diff --git a/CMakeLists.txt b/CMakeLists.txt
index 22cecac16f5694c0e7b7610e42a75b611180690b..0512280a636d8ac94b41cb60ed60096c5cc41ec7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -96,27 +96,33 @@ endif()
set(CMAKE_MACOSX_RPATH 1) # Unsure if this works for CMAKE_BUIlD_RPATH, or just CMAKE_INSTALL_RPATH
set(CMAKE_BUILD_RPATH "${CMAKE_CUDA_IMPLICIT_LINK_DIRECTORIES}")
+## Set up doctest
+# option(ENABLE_DOCTESTS "Include tests in the library. Setting this to OFF will remove all doctest related code.
+# Tests in tests/*.cpp will still be enabled." ON)
+# set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/")
+# include(doctest)
+
+## Add subdirectories
+add_subdirectory(src)
+add_subdirectory(src/Tests)
+
# set(CMAKE_VERBOSE_MAKEFILE True)
add_executable("${PROJECT_NAME}" src/arbd.cpp
- src/ParticlePatch.cpp
- src/Integrator.cpp
- src/Integrator/CPU.cpp
- src/Integrator/CUDA.cu
- src/SignalManager.cpp
- src/GPUManager.cpp
- src/SimManager.cpp
- src/useful.cu
- )
+src/SimManager.cpp
+src/useful.cu
+)
+
+target_link_libraries("${PROJECT_NAME}" PUBLIC "lib${PROJECT_NAME}")
## Add optional libraries
if(USE_CUDA)
- target_link_libraries("${PROJECT_NAME}" PRIVATE curand)
+ target_link_libraries("${PROJECT_NAME}" PUBLIC curand)
endif()
if(USE_NCCL)
- target_link_libraries("${PROJECT_NAME}" PRIVATE nccl)
+ target_link_libraries("${PROJECT_NAME}" PUBLIC nccl)
endif()
if(USE_NVTX)
- target_link_libraries("${PROJECT_NAME}" PRIVATE nvToolsExt)
+ target_link_libraries("${PROJECT_NAME}" PUBLIC nvToolsExt)
endif()
install(TARGETS "${PROJECT_NAME}")
diff --git a/src/GPUManager.h b/src/GPUManager.h
index 2086361712b1ddc837091702c16db9a94faf63b9..d4b8d91d654beb68a4041e8e6c063289cb9ecc36 100644
--- a/src/GPUManager.h
+++ b/src/GPUManager.h
@@ -6,7 +6,7 @@
#include <cuda.h>
#include <cuda_runtime_api.h>
-#include "useful.h"
+// #include "useful.h"
#ifdef USE_NCCL
#include <nccl.h>
diff --git a/src/Integrator.h b/src/Integrator.h
index 8e71eb99b1ac001617a71325c85bea71a4799978..7ccb0f941b79f8cb9ae3134aea2100702fdc15e1 100644
--- a/src/Integrator.h
+++ b/src/Integrator.h
@@ -1,26 +1,22 @@
+/*********************************************************************
+ * @file Integrator.h
+ *
+ * @brief Declaration of Integrator class with factory-like method
+ * GetIntegrator()
+ *
+ * Defines hashable Integrator::Conf struct that allows operator
+ * resuse. Common CPU/GPU kernels implemented in Integrator/kernels.h
+ * with various BD/MD integrators implemented on different backends in
+ * Integrator/CUDA.h and Integrator/CPU.h
+ *********************************************************************/
#pragma once
#include <cassert>
#include <iostream>
#include <map>
-#include "PatchOps.h"
+#include "PatchOp.h"
-#ifdef __CUDACC__
- #define HOST __host__
- #define DEVICE __device__
-#else
- #define HOST
- #define DEVICE
-#endif
-
-namespace IntegratorKernels {
- HOST DEVICE void __inline__ BDIntegrate() {
- // std::cout << "Computes::BDIntegrate_inline" << std::endl;
- printf("Integrator::BDIntegrate\n");
- };
-}
-
-class Integrator : public BaseCompute {
+class Integrator : public BasePatchOp {
public:
virtual void compute(Patch* patch) = 0;
