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Data Structures
struct	Proc
	Processors information. More...

struct	Grid
	Grid information. More...

struct	Simu
	Simulation parameters. More...

struct	Obs
	Osbtacles parameters. More...

struct	Vectors
	Petsc Vectors. More...

struct	Fields
	Vector fields (at iteration, n, n+1, ...) More...

struct	Pointers
	The arrays associated to the petsc vectors. More...

struct	Arrays
	Arrays fields (at iteration, n, n+1, ...) More...

struct	Linear
	Vector and matrices for linear systems. More...

struct	Obs.mouv
	Motion parameters. More...

struct	Obs.coef
	Forces, Torques, Power, Energy, ... More...

struct	Obs.geom
	Geometry parameters. More...

struct	Obs.elast
	Lagrangian elasticity parameters. More...

struct	Linear.vec
	Petsc Vectors. More...

struct	Linear.arr
	Arrays associated to petsc vectors. More...

Macros
#define	RESET "\033[0m"

#define	BLACK "\033[30m" /* Black */

#define	RED "\033[31m" /* Red */

#define	GREEN "\033[32m" /* Green */

#define	YELLOW "\033[33m" /* Yellow */

#define	BLUE "\033[34m" /* Blue */

#define	MAGENTA "\033[35m" /* Magenta */

#define	CYAN "\033[36m" /* Cyan */

#define	WHITE "\033[37m" /* White */

#define	BOLDBLACK "\033[1m" /* Bold Black */

#define	BOLDRED "\033[1m\033[31m" /* Bold Red */

#define	BOLDGREEN "\033[1m\033[32m" /* Bold Green */

#define	BOLDYELLOW "\033[1m\033[33m" /* Bold Yellow */

#define	BOLDBLUE "\033[1m\033[34m" /* Bold Blue */

#define	BOLDMAGENTA "\033[1m\033[35m" /* Bold Magenta */

#define	BOLDCYAN "\033[1m\033[36m" /* Bold Cyan */

#define	BOLDWHITE "\033[1m\033[37m" /* Bold White */

Data Structure Documentation

◆ Proc

struct Proc

Processors information.

Data Fields
int	gxm	number of points in the X direction for the current processors with ghost nodes
int	gxs	Index of the first mesh point in the X direction for the corrent processor with ghost nodes
int	gym	number of points in the Y direction for the current processors with ghost nodes
int	gys	Index of the first mesh point in the Y direction for the corrent processor with ghost nodes
int	gzm	number of points in the Z direction for the current processors with ghost nodes
int	gzs	Index of the first mesh point in the Y direction for the corrent processor with ghost nodes
PetscMPIInt	rank	Rank of the current processor
PetscMPIInt	size	Number of processors used
int	xm	number of points in the X direction for the current processors
int	xs	Index of the first mesh point in the X direction for the corrent processor
int	ym	number of points in the Y direction for the current processors
int	ys	Index of the first mesh point in the Y direction for the current processor
int	zm	number of points in the Z direction for the current processors
int	zs	Index of the first mesh point in the Z direction for the current processor

◆ Grid

struct Grid

Grid information.

Data Fields
DM	da	petsc Distributed Array (3D Cartesian Grid)
double	dx	\( \Delta x \): space step in the X direction
double	dy	\( \Delta y \): space step in the Y direction
double	dz	\( \Delta z \): space step in the Z direction
double	epsilon	\( \varepsilon \) : interface regularization
int	ip	Shift if xperiodic=TRUE
int	jp	Shift if yperiodic=TRUE
int	kp	Shift if zperiodic=TRUE
int	nx	\( N_X \): number of points in the X direction
int	ny	\( N_Y \): number of points in the Y direction
int	nz	\( N_Z \): number of points in the Z direction
double	xmax	\( x_{max} \) for computational domain
double	xmin	\( x_{min} \) for computational domain
PetscBool	xperiodic	X-periodic boundary condition if TRUE
double	ymax	\( y_{max} \) for computational domain
double	ymin	\( y_{min} \) for computational domain
PetscBool	yperiodic	Y-periodic boundary condition if TRUE
double	zmax	\( z_{max} \) for computational domain
double	zmin	\( z_{min} \) for computational domain
PetscBool	zperiodic	Z-periodic boundary condition if TRUE

◆ Simu

struct Simu

Simulation parameters.

