!
! The following is just to define auxiliary variables used in angle conversion
!
+! ifirstrun=0
pi=4.0D0*datan(1.0D0)
dwapi=2.0D0*pi
dwapi3=dwapi/3.0D0
icsa_in=40
!rc for ifc error 118
icsa_pdb=42
+ irotam_end=43
#endif
iscpp=25
icbase=16
isidep_peppho=144
iliptranpar=60
+
itube=61
+! LIPID MARTINI
+ ilipbond=301
+ ilipnonbond=302
+ imartprot=303 ! this parameters are between protein and martini form of lipid
! IONS
iion=401
+ iionnucl=402
+ iiontran=403 ! this is parameter file for transition metals
+ iwaterwater=404
+ iwatersc=405
#if defined(WHAM_RUN) || defined(CLUSTER)
!
! setting the mpi variables for WHAM
!
!c maxfun=5000
!c maxit=2000
- maxfun=500
- maxit=200
+ maxfun=1000
+ maxit=1000
tolf=1.0D-2
rtolf=5.0D-4
!
nscp_int_tot,my_scp_inds,my_scp_inde,ind_scpint,&
ind_scpint_old,nsumgrad,nlen,ngrad_start,ngrad_end,&
ierror,k,ierr,iaux,ncheck_to,ncheck_from,ind_typ,&
- ichunk,int_index_old
+ ichunk,int_index_old,ibra
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
+ my_scp_inde_nucl,ind_scpint_nucl,ind_scpint_old_nucl,impishi
+ integer(kind=1),dimension(:,:),allocatable :: remmat
! 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)
!... Determine the numbers of start and end SC-SC interaction
!... to deal with by current processor.
!write (iout,*) '******INIT_INT_TABLE nres=',nres,' nnt=',nnt,' nct=',nct
+ print *,"in spliting contacts"
do i=0,nfgtasks-1
itask_cont_from(i)=fg_rank
itask_cont_to(i)=fg_rank
lprint=energy_dec
itmp=0
do i=1,5
+ print *,i,nres_molec(i)
if (nres_molec(i).eq.0) cycle
itmp=itmp+nres_molec(i)
if (itype(itmp,i).eq.ntyp1_molec(i)) then
nnt_molec(i)=itmp+1
endif
enddo
+! if (.not.allocated(nres_molec)) print *,"WHATS WRONG"
print *,"nres_molec",nres_molec(:)
print *,"nnt_molec",nnt_molec(:)
print *,"nct_molec",nct_molec(:)
iatsc_s=0
iatsc_e=0
#endif
+ if(.not.allocated(ielstart_all)) then
!el common /przechowalnia/
allocate(iturn3_start_all(0:nfgtasks))
allocate(iturn3_end_all(0:nfgtasks))
allocate(itask_cont_from_all(0:nfgtasks-1,0:nfgtasks-1))
allocate(itask_cont_to_all(0:nfgtasks-1,0:nfgtasks-1))
!el----------
+ endif
! lprint=.false.
print *,"NCT",nct_molec(1),nct
do i=1,nres !el !maxres
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
iturn3_end=iturn3_end+nnt
iphi_end=iturn3_end+2
iturn3_start=iturn3_start-1
+ if (iturn3_start.eq.0) iturn3_start=1
iturn3_end=iturn3_end-1
call int_bounds(nct_molec(2)-nnt_molec(2)-2,iphi_nucl_start,iphi_nucl_end)
iphi_nucl_start=iphi_nucl_start+nnt_molec(2)+2
iphid_end=iturn4_end+2
iturn4_start=iturn4_start-1
iturn4_end=iturn4_end-1
+ if (iturn4_start.eq.0) iturn4_start=1
! print *,"TUTUTU",nres_molec(1),nres
call int_bounds(nres_molec(1)-2,ibond_start,ibond_end)
ibond_start=ibond_start+1
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)
+ call int_bounds(nres_molec(2)-1,ibondp_nucl_start,ibondp_nucl_end)
+ ibondp_nucl_start=ibondp_nucl_start+nnt_molec(2)-1
+ ibondp_nucl_end=ibondp_nucl_end+nnt_molec(2)-1
+ else
+ ibondp_nucl_start=1
+ ibondp_nucl_end=0
+ endif
print *,"NUCLibond2",ibondp_nucl_start,ibondp_nucl_end
call int_bounds &
(ntheta_constr,ithetaconstr_start,ithetaconstr_end)
endif
+! HERE MAKING LISTS FOR MARTINI
+ itmp=0
+ do i=1,3
+ itmp=itmp+nres_molec(i)
+ enddo
+!First bonding
+! call int_bounds(nres_molec(4)-1,ilipbond_start,ilipbond_end)
+ ilipbond_start=1+itmp
