1.6606077 5.9355397 0 0 0 0 3.0000000
1.3228511 5.4343948 0 0 0 0 3.0000000
1.3228511 5.4343948 0 0 0 0 3.0000000
+ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
+ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
+ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
+ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
+ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
+ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
+ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
+
set (CMAKE_Fortran_FLAGS_RELEASE " ")
set (CMAKE_Fortran_FLAGS_DEBUG "-O0 -g -traceback")
# set(FFLAGS0 "-fpp -c -CB -g -ip " )
- set(FFLAGS0 "-CB -g -ip -fpp -heap-arrays -mcmodel=large" )
+ set(FFLAGS0 "-O3 -g -ip -fpp -mcmodel=large" )
# set(FFLAGS0 "-O0 -CB -CA -g" )
set(FFLAGS1 "-fpp -c -O " )
set(FFLAGS2 "-fpp -c -g -CA -CB ")
do j=1,3
incr(j)=d_t(j,0)
enddo
- do i=nnt,nct-1
+ do i=nnt,nct-1 !czy na pewno nct-1??
mnum=molnum(i)
!c write (iout,*) "Kinetic trp:",i,(incr(j),j=1,3
!c Skip dummy peptide groups
do j=1,3
v(j)=incr(j)+0.5d0*d_t(j,i)
enddo
- if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
+ if (mnum.eq.5) mp(mnum)=0.0d0
+! if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
!c write (iout,*) "Kinetic trp:",i,(v(j),j=1,3)
vtot(i)=v(1)*v(1)+v(2)*v(2)+v(3)*v(3)
KEt_p=KEt_p+mp(mnum)*(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
do i=nnt,nct
mnum=molnum(i)
iti=iabs(itype(i,mnum))
+ if (mnum.eq.5) iti=itype(i,mnum)
if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum)&
.or.mnum.ge.3) then
do j=1,3
v(j)=incr(j)+d_t(j,nres+i)
enddo
endif
- write (iout,*) "Kinetic trsc:",i,(incr(j),j=1,3)
- write (iout,*) "i",i," msc",msc(iti,1)," v",(v(j),j=1,3)
+! if (mnum.ne.5) then
+! write (iout,*) "Kinetic trsc:",i,(incr(j),j=1,3)
+! write (iout,*) "i",i," msc",msc(iti,mnum)," v",(v(j),j=1,3)
KEt_sc=KEt_sc+msc(iti,mnum)*(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
vtot(i+nres)=v(1)*v(1)+v(2)*v(2)+v(3)*v(3)
+! endif
do j=1,3
incr(j)=incr(j)+d_t(j,i)
enddo
enddo
!c The total kinetic energy
111 continue
-!c write(iout,*) ' KEt_p',KEt_p,' KEt_sc',KEt_sc,' KEr_p',KEr_p,
-!c & ' KEr_sc', KEr_sc
+! write(iout,*) ' KEt_p',KEt_p,' KEt_sc',KEt_sc,' KEr_p',KEr_p, &
+! ' KEr_sc', KEr_sc
KE_total=0.5d0*(KEt_p+KEt_sc+0.25d0*KEr_p+KEr_sc)
!c write (iout,*) "KE_total",KE_total
return
do i=innt,inct-1
mnum=molnum(i)
if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
+ if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
!c write (iout,*) i,(d_t(j,i),j=1,3),(d_t(j,i+1),j=1,3)
do j=1,3
v(j)=0.5d0*(d_t(j,i)+d_t(j,i+1))
endif
if (mod(itime,ntwx).eq.0) then
call returnbox
+ call enerprint(potEcomp)
+
write (tytul,'("time",f8.2)') totT
if(mdpdb) then
call hairpin(.true.,nharp,iharp)
call secondary2(.true.)
