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MuscularActivation.f90
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MuscularActivation.f90
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! '''
! Neuromuscular simulator in Fortran.
! Copyright (C) 2020 Renato Naville Watanabe
! Marina Oliveira
! This program is free software: you can redistribute it and/or modify
! it under the terms of the GNU General Public License as published by
! the Free Software Foundation, either version 3 of the License, or
! any later version.
! This program is distributed in the hope that it will be useful,
! but WITHOUT ANY WARRANTY; without even the implied warranty of
! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
! GNU General Public License for more details.
! You should have received a copy of the GNU General Public License
! along with this program. If not, see <http://www.gnu.org/licenses/>.
! Contact: [email protected]
! '''
module MuscularActivationClass
use ConfigurationClass
use DynamicalArrays
use MotorUnitClass
implicit none
private
integer, parameter :: wp = kind( 1.0d0 )
real(wp), parameter :: PI = 4 * atan(1.0_wp)
public :: MuscularActivation
type MuscularActivation
type(Configuration), pointer :: conf
character(len = 6) :: pool
integer :: MUnumber
character(len = 80) :: activationModel
real(wp), dimension(:,:), allocatable :: ActMatrix
real(wp), dimension(:), allocatable :: an, activation_nonSat, k, p, m, bSat, bSatRaikova,activation_Sat
real(wp), dimension(:), allocatable :: activationRaikova
real(wp), dimension(:), allocatable :: diracDeltaValue
type(MotorUnit), pointer:: unit(:)
contains
procedure :: atualizeActivationSignal
procedure :: reset
end type MuscularActivation
interface MuscularActivation
module procedure init_MuscularActivation
end interface MuscularActivation
contains
type(MuscularActivation) function init_MuscularActivation(conf, pool, MUnumber, unit)
class(Configuration), intent(in), target :: conf
character(len = 6), intent(in) :: pool
integer, intent(in) :: MUnumber
class(MotorUnit), dimension(MUnumber), intent(in), target:: unit
character(len = 80) :: paramTag
integer :: i, j, stat
init_MuscularActivation%conf => conf
init_MuscularActivation%pool = pool
init_MuscularActivation%MUnumber = MUnumber
nullify(init_MuscularActivation%unit)
init_MuscularActivation%unit => unit(:)
!## Model of the activation signal. For now, it can be *SOCDS* (second order critically damped system) or Raikova.
paramTag = 'activationModel'
init_MuscularActivation%activationModel = init_MuscularActivation%conf%parameterSet(paramTag, pool, 0)
if (trim(init_MuscularActivation%activationModel).eq.'SOCDS') then
allocate(init_MuscularActivation%ActMatrix(init_MuscularActivation%MUnumber, 3*init_MuscularActivation%MUnumber))
init_MuscularActivation%ActMatrix(:,:) = 0.0
do i = 1, init_MuscularActivation%MUnumber
init_MuscularActivation%ActMatrix(i,3*(i-1)+1:3*(i-1)+3) = &
[2*exp(-init_MuscularActivation%conf%timeStep_ms/init_MuscularActivation%unit(i)%TwitchTc_ms), &
-exp(-2*init_MuscularActivation%conf%timeStep_ms/init_MuscularActivation%unit(i)%TwitchTc_ms), &
(init_MuscularActivation%conf%timeStep_ms**2)/init_MuscularActivation%unit(i)%TwitchTc_ms*exp(1.0-init_MuscularActivation%conf%timeStep_ms/init_MuscularActivation%unit(i)%TwitchTc_ms)]
end do
allocate(init_MuscularActivation%an(3*init_MuscularActivation%MUnumber))
init_MuscularActivation%an(:) = 0.0
allocate(init_MuscularActivation%bSat(init_MuscularActivation%MUnumber))
do i = 1, init_MuscularActivation%MUnumber
init_MuscularActivation%bSat(i) = init_MuscularActivation%unit(i)%bSat
end do
init_MuscularActivation%diracDeltaValue = - init_MuscularActivation%bSat / init_MuscularActivation%conf%timeStep_ms
print *, 'SOCDS activation model built'
else
allocate(init_MuscularActivation%k(init_MuscularActivation%MUnumber))
