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Commit f5acdd7a authored by peastman's avatar peastman
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CustomManyParticleForce offers two different "permutation modes". Implemented... 

CustomManyParticleForce offers two different "permutation modes".  Implemented it for Reference and CPU platforms.
parent bf464848
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openmmapi/include/openmm/CustomManyParticleForce.h
View file @ f5acdd7a
...@@ -75,8 +75,8 @@ namespace OpenMM { ...@@ -75,8 +75,8 @@ namespace OpenMM {
* you can modify its parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist * you can modify its parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist
* unless you call updateParametersInContext(). * unless you call updateParametersInContext().
* *
* Multi-particle interactions can be very expensive to evaluate, so they are usually used with a cutoff distance. If two particles * Multi-particle interactions can be very expensive to evaluate, so they are usually used with a cutoff distance. The exact
* are further apart than the cutoff, <i>all</i> sets that include those two particles will be omitted. * interpretation of the cutoff depends on the permutation mode, as discussed below.
* *
* CustomManyParticleForce also lets you specify "exclusions", particular pairs of particles whose interactions should be * CustomManyParticleForce also lets you specify "exclusions", particular pairs of particles whose interactions should be
* omitted from force and energy calculations. This is most often used for particles that are bonded to each other. * omitted from force and energy calculations. This is most often used for particles that are bonded to each other.
...@@ -89,7 +89,8 @@ namespace OpenMM { ...@@ -89,7 +89,8 @@ namespace OpenMM {
* "C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;" * "C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
* "theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);" * "theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
* "r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)"); * "r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
* <pre></tt> * force->setPermutationMode(CustomManyParticleForce::SinglePermutation);
* </pre></tt>
* *
* This force depends on one parameter, C. The following code defines it as a global parameter: * This force depends on one parameter, C. The following code defines it as a global parameter:
* *
...@@ -97,16 +98,38 @@ namespace OpenMM { ...@@ -97,16 +98,38 @@ namespace OpenMM {
* force->addGlobalParameter("C", 1.0); * force->addGlobalParameter("C", 1.0);
* </pre></tt> * </pre></tt>
* *
* The expression <i>must</i> be symmetric with respect to the particles. It typically will only be evaluated once for * Notice that the expression is symmetric with respect to the particles. It only depends on the products
* each set of particles, and no guarantee is made about which particle will be identified as "particle 1". In the above * cos(theta1)*cos(theta2)*cos(theta3) and r12*r13*r23, both of which are unchanged if the labels p1, p2, and p3 are permuted.
* example, the energy only depends on the products cos(theta1)*cos(theta2)*cos(theta3) and r12*r13*r23, both of which are * This is required because we specified SinglePermutation as the permutation mode. (This is the default, so we did not
* unchanged if the labels p1, p2, and p3 are permuted. If that were not true, the results would be undefined, because * really need to set it, but doing so makes the example clearer.) In this mode, the expression is only evaluated once for
* each set of particles. No guarantee is made about which particle will be identified as p1, p2, etc. Therefore, the
* energy <i>must</i> be symmetric with respect to exchange of particles. Otherwise, the results would be undefined because
* permuting the labels would change the energy. * permuting the labels would change the energy.
* *
* In some cases this requirement is overly restrictive. When some particles are fundamentally different from others, * Not all many-particle interactions work this way. Another common pattern is for the expression to describe an interaction
* the expression may be inherently non-symmetric. An example would be a water model that involves three particles, * between one central particle and other nearby particles. An example of this is the 3-particle piece of the Stillinger-Weber
* two of which <i>must</i> be hydrogen and one of which <i>must</i> be oxygen. Cases like this can be implemented * potential:
* using particle types. *
* <tt><pre>CustomManyParticleForce* force = new CustomManyParticleForce(3,
* "L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));"
"r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)");
* force->setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
* </pre></tt>
*
* When the permutation mode is set to UniqueCentralParticle, particle p1 is treated as the central particle. For a set of
* N particles, the expression is evaluated N times, once with each particle as p1. The expression can therefore treat
* p1 differently from the other particles. Notice that it is still symmetric with respect to p2 and p3, however. There
* is no guarantee about how those labels will be assigned to particles.
