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Commit fd473eea authored by Peter Eastman's avatar Peter Eastman
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Merge branch 'master' into nucleic

parents 0a751b5b 6a985cfd
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Showing with 443 additions and 2202 deletions
platforms/cpu/include/CpuNeighborList.h
View file @ fd473eea
......@@ -35,6 +35,7 @@
#include "AlignedArray.h"
#include "RealVec.h"
#include "windowsExportCpu.h"
#include "openmm/internal/gmx_atomic.h"
#include "openmm/internal/ThreadPool.h"
#include <set>
#include <utility>
......@@ -74,6 +75,7 @@ private:
int numAtoms;
bool usePeriodic;
float maxDistance;
gmx_atomic_t atomicCounter;
};
} // namespace OpenMM
......
platforms/cpu/sharedTarget/CMakeLists.txt
View file @ fd473eea
......@@ -18,6 +18,6 @@ ENDFOREACH(file)
ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_SHARED_LIBRARY")
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_SHARED_LIBRARY")
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
platforms/cpu/src/CpuCustomGBForce.cpp
View file @ fd473eea
......@@ -28,7 +28,7 @@
#include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h"
#include "CpuCustomGBForce.h"
#include "gmx_atomic.h"
#include "openmm/internal/gmx_atomic.h"
using namespace OpenMM;
using namespace std;
......
platforms/cpu/src/CpuCustomManyParticleForce.cpp
View file @ fd473eea
......@@ -32,7 +32,7 @@
#include "ReferenceTabulatedFunction.h"
#include "openmm/internal/CustomManyParticleForceImpl.h"
#include "lepton/CustomFunction.h"
#include "gmx_atomic.h"
#include "openmm/internal/gmx_atomic.h"
using namespace OpenMM;
using namespace std;
......
platforms/cpu/src/CpuCustomNonbondedForce.cpp
View file @ fd473eea
......@@ -28,7 +28,7 @@
#include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h"
#include "CpuCustomNonbondedForce.h"
#include "gmx_atomic.h"
#include "openmm/internal/gmx_atomic.h"
using namespace OpenMM;
using namespace std;
......
platforms/cpu/src/CpuGBSAOBCForce.cpp
View file @ fd473eea
......@@ -25,7 +25,7 @@
#include "CpuGBSAOBCForce.h"
#include "SimTKOpenMMRealType.h"
#include "openmm/internal/vectorize.h"
#include "gmx_atomic.h"
#include "openmm/internal/gmx_atomic.h"
#include <algorithm>
#include <cmath>
#include <cstdlib>
......@@ -279,7 +279,7 @@ void CpuGBSAOBCForce::threadComputeForce(ThreadPool& threads, int threadIndex) {
fvec4 r = sqrt(r2);
fvec4 alpha2_ij = radii*bornRadii[atomJ];
fvec4 D_ij = r2/(4.0f*alpha2_ij);
fvec4 expTerm(expf(-D_ij[0]), expf(-D_ij[1]), expf(-D_ij[2]), expf(-D_ij[3]));
fvec4 expTerm = exp(-D_ij);
fvec4 denominator2 = r2 + alpha2_ij*expTerm;
fvec4 denominator = sqrt(denominator2);
fvec4 Gpol = (partialChargeI*posJ[3])/denominator;
......
platforms/cpu/src/CpuKernelFactory.cpp
View file @ fd473eea
......@@ -41,6 +41,8 @@ KernelImpl* CpuKernelFactory::createKernelImpl(std::string name, const Platform&
CpuPlatform::PlatformData& data = CpuPlatform::getPlatformData(context);
if (name == CalcForcesAndEnergyKernel::Name())
return new CpuCalcForcesAndEnergyKernel(name, platform, data, context);
if (name == CalcHarmonicAngleForceKernel::Name())
return new CpuCalcHarmonicAngleForceKernel(name, platform, data);
if (name == CalcPeriodicTorsionForceKernel::Name())
return new CpuCalcPeriodicTorsionForceKernel(name, platform, data);
if (name == CalcRBTorsionForceKernel::Name())
......
platforms/cpu/src/CpuKernels.cpp
View file @ fd473eea
......@@ -30,6 +30,7 @@
* -------------------------------------------------------------------------- */
#include "CpuKernels.h"
#include "ReferenceAngleBondIxn.h"
#include "ReferenceBondForce.h"
#include "ReferenceConstraints.h"
#include "ReferenceKernelFactory.h"
......@@ -47,6 +48,7 @@
#include "RealVec.h"
#include "lepton/CompiledExpression.h"
#include "lepton/CustomFunction.h"
#include "lepton/Operation.h"
#include "lepton/Parser.h"
#include "lepton/ParsedExpression.h"
......@@ -83,6 +85,17 @@ static ReferenceConstraints& extractConstraints(ContextImpl& context) {
return *(ReferenceConstraints*) data->constraints;
}
/**
* Make sure an expression doesn't use any undefined variables.
