itordp_nucl= 130
! ielep_nucl= 131
isidep_nucl=132
-
-
+ iscpp_nucl=133
+ isidep_scbase=141
+ isidep_pepbase=142
+ isidep_scpho=143
+ isidep_peppho=144
iliptranpar=60
itube=61
+! IONS
+ iion=401
#if defined(WHAM_RUN) || defined(CLUSTER)
!
! setting the mpi variables for WHAM
!el local variables
integer :: ind_scint=0,ind_scint_old,ii,jj,i,j,iint,itmp
-
+ integer :: ind_scint_nucl=0
#ifdef MPI
integer :: my_sc_int(0:nfgtasks-1),my_ele_int(0:nfgtasks-1)
integer :: my_sc_intt(0:nfgtasks),my_ele_intt(0:nfgtasks)
integer :: n_sc_int_tot,my_sc_inde,my_sc_inds,ind_sctint,npept
+ integer :: n_sc_int_tot_nucl,my_sc_inde_nucl,my_sc_inds_nucl, &
+ ind_sctint_nucl,npept_nucl
+
integer :: nele_int_tot,my_ele_inds,my_ele_inde,ind_eleint_old,&
ind_eleint,ijunk,nele_int_tot_vdw,my_ele_inds_vdw,&
my_ele_inde_vdw,ind_eleint_vdw,ind_eleint_vdw_old,&
ind_scpint_old,nsumgrad,nlen,ngrad_start,ngrad_end,&
ierror,k,ierr,iaux,ncheck_to,ncheck_from,ind_typ,&
ichunk,int_index_old
- integer,dimension(5) :: nct_molec,nnt_molec
+ integer :: nele_int_tot_nucl,my_ele_inds_nucl,my_ele_inde_nucl,&
+ ind_eleint_old_nucl,ind_eleint_nucl,nele_int_tot_vdw_nucl,&
+ my_ele_inds_vdw_nucl,my_ele_inde_vdw_nucl,ind_eleint_vdw_nucl,&
+ ind_eleint_vdw_old_nucl,nscp_int_tot_nucl,my_scp_inds_nucl,&
+ my_scp_inde_nucl,ind_scpint_nucl,ind_scpint_old_nucl,impishi
+! integer,dimension(5) :: nct_molec,nnt_molec
!el allocate(itask_cont_from(0:nfgtasks-1)) !(0:max_fg_procs-1)
!el allocate(itask_cont_to(0:nfgtasks-1)) !(0:max_fg_procs-1)
iatsc_e=nct-1
#endif
if (iatsc_s.eq.0) iatsc_s=1
+!----------------- scaling for nucleic acid GB
+ n_sc_int_tot_nucl=(nct_molec(2)-nnt_molec(2)+1)*(nct_molec(2)-nnt_molec(2))/2
+ call int_bounds(n_sc_int_tot_nucl,my_sc_inds_nucl,my_sc_inde_nucl)
+!write (iout,*) 'INIT_INT_TABLE nres=',nres,' nnt=',nnt,' nct=',nct
+ if (lprint) &
+ write (iout,*) 'Processor',fg_rank,' CG group',kolor,&
+ ' absolute rank',MyRank,&
+ ' n_sc_int_tot',n_sc_int_tot_nucl,' my_sc_inds=',my_sc_inds_nucl,&
+ ' my_sc_inde',my_sc_inde_nucl
+ ind_sctint_nucl=0
+ iatsc_s_nucl=0
+ iatsc_e_nucl=0
+ do i=1,nres !el !maxres
+ nint_gr_nucl(i)=0
+ nscp_gr_nucl(i)=0
+ ielstart_nucl(i)=0
+ ielend_nucl(i)=0
+ do j=1,maxint_gr
+ istart_nucl(i,j)=0
+ iend_nucl(i,j)=0
+ iscpstart_nucl(i,j)=0
+ iscpend_nucl(i,j)=0
+ enddo
+ enddo
+ do i=nnt_molec(2),nct_molec(2)-1
+ print*, "inloop2",i
+ call int_partition(ind_scint_nucl,my_sc_inds_nucl,my_sc_inde_nucl,i,&
+ iatsc_s_nucl,iatsc_e_nucl,i+1,nct_molec(2),nint_gr_nucl(i), &
+ istart_nucl(i,1),iend_nucl(i,1),*112)
+ print *,istart_nucl(i,1)
+ enddo
+ 112 continue
+ if (iatsc_s_nucl.eq.0) iatsc_s_nucl=1
+ print *,"tu mam",iatsc_s_nucl,iatsc_e_nucl
+
#ifdef MPI
if (lprint) write (*,*) 'Processor',fg_rank,' CG Group',kolor,&
' absolute rank',myrank,' iatsc_s=',iatsc_s,' iatsc_e=',iatsc_e
write (iout,'(i3,2(2x,2i3))') &
i,(istart(i,iint),iend(i,iint),iint=1,nint_gr(i))
enddo
- endif
+! endif
! lprint=.false.