*
* Distance cutoffs are applied in different ways depending on the permutation mode. In SinglePermutation mode, every particle
* in the set must be within the cutoff distance of every other particle. If <i>any</i> two particles are further apart than
* the cutoff distance, the interaction is skipped. In UniqueCentralParticle mode, each particle must be within the cutoff
* distance of the central particle, but not necessarily of all the other particles. The cutoff may therefore exclude a subset
* of the permutations of a set of particles.
*
* Another common situation is that some particles are fundamentally different from others, causing the expression to be
* inherently non-symmetric. An example would be a water model that involves three particles, two of which <i>must</i> be
* hydrogen and one of which <i>must</i> be oxygen. Cases like this can be implemented using particle types.
* *
* A particle type is an integer that you specify when you call addParticle(). (If you omit the argument, it defaults * A particle type is an integer that you specify when you call addParticle(). (If you omit the argument, it defaults
* to 0.) For the water model, you could specify 0 for all oxygen atoms and 1 for all hydrogen atoms. You can then * to 0.) For the water model, you could specify 0 for all oxygen atoms and 1 for all hydrogen atoms. You can then
...@@ -157,6 +180,26 @@ public: ...@@ -157,6 +180,26 @@ public:
*/ */
CutoffPeriodic = 2, CutoffPeriodic = 2,
}; };
/**
* This is an enumeration of the different modes for selecting which permutations of a set of particles to evaluate the
* interaction for.
*/
enum PermutationMode {
/**
* For any set of particles, the interaction is evaluated only once for a single permutation of the particles.
* There is no guarantee about which permutation will be used (aside from the requirement to satisfy type filters),
* so the expression must be symmetric. If cutoffs are used, then every particle in the set must be within the
* cutoff distance of every other particle.
*/
SinglePermutation = 0,
/**
* The interaction is treated as an interaction between one central particle (p1) and various other nearby particles
* (p2, p3, ...). For a set of N particles it will be evaluated N times, once with each particle as p1. The expression
* must be symmetric with respect to the other particles, but may treat p1 differently. If cutoffs are used, then
* every particle must be within the cutoff distance of p1.
*/
UniqueCentralParticle = 1
};
/** /**
* Create a CustomManyParticleForce. * Create a CustomManyParticleForce.
* *
...@@ -218,6 +261,14 @@ public: ...@@ -218,6 +261,14 @@ public:
* Set the method used for handling long range nonbonded interactions. * Set the method used for handling long range nonbonded interactions.
*/ */
void setNonbondedMethod(NonbondedMethod method); void setNonbondedMethod(NonbondedMethod method);
/**
* Get the mode that selects which permutations of a set of particles to evaluate the interaction for.
*/
PermutationMode getPermutationMode() const;
/**
* Set the mode that selects which permutations of a set of particles to evaluate the interaction for.
*/
void setPermutationMode(PermutationMode mode);
/** /**
* Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use * Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect. * is NoCutoff, this value will have no effect.
...@@ -420,6 +471,7 @@ private: ...@@ -420,6 +471,7 @@ private:
class FunctionInfo; class FunctionInfo;
int particlesPerSet; int particlesPerSet;
NonbondedMethod nonbondedMethod; NonbondedMethod nonbondedMethod;
PermutationMode permutationMode;
double cutoffDistance; double cutoffDistance;
std::string energyExpression; std::string energyExpression;
std::vector<ParticleParameterInfo> particleParameters; std::vector<ParticleParameterInfo> particleParameters;
......