*/
static void validateVariables(const Lepton::ExpressionTreeNode& node, const set<string>& variables) {
const Lepton::Operation& op = node.getOperation();
if (op.getId() == Lepton::Operation::VARIABLE && variables.find(op.getName()) == variables.end())
throw OpenMMException("Unknown variable in expression: "+op.getName());
for (int i = 0; i < (int) node.getChildren().size(); i++)
validateVariables(node.getChildren()[i], variables);
}
/**
* Compute the kinetic energy of the system, possibly shifting the velocities in time to account
* for a leapfrog integrator.
......@@ -240,6 +253,64 @@ double CpuCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, boo
return referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().finishComputation(context, includeForce, includeEnergy, groups, valid);
}
CpuCalcHarmonicAngleForceKernel::~CpuCalcHarmonicAngleForceKernel() {
if (angleIndexArray != NULL) {
for (int i = 0; i < numAngles; i++) {
delete[] angleIndexArray[i];
delete[] angleParamArray[i];
}
delete[] angleIndexArray;
delete[] angleParamArray;
}
}
void CpuCalcHarmonicAngleForceKernel::initialize(const System& system, const HarmonicAngleForce& force) {
numAngles = force.getNumAngles();
angleIndexArray = new int*[numAngles];
for (int i = 0; i < numAngles; i++)
angleIndexArray[i] = new int[3];
angleParamArray = new RealOpenMM*[numAngles];
for (int i = 0; i < numAngles; i++)
angleParamArray[i] = new RealOpenMM[2];
for (int i = 0; i < numAngles; ++i) {
int particle1, particle2, particle3;
double angle, k;
force.getAngleParameters(i, particle1, particle2, particle3, angle, k);
angleIndexArray[i][0] = particle1;
angleIndexArray[i][1] = particle2;
angleIndexArray[i][2] = particle3;
angleParamArray[i][0] = (RealOpenMM) angle;
angleParamArray[i][1] = (RealOpenMM) k;
}
bondForce.initialize(system.getNumParticles(), numAngles, 3, angleIndexArray, data.threads);
}
double CpuCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = 0;
ReferenceAngleBondIxn angleBond;
bondForce.calculateForce(posData, angleParamArray, forceData, includeEnergy ? &energy : NULL, angleBond);
return energy;
}
void CpuCalcHarmonicAngleForceKernel::copyParametersToContext(ContextImpl& context, const HarmonicAngleForce& force) {
if (numAngles != force.getNumAngles())
throw OpenMMException("updateParametersInContext: The number of angles has changed");
// Record the values.
for (int i = 0; i < numAngles; ++i) {
int particle1, particle2, particle3;
double angle, k;
force.getAngleParameters(i, particle1, particle2, particle3, angle, k);
if (particle1 != angleIndexArray[i][0] || particle2 != angleIndexArray[i][1] || particle3 != angleIndexArray[i][2])
throw OpenMMException("updateParametersInContext: The set of particles in an angle has changed");
angleParamArray[i][0] = (RealOpenMM) angle;
angleParamArray[i][1] = (RealOpenMM) k;
}
}
CpuCalcPeriodicTorsionForceKernel::~CpuCalcPeriodicTorsionForceKernel() {
if (torsionIndexArray != NULL) {
for (int i = 0; i < numTorsions; i++) {
......@@ -467,6 +538,7 @@ void CpuCalcNonbondedForceKernel::initialize(const System& system, const Nonbond
bonded14ParamArray[i][1] = static_cast<RealOpenMM>(4.0*depth);
bonded14ParamArray[i][2] = static_cast<RealOpenMM>(charge);
}
bondForce.initialize(system.getNumParticles(), num14, 2, bonded14IndexArray, data.threads);
// Record other parameters.
