'ode_method' is available in rdesineur.

Fixed compilation process; merged master branch.

Author: Dilawar Singh

CMakeLists.txt

@@ -119,17 +119,15 @@ if(WITH_BOOST)
 endif(WITH_BOOST)
 
 # If using BOOST ODE2 library to solve ODE system, then don't use GSL.
-if(WITH_BOOST_ODE OR WITH_BOOST)
-    message(STATUS "Turning off GSL")
+if(WITH_BOOST_ODE)
     set(WITH_GSL OFF)
-endif()
+endif(WITH_BOOST_ODE)
 
 set_target_properties(libmoose PROPERTIES COMPILE_DEFINITIONS  "MOOSE_LIB")
 set_target_properties(libmoose PROPERTIES PREFIX "")
 
 ## Variable to collect all static libraries.
 set(STATIC_LIBRARIES "" )
-
 # Collect all shared libraries here.
 set(SYSTEM_SHARED_LIBS ${LibXML2_LIBRARIES})
 
@@ -179,16 +177,14 @@ if(WITH_MPI)
     endif()
 endif(WITH_MPI)
 
-if(WITH_BOOST OR WITH_BOOST_ODE)
+if(WITH_BOOST_ODE)
     list(APPEND SYSTEM_SHARED_LIBS ${LAPACK_LIBRARIES})
     list(APPEND SYSTEM_SHARED_LIBS ${Boost_LIBRARIES})
 endif(WITH_BOOST_ODE)
 
 find_package( Threads )
 list(APPEND SYSTEM_SHARED_LIBS ${CMAKE_THREAD_LIBS_INIT})
 
-list(APPEND SYSTEM_SHARED_LIBS ${CMAKE_THREAD_LIBS_INIT})
-
 # These libraries could be static of dynamic. We need to discrimate between
 # these two types because of --whole-archive option. See
 # BhallaLab/moose-core#66,
@@ -240,10 +236,6 @@ add_subdirectory(kinetics)
 add_subdirectory(synapse)
 add_subdirectory(intfire)
 add_subdirectory(external/libsoda)
-add_subdirectory(external/muparser)
-
-list(APPEND MOOSE_LIBRARIES muparser)
-
 
 ###################################### LINKING #################################
 list(APPEND MOOSE_LIBRARIES
@@ -273,7 +265,7 @@ list(APPEND MOOSE_LIBRARIES
 list(REMOVE_DUPLICATES STATIC_LIBRARIES)
 if(SYSTEM_SHARED_LIBS)
     list(REMOVE_DUPLICATES SYSTEM_SHARED_LIBS)
-endif()
+endif( )
 
 # cmake --help-policy CMP0042. Also in pymoose/CMakeLists.txt
 # More details:
@@ -312,7 +304,7 @@ target_link_libraries(moose.bin moose ${CMAKE_DL_LIBS})
 
 if( WITH_BOOST )
     target_link_libraries( moose.bin ${Boost_LIBRARIES} )
-endif( )
+endif( WITH_BOOST )
 
 
 ######################### BUILD PYMOOSE ########################################

basecode/global.h

@@ -65,8 +65,6 @@ namespace moose
 
     extern map<string, valarray<double>> solverProfMap;
 
-    extern map<string, valarray<double>> solverProfMap;
-
     /**
      * @brief A global seed for all RNGs in moose. When moose.seed( x ) is called,
      * this variable is set. Other's RNGs (except muparser) uses this seed to

external/libsoda/CMakeLists.txt

@@ -1,32 +1,16 @@
 cmake_minimum_required(VERSION 2.8)
 
-set(CMAKE_BUILD_TYPE Release)
-add_definitions( -std=c++11 ) 
-
-add_library( lsoda ${CMAKE_CURRENT_SOURCE_DIR}/LSODA.cpp)
-
-if( "${CMAKE_BUILD_TYPE}" STREQUAL "Release" )
-    message( STATUS "Building for release" )
-    set_target_properties( lsoda PROPERTIES COMPILE_FLAGS "-Werror -Wall")
-else()
-    message( STATUS "Building for DEBUG mode" )
-endif()
+add_library(lsoda ${CMAKE_CURRENT_SOURCE_DIR}/LSODA.cpp)
 
 find_package(Threads REQUIRED)
 
