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MotorUnitPool.f90
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MotorUnitPool.f90
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! '''
! Neuromuscular simulator in Fortran.
! Copyright (C) 2021 Renato Naville Watanabe
! Pablo Alejandro
! 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: renato.watanabe@ufabc.edu.br
! '''
module MotorUnitPoolClass
! '''
! Class that implements a motor unit pool. Encompasses a set of motor
! units that controls a single muscle.
! '''
use ConfigurationClass
use DynamicalArrays
use MotorUnitClass
use MuscularActivationClass
use MuscleNoHillClass
use MuscleHillClass
use MuscleSpindleClass
use GolgiTendonOrganClass
use, intrinsic :: iso_c_binding, only: c_int, c_double
implicit none
private
integer, parameter :: wp = kind(1.0d0)
real(wp), parameter :: pi = 4 * atan(1.0_wp)
real(wp),private :: pic, poc !tst!
public :: MotorUnitPool
type MotorUnitPool
real(wp) :: t
character(len = 2) :: poolKind
type(Configuration), pointer :: conf
character(len = 6) :: pool
integer :: MUnumber, totalNumberOfCompartments
real(wp) :: muscleThickness_mm
type(MotorUnit), dimension(:), allocatable:: unit
real(wp), dimension(:), allocatable :: v_mV
real(wp), dimension(:,:), allocatable :: G
real(wp), dimension(:), allocatable :: iInjected, capacitanceInv, iIonic, EqCurrent_nA
real(wp), dimension(:,:), allocatable :: poolSomaSpikes! ## Vector with the instants of spikes in the soma compartment, in ms.
real(wp), dimension(:,:), allocatable :: poolLastCompSpikes ! ## Vector with the instants of spikes in the last dynamical compartment, in ms.
real(wp), dimension(:,:), allocatable :: poolTerminalSpikes ! ## Vector with the instants of spikes in the terminal, in ms.
real(wp), dimension(:), allocatable :: emg
type(MuscularActivation) :: Activation
type(MuscleNoHill) :: NoHillMuscle
type(MuscleHill) :: HillMuscle
type(MuscleSpindle) :: spindle
type(GolgiTendonOrgan) :: GTO
character(len=80) :: hillModel
integer(c_int) :: spIndexing, spRows, spCols, spNumberOfElements, spOperation
integer(c_int), dimension(:), allocatable :: spRowStart, spRowEnd, spColIdx
real(wp), dimension(:), allocatable :: spValues
contains
procedure :: dVdt
procedure :: atualizeMotorUnitPool
procedure :: getMotorUnitPoolInstantEMG
procedure :: getMotorUnitPoolEMG
procedure :: listSpikes
procedure :: reset
end type MotorUnitPool
interface MotorUnitPool
module procedure init_MotorUnitPool
end interface MotorUnitPool
contains
type (MotorUnitPool) function init_MotorUnitPool(conf, pool)
! '''
! Constructor
! - Inputs:
! + **conf**: Configuration object with the simulation parameters.
! + **pool**: string with Motor unit pool to which the motor unit belongs.
! '''
class(Configuration), intent(in), target :: conf
character(*), intent(in):: pool
character(len = 80) :: paramTag, paramChar
integer :: MUnumber_S, MUnumber_FR, MUnumber_FF
real(wp) :: paramReal
integer(c_int) :: i, j
character(len = 2) :: neuronKind
integer :: simDurationSteps, lastIndex, stat
init_MotorUnitPool%t = 0.0
! ## Indicates that is Motor Unit pool.
init_MotorUnitPool%poolKind = 'MU'
! ## Configuration object with the simulation parameters.
init_MotorUnitPool%conf => conf
! ## String with Motor unit pool to which the motor unit belongs.
