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) {
    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];
        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);
        t.x = (t.x-floor(t.x))*GRID_SIZE_X;
        t.y = (t.y-floor(t.y))*GRID_SIZE_Y;
        t.z = (t.z-floor(t.z))*GRID_SIZE_Z;
        real4 dr = (real4) (t.x-(int) t.x, t.y-(int) t.y, t.z-(int) t.z, 0.0f);
        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);
#ifndef SUPPORTS_64_BIT_ATOMICS
        data[PME_ORDER-1] = 0.0f;
        data[1] = dr;
        data[0] = 1.0f-dr;
        for (int j = 3; j < PME_ORDER; j++) {
            real div = RECIP(j-1.0f);
            data[j-1] = div*dr*data[j-2];
            for (int k = 1; k < (j-1); k++)
                data[j-k-1] = div*((dr+(real4) k) *data[j-k-2] + (-dr+(real4) (j-k))*data[j-k-1]);
            data[0] = div*(- dr+1.0f)*data[0];
        }
        data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2];
        for (int j = 1; j < (PME_ORDER-1); j++)
            data[PME_ORDER-j-1] = scale*((dr+(real4) j)*data[PME_ORDER-j-2] + (-dr+(real4) (PME_ORDER-j))*data[PME_ORDER-j-1]);
        data[0] = scale*(-dr+1.0f)*data[0];
        for (int j = 0; j < PME_ORDER; j++) {
            data[j].w = pos.w; // Storing the charge here improves cache coherency in the charge spreading kernel
            pmeBsplineTheta[i+j*NUM_ATOMS] = data[j];
        }
#endif
    }
}

/**
 * For each grid point, find the range of sorted atoms associated with that point.
 */
__kernel void findAtomRangeForGrid(__global int2* restrict pmeAtomGridIndex, __global int* restrict pmeAtomRange, __global const real4* restrict posq) {
    int start = (NUM_ATOMS*get_global_id(0))/get_global_size(0);
    int end = (NUM_ATOMS*(get_global_id(0)+1))/get_global_size(0);
    int last = (start == 0 ? -1 : pmeAtomGridIndex[start-1].y);
    for (int i = start; i < end; ++i) {
        int2 atomData = pmeAtomGridIndex[i];
        int gridIndex = atomData.y;
        if (gridIndex != last) {
            for (int j = last+1; j <= gridIndex; ++j)
                pmeAtomRange[j] = i;
            last = gridIndex;
        }
    }

    // Fill in values beyond the last atom.

    if (get_global_id(0) == get_global_size(0)-1) {
        int gridSize = GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z;
        for (int j = last+1; j <= gridSize; ++j)
            pmeAtomRange[j] = NUM_ATOMS;
    }
}

/**
 * The grid index won't be needed again.  Reuse that component to hold the z index, thus saving
 * some work in the charge spreading kernel.
 */
__kernel void recordZIndex(__global int2* restrict pmeAtomGridIndex, __global const real4* restrict posq, real4 periodicBoxSize, real4 recipBoxVecZ) {
    int start = (NUM_ATOMS*get_global_id(0))/get_global_size(0);
    int end = (NUM_ATOMS*(get_global_id(0)+1))/get_global_size(0);
    for (int i = start; i < end; ++i) {
        real posz = posq[pmeAtomGridIndex[i].x].z;
        posz -= floor(posz*recipBoxVecZ.z)*periodicBoxSize.z;
        int z = ((int) ((posz*recipBoxVecZ.z)*GRID_SIZE_Z)) % GRID_SIZE_Z;
        pmeAtomGridIndex[i].y = z;
    }
}

#ifdef SUPPORTS_64_BIT_ATOMICS
#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) {
    const real4 scale = 1/(real) (PME_ORDER-1);
    real4 data[PME_ORDER];
    
    // Process the atoms in spatially sorted order.  This improves efficiency when writing
    // the grid values.
    