int num_patches() const { return 1; };
@@ -45,5 +41,6 @@ protected:
};
+#include "Integrator/kernels.h"
#include "Integrator/CUDA.h"
#include "Integrator/CPU.h"
diff --git a/src/Interaction.h b/src/Interaction.h
new file mode 100644
index 0000000000000000000000000000000000000000..cad0850688f8f38b27abf8a87bd784f8914ae311
--- /dev/null
+++ b/src/Interaction.h
@@ -0,0 +1,87 @@
+#pragma once
+
+#include <cassert>
+#include <iostream>
+#include <map>
+#include "PatchOp.h"
+
+class LocalInteraction : public BasePatchOp {
+public:
+ virtual void compute(Patch* patch) = 0;
+ int num_patches() const { return 1; };
+
+ // Following relates to lazy initialized factory method
+ struct Conf {
+ enum Object {Particle, RigidBody };
+ enum DoF {Bond, Angle, Dihedral, Bonded, NeighborhoodPair};
+ enum Form {Harmonic, Tabulated, LennardJones, Coulomb, LJ};
+ enum Backend { Default, CUDA, CPU };
+
+ Object object_type;
+ DoF dof;
+ Form form;
+ Backend backend;
+
+ explicit operator int() const {return object_type*64 + dof*16 + form*4 + backend;};
+ };
+
+ static LocalInteraction* GetInteraction(Conf& conf);
+
+private:
+ size_t num_interactions;
+
+protected:
+ static std::map<Conf, LocalInteraction*> _interactions;
+
+};
+
+// class LocalNonbondedInteraction : public BasePatchOp {
+// public:
+// virtual void compute(Patch* patch) = 0;
+// int num_patches() const { return 1; };
+
+// // Following relates to lazy initialized factory method
+// struct Conf {
+// enum Object {Particle, RigidBody };
+// enum Electrostatics {None, Coulomb, DebyeHuckel}
+// enum Form {Tabulated, LennardJones, Coulomb, LJ, DebyeHueckel};
+// enum Backend { Default, CUDA, CPU };
+
+// Object object_type;
+
+// std::string tabulated_file = "";
+// Algorithm algorithm;
+// Backend backend;
+
+// explicit operator int() const {return object_type*16 + algorithm*4 + backend;};
+// };
+
+// static Integrator* GetIntegrator(Conf& conf);
+
+// private:
+// size_t num_interactions;
+
+// protected:
+// static std::map<Conf, Integrator*> _integrators;
+
+// };
+
+// class LocalBonded : public LocalInteraction {
+
+// private:
+// size_t bondlist; // Encode bond, angle, dihedral
+
+// };
+
+// class LocalBonds : public LocalInteraction {
+
+// private:
+// // static const char* type = "Bond";
+// size_t bondlist;
+
+// };
+
+
+#include "Interaction/kernels.h"
+#include "Interaction/CUDA.h"
+#include "Interaction/CPU.h"
diff --git a/src/Interactions.h b/src/Interactions.h
deleted file mode 100644
index d58ae497e9eefdb54463b50689a0f28b12042859..0000000000000000000000000000000000000000
--- a/src/Interactions.h
+++ /dev/null
@@ -1,18 +0,0 @@
-#pragma once
-
-#include "useful.h"
-
-class Interactions {
- // Object to store all kinds of info about the simulation system, but no particle data
-
-public:
- size_t num_interactions;
-
-};
-
-class BondInteractions : public Interactions {
-
-private:
- static const char* type = "Bond";
- size_t bondlist;
-};
diff --git a/src/ParticlePatch.cpp b/src/ParticlePatch.cpp
index 1977e1fbcfdffebddc54a55989e69e0f399261df..a4464acaff0c9d677521770f70eb16154012b532 100644
--- a/src/ParticlePatch.cpp
+++ b/src/ParticlePatch.cpp
