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Unverified Commit 73cac8e6 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #2085 from peastman/charges 

Support multiple NonbondedForces in one System
parents a885a6ae daa9de8a
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Showing with 72 additions and 11 deletions
platforms/opencl/src/kernels/pme.cl
View file @ 73cac8e6
......@@ -3,12 +3,14 @@ __kernel void updateBsplines(__global const real4* restrict posq, __global real4
real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ
#ifdef USE_LJPME
, __global const float2* restrict sigmaEpsilon
#else
, __global const real* restrict charges
#endif
) {
const real4 scale = 1/(real) (PME_ORDER-1);
for (int i = get_global_id(0); i < NUM_ATOMS; i += get_global_size(0)) {
for (int atom = get_global_id(0); atom < NUM_ATOMS; atom += get_global_size(0)) {
__local real4* data = &bsplinesCache[get_local_id(0)*PME_ORDER];
real4 pos = posq[i];
real4 pos = posq[atom];
APPLY_PERIODIC_TO_POS(pos)
real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
......@@ -20,7 +22,7 @@ __kernel void updateBsplines(__global const real4* restrict posq, __global real4
int4 gridIndex = (int4) (((int) t.x) % GRID_SIZE_X,
((int) t.y) % GRID_SIZE_Y,
((int) t.z) % GRID_SIZE_Z, 0);
pmeAtomGridIndex[i] = (int2) (i, gridIndex.x*GRID_SIZE_Y*GRID_SIZE_Z+gridIndex.y*GRID_SIZE_Z+gridIndex.z);
pmeAtomGridIndex[atom] = (int2) (atom, gridIndex.x*GRID_SIZE_Y*GRID_SIZE_Z+gridIndex.y*GRID_SIZE_Z+gridIndex.z);
#ifndef SUPPORTS_64_BIT_ATOMICS
data[PME_ORDER-1] = 0.0f;
data[1] = dr;
......@@ -38,13 +40,13 @@ __kernel void updateBsplines(__global const real4* restrict posq, __global real4
data[0] = scale*(-dr+1.0f)*data[0];
for (int j = 0; j < PME_ORDER; j++) {
#ifdef USE_LJPME
const float2 sigEps = sigmaEpsilon[i];
const float2 sigEps = sigmaEpsilon[atom];
const real charge = 8*sigEps.x*sigEps.x*sigEps.x*sigEps.y;
#else
const real charge = pos.w;
const real charge = CHARGE;
#endif
data[j].w = charge; // Storing the charge here improves cache coherency in the charge spreading kernel
pmeBsplineTheta[i+j*NUM_ATOMS] = data[j];
pmeBsplineTheta[atom+j*NUM_ATOMS] = data[j];
}
#endif
}
......@@ -99,6 +101,8 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ
#ifdef USE_LJPME
, __global const float2* restrict sigmaEpsilon
#else
, __global const real* restrict charges
#endif
) {
const real scale = 1/(real) (PME_ORDER-1);
......@@ -114,7 +118,7 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
const float2 sigEps = sigmaEpsilon[atom];
const real charge = 8*sigEps.x*sigEps.x*sigEps.x*sigEps.y;
#else
const real charge = pos.w;
const real charge = CHARGE;
#endif
if (charge == 0)
continue;
......@@ -192,6 +196,8 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ
#ifdef USE_LJPME
, __global const float2* restrict sigmaEpsilon
#else
, __global const real* restrict charges
#endif
) {
const int firstx = get_global_id(0)*GRID_SIZE_X/get_global_size(0);
......@@ -224,7 +230,7 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
const float2 sigEps = sigmaEpsilon[atom];
const real charge = 8*sigEps.x*sigEps.x*sigEps.x*sigEps.y;
#else
const real charge = pos.w;
const real charge = CHARGE;
#endif
if (charge == 0)
continue;
......@@ -274,6 +280,8 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
__global real* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta
#ifdef USE_LJPME
, __global const float2* restrict sigmaEpsilon
#else
, __global const real* restrict charges
#endif
) {
unsigned int numGridPoints = GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z;
......@@ -452,6 +460,8 @@ __kernel void gridInterpolateForce(__global const real4* restrict posq, __global
real4 recipBoxVecY, real4 recipBoxVecZ, __global int2* restrict pmeAtomGridIndex
#ifdef USE_LJPME
, __global const float2* restrict sigmaEpsilon
#else
, __global const real* restrict charges
#endif
) {
const real scale = 1/(real) (PME_ORDER-1);
......@@ -522,7 +532,7 @@ __kernel void gridInterpolateForce(__global const real4* restrict posq, __global
const float2 sigEps = sigmaEpsilon[atom];
real q = 8*sigEps.x*sigEps.x*sigEps.x*sigEps.y;
#else
real q = pos.w*EPSILON_FACTOR;
real q = CHARGE*EPSILON_FACTOR;
#endif
totalForce.x -= q*(force.x*GRID_SIZE_X*recipBoxVecX.x);
totalForce.y -= q*(force.x*GRID_SIZE_X*recipBoxVecY.x+force.y*GRID_SIZE_Y*recipBoxVecY.y);
......