-add_executable( test_lsoda ${CMAKE_CURRENT_SOURCE_DIR}/test_LSODA.cpp)
-target_link_libraries( test_lsoda lsoda )
+add_executable(test_lsoda test_LSODA.cpp)
+target_link_libraries(test_lsoda lsoda)
 
-add_executable( benchmark_lsoda ${CMAKE_CURRENT_SOURCE_DIR}/benchmark_LSODA.cpp)
-target_link_libraries( benchmark_lsoda lsoda )
-
-set_target_properties(test_lsoda PROPERTIES COMPILE_FLAGS "-g -UNDEBUG" )
-set_target_properties(benchmark_lsoda 
-    PROPERTIES COMPILE_FLAGS "-O3" LINK_FLAGS "-pthread"
-    ) 
+add_executable(benchmark_lsoda benchmark_LSODA.cpp)
+target_link_libraries(benchmark_lsoda lsoda)
 target_link_libraries(benchmark_lsoda ${CMAKE_THREAD_LIBS_INIT})
 
 enable_testing()
 add_test(NAME test_lsoda COMMAND $<TARGET_FILE:test_lsoda>)
 add_test(NAME test_benchmark COMMAND $<TARGET_FILE:benchmark_lsoda>)
-

ksolve/CMakeLists.txt

@@ -4,7 +4,7 @@ include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
 
 if(WITH_BOOST)
     find_package(Boost 1.53 REQUIRED COMPONENTS thread)
-    add_definitions( -DUSE_BOOST_ASYNC )
+    add_definitions(-DUSE_BOOST )
     set(WITH_BOOST_ODE ON)
     include_directories( ${Boost_INCLUDE_DIRS} )
     # This is still not part of official bindings.
@@ -18,7 +18,7 @@ if(WITH_BOOST_ODE)
     include_directories(${CMAKE_CURRENT_SOURCE_DIR}/../external/boost-numeric-bindings)
 elseif(WITH_GSL)
     include_directories( ${GSL_INCLUDE_DIRS} )
-    add_definitions(-DUSE_GSL -UUSE_BOOST_ODE)
+    add_definitions(-DUSE_GSL -UUSE_BOOST_ODE -UUSE_BOOST)
 endif(WITH_BOOST_ODE)
 
 set(KSOLVE_SRCS

ksolve/Gsolve.cpp

@@ -562,18 +562,6 @@ size_t Gsolve::advance_chunk( const size_t begin, const size_t end, ProcPtr p )
     return tot;
 }
 
-void Gsolve::recalcTimeChunk( const size_t begin, const size_t end, ProcPtr p)
-{
-    for (size_t i = begin; i < std::min(pools_.size(), end); i++) 
-        pools_[i].recalcTime( &sys_, p->currTime );
-}
-
-void Gsolve::advance_chunk( const size_t begin, const size_t end, ProcPtr p )
-{
-    for (size_t i = begin; i < std::min(end, pools_.size() ); i++)
-        pools_[i].advance( p, &sys_ );
-}
-
 void Gsolve::reinit( const Eref& e, ProcPtr p )
 {
     if ( !stoichPtr_ )
@@ -903,8 +891,7 @@ void Gsolve::makeReacDepsUnique()
         vector< unsigned int >& dep = sys_.dependency[ i ];
         // Here we want to remove self-entries as well as duplicates.
         sort( dep.begin(), dep.end() );
-
-        // vector< unsigned int >::iterator k = dep.begin();
+        vector< unsigned int >::iterator k = dep.begin();
 