Data Fields
PetscBool	bi_fluid	Bi-fluid computation if TRUE
int	carac
double	Cc	Stability condition for convective terms
double	cfl
double	Cg	Stability condition for gravity
double	Cs	Stability condition for surface tension
int	cscheme	Choice of the scheme for convective terms
double	Cv	Stability condition for vicous terms
double	dt
double	dtelast
double	E
int	fluid	Choice of the fluid (air, water, both)
PetscBool	force_exa	Compute forces and torques with surface appraoch if TRUE
PetscBool	force_ext1	Compute forces and torques with volume appraoch (small box) if TRUE
PetscBool	force_ext2	Compute forces and torques with volume appraoch (large box) if TRUE
double	g
double	hsurf	Initial bi-fuid position
int	ischeme	Choice of explicit/implicit diffusive term
int	kk
double	lambda
double	mu1
double	mu2
double	mue
int	ni	Number of iteration in time
PetscBool	redist	Level Set reinitialisation if TRUE
double	rho1
double	rho2
double	rhoe
double	st
int	test	Choice of the predifined test case in TEST_CASES.DAT
double	time
double	timeac
double	timeac2
double	volume

◆ Obs

struct Obs

Osbtacles parameters.

Data Fields
int *	choice	Choice of the kind of obstacle (Fish, torus, etc)
struct Obs.coef	coef	Forces, Torques, Power, Energy, ...
struct Obs.elast	elast	Lagrangian elasticity parameters.
int *	file_format	User defined or obj geometry
struct Obs.geom	geom	Geometry parameters.
int	ib	\( ib \): index of the structures
struct Obs.mouv	mouv	Motion parameters.
int	nb	\( N_b \): number of non elastc structures
int	nbe	\( N_{be} \): number of elastc structures
int *	ne	\( N_E \): number of points on each slice (for regular body mesh)
int	nexp
int	nexp2
int	nexp3
int *	no	\( N_0 \):
int *	ns	\( N_S \): number of slices on the body (for regular body mesh)
int *	nst
char	OBJ_FILE[30][PETSC_MAX_PATH_LEN]
double *	St
double *	St_swim
int	test
double	thetafood
double	xfood
double *	xhead
double *	xtail
double	yfood
double *	yhead
double *	ytail
double	zfood
double *	zhead
double *	ztail

◆ Vectors

struct Vectors

Petsc Vectors.

Data Fields
Vec	a
Vec	an
Vec	as
Vec	DIV	Global vector for the velocity divergence
Vec	DU	Global vector for the stress tensor (possibly with elasticity)
Vec	la
Vec	lan
Vec	las
Vec	lD	Local vector for bi-flui Dirac function
Vec	ldPdy	Local vector for the pressure gradient in the gravity direction Y
Vec	lDU	Local vector for the stress tensor (possibly with elasticity)
Vec	lH	Local vector for bi-fluid Heaviside function
Vec	lLS	Local vector for the Level Set
Vec	lLSind	Local vector to indcate which is the closest body
Vec	lnx	Local vector for the X derivative of the elastic Level Set function
Vec	lny	Local vector for the Y derivative of the elastic Level Set function
Vec	lnz	Local vector for the Z derivative of the elastic Level Set function
Vec	lOn	Local vector for the norma of the Vorticity
Vec	lOx	Local vector for the X-Vorticity
Vec	lOy	Local vector for the Y-Vorticity
Vec	lOz	Local vector for the Z-Vorticity
Vec	lP	Local vector for tye pressure
Vec	lPHI	Local vector for solution of the Poisson equation
Vec	lPSI	Local vector the bi-fluid Level Set
Vec	lQ	Local vector for Q-criterion
Vec	lU	Local vector for cell center x-velocity U
Vec	lUf	Local vector for face center x-velocity Uf
Vec	lV	Local vector for cell center y-velocity V
Vec	lVf	Local vector for face center y-velocity Vf
Vec	lW	Local vector for cell center z-velocity W
Vec	lWf	Local vector for face center z-velocity Wf
Vec	lYx	Local vector for backward characteristics in X direction
Vec	lYy	Local vector for backward characteristics in Y direction
Vec	lYz	Local vector for backward characteristics in Z direction
Vec	PHI	Global vector for solution of the Poisson equation
Vec	U	Global vector for cell center x-velocity U
Vec	Uf	Global vector for face center x-velocity Uf
Vec	V	Global vector for cell center y-velocity V
Vec	Vf	Global vector for face center y-velocity Vf
Vec	W	Global vector for cell center z-velocity W
Vec	Wf	Global vector for face center z-velocity Wf
Vec	Yx	Global vector for backward characteristics in X direction
Vec	Yy	Global vector for backward characteristics in Y direction
Vec	Yz	Global vector for backward characteristics in Z direction

◆ Fields

struct Fields

Vector fields (at iteration, n, n+1, ...)

