Reaction-diffusion module (physics routines) More...

Functions/Subroutines
subroutine	rd_write_info (fh)
	Write this module's parameters to a snapshot. More...

subroutine, public	rd_phys_init ()

subroutine	rd_check_params

subroutine	rd_to_conserved (ixIL, ixOL, w, x)

subroutine	rd_to_primitive (ixIL, ixOL, w, x)

subroutine	rd_get_cmax (w, x, ixIL, ixOL, idim, cmax)

subroutine	rd_get_cbounds (wLC, wRC, wLp, wRp, x, ixIL, ixOL, idim, Hspeed, cmax, cmin)

subroutine	rd_get_dt (w, ixIL, ixOL, dtnew, dxD, x)

subroutine	rd_get_flux (wC, w, x, ixIL, ixOL, idim, f)

subroutine	rd_add_source (qdt, dtfactor, ixIL, ixOL, wCT, wCTprim, w, x, qsourcesplit, active)

subroutine	rd_laplacian (ixIL, ixOL, var, lpl)
	Compute the Laplacian using a standard second order scheme. For now this method only works in slab geometries. Requires one ghost cell only. More...

subroutine	put_laplacians_onegrid (ixIL, ixOL, w)

subroutine	rd_evaluate_implicit (qtC, psa)
	inplace update of psa==>F_im(psa) More...

subroutine	rd_implicit_update (dtfactor, qdt, qtC, psa, psb)
	Implicit solve of psa=psb+dtfactordtF_im(psa) More...

Variables
integer, public, protected	u_ = 1

integer, public, protected	v_ = 2
	For 2 or more equations. More...

integer, public, protected	w_ = 3
	For 3 or more equations. More...

logical, public, protected	rd_particles = .false.
	Whether particles module is added. More...

double precision, public, protected	dtreacpar = 0.5d0
	Parameter with which to multiply the reaction timestep restriction. More...

character(len=20), public, protected	equation_name = "gray-scott"
	Name of the system to be solved. More...

double precision, public, protected	d1 = 0.05d0
	Diffusion coefficient for first species (u) More...

double precision, public, protected	d2 = 1.0d0
	Diffusion coefficient for second species (v) (if applicable) More...

double precision, public, protected	d3 = 1.0d0
	Diffusion coefficient for third species (w) (if applicable) More...

double precision, public, protected	sb_alpha = 0.1305d0
	Parameter for Schnakenberg model. More...

double precision, public, protected	sb_beta = 0.7695d0
	Parameter for Schnakenberg model. More...

double precision, public, protected	sb_kappa = 100.0d0
	Parameter for Schnakenberg model. More...

double precision, public, protected	gs_f = 0.046d0
	Feed rate for Gray-Scott model. More...

double precision, public, protected	gs_k = 0.063d0
	Kill rate for Gray-Scott model. More...

double precision, public, protected	br_a = 4.5d0
	Parameter for Brusselator model. More...

double precision, public, protected	br_b = 8.0d0
	Parameter for Brusselator model. More...

double precision, public, protected	br_c = 1.0d0
	Parameter for extended Brusselator model. More...

double precision, public, protected	br_d = 1.0d0
	Parameter for extended Brusselator model. More...

double precision, public, protected	lg_lambda = 1.0d0
	Parameter for logistic model (Fisher / KPP equation) More...

double precision, public, protected	bzfn_epsilon = 1.0d0
	Parameter for the Field-Noyes model of the Belousov-Zhabotinsky reaction. More...

double precision, public, protected	bzfn_delta = 1.0d0
	Parameter for the Field-Noyes model of the Belousov-Zhabotinsky reaction. More...

double precision, public, protected	bzfn_lambda = 1.0d0
	Parameter for the Field-Noyes model of the Belousov-Zhabotinsky reaction. More...

double precision, public, protected	bzfn_mu = 1.0d0
	Parameter for the Field-Noyes model of the Belousov-Zhabotinsky reaction. More...

double precision, public, protected	lor_r = 28.0d0
	Parameter for Lorenz system (Rayleigh number) More...

double precision, public, protected	lor_sigma = 10.0d0
	Parameter for Lorenz system (Prandtl number) More...

double precision, public, protected	lor_b = 8.0d0 / 3.0d0
	Parameter for Lorenz system (aspect ratio of the convection rolls) More...

type(mg_bc_t), dimension(3, mg_num_neighbors), public	rd_mg_bc
	Boundary condition information for the multigrid method. More...

