DERIVED TYPE ode_output: handles output for PDE/ODE simulations More...

Data Types
interface	assemble
	assemble the output (finalise construction) More...

interface	clear

interface	ode_output
	The type ode_output handles output for ODE simulations. More...

interface	print
	print a short description More...

interface	set
	set the output parameters More...

Functions/Subroutines
subroutine	ode_output_clear (out)
	destructor for ode_output More...

type(ode_output) function	ode_output_create (t0, T, N)
	Constructor for the type ode_output More...

subroutine	ode_output_set (out, verb, Ytn_period, Vtn_period, Vtn_rec_prd, Vtn_plot, act_type, act_rec, act_plot, stop_if_dep, act_Vth, Vtn_file, act_file, outDir, pos, xn_list, Vxn_period, Vxn_plot, Vxn_file)
	set the following parameters = optional see ode_output_mod::ode_output for the default values More...

subroutine	ode_output_assemble (out, dt, X_h)
	assemble the output, follows set(out, ...) More...

integer function	def_nv (method)
	size of V required to compute act More...

subroutine	ode_output_print (out)
	print ode_output More...

subroutine, public	output_proc (out, time, s, final)
	Pre-defined output for ODE resolution More...

subroutine	ode_output_last_output (out)
	ends computation output More...

subroutine	plot_vtn (out)
	Plot V(x, tn) "co$outDir/vn.dat", n=1..Ytn_cpt. More...

subroutine	plot_vtn_gnuplot (out)
	plot ../temp/vn.dat More...

subroutine	plot_vtn_gmsh (out)

subroutine	plot_vxn_gnuplot (out)

subroutine	plot_act (out)
	plot activation times More...

subroutine	plot_act_gnuplot (out)

subroutine	plot_act_gmsh (out)

subroutine	comp_act_0 (act, V, time, Vth)
	Computation of activation times : cut off. More...

subroutine	comp_act_1 (act, V, time, dt, Vth)
	Computation of activation times : linear interp. More...

subroutine	comp_act_2 (act, V, time, dt, Vth)
	Computation of activation times : quadradic interp. More...

subroutine	comp_act_4 (act, V, time, dt, Vth)
	Computation of activation times : bi-quadradic interp. More...

real(rp) function, public	celerity_l2_dist (u1, u2, X_h, qdm, weight)
	returns \|\| (c(u1) - c(u2)) * weight(x) \|\|_L2() More...

real(rp) function, public	celerity_l2_norm (u1, X_h, qdm, weight)
	returns \|\| c(u1) * weight(x) \|\|_L2 More...

Detailed Description

DERIVED TYPE ode_output: handles output for PDE/ODE simulations

The type ode_output conatins a procedural element

out%output

that can be passed as an argument to an ode_solver.

It is constructed in 3 steps

Creation:
out = ode_output(t0, t, n)
for an ODE on the tiem interval (t0,T) and with 'n' unknowns per node ( $ Y(x,t)\in\R^n$), documentation.
Settings:
call set(out, args)
see ode_output_set documentation.
Assembling:
call assemble(out, dt, ...)

ends up the construction before to solve see ode_output_assemble documentation.

Tutorial examples:

ode_Lin_0d.f90: solve $ y'= y$ and visualise the solution,
cardio_0d.f90: a non linear ODE system in cardiac electrophysiology.
monodomain_2d.f90: a parabolic reaction-diffusion equation coupled with an ODE system,
discretised in space with finite elements on a 2D mesh.

In these examples, see the subroutine 'output_proc' or 'cardio_output'.

Author: Charles Pierre

Function/Subroutine Documentation

◆ celerity_l2_dist()

real(rp) function, public ode_output_mod::celerity_l2_dist	(	real(rp), dimension(:), intent(in)	u1,
		real(rp), dimension(:), intent(in)	u2,
		type(fespace), intent(in)	X_h,
		type(quadmesh), intent(in)	qdm,
		procedure(r3tor)	weight
	)

returns || (c(u1) - c(u2)) * weight(x) ||_L2()

c = wafe front celerity

u1 and u2 are activation times for the finite element space X_h

integration method is described by qdm

weight allows to compute the norm on a subset of Omega

Definition at line 1211 of file ode_output_mod.F90.

