subroutine initialize
C 
C Define constants and zero out tables.
C
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
#ifdef MPI
      include 'mpif.h'
      include "COMMON.MPI"
      integer ierror
#endif
      include 'COMMON.IOUNITS'
      include 'COMMON.CHAIN'
      include 'COMMON.INTERACT'
      include 'COMMON.GEO'
      include 'COMMON.LOCAL'
      include 'COMMON.TORSION'
      include 'COMMON.FFIELD'
      include 'COMMON.SBRIDGE'
      include 'COMMON.MINIM' 
      include 'COMMON.DERIV'
      include "COMMON.WEIGHTS"
      include "COMMON.NAMES"
      include "COMMON.TIME1"
      include "COMMON.THERMAL"
      include "COMMON.TORCNSTR"
      include "COMMON.ENERGIES"
C
C The following is just to define auxiliary variables used in angle conversion
C
      pi=4.0D0*datan(1.0D0)
      dwapi=2.0D0*pi
      dwapi3=dwapi/3.0D0
      pipol=0.5D0*pi
      deg2rad=pi/180.0D0
      rad2deg=1.0D0/deg2rad
      angmin=10.0D0*deg2rad
      Rgas = 1.987D-3
      eps_out = 80.0d0
C
C Define I/O units.
C
      inp=    1
      iout=   2
      ipdbin= 3
      ipdb=   7
      imol2=  4
      igeom=  8
      intin=  9
      ithep= 11
      irotam=12
      itorp= 13
      itordp= 23
      ielep= 14
      isidep=15 
      isidep1=22
      iscpp=25
      icbase=16
      ifourier=20
      istat= 17
      ientin=18
      ientout=19
      ibond=28
      isccor=29
C
C CSA I/O units (separated from others especially for Jooyoung)
C
      icsa_rbank=30
      icsa_seed=31
      icsa_history=32
      icsa_bank=33
      icsa_bank1=34
      icsa_alpha=35
      icsa_alpha1=36
      icsa_bankt=37
      icsa_int=39
      icsa_bank_reminimized=38
      icsa_native_int=41
      icsa_in=40
C
C Set default weights of the energy terms.
C
      wlong=1.0D0
      welec=1.0D0
      wtor =1.0D0
      wang =1.0D0
      wscloc=1.0D0
      wstrain=1.0D0
C
C Zero out tables.
C
      ndih_constr=0
      do i=1,maxres2
	do j=1,3
	  c(j,i)=0.0D0
	  dc(j,i)=0.0D0
        enddo
      enddo
      do i=1,maxres
	do j=1,3
	  xloc(j,i)=0.0D0
        enddo
      enddo
      do i=1,ntyp
	do j=1,ntyp
	  aa(i,j)=0.0D0
	  bb(i,j)=0.0D0
	  augm(i,j)=0.0D0
	  sigma(i,j)=0.0D0
	  r0(i,j)=0.0D0
	  chi(i,j)=0.0D0
        enddo
	do j=1,2
	  bad(i,j)=0.0D0
        enddo
	chip(i)=0.0D0
	alp(i)=0.0D0
	sigma0(i)=0.0D0
	sigii(i)=0.0D0
	rr0(i)=0.0D0
	a0thet(i)=0.0D0
        do j=1,2
         do ichir1=-1,1
          do ichir2=-1,1
          athet(j,i,ichir1,ichir2)=0.0D0
          bthet(j,i,ichir1,ichir2)=0.0D0
          enddo
         enddo
        enddo
	do j=0,3
	  polthet(j,i)=0.0D0
        enddo
	do j=1,3
	  gthet(j,i)=0.0D0
        enddo
	theta0(i)=0.0D0
	sig0(i)=0.0D0
	sigc0(i)=0.0D0
	do j=1,maxlob
	  bsc(j,i)=0.0D0
	  do k=1,3
	    censc(k,j,i)=0.0D0
          enddo
          do k=1,3
	    do l=1,3
	      gaussc(l,k,j,i)=0.0D0
            enddo
          enddo
	  nlob(i)=0
        enddo
      enddo
      nlob(ntyp1)=0
      dsc(ntyp1)=0.0D0
      do iblock=1,2
      do i=1,maxtor
	itortyp(i)=0
	do j=1,maxtor
	  do k=1,maxterm
	    v1(k,j,i,iblock)=0.0D0
	    v2(k,j,i,iblock)=0.0D0
          enddo
        enddo
      enddo
      enddo
      do i=1,maxres
	itype(i)=0
	itel(i)=0
      enddo
C Initialize the bridge arrays
      ns=0
      nss=0 
      nhpb=0
      do i=1,maxss
	iss(i)=0
      enddo
      do i=1,maxdim
	dhpb(i)=0.0D0
      enddo
      do i=1,maxres
	ihpb(i)=0
	jhpb(i)=0
      enddo
C
C Initialize timing.
C
      call set_timers
C
C Initialize variables used in minimization.
