Merge branch 'master' into gayberne

platforms/cuda/src/CudaKernels.cpp

@@ -1938,12 +1938,14 @@ double CudaCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeF
         // Execute the reciprocal space kernels.
 
         void* gridIndexArgs[] = {&cu.getPosq().getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxSizePointer(),
+                cu.getInvPeriodicBoxSizePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
                 recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
         cu.executeKernel(pmeGridIndexKernel, gridIndexArgs, cu.getNumAtoms());
 
         sort->sort(*pmeAtomGridIndex);
 
         void* spreadArgs[] = {&cu.getPosq().getDevicePointer(), &directPmeGrid->getDevicePointer(), cu.getPeriodicBoxSizePointer(),
+                cu.getInvPeriodicBoxSizePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
                 recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2], &pmeAtomGridIndex->getDevicePointer()};
         cu.executeKernel(pmeSpreadChargeKernel, spreadArgs, cu.getNumAtoms(), 128);
 
@@ -1984,8 +1986,9 @@ double CudaCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeF
             fft->execFFT(*reciprocalPmeGrid, *directPmeGrid, false);
         }
 
-        void* interpolateArgs[] = {&cu.getPosq().getDevicePointer(), &cu.getForce().getDevicePointer(), &directPmeGrid->getDevicePointer(),
-                cu.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2], &pmeAtomGridIndex->getDevicePointer()};
+        void* interpolateArgs[] = {&cu.getPosq().getDevicePointer(), &cu.getForce().getDevicePointer(), &directPmeGrid->getDevicePointer(), cu.getPeriodicBoxSizePointer(),
+                cu.getInvPeriodicBoxSizePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
+                recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2], &pmeAtomGridIndex->getDevicePointer()};
         cu.executeKernel(pmeInterpolateForceKernel, interpolateArgs, cu.getNumAtoms(), 128);
         if (usePmeStream) {
             cuEventRecord(pmeSyncEvent, pmeStream);

platforms/cuda/src/kernels/pme.cu

 extern "C" __global__ void findAtomGridIndex(const real4* __restrict__ posq, int2* __restrict__ pmeAtomGridIndex,
-            real4 periodicBoxSize, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
+            real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
+            real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
     // Compute the index of the grid point each atom is associated with.
     
     for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < NUM_ATOMS; i += blockDim.x*gridDim.x) {
         real4 pos = posq[i];
+        APPLY_PERIODIC_TO_POS(pos)
         real3 t = make_real3(pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
                              pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
                              pos.z*recipBoxVecZ.z);
@@ -18,7 +20,8 @@ extern "C" __global__ void findAtomGridIndex(const real4* __restrict__ posq, int
 }
 
 extern "C" __global__ void gridSpreadCharge(const real4* __restrict__ posq, real* __restrict__ originalPmeGrid,
-        real4 periodicBoxSize, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ, const int2* __restrict__ pmeAtomGridIndex) {
+        real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
+        real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ, const int2* __restrict__ pmeAtomGridIndex) {
     real3 data[PME_ORDER];
     const real scale = RECIP(PME_ORDER-1);
     
@@ -28,9 +31,7 @@ extern "C" __global__ void gridSpreadCharge(const real4* __restrict__ posq, real
     for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < NUM_ATOMS; i += blockDim.x*gridDim.x) {
         int atom = pmeAtomGridIndex[i].x;
         real4 pos = posq[atom];
-        pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
-        pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
-        pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
+        APPLY_PERIODIC_TO_POS(pos)
         real3 t = make_real3(pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
                              pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
                              pos.z*recipBoxVecZ.z);
@@ -197,7 +198,8 @@ gridEvaluateEnergy(real2* __restrict__ halfcomplex_pmeGrid, mixed* __restrict__
 
 extern "C" __global__
 void gridInterpolateForce(const real4* __restrict__ posq, unsigned long long* __restrict__ forceBuffers, const real* __restrict__ originalPmeGrid,
-        real4 periodicBoxSize, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ, const int2* __restrict__ pmeAtomGridIndex) {
+        real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
+        real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ, const int2* __restrict__ pmeAtomGridIndex) {
     real3 data[PME_ORDER];
     real3 ddata[PME_ORDER];
     const real scale = RECIP(PME_ORDER-1);
@@ -209,9 +211,7 @@ void gridInterpolateForce(const real4* __restrict__ posq, unsigned long long* __
         int atom = pmeAtomGridIndex[i].x;
         real3 force = make_real3(0);
         real4 pos = posq[atom];
-        pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
-        pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
-        pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
+        APPLY_PERIODIC_TO_POS(pos)
         real3 t = make_real3(pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
                              pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
                              pos.z*recipBoxVecZ.z);