@@ -1,11 +1,5 @@
#include "ParticlePatch.h"
-// BasePatch::BasePatch(size_t num, short thread_id, short gpu_id) { ;};
-// BasePatch::BasePatch() {};
-// BasePatch::~BasePatch() {};
-
-// Patch::Patch(size_t num, short thread_id, short gpu_id) {};
-
void Patch::compute() {
for (auto& c_p: local_computes) {
c_p->compute(this);
diff --git a/src/ParticlePatch.cu b/src/ParticlePatch.cu
deleted file mode 100644
index 3628b208e26278975b34866e6cf9272c943524eb..0000000000000000000000000000000000000000
--- a/src/ParticlePatch.cu
+++ /dev/null
@@ -1,14 +0,0 @@
-#include "ParticlePatch.h"
-
-// BasePatch::BasePatch(size_t num, short thread_id, short gpu_id) { ;};
-// BasePatch::BasePatch() {};
-// BasePatch::~BasePatch() {};
-
-Patch::Patch(size_t num, short thread_id, short gpu_id) {};
-
-void Patch::compute() {
- for (auto& c_p: local_computes) {
- c_p->compute(this);
- }
-};
-
diff --git a/src/ParticlePatch.h b/src/ParticlePatch.h
index 3f337868a2f28cdff0344a4b92e4dbd76ade774e..2efcda21b9598d6a17d8bee71c93afeb30e3bd2e 100644
--- a/src/ParticlePatch.h
+++ b/src/ParticlePatch.h
@@ -18,10 +18,10 @@
#endif
#include "SimSystem.h"
-#include "useful.h"
+// #include "useful.h"
+#include "Types.h"
-#include "PatchOps.h"
-//class BaseCompute;
+#include "PatchOp.h"
class BasePatch {
public:
@@ -56,10 +56,10 @@ public:
// void addParticles(int n, int typ);
// template<class T>
// void add_compute(std::unique_ptr<T>&& p) {
- // std::unique_ptr<BaseCompute> base_p = static_cast<std::unique_ptr<BaseCompute>>(p);
+ // std::unique_ptr<BasePatchOp> base_p = static_cast<std::unique_ptr<BasePatchOp>>(p);
// local_computes.emplace_back(p);
// };
- void add_compute(std::unique_ptr<BaseCompute>&& p) {
+ void add_compute(std::unique_ptr<BasePatchOp>&& p) {
local_computes.emplace_back(std::move(p));
};
@@ -67,8 +67,8 @@ public:
private:
// std::vector<PatchProxy> neighbors;
- std::vector<std::unique_ptr<BaseCompute>> local_computes; // Operations that will be performed on this patch each timestep
- std::vector<std::unique_ptr<BaseCompute>> nonlocal_computes; // Operations that will be performed on this patch each timestep
+ std::vector<std::unique_ptr<BasePatchOp>> local_computes; // Operations that will be performed on this patch each timestep
+ std::vector<std::unique_ptr<BasePatchOp>> nonlocal_computes; // Operations that will be performed on this patch each timestep
static int patch_idx; // Unique ID across ranks
diff --git a/src/PatchOp.h b/src/PatchOp.h
new file mode 100644
index 0000000000000000000000000000000000000000..b1a4223dde39f3ca6c8acb4e6d4586b83b49c214
--- /dev/null
+++ b/src/PatchOp.h
@@ -0,0 +1,25 @@
+/*********************************************************************
+ * @file PatchOp.h
+ *
+ * @brief Declaration of BasePatchOp class.
+ *
+ * Includes headers of derived classes for convenient access to
+ * factory methods. Virtual method `BasePatchOp::compute(Patch*
+ * patch)` called by `patch->compute()` by any Patch to which the
+ * PatchOp has been added.
+ *********************************************************************/
+#pragma once
+
+class Patch;
+
+/// Abstract base class that operates on Patch data.