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◆ celerity_l2_norm()

real(rp) function, public ode_output_mod::celerity_l2_norm	(	real(rp), dimension(:), intent(in)	u1,
		type(fespace), intent(in)	X_h,
		type(quadmesh), intent(in)	qdm,
		procedure(r3tor)	weight
	)

returns || c(u1) * weight(x) ||_L2

c = wafe front celerity

u1 = activation times for the finite element space X_h

integration method is described by qdm

weight allows to compute the norm on a subset of Omega

Definition at line 1249 of file ode_output_mod.F90.

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◆ comp_act_0()

subroutine ode_output_mod::comp_act_0	(	real(rp), dimension(:), intent(out)	act,
		real(rp), dimension(:,:), intent(in)	V,
		real(rp), intent(in)	time,
		real(rp), intent(in)	Vth
	)

private

Computation of activation times : cut off.

Definition at line 1017 of file ode_output_mod.F90.

◆ comp_act_1()

subroutine ode_output_mod::comp_act_1	(	real(rp), dimension(:), intent(out)	act,
		real(rp), dimension(:,:), intent(in)	V,
		real(rp), intent(in)	time,
		real(rp), intent(in)	dt,
		real(rp), intent(in)	Vth
	)

private

Computation of activation times : linear interp.

Definition at line 1040 of file ode_output_mod.F90.

◆ comp_act_2()

subroutine ode_output_mod::comp_act_2	(	real(rp), dimension(:), intent(out)	act,
		real(rp), dimension(:,:), intent(in)	V,
		real(rp), intent(in)	time,
		real(rp), intent(in)	dt,
		real(rp), intent(in)	Vth
	)

private

Computation of activation times : quadradic interp.

Definition at line 1065 of file ode_output_mod.F90.

◆ comp_act_4()

subroutine ode_output_mod::comp_act_4	(	real(rp), dimension(:), intent(out)	act,
		real(rp), dimension(:,:), intent(in)	V,
		real(rp), intent(in)	time,
		real(rp), intent(in)	dt,
		real(rp), intent(in)	Vth
	)

private

Computation of activation times : bi-quadradic interp.

Definition at line 1101 of file ode_output_mod.F90.

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◆ def_nv()

integer function ode_output_mod::def_nv ( integer method )

private

size of V required to compute act

Definition at line 481 of file ode_output_mod.F90.

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◆ ode_output_assemble()

subroutine ode_output_mod::ode_output_assemble	(	type(ode_output), intent(inout)	out,
		real(rp), intent(in)	dt,
		type(fespace), optional, target	X_h
	)

private

assemble the output, follows set(out, ...)

Parameters :

dt = time step
X_h = finite element space

To run before any simulation

Definition at line 392 of file ode_output_mod.F90.

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◆ ode_output_clear()

subroutine ode_output_mod::ode_output_clear ( type(ode_output), intent(inout) out )

private

destructor for ode_output

Definition at line 227 of file ode_output_mod.F90.

◆ ode_output_create()

type(ode_output) function ode_output_mod::ode_output_create	(	real(rp), intent(in)	t0,
		real(rp), intent(in)	T,
		integer, intent(in)	N
	)

private

Constructor for the type ode_output

OUTPUT:
- out = ode_output

INPUT:
- dim = dimension in space
- t0, T = starting and final time
- N = number of unknowns per node

Definition at line 256 of file ode_output_mod.F90.

◆ ode_output_last_output()

subroutine ode_output_mod::ode_output_last_output ( type(ode_output), intent(in) out )

private

ends computation output

Definition at line 769 of file ode_output_mod.F90.

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◆ ode_output_print()

subroutine ode_output_mod::ode_output_print ( type(ode_output), intent(in) out )

private

print ode_output

Definition at line 506 of file ode_output_mod.F90.

