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Commit 73183c61 authored by ChayaSt's avatar ChayaSt
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resolved conflict

parents 0e218233 32e08b87
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openmmapi/src/MonteCarloAnisotropicBarostat.cpp
View file @ 73183c61
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -34,8 +34,8 @@
using namespace OpenMM;
MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double temperature, bool scaleX, bool scaleY, bool scaleZ, int frequency) :
defaultPressure(defaultPressure), temperature(temperature), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ), frequency(frequency) {
MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double defaultTemperature, bool scaleX, bool scaleY, bool scaleZ, int frequency) :
defaultPressure(defaultPressure), defaultTemperature(defaultTemperature), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ), frequency(frequency) {
setRandomNumberSeed(0);
}
......
openmmapi/src/MonteCarloAnisotropicBarostatImpl.cpp
View file @ 73183c61
......@@ -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) 2010-2013 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman, Lee-Ping Wang *
* Contributors: *
* *
......@@ -119,7 +119,7 @@ void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context)
// Compute the energy of the modified system.
double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
double kT = BOLTZ*owner.getTemperature();
double kT = BOLTZ*context.getParameter(MonteCarloAnisotropicBarostat::Temperature());
double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
// Reject the step.
......@@ -150,6 +150,7 @@ std::map<std::string, double> MonteCarloAnisotropicBarostatImpl::getDefaultParam
parameters[MonteCarloAnisotropicBarostat::PressureX()] = getOwner().getDefaultPressure()[0];
parameters[MonteCarloAnisotropicBarostat::PressureY()] = getOwner().getDefaultPressure()[1];
parameters[MonteCarloAnisotropicBarostat::PressureZ()] = getOwner().getDefaultPressure()[2];
parameters[MonteCarloAnisotropicBarostat::Temperature()] = getOwner().getDefaultTemperature();
return parameters;
}
......
openmmapi/src/MonteCarloBarostat.cpp
View file @ 73183c61
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -34,8 +34,8 @@
using namespace OpenMM;
MonteCarloBarostat::MonteCarloBarostat(double defaultPressure, double temperature, int frequency) :
defaultPressure(defaultPressure), temperature(temperature), frequency(frequency) {
MonteCarloBarostat::MonteCarloBarostat(double defaultPressure, double defaultTemperature, int frequency) :
defaultPressure(defaultPressure), defaultTemperature(defaultTemperature), frequency(frequency) {
setRandomNumberSeed(0);
}
......
openmmapi/src/MonteCarloBarostatImpl.cpp
View file @ 73183c61
......@@ -89,7 +89,7 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context) {
double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
double pressure = context.getParameter(MonteCarloBarostat::Pressure())*(AVOGADRO*1e-25);
double kT = BOLTZ*owner.getTemperature();
double kT = BOLTZ*context.getParameter(MonteCarloBarostat::Temperature());
double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
// Reject the step.
......@@ -118,6 +118,7 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context) {
std::map<std::string, double> MonteCarloBarostatImpl::getDefaultParameters() {
std::map<std::string, double> parameters;
parameters[MonteCarloBarostat::Pressure()] = getOwner().getDefaultPressure();
parameters[MonteCarloBarostat::Temperature()] = getOwner().getDefaultTemperature();
return parameters;
}
......
openmmapi/src/MonteCarloMembraneBarostat.cpp
View file @ 73183c61
......@@ -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) 2010-2014 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -34,8 +34,8 @@
using namespace OpenMM;
MonteCarloMembraneBarostat::MonteCarloMembraneBarostat(double defaultPressure, double defaultSurfaceTension, double temperature, XYMode xymode, ZMode zmode, int frequency) :
defaultPressure(defaultPressure), defaultSurfaceTension(defaultSurfaceTension), temperature(temperature),
MonteCarloMembraneBarostat::MonteCarloMembraneBarostat(double defaultPressure, double defaultSurfaceTension, double defaultTemperature, XYMode xymode, ZMode zmode, int frequency) :
defaultPressure(defaultPressure), defaultSurfaceTension(defaultSurfaceTension), defaultTemperature(defaultTemperature),
xymode(xymode), zmode(zmode), frequency(frequency) {
setRandomNumberSeed(0);
}
......
openmmapi/src/MonteCarloMembraneBarostatImpl.cpp
View file @ 73183c61
......@@ -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) 2010-2014 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman, Lee-Ping Wang *
* Contributors: *
* *
......@@ -120,7 +120,7 @@ void MonteCarloMembraneBarostatImpl::updateContextState(ContextImpl& context) {
// Compute the energy of the modified system.
double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
double kT = BOLTZ*owner.getTemperature();
double kT = BOLTZ*context.getParameter(MonteCarloMembraneBarostat::Temperature());
double w = finalEnergy-initialEnergy + pressure*deltaVolume - tension*deltaArea - context.getMolecules().size()*kT*std::log(newVolume/volume);
if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
// Reject the step.
