From: Adam Kazimierz Sieradzan Date: Thu, 5 Jul 2012 08:06:02 +0000 (-0400) Subject: hotfix of SCCOR potentials X-Git-Tag: v.3.2~61^2~6 X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;h=8421ab63ce0b8bbbfae73b37d47281229365565b;hp=c6be8f83ca143883c107a6f1a56ae1716e02fd63;p=unres.git hotfix of SCCOR potentials --- diff --git a/bin/unres/MD/unres_ifort_MPICH_GAB.exe b/bin/unres/MD/unres_ifort_MPICH_GAB.exe index 2ffec15..da4efff 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_GAB.exe b/bin/unres/MD/unres_ifort_single_GAB.exe index 66109ea..228bcd7 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/wham/wham_multparm-ham_rep-oldparm b/bin/wham/wham_multparm-ham_rep-oldparm index 2ddc49d..4a34607 100755 Binary files a/bin/wham/wham_multparm-ham_rep-oldparm and b/bin/wham/wham_multparm-ham_rep-oldparm differ diff --git a/source/unres/src_MD/Makefile b/source/unres/src_MD/Makefile deleted file mode 120000 index 6584c5e..0000000 --- a/source/unres/src_MD/Makefile +++ /dev/null @@ -1 +0,0 @@ -Makefile_single_ifort \ No newline at end of file diff --git a/source/unres/src_MD/Makefile b/source/unres/src_MD/Makefile new file mode 100644 index 0000000..ec1bcf3 --- /dev/null +++ b/source/unres/src_MD/Makefile @@ -0,0 +1,123 @@ +INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh + + +FC= ifort + +OPT = -g -ip -w -CB + +FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include +FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)/include +FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include +FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report -I$(INSTALL_DIR)/include + + +LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a + +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.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 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.o \ + banach.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 test.o + +GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES -DISNAN -DMP -DMPI \ + -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC +GAB: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_GAB.exe +GAB: ${object} xdrf/libxdrf.a + cc -o compinfo compinfo.c + ./compinfo | true + ${FC} ${FFLAGS} cinfo.f + ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN} + +E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES -DISNAN -DMP -DMPI \ + -DSPLITELE -DLANG0 +E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe +E0LL2Y: ${object} xdrf/libxdrf.a + cc -o compinfo compinfo.c + ./compinfo | true + ${FC} ${FFLAGS} cinfo.f + ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN} + +xdrf/libxdrf.a: + cd xdrf && make + + +clean: + /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean + +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 + +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 + +energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F + ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F + +lagrangian_lesyng.o : lagrangian_lesyng.F + ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F + +MD_A-MTS.o : MD_A-MTS.F + ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F + +blas.o : blas.f + ${FC} ${FFLAGS1} blas.f + +add.o : add.f + ${FC} ${FFLAGS1} add.f + +eigen.o : eigen.f + ${FC} ${FFLAGS2} eigen.f + +proc_proc.o: proc_proc.c + ${CC} ${CFLAGS} proc_proc.c diff --git a/source/unres/src_MD/Makefile_MPICH_ifort b/source/unres/src_MD/Makefile_MPICH_ifort deleted file mode 100644 index ec1bcf3..0000000 --- a/source/unres/src_MD/Makefile_MPICH_ifort +++ /dev/null @@ -1,123 +0,0 @@ -INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh - - -FC= ifort - -OPT = -g -ip -w -CB - -FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include -FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)/include -FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include -FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report -I$(INSTALL_DIR)/include - - -LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a - -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.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 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.o \ - banach.