This adds on the hierarchical grid code for 3D problems. More...

#include <HGRID_3D.h>

Inheritance diagram for HGRID_3D:

Public Member Functions
	HGRID_3D ()
	This is the default constructor. All it does is set senible defaults. More...

	HGRID_3D (MD &other)
	Copy-constructor for creates an HGRID problem from an existing MD problem. More...

	HGRID_3D (HGRID_base &other)

void	constructor ()
	This is the actually constructor it is called do both constructors above. More...

Public Member Functions inherited from HGRID_base
	HGRID_base ()
	This is the default constructor. All it does is set senible defaults. More...

	~HGRID_base ()
	This is the default destructor. More...

	HGRID_base (MD &other)
	Copy-constructor for creates an HGRID problem from an existing MD problem. More...

void	constructor ()
	This is the actually constructor it is called do both constructors above. More...

void	HGRID_actions_before_time_loop ()
	This sets up the broad phase information, has to be done at this stage becuase it requires the partcle size. More...

void	HGRID_actions_before_time_step ()
	This resets all the bucket information. More...

void	set_HGRID_num_buckets (unsigned int new_num_buckets)
	This sets the number of buckets for the HGRID. More...

void	set_HGRID_num_buckets_to_power ()
	set number of buckets to the smallest power of two bigger than the number of particles More...

void	set_HGRID_num_buckets_to_power (unsigned int N)
	set number of buckets to the smallest power of two bigger than N More...

void	read (std::istream &is)
	This function reads all HGRID data. More...

void	write (std::ostream &os)
	This function writes all HGRID data. More...

void	print (std::ostream &os, bool print_all)
	This function outputs all HGRID data. More...

Mdouble	getHGridCurrentMaxRelativeDisplacement ()

Mdouble	getHGridTotalCurrentMaxRelativeDisplacement ()

void	setHGridUpdateEachTimeStep (bool updateEachTimeStep)

bool	getHGridUpdateEachTimeStep ()

void	setHGridMaxLevels (int HGridMaxLevels)

int	getHGridMaxLevels ()

HGridMethod	getHGridMethod ()

void	setHGridMethod (HGridMethod hGridMethod)

HGridDistribution	getHGridDistribution ()

void	setHGridDistribution (HGridDistribution hGridDistribution)

Mdouble	getHGridCellOverSizeRatio ()

void	setHGridCellOverSizeRatio (Mdouble cellOverSizeRatio)

Public Member Functions inherited from MD
void	constructor ()
	A public constructor, which sets defaults so the problem can be solved off the shelf. More...

	MD ()

	MD (STD_save &other)

virtual	~MD ()

void	info ()
	Set up a virtual info this will be provided from the inhertiance. More...

void	solve ()
	The work horse of the code. More...

void	solve (unsigned int argc, char *argv[])
	Read arguments before solving. More...

void	solveWithMDCLR ()
	Tries to solve the problem using MDCLR. More...

Mdouble	get_t ()
	Access function for the time. More...

void	set_t (Mdouble new_t)
	Access function for the time. More...

int	get_NSpecies ()
	Allows the number of Species to be accessed. More...

std::vector< CSpecies > &	get_Species (void)
	Allows the species to be copied. More...

CSpecies *	get_Species (int i)
	Allows the species to be accessed. More...

CSpecies *	get_MixedSpecies (int i, int j)
	Allows the mixed species to be accessed. More...

void	set_MixedSpecies (int i, int j, CSpecies &S)
	Allows the mixed species to be set. More...

void	set_tmax (Mdouble new_tmax)
	Allows the upper time limit to be changed. More...

Mdouble	get_tmax ()
	Allows the upper time limit to be accessed. More...

ParticleHandler &	getParticleHandler ()

WallHandler &	getWallHandler ()

BoundaryHandler &	getBoundaryHandler ()

void	set_savecount (int new_)
	Allows the number of time steps between saves to be changed, see also set_number_of_saves. More...

void	set_save_count_all (int new_)

void	set_save_count_data (int new_)

void	set_save_count_ene (int new_)

void	set_save_count_stat (int new_)

void	set_save_count_fstat (int new_)

int	get_savecount ()
	Allows the number of time steps between saves to be accessed. More...

int	get_save_count ()

int	get_save_count_data ()

int	get_save_count_ene ()

int	get_save_count_stat ()

int	get_save_count_fstat ()

void	set_do_stat_always (bool new_)
	Sets how often the data is saved using the number of saves wanted, tmax, and dt. See also set_savecount. More...

void	set_number_of_saves (Mdouble N)

void	set_number_of_saves_all (Mdouble N)

void	set_number_of_saves_data (Mdouble N)

void	set_number_of_saves_ene (Mdouble N)

void	set_number_of_saves_stat (Mdouble N)

void	set_number_of_saves_fstat (Mdouble N)

void	set_plastic_k1_k2max_kc_depth (Mdouble k1_, Mdouble k2max_, Mdouble kc_, Mdouble depth_, unsigned int indSpecies=0)
	Allows the plastic constants to be changed. More...

void	set_k1 (Mdouble new_, unsigned int indSpecies=0)

void	set_k2max (Mdouble new_, unsigned int indSpecies=0)

void	set_kc (Mdouble new_, unsigned int indSpecies=0)

void	set_depth (Mdouble new_, unsigned int indSpecies=0)

Mdouble	get_k1 (unsigned int indSpecies=0)
	Allows the plastic constants to be accessed. More...

Mdouble	get_k2max (unsigned int indSpecies=0)

Mdouble	get_kc (unsigned int indSpecies=0)

Mdouble	get_depth (unsigned int indSpecies=0)

Mdouble	get_plastic_dt (Mdouble mass, unsigned int indSpecies=0)

void	set_k (Mdouble new_, unsigned int indSpecies=0)
	Allows the spring constant to be changed. More...

Mdouble	get_k (int indSpecies=0)
	Allows the spring constant to be accessed. More...

void	set_kt (Mdouble new_, unsigned int indSpecies=0)
	Allows the spring constant to be changed. More...

