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Commit b2af59a8 authored by peastman's avatar peastman
Browse files

Bug fixes to interaction groups

parent 4ea10969
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Showing with 222 additions and 42 deletions
openmmapi/include/openmm/CustomNonbondedForce.h
View file @ b2af59a8
......@@ -404,6 +404,14 @@ public:
* @param set2 the second set of particles forming the interaction group
*/
void getInteractionGroupParameters(int index, std::set<int>& set1, std::set<int>& set2) const;
/**
* Set the parameters for an interaction group.
*
* @param index the index of the interaction group for which to set parameters
* @param set1 the first set of particles forming the interaction group
* @param set2 the second set of particles forming the interaction group
*/
void setInteractionGroupParameters(int index, const std::set<int>& set1, const std::set<int>& set2);
/**
* Update the per-particle parameters in a Context to match those stored in this Force object. This method provides
* an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
......
openmmapi/src/CustomNonbondedForce.cpp
View file @ b2af59a8
......@@ -210,6 +210,12 @@ void CustomNonbondedForce::getInteractionGroupParameters(int index, std::set<int
set2 = interactionGroups[index].set2;
}
void CustomNonbondedForce::setInteractionGroupParameters(int index, const std::set<int>& set1, const std::set<int>& set2) {
ASSERT_VALID_INDEX(index, interactionGroups);
interactionGroups[index].set1 = set1;
interactionGroups[index].set2 = set2;
}
ForceImpl* CustomNonbondedForce::createImpl() const {
return new CustomNonbondedForceImpl(*this);
}
......
platforms/cuda/src/CudaKernels.cpp
View file @ b2af59a8
......@@ -2059,6 +2059,7 @@ void CudaCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbo
vector<vector<int> > atomLists;
vector<pair<int, int> > tiles;
map<pair<int, int>, int> duplicateInteractions;
for (int group = 0; group < force.getNumInteractionGroups(); group++) {
// Get the list of atoms in this group and sort them.
......@@ -2100,6 +2101,23 @@ void CudaCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbo
atoms.push_back(atoms2[j]);
atomLists.push_back(atoms);
}
// If this group contains duplicate interactions, record that we need to skip them once.
for (int i = 0; i < (int) atoms1.size(); i++) {
int a1 = atoms1[i];
if (set2.find(a1) == set2.end())
continue;
for (int j = 0; j < (int) atoms2.size() && atoms2[j] < a1; j++) {
int a2 = atoms2[j];
if (set1.find(a2) != set1.end()) {
pair<int, int> key = make_pair(a2, a1);
if (duplicateInteractions.find(key) == duplicateInteractions.end())
duplicateInteractions[key] = 0;
duplicateInteractions[key]++;
}
}
}
}
// Build a lookup table for quickly identifying excluded interactions.
......@@ -2108,7 +2126,7 @@ void CudaCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbo
for (int i = 0; i < force.getNumExclusions(); i++) {
int p1, p2;
force.getExclusionParticles(i, p1, p2);
exclusions.insert(make_pair(p1, p2));
exclusions.insert(make_pair(min(p1, p2), max(p1, p2)));
}
// Build the exclusion flags for each tile. While we're at it, filter out tiles
......@@ -2126,13 +2144,23 @@ void CudaCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbo
}
vector<int>& atoms1 = atomLists[tiles[tile].first];
vector<int>& atoms2 = atomLists[tiles[tile].second];
vector<int> flags(atoms1.size(), (1<<atoms2.size())-1);
vector<int> flags(atoms1.size(), (1L<<atoms2.size())-1);
int numExcluded = 0;
for (int i = 0; i < (int) atoms1.size(); i++)
for (int j = 0; j < (int) atoms2.size(); j++) {
int a1 = atoms1[i];
int a2 = atoms2[j];
if (a1 == a2 || exclusions.find(make_pair(a1, a2)) != exclusions.end() || exclusions.find(make_pair(a2, a1)) != exclusions.end()) {
bool isExcluded = false;
pair<int, int> key = make_pair(min(a1, a2), max(a1, a2));
if (a1 == a2 || exclusions.find(key) != exclusions.end())
isExcluded = true; // This is an excluded interaction.
else if (duplicateInteractions.find(key) != duplicateInteractions.end() && duplicateInteractions[key] > 0) {
// Both atoms are in both sets, so skip duplicate interactions.
isExcluded = true;
duplicateInteractions[key]--;
}
if (isExcluded) {
flags[i] &= -1-(1<<j);
numExcluded++;
}
......@@ -2140,8 +2168,7 @@ void CudaCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbo
if (numExcluded == atoms1.size()*atoms2.size())
continue; // All interactions are excluded.
