--- /dev/null
+ implicit none
+ include "DIMENSIONS"
+ include "COMMON.CALC"
+ integer i,j,k,l,ii,nf,n,uiparm(1)
+ double precision x(maxene)
+ double precision rmsave(maxT),fdum,rr
+ external fdum,funclik
+ double precision quot,quotl,f,T0 /300.0d0/
+ character*8 ename(maxene)
+ common /names/ ename
+ character*1 restyp(nbase)
+ data restyp /'A','G','C','T','U'/
+ character maskchar(0:1) /' ','*'/
+ character*80 Naresfile,Fracfile
+ double precision g(100)
+c print *,"start"
+ read(1,*) nene,sigma2,wsq
+ write (2,*) "nene",nene," nT",nT," sigma",sigma2
+ read(1,*) (ename(i),i=1,nene)
+ read(1,*) (weight(i),i=1,nene)
+ read(1,*) (iweight(i),i=1,nene)
+ read(1,*) (mask(i),i=1,nene)
+ do i=1,nnbase
+ read(1,*) sig0(i),(weightel(3*(i-1)+j),maskel(3*(i-1)+j),j=1,3)
+ enddo
+ read(1,'(a)') Naresfile
+ read(1,'(a)') Fracfile
+ close(1)
+ open(7,file=Naresfile,status='old')
+ i=0
+ do
+c print *,"i=",i
+ read(7,*,end=10,err=10) ii,(enetb(j,i+1),j=1,nene),
+ & ((eletb(3*(j-1)+k,i+1),j=1,nnbase),k=1,3),
+ & entfac(i+1),
+ & qtab(i+1),rmstab(i+1),rgytab(i+1),
+ & fpair(i+1),rr,fdup(i+1)
+ i=i+1
+ enddo
+ 10 continue
+ nconf=i
+ close(7)
+ write (2,*) "nconf",nconf
+ write (2,'(/"Initial energy-term weights (* optimized)")')
+ write (2,'(i5,2x,a4,f10.5,1x,a1,i5)')
+ & (j,ename(j),weight(j),maskchar(mask(j)),iweight(j),j=1,nene)
+ ii=0
+ write (2,*)
+ & "Initial base-dipole-interaction parameters (* optimizable)"
+ do i=1,nbase
+ do j=1,i
+ ii=ii+1
+ write (2,'(2a2,f10.5,3(f10.5,1x,a1))') restyp(i),restyp(j),
+ & sig0(ii),(weightel(3*(ii-1)+k),maskchar(maskel(3*(ii-1)+k)),
+ & k=1,3)
+ enddo
+ enddo
+ write (2,*) "sigma",sigma2," wsq",wsq
+ sigma2=sigma2*sigma2
+ close(7)
+ open(7,file=Fracfile,status='old')
+ i=0
+ do
+ read(7,*,end=11,err=11) temper(i+1),frac(i+1)
+ i=i+1
+ enddo
+ 11 continue
+ nT=i
+ close(7)
+ write (2,*) "Fractions of base pairs"
+ do i=1,nT
+ write (2,'(i5,f8.1,f10.5)') i,temper(i),frac(i)
+ enddo
+c Transfer weights to variables
+ call w2x(n,x)
+ write (2,*) "n",n
+c Compute the temperature scale factors
+ do i=1,nT
+ ft(1,i)=1.0d0
+ quot=temper(i)/T0
+ quotl=1.0d0
+ do l=2,2
+ quotl=quotl*quot
+ fT(l,i)=1.12692801104297249644d0/
+ & dlog(dexp(quotl)+dexp(-quotl))
+ enddo
+ enddo
+c do i=1,nT
+c write (2,'(i5,f8.3,f10.5)') (i,(ft(j,i),j=1,2),i=1,nT)
+c enddo
+
+ call funclik(n,x,nf,f,uiparm,rmsave,fdum)
+ write (2,*) "f",f
+ write(2,'(/a3,a8,3a10)')" Nr"," Temp"," rmsave",
+ & " fave"," fave(exp)"
+ do i=1,nT
+ write (2,'(i3,f8.1,3f10.5)') i,temper(i),rmsave(i),
+ & fave(i),frac(i)
+ enddo
+c call grad(n,x,nf,g,uiparm,rmsave,fdum)
+c write (2,*) "rmsave",(rmsave(i),i=1,nT),"f",f
+c stop
+ call minsumsl(n,x,f)
+ call funclik(n,x,nf,f,uiparm,rmsave,fdum)
+ write (2,'(/"Final parameters (",i5,")")') n
+ do i=1,n
