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Commit 4b6f53e5 authored by peastman's avatar peastman
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Began implementing triclinic boxes for CPU platform

parent 9c6011f8
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Showing with 167 additions and 37 deletions
platforms/cpu/include/CpuNonbondedForce.h
View file @ 4b6f53e5
......@@ -83,11 +83,11 @@ class CpuNonbondedForce {
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@param periodicBoxVectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(float* periodicBoxSize);
void setPeriodic(RealVec* periodicBoxVectors);
/**---------------------------------------------------------------------------------------
......@@ -161,11 +161,14 @@ protected:
bool cutoff;
bool useSwitch;
bool periodic;
bool triclinic;
bool ewald;
bool pme;
bool tableIsValid;
const CpuNeighborList* neighborList;
float periodicBoxSize[3];
float recipBoxSize[3];
RealVec periodicBoxVectors[3];
AlignedArray<fvec4> periodicBoxVec4;
float cutoffDistance, switchingDistance;
float krf, crf;
float alphaEwald;
......
platforms/cpu/src/CpuKernels.cpp
View file @ 4b6f53e5
......@@ -73,6 +73,11 @@ static RealVec& extractBoxSize(ContextImpl& context) {
return *(RealVec*) data->periodicBoxSize;
}
static RealVec* extractBoxVectors(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return (RealVec*) data->periodicBoxVectors;
}
static ReferenceConstraints& extractConstraints(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return *(ReferenceConstraints*) data->constraints;
......@@ -147,19 +152,36 @@ public:
AlignedArray<float>& posq = data.posq;
vector<RealVec>& posData = extractPositions(context);
RealVec boxSize = extractBoxSize(context);
double invBoxSize[3] = {1/boxSize[0], 1/boxSize[1], 1/boxSize[2]};
RealVec* boxVectors = extractBoxVectors(context);
double boxSize[3] = {boxVectors[0][0], boxVectors[1][1], boxVectors[2][2]};
double invBoxSize[3] = {1/boxVectors[0][0], 1/boxVectors[1][1], 1/boxVectors[2][2]};
bool triclinic = (boxVectors[0][1] != 0 || boxVectors[0][2] != 0 || boxVectors[1][0] != 0 || boxVectors[1][2] != 0 || boxVectors[2][0] != 0 || boxVectors[2][1] != 0);
int numParticles = context.getSystem().getNumParticles();
int numThreads = threads.getNumThreads();
int start = threadIndex*numParticles/numThreads;
int end = (threadIndex+1)*numParticles/numThreads;
if (data.isPeriodic)
for (int i = start; i < end; i++)
if (data.isPeriodic) {
if (triclinic) {
for (int i = start; i < end; i++) {
RealVec pos = posData[i];
pos -= boxVectors[2]*floor(pos[2]*invBoxSize[2]);
pos -= boxVectors[1]*floor(pos[1]*invBoxSize[1]);
pos -= boxVectors[0]*floor(pos[0]*invBoxSize[0]);
posq[4*i] = (float) pos[0];
posq[4*i+1] = (float) pos[1];
posq[4*i+2] = (float) pos[2];
}
}
else {
for (int i = start; i < end; i++) {
for (int j = 0; j < 3; j++) {
RealOpenMM x = posData[i][j];
double base = floor(x*invBoxSize[j])*boxSize[j];
posq[4*i+j] = (float) (x-base);
}
}
}
}
else
for (int i = start; i < end; i++) {
posq[4*i] = (float) posData[i][0];
......@@ -543,10 +565,11 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
nonbonded->setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric);
}
if (data.isPeriodic) {
RealVec* boxVectors = extractBoxVectors(context);
double minAllowedSize = 1.999999*nonbondedCutoff;
if (boxSize[0] < minAllowedSize || boxSize[1] < minAllowedSize || boxSize[2] < minAllowedSize)
if (boxVectors[0][0] < minAllowedSize || boxVectors[1][1] < minAllowedSize || boxVectors[2][2] < minAllowedSize)
throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
nonbonded->setPeriodic(floatBoxSize);
nonbonded->setPeriodic(boxVectors);
}
if (ewald)
nonbonded->setUseEwald(ewaldAlpha, kmax[0], kmax[1], kmax[2]);
......