openmmapi/src/CustomManyParticleForce.cpp
View file @ f5acdd7a
...@@ -44,7 +44,7 @@ using namespace OpenMM; ...@@ -44,7 +44,7 @@ using namespace OpenMM;
using namespace std; using namespace std;
CustomManyParticleForce::CustomManyParticleForce(int particlesPerSet, const string& energy) : CustomManyParticleForce::CustomManyParticleForce(int particlesPerSet, const string& energy) :
particlesPerSet(particlesPerSet), energyExpression(energy), nonbondedMethod(NoCutoff), cutoffDistance(1.0), typeFilters(particlesPerSet) { particlesPerSet(particlesPerSet), energyExpression(energy), nonbondedMethod(NoCutoff), permutationMode(SinglePermutation), cutoffDistance(1.0), typeFilters(particlesPerSet) {
} }
CustomManyParticleForce::~CustomManyParticleForce() { CustomManyParticleForce::~CustomManyParticleForce() {
...@@ -68,6 +68,14 @@ void CustomManyParticleForce::setNonbondedMethod(NonbondedMethod method) { ...@@ -68,6 +68,14 @@ void CustomManyParticleForce::setNonbondedMethod(NonbondedMethod method) {
nonbondedMethod = method; nonbondedMethod = method;
} }
CustomManyParticleForce::PermutationMode CustomManyParticleForce::getPermutationMode() const {
return permutationMode;
}
void CustomManyParticleForce::setPermutationMode(PermutationMode mode) {
permutationMode = mode;
}
double CustomManyParticleForce::getCutoffDistance() const { double CustomManyParticleForce::getCutoffDistance() const {
return cutoffDistance; return cutoffDistance;
} }
......
platforms/cpu/include/CpuCustomManyParticleForce.h
View file @ f5acdd7a
...@@ -51,7 +51,7 @@ private: ...@@ -51,7 +51,7 @@ private:
class ComputeForceTask; class ComputeForceTask;
class ThreadData; class ThreadData;
int numParticles, numParticlesPerSet, numPerParticleParameters, numTypes; int numParticles, numParticlesPerSet, numPerParticleParameters, numTypes;
bool useCutoff, usePeriodic; bool useCutoff, usePeriodic, centralParticleMode;
RealOpenMM cutoffDistance; RealOpenMM cutoffDistance;
RealOpenMM periodicBoxSize[3]; RealOpenMM periodicBoxSize[3];
CpuNeighborList* neighborList; CpuNeighborList* neighborList;
...@@ -60,6 +60,7 @@ private: ...@@ -60,6 +60,7 @@ private:
std::vector<int> particleTypes; std::vector<int> particleTypes;
std::vector<int> orderIndex; std::vector<int> orderIndex;
std::vector<std::vector<int> > particleOrder; std::vector<std::vector<int> > particleOrder;
std::vector<std::vector<int> > particleNeighbors;
std::vector<ThreadData*> threadData; std::vector<ThreadData*> threadData;
// The following variables are used to make information accessible to the individual threads. // The following variables are used to make information accessible to the individual threads.
float* posq; float* posq;
......
platforms/cpu/src/CpuCustomManyParticleForce.cpp
View file @ f5acdd7a
...@@ -54,6 +54,7 @@ CpuCustomManyParticleForce::CpuCustomManyParticleForce(const CustomManyParticleF ...@@ -54,6 +54,7 @@ CpuCustomManyParticleForce::CpuCustomManyParticleForce(const CustomManyParticleF
numParticles = force.getNumParticles(); numParticles = force.getNumParticles();
numParticlesPerSet = force.getNumParticlesPerSet(); numParticlesPerSet = force.getNumParticlesPerSet();
numPerParticleParameters = force.getNumPerParticleParameters(); numPerParticleParameters = force.getNumPerParticleParameters();
centralParticleMode = (force.getPermutationMode() == CustomManyParticleForce::UniqueCentralParticle);
// Create custom functions for the tabulated functions. // Create custom functions for the tabulated functions.
...@@ -114,10 +115,31 @@ void CpuCustomManyParticleForce::calculateIxn(AlignedArray<float>& posq, RealOpe ...@@ -114,10 +115,31 @@ void CpuCustomManyParticleForce::calculateIxn(AlignedArray<float>& posq, RealOpe
gmx_atomic_set(&counter, 0); gmx_atomic_set(&counter, 0);
this->atomicCounter = &counter; this->atomicCounter = &counter;
if (useCutoff) { if (useCutoff) {
// Construct a neighbor list. // Construct a neighbor list. We use CpuNeighborList to do this, but then copy the result
// into a new data structure. This is needed because in UniqueCentralParticle mode, the
// the neighbor list needs to include symmetric pairs.