+ write (iout,'(a)') 'Interaction array2:'
+ do i=iatsc_s_nucl,iatsc_e_nucl
+ write (iout,'(i3,2(2x,2i4))') &
+ i,(istart_nucl(i,iint),iend_nucl(i,iint),iint=1,nint_gr_nucl(i))
+ enddo
+ endif
ispp=4 !?? wham ispp=2
#ifdef MPI
! Now partition the electrostatic-interaction array
- if (itype(nres_molec(1),1).eq.ntyp1_molec(1)) then
+ if (nres_molec(1).eq.0) then
+ npept=0
+ elseif (itype(nres_molec(1),1).eq.ntyp1_molec(1)) then
npept=nres_molec(1)-nnt-1
else
npept=nres_molec(1)-nnt
enddo ! i
13 continue
if (iatel_s.eq.0) iatel_s=1
+!----------now nucleic acid
+! if (itype(nres_molec(2),2).eq.ntyp1_molec(2)) then
+ npept_nucl=nct_molec(2)-nnt_molec(2)
+! else
+! npept_nucl=nct_molec(2)-nnt_molec(2)
+! endif
+ nele_int_tot_nucl=(npept_nucl-ispp)*(npept_nucl-ispp+1)/2
+ call int_bounds(nele_int_tot_nucl,my_ele_inds_nucl,my_ele_inde_nucl)
+ if (lprint) &
+ write (*,*) 'Processor',fg_rank,' CG group',kolor,&
+ ' absolute rank',MyRank,&
+ ' nele_int_tot',nele_int_tot,' my_ele_inds=',my_ele_inds,&
+ ' my_ele_inde',my_ele_inde
+ iatel_s_nucl=0
+ iatel_e_nucl=0
+ ind_eleint_nucl=0
+ ind_eleint_old_nucl=0
+! if (itype(nres_molec(1),1).eq.ntyp1_molec(1)) then
+! nct_molec(1)=nres_molec(1)-1
+! else
+! nct_molec(1)=nres_molec(1)
+! endif
+! print *,"nct",nct,nct_molec(1),itype(nres_molec(1),1),ntyp_molec(1)
+ do i=nnt_molec(2),nct_molec(2)-3
+ ijunk=0
+ call int_partition(ind_eleint_nucl,my_ele_inds_nucl,my_ele_inde_nucl,i,&
+ iatel_s_nucl,iatel_e_nucl,i+ispp,nct_molec(2)-1,&
+ ijunk,ielstart_nucl(i),ielend_nucl(i),*113)
+ enddo ! i
+ 113 continue
+ if (iatel_s_nucl.eq.0) iatel_s_nucl=1
+
nele_int_tot_vdw=(npept-2)*(npept-2+1)/2
! write (iout,*) "nele_int_tot_vdw",nele_int_tot_vdw
call int_bounds(nele_int_tot_vdw,my_ele_inds_vdw,my_ele_inde_vdw)
enddo ! i
if (iatel_s_vdw.eq.0) iatel_s_vdw=1
15 continue
+ if (iatel_s.eq.0) iatel_s=1
+ if (iatel_s_vdw.eq.0) iatel_s_vdw=1
+ nele_int_tot_vdw_nucl=(npept_nucl-2)*(npept_nucl-2+1)/2
+! write (iout,*) "nele_int_tot_vdw",nele_int_tot_vdw
+ call int_bounds(nele_int_tot_vdw_nucl,my_ele_inds_vdw_nucl,&
+ my_ele_inde_vdw_nucl)
+! write (iout,*) "my_ele_inds_vdw",my_ele_inds_vdw,
+! & " my_ele_inde_vdw",my_ele_inde_vdw
+ ind_eleint_vdw_nucl=0
+ ind_eleint_vdw_old_nucl=0
+ iatel_s_vdw_nucl=0
+ iatel_e_vdw_nucl=0
+ do i=nnt_molec(2),nct_molec(2)-3
+ ijunk=0