    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;
        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);
        t.x = (t.x-floor(t.x))*GRID_SIZE_X;
        t.y = (t.y-floor(t.y))*GRID_SIZE_Y;
        t.z = (t.z-floor(t.z))*GRID_SIZE_Z;
        int4 gridIndex = (int4) (((int) t.x) % GRID_SIZE_X,
                                 ((int) t.y) % GRID_SIZE_Y,
                                 ((int) t.z) % GRID_SIZE_Z, 0);

        // Since we need the full set of thetas, it's faster to compute them here than load them
        // from global memory.

        real4 dr = (real4) (t.x-(int) t.x, t.y-(int) t.y, t.z-(int) t.z, 0.0f);
        data[PME_ORDER-1] = 0.0f;
        data[1] = dr;
        data[0] = 1.0f-dr;
        for (int j = 3; j < PME_ORDER; j++) {
            real div = RECIP(j-1.0f);
            data[j-1] = div*dr*data[j-2];
            for (int k = 1; k < (j-1); k++)
                data[j-k-1] = div*((dr+(real4) k) *data[j-k-2] + (-dr+(real4) (j-k))*data[j-k-1]);
            data[0] = div*(- dr+1.0f)*data[0];
        }
        data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2];
        for (int j = 1; j < (PME_ORDER-1); j++)
            data[PME_ORDER-j-1] = scale*((dr+(real4) j)*data[PME_ORDER-j-2] + (-dr+(real4) (PME_ORDER-j))*data[PME_ORDER-j-1]);
        data[0] = scale*(-dr+1.0f)*data[0];

        // Spread the charge from this atom onto each grid point.

        for (int ix = 0; ix < PME_ORDER; ix++) {
            int xindex = gridIndex.x+ix;
            xindex -= (xindex >= GRID_SIZE_X ? GRID_SIZE_X : 0);
            for (int iy = 0; iy < PME_ORDER; iy++) {
                int yindex = gridIndex.y+iy;
                yindex -= (yindex >= GRID_SIZE_Y ? GRID_SIZE_Y : 0);
                for (int iz = 0; iz < PME_ORDER; iz++) {
                    int zindex = gridIndex.z+iz;
                    zindex -= (zindex >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
                    int index = xindex*GRID_SIZE_Y*GRID_SIZE_Z + yindex*GRID_SIZE_Z + zindex;
                    real add = pos.w*data[ix].x*data[iy].y*data[iz].z;
                    atom_add(&pmeGrid[index], (long) (add*0x100000000));
                }
            }
        }
    }
}

__kernel void finishSpreadCharge(__global long* restrict fixedGrid, __global real* restrict realGrid) {
    const unsigned int gridSize = GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z;
    real scale = EPSILON_FACTOR/(real) 0x100000000;
    for (int index = get_global_id(0); index < gridSize; index += get_global_size(0)) {
        long value = fixedGrid[index];
        realGrid[index] = (real) (value*scale);
    }
}
#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) {
    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)
        return;
    const real4 scale = 1/(real) (PME_ORDER-1);
    real4 data[PME_ORDER];
    
    // Process the atoms in spatially sorted order.  This improves efficiency when writing
    // the grid values.
    
    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;
        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);
        t.x = (t.x-floor(t.x))*GRID_SIZE_X;
        t.y = (t.y-floor(t.y))*GRID_SIZE_Y;
        t.z = (t.z-floor(t.z))*GRID_SIZE_Z;
        int4 gridIndex = (int4) (((int) t.x) % GRID_SIZE_X,
                                 ((int) t.y) % GRID_SIZE_Y,
                                 ((int) t.z) % GRID_SIZE_Z, 0);

        // Spread the charge from this atom onto each grid point.

        bool hasComputedThetas = false;
        for (int ix = 0; ix < PME_ORDER; ix++) {
            int xindex = gridIndex.x+ix;
            xindex -= (xindex >= GRID_SIZE_X ? GRID_SIZE_X : 0);
            if (xindex < firstx || xindex >= lastx)
                continue;
            if (!hasComputedThetas) {
                hasComputedThetas = true;
                
                // Since we need the full set of thetas, it's faster to compute them here than load them
                // from global memory.