particleNeighbors.resize(numParticles);
for (int i = 0; i < numParticles; i++)
particleNeighbors[i].clear();
float boxSizeFloat[] = {(float) periodicBoxSize[0], (float) periodicBoxSize[1], (float) periodicBoxSize[2]}; float boxSizeFloat[] = {(float) periodicBoxSize[0], (float) periodicBoxSize[1], (float) periodicBoxSize[2]};
neighborList->computeNeighborList(numParticles, posq, exclusions, boxSizeFloat, usePeriodic, cutoffDistance, threads); neighborList->computeNeighborList(numParticles, posq, exclusions, boxSizeFloat, usePeriodic, cutoffDistance, threads);
for (int blockIndex = 0; blockIndex < neighborList->getNumBlocks(); blockIndex++) {
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
int numNeighbors = neighbors.size();
for (int i = 0; i < 4; i++) {
int p1 = neighborList->getSortedAtoms()[4*blockIndex+i];
for (int j = 0; j < numNeighbors; j++) {
if ((exclusions[j] & (1<<i)) == 0) {
int p2 = neighbors[j];
particleNeighbors[p1].push_back(p2);
if (centralParticleMode)
particleNeighbors[p2].push_back(p1);
}
}
}
}
} }
// Signal the threads to start running and wait for them to finish. // Signal the threads to start running and wait for them to finish.
...@@ -147,27 +169,12 @@ void CpuCustomManyParticleForce::threadComputeForce(ThreadPool& threads, int thr ...@@ -147,27 +169,12 @@ void CpuCustomManyParticleForce::threadComputeForce(ThreadPool& threads, int thr
if (useCutoff) { if (useCutoff) {
// Loop over interactions from the neighbor list. // Loop over interactions from the neighbor list.
vector<int> particles;
while (true) { while (true) {
int blockIndex = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1); int i = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
if (blockIndex >= neighborList->getNumBlocks()) if (i >= numParticles)
break; break;
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex); particleIndices[0] = i;
const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex); loopOverInteractions(particleNeighbors[i], particleIndices, 1, 0, particleParameters, forces, data, boxSize, invBoxSize);
int numNeighbors = neighbors.size();
for (int i = 0; i < 4; i++) {
particleIndices[0] = neighborList->getSortedAtoms()[4*blockIndex+i];
// Build a filtered list of neighbors after removing exclusions. We'll check for actual exclusions
// again later, but the neighbor list also includes padding atoms that it marks as exclusions, so
// we need to remove those now.
particles.resize(0);
for (int j = 0; j < numNeighbors; j++)
if ((exclusions[j] & (1<<i)) == 0)
particles.push_back(neighbors[j]);
loopOverInteractions(particles, particleIndices, 1, 0, particleParameters, forces, data, boxSize, invBoxSize);
}
} }
} }
else { else {
...@@ -181,7 +188,8 @@ void CpuCustomManyParticleForce::threadComputeForce(ThreadPool& threads, int thr ...@@ -181,7 +188,8 @@ void CpuCustomManyParticleForce::threadComputeForce(ThreadPool& threads, int thr
if (i >= numParticles) if (i >= numParticles)
break; break;
particleIndices[0] = i; particleIndices[0] = i;
loopOverInteractions(particles, particleIndices, 1, i+1, particleParameters, forces, data, boxSize, invBoxSize); int startIndex = (centralParticleMode ? 0 : i+1);
loopOverInteractions(particles, particleIndices, 1, startIndex, particleParameters, forces, data, boxSize, invBoxSize);
} }
} }
} }
...@@ -208,6 +216,7 @@ void CpuCustomManyParticleForce::loopOverInteractions(vector<int>& availablePart ...@@ -208,6 +216,7 @@ void CpuCustomManyParticleForce::loopOverInteractions(vector<int>& availablePart