......@@ -527,7 +599,7 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
if (nonbondedMethod != NoCutoff) {
// Determine whether we need to recompute the neighbor list.
double padding = 0.15*nonbondedCutoff;
double padding = 0.25*nonbondedCutoff;
bool needRecompute = false;
double closeCutoff2 = 0.25*padding*padding;
double farCutoff2 = 0.5*padding*padding;
......@@ -599,9 +671,8 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
}
energy += nonbondedEnergy;
if (includeDirect) {
ReferenceBondForce refBondForce;
ReferenceLJCoulomb14 nonbonded14;
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, includeEnergy ? &energy : NULL, nonbonded14);
bondForce.calculateForce(posData, bonded14ParamArray, forceData, includeEnergy ? &energy : NULL, nonbonded14);
if (data.isPeriodic)
energy += dispersionCoefficient/(boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2]);
}
......@@ -654,6 +725,19 @@ void CpuCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context,
dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(context.getSystem(), force);
}
void CpuCalcNonbondedForceKernel::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
if (nonbondedMethod != PME)
throw OpenMMException("getPMEParametersInContext: This Context is not using PME");
if (useOptimizedPme)
optimizedPme.getAs<const CalcPmeReciprocalForceKernel>().getPMEParameters(alpha, nx, ny, nz);
else {
alpha = ewaldAlpha;
nx = gridSize[0];
ny = gridSize[1];
nz = gridSize[2];
}
}
CpuCalcCustomNonbondedForceKernel::CpuCalcCustomNonbondedForceKernel(string name, const Platform& platform, CpuPlatform::PlatformData& data) :
CalcCustomNonbondedForceKernel(name, platform), data(data), forceCopy(NULL), neighborList(NULL), nonbonded(NULL) {
}
......@@ -724,6 +808,14 @@ void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const C
globalParameterNames.push_back(force.getGlobalParameterName(i));
globalParamValues[force.getGlobalParameterName(i)] = force.getGlobalParameterDefaultValue(i);
}
set<string> variables;
variables.insert("r");
for (int i = 0; i < numParameters; i++) {
variables.insert(parameterNames[i]+"1");
variables.insert(parameterNames[i]+"2");
}
variables.insert(globalParameterNames.begin(), globalParameterNames.end());
validateVariables(expression.getRootNode(), variables);
// Delete the custom functions.
......@@ -937,6 +1029,18 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
vector<vector<Lepton::CompiledExpression> > valueGradientExpressions(force.getNumComputedValues());
vector<Lepton::CompiledExpression> valueExpressions;
vector<Lepton::CompiledExpression> energyExpressions;
set<string> particleVariables, pairVariables;
pairVariables.insert("r");
particleVariables.insert("x");
particleVariables.insert("y");
particleVariables.insert("z");
for (int i = 0; i < numPerParticleParameters; i++) {
particleVariables.insert(particleParameterNames[i]);
pairVariables.insert(particleParameterNames[i]+"1");
pairVariables.insert(particleParameterNames[i]+"2");
}
particleVariables.insert(globalParameterNames.begin(), globalParameterNames.end());
pairVariables.insert(globalParameterNames.begin(), globalParameterNames.end());
for (int i = 0; i < force.getNumComputedValues(); i++) {
string name, expression;
CustomGBForce::ComputationType type;
......@@ -945,15 +1049,21 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
valueExpressions.push_back(ex.createCompiledExpression());
valueTypes.push_back(type);
valueNames.push_back(name);
if (i == 0)
if (i == 0) {
valueDerivExpressions[i].push_back(ex.differentiate("r").createCompiledExpression());
validateVariables(ex.getRootNode(), pairVariables);
}
else {
valueGradientExpressions[i].push_back(ex.differentiate("x").createCompiledExpression());
valueGradientExpressions[i].push_back(ex.differentiate("y").createCompiledExpression());
valueGradientExpressions[i].push_back(ex.differentiate("z").createCompiledExpression());
for (int j = 0; j < i; j++)
valueDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).createCompiledExpression());
validateVariables(ex.getRootNode(), particleVariables);
}
particleVariables.insert(name);
pairVariables.insert(name+"1");
pairVariables.insert(name+"2");
}
// Parse the expressions for energy terms.
......@@ -975,10 +1085,12 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
energyGradientExpressions[i].push_back(ex.differentiate("x").createCompiledExpression());
energyGradientExpressions[i].push_back(ex.differentiate("y").createCompiledExpression());
energyGradientExpressions[i].push_back(ex.differentiate("z").createCompiledExpression());
validateVariables(ex.getRootNode(), particleVariables);
}
else {
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"1").createCompiledExpression());
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"2").createCompiledExpression());
validateVariables(ex.getRootNode(), pairVariables);
}
}
}
......