         /// STL stuff follows, with the usual weirdness.
         vector<unsigned int>::iterator pos = unique( dep.begin(), dep.end() );

ksolve/Ksolve.cpp

@@ -17,23 +17,21 @@
 #include <gsl/gsl_odeiv2.h>
 #endif
 
-#include "../shell/Shell.h"
-
-#include "../mesh/MeshEntry.h"
-#include "../mesh/Boundary.h"
-#include "../mesh/ChemCompt.h"
-#include "../mesh/VoxelJunction.h"
-
-#include "../utility/print_function.hpp"
-
 #include "OdeSystem.h"
 #include "VoxelPoolsBase.h"
 #include "VoxelPools.h"
+#include "../mesh/VoxelJunction.h"
 #include "ZombiePoolInterface.h"
+
 #include "RateTerm.h"
 #include "../basecode/SparseMatrix.h"
 #include "KinSparseMatrix.h"
 #include "Stoich.h"
+#include "../shell/Shell.h"
+
+#include "../mesh/MeshEntry.h"
+#include "../mesh/Boundary.h"
+#include "../mesh/ChemCompt.h"
 #include "Ksolve.h"
 
 #include <chrono>
@@ -246,15 +244,7 @@ Ksolve::Ksolve()
 
 Ksolve::~Ksolve()
 {
-#if 0
-    char* p = getenv( "MOOSE_SHOW_SOLVER_PERF" );
-    if( p != NULL )
-    {
-        cout << "Info: Ksolve (+Dsolve) took " << totalTime_ << " seconds and took " << numSteps_
-             << " steps." << endl;
-
-    }
-#endif
+    ;
 }
 
 //////////////////////////////////////////////////////////////
@@ -269,7 +259,6 @@ string Ksolve::getMethod() const
 void Ksolve::setMethod( string method )
 {
     std::transform(method.begin(), method.end(), method.begin(), ::tolower);
-
     // If user is trying to set ksolve method after ksolve has been initialized,
     // show a warning.
     if( isBuilt_ )
@@ -288,44 +277,27 @@ void Ksolve::setMethod( string method )
         method_ = "rk5";
     }
     else if ( method == "rk4"  || method == "rk2" ||
-              method == "rk8" || method == "rkck" || method == "lsoda"
-            )
+              method == "rk8" || method == "rkck" || method == "lsoda" )
     {
         method_ = method;
     }
     else
     {
         cout << "Warning: Ksolve::setMethod: '" << method <<
-             "' not known, using default rk5\n";
+             "' is not known, using default rk5\n";
         method_ = "rk5";
     }
 #elif USE_BOOST_ODE
     // TODO: Check for boost related methods.
     method_ = method;
 #endif
-
 }
 
 double Ksolve::getEpsAbs() const
 {
     return epsAbs_;
 }
 
-double Ksolve::getEpsRel() const
-{
-    return epsRel_;
-}
-
-double Ksolve::getRelativeAccuracy( ) const
-{
-    return getEpsRel();
-}
-
-double Ksolve::getAbsoluteAccuracy( ) const
-{
-    return getEpsAbs();
-}
-
 void Ksolve::setEpsAbs( double epsAbs )
 {
     if ( epsAbs < 0 )
@@ -334,6 +306,12 @@ void Ksolve::setEpsAbs( double epsAbs )
         epsAbs_ = epsAbs;
 }
 
+
+double Ksolve::getEpsRel() const
+{
+    return epsRel_;
+}
+
 void Ksolve::setEpsRel( double epsRel )
 {
     if ( epsRel < 0 )
@@ -537,8 +515,6 @@ double Ksolve::getEstimatedDt() const
 //////////////////////////////////////////////////////////////
 void Ksolve::process( const Eref& e, ProcPtr p )
 {
-
-
     if ( isBuilt_ == false )
         return;
 

ksolve/OdeSystem.h

@@ -16,14 +16,13 @@
 #include <gsl/gsl_odeiv2.h>
 #endif     /* -----  not USE_BOOST_ODE  ----- */
 
-class OdeSystem
-{
-public:
-    OdeSystem()
-        : method( "rk5" ),
-          initStepSize( 0.001 ),
-          epsAbs( 1e-6 ),
-          epsRel( 1e-6 )
+class OdeSystem {
+    public:
+        OdeSystem()
+            : method( "rk5" ),
+            initStepSize( 0.001 ),
+            epsAbs( 1e-6 ),
+            epsRel( 1e-6 )
     {;}
 
         std::string method;