platforms/cpu/src/CpuNonbondedForce.cpp
View file @ 4b6f53e5
......@@ -103,20 +103,30 @@ void CpuNonbondedForce::setUseSwitchingFunction(float distance) {
also been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@param periodicBoxVectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void CpuNonbondedForce::setPeriodic(float* periodicBoxSize) {
void CpuNonbondedForce::setPeriodic(RealVec* periodicBoxVectors) {
assert(cutoff);
assert(periodicBoxSize[0] >= 2*cutoffDistance);
assert(periodicBoxSize[1] >= 2*cutoffDistance);
assert(periodicBoxSize[2] >= 2*cutoffDistance);
assert(periodicBoxVectors[0][0] >= 2.0*cutoffDistance);
assert(periodicBoxVectors[1][1] >= 2.0*cutoffDistance);
assert(periodicBoxVectors[2][2] >= 2.0*cutoffDistance);
periodic = true;
this->periodicBoxSize[0] = periodicBoxSize[0];
this->periodicBoxSize[1] = periodicBoxSize[1];
this->periodicBoxSize[2] = periodicBoxSize[2];
this->periodicBoxVectors[0] = periodicBoxVectors[0];
this->periodicBoxVectors[1] = periodicBoxVectors[1];
this->periodicBoxVectors[2] = periodicBoxVectors[2];
recipBoxSize[0] = (float) (1.0/periodicBoxVectors[0][0]);
recipBoxSize[1] = (float) (1.0/periodicBoxVectors[1][1]);
recipBoxSize[2] = (float) (1.0/periodicBoxVectors[2][2]);
periodicBoxVec4.resize(3);
periodicBoxVec4[0] = fvec4(periodicBoxVectors[0][0], periodicBoxVectors[0][1], periodicBoxVectors[0][2], 0);
periodicBoxVec4[1] = fvec4(periodicBoxVectors[1][0], periodicBoxVectors[1][1], periodicBoxVectors[1][2], 0);
periodicBoxVec4[2] = fvec4(periodicBoxVectors[2][0], periodicBoxVectors[2][1], periodicBoxVectors[2][2], 0);
triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 ||
periodicBoxVectors[1][0] != 0.0 || periodicBoxVectors[1][2] != 0.0 ||
periodicBoxVectors[2][0] != 0.0 || periodicBoxVectors[2][1] != 0.0);
}
/**---------------------------------------------------------------------------------------
......@@ -186,7 +196,7 @@ void CpuNonbondedForce::calculateReciprocalIxn(int numberOfAtoms, float* posq, c
int kmax = (ewald ? max(numRx, max(numRy,numRz)) : 0);
float factorEwald = -1 / (4*alphaEwald*alphaEwald);
float TWO_PI = 2.0 * PI_M;
float recipCoeff = (float)(ONE_4PI_EPS0*4*PI_M/(periodicBoxSize[0] * periodicBoxSize[1] * periodicBoxSize[2]) /epsilon);
float recipCoeff = (float)(ONE_4PI_EPS0*4*PI_M/(periodicBoxVectors[0][0] * periodicBoxVectors[1][1] * periodicBoxVectors[2][2]) /epsilon);
if (pme) {
pme_t pmedata;
......@@ -194,9 +204,8 @@ void CpuNonbondedForce::calculateReciprocalIxn(int numberOfAtoms, float* posq, c
vector<RealOpenMM> charges(numberOfAtoms);
for (int i = 0; i < numberOfAtoms; i++)
charges[i] = posq[4*i+3];
RealVec boxVectors[3] = {Vec3(periodicBoxSize[0], 0, 0), Vec3(0, periodicBoxSize[1], 0), Vec3(0, 0, periodicBoxSize[2])};
RealOpenMM recipEnergy = 0.0;
pme_exec(pmedata, atomCoordinates, forces, charges, boxVectors, &recipEnergy);
pme_exec(pmedata, atomCoordinates, forces, charges, periodicBoxVectors, &recipEnergy);
if (totalEnergy)
*totalEnergy += recipEnergy;
pme_destroy(pmedata);
......@@ -208,7 +217,7 @@ void CpuNonbondedForce::calculateReciprocalIxn(int numberOfAtoms, float* posq, c
