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"...openmmapi/src/AmoebaHarmonicInPlaneAngleForceImpl.cpp" did not exist on "3d750e8517a73f39fce1de63a5f36d26f6a3d38c"
Commit 94ecc958 authored by Peter Eastman's avatar Peter Eastman
Browse files

OpenCL implementation of virtual sites

parent bfc1b529
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Showing with 818 additions and 34 deletions
platforms/opencl/src/OpenCLContext.cpp
View file @ 94ecc958
......@@ -38,10 +38,12 @@
#include "hilbert.h"
#include "openmm/Platform.h"
#include "openmm/System.h"
#include "openmm/VirtualSite.h"
#include <algorithm>
#include <fstream>
#include <iostream>
#include <sstream>
#include <typeinfo>
using namespace OpenMM;
using namespace std;
......@@ -230,8 +232,10 @@ OpenCLContext::~OpenCLContext() {
}
void OpenCLContext::initialize(const System& system) {
for (int i = 0; i < numAtoms; i++)
(*velm)[i].w = (float) (1.0/system.getParticleMass(i));
for (int i = 0; i < numAtoms; i++) {
double mass = system.getParticleMass(i);
(*velm)[i].w = (float) (mass == 0.0 ? 0.0 : 1.0/mass);
}
velm->upload();
bonded->initialize(system);
numForceBuffers = platformData.contexts.size();
......@@ -462,7 +466,77 @@ struct OpenCLContext::Molecule {
vector<vector<int> > groups;
};
/**
* This class ensures that atom reordering doesn't break virtual sites.
*/
class OpenCLContext::VirtualSiteInfo : public OpenCLForceInfo {
public:
VirtualSiteInfo(const System& system) : OpenCLForceInfo(0) {
for (int i = 0; i < system.getNumParticles(); i++) {
if (system.isVirtualSite(i)) {
siteTypes.push_back(&typeid(system.getVirtualSite(i)));
vector<int> particles;
particles.push_back(i);
for (int j = 0; j < system.getVirtualSite(i).getNumParticles(); j++)
particles.push_back(system.getVirtualSite(i).getParticle(j));
siteParticles.push_back(particles);
vector<double> weights;
if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
// A two particle average.
const TwoParticleAverageSite& site = dynamic_cast<const TwoParticleAverageSite&>(system.getVirtualSite(i));
weights.push_back(site.getWeight(0));
weights.push_back(site.getWeight(1));
}
else if (dynamic_cast<const ThreeParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
// A three particle average.
const ThreeParticleAverageSite& site = dynamic_cast<const ThreeParticleAverageSite&>(system.getVirtualSite(i));
weights.push_back(site.getWeight(0));
weights.push_back(site.getWeight(1));
weights.push_back(site.getWeight(2));
}
else if (dynamic_cast<const OutOfPlaneSite*>(&system.getVirtualSite(i)) != NULL) {
// An out of plane site.
const OutOfPlaneSite& site = dynamic_cast<const OutOfPlaneSite&>(system.getVirtualSite(i));
weights.push_back(site.getWeight12());
weights.push_back(site.getWeight13());
weights.push_back(site.getWeightCross());
}
siteWeights.push_back(weights);
}
}
}
int getNumParticleGroups() {
return siteTypes.size();
}
void getParticlesInGroup(int index, std::vector<int>& particles) {
particles = siteParticles[index];
}
bool areGroupsIdentical(int group1, int group2) {
if (siteTypes[group1] != siteTypes[group2])
return false;
int numParticles = siteWeights[group1].size();
if (siteWeights[group2].size() != numParticles)
return false;
for (int i = 0; i < numParticles; i++)
if (siteWeights[group1][i] != siteWeights[group2][i])
return false;
return true;
}
private:
vector<const type_info*> siteTypes;
vector<vector<int> > siteParticles;
vector<vector<double> > siteWeights;
};
void OpenCLContext::findMoleculeGroups(const System& system) {
// Add a ForceInfo that makes sure reordering doesn't break virtual sites.
addForce(new VirtualSiteInfo(system));
// First make a list of every other atom to which each atom is connect by a constraint or force group.
vector<vector<int> > atomBonds(system.getNumParticles());
......
platforms/opencl/src/OpenCLContext.h
View file @ 94ecc958
......@@ -476,6 +476,7 @@ public:
private:
struct Molecule;
struct MoleculeGroup;
class VirtualSiteInfo;
void findMoleculeGroups(const System& system);
static void tagAtomsInMolecule(int atom, int molecule, std::vector<int>& atomMolecule, std::vector<std::vector<int> >& atomBonds);
double time;
......
platforms/opencl/src/OpenCLIntegrationUtilities.cpp
View file @ 94ecc958
......@@ -28,6 +28,7 @@
#include "OpenCLArray.h"
#include "OpenCLKernelSources.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/VirtualSite.h"
#include "quern.h"
#include "OpenCLExpressionUtilities.h"
#include <algorithm>
......@@ -91,10 +92,13 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
random(NULL), randomSeed(NULL), randomPos(0), stepSize(NULL), ccmaAtoms(NULL), ccmaDistance(NULL),
ccmaReducedMass(NULL), ccmaAtomConstraints(NULL), ccmaNumAtomConstraints(NULL), ccmaConstraintMatrixColumn(NULL),
ccmaConstraintMatrixValue(NULL), ccmaDelta1(NULL), ccmaDelta2(NULL), ccmaConverged(NULL),
ccmaConvergedBuffer(NULL), hasInitializedPosConstraintKernels(false), hasInitializedVelConstraintKernels(false) {
ccmaConvergedBuffer(NULL), vsite2AvgAtoms(NULL), vsite2AvgWeights(NULL), vsite3AvgAtoms(NULL), vsite3AvgWeights(NULL),
vsiteOutOfPlaneAtoms(NULL), vsiteOutOfPlaneWeights(NULL), hasInitializedPosConstraintKernels(false), hasInitializedVelConstraintKernels(false) {
// Create workspace arrays.