......@@ -150,6 +150,7 @@ std::map<std::string, double> MonteCarloMembraneBarostatImpl::getDefaultParamete
std::map<std::string, double> parameters;
parameters[MonteCarloMembraneBarostat::Pressure()] = getOwner().getDefaultPressure();
parameters[MonteCarloMembraneBarostat::SurfaceTension()] = getOwner().getDefaultSurfaceTension();
parameters[MonteCarloMembraneBarostat::Temperature()] = getOwner().getDefaultTemperature();
return parameters;
}
......
openmmapi/src/PeriodicTorsionForce.cpp
View file @ 73183c61
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -37,7 +37,7 @@
using namespace OpenMM;
PeriodicTorsionForce::PeriodicTorsionForce() {
PeriodicTorsionForce::PeriodicTorsionForce() : usePeriodic(false) {
}
int PeriodicTorsionForce::addTorsion(int particle1, int particle2, int particle3, int particle4, int periodicity, double phase, double k) {
......@@ -74,3 +74,11 @@ ForceImpl* PeriodicTorsionForce::createImpl() const {
void PeriodicTorsionForce::updateParametersInContext(Context& context) {
dynamic_cast<PeriodicTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void PeriodicTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool PeriodicTorsionForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/RBTorsionForce.cpp
View file @ 73183c61
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -37,7 +37,7 @@
using namespace OpenMM;
RBTorsionForce::RBTorsionForce() {
RBTorsionForce::RBTorsionForce() : usePeriodic(false) {
}
int RBTorsionForce::addTorsion(int particle1, int particle2, int particle3, int particle4, double c0, double c1, double c2, double c3, double c4, double c5) {
......@@ -80,3 +80,11 @@ ForceImpl* RBTorsionForce::createImpl() const {
void RBTorsionForce::updateParametersInContext(Context& context) {
dynamic_cast<RBTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void RBTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool RBTorsionForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
platforms/cpu/include/CpuKernels.h
View file @ 73183c61
......@@ -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) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -90,6 +90,7 @@ public:
private:
CpuPlatform::PlatformData& data;
Kernel referenceKernel;
std::vector<RealVec> lastPositions;
};
/**
......@@ -98,7 +99,7 @@ private:
class CpuCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
public:
CpuCalcHarmonicAngleForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) :
CalcHarmonicAngleForceKernel(name, platform), data(data), angleIndexArray(NULL), angleParamArray(NULL) {
CalcHarmonicAngleForceKernel(name, platform), data(data), angleIndexArray(NULL), angleParamArray(NULL), usePeriodic(false) {
}
~CpuCalcHarmonicAngleForceKernel();
/**
......@@ -130,6 +131,7 @@ private:
int **angleIndexArray;
RealOpenMM **angleParamArray;
CpuBondForce bondForce;
bool usePeriodic;
};
/**
......@@ -138,7 +140,7 @@ private:
class CpuCalcPeriodicTorsionForceKernel : public CalcPeriodicTorsionForceKernel {
public:
CpuCalcPeriodicTorsionForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) :
CalcPeriodicTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL) {
CalcPeriodicTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL), usePeriodic(false) {
}
~CpuCalcPeriodicTorsionForceKernel();
/**
......@@ -170,6 +172,7 @@ private:
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
CpuBondForce bondForce;
bool usePeriodic;
};
/**
......@@ -178,7 +181,7 @@ private:
class CpuCalcRBTorsionForceKernel : public CalcRBTorsionForceKernel {
public:
CpuCalcRBTorsionForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) :
CalcRBTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL) {
CalcRBTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL), usePeriodic(false) {
}
~CpuCalcRBTorsionForceKernel();
/**
......@@ -210,6 +213,7 @@ private:
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
CpuBondForce bondForce;
bool usePeriodic;
};
/**
......@@ -264,9 +268,7 @@ private:
bool useSwitchingFunction, useOptimizedPme, hasInitializedPme;
std::vector<std::set<int> > exclusions;
std::vector<std::pair<float, float> > particleParams;
std::vector<RealVec> lastPositions;
NonbondedMethod nonbondedMethod;
CpuNeighborList* neighborList;
CpuNonbondedForce* nonbonded;
Kernel optimizedPme;
CpuBondForce bondForce;
......@@ -314,7 +316,6 @@ private:
std::vector<std::string> parameterNames, globalParameterNames;
std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
NonbondedMethod nonbondedMethod;
CpuNeighborList* neighborList;
CpuCustomNonbondedForce* nonbonded;
};
......@@ -400,7 +401,6 @@ private:
std::vector<OpenMM::CustomGBForce::ComputationType> valueTypes;
std::vector<OpenMM::CustomGBForce::ComputationType> energyTypes;
NonbondedMethod nonbondedMethod;
CpuNeighborList* neighborList;
};
/**
......
