6/11/2012 Changes of the CSA version

diff --git a/.gitignore b/.gitignore
index 7d78886..45bb905 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 *.[oa] 
 *~
 *.swp
+*.[eo][0-9][0-9][0-9][0-9]*

diff --git a/examples/unres/CSA/CASP3/ENERGY/prota_nmr.pdb.gz b/examples/unres/CSA/CASP3/ENERGY/prota_nmr.pdb.gz
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diff --git a/source/cluster/wham/src/COMMON.SBRIDGE b/source/cluster/wham/src/COMMON.SBRIDGE
deleted file mode 100644 (file)
index 92150c5..0000000
--- a/source/cluster/wham/src/COMMON.SBRIDGE
+++ /dev/null
@@ -1,7 +0,0 @@
-      integer ns,nss,nfree,iss,ihpb,jhpb,nhpb,link_start,link_end
-      double precision ebr,dbr,fbr,dhpb,forcon,weidis
-      common /sbridge/ ebr,dbr,fbr,ns,nss,nfree,iss(maxss)
-      common /links/ dhpb(maxss),forcon(maxss),ihpb(maxss),
-     & jhpb(maxss),nhpb
-      common /restraints/ weidis
-      common /links_split/ link_start,link_end

diff --git a/source/cluster/wham/src/Makefile-MPI-INTEL b/source/cluster/wham/src/Makefile-MPI-INTEL
deleted file mode 100644 (file)
index ff2c438..0000000
--- a/source/cluster/wham/src/Makefile-MPI-INTEL
+++ /dev/null
@@ -1,33 +0,0 @@
-INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
-BIN=/users/adam/ZSCOREZ/bin
-FC = ifort
-OPT = -O3 -ip -w
-#OPT = -CB -g 
-FFLAGS =  ${OPT} -c -I. -I../src_MD_T-sccor/include_unres -I../src_MD_T-sccor -I/users/adam/MEY_MD/src_Tc-czarek -I$(INSTALL_DIR)/include
-CPPFLAGS = -DLINUX -DPGI -DSPLITELE -DPROCOR -DMP -DMPI
-LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a -g -d2 -CA -CB
-
-.c.o:
-       cc -c -DLINUX -DPGI $*.c
-
-.f.o:
-       ${FC} ${FFLAGS} $*.f
-
-.F.o:
-       ${FC} ${FFLAGS} ${CPPFLAGS} ${FFLAGS} $*.F
-
-objects = main_clust.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
-       matmult.o readrtns.o pinorm.o rescode.o intcor.o timing.o misc.o \
-       geomout.o readpdb.o read_coords.o parmread.o probabl.o fitsq.o hc.o  \
-       track.o wrtclust.o srtclust.o noyes.o contact.o printmat.o \
-       int_from_cart1.o energy_p_new.o icant.o proc_proc.o work_partition.o \
-       setup_var.o read_ref_str.o
-
-unres_clust: $(objects)
-       $(FC) ${OPT} ${objects} ${LIBS} -o ${BIN}/unres_clustMD_MPI-oldparm
-
-clean:
-       /bin/rm *.o
-
-move:
-       mv *.o ${OBJ}

