+++ /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