+ write (2,'(i5,f10.5)') i,x(i)
+ enddo
+ write (2,'(/"Energy-term weights (* optimized)")')
+ write (2,'(i5,2x,a4,f10.5,1x,a1,i5)')
+ & (j,ename(j),weight(j),maskchar(mask(j)),iweight(j),j=1,nene)
+ write (2,*) "Base-dipole-interaction parameters (* optimized)"
+ ii=0
+ do i=1,nbase
+ do j=1,i
+ ii=ii+1
+ write (2,'(2a2,f10.5,3(f10.5,1x,a1))') restyp(i),restyp(j),
+ & sig0(ii),(weightel(3*(ii-1)+k),maskchar(maskel(3*(ii-1)+k)),
+ & k=1,3)
+ enddo
+ enddo
+ write (2,*) "f",f
+ write(2,'(/a3,a8,3a10)')" Nr"," Temp"," rmsave",
+ & " fave"," fave(exp)"
+ do i=1,nT
+ write (2,'(i3,f8.1,3f10.5)') i,temper(i),rmsave(i),
+ & fave(i),frac(i)
+ enddo
+
+c do i=10,30
+c do k=10,30
+c weight(6)=0.1d0*i
+c weight(1)=0.1d0*k
+c write (2,'(i5,2x,a4,f10.5,i5)')
+c & (j,ename(j),weight(j),iweight(j),j=1,nene)
+c call funclik(nene,weight,nf,f,uiparm,rmsave,fdum)
+c write (2,*) "f",f
+c enddo
+c enddo
+ stop
+ end
+c-------------------------------------------------------------------------------
+ subroutine funclik(n,x,nf,f,uiparm,rmsave,ufparm)
+ implicit none
+ include "DIMENSIONS"
+ include "COMMON.CALC"
+ character*8 ename(maxene)
+ common /names/ ename
+ integer n,nf
+ double precision f,loglik,chisq
+ double precision x(n)
+ integer uiparm
+ double precision ufparm
+ external ufparm
+ double precision ww(maxene),sumlik(maxT),rmsave(maxT)
+ integer it,i,j,k
+ double precision beta,over,boltz,sumQ,ener(maxconf),emin,ee,enel,
+ & sumover,eboltz
+ call x2w(n,x)
+ loglik=0.0d0
+ chisq=0.0d0
+ do iT=1,nT
+ do i=1,nene
+ ww(i)=weight(i)*ft(iweight(i),iT)
+ enddo
+c write (2,*) "iT",iT," temper",temper(iT)," beta",beta
+c write (2,'(i5,2x,a4,2f10.5,i5,f10.5)')
+c & (i,ename(i),weight(i),ww(i),iweight(i),ft(iweight(i),iT),
+c & i=1,n)
+ beta=1.0d0/(temper(iT)*1.987D-3)
+c write (2,*) "beta",beta
+ emin=1.0d10
+ do i=1,nconf
+ enel=0.0d0
+ do j=1,nnbase
+c write (2,*)
+c & i,j,sig0(j),(weightel(3*(j-1)+k),eletb(3*(j-1)+k,i),k=1,3)
+ enel=enel+weightel(3*(j-1)+1)*sig0(j)**6*eletb(3*(j-1)+1,i)
+ & +weightel(3*(j-1)+2)*sig0(j)**3*eletb(3*(j-1)+2,i)
+ & +weightel(3*j)*sig0(j)**6*eletb(3*j,i)
+ enddo
+c write (2,*) i,enel,enetb(6,i)
+ enetb(6,i)=enel
+ ener(i)=0.0d0
+ do j=1,nene
+ ener(i)=ener(i)+ww(j)*enetb(j,i)
+ enddo
+ ee = ener(i)-entfac(i)/beta
+ if (ee.lt.emin) emin=ee
+ enddo
+ rmsave(it)=0.0d0
+ sumlik(it)=0.0d0
+ fave(it)=0.0d0
+ sumQ=0.0d0
+ sumover=0.0d0
+ do i=1,nconf
+ boltz=-beta*(ener(i)-emin)+entfac(i)
+ eboltz=dexp(boltz)
+ rmsave(iT)=rmsave(iT)+rmstab(i)*dexp(boltz)
+ over=dexp(-0.5d0*rmstab(i)**2/sigma2)
+ if (frac(iT).lt.0.5d0) over=1.0d0-over
+ sumover=sumover+over
+c write (2,*) i,ener(i),entfac(i),rmstab(i),fpair(i),fdup(i),
+c & over,boltz,eboltz
+ fave(iT)=fave(iT)+fdup(i)*eboltz
+ sumQ=sumQ+eboltz
+ sumlik(iT)=sumlik(iT)+over*boltz