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diff --git a/source/wham/src/Makefile1_matrix b/source/wham/src/Makefile1_matrix
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+++ /dev/null
@@ -1,73 +0,0 @@
-INSTALL_DIR = /usr/local/mpich-1.2.7p1_pgi64-6.2-3_ssh
-BIN = ./
-CC = cc
-FC = pgf90
-#FC = ifc
-OPT = -mcmodel=medium -Mlarge_arrays -fast -pc 64 -tp amd64
-#OPT = -mcmodel=medium -Mlarge_arrays -tp amd64
-#FFLAGS =  ${OPT} -g -c -I. -I../src_MD -I/users/adam/UNRES/NEW/src -I$(INSTALL_DIR)/include
-#FFLAGS =  ${OPT} -c -C -g -I. -I../src_MD -I/users/adam/UNRES/NEW/src -I$(INSTALL_DIR)/include
-#FFLAGS = ${OPT} -c -I. -I/users/adam/ZSCOREZ/src_MD -I/users/adam/UNRES/NEW/src -I$(INSTALL_DIR)/include
-FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include
-LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich
-#LIBS = -L$(INSTALL_DIR)/lib_pgi -lmpich -lpmpich -Vaxlib
-#CPPFLAGS = -DMPI -DLINUX -DUNRES -DMOMENT -DCHECKGRAD -DPGI
-#CPPFLAGS = -DMPI -DLINUX -DUNRES -DCHECKGRAD -DPGI -DMYGETENV
-CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI
-#CPPFLAGS = -DMPI -DLINUX -DUNRES -DPGI
-#CPPFLAGS = -DMPI -DLINUX -DUNRES
-
-.f.o:
-       ${FC} ${FFLAGS} $*.f
-
-.F.o:
-       ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
-
-all: make_dbase
-
-objects = \
-       wham_multparm.o \
-       enecalc1.o \
-       energy_p_new.o \
-       initialize_p.o \
-       molread_zs.o \
-       openunits.o \
-       readrtns.o \
-       arcos.o \
-       cartder.o \
-       cartprint.o \
-       chainbuild.o \
-       geomout.o \
-       icant.o \
-       intcor.o \
-       int_from_cart.o \
-       make_ensemble1.o \
-       matmult.o \
-       misc.o \
-       mygetenv.o \
-       parmread.o \
-       pinorm.o \
-       printmat.o \
-       proc_proc.o \
-       rescode.o \
-       setup_var.o \
-       store_parm.o \
-       timing.o \
-       wham_calc1.o
-
-objects_compar = \
-        readrtns_compar.o \
-        readpdb.o fitsq.o contact.o \
-        elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \
-        angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \
-        rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o
-
-make_dbase: ${objects} ${objects_compar}
-       cc -o compinfo compinfo.c
-       ./compinfo
-       ${FC} -c ${FFLAGS} cinfo.f
-       $(FC) ${OPT} -Wl,-Bstatic ${objects} ${objects_compar} cinfo.o \
-       ${LIBS} -o ${BIN}/wham_multparm1-OPTERON-T__
-
-clean:
-       /bin/rm *.o

diff --git a/source/wham/src/Makefile_matrix-oldparm b/source/wham/src/Makefile_matrix-oldparm
deleted file mode 100644 (file)
index 97240fb..0000000
--- a/source/wham/src/Makefile_matrix-oldparm
+++ /dev/null
@@ -1,68 +0,0 @@
-INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
-BIN = ../bin
-FC= ifort
-#OPT = -mcmodel=medium -O3 -ip -w
-OPT = -mcmodel=medium -g -CB
-FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include
-LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xdrf/libxdrf.a
-CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 \
-       -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
-
-.f.o:
-       ${FC} ${FFLAGS} $*.f
-
-.F.o:
-       ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
-
-all: make_dbase
-
-objects = \
-       wham_multparm.o \
-       bxread.o \
-       xread.o \
-       cxread.o \
-       enecalc1.o \
-       energy_p_new.o \
-       initialize_p.o \
-       molread_zs.o \
-       openunits.o \
-       readrtns.o \
-       arcos.o \
-       cartder.o \
-       cartprint.o \
-       chainbuild.o \
-       geomout.o \
-       icant.o \
-       intcor.o \
-       int_from_cart.o \
-       make_ensemble1.o \
-       matmult.o \
-       misc.o \
-       mygetenv.o \
-       parmread.o \
-       pinorm.o \
-       printmat.o \
-       proc_proc.o \
-       rescode.o \
-       setup_var.o \
-       slices.o \
-       store_parm.o \
-       timing.o \
-       wham_calc1.o
-
-objects_compar = \
-        readrtns_compar.o \
-        readpdb.o fitsq.o contact.o \
-        elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \
-        angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \
-        rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o
-
-make_dbase: ${objects} ${objects_compar}
-       cc -o compinfo compinfo.c
-       ./compinfo
-       ${FC} -c ${FFLAGS} cinfo.f
-       $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
-       ${LIBS} -static-intel -o ${BIN}/wham_multparm-ham_rep-oldparm
-
-clean:
-       /bin/rm *.o

diff --git a/source/wham/src/compinfo b/source/wham/src/compinfo
deleted file mode 100755 (executable)
index a9d3c1d..0000000
Binary files a/source/wham/src/compinfo and /dev/null differ

diff --git a/source/wham/src/xdrf/ftocstr.o b/source/wham/src/xdrf/ftocstr.o
deleted file mode 100644 (file)
index c032adf..0000000
Binary files a/source/wham/src/xdrf/ftocstr.o and /dev/null differ

diff --git a/source/wham/src/xdrf/libxdrf.a b/source/wham/src/xdrf/libxdrf.a
deleted file mode 100644 (file)
index 95d935f..0000000
Binary files a/source/wham/src/xdrf/libxdrf.a and /dev/null differ

diff --git a/source/wham/src/xdrf/libxdrf.o b/source/wham/src/xdrf/libxdrf.o
deleted file mode 100644 (file)
index 4d44318..0000000
Binary files a/source/wham/src/xdrf/libxdrf.o and /dev/null differ