From: Adam Liwo Date: Fri, 23 Jan 2015 20:29:12 +0000 (+0100) Subject: Corrected refsys.f in src_MD-M X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;ds=sidebyside;h=e39b9b369e87de20bb1826764be18633ea348f58;p=unres.git Corrected refsys.f in src_MD-M --- diff --git a/bin/unres/MD/unres-mult-symetr_ifort_MPICH_E0LL2Y.exe b/bin/unres/MD/unres-mult-symetr_ifort_MPICH_E0LL2Y.exe index 362485e..3128072 100755 Binary files a/bin/unres/MD/unres-mult-symetr_ifort_MPICH_E0LL2Y.exe and b/bin/unres/MD/unres-mult-symetr_ifort_MPICH_E0LL2Y.exe differ diff --git a/source/unres/src_MD-M/Makefile b/source/unres/src_MD-M/Makefile deleted file mode 100644 index 4960339..0000000 --- a/source/unres/src_MD-M/Makefile +++ /dev/null @@ -1,131 +0,0 @@ -CPPFLAGS = -DLINUX -DUNRES -DMP -DMPI \ - -DPGI -DSPLITELE -DISNAN -DAMD64 \ - -DPROCOR -DLANG0 \ - -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB -## -DPROCOR -## -DMOMENT -#-DCO_BIAS -#-DCRYST_TOR -#-DDEBUG - -#INSTALL_DIR = /usr/local/mpich-1.2.0 -INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh -# -#FC= /usr/local/opt/intel/compiler60/ia32/bin/ifc -FC= ifort - -OPT = -O3 -ip -w -#OPT = -g -CB -#OPT = -g -CFLAGS = -DSGI -c - -FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include -FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)/include -FFLAGS2 = -c -w -O0 -I$(INSTALL_DIR)/include -FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report -I$(INSTALL_DIR)/include - -BIN = ../../../bin/unres/MD-M/unres_Tc_procor_oldparm_em64-D-symetr.exe -#LIBS = -L$(INSTALL_DIR)/lib_pgi -lmpich xdrf/libxdrf.a -#LIBS = -L$(INSTALL_DIR)/lib_ifort -lmpich xdrf/libxdrf.a -LIBS = -L$(INSTALL_DIR)/lib -lmpich ../../lib/xdrf_em64/libxdrf.a -g -d2 -CA -CB - -ARCH = LINUX -PP = /lib/cpp -P - - -all: unres - -.SUFFIXES: .F -.F.o: - ${FC} ${FFLAGS} ${CPPFLAGS} $*.F - - -object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \ - matmult.o readrtns_CSA.o parmread.o gen_rand_conf.o printmat.o map.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 \ - energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \ - cored.o rmdd.o geomout.o readpdb.o permut.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 \ - together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \ - indexx.o MP.o compare_s1.o prng_32.o \ - test.o banach.o distfit.o rmsd.o elecont.o dihed_cons.o \ - sc_move.o local_move.o \ - intcartderiv.o lagrangian_lesyng.o\ - stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \ - surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \ - q_measure.o gnmr1.o - -unres: ${object} proc_proc.o - cc -o compinfo compinfo.c - ./compinfo | true - ${FC} ${FFLAGS} cinfo.f - ${FC} ${OPT} -Wl,-M ${object} proc_proc.o cinfo.o ${LIBS} -o ${BIN} - - -clean: - /bin/rm *.o - -newconf.o: newconf.f - ${FC} ${FFLAGS} ${CPPFLAGS} newconf.f - -bank.o: bank.F - ${FC} ${FFLAGS} ${CPPFLAGS} bank.F - -diff12.o: diff12.f - ${FC} ${FFLAGS} ${CPPFLAGS} diff12.f - -csa.o: csa.f - ${FC} ${FFLAGS} ${CPPFLAGS} csa.f - -shift.o: shift.F - ${FC} ${FFLAGS} ${CPPFLAGS} shift.F - -ran.o: ran.f - ${FC} ${FFLAGS} ${CPPFLAGS} ran.f - -together.o: together.F - ${FC} ${FFLAGS} ${CPPFLAGS} together.F - -test.o: test.F - ${FC} ${FFLAGS} ${CPPFLAGS} test.F - -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 - -permut.o : permut.F - ${FC} ${FFLAGS2} ${CPPFLAGS} permut.