posDelta = new OpenCLArray<mm_float4>(context, context.getPaddedNumAtoms(), "posDelta");
vector<mm_float4> deltas(posDelta->getSize(), mm_float4(0.0, 0.0, 0.0, 0.0));
posDelta->upload(deltas);
stepSize = new OpenCLArray<mm_float2>(context, 1, "stepSize", true);
stepSize->set(0, mm_float2(0.0f, 0.0f));
stepSize->upload();
......@@ -515,6 +519,87 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
ccmaVelForceKernel = cl::Kernel(ccmaProgram, "computeConstraintForce");
ccmaVelUpdateKernel = cl::Kernel(ccmaProgram, "updateAtomPositions");
}
// Build the list of virtual sites.
vector<mm_int4> vsite2AvgAtomVec;
vector<mm_float2> vsite2AvgWeightVec;
vector<mm_int4> vsite3AvgAtomVec;
vector<mm_float4> vsite3AvgWeightVec;
vector<mm_int4> vsiteOutOfPlaneAtomVec;
vector<mm_float4> vsiteOutOfPlaneWeightVec;
for (int i = 0; i < numAtoms; i++) {
if (system.isVirtualSite(i)) {
if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
// A two particle average.
const TwoParticleAverageSite& site = dynamic_cast<const TwoParticleAverageSite&>(system.getVirtualSite(i));
vsite2AvgAtomVec.push_back(mm_int4(i, site.getParticle(0), site.getParticle(1), 0));
vsite2AvgWeightVec.push_back(mm_float2((float) site.getWeight(0), (float) site.getWeight(1)));
}
else if (dynamic_cast<const ThreeParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
// A three particle average.
const ThreeParticleAverageSite& site = dynamic_cast<const ThreeParticleAverageSite&>(system.getVirtualSite(i));
vsite3AvgAtomVec.push_back(mm_int4(i, site.getParticle(0), site.getParticle(1), site.getParticle(2)));
vsite3AvgWeightVec.push_back(mm_float4((float) site.getWeight(0), (float) site.getWeight(1), (float) site.getWeight(2), 0.0f));
}
else if (dynamic_cast<const OutOfPlaneSite*>(&system.getVirtualSite(i)) != NULL) {
// An out of plane site.
const OutOfPlaneSite& site = dynamic_cast<const OutOfPlaneSite&>(system.getVirtualSite(i));
vsiteOutOfPlaneAtomVec.push_back(mm_int4(i, site.getParticle(0), site.getParticle(1), site.getParticle(2)));
vsiteOutOfPlaneWeightVec.push_back(mm_float4((float) site.getWeight12(), (float) site.getWeight13(), (float) site.getWeightCross(), 0.0f));
}
}
}
int num2Avg = vsite2AvgAtomVec.size();
int num3Avg = vsite3AvgAtomVec.size();
int numOutOfPlane = vsiteOutOfPlaneAtomVec.size();
vsite2AvgAtoms = new OpenCLArray<mm_int4>(context, max(1, num2Avg), "vsite2AvgAtoms");
vsite2AvgWeights = new OpenCLArray<mm_float2>(context, max(1, num2Avg), "vsite2AvgWeights");
vsite3AvgAtoms = new OpenCLArray<mm_int4>(context, max(1, num3Avg), "vsite3AvgAtoms");
vsite3AvgWeights = new OpenCLArray<mm_float4>(context, max(1, num3Avg), "vsite3AvgWeights");
vsiteOutOfPlaneAtoms = new OpenCLArray<mm_int4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneAtoms");
vsiteOutOfPlaneWeights = new OpenCLArray<mm_float4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneWeights");
if (num2Avg > 0) {
vsite2AvgAtoms->upload(vsite2AvgAtomVec);
vsite2AvgWeights->upload(vsite2AvgWeightVec);
}
if (num3Avg > 0) {
vsite3AvgAtoms->upload(vsite3AvgAtomVec);
vsite3AvgWeights->upload(vsite3AvgWeightVec);
}
if (numOutOfPlane > 0) {
vsiteOutOfPlaneAtoms->upload(vsiteOutOfPlaneAtomVec);
vsiteOutOfPlaneWeights->upload(vsiteOutOfPlaneWeightVec);
}
// Create the kernels for virtual sites.