tileOrder.push_back(make_pair((int) -atoms2.size(), tile));
if (numExcluded > 0)
exclusionFlags[tile] = flags;
exclusionFlags[tile] = flags;
}
sort(tileOrder.begin(), tileOrder.end());
......
platforms/cuda/src/kernels/customNonbondedGroups.cu
View file @ b2af59a8
......@@ -80,10 +80,10 @@ extern "C" __global__ void computeInteractionGroups(
atomicAdd(&forceBuffers[atom1], static_cast<unsigned long long>((long long) (force.x*0x100000000)));
atomicAdd(&forceBuffers[atom1+PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (force.y*0x100000000)));
atomicAdd(&forceBuffers[atom1+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (force.z*0x100000000)));
atomicAdd(&forceBuffers[atom2], static_cast<unsigned long long>((long long) (localData[threadIdx.x].fx*0x100000000)));
atomicAdd(&forceBuffers[atom2+PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (localData[threadIdx.x].fy*0x100000000)));
atomicAdd(&forceBuffers[atom2+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (localData[threadIdx.x].fz*0x100000000)));
}
atomicAdd(&forceBuffers[atom2], static_cast<unsigned long long>((long long) (localData[threadIdx.x].fx*0x100000000)));
atomicAdd(&forceBuffers[atom2+PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (localData[threadIdx.x].fy*0x100000000)));
atomicAdd(&forceBuffers[atom2+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (localData[threadIdx.x].fz*0x100000000)));
}
energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] += energy;
}
\ No newline at end of file
platforms/cuda/tests/TestCudaCustomNonbondedForce.cpp
View file @ b2af59a8
......@@ -582,6 +582,7 @@ void testLargeInteractionGroup() {
// Create a large system.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
CustomNonbondedForce* nonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6)+138.935456*q/r; q=q1*q2; sigma=0.5*(sigma1+sigma2); eps=sqrt(eps1*eps2)");
......@@ -639,6 +640,18 @@ void testLargeInteractionGroup() {
// The force on that one particle should be the same.
ASSERT_EQUAL_VEC(state1.getForces()[151], state2.getForces()[151], 1e-4);
// Modify the interaction group so it includes all interactions. This should now reproduce the original forces
// on all atoms.
for (int i = 0; i < numParticles; i++)
set1.insert(i);
nonbonded->setInteractionGroupParameters(0, set1, set2);
context.reinitialize();
context.setPositions(positions);
State state3 = context.getState(State::Forces);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state3.getForces()[i], 1e-4);
}
int main(int argc, char* argv[]) {
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ b2af59a8
......@@ -2070,6 +2070,7 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
vector<vector<int> > atomLists;
vector<pair<int, int> > tiles;
map<pair<int, int>, int> duplicateInteractions;
for (int group = 0; group < force.getNumInteractionGroups(); group++) {
// Get the list of atoms in this group and sort them.
......@@ -2111,6 +2112,23 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
atoms.push_back(atoms2[j]);
atomLists.push_back(atoms);
}
// If this group contains duplicate interactions, record that we need to skip them once.
for (int i = 0; i < (int) atoms1.size(); i++) {
int a1 = atoms1[i];
if (set2.find(a1) == set2.end())
continue;
for (int j = 0; j < (int) atoms2.size() && atoms2[j] < a1; j++) {
int a2 = atoms2[j];
if (set1.find(a2) != set1.end()) {
pair<int, int> key = make_pair(a2, a1);
if (duplicateInteractions.find(key) == duplicateInteractions.end())
duplicateInteractions[key] = 0;
duplicateInteractions[key]++;
}
}
}
}
// Build a lookup table for quickly identifying excluded interactions.
......@@ -2119,7 +2137,7 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
for (int i = 0; i < force.getNumExclusions(); i++) {
int p1, p2;
force.getExclusionParticles(i, p1, p2);
exclusions.insert(make_pair(p1, p2));
exclusions.insert(make_pair(min(p1, p2), max(p1, p2)));
}
// Build the exclusion flags for each tile. While we're at it, filter out tiles
......@@ -2137,13 +2155,23 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
}
vector<int>& atoms1 = atomLists[tiles[tile].first];
vector<int>& atoms2 = atomLists[tiles[tile].second];
vector<int> flags(atoms1.size(), (1<<atoms2.size())-1);
vector<int> flags(atoms1.size(), (1L<<atoms2.size())-1);
int numExcluded = 0;
for (int i = 0; i < (int) atoms1.size(); i++)
for (int j = 0; j < (int) atoms2.size(); j++) {
int a1 = atoms1[i];
int a2 = atoms2[j];
if (a1 == a2 || exclusions.find(make_pair(a1, a2)) != exclusions.end() || exclusions.find(make_pair(a2, a1)) != exclusions.end()) {
bool isExcluded = false;
pair<int, int> key = make_pair(min(a1, a2), max(a1, a2));
if (a1 == a2 || exclusions.find(key) != exclusions.end())
isExcluded = true; // This is an excluded interaction.