call pdbout(potE,tytul,ipdb)
- call enerprint(potEcomp)
+! call enerprint(potEcomp)
else
call cartout(totT)
endif
if(me.eq.king.or..not.out1file)then
write (iout,*) "Initial velocities"
do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
+ write (iout,'(i6,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
(d_t(j,i+nres),j=1,3)
enddo
! Zeroing the total angular momentum of the system
write (iout,*) "Initial velocities"
write (iout,"(13x,' backbone ',23x,' side chain')")
do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
+ write (iout,'(i6,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
(d_t(j,i+nres),j=1,3)
enddo
write (iout,*) "Initial accelerations"
real(kind=8) :: xv,sigv,lowb,highb ,Ek1
#ifdef FIVEDIAG
integer ichain,n,innt,inct,ibeg,ierr
- double precision work(48*nres)
- integer iwork(6*nres)
+ real(kind=8) ,allocatable, dimension(:):: work
+ integer,allocatable,dimension(:) :: iwork
! double precision Ghalf(mmaxres2_chain),Geigen(maxres2_chain),&
! Gvec(maxres2_chain,maxres2_chain)
! common /przechowalnia/Ghalf,Geigen,Gvec
-#ifdef DEBUG
- double precision inertia(maxres2_chain,maxres2_chain)
-#endif
+!#ifdef DEBUG
+! double precision inertia(maxres2_chain,maxres2_chain)
+!#endif
#endif
-#define DEBUG
+!#define DEBUG
#ifdef FIVEDIAG
- real(kind=8) ,allocatable, dimension(:) :: DDU1,DDU2,DL2,DL1,xsolv,DML,rs
+ real(kind=8) ,allocatable, dimension(:) :: xsolv,DML,rs
real(kind=8) :: sumx,Ek2,Ek3,aux
#ifdef DEBUG
real(kind=8) ,allocatable, dimension(:) :: rsold
real (kind=8),allocatable,dimension(:,:) :: matold,inertia
integer :: iti
#endif
- integer :: i,j,ii,k,ind,mark,imark,mnum
+#endif
+ integer :: i,j,ii,k,mark,imark,mnum,nres2
+ integer(kind=8) :: ind
! Generate random velocities from Gaussian distribution of mean 0 and std of KT/m
+!#undef DEBUG
! First generate velocities in the eigenspace of the G matrix
! write (iout,*) "Calling random_vel dimen dimen3",dimen,dimen3
! call flush(iout)
-!#define DEBUG
+#ifdef FIVEDIAG
+ if(.not.allocated(work)) then
+ allocate(work(48*nres))
+ allocate(iwork(6*nres))
+ endif
+ print *,"IN RANDOM VEL"
+ nres2=2*nres
+! print *,size(ghalf)
+#undef DEBUG
#ifdef DEBUG
write (iout,*) "Random_vel, fivediag"
+ flush(iout)
allocate(inertia(2*nres,2*nres))
#endif
d_t=0.0d0
#endif
do ichain=1,nchain
ind=0
+ if(.not.allocated(ghalf)) print *,"COCO"
+ if(.not.allocated(Ghalf)) allocate(Ghalf(nres2*(nres2+1)/2))
ghalf=0.0d0
n=dimen_chain(ichain)
innt=iposd_chain(ichain)
mnum1=molnum(i+1)
if (itype(i,mnum).eq.ntyp1_molec(mnum)&
.or. itype(i+1,mnum1).eq.ntyp1_molec(mnum1)) cycle
- if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
+! if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
+ if (mnum.ge.5) mp(mnum)=0.0d0
M_PEP=M_PEP+mp(mnum)
do j=1,3
do i=nnt,nct-1
mnum=molnum(i)
mnum1=molnum(i+1)
- if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
+! if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
+ if (mnum.ge.5) mp(mnum)=0.0d0
if (itype(i,mnum).eq.ntyp1_molec(mnum)&
.or. itype(i+1,mnum1).eq.ntyp1_molec(mnum1)) cycle
do j=1,3
do i=nnt,nct-1
mnum=molnum(i)
mnum1=molnum(i+1)
- if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
+! if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
+ if (mnum.ge.5) mp(mnum)=0.0d0
if (itype(i,mnum).eq.ntyp1_molec(mnum)&
.or. itype(i+1,mnum1).eq.ntyp1_molec(mnum1)) cycle
do j=1,3
call vecpr(pr(1),v(1),vp)
!c write (iout,*) "i",i," iti",iti," pr",(pr(j),j=1,3),
!c & " v",(v(j),j=1,3)," vp",(vp(j),j=1,3)
- if (mnum.gt.4) then
- mscab=0.0d0
- else
+! if (mnum.gt.4) then
+! mscab=0.0d0
+! else
mscab=msc(iti,mnum)
- endif
+! endif
do j=1,3
L(j)=L(j)+mscab*vp(j)
enddo
! commom.langevin.lang0
! common /langforc/
allocate(friction(3,0:nres2),stochforc(3,0:nres2)) !(3,0:MAXRES2)
+#ifndef FIVEDIAG
if(.not.allocated(fricmat)) allocate(fricmat(nres2,nres2))
allocate(fricvec(nres2,nres2)) !(MAXRES2,MAXRES2)
+#endif
allocate(fric_work(nres6),stoch_work(nres6),fricgam(nres6)) !(MAXRES6)
allocate(flag_stoch(0:maxflag_stoch)) !(0:maxflag_stoch)
#endif
-
+#ifndef FIVEDIAG
if(.not.allocated(fcopy)) allocate(fcopy(nres2,nres2))
+#endif
!----------------------
! commom.hairpin in CSA module
!----------------------
#ifdef FIVEDIAG
allocate(DM(nres2),DU1(nres2),DU2(nres2))
allocate(DMorig(nres2),DU1orig(nres2),DU2orig(nres2))
+!#ifdef DEBUG
allocate(Gvec(nres2,nres2))
+!#endif
#else
write (iout,*) "Before A Allocation",nfgtasks-1
call flush(iout)
! include 'DIMENSIONS'
use comm_cipiszcze
use energy_data
+#ifdef FIVEDIAG
use energy, only: grad_transform
+#endif
use geometry_data, only: nres
use control_data !el, only: mucadyn,lmuca
#ifdef MPI
real(kind=8) :: rscheck(2*nres),rsold(2*nres)
#endif
#endif
- logical :: lprn = .true.
+ logical :: lprn = .false.
