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Commit 51e51c3b authored by John Chodera (MSKCC)'s avatar John Chodera (MSKCC)
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Merge remote-tracking branch 'upstream/master'

parents bc240d4a 373c3878
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Showing with 611 additions and 302 deletions
platforms/cuda/tests/TestCudaNonbondedForce.cpp
View file @ 51e51c3b
......@@ -748,7 +748,7 @@ void testChangingParameters() {
ASSERT_EQUAL_TOL(cuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
}
void testParallelComputation(bool useCutoff) {
void testParallelComputation(NonbondedForce::NonbondedMethod method) {
System system;
const int numParticles = 200;
for (int i = 0; i < numParticles; i++)
......@@ -756,9 +756,9 @@ void testParallelComputation(bool useCutoff) {
NonbondedForce* force = new NonbondedForce();
for (int i = 0; i < numParticles; i++)
force->addParticle(i%2-0.5, 0.5, 1.0);
if (useCutoff)
force->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
force->setNonbondedMethod(method);
system.addForce(force);
system.setDefaultPeriodicBoxVectors(Vec3(5,0,0), Vec3(0,5,0), Vec3(0,0,5));
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
......@@ -877,8 +877,9 @@ int main(int argc, char* argv[]) {
//testBlockInteractions(true);
testDispersionCorrection();
testChangingParameters();
testParallelComputation(false);
testParallelComputation(true);
testParallelComputation(NonbondedForce::NoCutoff);
testParallelComputation(NonbondedForce::Ewald);
testParallelComputation(NonbondedForce::PME);
testSwitchingFunction(NonbondedForce::CutoffNonPeriodic);
testSwitchingFunction(NonbondedForce::PME);
}
......
platforms/cuda/tests/TestCudaVirtualSites.cpp
View file @ 51e51c3b
......@@ -524,6 +524,47 @@ void testReordering() {
}
}
/**
* Test a System where multiple virtual sites are all calculated from the same particles.
*/
void testOverlappingSites() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
NonbondedForce* nonbonded = new NonbondedForce();
system.addForce(nonbonded);
nonbonded->addParticle(1.0, 0.0, 0.0);
nonbonded->addParticle(-0.5, 0.0, 0.0);
nonbonded->addParticle(-0.5, 0.0, 0.0);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(10, 0, 0));
positions.push_back(Vec3(0, 10, 0));
for (int i = 0; i < 20; i++) {
system.addParticle(0.0);
double u = 0.1*((i+1)%4);
double v = 0.05*i;
system.setVirtualSite(3+i, new ThreeParticleAverageSite(0, 1, 2, u, v, 1-u-v));
nonbonded->addParticle(i%2 == 0 ? -1.0 : 1.0, 0.0, 0.0);
positions.push_back(Vec3());
}
VerletIntegrator i1(0.002);
VerletIntegrator i2(0.002);
Context c1(system, i1, Platform::getPlatformByName("Reference"));
Context c2(system, i2, platform);
c1.setPositions(positions);
c2.setPositions(positions);
c1.applyConstraints(0.0001);
c2.applyConstraints(0.0001);
State s1 = c1.getState(State::Positions | State::Forces);
State s2 = c2.getState(State::Positions | State::Forces);
for (int i = 0; i < system.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getPositions()[i], s2.getPositions()[i], 1e-5);
for (int i = 0; i < 3; i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
......@@ -535,6 +576,7 @@ int main(int argc, char* argv[]) {
testLocalCoordinates();
testConservationLaws();
testReordering();
testOverlappingSites();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/opencl/include/OpenCLIntegrationUtilities.h
View file @ 51e51c3b
......@@ -121,7 +121,7 @@ private:
cl::Kernel ccmaPosForceKernel, ccmaVelForceKernel;
cl::Kernel ccmaMultiplyKernel;
cl::Kernel ccmaPosUpdateKernel, ccmaVelUpdateKernel;
cl::Kernel vsitePositionKernel, vsiteForceKernel;
cl::Kernel vsitePositionKernel, vsiteForceKernel, vsiteAddForcesKernel;
cl::Kernel randomKernel, timeShiftKernel;
OpenCLArray* posDelta;
OpenCLArray* settleAtoms;
......@@ -152,7 +152,7 @@ private:
OpenCLArray* vsiteLocalCoordsParams;
int randomPos;
int lastSeed, numVsites;
bool hasInitializedPosConstraintKernels, hasInitializedVelConstraintKernels, ccmaUseDirectBuffer;
bool hasInitializedPosConstraintKernels, hasInitializedVelConstraintKernels, ccmaUseDirectBuffer, hasOverlappingVsites;
struct ShakeCluster;
struct ConstraintOrderer;
};
......
platforms/opencl/src/OpenCLIntegrationUtilities.cpp
View file @ 51e51c3b
......@@ -101,7 +101,7 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
ccmaConstraintMatrixValue(NULL), ccmaDelta1(NULL), ccmaDelta2(NULL), ccmaConverged(NULL), ccmaConvergedHostBuffer(NULL),
vsite2AvgAtoms(NULL), vsite2AvgWeights(NULL), vsite3AvgAtoms(NULL), vsite3AvgWeights(NULL),
vsiteOutOfPlaneAtoms(NULL), vsiteOutOfPlaneWeights(NULL), vsiteLocalCoordsAtoms(NULL), vsiteLocalCoordsParams(NULL),
hasInitializedPosConstraintKernels(false), hasInitializedVelConstraintKernels(false) {
hasInitializedPosConstraintKernels(false), hasInitializedVelConstraintKernels(false), hasOverlappingVsites(false) {
// Create workspace arrays.
if (context.getUseDoublePrecision() || context.getUseMixedPrecision()) {
......@@ -649,6 +649,7 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
int num3Avg = vsite3AvgAtomVec.size();
int numOutOfPlane = vsiteOutOfPlaneAtomVec.size();
int numLocalCoords = vsiteLocalCoordsAtomVec.size();
numVsites = num2Avg+num3Avg+numOutOfPlane+numLocalCoords;
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");
......@@ -706,6 +707,20 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
}
}
// If multiple virtual sites depend on the same particle, make sure the force distribution
// can be done safely.
vector<int> atomCounts(numAtoms, 0);
for (int i = 0; i < numAtoms; i++)
if (system.isVirtualSite(i))
for (int j = 0; j < system.getVirtualSite(i).getNumParticles(); j++)
atomCounts[system.getVirtualSite(i).getParticle(j)]++;
for (int i = 0; i < numAtoms; i++)
if (atomCounts[i] > 1)
hasOverlappingVsites = true;
if (hasOverlappingVsites && context.getUseDoublePrecision() && !context.getSupports64BitGlobalAtomics())
throw OpenMMException("This device does not support 64 bit atomics. Cannot use double precision when multiple virtual sites depend on the same atom.");
// Create the kernels for virtual sites.