init_MotorUnitPool%pool = pool
paramTag = 'MUnumber_' // trim(pool) // '-S'
paramChar = init_MotorUnitPool%conf%parameterSet(paramTag, pool, 0)
read(paramChar, *)paramReal
MUnumber_S = int(paramReal)
paramTag = 'MUnumber_' // trim(pool) // '-FR'
paramChar = init_MotorUnitPool%conf%parameterSet(paramTag, pool, 0)
read(paramChar, *)paramReal
MUnumber_FR = int(paramReal)
paramTag = 'MUnumber_' // trim(pool) // '-FF'
paramChar = init_MotorUnitPool%conf%parameterSet(paramTag, pool, 0)
read(paramChar, *)paramReal
MUnumber_FF = int(paramReal)
! ## Number of motor units.
init_MotorUnitPool%MUnumber = MUnumber_S + MUnumber_FR + MUnumber_FF
! ## Muscle thickness, in mm.
paramTag = 'thickness:' // trim(pool)
paramChar = init_MotorUnitPool%conf%parameterSet(paramTag, pool, 0)
read(paramChar, *)init_MotorUnitPool%muscleThickness_mm
! ## Vector of MotorUnit objects.
allocate(init_MotorUnitPool%unit(init_MotorUnitPool%MUnumber))
call cpu_time(pic) !tst!
print *, init_MotorUnitPool%MUnumber, ' <-- init_MotorUnitPool%MUnumber MotorUnit' !tst! 900
print *, 'init_MotorUnitPool%MUnumber=',init_MotorUnitPool%MUnumber,';MUnumber_S=',MUnumber_S,';MUnumber_FR=',MUnumber_FR,';MUnumber_FF=',MUnumber_FF,'[MotorUnitPool.f90]#tst#' !tst! 900
do i = 1, init_MotorUnitPool%MUnumber
if (i <= MUnumber_S) then
neuronKind = 'S'
init_MotorUnitPool%unit(i) = MotorUnit(init_MotorUnitPool%conf, init_MotorUnitPool%pool,&
i, neuronKind, init_MotorUnitPool%muscleThickness_mm,&
init_MotorUnitPool%conf%skinThickness_mm)
else if (i <= MUnumber_S + MUnumber_FR) then
neuronKind = 'FR'
init_MotorUnitPool%unit(i) = MotorUnit(init_MotorUnitPool%conf, init_MotorUnitPool%pool,&
i, neuronKind, init_MotorUnitPool%muscleThickness_mm,&
init_MotorUnitPool%conf%skinThickness_mm)
else
neuronKind = 'FF'
init_MotorUnitPool%unit(i) = MotorUnit(init_MotorUnitPool%conf, init_MotorUnitPool%pool,&
i, neuronKind, init_MotorUnitPool%muscleThickness_mm,&
init_MotorUnitPool%conf%skinThickness_mm)
end if
end do
call cpu_time(poc) !tst!
print '(F15.6, A)', poc - pic, ' seconds (... init_MotorUnitPool%MUnumber MotorUnit)' !tst! 306.968750 seconds para 900
! # This is used to get values from MotorUnit.py and make computations
! # in MotorUnitPool.py
init_MotorUnitPool%totalNumberOfCompartments = 0
do i = 1, init_MotorUnitPool%MUnumber
init_MotorUnitPool%totalNumberOfCompartments = init_MotorUnitPool%totalNumberOfCompartments &
+ init_MotorUnitPool%unit(i)%compNumber
!print *,'i=',i,';init_MotorUnitPool%unit(i)%compNumber=',init_MotorUnitPool%unit(i)%compNumber,'[MotorUnitPool.f90]#tst#' !tst!
