Implement minor changes on branch adam

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
index 3b52754..d83f6f7 100755 (executable)
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diff --git a/source/cluster/wham/src-M/arcos.o b/source/cluster/wham/src-M/arcos.o
deleted file mode 100644 (file)
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
deleted file mode 100644 (file)
index 5094de3..0000000
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diff --git a/source/cluster/wham/src-M/chainbuild.o b/source/cluster/wham/src-M/chainbuild.o
deleted file mode 100644 (file)
index 91e249f..0000000
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diff --git a/source/cluster/wham/src-M/contact.o b/source/cluster/wham/src-M/contact.o
deleted file mode 100644 (file)
index 07d23b9..0000000
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diff --git a/source/cluster/wham/src-M/convert.o b/source/cluster/wham/src-M/convert.o
deleted file mode 100644 (file)
index 62c02ae..0000000
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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
deleted file mode 100644 (file)
index 6b5c262..0000000
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diff --git a/source/cluster/wham/src-M/fitsq.o b/source/cluster/wham/src-M/fitsq.o
deleted file mode 100644 (file)
index b6edd7b..0000000
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diff --git a/source/cluster/wham/src-M/geomout.o b/source/cluster/wham/src-M/geomout.o
deleted file mode 100644 (file)
index bfb6f26..0000000
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diff --git a/source/cluster/wham/src-M/gnmr1.o b/source/cluster/wham/src-M/gnmr1.o
deleted file mode 100644 (file)
index e112fd1..0000000
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diff --git a/source/cluster/wham/src-M/hc.o b/source/cluster/wham/src-M/hc.o
deleted file mode 100644 (file)
index ae35516..0000000
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diff --git a/source/cluster/wham/src-M/icant.o b/source/cluster/wham/src-M/icant.o
deleted file mode 100644 (file)
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
deleted file mode 100644 (file)
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
deleted file mode 100644 (file)
index 111cbfe..0000000
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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)
index cfc4e71..0000000
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diff --git a/source/cluster/wham/src-M/main_clust.o b/source/cluster/wham/src-M/main_clust.o
deleted file mode 100644 (file)
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
deleted file mode 100644 (file)
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
deleted file mode 100644 (file)
index e7f70c0..0000000
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diff --git a/source/cluster/wham/src-M/parmread.o b/source/cluster/wham/src-M/parmread.o
deleted file mode 100644 (file)
index 0733796..0000000
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diff --git a/source/cluster/wham/src-M/permut.o b/source/cluster/wham/src-M/permut.o
deleted file mode 100644 (file)
index 3a49989..0000000
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diff --git a/source/cluster/wham/src-M/pinorm.o b/source/cluster/wham/src-M/pinorm.o
deleted file mode 100644 (file)
index b9f7de8..0000000
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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)
index 81bb89a..0000000
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diff --git a/source/cluster/wham/src-M/probabl.o b/source/cluster/wham/src-M/probabl.o
deleted file mode 100644 (file)
index 1cb97cf..0000000
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diff --git a/source/cluster/wham/src-M/proc_proc.o b/source/cluster/wham/src-M/proc_proc.o
deleted file mode 100644 (file)
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)
index 7b8eb30..0000000
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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
deleted file mode 100644 (file)
index 91d152b..0000000
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diff --git a/source/cluster/wham/src-M/readpdb.o b/source/cluster/wham/src-M/readpdb.o
deleted file mode 100644 (file)
index 3ad016d..0000000
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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
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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 2f5d84f..6c9226d 100644 (file)
--- a/source/cluster/wham/src/Makefile
+++ b/source/cluster/wham/src/Makefile
@@ -3,9 +3,9 @@ BIN=../../../../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
+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$(INSTALL_DIR)/lib -lmpich ../../../wham/src/xdrf/libxdrf.a -g -d2 -CA -CB
+LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a -g -d2 -CA -CB
 
 .c.o:
        cc -c -DLINUX -DPGI $*.c
@@ -21,7 +21,7 @@ objects = main_clust.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.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
+       setup_var.o read_ref_str.o gnmr1.o
 
 unres_clust: $(objects)
        $(FC) ${OPT} ${objects} ${LIBS} -o ${BIN}/unres_clustMD_MPI-oldparm

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
index 08263ac..71fc6a6 100644 (file)
--- 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 5 298
+C 2 5 299
       subroutine cinfo
       include 'COMMON.IOUNITS'
       write(iout,*)'++++ Compile info ++++'
-      write(iout,*)'Version 2.5 build 298'
-      write(iout,*)'compiled Thu Jul  5 05:49:13 2012'
+      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 '

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
index ae30211..641b295 100644 (file)
--- a/source/wham/src/cinfo.f
+++ b/source/wham/src/cinfo.f
@@ -1,10 +1,10 @@
 C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 0 0 570
+C 0 0 573
       subroutine cinfo
       include 'COMMON.IOUNITS'
       write(iout,*)'++++ Compile info ++++'
-      write(iout,*)'Version 0.0 build 570'
-      write(iout,*)'compiled Thu Jul  5 03:32:30 2012'
+      write(iout,*)'Version 0.0 build 573'
+      write(iout,*)'compiled Wed Jul 18 03:05:03 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 '
@@ -16,7 +16,7 @@ C 0 0 570
       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$(INSTALL_DIR)/lib -lmpich -lpmpich .....'
+      write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xd...'
       write(iout,*)'objects = \\'
       write(iout,*)'   wham_multparm.o \\'
       write(iout,*)'   bxread.o \\'