map<string, string> defines;
......@@ -713,6 +728,10 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
defines["NUM_3_AVERAGE"] = context.intToString(num3Avg);
defines["NUM_OUT_OF_PLANE"] = context.intToString(numOutOfPlane);
defines["NUM_LOCAL_COORDS"] = context.intToString(numLocalCoords);
defines["NUM_ATOMS"] = context.intToString(numAtoms);
defines["PADDED_NUM_ATOMS"] = context.intToString(context.getPaddedNumAtoms());
if (hasOverlappingVsites)
defines["HAS_OVERLAPPING_VSITES"] = "1";
cl::Program vsiteProgram = context.createProgram(OpenCLKernelSources::virtualSites, defines);
vsitePositionKernel = cl::Kernel(vsiteProgram, "computeVirtualSites");
int index = 0;
......@@ -731,6 +750,8 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
index = 0;
vsiteForceKernel.setArg<cl::Buffer>(index++, context.getPosq().getDeviceBuffer());
index++; // Skip argument 1: the force array hasn't been created yet.
if (context.getSupports64BitGlobalAtomics())
index++; // Skip argument 2: the force array hasn't been created yet.
if (context.getUseMixedPrecision())
vsiteForceKernel.setArg<cl::Buffer>(index++, context.getPosqCorrection().getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(index++, vsite2AvgAtoms->getDeviceBuffer());
......@@ -741,7 +762,8 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteOutOfPlaneWeights->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsAtoms->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsParams->getDeviceBuffer());
numVsites = num2Avg+num3Avg+numOutOfPlane+numLocalCoords;
if (hasOverlappingVsites && context.getSupports64BitGlobalAtomics())
vsiteAddForcesKernel = cl::Kernel(vsiteProgram, "addDistributedForces");
}
OpenCLIntegrationUtilities::~OpenCLIntegrationUtilities() {
......@@ -941,8 +963,25 @@ void OpenCLIntegrationUtilities::computeVirtualSites() {
void OpenCLIntegrationUtilities::distributeForcesFromVirtualSites() {
if (numVsites > 0) {
// Set arguments that didn't exist yet in the constructor.
vsiteForceKernel.setArg<cl::Buffer>(1, context.getForce().getDeviceBuffer());
if (context.getSupports64BitGlobalAtomics()) {
vsiteForceKernel.setArg<cl::Buffer>(2, context.getLongForceBuffer().getDeviceBuffer());
if (hasOverlappingVsites) {
// We'll be using 64 bit atomics for the force redistribution, so clear the buffer.
context.clearBuffer(context.getLongForceBuffer());
}
}
context.executeKernel(vsiteForceKernel, numVsites);
if (context.getSupports64BitGlobalAtomics() && hasOverlappingVsites) {
// Add the redistributed forces from the virtual sites to the main force array.
vsiteAddForcesKernel.setArg<cl::Buffer>(0, context.getLongForceBuffer().getDeviceBuffer());
vsiteAddForcesKernel.setArg<cl::Buffer>(1, context.getForce().getDeviceBuffer());
context.executeKernel(vsiteAddForcesKernel, context.getNumAtoms());
}
}
}
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 51e51c3b
......@@ -1492,7 +1492,7 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
else
dispersionCoefficient = 0.0;
alpha = 0;
if (force.getNonbondedMethod() == NonbondedForce::Ewald && cl.getContextIndex() == 0) {
if (force.getNonbondedMethod() == NonbondedForce::Ewald) {
// Compute the Ewald parameters.
int kmaxx, kmaxy, kmaxz;
......@@ -1500,23 +1500,25 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
defines["EWALD_ALPHA"] = cl.doubleToString(alpha);
defines["TWO_OVER_SQRT_PI"] = cl.doubleToString(2.0/sqrt(M_PI));
defines["USE_EWALD"] = "1";
ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
if (cl.getContextIndex() == 0) {
ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
// Create the reciprocal space kernels.
// Create the reciprocal space kernels.
map<string, string> replacements;
replacements["NUM_ATOMS"] = cl.intToString(numParticles);
replacements["KMAX_X"] = cl.intToString(kmaxx);
replacements["KMAX_Y"] = cl.intToString(kmaxy);
replacements["KMAX_Z"] = cl.intToString(kmaxz);
replacements["EXP_COEFFICIENT"] = cl.doubleToString(-1.0/(4.0*alpha*alpha));
cl::Program program = cl.createProgram(OpenCLKernelSources::ewald, replacements);
ewaldSumsKernel = cl::Kernel(program, "calculateEwaldCosSinSums");
ewaldForcesKernel = cl::Kernel(program, "calculateEwaldForces");
int elementSize = (cl.getUseDoublePrecision() ? sizeof(mm_double2) : sizeof(mm_float2));
cosSinSums = new OpenCLArray(cl, (2*kmaxx-1)*(2*kmaxy-1)*(2*kmaxz-1), elementSize, "cosSinSums");
}
else if (force.getNonbondedMethod() == NonbondedForce::PME && cl.getContextIndex() == 0) {
map<string, string> replacements;
replacements["NUM_ATOMS"] = cl.intToString(numParticles);
replacements["KMAX_X"] = cl.intToString(kmaxx);
replacements["KMAX_Y"] = cl.intToString(kmaxy);
replacements["KMAX_Z"] = cl.intToString(kmaxz);
replacements["EXP_COEFFICIENT"] = cl.doubleToString(-1.0/(4.0*alpha*alpha));
cl::Program program = cl.createProgram(OpenCLKernelSources::ewald, replacements);
ewaldSumsKernel = cl::Kernel(program, "calculateEwaldCosSinSums");
ewaldForcesKernel = cl::Kernel(program, "calculateEwaldForces");
int elementSize = (cl.getUseDoublePrecision() ? sizeof(mm_double2) : sizeof(mm_float2));
cosSinSums = new OpenCLArray(cl, (2*kmaxx-1)*(2*kmaxy-1)*(2*kmaxz-1), elementSize, "cosSinSums");
}
}
else if (force.getNonbondedMethod() == NonbondedForce::PME) {
// Compute the PME parameters.
int gridSizeX, gridSizeY, gridSizeZ;
......@@ -1527,119 +1529,121 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
defines["EWALD_ALPHA"] = cl.doubleToString(alpha);
defines["TWO_OVER_SQRT_PI"] = cl.doubleToString(2.0/sqrt(M_PI));
defines["USE_EWALD"] = "1";
ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
pmeDefines["PME_ORDER"] = cl.intToString(PmeOrder);
pmeDefines["NUM_ATOMS"] = cl.intToString(numParticles);
pmeDefines["RECIP_EXP_FACTOR"] = cl.doubleToString(M_PI*M_PI/(alpha*alpha));
pmeDefines["GRID_SIZE_X"] = cl.intToString(gridSizeX);
pmeDefines["GRID_SIZE_Y"] = cl.intToString(gridSizeY);
pmeDefines["GRID_SIZE_Z"] = cl.intToString(gridSizeZ);
pmeDefines["EPSILON_FACTOR"] = cl.doubleToString(sqrt(ONE_4PI_EPS0));
bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
if (deviceIsCpu)
pmeDefines["DEVICE_IS_CPU"] = "1";
if (cl.getPlatformData().useCpuPme) {
// Create the CPU PME kernel.
try {
cpuPme = getPlatform().createKernel(CalcPmeReciprocalForceKernel::Name(), *cl.getPlatformData().context);
cpuPme.getAs<CalcPmeReciprocalForceKernel>().initialize(gridSizeX, gridSizeY, gridSizeZ, numParticles, alpha);
cl::Program program = cl.createProgram(OpenCLKernelSources::pme, pmeDefines);
cl::Kernel addForcesKernel = cl::Kernel(program, "addForces");
pmeio = new PmeIO(cl, addForcesKernel);
cl.addPreComputation(new PmePreComputation(cl, cpuPme, *pmeio));
cl.addPostComputation(new PmePostComputation(cpuPme, *pmeio));
}
catch (OpenMMException& ex) {
// The CPU PME plugin isn't available.