platforms/cpu/src/CpuLangevinDynamics.cpp
View file @ fd473eea
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
* Authors: Peter Eastman
* Contributors:
*
......@@ -49,6 +49,16 @@ public:
CpuLangevinDynamics& owner;
};
class CpuLangevinDynamics::Update3Task : public ThreadPool::Task {
public:
Update3Task(CpuLangevinDynamics& owner) : owner(owner) {
}
void execute(ThreadPool& threads, int threadIndex) {
owner.threadUpdate3(threadIndex);
}
CpuLangevinDynamics& owner;
};
CpuLangevinDynamics::CpuLangevinDynamics(int numberOfAtoms, RealOpenMM deltaT, RealOpenMM tau, RealOpenMM temperature, ThreadPool& threads, CpuRandom& random) :
ReferenceStochasticDynamics(numberOfAtoms, deltaT, tau, temperature), threads(threads), random(random) {
}
......@@ -92,6 +102,23 @@ void CpuLangevinDynamics::updatePart2(int numberOfAtoms, vector<RealVec>& atomCo
threads.waitForThreads();
}
void CpuLangevinDynamics::updatePart3(int numberOfAtoms, vector<RealVec>& atomCoordinates, vector<RealVec>& velocities,
vector<RealOpenMM>& inverseMasses, vector<RealVec>& xPrime) {
// Record the parameters for the threads.
this->numberOfAtoms = numberOfAtoms;
this->atomCoordinates = &atomCoordinates[0];
this->velocities = &velocities[0];
this->inverseMasses = &inverseMasses[0];
this->xPrime = &xPrime[0];
// Signal the threads to start running and wait for them to finish.
Update3Task task(*this);
threads.execute(task);
threads.waitForThreads();
}
void CpuLangevinDynamics::threadUpdate1(int threadIndex) {
const RealOpenMM tau = getTau();
const RealOpenMM vscale = EXP(-getDeltaT()/tau);
......@@ -122,3 +149,16 @@ void CpuLangevinDynamics::threadUpdate2(int threadIndex) {
}
}
}
void CpuLangevinDynamics::threadUpdate3(int threadIndex) {
const RealOpenMM invStepSize = 1.0/getDeltaT();
int start = threadIndex*numberOfAtoms/threads.getNumThreads();
int end = (threadIndex+1)*numberOfAtoms/threads.getNumThreads();
for (int i = start; i < end; ++i)
if (inverseMasses[i] != 0.0) {
velocities[i] = (xPrime[i]-atomCoordinates[i])*invStepSize;
atomCoordinates[i] = xPrime[i];
}
}
platforms/cpu/src/CpuNeighborList.cpp
View file @ fd473eea
......@@ -59,22 +59,25 @@ public:
*/
class CpuNeighborList::Voxels {
public:
Voxels(int blockSize, float vsy, float vsz, float miny, float maxy, float minz, float maxz, const RealVec* periodicBoxVectors, bool usePeriodic) :
blockSize(blockSize), voxelSizeY(vsy), voxelSizeZ(vsz), miny(miny), maxy(maxy), minz(minz), maxz(maxz), periodicBoxVectors(periodicBoxVectors), usePeriodic(usePeriodic) {
periodicBoxSize[0] = (float) periodicBoxVectors[0][0];
periodicBoxSize[1] = (float) periodicBoxVectors[1][1];
periodicBoxSize[2] = (float) periodicBoxVectors[2][2];
recipBoxSize[0] = (float) (1/periodicBoxVectors[0][0]);
recipBoxSize[1] = (float) (1/periodicBoxVectors[1][1]);
recipBoxSize[2] = (float) (1/periodicBoxVectors[2][2]);
triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 ||
periodicBoxVectors[1][0] != 0.0 || periodicBoxVectors[1][2] != 0.0 ||
periodicBoxVectors[2][0] != 0.0 || periodicBoxVectors[2][1] != 0.0);
Voxels(int blockSize, float vsy, float vsz, float miny, float maxy, float minz, float maxz, const RealVec* boxVectors, bool usePeriodic) :
blockSize(blockSize), voxelSizeY(vsy), voxelSizeZ(vsz), miny(miny), maxy(maxy), minz(minz), maxz(maxz), usePeriodic(usePeriodic) {
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
periodicBoxVectors[i][j] = (float) boxVectors[i][j];
periodicBoxSize[0] = (float) boxVectors[0][0];
periodicBoxSize[1] = (float) boxVectors[1][1];
periodicBoxSize[2] = (float) boxVectors[2][2];
recipBoxSize[0] = (float) (1/boxVectors[0][0]);
recipBoxSize[1] = (float) (1/boxVectors[1][1]);
recipBoxSize[2] = (float) (1/boxVectors[2][2]);
triclinic = (boxVectors[0][1] != 0.0 || boxVectors[0][2] != 0.0 ||
boxVectors[1][0] != 0.0 || boxVectors[1][2] != 0.0 ||
boxVectors[2][0] != 0.0 || boxVectors[2][1] != 0.0);
if (usePeriodic) {
ny = (int) floorf(periodicBoxVectors[1][1]/voxelSizeY+0.5f);
nz = (int) floorf(periodicBoxVectors[2][2]/voxelSizeZ+0.5f);
voxelSizeY = periodicBoxVectors[1][1]/ny;
voxelSizeZ = periodicBoxVectors[2][2]/nz;
ny = (int) floorf(boxVectors[1][1]/voxelSizeY+0.5f);
nz = (int) floorf(boxVectors[2][2]/voxelSizeZ+0.5f);
voxelSizeY = boxVectors[1][1]/ny;
voxelSizeZ = boxVectors[2][2]/nz;
}
else {
ny = max(1, (int) floorf((maxy-miny)/voxelSizeY+0.5f));
......@@ -110,12 +113,10 @@ public:
}
/**
* Find the index of the first particle in voxel (y,z) whose x coordinate in >= the specified value.