+ call int_partition(ind_eleint_vdw_nucl,my_ele_inds_vdw_nucl,&
+ my_ele_inde_vdw_nucl,i,&
+ iatel_s_vdw_nucl,iatel_e_vdw_nucl,i+2,nct_molec(2)-1,&
+ ijunk,ielstart_vdw_nucl(i),&
+ ielend_vdw(i),*115)
+! write (iout,*) i," ielstart_vdw",ielstart_vdw(i),
+! & " ielend_vdw",ielend_vdw(i)
+ enddo ! i
+ if (iatel_s_vdw.eq.0) iatel_s_vdw_nucl=1
+ 115 continue
+
#else
iatel_s=nnt
iatel_e=nct_molec(1)-5 ! ?? wham iatel_e=nct-3
endif ! lprint
! iscp=3
iscp=2
+ iscp_nucl=2
! Partition the SC-p interaction array
#ifdef MPI
nscp_int_tot=(npept-iscp+1)*(npept-iscp+1)
endif
enddo ! i
14 continue
+ print *,"before inloop3",iatscp_s,iatscp_e,iscp_nucl
+ nscp_int_tot_nucl=(npept_nucl-iscp_nucl+1)*(npept_nucl-iscp_nucl+1)
+ call int_bounds(nscp_int_tot_nucl,my_scp_inds_nucl,my_scp_inde_nucl)
+ if (lprint) write (iout,*) 'Processor',fg_rank,' CG group',kolor,&
+ ' absolute rank',myrank,&
+ ' nscp_int_tot',nscp_int_tot_nucl,' my_scp_inds=',my_scp_inds_nucl,&
+ ' my_scp_inde',my_scp_inde_nucl
+ print *,"nscp_int_tot_nucl",nscp_int_tot_nucl,my_scp_inds_nucl,my_scp_inde_nucl
+ iatscp_s_nucl=0
+ iatscp_e_nucl=0
+ ind_scpint_nucl=0
+ ind_scpint_old_nucl=0
+ do i=nnt_molec(2),nct_molec(2)-1
+ print *,"inloop3",i,nnt_molec(2)+iscp,nct_molec(2)-iscp
+ if (i.lt.nnt_molec(2)+iscp) then
+!d write (iout,*) 'i.le.nnt+iscp'
+ call int_partition(ind_scpint_nucl,my_scp_inds_nucl,&
+ my_scp_inde_nucl,i,iatscp_s_nucl,iatscp_e_nucl,i+iscp,&
+ nct_molec(2),nscp_gr_nucl(i),iscpstart_nucl(i,1),&
+ iscpend_nucl(i,1),*114)
+ else if (i.gt.nct_molec(2)-iscp) then
+!d write (iout,*) 'i.gt.nct-iscp'
+ call int_partition(ind_scpint_nucl,my_scp_inds_nucl,&
+ my_scp_inde_nucl,i,&
+ iatscp_s_nucl,iatscp_e_nucl,nnt_molec(2),i-iscp,nscp_gr_nucl(i),&
+ iscpstart_nucl(i,1),&
+ iscpend_nucl(i,1),*114)
+ else
+ call int_partition(ind_scpint_nucl,my_scp_inds_nucl,&
+ my_scp_inde_nucl,i,iatscp_s_nucl,iatscp_e_nucl,nnt_molec(2),&
+ i-iscp,nscp_gr_nucl(i),iscpstart_nucl(i,1),&
+ iscpend_nucl(i,1),*114)
+ ii=nscp_gr_nucl(i)+1
+ call int_partition(ind_scpint_nucl,my_scp_inds_nucl,&
+ my_scp_inde_nucl,i,iatscp_s_nucl,iatscp_e_nucl,i+iscp,&
+ nct_molec(2),nscp_gr_nucl(i),iscpstart_nucl(i,ii),&
+ iscpend_nucl(i,ii),*114)
+ endif
+ enddo ! i
+ 114 continue
+ print *, "after inloop3",iatscp_s_nucl,iatscp_e_nucl
+ if (iatscp_s_nucl.eq.0) iatscp_s_nucl=1