!el common /cipiszcze/ itime
itime = itt_comm
enddo
inct_prev=inct+1
do i=innt,inct
- if (itype(i).ne.10) then
+ mnum=molnum(i)
+ if ((itype(i).ne.10).and.(mnum.le.3)) then
do j=1,3
d_a(j,i+nres)=d_a(j,i+nres)-d_a(j,i)
enddo
include 'mpif.h'
integer :: ierror
real(kind=8) :: time00
- real(kind=8) ,allocatable, dimension(:) :: DDM,DDU1,DDU2
+! real(kind=8) ,allocatable, dimension(:) :: DDM,DDU1,DDU2
#endif
! include 'COMMON.SETUP'
! include 'COMMON.VAR'
real(kind=8),allocatable,dimension(:,:) :: Bmat,matmult
#endif
real(kind=8) :: dtdi
- real(kind=8),dimension(2*nres) :: massvec,sqreig !(maxres2) maxres2=2*maxres
+ real(kind=8),dimension(:),allocatable :: massvec,sqreig !(maxres2) maxres2=2*maxres
real(kind=8) :: relfeh,eps1,eps2
!el real(kind=8),dimension(:),allocatable :: Ghalf
!el real(kind=8),dimension(2*nres*(2*nres+1)/2) :: Ghalf !(mmaxres2) (mmaxres2=(maxres2*(maxres2+1)/2))
!el real(kind=8),dimension(2*nres,2*nres) :: Gcopy !(maxres2,maxres2)
!el real(kind=8),dimension(:,:),allocatable :: Gcopy
- real(kind=8),dimension(8*6*nres) :: work !(8*maxres6)
- integer,dimension(6*nres) :: iwork !(maxres6) maxres6=6*maxres
+ real(kind=8),dimension(:),allocatable :: work !(8*maxres6)
+ integer,dimension(:),allocatable :: iwork !(maxres6) maxres6=6*maxres
+! common /jakistam/ iwork,work,massvec,sqreig
!el common /przechowalnia/ Gcopy,Ghalf
real(kind=8) :: coeff,mscab
integer :: i,j,ind,ind1,k,l,ii,jj,m,m1,ii1,iti,nres2,ierr,nind,mark
real(kind=8) :: ip4
integer :: iz,mnum,ichain,n,dimenp,innt,inct
+ if(.not.allocated(massvec)) then
+ allocate(massvec(2*nres),sqreig(2*nres))
+ allocate(work(8*6*nres))
+ allocate(iwork(6*nres))
+ endif
print *,"just entered"
relfeh=1.0d-14
nres2=2*nres
print *,"FIVEDIAG"
write (iout,*) "before FIVEDIAG"
+#ifdef FIVEDIAG
if(.not.allocated(Ghalf)) allocate(Ghalf(nres2*(nres2+1)/2)) !mmaxres2=(maxres2*(maxres+1)/2)
+#endif
#ifndef FIVEDIAG
+ if(.not.allocated(Ghalf)) allocate(Ghalf(nres2*(nres2+1)/2)) !mmaxres2=(maxres2*(maxres+1)/2)
write (iout,*) "ALLOCATE"
print *,"ALLOCATE"
if(.not.allocated(Gcopy)) allocate(Gcopy(nres2,nres2)) !(maxres2,maxres2)
innt=chain_border(1,ichain)
mnum=molnum(innt)
inct=chain_border(2,ichain)
+ if (mnum.eq.5) mp(mnum)=0.0
+! if (mnum.eq.5) mp(mnum)=msc(itype(innt,mnum),mnum)
DM(ind)=mp(mnum)/4+ip(mnum)/4
if (iabs(itype(innt,1)).eq.10.or.molnum(innt).gt.2) then
- DM(ind)=DM(ind)+msc(itype(innt,mnum),mnum)
+ DM(ind)=DM(ind)+msc(itype(innt,mnum),mnum)
ind=ind+1
nind=1
else
do i=innt+1,inct-1
mnum=molnum(i)
! if (iabs(itype(i)).eq.ntyp1) cycle
- if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
- if (mnum.eq.5) ip(mnum)=isc(itype(i,mnum),mnum)
+! if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
+! if (mnum.eq.5) ip(mnum)=isc(itype(i,mnum),mnum)
+ if (mnum.eq.5) mp(mnum)=0.0
+! if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
DM(ind)=2*ip(mnum)/4+mp(mnum)/2
if (iabs(itype(i,1)).eq.10.or.molnum(i).gt.2) then
- if (iabs(itype(i,1)).eq.10.or.molnum(i).gt.2)&
- DM(ind)=DM(ind)+msc(itype(i,molnum(i)),mnum)
+! if (iabs(itype(i,1)).eq.10.or.molnum(i).gt.2)&
+! DM(ind)=DM(ind)+msc(itype(i,molnum(i)),mnum)
+ DM(ind)=DM(ind)+msc(itype(i,mnum),mnum)
ind=ind+1
nind=nind+1
else
if (inct.gt.innt) then
! DM(ind)=ip4+mp(molnum(inct))/4
mnum=molnum(inct)
+ if (mnum.eq.5) mp(mnum)=0.0
+! if (mnum.eq.5) mp(mnum)=msc(itype(inct,molnum(inct)),molnum(inct))
+
DM(ind)=mp(mnum)/4+ip(mnum)/4
if (iabs(itype(inct,mnum)).eq.10.or.molnum(inct).gt.2) then
- DM(ind)=DM(ind)+msc(itype(inct,molnum(inct)),molnum(inct))
+ DM(ind)=DM(ind)+msc(itype(inct,molnum(inct)),molnum(inct))
ind=ind+1
nind=nind+1
else
DU1(ind+1)=0.0d0
ind=ind+2
else
- if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
- if (mnum.eq.5) ip(mnum)=isc(itype(i,mnum),mnum)
+! if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
+! if (mnum.eq.5) ip(mnum)=isc(itype(i,mnum),mnum)
