From: Adam Kazimierz Sieradzan Date: Mon, 18 Jun 2012 10:22:21 +0000 (-0400) Subject: Merge branch 'adasko' into devel X-Git-Tag: v.3.2~83 X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;h=478f5fd9e95bd5665ab58ee691f517d7dab379b3;hp=-c;p=unres.git Merge branch 'adasko' into devel Conflicts: .gitignore --- 478f5fd9e95bd5665ab58ee691f517d7dab379b3 diff --combined .gitignore index 918a787,d5615a4..abb3640 --- a/.gitignore +++ b/.gitignore @@@ -1,11 -1,6 +1,19 @@@ ++<<<<<<< HEAD +# ignore compiled stuff +*.[oa] + +# ignore texteditors +*.swp +*~ + + +# ifnore build dir +build/ ++======= + ~.[ao] + gradcheck/ + mapcheck/ + run/ + sympcheck/ ++>>>>>>> adasko diff --combined source/unres/src_MD/energy_p_new_barrier.F index 1692c50,851ad39..1a99285 --- a/source/unres/src_MD/energy_p_new_barrier.F +++ b/source/unres/src_MD/energy_p_new_barrier.F @@@ -471,7 -471,7 +471,7 @@@ cMS$ATTRIBUTES C :: proc_pro include 'mpif.h' #endif double precision gradbufc(3,maxres),gradbufx(3,maxres), - & glocbuf(4*maxres),gradbufc_sum(3,maxres) + & glocbuf(4*maxres),gradbufc_sum(3,maxres),gloc_scbuf(3,maxres) include 'COMMON.SETUP' include 'COMMON.IOUNITS' include 'COMMON.FFIELD' @@@ -483,6 -483,7 +483,7 @@@ include 'COMMON.CONTROL' include 'COMMON.TIME1' include 'COMMON.MAXGRAD' + include 'COMMON.SCCOR' #ifdef TIMING #ifdef MPI time01=MPI_Wtime() @@@ -755,7 -756,6 +756,6 @@@ c endd & +wturn3*gel_loc_turn3(i) & +wturn6*gel_loc_turn6(i) & +wel_loc*gel_loc_loc(i) - & +wsccor*gsccor_loc(i) enddo #ifdef DEBUG write (iout,*) "gloc after adding corr" @@@ -774,6 -774,21 +774,21 @@@ do i=1,4*nres glocbuf(i)=gloc(i,icg) enddo + #define DEBUG + #ifdef DEBUG + write (iout,*) "gloc_sc before reduce" + do i=1,nres + do j=1,3 + write (iout,*) i,j,gloc_sc(j,i,icg) + enddo + enddo + #endif + #undef DEBUG + do i=1,nres + do j=1,3 + gloc_scbuf(j,i)=gloc_sc(j,i,icg) + enddo + enddo time00=MPI_Wtime() call MPI_Barrier(FG_COMM,IERR) time_barrier_g=time_barrier_g+MPI_Wtime()-time00 @@@ -784,7 -799,19 +799,19 @@@ & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) call MPI_Reduce(glocbuf(1),gloc(1,icg),4*nres, & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) + call MPI_Reduce(gloc_scbuf(1,1),gloc_sc(1,1,icg),3*nres, + & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) time_reduce=time_reduce+MPI_Wtime()-time00 + #define DEBUG + #ifdef DEBUG + write (iout,*) "gloc_sc after reduce" + do i=1,nres + do j=1,3 + write (iout,*) i,j,gloc_sc(j,i,icg) + enddo + enddo + #endif + #undef DEBUG #ifdef DEBUG write (iout,*) "gloc after reduce" do i=1,4*nres @@@ -5650,7 -5677,7 +5677,7 @@@ C Proline-Proline pair is a special cas & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1, & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6) gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci - c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) + write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) enddo ! 6/20/98 - dihedral angle constraints edihcnstr=0.0d0 @@@ -5765,6 -5792,7 +5792,7 @@@ c do i=1,ndih_const else difi=0.0 endif + c write (iout,*) "gloci", gloc(i-3,icg) cd write (iout,'(2i5,4f8.3,2e14.5)') i,itori,rad2deg*phii, cd & rad2deg*phi0(i), rad2deg*drange(i), cd & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg) @@@ -5801,7 -5829,6 +5829,6 @@@ c lprn=.true phii1=phi(i+1) gloci1=0.0D0 gloci2=0.0D0 - C Regular cosine and sine terms do j=1,ntermd_1(itori,itori1,itori2) v1cij=v1c(1,j,itori,itori1,itori2) v1sij=v1s(1,j,itori,itori1,itori2) @@@ -5836,6 -5863,7 +5863,7 @@@ enddo gloc(i-3,icg)=gloc(i-3,icg)+wtor_d*gloci1 gloc(i-2,icg)=gloc(i-2,icg)+wtor_d*gloci2 + c write (iout,*) "gloci", gloc(i-3,icg) enddo return end @@@ -5868,26 -5896,57 +5896,57 @@@ C Set lprn=.true. for debuggin c lprn=.true. c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor esccor=0.0D0 - do i=iphi_start,iphi_end + do i=itau_start,itau_end esccor_ii=0.0D0 - itori=itype(i-2) - itori1=itype(i-1) + isccori=isccortyp(itype(i-2)) + isccori1=isccortyp(itype(i-1)) phii=phi(i) + cccc