init_MuscularActivation%k(:) = 0.0
allocate(init_MuscularActivation%p(init_MuscularActivation%MUnumber))
init_MuscularActivation%p(:) = 0.0
allocate(init_MuscularActivation%m(init_MuscularActivation%MUnumber))
init_MuscularActivation%m(:) = 0.0
allocate(init_MuscularActivation%bSatRaikova(init_MuscularActivation%MUnumber))
init_MuscularActivation%bSatRaikova(:) = 0.0
allocate(init_MuscularActivation%activationRaikova(init_MuscularActivation%MUnumber))
init_MuscularActivation%activationRaikova(:) = 0.0
do i = 1, init_MuscularActivation%MUnumber
init_MuscularActivation%k(i) = log(2.0)/(-init_MuscularActivation%unit(i)%TwitchTcRaikova_ms * log((init_MuscularActivation%unit(i)%TwitchHrRaikova_ms)/(init_MuscularActivation%unit(i)%TwitchTcRaikova_ms)) + init_MuscularActivation%unit(i)%TwitchHrRaikova_ms - init_MuscularActivation%unit(i)%TwitchTcRaikova_ms)
init_MuscularActivation%p(i) = exp(-init_MuscularActivation%k(i) * init_MuscularActivation%unit(i)%TwitchTcRaikova_ms * log(init_MuscularActivation%unit(i)%TwitchTcRaikova_ms) - (-init_MuscularActivation%k(i) * init_MuscularActivation%unit(i)%TwitchTcRaikova_ms))
init_MuscularActivation%m(i) = init_MuscularActivation%k(i) * init_MuscularActivation%unit(i)%TwitchTcRaikova_ms
init_MuscularActivation%bSatRaikova(i) = init_MuscularActivation%unit(i)%bSatRaikova
end do
print *, 'Raikova activation model built'
end if
! ## The non-saturated activation signal of all motor units (see actMatrix explanation).
allocate(init_MuscularActivation%activation_nonSat(init_MuscularActivation%MUnumber))
init_MuscularActivation%activation_nonSat(:) = 0.0
! ## The parameter \f$b\f$ (see twitchSaturation function explanation) of
! ## each motor unit.
! ## The non-saturated activation signal of all motor units (see actMatrix explanation).
allocate(init_MuscularActivation%activation_Sat(init_MuscularActivation%MUnumber))
init_MuscularActivation%activation_Sat(:) = 0.0
! ## Dirac's delta approximation amplitude value. Is the inverse
! ## of the simulation time step (\f$1/T\f$).
end function
subroutine atualizeActivationSignal(self, t)
! '''
! Update the activation signal of the motor units.
!
! - Inputs:
! + **t**: current instant, in ms.
! '''
class(MuscularActivation), intent(inout) :: self
real(wp), intent(in) :: t
real(wp), dimension(self%MUnumber) :: temp!
integer :: i, j, sizeTrain, stat
if (trim(self%activationModel).eq.'SOCDS') then
do i = 1, self%MUnumber
self%an(3*(i-1)+2) = self%an(3*(i-1)+1)
self%an(3*(i-1)+1) = self%activation_nonSat(i)
if (allocated(self%unit(i)%terminalSpikeTrain)) then
sizeTrain = size(self%unit(i)%terminalSpikeTrain)
if (abs(t - self%unit(i)%terminalSpikeTrain(sizeTrain)) < 1e-6) then
self%an(3*(i-1)+3) = self%diracDeltaValue(i)
else
self%an(3*(i-1)+3) = 0.0
end if
else
self%an(3*(i-1)+3) = 0.0
end if
end do
self%activation_nonSat = matmul(self%ActMatrix, self%an)
else
do i = 1, self%MUnumber
temp(i) = 0
self%activationRaikova(i) = 0
if (allocated(self%unit(i)%terminalSpikeTrain)) then
sizeTrain = size(self%unit(i)%terminalSpikeTrain)
do j = 1, sizeTrain
if(t >= 0 .and. (t-self%unit(i)%terminalSpikeTrain(j))< 10.0*self%unit(i)%TwitchHrRaikova_ms) then
temp(i) = self%p(i) * (t-self%unit(i)%terminalSpikeTrain(j))**self%m(i) * exp(-self%k(i) * (t-self%unit(i)%terminalSpikeTrain(j)));
self%activationRaikova(i) = temp(i) + self%activationRaikova(i)
end if
end do
end if
end do
self%activation_nonSat = - self%bSatRaikova * self%activationRaikova
end if
self%activation_Sat(:) = 2.0 / (1.0 + exp(self%activation_nonSat)) - 1.0
end subroutine
subroutine reset(self)
! '''
!
! '''
class(MuscularActivation), intent(inout) :: self
if (trim(self%activationModel).eq.'SOCDS') then
self%an(:) = 0.0
else
self%activationRaikova(:) = 0.0
end if
self%activation_nonSat(:) = 0.0
self%activation_Sat(:) = 0.0
end subroutine
end module MuscularActivationClass