
- redist_options.interval_check_convergence = 1;
- redist_options.width_NB_in_grid_points = 6;
- redist_options.print_current_iterChangeResidual = true;
- redist_options.print_steadyState_iter = true;
- //! @cond [Redistancing options] @endcond
-
- /**
- * @page example_sussman_disk Disk 2D
- *
- * ## Run the redistancing ## {#e2d_c_runredist}
- *
- * Now, we can instantiate the Sussman-redistancing class using the redist_options we have just set (or use the
- * defaults) and run the redistancing. If we are interested in the time-step that was automatically computed
- * internally according to the CFL-condition, we can access it with #RedistancingSussman::get_time_step(). If, for
- * whatever reason, we wish to change this timestep, we can do that with #RedistancingSussman::set_user_time_step
- * (T dt). However, be careful when setting your own timestep: if chosen too large, the CFL-condition may be no
- * longer fulfilled and the method can become unstable. For the #RedistancingSussman::run_redistancing we need to
- * provide two template parameters. These are the indices of the respective property that: 1.) contains the
- * initial Phi, 2.) should
- * contain the output of the redistancing. You can use the same index twice, if you want that your input will be
- * overwritten by the output. This time, it makes sense, to save the output grid, since this is already our grid
- * 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_disk/main.cpp Run redistancing
- */
- //! @cond [Run redistancing] @endcond
- RedistancingSussman<grid_in_type> redist_obj(g_dist, redist_options); // Instantiation of Sussman-redistancing class
- // std::cout << "dt = " << redist_obj.get_time_step() << std::endl;
- // Run the redistancing. In the <> brackets provide property-index where 1.) your initial Phi is stored and 2.)
- // where the resulting SDF should be written to.
- redist_obj.run_redistancing<Phi_0_grid, Phi_SDF_grid>();
-
- 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_disk Disk 2D
- *
- * ## Initialize empty vector for narrow band particles ## {#e2d_c_initnbvector}
- *
- * Next, we want to place particles in a narrow band around the interface. For this, we need to create an empty
- * vector in the same domain as our grid from before. We therefore re-use the \p box and \p ghost that we defined
- * during grid creation. This time, we have to set the boundary conditions (see general OpenFPM vector_dist
- * documentation for details.) We also have to choose now, how many properties our particle should store. Minimum is
- * 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_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)
- size_t bc[grid_dim] = {PERIODIC, PERIODIC};
- // Create an empty vector to which narrow-band particles will be added. You can choose, how many properties you want.
- // 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, 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);
- vd_narrow_band.setPropNames({"Phi_SDF", "Phi_grad", "Phi_magnOfGrad"});
- //! @cond [Initialize narrow band] @endcond
-
- /**
- * @page example_sussman_disk Disk 2D
- *
- * ## Instantiate narrow band ## {#e2d_c_instnarrowband}
- *
- * Before we fill the empty vector that we just created with particles, we define how thick the narrow band
- * around the interface should be.
- * This is independent of the redist_options.width_NB_in_grid_points that we chose before. However, it makes
- * sense to use a width during redistancing which is at least as large as the width that we want to place the
- * particles in. The reason is that convergence criteria were checked for that part of the grid only, which
- * belonged to the narrow band.
- *
- * Depending on the type of the variable which you define, the width can be either set in terms of number of
- * 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_disk/main.cpp Instantiate narrow band
- */
- //! @cond [Instantiate narrow band] @endcond
- size_t thickness_of_narrowBand_in_grid_points = 6;
- NarrowBand<grid_in_type> narrowBand(g_dist, thickness_of_narrowBand_in_grid_points); // Instantiation of NarrowBand class
- //! @cond [Instantiate narrow band] @endcond
-
- /**
- * @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_disk/main.cpp Indices narrow band
- *
- */
- //////////////////////////////////////////////////////////////////////////////////////////////
- //! @cond [Indices narrow band] @endcond
- // Some indices
- const size_t Phi_SDF_vd = 0;
- const size_t Phi_grad_vd = 1;
- const size_t Phi_magnOfGrad_vd = 2;
- //! @cond [Indices narrow band] @endcond
-
- /**
- * @page example_sussman_disk Disk 2D
- *
- * ## Fill the vector with particles placed within a narrow band around the interface ## {#e2d_c_getnarrowband}
- *
- * Now, we finally fill the vector with particles placed in a narrow band around the interface. The first
- * template parameter that we pass, must always be the index of the grid property that contains the Phi_SDF.
- *
- * Then you can decide between the following options, what you want to copy from the grid to the particles:
- * * Only copy the Phi_SDF: \p narrowBand.get_narrow_band<Phi_SDF_grid, Phi_SDF_vd>(g_dist, vd_narrow_band);
- * * Copy Phi_SDF as well as the first order upwind gradient of Phi_SDF: \p narrowBand
- * .get_narrow_band<Phi_SDF_grid, Phi_SDF_vd, Phi_grad_vd>(g_dist, vd_narrow_band);
- * * Copy Phi_SDF as well as the first order upwind gradient of Phi_SDF and the corresponding gradient magnitude:
- * \p narrowBand.get_narrow_band<Phi_SDF_grid, Phi_SDF_vd, Phi_grad_vd, Phi_magnOfGrad_vd>(g_dist,
- * vd_narrow_band);
- * * Copy an arbitrary property: \p narrowBand.get_narrow_band_copy_specific_property<Phi_SDF_grid,
- * Prop_index_grid, Prop_index_vector>(g_dist, vd_narrow_band);
- *
- * 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_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.
- // The function will know depending on how many property-indices you provide in the <> brackets.
- // First property-index must always be the index of the SDF on the grid!
- // E.g.: The following line would only write only the Phi_SDF from the grid to your narrow-band particles
- // narrowBand.get_narrow_band<Phi_SDF_grid, Phi_SDF_vd>(g_dist, vd_narrow_band);
- // Whereas this will give you the gradients and magnOfGrad of Phi as well:
- //! @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_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_disk Disk 2D
- *
- * ## Terminate ## {#e2d_c_terminate}
- *
- * We end with terminating OpenFPM
- *
- * @snippet example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp Terminate
- */
- //! @cond [Terminate] @endcond
- openfpm_finalize(); // Finalize openFPM library
- return 0;
-}
-//! @cond [Terminate] @endcond
-
-/**
- * @page example_sussman_disk Disk 2D
- *
- * ## Full code ## {#e2d_c_full}
- *
- * @include example/Numerics/Sussman_redistancing/example_sussman_disk/main.cpp
- */
-
-
-
-
-
--
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