From 1da1cacdb0bc45ab8961dbaad1cb2eeed5530ef5 Mon Sep 17 00:00:00 2001 From: Adam Kazimierz Sieradzan Date: Mon, 18 Jun 2012 05:56:28 -0400 Subject: [PATCH] zmiany po usunieciu diagnostyki... --- examples/unres/MD/ff_gab/1L2Y_minim.inp | 2 +- examples/unres/MD/ff_gab/unres.pbs | 2 +- source/unres/src_MD/COMMON.LOCAL | 6 +++-- source/unres/src_MD/Makefile_MPICH_ifort | 2 +- source/unres/src_MD/cinfo.f | 6 ++--- source/unres/src_MD/energy_p_new_barrier.F | 38 ++++++++++++++++++++++++---- source/unres/src_MD/initialize_p.F | 5 ++++ source/unres/src_MD/int_to_cart.f | 10 ++++---- source/unres/src_MD/intcartderiv.F | 20 +++++++-------- source/unres/src_MD/map.f | 1 + source/unres/src_MD/readrtns.F | 5 ++++ 11 files changed, 69 insertions(+), 28 deletions(-) diff --git a/examples/unres/MD/ff_gab/1L2Y_minim.inp b/examples/unres/MD/ff_gab/1L2Y_minim.inp index 286b667..b6e6e25 100644 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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') -- 1.7.9.5