platforms/opencl/src/OpenCLKernels.cpp

@@ -1913,7 +1913,7 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
             pmeInterpolateForceKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
             pmeInterpolateForceKernel.setArg<cl::Buffer>(1, cl.getForceBuffers().getDeviceBuffer());
             pmeInterpolateForceKernel.setArg<cl::Buffer>(2, pmeGrid->getDeviceBuffer());
-            pmeInterpolateForceKernel.setArg<cl::Buffer>(7, pmeAtomGridIndex->getDeviceBuffer());
+            pmeInterpolateForceKernel.setArg<cl::Buffer>(11, pmeAtomGridIndex->getDeviceBuffer());
             if (cl.getSupports64BitGlobalAtomics()) {
                 pmeFinishSpreadChargeKernel = cl::Kernel(program, "finishSpreadCharge");
                 pmeFinishSpreadChargeKernel.setArg<cl::Buffer>(0, pmeGrid2->getDeviceBuffer());
@@ -1962,45 +1962,45 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
         
         // Execute the reciprocal space kernels.
 
-        setPeriodicBoxSizeArg(cl, pmeUpdateBsplinesKernel, 4);
+        setPeriodicBoxArgs(cl, pmeUpdateBsplinesKernel, 4);
         if (cl.getUseDoublePrecision()) {
-            pmeUpdateBsplinesKernel.setArg<mm_double4>(5, recipBoxVectors[0]);
-            pmeUpdateBsplinesKernel.setArg<mm_double4>(6, recipBoxVectors[1]);
-            pmeUpdateBsplinesKernel.setArg<mm_double4>(7, recipBoxVectors[2]);
+            pmeUpdateBsplinesKernel.setArg<mm_double4>(9, recipBoxVectors[0]);
+            pmeUpdateBsplinesKernel.setArg<mm_double4>(10, recipBoxVectors[1]);
+            pmeUpdateBsplinesKernel.setArg<mm_double4>(11, recipBoxVectors[2]);
         }
         else {
-            pmeUpdateBsplinesKernel.setArg<mm_float4>(5, recipBoxVectorsFloat[0]);
-            pmeUpdateBsplinesKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[1]);
-            pmeUpdateBsplinesKernel.setArg<mm_float4>(7, recipBoxVectorsFloat[2]);
+            pmeUpdateBsplinesKernel.setArg<mm_float4>(9, recipBoxVectorsFloat[0]);
+            pmeUpdateBsplinesKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[1]);
+            pmeUpdateBsplinesKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[2]);
         }
         cl.executeKernel(pmeUpdateBsplinesKernel, cl.getNumAtoms());
         if (deviceIsCpu && !cl.getSupports64BitGlobalAtomics()) {
-            setPeriodicBoxSizeArg(cl, pmeSpreadChargeKernel, 5);
+            setPeriodicBoxArgs(cl, pmeSpreadChargeKernel, 5);
             if (cl.getUseDoublePrecision()) {
-                pmeSpreadChargeKernel.setArg<mm_double4>(6, recipBoxVectors[0]);
-                pmeSpreadChargeKernel.setArg<mm_double4>(7, recipBoxVectors[1]);
-                pmeSpreadChargeKernel.setArg<mm_double4>(8, recipBoxVectors[2]);
+                pmeSpreadChargeKernel.setArg<mm_double4>(10, recipBoxVectors[0]);
+                pmeSpreadChargeKernel.setArg<mm_double4>(11, recipBoxVectors[1]);
+                pmeSpreadChargeKernel.setArg<mm_double4>(12, recipBoxVectors[2]);
             }
             else {
-                pmeSpreadChargeKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[0]);
-                pmeSpreadChargeKernel.setArg<mm_float4>(7, recipBoxVectorsFloat[1]);
-                pmeSpreadChargeKernel.setArg<mm_float4>(8, recipBoxVectorsFloat[2]);
+                pmeSpreadChargeKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[0]);
+                pmeSpreadChargeKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[1]);
+                pmeSpreadChargeKernel.setArg<mm_float4>(12, recipBoxVectorsFloat[2]);
             }
             cl.executeKernel(pmeSpreadChargeKernel, 2*cl.getDevice().getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>(), 1);
         }
         else {
             sort->sort(*pmeAtomGridIndex);
             if (cl.getSupports64BitGlobalAtomics()) {
-                setPeriodicBoxSizeArg(cl, pmeSpreadChargeKernel, 5);
+            setPeriodicBoxArgs(cl, pmeSpreadChargeKernel, 5);
