Classes
class	Cell
	Individual cell for contact detection. More...

class	Cells< d >
	All the cells making the space, with related function for creating the cell array, neighbour arrays etc. Currently non implemented TODO: no pbc handling, no handling of moving boundaries. More...

class	Action< d >
	Handle force and torque contact information. More...

class	SpecificAction< d >
	Action on a specific particle for a specific duration. More...

class	cp< d >
	Contact properties class. More...

class	cpm< d >
	Contact properties for mesh contacts (mainly), including contact point location, specialising cp. More...

class	ContactList< d >
	Handles lists of contacts. More...

class	ContactListMesh< d >
	Handles lists of contacts with meshes. More...

class	Contacts< d >
	Calculate contact forces. More...

class	Simulation< d >

struct	CLp_it_t< d >
	Simple packing structure for the iterators to the contact list regions per particle. More...

class	Multiproc< d >
	Manual multiprocessor handling for OpenMP, for max efficiency & avoiding bugs & race conditions, hopefully. More...

class	number_gen< T >
	Small class to handle number generator (ie. first:step:last syntax) More...

class	Parameters< d >
	Generic class to handle the simulation set up. More...

class	TensorInfos
	Limited use: used to transfer data to the VTK writer. More...

class	Tools_2D
	Dimension specific mathematics. More...

class	Tools< d >
	Static class to handle multi-dimensional mathematics, and more. It gets specialised for speed with template parameter d:dimension. More...

Macros
#define	CONTACTLIST

#define	MAXDIM 4

#define	MACRO(r, state) case BOOST_PP_TUPLE_ELEM(2, 0, state): templatedmain<BOOST_PP_TUPLE_ELEM(2, 0, state)>(argv);break;

#define	STR_PROTECT(s) s

#define	MAXDEFDIM 30
	For larger number of dimension, be taken in particular for periodic boundary conditions. More...

Typedefs
using	json = nddem::json

using	uint = unsigned int

using	v1d = vector< double >

using	v2d = vector< vector< double > >

using	v3d = vector< vector< vector< double > >>

using	v1f = vector< float >

using	cv1d = const vector< double >

using	cv2d = const vector< vector< double > >

using	cv3d = const vector< vector< vector< double > >>

using	cv1f = const vector< float >

using	bitdim = unsigned int

using	v1i = vector< int >

Enumerations
enum class	ExportType { NONE =0 , CSV =1 , VTK =2 , NETCDFF =4 , XML =8 , XMLbase64 =16 , CSVA =32 , CSVCONTACT =64 }

enum class	ExportData { NONE =0 , POSITION =0x1 , VELOCITY =0x2 , OMEGA =0x4 , OMEGAMAG =0x8 , ORIENTATION =0x10 , COORDINATION =0x20 , RADIUS =0x40 , IDS =0x80 , FN =0x100 , FT =0x200 , TORQUE =0x400 , GHOSTMASK =0x800 , GHOSTDIR =0x1000 , BRANCHVECTOR =0x2000 , FN_EL =0x4000 , FN_VISC =0x8000 , FT_EL =0x10000 , FT_VISC =0x20000 , FT_FRIC =0x40000 , FT_FRICTYPE =0x80000 , CONTACTPOSITION =0x100000 , MASS =0x200000 }

enum class	TensorType { SCALAR , VECTOR , TENSOR , SYMTENSOR , SKEWTENSOR , SCALARMASK , NONE }

enum	DataValue { radius , mass , Imom , pos , vel , omega , id1 , id2 , pospq , lpq , fpq , mpq , mqp , orient , extra_named , radius , mass , Imom , pos , vel , omega , id1 , id2 , pospq , lpq , fpq , mpq , mqp , orient , extra_named }

enum	ContactModels { HOOKE =0 , HERTZ }

enum	ContactStrategies { NAIVE =0 , CELLS =1 , OCTREE =2 }

enum class	WallType { PBC =0 , WALL =1 , MOVINGWALL =2 , SPHERE =3 , ROTATINGSPHERE =4 , PBC_LE =5 , ELLIPSE =6 , HEMISPHERE =7 , AXIALCYLINDER , UNDEFINED }

Functions
template<int d>
bool	operator< (const cp< d > &a, const cp< d > &b)
	The contact list is order in increasing order of index i, and for two identical i in increasing order of j. More...

template<int d>
bool	operator== (const cp< d > &a, const cp< d > &b)
	Contact equivalence is based solely on the index of objects in contact i and j. More...

void	sig_handler (int p)
	Function handling signal reception for clean closing on SIGINT for example. More...

template<int d>
int	templatedmain (char *argv[])
	Main simulation run. All the simulation is handled by this function. More...

int	main (int argc, char *argv[])
	Calls the appropriate templatedmain() function. Templated function are used to allow compiler optimisation for speed. Only a handful of dimension are compiled on the base code to limit compilation time and memory. If you need dimensions that are not cmpiled by default, have a look at the code it's pretty straightforward to activate the needed dimension. If the compilation failed with low meomry, in particular on older system, head to the code and comment the dimensions which are unused. More...