Mdouble	get_kt (int indSpecies=0)
	Allows the spring constant to be accessed. More...

void	set_krolling (Mdouble new_, unsigned int indSpecies=0)
	Allows the spring constant to be changed. More...

Mdouble	get_krolling (int indSpecies=0)
	Allows the spring constant to be accessed. More...

void	set_ktorsion (Mdouble new_, unsigned int indSpecies=0)
	Allows the spring constant to be changed. More...

Mdouble	get_ktorsion (int indSpecies=0)
	Allows the spring constant to be accessed. More...

void	set_rho (Mdouble new_, unsigned int indSpecies=0)
	Allows the density to be changed. More...

Mdouble	get_rho (int indSpecies=0)
	Allows the density to be accessed. More...

void	set_dispt (Mdouble new_, unsigned int indSpecies=0)
	Allows the tangential viscosity to be changed. More...

Mdouble	get_dispt (unsigned int indSpecies=0)
	Allows the tangential viscosity to be accessed. More...

void	set_disprolling (Mdouble new_, unsigned int indSpecies=0)
	Allows the tangential viscosity to be changed. More...

Mdouble	get_disprolling (unsigned int indSpecies=0)
	Allows the tangential viscosity to be accessed. More...

void	set_disptorsion (Mdouble new_, unsigned int indSpecies=0)
	Allows the tangential viscosity to be changed. More...

Mdouble	get_disptorsion (unsigned int indSpecies=0)
	Allows the tangential viscosity to be accessed. More...

void	set_disp (Mdouble new_, unsigned int indSpecies=0)
	Allows the normal dissipation to be changed. More...

Mdouble	get_disp (unsigned int indSpecies=0)
	Allows the normal dissipation to be accessed. More...

void	set_dissipation (Mdouble new_, unsigned int indSpecies=0)
	Allows the normal dissipation to be changed. More...

Mdouble	get_dissipation (unsigned int indSpecies=0)
	Allows the normal dissipation to be accessed. More...

void	set_mu (Mdouble new_, unsigned int indSpecies=0)
	Allows the Coulomb friction coefficient to be changed. More...

Mdouble	get_mu (unsigned int indSpecies=0)
	Allows the Coulomb friction coefficient to be accessed. More...

void	set_murolling (Mdouble new_, unsigned int indSpecies=0)
	Allows the Coulomb friction coefficient to be changed. More...

Mdouble	get_murolling (unsigned int indSpecies=0)
	Allows the Coulomb friction coefficient to be accessed. More...

void	set_mutorsion (Mdouble new_, unsigned int indSpecies=0)
	Allows the Coulomb friction coefficient to be changed. More...

Mdouble	get_mutorsion (unsigned int indSpecies=0)
	Allows the Coulomb friction coefficient to be accessed. More...

void	set_rotation (bool new_)

bool	get_rotation ()

void	set_dim_particle (int new_, unsigned int indSpecies=0)
	Allows the dimension of the particle (f.e. for mass) to be changed. More...

int	get_dim_particle (unsigned int indSpecies=0)
	Allows the dimension of the particle (f.e. for mass) to be accessed. More...

bool	get_save_data_data ()
	Returns the data counter. More...

bool	get_save_data_ene ()

bool	get_save_data_fstat ()

bool	get_save_data_stat ()

bool	get_do_stat_always ()

void	set_k_and_restitution_coefficient (Mdouble k_, Mdouble eps, Mdouble mass, unsigned int indSpecies=0)
	Sets k, disp such that it matches a given tc and eps for a collision of two copies of P. More...

void	set_collision_time_and_restitution_coefficient (Mdouble tc, Mdouble eps, Mdouble mass, unsigned int indSpecies=0)
	Sets k, disp such that it matches a given tc and eps for a collision of two copies of P. More...

void	set_collision_time_and_restitution_coefficient (Mdouble tc, Mdouble eps, Mdouble mass1, Mdouble mass2, unsigned int indSpecies=0)
	Set k, disp such that is matches a given tc and eps for a collision of two different masses. More...

void	set_collision_time_and_normal_and_tangential_restitution_coefficient (Mdouble tc, Mdouble eps, Mdouble beta, Mdouble mass1, Mdouble mass2, unsigned int indSpecies=0)
	See CSpecies::set_collision_time_and_normal_and_tangential_restitution_coefficient. More...

void	set_collision_time_and_normal_and_tangential_restitution_coefficient_nodispt (Mdouble tc, Mdouble eps, Mdouble beta, Mdouble mass1, Mdouble mass2, unsigned int indSpecies=0)
	See CSpecies::set_collision_time_and_normal_and_tangential_restitution_coefficient. More...

Mdouble	get_collision_time (Mdouble mass, unsigned int indSpecies=0)
	Calculates collision time for two copies of a particle of given disp, k, mass. More...

Mdouble	get_restitution_coefficient (Mdouble mass, unsigned int indSpecies=0)
	Calculates restitution coefficient for two copies of given disp, k, mass. More...

Mdouble	get_xmin ()
	Get xmin. More...

Mdouble	get_xmax ()
	Get xmax. More...

Mdouble	get_ymin ()
	Gets ymin. More...

Mdouble	get_ymax ()
	Gets ymax. More...

Mdouble	get_zmin ()
	Gets zmin. More...

Mdouble	get_zmax ()
	Gets zmax. More...

void	set_xmin (Mdouble new_xmin)
	Sets xmin and walls, assuming the standard definition of walls as in the default constructor. More...

void	set_ymin (Mdouble new_ymin)

void	set_zmin (Mdouble new_zmin)
	Sets ymin and walls, assuming the standard definition of walls as in the default constructor. More...

void	set_xmax (Mdouble new_xmax)
	Sets xmax and walls, assuming the standard definition of walls as in the default constructor. More...

void	set_ymax (Mdouble new_ymax)
	Sets ymax and walls, assuming the standard definition of walls as in the default constructor. More...

void	set_zmax (Mdouble new_zmax)
	Sets ymax and walls, assuming the standard definition of walls as in the default constructor. More...

void	set_dt (Mdouble new_dt)
	Allows the time step dt to be changed. More...