Added 9 May 2012 + cc Tauangle is torsional engle depending on the value of first digit + c(see comment below) + cc Omicron is flat angle depending on the value of first digit + c(see comment below) + + + do intertyp=1,3 !intertyp + cc Added 09 May 2012 (Adasko) + cc Intertyp means interaction type of backbone mainchain correlation: + c 1 = SC...Ca...Ca...Ca + c 2 = Ca...Ca...Ca...SC + c 3 = SC...Ca...Ca...SCi gloci=0.0D0 - do j=1,nterm_sccor - v1ij=v1sccor(j,itori,itori1) - v2ij=v2sccor(j,itori,itori1) - cosphi=dcos(j*phii) - sinphi=dsin(j*phii) + if (((intertyp.eq.3).and.((itype(i-2).eq.10).or. + & (itype(i-1).eq.10).or.(itype(i-2).eq.21).or. + & (itype(i-1).eq.21))) + & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10) + & .or.(itype(i-2).eq.21))) + & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or. + & (itype(i-1).eq.21)))) cycle + if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.21)) cycle + if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.21)) + & cycle + do j=1,nterm_sccor(isccori,isccori1) + v1ij=v1sccor(j,intertyp,isccori,isccori1) + v2ij=v2sccor(j,intertyp,isccori,isccori1) + cosphi=dcos(j*tauangle(intertyp,i)) + sinphi=dsin(j*tauangle(intertyp,i)) esccor=esccor+v1ij*cosphi+v2ij*sinphi gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi) enddo + gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci + c write (iout,*) "WTF",intertyp,i,itype(i),v1ij*cosphi+v2ij*sinphi + c &gloc_sc(intertyp,i-3,icg) if (lprn) & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1, - & (v1sccor(j,itori,itori1),j=1,6),(v2sccor(j,itori,itori1),j=1,6) + & (v1sccor(j,intertyp,itori,itori1),j=1,6) + & ,(v2sccor(j,intertyp,itori,itori1),j=1,6) gsccor_loc(i-3)=gsccor_loc(i-3)+gloci + enddo !intertyp enddo + c do i=1,nres + c write (iout,*) "W@T@F", gloc_sc(1,i,icg),gloc(i,icg) + c enddo return end c---------------------------------------------------------------------------- @@@ -7994,9 -8053,9 +8053,9 @@@ C Parallel Antiparallel C C o o -C /l\ /j\ -C / \ / \ -C /| o | | o |\ +C /l\ /j\ +C / \ / \ +C /| o | | o |\ C \ j|/k\| / \ |/k\|l / C \ / \ / \ / \ / C o o o o @@@ -8095,18 -8154,18 +8154,18 @@@ c-------------------------------------- logical lprn common /kutas/ lprn CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC -C -C Parallel Antiparallel -C -C o o -C \ /l\ /j\ / -C \ / \ / \ / -C o| o | | o |o -C \ j|/k\| \ |/k\|l -C \ / \ \ / \ -C o o -C i i -C +C C +C Parallel Antiparallel C +C C +C o o C +C \ /l\ /j\ / C +C \ / \ / \ / C +C o| o | | o |o C +C \ j|/k\| \ |/k\|l C +C \ / \ \ / \ C +C o o C +C i i C +C C CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC cd write (2,*) 'eello6_graph2: i,',i,' j',j,' k',k,' l',l C AL 7/4/01 s1 would occur in the sixth-order moment, @@@ -8277,18 -8336,18 +8336,18 @@@ c-------------------------------------- double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2) logical swap CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC -C -C Parallel Antiparallel -C -C o o -C /l\ / \ /j\ -C / \ / \ / \ -C /| o |o o| o |\ -C j|/k\| / |/k\|l / -C / \ / / \ / -C / o / o -C i i -C +C C +C Parallel Antiparallel C +C C +C o o C +C /l\ / \ /j\ C +C / \ / \ / \ C +C /| o |o o| o |\ C +C j|/k\| / |/k\|l / C +C / \ / / \ / C +C / o / o C +C i i C +C C CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC C C 4/7/01 AL Component s1 was removed, because it pertains to the respective @@@ -8394,18 -8453,18 +8453,18 @@@ c-------------------------------------- & auxvec1(2),auxmat1(2,2) logical swap CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC -C -C Parallel Antiparallel -C -C o o -C /l\ / \ /j\ -C / \ / \ / \ -C /| o |o o| o |\ -C \ j|/k\| \ |/k\|l -C \ / \ \ / \ -C o \ o \ -C i i -C +C C +C Parallel Antiparallel C +C C +C o o C +C /l\ / \ /j\ C +C / \ / \ / \ C +C /| o |o o| o |\ C +C \ j|/k\| \ |/k\|l C +C \ / \ \ / \ C +C o \ o \ C +C i i C +C C CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC C C 4/7/01 AL Component s1 was removed, because it pertains to the respective diff --combined source/unres/src_MD/readrtns.F index 684c376,988983e..abd3911 --- a/source/unres/src_MD/readrtns.F +++ b/source/unres/src_MD/readrtns.F @@@ -2080,38 -2080,38 +2080,38 @@@ C Get parameter filenames and open the open (isidep,file=sidename,status='old') #else open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old', - & readonly) + &action='read') open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown') C open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown') C Get parameter filenames and open the parameter files. call getenv_loc('BONDPAR',bondname) - open (ibond,file=bondname,status='old',readonly) + open (ibond,file=bondname,status='old',action='read') call getenv_loc('THETPAR',thetname) - open (ithep,file=thetname,status='old',readonly) + open (ithep,file=thetname,status='old',action='read') #ifndef CRYST_THETA call getenv_loc('THETPARPDB',thetname_pdb) print *,"thetname_pdb ",thetname_pdb - open (ithep_pdb,file=thetname_pdb,status='old',readonly) + open (ithep_pdb,file=thetname_pdb,status='old',action='read') print *,ithep_pdb," opened" #endif call getenv_loc('ROTPAR',rotname) - open (irotam,file=rotname,status='old',readonly) + open (irotam,file=rotname,status='old',action='read') #ifndef CRYST_SC call getenv_loc('ROTPARPDB',rotname_pdb) - open (irotam_pdb,file=rotname_pdb,status='old',readonly) + open (irotam_pdb,file=rotname_pdb,status='old',action='read') #endif call getenv_loc('TORPAR',torname) - open (itorp,file=torname,status='old',readonly) + open (itorp,file=torname,status='old',action='read') call getenv_loc('TORDPAR',tordname) - open (itordp,file=tordname,status='old',readonly) + open (itordp,file=tordname,status='old',action='read') call getenv_loc('SCCORPAR',sccorname) - open (isccor,file=sccorname,status='old',readonly) + open (isccor,file=sccorname,status='old',action='read') call getenv_loc('FOURIER',fouriername) - open (ifourier,file=fouriername,status='old',readonly) + open (ifourier,file=fouriername,status='old',action='read') call getenv_loc('ELEPAR',elename) - open (ielep,file=elename,status='old',readonly) + open (ielep,file=elename,status='old',action='read') call getenv_loc('SIDEPAR',sidename) - open (isidep,file=sidename,status='old',readonly) + open (isidep,file=sidename,status='old',action='read') #endif #ifndef OLDSCP C @@@ -2126,7 -2126,7 +2126,7 @@@ #elif (defined G77) open (iscpp,file=scpname,status='old') #else - open (iscpp,file=scpname,status='old',readonly) + open (iscpp,file=scpname,status='old',action='read') #endif #endif call getenv_loc('PATTERN',patname) @@@ -2137,7 -2137,7 +2137,7 @@@ #elif (defined G77) open (icbase,file=patname,status='old') #else - open (icbase,file=patname,status='old',readonly) + open (icbase,file=patname,status='old',action='read') #endif #ifdef MPI C Open output file only for CG processes @@@ -2192,6 -2192,7 +2192,7 @@@ c print *,"Processor",myrank," fg_ #if defined(AIX) || defined(PGI) if (me.eq.king .or. .not. out1file) & open(iout,file=outname,status='unknown') + c#define DEBUG #ifdef DEBUG if (fg_rank.gt.0) then write (liczba,'(i3.3)') myrank/nfgtasks @@@ -2200,6 -2201,7 +2201,7 @@@ & status='unknown') endif #endif + c#undef DEBUG if(me.eq.king) then open(igeom,file=intname,status='unknown',position='append') open(ipdb,file=pdbname,status='unknown') @@@ -2211,14 -2213,17 +2213,17 @@@ c1out open(iout,file=outname,stat #else if (me.eq.king .or. .not.out1file) & open(iout,file=outname,status='unknown') + c#define DEBUG #ifdef DEBUG if (fg_rank.gt.0) then + print "Processor",fg_rank," opening output file" write (liczba,'(i3.3)') myrank/nfgtasks write (ll,'(bz,i3.3)') fg_rank open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll, & status='unknown') endif #endif + c#undef DEBUG if(me.eq.king) then open(igeom,file=intname,status='unknown',access='append') open(ipdb,file=pdbname,status='unknown')