+ if (mnum.eq.5) mp(mnum)=0.0
DU1(ind)=mp(mnum)/4-ip(mnum)/4
ind=ind+1
endif
! if (iabs(itype(i)).eq.ntyp1) cycle
!c write (iout,*) "i",i," itype",itype(i),ntyp1
if (iabs(itype(i,1)).ne.10 .and. iabs(itype(i,mnum)).ne.ntyp1_molec(mnum).and.mnum.le.2) then
- if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
+! if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
+ if (mnum.eq.5) mp(mnum)=0.0
DU2(ind)=mp(mnum)/4-ip(mnum)/4
DU2(ind+1)=0.0d0
ind=ind+2
if(.not.allocated(bfrag)) allocate(bfrag(4,nres/3)) !(4,maxres/3)
if(.not.allocated(hfrag)) allocate(hfrag(2,nres/3)) !(2,maxres/3)
! COMMON /WAGI/
+#ifndef FIVEDIAG
if(.not.allocated(w)) allocate(w(maxres22),d0(maxres22)) !(maxres22)
! COMMON /POCHODNE/
!el allocate(DRDG(maxres22,maxres22)) !(MAXRES22,MAXRES)
if (.not.allocated(DDD)) allocate(DDD(maxres22)) !(maxres22)
if (.not.allocated(H)) allocate(H(nres,nres)) !(MAXRES,MAXRES)
+#endif
if (.not.allocated(XX)) allocate(XX(nres)) !(MAXRES)
! COMMON /frozen/
if (.not.allocated(mask)) allocate(mask(nres)) !(maxres)
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(nres,nres) :: remmat
+ 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(:)
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
! 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)
! 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,&
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
!-----------------------------------------------------------------------------
! common.sbridge
! common /dyn_ssbond/
- real(kind=8),dimension(:,:),allocatable :: dyn_ssbond_ij !(maxres,maxres)
+ real(kind=8),dimension(:),allocatable :: dyn_ssbond_ij !(maxres,maxres)
!-----------------------------------------------------------------------------
! common.sccor
! Parameters of the SCCOR term
#ifdef MPI
real(kind=8) :: weights_(n_ene) !,time_Bcast,time_Bcastw
! shielding effect varibles for MPI
- real(kind=8) :: fac_shieldbuf(nres), &
- grad_shield_locbuf1(3*maxcontsshi*nres), &
- grad_shield_sidebuf1(3*maxcontsshi*nres), &
- grad_shield_locbuf2(3*maxcontsshi*nres), &
- grad_shield_sidebuf2(3*maxcontsshi*nres), &
- grad_shieldbuf1(3*nres), &
- grad_shieldbuf2(3*nres)
-
- integer ishield_listbuf(-1:nres), &
- shield_listbuf(maxcontsshi,-1:nres),k,j,i,iii,impishi,mojint,jjj
+ real(kind=8) :: fac_shieldbuf(nres_molec(1)), &
+ grad_shield_locbuf1(3*maxcontsshi*nres_molec(1)), &
+ grad_shield_sidebuf1(3*maxcontsshi*nres_molec(1)), &
+ grad_shield_locbuf2(3*maxcontsshi*nres_molec(1)), &
+ grad_shield_sidebuf2(3*maxcontsshi*nres_molec(1)), &
+ grad_shieldbuf1(3*nres_molec(1)), &
+ grad_shieldbuf2(3*nres_molec(1))
+
+ integer ishield_listbuf(-1:nres_molec(1)), &
+ shield_listbuf(maxcontsshi,-1:nres_molec(1)),k,j,i,iii,impishi,mojint,jjj
! print *,"I START ENERGY"
imatupdate=100
! if (mod(itime_mat,imatupdate).eq.0) call make_SCSC_inter_list
time_Bcastw=time_Bcastw+MPI_Wtime()-time00
! call chainbuild_cart
endif
-! print *,"itime_mat",itime_mat,imatupdate
+ print *,"itime_mat",itime_mat,imatupdate
if (nfgtasks.gt.1) then
call MPI_Bcast(itime_mat,1,MPI_INT,king,FG_COMM,IERROR)
endif
Eafmforce=0.0d0
endif
endif
-! print *,"before tubemode",tubemode
+ print *,"before tubemode",tubemode
if (tubemode.eq.1) then
call calctube(etube)
else if (tubemode.eq.2) then
else
etube=0.0d0
endif
-! print *, "TU JEST PRZED EHPB"
+ print *, "TU JEST PRZED EHPB"
call edis(ehpb)
!--------------------------------------------------------
! include 'COMMON.SBRIDGE'
logical :: lprn
!el local variables
- integer :: iint,itypi,itypi1,itypj,subchap,icont
+ integer :: iint,itypi,itypi1,itypj,subchap,icont,countss
real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
real(kind=8) :: evdw,sig0ij
real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
! print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
lprn=.false.