Mdouble	get_dt ()
	Allows the time step dt to be accessed. More...

void	set_name (const char *name)
	Sets the name of the problem, used for the same data files. More...

void	set_xballs_colour_mode (int new_cmode)
	Set the xball output mode. More...

void	set_xballs_cmode (int new_cmode)

int	get_xballs_cmode ()

void	set_xballs_vector_scale (double new_vscale)
	Set the scale of vectors in xballs. More...

double	get_xballs_vscale ()

void	set_xballs_additional_arguments (std::string new_)
	Set the additional arguments for xballs. More...

std::string	get_xballs_additional_arguments ()

void	set_xballs_scale (Mdouble new_scale)
	Set the scale of the xballs problem. The default is fit to screen. More...

double	get_xballs_scale ()

void	set_gravity (Vec3D new_gravity)
	Allows the gravitational acceleration to be changed. More...

Vec3D	get_gravity ()
	Allows the gravitational acceleration to be accessed. More...

void	set_dim (int new_dim)
	Allows the dimension of the simulation to be changed. More...

int	get_dim ()
	Allows the dimension of the simulation to be accessed. More...

int	get_restart_version ()
	Gets restart_version. More...

void	set_restart_version (int new_)
	Sets restart_version. More...

bool	get_restarted ()
	Gets restarted. More...

Mdouble	get_max_radius ()
	Sets restarted. More...

void	set_restarted (bool new_)

bool	get_append ()
	Gets restarted. More...

void	set_append (bool new_)
	Sets restarted. More...

Mdouble	get_ene_ela ()
	Gets ene_ela. More...

void	set_ene_ela (Mdouble new_)
	Sets ene_ela. More...

void	add_ene_ela (Mdouble new_)
	Sets ene_ela. More...

void	Remove_Particle (int IP)
	This function removes partice IP from the vector of particles by moving the last particle in the vector to the position if IP Also it checks if the moved Particle has any tangentialsspring-information, which needs to be moved to a different particle, because tangential spring information always needs to be stored in the real particle with highest particle index. More...

Mdouble	get_Mass_from_Radius (Mdouble radius, int indSpecies=0)

Mdouble	get_maximum_velocity (BaseParticle &P)
	Calculates the maximum velocity allowed for a collision of two copies of P (for higher velocities particles could pass through each other) More...

virtual BaseParticle *	getSmallestParticle ()

virtual BaseParticle *	getLargestParticle ()

virtual void	removeParticle (int iP)

Mdouble	get_maximum_velocity ()

void	set_dt_by_mass (Mdouble mass)
	Sets dt to 1/50-th of the collision time for two particles of mass P. More...

void	set_dt (BaseParticle &P)
	Sets dt to 1/50-th of the collision time for two copies of P. More...

void	set_dt ()
	Sets dt to 1/50-th of the smallest possible collision time. More...

virtual void	setup_particles_initial_conditions ()
	This function allows the initial conditions of the particles to be set, by default locations is random. More...

virtual void	create_xballs_script ()
	This creates a scipt which can be used to load the xballs problem to display the data just generated. More...

virtual double	getInfo (BaseParticle &P)
	Allows the user to set what is written into the info column in the data file. By default is store the Species ID number. More...

virtual void	save_restart_data ()
	Stores all MD data. More...

int	load_restart_data ()
	Loads all MD data. More...

int	load_restart_data (std::string filename)

void	statistics_from_restart_data (const char *name)
	Loads all MD data and plots statistics for all timesteps in the .data file. More...

virtual void	write_v1 (std::ostream &os)
	Writes all MD data. More...

virtual void	read_v1 (std::istream &is)
	Reads all MD data. More...

virtual void	read_v2 (std::istream &is)

bool	load_from_data_file (const char *filename, unsigned int format=0)
	This allows particle data to be reloaded from data files. More...

bool	load_par_ini_file (const char *filename)
	allows the user to read par.ini files (useful to read MDCLR files) More...

bool	read_next_from_data_file (unsigned int format=0)
	by default format do not pass an argument; only specify format if you have to read a special format (f.e. dim=2, but format=14 (3d format)) More...

int	read_dim_from_data_file ()

bool	find_next_data_file (Mdouble tmin, bool verbose=true)

void	add_Species (CSpecies &S)

void	add_Species (void)

void	set_format (int new_)

int	get_format ()

int	readArguments (unsigned int argc, char *argv[])
	Can interpret main function input arguments that are passed by the driver codes. More...

Public Member Functions inherited from STD_save
	STD_save ()
	Default constructor: sets the counter to 0 (i.e. no number will be included). More...

	STD_save (STD_save &other)
	Copy constructor. More...

void	constructor ()

void	inc_counter_in_file ()
	Increament the counter value stored in the file_counter by 1 and store the new value. More...

int	read_run_num_from_file ()
	Read rom the counter file the counter. More...

void	set_counter_from_file ()
	Sets the counter based on the current number stored in the counter file. More...

void	save_info_to_disk ()
	Saves the information generated by info to disk in a file. More...

void	set_counter (int new_counter)
	This set the counter, overriding the defaults. More...

int	get_counter ()
	This returns the current value of the counter. More...

bool	FileExists (std::string strFilename)
	Function to check if a file exists, is used to check if a run has already need done. More...

void	auto_number ()

std::vector< int >	get_numbers (int size_x, int size_y)
	This turns a counter into two indexs for doing parmater studies. The indexs run from 1:size_x and 1:size_y where as the study number starts at 0. More...

int	launch_new (const char *name, bool quick=false)
	This launch a code from within this code. Please pass the name of the code to run. More...

void	set_name (const char *name)
	Sets the name of the problem, used for the same data files. More...

std::string	get_name ()
	Allows the problem_name to be accessed. More...

std::fstream &	get_data_file ()
	Allows the problem_name to be accessed. More...

std::fstream &	get_stat_file ()
	Allows the problem_name to be accessed. More...

std::fstream &	get_fstat_file ()
	Allows the problem_name to be accessed. More...

std::fstream &	get_ene_file ()
	Allows the problem_name to be accessed. More...