platforms/cpu/include/CpuNeighborList.h
View file @ 73183c61
......@@ -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) 2013-2015 Stanford University and the Authors. *
* Portions copyright (c) 2013-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -51,6 +51,7 @@ public:
void computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const std::vector<std::set<int> >& exclusions,
const RealVec* periodicBoxVectors, bool usePeriodic, float maxDistance, ThreadPool& threads);
int getNumBlocks() const;
int getBlockSize() const;
const std::vector<int>& getSortedAtoms() const;
const std::vector<int>& getBlockNeighbors(int blockIndex) const;
const std::vector<char>& getBlockExclusions(int blockIndex) const;
......
platforms/cpu/include/CpuPlatform.h
View file @ 73183c61
......@@ -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) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -34,6 +34,7 @@
#include "AlignedArray.h"
#include "CpuRandom.h"
#include "CpuNeighborList.h"
#include "ReferencePlatform.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/ThreadPool.h"
......@@ -64,7 +65,7 @@ public:
* This is the name of the parameter for selecting the number of threads to use.
*/
static const std::string& CpuThreads() {
static const std::string key = "CpuThreads";
static const std::string key = "Threads";
return key;
}
/**
......@@ -80,12 +81,18 @@ private:
class CpuPlatform::PlatformData {
public:
PlatformData(int numParticles, int numThreads);
~PlatformData();
void requestNeighborList(double cutoffDistance, double padding, bool useExclusions, std::vector<std::set<int> >& exclusionList);
AlignedArray<float> posq;
std::vector<AlignedArray<float> > threadForce;
ThreadPool threads;
bool isPeriodic;
CpuRandom random;
std::map<std::string, std::string> propertyValues;
CpuNeighborList* neighborList;
double cutoff, paddedCutoff;
bool anyExclusions;
std::vector<std::set<int> > exclusions;
};
} // namespace OpenMM
......
platforms/cpu/src/CpuCustomGBForce.cpp
View file @ 73183c61
/* Portions copyright (c) 2009-2014 Stanford University and Simbios.
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -294,12 +294,13 @@ void CpuCustomGBForce::calculateParticlePairValue(int index, ThreadData& data, i
int blockIndex = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
if (blockIndex >= neighborList->getNumBlocks())
break;
const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
const int blockSize = neighborList->getBlockSize();
const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& blockExclusions = neighborList->getBlockExclusions(blockIndex);
for (int i = 0; i < (int) neighbors.size(); i++) {
int first = neighbors[i];
for (int k = 0; k < 4; k++) {
for (int k = 0; k < blockSize; k++) {
if ((blockExclusions[i] & (1<<k)) == 0) {
int second = blockAtom[k];
if (useExclusions && exclusions[first].find(second) != exclusions[first].end())
......@@ -379,12 +380,13 @@ void CpuCustomGBForce::calculateParticlePairEnergyTerm(int index, ThreadData& da
int blockIndex = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
if (blockIndex >= neighborList->getNumBlocks())
break;
const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
const int blockSize = neighborList->getBlockSize();
const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& blockExclusions = neighborList->getBlockExclusions(blockIndex);
for (int i = 0; i < (int) neighbors.size(); i++) {
int first = neighbors[i];
for (int k = 0; k < 4; k++) {
for (int k = 0; k < blockSize; k++) {
if ((blockExclusions[i] & (1<<k)) == 0) {
int second = blockAtom[k];
if (useExclusions && exclusions[first].find(second) != exclusions[first].end())
......@@ -460,12 +462,13 @@ void CpuCustomGBForce::calculateChainRuleForces(ThreadData& data, int numAtoms,
int blockIndex = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
if (blockIndex >= neighborList->getNumBlocks())
break;
const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
const int blockSize = neighborList->getBlockSize();
const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& blockExclusions = neighborList->getBlockExclusions(blockIndex);
for (int i = 0; i < (int) neighbors.size(); i++) {
int first = neighbors[i];
for (int k = 0; k < 4; k++) {
for (int k = 0; k < blockSize; k++) {
if ((blockExclusions[i] & (1<<k)) == 0) {
int second = blockAtom[k];
bool isExcluded = (exclusions[first].find(second) != exclusions[first].end());
......
platforms/cpu/src/CpuCustomNonbondedForce.cpp
View file @ 73183c61
/* Portions copyright (c) 2009-2014 Stanford University and Simbios.
