Commit a75f7554 authored by David Moxey's avatar David Moxey

Merge branch 'master' into fix/output-gmsh

parents de97118c 7d2a4f8f
......@@ -14,4 +14,3 @@ IndentCaseLabels: true
Standard: Cpp03
AccessModifierOffset: -4
BinPackParameters: false
BinPackArguments: false
......@@ -3,23 +3,52 @@ Changelog
v4.4.0
------
**Library:**
**Library**:
- Add support for variable polynomial order for 3D simulations with continuous
Galerkin discretisation (!604)
- Bump version of gsmpi to suppress autotuning output unless `--verbose` is
specified (!652)
- Add support for variable polynomial order with periodic boundary conditions
(!658)
- Statistics are now printed for lowest level of multi-level static condensation
(!656)
- Sped up interpolataion from pts files and fixed parallel pts import (!584)
- Increased required boost version to 1.56.0 (!584)
- New FieldUtils library allows support for most `FieldConvert` post-processing
operations during simulation using a new filter (!589)
- Adjust CMake dependencies to reduce compile time (!671)
- Homogeneous1D dealiasing improvements (!622)
**ADRSolver:**
- Add a projection equation system for C^0 projections (!675)
**APESolver:**
- Use a continuous basefield projection and revert to constant c formulation (!664)
- Added ability to compute CFL number (!664)
- Output Sourceterm (!664)
**IncNavierStokesSolver:**
- Add ability to simulate additional scalar fields (!624)
- Improve performance when using homogeneous dealiasing (!622)
**NekMesh:**
- Modify curve module to allow for spline input (!628)
- Add STL surface writer module (!668)
- New module for inserting an alternate high-order surface into the working
mesh (!669)
- Improvements to mesh linearisation module (!659)
**FieldConvert:**
- Move all modules to a new library, FieldUtils, to support post-processing
during simulations (!589)
- Add module to stretch homogeneous direction (!609)
v4.3.4
------
**Library:**
- Fix performance issue with `v_ExtractDataToCoeffs` for post-processing of large
simulations (!672)
v4.3.3
------
**Library**:
......
......@@ -97,7 +97,9 @@ MARK_AS_ADVANCED(NEKTAR_BUILD_PACKAGES)
OPTION(NEKTAR_TEST_ALL "Include full set of regression tests to this build." OFF)
# Meshing utilities and library
OPTION(NEKTAR_USE_MESHGEN "Build mesh generation utilities." OFF)
IF (NOT WIN32)
OPTION(NEKTAR_USE_MESHGEN "Build mesh generation utilities." OFF)
ENDIF()
# Build options
OPTION(NEKTAR_FULL_DEBUG "Enable Full Debugging." OFF)
......@@ -180,15 +182,15 @@ INCLUDE (ThirdPartyScotch)
INCLUDE (ThirdPartyZlib)
INCLUDE (ThirdPartyBoost)
INCLUDE (ThirdPartyFFTW)
INCLUDE (ThirdPartyOCC)
INCLUDE (ThirdPartyArpack)
INCLUDE (ThirdPartyMPI)
INCLUDE (ThirdPartyPETSc)
INCLUDE (ThirdPartyVTK)
INCLUDE (ThirdPartyQT4)
INCLUDE (ThirdPartySMV)
INCLUDE (ThirdPartyTriangle)
INCLUDE (ThirdPartyOCC)
INCLUDE (ThirdPartyTetGen)
INCLUDE (ThirdPartyANN)
INCLUDE (ThirdPartyCCM)
INCLUDE (Doxygen)
......@@ -283,7 +285,7 @@ INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR})
# Build active components
IF (NEKTAR_BUILD_LIBRARY)
SET(NEKTAR++_LIBRARIES SolverUtils LibUtilities StdRegions SpatialDomains LocalRegions
MultiRegions Collections GlobalMapping NekMeshUtils)
MultiRegions Collections GlobalMapping FieldUtils NekMeshUtils)
INCLUDE_DIRECTORIES(library)
ADD_SUBDIRECTORY(library)
INSTALL(EXPORT Nektar++Libraries DESTINATION ${LIB_DIR}/cmake COMPONENT dev)
......