+ enddo
+ fave(iT)=fave(iT)/sumq
+ sumlik(it)=sumlik(iT)-dlog(sumQ)*sumover
+ rmsave(iT)=rmsave(iT)/sumQ
+ if (frac(iT).gt.0.95d0 .or. frac(iT).lt.0.05d0) then
+ loglik=loglik-sumlik(iT)
+ endif
+ chisq=chisq+(frac(iT)-fave(iT))**2
+c write (2,*) iT,temper(iT),rmsave(iT),sumlik(iT),sumQ,sumover,
+c & fave(iT),frac(iT)
+c call flush(2)
+ enddo
+ f = loglik/nconf+wsq*chisq
+c write (2,*) "loglik",loglik/nconf," chisq",chisq," f",f
+ return
+ end
+c-------------------------------------------------------------------------------
+ subroutine grad(n,x,nf,g,uiparm,urparm,ufparm)
+ implicit none
+ integer n,nf,uiparm(1)
+ double precision x(n),g(n),urparm(1),ufparm
+ external ufparm
+ integer i
+ double precision xi,fplus,fminus,delta/1.0d-9/,delta2/2.0d-9/
+ do i=1,n
+ xi=x(i)
+ x(i)=xi+delta
+ call funclik(n,x,nf,fplus,uiparm,urparm,ufparm)
+ x(i)=xi-delta
+ call funclik(n,x,nf,fminus,uiparm,urparm,ufparm)
+ g(i)=(fplus-fminus)/delta2
+c write(2,*) i,fplus,fminus,g(i)
+ enddo
+ return
+ end
+c-------------------------------------------------------------------------------
+ double precision function fdum()
+ fdum=0.0d0
+ return
+ end
+c-------------------------------------------------------------------------------
+ logical function stopx(idum)
+ integer idum
+ stopx=.false.
+ return
+ end
+c-------------------------------------------------------------------------------
+ subroutine x2w(n,x)
+ include "DIMENSIONS"
+ include "COMMON.CALC"
+ double precision fabs
+ integer n,i,ii
+ double precision x(n)
+ ii=0
+ do i=1,nene
+ if (mask(i).gt.0) then
+ ii=ii+1
+ weight(i)=fabs(x(ii))
+ endif
+ enddo
+ do i=1,nnbase
+ if (maskel(3*(i-1)+1).gt.0) then
+ ii=ii+1
+ weightel(3*(i-1)+1)=-fabs(x(ii))
+ endif
+ if (maskel(3*(i-1)+2).gt.0) then
+ ii=ii+1
+ weightel(3*(i-1)+2)=x(ii)
+ endif
+ if (maskel(3*i).gt.0) then
+ ii=ii+1
+ weightel(3*i)=-fabs(x(ii))
+ endif
+ enddo
+ return
+ end
+c-------------------------------------------------------------------------------
+ subroutine w2x(n,x)
+ include "DIMENSIONS"
+ include "COMMON.CALC"
+ integer n,i,ii
+ double precision x(maxene+3*nnbase)
+ ii=0
+ do i=1,nene
+c write (2,*) "i",i," mask",mask(i)," ii",ii
+ if (mask(i).gt.0) then
+ ii=ii+1
+ x(ii)=weight(i)
+ endif
+ enddo
+ do i=1,3*nnbase
+c write (2,*) "i",i," maskel",maskel(i)," ii",ii
+ if (maskel(i).gt.0) then
+ ii=ii+1
+ x(ii)=weightel(i)
+ endif
+ enddo
+ n=ii
+c write (2,*) "W2X: n=",n
+ return
+ end
+c------------------------------------------------------------------------------------
+ double precision function fabs(x)
+ double precision x
+ double precision a /100.0d0/
+ if (dabs(x).gt.1.0d-2) then
+ fabs = dabs(x)
+ else
+ fabs = dlog(dexp(a*x)+dexp(-a*x))/a
+ endif
+ return
+ end
projects / unres.git / blobdiff