Merge branch 'prerelease-3.2.1' into devel

Conflicts:
	.gitignore
	CMakeLists.txt
	source/cluster/wham/src/COMMON.SCCOR
	source/maxlik/src_CSA/CMakeLists.txt
	source/unres/src_CSA_DiL/CMakeLists.txt
	source/unres/src_MD-M/CMakeLists.txt
	source/unres/src_MD-M/Makefile
	source/unres/src_MD-M/energy_p_new_barrier.F
	source/unres/src_MD-M/ssMD.F
	source/unres/src_MD/CMakeLists.txt
	source/unres/src_MIN/CMakeLists.txt
	source/wham/src/DIMENSIONS.FREE
	source/xdrfpdb/src/CMakeLists.txt

diff --cc CMakeLists.txt
Simple merge

diff --cc source/maxlik/src_CSA/CMakeLists.txt
index 82884df,e80d110..a990836
--- 1/source/maxlik/src_CSA/CMakeLists.txt
--- 2/source/maxlik/src_CSA/CMakeLists.txt
+++ b/source/maxlik/src_CSA/CMakeLists.txt
@@@ -52,9 -52,10 +52,11 @@@ set(MAXLIK_SRCS ${MAXLIK_SRC0} 
  #=========================================
  add_executable(MAXLIK ${MAXLIK_SRCS} )
  set_target_properties(MAXLIK PROPERTIES OUTPUT_NAME ${MAXLIK_BIN})
+ set_property(TARGET MAXLIK PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
  
  #=========================================
 -# Install Path
 +# Install maxlik binary (used by "make install")
  #=========================================
+ install(TARGETS MAXLIK DESTINATION ${CMAKE_INSTALL_PREFIX})
  
 +install(TARGETS MAXLIK RUNTIME DESTINATION unrespack/bin)

diff --cc source/unres/src_MD-M/CMakeLists.txt
Simple merge

diff --cc source/unres/src_MD-M/energy_p_new_barrier.F
index 5ad53f1,91046c3..0ba8f26
--- 1/source/unres/src_MD-M/energy_p_new_barrier.F
--- 2/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@@ -4081,12 -4043,12 +4081,18 @@@ cmc        if (ii.gt.nres .and. itype(i
  C 18/07/06 MC: Use the convention that the first nss pairs are SS bonds
          if (.not.dyn_ss .and. i.le.nss) then
  C 15/02/13 CC dynamic SSbond - additional check
++<<<<<<< HEAD
 +         if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
 +     & iabs(itype(jjj)).eq.1) then
++=======
+          if (ii.gt.nres 
+      &       .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then 
++>>>>>>> prerelease-3.2.1
            call ssbond_ene(iii,jjj,eij)
            ehpb=ehpb+2*eij
+          endif
  cd          write (iout,*) "eij",eij
 +         endif
          else
  C Calculate the distance between the two points and its difference from the
  C target distance.

diff --cc source/unres/src_MD-M/readrtns_CSA.F
Simple merge

diff --cc source/unres/src_MD/CMakeLists.txt
index 1c4a879,ea7776c..0cec201
--- 1/source/unres/src_MD/CMakeLists.txt
--- 2/source/unres/src_MD/CMakeLists.txt
+++ b/source/unres/src_MD/CMakeLists.txt
@@@ -350,10 -322,10 +340,10 @@@ FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/
  export POT=GB
  export PREFIX=ala10
  #-----------------------------------------------------------------------------
- UNRES_BIN=./${UNRES_BIN}
+ UNRES_BIN=${CMAKE_BINARY_DIR}/bin/${UNRES_BIN}
  #-----------------------------------------------------------------------------
  DD=${CMAKE_SOURCE_DIR}/PARAM
 -export BONDPAR=$DD/bond.parm
 +export BONDPAR=$DD/${UNRES_BONDPAR}
  export THETPAR=$DD/thetaml.5parm
  export ROTPAR=$DD/scgauss.parm
  export TORPAR=$DD/torsion_631Gdp.parm

