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Commit 51828eaa authored by Peter Eastman's avatar Peter Eastman
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Merge branch 'master' into qc

parents cf8a03e8 5ed9dd65
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platforms/cuda/tests/TestCudaVirtualSites.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2012 Stanford University and the Authors. *
* Portions copyright (c) 2012-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -213,6 +213,84 @@ void testOutOfPlane() {
}
}
/**
* Test a LocalCoordinatesSite virtual site.
*/
void testLocalCoordinates() {
const Vec3 originWeights(0.2, 0.3, 0.5);
const Vec3 xWeights(-1.0, 0.5, 0.5);
const Vec3 yWeights(0.0, -1.0, 1.0);
const Vec3 localPosition(0.4, 0.3, 0.2);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(3, new LocalCoordinatesSite(0, 1, 2, originWeights, xWeights, yWeights, localPosition));
CustomExternalForce* forceField = new CustomExternalForce("2*x^2+3*y^2+4*z^2");
system.addForce(forceField);
vector<double> params;
forceField->addParticle(0, params);
forceField->addParticle(1, params);
forceField->addParticle(2, params);
forceField->addParticle(3, params);
LangevinIntegrator integrator(300.0, 0.1, 0.002);
Context context(system, integrator, platform);
vector<Vec3> positions(4), positions2(4), positions3(4);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < 100; i++) {
// Set the particles at random positions.
Vec3 xdir, ydir, zdir;
do {
for (int j = 0; j < 3; j++)
positions[j] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
xdir = positions[0]*xWeights[0] + positions[1]*xWeights[1] + positions[2]*xWeights[2];
ydir = positions[0]*yWeights[0] + positions[1]*yWeights[1] + positions[2]*yWeights[2];
zdir = xdir.cross(ydir);
if (sqrt(xdir.dot(xdir)) > 0.1 && sqrt(ydir.dot(ydir)) > 0.1 && sqrt(zdir.dot(zdir)) > 0.1)
break; // These positions give a reasonable coordinate system.
} while (true);
context.setPositions(positions);
context.applyConstraints(0.0001);
// See if the virtual site is positioned correctly.
State state = context.getState(State::Positions | State::Forces);
const vector<Vec3>& pos = state.getPositions();
Vec3 origin = pos[0]*originWeights[0] + pos[1]*originWeights[1] + pos[2]*originWeights[2];
xdir /= sqrt(xdir.dot(xdir));
zdir /= sqrt(zdir.dot(zdir));
ydir = zdir.cross(xdir);
ASSERT_EQUAL_VEC(origin+xdir*localPosition[0]+ydir*localPosition[1]+zdir*localPosition[2], pos[3], 1e-5);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < 3; ++i) {
Vec3 f = state.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
}
norm = std::sqrt(norm);
const double delta = 1e-2;
double step = 0.5*delta/norm;
for (int i = 0; i < 3; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
context.applyConstraints(0.0001);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
context.applyConstraints(0.0001);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/delta, 1e-3)
}
}
/**
* Make sure that energy, linear momentum, and angular momentum are all conserved
* when using virtual sites.
......@@ -279,6 +357,26 @@ void testConservationLaws() {
positions.push_back(Vec3(1, 1, -1));
positions.push_back(Vec3());
// Create a molecule with a LocalCoordinatesSite virtual site.
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(14, new LocalCoordinatesSite(11, 12, 13, Vec3(0.3, 0.3, 0.4), Vec3(1.0, -0.5, -0.5), Vec3(0, -1.0, 1.0), Vec3(0.2, 0.2, 1.0)));
system.addConstraint(11, 12, 1.0);
system.addConstraint(11, 13, 1.0);
system.addConstraint(12, 13, sqrt(2.0));
for (int i = 0; i < 4; i++) {
forceField->addParticle(0, 1, 10);
for (int j = 0; j < i; j++)
forceField->addException(i+11, j+11, 0, 1, 0);
}
positions.push_back(Vec3(1, 2, 0));
positions.push_back(Vec3(2, 2, 0));
positions.push_back(Vec3(1, 3, 0));
positions.push_back(Vec3());
// Simulate it and check conservation laws.
VerletIntegrator integrator(0.002);
......@@ -315,7 +413,7 @@ void testConservationLaws() {
if (i == 0)
initialAngularMomentum = angularMomentum;
else
ASSERT_EQUAL_VEC(initialAngularMomentum, angularMomentum, 0.02);
ASSERT_EQUAL_VEC(initialAngularMomentum, angularMomentum, 0.03);
integrator.step(1);
}
}
......@@ -434,6 +532,7 @@ int main(int argc, char* argv[]) {
testTwoParticleAverage();
testThreeParticleAverage();
testOutOfPlane();
testLocalCoordinates();
testConservationLaws();
testReordering();
}
......
