From: Adam Liwo Date: Thu, 20 Sep 2012 12:50:23 +0000 (-0400) Subject: Update X-Git-Tag: v.3.2~70 X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=ffdab8e1a4782a031ac72eef5416fd12a1dd3722 Update --- diff --git a/bin/unres/MD/unres_ifort_MPICH_GAB.exe b/bin/unres/MD/unres_ifort_MPICH_GAB.exe index da4efff..c5b7bf1 100755 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/bin/unres/MD/unres_ifort_single_E0LL2Y.exe b/bin/unres/MD/unres_ifort_single_E0LL2Y.exe index 10f5546..651864e 100755 Binary files a/bin/unres/MD/unres_ifort_single_E0LL2Y.exe and b/bin/unres/MD/unres_ifort_single_E0LL2Y.exe differ diff --git a/bin/wham/wham_ifort_MPICH_E0LL2Y.exe b/bin/wham/wham_ifort_MPICH_E0LL2Y.exe index c93d86e..b84ec07 100755 Binary files a/bin/wham/wham_ifort_MPICH_E0LL2Y.exe and b/bin/wham/wham_ifort_MPICH_E0LL2Y.exe differ diff --git a/source/unres/src_MD/Makefile_MPICH_ifort b/source/unres/src_MD/Makefile_MPICH_ifort index 5af741c..4505541 100644 --- a/source/unres/src_MD/Makefile_MPICH_ifort +++ b/source/unres/src_MD/Makefile_MPICH_ifort @@ -52,7 +52,7 @@ GAB: ${object} xdrf/libxdrf.a E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES -DISNAN -DMP -DMPI \ -DSPLITELE -DLANG0 -E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_E0LL2Y-test.exe +E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe E0LL2Y: ${object} xdrf/libxdrf.a cc -o compinfo compinfo.c ./compinfo | true diff --git a/source/unres/src_MD/cinfo.f b/source/unres/src_MD/cinfo.f deleted file mode 100644 index 71fc6a6..0000000 --- a/source/unres/src_MD/cinfo.f +++ /dev/null @@ -1,31 +0,0 @@ -C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C -C 2 5 299 - subroutine cinfo - include 'COMMON.IOUNITS' - write(iout,*)'++++ Compile info ++++' - write(iout,*)'Version 2.5 build 299' - write(iout,*)'compiled Wed Jul 18 03:29:18 2012' - write(iout,*)'compiled by jal47@matrix.chem.cornell.edu' - write(iout,*)'OS name: Linux ' - write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 ' - write(iout,*)'OS version:', - & ' #1 SMP Tue May 3 09:23:03 UTC 2011 ' - write(iout,*)'flags:' - write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...' - write(iout,*)'FC= ifort' - write(iout,*)'OPT = -g -ip -w -CB ' - write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include ' - write(iout,*)'FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...' - write(iout,*)'FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include ' - write(iout,*)'FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ...' - write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...' - write(iout,*)'ARCH = LINUX' - write(iout,*)'PP = /lib/cpp -P' - write(iout,*)'object = unres.o arcos.o cartprint.o chainbuild...' - write(iout,*)'GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...' - write(iout,*)'GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP...' - write(iout,*)'E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...' - write(iout,*)'E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...' - write(iout,*)'++++ End of compile info ++++' - return - end diff --git a/source/unres/src_MD/energy_p_new_barrier.F