+ countss=0
! if (icall.eq.0) lprn=.false.
!el ind=0
dCAVdOM2=0.0d0
! do iint=1,nint_gr(i)
! do j=istart(i,iint),iend(i,iint)
IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
- call dyn_ssbond_ene(i,j,evdwij)
+ countss=countss+1
+ call dyn_ssbond_ene(i,j,evdwij,countss)
evdw=evdw+evdwij
if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') &
'evdw',i,j,evdwij,' ss'
! include 'COMMON.CONTROL'
logical :: lprn
!el local variables
- integer :: iint,itypi,itypi1,itypj,subchap
+ integer :: iint,itypi,itypi1,itypj,subchap,countss
real(kind=8) :: rrij,xi,yi,zi,fac,sigm,epsi,sig0ij,sig
real(kind=8) :: sss,e1,e2,evdw,rij_shift,sss_grad
real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
! print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
lprn=.false.
+ countss=0
! if (icall.eq.0) lprn=.false.
!el ind=0
do i=iatsc_s,iatsc_e
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
- call dyn_ssbond_ene(i,j,evdwij)
+ countss=countss+1
+ call dyn_ssbond_ene(i,j,evdwij,countss)
evdw=evdw+evdwij
if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') &
'evdw',i,j,evdwij,' ss'
!EL external ran_number
! Local variables
- integer :: i,j,k,l,lmax,p,pmax
+ integer :: i,j,k,l,lmax,p,pmax,countss
real(kind=8) :: rmin,rmax
real(kind=8) :: eij
real(kind=8) :: d
real(kind=8) :: wi,rij,tj,pj
! return
-
+ countss=1
i=5
j=14
dc_norm(k,nres+j)=dc(k,nres+j)/d
enddo
- call dyn_ssbond_ene(i,j,eij)
+ call dyn_ssbond_ene(i,j,eij,countss)
enddo
enddo
call exit(1)
return
end subroutine check_energies
!-----------------------------------------------------------------------------
- subroutine dyn_ssbond_ene(resi,resj,eij)
+ subroutine dyn_ssbond_ene(resi,resj,eij,countss)
! implicit none
! Includes
use calc_data
! Local variables
logical :: havebond
- integer itypi,itypj
+ integer itypi,itypj,countss
real(kind=8) :: rrij,ssd,deltat1,deltat2,deltat12,cosphi
real(kind=8) :: sig0ij,ljd,sig,fac,e1,e2
real(kind=8),dimension(3) :: dcosom1,dcosom2
! endif
!#endif
!#endif
- dyn_ssbond_ij(i,j)=eij
- else if (.not.havebond .and. dyn_ssbond_ij(i,j).lt.1.0d300) then
- dyn_ssbond_ij(i,j)=1.0d300
+ dyn_ssbond_ij(countss)=eij
+ else if (.not.havebond .and. dyn_ssbond_ij(countss).lt.1.0d300) then
+ dyn_ssbond_ij(countss)=1.0d300
!#ifndef CLUST
!#ifndef WHAM
! write(iout,'(a15,f12.2,f8.1,2i5)')
! include 'COMMON.MD'
! Local variables
real(kind=8) :: emin
- integer :: i,j,imin,ierr
+ integer :: i,j,imin,ierr,k
integer :: diff,allnss,newnss
integer,dimension(maxdim) :: allflag,allihpb,alljhpb,& !(maxdim)(maxdim=(maxres-1)*(maxres-2)/2)
- newihpb,newjhpb
+ newihpb,newjhpb,aliass
logical :: found
integer,dimension(0:nfgtasks) :: i_newnss
integer,dimension(0:nfgtasks) :: displ
integer :: g_newnss
allnss=0
+ k=0
do i=1,nres-1
do j=i+1,nres
- if (dyn_ssbond_ij(i,j).lt.1.0d300) then
+ if ((itype(i,1).eq.1).and.(itype(j,1).eq.1)) then
+ k=k+1
+ if (dyn_ssbond_ij(k).lt.1.0d300) then
allnss=allnss+1
allflag(allnss)=0
allihpb(allnss)=i
alljhpb(allnss)=j
- endif
+ aliass(allnss)=k
+ endif
+ endif
enddo
enddo
1 emin=1.0d300
do i=1,allnss
if (allflag(i).eq.0 .and. &
- dyn_ssbond_ij(allihpb(i),alljhpb(i)).lt.emin) then
- emin=dyn_ssbond_ij(allihpb(i),alljhpb(i))
+ dyn_ssbond_ij(aliass(allnss)).lt.emin) then
+ emin=dyn_ssbond_ij(aliass(allnss))
imin=i
endif
enddo
!C fac=fac+faccav
!C 667 continue
endif
- if (energy_dec) write(iout,*),i,rdiff,enetube(i),enecavtube(i)
+ if (energy_dec) write(iout,*),"ETUBE_PEP",i,rdiff,enetube(i),enecavtube(i)
do j=1,3
gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0
gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac
gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
enddo
- if (energy_dec) write(iout,*),i,rdiff,enetube(i+nres),enecavtube(i+nres)