end do
allocate(init_MotorUnitPool%v_mV(init_MotorUnitPool%totalNumberOfCompartments))
init_MotorUnitPool%v_mV(:) = 0.0
allocate(init_MotorUnitPool%G(init_MotorUnitPool%totalNumberOfCompartments, init_MotorUnitPool%totalNumberOfCompartments))
allocate(init_MotorUnitPool%iInjected(init_MotorUnitPool%totalNumberOfCompartments))
init_MotorUnitPool%iInjected(:) = 0.0
allocate(init_MotorUnitPool%capacitanceInv(init_MotorUnitPool%totalNumberOfCompartments))
allocate(init_MotorUnitPool%iIonic(init_MotorUnitPool%totalNumberOfCompartments))
init_MotorUnitPool%iIonic(:) = 0.0
allocate(init_MotorUnitPool%EqCurrent_nA(init_MotorUnitPool%totalNumberOfCompartments))
init_MotorUnitPool%G(:,:) = 0.0
! # Retrieving data from Motorneuron class
! # Vectors or matrices from Motorneuron compartments are copied,
! # populating larger vectors or matrices that will be used for computations
!call cpu_time(pic) !tst!
!print *, init_MotorUnitPool%MUnumber, ' <-- init_MotorUnitPool%MUnumber v_mV capacitanceInv' !tst!
do i = 1, init_MotorUnitPool%MUnumber
init_MotorUnitPool%v_mV((i-1)*init_MotorUnitPool%unit(i)%compNumber+1:&
(i)*init_MotorUnitPool%unit(i)%compNumber)&
= init_MotorUnitPool%unit(i)%v_mV
! # Consists of smaller matrices on its diagonal
init_MotorUnitPool%G((i-1)*init_MotorUnitPool%unit(i)%compNumber+1:&
(i)*init_MotorUnitPool%unit(i)%compNumber, &
(i-1)*init_MotorUnitPool%unit(i)%compNumber+1:&
i*init_MotorUnitPool%unit(i)%compNumber) &
= init_MotorUnitPool%unit(i)%G
init_MotorUnitPool%capacitanceInv((i-1)*init_MotorUnitPool%unit(i)%compNumber+1: &
i*init_MotorUnitPool%unit(i)%compNumber) &
= init_MotorUnitPool%unit(i)%capacitanceInv
init_MotorUnitPool%EqCurrent_nA((i-1)*init_MotorUnitPool%unit(i)%compNumber+1: &
i*init_MotorUnitPool%unit(i)%compNumber) &
= init_MotorUnitPool%unit(i)%EqCurrent_nA
end do
!call cpu_time(poc) !tst!
!print '(F15.6, A)', poc - pic, ' seconds (... init_MotorUnitPool%MUnumber v_mV capacitanceInv)' !tst!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
init_MotorUnitPool%spIndexing = 1
init_MotorUnitPool%spRows = init_MotorUnitPool%totalNumberOfCompartments
init_MotorUnitPool%spCols = init_MotorUnitPool%totalNumberOfCompartments
init_MotorUnitPool%spNumberOfElements = 0
allocate(init_MotorUnitPool%spRowStart(init_MotorUnitPool%spRows))
allocate(init_MotorUnitPool%spRowEnd(init_MotorUnitPool%spRows))
init_MotorUnitPool%spRowStart(:) = 0
!call cpu_time(pic) !tst!
!print *, init_MotorUnitPool%totalNumberOfCompartments, ' <-- init_MotorUnitPool%totalNumberOfCompartments' !tst!
do i = 1, init_MotorUnitPool%totalNumberOfCompartments
do j = 1, init_MotorUnitPool%totalNumberOfCompartments
if (abs(init_MotorUnitPool%G(i,j))>1e-10) then
init_MotorUnitPool%spNumberOfElements = init_MotorUnitPool%spNumberOfElements + 1
if (init_MotorUnitPool%spRowStart(i) == 0) then
init_MotorUnitPool%spRowStart(i) = init_MotorUnitPool%spNumberOfElements
end if
call AddToList(init_MotorUnitPool%spValues, init_MotorUnitPool%G(i,j)) !L! obs: spValues !!!
call integerAddToList(init_MotorUnitPool%spColIdx, j)
end if
end do
init_MotorUnitPool%spRowEnd(i) = init_MotorUnitPool%spNumberOfElements+1
end do
!call cpu_time(poc) !tst!