ExportType &	operator\|= (ExportType &a, const ExportType b)

ExportData &	operator\|= (ExportData &a, const ExportData b)

ExportData	operator\| (ExportData a, ExportData b)

ExportData	operator~ (ExportData a)

ExportData &	operator&= (ExportData &a, const ExportData b)

ExportData &	operator>>= (ExportData &w, int u)

ExportData &	operator<<= (ExportData &w, int u)

bool	operator& (ExportType &a, ExportType b)

bool	operator& (ExportData &a, ExportData b)

template<typename T >
std::istream &	operator>> (std::istream &in, number_gen< T > &n)

v1d	operator* (v1d a, double b)

v1f	operator* (v1f a, float b)

v1d	operator* (v1d a, cv1d &b)

v1f	operator* (v1f a, cv1f &b)

v1d	operator+ (v1d a, double b)

v1d	operator+ (v1d a, cv1d &b)

v1f	operator+ (v1f a, cv1f &b)

v1d	operator- (v1d a, double &b)

v1d	operator- (v1d a, cv1d &b)

v1d	operator- (v1d a, const double *b)

v1d	operator- (const double *a, v1d b)

v1d	operator- (v1d a)

v1f	operator- (v1f a, cv1f &b)

v1d	operator/ (v1d a, double b)

v1d &	operator-= (v1d &a, cv1d &b)

v1d &	operator*= (v1d &a, double b)

v1f &	operator*= (v1f &a, double b)

v1d &	operator+= (v1d &a, cv1d &b)

v1f &	operator+= (v1f &a, cv1f &b)

v1f &	operator/= (v1f &a, cv1f &b)

v1d &	operator/= (v1d &a, double b)

v1f &	operator/= (v1f &a, double b)

v1d	operator- (v1d a, double b)

int	ContactList< d >::insert (const cp< d > &a)
	Insert a contact, maintaining sorting with increasing i, and removing missing contacts on traversal. More...

int	ContactListMesh< d >::insert (const cpm< d > &a)
	Insert a contact, maintaining sorting with increasing i, and removing missing contacts on traversal. More...

bool	ContactList< d >::check_ghost_regular (bitdim gst, const Parameters< d > &P, cv1d &X1, cv1d &X2, double r1, double r2, cp< d > &tmpcp, int startd=0, double partialsum=0, bitdim mask=0)
	Find ghost-particle contact, going though pbc recursively. A beautiful piece of optimised algorithm if I may say so myself. More...

bool	ContactList< d >::check_ghost_LE (bitdim gst, const Parameters< d > &P, cv1d &X1, cv1d &X2, double r1, double r2, cp< d > &tmpcp, int startd=0, double partialsum=0, bitdim mask=0)

void	ContactList< d >::check_ghost_dst (uint32_t gst, int n, double partialsum, uint32_t mask, const Parameters< d > &P, cv1d &X1, cv1d &X2, cp< d > &contact)

void	ContactList< d >::coordinance (v1d &Z)
	Calculate and store coordination number in Z. More...

	Contacts< d >::Contacts (Parameters< d > &PP)

void	Contacts< d >::particle_particle (cv1d &Xi, cv1d &Vi, cv1d &Omegai, double ri, double mi, cv1d &Xj, cv1d &Vj, cv1d &Omegaj, double rj, double mj, cp< d > &Contact, bool isdumptime)
	Force & torque between 2 particles. More...

void	Contacts< d >::particle_wall (cv1d &Vi, cv1d &Omegai, double ri, double mi, cv1d &cn, cp< d > &Contact)
	Force & torque between a particle and a wall. More...

void	Contacts< d >::particle_movingwall (cv1d &Vi, cv1d &Omegai, double ri, double mi, cv1d &cn, cv1d &Vj, cp< d > &Contact)
	Force & torque between a particle and a moving wall. Vj is the velocity of the wall at the contact point. More...

void	Contacts< d >::particle_mesh (cv1d &Xi, cv1d &Vi, cv1d &Omegai, double ri, double mi, cpm< d > &Contact)
	Force & torque between particle and mesh. More...

void	Multiproc< d >::disp_share ()
	Display the # of particle on each thread. More...

void	Multiproc< d >::split (int N, int P)
	Function to allocate the grains to threads taking into account the load balance in the contact detection. load_balance() takes over after a few iteration have run, and is usually more efficient. More...

void	Multiproc< d >::splitcells (int C)

void	Multiproc< d >::delaying (int ID, int j, Action< d > &act)
	Record the action to be added later to the relevent atom in sequencial settings, avoid potential race condition if an action was added to an atom that is not owned by the thread. This is for a particle-particle contact. More...

void	Multiproc< d >::delayingwall (int ID, int j, Action< d > &act)
	Record the action on the wall. Only usefull if the force on the wall needs to be calculated. More...

void	Multiproc< d >::delayed_clean ()
	Clean the record list. More...

void	Multiproc< d >::delayedwall_clean ()
	Clean the record of the force on the wal. More...

void	Multiproc< d >::load_balance (ContactStrategies contactstrategy)
	Modify the atom share between threads to achieve better load balance between the threads based on the current speed of each one during the previous iterations. More...

auto	Multiproc< d >::contacts2array (ExportData exp, cv2d &X, Parameters< d > &P)
	pack the contact data in a 2d array More...

Variables
vector< std::pair< ExportType, ExportData > > *	toclean

XMLWriter *	xmlout

vector< std::pair< ExportType, ExportData > > *	toclean

XMLWriter *	xmlout

static vector< vector< int > >	Tools< d >::MSigns
	For skew symetric matrix. -1 below the diagonal, 0 on the diagonal, +1 above the diagnal. More...

static vector< vector< int > >	Tools< d >::MIndexAS
	For skew symmetric matrix, make the correspondance between linear index of a full matrix with the linear index of the skew-symetric storage. More...

static vector< pair< int, int > >	Tools< d >::MASIndex
	For skew symmetric matrix, make the correspondance between linear index and (row,column) index. More...

static v1d	Tools< d >::Eye
	The identity matrix in dimension <d> More...

static vector< FILE * >	Tools< d >::outs
	Store the output file descriptors. More...

static boost::random::mt19937	Tools< d >::rng
	Random number generator. More...

static boost::random::uniform_01< boost::mt19937 >	Tools< d >::rand
	Returns a random number between 0 and 1. More...