# Try to find OCE / OCC
# Once done this will define
#
# OCC_FOUND - system has OCC - OpenCASCADE
# OCC_INCLUDE_DIR - where the OCC include directory can be found
# OCC_LIBRARY_DIR - where the OCC library directory can be found
# OCC_LIBRARIES - Link this to use OCC
# OCC_OCAF_LIBRARIES - Link this to use OCC OCAF framework
#
# Adapted from FreeCAD: http://free-cad.sf.net
set(TEST_ENV $ENV{OCE_ROOT})
if(NOT DEFINED OCE_DIR AND DEFINED TEST_ENV)
file(GLOB OCE_DIR $ENV{OCE_ROOT}/lib/oce-*)
endif()
# First try to find OpenCASCADE Community Edition
if(NOT DEFINED OCE_DIR)
# Check for OSX needs to come first because UNIX evaluates to true on OSX
if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
if(DEFINED MACPORTS_PREFIX)
find_package(OCE HINTS ${MACPORTS_PREFIX}/Library/Frameworks)
elseif(DEFINED HOMEBREW_PREFIX)
find_package(OCE HINTS ${HOMEBREW_PREFIX}/Cellar/oce/*)
endif()
elseif(UNIX)
set(OCE_DIR "/usr/local/share/cmake/")
elseif(WIN32)
set(OCE_DIR "c:/OCE-0.4.0/share/cmake")
endif()
endif()
find_package(OCE QUIET)
if(OCE_FOUND)
message(STATUS "-- OpenCASCADE Community Edition has been found.")
# Disable this define. For more details see bug #0001872
#add_definitions (-DHAVE_CONFIG_H)
set(OCC_INCLUDE_DIR ${OCE_INCLUDE_DIRS})
#set(OCC_LIBRARY_DIR ${OCE_LIBRARY_DIR})
else(OCE_FOUND) #look for OpenCASCADE
if(WIN32)
if(CYGWIN OR MINGW)
FIND_PATH(OCC_INCLUDE_DIR Standard_Version.hxx
/usr/include/opencascade
/usr/local/include/opencascade
/usr/local/opt/opencascade/include
/opt/opencascade/include
/opt/opencascade/inc
)
FIND_LIBRARY(OCC_LIBRARY TKernel
/usr/lib
/usr/local/lib
/usr/local/opt/opencascade/lib
/opt/opencascade/lib
)
else(CYGWIN OR MINGW)
FIND_PATH(OCC_INCLUDE_DIR Standard_Version.hxx
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\SIM\\OCC\\2;Installation Path]/include"
)
FIND_LIBRARY(OCC_LIBRARY TKernel
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\SIM\\OCC\\2;Installation Path]/lib"
)
endif(CYGWIN OR MINGW)
else(WIN32)
FIND_PATH(OCC_INCLUDE_DIR Standard_Version.hxx
/usr/include/opencascade
/usr/local/include/opencascade
/usr/local/opt/opencascade/include
/opt/opencascade/include
/opt/opencascade/inc
/opt/local/include/oce
)
FIND_LIBRARY(OCC_LIBRARY TKernel
/usr/lib
/usr/local/lib
/usr/local/opt/opencascade/lib
/opt/opencascade/lib