void	set_fstat_filename (std::string filename)

void	set_data_filename (std::string filename)

void	set_stat_filename (std::string filename)

void	set_ene_filename (std::string filename)

void	set_fstat_filename ()

void	set_data_filename ()

void	set_stat_filename ()

void	set_ene_filename ()

std::string	get_fstat_filename ()

std::string	get_data_filename ()

std::string	get_stat_filename ()

std::string	get_ene_filename ()

void	set_step_size (unsigned int new_)

unsigned int	get_step_size ()

void	set_options_fstat (unsigned int new_)
	set and get for file options More...

unsigned int	get_options_fstat (void)

void	set_options_data (unsigned int new_)

unsigned int	get_options_data (void)

void	set_options_stat (unsigned int new_)

unsigned int	get_options_stat (void)

void	set_options_restart (unsigned int new_)

unsigned int	get_options_restart (void)

void	set_options_ene (unsigned int new_)

unsigned int	get_options_ene (void)

bool	open_file (std::fstream &file, std::string filename, unsigned int options, std::fstream::openmode mode)

bool	open_fstat_file (std::fstream::openmode mode=std::fstream::out)

bool	open_data_file (std::fstream::openmode mode=std::fstream::out)

bool	open_stat_file (std::fstream::openmode mode=std::fstream::out)

bool	open_ene_file (std::fstream::openmode mode=std::fstream::out)

bool	open_counted_file (std::fstream &file, std::string filenameNoCount, std::fstream::openmode mode)
	opens file needed if data is written in multiple files More...

bool	increase_counter_fstat (std::fstream::openmode mode)

bool	increase_counter_data (std::fstream::openmode mode)

bool	increase_counter_stat (std::fstream::openmode mode)

bool	increase_counter_ene (std::fstream::openmode mode)

void	set_file_counter (int new_)

int	get_file_counter ()

Protected Member Functions
void	HGRID_UpdateParticleInHgrid (BaseParticle *obj)
	This adds a partcile to the Grid, called in the grid setup routies. More...

void	HGRID_RemoveParticleFromHgrid (BaseParticle *obj)

virtual void	CheckCell (int x, int y, int z, int l, BaseParticle obj, HGrid grid)
	Check collisions for a general cell. More...

virtual void	CheckCell_current (int x, int y, int z, int l, HGrid *grid)
	Checks for a collision in the particles own cell. More...

void	CheckObjAgainstGrid (HGrid grid, BaseParticle obj)
	Check if an Particle has a collision in the grid; avoids multiple checks. More...

void	CheckObjAgainstWholeGrid (HGrid grid, BaseParticle obj)
	Check if an Particle has a collision in the grid. More...

bool	TestCell (int x, int y, int z, int l, BaseParticle obj, HGrid grid)
	Tests obj against all particles in cell similar to CheckCell, but links to TestObject instead of compute_internal_forces. More...

bool	TestObjAgainstGrid (HGrid grid, BaseParticle obj)
	Tests obj against all neighbouring particles similar to CheckObjAgainstGrid, but links to TestCell instead of CheckCell. More...

Protected Member Functions inherited from HGRID_base
void	InitBroadPhase ()
	This sets up the parameters required for the contact model. More...

void	HGRID_InsertParticleToHgrid (BaseParticle *obj)
	Inserts a single Particle to current grid. More...

void	broad_phase (BaseParticle *i)
	This makes the board_phase of contact point at the HGRID code. More...

virtual bool	TestObject (BaseParticle pI, BaseParticle pJ)
	criterium for inserting a particle (returns false, if particles overlap;) More...

void	HGRID_update_move (BaseParticle *iP, Mdouble move)

void	HGRID_actions_before_integration ()

void	HGRID_actions_after_integration ()

int	readNextArgument (unsigned int &i, unsigned int argc, char *argv[])

Protected Member Functions inherited from MD
virtual void	compute_all_forces ()
	This does the force computation. More...

virtual void	compute_internal_forces (BaseParticle *i)
	Computes the forces between particles (internal in the sence that the sum over all these forces is zero i.e. fully modelled forces) More...

CTangentialSpring *	getTangentialSpring (BaseParticle PI, BaseParticle PJ, BaseParticle *PJreal)

CTangentialSpring *	getTangentialSpringWall (BaseParticle *pI, int w)

virtual void	compute_internal_forces (BaseParticle P1, BaseParticle P2)
	Computes the forces between particles (internal in the sence that the sum over all these forces is zero i.e. fully modelled forces) More...

void	compute_plastic_internal_forces (BaseParticle P1, BaseParticle P2)
	Computes plastic forces between particles. More...

virtual void	compute_external_forces (BaseParticle *PI)
	This is were the computation of external forces takes place (e.g. gravity) More...

virtual void	compute_walls (BaseParticle *PI)
	This is were the walls are. More...

Mdouble	computeShortRangeForceWithWall (BaseParticle pI, int wall, CSpecies pSpecies, Mdouble dist)

Mdouble	computeShortRangeForceWithParticle (BaseParticle PI, BaseParticle PJ, BaseParticle PJreal, CSpecies pSpecies, Mdouble dist)

virtual void	actions_before_time_loop ()
	This is actions before the start of the main time loop. More...

virtual void	HGRID_InsertParticleToHgrid (BaseParticle *obj UNUSED)
	This is action before the time step is started. More...

virtual void	HGRID_UpdateParticleInHgrid (BaseParticle *obj UNUSED)

virtual void	HGRID_RemoveParticleFromHgrid (BaseParticle *obj UNUSED)

virtual bool	get_HGRID_UpdateEachTimeStep ()

virtual void	actions_before_time_step ()
	This is action before the time step is started. More...

virtual void	actions_after_solve ()
	This is actions at the end of the code, but before the files are closed. More...

virtual void	actions_after_time_step ()
	This is action after the time step is finished. More...

virtual void	output_xballs_data ()
	Output xball data for Particle i. More...

virtual void	output_xballs_data_particle (int i)
	This function outputs the location and velocity of the particle in a format the xballs progream can read. More...

virtual void	start_ene ()
	Functions for ene file. More...