RealOpenMM** particleParameters, float* forces, ThreadData& data, const fvec4& boxSize, const fvec4& invBoxSize) { RealOpenMM** particleParameters, float* forces, ThreadData& data, const fvec4& boxSize, const fvec4& invBoxSize) {
int numParticles = availableParticles.size(); int numParticles = availableParticles.size();
double cutoff2 = cutoffDistance*cutoffDistance; double cutoff2 = cutoffDistance*cutoffDistance;
int checkRange = (centralParticleMode ? 1 : loopIndex);
for (int i = startIndex; i < numParticles; i++) { for (int i = startIndex; i < numParticles; i++) {
int particle = availableParticles[i]; int particle = availableParticles[i];
...@@ -218,7 +227,7 @@ void CpuCustomManyParticleForce::loopOverInteractions(vector<int>& availablePart ...@@ -218,7 +227,7 @@ void CpuCustomManyParticleForce::loopOverInteractions(vector<int>& availablePart
fvec4 deltaR; fvec4 deltaR;
fvec4 pos1(posq+4*particle); fvec4 pos1(posq+4*particle);
float r2; float r2;
for (int j = 0; j < loopIndex && include; j++) { for (int j = 0; j < checkRange && include; j++) {
fvec4 pos2(posq+4*particleSet[j]); fvec4 pos2(posq+4*particleSet[j]);
computeDelta(pos1, pos2, deltaR, r2, boxSize, invBoxSize); computeDelta(pos1, pos2, deltaR, r2, boxSize, invBoxSize);
include &= (r2 < cutoff2); include &= (r2 < cutoff2);
...@@ -227,6 +236,8 @@ void CpuCustomManyParticleForce::loopOverInteractions(vector<int>& availablePart ...@@ -227,6 +236,8 @@ void CpuCustomManyParticleForce::loopOverInteractions(vector<int>& availablePart
for (int j = 0; j < loopIndex && include; j++) for (int j = 0; j < loopIndex && include; j++)
include &= (exclusions[particle].find(particleSet[j]) == exclusions[particle].end()); include &= (exclusions[particle].find(particleSet[j]) == exclusions[particle].end());
if (include) { if (include) {
if (loopIndex > 0 && availableParticles[i] == particleSet[0])
continue;
particleSet[loopIndex] = availableParticles[i]; particleSet[loopIndex] = availableParticles[i];
if (loopIndex == numParticlesPerSet-1) if (loopIndex == numParticlesPerSet-1)
calculateOneIxn(particleSet, particleParameters, forces, data, boxSize, invBoxSize); calculateOneIxn(particleSet, particleParameters, forces, data, boxSize, invBoxSize);
......
platforms/cpu/tests/TestCpuCustomManyParticleForce.cpp
View file @ f5acdd7a
...@@ -121,6 +121,77 @@ void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& p ...@@ -121,6 +121,77 @@ void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& p
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-4); ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-4);
} }
void validateStillingerWeber(CustomManyParticleForce* force, const vector<Vec3>& positions, const vector<const int*>& expectedSets, double boxSize) {
// Create a System and Context.
int numParticles = force->getNumParticles();
CustomManyParticleForce::NonbondedMethod nonbondedMethod = force->getNonbondedMethod();
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(force);
VerletIntegrator integrator(0.001);
CpuPlatform platform;
Context context(system, integrator, platform);
context.setPositions(positions);
State state1 = context.getState(State::Forces | State::Energy);
double L = context.getParameter("L");
double eps = context.getParameter("eps");
double a = context.getParameter("a");
double gamma = context.getParameter("gamma");
double sigma = context.getParameter("sigma");
// See if the energy matches the expected value.