opt/local/lib
)
endif(WIN32)
if(OCC_LIBRARY)
GET_FILENAME_COMPONENT(OCC_LIBRARY_DIR ${OCC_LIBRARY} PATH)
IF(NOT OCC_INCLUDE_DIR)
FIND_PATH(OCC_INCLUDE_DIR Standard_Version.hxx
${OCC_LIBRARY_DIR}/../inc
)
ENDIF()
endif(OCC_LIBRARY)
endif(OCE_FOUND)
if(OCC_INCLUDE_DIR)
file(STRINGS ${OCC_INCLUDE_DIR}/Standard_Version.hxx OCC_MAJOR
REGEX "#define OCC_VERSION_MAJOR.*"
)
string(REGEX MATCH "[0-9]+" OCC_MAJOR ${OCC_MAJOR})
file(STRINGS ${OCC_INCLUDE_DIR}/Standard_Version.hxx OCC_MINOR
REGEX "#define OCC_VERSION_MINOR.*"
)
string(REGEX MATCH "[0-9]+" OCC_MINOR ${OCC_MINOR})
file(STRINGS ${OCC_INCLUDE_DIR}/Standard_Version.hxx OCC_MAINT
REGEX "#define OCC_VERSION_MAINTENANCE.*"
)
string(REGEX MATCH "[0-9]+" OCC_MAINT ${OCC_MAINT})
set(OCC_VERSION_STRING "${OCC_MAJOR}.${OCC_MINOR}.${OCC_MAINT}")
endif(OCC_INCLUDE_DIR)
# handle the QUIETLY and REQUIRED arguments and set OCC_FOUND to TRUE if
# all listed variables are TRUE
include(FindPackageHandleStandardArgs)
FIND_PACKAGE_HANDLE_STANDARD_ARGS(OCC REQUIRED_VARS OCC_INCLUDE_DIR VERSION_VAR OCC_VERSION_STRING)
if(OCC_FOUND)
set(OCC_LIBRARIES
TKFillet
TKMesh
TKernel
TKG2d
TKG3d
TKMath
TKIGES
TKSTL
TKShHealing
TKXSBase
TKBool
TKBO
TKBRep
TKTopAlgo
TKGeomAlgo
TKGeomBase
TKOffset
TKPrim
TKSTEP
TKSTEPBase
TKSTEPAttr
TKHLR
TKFeat
)
set(OCC_OCAF_LIBRARIES
TKCAF
TKXCAF
TKLCAF
TKXDESTEP
TKXDEIGES
TKMeshVS
)
if(OCC_VERSION_STRING VERSION_LESS 6.7.3)
list(APPEND OCC_OCAF_LIBRARIES TKAdvTools)
endif(OCC_VERSION_STRING VERSION_LESS 6.7.3)
message(STATUS "-- Found OCE/OpenCASCADE version: ${OCC_VERSION_STRING}")
message(STATUS "-- OCE/OpenCASCADE include directory: ${OCC_INCLUDE_DIR}")
message(STATUS "-- OCE/OpenCASCADE shared libraries directory: ${OCC_LIBRARY_DIR}")
else(OCC_FOUND)
#message(SEND_ERROR "Neither OpenCASCADE Community Edition nor OpenCasCade were found: will not build CAD modules!")
endif(OCC_FOUND)
########################################################################
#
# ThirdParty configuration for Nektar++
#
# libann partitioner
#
########################################################################
IF (NOT WIN32)
OPTION(NEKTAR_USE_ANN
"Use ANN routines for performing Approximate Nearest Neighbour searches." OFF)
ENDIF(NOT WIN32)
IF( NEKTAR_USE_MESHGEN )
SET(NEKTAR_USE_ANN ON CACHE BOOL "" FORCE)
ENDIF()
IF (NEKTAR_USE_ANN)
