merge from main

Author: hamidrezanorouzi

.gitignore

@@ -1,6 +1,12 @@
+# files 
+.clang-format
+.vscode
+.dependencygraph
+
 # Prerequisites
 *.d
 
+
 # Compiled Object files
 *.slo
 *.lo

CMakeLists.txt

@@ -1,88 +1,83 @@
 cmake_minimum_required(VERSION 3.16 FATAL_ERROR)
 
 # set the project name and version
-project(phasicFlow VERSION 0.1 )
+project(phasicFlow VERSION 1.0 )
 
 set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 set(CMAKE_INSTALL_PREFIX ${phasicFlow_SOURCE_DIR} CACHE PATH "Install path of phasicFlow" FORCE)
-set(CMAKE_BUILD_TYPE Release CACHE STRING "build type" FORCE)
+set(CMAKE_BUILD_TYPE Debug CACHE STRING "build type" FORCE)
+set(BUILD_SHARED_LIBS ON CACHE BOOL "Build using shared libraries" FORCE)
+mark_as_advanced(FORCE var BUILD_SHARED_LIBS)
 
 message(STATUS ${CMAKE_INSTALL_PREFIX})
 
-mark_as_advanced(FORCE var Kokkos_ENABLE_CUDA_LAMBDA)
-mark_as_advanced(FORCE var Kokkos_ENABLE_OPENMP)
-mark_as_advanced(FORCE var Kokkos_ENABLE_SERIAL)
-mark_as_advanced(FORCE var Kokkos_ENABLE_CUDA_LAMBDA)
-mark_as_advanced(FORCE var BUILD_SHARED_LIBS)
+include(cmake/globals.cmake)
+
+#Kokkos directory to be included 
+set(Kokkos_Source_DIR)
+
+if(DEFINED ENV{Kokkos_DIR})
+   set(Kokkos_Source_DIR $ENV{Kokkos_DIR})
+else()
+  set(Kokkos_Source_DIR $ENV{HOME}/Kokkos/kokkos)
+endif()
+message(STATUS "Kokkos source directory is ${Kokkos_Source_DIR}")
+add_subdirectory(${Kokkos_Source_DIR} ./kokkos)
+Kokkos_cmake_settings()
+
 
-option(USE_STD_PARALLEL_ALG "Use TTB std parallel algorithms" ON)
+option(pFlow_STD_Parallel_Alg "Use TTB std parallel algorithms" ON)
 option(pFlow_Build_Serial "Build phasicFlow and backends for serial execution" OFF)
 option(pFlow_Build_OpenMP "Build phasicFlow and backends for OpenMP execution" OFF)
 option(pFlow_Build_Cuda   "Build phasicFlow and backends for Cuda execution" OFF)
-option(pFlow_Build_Double "Build phasicFlow with double precision variables" ON)
+option(pFlow_Build_Double "Build phasicFlow with double precision floating-oint variables" ON)
+option(pFlow_Build_MPI    "Build for MPI parallelization. This will enable multi-gpu run, CPU run on clusters (distributed memory machine). Use this combination Cuda+MPI, OpenMP + MPI or Serial+MPI " OFF)
 
-set(BUILD_SHARED_LIBS ON CACHE BOOL "Build using shared libraries" FORCE)
 
 if(pFlow_Build_Serial)
 	set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "Serial execution" FORCE) 
 	set(Kokkos_ENABLE_OPENMP OFF CACHE BOOL "OpenMP execution" FORCE)
 	set(Kokkos_ENABLE_CUDA OFF CACHE BOOL "Cuda execution" FORCE)
 	set(Kokkos_ENABLE_CUDA_LAMBDA OFF CACHE BOOL "Cuda execution" FORCE)
+	set(Kokkos_ENABLE_CUDA_CONSTEXPR OFF CACHE BOOL "Enable constexpr on cuda code" FORCE)
 elseif(pFlow_Build_OpenMP )
 	set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "Serial execution" FORCE) 
 	set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "OpenMP execution" FORCE)
 	set(Kokkos_ENABLE_CUDA OFF CACHE BOOL "Cuda execution" FORCE)
 	set(Kokkos_ENABLE_CUDA_LAMBDA OFF CACHE BOOL "Cuda execution" FORCE)
 	set(Kokkos_DEFAULT_HOST_PARALLEL_EXECUTION_SPACE SERIAL CACHE STRING "" FORCE)
+	set(Kokkos_ENABLE_CUDA_CONSTEXPR OFF CACHE BOOL "Enable constexpr on cuda code" FORCE)
 elseif(pFlow_Build_Cuda)
 	set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "Serial execution" FORCE) 
 	set(Kokkos_ENABLE_OPENMP OFF CACHE BOOL "OpenMP execution" FORCE)
 	set(Kokkos_ENABLE_CUDA ON CACHE BOOL "Cuda execution" FORCE)
 	set(Kokkos_ENABLE_CUDA_LAMBDA ON CACHE BOOL "Cuda execution" FORCE)
+	set(Kokkos_ENABLE_CUDA_CONSTEXPR ON CACHE BOOL "Enable constexpr on cuda code" FORCE)
 endif()
 
-
-
-include(cmake/globals.cmake)
-message(STATUS "Valid file extensions are ${validFiles}")
+if(pFlow_Build_MPI)
+	find_package(MPI REQUIRED)
+endif()
 
 include(cmake/makeLibraryGlobals.cmake)
 include(cmake/makeExecutableGlobals.cmake)
 
 configure_file(phasicFlowConfig.H.in phasicFlowConfig.H)
-
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 #add a global include directory 
 include_directories(src/setHelpers src/demComponent "${PROJECT_BINARY_DIR}")
 
-#main subdirectories of the code 
-set(Kokkos_Source_DIR)
-
-if(DEFINED ENV{Kokkos_DIR})
-   set(Kokkos_Source_DIR $ENV{Kokkos_DIR})
-#  add_subdirectory($ENV{Kokkos_DIR} ${phasicFlow_BINARY_DIR}/kokkos)
-#  message(STATUS "Kokkos directory is $ENV{Kokkos_DIR}")
-else()
-#  add_subdirectory($ENV{HOME}/Kokkos/kokkos ${phasicFlow_BINARY_DIR}/kokkos)
-  set(Kokkos_Source_DIR $ENV{HOME}/Kokkos/kokkos)
-endif()
-
-message(STATUS "Kokkos source directory is ${Kokkos_Source_DIR}")
-add_subdirectory(${Kokkos_Source_DIR} ${phasicFlow_BINARY_DIR}/kokkos)
-
 add_subdirectory(src)
 
 add_subdirectory(solvers)
 
 add_subdirectory(utilities)
 
 add_subdirectory(DEMSystems)
-#add_subdirectory(testIO)
-
 
 install(FILES "${PROJECT_BINARY_DIR}/phasicFlowConfig.H"
-  DESTINATION include
-)
+  DESTINATION include)
 
 include(InstallRequiredSystemLibraries)
 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")

DEMSystems/CMakeLists.txt

@@ -1,9 +1,11 @@
 
 set(SourceFiles 
+domainDistribute/domainDistribute.cpp
 DEMSystem/DEMSystem.cpp
-sphereDEMSystem/sphereDEMSystem.cpp
 sphereDEMSystem/sphereFluidParticles.cpp
-domainDistribute/domainDistribute.cpp
+sphereDEMSystem/sphereDEMSystem.cpp
+grainDEMSystem/grainFluidParticles.cpp
+grainDEMSystem/grainDEMSystem.cpp
 )
 
 set(link_libs Kokkos::kokkos phasicFlow Particles Geometry Property Interaction Interaction Utilities)

DEMSystems/DEMSystem/DEMSystem.cpp

@@ -33,14 +33,14 @@ pFlow::DEMSystem::DEMSystem(
 	ControlDict_()
 {
 
-  REPORT(0)<<"Initializing host/device execution spaces . . . \n";
-	REPORT(1)<<"Host execution space is "<< greenText(DefaultHostExecutionSpace::name())<<endREPORT;
-	REPORT(1)<<"Device execution space is "<<greenText(DefaultExecutionSpace::name())<<endREPORT;
+	REPORT(0)<<"Initializing host/device execution spaces . . . \n";
+	REPORT(1)<<"Host execution space is "<< Green_Text(DefaultHostExecutionSpace::name())<<END_REPORT;
+	REPORT(1)<<"Device execution space is "<<Green_Text(DefaultExecutionSpace::name())<<END_REPORT;
 
  	// initialize Kokkos
 	Kokkos::initialize( argc, argv ); 
 