                 if (cl.getUseDoublePrecision()) {
-                    pmeSpreadChargeKernel.setArg<mm_double4>(6, recipBoxVectors[0]);
-                    pmeSpreadChargeKernel.setArg<mm_double4>(7, recipBoxVectors[1]);
-                    pmeSpreadChargeKernel.setArg<mm_double4>(8, recipBoxVectors[2]);
+                    pmeSpreadChargeKernel.setArg<mm_double4>(10, recipBoxVectors[0]);
+                    pmeSpreadChargeKernel.setArg<mm_double4>(11, recipBoxVectors[1]);
+                    pmeSpreadChargeKernel.setArg<mm_double4>(12, recipBoxVectors[2]);
                 }
                 else {
-                    pmeSpreadChargeKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[0]);
-                    pmeSpreadChargeKernel.setArg<mm_float4>(7, recipBoxVectorsFloat[1]);
-                    pmeSpreadChargeKernel.setArg<mm_float4>(8, recipBoxVectorsFloat[2]);
+                    pmeSpreadChargeKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[0]);
+                    pmeSpreadChargeKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[1]);
+                    pmeSpreadChargeKernel.setArg<mm_float4>(12, recipBoxVectorsFloat[2]);
                 }
                 cl.executeKernel(pmeSpreadChargeKernel, cl.getNumAtoms());
                 cl.executeKernel(pmeFinishSpreadChargeKernel, pmeGrid->getSize());
@@ -2038,16 +2038,16 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
             cl.executeKernel(pmeEvalEnergyKernel, cl.getNumAtoms());
         cl.executeKernel(pmeConvolutionKernel, cl.getNumAtoms());
         fft->execFFT(*pmeGrid2, *pmeGrid, false);
-        setPeriodicBoxSizeArg(cl, pmeInterpolateForceKernel, 3);
+        setPeriodicBoxArgs(cl, pmeInterpolateForceKernel, 3);
         if (cl.getUseDoublePrecision()) {
-            pmeInterpolateForceKernel.setArg<mm_double4>(4, recipBoxVectors[0]);
-            pmeInterpolateForceKernel.setArg<mm_double4>(5, recipBoxVectors[1]);
-            pmeInterpolateForceKernel.setArg<mm_double4>(6, recipBoxVectors[2]);
+            pmeInterpolateForceKernel.setArg<mm_double4>(8, recipBoxVectors[0]);
+            pmeInterpolateForceKernel.setArg<mm_double4>(9, recipBoxVectors[1]);
+            pmeInterpolateForceKernel.setArg<mm_double4>(10, recipBoxVectors[2]);
         }
         else {
-            pmeInterpolateForceKernel.setArg<mm_float4>(4, recipBoxVectorsFloat[0]);
-            pmeInterpolateForceKernel.setArg<mm_float4>(5, recipBoxVectorsFloat[1]);
-            pmeInterpolateForceKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[2]);
+            pmeInterpolateForceKernel.setArg<mm_float4>(8, recipBoxVectorsFloat[0]);
+            pmeInterpolateForceKernel.setArg<mm_float4>(9, recipBoxVectorsFloat[1]);
+            pmeInterpolateForceKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[2]);
         }
         if (deviceIsCpu)
             cl.executeKernel(pmeInterpolateForceKernel, 2*cl.getDevice().getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>(), 1);

platforms/opencl/src/kernels/pme.cl

 __kernel void updateBsplines(__global const real4* restrict posq, __global real4* restrict pmeBsplineTheta, __local real4* restrict bsplinesCache,
-        __global int2* restrict pmeAtomGridIndex, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
+        __global int2* restrict pmeAtomGridIndex, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
+        real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
     const real4 scale = 1/(real) (PME_ORDER-1);
     for (int i = get_global_id(0); i < NUM_ATOMS; i += get_global_size(0)) {
         __local real4* data = &bsplinesCache[get_local_id(0)*PME_ORDER];
         real4 pos = posq[i];
+        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,
                            pos.z*recipBoxVecZ.z);
@@ -83,7 +85,8 @@ __kernel void recordZIndex(__global int2* restrict pmeAtomGridIndex, __global co
 #pragma OPENCL EXTENSION cl_khr_int64_base_atomics : enable
 