platforms/opencl/CMakeLists.txt
View file @ 51828eaa
#---------------------------------------------------
# OpenMM OpenCL Platform
#
# Creates OpenMM library, base name=OpenMMOpenCL.
# Default libraries are shared & optimized. Variants
# are created for static (_static) and debug (_d).
# Creates OpenMMOpenCL library.
#
# Windows:
# OpenMMOpenCL[_d].dll
# OpenMMOpenCL[_d].lib
# OpenMMOpenCL_static[_d].lib
# OpenMMOpenCL.dll
# OpenMMOpenCL.lib
# OpenMMOpenCL_static.lib
# Unix:
# libOpenMMOpenCL[_d].so
# libOpenMMOpenCL_static[_d].a
# libOpenMMOpenCL.so
# libOpenMMOpenCL_static.a
#----------------------------------------------------
set(OPENMM_BUILD_OPENCL_TESTS TRUE CACHE BOOL "Whether to build OpenCL test cases")
......@@ -33,19 +31,6 @@ SET(SHARED_TARGET ${OPENMMOPENCL_LIBRARY_NAME})
SET(STATIC_TARGET ${OPENMMOPENCL_LIBRARY_NAME}_static)
# Ensure that debug libraries have "_d" appended to their names.
# CMake gets this right on Windows automatically with this definition.
IF (MSVC)
SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
ENDIF (MSVC)
# But on Unix or Cygwin we have to add the suffix manually
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(SHARED_TARGET ${SHARED_TARGET}_d)
SET(STATIC_TARGET ${STATIC_TARGET}_d)
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
# These are all the places to search for header files which are
# to be part of the API.
SET(API_INCLUDE_DIRS) # start empty
......
platforms/opencl/include/OpenCLIntegrationUtilities.h
View file @ 51828eaa
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009-2013 Stanford University and the Authors. *
* Portions copyright (c) 2009-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -148,6 +148,8 @@ private:
OpenCLArray* vsite3AvgWeights;
OpenCLArray* vsiteOutOfPlaneAtoms;
OpenCLArray* vsiteOutOfPlaneWeights;
OpenCLArray* vsiteLocalCoordsAtoms;
OpenCLArray* vsiteLocalCoordsParams;
int randomPos;
int lastSeed, numVsites;
bool hasInitializedPosConstraintKernels, hasInitializedVelConstraintKernels, ccmaUseDirectBuffer;
......
platforms/opencl/include/OpenCLPlatform.h
View file @ 51828eaa
......@@ -48,6 +48,7 @@ public:
}
double getSpeed() const;
bool supportsDoublePrecision() const;
static bool isPlatformSupported();
const std::string& getPropertyValue(const Context& context, const std::string& property) const;
void setPropertyValue(Context& context, const std::string& property, const std::string& value) const;
void contextCreated(ContextImpl& context, const std::map<std::string, std::string>& properties) const;
......
platforms/opencl/sharedTarget/CMakeLists.txt
View file @ 51828eaa
......@@ -13,12 +13,7 @@ ADD_CUSTOM_COMMAND(OUTPUT ${CL_KERNELS_CPP} ${CL_KERNELS_H}
SET_SOURCE_FILES_PROPERTIES(${CL_KERNELS_CPP} ${CL_KERNELS_H} PROPERTIES GENERATED TRUE)
ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME}_d)
ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME})
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB} ${OPENCL_LIBRARIES} ${PTHREADS_LIB})
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${OPENCL_LIBRARIES} ${PTHREADS_LIB})
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_OPENCL_BUILDING_SHARED_LIBRARY")
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
platforms/opencl/src/OpenCLIntegrationUtilities.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009-2013 Stanford University and the Authors. *
* Portions copyright (c) 2009-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -100,7 +100,8 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
ccmaReducedMass(NULL), ccmaAtomConstraints(NULL), ccmaNumAtomConstraints(NULL), ccmaConstraintMatrixColumn(NULL),
ccmaConstraintMatrixValue(NULL), ccmaDelta1(NULL), ccmaDelta2(NULL), ccmaConverged(NULL), ccmaConvergedHostBuffer(NULL),
vsite2AvgAtoms(NULL), vsite2AvgWeights(NULL), vsite3AvgAtoms(NULL), vsite3AvgWeights(NULL),
vsiteOutOfPlaneAtoms(NULL), vsiteOutOfPlaneWeights(NULL), hasInitializedPosConstraintKernels(false), hasInitializedVelConstraintKernels(false) {
vsiteOutOfPlaneAtoms(NULL), vsiteOutOfPlaneWeights(NULL), vsiteLocalCoordsAtoms(NULL), vsiteLocalCoordsParams(NULL),
hasInitializedPosConstraintKernels(false), hasInitializedVelConstraintKernels(false) {
// Create workspace arrays.
if (context.getUseDoublePrecision() || context.getUseMixedPrecision()) {
......@@ -595,6 +596,8 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
vector<mm_double4> vsite3AvgWeightVec;
vector<mm_int4> vsiteOutOfPlaneAtomVec;
vector<mm_double4> vsiteOutOfPlaneWeightVec;
vector<mm_int4> vsiteLocalCoordsAtomVec;
vector<cl_double> vsiteLocalCoordsParamVec;
for (int i = 0; i < numAtoms; i++) {
if (system.isVirtualSite(i)) {
if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
......@@ -618,35 +621,65 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
vsiteOutOfPlaneAtomVec.push_back(mm_int4(i, site.getParticle(0), site.getParticle(1), site.getParticle(2)));
vsiteOutOfPlaneWeightVec.push_back(mm_double4(site.getWeight12(), site.getWeight13(), site.getWeightCross(), 0.0));
}
else if (dynamic_cast<const LocalCoordinatesSite*>(&system.getVirtualSite(i)) != NULL) {
// An out of plane site.