+class BasePatchOp {
+public:
+ virtual void compute(Patch* patch) = 0;
+ virtual int num_patches() const = 0;
+private:
+ void* compute_data;
+};
+
+#include "Integrator.h"
+#include "Interaction.h"
diff --git a/src/PatchOps.h b/src/PatchOps.h
deleted file mode 100644
index 13115b01602576f6ad286f11ac8d3b99d67ead1b..0000000000000000000000000000000000000000
--- a/src/PatchOps.h
+++ /dev/null
@@ -1,14 +0,0 @@
-#pragma once
-
-class Patch;
-
-class BaseCompute {
- // Low level class that operates on Patch data
-public:
- virtual void compute(Patch* patch) = 0;
- virtual int num_patches() const = 0;
-private:
- void* compute_data;
-};
-
-#include "Integrator.h"
diff --git a/src/SimManager.cpp b/src/SimManager.cpp
index 8fee0dc43450a373c057abf40cd39113954d9e6e..defd93cbe810281df01ac503389b26fbee47a4f0 100644
--- a/src/SimManager.cpp
+++ b/src/SimManager.cpp
@@ -1,16 +1,14 @@
#include "SimManager.h"
#include <memory>
-// class LocalPairForce;
-// class NeighborPairForce;
-// class BDIntegrate;
-// #include "Computes.h"
-
void SimManager::run() {
std::cout << "running" << std::endl;
+
// SimSystem sys = SimSystem();
// Patch p(10,0,0,sys);
+
Patch p(10,0,0);
+
//ProxyPatch p2(10,0,0);
// p.add_compute( std::make_unique<LocalPairForce>() );
@@ -18,11 +16,14 @@ void SimManager::run() {
#ifdef USE_CUDA
p.add_compute( std::make_unique<BDIntegrateCUDA>() );
+ p.add_compute( std::make_unique<LocalBondedCUDA>() );
#else
p.add_compute( std::make_unique<BDIntegrate>() );
+ p.add_compute( std::make_unique<LocalBonded>() );
#endif
for (size_t step = 0; step < 10; ++step) {
+ printf("Step\n");
p.compute();
#ifdef USE_CUDA
cudaDeviceSynchronize();
diff --git a/src/SimManager.h b/src/SimManager.h
index f48f00176af5dddd04ee475bd6a9e91ec14a17ad..a379954a2834ac67b194725e0127399a37327302 100644
--- a/src/SimManager.h
+++ b/src/SimManager.h
@@ -1,7 +1,7 @@
#pragma once
#include <iostream>
#include "ParticlePatch.h"
-#include "PatchOps.h"
+#include "PatchOp.h"
class SimManager {
public:
diff --git a/version.cmake b/version.cmake
deleted file mode 100644
index c366f35dd4c189dda3c9185b9687cb4b6d93c54d..0000000000000000000000000000000000000000
--- a/version.cmake
+++ /dev/null
@@ -1,43 +0,0 @@
-execute_process(COMMAND git log --pretty=format:'%h' -n 1
- OUTPUT_VARIABLE GIT_REV
- ERROR_QUIET)
-
-# Check whether we got any revision (which isn't
-# always the case, e.g. when someone downloaded a zip
-# file from Github instead of a checkout)
-if ("${GIT_REV}" STREQUAL "")
- set(GIT_REV "N/A")
- set(GIT_DIFF "")
- set(GIT_TAG "N/A")
- set(GIT_BRANCH "N/A")
- else()
- execute_process(
- COMMAND bash -c "git diff --quiet --exit-code || echo +"
- OUTPUT_VARIABLE GIT_DIFF)
- execute_process(
- COMMAND git describe --exact-match --tags
- OUTPUT_VARIABLE GIT_TAG ERROR_QUIET)
- execute_process(
- COMMAND git rev-parse --abbrev-ref HEAD
- OUTPUT_VARIABLE GIT_BRANCH)
-
- string(STRIP "${GIT_REV}" GIT_REV)
- string(SUBSTRING "${GIT_REV}" 1 7 GIT_REV)
- string(STRIP "${GIT_DIFF}" GIT_DIFF)
- string(STRIP "${GIT_TAG}" GIT_TAG)
- string(STRIP "${GIT_BRANCH}" GIT_BRANCH)
- endif()
-
-set(VERSION "const char* GIT_REV=\"${GIT_REV}${GIT_DIFF}\";
-const char* GIT_TAG=\"${GIT_TAG}\";
-const char* GIT_BRANCH=\"${GIT_BRANCH}\";")
-
-if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/version.cpp)
- file(READ ${CMAKE_CURRENT_SOURCE_DIR}/version.cpp VERSION_)
- else()
- set(VERSION_ "")
- endif()
-
-if (NOT "${VERSION}" STREQUAL "${VERSION_}")
- file(WRITE ${CMAKE_CURRENT_SOURCE_DIR}/version.cpp "${VERSION}")
-endif()
\ No newline at end of file