map<string, string> defines;
defines["NUM_2_AVERAGE"] = OpenCLExpressionUtilities::intToString(num2Avg);
defines["NUM_3_AVERAGE"] = OpenCLExpressionUtilities::intToString(num3Avg);
defines["NUM_OUT_OF_PLANE"] = OpenCLExpressionUtilities::intToString(numOutOfPlane);
cl::Program ccmaProgram = context.createProgram(OpenCLKernelSources::virtualSites, defines);
vsitePositionKernel = cl::Kernel(ccmaProgram, "computeVirtualSites");
vsitePositionKernel.setArg<cl::Buffer>(0, context.getPosq().getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(1, vsite2AvgAtoms->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(2, vsite2AvgWeights->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(3, vsite3AvgAtoms->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(4, vsite3AvgWeights->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(5, vsiteOutOfPlaneAtoms->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(6, vsiteOutOfPlaneWeights->getDeviceBuffer());
vsiteForceKernel = cl::Kernel(ccmaProgram, "distributeForces");
vsiteForceKernel.setArg<cl::Buffer>(0, context.getPosq().getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(1, context.getForce().getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(2, vsite2AvgAtoms->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(3, vsite2AvgWeights->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(4, vsite3AvgAtoms->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(5, vsite3AvgWeights->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(6, vsiteOutOfPlaneAtoms->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(7, vsiteOutOfPlaneWeights->getDeviceBuffer());
numVsites = num2Avg+num3Avg+numOutOfPlane;
}
OpenCLIntegrationUtilities::~OpenCLIntegrationUtilities() {
......@@ -556,6 +641,18 @@ OpenCLIntegrationUtilities::~OpenCLIntegrationUtilities() {
delete ccmaConverged;
if (ccmaConvergedBuffer != NULL)
delete ccmaConvergedBuffer;
if (vsite2AvgAtoms != NULL)
delete vsite2AvgAtoms;
if (vsite2AvgWeights != NULL)
delete vsite2AvgWeights;
if (vsite3AvgAtoms != NULL)
delete vsite3AvgAtoms;
if (vsite3AvgWeights != NULL)
delete vsite3AvgWeights;
if (vsiteOutOfPlaneAtoms != NULL)
delete vsiteOutOfPlaneAtoms;
if (vsiteOutOfPlaneWeights != NULL)
delete vsiteOutOfPlaneWeights;
}
void OpenCLIntegrationUtilities::applyConstraints(double tol) {
......@@ -660,6 +757,16 @@ void OpenCLIntegrationUtilities::applyConstraints(bool constrainVelocities, doub
}
}
void OpenCLIntegrationUtilities::computeVirtualSites() {
if (numVsites > 0)
context.executeKernel(vsitePositionKernel, numVsites);
}
void OpenCLIntegrationUtilities::distributeForcesFromVirtualSites() {
if (numVsites > 0)
context.executeKernel(vsiteForceKernel, numVsites);
}
void OpenCLIntegrationUtilities::initRandomNumberGenerator(unsigned int randomNumberSeed) {
if (random != NULL) {
if (randomNumberSeed != lastSeed)
......
platforms/opencl/src/OpenCLIntegrationUtilities.h
View file @ 94ecc958
......@@ -84,6 +84,14 @@ public:
* @return the index in the array at which to start reading
*/
int prepareRandomNumbers(int numValues);
/**
* Compute the positions of virtual sites.
*/
void computeVirtualSites();
/**
* Distribute forces from virtual sites to the atoms they are based on.
*/
void distributeForcesFromVirtualSites();
private:
void applyConstraints(bool constrainVelocities, double tol);
OpenCLContext& context;
......@@ -93,6 +101,7 @@ private:
cl::Kernel ccmaPosForceKernel, ccmaVelForceKernel;
cl::Kernel ccmaMultiplyKernel;
cl::Kernel ccmaPosUpdateKernel, ccmaVelUpdateKernel;
cl::Kernel vsitePositionKernel, vsiteForceKernel;
cl::Kernel randomKernel;
OpenCLArray<mm_float4>* posDelta;
OpenCLArray<mm_int4>* settleAtoms;
......@@ -114,8 +123,14 @@ private:
OpenCLArray<cl_int>* ccmaConverged;
cl::Buffer* ccmaConvergedBuffer;
cl_int* ccmaConvergedMemory;
OpenCLArray<mm_int4>* vsite2AvgAtoms;
OpenCLArray<mm_float2>* vsite2AvgWeights;
OpenCLArray<mm_int4>* vsite3AvgAtoms;
OpenCLArray<mm_float4>* vsite3AvgWeights;
OpenCLArray<mm_int4>* vsiteOutOfPlaneAtoms;
OpenCLArray<mm_float4>* vsiteOutOfPlaneWeights;
int randomPos;
int lastSeed;
int lastSeed, numVsites;
bool hasInitializedPosConstraintKernels, hasInitializedVelConstraintKernels;
struct ShakeCluster;
struct ConstraintOrderer;
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 94ecc958
......@@ -108,6 +108,7 @@ double OpenCLCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context,
cl.getBondedUtilities().computeInteractions();
cl.getNonbondedUtilities().computeInteractions();
cl.reduceForces();
cl.getIntegrationUtilities().distributeForcesFromVirtualSites();
double sum = 0.0f;
if (includeEnergy) {
OpenCLArray<cl_float>& energy = cl.getEnergyBuffer();
......@@ -221,6 +222,7 @@ void OpenCLApplyConstraintsKernel::initialize(const System& system) {
void OpenCLApplyConstraintsKernel::apply(ContextImpl& context, double tol) {
cl.getIntegrationUtilities().applyConstraints(tol);
cl.getIntegrationUtilities().computeVirtualSites();
}
class OpenCLBondForceInfo : public OpenCLForceInfo {
......@@ -3216,6 +3218,7 @@ void OpenCLIntegrateVerletStepKernel::execute(ContextImpl& context, const Verlet
// Call the second integration kernel.
cl.executeKernel(kernel2, numAtoms);
integration.computeVirtualSites();
// Update the time and step count.
