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Commit df4b64cb authored by Peter Eastman's avatar Peter Eastman
Browse files

Checked in explicit solvent implementation for Cuda platform (cutoffs,... 

Checked in explicit solvent implementation for Cuda platform (cutoffs, periodic boundary conditions, SETTLE)
parent 08d6cc4c
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openmmapi/include/GBSAOBCForce.h
View file @ df4b64cb
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -40,6 +40,9 @@ namespace OpenMM { ...@@ -40,6 +40,9 @@ namespace OpenMM {
/** /**
* This class implements an implicit solvation force using the GBSA-OBC model. * This class implements an implicit solvation force using the GBSA-OBC model.
* <p>
* If the System also contains a NonbondedForce, this force will use the cutoffs
* and periodic boundary conditions specified in it.
*/ */
class OPENMM_EXPORT GBSAOBCForce : public Force { class OPENMM_EXPORT GBSAOBCForce : public Force {
...@@ -104,20 +107,20 @@ private: ...@@ -104,20 +107,20 @@ private:
class ParticleInfo; class ParticleInfo;
double solventDielectric, soluteDielectric; double solventDielectric, soluteDielectric;
// Retarded visual studio compiler complains about being unable to // Retarded visual studio compiler complains about being unable to
// export private stl class members. // export private stl class members.
// This stanza explains that it should temporarily shut up. // This stanza explains that it should temporarily shut up.
#if defined(_MSC_VER) #if defined(_MSC_VER)
#pragma warning(push) #pragma warning(push)
#pragma warning(disable:4251) #pragma warning(disable:4251)
#endif #endif
std::vector<ParticleInfo> particles; std::vector<ParticleInfo> particles;
#if defined(_MSC_VER) #if defined(_MSC_VER)
#pragma warning(pop) #pragma warning(pop)
#endif #endif
}; };
class GBSAOBCForce::ParticleInfo { class GBSAOBCForce::ParticleInfo {
......
openmmapi/include/System.h
View file @ df4b64cb
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -130,6 +130,14 @@ public: ...@@ -130,6 +130,14 @@ public:
* *
* @param index the index of the Force to get * @param index the index of the Force to get
*/ */
const Force& getForce(int index) const {
return *forces[index];
}
/**
* Get a reference to one of the Forces in this System.
*
* @param index the index of the Force to get
*/
Force& getForce(int index) { Force& getForce(int index) {
return *forces[index]; return *forces[index];
} }
......
openmmapi/include/internal/ForceImpl.h
View file @ df4b64cb
...@@ -33,6 +33,7 @@ ...@@ -33,6 +33,7 @@
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include <map> #include <map>
#include <string>
#include <vector> #include <vector>
namespace OpenMM { namespace OpenMM {
......
platforms/cuda/cudpp/license.txt 0 → 100644
View file @ df4b64cb
CUDA Data-Parallel Primitives Library (CUDPP) is the proprietary
property of The Regents of the University of California ("The
Regents") and NVIDIA Corporation ("NVIDIA").
Copyright (c) 2007-2008 The Regents of the University of California, Davis
campus and NVIDIA Corporation. All Rights Reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
- Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
- Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
- Neither the name of The Regents, NVIDIA, nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
The end-user understands that the program was developed for research
purposes and is advised not to rely exclusively on the program for any
reason. No other rights or permissions are granted beyond what is stated
explictely herein.
THE SOFTWARE PROVIDED IS ON AN "AS IS" BASIS, AND THE REGENTS, NVIDIA
AND CONTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE REGENTS, NVIDIA AND
CONTRIBUTORS SPECIFICALLY DISCLAIM ANY EXPRESS OR IMPLIED WARRANTIES,
INCLUDING BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE REGENTS, NVIDIA OR CONTRIBUTORS BE LIABLE TO ANY
PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, 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 UNDER 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 AND ITS DOCUMENTATION, EVEN IF ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.
If you do not agree to these terms, do not download or use the
software. This license may be modified only in a writing signed by
authorized signatory of all parties. For The Regents contact
copyright@ucdavis.edu.
Relating to funding received by the Regents-
Acknowledgment: This material is based in part upon work supported by
the Department of Energy under Award Numbers DE-FG02-04ER25609 and
DE-FC02-06ER25777.
Disclaimer: This report was prepared as an account of work sponsored
by an agency of the United States Government. Neither the United
States Government nor any agency thereof, nor any of their employees,
makes any warranty, express or implied, or assumes any legal liability
or responsibility for the accuracy, completeness, or usefulness of any
information, apparatus, product, or process disclosed, or represents
that its use would not infringe privately owned rights. Reference
herein to any specific commercial product, process, or service by
trade name, trademark, manufacturer, or otherwise does not necessarily
constitute or imply its endorsement, recommendation, or favoring by
the United States Government or any agency thereof. The views and
opinions of authors expressed herein do not necessarily state or
reflect those of the United States Government or any agency hereof.
platforms/cuda/cudpp/license_nv.txt 0 → 100644
View file @ df4b64cb
This portion of the CUDA Data-Parallel Primitives Library (CUDPP) is the
proprietary property of NVIDIA Corporation ("NVIDIA").
Copyright (c) 2007-2008 NVIDIA Corporation. All Rights Reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
- Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
- Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
- Neither the name of NVIDIA, nor the names of its contributors may be used to
endorse or promote products derived from this software without specific prior
written permission.
The end-user understands that the program was developed for research
purposes and is advised not to rely exclusively on the program for any
reason. No other rights or permissions are granted beyond what is stated
explictely herein.
THE SOFTWARE PROVIDED IS ON AN "AS IS" BASIS, AND NVIDIA
AND CONTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
UPDATES, ENHANCEMENTS, OR MODIFICATIONS. NVIDIA AND CONTRIBUTORS
SPECIFICALLY DISCLAIM ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING
BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
SHALL NVIDIA OR CONTRIBUTORS BE LIABLE TO ANY PARTY FOR DIRECT,
INDIRECT, SPECIAL, INCIDENTAL, 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 UNDER 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 AND ITS
DOCUMENTATION, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
If you do not agree to these terms, do not download or use the
software. This license may be modified only in a writing signed by
authorized signatory of all parties.
\ No newline at end of file
platforms/cuda/include/CudaPlatform.h
View file @ df4b64cb
...@@ -65,14 +65,16 @@ private: ...@@ -65,14 +65,16 @@ private:
class CudaPlatform::PlatformData { class CudaPlatform::PlatformData {
public: public:
PlatformData(_gpuContext* gpu) : gpu(gpu), removeCM(false), useOBC(false), hasBonds(false), hasAngles(false), PlatformData(_gpuContext* gpu) : gpu(gpu), removeCM(false), nonbondedMethod(0), hasBonds(false), hasAngles(false),
hasPeriodicTorsions(false), hasRB(false), hasNonbonded(false), primaryKernel(NULL) { hasPeriodicTorsions(false), hasRB(false), hasNonbonded(false), primaryKernel(NULL), stepCount(0) {
} }
_gpuContext* gpu; _gpuContext* gpu;
KernelImpl* primaryKernel; KernelImpl* primaryKernel;
bool removeCM, useOBC; bool removeCM;
bool hasBonds, hasAngles, hasPeriodicTorsions, hasRB, hasNonbonded; bool hasBonds, hasAngles, hasPeriodicTorsions, hasRB, hasNonbonded;
int nonbondedMethod;
int cmMotionFrequency; int cmMotionFrequency;
int stepCount;
}; };
} // namespace OpenMM } // namespace OpenMM
......