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.o : energy_p_new.F - ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new.F - -lagrangian_lesyng.o : lagrangian_lesyng.F - ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F - -proc_proc.o: proc_proc.c - ${CC} ${CFLAGS} proc_proc.c diff --git a/source/unres/src_MD-M/Makefile b/source/unres/src_MD-M/Makefile new file mode 120000 index 0000000..8453cdd --- /dev/null +++ b/source/unres/src_MD-M/Makefile @@ -0,0 +1 @@ +Makefile_MPICH_ifort \ No newline at end of file diff --git a/source/unres/src_MD-M/cinfo.f b/source/unres/src_MD-M/cinfo.f index 708ae58..c7b5141 100644 --- a/source/unres/src_MD-M/cinfo.f +++ b/source/unres/src_MD-M/cinfo.f @@ -1,66 +1,33 @@ C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C -<<<<<<< HEAD -C 0 40360 35 +C 0 40360 9 subroutine cinfo include 'COMMON.IOUNITS' write(iout,*)'++++ Compile info ++++' - write(iout,*)'Version 0.40360 build 35' - write(iout,*)'compiled Mon Jan 5 06:42:38 2015' - write(iout,*)'compiled by adam@piasek4' + write(iout,*)'Version 0.40360 build 9' + write(iout,*)'compiled Fri Jan 23 21:00:08 2015' + write(iout,*)'compiled by adam@mmka' write(iout,*)'OS name: Linux ' - write(iout,*)'OS release: 3.2.0-70-generic ' + write(iout,*)'OS release: 3.2.0-72-generic ' write(iout,*)'OS version:', - & ' #105-Ubuntu SMP Wed Sep 24 19:49:16 UTC 2014 ' + & ' #107-Ubuntu SMP Thu Nov 6 14:24:01 UTC 2014 ' write(iout,*)'flags:' - write(iout,*)'INSTALL_DIR = /users/software/mpich2-1.0.7' - write(iout,*)'FC= gfortran' - write(iout,*)'OPT = -O' - write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include' - write(iout,*)'FFLAGS1 = -c -I$(INSTALL_DIR)/include' - write(iout,*)'FFLAGS2 = -c -O0 -I$(INSTALL_DIR)/include' - write(iout,*)'FFLAGS3 = -c -O -I$(INSTALL_DIR)/include' - write(iout,*)'FFLAGSE = -c -O3 -I$(INSTALL_DIR)/include' - write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpthread x...' - 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 -DG77 -DAMD64 ...' - write(iout,*)'GAB: BIN = ../../../bin/unres/MD/unres-D-symetr...' - write(iout,*)'4P: CPPFLAGS = -DLINUX -DG77 -DAMD64 -DUNRES -D...' - write(iout,*)'4P: BIN = ../../../bin/unres/MD/unres-mult-syme...' - write(iout,*)'E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DG77 -DAMD...' - write(iout,*)'E0LL2Y: BIN = ../../../bin/unres/MD/unres-mult-...' -======= -C 2 3 3460 - subroutine cinfo - include 'COMMON.IOUNITS' - write(iout,*)'++++ Compile info ++++' - write(iout,*)'Version 2.3 build 3460' - write(iout,*)'compiled Mon Oct 29 07:58:47 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 ' - write(iout,*)'OS version:', - & ' #1 SMP Tue May 3 09:23:03 UTC 2011 ' - write(iout,*)'flags:' - write(iout,*)'CPPFLAGS = -DLINUX -DUNRES -DMP -DMPI \\' - write(iout,*)' -DPGI -DSPLITELE -DISNAN -DAMD64 \\' - write(iout,*)' -DPROCOR -DLANG0 \\' - write(iout,*)' -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORP...' write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...' write(iout,*)'FC= ifort' - write(iout,*)'OPT = -O3 -ip -w' - write(iout,*)'CFLAGS = -DSGI -c' - write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include' - write(iout,*)'FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...' - write(iout,*)'FFLAGS2 = -c -w -O0 -I$(INSTALL_DIR)/include' - write(iout,*)'FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ...' - write(iout,*)'BIN = ../../../bin/unres/MD-M/unres_Tc_procor_o...' - write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich ../../lib/x...' + write(iout,*)'OPT = -O3 -ip ' + write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include ' + write(iout,*)'FFLAGS1 = -c -g -CA -CB -I$(INSTALL_DIR)/inclu...' + write(iout,*)'FFLAGS2 = -c -g -O0 -I$(INSTALL_DIR)/include ' + write(iout,*)'FFLAGSE = -c -O3 -ipo -opt_report -I$(INSTALL...' + write(iout,*)'LIBS = -L$(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...' ->>>>>>> 641d04ddae7b3a57c3c949f3f980374896c94b58 + write(iout,*)'GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 ...' + write(iout,*)'GAB: BIN = ../../../bin/unres/MD/unres-mult-sym...' + write(iout,*)'4P: CPPFLAGS = -DLINUX -DPGI -DAMD64 -DUNRES -D...' + write(iout,*)'4P: BIN = ../../../bin/unres/MD/unres-mult-syme...' + write(iout,*)'E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD...' + write(iout,*)'E0LL2Y: BIN = ../../../bin/unres/MD/unres-mult-...' write(iout,*)'++++ End of compile info ++++' return end diff --git a/source/unres/src_MD-M/readpdb.F b/source/unres/src_MD-M/readpdb.F index 8b6f331..c7f0ddd 100644 --- a/source/unres/src_MD-M/readpdb.F +++ b/source/unres/src_MD-M/readpdb.F @@ -169,7 +169,7 @@ C 2/15/2013 by Adam: corrected insertion of the last dummy residue c(j,nres+1)=c(j,1) c(j,2*nres)=c(j,nres) enddo - if (itype(1).eq.21) then + if (itype(1).eq.21) then nsup=nsup-1 nstart_sup=2 if (unres_pdb) then diff --git a/source/unres/src_MD-M/readrtns_CSA.F b/source/unres/src_MD-M/readrtns_CSA.F index c2d0887..0b08ab7 100644 --- a/source/unres/src_MD-M/readrtns_CSA.F +++ b/source/unres/src_MD-M/readrtns_CSA.F @@ -722,9 +722,11 @@ C 12/1/95 Added weight for the multi-body term WCORR 33 write (iout,'(a)') 'Error opening PDB file.' stop 34 continue -c print *,'Begin reading pdb data' +c write (iout,*) 'Begin reading pdb data' +c call flush(iout) call readpdb -c print *,'Finished reading pdb data' +c write (iout,*) 'Finished reading pdb data' +c call flush(iout) if(me.eq.king.or..not.out1file) & write (iout,'(a,i3,a,i3)')'nsup=',nsup, & ' nstart_sup=',nstart_sup diff --git a/source/unres/src_MD-M/refsys.f b/source/unres/src_MD-M/refsys.f index 86b0524..b57c201 100644 --- a/source/unres/src_MD-M/refsys.f +++ b/source/unres/src_MD-M/refsys.f @@ -1,22 +1,22 @@ - subroutine refsys(fail) -c This subroutine calculates unit vectors of a local reference system -c defined by atoms (i2), (i3), and (i4). The x axis is the axis from + subroutine refsys(i2,i3,i4,e1,e2,e3,fail) + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' +c this subroutine calculates unity vectors of a local reference system +c defined by atoms (i2), (i3), and (i4). the x axis is the axis from c atom (i3) to atom (i2), and the xy plane is the plane defined by atoms c (i2), (i3), and (i4). z axis is directed according to the sign of the -c vector product (i3)-(i2) and (i3)-(i4). Sets