......@@ -3292,6 +3295,7 @@ void OpenCLIntegrateLangevinStepKernel::execute(ContextImpl& context, const Lang
// Call the second integration kernel.
cl.executeKernel(kernel2, numAtoms);
integration.computeVirtualSites();
// Update the time and step count.
......@@ -3351,6 +3355,7 @@ void OpenCLIntegrateBrownianStepKernel::execute(ContextImpl& context, const Brow
// Call the second integration kernel.
cl.executeKernel(kernel2, numAtoms);
integration.computeVirtualSites();
// Update the time and step count.
......@@ -3411,6 +3416,7 @@ void OpenCLIntegrateVariableVerletStepKernel::execute(ContextImpl& context, cons
// Call the second integration kernel.
cl.executeKernel(kernel2, numAtoms);
integration.computeVirtualSites();
// Update the time and step count.
......@@ -3488,6 +3494,7 @@ void OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, co
// Call the second integration kernel.
cl.executeKernel(kernel2, numAtoms);
integration.computeVirtualSites();
// Update the time and step count.
......@@ -3958,6 +3965,7 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
else if (stepType[i] == CustomIntegrator::ConstrainPositions) {
cl.getIntegrationUtilities().applyConstraints(integrator.getConstraintTolerance());
cl.executeKernel(kernels[i][0], numAtoms);
cl.getIntegrationUtilities().computeVirtualSites();
}
else if (stepType[i] == CustomIntegrator::ConstrainVelocities) {
cl.getIntegrationUtilities().applyVelocityConstraints(integrator.getConstraintTolerance());
......
platforms/opencl/src/kernels/brownian.cl
View file @ 94ecc958
......@@ -7,6 +7,7 @@ __kernel void integrateBrownianPart1(float tauDeltaT, float noiseAmplitude, __gl
randomIndex += get_global_id(0);
for (int index = get_global_id(0); index < NUM_ATOMS; index += get_global_size(0)) {
float invMass = velm[index].w;
if (invMass != 0.0)
posDelta[index] = (float4) (tauDeltaT*invMass*force[index].xyz + noiseAmplitude*sqrt(invMass)*random[randomIndex].xyz, 0.0f);
randomIndex += get_global_size(0);
}
......@@ -18,8 +19,10 @@ __kernel void integrateBrownianPart1(float tauDeltaT, float noiseAmplitude, __gl
__kernel void integrateBrownianPart2(float oneOverDeltaT, __global float4* posq, __global float4* velm, __global const float4* restrict posDelta) {
for (int index = get_global_id(0); index < NUM_ATOMS; index += get_global_size(0)) {
if (velm[index].w != 0.0) {
float4 delta = posDelta[index];
velm[index].xyz = oneOverDeltaT*delta.xyz;
posq[index].xyz = posq[index].xyz + delta.xyz;
}
}
}
platforms/opencl/src/kernels/customIntegratorPerDof.cl
View file @ 94ecc958
......@@ -30,9 +30,11 @@ __kernel void computePerDof(__global float4* restrict posq, __global float4* res
float4 f = force[index];
float mass = 1.0f/velocity.w;
#endif
if (velocity.w != 0.0) {
float4 gaussian = gaussianValues[randomIndex];
float4 uniform = uniformValues[index];
COMPUTE_STEP
}
randomIndex += get_global_size(0);
index += get_global_size(0);
}
......
platforms/opencl/src/kernels/langevin.cl
View file @ 94ecc958
......@@ -18,10 +18,12 @@ __kernel void integrateLangevinPart1(__global float4* restrict velm, __global co
randomIndex += index;
while (index < NUM_ATOMS) {
float4 velocity = velm[index];
if (velocity.w != 0.0) {
float sqrtInvMass = sqrt(velocity.w);
velocity.xyz = vscale*velocity.xyz + fscale*velocity.w*force[index].xyz + noisescale*sqrtInvMass*random[randomIndex].xyz;
velm[index] = velocity;
posDelta[index] = stepSize*velocity;
}
randomIndex += get_global_size(0);
index += get_global_size(0);
}
......@@ -39,9 +41,10 @@ __kernel void integrateLangevinPart2(__global float4* restrict posq, __global co
#endif
int index = get_global_id(0);
while (index < NUM_ATOMS) {
float4 vel = velm[index];
if (vel.w != 0.0) {
float4 pos = posq[index];
float4 delta = posDelta[index];
float4 vel = velm[index];
pos.xyz += delta.xyz;
#ifdef SUPPORTS_DOUBLE_PRECISION
vel.xyz = convert_float4(invStepSize*convert_double4(delta)).xyz;
......@@ -50,6 +53,7 @@ __kernel void integrateLangevinPart2(__global float4* restrict posq, __global co
#endif
posq[index] = pos;
velm[index] = vel;
}
index += get_global_size(0);
}
}
......