tests/TestDispersionPME.h
View file @ 73cac8e6
......@@ -1269,7 +1269,7 @@ void testWater2DpmeEnergiesForcesWithExclusions() {
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_TOL(refenergy, energy, 1E-4);
ASSERT_EQUAL_TOL(refenergy, energy, 5E-4);
for (int n = 0; n < numAtoms; ++n)
ASSERT_EQUAL_VEC(refforces[n], forces[n], 5E-4);
}
......
tests/TestNonbondedForce.h
View file @ 73cac8e6
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2018 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -684,6 +684,56 @@ void testSwitchingFunction(NonbondedForce::NonbondedMethod method) {
}
}
void testTwoForces() {
// Create a system with two NonbondedForces.
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* nb1 = new NonbondedForce();
nb1->addParticle(-1.5, 1, 1.2);
nb1->addParticle(0.5, 1, 1.0);
system.addForce(nb1);
NonbondedForce* nb2 = new NonbondedForce();
nb2->addParticle(0.4, 1.4, 0.5);
nb2->addParticle(0.3, 1.8, 1.0);
nb2->setForceGroup(1);
system.addForce(nb2);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1.5, 0, 0);
context.setPositions(positions);
State state1 = context.getState(State::Energy, false, 1<<0);
ASSERT_EQUAL_TOL(ONE_4PI_EPS0*(-1.5*0.5)/1.5 + 4.0*sqrt(1.2*1.0)*(pow(1.0/1.5, 12.0)-pow(1.0/1.5, 6.0)), state1.getPotentialEnergy(), TOL);
State state2 = context.getState(State::Energy, false, 1<<1);
ASSERT_EQUAL_TOL(ONE_4PI_EPS0*(0.4*0.3)/1.5 + 4.0*sqrt(0.5*1.0)*(pow(1.6/1.5, 12.0)-pow(1.6/1.5, 6.0)), state2.getPotentialEnergy(), TOL);
State state = context.getState(State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy()+state2.getPotentialEnergy(), state.getPotentialEnergy(), TOL);
// Try modifying them and see if they're still correct.
nb1->setParticleParameters(0, -1.2, 1.1, 1.4);
nb1->updateParametersInContext(context);
nb2->setParticleParameters(0, 0.5, 1.6, 0.6);
nb2->updateParametersInContext(context);
state1 = context.getState(State::Energy, false, 1<<0);
ASSERT_EQUAL_TOL(ONE_4PI_EPS0*(-1.2*0.5)/1.5 + 4.0*sqrt(1.4*1.0)*(pow(1.05/1.5, 12.0)-pow(1.05/1.5, 6.0)), state1.getPotentialEnergy(), TOL);
state2 = context.getState(State::Energy, false, 1<<1);
ASSERT_EQUAL_TOL(ONE_4PI_EPS0*(0.5*0.3)/1.5 + 4.0*sqrt(0.6*1.0)*(pow(1.7/1.5, 12.0)-pow(1.7/1.5, 6.0)), state2.getPotentialEnergy(), TOL);
// Make sure it also works with PME.
nb1->setNonbondedMethod(NonbondedForce::PME);
nb2->setNonbondedMethod(NonbondedForce::PME);
context.reinitialize(true);
state1 = context.getState(State::Energy, false, 1<<0);
state2 = context.getState(State::Energy, false, 1<<1);
state = context.getState(State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy()+state2.getPotentialEnergy(), state.getPotentialEnergy(), TOL);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -701,6 +751,7 @@ int main(int argc, char* argv[]) {
testChangingParameters();
testSwitchingFunction(NonbondedForce::CutoffNonPeriodic);
testSwitchingFunction(NonbondedForce::PME);
testTwoForces();
runPlatformTests();
}
catch(const exception& e) {
......
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