!print '(F15.6, A)', poc - pic, ' seconds (... totalNumberOfCompartments)' !tst! 0.046875 seconds
!L! stat = mkl_sparse_d_create_csr(init_MotorUnitPool%GSp, &
!L! init_MotorUnitPool%spIndexing, &
!L! init_MotorUnitPool%spRows, &
!L! init_MotorUnitPool%spCols, &
!L! init_MotorUnitPool%spRowStart, &
!L! init_MotorUnitPool%spRowEnd, &
!L! init_MotorUnitPool%spColIdx, &
!L! init_MotorUnitPool%spValues)
! Values for the matrix-vector operation matInt = GV
!L! init_MotorUnitPool%spDescr%type = SPARSE_MATRIX_TYPE_GENERAL
!L! init_MotorUnitPool%spAlpha = 1.0
!L! init_MotorUnitPool%spOperation = SPARSE_OPERATION_NON_TRANSPOSE
!L! init_MotorUnitPool%spBeta = 0.0
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! #activation signal
init_MotorUnitPool%Activation = MuscularActivation(init_MotorUnitPool%conf,init_MotorUnitPool%pool,&
init_MotorUnitPool%MUnumber, init_MotorUnitPool%unit)
! #Force
! ## String indicating whther a Hill model is used or not. For now, it can be *No*.
paramTag = 'hillModel'
init_MotorUnitPool%hillModel = init_MotorUnitPool%conf%parameterSet(paramTag, pool, 0)
if (trim(init_MotorUnitPool%hillModel).eq.'No') then
init_MotorUnitPool%NoHillMuscle = MuscleNoHill(init_MotorUnitPool%conf, &
init_MotorUnitPool%pool, &
init_MotorUnitPool%MUnumber, &
MUnumber_S, init_MotorUnitPool%unit)
else
init_MotorUnitPool%HillMuscle = MuscleHill(init_MotorUnitPool%conf, &
init_MotorUnitPool%pool, &
init_MotorUnitPool%MUnumber, &
MUnumber_S, init_MotorUnitPool%unit)
end if
! # EMG
! ## EMG along time, in mV.
simDurationSteps = nint(init_MotorUnitPool%conf%simDuration_ms/init_MotorUnitPool%conf%timeStep_ms)
allocate(init_MotorUnitPool%emg(simDurationSteps))
init_MotorUnitPool%emg(:) = 0.0
! Spindle
init_MotorUnitPool%spindle = MuscleSpindle(init_MotorUnitPool%conf, init_MotorUnitPool%pool)
! GTO
init_MotorUnitPool%GTO = GolgiTendonOrgan(init_MotorUnitPool%conf, init_MotorUnitPool%pool)
! ##
print '(A)', 'Motor Unit Pool ' // trim(pool) // ' built'
end function
function dVdt(self, t, V)
class(MotorUnitPool), intent(inout) :: self
real(wp), intent(in) :: t
real(wp), intent(in) :: V(:)
real(wp), dimension(self%totalNumberOfCompartments) :: dVdt
integer :: i, j, stat
real(wp), dimension(:), allocatable :: matInt
real(wp) :: pic, poc !tst!
allocate(matInt(self%totalNumberOfCompartments))
do i = 1, self%MUnumber
do j = 1, self%unit(i)%compNumber
self%iIonic((i-1)*self%unit(i)%compNumber+j) = &
self%unit(i)%Compartments(j)%computeCurrent(t, &
V((i-1)*self%unit(i)%compNumber+j))
end do
end do
matInt = matmul(self%G, V) !<--- !L!
dVdt = (self%iIonic + matInt + self%iInjected &
+ self%EqCurrent_nA) * self%capacitanceInv
if (allocated(matInt)) deallocate(matInt)
end function
subroutine atualizeMotorUnitPool(self, t, dynGamma, statGamma)
! '''
! Update all parts of the Motor Unit pool. It consists
! to update all motor units, the activation signal and
! the muscle force.
! - Inputs:
! + **t**: current instant, in ms.