platforms/opencl/src/kernels/verlet.cl
View file @ 94ecc958
......@@ -12,12 +12,14 @@ __kernel void integrateVerletPart1(int numAtoms, __global const float2* restrict
float dtVel = 0.5f*(stepSize.x+stepSize.y);
int index = get_global_id(0);
while (index < numAtoms) {
float4 pos = posq[index];
float4 velocity = velm[index];
if (velocity.w != 0.0) {
float4 pos = posq[index];
velocity.xyz += force[index].xyz*dtVel*velocity.w;
pos.xyz = velocity.xyz*dtPos;
posDelta[index] = pos;
velm[index] = velocity;
}
index += get_global_size(0);
}
}
......@@ -38,9 +40,10 @@ __kernel void integrateVerletPart2(int numAtoms, __global float2* restrict dt, _
barrier(CLK_LOCAL_MEM_FENCE);
int index = get_global_id(0);
while (index < numAtoms) {
float4 velocity = velm[index];
if (velocity.w != 0.0) {
float4 pos = posq[index];
float4 delta = posDelta[index];
float4 velocity = velm[index];
pos.xyz += delta.xyz;
#ifdef SUPPORTS_DOUBLE_PRECISION
velocity.xyz = convert_float4(convert_double4(delta)*oneOverDt).xyz;
......@@ -49,6 +52,7 @@ __kernel void integrateVerletPart2(int numAtoms, __global float2* restrict dt, _
#endif
posq[index] = pos;
velm[index] = velocity;
}
index += get_global_size(0);
}
}
......
platforms/opencl/src/kernels/virtualSites.cl 0 → 100644
View file @ 94ecc958
/**
* Compute the positions of virtual sites
*/
__kernel void computeVirtualSites(__global float4* restrict posq, __global const int4* restrict avg2Atoms, __global const float2* restrict avg2Weights,
__global const int4* restrict avg3Atoms, __global const float4* restrict avg3Weights,
__global const int4* restrict outOfPlaneAtoms, __global const float4* restrict outOfPlaneWeights) {
// Two particle average sites.
for (int index = get_global_id(0); index < NUM_2_AVERAGE; index += get_global_size(0)) {
int4 atoms = avg2Atoms[index];
float2 weights = avg2Weights[index];
float4 pos = posq[atoms.x];
float4 pos1 = posq[atoms.y];
float4 pos2 = posq[atoms.z];
pos.xyz = pos1.xyz*weights.x + pos2.xyz*weights.y;
posq[atoms.x] = pos;
}
// Three particle average sites.
for (int index = get_global_id(0); index < NUM_3_AVERAGE; index += get_global_size(0)) {
int4 atoms = avg3Atoms[index];
float4 weights = avg3Weights[index];
float4 pos = posq[atoms.x];
float4 pos1 = posq[atoms.y];
float4 pos2 = posq[atoms.z];
float4 pos3 = posq[atoms.w];
pos.xyz = pos1.xyz*weights.x + pos2.xyz*weights.y + pos3.xyz*weights.z;
posq[atoms.x] = pos;
}
// Out of plane sites.
for (int index = get_global_id(0); index < NUM_OUT_OF_PLANE; index += get_global_size(0)) {
int4 atoms = outOfPlaneAtoms[index];
float4 weights = outOfPlaneWeights[index];
float4 pos = posq[atoms.x];
float4 pos1 = posq[atoms.y];
float4 pos2 = posq[atoms.z];
float4 pos3 = posq[atoms.w];
float4 v12 = pos2-pos1;
float4 v13 = pos3-pos1;
pos.xyz = pos1.xyz + v12.xyz*weights.x + v13.xyz*weights.y + cross(v12, v13).xyz*weights.z;
posq[atoms.x] = pos;
}
}
/**
* Distribute forces from virtual sites to the atoms they are based on.
*/
__kernel void distributeForces(__global const float4* restrict posq, __global float4* restrict force,
__global const int4* restrict avg2Atoms, __global const float2* restrict avg2Weights,
__global const int4* restrict avg3Atoms, __global const float4* restrict avg3Weights,
__global const int4* restrict outOfPlaneAtoms, __global const float4* restrict outOfPlaneWeights) {
// Two particle average sites.
for (int index = get_global_id(0); index < NUM_2_AVERAGE; index += get_global_size(0)) {
int4 atoms = avg2Atoms[index];
float2 weights = avg2Weights[index];
float4 f = force[atoms.x];
float4 f1 = force[atoms.y];
float4 f2 = force[atoms.z];
f1.xyz += f.xyz*weights.x;
f2.xyz += f.xyz*weights.y;
force[atoms.y] = f1;
force[atoms.z] = f2;
}
// Three particle average sites.
for (int index = get_global_id(0); index < NUM_3_AVERAGE; index += get_global_size(0)) {
int4 atoms = avg3Atoms[index];
float4 weights = avg3Weights[index];
float4 f = force[atoms.x];
float4 f1 = force[atoms.y];
float4 f2 = force[atoms.z];
float4 f3 = force[atoms.w];
f1.xyz += f.xyz*weights.x;
f2.xyz += f.xyz*weights.y;
f3.xyz += f.xyz*weights.z;
force[atoms.y] = f1;
force[atoms.z] = f2;
force[atoms.w] = f3;
}
// Out of plane sites.