b/source/unres/src_MD/energy_p_new_barrier.F index 9edadf8..03a7825 100644 --- a/source/unres/src_MD/energy_p_new_barrier.F +++ b/source/unres/src_MD/energy_p_new_barrier.F @@ -774,7 +774,6 @@ 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 @@ -783,7 +782,6 @@ c enddo enddo enddo #endif -#undef DEBUG do i=1,nres do j=1,3 gloc_scbuf(j,i)=gloc_sc(j,i,icg) @@ -802,7 +800,6 @@ c enddo 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 @@ -811,7 +808,6 @@ c enddo enddo enddo #endif -#undef DEBUG #ifdef DEBUG write (iout,*) "gloc after reduce" do i=1,4*nres diff --git a/source/unres/src_MIN/Makefile b/source/unres/src_MIN/Makefile deleted file mode 120000 index 27e5786..0000000 --- a/source/unres/src_MIN/Makefile +++ /dev/null @@ -1 +0,0 @@ -Makefile_OLDPARM_ifort \ No newline at end of file diff --git a/source/unres/src_MIN/cinfo.f b/source/unres/src_MIN/cinfo.f deleted file mode 100644 index f9fdbc8..0000000 --- a/source/unres/src_MIN/cinfo.f +++ /dev/null @@ -1,8 +0,0 @@ -C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C -C 2 4 3232 - subroutine cinfo - include 'COMMON.IOUNITS' - write(iout,*)'++++ Compile info ++++' - write(iout,*)'Version MINI energy and minimization only' - return - end diff --git a/source/unres/src_MIN/readrtns_min.F b/source/unres/src_MIN/readrtns_min.F index b6f8e2e..dee929a 100644 --- a/source/unres/src_MIN/readrtns_min.F +++ b/source/unres/src_MIN/readrtns_min.F @@ -118,8 +118,7 @@ C Set up the time limit (caution! The time must be input in minutes!) dccart=(index(controlcard,'CART').gt.0) overlapsc=(index(controlcard,'OVERLAP').gt.0) overlapsc=.not.overlapsc - searchsc=(index(controlcard,'NOSEARCHSC').gt.0) - searchsc=.not.searchsc + searchsc=(index(controlcard,'SEARCHSC').gt.0) sideadd=(index(controlcard,'SIDEADD').gt.0) energy_dec=(index(controlcard,'ENERGY_DEC').gt.0) outpdb=(index(controlcard,'PDBOUT').gt.0) @@ -432,7 +431,7 @@ c call contact(.false.,ncont_ref,icont_ref,co) nsi=0 fail=.true. do while (fail.and.nsi.le.maxsi) -c call gen_side(iti,theta(i+1),alph(i),omeg(i),fail) + call gen_side(iti,theta(i+1),alph(i),omeg(i),fail) nsi=nsi+1 enddo if(fail) write(iout,*)'Adding sidechain failed for res ', @@ -691,7 +690,7 @@ C initial geometry. #endif do itrial=1,100 itmp=1 -c call gen_rand_conf(itmp,*30) + call gen_rand_conf(itmp,*30) goto 40 30 write (iout,*) 'Failed to generate random conformation', & ', itrial=',itrial @@ -718,7 +717,7 @@ c call gen_rand_conf(itmp,*30) #else do itrial=1,100 itmp=1 -c call gen_rand_conf(itmp,*31) + call gen_rand_conf(itmp,*31) goto 40 31 write (iout,*) 'Failed to generate random conformation', & ', itrial=',itrial diff --git a/source/unres/src_MIN/unres_min.F b/source/unres/src_MIN/unres_min.F index 1e97d6e..3cdbeef 100644 --- a/source/unres/src_MIN/unres_min.F +++ b/source/unres/src_MIN/unres_min.F @@ -141,6 +141,18 @@ c call hairpin(.true.,nharp,iharp) c call secondary2(.true.) if (minim) then +crc overlap test + if (overlapsc) then + print *, 'Calling OVERLAP_SC' + call overlap_sc(fail) + endif + + if (searchsc) then + call sc_move(2,nres-1,10,1d10,nft_sc,etot) + print *,'SC_move',nft_sc,etot + write(iout,*) 