C   
c     maxfun=5000
c     maxit=2000
      maxfun=500
      maxit=200
      tolf=1.0D-2
      rtolf=5.0D-4
C 
C Initialize the variables responsible for the mode of gradient storage.
C
      nfl=0
      icg=1
      do i=1,14
        do j=1,14
          if (print_order(i).eq.j) then
            iw(print_order(i))=j
            goto 1121
          endif
        enddo
1121    continue
      enddo
      calc_grad=.false.
C Set timers and counters for the respective routines
      t_func = 0.0d0
      t_grad = 0.0d0
      t_fhel = 0.0d0
      t_fbet = 0.0d0
      t_ghel = 0.0d0
      t_gbet = 0.0d0
      t_viol = 0.0d0
      t_gviol = 0.0d0
      n_func = 0
      n_grad = 0
      n_fhel = 0
      n_fbet = 0
      n_ghel = 0
      n_gbet = 0
      n_viol = 0
      n_gviol = 0
      n_map = 0
#ifndef SPLITELE
      nprint_ene=nprint_ene-1
#endif
      enetb=0.0d0
      nfgtasks=1
#ifdef MPI
c      write (iout,*) "maxres6",maxres6
c      write (iout,*) "Calling MPI_Type_contiguous"
c      call flush(iout)
      call MPI_Type_contiguous(maxres6,MPI_DOUBLE_PRECISION,MPI_FORCE,
     &  IERROR)
      call MPI_Type_commit(MPI_FORCE,ierror)
c      write (iout,*) "After MPI_Type_contiguous ierror",ierror
#endif
      return
      end
c-------------------------------------------------------------------------
      block data nazwy
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'COMMON.NAMES'
      include 'COMMON.WEIGHTS'
      include 'COMMON.FFIELD'
      data restyp /
     &'DD','DAU','DAI','DDB','DSM','DPR','DLY','DAR','DHI','DAS','DGL',
     & 'DSG','DGN','DSN','DTH',
     &'DYY','DAL','DTY','DTR','DVA','DLE','DIL','DPN','MED','DCY','ZER',
     &'CYS','MET','PHE','ILE','LEU','VAL','TRP','TYR','ALA','GLY','THR',
     &'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','SME','DBZ',
     &'AIB','ABU','D'/
      data onelet /
     &'z','z','z','z','z','p','k','r','h','d','e','n','q','s','t','g',
     &'a','y','w','v','l','i','f','m','c','x',
     &'C','M','F','I','L','V','W','Y','A','G','T',
     &'S','Q','N','E','D','H','R','K','P','z','z','z','z','X'/
      data potname /'LJ','LJK','BP','GB','GBV','MM'/
      data ename /
     &   "EVDW SC-SC","EVDW2 SC-p","EES p-p","ECORR4 ","ECORR5 ",
     &   "ECORR6 ","EELLO ","ETURN3 ","ETURN4 ","ETURN6 ",
     &   "EBE bend","ESC SCloc","ETORS ","ETORSD ","EHPB","EVDWPP",
     &   "ESTR","EVDW2_14","ESCCOR","EDIHC","EVDW_T","ELIPTRAN",
     &   "EAFM","ETHETC","EMPTY"/
      data wname /
     &   "WSC","WSCP","WELEC","WCORR","WCORR5","WCORR6","WEL_LOC",
     &   "WTURN3","WTURN4","WTURN6","WANG","WSCLOC","WTOR","WTORD",
     &   "WHPB","WVDWPP","WBOND","WSCP14","WSCCOR","WDIHC","WSC_T",
     &   "WLIPTRAN","WAFM","WTHETC","WSHIELD"/
      data ww0 /1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,
     &    1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,0.0d0,1.0d0,
     &    0.0d0,0.0,0.0d0,0.0d0,0.0d0,0.0d0/
      data nprint_ene /25/
      data print_order /1,2,3,17,11,12,13,14,4,5,6,7,8,9,10,19,16,15,18,
     &  20,21,22,23,24,25/
      end 
c---------------------------------------------------------------------------
      subroutine init_int_table
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
#ifdef MPI
      include 'mpif.h'
#endif
#ifdef MP
      include 'COMMON.INFO'
#endif
      include 'COMMON.CHAIN'
      include 'COMMON.INTERACT'
      include 'COMMON.LOCAL'
      include 'COMMON.SBRIDGE'
      include 'COMMON.IOUNITS'
      logical scheck,lprint
      lprint=.false.
      do i=1,maxres
        nint_gr(i)=0
        nscp_gr(i)=0
        do j=1,maxint_gr
          istart(i,1)=0
          iend(i,1)=0
          ielstart(i)=0
          ielend(i)=0
          iscpstart(i,1)=0
          iscpend(i,1)=0    
        enddo
      enddo
      ind_scint=0
      ind_scint_old=0
cd    write (iout,*) 'ns=',ns,' nss=',nss,' ihpb,jhpb',
cd   &   (ihpb(i),jhpb(i),i=1,nss)
      do i=nnt,nct-1
        scheck=.false.
        do ii=1,nss
          if (ihpb(ii).eq.i+nres) then
            scheck=.true.