for (int index = get_global_id(0); index < NUM_OUT_OF_PLANE; index += get_global_size(0)) {
int4 atoms = outOfPlaneAtoms[index];
float4 weights = outOfPlaneWeights[index];
float4 pos1 = posq[atoms.y];
float4 pos2 = posq[atoms.z];
float4 pos3 = posq[atoms.w];
float4 v12 = pos2-pos1;
float4 v13 = pos3-pos1;
float4 f = force[atoms.x];
float4 f1 = force[atoms.y];
float4 f2 = force[atoms.z];
float4 f3 = force[atoms.w];
float4 fp2 = (float4) (weights.x*f.x - weights.z*v13.z*f.y + weights.z*v13.y*f[2],
weights.z*v13.z*f.x + weights.x*f.y - weights.z*v13.x*f[2],
-weights.z*v13.y*f.x + weights.z*v13.x*f.y + weights.x*f.z, 0.0f);
float4 fp3 = (float4) (weights.y*f.x + weights.z*v12[2]*f.y - weights.z*v12.y*f.z,
-weights.z*v12[2]*f.x + weights.y*f.y + weights.z*v12.x*f.z,
weights.z*v12.y*f.x - weights.z*v12.x*f.y + weights.y*f[2], 0.0f);
f1.xyz += f.xyz-fp2.xyz-fp3.xyz;
f2.xyz += fp2.xyz;
f3.xyz += fp3.xyz;
force[atoms.y] = f1;
force[atoms.z] = f2;
force[atoms.w] = f3;
}
}
platforms/opencl/tests/TestOpenCLVirtualSites.cpp 0 → 100644
View file @ 94ecc958
/* -------------------------------------------------------------------------- *
* 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 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. *
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of virtual sites.
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/CustomBondForce.h"
#include "openmm/CustomExternalForce.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/VirtualSite.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
/**
* Check that massless particles are handled correctly.
*/
void testMasslessParticle() {
OpenCLPlatform platform;
System system;
system.addParticle(0.0);
system.addParticle(1.0);
CustomBondForce* bonds = new CustomBondForce("-1/r");
system.addForce(bonds);
vector<double> params;
bonds->addBond(0, 1, params);
VerletIntegrator integrator(0.002);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
vector<Vec3> velocities(2);
velocities[0] = Vec3(0, 0, 0);
velocities[1] = Vec3(0, 1, 0);
context.setVelocities(velocities);
// The second particle should move in a circular orbit around the first one.
// Compare it to the analytical solution.
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Velocities | State::Forces);
double time = state.getTime();
ASSERT_EQUAL_VEC(Vec3(), state.getPositions()[0], 0.0);
ASSERT_EQUAL_VEC(Vec3(), state.getVelocities()[0], 0.0);
ASSERT_EQUAL_VEC(Vec3(cos(time), sin(time), 0), state.getPositions()[1], 0.01);
ASSERT_EQUAL_VEC(Vec3(-sin(time), cos(time), 0), state.getVelocities()[1], 0.01);
integrator.step(1);
}
}
/**
* Test a TwoParticleAverageSite virtual site.
*/
void testTwoParticleAverage() {
OpenCLPlatform platform;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(2, new TwoParticleAverageSite(0, 1, 0.8, 0.2));
CustomExternalForce* forceField = new CustomExternalForce("-a*x");
system.addForce(forceField);
forceField->addPerParticleParameter("a");
vector<double> params(1);
params[0] = 0.1;
forceField->addParticle(0, params);
params[0] = 0.2;
forceField->addParticle(1, params);
params[0] = 0.3;
forceField->addParticle(2, params);
LangevinIntegrator integrator(300.0, 0.1, 0.002);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
context.applyConstraints(0.0001);
for (int i = 0; i < 1000; i++) {
State state = context.getState(State::Positions | State::Forces);
const vector<Vec3>& pos = state.getPositions();
ASSERT_EQUAL_VEC(pos[0]*0.8+pos[1]*0.2, pos[2], 1e-5);
ASSERT_EQUAL_VEC(Vec3(0.1+0.3*0.8, 0, 0), state.getForces()[0], 1e-4);
ASSERT_EQUAL_VEC(Vec3(0.2+0.3*0.2, 0, 0), state.getForces()[1], 1e-4);
integrator.step(1);
}
}
/**
* Test a ThreeParticleAverageSite virtual site.
*/
void testThreeParticleAverage() {
OpenCLPlatform platform;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(3, new ThreeParticleAverageSite(0, 1, 2, 0.2, 0.3, 0.5));
CustomExternalForce* forceField = new CustomExternalForce("-a*x");
system.addForce(forceField);
forceField->addPerParticleParameter("a");
vector<double> params(1);
params[0] = 0.1;
forceField->addParticle(0, params);
params[0] = 0.2;
forceField->addParticle(1, params);
params[0] = 0.3;
forceField->addParticle(2, params);
params[0] = 0.4;
forceField->addParticle(3, params);
LangevinIntegrator integrator(300.0, 0.1, 0.002);
Context context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
positions[2] = Vec3(0, 1, 0);
context.setPositions(positions);
context.applyConstraints(0.0001);
for (int i = 0; i < 1000; i++) {
State state = context.getState(State::Positions | State::Forces);
const vector<Vec3>& pos = state.getPositions();
ASSERT_EQUAL_VEC(pos[0]*0.2+pos[1]*0.3+pos[2]*0.5, pos[3], 1e-5);
ASSERT_EQUAL_VEC(Vec3(0.1+0.4*0.2, 0, 0), state.getForces()[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(0.2+0.4*0.3, 0, 0), state.getForces()[1], 1e-5);
ASSERT_EQUAL_VEC(Vec3(0.3+0.4*0.5, 0, 0), state.getForces()[2], 1e-5);
integrator.step(1);
}
}
/**
* Test an OutOfPlaneSite virtual site.