+ ilipbond_end=nres_molec(4)-1+itmp
+!angles
+ call int_bounds(nres_molec(4)-1,ilipbond_start_tub,ilipbond_end_tub)
+ ilipbond_start_tub=1+itmp
+ ilipbond_end_tub=nres_molec(4)-1+itmp
+! call int_bounds(nres_molec(4)-2,ilipang_start,ilipang_end)
+ ilipang_start=2+itmp
+ ilipang_end=itmp+nres_molec(4)-1
+! create LJ LIST MAXIMUM
+! Eliminate branching from list
+ if(.not.allocated(remmat))&
+ allocate(remmat(itmp+1:nres_molec(4)+itmp,itmp+1:nres_molec(4)+itmp))
+ remmat=0
+ do i=1+itmp,nres_molec(4)-1+itmp
+ if (itype(i,4).eq.12) ibra=i
+ if (itype(i,4).eq.ntyp1_molec(4)-1) then
+! remmat(ibra-1,i+1)=1
+ remmat(ibra,i+1)=1
+! remmat(ibra+1,i+1)=1
+ endif
+ enddo
+ maxljliplist=0
+ if (.not.allocated(mlipljlisti)) then
+ allocate (mlipljlisti(nres_molec(4)*nres_molec(4)/2))
+ allocate (mlipljlistj(nres_molec(4)*nres_molec(4)/2))
+ endif
+ do i=1+itmp,nres_molec(4)-1+itmp
+ do j=i+2,nres_molec(4)+itmp
+ if ((itype(i,4).le.ntyp_molec(4)).and.(itype(j,4).le.ntyp_molec(4))&
+ .and.(remmat(i,j).eq.0)) then
+ maxljliplist=maxljliplist+1
+ mlipljlisti(maxljliplist)=i
+ mlipljlistj(maxljliplist)=j
+ if (energy_dec) print *,i,j,remmat(i,j),"lj lip list"
+ endif
+ enddo
+ enddo
+! split the bound of the list
+ call int_bounds(maxljliplist,iliplj_start,iliplj_end)
+ iliplj_start=iliplj_start
+ iliplj_end=iliplj_end
+! now the electrostatic list
+ maxelecliplist=0
+ if (.not.allocated(mlipeleclisti)) then
+ allocate (mlipeleclisti(nres_molec(4)*nres_molec(4)/2))
+ allocate (mlipeleclistj(nres_molec(4)*nres_molec(4)/2))
+ endif
+ do i=1+itmp,nres_molec(4)-1+itmp
+ do j=i+2,nres_molec(4)+itmp
+ if ((itype(i,4).le.4).and.(itype(j,4).le.4)) then
+ maxelecliplist=maxelecliplist+1
+ mlipeleclisti(maxelecliplist)=i
+ mlipeleclistj(maxelecliplist)=j
+ endif
+ enddo
+ enddo
+ call int_bounds(maxelecliplist,ilip_elec_start,ilipelec_end)
+ ilip_elec_start=ilip_elec_start
+ ilipelec_end=ilipelec_end
! nsumgrad=(nres-nnt)*(nres-nnt+1)/2
! nlen=nres-nnt+1
nsumgrad=(nres-nnt)*(nres-nnt+1)/2
jgrad_start(i)=i+1
jgrad_end(i)=nres
enddo
+! THIS SHOULD BE FIXED
+ itmp=0
+ do i=1,4
+ itmp=itmp+nres_molec(i)
+ enddo
+ call int_bounds(nres_molec(5),icatb_start,icatb_end)
+ icatb_start=icatb_start+itmp
+ icatb_end=icatb_end+itmp
+
+
+
if (lprint) then
write (*,*) 'Processor:',fg_rank,' CG group',kolor,&
' absolute rank',myrank,&
write (iout,*) "iturn4_end_all",&
(iturn4_end_all(i),i=0,nfgtasks-1)
write (iout,*) "The ielstart_all array"
+! do i=0,nfgtasks-1
+! if (iturn3_start_all(i).le.0) iturn3_start_all(i)=1
+! if (iturn4_start_all(i).le.0) iturn4_start_all(i)=1
+! enddo
do i=nnt,nct
write (iout,'(20i4)') i,(ielstart_all(i,j),j=0,nfgtasks-1)
enddo
! write (iout,*) "Loop backward iatel_e-1",iatel_e-1,
! & " iatel_e",iatel_e
! call flush(iout)
+#ifndef NEWCORR
nat_sent=0
do i=iatel_s,iatel_e
! write (iout,*) "i",i," ielstart",ielstart(i),
iat_sent(nat_sent)=i
endif
enddo
+#endif
if (lprint) then
write (iout,*)"After longrange ntask_cont_from",ntask_cont_from,&
" ntask_cont_to",ntask_cont_to
write (iout,*) "itask_cont_to",&
(itask_cont_to(i),i=1,ntask_cont_to)
call flush(iout)
+#ifndef NEWCORR
write (iout,*) "iint_sent"
do i=1,nat_sent
ii=iat_sent(i)
write (iout,'(20i4)') ii,(j,(iint_sent(k,j,i),k=1,4),&
j=ielstart(ii),ielend(ii))
enddo
+#endif
write (iout,*) "iturn3_sent iturn3_start",iturn3_start,&
" iturn3_end",iturn3_end
