Add symengine #238

CMakeLists.txt

@@ -89,7 +89,7 @@ set(ENABLE_COVERAGE OFF CACHE BOOL "Enable code coverage")
 set(ENABLE_ARRAY_INDEX_CHECKING OFF CACHE BOOL "Enable Array index checking")
 set(SV_LOCAL_VTK_PATH "" CACHE STRING "Path to a local build of VTK.")
 set(ENABLE_UNIT_TEST OFF CACHE BOOL "Enable Unit Test by Google Test")
-
+set(SV_USE_SYMENGINE OFF CACHE BOOL "Build with the SymEngine symbolic algebra package")
 #-----------------------------------------------------------------------------
 # RPATH handling
 # No objects built directly with project. Not needed!
@@ -145,6 +145,7 @@ ExternalProject_Add(svFSI
  -DSV_EXTERNALS_USE_TOPLEVEL_DIR:BOOL=ON
  -DSV_EXTERNALS_TOPLEVEL_DIR:PATH=${SV_EXTERNALS_TOPLEVEL_DIR}
  -DSV_USE_TRILINOS:BOOL=${SV_USE_TRILINOS}
+ -DSV_USE_SYMENGINE:BOOL=${SV_USE_SYMENGINE}
  #-DSV_USE_PETSC:BOOL=${SV_USE_PETSC}
  -DSV_PETSC_DIR:STRING=${SV_PETSC_DIR}
  -DENABLE_COVERAGE:BOOL=${ENABLE_COVERAGE}

Code/CMake/SimVascularInternals.cmake

@@ -4,6 +4,7 @@ set(SV_LIBS
  THIRDPARTY_GKLIB_SVFSI
  THIRDPARTY_TETGEN
  THIRDPARTY_TINYXML
+ THIRDPARTY_EXPRTK
  THIRDPARTY_ZLIB
  SVFSILS
  SVFSI_CINTERFACE

Code/CMake/SimVascularThirdParty.cmake

@@ -47,5 +47,6 @@ endif()
 simvascular_third_party(tinyxml)
 set(TINYXML_LIBRARY ${SV_LIB_THIRDPARTY_TINYXML_NAME})
 
-
-
+# EXPRTK
+simvascular_third_party(exprtk)
+set(EXPRTK_LIBRARY ${SV_LIB_THIRDPARTY_EXPRTK_NAME})

Code/Source/svFSI/CMakeLists.txt

@@ -29,6 +29,7 @@ set(CMAKE_CXX_STANDARD_REQUIRED True)
 include_directories(${SV_SOURCE_DIR}/ThirdParty/parmetis_svfsi/simvascular_parmetis_svfsi/ParMETISLib)
 include_directories(${SV_SOURCE_DIR}/ThirdParty/tetgen/simvascular_tetgen)
 include_directories(${SV_SOURCE_DIR}/ThirdParty/tinyxml/simvascular_tinyxml)
+include_directories(${SV_SOURCE_DIR}/ThirdParty/exprtk/simvascular_exprtk)
 include_directories(${MPI_C_INCLUDE_PATH})
 
 # Find Trilinos package if requested
@@ -124,6 +125,30 @@ else()
 
 endif()
 
+# Build with the SymEngine library.
+if(SV_USE_SYMENGINE)
+ include(FetchContent)
+ set(FETCHCONTENT_BASE_DIR "${CMAKE_BINARY_DIR}/ThirdParty/symengine")
+ FetchContent_Declare(
+ symengine
+ GIT_REPOSITORY https://github.com/symengine/symengine.git
+ GIT_TAG v0.12.0
+ GIT_SHALLOW TRUE
+ GIT_PROGRESS TRUE
+ )
+ set(FETCHCONTENT_QUIET FALSE)
+ FetchContent_GetProperties(symengine)
+ if(NOT symengine_POPULATED)
+ FetchContent_Populate(symengine)
+ set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build." FORCE) # Set the build type for SymEngine
+ #add_subdirectory(${symengine_SOURCE_DIR} ${symengine_BINARY_DIR})
+ endif()
+ message(STATUS "SymEngine fetched from source.")
+ set(USE_SYMENGINE 1)
+else()
+ set(USE_SYMENGINE 0)
+endif()
+
 if(ENABLE_ARRAY_INDEX_CHECKING)
  ADD_DEFINITIONS(-DENABLE_ARRAY_INDEX_CHECKING)
 endif()
@@ -238,6 +263,8 @@ if(USE_TRILINOS)
  link_directories(${Trilinos_TPL_LIBRARY_DIRS})
 endif()
 