Collaboration diagram for Fields:

[legend]

Data Fields
Vectors	e	iteration \( \ast \) (for the predicted fields)
Vectors	el[10]
Vectors	elm1[10]
Vectors	elt[10]
Vectors	i[10]
Vectors	im1[10]
Vectors	it[10]
Vectors	k[10]
Vectors	l[10]
Vectors	m
Vectors	mat[6][3][3]
Vectors	n	iteration \( n \)
Vectors	nm1	iteration \( n-1 \)
Vectors	np1	iteration \( n+1 \)
Vectors	t

◆ Pointers

struct Pointers

The arrays associated to the petsc vectors.

Data Fields
double ***	a
double ***	an
double ***	as
double ***	D	Array for the bi-fluid Dirac function
double ***	DIV	Array for the velocity divergence
double ***	dPdy	Array for the cell center pressure gradient in the gravity Y direction
double ***	DU	Array for the stress tensor (possibly with elasticity)
double ***	H	Array for the bi-fluid Heaviside function
double ***	LS	Array for the body Level Set
int ***	LSind
double ***	nx	Array for the X derivative of the elastic Level Set function
double ***	ny	Array for the Y derivative of the elastic Level Set function
double ***	nz	Array for the Z derivative of the elastic Level Set function
double ***	On	Array for norm of the Vorticity
double ***	Ox	Array for X-Vorticity
double ***	Oy	Array for Y-Vorticity
double ***	Oz	Array for Z-Vorticity
double ***	P	Array for the cell center pressure P
double ***	PHI	Array for the Poisson solution
double ***	PSI	Array for bi-fluid Level Set
double ***	Q	Array for Q-criterion
double ***	U	Array for the X-cell center velocity U
double ***	Uf	Array for the X-face center velocity Uf
double ***	V	Array for the Y-cell center velocity V
double ***	Vf	Array for the Y-face center velocity Vf
double ***	W	Array for the Z-cell center velocity W
double ***	Wf	Array for the Z-face center velocity Wf
double ***	Yx	Array for the X- backward characterisctics
double ***	Yy	Array for the Y- backward characterisctics
double ***	Yz	Array for the Z- backward characterisctics

◆ Arrays

struct Arrays

Arrays fields (at iteration, n, n+1, ...)

Collaboration diagram for Arrays:

[legend]

Data Fields
Pointers	cl
Pointers	e	iteration \( \ast \) (for the predicted fields)
Pointers	el[10]
Pointers	elm1[10]
Pointers	elt[10]
Pointers	i[10]
Pointers	im1[10]
Pointers	it[10]
Pointers	k[10]
Pointers	l[10]
Pointers	m
Pointers	mat[6][3][3]
Pointers	n	iteration \( n \)
Pointers	nm1	iteration \( n-1 \)
Pointers	np1	iteration \( n+1 \)
Pointers	t

◆ Linear

struct Linear

Vector and matrices for linear systems.

Data Fields
Mat	Ap	Matrix for Poisson equation
struct Linear.arr	arr	Arrays associated to petsc vectors.
Mat	Au	Matrix for Momentum equation
int	itp	number of iterations for Poisson equation
int	itu	number of iterations for X-Momentum equation
int	itv	number of iterations for Y-Momentum equation
int	itw	number of iterations for Y-Momentum equation
KSP	kspp	Krylov solver for Poisson equation
KSP	kspu	Krylov solver for Momentum equation
MatNullSpace	nullsp	nullspace: to solve Poisson equation with Homogeneous Neumann Boundary Conditions
struct Linear.vec	vec	Petsc Vectors.

◆ Obs.mouv

struct Obs.mouv

Motion parameters.

Data Fields
double	a
double *	cp
double	f
double **	Omega
double **	Omegat
double	rpm
double **	Theta	\( \theta \): Angle (position) of the body
double	theta
double **	Theta_def	\( \theta_d \): Angle generated by the body deformation
double **	Thetai	\( \theta_i \): Initial angle of the body
double **	u
double ***	Ub	\( u_b \): x-velocity of each body mesh point
double *	ubar	\( \overline{u} \): linear x-velocity (mass center)
double	Uin	\( U_0 \): initial condition for x-velocity
double **	v
double ***	Vb	\( v_b \): y-velocity of each body mesh point
double *	vbar	\( \overline{v} \): linear y-velocity (mass center)
double	Vin	\( V_0 \): initial condition for y-velocity
double	Vref	\( U_{ref} \): Reference velocity
double ***	Wb	\( w_b \): z-velocity of each body mesh point
double *	wbar	\( \overline{w} \): linear z-velocity (mass center)
double	Win	\( W_0 \): initial condition for z-velocity
double *	xbar	\( \overline{x} \): linear x-displacement (mass center)
double *	ybar	\( \overline{y} \): linear y-displacement (mass center)
double *	zbar	\( \overline{z} \): linear z-displacement (mass center)

◆ Obs.coef

struct Obs.coef

Forces, Torques, Power, Energy, ...