General functions
static void	Tools< d >::initialise ()
	Initialise the member variables, in particular the variables to handle skew-symmetric flattened matrix, cf. the class detailed description. More...

static void	Tools< d >::clear ()
	Get the class ready for a different dimension. More...

static std::pair< double, double >	Tools< d >::two_max_element (cv1d &v)
	Return the two largest elements of v. More...

static bool	Tools< d >::check_initialised (int dd)

static int	Tools< d >::sgn (uint8_t a)
	Sign function. More...

static int	Tools< d >::sgn (double a)
	Sign function. More...

Saving and writing functions
static int	Tools< d >::savetxt (char path[], const v2d &table, char const header[])

static int	Tools< d >::write1D (char path[], v1d table)

static void	Tools< d >::savecsv (char path[], cv2d &X, cv1d &r, const vector< uint32_t > &PBCFlags, cv1d &Vmag, cv1d &OmegaMag, [[maybe_unused]] cv1d &Z)
	Save the location and a few more informations in a CSV file. More...

static void	Tools< d >::savecsv (char path[], cv2d &X, cv2d &V, cv1d &r, const vector< uint32_t > &PBCFlags, cv1d &Vmag, cv1d &OmegaMag, [[maybe_unused]] cv1d &Z)
	Save the location and a few more informations in a CSV file. More...

static void	Tools< d >::savecsv (char path[], cv2d &A)
	Save the orientation in a CSV file. More...

static void	Tools< d >::savevtk (char path[], int N, cv2d &Boundaries, cv2d &X, cv1d &r, vector< TensorInfos > data)
	Save as a vtk file. Dimensions higher than 3 are stored as additional scalars. Additional informations can be passed as a vector of TensorInfos. More...

static int	Tools< d >::writeinline (initializer_list< v1d >)

static int	Tools< d >::writeinline_close (void)

static void	Tools< d >::print (cv1d M)

Vector and matrix initialisation and normalisation
static v1d	Tools< d >::randomize_vec (cv1d v)
	Produce a random vector. More...

static void	Tools< d >::unitvec (vector< double > &v, int n)
	Construct a unit vector in place. More...

static void	Tools< d >::orthonormalise (v1d &A)
	Orthonormalise A using the Gram-Shmidt process, in place. More...

static v1d	Tools< d >::unitvec (int n)
	Construct & return a unit vector. More...

static void	Tools< d >::setzero (v2d &a)
	Set a matrix to zero in-place. More...

static void	Tools< d >::setzero (v1d &a)
	Set a vector to zero in-place. More...

static double	Tools< d >::norm (const vector< double > &a)
	Norm of a vector. More...

static void	Tools< d >::norm (v1d &res, cv2d &a)
	Norm of a 2D-matrix, returns a 1D vector with the norms of the individual vectors. More...

static double	Tools< d >::normdiff (cv1d &a, cv1d &b)
	Norm of a vector difference . More...

static double	Tools< d >::normsq (const vector< double > &a)
	Norm squared. More...

static double	Tools< d >::normdiffsq (cv1d &a, cv1d &b)
	Norm squared of a vector difference . More...

static double	Tools< d >::skewnorm (cv1d &a)
	Norm of a skew-symetric matrix. More...

static double	Tools< d >::skewnormsq (cv1d &a)
	Norm squared of a skew-symetrix matrix. More...

static double	Tools< d >::dot (cv1d &a, cv1d &b)
	Dot product. More...

static v1f	Tools< d >::vsqrt (cv1f &a)
	Component-wise square root. More...

static v1f	Tools< d >::vsq (cv1f &a)
	Component-wise squaring. More...

static void	Tools< d >::surfacevelocity (v1d &res, cv1d &p, double com, double vel_com, double *omega_com)

static void	Tools< d >::setgravity (v2d &a, v1d &g, v1d &m)
	Set the gravity. $\vec a_i = m_i * \vec g$ . More...

Matrix operations, usually operating on flattened matrices, cf. the description for more information on matrix storage
static v1d	Tools< d >::skewmatvecmult (cv1d &M, cv1d &v)
	Multiply the skew symetric matrix M with vector v. More...

static v1d	Tools< d >::skewmatvecmult (const double *M, cv1d &v)
	Multiply the skew symetric matrix M with vector v. More...

static void	Tools< d >::skewmatvecmult (v1d &r, cv1d &M, cv1d &v)
	Multiply the skew symetric matrix M with vector v in place. More...

static void	Tools< d >::skewmatvecmult (v1d &r, const double *M, cv1d &v)
	Multiply the skew symetric matrix M with vector v in place (overload) More...

static v1d	Tools< d >::skewmatsquare (cv1d &A)
	Square the skew symetric matrix M. More...

static void	Tools< d >::skewmatsquare (v1d &r, cv1d &A)
	Square the skew symetric matrix M in place. More...

static v1d	Tools< d >::skewexpand (cv1d &A)
	Return the skew symetrix matrix M stored on d(d-1)/2 component as a full flattened matrix with d^2 components. More...

static void	Tools< d >::skewexpand (v1d &r, cv1d &A)
	Return the skew symetrix matrix M stored on d(d-1)/2 component as a full flattened matrix with d^2 components in place. More...