* Find the index of the first particle in voxel (y,z) whose x coordinate is >= the specified value.
*/
int findLowerBound(int y, int z, double x) const {
int findLowerBound(int y, int z, double x, int lower, int upper) const {
const vector<pair<float, int> >& bin = bins[y][z];
int lower = 0;
int upper = bin.size();
while (lower < upper) {
int middle = (lower+upper)/2;
if (bin[middle].first < x)
......@@ -127,12 +128,10 @@ public:
}
/**
* Find the index of the first particle in voxel (y,z) whose x coordinate in greater than the specified value.
* Find the index of the first particle in voxel (y,z) whose x coordinate is greater than the specified value.
*/
int findUpperBound(int y, int z, double x) const {
int findUpperBound(int y, int z, double x, int lower, int upper) const {
const vector<pair<float, int> >& bin = bins[y][z];
int lower = 0;
int upper = bin.size();
while (lower < upper) {
int middle = (lower+upper)/2;
if (bin[middle].first > x)
......@@ -208,7 +207,7 @@ public:
// Loop over voxels along the y axis.
int boxz = (int) floor((float) z/nz);
float boxz = floor((float) z/nz);
int starty = centerVoxelIndex.y-dIndexY;
int endy = centerVoxelIndex.y+dIndexY;
float yoffset = (float) (usePeriodic ? boxz*periodicBoxVectors[2][1] : 0);
......@@ -225,7 +224,7 @@ public:
voxelIndex.y = y;
if (usePeriodic)
voxelIndex.y = (y < 0 ? y+ny : (y >= ny ? y-ny : y));
int boxy = (int) floor((float) y/ny);
float boxy = floor((float) y/ny);
float xoffset = (float) (usePeriodic ? boxy*periodicBoxVectors[1][0]+boxz*periodicBoxVectors[2][0] : 0);
// Identify the range of atoms within this bin we need to search. When using periodic boundary
......@@ -261,30 +260,34 @@ public:
int numRanges;
int rangeStart[2];
int rangeEnd[2];
rangeStart[0] = findLowerBound(voxelIndex.y, voxelIndex.z, minx);
int binSize = bins[voxelIndex.y][voxelIndex.z].size();
rangeStart[0] = findLowerBound(voxelIndex.y, voxelIndex.z, minx, 0, binSize);
if (needPeriodic) {
numRanges = 2;
rangeEnd[0] = findUpperBound(voxelIndex.y, voxelIndex.z, maxx);
if (rangeStart[0] > 0) {
rangeEnd[0] = findUpperBound(voxelIndex.y, voxelIndex.z, maxx, rangeStart[0], binSize);
if (rangeStart[0] > 0 && rangeEnd[0] < binSize)
numRanges = 1;
else if (rangeStart[0] > 0) {
rangeStart[1] = 0;
rangeEnd[1] = min(findUpperBound(voxelIndex.y, voxelIndex.z, maxx-periodicBoxSize[0]), rangeStart[0]);
rangeEnd[1] = min(findUpperBound(voxelIndex.y, voxelIndex.z, maxx-periodicBoxSize[0], 0, rangeStart[0]), rangeStart[0]);
}
else {
rangeStart[1] = max(findLowerBound(voxelIndex.y, voxelIndex.z, minx+periodicBoxSize[0]), rangeEnd[0]);
rangeStart[1] = max(findLowerBound(voxelIndex.y, voxelIndex.z, minx+periodicBoxSize[0], rangeEnd[0], binSize), rangeEnd[0]);
rangeEnd[1] = bins[voxelIndex.y][voxelIndex.z].size();
}
}
else {
numRanges = 1;
rangeEnd[0] = findUpperBound(voxelIndex.y, voxelIndex.z, maxx);
rangeEnd[0] = findUpperBound(voxelIndex.y, voxelIndex.z, maxx, rangeStart[0], binSize);
}
bool periodicRectangular = (needPeriodic && !triclinic);
// Loop over atoms and check to see if they are neighbors of this block.