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -190,7 +190,8 @@ void CpuCustomNonbondedForce::threadComputeForce(ThreadPool& threads, int thread
int blockIndex = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
if (blockIndex >= neighborList->getNumBlocks())
break;
const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
const int blockSize = neighborList->getBlockSize();
const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
for (int i = 0; i < (int) neighbors.size(); i++) {
......@@ -199,7 +200,7 @@ void CpuCustomNonbondedForce::threadComputeForce(ThreadPool& threads, int thread
ReferenceForce::setVariable(data.energyParticleParams[j*2], atomParameters[first][j]);
ReferenceForce::setVariable(data.forceParticleParams[j*2], atomParameters[first][j]);
}
for (int k = 0; k < 4; k++) {
for (int k = 0; k < blockSize; k++) {
if ((exclusions[i] & (1<<k)) == 0) {
int second = blockAtom[k];
for (int j = 0; j < (int) paramNames.size(); j++) {
......
platforms/cpu/src/CpuKernels.cpp
View file @ 73183c61
......@@ -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) 2013-2015 Stanford University and the Authors. *
* Portions copyright (c) 2013-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -230,6 +230,7 @@ CpuCalcForcesAndEnergyKernel::CpuCalcForcesAndEnergyKernel(std::string name, con
void CpuCalcForcesAndEnergyKernel::initialize(const System& system) {
referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().initialize(system);
lastPositions.resize(system.getNumParticles(), Vec3(1e10, 1e10, 1e10));
}
void CpuCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups) {
......@@ -237,11 +238,60 @@ void CpuCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool i
// Convert positions to single precision and clear the forces.
InitForceTask task(context.getSystem().getNumParticles(), context, data);
int numParticles = context.getSystem().getNumParticles();
InitForceTask task(numParticles, context, data);
data.threads.execute(task);
data.threads.waitForThreads();
if (!task.positionsValid)
throw OpenMMException("Particle coordinate is nan");
// Determine whether we need to recompute the neighbor list.
if (data.neighborList != NULL) {
double padding = data.paddedCutoff-data.cutoff;;
bool needRecompute = false;
double closeCutoff2 = 0.25*padding*padding;
double farCutoff2 = 0.5*padding*padding;
int maxNumMoved = numParticles/10;
vector<int> moved;
vector<RealVec>& posData = extractPositions(context);
for (int i = 0; i < numParticles; i++) {
RealVec delta = posData[i]-lastPositions[i];
double dist2 = delta.dot(delta);
if (dist2 > closeCutoff2) {
moved.push_back(i);
if (dist2 > farCutoff2 || moved.size() > maxNumMoved) {
needRecompute = true;
break;
}
}
}
if (!needRecompute && moved.size() > 0) {
// Some particles have moved further than half the padding distance. Look for pairs
// that are missing from the neighbor list.
int numMoved = moved.size();
double cutoff2 = data.cutoff*data.cutoff;
double paddedCutoff2 = data.paddedCutoff*data.paddedCutoff;
for (int i = 1; i < numMoved && !needRecompute; i++)
for (int j = 0; j < i; j++) {
RealVec delta = posData[moved[i]]-posData[moved[j]];
if (delta.dot(delta) < cutoff2) {
// These particles should interact. See if they are in the neighbor list.
RealVec oldDelta = lastPositions[moved[i]]-lastPositions[moved[j]];
if (oldDelta.dot(oldDelta) > paddedCutoff2) {
needRecompute = true;
break;
}
}
}
}
if (needRecompute) {
data.neighborList->computeNeighborList(numParticles, data.posq, data.exclusions, extractBoxVectors(context), data.isPeriodic, data.paddedCutoff, data.threads);
lastPositions = posData;
}
}
}
double CpuCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups, bool& valid) {
......@@ -283,6 +333,7 @@ void CpuCalcHarmonicAngleForceKernel::initialize(const System& system, const Har
angleParamArray[i][1] = (RealOpenMM) k;
}
bondForce.initialize(system.getNumParticles(), numAngles, 3, angleIndexArray, data.threads);
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double CpuCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -290,6 +341,8 @@ double CpuCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool inclu
vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = 0;
ReferenceAngleBondIxn angleBond;
if (usePeriodic)
angleBond.setPeriodic(extractBoxVectors(context));
bondForce.calculateForce(posData, angleParamArray, forceData, includeEnergy ? &energy : NULL, angleBond);
return energy;
}
......@@ -343,6 +396,7 @@ void CpuCalcPeriodicTorsionForceKernel::initialize(const System& system, const P