}
}
if (pmeio == NULL) {
// Create required data structures.
int elementSize = (cl.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
pmeGrid = new OpenCLArray(cl, gridSizeX*gridSizeY*gridSizeZ, 2*elementSize, "pmeGrid");
cl.addAutoclearBuffer(*pmeGrid);
pmeGrid2 = new OpenCLArray(cl, gridSizeX*gridSizeY*gridSizeZ, 2*elementSize, "pmeGrid2");
pmeBsplineModuliX = new OpenCLArray(cl, gridSizeX, elementSize, "pmeBsplineModuliX");
pmeBsplineModuliY = new OpenCLArray(cl, gridSizeY, elementSize, "pmeBsplineModuliY");
pmeBsplineModuliZ = new OpenCLArray(cl, gridSizeZ, elementSize, "pmeBsplineModuliZ");
pmeBsplineTheta = new OpenCLArray(cl, PmeOrder*numParticles, 4*elementSize, "pmeBsplineTheta");
pmeAtomRange = OpenCLArray::create<cl_int>(cl, gridSizeX*gridSizeY*gridSizeZ+1, "pmeAtomRange");
pmeAtomGridIndex = OpenCLArray::create<mm_int2>(cl, numParticles, "pmeAtomGridIndex");
sort = new OpenCLSort(cl, new SortTrait(), cl.getNumAtoms());
fft = new OpenCLFFT3D(cl, gridSizeX, gridSizeY, gridSizeZ);
// Initialize the b-spline moduli.
int maxSize = max(max(gridSizeX, gridSizeY), gridSizeZ);
vector<double> data(PmeOrder);
vector<double> ddata(PmeOrder);
vector<double> bsplines_data(maxSize);
data[PmeOrder-1] = 0.0;
data[1] = 0.0;
data[0] = 1.0;
for (int i = 3; i < PmeOrder; i++) {
double div = 1.0/(i-1.0);
data[i-1] = 0.0;
for (int j = 1; j < (i-1); j++)
data[i-j-1] = div*(j*data[i-j-2]+(i-j)*data[i-j-1]);
data[0] = div*data[0];
}
// Differentiate.
ddata[0] = -data[0];
for (int i = 1; i < PmeOrder; i++)
ddata[i] = data[i-1]-data[i];
double div = 1.0/(PmeOrder-1);
data[PmeOrder-1] = 0.0;
for (int i = 1; i < (PmeOrder-1); i++)
data[PmeOrder-i-1] = div*(i*data[PmeOrder-i-2]+(PmeOrder-i)*data[PmeOrder-i-1]);
data[0] = div*data[0];
for (int i = 0; i < maxSize; i++)
bsplines_data[i] = 0.0;
for (int i = 1; i <= PmeOrder; i++)
bsplines_data[i] = data[i-1];
// Evaluate the actual bspline moduli for X/Y/Z.
for(int dim = 0; dim < 3; dim++) {
int ndata = (dim == 0 ? gridSizeX : dim == 1 ? gridSizeY : gridSizeZ);
vector<cl_double> moduli(ndata);
for (int i = 0; i < ndata; i++) {
double sc = 0.0;
double ss = 0.0;
for (int j = 0; j < ndata; j++) {
double arg = (2.0*M_PI*i*j)/ndata;
sc += bsplines_data[j]*cos(arg);
ss += bsplines_data[j]*sin(arg);
}
moduli[i] = (float) (sc*sc+ss*ss);
if (cl.getContextIndex() == 0) {
ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
pmeDefines["PME_ORDER"] = cl.intToString(PmeOrder);
pmeDefines["NUM_ATOMS"] = cl.intToString(numParticles);
pmeDefines["RECIP_EXP_FACTOR"] = cl.doubleToString(M_PI*M_PI/(alpha*alpha));
pmeDefines["GRID_SIZE_X"] = cl.intToString(gridSizeX);
pmeDefines["GRID_SIZE_Y"] = cl.intToString(gridSizeY);
pmeDefines["GRID_SIZE_Z"] = cl.intToString(gridSizeZ);
pmeDefines["EPSILON_FACTOR"] = cl.doubleToString(sqrt(ONE_4PI_EPS0));
bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
if (deviceIsCpu)
pmeDefines["DEVICE_IS_CPU"] = "1";
if (cl.getPlatformData().useCpuPme) {
// Create the CPU PME kernel.
try {
cpuPme = getPlatform().createKernel(CalcPmeReciprocalForceKernel::Name(), *cl.getPlatformData().context);
cpuPme.getAs<CalcPmeReciprocalForceKernel>().initialize(gridSizeX, gridSizeY, gridSizeZ, numParticles, alpha);
cl::Program program = cl.createProgram(OpenCLKernelSources::pme, pmeDefines);
cl::Kernel addForcesKernel = cl::Kernel(program, "addForces");
pmeio = new PmeIO(cl, addForcesKernel);
cl.addPreComputation(new PmePreComputation(cl, cpuPme, *pmeio));
cl.addPostComputation(new PmePostComputation(cpuPme, *pmeio));
}
for (int i = 0; i < ndata; i++)
{
if (moduli[i] < 1.0e-7)
moduli[i] = (moduli[i-1]+moduli[i+1])*0.5f;
catch (OpenMMException& ex) {
// The CPU PME plugin isn't available.
}
if (cl.getUseDoublePrecision()) {
if (dim == 0)
pmeBsplineModuliX->upload(moduli);
else if (dim == 1)
pmeBsplineModuliY->upload(moduli);
else
pmeBsplineModuliZ->upload(moduli);
}
if (pmeio == NULL) {
// Create required data structures.
int elementSize = (cl.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
pmeGrid = new OpenCLArray(cl, gridSizeX*gridSizeY*gridSizeZ, 2*elementSize, "pmeGrid");
cl.addAutoclearBuffer(*pmeGrid);
pmeGrid2 = new OpenCLArray(cl, gridSizeX*gridSizeY*gridSizeZ, 2*elementSize, "pmeGrid2");
pmeBsplineModuliX = new OpenCLArray(cl, gridSizeX, elementSize, "pmeBsplineModuliX");
pmeBsplineModuliY = new OpenCLArray(cl, gridSizeY, elementSize, "pmeBsplineModuliY");
pmeBsplineModuliZ = new OpenCLArray(cl, gridSizeZ, elementSize, "pmeBsplineModuliZ");
pmeBsplineTheta = new OpenCLArray(cl, PmeOrder*numParticles, 4*elementSize, "pmeBsplineTheta");
pmeAtomRange = OpenCLArray::create<cl_int>(cl, gridSizeX*gridSizeY*gridSizeZ+1, "pmeAtomRange");
pmeAtomGridIndex = OpenCLArray::create<mm_int2>(cl, numParticles, "pmeAtomGridIndex");
sort = new OpenCLSort(cl, new SortTrait(), cl.getNumAtoms());
fft = new OpenCLFFT3D(cl, gridSizeX, gridSizeY, gridSizeZ);
// Initialize the b-spline moduli.