Detailed Description

Reaction-diffusion module (physics routines)

Multiple reaction-diffusion systems are included: the Gray-Scott model, the Schnakenberg model, the Brusselator model, the diffusive logistic equation, an analytical testcase from "Numerical solution of time-dependent advection- diffusion-reaction equations" by Hundsdorfer & Verwer, the Oregonator model, the extended Brusselator model, and the diffusive Lorenz system. See the documentation of the reaction-diffusion module for more information.

IMEX methods are also supported. The implicit system is solved by a multigrid solver coupled into MPI-AMRVAC.

Function/Subroutine Documentation

◆ put_laplacians_onegrid()

subroutine mod_rd_phys::put_laplacians_onegrid	(	integer, intent(in)	ixI,
		integer, intent(in)	L,
		integer, intent(in)	ixO,
			L,
		double precision, dimension(ixi^s, 1:nw), intent(inout)	w
	)

Definition at line 505 of file mod_rd_phys.t.

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◆ rd_add_source()

subroutine mod_rd_phys::rd_add_source	(	double precision, intent(in)	qdt,
		double precision, intent(in)	dtfactor,
		integer, intent(in)	ixI,
		integer, intent(in)	L,
		integer, intent(in)	ixO,
			L,
		double precision, dimension(ixi^s, 1:nw), intent(in)	wCT,
		double precision, dimension(ixi^s,1:nw), intent(in)	wCTprim,
		double precision, dimension(ixi^s, 1:nw), intent(inout)	w,
		double precision, dimension(ixi^s, 1:ndim), intent(in)	x,
		logical, intent(in)	qsourcesplit,
		logical, intent(inout)	active
	)

Definition at line 386 of file mod_rd_phys.t.

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◆ rd_check_params()

subroutine mod_rd_phys::rd_check_params

Definition at line 215 of file mod_rd_phys.t.

◆ rd_evaluate_implicit()

subroutine mod_rd_phys::rd_evaluate_implicit	(	double precision, intent(in)	qtC,
		type(state), dimension(max_blocks), target	psa
	)

inplace update of psa==>F_im(psa)

Definition at line 531 of file mod_rd_phys.t.

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◆ rd_get_cbounds()

subroutine mod_rd_phys::rd_get_cbounds	(	double precision, dimension(ixi^s, nw), intent(in)	wLC,
		double precision, dimension(ixi^s,nw), intent(in)	wRC,
		double precision, dimension(ixi^s, nw), intent(in)	wLp,
		double precision, dimension(ixi^s,nw), intent(in)	wRp,
		double precision, dimension(ixi^s, 1:^nd), intent(in)	x,
		integer, intent(in)	ixI,
		integer, intent(in)	L,
		integer, intent(in)	ixO,
			L,
		integer, intent(in)	idim,
		double precision, dimension(ixi^s,1:number_species), intent(in)	Hspeed,
		double precision, dimension(ixi^s,1:number_species), intent(inout)	cmax,
		double precision, dimension(ixi^s,1:number_species), intent(inout), optional	cmin
	)

Definition at line 297 of file mod_rd_phys.t.

◆ rd_get_cmax()

subroutine mod_rd_phys::rd_get_cmax	(	double precision, dimension(ixi^s, nw), intent(in)	w,
		double precision, dimension(ixi^s, 1:^nd), intent(in)	x,
		integer, intent(in)	ixI,
		integer, intent(in)	L,
		integer, intent(in)	ixO,
			L,
		integer, intent(in)	idim,
		double precision, dimension(ixi^s), intent(inout)	cmax
	)

Definition at line 288 of file mod_rd_phys.t.

◆ rd_get_dt()

subroutine mod_rd_phys::rd_get_dt	(	double precision, dimension(ixi^s, 1:nw), intent(in)	w,
		integer, intent(in)	ixI,
		integer, intent(in)	L,
		integer, intent(in)	ixO,
			L,
		double precision, intent(inout)	dtnew,
		double precision, intent(in)	dx,
		double precision, intent(in)	D,
		double precision, dimension(ixi^s, 1:^nd), intent(in)	x
	)

Definition at line 317 of file mod_rd_phys.t.

◆ rd_get_flux()

subroutine mod_rd_phys::rd_get_flux	(	double precision, dimension(ixi^s, 1:nw), intent(in)	wC,
		double precision, dimension(ixi^s, 1:nw), intent(in)	w,
		double precision, dimension(ixi^s, 1:^nd), intent(in)	x,
		integer, intent(in)	ixI,
		integer, intent(in)	L,
		integer, intent(in)	ixO,
			L,
		integer, intent(in)	idim,
		double precision, dimension(ixi^s, nwflux), intent(out)	f
	)

Definition at line 374 of file mod_rd_phys.t.

