zmiany po usunieciu diagnostyki...

diff --git a/bin/unres/MD/unres_ifort_MPICH_GAB.exe b/bin/unres/MD/unres_ifort_MPICH_GAB.exe
index 17aa073..51bbafe 100755 (executable)
Binary files a/bin/unres/MD/unres_ifort_MPICH_GAB.exe and b/bin/unres/MD/unres_ifort_MPICH_GAB.exe differ

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim.inp b/examples/unres/MD/ff_gab/1L2Y_minim.inp
index 286b667..b6e6e25 100644 (file)
--- a/examples/unres/MD/ff_gab/1L2Y_minim.inp
+++ b/examples/unres/MD/ff_gab/1L2Y_minim.inp
@@ -1,5 +1,5 @@
 1L2Y
-SEED=-3059743 PDBREF MINIMIZE
+SEED=-3059743 PDBREF ENE
 maxmin=1000
 WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873            &
 WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000        &

diff --git a/examples/unres/MD/ff_gab/unres.pbs b/examples/unres/MD/ff_gab/unres.pbs
index 367e87f..f983fb9 100755 (executable)
--- a/examples/unres/MD/ff_gab/unres.pbs
+++ b/examples/unres/MD/ff_gab/unres.pbs
@@ -1,7 +1,7 @@
 #!/bin/sh
 #PBS -N PGA
 #PBS -q dque
-#PBS -l nodes=58:ppn=2
+#PBS -l nodes=1:ppn=1
 #PBS -l walltime=24:00:00
 #-----------------------------------------------------------------------------
 export POT=GB

diff --git a/source/unres/src_MD/COMMON.LOCAL b/source/unres/src_MD/COMMON.LOCAL
index 837a7a3..a3f68dc 100644 (file)
--- a/source/unres/src_MD/COMMON.LOCAL
+++ b/source/unres/src_MD/COMMON.LOCAL
@@ -29,7 +29,8 @@ C Parameters of ab initio-derived potential of virtual-bond-angle bending
 C Virtual-bond lenghts
       double precision vbl,vblinv,vblinv2,vbl_cis,vbl0,vbld_inv
       integer loc_start,loc_end,ithet_start,ithet_end,iphi_start,
-     & iphi_end,iphid_start,iphid_end,ibond_start,ibond_end,
+     & iphi_end,iphid_start,iphid_end,itau_start,itau_end,ibond_start,
+     & ibond_end,
      & ibondp_start,ibondp_end,ivec_start,ivec_end,iset_start,iset_end,
      & iturn3_start,iturn3_end,iturn4_start,iturn4_end,iint_start,
      & iint_end,iphi1_start,iphi1_end,
@@ -42,7 +43,8 @@ C Virtual-bond lenghts
      & iint_count(0:max_fg_procs-1),iint_displ(0:max_fg_procs-1)
       common /peptbond/ vbl,vblinv,vblinv2,vbl_cis,vbl0
       common /indices/ loc_start,loc_end,ithet_start,ithet_end,
-     & iphi_start,iphi_end,iphid_start,iphid_end,ibond_start,ibond_end,
+     & iphi_start,iphi_end,iphid_start,iphid_end,itau_start,itau_end,
+     & ibond_start,ibond_end,
      & ibondp_start,ibondp_end,ivec_start,ivec_end,iset_start,iset_end,
      & iturn3_start,iturn3_end,iturn4_start,iturn4_end,iint_start,
      & iint_end,iphi1_start,iphi1_end,iint_count,iint_displ,ivec_displ,

diff --git a/source/unres/src_MD/Makefile_MPICH_ifort b/source/unres/src_MD/Makefile_MPICH_ifort
index 8846882..d60f106 100644 (file)
--- a/source/unres/src_MD/Makefile_MPICH_ifort
+++ b/source/unres/src_MD/Makefile_MPICH_ifort
@@ -44,7 +44,7 @@ object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
         cored.o rmdd.o geomout.o readpdb.o regularize.o thread.o fitsq.o mcm.o \
         mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
         eigen.o blas.o add.o entmcm.o minim_mcmf.o \
-        MP.o compare_s1.o prng_32.o \
+        MP.o compare_s1.o prng.o \
         banach.o rmsd.o elecont.o dihed_cons.o \
         sc_move.o local_move.o \
         intcartderiv.o lagrangian_lesyng.o\

diff --git a/source/unres/src_MD/cinfo.f b/source/unres/src_MD/cinfo.f
index a0005f6..9b22a2e 100644 (file)
--- a/source/unres/src_MD/cinfo.f
+++ b/source/unres/src_MD/cinfo.f
@@ -1,10 +1,10 @@
 C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 2 5 274
+C 2 5 295
       subroutine cinfo
       include 'COMMON.IOUNITS'
       write(iout,*)'++++ Compile info ++++'
-      write(iout,*)'Version 2.5 build 274'
-      write(iout,*)'compiled Fri Jun 15 02:51:50 2012'
+      write(iout,*)'Version 2.5 build 295'
+      write(iout,*)'compiled Mon Jun 18 05:08:20 2012'
       write(iout,*)'compiled by aks255@matrix.chem.cornell.edu'
       write(iout,*)'OS name:    Linux '
       write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '

diff --git a/source/unres/src_MD/energy_p_new_barrier.F b/source/unres/src_MD/energy_p_new_barrier.F
index f07517b..851ad39 100644 (file)
--- a/source/unres/src_MD/energy_p_new_barrier.F
+++ b/source/unres/src_MD/energy_p_new_barrier.F
@@ -471,7 +471,7 @@ cMS$ATTRIBUTES C ::  proc_proc
       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'
@@ -774,6 +774,21 @@ c      enddo
         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 @@ c      enddo
      &    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
@@ -5869,7 +5896,7 @@ C Set lprn=.true. for debugging
 c      lprn=.true.
 c      write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
       esccor=0.0D0
-      do i=iphi_start-1,iphi_end+1
+      do i=itau_start,itau_end
         esccor_ii=0.0D0
         isccori=isccortyp(itype(i-2))
         isccori1=isccortyp(itype(i-1))
@@ -5895,8 +5922,9 @@ c   3 = SC...Ca...Ca...SCi
      &     .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.le.iphi_start-1)) cycle
-        if ((intertyp.eq.1).and.(i.ge.iphi_end+1)) 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)
@@ -5906,7 +5934,7 @@ c   3 = SC...Ca...Ca...SCi
           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),
+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/)')

diff --git a/source/unres/src_MD/initialize_p.F b/source/unres/src_MD/initialize_p.F
index 75c98de..7db117d 100644 (file)
--- a/source/unres/src_MD/initialize_p.F
+++ b/source/unres/src_MD/initialize_p.F
@@ -564,6 +564,9 @@ C Partition local interactions
       iphi_end=iturn3_end+2
       iturn3_start=iturn3_start-1
       iturn3_end=iturn3_end-1
+      call int_bounds(nres-3,itau_start,itau_end) 
+      itau_start=itau_start+3
+      itau_end=itau_end+3
       call int_bounds(nres-3,iphi1_start,iphi1_end)
       iphi1_start=iphi1_start+3
       iphi1_end=iphi1_end+3
@@ -1090,6 +1093,8 @@ c        write (iout,*) "MPI_ROTAT2",MPI_ROTAT2
       idihconstr_end=ndih_constr
       iphid_start=iphi_start
       iphid_end=iphi_end-1
+      itau_start=4
+      itau_end=nres
       ibond_start=2
       ibond_end=nres-1
       ibondp_start=nnt+1

diff --git a/source/unres/src_MD/int_to_cart.f b/source/unres/src_MD/int_to_cart.f
index b2d378e..73e8384 100644 (file)
--- a/source/unres/src_MD/int_to_cart.f
+++ b/source/unres/src_MD/int_to_cart.f
@@ -181,7 +181,7 @@ c           write(iout,*)  gloc_sc(1,0,icg),dtauangle(j,1,3,3)
          endif
          if ((itype(3).ne.10).and.(nres.ge.3)) then
           gcart(j,2)=gcart(j,2)+gloc_sc(2,1,icg)*dtauangle(j,2,2,4)
-           write(iout,*) gloc_sc(2,1,icg),dtauangle(j,2,2,4)
+c           write(iout,*) gloc_sc(2,1,icg),dtauangle(j,2,2,4)
          endif
          if ((itype(4).ne.10).and.(nres.ge.4)) then
           gcart(j,2)=gcart(j,2)+gloc_sc(2,2,icg)*dtauangle(j,2,1,5)
@@ -238,8 +238,8 @@ c  Setting dE/ddnres-1
          if ((itype(nres-1).ne.10).and.(itype(nres-1).ne.21)) then
          gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(2,nres-3,icg)
      &    *dtauangle(j,2,3,nres)
-          write (iout,*) "gxcart(nres-1)", gloc_sc(2,nres-3,icg),
-     &     dtauangle(j,2,3,nres), gxcart(j,nres-1)
+c          write (iout,*) "gxcart(nres-1)", gloc_sc(2,nres-3,icg),
+c     &     dtauangle(j,2,3,nres), gxcart(j,nres-1)
          if (itype(nres-2).ne.10) then
         gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(3,nres-3,icg)
      &    *dtauangle(j,3,3,nres)
@@ -258,8 +258,8 @@ c  Setting dE/ddnres-1
           if ((itype(nres).ne.10).and.(itype(nres).ne.21)) then
             gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(2,nres-2,icg)*
      &     dtauangle(j,2,2,nres+1)
-           write (iout,*) "gcart(nres-1)", gloc_sc(2,nres-2,icg),
-     &     dtauangle(j,2,2,nres+1), itype(nres-1),itype(nres)
+c           write (iout,*) "gcart(nres-1)", gloc_sc(2,nres-2,icg),
+c     &     dtauangle(j,2,2,nres+1), itype(nres-1),itype(nres)
            endif
          enddo
       endif 