int maxSize = max(max(gridSizeX, gridSizeY), gridSizeZ);
vector<double> data(PmeOrder);
vector<double> ddata(PmeOrder);
vector<double> bsplines_data(maxSize);
data[PmeOrder-1] = 0.0;
data[1] = 0.0;
data[0] = 1.0;
for (int i = 3; i < PmeOrder; i++) {
double div = 1.0/(i-1.0);
data[i-1] = 0.0;
for (int j = 1; j < (i-1); j++)
data[i-j-1] = div*(j*data[i-j-2]+(i-j)*data[i-j-1]);
data[0] = div*data[0];
}
else {
vector<float> modulif(ndata);
// Differentiate.
ddata[0] = -data[0];
for (int i = 1; i < PmeOrder; i++)
ddata[i] = data[i-1]-data[i];
double div = 1.0/(PmeOrder-1);
data[PmeOrder-1] = 0.0;
for (int i = 1; i < (PmeOrder-1); i++)
data[PmeOrder-i-1] = div*(i*data[PmeOrder-i-2]+(PmeOrder-i)*data[PmeOrder-i-1]);
data[0] = div*data[0];
for (int i = 0; i < maxSize; i++)
bsplines_data[i] = 0.0;
for (int i = 1; i <= PmeOrder; i++)
bsplines_data[i] = data[i-1];
// Evaluate the actual bspline moduli for X/Y/Z.
for(int dim = 0; dim < 3; dim++) {
int ndata = (dim == 0 ? gridSizeX : dim == 1 ? gridSizeY : gridSizeZ);
vector<cl_double> moduli(ndata);
for (int i = 0; i < ndata; i++) {
double sc = 0.0;
double ss = 0.0;
for (int j = 0; j < ndata; j++) {
double arg = (2.0*M_PI*i*j)/ndata;
sc += bsplines_data[j]*cos(arg);
ss += bsplines_data[j]*sin(arg);
}
moduli[i] = (float) (sc*sc+ss*ss);
}
for (int i = 0; i < ndata; i++)
modulif[i] = (float) moduli[i];
if (dim == 0)
pmeBsplineModuliX->upload(modulif);
else if (dim == 1)
pmeBsplineModuliY->upload(modulif);
else
pmeBsplineModuliZ->upload(modulif);
{
if (moduli[i] < 1.0e-7)
moduli[i] = (moduli[i-1]+moduli[i+1])*0.5f;
}
if (cl.getUseDoublePrecision()) {
if (dim == 0)
pmeBsplineModuliX->upload(moduli);
else if (dim == 1)
pmeBsplineModuliY->upload(moduli);
else
pmeBsplineModuliZ->upload(moduli);
}
else {
vector<float> modulif(ndata);
for (int i = 0; i < ndata; i++)
modulif[i] = (float) moduli[i];
if (dim == 0)
pmeBsplineModuliX->upload(modulif);
else if (dim == 1)
pmeBsplineModuliY->upload(modulif);
else
pmeBsplineModuliZ->upload(modulif);
}
}
}
}
......
platforms/opencl/src/kernels/virtualSites.cl
View file @ 51e51c3b
......@@ -108,10 +108,66 @@ __kernel void computeVirtualSites(__global real4* restrict posq,
}
}
#ifdef HAS_OVERLAPPING_VSITES
#ifdef SUPPORTS_64_BIT_ATOMICS
// We will use 64 bit atomics for force redistribution.
#define ADD_FORCE(index, f) addForce(index, f, longForce);
#pragma OPENCL EXTENSION cl_khr_int64_base_atomics : enable
void addForce(int index, real4 f, __global long* longForce) {
atom_add(&longForce[index], (long) (f.x*0x100000000));
atom_add(&longForce[index+PADDED_NUM_ATOMS], (long) (f.y*0x100000000));
atom_add(&longForce[index+2*PADDED_NUM_ATOMS], (long) (f.z*0x100000000));
}
__kernel void addDistributedForces(__global const long* restrict longForces, __global real4* restrict forces) {
real scale = 1/(real) 0x100000000;
for (int index = get_global_id(0); index < NUM_ATOMS; index += get_global_size(0)) {
real4 f = (real4) (scale*longForces[index], scale*longForces[index+PADDED_NUM_ATOMS], scale*longForces[index+2*PADDED_NUM_ATOMS], 0);
forces[index] += f;
}
}
#else
// 64 bit atomics aren't supported, so we have to use atomic_cmpxchg() for force redistribution.
#define ADD_FORCE(index, f) addForce(index, f, force);
void atomicAddFloat(__global float* p, float v) {
__global int* ip = (__global int*) p;
while (true) {
union {
float f;
int i;
} oldval, newval;
oldval.f = *p;
newval.f = oldval.f+v;
if (atomic_cmpxchg(ip, oldval.i, newval.i) == oldval.i)
return;
}
}
void addForce(int index, float4 f, __global float4* force) {
__global float* components = (__global float*) force;
atomicAddFloat(&components[4*index], f.x);
atomicAddFloat(&components[4*index+1], f.y);
atomicAddFloat(&components[4*index+2], f.z);
}
#endif
#else
// There are no overlapping virtual sites, so we can just store forces directly.
#define ADD_FORCE(index, f) force[index].xyz += (f).xyz;
#endif
/**
* Distribute forces from virtual sites to the atoms they are based on.
*/
__kernel void distributeForces(__global const real4* restrict posq, __global real4* restrict force,
#ifdef SUPPORTS_64_BIT_ATOMICS
__global long* restrict longForce,
#endif
#ifdef USE_MIXED_PRECISION
__global real4* restrict posqCorrection,
#endif
......@@ -129,12 +185,8 @@ __kernel void distributeForces(__global const real4* restrict posq, __global rea
int4 atoms = avg2Atoms[index];
real2 weights = avg2Weights[index];
real4 f = force[atoms.x];
real4 f1 = force[atoms.y];
real4 f2 = force[atoms.z];
f1.xyz += f.xyz*weights.x;
f2.xyz += f.xyz*weights.y;
force[atoms.y] = f1;
force[atoms.z] = f2;
ADD_FORCE(atoms.y, f*weights.x);
ADD_FORCE(atoms.z, f*weights.y);
}
// Three particle average sites.
......@@ -143,15 +195,9 @@ __kernel void distributeForces(__global const real4* restrict posq, __global rea
int4 atoms = avg3Atoms[index];
real4 weights = avg3Weights[index];
real4 f = force[atoms.x];
real4 f1 = force[atoms.y];
real4 f2 = force[atoms.z];
real4 f3 = force[atoms.w];
f1.xyz += f.xyz*weights.x;
f2.xyz += f.xyz*weights.y;
f3.xyz += f.xyz*weights.z;
force[atoms.y] = f1;
force[atoms.z] = f2;
force[atoms.w] = f3;
ADD_FORCE(atoms.y, f*weights.x);
ADD_FORCE(atoms.z, f*weights.y);
ADD_FORCE(atoms.w, f*weights.z);
}
// Out of plane sites.
......@@ -165,21 +211,15 @@ __kernel void distributeForces(__global const real4* restrict posq, __global rea
mixed4 v12 = pos2-pos1;
mixed4 v13 = pos3-pos1;
real4 f = force[atoms.x];
real4 f1 = force[atoms.y];
real4 f2 = force[atoms.z];
real4 f3 = force[atoms.w];
real4 fp2 = (real4) (weights.x*f.x - weights.z*v13.z*f.y + weights.z*v13.y*f.z,
weights.z*v13.z*f.x + weights.x*f.y - weights.z*v13.x*f.z,
-weights.z*v13.y*f.x + weights.z*v13.x*f.y + weights.x*f.z, 0.0f);
real4 fp3 = (real4) (weights.y*f.x + weights.z*v12.z*f.y - weights.z*v12.y*f.z,
-weights.z*v12.z*f.x + weights.y*f.y + weights.z*v12.x*f.z,
weights.z*v12.y*f.x - weights.z*v12.x*f.y + weights.y*f.z, 0.0f);
f1.xyz += f.xyz-fp2.xyz-fp3.xyz;
f2.xyz += fp2.xyz;
f3.xyz += fp3.xyz;
force[atoms.y] = f1;
force[atoms.z] = f2;
force[atoms.w] = f3;
ADD_FORCE(atoms.y, f-fp2-fp3);
ADD_FORCE(atoms.z, fp2);
ADD_FORCE(atoms.w, fp3);
}
// Local coordinates sites.
......@@ -230,9 +270,9 @@ __kernel void distributeForces(__global const real4* restrict posq, __global rea
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];
real4 f1 = 0;
real4 f2 = 0;
real4 f3 = 0;
mixed4 fp1 = localPosition*f.x;
mixed4 fp2 = localPosition*f.y;
mixed4 fp3 = localPosition*f.z;
......@@ -263,8 +303,8 @@ __kernel void distributeForces(__global const real4* restrict posq, __global rea
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;
ADD_FORCE(atoms.y, f1);
ADD_FORCE(atoms.z, f2);
ADD_FORCE(atoms.w, f3);
}
}
platforms/opencl/tests/TestOpenCLLocalEnergyMinimizer.cpp
View file @ 51e51c3b
......@@ -7,7 +7,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -170,6 +170,7 @@ void testVirtualSites() {
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
context.applyConstraints(1e-5);
State initialState = context.getState(State::Forces | State::Energy);
LocalEnergyMinimizer::minimize(context, tolerance);
State finalState = context.getState(State::Forces | State::Energy | State::Positions);
......
platforms/opencl/tests/TestOpenCLNonbondedForce.cpp
View file @ 51e51c3b
......@@ -751,7 +751,7 @@ void testChangingParameters() {
ASSERT_EQUAL_TOL(clState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
}
void testParallelComputation(bool useCutoff) {
void testParallelComputation(NonbondedForce::NonbondedMethod method) {
System system;
const int numParticles = 200;
for (int i = 0; i < numParticles; i++)
......@@ -759,9 +759,9 @@ void testParallelComputation(bool useCutoff) {
NonbondedForce* force = new NonbondedForce();
for (int i = 0; i < numParticles; i++)
force->addParticle(i%2-0.5, 0.5, 1.0);
if (useCutoff)
force->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
force->setNonbondedMethod(method);
system.addForce(force);
system.setDefaultPeriodicBoxVectors(Vec3(5,0,0), Vec3(0,5,0), Vec3(0,0,5));
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
......@@ -880,8 +880,9 @@ int main(int argc, char* argv[]) {
// testBlockInteractions(true);
testDispersionCorrection();
testChangingParameters();
testParallelComputation(false);
testParallelComputation(true);
testParallelComputation(NonbondedForce::NoCutoff);
testParallelComputation(NonbondedForce::Ewald);
testParallelComputation(NonbondedForce::PME);
testSwitchingFunction(NonbondedForce::CutoffNonPeriodic);
testSwitchingFunction(NonbondedForce::PME);
}
......
platforms/opencl/tests/TestOpenCLVirtualSites.cpp
View file @ 51e51c3b
......@@ -524,6 +524,47 @@ void testReordering() {
}
}
/**
* Test a System where multiple virtual sites are all calculated from the same particles.
*/
void testOverlappingSites() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
NonbondedForce* nonbonded = new NonbondedForce();
system.addForce(nonbonded);
nonbonded->addParticle(1.0, 0.0, 0.0);
nonbonded->addParticle(-0.5, 0.0, 0.0);
nonbonded->addParticle(-0.5, 0.0, 0.0);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(10, 0, 0));
positions.push_back(Vec3(0, 10, 0));
for (int i = 0; i < 20; i++) {
system.addParticle(0.0);
double u = 0.1*((i+1)%4);
double v = 0.05*i;
system.setVirtualSite(3+i, new ThreeParticleAverageSite(0, 1, 2, u, v, 1-u-v));
nonbonded->addParticle(i%2 == 0 ? -1.0 : 1.0, 0.0, 0.0);
positions.push_back(Vec3());
}
VerletIntegrator i1(0.002);
VerletIntegrator i2(0.002);
Context c1(system, i1, Platform::getPlatformByName("Reference"));
Context c2(system, i2, platform);
c1.setPositions(positions);
c2.setPositions(positions);
c1.applyConstraints(0.0001);
c2.applyConstraints(0.0001);
State s1 = c1.getState(State::Positions | State::Forces);
State s2 = c2.getState(State::Positions | State::Forces);
for (int i = 0; i < system.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getPositions()[i], s2.getPositions()[i], 1e-5);
for (int i = 0; i < 3; i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
......@@ -535,6 +576,7 @@ int main(int argc, char* argv[]) {
testLocalCoordinates();
testConservationLaws();
testReordering();
testOverlappingSites();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/reference/tests/TestReferenceLocalEnergyMinimizer.cpp
View file @ 51e51c3b
......@@ -7,7 +7,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -171,6 +171,7 @@ void testVirtualSites() {
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
context.applyConstraints(1e-5);
State initialState = context.getState(State::Forces | State::Energy);
LocalEnergyMinimizer::minimize(context, tolerance);
State finalState = context.getState(State::Forces | State::Energy | State::Positions);
......
plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h
View file @ 51e51c3b
......@@ -126,13 +126,15 @@ public:
* Set the torsion-torsion grid at the specified index
*
* @param index the index of the torsion-torsion for which to get parameters
* @param grid grid
* @param grid either 3 or 6 values may be specified per grid point. If the derivatives
* are omitted, they are calculated automatically by fitting a 2D spline to
* the energies.
* grid[x][y][0] = x value
* grid[x][y][1] = y value
* grid[x][y][2] = function value
* grid[x][y][3] = dfdx value
* grid[x][y][4] = dfdy value
* grid[x][y][5] = dfd(xy) value
* grid[x][y][2] = energy
* grid[x][y][3] = dEdx value
* grid[x][y][4] = dEdy value
* grid[x][y][5] = dEd(xy) value
*/
void setTorsionTorsionGrid(int index, const std::vector<std::vector<std::vector<double> > >& grid);
......@@ -181,29 +183,7 @@ public:
_spacing[0] = _spacing[1] = 1.0;
}
TorsionTorsionGridInfo(const TorsionTorsionGrid& grid) {
_grid.resize(grid.size());
for(unsigned int kk = 0; kk < grid.size(); kk++){
_grid[kk].resize(grid[kk].size());
for(unsigned int jj = 0; jj < grid[kk].size(); jj++){
_grid[kk][jj].resize(grid[kk][jj].size());
for(unsigned int ii = 0; ii < grid[kk][jj].size(); ii++){
_grid[kk][jj][ii] = grid[kk][jj][ii];
}
}
}
_startValues[0] = _grid[0][0][0];
_startValues[1] = _grid[0][0][1];
_spacing[0] = static_cast<double>(_grid.size()-1)/360.0;
_spacing[1] = static_cast<double>(grid.size()-1)/360.0;
_size[0] = static_cast<int>(grid.size());
_size[1] = static_cast<int>(grid[0].size());
}
TorsionTorsionGridInfo(const TorsionTorsionGrid& grid);
const TorsionTorsionGrid& getTorsionTorsionGrid(void) const {
return _grid;
......
plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForce.cpp
View file @ 51e51c3b
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -33,8 +33,10 @@
#include "openmm/OpenMMException.h"
#include "openmm/AmoebaTorsionTorsionForce.h"
#include "openmm/internal/AmoebaTorsionTorsionForceImpl.h"
#include "openmm/internal/SplineFitter.h"
using namespace OpenMM;
using namespace std;
AmoebaTorsionTorsionForce::AmoebaTorsionTorsionForce() {
}
......@@ -82,3 +84,102 @@ void AmoebaTorsionTorsionForce::setTorsionTorsionGrid(int index, const TorsionTo
ForceImpl* AmoebaTorsionTorsionForce::createImpl() const {
return new AmoebaTorsionTorsionForceImpl(*this);
}
AmoebaTorsionTorsionForce::TorsionTorsionGridInfo::TorsionTorsionGridInfo(const TorsionTorsionGrid& grid) {
if (grid[0][0][0] != grid[1][0][0])
_grid = grid;
else {
// We need to transpose the grid.
int xsize = grid[0].size();
int ysize = grid.size();
_grid.resize(xsize);
for (int i = 0; i < xsize; i++) {
_grid[i].resize(ysize);
for (int j = 0; j < ysize; j++)
_grid[i][j] = grid[j][i];
}
}
_startValues[0] = _grid[0][0][0];
_startValues[1] = _grid[0][0][1];
_spacing[0] = static_cast<double>(_grid.size()-1)/360.0;
_spacing[1] = static_cast<double>(_grid.size()-1)/360.0;
_size[0] = static_cast<int>(_grid.size());
_size[1] = static_cast<int>(_grid[0].size());
if (_grid[0][0].size() == 3) {
// We need to compute the derivatives ourselves. First determine if the grid is periodic.
int xsize = _size[0];
int ysize = _size[1];
bool periodic = true;
for (int i = 0; i < xsize; i++)
if (_grid[i][0][2] != _grid[i][ysize-1][2])
periodic = false;
for (int i = 0; i < ysize; i++)
if (_grid[0][i][2] != _grid[xsize-1][i][2])
periodic = false;
// Compute derivatives with respect to the first angle.
vector<double> x(xsize), y(ysize);
for (int i = 0; i < xsize; i++)
x[i] = _grid[i][0][0];
for (int i = 0; i < ysize; i++)
y[i] = _grid[0][i][1];
vector<double> d1(xsize*ysize), d2(xsize*ysize), d12(xsize*ysize);
vector<double> t(xsize), deriv(xsize);
for (int i = 0; i < ysize; i++) {
for (int j = 0; j < xsize; j++)
t[j] = _grid[j][i][2];
if (periodic)
SplineFitter::createPeriodicSpline(x, t, deriv);
else
SplineFitter::createNaturalSpline(x, t, deriv);
for (int j = 0; j < xsize; j++)
d1[j+xsize*i] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[j]);
}
// Compute derivatives with respect to the second angle.
t.resize(ysize);
deriv.resize(ysize);
for (int i = 0; i < xsize; i++) {
for (int j = 0; j < ysize; j++)
t[j] = _grid[i][j][2];
if (periodic)
SplineFitter::createPeriodicSpline(y, t, deriv);
else
SplineFitter::createNaturalSpline(y, t, deriv);
for (int j = 0; j < ysize; j++)
d2[i+xsize*j] = SplineFitter::evaluateSplineDerivative(y, t, deriv, y[j]);
}
// Compute cross derivatives.
t.resize(xsize);
deriv.resize(xsize);
for (int i = 0; i < ysize; i++) {
for (int j = 0; j < xsize; j++)
t[j] = d2[j+xsize*i];
if (periodic)
SplineFitter::createPeriodicSpline(x, t, deriv);
else
SplineFitter::createNaturalSpline(x, t, deriv);
for (int j = 0; j < xsize; j++)
d12[j+xsize*i] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[j]);
}
// Add the derivatives to the grid.
for (int i = 0; i < xsize; i++)
for (int j = 0; j < ysize; j++) {
_grid[i][j].push_back(d1[i+xsize*j]);
_grid[i][j].push_back(d2[i+xsize*j]);
_grid[i][j].push_back(d12[i+xsize*j]);
}
}
}
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaTorsionTorsionForce.cpp
View file @ 51e51c3b
......@@ -49,7 +49,7 @@ extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
const double TOL = 1e-4;
TorsionTorsionGrid& getTorsionGrid( int gridIndex ) {
TorsionTorsionGrid getTorsionGrid(int gridIndex, bool includeDerivs) {
static double grid[4][625][6] = {
{
......@@ -2557,35 +2557,32 @@ static double grid[4][625][6] = {
{ 165.0000, 180.0000, -0.182999000E+01, 0.377952854E-01, 0.233583295E-01, -0.109828932E-02 },
{ 180.0000, 180.0000, -0.146854000E+01, 0.491175487E-02, 0.195601580E-02, -0.163177030E-02 } } };
// static std::vector< std::vector< std::vector<double> > > TorsionTorsionGrid
static std::vector<TorsionTorsionGrid> grids;
if( grids.size() == 0 ){
grids.resize(4);
for( int ii = 0; ii < 4; ii++ ){
grids[ii].resize( 25 );
for( int jj = 0; jj < 25; jj++ ){
grids[ii][jj].resize(25);
for( int kk = 0; kk < 25; kk++ ){
grids[ii][jj][kk].resize(6);
}
int elementCount = (includeDerivs ? 6 : 3);
std::vector<TorsionTorsionGrid> grids(4);
for( int ii = 0; ii < 4; ii++ ){
grids[ii].resize( 25 );
for( int jj = 0; jj < 25; jj++ ){
grids[ii][jj].resize(25);
for( int kk = 0; kk < 25; kk++ ){
grids[ii][jj][kk].resize(elementCount);
}
int index = 0;
for( int jj = 0; jj < 25; jj++ ){
for( int kk = 0; kk < 25; kk++ ){
int jjIndex = static_cast<int>(((grid[ii][index][0] + 180.0)/15.0)+1.0e-05);
int kkIndex = static_cast<int>(((grid[ii][index][1] + 180.0)/15.0)+1.0e-05);
for( int ll = 0; ll < 6; ll++ ){
grids[ii][kk][jj][ll] = grid[ii][index][ll];
}
index++;
}
int index = 0;
for( int jj = 0; jj < 25; jj++ ){
for( int kk = 0; kk < 25; kk++ ){
int jjIndex = static_cast<int>(((grid[ii][index][0] + 180.0)/15.0)+1.0e-05);
int kkIndex = static_cast<int>(((grid[ii][index][1] + 180.0)/15.0)+1.0e-05);
for( int ll = 0; ll < elementCount; ll++ ){
grids[ii][kk][jj][ll] = grid[ii][index][ll];
}
index++;
}
}
}
return grids[gridIndex];
}
void testTorsionTorsion( FILE* log, int systemId ) {
void testTorsionTorsion(int systemId, bool includeDerivs) {
System system;
int numberOfParticles = 6;
......@@ -2645,11 +2642,11 @@ void testTorsionTorsion( FILE* log, int systemId ) {
expectedEnergy = -3.372536909E+00;
}
amoebaTorsionTorsionForce->addTorsionTorsion( 0, 1, 2, 3, 4, chiralCheckAtomIndex, 0 );
amoebaTorsionTorsionForce->setTorsionTorsionGrid( 0, getTorsionGrid( gridIndex ) );
amoebaTorsionTorsionForce->addTorsionTorsion(0, 1, 2, 3, 4, chiralCheckAtomIndex, 0);
amoebaTorsionTorsionForce->setTorsionTorsionGrid(0, getTorsionGrid(gridIndex, includeDerivs));
system.addForce(amoebaTorsionTorsionForce);
Context context(system, integrator, Platform::getPlatformByName( "Reference"));
Context context(system, integrator, Platform::getPlatformByName("Reference"));
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
......@@ -2662,18 +2659,6 @@ void testTorsionTorsion( FILE* log, int systemId ) {
forces[ii][2] *= conversion;
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaTorsionTorsionForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2],
forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
}
#endif
double tolerance = 1.0e-03;
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
......@@ -2687,10 +2672,8 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestReferenceAmoebaTorsionTorsionForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
//registerAmoebaCudaKernelFactories();
FILE* log = NULL;
testTorsionTorsion( log, 1 );
testTorsionTorsion(1, true);
testTorsionTorsion(1, false);
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
std::cout << "FAIL - ERROR. Test failed." << std::endl;
......
plugins/drude/openmmapi/src/DrudeLangevinIntegrator.cpp
View file @ 51e51c3b
......@@ -33,8 +33,8 @@
#include "openmm/Context.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/DrudeKernels.h"
#include <cmath>
#include <ctime>
#include <string>
......@@ -49,7 +49,7 @@ DrudeLangevinIntegrator::DrudeLangevinIntegrator(double temperature, double fric
setDrudeFriction(drudeFrictionCoeff);
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setRandomNumberSeed((int) time(NULL));
setRandomNumberSeed(osrngseed());
}
void DrudeLangevinIntegrator::initialize(ContextImpl& contextRef) {
......
plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp
View file @ 51e51c3b
......@@ -33,10 +33,10 @@
#include "openmm/Context.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/RpmdKernels.h"
#include "SimTKOpenMMRealType.h"
#include <cmath>
#include <ctime>
#include <string>
using namespace OpenMM;
......@@ -48,7 +48,7 @@ RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictio
setFriction(frictionCoeff);
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setRandomNumberSeed((int) time(NULL));
setRandomNumberSeed(osrngseed());
}
RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize) :
......@@ -57,7 +57,7 @@ RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictio
setFriction(frictionCoeff);
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setRandomNumberSeed((int) time(NULL));
setRandomNumberSeed(osrngseed());
}
void RPMDIntegrator::initialize(ContextImpl& contextRef) {
......
serialization/include/openmm/serialization/XmlSerializer.h
View file @ 51e51c3b
......@@ -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) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -79,7 +79,7 @@ public:
private:
static void serialize(const SerializationNode& node, std::ostream& stream);
static void* deserializeStream(std::istream& stream);
static TiXmlElement* encodeNode(const SerializationNode& node);
static void encodeNode(const SerializationNode& node, std::ostream& stream, int depth);
static void decodeNode(SerializationNode& node, const TiXmlElement& element);
};
......
serialization/src/XmlSerializer.cpp
View file @ 51e51c3b
......@@ -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) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -36,25 +36,32 @@ using namespace OpenMM;
using namespace std;
void XmlSerializer::serialize(const SerializationNode& node, std::ostream& stream) {
TiXmlDocument doc;
TiXmlDeclaration* decl = new TiXmlDeclaration( "1.0", "", "" );
doc.LinkEndChild(decl);
doc.LinkEndChild(encodeNode(node));
TiXmlPrinter printer;
printer.SetIndent("\t");
doc.Accept(&printer);
stream << printer.Str();
stream << "<?xml version=\"1.0\" ?>\n";
encodeNode(node, stream, 0);
}
TiXmlElement* XmlSerializer::encodeNode(const SerializationNode& node) {
TiXmlElement* element = new TiXmlElement(node.getName());
void XmlSerializer::encodeNode(const SerializationNode& node, std::ostream& stream, int depth) {
for (int i = 0; i < depth; i++)
stream << '\t';
stream << '<' << node.getName();
const map<string, string>& properties = node.getProperties();
for (map<string, string>::const_iterator iter = properties.begin(); iter != properties.end(); ++iter)
element->SetAttribute(iter->first.c_str(), iter->second.c_str());
for (map<string, string>::const_iterator iter = properties.begin(); iter != properties.end(); ++iter) {
string name, value;
TiXmlBase::EncodeString(iter->first, &name);
TiXmlBase::EncodeString(iter->second, &value);
stream << ' ' << name << "=\"" << value << '\"';
}
const vector<SerializationNode>& children = node.getChildren();
for (int i = 0; i < (int) children.size(); i++)
element->LinkEndChild(encodeNode(children[i]));
return element;
if (children.size() == 0)
stream << "/>\n";
else {
stream << ">\n";
for (int i = 0; i < (int) children.size(); i++)
encodeNode(children[i], stream, depth+1);
for (int i = 0; i < depth; i++)
stream << '\t';
stream << "</" << node.getName() << ">\n";
}
}
void* XmlSerializer::deserializeStream(std::istream& stream) {
......
tests/TestFindExclusions.cpp
View file @ 51e51c3b
......@@ -30,6 +30,7 @@
* -------------------------------------------------------------------------- */
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/CustomNonbondedForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/OpenMMException.h"
#include <iostream>
......@@ -166,10 +167,62 @@ void testReplaceExceptions() {
ASSERT(charge == 5.0);
}
/**
* This is the same as testFindExceptions(), except it tests adding exclusions to a CustomNonbondedForce.