static v1d	Tools< d >::matmult (cv1d &A, cv1d &B)
	Multiply 2 matrix together. More...

static void	Tools< d >::matmult (v1d &r, cv1d &A, cv1d &B)
	Multiply 2 matrix together in place. More...

static void	Tools< d >::matvecmult (v1d &res, cv1d &A, cv1d &B)
	Multiply a matrix with a vector, in place. More...

static v1d	Tools< d >::wedgeproduct (cv1d &a, cv1d &b)
	Wedge product of vectors. More...

static void	Tools< d >::wedgeproduct (v1d &res, cv1d &a, cv1d &b)
	Wedge product in-place. More...

static double	Tools< d >::det (cv2d &M)
	compute the matrix determinant (probably quite slow, but doesn't really really matters for the usage) More...

static double	Tools< d >::det (cv1d &M)
	compute the matrix determinant (probably quite slow, but shouldn't really really matters for the usage) More...

static double	Tools< d >::det (double M[d][d])
	compute the matrix determinant using array on the stack (avoids malloc/free) More...

static v1d	Tools< d >::inverse (cv1d &M)
	compute the matrix inverse (very slow and redundant calculation of the determinant for the comatrix, but shouldn't really really matters for the usage) More...

static v1d	Tools< d >::transpose (cv1d &a)
	Transposition. More...

static void	Tools< d >::transpose_inplace (v1d &a)
	Transpose in-place. More...

Special physics computation
static double	Tools< d >::Volume (double R)
	Compute the hypersphere volume. More...

static double	Tools< d >::InertiaMomentum (double R, double rho)
	Compute the hypersphere moment of inertia. More...

Coordinate system change
static double	Tools< d >::hyperspherical_xtophi (cv1d &x, v1d &phi)
	Convert from cartesian to hyperspherical coordinates. More...

static void	Tools< d >::hyperspherical_phitox (double r, cv1d &phi, v1d &x)
	Convert from hyperspherical to cartesian coordinates. More...

Detailed Description

This module handles the Discrete Element Simulations.

Macro Definition Documentation

◆ CONTACTLIST

#define CONTACTLIST

◆ MACRO

#define MACRO	(	r,
		state
	)	case BOOST_PP_TUPLE_ELEM(2, 0, state): templatedmain<BOOST_PP_TUPLE_ELEM(2, 0, state)>(argv);break;

◆ MAXDEFDIM

#define MAXDEFDIM 30

For larger number of dimension, be taken in particular for periodic boundary conditions.

◆ MAXDIM

#define MAXDIM 4

◆ STR_PROTECT

#define STR_PROTECT ( s ) s

Typedef Documentation

◆ bitdim

using bitdim = unsigned int

◆ cv1d

using cv1d = const vector <double>

◆ cv1f

using cv1f = const vector <float>

◆ cv2d

using cv2d = const vector < vector <double> >

◆ cv3d

using cv3d = const vector<vector<vector<double> >>

◆ json

using json = nddem::json

◆ uint

using uint = unsigned int

◆ v1d

using v1d = vector < double >

◆ v1f

using v1f = vector <float>

◆ v1i

using v1i = vector <int>

◆ v2d

using v2d = vector < vector <double> >

◆ v3d

using v3d = vector<vector<vector<double> >>

Enumeration Type Documentation

◆ ContactModels

enum ContactModels

Enumerator
HOOKE
HERTZ

◆ ContactStrategies

enum ContactStrategies

Enumerator
NAIVE
CELLS
OCTREE

◆ DataValue

enum DataValue

Enumerator
radius
mass
Imom
pos
vel
omega
id1
id2
pospq
lpq
fpq
mpq
mqp
orient
extra_named
radius
mass
Imom
pos
vel
omega
id1
id2
pospq
lpq
fpq
mpq
mqp
orient
extra_named

◆ ExportData

enum ExportData

strong

Enumerator
NONE
POSITION
VELOCITY
OMEGA
OMEGAMAG
ORIENTATION
COORDINATION
RADIUS
IDS
FN
FT
TORQUE
GHOSTMASK
GHOSTDIR
BRANCHVECTOR
FN_EL
FN_VISC
FT_EL
FT_VISC
FT_FRIC
FT_FRICTYPE
CONTACTPOSITION
MASS

◆ ExportType

enum ExportType

strong

Enumerator
NONE
CSV
VTK
NETCDFF
XML
XMLbase64
CSVA
CSVCONTACT

◆ TensorType

enum TensorType

strong

Enumerator
SCALAR
VECTOR
TENSOR
SYMTENSOR
SKEWTENSOR
SCALARMASK
NONE

◆ WallType

enum WallType

strong

Enumerator
PBC
WALL
MOVINGWALL
SPHERE
ROTATINGSPHERE
PBC_LE
ELLIPSE
HEMISPHERE
AXIALCYLINDER
UNDEFINED

Function Documentation

◆ check_ghost_dst()

template<int d>

void ContactList< d >::check_ghost_dst	(	uint32_t	gst,
		int	n,
		double	partialsum,
		uint32_t	mask,
		const Parameters< d > &	P,
		cv1d &	X1,
		cv1d &	X2,
		cp< d > &	contact
	)

Deprecated:: Measure distance between a ghost and a particle

◆ check_ghost_LE()

template<int d>

bool ContactList< d >::check_ghost_LE	(	bitdim	gst,
		const Parameters< d > &	P,
		cv1d &	X1,
		cv1d &	X2,
		double	r1,
		double	r2,
		cp< d > &	tmpcp,
		int	startd = `0`,
		double	partialsum = `0`,
		bitdim	mask = `0`
	)

◆ check_ghost_regular()

template<int d>

bool ContactList< d >::check_ghost_regular	(	bitdim	gst,
		const Parameters< d > &	P,
		cv1d &	X1,
		cv1d &	X2,
		double	r1,
		double	r2,
		cp< d > &	tmpcp,
		int	startd = `0`,
		double	partialsum = `0`,
		bitdim	mask = `0`
	)

Find ghost-particle contact, going though pbc recursively. A beautiful piece of optimised algorithm if I may say so myself.