write (iout,'(20i4)') (i,(iturn3_sent(j,i),j=1,4),&
itask_cont_from(0),CONT_FROM_GROUP,IERR)
call MPI_Group_incl(fg_group,ntask_cont_to+1,itask_cont_to(0),&
CONT_TO_GROUP,IERR)
+#ifndef NEWCORR
do i=1,nat_sent
ii=iat_sent(i)
iaux=4*(ielend(ii)-ielstart(ii)+1)
+ if (iaux.lt.0) iaux=0
call MPI_Group_translate_ranks(fg_group,iaux,&
iint_sent(1,ielstart(ii),i),CONT_TO_GROUP,&
iint_sent_local(1,ielstart(ii),i),IERR )
! write (iout,*) "Ranks translated i=",i
! call flush(iout)
enddo
+#endif
iaux=4*(iturn3_end-iturn3_start+1)
+ if (iaux.lt.0) iaux=0
call MPI_Group_translate_ranks(fg_group,iaux,&
iturn3_sent(1,iturn3_start),CONT_TO_GROUP,&
iturn3_sent_local(1,iturn3_start),IERR)
iaux=4*(iturn4_end-iturn4_start+1)
+ if (iaux.lt.0) iaux=0
call MPI_Group_translate_ranks(fg_group,iaux,&
iturn4_sent(1,iturn4_start),CONT_TO_GROUP,&
iturn4_sent_local(1,iturn4_start),IERR)
if (lprint) then
+#ifndef NEWCORR
+
write (iout,*) "iint_sent_local"
do i=1,nat_sent
ii=iat_sent(i)
j=ielstart(ii),ielend(ii))
call flush(iout)
enddo
+#endif
+ if (iturn3_end.gt.0) then
write (iout,*) "iturn3_sent_local iturn3_start",iturn3_start,&
" iturn3_end",iturn3_end
write (iout,'(20i4)') (i,(iturn3_sent_local(j,i),j=1,4),&
i=iturn4_start,iturn4_end)
call flush(iout)
endif
+ endif
call MPI_Group_free(fg_group,ierr)
call MPI_Group_free(cont_from_group,ierr)
call MPI_Group_free(cont_to_group,ierr)
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)
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,mnum).ne.ntyp1_molec(mnum) .and. mnum.ne.5) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum) .and. mnum.lt.4) 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 $
end subroutine print_detailed_timing
#endif
!-----------------------------------------------------------------------------
+ subroutine homology_partition
+ implicit none
+! include 'DIMENSIONS'
+!#ifdef MPI
+! include 'mpif.h'
+!#endif
+! include 'COMMON.SBRIDGE'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.SETUP'
+! include 'COMMON.CONTROL'
+! include 'COMMON.INTERACT'
+! include 'COMMON.HOMOLOGY'
+!d write(iout,*)"homology_partition: lim_odl=",lim_odl,
+!d & " lim_dih",lim_dih
+#ifdef MPI
+ if (me.eq.king .or. .not. out1file) write (iout,*) "MPI"
+ call int_bounds(lim_odl,link_start_homo,link_end_homo)
+ call int_bounds(lim_dih,idihconstr_start_homo, &
+ idihconstr_end_homo)
+ idihconstr_start_homo=idihconstr_start_homo+nnt-1+3
+ idihconstr_end_homo=idihconstr_end_homo+nnt-1+3
+ if (me.eq.king .or. .not. out1file)&
+ write (iout,*) 'Processor',fg_rank,' CG group',kolor,&
+ ' absolute rank',MyRank,&
+ ' lim_odl',lim_odl,' link_start=',link_start_homo,&
+ ' link_end',link_end_homo,' lim_dih',lim_dih,&
+ ' idihconstr_start_homo',idihconstr_start_homo,&
+ ' idihconstr_end_homo',idihconstr_end_homo
+#else
+ write (iout,*) "Not MPI"
+ link_start_homo=1
+ link_end_homo=lim_odl
+ idihconstr_start_homo=nnt+3
+ idihconstr_end_homo=lim_dih+nnt-1+3
+ write (iout,*) &
+ ' lim_odl',lim_odl,' link_start=',link_start_homo, &
+ ' link_end',link_end_homo,' lim_dih',lim_dih,&
+ ' idihconstr_start_homo',idihconstr_start_homo,&
+ ' idihconstr_end_homo',idihconstr_end_homo
+#endif
+ return
+ end subroutine homology_partition
+
!-----------------------------------------------------------------------------
end module control
projects / unres4.git / blobdiff