const vector<pair<float, int> >& voxelBins = bins[voxelIndex.y][voxelIndex.z];
for (int range = 0; range < numRanges; range++) {
for (int item = rangeStart[range]; item < rangeEnd[range]; item++) {
const int sortedIndex = bins[voxelIndex.y][voxelIndex.z][item].second;
const int sortedIndex = voxelBins[item].second;
// Avoid duplicate entries.
if (sortedIndex >= lastSortedIndex)
......@@ -361,7 +364,7 @@ private:
int ny, nz;
float periodicBoxSize[3], recipBoxSize[3];
bool triclinic;
const RealVec* periodicBoxVectors;
float periodicBoxVectors[3][3];
const bool usePeriodic;
vector<vector<vector<pair<float, int> > > > bins;
};
......@@ -444,6 +447,7 @@ void CpuNeighborList::computeNeighborList(int numAtoms, const AlignedArray<float
// Signal the threads to start running and wait for them to finish.
gmx_atomic_set(&atomicCounter, 0);
threads.resumeThreads();
threads.waitForThreads();
......@@ -500,7 +504,11 @@ void CpuNeighborList::threadComputeNeighborList(ThreadPool& threads, int threadI
vector<int> blockAtoms;
vector<float> blockAtomX(blockSize), blockAtomY(blockSize), blockAtomZ(blockSize);
vector<VoxelIndex> atomVoxelIndex;
for (int i = threadIndex; i < numBlocks; i += numThreads) {
while (true) {
int i = gmx_atomic_fetch_add(&atomicCounter, 1);
if (i >= numBlocks)
break;
// Find the atoms in this block and compute their bounding box.
int firstIndex = blockSize*i;
......@@ -532,14 +540,24 @@ void CpuNeighborList::threadComputeNeighborList(ThreadPool& threads, int threadI
// Record the exclusions for this block.
map<int, char> atomFlags;
for (int j = 0; j < atomsInBlock; j++) {
const set<int>& atomExclusions = (*exclusions)[sortedAtoms[firstIndex+j]];
char mask = 1<<j;
for (int k = 0; k < (int) blockNeighbors[i].size(); k++) {
int atomIndex = blockNeighbors[i][k];
if (atomExclusions.find(atomIndex) != atomExclusions.end())
blockExclusions[i][k] |= mask;
for (set<int>::const_iterator iter = atomExclusions.begin(); iter != atomExclusions.end(); ++iter) {
map<int, char>::iterator thisAtomFlags = atomFlags.find(*iter);
if (thisAtomFlags == atomFlags.end())
atomFlags[*iter] = mask;
else
thisAtomFlags->second |= mask;
}
}
int numNeighbors = blockNeighbors[i].size();
for (int k = 0; k < numNeighbors; k++) {
int atomIndex = blockNeighbors[i][k];
map<int, char>::iterator thisAtomFlags = atomFlags.find(atomIndex);
if (thisAtomFlags != atomFlags.end())
blockExclusions[i][k] |= thisAtomFlags->second;
}
}
}
......
platforms/cpu/src/CpuNonbondedForce.cpp
View file @ fd473eea
......@@ -28,7 +28,7 @@
#include "CpuNonbondedForce.h"
#include "ReferenceForce.h"
#include "ReferencePME.h"
#include "gmx_atomic.h"
#include "openmm/internal/gmx_atomic.h"
#include <algorithm>
// In case we're using some primitive version of Visual Studio this will
......@@ -322,6 +322,14 @@ void CpuNonbondedForce::calculateDirectIxn(int numberOfAtoms, float* posq, const
threads.execute(task);
threads.waitForThreads();
// Signal the threads to subtract the exclusions.
if (ewald || pme) {
gmx_atomic_set(&counter, 0);
threads.resumeThreads();
threads.waitForThreads();
}
// Combine the energies from all the threads.
if (totalEnergy != NULL) {
......@@ -354,8 +362,16 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex
// Now subtract off the exclusions, since they were implicitly included in the reciprocal space sum.