const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i));
vsiteLocalCoordsAtomVec.push_back(mm_int4(i, site.getParticle(0), site.getParticle(1), site.getParticle(2)));
Vec3 origin = site.getOriginWeights();
Vec3 x = site.getXWeights();
Vec3 y = site.getYWeights();
Vec3 pos = site.getLocalPosition();
vsiteLocalCoordsParamVec.push_back(origin[0]);
vsiteLocalCoordsParamVec.push_back(origin[1]);
vsiteLocalCoordsParamVec.push_back(origin[2]);
vsiteLocalCoordsParamVec.push_back(x[0]);
vsiteLocalCoordsParamVec.push_back(x[1]);
vsiteLocalCoordsParamVec.push_back(x[2]);
vsiteLocalCoordsParamVec.push_back(y[0]);
vsiteLocalCoordsParamVec.push_back(y[1]);
vsiteLocalCoordsParamVec.push_back(y[2]);
vsiteLocalCoordsParamVec.push_back(pos[0]);
vsiteLocalCoordsParamVec.push_back(pos[1]);
vsiteLocalCoordsParamVec.push_back(pos[2]);
}
}
}
int num2Avg = vsite2AvgAtomVec.size();
int num3Avg = vsite3AvgAtomVec.size();
int numOutOfPlane = vsiteOutOfPlaneAtomVec.size();
int numLocalCoords = vsiteLocalCoordsAtomVec.size();
vsite2AvgAtoms = OpenCLArray::create<mm_int4>(context, max(1, num2Avg), "vsite2AvgAtoms");
vsite3AvgAtoms = OpenCLArray::create<mm_int4>(context, max(1, num3Avg), "vsite3AvgAtoms");
vsiteOutOfPlaneAtoms = OpenCLArray::create<mm_int4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneAtoms");
vsiteLocalCoordsAtoms = OpenCLArray::create<mm_int4>(context, max(1, numLocalCoords), "vsiteLocalCoordinatesAtoms");
if (num2Avg > 0)
vsite2AvgAtoms->upload(vsite2AvgAtomVec);
if (num3Avg > 0)
vsite3AvgAtoms->upload(vsite3AvgAtomVec);
if (numOutOfPlane > 0)
vsiteOutOfPlaneAtoms->upload(vsiteOutOfPlaneAtomVec);
if (numLocalCoords > 0)
vsiteLocalCoordsAtoms->upload(vsiteLocalCoordsAtomVec);
if (context.getUseDoublePrecision()) {
vsite2AvgWeights = OpenCLArray::create<mm_double2>(context, max(1, num2Avg), "vsite2AvgWeights");
vsite3AvgWeights = OpenCLArray::create<mm_double4>(context, max(1, num3Avg), "vsite3AvgWeights");
vsiteOutOfPlaneWeights = OpenCLArray::create<mm_double4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneWeights");
vsiteLocalCoordsParams = OpenCLArray::create<cl_double>(context, max(1, 12*numLocalCoords), "vsiteLocalCoordinatesParams");
if (num2Avg > 0)
vsite2AvgWeights->upload(vsite2AvgWeightVec);
if (num3Avg > 0)
vsite3AvgWeights->upload(vsite3AvgWeightVec);
if (numOutOfPlane > 0)
vsiteOutOfPlaneWeights->upload(vsiteOutOfPlaneWeightVec);
if (numLocalCoords > 0)
vsiteLocalCoordsParams->upload(vsiteLocalCoordsParamVec);
}
else {
vsite2AvgWeights = OpenCLArray::create<mm_float2>(context, max(1, num2Avg), "vsite2AvgWeights");
vsite3AvgWeights = OpenCLArray::create<mm_float4>(context, max(1, num3Avg), "vsite3AvgWeights");
vsiteOutOfPlaneWeights = OpenCLArray::create<mm_float4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneWeights");
vsiteLocalCoordsParams = OpenCLArray::create<float>(context, max(1, 12*numLocalCoords), "vsiteLocalCoordinatesParams");
if (num2Avg > 0) {
vector<mm_float2> floatWeights(num2Avg);
for (int i = 0; i < num2Avg; i++)
......@@ -665,6 +698,12 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
floatWeights[i] = mm_float4((float) vsiteOutOfPlaneWeightVec[i].x, (float) vsiteOutOfPlaneWeightVec[i].y, (float) vsiteOutOfPlaneWeightVec[i].z, 0.0f);
vsiteOutOfPlaneWeights->upload(floatWeights);
}
if (numLocalCoords > 0) {
vector<cl_float> floatParams(vsiteLocalCoordsParamVec.size());
for (int i = 0; i < (int) vsiteLocalCoordsParamVec.size(); i++)
floatParams[i] = (cl_float) vsiteLocalCoordsParamVec[i];
vsiteLocalCoordsParams->upload(floatParams);
}
}
// Create the kernels for virtual sites.
......@@ -673,6 +712,7 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
defines["NUM_2_AVERAGE"] = context.intToString(num2Avg);
defines["NUM_3_AVERAGE"] = context.intToString(num3Avg);
defines["NUM_OUT_OF_PLANE"] = context.intToString(numOutOfPlane);
defines["NUM_LOCAL_COORDS"] = context.intToString(numLocalCoords);
cl::Program vsiteProgram = context.createProgram(OpenCLKernelSources::virtualSites, defines);
vsitePositionKernel = cl::Kernel(vsiteProgram, "computeVirtualSites");
int index = 0;
......@@ -685,6 +725,8 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
vsitePositionKernel.setArg<cl::Buffer>(index++, vsite3AvgWeights->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteOutOfPlaneAtoms->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteOutOfPlaneWeights->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsAtoms->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsParams->getDeviceBuffer());
vsiteForceKernel = cl::Kernel(vsiteProgram, "distributeForces");
index = 0;
vsiteForceKernel.setArg<cl::Buffer>(index++, context.getPosq().getDeviceBuffer());
......@@ -697,7 +739,9 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
vsiteForceKernel.setArg<cl::Buffer>(index++, vsite3AvgWeights->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteOutOfPlaneAtoms->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteOutOfPlaneWeights->getDeviceBuffer());
numVsites = num2Avg+num3Avg+numOutOfPlane;
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsAtoms->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsParams->getDeviceBuffer());
numVsites = num2Avg+num3Avg+numOutOfPlane+numLocalCoords;
}
OpenCLIntegrationUtilities::~OpenCLIntegrationUtilities() {
......@@ -751,6 +795,10 @@ OpenCLIntegrationUtilities::~OpenCLIntegrationUtilities() {
delete vsiteOutOfPlaneAtoms;
if (vsiteOutOfPlaneWeights != NULL)
delete vsiteOutOfPlaneWeights;
if (vsiteLocalCoordsAtoms != NULL)
delete vsiteLocalCoordsAtoms;
if (vsiteLocalCoordsParams != NULL)
delete vsiteLocalCoordsParams;
}
void OpenCLIntegrationUtilities::applyConstraints(double tol) {
......