diff --cc source/unres/src_MD/COMMON.SCCOR
index 154de36,8de6d3c..7952bd1
--- 1/source/unres/src_MD/COMMON.SCCOR
--- 2/source/unres/src_MD/COMMON.SCCOR
+++ b/source/unres/src_MD/COMMON.SCCOR
@@@ -2,14 -2,10 +2,14 @@@ cc Parameters of the SCCOR ter
        double precision v1sccor,v2sccor,vlor1sccor,
       &                 vlor2sccor,vlor3sccor,gloc_sc,
       &                 dcostau,dsintau,dtauangle,dcosomicron,
-      &                 domicron
+      &                 domicron,v0sccor
        integer nterm_sccor,isccortyp,nsccortyp,nlor_sccor
 -      common/sccor/v1sccor(maxterm_sccor,3,20,20),
 -     &    v2sccor(maxterm_sccor,3,20,20),
 +      common/sccor/v1sccor(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp),
 +     &    v2sccor(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp),
 +     &    v0sccor(maxterm_sccor,-ntyp:ntyp,-ntyp:ntyp),
 +     &    nterm_sccor(-ntyp:ntyp,-ntyp:ntyp),isccortyp(-ntyp:ntyp),
 +     &    nsccortyp,
 +     &    nlor_sccor(-ntyp:ntyp,-ntyp:ntyp),
       &    vlor1sccor(maxterm_sccor,20,20),
       &    vlor2sccor(maxterm_sccor,20,20),
       &    vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,0:maxres2,10),

diff --cc source/unres/src_MD/energy_p_new_barrier.F
Simple merge

diff --cc source/unres/src_MIN/CMakeLists.txt
Simple merge

diff --cc source/wham/src-M/CMakeLists.txt
Simple merge

diff --cc source/wham/src/CMakeLists.txt
index e1c1c1c,e7f990e..d441588
--- 1/source/wham/src/CMakeLists.txt
--- 2/source/wham/src/CMakeLists.txt
+++ b/source/wham/src/CMakeLists.txt
@@@ -94,9 -94,11 +94,11 @@@ set(UNRES_WHAM_PP_SR
  # Set comipiler flags for different sourcefiles  
  #================================================
  if (Fortran_COMPILER_NAME STREQUAL "ifort")
 -  set(FFLAGS0 "-mcmodel=medium -g -CB -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" ) 
 +  set(FFLAGS0 "-mcmodel=large -g -CB -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" ) 
  elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
    set(FFLAGS0 "-std=legacy -g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" ) 
+ else ()
+   set(FFLAGS0 "-g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" )   
  endif (Fortran_COMPILER_NAME STREQUAL "ifort")
  
  

diff --cc source/wham/src/energy_p_new.F
Simple merge

diff --cc source/xdrfpdb/src/CMakeLists.txt
index ac5142d,b4195e5..ba946f4
--- 1/source/xdrfpdb/src/CMakeLists.txt
--- 2/source/xdrfpdb/src/CMakeLists.txt
+++ b/source/xdrfpdb/src/CMakeLists.txt
@@@ -71,9 -71,10 +71,10 @@@ set_property(SOURCE ${UNRES_XDRF_PP_SRC
  
   
  #=========================================
 -# Build the binaries
 +# Build the binaries (used by "make")
  #=========================================
  add_executable(xdrf2pdb   ${UNRES_XDRF_XDRF2PDB_SRC} )
+ set_property(TARGET xdrf2pdb PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
  target_link_libraries( xdrf2pdb xdrf )
  
  add_executable(xdrf2pdb-m ${UNRES_XDRF_XDRF2PDB-M_SRC} )
@@@ -87,15 -91,16 +91,16 @@@ target_link_libraries( xdrf2ang xdrf 
  
  
  #=========================================
- # INSTALL (used by "make install")
+ # Install Path
  #=========================================
- install(TARGETS xdrf2pdb      RUNTIME DESTINATION unrespack/bin)
- install(TARGETS xdrf2pdb-m    RUNTIME DESTINATION unrespack/bin)
- install(TARGETS xdrf2x                RUNTIME DESTINATION unrespack/bin)
- install(TARGETS xdrf2ang      RUNTIME DESTINATION unrespack/bin)
 -install(TARGETS xdrf2pdb DESTINATION ${CMAKE_INSTALL_PREFIX})
 -install(TARGETS xdrf2pdb-m DESTINATION ${CMAKE_INSTALL_PREFIX})
 -install(TARGETS xdrf2x DESTINATION ${CMAKE_INSTALL_PREFIX})
 -install(TARGETS xdrf2ang DESTINATION ${CMAKE_INSTALL_PREFIX})
++install(TARGETS xdrf2pdb      DESTINATION ${CMAKE_INSTALL_PREFIX})
++install(TARGETS xdrf2pdb-m    DESTINATION ${CMAKE_INSTALL_PREFIX})
++install(TARGETS xdrf2x                DESTINATION ${CMAKE_INSTALL_PREFIX})
++install(TARGETS xdrf2ang      DESTINATION ${CMAKE_INSTALL_PREFIX})
+ 
  
  #=========================================
- # TESTS (used by "ctest") 
+ # TESTS
  #=========================================