            jj=jhpb(ii)-nres
            goto 10
          endif
        enddo
   10   continue
cd      write (iout,*) 'i=',i,' scheck=',scheck,' jj=',jj
        if (scheck) then
          if (jj.eq.i+1) then
            nint_gr(i)=1
            istart(i,1)=i+2
            iend(i,1)=nct
          else if (jj.eq.nct) then
            nint_gr(i)=1
            istart(i,1)=i+1
            iend(i,1)=nct-1
          else
            nint_gr(i)=2
            istart(i,1)=i+1
            iend(i,1)=jj-1
            istart(i,2)=jj+1
            iend(i,2)=nct
          endif
        else
          nint_gr(i)=1
          istart(i,1)=i+1
          iend(i,1)=nct
          ind_scint=int_scint+nct-i
        endif
      enddo
   12 continue
      iatsc_s=nnt
      iatsc_e=nct-1
      if (lprint) then
      write (iout,'(a)') 'Interaction array:'
      do i=iatsc_s,iatsc_e
        write (iout,'(i3,2(2x,2i3))') 
     & i,(istart(i,iint),iend(i,iint),iint=1,nint_gr(i))
      enddo
      endif
      ispp=2
      iatel_s=nnt
      iatel_e=nct-3
      do i=iatel_s,iatel_e
        ielstart(i)=i+4
        ielend(i)=nct-1
      enddo
      if (lprint) then
        write (iout,'(a)') 'Electrostatic interaction array:'
        do i=iatel_s,iatel_e
          write (iout,'(i3,2(2x,2i3))') i,ielstart(i),ielend(i)
        enddo
      endif ! lprint
c     iscp=3
      iscp=2
C Partition the SC-p interaction array
      iatscp_s=nnt
      iatscp_e=nct-1
      do i=nnt,nct-1
        if (i.lt.nnt+iscp) then
          nscp_gr(i)=1
          iscpstart(i,1)=i+iscp
          iscpend(i,1)=nct
        elseif (i.gt.nct-iscp) then
          nscp_gr(i)=1
          iscpstart(i,1)=nnt
          iscpend(i,1)=i-iscp
        else
          nscp_gr(i)=2
          iscpstart(i,1)=nnt
          iscpend(i,1)=i-iscp
          iscpstart(i,2)=i+iscp
          iscpend(i,2)=nct
        endif 
      enddo ! i
      if (lprint) then
        write (iout,'(a)') 'SC-p interaction array:'
        do i=iatscp_s,iatscp_e
          write (iout,'(i3,2(2x,2i3))') 
     &         i,(iscpstart(i,j),iscpend(i,j),j=1,nscp_gr(i))
        enddo
      endif ! lprint
C Partition local interactions
      loc_start=2
      loc_end=nres-1
      ithet_start=3 
      ithet_end=nres
      iturn3_start=nnt
      iturn3_end=nct-3
      iturn4_start=nnt
      iturn4_end=nct-4
      iphi_start=nnt+3
      iphi_end=nct
      idihconstr_start=1
      idihconstr_end=ndih_constr
      ithetaconstr_start=1
      ithetaconstr_end=ntheta_constr
      itau_start=4
      itau_end=nres
      return
      end 
c---------------------------------------------------------------------------
      subroutine int_partition(int_index,lower_index,upper_index,atom,
     & at_start,at_end,first_atom,last_atom,int_gr,jat_start,jat_end,*)
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'COMMON.IOUNITS'
      integer int_index,lower_index,upper_index,atom,at_start,at_end,
     & first_atom,last_atom,int_gr,jat_start,jat_end
      logical lprn
      lprn=.false.
      if (lprn) write (iout,*) 'int_index=',int_index
      int_index_old=int_index
      int_index=int_index+last_atom-first_atom+1
      if (lprn) 
     &   write (iout,*) 'int_index=',int_index,
     &               ' int_index_old',int_index_old,
     &               ' lower_index=',lower_index,
     &               ' upper_index=',upper_index,
     &               ' atom=',atom,' first_atom=',first_atom,
     &               ' last_atom=',last_atom
      if (int_index.ge.lower_index) then
        int_gr=int_gr+1
        if (at_start.eq.0) then
          at_start=atom
          jat_start=first_atom-1+lower_index-int_index_old
        else
          jat_start=first_atom
        endif
        if (lprn) write (iout,*) 'jat_start',jat_start
        if (int_index.ge.upper_index) then
          at_end=atom
          jat_end=first_atom-1+upper_index-int_index_old
          return1
        else
          jat_end=last_atom
        endif
        if (lprn) write (iout,*) 'jat_end',jat_end
      endif
      return
      end
c------------------------------------------------------------------------------
      subroutine hpb_partition
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'COMMON.SBRIDGE'
      include 'COMMON.IOUNITS'
      link_start=1
      link_end=nhpb
cd    write (iout,*) 'Processor',MyID,' MyRank',MyRank,
cd   &  ' nhpb',nhpb,' link_start=',link_start,
cd   &  ' link_end',link_end
      return
      end