platforms/cuda/sharedTarget/CMakeLists.txt
View file @ df4b64cb
...@@ -5,19 +5,18 @@ INCLUDE(${FINDCUDA_DIR}/FindCuda.cmake) ...@@ -5,19 +5,18 @@ INCLUDE(${FINDCUDA_DIR}/FindCuda.cmake)
INCLUDE_DIRECTORIES(${CUDA_INCLUDE}) INCLUDE_DIRECTORIES(${CUDA_INCLUDE})
LINK_DIRECTORIES(${CUDA_TARGET_LINK}) LINK_DIRECTORIES(${CUDA_TARGET_LINK})
FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS}) FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
FILE(GLOB src_files ${CMAKE_SOURCE_DIR}/platforms/cuda/${subdir}/src/*.cu ${CMAKE_SOURCE_DIR}/platforms/cuda/src/*/*.cu) FILE(GLOB src_files ${CMAKE_SOURCE_DIR}/platforms/cuda/${subdir}/src/*.cu ${CMAKE_SOURCE_DIR}/platforms/cuda/${subdir}/src/*/*.cu)
FOREACH(file ${src_files}) FOREACH(file ${src_files})
FILE(RELATIVE_PATH file ${CMAKE_SOURCE_DIR}/platforms/cuda ${file}) FILE(RELATIVE_PATH file ${CMAKE_SOURCE_DIR}/platforms/cuda ${file})
SET(SOURCE_FILES ${SOURCE_FILES} ${file}) #append SET(SOURCE_FILES ${SOURCE_FILES} ${file}) #append
ENDFOREACH(file) ENDFOREACH(file)
CUDA_INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda/../${subdir}/include) CUDA_INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda/${subdir}/include)
CUDA_INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda/${subdir}/src)
ENDFOREACH(subdir) ENDFOREACH(subdir)
CUDA_INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda/../src)
CUDA_ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES}) CUDA_ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}_d optimized ${OPENMM_LIBRARY_NAME}) TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}_d optimized ${OPENMM_LIBRARY_NAME} cudpp cutil)
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY") SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY")
INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_TARGET}) INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_TARGET})
platforms/cuda/src/CudaKernels.cpp
View file @ df4b64cb
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -47,24 +47,30 @@ using namespace std; ...@@ -47,24 +47,30 @@ using namespace std;
static void calcForces(OpenMMContextImpl& context, CudaPlatform::PlatformData& data) { static void calcForces(OpenMMContextImpl& context, CudaPlatform::PlatformData& data) {
_gpuContext* gpu = data.gpu; _gpuContext* gpu = data.gpu;
if (data.useOBC) { if (data.stepCount%100 == 0)
gpuReorderAtoms(gpu);
data.stepCount++;
kClearForces(gpu);
if (gpu->bIncludeGBSA) {
gpu->bRecalculateBornRadii = true; gpu->bRecalculateBornRadii = true;
kCalculateCDLJObcGbsaForces1(gpu); kCalculateCDLJObcGbsaForces1(gpu);
kReduceObcGbsaBornForces(gpu); kReduceObcGbsaBornForces(gpu);
kCalculateObcGbsaForces2(gpu); kCalculateObcGbsaForces2(gpu);
} }
else { else if (data.hasNonbonded) {
kClearForces(gpu);
kCalculateCDLJForces(gpu); kCalculateCDLJForces(gpu);
} }
kCalculateLocalForces(gpu); kCalculateLocalForces(gpu);
kReduceBornSumAndForces(gpu); if (gpu->bIncludeGBSA)
kReduceBornSumAndForces(gpu);
else
kReduceForces(gpu);
} }
static double calcEnergy(OpenMMContextImpl& context, System& system) { static double calcEnergy(OpenMMContextImpl& context, System& system) {
// We don't currently have GPU kernels to calculate energy, so instead we have the reference // We don't currently have GPU kernels to calculate energy, so instead we have the reference
// platform do it. This is VERY slow. // platform do it. This is VERY slow.
LangevinIntegrator integrator(0.0, 1.0, 0.0); LangevinIntegrator integrator(0.0, 1.0, 0.0);
ReferencePlatform platform; ReferencePlatform platform;
OpenMMContext refContext(system, integrator, platform); OpenMMContext refContext(system, integrator, platform);
...@@ -259,7 +265,19 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon ...@@ -259,7 +265,19 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
exclusionList[i] = vector<int>(exclusions[i].begin(), exclusions[i].end()); exclusionList[i] = vector<int>(exclusions[i].begin(), exclusions[i].end());
exclusionList[i].push_back(i); exclusionList[i].push_back(i);
} }
gpuSetCoulombParameters(gpu, 138.935485f, particle, c6, c12, q, symbol, exclusionList); CudaNonbondedMethod method = NO_CUTOFF;
if (force.getNonbondedMethod() != NonbondedForce::NoCutoff) {
gpuSetNonbondedCutoff(gpu, force.getCutoffDistance(), 78.3f);
method = CUTOFF;
}
if (force.getNonbondedMethod() == NonbondedForce::CutoffPeriodic) {
Vec3 boxVectors[3];
force.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
gpuSetPeriodicBoxSize(gpu, boxVectors[0][0], boxVectors[1][1], boxVectors[2][2]);
method = PERIODIC;
}
data.nonbondedMethod = method;
gpuSetCoulombParameters(gpu, 138.935485f, particle, c6, c12, q, symbol, exclusionList, method);
} }
// Initialize 1-4 nonbonded interactions. // Initialize 1-4 nonbonded interactions.
...@@ -312,7 +330,6 @@ void CudaCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCF ...@@ -312,7 +330,6 @@ void CudaCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCF
scale[i] = (float) scalingFactor; scale[i] = (float) scalingFactor;
} }
gpuSetObcParameters(gpu, (float) force.getSoluteDielectric(), (float) force.getSolventDielectric(), particle, radius, scale); gpuSetObcParameters(gpu, (float) force.getSoluteDielectric(), (float) force.getSolventDielectric(), particle, radius, scale);
data.useOBC = true;
} }
void CudaCalcGBSAOBCForceKernel::executeForces(OpenMMContextImpl& context) { void CudaCalcGBSAOBCForceKernel::executeForces(OpenMMContextImpl& context) {
...@@ -361,12 +378,12 @@ static void initializeIntegration(const System& system, CudaPlatform::PlatformDa ...@@ -361,12 +378,12 @@ static void initializeIntegration(const System& system, CudaPlatform::PlatformDa
gpuSetRbDihedralParameters(gpu, vector<int>(), vector<int>(), vector<int>(), vector<int>(), vector<float>(), vector<float>(), gpuSetRbDihedralParameters(gpu, vector<int>(), vector<int>(), vector<int>(), vector<int>(), vector<float>(), vector<float>(),
vector<float>(), vector<float>(), vector<float>(), vector<float>()); vector<float>(), vector<float>(), vector<float>(), vector<float>());
if (!data.hasNonbonded) { if (!data.hasNonbonded) {
gpuSetCoulombParameters(gpu, 138.935485f, vector<int>(), vector<float>(), vector<float>(), vector<float>(), vector<char>(), vector<vector<int> >()); gpuSetCoulombParameters(gpu, 138.935485f, vector<int>(), vector<float>(), vector<float>(), vector<float>(), vector<char>(), vector<vector<int> >(), NO_CUTOFF);
gpuSetLJ14Parameters(gpu, 138.935485f, 1.0f, vector<int>(), vector<int>(), vector<float>(), vector<float>(), vector<float>(), vector<float>()); gpuSetLJ14Parameters(gpu, 138.935485f, 1.0f, vector<int>(), vector<int>(), vector<float>(), vector<float>(), vector<float>(), vector<float>());
} }
// Finish initialization. // Finish initialization.