 __kernel void gridSpreadCharge(__global const real4* restrict posq, __global const int2* restrict pmeAtomGridIndex, __global const int* restrict pmeAtomRange,
-        __global long* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
+        __global long* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 invPeriodicBoxSize,
+        real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
     const real scale = 1/(real) (PME_ORDER-1);
     real4 data[PME_ORDER];
     
@@ -93,9 +96,7 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
     for (int i = get_global_id(0); i < NUM_ATOMS; i += get_global_size(0)) {
         int atom = pmeAtomGridIndex[i].x;
         real4 pos = posq[atom];
-        pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
-        pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
-        pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
+        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,
                            pos.z*recipBoxVecZ.z);
@@ -165,7 +166,8 @@ __kernel void finishSpreadCharge(__global long* restrict fixedGrid, __global rea
 }
 #elif defined(DEVICE_IS_CPU)
 __kernel void gridSpreadCharge(__global const real4* restrict posq, __global const int2* restrict pmeAtomGridIndex, __global const int* restrict pmeAtomRange,
-        __global real* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
+        __global real* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 invPeriodicBoxSize,
+        real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
     const int firstx = get_global_id(0)*GRID_SIZE_X/get_global_size(0);
     const int lastx = (get_global_id(0)+1)*GRID_SIZE_X/get_global_size(0);
     if (firstx == lastx)
@@ -179,9 +181,7 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
     for (int i = 0; i < NUM_ATOMS; i++) {
         int atom = i;//pmeAtomGridIndex[i].x;
         real4 pos = posq[atom];
-        pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
-        pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
-        pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
+        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,
                            pos.z*recipBoxVecZ.z);
@@ -370,7 +370,8 @@ __kernel void gridEvaluateEnergy(__global real2* restrict pmeGrid, __global mixe
 }
 
 __kernel void gridInterpolateForce(__global const real4* restrict posq, __global real4* restrict forceBuffers, __global const real* restrict pmeGrid,
-        real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ, __global int2* restrict pmeAtomGridIndex) {
+        real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX,
+        real4 recipBoxVecY, real4 recipBoxVecZ, __global int2* restrict pmeAtomGridIndex) {
     const real scale = 1/(real) (PME_ORDER-1);
     real4 data[PME_ORDER];
     real4 ddata[PME_ORDER];
@@ -382,9 +383,7 @@ __kernel void gridInterpolateForce(__global const real4* restrict posq, __global
         int atom = pmeAtomGridIndex[i].x;
         real4 force = 0.0f;
         real4 pos = posq[atom];
-        pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
-        pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
-        pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
+        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,
                            pos.z*recipBoxVecZ.z);

tests/TestEwald.h

@@ -270,6 +270,49 @@ void testTriclinic() {
     ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-4);
 }
 