#else
iatscp_s=nnt
iatscp_e=nct_molec(1)-1
call int_bounds(nres_molec(1)-2,loc_start,loc_end)
loc_start=loc_start+1
loc_end=loc_end+1
+ call int_bounds(nres_molec(2)-2,loc_start_nucl,loc_end_nucl)
+ loc_start_nucl=loc_start_nucl+1+nres_molec(1)
+ loc_end_nucl=loc_end_nucl+1+nres_molec(1)
call int_bounds(nres_molec(1)-2,ithet_start,ithet_end)
ithet_start=ithet_start+2
ithet_end=ithet_end+2
ibond_nucl_start=ibond_nucl_start+nnt_molec(2)-1
ibond_nucl_end=ibond_nucl_end+nnt_molec(2)-1
print *,"NUCLibond",ibond_nucl_start,ibond_nucl_end
+ if (nres_molec(2).ne.0) then
print *, "before devision",nnt_molec(2),nct_molec(2)-nnt_molec(2)
call int_bounds(nct_molec(2)-nnt_molec(2),ibondp_nucl_start,ibondp_nucl_end)
ibondp_nucl_start=ibondp_nucl_start+nnt_molec(2)
ibondp_nucl_end=ibondp_nucl_end+nnt_molec(2)
+ else
+ ibondp_nucl_start=1
+ ibondp_nucl_end=0
+ endif
print *,"NUCLibond2",ibondp_nucl_start,ibondp_nucl_end
write (*,*) 'Processor:',fg_rank,myrank,' igrad_start',&
igrad_start,' igrad_end',igrad_end,' ngrad_start',ngrad_start,&
' ngrad_end',ngrad_end
- do i=igrad_start,igrad_end
- write(*,*) 'Processor:',fg_rank,myrank,i,&
- jgrad_start(i),jgrad_end(i)
- enddo
+! do i=igrad_start,igrad_end
+! write(*,*) 'Processor:',fg_rank,myrank,i,&
+! jgrad_start(i),jgrad_end(i)
+! enddo
endif
if (nfgtasks.gt.1) then
call MPI_Allgather(ivec_start,1,MPI_INTEGER,ivec_displ(0),1,&
call MPI_Type_contiguous(18,MPI_DOUBLE_PRECISION,MPI_UYZGRAD,&
IERROR)
call MPI_Type_commit(MPI_UYZGRAD,IERROR)
+ call MPI_Type_contiguous(maxcontsshi,MPI_INTEGER,MPI_I50,IERROR)
+ call MPI_Type_commit(MPI_I50,IERROR)
+ call MPI_Type_contiguous(maxcontsshi,MPI_DOUBLE_PRECISION,MPI_D50,IERROR)
+ call MPI_Type_commit(MPI_D50,IERROR)
+
+ impishi=maxcontsshi*3
+! call MPI_Type_contiguous(impishi,MPI_DOUBLE_PRECISION, &
+! MPI_SHI,IERROR)
+! call MPI_Type_commit(MPI_SHI,IERROR)
+! print *,MPI_SHI,"MPI_SHI",MPI_D50
call MPI_Type_contiguous(2,MPI_DOUBLE_PRECISION,MPI_MU,IERROR)
call MPI_Type_commit(MPI_MU,IERROR)
call MPI_Type_contiguous(4,MPI_DOUBLE_PRECISION,MPI_MAT1,IERROR)
!-----------------------------------------------------------------------------
subroutine setup_var
- integer :: i
+ integer :: i,mnum
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
! include 'COMMON.IOUNITS'
nvar=ntheta+nphi