! '''
class(MotorUnitPool) , intent(inout), target:: self
real(wp), intent(in) :: t
real(wp), intent(in) :: dynGamma, statGamma
real(wp), dimension(:), allocatable :: k1, k2, k3, k4, newStateTemp
real(wp), dimension(:), allocatable :: vUnit
real(wp) :: newtTemp
integer :: i
real(wp) :: vmax, vmin
real(wp) :: length, velocity, acceleration, tendonForce
allocate(k1(self%totalNumberOfCompartments))
allocate(k2(self%totalNumberOfCompartments))
allocate(k3(self%totalNumberOfCompartments))
allocate(k4(self%totalNumberOfCompartments))
allocate(newStateTemp(self%totalNumberOfCompartments))
vmin = -30.0
vmax = 120.0
k1 = self%dVdt(t, self%v_mV)
newStateTemp = self%v_mV + self%conf%timeStepByTwo_ms * k1
newtTemp = t + self%conf%timeStepByTwo_ms
k2 = self%dVdt(newtTemp, newStateTemp)
newStateTemp = self%v_mV + self%conf%timeStepByTwo_ms * k2
k3 = self%dVdt(newtTemp, newStateTemp)
newStateTemp = self%v_mV + self%conf%timeStep_ms * k3
newtTemp = t + self%conf%timeStep_ms
k4 = self%dVdt(newtTemp, newStateTemp)
self%v_mV = self%v_mV + self%conf%timeStepBySix_ms * (k1+ 2.0*k2 + 2.0*k3 + k4)
self%v_mV = merge(self%v_mV, vmax, self%v_mV < vmax)
self%v_mV = merge(self%v_mV, vmin, self%v_mV > vmin)
allocate(vUnit(self%unit(1)%compNumber))
do i = 1, self%MUnumber
vUnit = self%v_mV((i-1)*self%unit(i)%compNumber+1:i*self%unit(i)%compNumber)
call self%unit(i)%atualizeMotorUnit(t, vUnit)
end do
self%Activation%unit => self%unit(:)
call self%Activation%atualizeActivationSignal(t)
if (trim(self%hillModel).eq.'No') then
call self%NoHillMuscle%atualizeForce(self%Activation%activation_Sat)
length = self%NoHillMuscle%lengthNorm
velocity = self%NoHillMuscle%velocityNorm
acceleration = self%NoHillMuscle%accelerationNorm
tendonForce = self%NoHillMuscle%force(nint(t/self%conf%timeStep_ms)+1)
else
call self%HillMuscle%atualizeForce(self%Activation%activation_Sat)
length = self%HillMuscle%lengthNorm
velocity = self%HillMuscle%velocityNorm
acceleration = self%HillMuscle%accelerationNorm
tendonForce = self%HillMuscle%tendonForce_N(nint(t/self%conf%timeStep_ms)+1)
end if
call self%spindle%atualizeMuscleSpindle(t, length, velocity, acceleration, dynGamma, statGamma)
call self%GTO%atualizeGolgiTendonOrgan(t, tendonForce) !Feedback
deallocate(k1)
deallocate(k2)
deallocate(k3)
deallocate(k4)
deallocate(vUnit)
end subroutine
subroutine listSpikes(self)
! '''
! List the spikes that occurred in the soma and in
! the terminal of the different motor units.