torsionParamArray[i][2] = (RealOpenMM) periodicity;
}
bondForce.initialize(system.getNumParticles(), numTorsions, 4, torsionIndexArray, data.threads);
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double CpuCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -350,6 +404,8 @@ double CpuCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool inc
vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = 0;
ReferenceProperDihedralBond periodicTorsionBond;
if (usePeriodic)
periodicTorsionBond.setPeriodic(extractBoxVectors(context));
bondForce.calculateForce(posData, torsionParamArray, forceData, includeEnergy ? &energy : NULL, periodicTorsionBond);
return energy;
}
......@@ -407,6 +463,7 @@ void CpuCalcRBTorsionForceKernel::initialize(const System& system, const RBTorsi
torsionParamArray[i][5] = (RealOpenMM) c5;
}
bondForce.initialize(system.getNumParticles(), numTorsions, 4, torsionIndexArray, data.threads);
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double CpuCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -414,6 +471,8 @@ double CpuCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeFo
vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = 0;
ReferenceRbDihedralBond rbTorsionBond;
if (usePeriodic)
rbTorsionBond.setPeriodic(extractBoxVectors(context));
bondForce.calculateForce(posData, torsionParamArray, forceData, includeEnergy ? &energy : NULL, rbTorsionBond);
return energy;
}
......@@ -464,15 +523,11 @@ CpuNonbondedForce* createCpuNonbondedForceVec4();
CpuNonbondedForce* createCpuNonbondedForceVec8();
CpuCalcNonbondedForceKernel::CpuCalcNonbondedForceKernel(string name, const Platform& platform, CpuPlatform::PlatformData& data) : CalcNonbondedForceKernel(name, platform),
data(data), bonded14IndexArray(NULL), bonded14ParamArray(NULL), hasInitializedPme(false), neighborList(NULL), nonbonded(NULL) {
if (isVec8Supported()) {
neighborList = new CpuNeighborList(8);
data(data), bonded14IndexArray(NULL), bonded14ParamArray(NULL), hasInitializedPme(false), nonbonded(NULL) {
if (isVec8Supported())
nonbonded = createCpuNonbondedForceVec8();
}
else {
neighborList = new CpuNeighborList(4);
else
nonbonded = createCpuNonbondedForceVec4();
}
}
CpuCalcNonbondedForceKernel::~CpuCalcNonbondedForceKernel() {
......@@ -486,8 +541,6 @@ CpuCalcNonbondedForceKernel::~CpuCalcNonbondedForceKernel() {
}
if (nonbonded != NULL)
delete nonbonded;
if (neighborList != NULL)
delete neighborList;
}
void CpuCalcNonbondedForceKernel::initialize(const System& system, const NonbondedForce& force) {
......@@ -547,6 +600,7 @@ void CpuCalcNonbondedForceKernel::initialize(const System& system, const Nonbond
if (nonbondedMethod == NoCutoff)
useSwitchingFunction = false;
else {
data.requestNeighborList(nonbondedCutoff, 0.25*nonbondedCutoff, true, exclusions);
useSwitchingFunction = force.getUseSwitchingFunction();
switchingDistance = force.getSwitchingDistance();
}
......@@ -569,7 +623,6 @@ void CpuCalcNonbondedForceKernel::initialize(const System& system, const Nonbond
dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(system, force);
else
dispersionCoefficient = 0.0;
lastPositions.resize(numParticles, Vec3(1e10, 1e10, 1e10));
data.isPeriodic = (nonbondedMethod == CutoffPeriodic || nonbondedMethod == Ewald || nonbondedMethod == PME);
}
......@@ -596,53 +649,8 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0);
bool ewald = (nonbondedMethod == Ewald);
bool pme = (nonbondedMethod == PME);
if (nonbondedMethod != NoCutoff) {
// Determine whether we need to recompute the neighbor list.
double padding = 0.25*nonbondedCutoff;
bool needRecompute = false;
double closeCutoff2 = 0.25*padding*padding;
double farCutoff2 = 0.5*padding*padding;
int maxNumMoved = numParticles/10;
vector<int> moved;
for (int i = 0; i < numParticles; i++) {
RealVec delta = posData[i]-lastPositions[i];
double dist2 = delta.dot(delta);
if (dist2 > closeCutoff2) {
moved.push_back(i);
if (dist2 > farCutoff2 || moved.size() > maxNumMoved) {
needRecompute = true;
break;
}
}
}
if (!needRecompute && moved.size() > 0) {
// Some particles have moved further than half the padding distance. Look for pairs
// that are missing from the neighbor list.
int numMoved = moved.size();
double cutoff2 = nonbondedCutoff*nonbondedCutoff;
double paddedCutoff2 = (nonbondedCutoff+padding)*(nonbondedCutoff+padding);
for (int i = 1; i < numMoved && !needRecompute; i++)
for (int j = 0; j < i; j++) {
RealVec delta = posData[moved[i]]-posData[moved[j]];
if (delta.dot(delta) < cutoff2) {
// These particles should interact. See if they are in the neighbor list.