                real4 dr = (real4) (t.x-(int) t.x, t.y-(int) t.y, t.z-(int) t.z, 0.0f);
                data[PME_ORDER-1] = 0.0f;
                data[1] = dr;
                data[0] = 1.0f-dr;
                for (int j = 3; j < PME_ORDER; j++) {
                    real div = RECIP(j-1.0f);
                    data[j-1] = div*dr*data[j-2];
                    for (int k = 1; k < (j-1); k++)
                        data[j-k-1] = div*((dr+(real4) k) *data[j-k-2] + (-dr+(real4) (j-k))*data[j-k-1]);
                    data[0] = div*(- dr+1.0f)*data[0];
                }
                data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2];
                for (int j = 1; j < (PME_ORDER-1); j++)
                    data[PME_ORDER-j-1] = scale*((dr+(real4) j)*data[PME_ORDER-j-2] + (-dr+(real4) (PME_ORDER-j))*data[PME_ORDER-j-1]);
                data[0] = scale*(-dr+1.0f)*data[0];
            }
            for (int iy = 0; iy < PME_ORDER; iy++) {
                int yindex = gridIndex.y+iy;
                yindex -= (yindex >= GRID_SIZE_Y ? GRID_SIZE_Y : 0);
                for (int iz = 0; iz < PME_ORDER; iz++) {
                    int zindex = gridIndex.z+iz;
                    zindex -= (zindex >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
                    int index = xindex*GRID_SIZE_Y*GRID_SIZE_Z + yindex*GRID_SIZE_Z + zindex;
                    pmeGrid[index] += EPSILON_FACTOR*pos.w*data[ix].x*data[iy].y*data[iz].z;
                }
            }
        }
    }
}
#else
__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) {
    unsigned int numGridPoints = GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z;
    for (int gridIndex = get_global_id(0); gridIndex < numGridPoints; gridIndex += get_global_size(0)) {
        // Compute the charge on a grid point.

        int4 gridPoint;
        gridPoint.x = gridIndex/(GRID_SIZE_Y*GRID_SIZE_Z);
        int remainder = gridIndex-gridPoint.x*GRID_SIZE_Y*GRID_SIZE_Z;
        gridPoint.y = remainder/GRID_SIZE_Z;
        gridPoint.z = remainder-gridPoint.y*GRID_SIZE_Z;
        real result = 0.0f;

        // Loop over all atoms that affect this grid point.

        for (int ix = 0; ix < PME_ORDER; ++ix) {
            int x = gridPoint.x-ix+(gridPoint.x >= ix ? 0 : GRID_SIZE_X);
            for (int iy = 0; iy < PME_ORDER; ++iy) {
                int y = gridPoint.y-iy+(gridPoint.y >= iy ? 0 : GRID_SIZE_Y);
                int z1 = gridPoint.z-PME_ORDER+1;
                z1 += (z1 >= 0 ? 0 : GRID_SIZE_Z);
                int z2 = (z1 < gridPoint.z ? gridPoint.z : GRID_SIZE_Z-1);
                int gridIndex1 = x*GRID_SIZE_Y*GRID_SIZE_Z+y*GRID_SIZE_Z+z1;
                int gridIndex2 = x*GRID_SIZE_Y*GRID_SIZE_Z+y*GRID_SIZE_Z+z2;
                int firstAtom = pmeAtomRange[gridIndex1];
                int lastAtom = pmeAtomRange[gridIndex2+1];
                for (int i = firstAtom; i < lastAtom; ++i)
                {
                    int2 atomData = pmeAtomGridIndex[i];
                    int atomIndex = atomData.x;
                    int z = atomData.y;
                    int iz = gridPoint.z-z+(gridPoint.z >= z ? 0 : GRID_SIZE_Z);
                    real atomCharge = pmeBsplineTheta[atomIndex+ix*NUM_ATOMS].w;
                    result += atomCharge*pmeBsplineTheta[atomIndex+ix*NUM_ATOMS].x*pmeBsplineTheta[atomIndex+iy*NUM_ATOMS].y*pmeBsplineTheta[atomIndex+iz*NUM_ATOMS].z;
                }
                if (z1 > gridPoint.z)
                {
                    gridIndex1 = x*GRID_SIZE_Y*GRID_SIZE_Z+y*GRID_SIZE_Z;
                    gridIndex2 = x*GRID_SIZE_Y*GRID_SIZE_Z+y*GRID_SIZE_Z+gridPoint.z;
                    firstAtom = pmeAtomRange[gridIndex1];
                    lastAtom = pmeAtomRange[gridIndex2+1];
                    for (int i = firstAtom; i < lastAtom; ++i)
                    {
                        int2 atomData = pmeAtomGridIndex[i];
                        int atomIndex = atomData.x;
                        int z = atomData.y;
                        int iz = gridPoint.z-z+(gridPoint.z >= z ? 0 : GRID_SIZE_Z);
                        real atomCharge = pmeBsplineTheta[atomIndex+ix*NUM_ATOMS].w;
                        result += atomCharge*pmeBsplineTheta[atomIndex+ix*NUM_ATOMS].x*pmeBsplineTheta[atomIndex+iy*NUM_ATOMS].y*pmeBsplineTheta[atomIndex+iz*NUM_ATOMS].z;
                    }
                }
            }
        }
        pmeGrid[gridIndex] = result*EPSILON_FACTOR;
    }
}
#endif

