From: Adam Liwo Date: Wed, 17 Oct 2012 04:52:06 +0000 (-0400) Subject: Merge branch 'adam' into devel X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;h=8f4ff43aff8e7c88469519e17fcd9f1d5ef73103;hp=c31fc30c9830b0e505fc4c5af6d07e13be4f3078;p=unres.git Merge branch 'adam' into devel Conflicts: bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe --- diff --git a/bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe b/bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe new file mode 100755 index 0000000..098d4e1 Binary files /dev/null and b/bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe differ diff --git a/bin/unres/MD/unres_ifort_single_GAB.exe b/bin/unres/MD/unres_ifort_single_GAB.exe index 228bcd7..df1e14c 100755 Binary files a/bin/unres/MD/unres_ifort_single_GAB.exe and b/bin/unres/MD/unres_ifort_single_GAB.exe differ diff --git a/bin/unres/MINIM/unres_ifort_MIN_single_GAB.exe b/bin/unres/MINIM/unres_ifort_MIN_single_GAB.exe index 394eaac..cfd83ee 100755 Binary files a/bin/unres/MINIM/unres_ifort_MIN_single_GAB.exe and b/bin/unres/MINIM/unres_ifort_MIN_single_GAB.exe differ diff --git a/source/unres/src_CSA/readpdb.F b/source/unres/src_CSA/readpdb.F index dacd12d..69ec3e1 100644 --- a/source/unres/src_CSA/readpdb.F +++ b/source/unres/src_CSA/readpdb.F @@ -258,6 +258,9 @@ c endif enddo iti=itype(i) di=dist(i,nres+i) +C 10/03/12 Adam: Correction for zero SC-SC bond length + if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0) + & di=dsc(itype(i)) vbld(i+nres)=di if (itype(i).ne.10) then vbld_inv(i+nres)=1.0d0/di diff --git a/source/unres/src_CSA/readrtns_csa.F b/source/unres/src_CSA/readrtns_csa.F index 17b2165..9ab4510 100644 --- a/source/unres/src_CSA/readrtns_csa.F +++ b/source/unres/src_CSA/readrtns_csa.F @@ -455,6 +455,9 @@ c print *,'Finished reading pdb data' call contact(.false.,ncont_ref,icont_ref,co) if (sideadd) then +C Following 2 lines for diagnostics; comment out if not needed + write (iout,*) "Before sideadd" + call intout if(me.eq.king.or..not.out1file) & write(iout,*)'Adding sidechains' maxsi=1000 @@ -472,6 +475,11 @@ c call gen_side(iti,theta(i+1),alph(i),omeg(i),fail) endif enddo endif +C 10/03/12 Adam: Recalculate coordinates with new side chain positions + call chainbuild +C Following 2 lines for diagnostics; comment out if not needed + write (iout,*) "After sideadd" + call intout endif if (indpdb.eq.0) then diff --git a/source/unres/src_MD/readpdb.F b/source/unres/src_MD/readpdb.F index 563941b..97e9aa8 100644 --- a/source/unres/src_MD/readpdb.F +++ b/source/unres/src_MD/readpdb.F @@ -260,6 +260,9 @@ c endif enddo iti=itype(i) di=dist(i,nres+i) +C 10/03/12 Adam: Correction for zero SC-SC bond length + if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0) + & di=dsc(itype(i)) vbld(i+nres)=di if (itype(i).ne.10) then vbld_inv(i+nres)=1.0d0/di diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F index 47850c2..6b0e362 100644 --- a/source/unres/src_MD/readrtns.F +++ b/source/unres/src_MD/readrtns.F @@ -893,6 +893,9 @@ c