RealVec oldDelta = lastPositions[moved[i]]-lastPositions[moved[j]];
if (oldDelta.dot(oldDelta) > paddedCutoff2) {
needRecompute = true;
break;
}
}
}
}
if (needRecompute) {
neighborList->computeNeighborList(numParticles, posq, exclusions, boxVectors, data.isPeriodic, nonbondedCutoff+padding, data.threads);
lastPositions = posData;
}
nonbonded->setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric);
}
if (nonbondedMethod != NoCutoff)
nonbonded->setUseCutoff(nonbondedCutoff, *data.neighborList, rfDielectric);
if (data.isPeriodic) {
RealVec* boxVectors = extractBoxVectors(context);
double minAllowedSize = 1.999999*nonbondedCutoff;
......@@ -739,7 +747,7 @@ void CpuCalcNonbondedForceKernel::getPMEParameters(double& alpha, int& nx, int&
}
CpuCalcCustomNonbondedForceKernel::CpuCalcCustomNonbondedForceKernel(string name, const Platform& platform, CpuPlatform::PlatformData& data) :
CalcCustomNonbondedForceKernel(name, platform), data(data), forceCopy(NULL), neighborList(NULL), nonbonded(NULL) {
CalcCustomNonbondedForceKernel(name, platform), data(data), forceCopy(NULL), nonbonded(NULL) {
}
CpuCalcCustomNonbondedForceKernel::~CpuCalcCustomNonbondedForceKernel() {
......@@ -748,8 +756,6 @@ CpuCalcCustomNonbondedForceKernel::~CpuCalcCustomNonbondedForceKernel() {
delete[] particleParamArray[i];
delete[] particleParamArray;
}
if (neighborList != NULL)
delete neighborList;
if (nonbonded != NULL)
delete nonbonded;
if (forceCopy != NULL)
......@@ -786,7 +792,7 @@ void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const C
if (nonbondedMethod == NoCutoff)
useSwitchingFunction = false;
else {
neighborList = new CpuNeighborList(4);
data.requestNeighborList(nonbondedCutoff, 0.25*nonbondedCutoff, true, exclusions);
useSwitchingFunction = force.getUseSwitchingFunction();
switchingDistance = force.getSwitchingDistance();
}
......@@ -852,10 +858,8 @@ double CpuCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool inc
RealVec* boxVectors = extractBoxVectors(context);
double energy = 0;
bool periodic = (nonbondedMethod == CutoffPeriodic);
if (nonbondedMethod != NoCutoff) {
neighborList->computeNeighborList(numParticles, data.posq, exclusions, boxVectors, data.isPeriodic, nonbondedCutoff, data.threads);
nonbonded->setUseCutoff(nonbondedCutoff, *neighborList);
}
if (nonbondedMethod != NoCutoff)
nonbonded->setUseCutoff(nonbondedCutoff, *data.neighborList);
if (periodic) {
double minAllowedSize = 2*nonbondedCutoff;
if (boxVectors[0][0] < minAllowedSize || boxVectors[1][1] < minAllowedSize || boxVectors[2][2] < minAllowedSize)
......@@ -963,8 +967,6 @@ CpuCalcCustomGBForceKernel::~CpuCalcCustomGBForceKernel() {
delete[] particleParamArray[i];
delete[] particleParamArray;
}
if (neighborList != NULL)
delete neighborList;
if (ixn != NULL)
delete ixn;
}
......@@ -1012,10 +1014,8 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
globalParameterNames.push_back(force.getGlobalParameterName(i));
nonbondedMethod = CalcCustomGBForceKernel::NonbondedMethod(force.getNonbondedMethod());
nonbondedCutoff = (RealOpenMM) force.getCutoffDistance();
if (nonbondedMethod == NoCutoff)
neighborList = NULL;
else
neighborList = new CpuNeighborList(4);
if (nonbondedMethod != NoCutoff)
data.requestNeighborList(nonbondedCutoff, 0.25*nonbondedCutoff, true, exclusions);
// Create custom functions for the tabulated functions.