fail to .true. if atoms +c vector product (i3)-(i2) and (i3)-(i4). sets fail to .true. if atoms c (i2) and (i3) or (i3) and (i4) coincide or atoms (i2), (i3), and (i4) -c form a linear fragment. Returns vectors e1, e2, and e3. - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' +c form a linear fragment. returns vectors e1, e2, and e3. logical fail double precision e1(3),e2(3),e3(3) double precision u(3),z(3) include 'COMMON.IOUNITS' - include 'COMMON.CHAIN' - double precision coinc/1.0D-13/,align /1.0D-13/ + include "COMMON.CHAIN" + data coinc /1.0d-13/,align /1.0d-13/ fail=.false. - s1=0.0 - s2=0.0 + s1=0.0d0 + s2=0.0d0 do 1 i=1,3 zi=c(i,i2)-c(i,i3) ui=c(i,i4)-c(i,i3) @@ -29,28 +29,22 @@ c form a linear fragment. Returns vectors e1, e2, and e3. if (s1.gt.coinc) goto 2 write (iout,1000) i2,i3,i1 fail=.true. -c do 3 i=1,3 -c 3 c(i,i1)=0.0D0 return 2 if (s2.gt.coinc) goto 4 write(iout,1000) i3,i4,i1 fail=.true. - do 5 i=1,3 - 5 c(i,i1)=0.0D0 return 4 s1=1.0/s1 s2=1.0/s2 v1=z(2)*u(3)-z(3)*u(2) v2=z(3)*u(1)-z(1)*u(3) v3=z(1)*u(2)-z(2)*u(1) - anorm=dsqrt(v1*v1+v2*v2+v3*v3) + anorm=sqrt(v1*v1+v2*v2+v3*v3) if (anorm.gt.align) goto 6 write (iout,1010) i2,i3,i4,i1 fail=.true. -c do 7 i=1,3 -c 7 c(i,i1)=0.0D0 return - 6 anorm=1.0D0/anorm + 6 anorm=1.0/anorm e3(1)=v1*anorm e3(2)=v2*anorm e3(3)=v3*anorm @@ -60,9 +54,7 @@ c 7 c(i,i1)=0.0D0 e2(1)=e1(3)*e3(2)-e1(2)*e3(3) e2(2)=e1(1)*e3(3)-e1(3)*e3(1) e2(3)=e1(2)*e3(1)-e1(1)*e3(2) - 1000 format (/1x,' * * * Error - atoms',i4,' and',i4,' coincide.', - 1 'coordinates of atom',i4,' are set to zero.') - 1010 format (/1x,' * * * Error - atoms',2(i4,2h, ),i4,' form a linear', - 1 ' fragment. coordinates of atom',i4,' are set to zero.') + 1000 format (/1x,' * * * error - atoms',i4,' and',i4,' coincide.') + 1010 format (/1x,' * * * error - atoms',2(i4,2h, ),i4,' form a linear') return end diff --git a/source/unres/src_MD-M/ssMD.F b/source/unres/src_MD-M/ssMD.F index eab3c70..15800ae 100644 --- a/source/unres/src_MD-M/ssMD.F +++ b/source/unres/src_MD-M/ssMD.F @@ -532,7 +532,7 @@ c Local variables & allihpb(maxdim),alljhpb(maxdim), & newnss,newihpb(maxdim),newjhpb(maxdim) logical found - integer i_newnss(max_fg_procs),displ(max_fg_procs) + integer i_newnss(max_fg_procs),displ(0:max_fg_procs) integer g_newihpb(maxdim),g_newjhpb(maxdim),g_newnss allnss=0 diff --git a/source/unres/src_MD-M/unres.F b/source/unres/src_MD-M/unres.F index 7addf74..83d9588 100644 --- a/source/unres/src_MD-M/unres.F +++ b/source/unres/src_MD-M/unres.F @@ -56,7 +56,6 @@ c call memmon_print_usage() if (me.eq.king) call cinfo C Read force field parameters and job setup data call readrtns - call flush(iout) C if (me.eq.king .or. .not. out1file) then write (iout,'(2a/)') @@ -137,9 +136,15 @@ c-------------------------------------------------------------------------- include 'COMMON.SETUP' include 'COMMON.CONTROL' include 'COMMON.IOUNITS' - if (me.eq.king .or. .not. out1file) - & write (iout,*) "Calling chainbuild" +c if (me.eq.king .or. .not. out1file) then +c write (iout,*) "Calling chainbuild" +c call flush(iout) +c endif call chainbuild +c if (me.eq.king .or. .not. out1file) then +c write (iout,*) "Calling MD" +c call flush(iout) +c endif call MD return end