platforms/opencl/src/OpenCLPlatform.cpp
View file @ 51828eaa
......@@ -33,6 +33,10 @@
#include "openmm/System.h"
#include <algorithm>
#include <sstream>
#ifdef __APPLE__
#include "sys/sysctl.h"
#endif
using namespace OpenMM;
using std::map;
......@@ -42,10 +46,12 @@ using std::vector;
#ifdef OPENMM_OPENCL_BUILDING_STATIC_LIBRARY
extern "C" void registerOpenCLPlatform() {
if (OpenCLPlatform::isPlatformSupported())
Platform::registerPlatform(new OpenCLPlatform());
}
#else
extern "C" OPENMM_EXPORT_OPENCL void registerPlatforms() {
if (OpenCLPlatform::isPlatformSupported())
Platform::registerPlatform(new OpenCLPlatform());
}
#endif
......@@ -102,6 +108,33 @@ bool OpenCLPlatform::supportsDoublePrecision() const {
return true;
}
bool OpenCLPlatform::isPlatformSupported() {
// Return false for OpenCL implementations that are known
// to be buggy (Apple OSX since 10.7.5)
#ifdef __APPLE__
char str[256];
size_t size = sizeof(str);
int ret = sysctlbyname("kern.osrelease", str, &size, NULL, 0);
if (ret != 0)
return false;
int major, minor, micro;
if (sscanf(str, "%d.%d.%d", &major, &minor, &micro) != 3)
return false;
if ((major > 11) || (major == 11 && minor > 4) || (major == 11 && minor == 4 && micro >= 2))
// 11.4.2 is the darwin release corresponding to OSX 10.7.5, which is the
// point at which a number of serious bugs were introduced into the
// Apple OpenCL libraries, resulting in catistrophically incorrect MD simulations
// (see https://github.com/SimTk/openmm/issues/395 for example). Once a fix is released,
// this version check should be updated.
return false;
#endif
return true;
}
const string& OpenCLPlatform::getPropertyValue(const Context& context, const string& property) const {
const ContextImpl& impl = getContextImpl(context);
const PlatformData* data = reinterpret_cast<const PlatformData*>(impl.getPlatformData());
......
platforms/opencl/src/kernels/gbsaObc_cpu.cl
View file @ 51828eaa
......@@ -468,11 +468,16 @@ __kernel void computeGBSAForce1(
real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator);
real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
if (atom1 != y*TILE_SIZE+j)
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += 0.5f*tempEnergy;
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
......@@ -527,11 +532,15 @@ __kernel void computeGBSAForce1(
real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator);
real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += tempEnergy;
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
......@@ -684,11 +693,15 @@ __kernel void computeGBSAForce1(
real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator);
real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += tempEnergy;
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
......@@ -744,11 +757,15 @@ __kernel void computeGBSAForce1(
real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator);
real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += tempEnergy;
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
......
platforms/opencl/src/kernels/virtualSites.cl
View file @ 51828eaa
......@@ -32,7 +32,8 @@ __kernel void computeVirtualSites(__global real4* restrict posq,
#endif
__global const int4* restrict avg2Atoms, __global const real2* restrict avg2Weights,
__global const int4* restrict avg3Atoms, __global const real4* restrict avg3Weights,
__global const int4* restrict outOfPlaneAtoms, __global const real4* restrict outOfPlaneWeights) {
__global const int4* restrict outOfPlaneAtoms, __global const real4* restrict outOfPlaneWeights,
__global const int4* restrict localCoordsAtoms, __global const real* restrict localCoordsParams) {
#ifndef USE_MIXED_PRECISION
__global real4* posqCorrection = 0;
#endif
......@@ -76,6 +77,35 @@ __kernel void computeVirtualSites(__global real4* restrict posq,
pos.xyz = pos1.xyz + v12.xyz*weights.x + v13.xyz*weights.y + cross(v12, v13).xyz*weights.z;
storePos(posq, posqCorrection, atoms.x, pos);
}
// Local coordinates sites.