......@@ -1112,8 +1112,7 @@ double CpuCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeFor
ixn->setPeriodic(extractBoxSize(context));
if (nonbondedMethod != NoCutoff) {
vector<set<int> > noExclusions(numParticles);
neighborList->computeNeighborList(numParticles, data.posq, exclusions, boxVectors, data.isPeriodic, nonbondedCutoff, data.threads);
ixn->setUseCutoff(nonbondedCutoff, *neighborList);
ixn->setUseCutoff(nonbondedCutoff, *data.neighborList);
}
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
......
platforms/cpu/src/CpuNeighborList.cpp
View file @ 73183c61
......@@ -508,6 +508,10 @@ int CpuNeighborList::getNumBlocks() const {
return sortedAtoms.size()/blockSize;
}
int CpuNeighborList::getBlockSize() const {
return blockSize;
}
const std::vector<int>& CpuNeighborList::getSortedAtoms() const {
return sortedAtoms;
}
......
platforms/cpu/src/CpuPlatform.cpp
View file @ 73183c61
......@@ -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) 2013-2014 Stanford University and the Authors. *
* Portions copyright (c) 2013-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -34,6 +34,7 @@
#include "CpuKernels.h"
#include "CpuSETTLE.h"
#include "ReferenceConstraints.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/hardware.h"
#include "openmm/internal/vectorize.h"
#include <sstream>
......@@ -59,6 +60,7 @@ extern "C" OPENMM_EXPORT_CPU void registerPlatforms() {
map<const ContextImpl*, CpuPlatform::PlatformData*> CpuPlatform::contextData;
CpuPlatform::CpuPlatform() {
deprecatedPropertyReplacements["CpuThreads"] = CpuThreads();
CpuKernelFactory* factory = new CpuKernelFactory();
registerKernelFactory(CalcForcesAndEnergyKernel::Name(), factory);
registerKernelFactory(CalcHarmonicAngleForceKernel::Name(), factory);
......@@ -83,7 +85,10 @@ CpuPlatform::CpuPlatform() {
const string& CpuPlatform::getPropertyValue(const Context& context, const string& property) const {
const ContextImpl& impl = getContextImpl(context);
const PlatformData& data = getPlatformData(impl);
map<string, string>::const_iterator value = data.propertyValues.find(property);
string propertyName = property;
if (deprecatedPropertyReplacements.find(property) != deprecatedPropertyReplacements.end())
propertyName = deprecatedPropertyReplacements.find(property)->second;
map<string, string>::const_iterator value = data.propertyValues.find(propertyName);
if (value != data.propertyValues.end())
return value->second;
return ReferencePlatform::getPropertyValue(context, property);
......@@ -131,7 +136,8 @@ const CpuPlatform::PlatformData& CpuPlatform::getPlatformData(const ContextImpl&
return *contextData[&context];
}
CpuPlatform::PlatformData::PlatformData(int numParticles, int numThreads) : posq(4*numParticles), threads(numThreads) {
CpuPlatform::PlatformData::PlatformData(int numParticles, int numThreads) : posq(4*numParticles), threads(numThreads),
neighborList(NULL), cutoff(0.0), paddedCutoff(0.0), anyExclusions(false) {
numThreads = threads.getNumThreads();
threadForce.resize(numThreads);
for (int i = 0; i < numThreads; i++)
......@@ -141,3 +147,27 @@ CpuPlatform::PlatformData::PlatformData(int numParticles, int numThreads) : posq
threadsProperty << numThreads;
propertyValues[CpuThreads()] = threadsProperty.str();
}
CpuPlatform::PlatformData::~PlatformData() {
if (neighborList != NULL)
delete neighborList;
}
bool isVec8Supported();
void CpuPlatform::PlatformData::requestNeighborList(double cutoffDistance, double padding, bool useExclusions, vector<set<int> >& exclusionList) {
if (neighborList == NULL)
neighborList = new CpuNeighborList(isVec8Supported() ? 8 : 4);
if (cutoffDistance > cutoff)
cutoff = cutoffDistance;
if (cutoffDistance+padding > paddedCutoff)
paddedCutoff = cutoffDistance+padding;
if (useExclusions) {
if (anyExclusions && exclusions != exclusionList)
throw OpenMMException("All Forces must have identical exclusions");
else {
exclusions = exclusionList;
anyExclusions = true;
}
}
}
platforms/cuda/include/CudaContext.h
View file @ 73183c61
......@@ -326,6 +326,18 @@ public:
void setStepsSinceReorder(int steps) {
stepsSinceReorder = steps;
}
/**
* Get the flag that marks whether the current force evaluation is valid.
*/
bool getForcesValid() const {
return forcesValid;
}
/**
* Get the flag that marks whether the current force evaluation is valid.
*/
void setForcesValid(bool valid) {
forcesValid = valid;
}
/**
* Get the number of atoms.