# First search for system ANN installs. Hint /opt/local for MacPorts and
# /usr/local/opt/ann for Homebrew.
FIND_LIBRARY(ANN_LIBRARY NAMES ANN
PATHS /opt/local/lib /usr/local/opt/ann/lib $ENV{ANN_ROOT}/lib)
FIND_PATH (ANN_INCLUDE_DIR ANN.h
PATHS /opt/local/include /usr/local/opt/ann/include $ENV{ANN_ROOT}/include
PATH_SUFFIXES ANN)
GET_FILENAME_COMPONENT(ANN_LIBRARY_PATH ${ANN_LIBRARY} PATH)
IF (ANN_LIBRARY AND ANN_INCLUDE_DIR)
SET(BUILD_ANN OFF)
ELSE()
SET(BUILD_ANN ON)
ENDIF ()
OPTION(THIRDPARTY_BUILD_ANN "Build ANN library from ThirdParty" ${BUILD_ANN})
IF (THIRDPARTY_BUILD_ANN)
# Note that ANN is compiled in the source-tree, so we unpack the
# source code in the ThirdParty builds directory.
SET(ANN_DIR ${TPBUILD}/ann-1.1.2)
SET(ANN_SRC ${ANN_DIR}/src)
IF (APPLE)
SET(ANN_CFLAGS "-O3 -fPIC")
SET(ANN_MAKELIB "libtool -static -o")
ELSE ()
SET(ANN_CFLAGS "-O3 -fPIC")
SET(ANN_MAKELIB "ar ruv")
ENDIF ()
INCLUDE(ExternalProject)
EXTERNALPROJECT_ADD(
ann-1.1.2
PREFIX ${TPSRC}
URL ${TPURL}/ann_1.1.2.tar.gz
URL_MD5 "9f99653b76798ecb1cfadc88950c4707"
STAMP_DIR ${TPBUILD}/stamp
DOWNLOAD_DIR ${TPSRC}
SOURCE_DIR ${TPBUILD}/ann-1.1.2
BINARY_DIR ${TPBUILD}/ann-1.1.2
TMP_DIR ${TPBUILD}/ann-1.1.2-tmp
INSTALL_DIR ${TPDIST}
CONFIGURE_COMMAND ${CMAKE_COMMAND} -E remove -f ${ANN_DIR}/Makefile
BUILD_COMMAND cd src
COMMAND $(MAKE) -C ${ANN_SRC} targets
"ANNLIB = libANN.a"
"C++ = ${CMAKE_CXX_COMPILER}"
"CFLAGS = ${ANN_CFLAGS}"
"MAKELIB = ${ANN_MAKELIB}"
"RANLIB = true"
INSTALL_COMMAND ${CMAKE_COMMAND} -E make_directory ${TPDIST}/lib
COMMAND ${CMAKE_COMMAND} -E copy ${ANN_DIR}/lib/libANN.a
${TPDIST}/lib
COMMAND ${CMAKE_COMMAND} -E copy_directory ${ANN_DIR}/include
${TPDIST}/include
)
SET(ANN_LIBRARY ANN CACHE FILEPATH
"ANN library" FORCE)
SET(ANN_INCLUDE_DIR ${TPDIST}/include CACHE FILEPATH
"ANN include directory" FORCE)
LINK_DIRECTORIES(${TPDIST}/lib)
MESSAGE(STATUS "Build ANN: ${TPDIST}/lib/lib${ANN_LIBRARY}.a")
SET(ANN_CONFIG_INCLUDE_DIR ${TPINC})
ELSE (THIRDPARTY_BUILD_ANN)
ADD_CUSTOM_TARGET(ann-1.1.2 ALL)
MESSAGE(STATUS "Found ANN: ${ANN_LIBRARY}")
SET(ANN_CONFIG_INCLUDE_DIR ${ANN_INCLUDE_DIR})
ENDIF (THIRDPARTY_BUILD_ANN)
INCLUDE_DIRECTORIES(${ANN_INCLUDE_DIR})
MARK_AS_ADVANCED(ANN_LIBRARY)
MARK_AS_ADVANCED(ANN_INCLUDE_DIR)
ENDIF()
......@@ -2,22 +2,30 @@
#
# ThirdParty configuration for Nektar++
#
# Star CCM i/o
# Star CCM i/o
#
########################################################################
OPTION(NEKTAR_USE_CCM
OPTION(NEKTAR_USE_CCM
"CCM star i/o library is available." OFF)
IF( NEKTAR_USE_CCM )
FIND_LIBRARY(CCMIO_LIBRARY NAMES "ccmio" "adf" PATHS /usr/local/lib ${Nektar++_TP_LIBRARY_DIRS})
set(CCMIO_LIBRARIES
ccmio
adf
)
FIND_LIBRARY(CCMIO_LIBRARY NAMES "ccmio" PATHS /usr/local/lib ${Nektar++_TP_LIBRARY_DIRS})
IF( CCMIO_LIBRARY )
MESSAGE(STATUS "Found Ccmio: ${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_PATH ${CCMIO_LIBRARY} PATH)
LINK_DIRECTORIES(${CCMIO_LIBRARY_PATH})
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()
......