gpuBuildThreadBlockWorkList(gpu); gpuBuildThreadBlockWorkList(gpu);
gpuBuildExclusionList(gpu); gpuBuildExclusionList(gpu);
gpuBuildOutputBuffers(gpu); gpuBuildOutputBuffers(gpu);
...@@ -401,6 +418,7 @@ void CudaIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, const Ve ...@@ -401,6 +418,7 @@ void CudaIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, const Ve
} }
kVerletUpdatePart1(gpu); kVerletUpdatePart1(gpu);
kApplyFirstShake(gpu); kApplyFirstShake(gpu);
kApplyFirstSettle(gpu);
if (data.removeCM) { if (data.removeCM) {
int step = (int) (context.getTime()/stepSize); int step = (int) (context.getTime()/stepSize);
if (step%data.cmMotionFrequency == 0) if (step%data.cmMotionFrequency == 0)
...@@ -415,7 +433,7 @@ CudaIntegrateLangevinStepKernel::~CudaIntegrateLangevinStepKernel() { ...@@ -415,7 +433,7 @@ CudaIntegrateLangevinStepKernel::~CudaIntegrateLangevinStepKernel() {
void CudaIntegrateLangevinStepKernel::initialize(const System& system, const LangevinIntegrator& integrator) { void CudaIntegrateLangevinStepKernel::initialize(const System& system, const LangevinIntegrator& integrator) {
initializeIntegration(system, data, integrator); initializeIntegration(system, data, integrator);
// if LangevinIntegrator seed does not equal default value or is less than/equal to 0, then // if LangevinIntegrator seed does not equal default value or is less than/equal to 0, then
// set gpu seed and redo random values // set gpu seed and redo random values
if( integrator.getRandomNumberSeed() <= 1 ){ if( integrator.getRandomNumberSeed() <= 1 ){
...@@ -444,6 +462,7 @@ void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const ...@@ -444,6 +462,7 @@ void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const
} }
kUpdatePart1(gpu); kUpdatePart1(gpu);
kApplyFirstShake(gpu); kApplyFirstShake(gpu);
kApplyFirstSettle(gpu);
if (data.removeCM) { if (data.removeCM) {
int step = (int) (context.getTime()/stepSize); int step = (int) (context.getTime()/stepSize);
if (step%data.cmMotionFrequency == 0) if (step%data.cmMotionFrequency == 0)
...@@ -451,6 +470,7 @@ void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const ...@@ -451,6 +470,7 @@ void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const
} }
kUpdatePart2(gpu); kUpdatePart2(gpu);
kApplySecondShake(gpu); kApplySecondShake(gpu);
kApplySecondSettle(gpu);
} }
CudaIntegrateBrownianStepKernel::~CudaIntegrateBrownianStepKernel() { CudaIntegrateBrownianStepKernel::~CudaIntegrateBrownianStepKernel() {
...@@ -479,6 +499,7 @@ void CudaIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, const ...@@ -479,6 +499,7 @@ void CudaIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, const
} }
kBrownianUpdatePart1(gpu); kBrownianUpdatePart1(gpu);
kApplyFirstShake(gpu); kApplyFirstShake(gpu);
kApplyFirstSettle(gpu);
if (data.removeCM) { if (data.removeCM) {
int step = (int) (context.getTime()/stepSize); int step = (int) (context.getTime()/stepSize);
if (step%data.cmMotionFrequency == 0) if (step%data.cmMotionFrequency == 0)
......
platforms/cuda/staticTarget/CMakeLists.txt
View file @ df4b64cb
...@@ -5,24 +5,23 @@ INCLUDE(${FINDCUDA_DIR}/FindCuda.cmake) ...@@ -5,24 +5,23 @@ INCLUDE(${FINDCUDA_DIR}/FindCuda.cmake)
INCLUDE_DIRECTORIES(${CUDA_INCLUDE}) INCLUDE_DIRECTORIES(${CUDA_INCLUDE})
LINK_DIRECTORIES(${CUDA_TARGET_LINK}) LINK_DIRECTORIES(${CUDA_TARGET_LINK})
FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS}) FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
FILE(GLOB src_files ${CMAKE_SOURCE_DIR}/platforms/cuda/${subdir}/src/*.cu ${CMAKE_SOURCE_DIR}/platforms/cuda/src/*/*.cu) FILE(GLOB src_files ${CMAKE_SOURCE_DIR}/platforms/cuda/${subdir}/src/*.cu ${CMAKE_SOURCE_DIR}/platforms/cuda/${subdir}/src/*/*.cu)
FOREACH(file ${src_files}) FOREACH(file ${src_files})
FILE(RELATIVE_PATH file ${CMAKE_SOURCE_DIR}/platforms/cuda ${file}) FILE(RELATIVE_PATH file ${CMAKE_SOURCE_DIR}/platforms/cuda ${file})
SET(SOURCE_FILES ${SOURCE_FILES} ${file}) #append SET(SOURCE_FILES ${SOURCE_FILES} ${file}) #append
ENDFOREACH(file) ENDFOREACH(file)
CUDA_INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda/../${subdir}/include) CUDA_INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda/${subdir}/include)
CUDA_INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda/${subdir}/src)
ENDFOREACH(subdir) ENDFOREACH(subdir)
CUDA_INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda/../src)
CUDA_ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES}) CUDA_ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
# required for getting OPENMM_EXPORT to be set correctly in 'class OPENMM_EXPORT CudaStreamFactory', ... # required for getting OPENMM_EXPORT to be set correctly in 'class OPENMM_EXPORT CudaStreamFactory', ...