Data Fields
double ***	C_other
double ***	C_total
double ***	C_useful
double ***	C_useless
double *	Cn
double ***	Cp	Pressure distribution on the body surface
double ***	Cpt
double ***	Cs
double ***	Cst
double ***	Ct_other
double ***	Ct_total
double ***	Ct_useful
double ***	Ct_useless
double *	Cx	\( C_X \): aero/hydrodynamique coefficient in the X-direction
double *	Cxt	\( \widetilde{C}_X \): Auxiliary aero/hydrodynamique coefficient in the X-direction
double *	Cy	\( C_Y \): aero/hydrodynamique coefficient in the Y-direction
double *	Cyt	\( \widetilde{C}_Y \): Auxiliary aero/hydrodynamique coefficient in the Y-direction
double *	Cz	\( C_Z \): aero/hydrodynamiquecoefficient in the Z-direction
double *	Czt	\( \widetilde{C}_Z \): Auxiliary aero/hydrodynamique coefficient in the Z-direction
double ***	dist
int ***	distk
int ***	distkt
double ***	distm1
double ***	distt
double	Ec
double	Ecm1
double	Ecm1t
double	Ect
double *	eta
double *	etas
double **	Fx	\( F_X \): aero/hydrodynamique force exerted by the fluid on the body in the X-direction
double **	Fxt	\( \widetilde{F}_X \): auxiliary aero/hydrodynamique force exerted by the fluid on the body in the X-direction
double ***	Fxx
double ***	Fxxt
double **	Fy	\( F_Y \): aero/hydrodynamique force exerted by the fluid on the body in the Y-direction
double **	Fyt	\( \widetilde{F}_Y \): auxiliary aero/hydrodynamique force exerted by the fluid on the body in the Y-direction
double ***	Fyy
double ***	Fyyt
double **	Fz	\( F_Z \): aero/hydrodynamique force exerted by the fluid on the body in the Z-direction
double **	Fzt	\( \widetilde{F}_Z \): auxiliary aero/hydrodynamique force exerted by the fluid on the body in the Y-direction
double ***	Fzz
double ***	Fzzt
int *	ie
int *	ie1
int *	ie2
int *	iet
int *	is
int *	is1
int *	is2
int *	ist
int *	je
int *	je1
int *	je2
int *	jet
int *	js
int *	js1
int *	js2
int *	jst
int *	ke
int *	ke1
int *	ke2
int *	ket
int *	ks
int *	ks1
int *	ks2
int *	kst
double	Mn_exa
double	Mn_ext
double *	Mx	\( M_X \): aero/hydrodynamique torque exerted by the fluid on the body on the X-direction
double *	Mxt	\( \widetilde{M}_X \): auxiliary aero/hydrodynamique torque exerted by the fluid on the body on the X-direction
double *	My	\( M_Y \): aero/hydrodynamique torque exerted by the fluid on the body on the Y-direction
double *	Myt	\( \widetilde{M}_Y \): auxiliary aero/hydrodynamique torque exerted by the fluid on the body on the Y-direction
double *	Mz	\( M_Z \): aero/hydrodynamique torque exerted by the fluid on the body on the Z-direction
double *	Mzt	\( \widetilde{M}_Z \): auxiliary aero/hydrodynamique torque exerted by the fluid on the body on the Z-direction
double	P
double **	P_other
double **	P_total
double **	P_useful
double **	P_useless
double	Pb
double	Pbt
double	Pc
double	Pct
double	Pext
double	Pextt
double	Pm
double *	Power
double *	Power_other
double *	Power_useful
double *	Power_useless
double *	Powert
double *	Powert_other
double *	Powert_useful
double *	Powert_useless
double	Pt
double	Pv
double	Pvt
double *	W_other
double *	W_total
double *	W_useful
double *	W_useless

◆ Obs.geom

struct Obs.geom

Geometry parameters.

Data Fields
double *	Amax
double *	Amin
double	h
int ***	ind_normal_q
int ***	ind_normal_t
int ***	ind_texture_q
int ***	ind_texture_t
int ***	ind_vertex_q
int ***	ind_vertex_t
double ***	Jinv	\( J^{-1} \): inverse of the body intertia matrix
double ***	Jxyz	\( J^{(n)}\): intertia matrix at time n
double ***	Jxyzm1	\( J^{(n-1)}\): intertia matrix at time n-1
double *	length	\( \ell \): body length
double	m1
double	m2
double ***	n	\( \bf{n} \): outward unit normal to each body mesh cell
int *	nb_normal	obj file: number of normals
int *	nb_quad	obj file: number of quads
int *	nb_texture	obj file: number of textures
int *	nb_triangle	obj file: number of triangles
int *	nb_vertex	obj file: number of vertex
int	nbarres[100]
double **	nx
double **	ny
double **	nz
double	r1
double	r2
double	rc
double	re
double	rh
double *	rho	\( \rho \): body density
double	ri
double *	S	\( S \): body surface
double *	St	\(\widetilde{S}\): auxiliary body surface
double **	theta	\( \theta^{(n)} \): angle between each backbone segment at time n
double **	theta_m1	\( \theta^{(n-1)} \): angle between each backbone segment at time n-1
double **	theta_m2	\( \theta^{(n-2)} \): angle between each backbone segment at time n-2
double **	tx
double **	ty
double **	tz
double **	ub
double *	V	\( V \): body volume
double **	vb
double *	Vs	\( V_S \): backup body volume
double *	Vt	\(\widetilde{V}\): auxiliary body volume
double **	vx
double **	vy
double **	vz
double **	wb
double ***	x	\( x^{(n)} \): X position of the body surface grid points at time \( n \)
double ***	x0
double ***	x0m1
double ***	x1
double **	xb	\( x_b \): X position of the backbone points (midline)
double **	xb_m1
double **	xbs
double *	xg	\( x_g \): X prosition of the center of mass
double *	xg1
double *	xg2
double *	xgd
double *	xgs
double *	xi	\( x_i \): initial X position of the mass center
double ***	xm1	\( x^{(n-1)} \): X position of the body surface grid points at time \( n-1 \)
double *	xmax
double *	xmin
double ***	xs
double ***	y	\( y^{(n)} \): Y position of the body surface grid points at time \( n \)
double ***	y0
double ***	y0m1
double ***	y1
double **	yb	\( y_b \): Y position of the backbone points (midline)
double **	yb_m1
double **	ybs
double	yc
double *	yg	\( y_g \): Y prosition of the center of mass
double *	yg1
double *	yg2
double *	ygd
double *	ygs
double *	yi	\( y_i \): initial Y position of the mass center
double	yl
double	ym
double ***	ym1	\( y^{(n-1)} \): Y position of the body surface grid points at time \( n-1 \)
double *	ymax
double *	ymin
double ***	ys
double	yt
double ***	z	\( z^{(n)} \): Z position of the body surface grid points at time \( n \)
double ***	z0
double ***	z0m1
double ***	z1
double **	zb	\( z_b \): Z position of the backbone points (midline)
double **	zb_m1
double **	zbs
double *	zg	\( z_g \): Z prosition of the center of mass
double *	zg1
double *	zg2
double *	zgd
double *	zgs
double *	zi	\( z_i \): initial Z position of the mass center
double ***	zm1	\( z^{(n-1)} \): Z position of the body surface grid points at time \( n-1 \)
double *	zmax
double *	zmin
double ***	zs

◆ Obs.elast

struct Obs.elast

Lagrangian elasticity parameters.

Data Fields
double **	a
double ***	A
double ***	A2
double **	Aibphi
double ***	Ap
double ***	Aphi
double **	b
double **	bphi
double **	ce
double **	cem1
double **	cem2
double **	curv
double *	Cx
double *	Cy
double **	d2ce
double **	d2phi
double **	d2se
double	dist
double	distance
double **	dphi
double **	e
double *	E
double ***	Gc
double ***	GcAp
double ***	GcApHc
double ***	GcApHs
double ***	Gs
double ***	GsAp
double ***	GsApHc
double ***	GsApHs
double ***	Hc
double ***	Hs
double **	In
double ***	Jn
double **	l
double **	m
double **	Mm
double **	Mmt
double *	mu
int	n[100]
double **	phi
double **	phim1
double **	phim2
double **	S
double **	se
double **	sem1
double **	sem2
double **	Wx
double **	Wxt
double **	Wy
double **	Wyt
double **	x
double **	xc
double **	xm1
double **	xm2
double **	y
double **	yc
double **	ym1
double **	ym2

◆ Linear.vec

struct Linear.vec