+
+
 simvascular_add_executable(${SV_SVFSI_EXE}
  SRCS ${CSRCS}
  DEV_SCRIPT_NAME "mysvfsi"
@@ -272,6 +299,10 @@ if(USE_PETSC)
  target_link_libraries(${SV_SVFSI_EXE} ${PETSC_LIBRARY_DIRS})
 endif()
 
+if(USE_SYMENGINE)
+ target_link_libraries(${SV_SVFSI_EXE} symengine)
+endif()
+
 # coverage
 if(ENABLE_COVERAGE)
  # set compiler flags

Code/ThirdParty/README.md

@@ -6,6 +6,8 @@ Applications
 
 eigen - A header-only application for matrix objects.
 
+exprtk - A header-only application for parsing and evaluating mathematical expressions.
+
 gklib_svfsi - A library used by METIS and ParMETIS applications.
 
 metis_svfsi - The METIS mesh partitioning application used by ParMETIS.

Code/ThirdParty/exprtk/CMakeLists.txt

@@ -0,0 +1,31 @@
+# Copyright (c) Stanford University, The Regents of the University of
+# California, and others.
+#
+# All Rights Reserved.
+#
+# See Copyright-SimVascular.txt for additional details.
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject
+# to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+simvascular_third_party(exprtk)

Code/ThirdParty/exprtk/simvascular_exprtk.h.in

@@ -0,0 +1,43 @@
+/* Copyright (c) Stanford University, The Regents of the University of
+ * California, and others.
+ *
+ * All Rights Reserved.
+ *
+ * See Copyright-SimVascular.txt for additional details.
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * "Software"), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject
+ * to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included
+ * in all copies or substantial portions of the Software.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+ * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#ifndef __simvascular_exprtk_h
+#define __simvascular_exprtk_h
+
+/* Use the exprtk library configured for SimVascular. */
+#cmakedefine SV_USE_SYSTEM_EXPRTK
+#ifdef SV_USE_SYSTEM_EXPRTK
+# include <exprtk.h>
+#else
+# include <simvascular_exprtk/exprtk.h>
+#endif
+
+#endif

Code/ThirdParty/exprtk/simvascular_exprtk/CMakeLists.txt

@@ -0,0 +1,57 @@
+# Copyright (c) Stanford University, The Regents of the University of
+# California, and others.
+#
+# All Rights Reserved.
+#
+# See Copyright-SimVascular.txt for additional details.
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject
+# to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+# Set the minimum required version of cmake for a project.
+cmake_minimum_required(VERSION 3.10)
+project(EXPRTK)
+
+# source files for exprtk
+SET(SRCS exprtk.cpp)
+SET(HDRS exprtk.h)
+
+set(lib ${SV_LIB_THIRDPARTY_EXPRTK_NAME})
+if(SV_USE_THIRDPARTY_SHARED_LIBRARIES)
+ add_library(${lib} SHARED ${SRCS} ${HDRS})
+else()
+ add_library(${lib} STATIC ${SRCS} ${HDRS})
+endif()
+
+if(SV_INSTALL_LIBS)
+ install(TARGETS ${lib}
+ RUNTIME DESTINATION ${SV_INSTALL_RUNTIME_DIR} COMPONENT ThirdPartyExecutables
+ LIBRARY DESTINATION ${SV_INSTALL_LIBRARY_DIR} COMPONENT ThirdPartyLibraries
+ ARCHIVE DESTINATION ${SV_INSTALL_ARCHIVE_DIR} COMPONENT ThirdPartyLibraries
+ )
+endif()
+if(SV_INSTALL_HEADERS)
+ install(FILES ${HDRS}
+ DESTINATION ${SV_INSTALL_INCLUDE_DIR}/thirdparty/exprtk COMPONENT ThirdPartyHeaders
+ )
+endif()

Code/ThirdParty/exprtk/simvascular_exprtk/LICENSE

@@ -0,0 +1,15 @@
+#
+# **************************************************************
+# * C++ Mathematical Expression Toolkit Library *
+# * *
+# * Author: Arash Partow (1999-2023) *
+# * URL: https://www.partow.net/programming/exprtk/index.html *
+# * *
+# * Copyright notice: *
+# * Free use of the Mathematical Expression Toolkit Library is *
+# * permitted under the guidelines and in accordance with the *
+# * most current version of the MIT License. *
+# * http://www.opensource.org/licenses/MIT *
+# * *
+# **************************************************************
+#

Code/ThirdParty/exprtk/simvascular_exprtk/exprtk.cpp

@@ -0,0 +1 @@
+// dummy file