# see OpenMM/openmmapi/include/internal/windowsExport.h for details # see OpenMM/openmmapi/include/internal/windowsExport.h for details
SET( CUDA_STATIC_COMPILE_FLAG "-DOPENMM_BUILDING_STATIC_LIBRARY -DOPENMM_USE_STATIC_LIBRARIES") SET( CUDA_STATIC_COMPILE_FLAG "-DOPENMM_BUILDING_STATIC_LIBRARY -DOPENMM_USE_STATIC_LIBRARIES")
SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES COMPILE_FLAGS ${CUDA_STATIC_COMPILE_FLAG}) SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES COMPILE_FLAGS ${CUDA_STATIC_COMPILE_FLAG})
TARGET_LINK_LIBRARIES(${STATIC_TARGET} debug ${OPENMM_LIBRARY_NAME}_static_d optimized ${OPENMM_LIBRARY_NAME}_static) TARGET_LINK_LIBRARIES(${STATIC_TARGET} debug ${OPENMM_LIBRARY_NAME}_static_d optimized ${OPENMM_LIBRARY_NAME}_static cudpp cutil)
INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${STATIC_TARGET}) INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${STATIC_TARGET})
platforms/cuda/tests/TestCudaGBSAOBCForce.cpp
View file @ df4b64cb
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -36,6 +36,7 @@ ...@@ -36,6 +36,7 @@
#include "../../../tests/AssertionUtilities.h" #include "../../../tests/AssertionUtilities.h"
#include "OpenMMContext.h" #include "OpenMMContext.h"
#include "CudaPlatform.h" #include "CudaPlatform.h"
#include "ReferencePlatform.h"
#include "GBSAOBCForce.h" #include "GBSAOBCForce.h"
#include "System.h" #include "System.h"
#include "LangevinIntegrator.h" #include "LangevinIntegrator.h"
...@@ -55,12 +56,12 @@ void testSingleParticle() { ...@@ -55,12 +56,12 @@ void testSingleParticle() {
System system(1, 0); System system(1, 0);
system.setParticleMass(0, 2.0); system.setParticleMass(0, 2.0);
LangevinIntegrator integrator(0, 0.1, 0.01); LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* forceField = new GBSAOBCForce(1); GBSAOBCForce* gbsa = new GBSAOBCForce(1);
NonbondedForce* standard = new NonbondedForce(1, 0); NonbondedForce* nonbonded = new NonbondedForce(1, 0);
forceField->setParticleParameters(0, 0.5, 0.15, 1); gbsa->setParticleParameters(0, 0.5, 0.15, 1);
standard->setParticleParameters(0, 0.5, 1, 0); nonbonded->setParticleParameters(0, 0.5, 1, 0);
system.addForce(forceField); system.addForce(gbsa);
system.addForce(standard); system.addForce(nonbonded);
OpenMMContext context(system, integrator, platform); OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(1); vector<Vec3> positions(1);
positions[0] = Vec3(0, 0, 0); positions[0] = Vec3(0, 0, 0);
...@@ -68,64 +69,145 @@ void testSingleParticle() { ...@@ -68,64 +69,145 @@ void testSingleParticle() {
State state = context.getState(State::Energy); State state = context.getState(State::Energy);
double bornRadius = 0.15-0.009; // dielectric offset double bornRadius = 0.15-0.009; // dielectric offset
double eps0 = EPSILON0; double eps0 = EPSILON0;
double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius; double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/gbsa->getSoluteDielectric()-1.0/gbsa->getSolventDielectric())/bornRadius;
double extendedRadius = bornRadius+0.14; // probe radius double extendedRadius = bornRadius+0.14; // probe radius
double nonpolarEnergy = CAL2JOULE*PI_M*0.0216*(10*extendedRadius)*(10*extendedRadius)*std::pow(0.15/bornRadius, 6.0); // Where did this formula come from? Just copied it from CpuImplicitSolvent.cpp double nonpolarEnergy = CAL2JOULE*PI_M*0.0216*(10*extendedRadius)*(10*extendedRadius)*std::pow(0.15/bornRadius, 6.0); // Where did this formula come from? Just copied it from CpuImplicitSolvent.cpp
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01); ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
} }
void testForce() { void testCutoffAndPeriodic() {
CudaPlatform platform; CudaPlatform cuda;
const int numParticles = 10; System system(2, 0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* gbsa = new GBSAOBCForce(2);
NonbondedForce* nonbonded = new NonbondedForce(2, 0);
gbsa->setParticleParameters(0, -1, 0.15, 1);
nonbonded->setParticleParameters(0, -1, 1, 0);
gbsa->setParticleParameters(1, 1, 0.15, 1);
nonbonded->setParticleParameters(1, 1, 1, 0);
const double cutoffDistance = 3.0;
const double boxSize = 10.0;
nonbonded->setCutoffDistance(cutoffDistance);
nonbonded->setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(gbsa);
system.addForce(nonbonded);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
// Calculate the forces for both cutoff and periodic with two different atom positions.
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
OpenMMContext context(system, integrator, cuda);
context.setPositions(positions);
State state1 = context.getState(State::Forces);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
context.reinitialize();
context.setPositions(positions);
State state2 = context.getState(State::Forces);
positions[1][0]+= boxSize;
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
context.reinitialize();
context.setPositions(positions);
State state3 = context.getState(State::Forces);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
context.reinitialize();
context.setPositions(positions);
State state4 = context.getState(State::Forces);
// All forces should be identical, exception state3 which should be zero.
ASSERT_EQUAL_VEC(state1.getForces()[0], state2.getForces()[0], 0.01);
ASSERT_EQUAL_VEC(state1.getForces()[1], state2.getForces()[1], 0.01);
ASSERT_EQUAL_VEC(state1.getForces()[0], state4.getForces()[0], 0.01);
ASSERT_EQUAL_VEC(state1.getForces()[1], state4.getForces()[1], 0.01);
ASSERT_EQUAL_VEC(state3.getForces()[0], Vec3(0, 0, 0), 0.01);
ASSERT_EQUAL_VEC(state3.getForces()[1], Vec3(0, 0, 0), 0.01);
}
void testForce(int numParticles, NonbondedForce::NonbondedMethod method) {
CudaPlatform cuda;
ReferencePlatform reference;
System system(numParticles, 0); System system(numParticles, 0);
LangevinIntegrator integrator(0, 0.1, 0.01); LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* forceField = new GBSAOBCForce(numParticles); GBSAOBCForce* gbsa = new GBSAOBCForce(numParticles);
NonbondedForce* standard = new NonbondedForce(numParticles, 0); NonbondedForce* nonbonded = new NonbondedForce(numParticles, 0);
for (int i = 0; i < numParticles; ++i) { for (int i = 0; i < numParticles; ++i) {
double charge = i%2 == 0 ? -1 : 1; double charge = i%2 == 0 ? -1 : 1;
forceField->setParticleParameters(i, charge, 0.15, 1); gbsa->setParticleParameters(i, charge, 0.15, 1);
standard->setParticleParameters(i, charge, 1, 0); nonbonded->setParticleParameters(i, charge, 1, 0);
} }
system.addForce(forceField); nonbonded->setNonbondedMethod(method);
system.addForce(standard); nonbonded->setCutoffDistance(3.0);
OpenMMContext context(system, integrator, platform); int grid = (int) floor(0.5+pow(numParticles, 1.0/3.0));
if (method == NonbondedForce::CutoffPeriodic) {
double boxSize = (grid+1)*2.0;
nonbonded->setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
}
system.addForce(gbsa);
system.addForce(nonbonded);
OpenMMContext context(system, integrator, cuda);
OpenMMContext refContext(system, integrator, reference);
// Set random positions for all the particles. // Set random (but uniformly distributed) positions for all the particles.
vector<Vec3> positions(numParticles); vector<Vec3> positions(numParticles);
init_gen_rand(0); init_gen_rand(0);
for (int i = 0; i < grid; i++)
for (int j = 0; j < grid; j++)
for (int k = 0; k < grid; k++)
positions[i*grid*grid+j*grid+k] = Vec3(i*2.0, j*2.0, k*2.0);
for (int i = 0; i < numParticles; ++i) for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3(5.0*genrand_real2(), 5.0*genrand_real2(), 5.0*genrand_real2()); positions[i] = positions[i] + Vec3(0.5*genrand_real2(), 0.5*genrand_real2(), 0.5*genrand_real2());
context.setPositions(positions); context.setPositions(positions);
refContext.setPositions(positions);
State state = context.getState(State::Forces | State::Energy); State state = context.getState(State::Forces | State::Energy);
State refState = refContext.getState(State::Forces | State::Energy);
// Take a small step in the direction of the energy gradient.
