Merge branch 'devel' into adam

Conflicts:
	bin/wham/wham_ifort_MPICH_GAB.exe
	source/cluster/wham/src/Makefile
	source/unres/src_MD/cinfo.f
	source/wham/src/cinfo.f

diff --git a/bin/unres_clustMD_MPI-oldparm b/bin/unres_clustMD_MPI-oldparm
new file mode 100755 (executable)
index 0000000..da1ec02
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diff --git a/bin/wham/wham_ifort_MPICH_GAB.exe b/bin/wham/wham_ifort_MPICH_GAB.exe
deleted file mode 100755 (executable)
index dcab164..0000000
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diff --git a/source/cluster/wham/src-M/arcos.o b/source/cluster/wham/src-M/arcos.o
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index 39795ca..0000000
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diff --git a/source/cluster/wham/src-M/cartprint.o b/source/cluster/wham/src-M/cartprint.o
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diff --git a/source/cluster/wham/src-M/chainbuild.o b/source/cluster/wham/src-M/chainbuild.o
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diff --git a/source/cluster/wham/src-M/contact.o b/source/cluster/wham/src-M/contact.o
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diff --git a/source/cluster/wham/src-M/convert.o b/source/cluster/wham/src-M/convert.o
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diff --git a/source/cluster/wham/src-M/energy_p_new.o b/source/cluster/wham/src-M/energy_p_new.o
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diff --git a/source/cluster/wham/src-M/gnmr1.o b/source/cluster/wham/src-M/gnmr1.o
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diff --git a/source/cluster/wham/src-M/hc.o b/source/cluster/wham/src-M/hc.o
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diff --git a/source/cluster/wham/src-M/icant.o b/source/cluster/wham/src-M/icant.o
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index bc7c902..0000000
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diff --git a/source/cluster/wham/src-M/initialize_p.o b/source/cluster/wham/src-M/initialize_p.o
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index 9115499..0000000
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diff --git a/source/cluster/wham/src-M/int_from_cart1.o b/source/cluster/wham/src-M/int_from_cart1.o
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diff --git a/source/cluster/wham/src-M/intcor.o b/source/cluster/wham/src-M/intcor.o
deleted file mode 100644 (file)
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diff --git a/source/cluster/wham/src-M/main_clust.o b/source/cluster/wham/src-M/main_clust.o
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index 78c2d48..0000000
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diff --git a/source/cluster/wham/src-M/matmult.o b/source/cluster/wham/src-M/matmult.o
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index f896532..0000000
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diff --git a/source/cluster/wham/src-M/misc.o b/source/cluster/wham/src-M/misc.o
deleted file mode 100644 (file)
index 031e467..0000000
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diff --git a/source/cluster/wham/src-M/noyes.o b/source/cluster/wham/src-M/noyes.o
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diff --git a/source/cluster/wham/src-M/parmread.o b/source/cluster/wham/src-M/parmread.o
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diff --git a/source/cluster/wham/src-M/permut.o b/source/cluster/wham/src-M/permut.o
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diff --git a/source/cluster/wham/src-M/pinorm.o b/source/cluster/wham/src-M/pinorm.o
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diff --git a/source/cluster/wham/src-M/printmat.o b/source/cluster/wham/src-M/printmat.o
deleted file mode 100644 (file)
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diff --git a/source/cluster/wham/src-M/probabl.o b/source/cluster/wham/src-M/probabl.o
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diff --git a/source/cluster/wham/src-M/proc_proc.o b/source/cluster/wham/src-M/proc_proc.o
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index a38ab2d..0000000
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diff --git a/source/cluster/wham/src-M/read_coords.o b/source/cluster/wham/src-M/read_coords.o
deleted file mode 100644 (file)
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diff --git a/source/cluster/wham/src-M/read_ref_str.o b/source/cluster/wham/src-M/read_ref_str.o
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diff --git a/source/cluster/wham/src-M/readpdb.o b/source/cluster/wham/src-M/readpdb.o
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diff --git a/source/cluster/wham/src-M/readrtns.o b/source/cluster/wham/src-M/readrtns.o
deleted file mode 100644 (file)
index eb4181e..0000000
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diff --git a/source/cluster/wham/src-M/rescode.o b/source/cluster/wham/src-M/rescode.o
deleted file mode 100644 (file)
index cc3968c..0000000
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diff --git a/source/cluster/wham/src-M/setup_var.o b/source/cluster/wham/src-M/setup_var.o
deleted file mode 100644 (file)
index 2d1f1c0..0000000
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diff --git a/source/cluster/wham/src-M/srtclust.o b/source/cluster/wham/src-M/srtclust.o
deleted file mode 100644 (file)
index dbc19a7..0000000
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diff --git a/source/cluster/wham/src-M/timing.o b/source/cluster/wham/src-M/timing.o
deleted file mode 100644 (file)
index 2386806..0000000
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diff --git a/source/cluster/wham/src-M/track.o b/source/cluster/wham/src-M/track.o
deleted file mode 100644 (file)
index 7cab1bf..0000000
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diff --git a/source/cluster/wham/src-M/work_partition.o b/source/cluster/wham/src-M/work_partition.o
deleted file mode 100644 (file)
index d5dfb8b..0000000
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diff --git a/source/cluster/wham/src-M/wrtclust.o b/source/cluster/wham/src-M/wrtclust.o
deleted file mode 100644 (file)
index 2289bf1..0000000
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diff --git a/source/cluster/wham/src-M/xdrf/ftocstr.o b/source/cluster/wham/src-M/xdrf/ftocstr.o
deleted file mode 100644 (file)
index f0102ea..0000000
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diff --git a/source/cluster/wham/src-M/xdrf/libxdrf.a b/source/cluster/wham/src-M/xdrf/libxdrf.a
deleted file mode 100644 (file)
index 755f9e6..0000000
Binary files a/source/cluster/wham/src-M/xdrf/libxdrf.a and /dev/null differ