for (int index = get_global_id(0); index < NUM_LOCAL_COORDS; index += get_global_size(0)) {
int4 atoms = localCoordsAtoms[index];
__global const real* params = &localCoordsParams[12*index];
mixed4 pos = loadPos(posq, posqCorrection, atoms.x);
mixed4 pos1_4 = loadPos(posq, posqCorrection, atoms.y);
mixed4 pos2_4 = loadPos(posq, posqCorrection, atoms.z);
mixed4 pos3_4 = loadPos(posq, posqCorrection, atoms.w);
mixed4 pos1 = (mixed4) (pos1_4.x, pos1_4.y, pos1_4.z, 0);
mixed4 pos2 = (mixed4) (pos2_4.x, pos2_4.y, pos2_4.z, 0);
mixed4 pos3 = (mixed4) (pos3_4.x, pos3_4.y, pos3_4.z, 0);
mixed4 originWeights = (mixed4) (params[0], params[1], params[2], 0);
mixed4 xWeights = (mixed4) (params[3], params[4], params[5], 0);
mixed4 yWeights = (mixed4) (params[6], params[7], params[8], 0);
mixed4 localPosition = (mixed4) (params[9], params[10], params[11], 0);
mixed4 origin = pos1*originWeights.x + pos2*originWeights.y + pos3*originWeights.z;
mixed4 xdir = pos1*xWeights.x + pos2*xWeights.y + pos3*xWeights.z;
mixed4 ydir = pos1*yWeights.x + pos2*yWeights.y + pos3*yWeights.z;
mixed4 zdir = cross(xdir, ydir);
xdir *= rsqrt(xdir.x*xdir.x+xdir.y*xdir.y+xdir.z*xdir.z);
zdir *= rsqrt(zdir.x*zdir.x+zdir.y*zdir.y+zdir.z*zdir.z);
ydir = cross(zdir, xdir);
pos.x = origin.x + xdir.x*localPosition.x + ydir.x*localPosition.y + zdir.x*localPosition.z;
pos.y = origin.y + xdir.y*localPosition.x + ydir.y*localPosition.y + zdir.y*localPosition.z;
pos.z = origin.z + xdir.z*localPosition.x + ydir.z*localPosition.y + zdir.z*localPosition.z;
storePos(posq, posqCorrection, atoms.x, pos);
}
}
/**
......@@ -87,7 +117,8 @@ __kernel void distributeForces(__global const real4* restrict posq, __global rea
#endif
__global const int4* restrict avg2Atoms, __global const real2* restrict avg2Weights,
__global const int4* restrict avg3Atoms, __global const real4* restrict avg3Weights,
__global const int4* restrict outOfPlaneAtoms, __global const real4* restrict outOfPlaneWeights) {
__global const int4* restrict outOfPlaneAtoms, __global const real4* restrict outOfPlaneWeights,
__global const int4* restrict localCoordsAtoms, __global const real* restrict localCoordsParams) {
#ifndef USE_MIXED_PRECISION
__global real4* posqCorrection = 0;
#endif
......@@ -150,4 +181,90 @@ __kernel void distributeForces(__global const real4* restrict posq, __global rea
force[atoms.z] = f2;
force[atoms.w] = f3;
}
// Local coordinates sites.
for (int index = get_global_id(0); index < NUM_LOCAL_COORDS; index += get_global_size(0)) {
int4 atoms = localCoordsAtoms[index];
__global const real* params = &localCoordsParams[12*index];
mixed4 pos = loadPos(posq, posqCorrection, atoms.x);
mixed4 pos1_4 = loadPos(posq, posqCorrection, atoms.y);
mixed4 pos2_4 = loadPos(posq, posqCorrection, atoms.z);
mixed4 pos3_4 = loadPos(posq, posqCorrection, atoms.w);
mixed4 pos1 = (mixed4) (pos1_4.x, pos1_4.y, pos1_4.z, 0);
mixed4 pos2 = (mixed4) (pos2_4.x, pos2_4.y, pos2_4.z, 0);
mixed4 pos3 = (mixed4) (pos3_4.x, pos3_4.y, pos3_4.z, 0);
mixed4 originWeights = (mixed4) (params[0], params[1], params[2], 0);
mixed4 wx = (mixed4) (params[3], params[4], params[5], 0);
mixed4 wy = (mixed4) (params[6], params[7], params[8], 0);
mixed4 localPosition = (mixed4) (params[9], params[10], params[11], 0);
mixed4 origin = pos1*originWeights.x + pos2*originWeights.y + pos3*originWeights.z;
mixed4 xdir = pos1*wx.x + pos2*wx.y + pos3*wx.z;
mixed4 ydir = pos1*wy.x + pos2*wy.y + pos3*wy.z;
mixed4 zdir = cross(xdir, ydir);
mixed invNormXdir = rsqrt(xdir.x*xdir.x+xdir.y*xdir.y+xdir.z*xdir.z);
mixed invNormZdir = rsqrt(zdir.x*zdir.x+zdir.y*zdir.y+zdir.z*zdir.z);
mixed4 dx = xdir*invNormXdir;
mixed4 dz = zdir*invNormZdir;
mixed4 dy = cross(dz, dx);
// The derivatives for this case are very complicated. They were computed with SymPy then simplified by hand.