// Make sure the Cuda and Reference platforms agree.
double norm = 0.0; double norm = 0.0;
double diff = 0.0;
for (int i = 0; i < numParticles; ++i) { for (int i = 0; i < numParticles; ++i) {
Vec3 f = state.getForces()[i]; Vec3 f = state.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2]; norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
Vec3 delta = f-refState.getForces()[i];
diff += delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2];
} }
norm = std::sqrt(norm); norm = std::sqrt(norm);
const double delta = 1e-2; diff = std::sqrt(diff);
double step = delta/norm; ASSERT_EQUAL_TOL(0.0, diff, 0.001*norm);
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i]; // Take a small step in the direction of the energy gradient. (This doesn't work with cutoffs, since the energy
Vec3 f = state.getForces()[i]; // changes discontinuously at the cutoff distance.)
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
if (method == NonbondedForce::NoCutoff)
{
const double delta = 1e-2;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
// See whether the potential energy changed by the expected amount.
State state2 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 1e-3*abs(state.getPotentialEnergy()));
} }
context.setPositions(positions);
// See whether the potential energy changed by the expected amount.
State state2 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.02)
} }
int main() { int main() {
try { try {
testSingleParticle(); testSingleParticle();
testForce(); testCutoffAndPeriodic();
for (int i = 2; i < 11; i++) {
testForce(i*i*i, NonbondedForce::NoCutoff);
testForce(i*i*i, NonbondedForce::CutoffNonPeriodic);
testForce(i*i*i, NonbondedForce::CutoffPeriodic);
}
} }
catch(const exception& e) { catch(const exception& e) {
cout << "exception: " << e.what() << endl; cout << "exception: " << e.what() << endl;
......
platforms/cuda/tests/TestCudaNonbondedForce.cpp
View file @ df4b64cb
...@@ -36,11 +36,16 @@ ...@@ -36,11 +36,16 @@
#include "../../../tests/AssertionUtilities.h" #include "../../../tests/AssertionUtilities.h"
#include "OpenMMContext.h" #include "OpenMMContext.h"
#include "CudaPlatform.h" #include "CudaPlatform.h"
#include "ReferencePlatform.h"
#include "HarmonicBondForce.h" #include "HarmonicBondForce.h"
#include "NonbondedForce.h" #include "NonbondedForce.h"
#include "System.h" #include "System.h"
#include "LangevinIntegrator.h" #include "LangevinIntegrator.h"
#include "VerletIntegrator.h"
#include "internal/OpenMMContextImpl.h"
#include "kernels/gputypes.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h" #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "../src/sfmt/SFMT.h"
#include <iostream> #include <iostream>
#include <vector> #include <vector>
...@@ -211,6 +216,8 @@ void testCutoff14() { ...@@ -211,6 +216,8 @@ void testCutoff14() {
system.addForce(bonds); system.addForce(bonds);
NonbondedForce* nonbonded = new NonbondedForce(5, 2); NonbondedForce* nonbonded = new NonbondedForce(5, 2);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic); nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
nonbonded->setNonbonded14Parameters(0, 0, 3, 0, 1.5, 0.0);
nonbonded->setNonbonded14Parameters(1, 1, 4, 0, 1.5, 0.0);
const double cutoff = 3.5; const double cutoff = 3.5;
nonbonded->setCutoffDistance(cutoff); nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded); system.addForce(nonbonded);
...@@ -316,14 +323,219 @@ void testPeriodic() { ...@@ -316,14 +323,219 @@ void testPeriodic() {
ASSERT_EQUAL_TOL(2*138.935485*(1.0)*(1.0+krf*1.0-crf), state.getPotentialEnergy(), TOL); ASSERT_EQUAL_TOL(2*138.935485*(1.0)*(1.0+krf*1.0-crf), state.getPotentialEnergy(), TOL);
} }
void testLargeSystem() {
const int numMolecules = 600;
const int numParticles = numMolecules*2;
const double cutoff = 2.0;
const double boxSize = 10.0;
const double tol = 1e-3;
CudaPlatform cuda;
ReferencePlatform reference;
System system(numParticles, 0);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce(numParticles, 0);
HarmonicBondForce* bonds = new HarmonicBondForce(numMolecules);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
nonbonded->setParticleParameters(2*i, 1.0, 0.2, 0.1);
nonbonded->setParticleParameters(2*i+1, 1.0, 0.1, 0.1);
}
else {
nonbonded->setParticleParameters(2*i, 1.0, 0.2, 0.2);
nonbonded->setParticleParameters(2*i+1, 1.0, 0.1, 0.2);
}
positions[2*i] = Vec3(boxSize*genrand_real2(), boxSize*genrand_real2(), boxSize*genrand_real2());
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(), genrand_real2(), genrand_real2());
velocities[2*i+1] = Vec3(genrand_real2(), genrand_real2(), genrand_real2());
bonds->setBondParameters(i, 2*i, 2*i+1, 1.0, 0.1);
}
// Try with cutoffs but not periodic boundary conditions, and make sure the Cuda and Reference
// platforms agree.
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
system.addForce(bonds);
OpenMMContext cudaContext(system, integrator, cuda);
OpenMMContext referenceContext(system, integrator, reference);
cudaContext.setPositions(positions);
cudaContext.setVelocities(velocities);
referenceContext.setPositions(positions);
referenceContext.setVelocities(velocities);
State cudaState = cudaContext.getState(State::Positions | State::Velocities | State::Forces);
State referenceState = referenceContext.getState(State::Positions | State::Velocities | State::Forces);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(cudaState.getPositions()[i], referenceState.getPositions()[i], tol);
ASSERT_EQUAL_VEC(cudaState.getVelocities()[i], referenceState.getVelocities()[i], tol);
ASSERT_EQUAL_VEC(cudaState.getForces()[i], referenceState.getForces()[i], tol);
}
// Now do the same thing with periodic boundary conditions.
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
nonbonded->setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
cudaContext.reinitialize();
referenceContext.reinitialize();
cudaContext.setPositions(positions);
cudaContext.setVelocities(velocities);
referenceContext.setPositions(positions);
referenceContext.setVelocities(velocities);
cudaState = cudaContext.getState(State::Positions | State::Velocities | State::Forces);
referenceState = referenceContext.getState(State::Positions | State::Velocities | State::Forces);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(cudaState.getPositions()[i], referenceState.getPositions()[i], tol);
ASSERT_EQUAL_VEC(cudaState.getVelocities()[i], referenceState.getVelocities()[i], tol);
ASSERT_EQUAL_VEC(cudaState.getForces()[i], referenceState.getForces()[i], tol);
}
}
void testBlockInteractions(bool periodic) {
const int blockSize = 32;
const int numBlocks = 100;
const int numParticles = blockSize*numBlocks;
const double cutoff = 1.0;
const double boxSize = (periodic ? 5.1 : 1.1);
CudaPlatform cuda;
System system(numParticles, 0);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce(numParticles, 0);
vector<Vec3> positions(numParticles);
init_gen_rand(0);
for (int i = 0; i < numParticles; i++) {
nonbonded->setParticleParameters(i, 1.0, 0.2, 0.2);
positions[i] = Vec3(boxSize*(3*genrand_real2()-1), boxSize*(3*genrand_real2()-1), boxSize*(3*genrand_real2()-1));
}
nonbonded->setNonbondedMethod(periodic ? NonbondedForce::CutoffPeriodic : NonbondedForce::CutoffNonPeriodic);
nonbonded->setCutoffDistance(cutoff);
nonbonded->setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(nonbonded);
OpenMMContext context(system, integrator, cuda);
context.setPositions(positions);
State state = context.getState(State::Positions | State::Velocities | State::Forces);
OpenMMContextImpl* contextImpl = *reinterpret_cast<OpenMMContextImpl**>(&context);
CudaPlatform::PlatformData& data = *static_cast<CudaPlatform::PlatformData*>(contextImpl->getPlatformData());
// Verify that the bounds of each block were calculated correctly.