virtual void	fstat_header ()

virtual void	output_ene ()
	This function outputs statistical data - The default is to compute the rotational kinetic engergy, linear kinetic energy, and the centre of mass. More...

virtual void	initialize_statistics ()
	Functions for statistics. More...

virtual void	output_statistics ()

virtual void	gather_statistics_collision (int index1 UNUSED, int index2 UNUSED, Vec3D Contact UNUSED, Mdouble delta UNUSED, Mdouble ctheta UNUSED, Mdouble fdotn UNUSED, Mdouble fdott UNUSED, Vec3D P1_P2_normal_ UNUSED, Vec3D P1_P2_tangential UNUSED)

virtual void	process_statistics (bool usethese UNUSED)

virtual void	finish_statistics ()

virtual void	set_initial_pressures_for_pressure_controlled_walls ()

virtual void	do_integration_before_force_computation (BaseParticle *pI)
	This is were the integration is done. More...

virtual void	checkInteractionWithBoundaries ()

virtual void	do_integration_after_force_computation (BaseParticle *pI)
	This is were the integration is done. More...

void	set_FixedParticles (unsigned int n)

void	initialize_tangential_springs ()

void	compute_particle_masses ()
	Computes the mass of each particle. More...

virtual void	cout_time ()
	std::couts time More...

virtual bool	continue_solve ()

void	reset_DeltaMax ()
	sets the history parameter DeltaMax of all particles to zero More...

void	reset_TangentialSprings ()
	sets the history parameter TangentialSprings of all particles to zero More...

Additional Inherited Members
Public Attributes inherited from HGRID_base
HGrid *	grid

Public Attributes inherited from MD
RNG	random

Protected Attributes inherited from MD
std::vector< CSpecies >	Species
	These are the particle parameters like dissipation etc. More...

Protected Attributes inherited from STD_save
std::stringstream	problem_name
	Stores the problem_name. More...

std::stringstream	data_filename
	These store the save file names, by default they are derived from problem_name. More...

std::stringstream	stat_filename

std::stringstream	fstat_filename

std::stringstream	ene_filename

std::fstream	data_file
	Stream used for data files. More...

std::fstream	stat_file

std::fstream	fstat_file

std::fstream	ene_file

unsigned int	options_fstat
	Indicators if files are created or not 0: file will not be created 1: file will be written in one file 2: file will be written in multiple files. More...

unsigned int	options_data

unsigned int	options_stat

unsigned int	options_ene

unsigned int	options_restart

unsigned int	file_counter
	Counter needed if file will be written in multiple files. More...

unsigned int	step_size

Detailed Description

This adds on the hierarchical grid code for 3D problems.

Definition at line 35 of file HGRID_3D.h.

Constructor & Destructor Documentation

HGRID_3D::HGRID_3D ( )

inline

This is the default constructor. All it does is set senible defaults.

Definition at line 40 of file HGRID_3D.h.

References constructor().

     {
         constructor();
         #ifdef CONSTUCTOR_OUTPUT
             std::cerr << "HGRID_3D() finished"<<std::endl;
         #endif
     }

HGRID_3D::HGRID_3D ( MD & other )

inline

Copy-constructor for creates an HGRID problem from an existing MD problem.

Bug:: Why is the constructor call commented out. This does not make sence to be Anthony. Dinant: I think this has something to do with somebody copying a 2D MD problem into a 3D Hgrid, then the 3D_Hgrid constructor changes properties of the MD class. Solution in my opinion is to change the HGRID_3D::constructor()

Definition at line 53 of file HGRID_3D.h.

                         : MD(other), HGRID_base(other)
     {
         /*constructor();*/
         #ifdef CONSTUCTOR_OUTPUT
             std::cerr << "HGRID_3D(MD& other) finished"<<std::endl;
         #endif  
     }

HGRID_3D::HGRID_3D ( HGRID_base & other )

inline

Definition at line 60 of file HGRID_3D.h.

                                 : MD(other), HGRID_base(other)
     {
         /*constructor();*/
         #ifdef CONSTUCTOR_OUTPUT
             std::cerr << "HGRID_3D(HGRID_base& other) finished"<<std::endl;
         #endif  
     }

Member Function Documentation

void HGRID_3D::CheckCell	(	int	x,
		int	y,
		int	z,
		int	l,
		BaseParticle *	obj,
		HGrid *	grid
	)

protectedvirtual

Check collisions for a general cell.

Check for collisions with a general cell.

Todo:: {What is the use of this check?}

Bug:: {TW: This check is not necessary, I believe. This is the most-expensive function in most codes (the two checks in this function slows down granular jet by 15%) and the selftests are not affected. DK: I do think this is neccesary, for example: If two cells hash to the same bucket and a particle in one of these cells check for collisions with the other cell. Then due to the hashingcollision it also gets all particles in it's own cell and thus generating false collisions.}

Definition at line 58 of file HGRID_3D.cc.

References MD::compute_internal_forces(), HGrid::ComputeHashBucketIndex(), BaseParticle::get_HGRID_Level(), BaseParticle::get_HGRID_NextObject(), BaseParticle::get_HGRID_x(), BaseParticle::get_HGRID_y(), BaseParticle::get_HGRID_z(), and HGrid::objectBucket.

Referenced by CheckObjAgainstGrid().

 {
     int bucket = grid->ComputeHashBucketIndex(x,y,z,l);
 
     if ((obj->get_HGRID_x() == x) && (obj->get_HGRID_y() == y) && (obj->get_HGRID_z() == z) && (obj->get_HGRID_Level() == l)) { return; }
 
     // Loop through all objects in the bucket to find nearby objects
     BaseParticle *p = grid->objectBucket[bucket];
 
     while (p!=NULL)
     {
         //Check if the particle realy is in the target cell (i.e. no hashing error has occured)
         if ((p->get_HGRID_x() == x) && (p->get_HGRID_y() == y) && (p->get_HGRID_z() == z) && (p->get_HGRID_Level() == l))
         {
             compute_internal_forces(obj,p);
         }
         p = p->get_HGRID_NextObject();
     }
 }

void HGRID_3D::CheckCell_current	(	int	x,
		int	y,
		int	z,
		int	l,
		HGrid *	grid
	)

protectedvirtual

Checks for a collision in the particles own cell.