for (int i = threadIndex; i < numberOfAtoms; i += numThreads) {
threads.syncThreads();
const int groupSize = max(1, numberOfAtoms/(10*numThreads));
while (true) {
int start = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), groupSize);
if (start >= numberOfAtoms)
break;
int end = min(start+groupSize, numberOfAtoms);
for (int i = start; i < end; i++) {
fvec4 posI((float) atomCoordinates[i][0], (float) atomCoordinates[i][1], (float) atomCoordinates[i][2], 0.0f);
float scaledChargeI = (float) (ONE_4PI_EPS0*posq[4*i+3]);
for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter) {
if (*iter > i) {
int j = *iter;
......@@ -364,18 +380,19 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex
float r2;
getDeltaR(posJ, posI, deltaR, r2, false, boxSize, invBoxSize);
float r = sqrtf(r2);
float inverseR = 1/r;
float chargeProd = ONE_4PI_EPS0*posq[4*i+3]*posq[4*j+3];
float alphaR = alphaEwald*r;
float erfAlphaR = erf(alphaR);
if (erfAlphaR > 1e-6f) {
float dEdR = (float) (chargeProd * inverseR * inverseR * inverseR);
dEdR = (float) (dEdR * (erfAlphaR-TWO_OVER_SQRT_PI*alphaR*exp(-alphaR*alphaR)));
float inverseR = 1/r;
float chargeProdOverR = scaledChargeI*posq[4*j+3]*inverseR;
float dEdR = chargeProdOverR*inverseR*inverseR;
dEdR = dEdR * (erfAlphaR-(float)TWO_OVER_SQRT_PI*alphaR*(float)exp(-alphaR*alphaR));
fvec4 result = deltaR*dEdR;
(fvec4(forces+4*i)-result).store(forces+4*i);
(fvec4(forces+4*j)+result).store(forces+4*j);
if (includeEnergy)
threadEnergy[threadIndex] -= chargeProd*inverseR*erfAlphaR;
threadEnergy[threadIndex] -= chargeProdOverR*erfAlphaR;
}
}
}
}
......
platforms/cpu/src/CpuPlatform.cpp
View file @ fd473eea
......@@ -61,6 +61,7 @@ map<const ContextImpl*, CpuPlatform::PlatformData*> CpuPlatform::contextData;
CpuPlatform::CpuPlatform() {
CpuKernelFactory* factory = new CpuKernelFactory();
registerKernelFactory(CalcForcesAndEnergyKernel::Name(), factory);
registerKernelFactory(CalcHarmonicAngleForceKernel::Name(), factory);
registerKernelFactory(CalcPeriodicTorsionForceKernel::Name(), factory);
registerKernelFactory(CalcRBTorsionForceKernel::Name(), factory);
registerKernelFactory(CalcNonbondedForceKernel::Name(), factory);
......
platforms/cpu/src/CpuSETTLE.cpp
View file @ fd473eea
......@@ -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 Stanford University and the Authors. *
* Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -30,6 +30,7 @@
* -------------------------------------------------------------------------- */
#include "CpuSETTLE.h"
#include "openmm/internal/gmx_atomic.h"
using namespace OpenMM;
using namespace std;
......@@ -39,10 +40,14 @@ public:
ApplyToPositionsTask(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses,
RealOpenMM tolerance, vector<ReferenceSETTLEAlgorithm*>& threadSettle) : atomCoordinates(atomCoordinates), atomCoordinatesP(atomCoordinatesP),
inverseMasses(inverseMasses), tolerance(tolerance), threadSettle(threadSettle) {
gmx_atomic_set(&atomicCounter, 0);
}
void execute(ThreadPool& threads, int threadIndex) {
if (threadIndex < threadSettle.size()) {
threadSettle[threadIndex]->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
while (true) {
int index = gmx_atomic_fetch_add(&atomicCounter, 1);
if (index >= threadSettle.size())
break;
threadSettle[index]->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
}
}
vector<OpenMM::RealVec>& atomCoordinates;
......@@ -50,6 +55,7 @@ public:
vector<RealOpenMM>& inverseMasses;
RealOpenMM tolerance;
vector<ReferenceSETTLEAlgorithm*>& threadSettle;
gmx_atomic_t atomicCounter;
};
class CpuSETTLE::ApplyToVelocitiesTask : public ThreadPool::Task {
......@@ -57,10 +63,14 @@ public:
ApplyToVelocitiesTask(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses,
RealOpenMM tolerance, vector<ReferenceSETTLEAlgorithm*>& threadSettle) : atomCoordinates(atomCoordinates), velocities(velocities),
inverseMasses(inverseMasses), tolerance(tolerance), threadSettle(threadSettle) {
gmx_atomic_set(&atomicCounter, 0);
}
void execute(ThreadPool& threads, int threadIndex) {
if (threadIndex < threadSettle.size()) {
threadSettle[threadIndex]->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
while (true) {
int index = gmx_atomic_fetch_add(&atomicCounter, 1);
if (index >= threadSettle.size())
break;
threadSettle[index]->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
}
}
vector<OpenMM::RealVec>& atomCoordinates;
......@@ -68,17 +78,18 @@ public:
vector<RealOpenMM>& inverseMasses;
RealOpenMM tolerance;
vector<ReferenceSETTLEAlgorithm*>& threadSettle;
gmx_atomic_t atomicCounter;
};
CpuSETTLE::CpuSETTLE(const System& system, const ReferenceSETTLEAlgorithm& settle, ThreadPool& threads) : threads(threads) {
int numThreads = threads.getNumThreads();
int numBlocks = 10*threads.getNumThreads();
int numClusters = settle.getNumClusters();
vector<RealOpenMM> mass(system.getNumParticles());
for (int i = 0; i < system.getNumParticles(); i++)
mass[i] = system.getParticleMass(i);
for (int i = 0; i < numThreads; i++) {
int start = i*numClusters/numThreads;
int end = (i+1)*numClusters/numThreads;
for (int i = 0; i < numBlocks; i++) {
int start = i*numClusters/numBlocks;
int end = (i+1)*numClusters/numBlocks;
if (start != end) {
int numThreadClusters = end-start;
vector<int> atom1(numThreadClusters), atom2(numThreadClusters), atom3(numThreadClusters);
......