// setup reciprocal box
float recipBoxSize[3] = { TWO_PI / periodicBoxSize[0], TWO_PI / periodicBoxSize[1], TWO_PI / periodicBoxSize[2]};
float recipBoxSize[3] = { TWO_PI / periodicBoxVectors[0][0], TWO_PI / periodicBoxVectors[1][1], TWO_PI / periodicBoxVectors[2][2]};
// setup K-vectors
......@@ -329,8 +338,8 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex
threadEnergy[threadIndex] = 0;
double* energyPtr = (includeEnergy ? &threadEnergy[threadIndex] : NULL);
float* forces = &(*threadForce)[threadIndex][0];
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0);
fvec4 invBoxSize((1/periodicBoxSize[0]), (1/periodicBoxSize[1]), (1/periodicBoxSize[2]), 0);
fvec4 boxSize(periodicBoxVectors[0][0], periodicBoxVectors[1][1], periodicBoxVectors[2][2], 0);
fvec4 invBoxSize(recipBoxSize[0], recipBoxSize[1], recipBoxSize[2], 0);
if (ewald || pme) {
// Compute the interactions from the neighbor list.
......@@ -343,8 +352,8 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex
// Now subtract off the exclusions, since they were implicitly included in the reciprocal space sum.
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0);
fvec4 invBoxSize((1/periodicBoxSize[0]), (1/periodicBoxSize[1]), (1/periodicBoxSize[2]), 0);
fvec4 boxSize(periodicBoxVectors[0][0], periodicBoxVectors[1][1], periodicBoxVectors[2][2], 0);
fvec4 invBoxSize(recipBoxSize[0], recipBoxSize[1], recipBoxSize[2], 0);
for (int i = threadIndex; i < numberOfAtoms; i += numThreads) {
fvec4 posI((float) atomCoordinates[i][0], (float) atomCoordinates[i][1], (float) atomCoordinates[i][2], 0.0f);
for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter) {
......@@ -453,9 +462,16 @@ void CpuNonbondedForce::calculateOneIxn(int ii, int jj, float* forces, double* t
void CpuNonbondedForce::getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& deltaR, float& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
deltaR = posJ-posI;
if (periodic) {
if (triclinic) {
deltaR -= periodicBoxVec4[2]*floor(deltaR[2]*recipBoxSize[2]+0.5f);
deltaR -= periodicBoxVec4[1]*floor(deltaR[1]*recipBoxSize[1]+0.5f);
deltaR -= periodicBoxVec4[0]*floor(deltaR[0]*recipBoxSize[0]+0.5f);
}
else {
fvec4 base = round(deltaR*invBoxSize)*boxSize;
deltaR = deltaR-base;
}
}
r2 = dot3(deltaR, deltaR);
}
......
platforms/cpu/src/CpuNonbondedForceVec4.cpp
View file @ 4b6f53e5
......@@ -262,10 +262,23 @@ void CpuNonbondedForceVec4::getDeltaR(const float* posI, const fvec4& x, const f
dy = y-posI[1];
dz = z-posI[2];
if (periodic) {
if (triclinic) {
fvec4 scale3 = floor(dz*recipBoxSize[2]+0.5f);
dx -= scale3*periodicBoxVectors[2][0];
dy -= scale3*periodicBoxVectors[2][1];
dz -= scale3*periodicBoxVectors[2][2];
fvec4 scale2 = floor(dy*recipBoxSize[1]+0.5f);
dx -= scale2*periodicBoxVectors[1][0];
dy -= scale2*periodicBoxVectors[1][1];
fvec4 scale1 = floor(dx*recipBoxSize[0]+0.5f);
dx -= scale1*periodicBoxVectors[0][0];
}
else {
dx -= round(dx*invBoxSize[0])*boxSize[0];
dy -= round(dy*invBoxSize[1])*boxSize[1];
dz -= round(dz*invBoxSize[2])*boxSize[2];
}
}
r2 = dx*dx + dy*dy + dz*dz;
}
......