double expectedEnergy = 0;
for (int i = 0; i < (int) expectedSets.size(); i++) {
int p1 = expectedSets[i][0];
int p2 = expectedSets[i][1];
int p3 = expectedSets[i][2];
Vec3 d12 = positions[p2]-positions[p1];
Vec3 d13 = positions[p3]-positions[p1];
Vec3 d23 = positions[p3]-positions[p2];
if (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic) {
for (int j = 0; j < 3; j++) {
d12[j] -= floor(d12[j]/boxSize+0.5f)*boxSize;
d13[j] -= floor(d13[j]/boxSize+0.5f)*boxSize;
d23[j] -= floor(d23[j]/boxSize+0.5f)*boxSize;
}
}
double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13));
double r23 = sqrt(d23.dot(d23));
double ctheta1 = d12.dot(d13)/(r12*r13);
double ctheta2 = -d12.dot(d23)/(r12*r23);
double ctheta3 = d13.dot(d23)/(r13*r23);
expectedEnergy += L*eps*(ctheta1+1.0/3.0)*(ctheta1+1.0/3.0)*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));
}
ASSERT_EQUAL_TOL(expectedEnergy, state1.getPotentialEnergy(), 1e-5);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
const vector<Vec3>& forces = state1.getForces();
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-4);
}
void testNoCutoff() { void testNoCutoff() {
CustomManyParticleForce* force = new CustomManyParticleForce(3, CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;" "C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
...@@ -504,6 +575,102 @@ void testLargeSystem() { ...@@ -504,6 +575,102 @@ void testLargeSystem() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4); ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
} }
void testCentralParticleModeNoCutoff() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));"
"r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)");
force->setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
force->addGlobalParameter("L", 23.13);
force->addGlobalParameter("eps", 25.894776);
force->addGlobalParameter("a", 1.8);
force->addGlobalParameter("sigma", 0.23925);
force->addGlobalParameter("gamma", 1.2);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
int sets[12][3] = {{0,1,2}, {0,1,3}, {0,2,3}, {1,0,2}, {1,0,3}, {1, 2, 3}, {2,0,1}, {2,0,3}, {2, 1, 3}, {3,0,1}, {3,0,2}, {3,1,2}};
vector<const int*> expectedSets(&sets[0], &sets[12]);
validateStillingerWeber(force, positions, expectedSets, 2.0);
}
void testCentralParticleModeCutoff() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));"
"r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)");
force->setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
force->addGlobalParameter("L", 23.13);
force->addGlobalParameter("eps", 25.894776);
force->addGlobalParameter("a", 1.8);
force->addGlobalParameter("sigma", 0.23925);
force->addGlobalParameter("gamma", 1.2);
force->setNonbondedMethod(CustomManyParticleForce::CutoffNonPeriodic);
force->setCutoffDistance(1.55);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
int sets[8][3] = {{0,1,2}, {0,1,3}, {0,2,3}, {1,0,2}, {1,0,3}, {1, 2, 3}, {2,0,1}, {3,0,1}};
vector<const int*> expectedSets(&sets[0], &sets[8]);
validateStillingerWeber(force, positions, expectedSets, 2.0);
}
void testCentralParticleModeLargeSystem() {
int gridSize = 8;
int numParticles = gridSize*gridSize*gridSize;
double boxSize = 2.0;
double spacing = boxSize/gridSize;
CpuPlatform platform;
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));"
"r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)");
force->setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
force->addGlobalParameter("L", 23.13);
force->addGlobalParameter("eps", 25.894776);
force->addGlobalParameter("a", 1.8);
force->addGlobalParameter("sigma", 0.23925);
force->addGlobalParameter("gamma", 1.2);
force->setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
force->setCutoffDistance(1.8*0.23925);
vector<double> params;
vector<Vec3> positions;
System system;
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
force->addParticle(params);
positions.push_back(Vec3((i+0.4*genrand_real2(sfmt))*spacing, (j+0.4*genrand_real2(sfmt))*spacing, (k+0.4*genrand_real2(sfmt))*spacing));
system.addParticle(1.0);
}
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(force);
VerletIntegrator integrator1(0.001);
VerletIntegrator integrator2(0.001);
Context context1(system, integrator1, Platform::getPlatformByName("Reference"));
Context context2(system, integrator2, platform);
context1.setPositions(positions);
context2.setPositions(positions);
State state1 = context1.getState(State::Forces | State::Energy);
State state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
int main() { int main() {
try { try {
testNoCutoff(); testNoCutoff();
...@@ -515,6 +682,9 @@ int main() { ...@@ -515,6 +682,9 @@ int main() {
testTabulatedFunctions(); testTabulatedFunctions();
testTypeFilters(); testTypeFilters();
testLargeSystem(); testLargeSystem();
testCentralParticleModeNoCutoff();
testCentralParticleModeCutoff();
testCentralParticleModeLargeSystem();
} }
catch(const exception& e) { catch(const exception& e) {
cout << "exception: " << e.what() << endl; cout << "exception: " << e.what() << endl;
......