! '''
class(MotorUnitPool) , intent(inout) :: self
integer :: i
integer, dimension(self%MUnumber) :: numberOfNewSpikesSoma, numberOfNewSpikesLastComp, numberOfNewSpikesTerminal
integer :: numberOfSpikesSoma, numberOfSpikesLastComp, numberOfSpikesTerminal
integer :: initInd, endInd
do i = 1, self%MUnumber
if (allocated(self%unit(i)%lastCompSpikeTrain)) then
numberOfNewSpikesLastComp(i) = size(self%unit(i)%lastCompSpikeTrain)
else
numberOfNewSpikesLastComp(i) = 0
end if
if (allocated(self%unit(i)%somaSpikeTrain)) then
numberOfNewSpikesSoma(i) = size(self%unit(i)%somaSpikeTrain)
else
numberOfNewSpikesSoma(i) = 0
end if
if (allocated(self%unit(i)%terminalSpikeTrain)) then
numberOfNewSpikesTerminal(i) = size(self%unit(i)%terminalSpikeTrain)
else
numberOfNewSpikesTerminal(i) = 0
end if
end do
numberOfSpikesSoma = sum(numberOfNewSpikesSoma)
numberOfSpikesTerminal = sum(numberOfNewSpikesTerminal)
numberOfSpikesLastComp = sum(numberOfNewSpikesLastComp)
print *, 'numberOfSpikesTerminal = ', numberOfSpikesTerminal
allocate(self%poolSomaSpikes(numberOfSpikesSoma,2))
allocate(self%poolLastCompSpikes(numberOfSpikesLastComp,2))
allocate(self%poolTerminalSpikes(numberOfSpikesTerminal,2))
initInd = 1
do i = 1, self%MUnumber
if (allocated(self%unit(i)%terminalSpikeTrain)) then
endInd = initInd + numberOfNewSpikesTerminal(i) - 1
self%poolTerminalSpikes(initInd:endInd,1) = self%unit(i)%terminalSpikeTrain
self%poolTerminalSpikes(initInd:endInd,2) = i
initInd = endInd+1
end if
end do
initInd = 1
do i = 1, self%MUnumber
if (allocated(self%unit(i)%somaSpikeTrain)) then
endInd = initInd + numberOfNewSpikesSoma(i) - 1
self%poolSomaSpikes(initInd:endInd,1) = self%unit(i)%somaSpikeTrain
self%poolSomaSpikes(initInd:endInd,2) = i
initInd = endInd + 1
end if
end do
initInd = 1
do i = 1, self%MUnumber
if (allocated(self%unit(i)%lastCompSpikeTrain)) then
endInd = initInd + numberOfNewSpikesLastComp(i) - 1
self%poolLastCompSpikes(initInd:endInd,1) = self%unit(i)%lastCompSpikeTrain
self%poolLastCompSpikes(initInd:endInd,2) = i
initInd = endInd + 1
end if
end do
end subroutine
real(wp) function getMotorUnitPoolInstantEMG(self, t) result(emg)
! '''
! '''
class(MotorUnitPool), intent(inout) :: self
real(wp), intent(in) :: t
integer :: j
real(wp), dimension(self%MUnumber) :: newEMG
do j = 1, self%MUnumber
newEMG(j) = self%unit(j)%getEMG(t)
end do
emg = sum(newEMG)
end function
subroutine getMotorUnitPoolEMG(self)
! '''
! '''
class(MotorUnitPool), intent(inout) :: self
integer :: i
real(wp) :: instant
integer :: simDuration
simDuration = size(self%emg)
do i = 1, simDuration
instant = (i-1) * self%conf%timeStep_ms
self%emg(i) = self%getMotorUnitPoolInstantEMG(instant)
end do
end subroutine
subroutine reset(self)
! '''
! '''
class(MotorUnitPool), intent(inout) :: self
integer :: i
if (allocated(self%poolSomaSpikes)) deallocate(self%poolSomaSpikes)
if (allocated(self%poolLastCompSpikes)) deallocate(self%poolLastCompSpikes)
if (allocated(self%poolTerminalSpikes)) deallocate(self%poolTerminalSpikes)
self%emg(:) = 0.0
do i = 1, self%MUnumber
call self%unit(i)%reset()
end do
do i = 1, self%MUnumber
self%v_mV((i-1)*self%unit(i)%compNumber+1:&
i*self%unit(i)%compNumber) = self%unit(i)%v_mV
end do
call self%Activation%reset()
if (trim(self%hillModel)=='No') then
call self%NoHillMuscle%reset()
else
call self%HillMuscle%reset()
end if
call self%spindle%reset()
print *, 'Motorneuron Pool reseted'
end subroutine
end module MotorUnitPoolClass