◆ rd_implicit_update()

subroutine mod_rd_phys::rd_implicit_update	(	double precision, intent(in)	dtfactor,
		double precision, intent(in)	qdt,
		double precision, intent(in)	qtC,
		type(state), dimension(max_blocks), target	psa,
		type(state), dimension(max_blocks), target	psb
	)

Implicit solve of psa=psb+dtfactor*dt*F_im(psa)

Definition at line 551 of file mod_rd_phys.t.

◆ rd_laplacian()

subroutine mod_rd_phys::rd_laplacian	(	integer, intent(in)	ixI,
		integer, intent(in)	L,
		integer, intent(in)	ixO,
			L,
		double precision, dimension(ixi^s), intent(in)	var,
		double precision, dimension(ixo^s), intent(out)	lpl
	)

Compute the Laplacian using a standard second order scheme. For now this method only works in slab geometries. Requires one ghost cell only.

Definition at line 482 of file mod_rd_phys.t.

◆ rd_phys_init()

subroutine, public mod_rd_phys::rd_phys_init

Definition at line 161 of file mod_rd_phys.t.

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◆ rd_to_conserved()

subroutine mod_rd_phys::rd_to_conserved	(	integer, intent(in)	ixI,
		integer, intent(in)	L,
		integer, intent(in)	ixO,
			L,
		double precision, dimension(ixi^s, nw), intent(inout)	w,
		double precision, dimension(ixi^s, 1:^nd), intent(in)	x
	)

Definition at line 270 of file mod_rd_phys.t.

◆ rd_to_primitive()

subroutine mod_rd_phys::rd_to_primitive	(	integer, intent(in)	ixI,
		integer, intent(in)	L,
		integer, intent(in)	ixO,
			L,
		double precision, dimension(ixi^s, nw), intent(inout)	w,
		double precision, dimension(ixi^s, 1:^nd), intent(in)	x
	)

Definition at line 279 of file mod_rd_phys.t.

◆ rd_write_info()

subroutine mod_rd_phys::rd_write_info ( integer, intent(in) fh )

Write this module's parameters to a snapshot.

Definition at line 150 of file mod_rd_phys.t.

Variable Documentation

◆ br_a

double precision, public, protected mod_rd_phys::br_a = 4.5d0

Parameter for Brusselator model.

Definition at line 64 of file mod_rd_phys.t.

◆ br_b

double precision, public, protected mod_rd_phys::br_b = 8.0d0

Parameter for Brusselator model.

Definition at line 66 of file mod_rd_phys.t.

◆ br_c

double precision, public, protected mod_rd_phys::br_c = 1.0d0

Parameter for extended Brusselator model.

Definition at line 68 of file mod_rd_phys.t.

◆ br_d

double precision, public, protected mod_rd_phys::br_d = 1.0d0

Parameter for extended Brusselator model.

Definition at line 70 of file mod_rd_phys.t.

◆ bzfn_delta

double precision, public, protected mod_rd_phys::bzfn_delta = 1.0d0

Parameter for the Field-Noyes model of the Belousov-Zhabotinsky reaction.

Definition at line 78 of file mod_rd_phys.t.

◆ bzfn_epsilon

double precision, public, protected mod_rd_phys::bzfn_epsilon = 1.0d0

Parameter for the Field-Noyes model of the Belousov-Zhabotinsky reaction.

Definition at line 76 of file mod_rd_phys.t.

◆ bzfn_lambda

double precision, public, protected mod_rd_phys::bzfn_lambda = 1.0d0

Parameter for the Field-Noyes model of the Belousov-Zhabotinsky reaction.

Definition at line 80 of file mod_rd_phys.t.

◆ bzfn_mu

double precision, public, protected mod_rd_phys::bzfn_mu = 1.0d0

Parameter for the Field-Noyes model of the Belousov-Zhabotinsky reaction.

Definition at line 82 of file mod_rd_phys.t.

◆ d1

double precision, public, protected mod_rd_phys::d1 = 0.05d0

Diffusion coefficient for first species (u)

Definition at line 45 of file mod_rd_phys.t.

◆ d2

double precision, public, protected mod_rd_phys::d2 = 1.0d0

Diffusion coefficient for second species (v) (if applicable)

Definition at line 47 of file mod_rd_phys.t.