Checks for collision in the particles own cell.

Bug:: {TW: This check is not necessary, I believe. This is the most-expensive function in most codes (the two checks in this function slows down granular jet by 15%) and the selftests are not affected. DK: I do think this is neccesary, for example: If two cells hash to the same bucket and a particle in one of these cells check for collisions with the other cell. Then due to the hashingcollision it also gets all particles in it's own cell and thus generating false collisions.}

Definition at line 31 of file HGRID_3D.cc.

References HGrid::bucketIsChecked, MD::compute_internal_forces(), HGrid::ComputeHashBucketIndex(), BaseParticle::get_HGRID_Level(), BaseParticle::get_HGRID_NextObject(), BaseParticle::get_HGRID_x(), BaseParticle::get_HGRID_y(), BaseParticle::get_HGRID_z(), and HGrid::objectBucket.

Referenced by CheckObjAgainstGrid().

 {
     int bucket = grid->ComputeHashBucketIndex(x,y,z,l);
     if (grid->bucketIsChecked[bucket]) { return; }
     BaseParticle* p1 = grid->objectBucket[bucket];
 
     while (p1!=NULL)
     {
         BaseParticle* p2 = p1->get_HGRID_NextObject();
         while (p2!=NULL)
         {
             //Check if the particle realy is in the target cell (i.e. no hashing error has occured)
             if ((p1->get_HGRID_x() == p2->get_HGRID_x()) && (p1->get_HGRID_y() == p2->get_HGRID_y()) && (p1->get_HGRID_z() == p2->get_HGRID_z()) && (p1->get_HGRID_Level() == p2->get_HGRID_Level()))
             {
                 compute_internal_forces(p1,p2);
             }
             p2 = p2->get_HGRID_NextObject();
         }
         p1 = p1->get_HGRID_NextObject();
     }
     grid->bucketIsChecked[bucket] = true;
 }

void HGRID_3D::CheckObjAgainstGrid	(	HGrid *	grid,
		BaseParticle *	obj
	)

protectedvirtual

Check if an Particle has a collision in the grid; avoids multiple checks.

Test collisions between object and all objects in hgrid.

Implements HGRID_base.

Definition at line 83 of file HGRID_3D.cc.

References BOTTOMUP, HGrid::cellSizes_, CheckCell(), CheckCell_current(), BaseParticle::get_HGRID_Level(), BaseParticle::get_HGRID_x(), BaseParticle::get_HGRID_y(), BaseParticle::get_HGRID_z(), BaseParticle::get_InteractionRadius(), BaseParticle::get_Position(), HGRID_base::getHGridMethod(), HGrid::invCellSizes_, HGrid::occupiedLevelsMask, TOPDOWN, Vec3D::X, Vec3D::Y, and Vec3D::Z.

 {
     unsigned int startLevel     = obj->get_HGRID_Level();
     
     int x, y, z;
     Mdouble inv_size;
 
     switch(getHGridMethod())
     {
     case BOTTOMUP:
         {
             int occupiedLevelsMask  = grid->occupiedLevelsMask >> obj->get_HGRID_Level();
             for (unsigned int level = startLevel; level < grid->cellSizes_.size(); occupiedLevelsMask >>= 1, level++) 
             {
                 // If no objects in rest of grid, stop now
                 if (occupiedLevelsMask == 0) break;
 
                 // If no objects at this level, go on to the next level
                 if ((occupiedLevelsMask & 1) == 0) continue;
 
                 if (level == startLevel)    
                 {
                     x = obj->get_HGRID_x();
                     y = obj->get_HGRID_y();
                     z = obj->get_HGRID_z();
 
                     CheckCell_current(x, y, z, level, grid);
 
                     CheckCell(x+1, y-1, z  , level, obj, grid);
                     CheckCell(x+1, y,   z  , level, obj, grid);
                     CheckCell(x+1, y+1, z  , level, obj, grid);
                     
                     CheckCell(x+1, y-1, z+1, level, obj, grid);
                     CheckCell(x+1, y,   z+1, level, obj, grid);
                     CheckCell(x+1, y+1, z+1, level, obj, grid);     
 
                     CheckCell(x+1, y-1, z-1, level, obj, grid);
                     CheckCell(x+1, y,   z-1, level, obj, grid);
                     CheckCell(x+1, y+1, z-1, level, obj, grid);
 
                     CheckCell(x  , y+1, z  , level, obj, grid);         
                     CheckCell(x  , y,   z-1, level, obj, grid);
                     CheckCell(x  , y+1, z-1, level, obj, grid);
                     CheckCell(x  , y+1, z+1, level, obj, grid);
                 }
                 else
                 {
                     int xs,ys,zs,xe,ye,ze;
                     inv_size = grid->invCellSizes_[level];
                     xs = (int) floor((obj->get_Position().X-obj->get_InteractionRadius()) * inv_size - 0.5);
                     xe = (int) floor((obj->get_Position().X+obj->get_InteractionRadius()) * inv_size + 0.5);
                     ys = (int) floor((obj->get_Position().Y-obj->get_InteractionRadius()) * inv_size - 0.5);
                     ye = (int) floor((obj->get_Position().Y+obj->get_InteractionRadius()) * inv_size + 0.5);
                     zs = (int) floor((obj->get_Position().Z-obj->get_InteractionRadius()) * inv_size - 0.5);
                     ze = (int) floor((obj->get_Position().Z+obj->get_InteractionRadius()) * inv_size + 0.5);
                     for(x=xs;x<=xe;x++)
                     {
                         for(y=ys;y<=ye;y++)
                         {
                             for(z=zs;z<=ze;z++)
                             {
                                 CheckCell(x,y,z,level,obj,grid);
                             }
                         }
                     }
                 }
             }
             break;
         }
         case TOPDOWN:
         {
             int occupiedLevelsMask  = grid->occupiedLevelsMask;
             for (unsigned int level = 0; level <=startLevel; occupiedLevelsMask >>= 1, level++) 
             {
                 // If no objects in rest of grid, stop now
                 if (occupiedLevelsMask == 0) break;
 
