preparing public version

c_tools/CMakeLists.txt

@@ -0,0 +1,50 @@
+
+include(FindPkgConfig)
+
+pkg_check_modules(CAIROMM cairomm-1.0)
+pkg_check_modules(SIGC sigc++-2.0)
+pkg_check_modules(CAIRO cairo)
+pkg_check_modules(FREETYPE freetype2)
+
+find_path(CAIROMMCONFIG_INCLUDE_PATH NAMES cairommconfig.h HINTS ${CAIROMM_INCLUDE_DIRS})
+find_path(CAIROMM_INCLUDE_PATH NAMES cairomm/cairomm.h HINTS ${CAIROMM_INCLUDE_DIRS})
+find_path(SIGC_INCLUDE_PATH NAMES sigc++/slot.h HINTS ${SIGC_INCLUDE_DIRS})
+find_path(SIGCCONFIG_INCLUDE_PATH NAMES sigc++config.h HINTS ${SIGC_INCLUDE_DIRS})
+find_path(CAIRO_INCLUDE_PATH NAMES cairo.h HINTS ${CAIRO_INCLUDE_DIRS})
+find_path(FREETYPE_INCLUDE_PATH NAMES freetype/config/ftheader.h HINTS ${FREETYPE_INCLUDE_DIRS})
+
+find_library(CAIROMM_LIB NAMES ${CAIROMM_LIBRARIES} HINTS CAIROMM_LIBRARY_DIRS)
+
+IF (CAIROMMCONFIG_INCLUDE_PATH AND CAIROMM_INCLUDE_PATH AND SIGC_INCLUDE_PATH AND SIGCCONFIG_INCLUDE_PATH AND CAIRO_INCLUDE_PATH AND FREETYPE_INCLUDE_PATH AND CAIROMM_LIB)
+
+  SET(CAIRO_FOUND 1)
+  SET(ALL_CAIROMM_LIBS ${CAIROMM_LIB})
+  SET(CAIRO_HEADERS ${CAIROMM_INCLUDE_PATH} 
+    ${CAIROMMCONFIG_INCLUDE_PATH} ${SIGC_INCLUDE_PATH} 
+    ${SIGCCONFIG_INCLUDE_PATH} ${CAIRO_INCLUDE_PATH}
+    ${FREETYPE_INCLUDE_PATH})
+
+ELSE (CAIROMMCONFIG_INCLUDE_PATH AND CAIROMM_INCLUDE_PATH AND SIGC_INCLUDE_PATH AND SIGCCONFIG_INCLUDE_PATH AND CAIRO_INCLUDE_PATH AND FREETYPE_INCLUDE_PATH AND CAIROMM_LIB)
+
+  SET(CAIRO_FOUND 0)
+
+ENDIF (CAIROMMCONFIG_INCLUDE_PATH AND CAIROMM_INCLUDE_PATH AND SIGC_INCLUDE_PATH AND SIGCCONFIG_INCLUDE_PATH AND CAIRO_INCLUDE_PATH AND FREETYPE_INCLUDE_PATH AND CAIROMM_LIB)
+
+SET(ZOB_LIBS zobovTool 
+  ${COSMOTOOL_LIBRARY} ${GSL_LIBRARIES}
+  ${NETCDF_LIBRARIES})
+
+
+include_directories(
+  ${QHULL_INCLUDES}
+  ${HEALPIX_INCLUDE_PATH}
+  ${CMAKE_CURRENT_BINARY_DIR}
+  ${CMAKE_CURRENT_SOURCE_DIR}/libzobov)
+
+
+set(computeAverageDistortion_SRCS computeAverageDistortion.cpp)
+add_genopt(computeAverageDistortion_SRCS computeAverageDistortion.ggo computeAverageDistortion_conf STRUCTNAME Params)
+add_executable(computeAverageDistortion ${computeAverageDistortion_SRCS})
+target_link_libraries(computeAverageDistortion ${ZOB_LIBS})
+
+subdirs(libzobov test mock  stacking visualization analysis zobov2 hod)

c_tools/analysis/CMakeLists.txt

@@ -0,0 +1,6 @@
+include_directories(${CMAKE_CURRENT_BINARY_DIR})
+
+SET(voidOverlap_SRCS voidOverlap.cpp)
+add_genopt(voidOverlap_SRCS voidOverlap.ggo voidOverlap_conf STRUCTNAME voidOverlap_info)
+add_executable(voidOverlap ${voidOverlap_SRCS})
+target_link_libraries(voidOverlap  ${ZOB_LIBS})

c_tools/hod/CMakeLists.txt

@@ -0,0 +1,21 @@
+include_directories(${CMAKE_CURRENT_BINARY_DIR})
+
+SET(hod_SRCS header.c main.c utility.c sigmac.c transfnc.c transfunc_file.c 
+  nonlinear_power_spectrum.c least_squares.c hod_functions.c 
+   xi_matter.c one_halo_rspace.c two_halo_rspace.c 
+  input_params.c dFdx.c mstar.c halo_concentration.c growthfactor.c 
+  halo_mass_conversion.c nfw_transform.c 
+  pair_density.c tasks.c wp_minimization.c 
+  kaiser_distortions.c 
+  tf_eisenstein_hu.c  jeans.c
+  populate_simulation.c test.c
+  dark_matter_statistics.c 
+  meshlink2.c nbrsfind2.c i3tensor_2.c 
+  mcmc.c halo_mass_function.c halo_bias.c
+  nrutil.c qromo.c midpnt.c midinf.c polint.c splint.c spline.c 
+  zbrent.c qtrap.c trapzd.c cisi.c complex.c amoeba.c amotry.c 
+  gaussj.c powell.c linmin.c f1dim.c mnbrak.c brent.c gasdev.c 
+  ran1.c jacobi.c splin2.c splie2.c ran2.c sort2.c
+)
+add_executable(hod ${hod_SRCS})
+target_link_libraries(hod  -lm)

c_tools/libzobov/CMakeLists.txt

@@ -0,0 +1,8 @@
+
+add_library(zobovTool loadZobov.cpp particleInfo.cpp contour_pixels.cpp)
+
+set_target_properties(zobovTool PROPERTIES COMPILE_FLAGS ${OpenMP_CXX_FLAGS} LINK_FLAGS ${OpenMP_CXX_FLAGS})
+
+SET(ZOB_LIBS zobovTool ${COSMOTOOL_LIBRARY} ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY} ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY})
+SET(ZOB_LIBS PARENT ${ZOB_LIBS})
+

c_tools/mock/CMakeLists.txt

@@ -0,0 +1,23 @@
+include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/loaders)
+
+IF(SDF_SUPPORT)
+  add_definitions(-DSDF_SUPPORT)
+ENDIF(SDF_SUPPORT)
+
+SET(generateMock_SRCS generateMock.cpp )
+add_genopt(generateMock_SRCS generateMock.ggo generateMock_conf STRUCTNAME generateMock_info)
+add_executable(generateMock ${generateMock_SRCS})
+target_link_libraries(generateMock simu_loaders ${ZOB_LIBS} ${HDF5HL_CPP_LIBRARY} ${HDF5_CPP_LIBRARY} ${HDF5_LIBRARY} ${LIBSDF_LIBRARY})
+
+add_executable(generateTestMock generateTestMock.cpp)
+target_link_libraries(generateTestMock ${ZOB_LIBS})
+
+
+SET(generateFromCatalog_SRCS generateFromCatalog.cpp)
+add_genopt(generateFromCatalog_SRCS generateFromCatalog.ggo generateFromCatalog_conf STRUCTNAME generateFromCatalog_info)
+add_executable(generateFromCatalog ${generateFromCatalog_SRCS})
+target_link_libraries(generateFromCatalog ${ZOB_LIBS} ${HDF5HL_CPP_LIBRARY} ${HDF5_CPP_LIBRARY} ${HEALPIX_LIBRARIES})
+
+set_target_properties(generateFromCatalog PROPERTIES COMPILE_FLAGS ${OpenMP_CXX_FLAGS} LINK_FLAGS ${OpenMP_CXX_FLAGS})
+
+subdirs(loaders)

c_tools/mock/loaders/CMakeLists.txt

@@ -0,0 +1,11 @@
+SET(SIMU_LOADERS_SRCS 
+   simulation_loader.cpp ramses_loader.cpp 
+   gadget_loader.cpp flash_loader.cpp)
+
+IF (SDF_SUPPORT)
+ add_definitions(-DSDF_SUPPORT)
+ SET(SIMU_LOADERS_SRCS ${SIMU_LOADERS_SRCS} sdf_loader.cpp multidark_loader.cpp)
+ENDIF (SDF_SUPPORT)
+
+
+add_library(simu_loaders ${SIMU_LOADERS_SRCS})

c_tools/stacking/CMakeLists.txt

@@ -0,0 +1,39 @@
+include_directories(${CMAKE_CURRENT_BINARY_DIR})
+
+SET(stackVoids_SRCS stackVoids.cpp)
+add_genopt(stackVoids_SRCS stackVoids.ggo stackVoids_conf STRUCTNAME stackVoids_info)
+add_executable(stackVoids ${stackVoids_SRCS})
+target_link_libraries(stackVoids  ${ZOB_LIBS})
+
+SET(stackVoidsZero_SRCS stackVoidsZero.cpp)
+add_genopt(stackVoidsZero_SRCS stackVoidsZero.ggo stackVoidsZero_conf STRUCTNAME stackVoidsZero_info)
+add_executable(stackVoidsZero ${stackVoidsZero_SRCS})
+target_link_libraries(stackVoidsZero ${ZOB_LIBS})
+
+set(computeVelocityProfile_SRCS computeVelocityProfile.cpp)
+add_genopt(computeVelocityProfile_SRCS computeVelocityProfile.ggo computeVelocityProfile_conf STRUCT Params)
+add_executable(computeVelocityProfile ${computeVelocityProfile_SRCS})
+target_link_libraries(computeVelocityProfile  ${ZOB_LIBS})
+
+
+set(stackDensityField_SRCS stackDensityField.cpp)
+add_genopt(stackDensityField_SRCS stackDensityField.ggo stackDensityField_conf STRUCT PARAMS)
+add_executable(stackDensityField ${stackDensityField_SRCS})
+target_link_libraries(stackDensityField ${ZOB_LIBS})
+
+
+
+set(stackVelocityField_SRCS stackVelocityField.cpp)
+add_genopt(stackVelocityField_SRCS stackVelocityField.ggo stackVelocityField_conf STRUCT PARAMS)
+add_executable(stackVelocityField ${stackVelocityField_SRCS})
+target_link_libraries(stackVelocityField ${ZOB_LIBS})
+
+SET(pruneVoids_SRCS pruneVoids.cpp)
+add_genopt(pruneVoids_SRCS pruneVoids.ggo pruneVoids_conf STRUCTNAME pruneVoids_info)
+add_executable(pruneVoids ${pruneVoids_SRCS})
+target_link_libraries(pruneVoids ${ZOB_LIBS})
+
+SET(makeAHFOutput_SRCS makeAHFOutput.cpp)
+add_genopt(makeAHFOutput_SRCS makeAHFOutput.ggo makeAHFOutput_conf STRUCTNAME makeAHFOutput_info)
+add_executable(makeAHFOutput ${makeAHFOutput_SRCS})
+target_link_libraries(makeAHFOutput ${ZOB_LIBS})

c_tools/zobov2/CMakeLists.txt

@@ -0,0 +1 @@
+subdirs(jozov2 voz1b1)

c_tools/zobov2/jozov2/CMakeLists.txt

@@ -0,0 +1,24 @@
+function(omp_add_flags TARGET LANG)
+   if(OPENMP_FOUND)
+     if(NOT LANG)
+       get_target_property(LANG ${TARGET} LINKER_LANGUAGE)
+     endif()
+     if(LANG MATCHES "C(XX)?")
+       set_property(TARGET ${TARGET} APPEND
+                    PROPERTY COMPILE_FLAGS ${OpenMP_${LANG}_FLAGS})
+       set_property(TARGET ${TARGET} APPEND
+                    PROPERTY LINK_FLAGS ${OpenMP_${LANG}_FLAGS})
+     else()
+       message(WARNING "omp_add_flags: target '${TARGET}'"
+                      " link language '${LANG}' is not supported")
+    endif()
+  endif()
+endfunction()
+
+add_executable(jozov2 jozov2.cpp jozov2_io.cpp jozov2_zones.cpp jozov2_watershed.cpp findrtop.c)
+
+if (ENABLE_OPENMP)
+  Find_Package(OpenMP)
+  omp_add_flags(jozov2 CXX)
+  add_definitions(-DOPENMP)
+ENDIF(ENABLE_OPENMP)

c_tools/zobov2/voz1b1/CMakeLists.txt

@@ -0,0 +1,4 @@
+add_executable(voz1b1_2 voz1b1.cpp vozutil.c voz_io.cpp)
+target_link_libraries(voz1b1_2 ${QHULL_LIBRARY} ${COSMOTOOL_LIBRARY} ${MATH_LIB})
+
+include_directories(${COSMOTOOL_INCLUDE_PATH} ${QHULL_INCLUDE_PATH})