*/
void testOutOfPlane() {
OpenCLPlatform platform;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(3, new OutOfPlaneSite(0, 1, 2, 0.3, 0.4, 0.5));
CustomExternalForce* forceField = new CustomExternalForce("-a*x");
system.addForce(forceField);
forceField->addPerParticleParameter("a");
vector<double> params(1);
params[0] = 0.1;
forceField->addParticle(0, params);
params[0] = 0.2;
forceField->addParticle(1, params);
params[0] = 0.3;
forceField->addParticle(2, params);
params[0] = 0.4;
forceField->addParticle(3, params);
LangevinIntegrator integrator(300.0, 0.1, 0.002);
Context context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
positions[2] = Vec3(0, 1, 0);
context.setPositions(positions);
context.applyConstraints(0.0001);
for (int i = 0; i < 1000; i++) {
State state = context.getState(State::Positions | State::Forces);
const vector<Vec3>& pos = state.getPositions();
Vec3 v12 = pos[1]-pos[0];
Vec3 v13 = pos[2]-pos[0];
Vec3 cross = v12.cross(v13);
ASSERT_EQUAL_VEC(pos[0]+v12*0.3+v13*0.4+cross*0.5, pos[3], 1e-5);
const vector<Vec3>& f = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0.1+0.2+0.3+0.4, 0, 0), f[0]+f[1]+f[2], 1e-5);
Vec3 f2(0.4*0.3, 0.4*0.5*v13[2], -0.4*0.5*v13[1]);
Vec3 f3(0.4*0.4, -0.4*0.5*v12[2], 0.4*0.5*v12[1]);
ASSERT_EQUAL_VEC(Vec3(0.1+0.4, 0, 0)-f2-f3, f[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(0.2, 0, 0)+f2, f[1], 1e-5);
ASSERT_EQUAL_VEC(Vec3(0.3, 0, 0)+f3, f[2], 1e-5);
integrator.step(1);
}
}
/**
* Make sure that energy, linear momentum, and angular momentum are all conserved
* when using virtual sites.
*/
void testConservationLaws() {
OpenCLPlatform platform;
System system;
NonbondedForce* forceField = new NonbondedForce();
system.addForce(forceField);
vector<Vec3> positions;
// Create a linear molecule with a TwoParticleAverage virtual site.
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(2, new TwoParticleAverageSite(0, 1, 0.4, 0.6));
system.addConstraint(0, 1, 2.0);
for (int i = 0; i < 3; i++) {
forceField->addParticle(0, 1, 10);
for (int j = 0; j < i; j++)
forceField->addException(i, j, 0, 1, 0);
}
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(2, 0, 0));
positions.push_back(Vec3());
// Create a planar molecule with a ThreeParticleAverage virtual site.
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(6, new ThreeParticleAverageSite(3, 4, 5, 0.3, 0.5, 0.2));
system.addConstraint(3, 4, 1.0);
system.addConstraint(3, 5, 1.0);
system.addConstraint(4, 5, sqrt(2.0));
for (int i = 0; i < 4; i++) {
forceField->addParticle(0, 1, 10);
for (int j = 0; j < i; j++)
forceField->addException(i+3, j+3, 0, 1, 0);
}
positions.push_back(Vec3(0, 0, 1));
positions.push_back(Vec3(1, 0, 1));
positions.push_back(Vec3(0, 1, 1));
positions.push_back(Vec3());
// Create a tetrahedral molecule with an OutOfPlane virtual site.
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(10, new OutOfPlaneSite(7, 8, 9, 0.3, 0.5, 0.2));
system.addConstraint(7, 8, 1.0);
system.addConstraint(7, 9, 1.0);
system.addConstraint(8, 9, sqrt(2.0));
for (int i = 0; i < 4; i++) {
forceField->addParticle(0, 1, 10);
for (int j = 0; j < i; j++)
forceField->addException(i+7, j+7, 0, 1, 0);
}
positions.push_back(Vec3(1, 0, -1));
positions.push_back(Vec3(2, 0, -1));
positions.push_back(Vec3(1, 1, -1));
positions.push_back(Vec3());
// Simulate it and check conservation laws.
VerletIntegrator integrator(0.002);
Context context(system, integrator, platform);
context.setPositions(positions);
context.applyConstraints(0.0001);
int numParticles = system.getNumParticles();
double initialEnergy;
Vec3 initialMomentum, initialAngularMomentum;
for (int i = 0; i < 1000; i++) {
State state = context.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
const vector<Vec3>& pos = state.getPositions();
const vector<Vec3>& vel = state.getVelocities();
const vector<Vec3>& f = state.getForces();
double energy = state.getPotentialEnergy();
for (int j = 0; j < numParticles; j++) {
Vec3 v = vel[j] + f[j]*0.5*integrator.getStepSize();
energy += 0.5*system.getParticleMass(j)*v.dot(v);
}
if (i == 0)
initialEnergy = energy;
else
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
Vec3 momentum;
for (int j = 0; j < numParticles; j++)
momentum += vel[j]*system.getParticleMass(j);
if (i == 0)
initialMomentum = momentum;
else
ASSERT_EQUAL_VEC(initialMomentum, momentum, 0.01);
Vec3 angularMomentum;
for (int j = 0; j < numParticles; j++)
angularMomentum += pos[j].cross(vel[j])*system.getParticleMass(j);
if (i == 0)
initialAngularMomentum = angularMomentum;
else
ASSERT_EQUAL_VEC(initialAngularMomentum, angularMomentum, 0.01);
integrator.step(1);
}
}
/**
* Make sure that atom reordering respects virtual sites.
