Set up cmake for physpack (do not build by default)

fastlib/branches/fastlib-cmake/CMakeLists.txt

@@ -32,3 +32,4 @@ set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib/)
 add_subdirectory(src) # fastlib
 add_subdirectory(mlpack) # mlpack
 add_subdirectory(contrib) # mlpack_contrib
+#add_subdirectory(physpack) # physpack  ## do not build by default

fastlib/branches/fastlib-cmake/physpack/CMakeLists.txt

@@ -0,0 +1,49 @@
+cmake_minimum_required(VERSION 2.8)
+project(MLPACK_CONTRIB C CXX Fortran)
+
+# compiler flags
+set(CMAKE_CXX_FLAGS "-g -Wall")
+add_definitions(-DDISABLE_DISK_MATRIX)
+
+# include directories
+include_directories(..)
+include_directories(../include)
+
+set(PHYSPACK_SRCS)
+
+# now we need to recurse into each of the contrib methods
+set(DIRS
+   mol_dynamics
+)
+
+foreach(dir ${DIRS})
+   add_subdirectory(${dir})
+endforeach()
+
+# PHYSPACK_SRCS is set in the subdirectories above
+add_library(physpack ${PHYSPACK_SRCS})
+add_dependencies(physpack fastlib)
+
+# move header files to the right directory
+file(GLOB_RECURSE INCLUDE_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.h)
+add_custom_command(TARGET physpack POST_BUILD
+   COMMENT "Moving header files to include/physpack/"
+   COMMAND ${CMAKE_COMMAND} ARGS -E make_directory ${CMAKE_BINARY_DIR}/include/physpack/)
+foreach(incl_file ${INCLUDE_FILES})
+   add_custom_command(TARGET mlpack_contrib POST_BUILD
+      COMMAND ${CMAKE_COMMAND} ARGS -E copy ${CMAKE_CURRENT_SOURCE_DIR}/${incl_file} ${CMAKE_BINARY_DIR}/include/physpack/${incl_file})
+endforeach()
+
+# set installation rules for include files
+#install(FILES ${CMAKE_BINARY_DIR}/include/physpack/
+#   DESTINATION include/physpack)
+
+# set installation rules for mlpack_contrib programs
+#install(PROGRAMS ${CMAKE_BINARY_DIR}/bin/
+#   DESTINATION bin)
+
+install(TARGETS physpack
+   RUNTIME DESTINATION bin
+   LIBRARY DESTINATION lib
+   ARCHIVE DESTINATION lib
+)

fastlib/branches/fastlib-cmake/physpack/mol_dynamics/CMakeLists.txt

@@ -0,0 +1,36 @@
+cmake_minimum_required(VERSION 2.8)
+
+# Define the files we need to compile
+# Anything not in this list will not be compiled into the output library
+# Do not include test programs here
+set(SOURCES
+   atom_tree.h
+   lennard_jones.h
+#   test_lennard_jones.h  ## exists in build.py but does not actually exist
+)
+
+# add directory name to sources
+set(DIR_SRCS)
+foreach(file ${SOURCES})
+  set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file})
+endforeach()
+# append sources (with directory name) to list of all PHYSPACK sources (used at the parent scope)
+set(PHYSPACK_SRCS ${PHYSPACK_SRCS} ${DIR_SRCS} PARENT_SCOPE)
+message("mol: ${PHYSPACK_SRCS}")
+
+add_executable(lennard_jones
+   LennardJones_main.cc
+)
+target_link_libraries(lennard_jones
+   physpack
+   fastlib
+)
+
+# Exists in build.py but does not actually exist
+#add_executable(lennard_jones_test
+#   test_lennard_jones.cc
+#)
+#target_link_libraries(lennard_jones_test
+#   physpack
+#   fastlib
+#)