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freenergysegments.f90
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freenergysegments.f90
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program freeenergysegments
use readandget
use netcdf
implicit none
character(len=50) :: infile, reffile, iname, rname, hname, sname, chrep, chat
logical :: netcdf,per,velin,startfound,endfound,normalize
integer :: i, j, k, at, nsteps, spatial, natoms, nrestr, rep, auxunit, auxunit2, bins, start, end, cutlenght
integer, allocatable, dimension (:) :: mask
real(4), allocatable, dimension (:) :: coordx, coordy, coordz
double precision, allocatable, dimension (:) :: hist_x, hist_y, segment_x, segment_y, singlecoord
double precision, allocatable, dimension (:) :: hist_x_cut, hist_y_cut, segment_x_cut, segment_y_cut
double precision, allocatable, dimension (:,:) :: rref
double precision, allocatable, dimension(:,:,:) :: coordall
double precision :: max, min, kref, temp, truncar, R, ini, fin
double precision, dimension(6) :: boxinfo
R=0.001987d0 !kcal/K mol
call readinputsegmentsfreenergy(nrestr,mask,infile,reffile,rep,netcdf,bins,kref,temp,per,velin,boxinfo,truncar,normalize)
allocate(hist_x(bins),hist_y(bins))
if (rep .le. 9) write(chrep,'(I1)') rep
if (rep .gt. 9 .and. rep .le. 99) write(chrep,'(I2)') rep
rname = trim(reffile) // "_"
rname = trim(rname) // trim(chrep)
rname = trim(rname) // ".rst7"
if (netcdf) then
iname = trim(infile) // "_"
iname = trim(iname) // trim(chrep)
iname = trim(iname) // ".nc"
call getdims(iname,nsteps,spatial,natoms)
if (allocated(coordx)) deallocate(coordx)
if (allocated(coordy)) deallocate(coordy)
if (allocated(coordz)) deallocate(coordz)
if (allocated(coordall)) deallocate(coordall)
allocate(coordx(nsteps),coordy(nsteps),coordz(nsteps),singlecoord(nsteps))
allocate(coordall(3,nrestr,nsteps),segment_x(nsteps),segment_y(nsteps),rref(3,natoms))
call getcoordfromnetcdf(iname,nsteps,natoms,spatial,coordx,coordy,coordz,coordall,nrestr,mask)
else
call getcoordfromfenebtraj(nsteps,coordall,nrestr,rep)
allocate(singlecoord(nsteps),segment_x(nsteps),segment_y(nsteps))
endif
segment_x=0.d0
segment_y=0.d0
call getrefcoord(rname,nrestr,mask,natoms,rref,boxinfo,per,velin)
do j=1,nrestr
at=mask(j)
do i=1,3
do k=1,nsteps
singlecoord(k)=coordall(i,j,k)
end do
min = MINVAL(singlecoord)
max = MAXVAL(singlecoord)
call histogram( singlecoord, nsteps, min, max, bins, hist_x, hist_y )
k=1
startfound=.false.
endfound=.false.
start=1
end=bins
do while (k .le. bins .and. (.not. startfound .or. .not. endfound))
if (hist_y(k) .ge. truncar .and. .not. startfound) then
start = k
startfound = .true.
endif
if (hist_y(bins-k+1) .ge. truncar .and. .not. endfound) then
end = bins-k+1
endfound = .true.
