Moved grompp from src/kernel/ to src/programs/grompp/.

Functions related to topology IO where moved to
src/gromacs/gmxpreprocess/ because they were also referenced by pdb2gmx.

IssueID #637

diff --git a/src/kernel/add_par.c b/src/gromacs/gmxpreprocess/add_par.c
similarity index 100%
rename from src/kernel/add_par.c
rename to src/gromacs/gmxpreprocess/add_par.c

diff --git a/src/kernel/add_par.h b/src/gromacs/gmxpreprocess/add_par.h
similarity index 100%
rename from src/kernel/add_par.h
rename to src/gromacs/gmxpreprocess/add_par.h

diff --git a/src/kernel/gpp_atomtype.c b/src/gromacs/gmxpreprocess/gpp_atomtype.c
similarity index 100%
rename from src/kernel/gpp_atomtype.c
rename to src/gromacs/gmxpreprocess/gpp_atomtype.c

diff --git a/src/kernel/gpp_bond_atomtype.c b/src/gromacs/gmxpreprocess/gpp_bond_atomtype.c
similarity index 100%
rename from src/kernel/gpp_bond_atomtype.c
rename to src/gromacs/gmxpreprocess/gpp_bond_atomtype.c

diff --git a/src/kernel/gpp_bond_atomtype.h b/src/gromacs/gmxpreprocess/gpp_bond_atomtype.h
similarity index 100%
rename from src/kernel/gpp_bond_atomtype.h
rename to src/gromacs/gmxpreprocess/gpp_bond_atomtype.h

diff --git a/src/kernel/readir.c b/src/gromacs/gmxpreprocess/readir.c
similarity index 100%
rename from src/kernel/readir.c
rename to src/gromacs/gmxpreprocess/readir.c

diff --git a/src/kernel/readir.h b/src/gromacs/gmxpreprocess/readir.h
similarity index 100%
rename from src/kernel/readir.h
rename to src/gromacs/gmxpreprocess/readir.h

diff --git a/src/kernel/readpull.c b/src/gromacs/gmxpreprocess/readpull.c
similarity index 100%
rename from src/kernel/readpull.c
rename to src/gromacs/gmxpreprocess/readpull.c

diff --git a/src/kernel/readrot.c b/src/gromacs/gmxpreprocess/readrot.c
similarity index 100%
rename from src/kernel/readrot.c
rename to src/gromacs/gmxpreprocess/readrot.c

diff --git a/src/kernel/topdirs.c b/src/gromacs/gmxpreprocess/topdirs.c
similarity index 100%
rename from src/kernel/topdirs.c
rename to src/gromacs/gmxpreprocess/topdirs.c

diff --git a/src/kernel/topdirs.h b/src/gromacs/gmxpreprocess/topdirs.h
similarity index 100%
rename from src/kernel/topdirs.h
rename to src/gromacs/gmxpreprocess/topdirs.h

diff --git a/src/kernel/topexcl.c b/src/gromacs/gmxpreprocess/topexcl.c
similarity index 100%
rename from src/kernel/topexcl.c
rename to src/gromacs/gmxpreprocess/topexcl.c

diff --git a/src/kernel/topexcl.h b/src/gromacs/gmxpreprocess/topexcl.h
similarity index 100%
rename from src/kernel/topexcl.h
rename to src/gromacs/gmxpreprocess/topexcl.h

diff --git a/src/kernel/topio.c b/src/gromacs/gmxpreprocess/topio.c
similarity index 100%
rename from src/kernel/topio.c
rename to src/gromacs/gmxpreprocess/topio.c

diff --git a/src/kernel/topio.h b/src/gromacs/gmxpreprocess/topio.h
similarity index 100%
rename from src/kernel/topio.h
rename to src/gromacs/gmxpreprocess/topio.h

diff --git a/src/kernel/toppush.c b/src/gromacs/gmxpreprocess/toppush.c
similarity index 100%
rename from src/kernel/toppush.c
rename to src/gromacs/gmxpreprocess/toppush.c

diff --git a/src/kernel/toppush.h b/src/gromacs/gmxpreprocess/toppush.h
similarity index 100%
rename from src/kernel/toppush.h
rename to src/gromacs/gmxpreprocess/toppush.h

diff --git a/src/kernel/topshake.c b/src/gromacs/gmxpreprocess/topshake.c
similarity index 100%
rename from src/kernel/topshake.c
rename to src/gromacs/gmxpreprocess/topshake.c

diff --git a/src/kernel/topshake.h b/src/gromacs/gmxpreprocess/topshake.h
similarity index 100%
rename from src/kernel/topshake.h
rename to src/gromacs/gmxpreprocess/topshake.h

diff --git a/src/kernel/toputil.c b/src/gromacs/gmxpreprocess/toputil.c
similarity index 100%
rename from src/kernel/toputil.c
rename to src/gromacs/gmxpreprocess/toputil.c

diff --git a/src/kernel/vsite_parm.c b/src/gromacs/gmxpreprocess/vsite_parm.c
similarity index 100%
rename from src/kernel/vsite_parm.c
rename to src/gromacs/gmxpreprocess/vsite_parm.c