◆ check_initialised()

template<int d>

static bool Tools< d >::check_initialised ( int dd )

inlinestatic

◆ clear()

template<int d>

void Tools< d >::clear

static

Get the class ready for a different dimension.

◆ Contacts()

template<int d>

Contacts< d >::Contacts ( Parameters< d > & PP )

◆ contacts2array()

template<int d>

auto Multiproc< d >::contacts2array	(	ExportData	exp,
		cv2d &	X,
		Parameters< d > &	P
	)

pack the contact data in a 2d array

◆ coordinance()

template<int d>

void ContactList< d >::coordinance ( v1d & Z )

Calculate and store coordination number in Z.

◆ delayed_clean()

template<int d>

void Multiproc< d >::delayed_clean

Clean the record list.

◆ delayedwall_clean()

template<int d>

void Multiproc< d >::delayedwall_clean

Clean the record of the force on the wal.

◆ delaying()

template<int d>

void Multiproc< d >::delaying	(	int	ID,
		int	j,
		Action< d > &	act
	)

Record the action to be added later to the relevent atom in sequencial settings, avoid potential race condition if an action was added to an atom that is not owned by the thread. This is for a particle-particle contact.

◆ delayingwall()

template<int d>

void Multiproc< d >::delayingwall	(	int	ID,
		int	j,
		Action< d > &	act
	)

Record the action on the wall. Only usefull if the force on the wall needs to be calculated.

◆ det() [1/3]

template<int d>

double Tools< d >::det ( cv1d & M )

static

compute the matrix determinant (probably quite slow, but shouldn't really really matters for the usage)

◆ det() [2/3]

template<int d>

double Tools< d >::det ( cv2d & M )

static

compute the matrix determinant (probably quite slow, but doesn't really really matters for the usage)

◆ det() [3/3]

template<int d>

double Tools< d >::det ( double M[d][d] )

static

compute the matrix determinant using array on the stack (avoids malloc/free)

◆ disp_share()

template<int d>

void Multiproc< d >::disp_share

Display the # of particle on each thread.

◆ dot()

template<int d>

static double Tools< d >::dot	(	cv1d &	a,
		cv1d &	b
	)

inlinestatic

Dot product.

◆ hyperspherical_phitox()

template<int d>

void Tools< d >::hyperspherical_phitox	(	double	r,
		cv1d &	phi,
		v1d &	x
	)

static

Convert from hyperspherical to cartesian coordinates.

◆ hyperspherical_xtophi()

template<int d>

double Tools< d >::hyperspherical_xtophi	(	cv1d &	x,
		v1d &	phi
	)

static

Convert from cartesian to hyperspherical coordinates.

◆ InertiaMomentum()

template<int d>

double Tools< d >::InertiaMomentum	(	double	R,
		double	rho
	)

static

Compute the hypersphere moment of inertia.

◆ initialise()

template<int d>

void Tools< d >::initialise

static

Initialise the member variables, in particular the variables to handle skew-symmetric flattened matrix, cf. the class detailed description.

◆ insert() [1/2]

template<int d>

int ContactList< d >::insert ( const cp< d > & a )

Insert a contact, maintaining sorting with increasing i, and removing missing contacts on traversal.

◆ insert() [2/2]

template<int d>

int ContactListMesh< d >::insert ( const cpm< d > & a )

Insert a contact, maintaining sorting with increasing i, and removing missing contacts on traversal.

◆ inverse()

template<int d>

vector< double > Tools< d >::inverse ( cv1d & M )

static

compute the matrix inverse (very slow and redundant calculation of the determinant for the comatrix, but shouldn't really really matters for the usage)

◆ load_balance()

template<int d>

void Multiproc< d >::load_balance ( ContactStrategies contactstrategy )

Modify the atom share between threads to achieve better load balance between the threads based on the current speed of each one during the previous iterations.

◆ main()

int main	(	int	argc,
		char *	argv[]
	)

Calls the appropriate templatedmain() function. Templated function are used to allow compiler optimisation for speed. Only a handful of dimension are compiled on the base code to limit compilation time and memory. If you need dimensions that are not cmpiled by default, have a look at the code it's pretty straightforward to activate the needed dimension. If the compilation failed with low meomry, in particular on older system, head to the code and comment the dimensions which are unused.

◆ matmult() [1/2]

template<int d>

v1d Tools< d >::matmult	(	cv1d &	A,
		cv1d &	B
	)

static

Multiply 2 matrix together.

◆ matmult() [2/2]

template<int d>

void Tools< d >::matmult	(	v1d &	r,
		cv1d &	A,
		cv1d &	B
	)

static

Multiply 2 matrix together in place.

◆ matvecmult()

template<int d>

void Tools< d >::matvecmult	(	v1d &	res,
		cv1d &	A,
		cv1d &	B
	)

static

Multiply a matrix with a vector, in place.

◆ norm() [1/2]

template<int d>

static double Tools< d >::norm ( const vector< double > & a )

inlinestatic

Norm of a vector.