platforms/cpu/src/CpuNonbondedForceVec8.cpp
View file @ 4b6f53e5
......@@ -292,10 +292,23 @@ void CpuNonbondedForceVec8::getDeltaR(const float* posI, const fvec8& x, const f
dy = y-posI[1];
dz = z-posI[2];
if (periodic) {
if (triclinic) {
fvec8 scale3 = floor(dz*recipBoxSize[2]+0.5f);
dx -= scale3*periodicBoxVectors[2][0];
dy -= scale3*periodicBoxVectors[2][1];
dz -= scale3*periodicBoxVectors[2][2];
fvec8 scale2 = floor(dy*recipBoxSize[1]+0.5f);
dx -= scale2*periodicBoxVectors[1][0];
dy -= scale2*periodicBoxVectors[1][1];
fvec8 scale1 = floor(dx*recipBoxSize[0]+0.5f);
dx -= scale1*periodicBoxVectors[0][0];
}
else {
dx -= round(dx*invBoxSize[0])*boxSize[0];
dy -= round(dy*invBoxSize[1])*boxSize[1];
dz -= round(dz*invBoxSize[2])*boxSize[2];
}
}
r2 = dx*dx + dy*dy + dz*dz;
}
......
platforms/cpu/tests/TestCpuNonbondedForce.cpp
View file @ 4b6f53e5
......@@ -353,6 +353,67 @@ void testPeriodic() {
ASSERT_EQUAL_TOL(2*ONE_4PI_EPS0*(1.0)*(1.0+krf*1.0-crf), state.getPotentialEnergy(), TOL);
}
void testTriclinic() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
Vec3 a(3.1, 0, 0);
Vec3 b(0.4, 3.5, 0);
Vec3 c(-0.1, -0.5, 4.0);
system.setDefaultPeriodicBoxVectors(a, b, c);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addParticle(1.0, 1, 0);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
const double cutoff = 1.5;
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
const double eps = 78.3;
const double krf = (1.0/(cutoff*cutoff*cutoff))*(eps-1.0)/(2.0*eps+1.0);
const double crf = (1.0/cutoff)*(3.0*eps)/(2.0*eps+1.0);
for (int iteration = 0; iteration < 50; iteration++) {
// Generate random positions for the two particles.
positions[0] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
positions[1] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
context.setPositions(positions);
// Loop over all possible periodic copies and find the nearest one.
Vec3 delta;
double distance2 = 100.0;
for (int i = -1; i < 2; i++)
for (int j = -1; j < 2; j++)
for (int k = -1; k < 2; k++) {
Vec3 d = positions[1]-positions[0]+a*i+b*j+c*k;
if (d.dot(d) < distance2) {
delta = d;
distance2 = d.dot(d);
}
}
double distance = sqrt(distance2);
// See if the force and energy are correct.
State state = context.getState(State::Forces | State::Energy);
if (distance >= cutoff) {
ASSERT_EQUAL(0.0, state.getPotentialEnergy());
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[0], 0);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[1], 0);
}
else {
const Vec3 force = delta*ONE_4PI_EPS0*(-1.0/(distance*distance*distance)+2.0*krf);
ASSERT_EQUAL_TOL(ONE_4PI_EPS0*(1.0/distance+krf*distance*distance-crf), state.getPotentialEnergy(), 1e-4);
ASSERT_EQUAL_VEC(force, state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(-force, state.getForces()[1], TOL);
}
}
}
void testLargeSystem() {
const int numMolecules = 600;
......@@ -635,6 +696,7 @@ int main(int argc, char* argv[]) {
testCutoff();
testCutoff14();
testPeriodic();
testTriclinic();
testLargeSystem();
testDispersionCorrection();
testChangingParameters();
......
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