data.gpu->psPosq4->Download();
data.gpu->psGridBoundingBox->Download();
data.gpu->psGridCenter->Download();
for (int i = 0; i < numBlocks; i++) {
float4 gridSize = data.gpu->psGridBoundingBox->_pSysData[i];
float4 center = data.gpu->psGridCenter->_pSysData[i];
if (periodic) {
ASSERT(gridSize.x < 0.5*boxSize);
ASSERT(gridSize.y < 0.5*boxSize);
ASSERT(gridSize.z < 0.5*boxSize);
}
float minx = 0.0, maxx = 0.0, miny = 0.0, maxy = 0.0, minz = 0.0, maxz = 0.0, radius = 0.0;
for (int j = 0; j < blockSize; j++) {
float4 pos = data.gpu->psPosq4->_pSysData[i*blockSize+j];
float dx = pos.x-center.x;
float dy = pos.y-center.y;
float dz = pos.z-center.z;
if (periodic) {
dx -= floor(0.5+dx/boxSize)*boxSize;
dy -= floor(0.5+dy/boxSize)*boxSize;
dz -= floor(0.5+dz/boxSize)*boxSize;
}
ASSERT(abs(dx) < gridSize.x+TOL);
ASSERT(abs(dy) < gridSize.y+TOL);
ASSERT(abs(dz) < gridSize.z+TOL);
minx = min(minx, dx);
maxx = max(maxx, dx);
miny = min(miny, dy);
maxy = max(maxy, dy);
minz = min(minz, dz);
maxz = max(maxz, dz);
}
ASSERT_EQUAL_TOL(-minx, gridSize.x, TOL);
ASSERT_EQUAL_TOL(maxx, gridSize.x, TOL);
ASSERT_EQUAL_TOL(-miny, gridSize.y, TOL);
ASSERT_EQUAL_TOL(maxy, gridSize.y, TOL);
ASSERT_EQUAL_TOL(-minz, gridSize.z, TOL);
ASSERT_EQUAL_TOL(maxz, gridSize.z, TOL);
}
// Verify that interactions were identified correctly.
data.gpu->psInteractionCount->Download();
int numWithInteractions = data.gpu->psInteractionCount->_pSysData[0];
vector<bool> hasInteractions(data.gpu->sim.workUnits, false);
data.gpu->psInteractingWorkUnit->Download();
data.gpu->psInteractionFlag->Download();
const unsigned int atoms = data.gpu->sim.paddedNumberOfAtoms;
const unsigned int grid = data.gpu->grid;
const unsigned int dim = (atoms+(grid-1))/grid;
for (int i = 0; i < numWithInteractions; i++) {
unsigned int workUnit = data.gpu->psInteractingWorkUnit->_pSysData[i];
unsigned int x = (workUnit >> 17);
unsigned int y = ((workUnit >> 2) & 0x7fff);
int tile = (x > y ? x+y*dim-y*(y+1)/2 : y+x*dim-x*(x+1)/2);
hasInteractions[tile] = true;
// Make sure this tile really should have been flagged based on bounding volumes.
float4 gridSize1 = data.gpu->psGridBoundingBox->_pSysData[x];
float4 gridSize2 = data.gpu->psGridBoundingBox->_pSysData[y];
float4 center1 = data.gpu->psGridCenter->_pSysData[x];
float4 center2 = data.gpu->psGridCenter->_pSysData[y];
float dx = center1.x-center2.x;
float dy = center1.y-center2.y;
float dz = center1.z-center2.z;
if (periodic) {
dx -= floor(0.5+dx/boxSize)*boxSize;
dy -= floor(0.5+dy/boxSize)*boxSize;
dz -= floor(0.5+dz/boxSize)*boxSize;
}
dx = max(0.0f, abs(dx)-gridSize1.x-gridSize2.x);
dy = max(0.0f, abs(dy)-gridSize1.y-gridSize2.y);
dz = max(0.0f, abs(dz)-gridSize1.z-gridSize2.z);
ASSERT(sqrt(dx*dx+dy*dy+dz*dz) < cutoff+TOL);
}
// Check the tiles that did not have interactions to make sure all atoms are beyond the cutoff.
data.gpu->psWorkUnit->Download();
for (int i = 0; i < hasInteractions.size(); i++)
if (!hasInteractions[i]) {
unsigned int workUnit = data.gpu->psWorkUnit->_pSysData[i];
unsigned int x = (workUnit >> 17);
unsigned int y = ((workUnit >> 2) & 0x7fff);
for (int atom1 = 0; atom1 < blockSize; ++atom1) {
float4 pos1 = data.gpu->psPosq4->_pSysData[x*blockSize+atom1];
for (int atom2 = 0; atom2 < blockSize; ++atom2) {
float4 pos2 = data.gpu->psPosq4->_pSysData[y*blockSize+atom2];
float dx = pos1.x-pos2.x;
float dy = pos1.y-pos2.y;
float dz = pos1.z-pos2.z;
if (periodic) {
dx -= floor(0.5+dx/boxSize)*boxSize;
dy -= floor(0.5+dy/boxSize)*boxSize;
dz -= floor(0.5+dz/boxSize)*boxSize;
}
ASSERT(dx*dx+dy*dy+dz*dz > cutoff*cutoff);
}
}
}
}
int main() { int main() {
try { try {
testCoulomb(); testCoulomb();
testLJ(); testLJ();
testExclusionsAnd14(); testExclusionsAnd14();
// testCutoff(); testCutoff();
// testCutoff14(); testCutoff14();
// testPeriodic(); testPeriodic();
testLargeSystem();
testBlockInteractions(false);
testBlockInteractions(true);
} }
catch(const exception& e) { catch(const exception& e) {
cout << "exception: " << e.what() << endl; cout << "exception: " << e.what() << endl;
......
platforms/cuda/tests/TestCudaSettle.cpp 0 → 100644
View file @ df4b64cb
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* 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. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the Cuda implementation of the SETTLE algorithm.