mixed t11 = (wx.x*ydir.x-wy.x*xdir.x)*invNormZdir;
mixed t12 = (wx.x*ydir.y-wy.x*xdir.y)*invNormZdir;
mixed t13 = (wx.x*ydir.z-wy.x*xdir.z)*invNormZdir;
mixed t21 = (wx.y*ydir.x-wy.y*xdir.x)*invNormZdir;
mixed t22 = (wx.y*ydir.y-wy.y*xdir.y)*invNormZdir;
mixed t23 = (wx.y*ydir.z-wy.y*xdir.z)*invNormZdir;
mixed t31 = (wx.z*ydir.x-wy.z*xdir.x)*invNormZdir;
mixed t32 = (wx.z*ydir.y-wy.z*xdir.y)*invNormZdir;
mixed t33 = (wx.z*ydir.z-wy.z*xdir.z)*invNormZdir;
mixed sx1 = t13*dz.y-t12*dz.z;
mixed sy1 = t11*dz.z-t13*dz.x;
mixed sz1 = t12*dz.x-t11*dz.y;
mixed sx2 = t23*dz.y-t22*dz.z;
mixed sy2 = t21*dz.z-t23*dz.x;
mixed sz2 = t22*dz.x-t21*dz.y;
mixed sx3 = t33*dz.y-t32*dz.z;
mixed sy3 = t31*dz.z-t33*dz.x;
mixed sz3 = t32*dz.x-t31*dz.y;
mixed4 wxScaled = wx*invNormXdir;
real4 f = force[atoms.x];
real4 f1 = force[atoms.y];
real4 f2 = force[atoms.z];
real4 f3 = force[atoms.w];
mixed4 fp1 = localPosition*f.x;
mixed4 fp2 = localPosition*f.y;
mixed4 fp3 = localPosition*f.z;
f1.x += fp1.x*wxScaled.x*(1-dx.x*dx.x) + fp1.z*(dz.x*sx1 ) + fp1.y*((-dx.x*dy.x )*wxScaled.x + dy.x*sx1 - dx.y*t12 - dx.z*t13) + f.x*originWeights.x;
f1.y += fp1.x*wxScaled.x*( -dx.x*dx.y) + fp1.z*(dz.x*sy1+t13) + fp1.y*((-dx.y*dy.x-dz.z)*wxScaled.x + dy.x*sy1 + dx.y*t11);
f1.z += fp1.x*wxScaled.x*( -dx.x*dx.z) + fp1.z*(dz.x*sz1-t12) + fp1.y*((-dx.z*dy.x+dz.y)*wxScaled.x + dy.x*sz1 + dx.z*t11);
f2.x += fp1.x*wxScaled.y*(1-dx.x*dx.x) + fp1.z*(dz.x*sx2 ) + fp1.y*((-dx.x*dy.x )*wxScaled.y + dy.x*sx2 - dx.y*t22 - dx.z*t23) + f.x*originWeights.y;
f2.y += fp1.x*wxScaled.y*( -dx.x*dx.y) + fp1.z*(dz.x*sy2+t23) + fp1.y*((-dx.y*dy.x-dz.z)*wxScaled.y + dy.x*sy2 + dx.y*t21);
f2.z += fp1.x*wxScaled.y*( -dx.x*dx.z) + fp1.z*(dz.x*sz2-t22) + fp1.y*((-dx.z*dy.x+dz.y)*wxScaled.y + dy.x*sz2 + dx.z*t21);
f3.x += fp1.x*wxScaled.z*(1-dx.x*dx.x) + fp1.z*(dz.x*sx3 ) + fp1.y*((-dx.x*dy.x )*wxScaled.z + dy.x*sx3 - dx.y*t32 - dx.z*t33) + f.x*originWeights.z;
f3.y += fp1.x*wxScaled.z*( -dx.x*dx.y) + fp1.z*(dz.x*sy3+t33) + fp1.y*((-dx.y*dy.x-dz.z)*wxScaled.z + dy.x*sy3 + dx.y*t31);
f3.z += fp1.x*wxScaled.z*( -dx.x*dx.z) + fp1.z*(dz.x*sz3-t32) + fp1.y*((-dx.z*dy.x+dz.y)*wxScaled.z + dy.x*sz3 + dx.z*t31);
f1.x += fp2.x*wxScaled.x*( -dx.y*dx.x) + fp2.z*(dz.y*sx1-t13) - fp2.y*(( dx.x*dy.y-dz.z)*wxScaled.x - dy.y*sx1 - dx.x*t12);
f1.y += fp2.x*wxScaled.x*(1-dx.y*dx.y) + fp2.z*(dz.y*sy1 ) - fp2.y*(( dx.y*dy.y )*wxScaled.x - dy.y*sy1 + dx.x*t11 + dx.z*t13) + f.y*originWeights.x;
f1.z += fp2.x*wxScaled.x*( -dx.y*dx.z) + fp2.z*(dz.y*sz1+t11) - fp2.y*(( dx.z*dy.y+dz.x)*wxScaled.x - dy.y*sz1 - dx.z*t12);
f2.x += fp2.x*wxScaled.y*( -dx.y*dx.x) + fp2.z*(dz.y*sx2-t23) - fp2.y*(( dx.x*dy.y-dz.z)*wxScaled.y - dy.y*sx2 - dx.x*t22);
f2.y += fp2.x*wxScaled.y*(1-dx.y*dx.y) + fp2.z*(dz.y*sy2 ) - fp2.y*(( dx.y*dy.y )*wxScaled.y - dy.y*sy2 + dx.x*t21 + dx.z*t23) + f.y*originWeights.y;
f2.z += fp2.x*wxScaled.y*( -dx.y*dx.z) + fp2.z*(dz.y*sz2+t21) - fp2.y*(( dx.z*dy.y+dz.x)*wxScaled.y - dy.y*sz2 - dx.z*t22);
f3.x += fp2.x*wxScaled.z*( -dx.y*dx.x) + fp2.z*(dz.y*sx3-t33) - fp2.y*(( dx.x*dy.y-dz.z)*wxScaled.z - dy.y*sx3 - dx.x*t32);
f3.y += fp2.x*wxScaled.z*(1-dx.y*dx.y) + fp2.z*(dz.y*sy3 ) - fp2.y*(( dx.y*dy.y )*wxScaled.z - dy.y*sy3 + dx.x*t31 + dx.z*t33) + f.y*originWeights.z;
f3.z += fp2.x*wxScaled.z*( -dx.y*dx.z) + fp2.z*(dz.y*sz3+t31) - fp2.y*(( dx.z*dy.y+dz.x)*wxScaled.z - dy.y*sz3 - dx.z*t32);
f1.x += fp3.x*wxScaled.x*( -dx.z*dx.x) + fp3.z*(dz.z*sx1+t12) + fp3.y*((-dx.x*dy.z-dz.y)*wxScaled.x + dy.z*sx1 + dx.x*t13);
f1.y += fp3.x*wxScaled.x*( -dx.z*dx.y) + fp3.z*(dz.z*sy1-t11) + fp3.y*((-dx.y*dy.z+dz.x)*wxScaled.x + dy.z*sy1 + dx.y*t13);
f1.z += fp3.x*wxScaled.x*(1-dx.z*dx.z) + fp3.z*(dz.z*sz1 ) + fp3.y*((-dx.z*dy.z )*wxScaled.x + dy.z*sz1 - dx.x*t11 - dx.y*t12) + f.z*originWeights.x;