......@@ -51,23 +51,23 @@ IF( NEKTAR_USE_MPI )
IF (THIRDPARTY_BUILD_GSMPI)
EXTERNALPROJECT_ADD(
gsmpi-1.2
URL ${TPURL}/gsmpi-1.2.tar.bz2
URL_MD5 35901be16791bfdeafa9c4d0e06d189b
gsmpi-1.2.1
URL ${TPURL}/gsmpi-1.2.1.tar.bz2
URL_MD5 18dcb4cd1dcc7876173465c404b1142d
STAMP_DIR ${TPBUILD}/stamp
DOWNLOAD_DIR ${TPSRC}
SOURCE_DIR ${TPSRC}/gsmpi-1.2
BINARY_DIR ${TPBUILD}/gsmpi-1.2
TMP_DIR ${TPBUILD}/gsmpi-1.2-tmp
SOURCE_DIR ${TPSRC}/gsmpi-1.2.1
BINARY_DIR ${TPBUILD}/gsmpi-1.2.1
TMP_DIR ${TPBUILD}/gsmpi-1.2.1-tmp
INSTALL_DIR ${TPDIST}
CONFIGURE_COMMAND
CONFIGURE_COMMAND
${CMAKE_COMMAND}
-G ${CMAKE_GENERATOR}
-DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
-DCMAKE_BUILD_TYPE:STRING=Debug
-DCMAKE_INSTALL_PREFIX:PATH=${TPDIST}
${TPSRC}/gsmpi-1.2
${TPSRC}/gsmpi-1.2.1
)
SET(GSMPI_LIBRARY gsmpi CACHE FILEPATH
"GSMPI path" FORCE)
......@@ -78,7 +78,7 @@ IF( NEKTAR_USE_MPI )
MESSAGE(STATUS "Build GSMPI: ${TPDIST}/lib/lib${GSMPI_LIBRARY}.a")
MESSAGE(STATUS "Build XXT: ${TPDIST}/lib/lib${XXT_LIBRARY}.a")
ELSE (THIRDPARTY_BUILD_GSMPI)
ADD_CUSTOM_TARGET(gsmpi-1.2 ALL)
ADD_CUSTOM_TARGET(gsmpi-1.2.1 ALL)
INCLUDE (FindGSMPI)
INCLUDE (FindXXT)
ENDIF (THIRDPARTY_BUILD_GSMPI)
......
......@@ -7,63 +7,66 @@
########################################################################
IF(NEKTAR_USE_MESHGEN)
SET(BUILD_OCC ON)
OPTION(THIRDPARTY_DOWNLOAD_OCC
"Download pre-compiled versions of OpenCascade." ${BUILD_OCC})
# Try to find installed version of OpenCascade
INCLUDE(FindOCC)
IF (THIRDPARTY_DOWNLOAD_OCC)
IF (OCC_FOUND)
SET(BUILD_OCC OFF)
ELSE()
SET(BUILD_OCC ON)
ENDIF()
OPTION(THIRDPARTY_BUILD_OCC "Build OpenCascade library from ThirdParty."