diff --git a/src/kernel/vsite_parm.h b/src/gromacs/gmxpreprocess/vsite_parm.h
similarity index 100%
rename from src/kernel/vsite_parm.h
rename to src/gromacs/gmxpreprocess/vsite_parm.h

diff --git a/src/kernel/CMakeLists.txt b/src/kernel/CMakeLists.txt
index 913489e6e775f7dcbfd4f635a587a3bc68533a99..c045ff2b8def61daa404615e8ca74883b64f07e9 100644 (file)
--- a/src/kernel/CMakeLists.txt
+++ b/src/kernel/CMakeLists.txt
@@ -1,35 +1,20 @@
 include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/gmxpreprocess)
 
 set(GMXPREPROCESS_SOURCES 
-    add_par.c       
-    convparm.c      
     gen_ad.c        
     gen_vsite.c     
     genhydro.c   
-    gpp_atomtype.c  
-    gpp_bond_atomtype.c     
     h_db.c          
     hackblock.c             
     hizzie.c        
     nm2type.c
     pdb2top.c       
     pgutil.c        
-    readir.c
-    readpull.c      
-    readrot.c
     resall.c        
     sorting.c       
     specbond.c      
     ter_db.c        
-    tomorse.c       
-    topdirs.c       
-    topexcl.c       
-    topio.c         
-    toppush.c       
-    topshake.c      
-    toputil.c       
     tpbcmp.c        
-    vsite_parm.c    
     fflibutil.c
     xlate.c)
 
@@ -41,10 +26,6 @@ if(NOT GMX_FAHCORE)
 
 list(APPEND GMX_EXTRA_LIBRARIES gmxpreprocess libgromacs)
 
-add_executable(grompp grompp.c)
-target_link_libraries(grompp ${GMX_EXTRA_LIBRARIES})
-set_target_properties(grompp PROPERTIES OUTPUT_NAME "grompp${GMX_BINARY_SUFFIX}")
-
 add_executable(tpbconv tpbconv.c)
 target_link_libraries(tpbconv ${GMX_EXTRA_LIBRARIES})
 set_target_properties(tpbconv PROPERTIES OUTPUT_NAME "tpbconv${GMX_BINARY_SUFFIX}")
@@ -75,7 +56,6 @@ set_target_properties(gmxcheck PROPERTIES OUTPUT_NAME "gmxcheck${GMX_BINARY_SUFF
 
 install(TARGETS gmxpreprocess DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries)
 install(TARGETS 
-        grompp
         tpbconv
         pdb2gmx
         g_protonate

diff --git a/src/programs/CMakeLists.txt b/src/programs/CMakeLists.txt
index b1c174f40c86abbe526eb751f0938a818e018333..d2f0dd28919566f6bfceff78445cabb6d6e96f8a 100644 (file)
--- a/src/programs/CMakeLists.txt
+++ b/src/programs/CMakeLists.txt
@@ -1,2 +1,5 @@
-add_subdirectory(g_ana)
 add_subdirectory(mdrun)
+if (NOT GMX_FAHCORE)
+    add_subdirectory(g_ana)
+    add_subdirectory(grompp)
+endif (NOT GMX_FAHCORE)

diff --git a/src/programs/grompp/CMakeLists.txt b/src/programs/grompp/CMakeLists.txt
new file mode 100644 (file)
index 0000000..70869e4
--- /dev/null
+++ b/src/programs/grompp/CMakeLists.txt
@@ -0,0 +1,8 @@
+include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/gmxpreprocess)
+
+file(GLOB GROMPP_SOURCES *.c)
+
+add_executable(grompp ${GROMPP_SOURCES})
+target_link_libraries(grompp ${GMX_EXTRA_LIBRARIES} libgromacs)
+set_target_properties(grompp PROPERTIES OUTPUT_NAME "grompp${GMX_BINARY_SUFFIX}")
+install(TARGETS grompp DESTINATION ${BIN_INSTALL_DIR} COMPONENT runtime)

diff --git a/src/kernel/convparm.c b/src/programs/grompp/convparm.c
similarity index 100%
rename from src/kernel/convparm.c
rename to src/programs/grompp/convparm.c

diff --git a/src/kernel/convparm.h b/src/programs/grompp/convparm.h
similarity index 100%
rename from src/kernel/convparm.h
rename to src/programs/grompp/convparm.h

diff --git a/src/kernel/gpp_tomorse.h b/src/programs/grompp/gpp_tomorse.h
similarity index 100%
rename from src/kernel/gpp_tomorse.h
rename to src/programs/grompp/gpp_tomorse.h

diff --git a/src/kernel/grompp.c b/src/programs/grompp/grompp.c
similarity index 100%
rename from src/kernel/grompp.c
rename to src/programs/grompp/grompp.c

diff --git a/src/kernel/tomorse.c b/src/programs/grompp/tomorse.c
similarity index 100%
rename from src/kernel/tomorse.c
rename to src/programs/grompp/tomorse.c