nside=0
do i=2,nres-1
+ mnum=molnum(i)
+ write(iout,*) "i",molnum(i)
#ifdef WHAM_RUN
if (itype(i,1).ne.10) then
#else
- if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum) .and. mnum.ne.5) then
#endif
nside=nside+1
ialph(i,1)=nvar+nside
return
end subroutine setup_var
!-----------------------------------------------------------------------------
-! rescode.f
-!-----------------------------------------------------------------------------
- integer function rescode(iseq,nam,itype,molecule)
-
- use io_base, only: ucase
-! implicit real*8 (a-h,o-z)
-! include 'DIMENSIONS'
-! include 'COMMON.NAMES'
-! include 'COMMON.IOUNITS'
- character(len=3) :: nam !,ucase
- integer :: iseq,itype,i
- integer :: molecule
- print *,molecule,nam
- if (molecule.eq.1) then
- if (itype.eq.0) then
-
- do i=-ntyp1_molec(molecule),ntyp1_molec(molecule)
- if (ucase(nam).eq.restyp(i,molecule)) then
- rescode=i
- return
- endif
- enddo
-
- else
-
- do i=-ntyp1_molec(molecule),ntyp1_molec(molecule)
- if (nam(1:1).eq.onelet(i)) then
- rescode=i
- return
- endif
- enddo
-
- endif
- else if (molecule.eq.2) then
- do i=1,ntyp1_molec(molecule)
- print *,nam(1:1),restyp(i,molecule)(1:1)
- if (nam(2:2).eq.restyp(i,molecule)(1:1)) then
- rescode=i
- return
- endif
- enddo
- else if (molecule.eq.3) then
- write(iout,*) "SUGAR not yet implemented"
- stop
- else if (molecule.eq.4) then
- write(iout,*) "Explicit LIPID not yet implemented"
- stop
- else if (molecule.eq.5) then
- do i=1,ntyp1_molec(molecule)
- print *,i,restyp(i,molecule)(1:2)
- if (ucase(nam(1:2)).eq.restyp(i,molecule)(1:2)) then
- rescode=i
- return
- endif
- enddo
- else
- write(iout,*) "molecule not defined"
- endif
- write (iout,10) iseq,nam
- stop
- 10 format ('**** Error - residue',i4,' has an unresolved name ',a3)
- end function rescode
- integer function sugarcode(sugar,ires)
- character sugar
- integer ires
- if (sugar.eq.'D') then
- sugarcode=1
- else if (sugar.eq.' ') then
- sugarcode=2
- else
- write (iout,*) 'UNKNOWN sugar type for residue',ires,' ',sugar
- stop
- endif
- return
- end function sugarcode
-
-!-----------------------------------------------------------------------------
! timing.F
!-----------------------------------------------------------------------------
! $Date: 1994/10/05 16:41:52 $
projects / unres4.git / blobdiff