*/
......@@ -572,7 +584,7 @@ private:
int paddedNumAtoms;
int numAtomBlocks;
int numThreadBlocks;
bool useBlockingSync, useDoublePrecision, useMixedPrecision, contextIsValid, atomsWereReordered, boxIsTriclinic, hasCompilerKernel;
bool useBlockingSync, useDoublePrecision, useMixedPrecision, contextIsValid, atomsWereReordered, boxIsTriclinic, hasCompilerKernel, forcesValid;
std::string compiler, tempDir, cacheDir, gpuArchitecture;
float4 periodicBoxVecXFloat, periodicBoxVecYFloat, periodicBoxVecZFloat, periodicBoxSizeFloat, invPeriodicBoxSizeFloat;
double4 periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ, periodicBoxSize, invPeriodicBoxSize;
......
platforms/cuda/include/CudaKernels.h
View file @ 73183c61
......@@ -178,7 +178,7 @@ public:
* @param b the vector defining the second edge of the periodic box
* @param c the vector defining the third edge of the periodic box
*/
void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const;
void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c);
/**
* Create a checkpoint recording the current state of the Context.
*
......@@ -718,7 +718,7 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force);
private:
void initInteractionGroups(const CustomNonbondedForce& force, const std::string& interactionSource);
void initInteractionGroups(const CustomNonbondedForce& force, const std::string& interactionSource, const std::vector<std::string>& tableTypes);
CudaContext& cu;
CudaParameterSet* params;
CudaArray* globals;
......
platforms/cuda/include/CudaNonbondedUtilities.h
View file @ 73183c61
......@@ -269,6 +269,8 @@ private:
CudaArray* oldPositions;
CudaArray* rebuildNeighborList;
CudaSort* blockSorter;
CUevent downloadCountEvent;
int* pinnedCountBuffer;
std::vector<void*> forceArgs, findBlockBoundsArgs, sortBoxDataArgs, findInteractingBlocksArgs;
std::vector<std::vector<int> > atomExclusions;
std::vector<ParameterInfo> parameters;
......
platforms/cuda/include/CudaPlatform.h
View file @ 73183c61
......@@ -58,35 +58,35 @@ public:
* This is the name of the parameter for selecting which CUDA device or devices to use.
*/
static const std::string& CudaDeviceIndex() {
static const std::string key = "CudaDeviceIndex";
static const std::string key = "DeviceIndex";
return key;
}
/**
* This is the name of the parameter that reports the CUDA device or devices being used.
*/
static const std::string& CudaDeviceName() {
static const std::string key = "CudaDeviceName";
static const std::string key = "DeviceName";
return key;
}
/**
* This is the name of the parameter for selecting whether CUDA should sync or spin loop while waiting for results.
*/
static const std::string& CudaUseBlockingSync() {
static const std::string key = "CudaUseBlockingSync";
static const std::string key = "UseBlockingSync";
return key;
}
/**
* This is the name of the parameter for selecting what numerical precision to use.
*/
static const std::string& CudaPrecision() {
static const std::string key = "CudaPrecision";
static const std::string key = "Precision";
return key;
}
/**
* This is the name of the parameter for selecting whether to use the CPU based PME calculation.
*/
static const std::string& CudaUseCpuPme() {
static const std::string key = "CudaUseCpuPme";
static const std::string key = "UseCpuPme";
return key;
}
/**
......@@ -107,14 +107,21 @@ public:
* This is the name of the parameter for specifying the path to the directory for creating temporary files.
*/
static const std::string& CudaTempDirectory() {
static const std::string key = "CudaTempDirectory";
static const std::string key = "TempDirectory";
return key;
}
/**
* This is the name of the parameter for selecting whether to disable use of a separate stream for PME.
*/
static const std::string& CudaDisablePmeStream() {
static const std::string key = "CudaDisablePmeStream";
static const std::string key = "DisablePmeStream";
return key;
}
/**
* This is the name of the parameter for requesting that force computations be fully deterministic.
*/
static const std::string& CudaDeterministicForces() {
static const std::string key = "DeterministicForces";
return key;
}
};
......@@ -123,14 +130,14 @@ class OPENMM_EXPORT_CUDA CudaPlatform::PlatformData {
public:
PlatformData(ContextImpl* context, const System& system, const std::string& deviceIndexProperty, const std::string& blockingProperty, const std::string& precisionProperty,
const std::string& cpuPmeProperty, const std::string& compilerProperty, const std::string& tempProperty, const std::string& hostCompilerProperty,
const std::string& pmeStreamProperty, int numThreads);
const std::string& pmeStreamProperty, const std::string& deterministicForcesProperty, int numThreads);
~PlatformData();
void initializeContexts(const System& system);
void syncContexts();
ContextImpl* context;
std::vector<CudaContext*> contexts;
std::vector<double> contextEnergy;
bool hasInitializedContexts, removeCM, peerAccessSupported, useCpuPme, disablePmeStream;
bool hasInitializedContexts, removeCM, peerAccessSupported, useCpuPme, disablePmeStream, deterministicForces;
int cmMotionFrequency;
int stepCount, computeForceCount;
double time;
......
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