diff --git a/source/unres/src_MD/intcartderiv.F b/source/unres/src_MD/intcartderiv.F
index dd4db24..c220540 100644 (file)
--- a/source/unres/src_MD/intcartderiv.F
+++ b/source/unres/src_MD/intcartderiv.F
@@ -151,7 +151,7 @@ c   Obtaining the gamma derivatives from cosine derivative
 
 Calculate derivative of Tauangle
 #ifdef PARINTDER
-      do i=iphi1_start-1,iphi1_end
+      do i=itau_start,itau_end
 #else
       do i=3,nres
 #endif
@@ -226,7 +226,7 @@ c        enddo
       enddo
 CC Second case Ca...Ca...Ca...SC
 #ifdef PARINTDER
-      do i=iphi1_start,iphi1_end
+      do i=itau_start,itau_end
 #else
       do i=4,nres
 #endif
@@ -291,7 +291,7 @@ c   Obtaining the gamma derivatives from cosine derivative
      &     dcosomicron(j,1,2,i)-fac0*(dc_norm(j,i-3)-scalp*
      &     dc_norm(j,i-1+nres))/vbld(i-1+nres)
            dtauangle(j,2,3,i)=-1/sing*dcostau(j,2,3,i)
-        write(iout,*) i,j,"else", dtauangle(j,2,3,i) 
+c        write(iout,*) i,j,"else", dtauangle(j,2,3,i) 
          enddo
         endif                                                                                            
       enddo
@@ -300,7 +300,7 @@ c   Obtaining the gamma derivatives from cosine derivative
 CCC third case SC...Ca...Ca...SC
 #ifdef PARINTDER
 
-      do i=iphi1_start-1,iphi1_end
+      do i=itau_start,itau_end
 #else
       do i=3,nres
 #endif
@@ -364,7 +364,7 @@ c   Obtaining the gamma derivatives from cosine derivative
      &     dcosomicron(j,1,2,i)-fac0*(dc_norm2(j,i-2+nres)-scalp*
      &     dc_norm(j,i-1+nres))/vbld(i-1+nres)
            dtauangle(j,3,3,i)=-1/sing*dcostau(j,3,3,i)
-          write(iout,*) "else",i 
+c          write(iout,*) "else",i 
          enddo
         endif                                                                                            
       enddo
@@ -458,12 +458,12 @@ c   obtaining the derivatives of omega from cosines
 #if defined(MPI) && defined(PARINTDER)
       if (nfgtasks.gt.1) then
 #ifdef DEBUG
-cd      write (iout,*) "Gather dtheta"
+       write (iout,*) "Gather dtheta"
 cd      call flush(iout)
-      write (iout,*) "dtheta before gather"
-      do i=1,nres
-        write (iout,'(i3,3(3f8.5,3x))') i,((dtheta(j,k,i),k=1,3),j=1,2)
-      enddo
+c      write (iout,*) "dtheta before gather"
+c      do i=1,nres
+c        write (iout,'(i3,3(3f8.5,3x))') i,((dtheta(j,k,i),k=1,3),j=1,2)
+c      enddo
 #endif
       call MPI_Gatherv(dtheta(1,1,ithet_start),ithet_count(fg_rank),
      &  MPI_THET,dtheta(1,1,1),ithet_count(0),ithet_displ(0),MPI_THET,

diff --git a/source/unres/src_MD/map.f b/source/unres/src_MD/map.f
index 6ea2632..9dbe64e 100644 (file)
--- a/source/unres/src_MD/map.f
+++ b/source/unres/src_MD/map.f
@@ -56,6 +56,7 @@ Cd      write (iout,*) i,iii,(nn(j),j=1,nmap)
           enddo ! k
         enddo ! j
         call chainbuild
+        call int_from_cart1(.false.)
         if (minim) then 
          call geom_to_var(nvar,x)
          call minimize(etot,x,iretcode,nfun)

diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F
index 6ce9ec3..988983e 100644 (file)
--- a/source/unres/src_MD/readrtns.F
+++ b/source/unres/src_MD/readrtns.F
@@ -2192,6 +2192,7 @@ c      print *,"Processor",myrank," fg_rank",fg_rank
 #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 @@ c      print *,"Processor",myrank," fg_rank",fg_rank
      &   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 @@ c1out       open(iout,file=outname,status='unknown')
 #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')