else if (duplicateInteractions.find(key) != duplicateInteractions.end() && duplicateInteractions[key] > 0) {
// Both atoms are in both sets, so skip duplicate interactions.
isExcluded = true;
duplicateInteractions[key]--;
}
if (isExcluded) {
flags[i] &= -1-(1<<j);
numExcluded++;
}
......@@ -2151,8 +2179,7 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
if (numExcluded == atoms1.size()*atoms2.size())
continue; // All interactions are excluded.
tileOrder.push_back(make_pair((int) -atoms2.size(), tile));
if (numExcluded > 0)
exclusionFlags[tile] = flags;
exclusionFlags[tile] = flags;
}
sort(tileOrder.begin(), tileOrder.end());
......
platforms/opencl/src/kernels/customNonbondedGroups.cl
View file @ b2af59a8
......@@ -78,32 +78,34 @@ __kernel void computeInteractionGroups(
int tj = tgx;
SYNC_WARPS;
for (int j = rangeStart; j < rangeEnd; j++) {
bool isExcluded = (((exclusions>>tj)&1) == 0);
int localIndex = tbx+tj;
posq2 = (real4) (localData[localIndex].x, localData[localIndex].y, localData[localIndex].z, localData[localIndex].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
if (tj < rangeEnd) {
bool isExcluded = (((exclusions>>tj)&1) == 0);
int localIndex = tbx+tj;
posq2 = (real4) (localData[localIndex].x, localData[localIndex].y, localData[localIndex].z, localData[localIndex].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
#endif
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
#ifdef USE_CUTOFF
if (!isExcluded && r2 < CUTOFF_SQUARED) {
if (!isExcluded && r2 < CUTOFF_SQUARED) {
#endif
real invR = RSQRT(r2);
real r = RECIP(invR);
LOAD_ATOM2_PARAMETERS
real dEdR = 0.0f;
real tempEnergy = 0.0f;
COMPUTE_INTERACTION
energy += tempEnergy;
delta *= dEdR;
force.xyz -= delta.xyz;
localData[localIndex].fx += delta.x;
localData[localIndex].fy += delta.y;
localData[localIndex].fz += delta.z;
real invR = RSQRT(r2);
real r = RECIP(invR);
LOAD_ATOM2_PARAMETERS
real dEdR = 0.0f;
real tempEnergy = 0.0f;
COMPUTE_INTERACTION
energy += tempEnergy;
delta *= dEdR;
force.xyz -= delta.xyz;
localData[localIndex].fx += delta.x;
localData[localIndex].fy += delta.y;
localData[localIndex].fz += delta.z;
#ifdef USE_CUTOFF
}
}
#endif
}
tj = (tj == rangeEnd-1 ? rangeStart : tj+1);
SYNC_WARPS;
}
......@@ -112,10 +114,10 @@ __kernel void computeInteractionGroups(
atom_add(&forceBuffers[atom1], (long) (force.x*0x100000000));
atom_add(&forceBuffers[atom1+PADDED_NUM_ATOMS], (long) (force.y*0x100000000));
atom_add(&forceBuffers[atom1+2*PADDED_NUM_ATOMS], (long) (force.z*0x100000000));
atom_add(&forceBuffers[atom2], (long) (localData[get_local_id(0)].fx*0x100000000));
atom_add(&forceBuffers[atom2+PADDED_NUM_ATOMS], (long) (localData[get_local_id(0)].fy*0x100000000));
atom_add(&forceBuffers[atom2+2*PADDED_NUM_ATOMS], (long) (localData[get_local_id(0)].fz*0x100000000));
}
atom_add(&forceBuffers[atom2], (long) (localData[get_local_id(0)].fx*0x100000000));
atom_add(&forceBuffers[atom2+PADDED_NUM_ATOMS], (long) (localData[get_local_id(0)].fy*0x100000000));
atom_add(&forceBuffers[atom2+2*PADDED_NUM_ATOMS], (long) (localData[get_local_id(0)].fz*0x100000000));
#else
writeForces(forceBuffers, localData, atom2);
localData[get_local_id(0)].fx = force.x;
......
platforms/opencl/tests/TestOpenCLCustomNonbondedForce.cpp
View file @ b2af59a8
......@@ -582,6 +582,7 @@ void testLargeInteractionGroup() {
// Create a large system.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
CustomNonbondedForce* nonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6)+138.935456*q/r; q=q1*q2; sigma=0.5*(sigma1+sigma2); eps=sqrt(eps1*eps2)");
......@@ -639,6 +640,18 @@ void testLargeInteractionGroup() {
// The force on that one particle should be the same.
