From ce029d82f9541e9434d7b016ad442b20526de7a2 Mon Sep 17 00:00:00 2001 From: Cezary Czaplewski Date: Tue, 15 Mar 2016 13:35:16 +0900 Subject: [PATCH] src_MIN sum_gradient from src_MD --- source/unres/src_MIN/energy_p_new_barrier.F | 217 ++++++++++++++++++--------- 1 file changed, 148 insertions(+), 69 deletions(-) diff --git a/source/unres/src_MIN/energy_p_new_barrier.F b/source/unres/src_MIN/energy_p_new_barrier.F index 072053a..8943726 100644 --- a/source/unres/src_MIN/energy_p_new_barrier.F +++ b/source/unres/src_MIN/energy_p_new_barrier.F @@ -441,12 +441,9 @@ cMS$ATTRIBUTES C :: proc_proc #endif #ifdef MPI include 'mpif.h' - double precision gradbufc(3,maxres),gradbufx(3,maxres), - & glocbuf(4*maxres),gradbufc_sum(3,maxres) -#else - double precision gradbufc(3,maxres),gradbufx(3,maxres), - & glocbuf(4*maxres),gradbufc_sum(3,maxres) #endif + double precision gradbufc(3,maxres),gradbufx(3,maxres), + & glocbuf(4*maxres),gradbufc_sum(3,maxres),gloc_scbuf(3,maxres) include 'COMMON.SETUP' include 'COMMON.IOUNITS' include 'COMMON.FFIELD' @@ -458,8 +455,13 @@ cMS$ATTRIBUTES C :: proc_proc include 'COMMON.CONTROL' include 'COMMON.TIME1' include 'COMMON.MAXGRAD' + include 'COMMON.SCCOR' #ifdef TIMING +#ifdef MPI time01=MPI_Wtime() +#else + time01=tcpu() +#endif #endif #ifdef DEBUG write (iout,*) "sum_gradient gvdwc, gvdwx" @@ -554,31 +556,61 @@ c enddo enddo call flush(iout) #endif - call MPI_AllReduce(gradbufc(1,1),gradbufc_sum(1,1),3*nres, - & MPI_DOUBLE_PRECISION,MPI_SUM,FG_COMM,IERR) - time_reduce=time_reduce+MPI_Wtime()-time00 -#ifdef DEBUG - write (iout,*) "gradbufc_sum after allreduce" do i=1,nres - write (iout,'(i3,3f10.5)') i,(gradbufc_sum(j,i),j=1,3) + do j=1,3 + gradbufc_sum(j,i)=gradbufc(j,i) + enddo enddo - call flush(iout) +c call MPI_AllReduce(gradbufc(1,1),gradbufc_sum(1,1),3*nres, +c & MPI_DOUBLE_PRECISION,MPI_SUM,FG_COMM,IERR) +c time_reduce=time_reduce+MPI_Wtime()-time00 +#ifdef DEBUG +c write (iout,*) "gradbufc_sum after allreduce" +c do i=1,nres +c write (iout,'(i3,3f10.5)') i,(gradbufc_sum(j,i),j=1,3) +c enddo +c call flush(iout) #endif #ifdef TIMING - time_allreduce=time_allreduce+MPI_Wtime()-time00 +c time_allreduce=time_allreduce+MPI_Wtime()-time00 #endif do i=nnt,nres do k=1,3 gradbufc(k,i)=0.0d0 enddo enddo - do i=igrad_start,igrad_end - do j=jgrad_start(i),jgrad_end(i) - do k=1,3 - gradbufc(k,i)=gradbufc(k,i)+gradbufc_sum(k,j) - enddo +#ifdef DEBUG + write (iout,*) "igrad_start",igrad_start," igrad_end",igrad_end + write (iout,*) (i," jgrad_start",jgrad_start(i), + & " jgrad_end ",jgrad_end(i), + & i=igrad_start,igrad_end) +#endif +c +c Obsolete and inefficient code; we can make the effort O(n) and, therefore, +c do not parallelize this part. +c +c do i=igrad_start,igrad_end +c do j=jgrad_start(i),jgrad_end(i) +c do k=1,3 +c gradbufc(k,i)=gradbufc(k,i)+gradbufc_sum(k,j) +c enddo +c enddo +c enddo + do j=1,3 + gradbufc(j,nres-1)=gradbufc_sum(j,nres) + enddo + do i=nres-2,nnt,-1 + do j=1,3 + gradbufc(j,i)=gradbufc(j,i+1)+gradbufc_sum(j,i+1) enddo enddo +#ifdef DEBUG + write (iout,*) "gradbufc after summing" + do i=1,nres + write (iout,'(i3,3f10.5)') i,(gradbufc(j,i),j=1,3) + enddo + call flush(iout) +#endif else #endif #ifdef DEBUG @@ -588,16 +620,37 @@ c enddo enddo call flush(iout) #endif - do i=nnt,nres-1 - do k=1,3 - gradbufc(k,i)=0.0d0 + do i=1,nres + do j=1,3 + gradbufc_sum(j,i)=gradbufc(j,i) + gradbufc(j,i)=0.0d0 enddo - do j=i+1,nres - do k=1,3 - gradbufc(k,i)=gradbufc(k,i)+gradbufc(k,j) - enddo + enddo + do j=1,3 + gradbufc(j,nres-1)=gradbufc_sum(j,nres) + enddo + do i=nres-2,nnt,-1 + do j=1,3 + gradbufc(j,i)=gradbufc(j,i+1)+gradbufc_sum(j,i+1) enddo enddo +c do i=nnt,nres-1 +c do k=1,3 +c gradbufc(k,i)=0.0d0 +c enddo +c do j=i+1,nres +c do k=1,3 +c gradbufc(k,i)=gradbufc(k,i)+gradbufc(k,j) +c enddo +c enddo +c enddo +#ifdef DEBUG + write (iout,*) "gradbufc after summing" + do i=1,nres + write (iout,'(i3,3f10.5)') i,(gradbufc(j,i),j=1,3) + enddo + call flush(iout) +#endif #ifdef MPI endif #endif @@ -675,7 +728,6 @@ c enddo & +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" @@ -694,6 +746,19 @@ c enddo do i=1,4*nres glocbuf(i)=gloc(i,icg) enddo +#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 + 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 @@ -704,8 +769,18 @@ 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 #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 +#ifdef DEBUG write (iout,*) "gloc after reduce" do i=1,4*nres write (iout,*) i,gloc(i,icg) @@ -831,7 +906,11 @@ c enddo #endif #ifdef TIMING +#ifdef MPI time_sumgradient=time_sumgradient+MPI_Wtime()-time01 +#else + time_sumgradient=time_sumgradient+tcpu()-time01 +#endif #endif return end @@ -945,25 +1024,25 @@ C------------------------------------------------------------------------ & edihcnstr,ebr*nss, & Uconst,etot 10 format (/'Virtual-chain energies:'// - & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ - & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ - & 'EES= ',1pE16.6,' WEIGHT=',1pD16.6,' (p-p)'/ - & 'EVDWPP=',1pE16.6,' WEIGHT=',1pD16.6,' (p-p VDW)'/ - & 'ESTR= ',1pE16.6,' WEIGHT=',1pD16.6,' (stretching)'/ - & 'EBE= ',1pE16.6,' WEIGHT=',1pD16.6,' (bending)'/ - & 'ESC= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC local)'/ - & 'ETORS= ',1pE16.6,' WEIGHT=',1pD16.6,' (torsional)'/ - & 'ETORSD=',1pE16.6,' WEIGHT=',1pD16.6,' (double torsional)'/ - & 'EHBP= ',1pE16.6,' WEIGHT=',1pD16.6, + & 'EVDW= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC-SC)'/ + & 'EVDW2= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC-p)'/ + & 'EES= ',1pE16.6,' WEIGHT=',1pE16.6,' (p-p)'/ + & 'EVDWPP=',1pE16.6,' WEIGHT=',1pE16.6,' (p-p VDW)'/ + & 'ESTR= ',1pE16.6,' WEIGHT=',1pE16.6,' (stretching)'/ + & 'EBE= ',1pE16.6,' WEIGHT=',1pE16.6,' (bending)'/ + & 'ESC= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC local)'/ + & 'ETORS= ',1pE16.6,' WEIGHT=',1pE16.6,' (torsional)'/ + & 'ETORSD=',1pE16.6,' WEIGHT=',1pE16.6,' (double torsional)'/ + & 'EHPB= ',1pE16.6,' WEIGHT=',1pE16.6, & ' (SS bridges & dist. cnstr.)'/ - & 'ECORR4=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/ - & 'ECORR5=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/ - & 'ECORR6=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/ - & 'EELLO= ',1pE16.6,' WEIGHT=',1pD16.6,' (electrostatic-local)'/ - & 'ETURN3=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 3rd order)'/ - & 'ETURN4=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 4th order)'/ - & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/ - & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/ + & 'ECORR4=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/ + & 'ECORR5=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/ + & 'ECORR6=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/ + & 'EELLO= ',1pE16.6,' WEIGHT=',1pE16.6,' (electrostatic-local)'/ + & 'ETURN3=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 3rd order)'/ + & 'ETURN4=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 4th order)'/ + & 'ETURN6=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 6th order)'/ + & 'ESCCOR=',1pE16.6,' WEIGHT=',1pE16.6,' (backbone-rotamer corr)'/ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ & 'UCONST= ',1pE16.6,' (Constraint energy)'/ @@ -4165,39 +4244,39 @@ cd write (iout,*) "eij",eij else C Calculate the distance between the two points and its difference from the C target distance. - dd=dist(ii,jj) - rdis=dd-dhpb(i) + dd=dist(ii,jj) + rdis=dd-dhpb(i) C Get the force constant corresponding to this distance. - waga=forcon(i) + waga=forcon(i) C Calculate the contribution to energy. - ehpb=ehpb+waga*rdis*rdis + ehpb=ehpb+waga*rdis*rdis C C Evaluate gradient. C - fac=waga*rdis/dd + fac=waga*rdis/dd cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd, cd & ' waga=',waga,' fac=',fac - do j=1,3 - ggg(j)=fac*(c(j,jj)-c(j,ii)) - enddo + do j=1,3 + ggg(j)=fac*(c(j,jj)-c(j,ii)) + enddo cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3) C If this is a SC-SC distance, we need to calculate the contributions to the C Cartesian gradient in the SC vectors (ghpbx). - if (iii.lt.ii) then + if (iii.lt.ii) then do j=1,3 ghpbx(j,iii)=ghpbx(j,iii)-ggg(j) ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j) enddo - endif + endif cgrad do j=iii,jjj-1 cgrad do k=1,3 cgrad ghpbc(k,j)=ghpbc(k,j)+ggg(k) cgrad enddo cgrad enddo - do k=1,3 - ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k) - ghpbc(k,iii)=ghpbc(k,iii)-ggg(k) - enddo + do k=1,3 + ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k) + ghpbc(k,iii)=ghpbc(k,iii)-ggg(k) + enddo endif enddo ehpb=0.5D0*ehpb @@ -5822,7 +5901,7 @@ cc Omicron is flat angle depending on the value of first digit c(see comment below) C print *,i,tauangle(1,i) - do intertyp=1,3 !intertyp + 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 @@ -8076,12 +8155,12 @@ C C C o o C C \ /l\ /j\ / C C \ / \ / \ / C -C o| o | | o |o 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 +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, @@ -8252,11 +8331,11 @@ c---------------------------------------------------------------------------- double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2) logical swap CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC -C C +C C C Parallel Antiparallel C C C C o o C -C /l\ / \ /j\ C +C /l\ / \ /j\ C C / \ / \ / \ C C /| o |o o| o |\ C C j|/k\| / |/k\|l / C @@ -8369,18 +8448,18 @@ c---------------------------------------------------------------------------- & auxvec1(2),auxmat1(2,2) logical swap CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC -C C +C C C Parallel Antiparallel C C C -C o o C +C o o C C /l\ / \ /j\ C C / \ / \ / \ C -C /| o |o o| o |\ C +C /| o |o o| o |\ C C \ j|/k\| \ |/k\|l C -C \ / \ \ / \ C +C \ / \ \ / \ C C o \ o \ C C i i C -C C +C C CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC C C 4/7/01 AL Component s1 was removed, because it pertains to the respective -- 1.7.9.5