◆ norm() [2/2]

template<int d>

static void Tools< d >::norm	(	v1d &	res,
		cv2d &	a
	)

inlinestatic

Norm of a 2D-matrix, returns a 1D vector with the norms of the individual vectors.

◆ normdiff()

template<int d>

static double Tools< d >::normdiff	(	cv1d &	a,
		cv1d &	b
	)

inlinestatic

Norm of a vector difference $|a-b|$ .

◆ normdiffsq()

template<int d>

static double Tools< d >::normdiffsq	(	cv1d &	a,
		cv1d &	b
	)

inlinestatic

Norm squared of a vector difference $|a-b|^2$ .

◆ normsq()

template<int d>

static double Tools< d >::normsq ( const vector< double > & a )

inlinestatic

Norm squared.

◆ operator&() [1/2]

bool operator&	(	ExportData &	a,
		ExportData	b
	)

inline

◆ operator&() [2/2]

bool operator&	(	ExportType &	a,
		ExportType	b
	)

inline

◆ operator&=()

ExportData& operator&=	(	ExportData &	a,
		const ExportData	b
	)

inline

◆ operator*() [1/4]

v1d operator*	(	v1d	a,
		cv1d &	b
	)

◆ operator*() [2/4]

v1d operator*	(	v1d	a,
		double	b
	)

◆ operator*() [3/4]

v1f operator*	(	v1f	a,
		cv1f &	b
	)

◆ operator*() [4/4]

v1f operator*	(	v1f	a,
		float	b
	)

◆ operator*=() [1/2]

v1d & operator*=	(	v1d &	a,
		double	b
	)

◆ operator*=() [2/2]

v1f & operator*=	(	v1f &	a,
		double	b
	)

◆ operator+() [1/3]

v1d operator+	(	v1d	a,
		cv1d &	b
	)

◆ operator+() [2/3]

v1d operator+	(	v1d	a,
		double	b
	)

◆ operator+() [3/3]

v1f operator+	(	v1f	a,
		cv1f &	b
	)

◆ operator+=() [1/2]

v1d & operator+=	(	v1d &	a,
		cv1d &	b
	)

◆ operator+=() [2/2]

v1f & operator+=	(	v1f &	a,
		cv1f &	b
	)

◆ operator-() [1/7]

v1d operator-	(	const double *	a,
		v1d	b
	)

◆ operator-() [2/7]

v1d operator- ( v1d a )

◆ operator-() [3/7]

v1d operator-	(	v1d	a,
		const double *	b
	)

◆ operator-() [4/7]

v1d operator-	(	v1d	a,
		cv1d &	b
	)

◆ operator-() [5/7]

v1d operator-	(	v1d	a,
		double &	b
	)

◆ operator-() [6/7]

v1d operator-	(	v1d	a,
		double	b
	)

◆ operator-() [7/7]

v1f operator-	(	v1f	a,
		cv1f &	b
	)

◆ operator-=()

v1d & operator-=	(	v1d &	a,
		cv1d &	b
	)

◆ operator/()

v1d operator/	(	v1d	a,
		double	b
	)

◆ operator/=() [1/3]

v1d & operator/=	(	v1d &	a,
		double	b
	)

◆ operator/=() [2/3]

v1f & operator/=	(	v1f &	a,
		cv1f &	b
	)

◆ operator/=() [3/3]

v1f & operator/=	(	v1f &	a,
		double	b
	)

◆ operator<()

template<int d>

bool operator<	(	const cp< d > &	a,
		const cp< d > &	b
	)

inline

The contact list is order in increasing order of index i, and for two identical i in increasing order of j.

◆ operator<<=()

ExportData& operator<<=	(	ExportData &	w,
		int	u
	)

inline

◆ operator==()

template<int d>

bool operator==	(	const cp< d > &	a,
		const cp< d > &	b
	)

inline

Contact equivalence is based solely on the index of objects in contact i and j.

◆ operator>>()

template<typename T >

std::istream& operator>>	(	std::istream &	in,
		number_gen< T > &	n
	)

◆ operator>>=()

ExportData& operator>>=	(	ExportData &	w,
		int	u
	)

inline

◆ operator|()

ExportData operator\|	(	ExportData	a,
		ExportData	b
	)

inline

◆ operator|=() [1/2]

ExportData& operator\|=	(	ExportData &	a,
		const ExportData	b
	)

inline

◆ operator|=() [2/2]

ExportType& operator\|=	(	ExportType &	a,
		const ExportType	b
	)

inline

◆ operator~()

ExportData operator~ ( ExportData a )

inline

◆ orthonormalise()

template<int d>

void Tools< d >::orthonormalise ( v1d & A )

static

Orthonormalise A using the Gram-Shmidt process, in place.

◆ particle_mesh()

template<int d>

void Contacts< d >::particle_mesh	(	cv1d &	Xi,
		cv1d &	Vi,
		cv1d &	Omegai,
		double	ri,
		double	mi,
		cpm< d > &	Contact
	)

Force & torque between particle and mesh.

◆ particle_movingwall()

template<int d>

void Contacts< d >::particle_movingwall	(	cv1d &	Vi,
		cv1d &	Omegai,
		double	ri,
		double	mi,
		cv1d &	cn,
		cv1d &	Vj,
		cp< d > &	Contact
	)

Force & torque between a particle and a moving wall. Vj is the velocity of the wall at the contact point.

◆ particle_particle()

template<int d>

void Contacts< d >::particle_particle	(	cv1d &	Xi,
		cv1d &	Vi,
		cv1d &	Omegai,
		double	ri,
		double	mi,
		cv1d &	Xj,
		cv1d &	Vj,
		cv1d &	Omegaj,
		double	rj,
		double	mj,
		cp< d > &	Contact,
		bool	isdumptime
	)

Force & torque between 2 particles.