${BUILD_OCC})
IF (THIRDPARTY_BUILD_OCC)
INCLUDE(ExternalProject)
SET(OCC_LIBS_TMP PTKernel TKernel TKMath TKBRep TKIGES TKSTEP TKSTEPAttr
SET(OCC_LIBRARIES_TMP PTKernel TKernel TKMath TKBRep TKIGES TKSTEP TKSTEPAttr
TKSTEP209 TKSTEPBase TKShapeSchema TKGeomBase TKGeomAlgo TKG3d TKG2d
TKXSBase TKPShape TKTopAlgo)
FOREACH(OCC_LIB ${OCC_LIBS_TMP})
LIST(APPEND OCC_LIBS ${TPDIST}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}${OCC_LIB}${CMAKE_SHARED_LIBRARY_SUFFIX})
TKXSBase TKPShape TKTopAlgo TKShHealing)
FOREACH(OCC_LIB ${OCC_LIBRARIES_TMP})
LIST(APPEND OCC_LIBRARIES ${TPDIST}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}${OCC_LIB}${CMAKE_SHARED_LIBRARY_SUFFIX})
ENDFOREACH()
UNSET(OCC_LIBRARIES_TMP)
IF(WIN32)
MESSAGE(SEND_ERROR "Cannot currently use OpenCascade with Nektar++ on Windows")
ELSEIF(APPLE)
EXTERNALPROJECT_ADD(
opencascade-6.8
PREFIX ${TPSRC}
URL ${TPURL}/OCC680osx64.tgz
URL_MD5 626292523b0691304f0fa271989fbc44
STAMP_DIR ${TPBUILD}/stamp
BINARY_DIR ${TPBUILD}/opencascade-6.8
DOWNLOAD_DIR ${TPSRC}
SOURCE_DIR ${TPSRC}/opencascade-6.8
INSTALL_DIR ${TPDIST}
UPDATE_COMMAND ""
CONFIGURE_COMMAND ""
BUILD_COMMAND ""
INSTALL_COMMAND cp -a ${TPSRC}/opencascade-6.8/i686/lib/. ${TPDIST}/lib/ COMMAND cp -a ${TPSRC}/opencascade-6.8/i686/inc/. ${TPDIST}/include/
)
# Patch OS X libraries to fix install name problems.
EXTERNALPROJECT_ADD_STEP(opencascade-6.8 patch-install-path
COMMAND bash ${CMAKE_SOURCE_DIR}/cmake/scripts/patch-occ.sh ${TPSRC}/opencascade-6.8/i686/lib ${CMAKE_INSTALL_PREFIX}/${NEKTAR_LIB_DIR}
DEPENDEES build
DEPENDERS install)
ELSE()
EXTERNALPROJECT_ADD(
opencascade-6.8
PREFIX ${TPSRC}
URL ${TPURL}/OCC680lin64.tgz
URL_MD5 d655b6f50998bb9600e081907c247793
STAMP_DIR ${TPBUILD}/stamp
DOWNLOAD_DIR ${TPSRC}
SOURCE_DIR ${TPSRC}/opencascade-6.8
INSTALL_DIR ${TPDIST}
UPDATE_COMMAND ""
CONFIGURE_COMMAND ""
BUILD_COMMAND ""
INSTALL_COMMAND cp -a ${TPSRC}/opencascade-6.8/lib/. ${TPDIST}/lib/ COMMAND cp -a ${TPSRC}/opencascade-6.8/inc/. ${TPDIST}/include/
)
ENDIF()
EXTERNALPROJECT_ADD(
opencascade-6.9
PREFIX ${TPSRC}
URL http://ae-nektar.ae.ic.ac.uk/~dmoxey/OCE-0.17.2.tar.gz
URL_MD5 bf2226be4cd192606af677cf178088e5
STAMP_DIR ${TPBUILD}/stamp