f2.x += fp3.x*wxScaled.y*( -dx.z*dx.x) + fp3.z*(dz.z*sx2+t22) + fp3.y*((-dx.x*dy.z-dz.y)*wxScaled.y + dy.z*sx2 + dx.x*t23);
f2.y += fp3.x*wxScaled.y*( -dx.z*dx.y) + fp3.z*(dz.z*sy2-t21) + fp3.y*((-dx.y*dy.z+dz.x)*wxScaled.y + dy.z*sy2 + dx.y*t23);
f2.z += fp3.x*wxScaled.y*(1-dx.z*dx.z) + fp3.z*(dz.z*sz2 ) + fp3.y*((-dx.z*dy.z )*wxScaled.y + dy.z*sz2 - dx.x*t21 - dx.y*t22) + f.z*originWeights.y;
f3.x += fp3.x*wxScaled.z*( -dx.z*dx.x) + fp3.z*(dz.z*sx3+t32) + fp3.y*((-dx.x*dy.z-dz.y)*wxScaled.z + dy.z*sx3 + dx.x*t33);
f3.y += fp3.x*wxScaled.z*( -dx.z*dx.y) + fp3.z*(dz.z*sy3-t31) + fp3.y*((-dx.y*dy.z+dz.x)*wxScaled.z + dy.z*sy3 + dx.y*t33);
f3.z += fp3.x*wxScaled.z*(1-dx.z*dx.z) + fp3.z*(dz.z*sz3 ) + fp3.y*((-dx.z*dy.z )*wxScaled.z + dy.z*sz3 - dx.x*t31 - dx.y*t32) + f.z*originWeights.z;
force[atoms.y] = f1;
force[atoms.z] = f2;
force[atoms.w] = f3;
}
}
platforms/opencl/staticTarget/CMakeLists.txt
View file @ 51828eaa
......@@ -13,12 +13,7 @@ ADD_CUSTOM_COMMAND(OUTPUT ${CL_KERNELS_CPP} ${CL_KERNELS_H}
SET_SOURCE_FILES_PROPERTIES(${CL_KERNELS_CPP} ${CL_KERNELS_H} PROPERTIES GENERATED TRUE)
ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME}_d)
ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME})
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${MAIN_OPENMM_LIB} ${OPENCL_LIBRARIES} ${PTHREADS_LIB_STATIC})
TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME} ${OPENCL_LIBRARIES} ${PTHREADS_LIB_STATIC})
#-DPTW32_STATIC_LIB only works for the windows pthreads.
SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_OPENCL_BUILDING_STATIC_LIBRARY -DPTW32_STATIC_LIB")
......
platforms/opencl/tests/TestOpenCLCustomCompoundBondForce.cpp
View file @ 51828eaa
......@@ -33,6 +33,9 @@
* This tests the OpenCL implementation of CustomCompoundBondForce.
*/
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
......@@ -313,7 +316,7 @@ void testMultipleBonds() {
parameters[0] = 1.0;
parameters[1] = 1.0;
parameters[2] = 2 * M_PI / 3;
parameters[3] = sqrt(3) / 2;
parameters[3] = sqrt(3.0) / 2;
vector<int> particles0(3);
particles0[0] = 0;
particles0[1] = 1;
......
platforms/opencl/tests/TestOpenCLVirtualSites.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2012 Stanford University and the Authors. *
* Portions copyright (c) 2012-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -213,6 +213,84 @@ void testOutOfPlane() {
}
}
/**
* Test a LocalCoordinatesSite virtual site.
*/
void testLocalCoordinates() {
const Vec3 originWeights(0.2, 0.3, 0.5);
const Vec3 xWeights(-1.0, 0.5, 0.5);
const Vec3 yWeights(0.0, -1.0, 1.0);
const Vec3 localPosition(0.4, 0.3, 0.2);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(3, new LocalCoordinatesSite(0, 1, 2, originWeights, xWeights, yWeights, localPosition));
CustomExternalForce* forceField = new CustomExternalForce("2*x^2+3*y^2+4*z^2");
system.addForce(forceField);
vector<double> params;
forceField->addParticle(0, params);
forceField->addParticle(1, params);
forceField->addParticle(2, params);
forceField->addParticle(3, params);
LangevinIntegrator integrator(300.0, 0.1, 0.002);
Context context(system, integrator, platform);
vector<Vec3> positions(4), positions2(4), positions3(4);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < 100; i++) {
// Set the particles at random positions.
Vec3 xdir, ydir, zdir;
do {
for (int j = 0; j < 3; j++)
positions[j] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
xdir = positions[0]*xWeights[0] + positions[1]*xWeights[1] + positions[2]*xWeights[2];
ydir = positions[0]*yWeights[0] + positions[1]*yWeights[1] + positions[2]*yWeights[2];
zdir = xdir.cross(ydir);
if (sqrt(xdir.dot(xdir)) > 0.1 && sqrt(ydir.dot(ydir)) > 0.1 && sqrt(zdir.dot(zdir)) > 0.1)
break; // These positions give a reasonable coordinate system.