                 // If no objects at this level, go on to the next level
                 if ((occupiedLevelsMask & 1) == 0) continue;
 
                 if (level == startLevel)    
                 {
                     x = obj->get_HGRID_x();
                     y = obj->get_HGRID_y();
                     z = obj->get_HGRID_z();
                     
                     CheckCell_current(x, y, z, level, grid);
                     
                     CheckCell(x+1, y-1, z  , level, obj, grid);
                     CheckCell(x+1, y,   z  , level, obj, grid);
                     CheckCell(x+1, y+1, z  , level, obj, grid);
                     
                     CheckCell(x+1, y-1, z+1, level, obj, grid);
                     CheckCell(x+1, y,   z+1, level, obj, grid);
                     CheckCell(x+1, y+1, z+1, level, obj, grid);     
 
                     CheckCell(x+1, y-1, z-1, level, obj, grid);
                     CheckCell(x+1, y,   z-1, level, obj, grid);
                     CheckCell(x+1, y+1, z-1, level, obj, grid);
 
                     CheckCell(x  , y+1, z  , level, obj, grid);         
                     CheckCell(x  , y,   z-1, level, obj, grid);
                     CheckCell(x  , y+1, z-1, level, obj, grid);
                     CheckCell(x  , y+1, z+1, level, obj, grid); 
                 }
                 else
                 {
                     int xs,ys,zs,xe,ye,ze;
                     inv_size = grid->invCellSizes_[level];
                     xs = (int) floor((obj->get_Position().X-obj->get_InteractionRadius()) * inv_size - 0.5);
                     xe = (int) floor((obj->get_Position().X+obj->get_InteractionRadius()) * inv_size + 0.5);
                     ys = (int) floor((obj->get_Position().Y-obj->get_InteractionRadius()) * inv_size - 0.5);
                     ye = (int) floor((obj->get_Position().Y+obj->get_InteractionRadius()) * inv_size + 0.5);
                     zs = (int) floor((obj->get_Position().Z-obj->get_InteractionRadius()) * inv_size - 0.5);
                     ze = (int) floor((obj->get_Position().Z+obj->get_InteractionRadius()) * inv_size + 0.5);
                     for(x=xs;x<=xe;x++)
                     {
                         for(y=ys;y<=ye;y++)
                         {
                             for(z=zs;z<=ze;z++)
                             {
                                 CheckCell(x,y,z,level,obj,grid);
                             }
                         }
                     }
                 }
             }
             break;
         }
     }
 }

void HGRID_3D::CheckObjAgainstWholeGrid	(	HGrid *	grid,
		BaseParticle *	obj
	)

protected

Check if an Particle has a collision in the grid.

void HGRID_3D::constructor ( )

inline

This is the actually constructor it is called do both constructors above.

Definition at line 69 of file HGRID_3D.h.

References MD::set_dim(), and MD::set_dim_particle().

Referenced by HGRID_3D().

                       {
         set_dim_particle(3);
         set_dim(3);
     }

void HGRID_3D::HGRID_RemoveParticleFromHgrid ( BaseParticle * obj )

protected

Definition at line 269 of file HGRID_3D.cc.

References HGrid::ComputeHashBucketIndex(), BaseParticle::get_HGRID_Level(), BaseParticle::get_HGRID_NextObject(), BaseParticle::get_HGRID_PrevObject(), BaseParticle::get_HGRID_x(), BaseParticle::get_HGRID_y(), BaseParticle::get_HGRID_z(), HGRID_base::grid, HGrid::objectBucket, BaseParticle::set_HGRID_NextObject(), and BaseParticle::set_HGRID_PrevObject().

Referenced by HGRID_UpdateParticleInHgrid().

 {
     int bucket = grid->ComputeHashBucketIndex(obj->get_HGRID_x(),obj->get_HGRID_y(), obj->get_HGRID_z(), obj->get_HGRID_Level());
     if(obj->get_HGRID_PrevObject())
         obj->get_HGRID_PrevObject()->set_HGRID_NextObject(obj->get_HGRID_NextObject());
     else
         if(grid->objectBucket[bucket]==obj)
             grid->objectBucket[bucket]=obj->get_HGRID_NextObject();
         
     if(obj->get_HGRID_NextObject())
         obj->get_HGRID_NextObject()->set_HGRID_PrevObject(obj->get_HGRID_PrevObject());
 }

void HGRID_3D::HGRID_UpdateParticleInHgrid ( BaseParticle * obj )

protected

This adds a partcile to the Grid, called in the grid setup routies.

Add object to grid square, and remember cell and level numbers, treating level as a third dimension coordinate.

Definition at line 220 of file HGRID_3D.cc.

References HGrid::ComputeHashBucketIndex(), BaseParticle::get_HGRID_Level(), BaseParticle::get_HGRID_x(), BaseParticle::get_HGRID_y(), BaseParticle::get_HGRID_z(), BaseParticle::get_PeriodicFromParticle(), BaseParticle::get_Position(), HGRID_base::grid, HGRID_RemoveParticleFromHgrid(), HGrid::invCellSizes_, HGrid::objectBucket, BaseParticle::set_HGRID_NextObject(), BaseParticle::set_HGRID_PrevObject(), BaseParticle::set_HGRID_x(), BaseParticle::set_HGRID_y(), BaseParticle::set_HGRID_z(), Vec3D::X, Vec3D::Y, and Vec3D::Z.

Referenced by Chute::add_particle(), and Chute::IsInsertable().