-	REPORT(0)<<"\nCreating Control repository . . ."<<endREPORT;
+	REPORT(0)<<"\nCreating Control repository . . ."<<END_REPORT;
 	Control_ = makeUnique<systemControl>(
 		ControlDict_.startTime(),
 		ControlDict_.endTime(),
@@ -87,4 +87,3 @@ pFlow::uniquePtr<pFlow::DEMSystem>
 
 	return nullptr;
 }
-

DEMSystems/DEMSystem/DEMSystem.hpp

@@ -25,6 +25,7 @@
 
 #include "types.hpp"
 #include "span.hpp"
+#include "box.hpp"
 #include "virtualConstructor.hpp"
 #include "uniquePtr.hpp"
 #include "systemControl.hpp"
@@ -60,6 +61,7 @@ class DEMSystem
 
 	DEMSystem(const DEMSystem&)=delete;
 
+	/// @brief no assignment 
 	DEMSystem& operator = (const DEMSystem&)=delete;
 
 	create_vCtor(
@@ -111,19 +113,34 @@ class DEMSystem
 	int32 numParInDomain(int32 di)const = 0;
 
 	virtual
-	std::vector<int32> numParInDomain()const = 0;
+	std::vector<int32> numParInDomains()const = 0;
 
 	virtual 
-	span<const int32> parIndexInDomain(int32 di)const = 0;
+	span<const int32> parIndexInDomain(int32 domIndx)const = 0;
 
 	virtual
-	span<real> parDiameter() = 0; 
+	span<real> diameter() = 0; 
+
+	virtual 
+	span<real> courseGrainFactor() = 0;
+
+	virtual
+	span<realx3> acceleration()=0;
 
 	virtual
-	span<realx3> parVelocity() = 0;
+	span<realx3> velocity() = 0;
 
 	virtual
-	span<realx3> parPosition() = 0;
+	span<realx3> position() = 0;
+
+	virtual
+	span<realx3> rAcceleration()=0;
+
+	virtual
+	span<realx3> rVelocity() = 0;
+
+	virtual
+	span<realx3> rPosition() = 0;
 
 	virtual
 	span<realx3> parFluidForce() = 0;
@@ -153,7 +170,6 @@ class DEMSystem
 	bool iterate(real upToTime) = 0;
 
 
-
 	static 
 	uniquePtr<DEMSystem>
 		create(
@@ -162,8 +178,6 @@ class DEMSystem
 			int argc, 
 			char* argv[]);
 
-
-
 };
 
 

DEMSystems/domainDistribute/domainDistribute.cpp

@@ -33,7 +33,7 @@ void pFlow::domainDistribute::clcDomains(const std::vector<box>& domains)
 
 
 pFlow::domainDistribute::domainDistribute(
-	const Vector<box>& domains,
+	const std::vector<box>& domains,
 	real maxBoundingBox)
 :
 numDomains_(domains.size()),
@@ -47,10 +47,10 @@ maxBoundingBoxSize_(maxBoundingBox)
 }
 
 bool pFlow::domainDistribute::locateParticles(
-		ViewType1D<realx3,HostSpace> points, includeMask mask)
+		ViewType1D<realx3,HostSpace> points, const pFlagTypeHost& mask)
 {
 
-	range activeRange = mask.activeRange();
+	const rangeU32 activeRange = mask.activeRange();
 
 
 	for(int32 di=0; di<numDomains_; di++)
@@ -59,7 +59,7 @@ bool pFlow::domainDistribute::locateParticles(
 	}
 
 
-	for(int32 i=activeRange.first; i<activeRange.second; i++)
+	for(int32 i=activeRange.start(); i<activeRange.end(); i++)
 	{
 		if(mask(i))
 		{

DEMSystems/domainDistribute/domainDistribute.hpp

@@ -43,19 +43,16 @@ class domainDistribute
 
 	int32Vector_H 							numParInDomain_;
 
-
 	real maxBoundingBoxSize_;
 
 	real domainExtension_ = 1.0;
 
-	using includeMask = typename pointStructure::activePointsHost;
-
 	void clcDomains(const std::vector<box>& domains);
 
 public:
 
 	domainDistribute(
-		const Vector<box>& domains,
+		const std::vector<box>& domains,
 		real maxBoundingBox);
 
 	~domainDistribute()=default;
@@ -78,7 +75,7 @@ class domainDistribute
 	{
 		return
 		span<const int32>(
-			particlesInDomains_[di].hostVectorAll().data(),
+			particlesInDomains_[di].hostViewAll().data(),
 			numParInDomain_[di]
 			);
 	}
@@ -91,7 +88,7 @@ class domainDistribute
 
 	//template<typename includeMask>
 	bool locateParticles(
-		ViewType1D<realx3,HostSpace> points, includeMask mask);
+		ViewType1D<realx3,HostSpace> points, const pFlagTypeHost& mask);
 
 };