◆ particle_wall()

template<int d>

void Contacts< d >::particle_wall	(	cv1d &	Vi,
		cv1d &	Omegai,
		double	ri,
		double	mi,
		cv1d &	cn,
		cp< d > &	Contact
	)

Force & torque between a particle and a wall.

◆ print()

template<int d>

static void Tools< d >::print ( cv1d M )

inlinestatic

◆ randomize_vec()

template<int d>

v1d Tools< d >::randomize_vec ( cv1d v )

static

Produce a random vector.

◆ savecsv() [1/3]

template<int d>

void Tools< d >::savecsv	(	char	path[],
		cv2d &	A
	)

static

Save the orientation in a CSV file.

◆ savecsv() [2/3]

template<int d>

void Tools< d >::savecsv	(	char	path[],
		cv2d &	X,
		cv1d &	r,
		const vector< uint32_t > &	PBCFlags,
		cv1d &	Vmag,
		cv1d &	OmegaMag,
		[[maybe_unused] ] cv1d &	Z
	)

static

Save the location and a few more informations in a CSV file.

◆ savecsv() [3/3]

template<int d>

void Tools< d >::savecsv	(	char	path[],
		cv2d &	X,
		cv2d &	V,
		cv1d &	r,
		const vector< uint32_t > &	PBCFlags,
		cv1d &	Vmag,
		cv1d &	OmegaMag,
		[[maybe_unused] ] cv1d &	Z
	)

static

Save the location and a few more informations in a CSV file.

◆ savetxt()

template<int d>

int Tools< d >::savetxt	(	char	path[],
		const v2d &	table,
		char const	header[]
	)

static

◆ savevtk()

template<int d>

void Tools< d >::savevtk	(	char	path[],
		int	N,
		cv2d &	Boundaries,
		cv2d &	X,
		cv1d &	r,
		vector< TensorInfos >	data
	)

static

Save as a vtk file. Dimensions higher than 3 are stored as additional scalars. Additional informations can be passed as a vector of TensorInfos.

◆ setgravity()

template<int d>

static void Tools< d >::setgravity	(	v2d &	a,
		v1d &	g,
		v1d &	m
	)

inlinestatic

Set the gravity. $\vec a_i = m_i * \vec g$ .

◆ setzero() [1/2]

template<int d>

static void Tools< d >::setzero ( v1d & a )

inlinestatic

Set a vector to zero in-place.

◆ setzero() [2/2]

template<int d>

static void Tools< d >::setzero ( v2d & a )

inlinestatic

Set a matrix to zero in-place.

◆ sgn() [1/2]

template<int d>

static int Tools< d >::sgn ( double a )

inlinestatic

Sign function.

◆ sgn() [2/2]

template<int d>

static int Tools< d >::sgn ( uint8_t a )

inlinestatic

Sign function.

◆ sig_handler()

void sig_handler ( int p )

Function handling signal reception for clean closing on SIGINT for example.

◆ skewexpand() [1/2]

template<int d>

v1d Tools< d >::skewexpand ( cv1d & A )

static

Return the skew symetrix matrix M stored on d(d-1)/2 component as a full flattened matrix with d^2 components.

◆ skewexpand() [2/2]

template<int d>

void Tools< d >::skewexpand	(	v1d &	r,
		cv1d &	A
	)

static

Return the skew symetrix matrix M stored on d(d-1)/2 component as a full flattened matrix with d^2 components in place.

◆ skewmatsquare() [1/2]

template<int d>

v1d Tools< d >::skewmatsquare ( cv1d & A )

static

Square the skew symetric matrix M.

◆ skewmatsquare() [2/2]

template<int d>

void Tools< d >::skewmatsquare	(	v1d &	r,
		cv1d &	A
	)

static

Square the skew symetric matrix M in place.

◆ skewmatvecmult() [1/4]

template<int d>

v1d Tools< d >::skewmatvecmult	(	const double *	M,
		cv1d &	v
	)

static

Multiply the skew symetric matrix M with vector v.

◆ skewmatvecmult() [2/4]

template<int d>

v1d Tools< d >::skewmatvecmult	(	cv1d &	M,
		cv1d &	v
	)

static

Multiply the skew symetric matrix M with vector v.

◆ skewmatvecmult() [3/4]

template<int d>

void Tools< d >::skewmatvecmult	(	v1d &	r,
		const double *	M,
		cv1d &	v
	)

static

Multiply the skew symetric matrix M with vector v in place (overload)

◆ skewmatvecmult() [4/4]

template<int d>

void Tools< d >::skewmatvecmult	(	v1d &	r,
		cv1d &	M,
		cv1d &	v
	)

static

Multiply the skew symetric matrix M with vector v in place.

◆ skewnorm()

template<int d>

static double Tools< d >::skewnorm ( cv1d & a )

inlinestatic

Norm of a skew-symetric matrix.

◆ skewnormsq()

template<int d>

static double Tools< d >::skewnormsq ( cv1d & a )

inlinestatic

Norm squared of a skew-symetrix matrix.

◆ split()

template<int d>

void Multiproc< d >::split	(	int	N,
		int	P
	)

private

Function to allocate the grains to threads taking into account the load balance in the contact detection. load_balance() takes over after a few iteration have run, and is usually more efficient.