+void testTriclinic2() {
+    // Create a triclinic box containing a large molecule made up of randomly positioned particles and make sure the
+    // results match the reference platform.
+
+    if (platform.getName() == "Reference")
+        return;
+    const int numParticles = 1000;
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(3.2, 0, 0), Vec3(-1.1, 3.1, 0), Vec3(-1.1, -1.5, 2.7));
+    vector<Vec3> positions(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    NonbondedForce* force = new NonbondedForce();
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(1.0);
+        force->addParticle(i%2 == 0 ? -1.0 : 1.0, 1.0, 0.0);
+        positions[i] = Vec3(10*genrand_real2(sfmt)-2, 10*genrand_real2(sfmt)-2, 10*genrand_real2(sfmt)-2);
+        if (i > 0) {
+            Vec3 delta = positions[i-1]-positions[i];
+            system.addConstraint(i-1, i, sqrt(delta.dot(delta)));
+        }
+    }
+    system.addForce(force);
+    force->setNonbondedMethod(NonbondedForce::PME);
+    force->setCutoffDistance(1.0);
+    force->setReciprocalSpaceForceGroup(1);
+    force->setPMEParameters(2.62826, 27, 25, 24);
+
+    // Compute the forces and energy.
+
+    VerletIntegrator integ1(0.001);
+    Context context1(system, integ1, platform);
+    context1.setPositions(positions);
+    VerletIntegrator integ2(0.001);
+    Context context2(system, integ2, Platform::getPlatformByName("Reference"));
+    context2.setPositions(positions);
+    State state1 = context1.getState(State::Forces | State::Energy, false, 2);
+    State state2 = context2.getState(State::Forces | State::Energy, false, 2);
+    ASSERT_EQUAL_TOL(state2.getPotentialEnergy(), state1.getPotentialEnergy(), 1e-4);
+    for (int i = 0; i < numParticles; i++)
+        ASSERT_EQUAL_VEC(state2.getForces()[i], state1.getForces()[i], 1e-4);
+}
+
 void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
     // Create a cloud of random point charges.
 
@@ -391,6 +434,7 @@ int main(int argc, char* argv[]) {
         testEwaldPME(false);
         testEwaldPME(true);
         testTriclinic();
+        testTriclinic2();
         testErrorTolerance(NonbondedForce::Ewald);
         testErrorTolerance(NonbondedForce::PME);
         testPMEParameters();

wrappers/python/simtk/openmm/app/gromacstopfile.py

@@ -6,7 +6,7 @@ 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) 2012-2015 Stanford University and the Authors.
+Portions copyright (c) 2012-2016 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors: Jason Swails
 
@@ -814,7 +814,7 @@ class GromacsTopFile(object):
                     map = []
                     for i in range(mapSize):
                         for j in range(mapSize):
-                            map.append(float(params[8+mapSize*((j+mapSize/2)%mapSize)+((i+mapSize/2)%mapSize)]))
+                            map.append(float(params[8+mapSize*((j+mapSize//2)%mapSize)+((i+mapSize//2)%mapSize)]))
                     map = tuple(map)
                     if map not in mapIndices:
                         mapIndices[map] = cmap.addMap(mapSize, map)

wrappers/python/simtk/openmm/app/internal/customgbforces.py

@@ -335,7 +335,7 @@ def _mbondi3_radii(topology):
 
 def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, kappa, offset):
     # Add the energy terms to the CustomGBForce.  These are identical for all the GB models.
-    
+
     params = "; solventDielectric=%.16g; soluteDielectric=%.16g; kappa=%.16g; offset=%.16g" % (solventDielectric, soluteDielectric, kappa, offset)
     if cutoff is not None:
         params += "; cutoff=%.16g" % cutoff
@@ -535,7 +535,7 @@ class GBSAGBnForce(CustomAmberGBForce):
 
     def addParticle(self, parameters):
         parameters = CustomAmberGBForce.addParticle(self, parameters)
-        if parameters[1] < 0.1 or parameters[1] > 0.2:
+        if parameters[1] + self.OFFSET < 0.1 or parameters[1] + self.OFFSET > 0.2:
             raise ValueError('Radii must be between 1 and 2 Angstroms for neck lookup')
 
     def setParticleParameters(self, idx, parameters):

wrappers/python/tests/TestAmberPrmtopFile.py

@@ -361,5 +361,17 @@ class TestAmberPrmtopFile(unittest.TestCase):
             # Make sure it says something about chamber
             self.assertTrue('chamber' in str(e).lower())
 
+    def testGBneckRadii(self):
+        """ Tests that GBneck radii limits are correctly enforced """
+        from simtk.openmm.app.internal.customgbforces import GBSAGBnForce
+        f = GBSAGBnForce()
+        # Make sure legal parameters do not raise
+        f.addParticle([0, 0.1, 0.5])
+        f.addParticle([0, 0.2, 0.5])
+        f.addParticle([0, 0.15, 0.5])
+        # Now make sure that out-of-range parameters *do* raise
+        self.assertRaises(ValueError, lambda: f.addParticle([0, 0.9, 0.5]))
+        self.assertRaises(ValueError, lambda: f.addParticle([0, 0.21, 0.5]))
+
 if __name__ == '__main__':
     unittest.main()