+ if (energy_dec) write(iout,*),"ETUBE",i,rdiff,enetube(i+nres),enecavtube(i+nres)
enddo
do j=1,3
gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
enddo
- if (energy_dec) write(iout,*),i,rdiff,enetube(i+nres)
+ if (energy_dec) write(iout,*) "ETUBLIP",i,rdiff,enetube(i+nres)
enddo
! common /contacts1/
allocate(num_cont(0:nres+4))
!(maxres)
+#ifndef NEWCORR
allocate(jcont(maxconts,nres))
!(maxconts,maxres)
allocate(facont(maxconts,nres))
allocate(ees0plist(maxconts,nres))
!(maxconts,maxres)
- allocate(num_cont_hb(nres))
!(maxres)
allocate(jcont_hb(maxconts,nres))
+#endif
+ allocate(num_cont_hb(nres))
!(maxconts,maxres)
! common /rotat/
allocate(Ug(2,2,nres))
allocate(sintab2(nres))
!(maxres)
! common /dipmat/
- allocate(a_chuj(2,2,maxconts,nres))
+! allocate(a_chuj(2,2,maxconts,nres))
!(2,2,maxconts,maxres)(maxconts=maxres/4)
- allocate(a_chuj_der(2,2,3,5,maxconts,nres))
+! allocate(a_chuj_der(2,2,3,5,maxconts,nres))
!(2,2,3,5,maxconts,maxres)(maxconts=maxres/4)
! common /contdistrib/
allocate(ncont_sent(nres))
allocate(iat_sent(nres))
!(maxres)
+#ifndef NEWCORR
+ print *,"before iint_sent allocate"
allocate(iint_sent(4,nres,nres))
allocate(iint_sent_local(4,nres,nres))
+ print *,"after iint_sent allocate"
+#endif
!(4,maxres,maxres)
allocate(iturn3_sent(4,0:nres+4))
allocate(iturn4_sent(4,0:nres+4))
!----------------------
! commom.deriv;
! common /derivat/
+#ifdef NEWCORR
+ print *,"before dcdv allocate"
+ allocate(dcdv(6,nres+2))
+ allocate(dxdv(6,nres+2))
+#else
+ print *,"before dcdv allocate"
allocate(dcdv(6,maxdim))
allocate(dxdv(6,maxdim))
+#endif
!(6,maxdim)
allocate(dxds(6,nres))
!(6,maxres)
!el integer,dimension(:),allocatable :: ihpb,jhpb,ibecarb !(maxdim) !el ibecarb !!! nie używane
! common /dyn_ssbond/
! and side-chain vectors in theta or phi.
- allocate(dyn_ssbond_ij(0:nres+4,0:nres+4))
+ allocate(dyn_ssbond_ij(10000))
!(maxres,maxres)
! do i=1,nres
! do j=i+1,nres
- dyn_ssbond_ij(:,:)=1.0d300
+ dyn_ssbond_ij(:)=1.0d300
! enddo
! enddo
allocate(uygrad(3,3,2,nres))
allocate(uzgrad(3,3,2,nres))
!(3,3,2,maxres)
+ print *,"before all 300"
! allocateion of lists JPRDLA
allocate(newcontlistppi(300*nres))
allocate(newcontlistscpi(350*nres))
! include 'COMMON.SBRIDGE'
logical :: lprn
!el local variables
- integer :: iint,itypi1,subchap,isel
+ integer :: iint,itypi1,subchap,isel,countss
real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,e1,e2,sigm,epsi
real(kind=8) :: evdw,aa,bb
real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
evdw=0.0d0
eps_out=80.0d0
sss_ele_cut=1.0d0
+ countss=0
! print *,"EVDW KURW",evdw,nres
do i=iatsc_s,iatsc_e
! print *,"I am in EVDW",i
do j=istart(i,iint),iend(i,iint)
! print *,"JA PIER",i,j,iint,istart(i,iint),iend(i,iint)
IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
- call dyn_ssbond_ene(i,j,evdwij)
+ call dyn_ssbond_ene(i,j,evdwij,countss)
evdw=evdw+evdwij
if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') &
'evdw',i,j,evdwij,' ss'
write (iout,1212) restyp(itype(i,1),1),i,dist(i-1,i),&
alfai,be,dist(nres+i,i),rad2deg*alpha(nres+i,i,nres2+2),be1
enddo
- 1212 format (a3,'(',i3,')',2(f10.5,2f10.2))
+ 1212 format (a3,'(',i6,')',2(f10.5,2f10.2))
endif
rad2deg*alph(i),rad2deg*omeg(i)
enddo
endif
- 1212 format (a3,'(',i3,')',2(f15.10,2f10.2))
+ 1212 format (a3,'(',i6,')',2(f15.10,2f10.2))
#ifdef TIMING
time_intfcart=time_intfcart+MPI_Wtime()-time01
#endif
' centroid coordinates'/ &
' ', 6X,'X',11X,'Y',11X,'Z',&
10X,'X',11X,'Y',11X,'Z')
- 110 format (a,'(',i3,')',6f12.5)
+ 110 format (a,'(',i6,')',6f12.5)
return
end subroutine cartprint
!-----------------------------------------------------------------------------
! common /rotmat/