◆ splitcells()

template<int d>

void Multiproc< d >::splitcells ( int C )

◆ surfacevelocity()

template<int d>

static void Tools< d >::surfacevelocity	(	v1d &	res,
		cv1d &	p,
		double *	com,
		double *	vel_com,
		double *	omega_com
	)

inlinestatic

◆ templatedmain()

template<int d>

int templatedmain ( char * argv[] )

Main simulation run. All the simulation is handled by this function.

◆ transpose()

template<int d>

static v1d Tools< d >::transpose ( cv1d & a )

inlinestatic

Transposition.

◆ transpose_inplace()

template<int d>

static void Tools< d >::transpose_inplace ( v1d & a )

inlinestatic

Transpose in-place.

◆ two_max_element()

template<int d>

std::pair< double, double > Tools< d >::two_max_element ( cv1d & v )

static

Return the two largest elements of v.

◆ unitvec() [1/2]

template<int d>

static v1d Tools< d >::unitvec ( int n )

inlinestatic

Construct & return a unit vector.

◆ unitvec() [2/2]

template<int d>

void Tools< d >::unitvec	(	vector< double > &	v,
		int	n
	)

static

Construct a unit vector in place.

◆ Volume()

template<int d>

double Tools< d >::Volume ( double R )

static

Compute the hypersphere volume.

◆ vsq()

template<int d>

static v1f Tools< d >::vsq ( cv1f & a )

inlinestatic

Component-wise squaring.

◆ vsqrt()

template<int d>

static v1f Tools< d >::vsqrt ( cv1f & a )

inlinestatic

Component-wise square root.

◆ wedgeproduct() [1/2]

template<int d>

v1d Tools< d >::wedgeproduct	(	cv1d &	a,
		cv1d &	b
	)

static

Wedge product of vectors.

◆ wedgeproduct() [2/2]

template<int d>

void Tools< d >::wedgeproduct	(	v1d &	res,
		cv1d &	a,
		cv1d &	b
	)

static

Wedge product in-place.

◆ write1D()

template<int d>

int Tools< d >::write1D	(	char	path[],
		v1d	table
	)

static

◆ writeinline()

template<int d>

int Tools< d >::writeinline ( initializer_list< v1d > list )

static

◆ writeinline_close()

template<int d>

int Tools< d >::writeinline_close ( void )

static

Variable Documentation

◆ Eye

template<int d>

vector< double > Tools< d >::Eye

static

The identity matrix in dimension <d>

◆ MASIndex

template<int d>

vector< pair< int, int > > Tools< d >::MASIndex

static

For skew symmetric matrix, make the correspondance between linear index and (row,column) index.

◆ MIndexAS

template<int d>

vector< vector< int > > Tools< d >::MIndexAS

staticprivate

For skew symmetric matrix, make the correspondance between linear index of a full matrix with the linear index of the skew-symetric storage.

◆ MSigns

template<int d>

vector< vector< int > > Tools< d >::MSigns

staticprivate

For skew symetric matrix. -1 below the diagonal, 0 on the diagonal, +1 above the diagnal.

◆ outs

template<int d>

vector< FILE * > Tools< d >::outs

staticprivate

Store the output file descriptors.

◆ rand

template<int d>

boost::random::uniform_01< boost::mt19937 > Tools< d >::rand

static

Returns a random number between 0 and 1.

◆ rng

template<int d>

boost::random::mt19937 Tools< d >::rng

static

Random number generator.

◆ toclean [1/2]

vector<std::pair<ExportType,ExportData> >* toclean

◆ toclean [2/2]

vector<std::pair<ExportType,ExportData> >* toclean

extern

◆ xmlout [1/2]

XMLWriter* xmlout

◆ xmlout [2/2]

XMLWriter* xmlout

extern

Classes

Macros

Typedefs

Enumerations

Functions

Variables

General functions

Saving and writing functions

Vector and matrix initialisation and normalisation

Matrix operations, usually operating on flattened matrices, cf. the description for more information on matrix storage

Special physics computation

Coordinate system change

Detailed Description

Macro Definition Documentation

◆ CONTACTLIST

◆ MACRO

◆ MAXDEFDIM

◆ MAXDIM

◆ STR_PROTECT

Typedef Documentation

◆ bitdim

◆ cv1d

◆ cv1f

◆ cv2d

◆ cv3d

◆ json

◆ uint

◆ v1d

◆ v1f

◆ v1i

◆ v2d

◆ v3d

Enumeration Type Documentation

◆ ContactModels

◆ ContactStrategies

◆ DataValue

◆ ExportData

◆ ExportType

◆ TensorType

◆ WallType

Function Documentation

◆ check_ghost_dst()

◆ check_ghost_LE()

◆ check_ghost_regular()

◆ check_initialised()

◆ clear()

◆ Contacts()

◆ contacts2array()

◆ coordinance()

◆ delayed_clean()

◆ delayedwall_clean()

◆ delaying()

◆ delayingwall()

◆ det() [1/3]

◆ det() [2/3]

◆ det() [3/3]

◆ disp_share()

◆ dot()

◆ hyperspherical_phitox()

◆ hyperspherical_xtophi()

◆ InertiaMomentum()

◆ initialise()

◆ insert() [1/2]

◆ insert() [2/2]

◆ inverse()

◆ load_balance()

◆ main()

◆ matmult() [1/2]

◆ matmult() [2/2]

◆ matvecmult()

◆ norm() [1/2]

◆ norm() [2/2]

◆ normdiff()

◆ normdiffsq()

◆ normsq()

◆ operator&() [1/2]

◆ operator&() [2/2]

◆ operator&=()

◆ operator*() [1/4]

◆ operator*() [2/4]