'SC_move',nft_sc,etot + endif + if (dccart) then print *, 'Calling MINIM_DC' #ifdef MPI diff --git a/source/wham/src/Makefile_MPICH_ifort b/source/wham/src/Makefile_MPICH_ifort index 2a95ca8..1d4a159 100644 --- a/source/wham/src/Makefile_MPICH_ifort +++ b/source/wham/src/Makefile_MPICH_ifort @@ -61,7 +61,7 @@ GAB: ${objects} ${objects_compar} xdrf/libxdrf.a ./compinfo ${FC} -c ${FFLAGS} cinfo.f $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \ - ${LIBS} -static-intel -o ${BIN}/wham_ifort_MPICH_GAB.exe + ${LIBS} -static-intel -o ${BIN}/wham_ifort_MPICH_GAB-DEBUG.exe E0LL2Y: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 E0LL2Y: ${objects} ${objects_compar} xdrf/libxdrf.a @@ -69,7 +69,7 @@ E0LL2Y: ${objects} ${objects_compar} xdrf/libxdrf.a ./compinfo ${FC} -c ${FFLAGS} cinfo.f $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \ - ${LIBS} -static-intel -o ${BIN}/wham_ifort_MPICH_E0LL2Y-debug.exe + ${LIBS} -static-intel -o ${BIN}/wham_ifort_MPICH_E0LL2Y-DEBUG.exe xdrf/libxdrf.a: cd xdrf && make diff --git a/source/wham/src/enecalc1.F b/source/wham/src/enecalc1.F index c431153..459f395 100644 --- a/source/wham/src/enecalc1.F +++ b/source/wham/src/enecalc1.F @@ -212,12 +212,11 @@ c call pdbout(ii+1,beta_h(ib,ipar),efree,energia(0),0.0d0,rmsdev) do k=1,21 enetb(k,iii+1,iparm)=energia(k) enddo +#define DEBUG #ifdef DEBUG write (iout,'(2i5,f10.1,3e15.5)') i,iii, & 1.0d0/(beta_h(ib,ipar)*1.987D-3),energia(0),eini,efree -c call enerprint(energia(0),fT) -#endif -#ifdef DEBUG + call enerprint(energia(0),fT) write (iout,'(8f10.5)') ((c(l,k),l=1,3),k=1,nres) write (iout,'(8f10.5)') ((c(l,k+nres),l=1,3),k=nnt,nct) write (iout,'(8f10.4)') (vbld(k),k=nnt+1,nct) @@ -230,8 +229,14 @@ c call enerprint(energia(0),fT) write (iout,'(8f10.5)') (q(k,iii+1),k=1,nQ) write (iout,'(f10.5,i10)') rmsdev,iscor call enerprint(energia(0),fT) + write(liczba,'(bz,i3.3)') me + nazwa="test"//liczba//".pdb" + write (iout,*) "pdb file",nazwa + open (ipdb,file=nazwa,position="append") call pdbout(ii+1,beta_h(ib,ipar),efree,energia(0),0.0d0,rmsdev) + close(ipdb) #endif +#undef DEBUG endif enddo ! iparm diff --git a/source/wham/src/energy_p_new.F b/source/wham/src/energy_p_new.F index cb4b7b0..e57397b 100644 --- a/source/wham/src/energy_p_new.F +++ b/source/wham/src/energy_p_new.F @@ -3100,8 +3100,8 @@ c nbi=nbondterm(iti) if (nbi.eq.1) then diff=vbld(i+nres)-vbldsc0(1,iti) -c write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff, -c & AKSC(1,iti),AKSC(1,iti)*diff*diff + write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff, + & AKSC(1,iti),AKSC(1,iti)*diff*diff estr=estr+0.5d0*AKSC(1,iti)*diff*diff do j=1,3 gradbx(j,i)=AKSC(1,iti)*diff*dc(j,i+nres)/vbld(i+nres) @@ -3130,8 +3130,8 @@ c & AKSC(1,iti),AKSC(1,iti)*diff*diff usum=usum+uprod1 usumsqder=usumsqder+ud(j)*uprod2 enddo -c write (iout,*) i,iti,vbld(i+nres),(vbldsc0(j,iti), -c & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi) + write (iout,*) i,iti,vbld(i+nres),(vbldsc0(j,iti), + & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi) estr=estr+uprod/usum do j=1,3 gradbx(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres)