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Commit fee4e4dd authored by Peter Eastman's avatar Peter Eastman
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Minor code cleanup

parent 0e6cbcea
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Showing with 47 additions and 47 deletions
platforms/opencl/src/OpenCLKernels.cpp
View file @ fee4e4dd
......@@ -137,7 +137,7 @@ void OpenCLUpdateStateDataKernel::setTime(ContextImpl& context, double time) {
contexts[i]->setTime(time);
}
void OpenCLUpdateStateDataKernel::getPositions(ContextImpl& context, std::vector<Vec3>& positions) {
void OpenCLUpdateStateDataKernel::getPositions(ContextImpl& context, vector<Vec3>& positions) {
OpenCLArray<mm_float4>& posq = cl.getPosq();
posq.download();
OpenCLArray<cl_int>& order = cl.getAtomIndex();
......@@ -151,7 +151,7 @@ void OpenCLUpdateStateDataKernel::getPositions(ContextImpl& context, std::vector
}
}
void OpenCLUpdateStateDataKernel::setPositions(ContextImpl& context, const std::vector<Vec3>& positions) {
void OpenCLUpdateStateDataKernel::setPositions(ContextImpl& context, const vector<Vec3>& positions) {
OpenCLArray<mm_float4>& posq = cl.getPosq();
OpenCLArray<cl_int>& order = cl.getAtomIndex();
int numParticles = context.getSystem().getNumParticles();
......@@ -169,7 +169,7 @@ void OpenCLUpdateStateDataKernel::setPositions(ContextImpl& context, const std::
cl.getPosCellOffsets()[i] = mm_int4(0, 0, 0, 0);
}
void OpenCLUpdateStateDataKernel::getVelocities(ContextImpl& context, std::vector<Vec3>& velocities) {
void OpenCLUpdateStateDataKernel::getVelocities(ContextImpl& context, vector<Vec3>& velocities) {
OpenCLArray<mm_float4>& velm = cl.getVelm();
velm.download();
OpenCLArray<cl_int>& order = cl.getAtomIndex();
......@@ -181,7 +181,7 @@ void OpenCLUpdateStateDataKernel::getVelocities(ContextImpl& context, std::vecto
}
}
void OpenCLUpdateStateDataKernel::setVelocities(ContextImpl& context, const std::vector<Vec3>& velocities) {
void OpenCLUpdateStateDataKernel::setVelocities(ContextImpl& context, const vector<Vec3>& velocities) {
OpenCLArray<mm_float4>& velm = cl.getVelm();
OpenCLArray<cl_int>& order = cl.getAtomIndex();
int numParticles = context.getSystem().getNumParticles();
......@@ -197,7 +197,7 @@ void OpenCLUpdateStateDataKernel::setVelocities(ContextImpl& context, const std:
velm.upload();
}
void OpenCLUpdateStateDataKernel::getForces(ContextImpl& context, std::vector<Vec3>& forces) {
void OpenCLUpdateStateDataKernel::getForces(ContextImpl& context, vector<Vec3>& forces) {
OpenCLArray<mm_float4>& force = cl.getForce();
force.download();
OpenCLArray<cl_int>& order = cl.getAtomIndex();
......@@ -251,12 +251,12 @@ void OpenCLVirtualSitesKernel::computePositions(ContextImpl& context) {
class OpenCLBondForceInfo : public OpenCLForceInfo {
public:
OpenCLBondForceInfo(int requiredBuffers, const HarmonicBondForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
OpenCLBondForceInfo(const HarmonicBondForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
}
void getParticlesInGroup(int index, std::vector<int>& particles) {
void getParticlesInGroup(int index, vector<int>& particles) {
int particle1, particle2;
double length, k;
force.getBondParameters(index, particle1, particle2, length, k);
......@@ -299,7 +299,7 @@ void OpenCLCalcHarmonicBondForceKernel::initialize(const System& system, const H
map<string, string> replacements;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float2");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::harmonicBondForce, replacements), force.getForceGroup());
cl.addForce(new OpenCLBondForceInfo(0, force));
cl.addForce(new OpenCLBondForceInfo(force));
}
double OpenCLCalcHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -308,12 +308,12 @@ double OpenCLCalcHarmonicBondForceKernel::execute(ContextImpl& context, bool inc
class OpenCLCustomBondForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomBondForceInfo(int requiredBuffers, const CustomBondForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
OpenCLCustomBondForceInfo(const CustomBondForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
}
void getParticlesInGroup(int index, std::vector<int>& particles) {
void getParticlesInGroup(int index, vector<int>& particles) {
int particle1, particle2;
vector<double> parameters;
force.getBondParameters(index, particle1, particle2, parameters);
......@@ -360,7 +360,7 @@ void OpenCLCalcCustomBondForceKernel::initialize(const System& system, const Cus
paramVector[i][j] = (cl_float) parameters[j];
}
params->setParameterValues(paramVector);
cl.addForce(new OpenCLCustomBondForceInfo(0, force));
cl.addForce(new OpenCLCustomBondForceInfo(force));
// Record information for the expressions.
......@@ -424,12 +424,12 @@ double OpenCLCalcCustomBondForceKernel::execute(ContextImpl& context, bool inclu
class OpenCLAngleForceInfo : public OpenCLForceInfo {
public:
OpenCLAngleForceInfo(int requiredBuffers, const HarmonicAngleForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
OpenCLAngleForceInfo(const HarmonicAngleForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumAngles();
}
void getParticlesInGroup(int index, std::vector<int>& particles) {
void getParticlesInGroup(int index, vector<int>& particles) {
int particle1, particle2, particle3;
double angle, k;
force.getAngleParameters(index, particle1, particle2, particle3, angle, k);
......@@ -474,7 +474,7 @@ void OpenCLCalcHarmonicAngleForceKernel::initialize(const System& system, const
map<string, string> replacements;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float2");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::harmonicAngleForce, replacements), force.getForceGroup());
cl.addForce(new OpenCLAngleForceInfo(0, force));
cl.addForce(new OpenCLAngleForceInfo(force));
}
double OpenCLCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -483,12 +483,12 @@ double OpenCLCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool in
class OpenCLCustomAngleForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomAngleForceInfo(int requiredBuffers, const CustomAngleForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
OpenCLCustomAngleForceInfo(const CustomAngleForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumAngles();
}
void getParticlesInGroup(int index, std::vector<int>& particles) {
void getParticlesInGroup(int index, vector<int>& particles) {
int particle1, particle2, particle3;
vector<double> parameters;
force.getAngleParameters(index, particle1, particle2, particle3, parameters);
......@@ -536,7 +536,7 @@ void OpenCLCalcCustomAngleForceKernel::initialize(const System& system, const Cu
paramVector[i][j] = (cl_float) parameters[j];
}
params->setParameterValues(paramVector);
cl.addForce(new OpenCLCustomAngleForceInfo(0, force));
cl.addForce(new OpenCLCustomAngleForceInfo(force));
// Record information for the expressions.
......@@ -600,12 +600,12 @@ double OpenCLCalcCustomAngleForceKernel::execute(ContextImpl& context, bool incl
class OpenCLPeriodicTorsionForceInfo : public OpenCLForceInfo {
public:
OpenCLPeriodicTorsionForceInfo(int requiredBuffers, const PeriodicTorsionForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
OpenCLPeriodicTorsionForceInfo(const PeriodicTorsionForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumTorsions();
}
void getParticlesInGroup(int index, std::vector<int>& particles) {
void getParticlesInGroup(int index, vector<int>& particles) {
int particle1, particle2, particle3, particle4, periodicity;
double phase, k;
force.getTorsionParameters(index, particle1, particle2, particle3, particle4, periodicity, phase, k);
......@@ -652,7 +652,7 @@ void OpenCLCalcPeriodicTorsionForceKernel::initialize(const System& system, cons
map<string, string> replacements;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float4");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::periodicTorsionForce, replacements), force.getForceGroup());
cl.addForce(new OpenCLPeriodicTorsionForceInfo(0, force));
cl.addForce(new OpenCLPeriodicTorsionForceInfo(force));
}
double OpenCLCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -661,12 +661,12 @@ double OpenCLCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool
class OpenCLRBTorsionForceInfo : public OpenCLForceInfo {
public:
OpenCLRBTorsionForceInfo(int requiredBuffers, const RBTorsionForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
OpenCLRBTorsionForceInfo(const RBTorsionForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumTorsions();
}
void getParticlesInGroup(int index, std::vector<int>& particles) {
void getParticlesInGroup(int index, vector<int>& particles) {
int particle1, particle2, particle3, particle4;
double c0, c1, c2, c3, c4, c5;
force.getTorsionParameters(index, particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5);
......@@ -712,7 +712,7 @@ void OpenCLCalcRBTorsionForceKernel::initialize(const System& system, const RBTo
map<string, string> replacements;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float8");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::rbTorsionForce, replacements), force.getForceGroup());
cl.addForce(new OpenCLRBTorsionForceInfo(0, force));
cl.addForce(new OpenCLRBTorsionForceInfo(force));
}
double OpenCLCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -721,12 +721,12 @@ double OpenCLCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includ
class OpenCLCMAPTorsionForceInfo : public OpenCLForceInfo {
public:
OpenCLCMAPTorsionForceInfo(int requiredBuffers, const CMAPTorsionForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
OpenCLCMAPTorsionForceInfo(const CMAPTorsionForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumTorsions();
}
void getParticlesInGroup(int index, std::vector<int>& particles) {
void getParticlesInGroup(int index, vector<int>& particles) {
int map, a1, a2, a3, a4, b1, b2, b3, b4;
force.getTorsionParameters(index, map, a1, a2, a3, a4, b1, b2, b3, b4);
particles.resize(8);
......@@ -799,7 +799,7 @@ void OpenCLCalcCMAPTorsionForceKernel::initialize(const System& system, const CM
replacements["MAP_POS"] = cl.getBondedUtilities().addArgument(mapPositions->getDeviceBuffer(), "int2");
replacements["MAPS"] = cl.getBondedUtilities().addArgument(torsionMaps->getDeviceBuffer(), "int");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::cmapTorsionForce, replacements), force.getForceGroup());
cl.addForce(new OpenCLCMAPTorsionForceInfo(0, force));
cl.addForce(new OpenCLCMAPTorsionForceInfo(force));
}
double OpenCLCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -808,12 +808,12 @@ double OpenCLCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool incl
class OpenCLCustomTorsionForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomTorsionForceInfo(int requiredBuffers, const CustomTorsionForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
OpenCLCustomTorsionForceInfo(const CustomTorsionForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumTorsions();
}
void getParticlesInGroup(int index, std::vector<int>& particles) {
void getParticlesInGroup(int index, vector<int>& particles) {
int particle1, particle2, particle3, particle4;
vector<double> parameters;
force.getTorsionParameters(index, particle1, particle2, particle3, particle4, parameters);
......@@ -862,7 +862,7 @@ void OpenCLCalcCustomTorsionForceKernel::initialize(const System& system, const
paramVector[i][j] = (cl_float) parameters[j];
}
params->setParameterValues(paramVector);
cl.addForce(new OpenCLCustomTorsionForceInfo(0, force));
cl.addForce(new OpenCLCustomTorsionForceInfo(force));
// Record information for the expressions.
......@@ -938,7 +938,7 @@ public:
int getNumParticleGroups() {
return force.getNumExceptions();
}
void getParticlesInGroup(int index, std::vector<int>& particles) {
void getParticlesInGroup(int index, vector<int>& particles) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
force.getExceptionParameters(index, particle1, particle2, chargeProd, sigma, epsilon);
......@@ -1057,7 +1057,7 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
defines["EWALD_ALPHA"] = doubleToString(alpha);
defines["TWO_OVER_SQRT_PI"] = doubleToString(2.0/sqrt(M_PI));
defines["USE_EWALD"] = "1";
ewaldSelfEnergy = (cl.getContextIndex() == 0 ? -ONE_4PI_EPS0*alpha*sumSquaredCharges/std::sqrt(M_PI) : 0.0);
ewaldSelfEnergy = (cl.getContextIndex() == 0 ? -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI) : 0.0);
// Create the reciprocal space kernels.
......@@ -1083,14 +1083,14 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
defines["EWALD_ALPHA"] = doubleToString(alpha);
defines["TWO_OVER_SQRT_PI"] = doubleToString(2.0/sqrt(M_PI));
defines["USE_EWALD"] = "1";
ewaldSelfEnergy = (cl.getContextIndex() == 0 ? -ONE_4PI_EPS0*alpha*sumSquaredCharges/std::sqrt(M_PI) : 0.0);
ewaldSelfEnergy = (cl.getContextIndex() == 0 ? -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI) : 0.0);
pmeDefines["PME_ORDER"] = intToString(PmeOrder);
pmeDefines["NUM_ATOMS"] = intToString(numParticles);
pmeDefines["RECIP_EXP_FACTOR"] = doubleToString(M_PI*M_PI/(alpha*alpha));
pmeDefines["GRID_SIZE_X"] = intToString(gridSizeX);
pmeDefines["GRID_SIZE_Y"] = intToString(gridSizeY);
pmeDefines["GRID_SIZE_Z"] = intToString(gridSizeZ);
pmeDefines["EPSILON_FACTOR"] = doubleToString(std::sqrt(ONE_4PI_EPS0));
pmeDefines["EPSILON_FACTOR"] = doubleToString(sqrt(ONE_4PI_EPS0));
// Create required data structures.
......@@ -1327,7 +1327,7 @@ public:
int getNumParticleGroups() {
return force.getNumExclusions();
}
void getParticlesInGroup(int index, std::vector<int>& particles) {
void getParticlesInGroup(int index, vector<int>& particles) {
int particle1, particle2;
force.getExclusionParticles(index, particle1, particle2);
particles.resize(2);
......@@ -1686,7 +1686,7 @@ public:
int getNumParticleGroups() {
return force.getNumExclusions();
}
void getParticlesInGroup(int index, std::vector<int>& particles) {
void getParticlesInGroup(int index, vector<int>& particles) {
int particle1, particle2;
force.getExclusionParticles(index, particle1, particle2);
particles.resize(2);
......@@ -2564,7 +2564,7 @@ double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool include
class OpenCLCustomExternalForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomExternalForceInfo(const CustomExternalForce& force, int numParticles) : OpenCLForceInfo(1), force(force), indices(numParticles, -1) {
OpenCLCustomExternalForceInfo(const CustomExternalForce& force, int numParticles) : OpenCLForceInfo(0), force(force), indices(numParticles, -1) {
vector<double> params;
for (int i = 0; i < force.getNumParticles(); i++) {
int particle;
......@@ -2697,7 +2697,7 @@ public:
int getNumParticleGroups() {
return force.getNumDonors()+force.getNumAcceptors()+force.getNumExclusions();
}
void getParticlesInGroup(int index, std::vector<int>& particles) {
void getParticlesInGroup(int index, vector<int>& particles) {
int p1, p2, p3;
vector<double> parameters;
if (index < force.getNumDonors()) {
......@@ -3190,16 +3190,16 @@ double OpenCLCalcCustomHbondForceKernel::execute(ContextImpl& context, bool incl
}
donorKernel.setArg<mm_float4>(8, cl.getPeriodicBoxSize());
donorKernel.setArg<mm_float4>(9, cl.getInvPeriodicBoxSize());
cl.executeKernel(donorKernel, std::max(numDonors, numAcceptors));
cl.executeKernel(donorKernel, max(numDonors, numAcceptors));
acceptorKernel.setArg<mm_float4>(8, cl.getPeriodicBoxSize());
acceptorKernel.setArg<mm_float4>(9, cl.getInvPeriodicBoxSize());
cl.executeKernel(acceptorKernel, std::max(numDonors, numAcceptors));
cl.executeKernel(acceptorKernel, max(numDonors, numAcceptors));
return 0.0;
}
class OpenCLCustomCompoundBondForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomCompoundBondForceInfo(const CustomCompoundBondForce& force) : OpenCLForceInfo(1), force(force) {
OpenCLCustomCompoundBondForceInfo(const CustomCompoundBondForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
......@@ -3586,9 +3586,9 @@ void OpenCLIntegrateLangevinStepKernel::execute(ContextImpl& context, const Lang
double tau = (friction == 0.0 ? 0.0 : 1.0/friction);
double kT = BOLTZ*temperature;
double vscale = std::exp(-stepSize/tau);
double vscale = exp(-stepSize/tau);
double fscale = (1-vscale)*tau;
double noisescale = std::sqrt(2*kT/tau)*std::sqrt(0.5*(1-vscale*vscale)*tau);
double noisescale = sqrt(2*kT/tau)*sqrt(0.5*(1-vscale*vscale)*tau);
vector<cl_float> p(params->getSize());
p[0] = (cl_float) vscale;
p[1] = (cl_float) fscale;
......@@ -3690,7 +3690,7 @@ void OpenCLIntegrateVariableVerletStepKernel::initialize(const System& system, c
kernel1 = cl::Kernel(program, "integrateVerletPart1");
kernel2 = cl::Kernel(program, "integrateVerletPart2");
selectSizeKernel = cl::Kernel(program, "selectVerletStepSize");
blockSize = std::min(std::min(256, system.getNumParticles()), (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>());
blockSize = min(min(256, system.getNumParticles()), (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>());
}
double OpenCLIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) {
......@@ -3764,9 +3764,9 @@ void OpenCLIntegrateVariableLangevinStepKernel::initialize(const System& system,
kernel2 = cl::Kernel(program, "integrateLangevinPart2");
selectSizeKernel = cl::Kernel(program, "selectLangevinStepSize");
params = new OpenCLArray<cl_float>(cl, 3, "langevinParams");
blockSize = std::min(256, system.getNumParticles());
blockSize = std::max(blockSize, params->getSize());
blockSize = std::min(blockSize, (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>());
blockSize = min(256, system.getNumParticles());
blockSize = max(blockSize, params->getSize());
blockSize = min(blockSize, (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>());
}
double OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) {
......@@ -3866,7 +3866,7 @@ private:
OpenCLParameterSet& perDofValues;
vector<vector<cl_float> >& localPerDofValues;
bool& deviceValuesAreCurrent;
std::vector<int> lastAtomOrder;
vector<int> lastAtomOrder;
};
OpenCLIntegrateCustomStepKernel::~OpenCLIntegrateCustomStepKernel() {
......
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