◆ ode_output_set()

subroutine ode_output_mod::ode_output_set	(	type(ode_output), intent(inout)	out,
		integer, intent(in), optional	verb,
		real(rp), intent(in), optional	Ytn_period,
		real(rp), intent(in), optional	Vtn_period,
		real(rp), intent(in), optional	Vtn_rec_prd,
		logical, intent(in), optional	Vtn_plot,
		integer, intent(in), optional	act_type,
		logical, intent(in), optional	act_rec,
		logical, intent(in), optional	act_plot,
		logical, intent(in), optional	stop_if_dep,
		real(rp), intent(in), optional	act_Vth,
		character(len=*), intent(in), optional	Vtn_file,
		character(len=*), intent(in), optional	act_file,
		character(len=*), intent(in), optional	outDir,
		integer, intent(in), optional	pos,
		integer, dimension(:), intent(in), optional	xn_list,
		real(rp), intent(in), optional	Vxn_period,
		logical, intent(in), optional	Vxn_plot,
		character(len=*), intent(in), optional	Vxn_file
	)

private

set the following parameters = optional see ode_output_mod::ode_output for the default values

verb = verbosity level
Ytn_period = memory storing period for Y(., t_n)
Vtn_period = memory storing period for V(., t_n)
Vtn_rec_prd = file record periof for V(., t_n)
Vtn_plot = Plot of V(tn,:) ?
act_type = computation method for activation times
act_Vth = threshold for activation times computation
act_plot = Plot activation times ?
act_rec = recording activation times to file act.dat ?
stop_if_dep = stop if fully depolarised domain ?
pos = plot file format
outdir = directory for file recordings
Vtn_FILE = prefix for potential recordings
ACT_FILE = prefix for activation time recordings

Definition at line 315 of file ode_output_mod.F90.

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◆ output_proc()

subroutine, public ode_output_mod::output_proc	(	class(ode_output), intent(inout)	out,
		real(rp), intent(in)	time,
		type(ode_solution), intent(in)	s,
		logical, intent(out)	final
	)

Pre-defined output for ODE resolution

This routine realises the output for ODE resolution relatively to the output setting in an ode_output

OUTPUT:
- final = final output call ?

INPUT/OUTPUT:
- out = ode_output settings

INPUT:
- time = running time
- s = ode_solution

Definition at line 570 of file ode_output_mod.F90.

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◆ plot_act()

subroutine ode_output_mod::plot_act ( type(ode_output), intent(in) out )

private

plot activation times

Definition at line 931 of file ode_output_mod.F90.

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◆ plot_act_gmsh()

subroutine ode_output_mod::plot_act_gmsh ( type(ode_output), intent(in) out )

private

Definition at line 974 of file ode_output_mod.F90.

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◆ plot_act_gnuplot()

subroutine ode_output_mod::plot_act_gnuplot ( type(ode_output), intent(in) out )

private

Definition at line 941 of file ode_output_mod.F90.

◆ plot_vtn()

subroutine ode_output_mod::plot_vtn ( type(ode_output), intent(in) out )

private

Plot V(x, tn) "co$outDir/vn.dat", n=1..Ytn_cpt.

Definition at line 789 of file ode_output_mod.F90.

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◆ plot_vtn_gmsh()

subroutine ode_output_mod::plot_vtn_gmsh ( type(ode_output), intent(in) out )

private

Definition at line 842 of file ode_output_mod.F90.

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◆ plot_vtn_gnuplot()

subroutine ode_output_mod::plot_vtn_gnuplot ( type(ode_output), intent(in) out )

private

plot ../temp/vn.dat

Definition at line 802 of file ode_output_mod.F90.

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◆ plot_vxn_gnuplot()

subroutine ode_output_mod::plot_vxn_gnuplot ( type(ode_output), intent(in) out )

private

Definition at line 895 of file ode_output_mod.F90.

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Data Types

Functions/Subroutines

Detailed Description

Function/Subroutine Documentation

◆ celerity_l2_dist()

◆ celerity_l2_norm()

◆ comp_act_0()

◆ comp_act_1()

◆ comp_act_2()

◆ comp_act_4()

◆ def_nv()

◆ ode_output_assemble()

◆ ode_output_clear()

◆ ode_output_create()

◆ ode_output_last_output()

◆ ode_output_print()

◆ ode_output_set()

◆ output_proc()

◆ plot_act()

◆ plot_act_gmsh()

◆ plot_act_gnuplot()

◆ plot_vtn()

◆ plot_vtn_gmsh()

◆ plot_vtn_gnuplot()

◆ plot_vxn_gnuplot()