} while (true);
context.setPositions(positions);
context.applyConstraints(0.0001);
// See if the virtual site is positioned correctly.
State state = context.getState(State::Positions | State::Forces);
const vector<Vec3>& pos = state.getPositions();
Vec3 origin = pos[0]*originWeights[0] + pos[1]*originWeights[1] + pos[2]*originWeights[2];
xdir /= sqrt(xdir.dot(xdir));
zdir /= sqrt(zdir.dot(zdir));
ydir = zdir.cross(xdir);
ASSERT_EQUAL_VEC(origin+xdir*localPosition[0]+ydir*localPosition[1]+zdir*localPosition[2], pos[3], 1e-5);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < 3; ++i) {
Vec3 f = state.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
}
norm = std::sqrt(norm);
const double delta = 1e-2;
double step = 0.5*delta/norm;
for (int i = 0; i < 3; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
context.applyConstraints(0.0001);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
context.applyConstraints(0.0001);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/delta, 1e-3)
}
}
/**
* Make sure that energy, linear momentum, and angular momentum are all conserved
* when using virtual sites.
......@@ -279,6 +357,26 @@ void testConservationLaws() {
positions.push_back(Vec3(1, 1, -1));
positions.push_back(Vec3());
// Create a molecule with a LocalCoordinatesSite virtual site.
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(14, new LocalCoordinatesSite(11, 12, 13, Vec3(0.3, 0.3, 0.4), Vec3(1.0, -0.5, -0.5), Vec3(0, -1.0, 1.0), Vec3(0.2, 0.2, 1.0)));
system.addConstraint(11, 12, 1.0);
system.addConstraint(11, 13, 1.0);
system.addConstraint(12, 13, sqrt(2.0));
for (int i = 0; i < 4; i++) {
forceField->addParticle(0, 1, 10);
for (int j = 0; j < i; j++)
forceField->addException(i+11, j+11, 0, 1, 0);
}
positions.push_back(Vec3(1, 2, 0));
positions.push_back(Vec3(2, 2, 0));
positions.push_back(Vec3(1, 3, 0));
positions.push_back(Vec3());
// Simulate it and check conservation laws.
VerletIntegrator integrator(0.002);
......@@ -315,7 +413,7 @@ void testConservationLaws() {
if (i == 0)
initialAngularMomentum = angularMomentum;
else
ASSERT_EQUAL_VEC(initialAngularMomentum, angularMomentum, 0.02);
ASSERT_EQUAL_VEC(initialAngularMomentum, angularMomentum, 0.03);
integrator.step(1);
}
}
......@@ -434,6 +532,7 @@ int main(int argc, char* argv[]) {
testTwoParticleAverage();
testThreeParticleAverage();
testOutOfPlane();
testLocalCoordinates();
testConservationLaws();
testReordering();
}
......
platforms/reference/include/CpuGBVI.h 100755 → 100644
View file @ 51828eaa
File mode changed from 100755 to 100644
platforms/reference/include/CpuObc.h 100755 → 100644
View file @ 51828eaa
File mode changed from 100755 to 100644
platforms/reference/include/GBVIParameters.h 100755 → 100644
View file @ 51828eaa
File mode changed from 100755 to 100644
platforms/reference/include/ObcParameters.h 100755 → 100644
View file @ 51828eaa
File mode changed from 100755 to 100644
platforms/reference/include/ReferenceNeighborList.h 100755 → 100644
View file @ 51828eaa
File mode changed from 100755 to 100644
platforms/reference/include/ReferenceTabulatedFunction.h
View file @ 51828eaa
......@@ -42,7 +42,7 @@ namespace OpenMM {
/**
* Given a TabulatedFunction, wrap it in an appropriate subclass of Lepton::CustomFunction.
*/
extern "C" Lepton::CustomFunction* createReferenceTabulatedFunction(const TabulatedFunction& function);
extern "C" OPENMM_EXPORT Lepton::CustomFunction* createReferenceTabulatedFunction(const TabulatedFunction& function);
/**
* This class adapts a Continuous1DFunction into a Lepton::CustomFunction.
......
platforms/reference/include/SimTKOpenMMRealType.h 100755 → 100644
View file @ 51828eaa
File mode changed from 100755 to 100644
platforms/reference/src/ReferenceTabulatedFunction.cpp
View file @ 51828eaa
......@@ -34,12 +34,19 @@
#include "openmm/internal/SplineFitter.h"
#ifdef _MSC_VER
#if _MSC_VER < 1800
/**
* We need to define this ourselves, since Visual Studio is missing round() from cmath.
*/
static int round(double x) {
return (int) (x+0.5);
}
#else
#include <cmath>
#endif // MSC_VER < 1800
#else
#include <cmath>
#endif
......@@ -48,7 +55,7 @@ using namespace OpenMM;
using namespace std;
using Lepton::CustomFunction;
extern "C" CustomFunction* createReferenceTabulatedFunction(const TabulatedFunction& function) {
extern "C" OPENMM_EXPORT CustomFunction* createReferenceTabulatedFunction(const TabulatedFunction& function) {
if (dynamic_cast<const Continuous1DFunction*>(&function) != NULL)
return new ReferenceContinuous1DFunction(dynamic_cast<const Continuous1DFunction&>(function));
if (dynamic_cast<const Continuous2DFunction*>(&function) != NULL)
......
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