end if
k = k + 1
end do
if (.not. startfound .or. .not. endfound) write(*,*) "WARNING, maybe histograms are looking weird"
do k=start,end
segment_x(k)=hist_x(k)
segment_y(k)=-R*temp*LOG(hist_y(k))-(kref/2.d0)*(hist_x(k)-rref(i,at))**2
end do
cutlenght=end-start+1
if (allocated(hist_x_cut)) deallocate(hist_x_cut)
if (allocated(hist_y_cut)) deallocate(hist_y_cut)
if (allocated(segment_x_cut)) deallocate(segment_x_cut)
if (allocated(segment_y_cut)) deallocate(segment_y_cut)
allocate(hist_x_cut(cutlenght), hist_y_cut(cutlenght), segment_x_cut(cutlenght), segment_y_cut(cutlenght))
do k=1,cutlenght
hist_x_cut(k)=hist_x(start+k-1)
hist_y_cut(k)=hist_y(start+k-1)
segment_x_cut(k)=segment_x(start+k-1)
segment_y_cut(k)=segment_y(start+k-1)
end do
min=MINVAL(segment_y_cut)
do k=1,cutlenght
segment_y_cut(k)=segment_y_cut(k)-min
end do
if(normalize) then
ini=segment_x_cut(1)
fin=segment_x_cut(cutlenght)
do k=1,cutlenght
segment_x_cut(k)=(segment_x_cut(k)-ini)/(fin-ini)
end do
! ini=MINVAL(segment_y_cut)
! fin=MAXVAL(segment_y_cut)
! do k=1,cutlenght
! segment_y_cut(k)=(segment_y_cut(k)-ini)/(fin-ini)
! end do
end if
if (i.eq.1) hname = "h.x.rep."//chrep
if (i.eq.2) hname = "h.y.rep."//chrep
if (i.eq.3) hname = "h.z.rep."//chrep
if (i.eq.1) sname = "s.x.rep."//chrep
if (i.eq.2) sname = "s.y.rep."//chrep
if (i.eq.3) sname = "s.z.rep."//chrep
if (at .le. 9) write(chat,'(I1)') at
if (at .gt. 9 .and. at .le. 99) write(chat,'(I2)') at
if (at .gt. 99 .and. at .le. 999) write(chat,'(I3)') at
if (at .gt. 999 .and. at .le. 9999) write(chat,'(I4)') at
hname = trim(hname)//".at."
hname = trim(hname)//trim(chat)
auxunit = 1000000*i+10000*j+rep
sname = trim(sname)//".at."
sname = trim(sname)//trim(chat)
auxunit2 = 99000000*i+990000*j+rep
if (auxunit.eq.auxunit2) write(*,*) "WARNING, auxunit = auxunit2"
open(auxunit, file = hname, status = 'unknown')
open(auxunit2, file = sname, status = 'unknown')
do k=1,cutlenght
write(auxunit,*) hist_x_cut(k), hist_y_cut(k)
write(auxunit2,*) segment_x_cut(k), segment_y_cut(k)
end do
close(auxunit)
close(auxunit2)
end do
end do
end program freeenergysegments
SUBROUTINE histogram( A, L, x_start, x_end, N, hist_x, hist_y )
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! Histogram takes an array A, of length L,
! starting and ending x values, x_start, x_end,
! and the number of bins, N, and outputs
! 2 arrays, hist_x and hist_y which contain the histogram
! data from A.
!
! extracted from https://searchcode.com/codesearch/raw/96378353/
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
IMPLICIT NONE
!! Inputs
INTEGER :: L
INTEGER :: N
REAL(KIND=8) :: x_start
REAL(KIND=8) :: x_end
REAL(KIND=8),DIMENSION(L) :: A
!! Outputs
REAL(KIND=8),DIMENSION(N) :: hist_x
REAL(KIND=8),DIMENSION(N) :: hist_y
!! Internal
INTEGER :: i
INTEGER :: j
INTEGER :: tot
REAL(KIND=8) :: dx
REAL(KIND=8) :: left
REAL(KIND=8) :: right
REAL(KIND=8) :: normalization_factor
!! Bin Width
dx = (x_end - x_start)/DBLE(N)
!! Loop over all bins
DO i=1,N
!! Set up hist_x, evenly spaced bin array with values of the bin centers
hist_x(i) = x_start + (i-1)*dx + dx/2.0D0
!! bin left value
left = hist_x(i) - dx/2.0D0
!! bin right value
right = hist_x(i) + dx/2.0D0
!! initialize counter for bin to 0
tot = 0
!! Loop over entire array A
DO j=1,L
!! Increment counter if value is within bin left and right
IF ( A(j) .GT. left .AND. A(j) .LT. right ) tot = tot+1
END DO
!! Set hist_y to bin counter
hist_y(i) = DBLE(tot)
END DO
! normalization (added by J. Semelak 2021)
normalization_factor=0.d0
DO i = 1, N
normalization_factor = normalization_factor + hist_y(i)*dx
END DO
DO i = 1, N
hist_y(i)=hist_y(i)/normalization_factor
END DO
END SUBROUTINE histogram