platforms/reference/include/ReferenceCustomManyParticleIxn.h
View file @ f5acdd7a
...@@ -44,7 +44,7 @@ class ReferenceCustomManyParticleIxn { ...@@ -44,7 +44,7 @@ class ReferenceCustomManyParticleIxn {
class AngleTermInfo; class AngleTermInfo;
class DihedralTermInfo; class DihedralTermInfo;
int numParticlesPerSet, numPerParticleParameters, numTypes; int numParticlesPerSet, numPerParticleParameters, numTypes;
bool useCutoff, usePeriodic; bool useCutoff, usePeriodic, centralParticleMode;
RealOpenMM cutoffDistance; RealOpenMM cutoffDistance;
RealOpenMM periodicBoxSize[3]; RealOpenMM periodicBoxSize[3];
Lepton::ExpressionProgram energyExpression; Lepton::ExpressionProgram energyExpression;
......
platforms/reference/src/SimTKReference/ReferenceCustomManyParticleIxn.cpp
View file @ f5acdd7a
...@@ -41,6 +41,7 @@ using namespace std; ...@@ -41,6 +41,7 @@ using namespace std;
ReferenceCustomManyParticleIxn::ReferenceCustomManyParticleIxn(const CustomManyParticleForce& force) : useCutoff(false), usePeriodic(false) { ReferenceCustomManyParticleIxn::ReferenceCustomManyParticleIxn(const CustomManyParticleForce& force) : useCutoff(false), usePeriodic(false) {
numParticlesPerSet = force.getNumParticlesPerSet(); numParticlesPerSet = force.getNumParticlesPerSet();
numPerParticleParameters = force.getNumPerParticleParameters(); numPerParticleParameters = force.getNumPerParticleParameters();
centralParticleMode = (force.getPermutationMode() == CustomManyParticleForce::UniqueCentralParticle);
// Create custom functions for the tabulated functions. // Create custom functions for the tabulated functions.
...@@ -134,8 +135,11 @@ void ReferenceCustomManyParticleIxn::loopOverInteractions(vector<int>& particles ...@@ -134,8 +135,11 @@ void ReferenceCustomManyParticleIxn::loopOverInteractions(vector<int>& particles
RealOpenMM** particleParameters, map<string, double>& variables, vector<OpenMM::RealVec>& forces, RealOpenMM** particleParameters, map<string, double>& variables, vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const { RealOpenMM* totalEnergy) const {
int numParticles = atomCoordinates.size(); int numParticles = atomCoordinates.size();
int start = (loopIndex == 0 ? 0 : particles[loopIndex-1]+1); int firstPartialLoop = (centralParticleMode ? 2 : 1);
int start = (loopIndex < firstPartialLoop ? 0 : particles[loopIndex-1]+1);
for (int i = start; i < numParticles; i++) { for (int i = start; i < numParticles; i++) {
if (loopIndex > 0 && i == particles[0])
continue;
particles[loopIndex] = i; particles[loopIndex] = i;
if (loopIndex == numParticlesPerSet-1) if (loopIndex == numParticlesPerSet-1)
calculateOneIxn(particles, atomCoordinates, particleParameters, variables, forces, totalEnergy); calculateOneIxn(particles, atomCoordinates, particleParameters, variables, forces, totalEnergy);
...@@ -173,7 +177,7 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle ...@@ -173,7 +177,7 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
int p2 = permutedParticles[j]; int p2 = permutedParticles[j];
if (exclusions[p1].find(p2) != exclusions[p1].end()) if (exclusions[p1].find(p2) != exclusions[p1].end())
return; return;
if (useCutoff) { if (useCutoff && (i == 0 || !centralParticleMode)) {
RealOpenMM delta[ReferenceForce::LastDeltaRIndex]; RealOpenMM delta[ReferenceForce::LastDeltaRIndex];
computeDelta(p1, p2, delta, atomCoordinates); computeDelta(p1, p2, delta, atomCoordinates);
if (delta[ReferenceForce::RIndex] >= cutoffDistance) if (delta[ReferenceForce::RIndex] >= cutoffDistance)
......
platforms/reference/tests/TestReferenceCustomManyParticleForce.cpp
View file @ f5acdd7a
...@@ -121,6 +121,77 @@ void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& p ...@@ -121,6 +121,77 @@ void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& p
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-4); ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-4);
} }
void validateStillingerWeber(CustomManyParticleForce* force, const vector<Vec3>& positions, const vector<const int*>& expectedSets, double boxSize) {
// Create a System and Context.