 {
     int l = obj->get_HGRID_Level();
     Mdouble inv_size = grid->invCellSizes_[l];
 
     int x=(int)floor(obj->get_Position().X * inv_size);
     int y=(int)floor(obj->get_Position().Y * inv_size);
     int z=(int)floor(obj->get_Position().Z * inv_size);
     
 #ifdef ContactListHgrid
     if(obj->get_HGRID_x()!=x||obj->get_HGRID_y()!=y||obj->get_HGRID_z()!=z||obj->get_PeriodicFromParticle())
     {
         if(!obj->get_PeriodicFromParticle())
         {
             int bucket = grid->ComputeHashBucketIndex(x, y, z, l);
                     
             //First the object has to be removed
             HGRID_RemoveParticleFromHgrid(obj);
             //Also remove all contact associated with it
             getPossibleContactList().remove_ParticlePosibleContacts(obj);
             
             //And now reinserted
             obj->set_HGRID_NextObject(grid->objectBucket[bucket]);
             if(grid->objectBucket[bucket])
                 grid->objectBucket[bucket]->set_HGRID_PrevObject(obj);
             obj->set_HGRID_PrevObject(0);
             grid->objectBucket[bucket] = obj;
         }
         
         obj->set_HGRID_x(x);
         obj->set_HGRID_y(y);
         obj->set_HGRID_z(z);            
         InsertObjAgainstGrid(grid, obj);
     }
 #else
     int bucket = grid->ComputeHashBucketIndex(x,y,z,l);
 
     obj->set_HGRID_NextObject(grid->objectBucket[bucket]);
     if(grid->objectBucket[bucket])
         grid->objectBucket[bucket]->set_HGRID_PrevObject(obj);
     obj->set_HGRID_PrevObject(0);
     grid->objectBucket[bucket] = obj;
 
     obj->set_HGRID_x(x);
     obj->set_HGRID_y(y);
     obj->set_HGRID_z(z);
 #endif
 }

bool HGRID_3D::TestCell	(	int	x,
		int	y,
		int	z,
		int	l,
		BaseParticle *	obj,
		HGrid *	grid
	)

protected

Tests obj against all particles in cell similar to CheckCell, but links to TestObject instead of compute_internal_forces.

Definition at line 286 of file HGRID_3D.cc.

References HGrid::ComputeHashBucketIndex(), BaseParticle::get_HGRID_Level(), BaseParticle::get_HGRID_NextObject(), BaseParticle::get_HGRID_x(), BaseParticle::get_HGRID_y(), BaseParticle::get_HGRID_z(), HGrid::objectBucket, and HGRID_base::TestObject().

Referenced by TestObjAgainstGrid().

 {
     bool Test = true;
         
     // Loop through all objects in the bucket to find nearby objects
     int bucket = grid->ComputeHashBucketIndex(x,y,z,l);
     BaseParticle *p = grid->objectBucket[bucket];
     
     while (Test && p!=NULL)
     {
         if ((p->get_HGRID_x() == x) && (p->get_HGRID_y() == y) && (p->get_HGRID_z() == z) && (p->get_HGRID_Level() == l)) 
         {
             Test = Test && TestObject(obj,p);       
         }
         p = p->get_HGRID_NextObject();
     }
 
     return Test;
 }

bool HGRID_3D::TestObjAgainstGrid	(	HGrid *	grid,
		BaseParticle *	obj
	)

protected

Tests obj against all neighbouring particles similar to CheckObjAgainstGrid, but links to TestCell instead of CheckCell.

Definition at line 310 of file HGRID_3D.cc.

References HGrid::cellSizes_, BaseParticle::get_Position(), HGrid::invCellSizes_, HGrid::occupiedLevelsMask, TestCell(), Vec3D::X, Vec3D::Y, and Vec3D::Z.

Referenced by Chute::IsInsertable().

 {
     bool Test = true;
     
     int x, y, z;
     Mdouble inv_size;
     int occupiedLevelsMask = grid->occupiedLevelsMask;
 
     for (unsigned int level = 0; level < grid->cellSizes_.size() && Test; occupiedLevelsMask >>= 1, level++) 
     {
         // If no objects in rest of grid, stop now
         if (occupiedLevelsMask == 0) break;
                 
         // If no objects at this level, go on to the next level
         if ((occupiedLevelsMask & 1) == 0) continue;
     
         // Treat level as a third dimension coordinate
         inv_size = grid->invCellSizes_[level];
 
         x = (int)floor(obj->get_Position().X * inv_size);
         y = (int)floor(obj->get_Position().Y * inv_size);
         z = (int)floor(obj->get_Position().Z * inv_size);
 
         Test = Test 
                 && TestCell(x  , y  , z  , level, obj, grid)
                 && TestCell(x  , y-1, z  , level, obj, grid)
                 && TestCell(x  , y+1, z  , level, obj, grid)
                 && TestCell(x-1, y  , z  , level, obj, grid)
                 && TestCell(x+1, y  , z  , level, obj, grid)
                 && TestCell(x-1, y-1, z  , level, obj, grid)
                 && TestCell(x-1, y+1, z  , level, obj, grid)
                 && TestCell(x+1, y-1, z  , level, obj, grid)
                 && TestCell(x+1, y+1, z  , level, obj, grid)
 
                 && TestCell(x  , y  , z-1, level, obj, grid)
                 && TestCell(x  , y-1, z-1, level, obj, grid)
                 && TestCell(x  , y+1, z-1, level, obj, grid)
                 && TestCell(x-1, y  , z-1, level, obj, grid)
                 && TestCell(x+1, y  , z-1, level, obj, grid)
                 && TestCell(x-1, y-1, z-1, level, obj, grid)
                 && TestCell(x-1, y+1, z-1, level, obj, grid)
                 && TestCell(x+1, y-1, z-1, level, obj, grid)
                 && TestCell(x+1, y+1, z-1, level, obj, grid)
 
                 && TestCell(x  , y  , z+1, level, obj, grid)
                 && TestCell(x  , y-1, z+1, level, obj, grid)
                 && TestCell(x  , y+1, z+1, level, obj, grid)
                 && TestCell(x-1, y  , z+1, level, obj, grid)
                 && TestCell(x+1, y  , z+1, level, obj, grid)
                 && TestCell(x-1, y-1, z+1, level, obj, grid)
                 && TestCell(x-1, y+1, z+1, level, obj, grid)
                 && TestCell(x+1, y-1, z+1, level, obj, grid)
                 && TestCell(x+1, y+1, z+1, level, obj, grid);
     } //end for level
 
     return Test;
 } 

The documentation for this class was generated from the following files:

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation