Merge branch 'feature/CMake_CCMIO' into 'master'

Thirdparty compilation of libccmio

See merge request !799

CHANGELOG.md

@@ -13,8 +13,10 @@ v5.0.0
 - Add periodic boundary condition meshing in 2D (!733)
 - Adjust boundary layer thickness in corners in 2D (!739)
 - Add non-O BL meshing in 2D (!757)
+- Add ability to compile CCIO library but tar file is not yet openly 
+  available whist we seek permission from Simens (!799)
 - Fix issue with reading CCM files due to definition of default arrays 
-- rather than a vector (!797)
+  rather than a vector (!797)
 - Fix inverted triangles and small memory issue in surface meshing (!798)
 
 **Library**

cmake/ThirdPartyCCM.cmake

@@ -6,28 +6,76 @@
 #
 ########################################################################
 OPTION(NEKTAR_USE_CCM
-   "CCM star i/o library is available." OFF)
+   "use CCM star i/o" OFF)
 
-IF( NEKTAR_USE_CCM )
+# First search for system ccmioL installs. Hint /usr/local 
+FIND_PATH   (CCMIO_INCLUDE_DIR ccmio.h PATHS /usr/local/include)
+FIND_LIBRARY(CCMIO_LIBRARY NAMES "ccmio" PATHS /usr/local/lib)
+
+# If we have our library then don't build CCMIO.
+IF (CCMIO_INCLUDE_DIR AND CCMIO_LIBRARY)
+    SET(BUILD_CCMIO OFF)
+ELSE()
+    SET(BUILD_CCMIO ON)
+ENDIF ()
+
+OPTION(THIRDPARTY_BUILD_CCMIO 
+    "Build CCMIO library from ThirdParty if permitted." ${BUILD_CCMIO})
+
+IF (THIRDPARTY_BUILD_CCMIO)
+    INCLUDE(ExternalProject)
+    MESSAGE(WARNING "We are seeking permission to distribute ccmio with Nektar++. If you are entitled to use libccmio please contact nektar-users@imperial.ac.uk and place the file ccmio-2.06.tar.bz2 in the director $NEKTAR/ThirdParty")
+    EXTERNALPROJECT_ADD(
+        ccmio-2.06
+        PREFIX ${TPSRC}
+        URL ${TPURL}/ccmio-2.06.tar.bz2
+        URL_MD5 809ee34a983cbc8931ca23879d92b4d0
+        STAMP_DIR ${TPBUILD}/stamp
+        DOWNLOAD_DIR ${TPSRC}
+        SOURCE_DIR ${TPSRC}/ccmio-2.06
+        BINARY_DIR ${TPBUILD}/ccmio-2.06
+        TMP_DIR ${TPBUILD}/ccmio-2.06-tmp
+        INSTALL_DIR ${TPDIST}
+        CONFIGURE_COMMAND ${CMAKE_COMMAND}
+            -G ${CMAKE_GENERATOR}
+            -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
+            -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
+            -DCMAKE_INSTALL_PREFIX:PATH=${TPDIST}
+            ${TPSRC}/ccmio-2.06
+    )
+    SET(CCMIO_LIBRARY ccmio CACHE FILEPATH
+        "CCMIO library" FORCE)
+    SET(CCMIO_INCLUDE_DIR ${TPDIST}/include CACHE FILEPATH
+        "CCMIO include" FORCE)
+
+    LINK_DIRECTORIES(${TPDIST}/lib)
+
+    INCLUDE_DIRECTORIES(NekMesh ${CCMIO_INCLUDE_DIR})
+
+    IF (WIN32)
+        MESSAGE(STATUS 
+                "Build CCMIO: ${TPDIST}/${LIB_DIR}/${CCMIO_LIBRARY}.dll")
+    ELSE ()
+        MESSAGE(STATUS 
+                "Build CCMIO: ${TPDIST}/${LIB_DIR}/lib${CCMIO_LIBRARY}.a")
+    ENDIF ()
+
+    SET(CCMIO_CONFIG_INCLUDE_DIR ${TPINC})
 
     set(CCMIO_LIBRARIES
         ccmio
         adf
     )
+ELSE()
+    ADD_CUSTOM_TARGET(ccmio-2.06 ALL)
+    MESSAGE(STATUS "Found CCMIO: ${CCMIO_LIBRARY}")
+    SET(CCMIO_CONFIG_INCLUDE_DIR ${CCMIO_INCLUDE_DIR})
+    INCLUDE_DIRECTORIES(NekMesh ${CCMIO_INCLUDE_DIR})
+    LINK_DIRECTORIES(${CCMIO_LIBRARY_DIR})
+
+ENDIF (THIRDPARTY_BUILD_CCMIO)
 
-    FIND_LIBRARY(CCMIO_LIBRARY NAMES "ccmio" PATHS /usr/local/lib ${Nektar++_TP_LIBRARY_DIRS})
-
-    IF( CCMIO_LIBRARY )
-        MESSAGE(STATUS "Found Ccmio: ${CCMIO_LIBRARY}")
-        MARK_AS_ADVANCED(CCMIO_LIBRARY)
-        ADD_DEFINITIONS(-DNEKTAR_USE_CCM)
-        FIND_PATH (CCMIO_INCLUDE_DIR ccmio.h)
-        GET_FILENAME_COMPONENT(CCMIO_LIBRARY_DIR ${CCMIO_LIBRARY} PATH)
-        INCLUDE_DIRECTORIES(NekMesh ${CCMIO_INCLUDE_DIR})
-        LINK_DIRECTORIES(${CCMIO_LIBRARY_DIR})
-        MESSAGE(STATUS ${CCMIO_LIBRARY_DIR})
-     ELSE()
-        MESSAGE(FATAL_ERROR "Cound not find ccmio library")
-     ENDIF()
-ENDIF( NEKTAR_USE_CCM )
+SET(CCMIO_LIBRARIES ccmio adf)
 
+MARK_AS_ADVANCED(CCMIO_INCLUDE_DIR)
+MARK_AS_ADVANCED(CCMIO_LIBRARY)

utilities/NekMesh/ProcessModules/ProcessSpherigon.cpp

@@ -233,7 +233,7 @@ void ProcessSpherigon::FindNormalFromPlyFile(MeshSharedPtr &plymesh,
     typedef bg::model::point<NekDouble, 3, bg::cs::cartesian> Point;
     typedef pair<Point, unsigned int> PointI;
 
-    int n_neighbs = 5;
+    int n_neighbs = 1;
 
     map<int,int>  TreeidtoPlyid;
 
@@ -263,17 +263,10 @@ void ProcessSpherigon::FindNormalFromPlyFile(MeshSharedPtr &plymesh,
                                                   "Nearest ply verts",prog);
         }
 
-
-        //I dont know why 5 nearest points are searched for when
-        //only the nearest point is used for the data
-        //was left like this in the ann->boost rewrite (MT 6/11/16)
         Point queryPt(vIt->second->m_x, vIt->second->m_y, vIt->second->m_z);
-        n_neighbs  = 5;
         vector<PointI> result;
-        rtree.query(bgi::nearest(queryPt, n_neighbs), std::back_inserter(result));
-
-        ASSERTL1(bg::distance(result[0].first,queryPt) < bg::distance(result[1].first,queryPt),
-            "Assumption that dist values are ordered from smallest to largest is not correct");
+        rtree.query(bgi::nearest(queryPt, n_neighbs),
+                    std::back_inserter(result));
 
         cntmin = TreeidtoPlyid[result[0].second];