Merge branch 'adasko' into devel

Dzialajacy D i L aminokwasy dla src_MD
Conflicts:
	bin/unres/MD/unres_ifort_MPICH_GAB.exe
	bin/wham/wham_multparm-ham_rep-oldparm
	source/unres/src_MD/Makefile
	source/unres/src_MD/Makefile_MPICH_ifort
	source/unres/src_MD/cinfo.f
	source/wham/src/Makefile
	source/wham/src/cinfo.f

diff --cc .gitignore
index 8b33225,3204def..3eaac99
--- 1/.gitignore
--- 2/.gitignore
+++ b/.gitignore
@@@ -21,6 -16,6 +21,8 @@@ gradcheck
  mapcheck/
  run/
  sympcheck/
+ bin/unres/MD/unres_ifort_MPICH_GAB_czyt.exe
+ DIL
  compinfo
 +DIL/
 +bin/unres/MD/unres_ifort_MPICH_GAB_czyt.exe

diff --cc bin/unres/MD/unres_ifort_MPICH_GAB.exe
index da4efff,b7cc647..3365b85
Binary files differ

diff --cc source/unres/src_MD/Makefile
index 0000000,8ebb82b..54399d1
mode 000000,100644..100644
--- /dev/null
--- 2/source/unres/src_MD/Makefile
+++ b/source/unres/src_MD/Makefile
@@@ -1,0 -1,124 +1,124 @@@
+ 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 -CB -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\
+         -DSCCORPDB
 -GAB: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_GAB_czyt.exe
++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 --cc source/unres/src_MD/cinfo.f
index 0000000,d3ab9f4..31a0d51
mode 000000,100644..100644
--- /dev/null
--- 2/source/unres/src_MD/cinfo.f
+++ b/source/unres/src_MD/cinfo.f
@@@ -1,0 -1,31 +1,31 @@@
+ C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
 -C 2 5 358
++C 2 5 360
+       subroutine cinfo
+       include 'COMMON.IOUNITS'
+       write(iout,*)'++++ Compile info ++++'
 -      write(iout,*)'Version 2.5 build 358'
 -      write(iout,*)'compiled Wed Jul 11 07:10:02 2012'
++      write(iout,*)'Version 2.5 build 360'
++      write(iout,*)'compiled Tue Jul 17 04:36:51 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,*)'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 -CB -ipo -ipo_obj  -opt_rep...'
+       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 --cc source/wham/src/energy_p_new.F
Simple merge