*/
#include "../../../tests/AssertionUtilities.h"
#include "OpenMMContext.h"
#include "CudaPlatform.h"
#include "NonbondedForce.h"
#include "System.h"
#include "LangevinIntegrator.h"
#include "../src/sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
void testConstraints() {
const int numMolecules = 10;
const int numParticles = numMolecules*3;
const int numConstraints = numMolecules*3;
const double temp = 100.0;
CudaPlatform platform;
System system(numParticles, numConstraints);
LangevinIntegrator integrator(temp, 2.0, 0.001);
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
for (int i = 0; i < numMolecules; ++i) {
system.setParticleMass(i*3, 16.0);
system.setParticleMass(i*3+1, 1.0);
system.setParticleMass(i*3+2, 1.0);
forceField->setParticleParameters(i*3, -0.82, 0.317, 0.65);
forceField->setParticleParameters(i*3+1, 0.41, 1.0, 0.0);
forceField->setParticleParameters(i*3+2, 0.41, 1.0, 0.0);
system.setConstraintParameters(i*3, i*3, i*3+1, 0.1);
system.setConstraintParameters(i*3+1, i*3, i*3+2, 0.1);
system.setConstraintParameters(i*3+2, i*3+1, i*3+2, 0.163);
}
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
for (int i = 0; i < numMolecules; ++i) {
positions[i*3] = Vec3((i%4)*0.4, (i/4)*0.4, 0);
positions[i*3+1] = positions[i*3]+Vec3(0.1, 0, 0);
positions[i*3+2] = positions[i*3]+Vec3(-0.03333, 0.09428, 0);
velocities[i*3] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
velocities[i*3+1] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
velocities[i*3+2] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
for (int i = 0; i < 1000; ++i) {
integrator.step(1);
State state = context.getState(State::Positions | State::Forces);
for (int j = 0; j < numConstraints; ++j) {
int particle1, particle2;
double distance;
system.getConstraintParameters(j, particle1, particle2, distance);
Vec3 p1 = state.getPositions()[particle1];
Vec3 p2 = state.getPositions()[particle2];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 1e-5);
}
}
}
int main() {
try {
testConstraints();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/cuda/tests/TestCudaStreams.cpp
View file @ df4b64cb
...@@ -35,7 +35,9 @@ ...@@ -35,7 +35,9 @@
#include "../../../tests/AssertionUtilities.h" #include "../../../tests/AssertionUtilities.h"
#include "CudaPlatform.h" #include "CudaPlatform.h"
#include "OpenMMContext.h"
#include "Stream.h" #include "Stream.h"
#include "VerletIntegrator.h"
#include <iostream> #include <iostream>
using namespace OpenMM; using namespace OpenMM;
...@@ -47,7 +49,10 @@ template <class T, int WIDTH> ...@@ -47,7 +49,10 @@ template <class T, int WIDTH>
void testStream(Stream::DataType type, T scale) { void testStream(Stream::DataType type, T scale) {
const int size = 100; const int size = 100;
CudaPlatform platform; CudaPlatform platform;
OpenMMContextImpl* impl = 0; // We need to pass an OpenMMContextImpl to createStream, but it will be ignored. System system(size, 0);
VerletIntegrator integrator(0.01);
OpenMMContext context(system, integrator, platform);
OpenMMContextImpl* impl = *reinterpret_cast<OpenMMContextImpl**>(&context);
Stream stream = platform.createStream("", size, type, *impl); Stream stream = platform.createStream("", size, type, *impl);
const int length = size*WIDTH; const int length = size*WIDTH;
T array[size*WIDTH+1]; T array[size*WIDTH+1];
......
platforms/reference/src/gbsa/CpuObc.cpp
View file @ df4b64cb
/* Portions copyright (c) 2006 Stanford University and Simbios. /* Portions copyright (c) 2006-2009 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -29,6 +29,7 @@ ...@@ -29,6 +29,7 @@
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "../SimTKUtilities/SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "../SimTKUtilities/SimTKOpenMMUtilities.h"
#include "CpuObc.h" #include "CpuObc.h"
#include "../SimTKReference/ReferenceForce.h"
#include <math.h> #include <math.h>
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -265,12 +266,14 @@ int CpuObc::computeBornRadii( RealOpenMM** atomCoordinates, RealOpenMM* bornRadi ...@@ -265,12 +266,14 @@ int CpuObc::computeBornRadii( RealOpenMM** atomCoordinates, RealOpenMM* bornRadi
if( atomJ != atomI ){ if( atomJ != atomI ){
RealOpenMM deltaX = atomCoordinates[atomJ][0] - atomCoordinates[atomI][0]; RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
RealOpenMM deltaY = atomCoordinates[atomJ][1] - atomCoordinates[atomI][1]; if (_obcParameters->getPeriodic())
RealOpenMM deltaZ = atomCoordinates[atomJ][2] - atomCoordinates[atomI][2]; ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR );
else
RealOpenMM r2 = deltaX*deltaX + deltaY*deltaY + deltaZ*deltaZ; ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
RealOpenMM r = SQRT( r2 ); RealOpenMM r = deltaR[ReferenceForce::RIndex];
if (_obcParameters->getUseCutoff() && r > _obcParameters->getCutoffDistance())
continue;
RealOpenMM offsetRadiusJ = atomicRadii[atomJ] - dielectricOffset; RealOpenMM offsetRadiusJ = atomicRadii[atomJ] - dielectricOffset;
RealOpenMM scaledRadiusJ = offsetRadiusJ*scaledRadiusFactor[atomJ]; RealOpenMM scaledRadiusJ = offsetRadiusJ*scaledRadiusFactor[atomJ];
RealOpenMM rScaledRadiusJ = r + scaledRadiusJ; RealOpenMM rScaledRadiusJ = r + scaledRadiusJ;
...@@ -417,15 +420,17 @@ int CpuObc::computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoo ...@@ -417,15 +420,17 @@ int CpuObc::computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoo
RealOpenMM partialChargeI = preFactor*partialCharges[atomI]; RealOpenMM partialChargeI = preFactor*partialCharges[atomI];
for( int atomJ = atomI; atomJ < numberOfAtoms; atomJ++ ){ for( int atomJ = atomI; atomJ < numberOfAtoms; atomJ++ ){
// 3 FLOP RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
if (_obcParameters->getPeriodic())
RealOpenMM deltaX = atomCoordinates[atomJ][0] - atomCoordinates[atomI][0]; ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR );
RealOpenMM deltaY = atomCoordinates[atomJ][1] - atomCoordinates[atomI][1]; else
RealOpenMM deltaZ = atomCoordinates[atomJ][2] - atomCoordinates[atomI][2]; ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _obcParameters->getCutoffDistance())
// 5 FLOP continue;
RealOpenMM r2 = deltaR[ReferenceForce::R2Index];
RealOpenMM r2 = deltaX*deltaX + deltaY*deltaY + deltaZ*deltaZ; RealOpenMM deltaX = deltaR[ReferenceForce::XIndex];
RealOpenMM deltaY = deltaR[ReferenceForce::YIndex];
RealOpenMM deltaZ = deltaR[ReferenceForce::ZIndex];
// 3 FLOP // 3 FLOP
...@@ -957,15 +962,17 @@ FILE* logFile = NULL; ...@@ -957,15 +962,17 @@ FILE* logFile = NULL;
RealOpenMM partialChargeI = preFactor*partialCharges[atomI]; RealOpenMM partialChargeI = preFactor*partialCharges[atomI];
for( int atomJ = atomI; atomJ < numberOfAtoms; atomJ++ ){ for( int atomJ = atomI; atomJ < numberOfAtoms; atomJ++ ){
// 3 FLOP RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
if (_obcParameters->getPeriodic())
RealOpenMM deltaX = atomCoordinates[atomJ][0] - atomCoordinates[atomI][0]; ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR );
RealOpenMM deltaY = atomCoordinates[atomJ][1] - atomCoordinates[atomI][1]; else
RealOpenMM deltaZ = atomCoordinates[atomJ][2] - atomCoordinates[atomI][2]; ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _obcParameters->getCutoffDistance())
// 5 FLOP continue;
RealOpenMM r2 = deltaR[ReferenceForce::R2Index];
RealOpenMM r2 = deltaX*deltaX + deltaY*deltaY + deltaZ*deltaZ; RealOpenMM deltaX = deltaR[ReferenceForce::XIndex];
RealOpenMM deltaY = deltaR[ReferenceForce::YIndex];
RealOpenMM deltaZ = deltaR[ReferenceForce::ZIndex];
// 3 FLOP // 3 FLOP
......