int numParticles = force->getNumParticles();
CustomManyParticleForce::NonbondedMethod nonbondedMethod = force->getNonbondedMethod();
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(force);
VerletIntegrator integrator(0.001);
ReferencePlatform platform;
Context context(system, integrator, platform);
context.setPositions(positions);
State state1 = context.getState(State::Forces | State::Energy);
double L = context.getParameter("L");
double eps = context.getParameter("eps");
double a = context.getParameter("a");
double gamma = context.getParameter("gamma");
double sigma = context.getParameter("sigma");
// See if the energy matches the expected value.
double expectedEnergy = 0;
for (int i = 0; i < (int) expectedSets.size(); i++) {
int p1 = expectedSets[i][0];
int p2 = expectedSets[i][1];
int p3 = expectedSets[i][2];
Vec3 d12 = positions[p2]-positions[p1];
Vec3 d13 = positions[p3]-positions[p1];
Vec3 d23 = positions[p3]-positions[p2];
if (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic) {
for (int j = 0; j < 3; j++) {
d12[j] -= floor(d12[j]/boxSize+0.5f)*boxSize;
d13[j] -= floor(d13[j]/boxSize+0.5f)*boxSize;
d23[j] -= floor(d23[j]/boxSize+0.5f)*boxSize;
}
}
double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13));
double r23 = sqrt(d23.dot(d23));
double ctheta1 = d12.dot(d13)/(r12*r13);
double ctheta2 = -d12.dot(d23)/(r12*r23);
double ctheta3 = d13.dot(d23)/(r13*r23);
expectedEnergy += L*eps*(ctheta1+1.0/3.0)*(ctheta1+1.0/3.0)*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));
}
ASSERT_EQUAL_TOL(expectedEnergy, state1.getPotentialEnergy(), 1e-5);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
const vector<Vec3>& forces = state1.getForces();
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-4);
}
void testNoCutoff() { void testNoCutoff() {
CustomManyParticleForce* force = new CustomManyParticleForce(3, CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;" "C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
...@@ -464,6 +535,58 @@ void testTypeFilters() { ...@@ -464,6 +535,58 @@ void testTypeFilters() {
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5); ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
} }
void testCentralParticleModeNoCutoff() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));"
"r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)");
force->setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
force->addGlobalParameter("L", 23.13);
force->addGlobalParameter("eps", 25.894776);
force->addGlobalParameter("a", 1.8);
force->addGlobalParameter("sigma", 0.23925);
force->addGlobalParameter("gamma", 1.2);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
int sets[12][3] = {{0,1,2}, {0,1,3}, {0,2,3}, {1,0,2}, {1,0,3}, {1, 2, 3}, {2,0,1}, {2,0,3}, {2, 1, 3}, {3,0,1}, {3,0,2}, {3,1,2}};
vector<const int*> expectedSets(&sets[0], &sets[12]);
validateStillingerWeber(force, positions, expectedSets, 2.0);
}
void testCentralParticleModeCutoff() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));"
"r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)");
force->setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
force->addGlobalParameter("L", 23.13);
force->addGlobalParameter("eps", 25.894776);
force->addGlobalParameter("a", 1.8);
force->addGlobalParameter("sigma", 0.23925);
force->addGlobalParameter("gamma", 1.2);
force->setNonbondedMethod(CustomManyParticleForce::CutoffNonPeriodic);
force->setCutoffDistance(1.55);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
int sets[8][3] = {{0,1,2}, {0,1,3}, {0,2,3}, {1,0,2}, {1,0,3}, {1, 2, 3}, {2,0,1}, {3,0,1}};
vector<const int*> expectedSets(&sets[0], &sets[8]);
validateStillingerWeber(force, positions, expectedSets, 2.0);
}
int main() { int main() {
try { try {
testNoCutoff(); testNoCutoff();
...@@ -474,6 +597,8 @@ int main() { ...@@ -474,6 +597,8 @@ int main() {
testParameters(); testParameters();
testTabulatedFunctions(); testTabulatedFunctions();
testTypeFilters(); testTypeFilters();
testCentralParticleModeNoCutoff();
testCentralParticleModeCutoff();
} }
catch(const exception& e) { catch(const exception& e) {
cout << "exception: " << e.what() << endl; cout << "exception: " << e.what() << endl;
......
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