*/
void testFindCustomExclusions() {
CustomNonbondedForce nonbonded("r");
vector<pair<int, int> > bonds;
vector<double> params;
for (int i = 0; i < NUM_ATOMS; i++)
nonbonded.addParticle(params);
// loop over all main-chain atoms (even numbered atoms)
for (int i = 0; i < NUM_ATOMS-1; i += 2)
{
// side-chain bonds
bonds.push_back(pair<int, int>(i, i+1));
// main-chain bonds
if (i < NUM_ATOMS-2) // penultimate atom (NUM_ATOMS-2) has no subsequent main-chain atom
bonds.push_back(pair<int, int>(i, i+2));
}
nonbonded.createExclusionsFromBonds(bonds, 3);
// Build lists of the expected exclusions.
vector<set<int> > expectedExclusions(NUM_ATOMS);
int totalExclusions = 0;
for (int i = 0; i < NUM_ATOMS; i += 2) {
addAtomsToExclusions(i, i+1, expectedExclusions, totalExclusions);
addAtomsToExclusions(i, i+2, expectedExclusions, totalExclusions);
addAtomsToExclusions(i, i+3, expectedExclusions, totalExclusions);
addAtomsToExclusions(i, i+4, expectedExclusions, totalExclusions);
addAtomsToExclusions(i+1, i+2, expectedExclusions, totalExclusions);
addAtomsToExclusions(i, i+5, expectedExclusions, totalExclusions);
addAtomsToExclusions(i, i+6, expectedExclusions, totalExclusions);
addAtomsToExclusions(i+1, i+3, expectedExclusions, totalExclusions);
addAtomsToExclusions(i+1, i+4, expectedExclusions, totalExclusions);
}
for (int i = 0; i < nonbonded.getNumExclusions(); i++) {
int particle1, particle2;
nonbonded.getExclusionParticles(i, particle1, particle2);
}
// Compare them to the exceptions that were generated.
ASSERT_EQUAL(totalExclusions, nonbonded.getNumExclusions());
for (int i = 0; i < nonbonded.getNumExclusions(); i++) {
int particle1, particle2;
nonbonded.getExclusionParticles(i, particle1, particle2);
ASSERT(expectedExclusions[particle1].find(particle2) != expectedExclusions[particle1].end());
}
}
int main() {
try {
testFindExceptions();
testReplaceExceptions();
testFindCustomExclusions();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
wrappers/python/CMakeLists.txt
View file @ 51e51c3b
......@@ -55,8 +55,12 @@ foreach(SUBDIR ${SUBDIRS})
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.xml"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdb"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.parm7"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.rst7"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.ncrst"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.dms"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.top"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.par"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*psf"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/charmm22.*"
)
......
wrappers/python/simtk/openmm/app/amberinpcrdfile.py
View file @ 51e51c3b
......@@ -6,9 +6,9 @@ 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) 2012 Stanford University and the Authors.
Portions copyright (c) 2012-2014 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Contributors: Jason Swails
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
......@@ -31,87 +31,97 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
__author__ = "Peter Eastman"
__version__ = "1.0"
from functools import wraps
from simtk.openmm.app.internal import amber_file_parser
from simtk.unit import Quantity, nanometers, picoseconds
import warnings
try:
import numpy
import numpy as np
except:
pass
np = None
def numpy_protector(func):
"""
Decorator to emit useful error messages if users try to request numpy
processing if numpy is not available. Raises ImportError if numpy could not
be found
"""
@wraps(func)
def wrapper(self, asNumpy=False):
if asNumpy and np is None:
raise ImportError('Could not import numpy. Cannot set asNumpy=True')
return func(self, asNumpy=asNumpy)
return wrapper
class AmberInpcrdFile(object):
"""AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it."""
def __init__(self, file, loadVelocities=False, loadBoxVectors=False):
def __init__(self, file, loadVelocities=None, loadBoxVectors=None):
"""Load an inpcrd file.
An inpcrd file contains atom positions and, optionally, velocities and periodic box dimensions.
Unfortunately, it is sometimes impossible to determine from the file itself exactly what data
it contains. You therefore must specify in advance what data to load. It is stored into this
object's "positions", "velocities", and "boxVectors" fields.
Parameters:
- file (string) the name of the file to load
- loadVelocities (boolean=False) whether to load velocities from the file
- loadBoxVectors (boolean=False) whether to load the periodic box vectors
- loadVelocities (boolean=None) deprecated. Velocities are loaded automatically if present
- loadBoxVectors (boolean=None) deprecated. Box vectors are loaded automatically if present
"""
results = amber_file_parser.readAmberCoordinates(file, read_velocities=loadVelocities, read_box=loadBoxVectors)
if loadVelocities:
## The atom positions read from the inpcrd file
self.positions = results[0]
if loadBoxVectors:
## The periodic box vectors read from the inpcrd file
self.boxVectors = results[1]
## The atom velocities read from the inpcrd file
self.velocities = results[2]
else:
self.velocities = results[1]
elif loadBoxVectors:
self.positions = results[0]
self.boxVectors = results[1]
else:
self.positions = results
self.file = file
if loadVelocities is not None or loadBoxVectors is not None:
warnings.warn('loadVelocities and loadBoxVectors have been '
'deprecated. velocities and box information '
'is loaded automatically if the inpcrd file contains '
'them.', DeprecationWarning)
results = amber_file_parser.readAmberCoordinates(file)
self.positions, self.velocities, self.boxVectors = results
# Cached numpy arrays
self._numpyPositions = None
if loadVelocities:
self._numpyVelocities = None
if loadBoxVectors:
self._numpyBoxVectors = None
self._numpyVelocities = None
self._numpyBoxVectors = None
@numpy_protector
def getPositions(self, asNumpy=False):
"""Get the atomic positions.
Parameters:
- asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
"""
"""
if asNumpy:
if self._numpyPositions is None:
self._numpyPositions = Quantity(numpy.array(self.positions.value_in_unit(nanometers)), nanometers)
self._numpyPositions = Quantity(np.array(self.positions.value_in_unit(nanometers)), nanometers)
return self._numpyPositions
return self.positions
@numpy_protector
def getVelocities(self, asNumpy=False):
"""Get the atomic velocities.
Parameters:
- asNumpy (boolean=False) if true, the vectors are returned as numpy arrays instead of Vec3s
"""
"""
if self.velocities is None:
raise AttributeError('velocities not found in %s' % self.file)
if asNumpy:
if self._numpyVelocities is None:
self._numpyVelocities = Quantity(numpy.array(self.velocities.value_in_unit(nanometers/picoseconds)), nanometers/picoseconds)
self._numpyVelocities = Quantity(np.array(self.velocities.value_in_unit(nanometers/picoseconds)), nanometers/picoseconds)
return self._numpyVelocities
return self.velocities
@numpy_protector
def getBoxVectors(self, asNumpy=False):
"""Get the periodic box vectors.
Parameters:
- asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
"""
"""
if self.boxVectors is None:
raise AttributeError('Box information not found in %s' % self.file)
if asNumpy:
if self._numpyBoxVectors is None:
self._numpyBoxVectors = []
self._numpyBoxVectors.append(Quantity(numpy.array(self.boxVectors[0].value_in_unit(nanometers)), nanometers))
self._numpyBoxVectors.append(Quantity(numpy.array(self.boxVectors[1].value_in_unit(nanometers)), nanometers))
self._numpyBoxVectors.append(Quantity(numpy.array(self.boxVectors[2].value_in_unit(nanometers)), nanometers))
self._numpyBoxVectors.append(Quantity(np.array(self.boxVectors[0].value_in_unit(nanometers)), nanometers))
self._numpyBoxVectors.append(Quantity(np.array(self.boxVectors[1].value_in_unit(nanometers)), nanometers))
self._numpyBoxVectors.append(Quantity(np.array(self.boxVectors[2].value_in_unit(nanometers)), nanometers))
return self._numpyBoxVectors
return self.boxVectors
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