platforms/reference/src/gbsa/ObcParameters.cpp
View file @ df4b64cb
/* Portions copyright (c) 2006 Stanford University and Simbios. /* Portions copyright (c) 2006-2009 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -101,7 +101,7 @@ const std::string ObcParameters::ParameterFileName = std::string( "params.agb" ) ...@@ -101,7 +101,7 @@ const std::string ObcParameters::ParameterFileName = std::string( "params.agb" )
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ObcParameters::ObcParameters( int numberOfAtoms, ObcParameters::ObcType obcType ) : ImplicitSolventParameters( numberOfAtoms ){ ObcParameters::ObcParameters( int numberOfAtoms, ObcParameters::ObcType obcType ) : ImplicitSolventParameters( numberOfAtoms ), cutoff(false), periodic(false) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -656,3 +656,84 @@ int ObcParameters::isNotReady( void ) const { ...@@ -656,3 +656,84 @@ int ObcParameters::isNotReady( void ) const {
return errors; return errors;
} }
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
@param distance the cutoff distance
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ObcParameters::setUseCutoff( RealOpenMM distance ) {
cutoff = true;
cutoffDistance = distance;
return SimTKOpenMMCommon::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Get whether to use a cutoff.
--------------------------------------------------------------------------------------- */
bool ObcParameters::getUseCutoff() {
return cutoff;
}
/**---------------------------------------------------------------------------------------
Get the cutoff distance.
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getCutoffDistance() {
return cutoffDistance;
}
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions. This requires that a cutoff has
also been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ObcParameters::setPeriodic( RealOpenMM* boxSize ) {
assert(cutoff);
assert(boxSize[0] >= 2.0*cutoffDistance);
assert(boxSize[1] >= 2.0*cutoffDistance);
assert(boxSize[2] >= 2.0*cutoffDistance);
periodic = true;
periodicBoxSize[0] = boxSize[0];
periodicBoxSize[1] = boxSize[1];
periodicBoxSize[2] = boxSize[2];
return SimTKOpenMMCommon::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Get whether to use periodic boundary conditions.
--------------------------------------------------------------------------------------- */
bool ObcParameters::getPeriodic() {
return periodic;
}
/**---------------------------------------------------------------------------------------
Get the periodic box dimension
--------------------------------------------------------------------------------------- */
const RealOpenMM* ObcParameters::getPeriodicBox() {
return periodicBoxSize;
}
platforms/reference/src/gbsa/ObcParameters.h
View file @ df4b64cb
/* Portions copyright (c) 2006 Stanford University and Simbios. /* Portions copyright (c) 2006-2009 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -55,6 +55,14 @@ class ObcParameters : public ImplicitSolventParameters { ...@@ -55,6 +55,14 @@ class ObcParameters : public ImplicitSolventParameters {
int _ownScaledRadiusFactors; int _ownScaledRadiusFactors;
RealOpenMM* _scaledRadiusFactors; RealOpenMM* _scaledRadiusFactors;
// cutoff and periodic boundary conditions
bool cutoff;
bool periodic;
RealOpenMM periodicBoxSize[3];
RealOpenMM cutoffDistance;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Set solvent dielectric (Simbios) Set solvent dielectric (Simbios)
...@@ -285,7 +293,65 @@ class ObcParameters : public ImplicitSolventParameters { ...@@ -285,7 +293,65 @@ class ObcParameters : public ImplicitSolventParameters {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int isNotReady( void ) const; int isNotReady( void ) const;
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
@param distance the cutoff distance
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
int setUseCutoff( RealOpenMM distance );
/**---------------------------------------------------------------------------------------
Get whether to use a cutoff.
--------------------------------------------------------------------------------------- */
bool getUseCutoff();
/**---------------------------------------------------------------------------------------
Get the cutoff distance.
--------------------------------------------------------------------------------------- */
RealOpenMM getCutoffDistance();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions. This requires that a cutoff has
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
int setPeriodic( RealOpenMM* boxSize );
/**---------------------------------------------------------------------------------------
Get whether to use periodic boundary conditions.
--------------------------------------------------------------------------------------- */
bool getPeriodic();
/**---------------------------------------------------------------------------------------
Get the periodic box dimension
--------------------------------------------------------------------------------------- */
const RealOpenMM* getPeriodicBox();
}; };
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/reference/tests/TestReferenceGBSAOBCForce.cpp
View file @ df4b64cb
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -39,6 +39,7 @@ ...@@ -39,6 +39,7 @@
#include "GBSAOBCForce.h" #include "GBSAOBCForce.h"
#include "System.h" #include "System.h"
#include "LangevinIntegrator.h" #include "LangevinIntegrator.h"
#include "NonbondedForce.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h" #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "../src/sfmt/SFMT.h" #include "../src/sfmt/SFMT.h"
#include <iostream> #include <iostream>
...@@ -70,6 +71,56 @@ void testSingleParticle() { ...@@ -70,6 +71,56 @@ void testSingleParticle() {
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01); ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
} }
void testCutoffAndPeriodic() {
ReferencePlatform platform;
System system(2, 0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* gbsa = new GBSAOBCForce(2);
NonbondedForce* nonbonded = new NonbondedForce(2, 0);
gbsa->setParticleParameters(0, -1, 0.15, 1);
nonbonded->setParticleParameters(0, -1, 1, 0);
gbsa->setParticleParameters(1, 1, 0.15, 1);
nonbonded->setParticleParameters(1, 1, 1, 0);
const double cutoffDistance = 3.0;
const double boxSize = 10.0;
nonbonded->setCutoffDistance(cutoffDistance);
nonbonded->setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(gbsa);
system.addForce(nonbonded);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
// Calculate the forces for both cutoff and periodic with two different atom positions.
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
OpenMMContext context(system, integrator, platform);
context.setPositions(positions);
State state1 = context.getState(State::Forces);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
context.reinitialize();
context.setPositions(positions);
State state2 = context.getState(State::Forces);
positions[1][0]+= boxSize;
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
context.reinitialize();
context.setPositions(positions);
State state3 = context.getState(State::Forces);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
context.reinitialize();
context.setPositions(positions);
State state4 = context.getState(State::Forces);
// All forces should be identical, exception state3 which should be zero.
ASSERT_EQUAL_VEC(state1.getForces()[0], state2.getForces()[0], 0.01);
ASSERT_EQUAL_VEC(state1.getForces()[1], state2.getForces()[1], 0.01);
ASSERT_EQUAL_VEC(state1.getForces()[0], state4.getForces()[0], 0.01);
ASSERT_EQUAL_VEC(state1.getForces()[1], state4.getForces()[1], 0.01);
ASSERT_EQUAL_VEC(state3.getForces()[0], Vec3(0, 0, 0), 0.01);
ASSERT_EQUAL_VEC(state3.getForces()[1], Vec3(0, 0, 0), 0.01);
}
void testForce() { void testForce() {
ReferencePlatform platform; ReferencePlatform platform;
const int numParticles = 10; const int numParticles = 10;
...@@ -116,6 +167,7 @@ void testForce() { ...@@ -116,6 +167,7 @@ void testForce() {
int main() { int main() {
try { try {
testSingleParticle(); testSingleParticle();
testCutoffAndPeriodic();
testForce(); testForce();
} }
catch(const exception& e) { catch(const exception& e) {
......
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