ASSERT_EQUAL_VEC(state1.getForces()[151], state2.getForces()[151], 1e-4);
// Modify the interaction group so it includes all interactions. This should now reproduce the original forces
// on all atoms.
for (int i = 0; i < numParticles; i++)
set1.insert(i);
nonbonded->setInteractionGroupParameters(0, set1, set2);
context.reinitialize();
context.setPositions(positions);
State state3 = context.getState(State::Forces);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state3.getForces()[i], 1e-4);
}
int main(int argc, char* argv[]) {
......
platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp
View file @ b2af59a8
......@@ -177,13 +177,15 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, vector<Re
const set<int>& set2 = interactionGroups[group].second;
for (set<int>::const_iterator atom1 = set1.begin(); atom1 != set1.end(); ++atom1) {
for (set<int>::const_iterator atom2 = set2.begin(); atom2 != set2.end(); ++atom2) {
if (*atom1 != *atom2 && exclusions[*atom1].find(*atom2) == exclusions[*atom1].end()) {
for (int j = 0; j < (int) paramNames.size(); j++) {
variables[particleParamNames[j*2]] = atomParameters[*atom1][j];
variables[particleParamNames[j*2+1]] = atomParameters[*atom2][j];
}
calculateOneIxn(*atom1, *atom2, atomCoordinates, variables, forces, energyByAtom, totalEnergy);
if (*atom1 == *atom2 || exclusions[*atom1].find(*atom2) != exclusions[*atom1].end())
continue; // This is an excluded interaction.
if (*atom1 > *atom2 && set1.find(*atom2) != set1.end() && set2.find(*atom1) != set2.end())
continue; // Both atoms are in both sets, so skip duplicate interactions.
for (int j = 0; j < (int) paramNames.size(); j++) {
variables[particleParamNames[j*2]] = atomParameters[*atom1][j];
variables[particleParamNames[j*2+1]] = atomParameters[*atom2][j];
}
calculateOneIxn(*atom1, *atom2, atomCoordinates, variables, forces, energyByAtom, totalEnergy);
}
}
}
......
platforms/reference/tests/TestReferenceCustomNonbondedForce.cpp
View file @ b2af59a8
......@@ -508,6 +508,87 @@ void testInteractionGroups() {
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), TOL);
}
void testLargeInteractionGroup() {
const int numMolecules = 300;
const int numParticles = numMolecules*2;
const double boxSize = 20.0;
// Create a large system.
ReferencePlatform platform;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
CustomNonbondedForce* nonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6)+138.935456*q/r; q=q1*q2; sigma=0.5*(sigma1+sigma2); eps=sqrt(eps1*eps2)");
nonbonded->addPerParticleParameter("q");
nonbonded->addPerParticleParameter("sigma");
nonbonded->addPerParticleParameter("eps");
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.1;
nonbonded->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
nonbonded->addParticle(params);
}
else {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.2;
nonbonded->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
nonbonded->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
nonbonded->addExclusion(2*i, 2*i+1);
}
nonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
system.addForce(nonbonded);
// Compute the forces.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state1 = context.getState(State::Forces);
// Modify the force so only one particle interacts with everything else.
set<int> set1, set2;
set1.insert(151);
for (int i = 0; i < numParticles; i++)
set2.insert(i);
nonbonded->addInteractionGroup(set1, set2);
context.reinitialize();
context.setPositions(positions);
State state2 = context.getState(State::Forces);
// The force on that one particle should be the same.
ASSERT_EQUAL_VEC(state1.getForces()[151], state2.getForces()[151], 1e-4);
// Modify the interaction group so it includes all interactions. This should now reproduce the original forces
// on all atoms.
for (int i = 0; i < numParticles; i++)
set1.insert(i);
nonbonded->setInteractionGroupParameters(0, set1, set2);
context.reinitialize();
context.setPositions(positions);
State state3 = context.getState(State::Forces);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state3.getForces()[i], 1e-4);
}
int main() {
try {
testSimpleExpression();
......@@ -520,6 +601,7 @@ int main() {
testSwitchingFunction();
testLongRangeCorrection();
testInteractionGroups();
testLargeInteractionGroup();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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