Merge release-4-5-patches into release-4-6

Changes in 4.5 for removed lines/files in 4.6:
	Makefile.am
	include/domdec.h
	include/domdec_network.h

Trivial conflict:
	include/types/commrec.h

Fixed GMX_THREADS into GMX_THREAD_MPI for those added in 4.5 in:
        include/mdrun.h
        src/gmxlib/shift_util.c
        src/mdlib/gmx_fft_fftw3.c

Change-Id: Id37bfbbacc945a7cf184fa21313c05e2680e1fba

diff --cc include/mdrun.h
index 2c40e49627e4d9b9f06646e80ab75c51e0f59221,6703169339683ee204b6167be43639e06b8e0b4e..81080968bae7bdf6798dcfe09150d7ecf1963866
--- 1/include/mdrun.h
--- 2/include/mdrun.h
+++ b/include/mdrun.h
@@@ -51,6 -51,11 +51,11 @@@
  #include "pull.h"
  #include "update.h"
  
 -#ifdef GMX_THREADS
+ 
++#ifdef GMX_THREAD_MPI
+ #include "thread_mpi/threads.h"
+ #endif
+ 
  #ifdef __cplusplus
  extern "C" {
  #endif

diff --cc include/types/commrec.h
index 1b30788441e6c5fbb08a833eeb583bf69f60679c,8201cf8c44730183d73be42e2d05275ceac5aa73..0d2fce9813e544359fab0a5e5574d324293378db
--- 1/include/types/commrec.h
--- 2/include/types/commrec.h
+++ b/include/types/commrec.h
@@@ -38,8 -38,9 +38,9 @@@
  #ifdef GMX_LIB_MPI
  #include <mpi.h>
  #else
 -#ifdef GMX_THREADS
 +#ifdef GMX_THREAD_MPI
- #include "../tmpi.h"
+ #include "../thread_mpi/tmpi.h"
+ #include "../thread_mpi/mpi_bindings.h"
  #else
  typedef void* MPI_Comm;
  typedef void* MPI_Request;

diff --cc src/gmxlib/shift_util.c
index 449e4d6fcff5bdacfba5acfc070fb478978eda47,43c3d20c91b76e5632df03a74d500e086657b48b..9df8e3dc53c1b7cb29d51ad857201a2de719edb5
--- 1/src/gmxlib/shift_util.c
--- 2/src/gmxlib/shift_util.c
+++ b/src/gmxlib/shift_util.c
@@@ -49,10 -49,11 +49,10 @@@
  #include "writeps.h"
  #include "macros.h"
  #include "xvgr.h"
 -#include "pppm.h"
  #include "gmxfio.h"
  
--#ifdef GMX_THREADS
- #include "thread_mpi.h"
++#ifdef GMX_THREAD_MPI
+ #include "thread_mpi/threads.h"
  #endif
  
  #define p2(x) ((x)*(x))

diff --cc src/gmxlib/tpxio.c
Simple merge

diff --cc src/kernel/md.c
Simple merge

diff --cc src/mdlib/CMakeLists.txt
index e50df463730959b3ce676f2b254e7193d9275fe8,b717496c17c0c57845b9f71324e6ecb0eb7e476d..50c249f1b33f10654509c5faa26ebae728a80e51
--- 1/src/mdlib/CMakeLists.txt
--- 2/src/mdlib/CMakeLists.txt
+++ b/src/mdlib/CMakeLists.txt
@@@ -3,7 -3,13 +3,11 @@@ file(GLOB MDLIB_SOURCES *.c
  
  # Files       called xxx_test.c are test drivers with a main() function for 
  # module xxx.c, so they should not be included in the library
 -file(GLOB_RECURSE NOT_MDLIB_SOURCES *_test.c *\#*)
 -list(REMOVE_ITEM MDLIB_SOURCES ${NOT_MDLIB_SOURCES})
  
+ if(NOT GMX_FFT_FFTPACK)
+ list(REMOVE_ITEM MDLIB_SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/fftpack.c)
+ endif()
+ 
  add_library(md ${MDLIB_SOURCES})
  target_link_libraries(md gmx ${GMX_EXTRA_LIBRARIES} ${FFT_LIBRARIES} ${XML_LIBRARIES})
  set_target_properties(md PROPERTIES OUTPUT_NAME "md${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}")

diff --cc src/mdlib/gmx_fft_fftw3.c
index c7b8c4c2f34085f7956e20b8a31039f5a68d6436,396b201e43fb05682b9e18da0961a4936e643fe2..f63d140fdf7eec544ba91ef07137ac741505e472
--- 1/src/mdlib/gmx_fft_fftw3.c
--- 2/src/mdlib/gmx_fft_fftw3.c
+++ b/src/mdlib/gmx_fft_fftw3.c
@@@ -35,9 -35,12 +35,12 @@@
  #define FFTWPREFIX(name) fftwf_ ## name
  #endif
  
 -#ifdef GMX_THREADS
++#ifdef GMX_THREAD_MPI
+ #include "thread_mpi/threads.h"
+ #endif
  
  
 -#ifdef GMX_THREADS
 +#ifdef GMX_THREAD_MPI
  /* none of the fftw3 calls, except execute(), are thread-safe, so 
     we need to serialize them with this mutex. */
  static tMPI_Thread_mutex_t big_fftw_mutex=TMPI_THREAD_MUTEX_INITIALIZER;

diff --cc src/tools/gmx_anaeig.c
Simple merge

diff --cc src/tools/gmx_density.c
Simple merge

diff --cc src/tools/gmx_editconf.c
Simple merge