allocate(t(3,3,nres),r(3,3,nres))
allocate(prod(3,3,nres),rt(3,3,nres)) !(3,3,maxres)
+ print *,"before permutations",maxperm,maxsym
+
! common /refstruct/
if(.not.allocated(cref)) allocate(cref(3,nres2+2,maxperm)) !(3,maxres2+2,maxperm)
+ print *,"cref"
!elwrite(iout,*) "jestem w alloc geo 2"
! allocate(crefjlee(3,nres2+2)) !(3,maxres2+2)
if (.not.allocated(crefjlee)) allocate (crefjlee(3,nres2+2))
if(.not.allocated(chain_rep)) allocate(chain_rep(3,nres2+2,maxsym)) !(3,maxres2+2,maxsym)
+ print *,"chain_rep"
if(.not.allocated(tabperm)) allocate(tabperm(maxperm,maxsym)) !(maxperm,maxsym)
! common /from_zscore/ in module.compare
!----------------------
! print *,'Finished reading pdb data'
if(me.eq.king.or..not.out1file) &
- write (iout,'(a,i3,a,i3)')'nsup=',nsup,&
+ write (iout,'(a,i7,a,i7)')'nsup=',nsup,&
' nstart_sup=',nstart_sup !,"ergwergewrgae"
!el if(.not.allocated(itype_pdb))
allocate(itype_pdb(nres))
! print *,"tu dochodze"
! znamy nres oraz nss można zaalokowac potrzebne tablice
call alloc_geo_arrays
+ print *,"after alloc_geo_arrays"
call alloc_ener_arrays
+ print *,"after alloc_ener_arrays"
!--------------------------------
! 8/13/98 Set limits to generating the dihedral angles
do i=1,nres
if (itype(nres,molnum(nres)).eq.ntyp1_molec(molnum(nres))) nct=nct-1
if (pdbref) then
if(me.eq.king.or..not.out1file) &
- write (iout,'(a,i3)') 'nsup=',nsup
+ write (iout,'(a,i7)') 'nsup=',nsup
nstart_seq=nnt
if (nsup.le.(nct-nnt+1)) then
do i=0,nct-nnt+1-nsup
implicit none
!-----------------------------------------------------------------------------
! Max. number of AA residues
- integer,parameter :: maxres=6500!1200
+ integer,parameter :: maxres=101000!1200
! Appr. max. number of interaction sites
integer,parameter :: maxres2=2*maxres
! parameter (maxres6=6*maxres)
do i=1,nres
iti=itype(i,1)
! print *,vbld(i),"vbld(i)",i
- write (iout,'(a3,i4,6f10.3)') restyp(iti,1),i,vbld(i),&
+ write (iout,'(a3,i6,6f10.3)') restyp(iti,1),i,vbld(i),&
rad2deg*theta(i),rad2deg*phi(i),vbld(nres+i),rad2deg*alph(i),&
rad2deg*omeg(i)
enddo
read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
print *,msc(i,5),restok(i,5)
enddo
- ip(5)=0.2
+ ! ip(5)=0.2
! mp(5)=0.2
pstok(5)=3.0
!DIR$ NOUNROLL
!
! *** assess candidate step (***sol version 2.3) ***
!
- integer :: liv, l,lv
+ integer :: liv, l
+ integer(kind=8) ::lv
integer :: iv(liv)
real(kind=8) :: v(lv)
!
! *** alg = 1 means regression constants.
! *** alg = 2 means general unconstrained optimization constants.
!
- integer :: liv, l,lv
- integer :: alg, iv(liv)
+ integer :: liv, l
+ integer(kind=8)::lv
+ integer :: iv(liv)
+ integer :: alg
real(kind=8) :: v(lv)
!
!el external imdcon, vdflt
!
! *** parameter declarations ***
!
- integer :: liv, lv, p
+ integer :: liv, p
+ integer(kind=8)::lv
integer :: iv(liv)
real(kind=8) :: d(p), g(p), v(lv), x(p)
!
!
! *** alg = 1 for regression, alg = 2 for general unconstrained opt.
!
- integer :: alg, liv, lv, n
+ integer :: alg, liv, n
+ integer(kind=8) :: lv
integer :: iv(liv)
real(kind=8) :: d(n), v(lv)
!
! *** alg = 1 means regression constants.
! *** alg = 2 means general unconstrained optimization constants.
!
- integer :: alg, l,lv
+ integer :: alg, l
+ integer(kind=8)::lv
real(kind=8) :: v(lv)
!/+
!el real(kind=8) :: dmax1
! *** minimize general unconstrained objective function using ***
! *** (analytic) gradient and hessian provided by the caller. ***
!
- integer :: liv, lv, n
- integer :: iv(liv), uiparm(1)
+ integer :: liv, n
+ integer(kind=8):: lv
+ integer:: iv(liv)
+ integer :: uiparm(1)
real(kind=8) :: d(n), x(n), v(lv), urparm(1)
real(kind=8),external :: ufparm
! dimension v(78 + n*(n+12)), uiparm(*), urparm(*)
! *** parameter declarations ***
!