*/
void testReordering() {
const double cutoff = 2.0;
const double boxSize = 20.0;
OpenCLPlatform platform;
System system;
NonbondedForce* nonbonded = new NonbondedForce();
system.addForce(nonbonded);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
nonbonded->setCutoffDistance(cutoff);
vector<Vec3> positions;
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
// Create linear molecules with TwoParticleAverage virtual sites.
for (int i = 0; i < 50; i++) {
int start = system.getNumParticles();
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(start+2, new TwoParticleAverageSite(start, start+1, 0.4, 0.6));
system.addConstraint(start, start+1, 2.0);
for (int i = 0; i < 3; i++) {
nonbonded->addParticle(0, 0.2, 1);
for (int j = 0; j < i; j++)
nonbonded->addException(start+i, start+j, 0, 1, 0);
}
Vec3 pos(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions.push_back(pos);
positions.push_back(pos+Vec3(2, 0, 0));
positions.push_back(Vec3());
}
// Create planar molecules with ThreeParticleAverage virtual sites.
for (int i = 0; i < 50; i++) {
int start = system.getNumParticles();
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(start+3, new ThreeParticleAverageSite(start, start+1, start+2, 0.3, 0.5, 0.2));
system.addConstraint(start, start+1, 1.0);
system.addConstraint(start, start+2, 1.0);
system.addConstraint(start+1, start+2, sqrt(2.0));
for (int i = 0; i < 4; i++) {
nonbonded->addParticle(0, 0.2, 1);
for (int j = 0; j < i; j++)
nonbonded->addException(start+i, start+j, 0, 1, 0);
}
Vec3 pos(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions.push_back(pos);
positions.push_back(pos+Vec3(1, 0, 0));
positions.push_back(pos+Vec3(0, 1, 0));
positions.push_back(Vec3());
}
// Create tetrahedral molecules with OutOfPlane virtual sites.
for (int i = 0; i < 50; i++) {
int start = system.getNumParticles();
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(start+3, new OutOfPlaneSite(start, start+1, start+2, 0.3, 0.5, 0.2));
system.addConstraint(start, start+1, 1.0);
system.addConstraint(start, start+2, 1.0);
system.addConstraint(start+1, start+2, sqrt(2.0));
for (int i = 0; i < 4; i++) {
nonbonded->addParticle(0, 0.2, 1);
for (int j = 0; j < i; j++)
nonbonded->addException(start+i, start+j, 0, 1, 0);
}
Vec3 pos(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions.push_back(pos);
positions.push_back(pos+Vec3(1, 0, 0));
positions.push_back(pos+Vec3(0, 1, 0));
positions.push_back(Vec3());
}
// Simulate it and check conservation laws.
LangevinIntegrator integrator(300.0, 0.1, 0.002);
Context context(system, integrator, platform);
context.setPositions(positions);
context.applyConstraints(0.0001);
for (int i = 0; i < 1000; i++) {
State state = context.getState(State::Positions);
const vector<Vec3>& pos = state.getPositions();
for (int j = 0; j < 150; j += 3)
ASSERT_EQUAL_VEC(pos[j]*0.4+pos[j+1]*0.6, pos[j+2], 1e-5);
for (int j = 150; j < 350; j += 4)
ASSERT_EQUAL_VEC(pos[j]*0.3+pos[j+1]*0.5+pos[j+2]*0.2, pos[j+3], 1e-5);
for (int j = 350; j < 550; j += 4) {
Vec3 v12 = pos[j+1]-pos[j];
Vec3 v13 = pos[j+2]-pos[j];
Vec3 cross = v12.cross(v13);
ASSERT_EQUAL_VEC(pos[j]+v12*0.3+v13*0.5+cross*0.2, pos[j+3], 1e-5);
}
integrator.step(1);
}
}
int main() {
try {
testMasslessParticle();
testTwoParticleAverage();
testThreeParticleAverage();
testOutOfPlane();
testConservationLaws();
testReordering();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/reference/tests/TestReferenceVirtualSites.cpp
View file @ 94ecc958
......@@ -120,6 +120,7 @@ void testTwoParticleAverage() {
ASSERT_EQUAL_VEC(pos[0]*0.8+pos[1]*0.2, pos[2], 1e-10);
ASSERT_EQUAL_VEC(Vec3(0.1+0.3*0.8, 0, 0), state.getForces()[0], 1e-10);
ASSERT_EQUAL_VEC(Vec3(0.2+0.3*0.2, 0, 0), state.getForces()[1], 1e-10);
integrator.step(1);
}
}
......@@ -161,6 +162,7 @@ void testThreeParticleAverage() {
ASSERT_EQUAL_VEC(Vec3(0.1+0.4*0.2, 0, 0), state.getForces()[0], 1e-10);
ASSERT_EQUAL_VEC(Vec3(0.2+0.4*0.3, 0, 0), state.getForces()[1], 1e-10);
ASSERT_EQUAL_VEC(Vec3(0.3+0.4*0.5, 0, 0), state.getForces()[2], 1e-10);
integrator.step(1);
}
}
......@@ -209,6 +211,7 @@ void testOutOfPlane() {
ASSERT_EQUAL_VEC(Vec3(0.1+0.4, 0, 0)-f2-f3, f[0], 1e-10);
ASSERT_EQUAL_VEC(Vec3(0.2, 0, 0)+f2, f[1], 1e-10);
ASSERT_EQUAL_VEC(Vec3(0.3, 0, 0)+f3, f[2], 1e-10);
integrator.step(1);
}
}
......
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