print *,'Finished reading pdb data' call contact(.false.,ncont_ref,icont_ref,co) if (sideadd) then +C Following 2 lines for diagnostics; comment out if not needed + write (iout,*) "Before sideadd" + call intout if(me.eq.king.or..not.out1file) & write(iout,*)'Adding sidechains' maxsi=1000 @@ -909,7 +912,12 @@ c print *,'Finished reading pdb data' & i,' after ',nsi,' trials' endif enddo +C 10/03/12 Adam: Recalculate coordinates with new side chain positions + call chainbuild endif +C Following 2 lines for diagnostics; comment out if not needed + write (iout,*) "After sideadd" + call intout endif if (indpdb.eq.0) then C Read sequence if not taken from the pdb file. diff --git a/source/unres/src_MIN/Makefile_OLDPARM_ifort b/source/unres/src_MIN/Makefile_OLDPARM_ifort deleted file mode 100644 index 598a89f..0000000 --- a/source/unres/src_MIN/Makefile_OLDPARM_ifort +++ /dev/null @@ -1,85 +0,0 @@ -CPPFLAGS = -DPROCOR -DLINUX -DPGI -DISNAN \ - -DSPLITELE -DAMD64 -DLANG0 \ - -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DPROCOR - -FC= ifort -g - -OPT = -O3 -ip -w - -FFLAGS = -c ${OPT} -FFLAGS1 = -c -w -g -d2 -CA -CB -FFLAGS2 = -c -w -g -O0 -FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report - - -BIN = ../../../bin/unres/MINIM/unres_Tc_procor_new_em64_min_sumsl_old.exe -LIBS = -lpthread - -ARCH = LINUX -PP = /lib/cpp -P - - -all: unres - -.SUFFIXES: .F.f -.F.o: - ${FC} ${FFLAGS} ${CPPFLAGS} $*.F -.f.o: - ${FC} ${FFLAGS} ${CPPFLAGS} $*.f - - -object = unres_min.o arcos.o cartprint.o chainbuild.o initialize_p.o \ - matmult.o readrtns_min.o parmread.o \ - pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \ - cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \ - gradient_p.o minimize_p.o sumsld.o \ - cored.o rmdd.o geomout_min.o readpdb.o \ - intcartderiv.o \ - MP.o printmat.o convert.o int_to_cart.o - -unres: ${object} -# cc -o compinfo compinfo.c -# ./compinfo | true - ${FC} ${FFLAGS} cinfo.f - ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN} - - -clean: - /bin/rm *.o - -chainbuild.o: chainbuild.F - ${FC} ${FFLAGS} ${CPPFLAGS} chainbuild.F - -matmult.o: matmult.f - ${FC} ${FFLAGS} ${CPPFLAGS} matmult.f - -parmread.o : parmread.F - ${FC} ${FFLAGS} ${CPPFLAGS} parmread.F - -intcor.o : intcor.f - ${FC} ${FFLAGS} ${CPPFLAGS} intcor.f - -cartder.o : cartder.F - ${FC} ${FFLAGS} ${CPPFLAGS} cartder.F - -readpdb.o : readpdb.F - ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb.F - -sumsld.o : sumsld.f - ${FC} ${FFLAGS} ${CPPFLAGS} sumsld.f - -cored.o : cored.f - ${FC} ${FFLAGS1} ${CPPFLAGS} cored.f - -rmdd.o : rmdd.f - ${FC} ${FFLAGS} ${CPPFLAGS} rmdd.f - -energy_p_new_barrier.o : energy_p_new_barrier.F - ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new_barrier.F - -gradient_p.o : gradient_p.F - ${FC} ${FFLAGSE} ${CPPFLAGS} gradient_p.F - - - - diff --git a/source/unres/src_MIN/Makefile_gfortran b/source/unres/src_MIN/Makefile_gfortran deleted file mode 100644 index 0c85368..0000000 --- a/source/unres/src_MIN/Makefile_gfortran +++ /dev/null @@ -1,92 +0,0 @@ -CPPFLAGS = -DPROCOR -DLINUX -DG77 -DISNAN \ - -DSPLITELE -DAMD64 -DLANG0 -# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -#-DCRYST_TOR -# -DPROCOR -# -DTSCSC -#-DTIMING \ -# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -# -DMOMENT -#-DPARVEC -#-DPARINT -DPARINTDER - -FC= gfortran - -OPT = -O - -FFLAGS = -c ${OPT} -FFLAGS1 = -c -g -C -FFLAGS2 = -c -g -O0 -FFLAGSE = -c -O3 - - -BIN = ../../../bin/unres/MIN/unres_min_gfortran.exe -LIBS = -#LIBS = -lpthread - -ARCH = LINUX -PP = /lib/cpp -P - - -all: unres - -.SUFFIXES: .F -.F.o: - ${FC} ${FFLAGS} ${CPPFLAGS} $*.F - - -object = unres_min.o arcos.o cartprint.o chainbuild.o initialize_p.o \ - matmult.o readrtns_min.o parmread.o \ - pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \ - cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \ - gradient_p.o minimize_p.o sumsld.o \ - cored.o rmdd.o geomout_min.o readpdb.o \ - intcartderiv.o \ - MP.o printmat.o convert.o int_to_cart.o - -unres: ${object} -# cc -o compinfo compinfo.c -# ./compinfo | true - ${FC} ${FFLAGS} cinfo.f - ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN} - - -clean: - /bin/rm *.o *.il - -chainbuild.o: chainbuild.F - ${FC} ${FFLAGS} ${CPPFLAGS} chainbuild.F - -matmult.o: matmult.f - ${FC} ${FFLAGS} ${CPPFLAGS} matmult.f - -parmread.o : parmread.F - ${FC} ${FFLAGS} ${CPPFLAGS} parmread.F - -intcor.o : intcor.f - ${FC} ${FFLAGS} ${CPPFLAGS} intcor.f - -cartder.o : cartder.F - ${FC} ${FFLAGS} ${CPPFLAGS} cartder.F - -readpdb.o : readpdb.F - ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb.F - -sumsld.o : sumsld.f - ${FC} ${FFLAGS} ${CPPFLAGS} sumsld.f - -cored.o : cored.f - ${FC} ${FFLAGS1} ${CPPFLAGS} cored.f - -rmdd.o : rmdd.f - ${FC} ${FFLAGS} ${CPPFLAGS} rmdd.f - -energy_p_new_barrier.o : energy_p_new_barrier.F - ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new_barrier.F - -gradient_p.o : gradient_p.F - ${FC} ${FFLAGSE} ${CPPFLAGS} gradient_p.F - - - - diff --git a/source/unres/src_MIN/Makefile_ifort b/source/unres/src_MIN/Makefile_ifort deleted file mode 100644 index 193d9e6..0000000 --- a/source/unres/src_MIN/Makefile_ifort +++ /dev/null @@ -1,91 +0,0 @@ -CPPFLAGS = -DPROCOR -DLINUX -DPGI -DISNAN \ - -DSPLITELE -DAMD64 -DLANG0 -# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -#-DCRYST_TOR -# -DPROCOR -# -DTSCSC -#-DTIMING \ -# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -# -DMOMENT -#-DPARVEC -#-DPARINT -DPARINTDER - -FC= ifort -g - -OPT = -O3 -ip -w - -FFLAGS = -c ${OPT} -FFLAGS1 = -c -w -g -d2 -CA -CB -FFLAGS2 = -c -w -g -O0 -FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report - - -BIN = ../bin/unres_Tc_procor_new_em64_nh_hremd_92110_min_sumsl.exe -LIBS = -lpthread - -ARCH = LINUX -PP = /lib/cpp -P - - -all: unres - -.SUFFIXES: .F -.F.o: - ${FC} ${FFLAGS} ${CPPFLAGS} $*.F - - -object = unres_min.o arcos.o cartprint.o chainbuild.o initialize_p.o \ - matmult.o readrtns_min.o parmread.o \ - pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \ - cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \ - gradient_p.o minimize_p.o sumsld.o \ - cored.o rmdd.o geomout_min.o readpdb.o \ - intcartderiv.o \ - MP.o printmat.o convert.o int_to_cart.o - -unres: ${object} -# cc -o compinfo compinfo.c -# ./compinfo | true - ${FC} ${FFLAGS} cinfo.f - ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN} - - -clean: - /bin/rm *.o *.il - -chainbuild.o: chainbuild.F - ${FC} ${FFLAGS} ${CPPFLAGS} chainbuild.F - -matmult.o: matmult.f - ${FC} ${FFLAGS} ${CPPFLAGS} matmult.f - -parmread.o : parmread.F - ${FC} ${FFLAGS} ${CPPFLAGS} parmread.F - -intcor.o : intcor.f - ${FC} ${FFLAGS} ${CPPFLAGS} intcor.f - -cartder.o : cartder.F - ${FC} ${FFLAGS} ${CPPFLAGS} cartder.F - -readpdb.o : readpdb.F - ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb.F - -sumsld.o : sumsld.f - ${FC} ${FFLAGS} ${CPPFLAGS} sumsld.f - -cored.o : cored.f - ${FC} ${FFLAGS1} ${CPPFLAGS} cored.f - -rmdd.o : rmdd.f - ${FC} ${FFLAGS} ${CPPFLAGS} rmdd.f - -energy_p_new_barrier.o : energy_p_new_barrier.F - ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new_barrier.F - -gradient_p.o : gradient_p.F - ${FC} ${FFLAGSE} ${CPPFLAGS} gradient_p.F - - - - diff --git a/source/unres/src_MIN/minimize_p.F b/source/unres/src_MIN/minimize_p.F index 1721510..72190e8 100644 --- a/source/unres/src_MIN/minimize_p.F +++ b/source/unres/src_MIN/minimize_p.F @@ -27,7 +27,10 @@ c common /przechowalnia/ v icall = 1 -c print *,"liv",liv," lv",lv +C Following 3 line for diagnostics; comment out if not needed + write(iout,*) "Enter MINIMIZE liv",liv," lv",lv + write (iout,*) "Coordinates before minimization" + call intout call deflt(2,iv,liv,lv,v) * 12 means fresh start, dont call deflt iv(1)=12 diff --git a/source/unres/src_MIN/readpdb.F b/source/unres/src_MIN/readpdb.F index dacd12d..1d79870 100644 --- a/source/unres/src_MIN/readpdb.F +++ b/source/unres/src_MIN/readpdb.F @@ -258,6 +258,9 @@ c endif enddo iti=itype(i) di=dist(i,nres+i) +C 9/29/12 Adam: Correction for zero SC-SC bond length + if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0) + & di=dsc(itype(i)) vbld(i+nres)=di if (itype(i).ne.10) then vbld_inv(i+nres)=1.0d0/di diff --git a/source/unres/src_MIN/readrtns_min.F b/source/unres/src_MIN/readrtns_min.F index dee929a..9d444cf 100644 --- a/source/unres/src_MIN/readrtns_min.F +++ b/source/unres/src_MIN/readrtns_min.F @@ -422,6 +422,9 @@ c print *,'Finished reading pdb data' c call contact(.false.,ncont_ref,icont_ref,co) if (sideadd) then +C Following 2 lines for diagnostics; comment out if not needed + write (iout,*) "Before sideadd" + call intout if(me.eq.king.or..not.out1file) & write(iout,*)'Adding sidechains' maxsi=1000 @@ -438,7 +441,12 @@ c call contact(.false.,ncont_ref,icont_ref,co) & i,' after ',nsi,' trials' endif enddo +C 9/29/12 Adam: Recalculate coordinates with new side chain positions + call chainbuild endif +C Following 2 lines for diagnostics; comment out if not needed + write (iout,*) "After sideadd" + call intout endif if (indpdb.eq.0) then C Read sequence if not taken from the pdb file.