◆ d3

double precision, public, protected mod_rd_phys::d3 = 1.0d0

Diffusion coefficient for third species (w) (if applicable)

Definition at line 49 of file mod_rd_phys.t.

◆ dtreacpar

double precision, public, protected mod_rd_phys::dtreacpar = 0.5d0

Parameter with which to multiply the reaction timestep restriction.

Definition at line 29 of file mod_rd_phys.t.

◆ equation_name

character(len=20), public, protected mod_rd_phys::equation_name = "gray-scott"

Name of the system to be solved.

Definition at line 32 of file mod_rd_phys.t.

◆ gs_f

double precision, public, protected mod_rd_phys::gs_f = 0.046d0

Feed rate for Gray-Scott model.

Definition at line 59 of file mod_rd_phys.t.

◆ gs_k

double precision, public, protected mod_rd_phys::gs_k = 0.063d0

Kill rate for Gray-Scott model.

Definition at line 61 of file mod_rd_phys.t.

◆ lg_lambda

double precision, public, protected mod_rd_phys::lg_lambda = 1.0d0

Parameter for logistic model (Fisher / KPP equation)

Definition at line 73 of file mod_rd_phys.t.

◆ lor_b

double precision, public, protected mod_rd_phys::lor_b = 8.0d0 / 3.0d0

Parameter for Lorenz system (aspect ratio of the convection rolls)

Definition at line 89 of file mod_rd_phys.t.

◆ lor_r

double precision, public, protected mod_rd_phys::lor_r = 28.0d0

Parameter for Lorenz system (Rayleigh number)

Definition at line 85 of file mod_rd_phys.t.

◆ lor_sigma

double precision, public, protected mod_rd_phys::lor_sigma = 10.0d0

Parameter for Lorenz system (Prandtl number)

Definition at line 87 of file mod_rd_phys.t.

◆ rd_mg_bc

type(mg_bc_t), dimension(3, mg_num_neighbors), public mod_rd_phys::rd_mg_bc

Boundary condition information for the multigrid method.

Definition at line 95 of file mod_rd_phys.t.

◆ rd_particles

logical, public, protected mod_rd_phys::rd_particles = .false.

Whether particles module is added.

Definition at line 26 of file mod_rd_phys.t.

◆ sb_alpha

double precision, public, protected mod_rd_phys::sb_alpha = 0.1305d0

Parameter for Schnakenberg model.

Definition at line 52 of file mod_rd_phys.t.

◆ sb_beta

double precision, public, protected mod_rd_phys::sb_beta = 0.7695d0

Parameter for Schnakenberg model.

Definition at line 54 of file mod_rd_phys.t.

◆ sb_kappa

double precision, public, protected mod_rd_phys::sb_kappa = 100.0d0

Parameter for Schnakenberg model.

Definition at line 56 of file mod_rd_phys.t.

◆ u_

integer, public, protected mod_rd_phys::u_ = 1

Definition at line 21 of file mod_rd_phys.t.

◆ v_

integer, public, protected mod_rd_phys::v_ = 2

For 2 or more equations.

Definition at line 22 of file mod_rd_phys.t.

◆ w_

integer, public, protected mod_rd_phys::w_ = 3

For 3 or more equations.

Definition at line 23 of file mod_rd_phys.t.

Functions/Subroutines

Variables

Detailed Description

Function/Subroutine Documentation

◆ put_laplacians_onegrid()

◆ rd_add_source()

◆ rd_check_params()

◆ rd_evaluate_implicit()

◆ rd_get_cbounds()

◆ rd_get_cmax()

◆ rd_get_dt()

◆ rd_get_flux()

◆ rd_implicit_update()

◆ rd_laplacian()

◆ rd_phys_init()

◆ rd_to_conserved()

◆ rd_to_primitive()

◆ rd_write_info()

Variable Documentation

◆ br_a

◆ br_b

◆ br_c

◆ br_d

◆ bzfn_delta

◆ bzfn_epsilon

◆ bzfn_lambda

◆ bzfn_mu

◆ d1

◆ d2

◆ d3

◆ dtreacpar

◆ equation_name

◆ gs_f

◆ gs_k

◆ lg_lambda

◆ lor_b

◆ lor_r

◆ lor_sigma

◆ rd_mg_bc

◆ rd_particles

◆ sb_alpha

◆ sb_beta

◆ sb_kappa

◆ u_

◆ v_

◆ w_