diff --git a/source/cluster/wham/src-M/xdrf/libxdrf.o b/source/cluster/wham/src-M/xdrf/libxdrf.o
deleted file mode 100644 (file)
index 1f81ca3..0000000
Binary files a/source/cluster/wham/src-M/xdrf/libxdrf.o and /dev/null differ

diff --git a/source/cluster/wham/src/Makefile b/source/cluster/wham/src/Makefile
index 333ebec..b192a7b 100644 (file)
--- a/source/cluster/wham/src/Makefile
+++ b/source/cluster/wham/src/Makefile
@@ -3,9 +3,15 @@ BIN=../../../../bin
 FC = ifort
 OPT = -O3 -ip -w
 OPT = -CB -g 
+<<<<<<< HEAD
+FFLAGS =  ${OPT} -c -I. -Iinclude_unres -I$(INSTALL_DIR)/include
+CPPFLAGS = -DLINUX -DPGI -DSPLITELE -DPROCOR -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DMP -DMPI
+LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a -g -d2 -CA -CB
+=======
 FFLAGS =  ${OPT} -c -I. -I./include_unres -I../src_MD_T-sccor -I/users/adam/MEY_MD/src_Tc-czarek -I$(INSTALL_DIR)/include
 CPPFLAGS = -DLINUX -DPGI -DSPLITELE -DPROCOR -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DMP -DMPI
 LIBS = -L$(INSTALL_DIR)/lib -lmpich ./xdrf/libxdrf.a -g -d2 -CA -CB
+>>>>>>> devel
 
 .c.o:
        cc -c -DLINUX -DPGI $*.c

diff --git a/source/unres/src_MD/Makefile_MPICH_ifort b/source/unres/src_MD/Makefile_MPICH_ifort
index 4505541..5af741c 100644 (file)
--- 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.exe
+E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_E0LL2Y-test.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
new file mode 100644 (file)
index 0000000..71fc6a6
--- /dev/null
+++ b/source/unres/src_MD/cinfo.f
@@ -0,0 +1,31 @@
+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/wham/src/DIMENSIONS.FREE b/source/wham/src/DIMENSIONS.FREE
index 1c483ee..a2eb4e5 100644 (file)
--- a/source/wham/src/DIMENSIONS.FREE
+++ b/source/wham/src/DIMENSIONS.FREE
@@ -3,7 +3,7 @@
       integer MaxR,MaxT_h
       integer MaxSlice
       parameter (Max_Parm=128)
-      parameter (MaxQ=1,MaxQ1=MaxQ+2)
+      parameter (MaxQ=4,MaxQ1=MaxQ+2)
       parameter(MaxR=1,MaxT_h=32)
       parameter(MaxSlice=40)
       integer MaxN

diff --git a/source/wham/src/Makefile_MPICH_ifort b/source/wham/src/Makefile_MPICH_ifort
index 0635d4d..2a95ca8 100644 (file)
--- a/source/wham/src/Makefile_MPICH_ifort
+++ b/source/wham/src/Makefile_MPICH_ifort
@@ -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.exe
+       ${LIBS} -static-intel -o ${BIN}/wham_ifort_MPICH_E0LL2Y-debug.exe
 
 xdrf/libxdrf.a:
        cd xdrf && make

diff --git a/source/wham/src/cinfo.f b/source/wham/src/cinfo.f
deleted file mode 100644 (file)
index 82c48ab..0000000
--- a/source/wham/src/cinfo.f
+++ /dev/null
@@ -1,62 +0,0 @@
-C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 0 4196011 2
-      subroutine cinfo
-      include 'COMMON.IOUNITS'
-      write(iout,*)'++++ Compile info ++++'
-      write(iout,*)'Version 0.4196011 build 2'
-      write(iout,*)'compiled Wed Jul 18 05:59:41 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,*)'BIN = ../../../bin/wham'
-      write(iout,*)'FC= ifort'
-      write(iout,*)'OPT = -mcmodel=medium -O3 -ip -w'
-      write(iout,*)'FFLAGS = ${OPT} -c -I. -I./include_unres -I$(IN...'
-      write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xd...'
-      write(iout,*)'objects = \\'
-      write(iout,*)'   wham_multparm.o \\'
-      write(iout,*)'   bxread.o \\'
-      write(iout,*)'   xread.o \\'
-      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,*)'   arcos.o \\'
-      write(iout,*)'   cartder.o \\'
-      write(iout,*)'   cartprint.o \\'
-      write(iout,*)'   chainbuild.o \\'
-      write(iout,*)'   geomout.o \\'
-      write(iout,*)'   icant.o \\'
-      write(iout,*)'   intcor.o \\'
-      write(iout,*)'   int_from_cart.o \\'
-      write(iout,*)'   make_ensemble1.o \\'
-      write(iout,*)'   matmult.o \\'
-      write(iout,*)'   misc.o \\'
-      write(iout,*)'   mygetenv.o \\'
-      write(iout,*)'   parmread.o \\'
-      write(iout,*)'   pinorm.o \\'
-      write(iout,*)'   printmat.o \\'
-      write(iout,*)'   proc_proc.o \\'
-      write(iout,*)'   rescode.o \\'
-      write(iout,*)'   setup_var.o \\'
-      write(iout,*)'   slices.o \\'
-      write(iout,*)'   store_parm.o \\'
-      write(iout,*)'   timing.o \\'
-      write(iout,*)'   wham_calc1.o'
-      write(iout,*)'objects_compar = \\'
-      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