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 test.o - -GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES -DISNAN -DMP -DMPI \ - -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -GAB: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_GAB.exe -GAB: ${object} xdrf/libxdrf.a - cc -o compinfo compinfo.c - ./compinfo | true - ${FC} ${FFLAGS} cinfo.f - ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN} - -E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES -DISNAN -DMP -DMPI \ - -DSPLITELE -DLANG0 -E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe -E0LL2Y: ${object} xdrf/libxdrf.a - cc -o compinfo compinfo.c - ./compinfo | true - ${FC} ${FFLAGS} cinfo.f - ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN} - -xdrf/libxdrf.a: - cd xdrf && make - - -clean: - /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean - -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 - -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 - -energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F - ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F - -lagrangian_lesyng.o : lagrangian_lesyng.F - ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F - -MD_A-MTS.o : MD_A-MTS.F - ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F - -blas.o : blas.f - ${FC} ${FFLAGS1} blas.f - -add.o : add.f - ${FC} ${FFLAGS1} add.f - -eigen.o : eigen.f - ${FC} ${FFLAGS2} eigen.f - -proc_proc.o: proc_proc.c - ${CC} ${CFLAGS} proc_proc.c diff --git a/source/unres/src_MD/cinfo.f b/source/unres/src_MD/cinfo.f index afd4fb8..3cc28df 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 5 297 +C 2 5 300 subroutine cinfo include 'COMMON.IOUNITS' write(iout,*)'++++ Compile info ++++' - write(iout,*)'Version 2.5 build 297' - write(iout,*)'compiled Mon Jun 25 07:29:48 2012' + write(iout,*)'Version 2.5 build 300' + write(iout,*)'compiled Thu Jul 5 03:59:46 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 ' @@ -16,17 +16,14 @@ C 2 5 297 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,*)'FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include ' write(iout,*)'FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ...' - write(iout,*)'CC = cc' - write(iout,*)'CFLAGS = -DLINUX -DPGI -c' - write(iout,*)'OPT = -O3 -ip -w' - write(iout,*)'LIBS = -Lxdrf -lxdrf' + write(iout,*)'LIBS = -L$(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_si...' + 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 ++++' diff --git a/source/unres/src_MD/tmptmp b/source/unres/src_MD/tmptmp deleted file mode 100644 index fb6f043..0000000 --- a/source/unres/src_MD/tmptmp +++ /dev/null @@ -1 +0,0 @@ -aks255 diff --git a/source/wham/src/Makefile b/source/wham/src/Makefile index 15fcd21..bba78b4 100644 --- a/source/wham/src/Makefile +++ b/source/wham/src/Makefile @@ -27,6 +27,7 @@ objects = \ molread_zs.o \ openunits.o \ readrtns.o \ + gnmr1.o\ arcos.o \ cartder.o \ cartprint.o \ diff --git a/source/wham/src/cinfo.f b/source/wham/src/cinfo.f index 97eabbe..5642820 100644 --- a/source/wham/src/cinfo.f +++ b/source/wham/src/cinfo.f @@ -1,21 +1,23 @@ C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C -C 0 0 565 +C 0 0 567 subroutine cinfo include 'COMMON.IOUNITS' write(iout,*)'++++ Compile info ++++' - write(iout,*)'Version 0.0 build 565' - write(iout,*)'compiled Tue May 29 04:48:26 2012' - write(iout,*)'compiled by adam@matrix.chem.cornell.edu' + write(iout,*)'Version 0.0 build 567' + write(iout,*)'compiled Thu Jul 5 04:03:19 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,*)'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,*)'BIN = ../../../bin/wham' + write(iout,*)'BIN = ../../../bin/wham/' write(iout,*)'FC= ifort' - write(iout,*)'OPT = -mcmodel=medium -O3 -ip -w' + write(iout,*)'OPT = -mcmodel=medium -g -CB' write(iout,*)'FFLAGS = ${OPT} -c -I. -I./include_unres -I$(IN...' write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xd...' + write(iout,*)'CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DP...' write(iout,*)'objects = \\' write(iout,*)' wham_multparm.o \\' write(iout,*)' bxread.o \\' @@ -23,11 +25,11 @@ C 0 0 565 write(iout,*)' cxread.o \\' write(iout,*)' enecalc1.o \\' write(iout,*)' energy_p_new.o \\' - write(iout,*)' gnmr1.o \\' write(iout,*)' initialize_p.o \\' write(iout,*)' molread_zs.o \\' write(iout,*)' openunits.o \\' write(iout,*)' readrtns.o \\' + write(iout,*)' gnmr1.o\\' write(iout,*)' arcos.o \\' write(iout,*)' cartder.o \\' write(iout,*)' cartprint.o \\' @@ -54,8 +56,6 @@ C 0 0 565 write(iout,*)' readrtns_compar.o \\' write(iout,*)' readpdb.o fitsq.o contact.o \\' write(iout,*)' elecont.o contfunc.o cont_frag.o conf_c...' - write(iout,*)'GAB: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITEL...' - write(iout,*)'E0LL2Y: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLI...' write(iout,*)'++++ End of compile info ++++' return end diff --git a/source/wham/src/include_unres/COMMON.SCCOR b/source/wham/src/include_unres/COMMON.SCCOR index efab24f..28d748a 100644 --- a/source/wham/src/include_unres/COMMON.SCCOR +++ b/source/wham/src/include_unres/COMMON.SCCOR @@ -6,7 +6,7 @@ cc Parameters of the SCCOR term integer nterm_sccor,isccortyp,nsccortyp,nlor_sccor common /sccor/ v1sccor(maxterm_sccor,3,20,20), & v2sccor(maxterm_sccor,3,20,20), - & v0sccor(maxterm_sccor,20), + & v0sccor(ntyp,ntyp), & vlor1sccor(maxterm_sccor,20,20), & vlor2sccor(maxterm_sccor,20,20), & vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,0:maxres2,10),