platforms/cpu/staticTarget/CMakeLists.txt
View file @ fd473eea
......@@ -17,6 +17,6 @@ ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${AP
TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME}_static ${PTHREADS_LIB_STATIC})
#-DPTW32_STATIC_LIB only works for the windows pthreads.
SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_STATIC_LIBRARY -DPTW32_STATIC_LIB")
SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_STATIC_LIBRARY -DPTW32_STATIC_LIB")
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${STATIC_TARGET})
platforms/cpu/tests/CMakeLists.txt
View file @ fd473eea
......@@ -23,7 +23,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
ELSE (OPENMM_BUILD_SHARED_LIB)
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${STATIC_TARGET})
ENDIF (OPENMM_BUILD_SHARED_LIB)
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
ENDFOREACH(TEST_PROG ${TEST_PROGS})
platforms/cpu/tests/CpuTests.h 0 → 100644
View file @ fd473eea
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "CpuPlatform.h"
#include <cstdlib>
#include <iostream>
OpenMM::CpuPlatform platform;
void initializeTests(int argc, char* argv[]) {
if (!OpenMM::CpuPlatform::isProcessorSupported()) {
std::cout << "CPU is not supported. Exiting." << std::endl;
exit(0);
}
}
platforms/cpu/tests/TestCpuCheckpoints.cpp 0 → 100644
View file @ fd473eea
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2012-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "CpuTests.h"
#include "TestCheckpoints.h"
void testCheckpoint() {
const int numParticles = 100;
const double boxSize = 5.0;
const double temperature = 200.0;
System system;
system.addForce(new AndersenThermostat(0.0, 100.0));
NonbondedForce* nonbonded = new NonbondedForce();
system.addForce(nonbonded);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
nonbonded->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.2, 0.1);
bool clash;
do {
clash = false;
positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
for (int j = 0; j < i; j++) {
Vec3 delta = positions[i]-positions[j];
if (sqrt(delta.dot(delta)) < 0.1)
clash = true;
}
} while (clash);
}
VerletIntegrator integrator(0.001);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
context.setParameter(AndersenThermostat::Temperature(), temperature);
// Run for a little while.
integrator.step(100);
// Record the current state and make a checkpoint.
State s1 = context.getState(State::Positions | State::Velocities | State::Parameters);
stringstream stream1(ios_base::out | ios_base::in | ios_base::binary);
context.createCheckpoint(stream1);
// Continue the simulation for a few more steps and record the state again.
integrator.step(10);
State s2 = context.getState(State::Positions | State::Velocities | State::Parameters);
// Restore from the checkpoint and see if everything gets restored correctly.
context.setPeriodicBoxVectors(Vec3(2*boxSize, 0, 0), Vec3(0, 2*boxSize, 0), Vec3(0, 0, 2*boxSize));
context.setParameter(AndersenThermostat::Temperature(), temperature+10);
context.loadCheckpoint(stream1);
State s3 = context.getState(State::Positions | State::Velocities | State::Parameters);
compareStates(s1, s3);
// Now simulate from there and see if the trajectory is identical.
integrator.step(10);
State s4 = context.getState(State::Positions | State::Velocities | State::Parameters);
compareStates(s2, s4);
}
void runPlatformTests() {
testCheckpoint();
}
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