- integer :: lh, liv, lv, n
- integer :: iv(liv)
+ integer :: lh, liv, n
+ integer(kind=8)::lv
+ integer :: iv(liv)
real(kind=8) :: d(n), fx, g(n), h(lh), v(lv), x(n)
!
!-------------------------- parameter usage --------------------------
!
! *** parameter declarations ***
!
- integer :: liv, lv, n
+ integer :: liv, n
+ integer(kind=8) ::lv
integer :: iv(liv)
real(kind=8) :: d(n), hdiag(n), v(lv)
!
logical :: not_done,change,reduce
!el common /przechowalnia/ v
!el local variables
- integer :: iretcode,nfun,lv,nvar_restr,idum(1),j
+ integer :: iretcode,nfun,nvar_restr,idum(1),j
+ integer (kind=8):: lv
real(kind=8) :: etot,rdum(1) !,fdum
lv=(77+(6*nres)*(6*nres+17)/2) !(77+maxvar*(maxvar+17)/2)) (maxvar=6*maxres)
! include 'COMMON.GEO'
! include 'COMMON.MINIM'
! include 'COMMON.CHAIN'
- integer :: iretcode,nfun,k,i,j,lv,idum(1)
+ integer :: iretcode,nfun,k,i,j,idum(1)
+ integer(kind=8) :: lv
integer,dimension(liv) :: iv
real(kind=8) :: minval !,v(1:77+(6*nres)*(6*nres+17)/2) !(1:lv)
real(kind=8),dimension(6*nres) :: x,d,xx !(maxvar) (maxvar=6*maxres)
real(kind=8) :: g(6*nres),f1,etot,rdum(1) !,fdum
lv=(77+(6*nres)*(6*nres+17)/2) !(77+maxvar*(maxvar+17)/2)) (maxvar=6*maxres)
-
+ print *,"lv value",lv
if (.not. allocated(v)) allocate(v(1:lv))
call deflt(2,iv,liv,lv,v)
+ print *,"after delft"
! 12 means fresh start, dont call deflt
iv(1)=12
! max num of fun calls
!el real(kind=8) :: v(1:77+(6*nres)*(6*nres+17)/2+1)
integer,dimension(6) :: indx
integer,dimension(liv) :: iv
- integer :: lv,idum(1),nf !
+ integer :: idum(1),nf !
+ integer(kind=8) :: lv
real(kind=8) :: rdum(1)
real(kind=8) :: przes(3),obrot(3,3),eee
logical :: non_conv
! external func_restr1,grad_restr1
logical :: not_done,change,reduce
!el common /przechowalnia/ v
-
- integer :: nvar_restr,lv,i,j
+ integer(kind=8):: lv
+ integer :: nvar_restr,i,j
integer :: idum(1)
real(kind=8) :: rdum(1),etot !,fdum
! *** analytic gradient and hessian approx. from secant update ***
!
! use control
- integer :: n, liv, lv
- integer :: iv(liv), uiparm(1)
+ integer :: n, liv
+ integer(kind=8)::lv
+ integer:: iv(liv)
+ integer :: uiparm(1)
real(kind=8) :: d(n), x(n), v(lv), urparm(1)
real(kind=8),external :: ufparm !funtion name as an argument
! sumit... reverse-communication routine that carries out sumsl algo-
! rithm.
!
- integer :: g1, iv1, nf
+ integer :: iv1, nf
real(kind=8) :: f
+ integer(kind=8)::g1
!
! *** subscripts for iv ***
!
if (iv1 .eq. 12) iv(1) = 13
go to 20
!
- 10 g1 = iv(g)
+ 10 g1 = iv(g)
+ print *,"my new g1",g1
!elwrite(iout,*) "in sumsl go to 10"
!
subroutine sumit(d,fx,g,iv,liv,lv,n,v,x)
use control, only:stopx
+ use MD_data, only: itime_mat
!
! *** carry out sumsl (unconstrained minimization) iterations, using
! *** double-dogleg/bfgs steps.
!
! *** parameter declarations ***
!
- integer :: liv, lv, n
+ integer :: liv, n
+ integer(kind=8) :: lv
integer :: iv(liv)
real(kind=8) :: d(n), fx, g(n), v(lv), x(n)
!
!
80 call itsum(d, g, iv, liv, lv, n, v, x)
90 k = iv(niter)
+ itime_mat=k
+! imat_update=k
if (k .lt. iv(mxiter)) go to 100
iv(1) = 10
go to 300
!
! *** parameter declarations ***
!
- integer :: lv, n
+ integer :: n
+ integer(kind=8) :: lv
real(kind=8) :: dig(n), nwtstp(n), step(n), v(lv)
!
! *** purpose ***
#endif
print *,'Start MD'
call alloc_MD_arrays
- call alloc_compare_arrays
print *,'After MD alloc'
+ call alloc_compare_arrays
+ print *,'After compare alloc'
if (me.eq.king .or. .not. out1file) &
write (iout,*) "Calling chainbuild"
if (extconf) then
projects / unres4.git / commitdiff