__kernel void reciprocalConvolution(__global real2* restrict pmeGrid, __global real* restrict energyBuffer, __global const real* restrict pmeBsplineModuliX,
        __global const real* restrict pmeBsplineModuliY, __global const real* restrict pmeBsplineModuliZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ, real recipScaleFactor) {
    const unsigned int gridSize = GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z;
    real energy = 0.0f;
    for (int index = get_global_id(0); index < gridSize; index += get_global_size(0)) {
        int kx = index/(GRID_SIZE_Y*GRID_SIZE_Z);
        int remainder = index-kx*GRID_SIZE_Y*GRID_SIZE_Z;
        int ky = remainder/GRID_SIZE_Z;
        int kz = remainder-ky*GRID_SIZE_Z;
        if (kx == 0 && ky == 0 && kz == 0)
            continue;
        int mx = (kx < (GRID_SIZE_X+1)/2) ? kx : (kx-GRID_SIZE_X);
        int my = (ky < (GRID_SIZE_Y+1)/2) ? ky : (ky-GRID_SIZE_Y);
        int mz = (kz < (GRID_SIZE_Z+1)/2) ? kz : (kz-GRID_SIZE_Z);
        real mhx = mx*recipBoxVecX.x;
        real mhy = mx*recipBoxVecY.x+my*recipBoxVecY.y;
        real mhz = mx*recipBoxVecZ.x+my*recipBoxVecZ.y+mz*recipBoxVecZ.z;
        real bx = pmeBsplineModuliX[kx];
        real by = pmeBsplineModuliY[ky];
        real bz = pmeBsplineModuliZ[kz];
        real2 grid = pmeGrid[index];
        real m2 = mhx*mhx+mhy*mhy+mhz*mhz;
        real denom = m2*bx*by*bz;
        real eterm = recipScaleFactor*EXP(-RECIP_EXP_FACTOR*m2)/denom;
        pmeGrid[index] = (real2) (grid.x*eterm, grid.y*eterm);
        energy += eterm*(grid.x*grid.x + grid.y*grid.y);
    }
    energyBuffer[get_global_id(0)] += 0.5f*energy;
}

__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) {
    const real4 scale = 1/(real) (PME_ORDER-1);
    real4 data[PME_ORDER];
    real4 ddata[PME_ORDER];
    
    // Process the atoms in spatially sorted order.  This improves cache performance when loading
    // the grid values.
    
    for (int i = get_global_id(0); i < NUM_ATOMS; i += get_global_size(0)) {
        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;
        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);
        t.x = (t.x-floor(t.x))*GRID_SIZE_X;
        t.y = (t.y-floor(t.y))*GRID_SIZE_Y;
        t.z = (t.z-floor(t.z))*GRID_SIZE_Z;
        int4 gridIndex = (int4) (((int) t.x) % GRID_SIZE_X,
                                 ((int) t.y) % GRID_SIZE_Y,
                                 ((int) t.z) % GRID_SIZE_Z, 0);

        // Since we need the full set of thetas, it's faster to compute them here than load them
        // from global memory.

        real4 dr = (real4) (t.x-(int) t.x, t.y-(int) t.y, t.z-(int) t.z, 0.0f);
        data[PME_ORDER-1] = 0.0f;
        data[1] = dr;
        data[0] = 1.0f-dr;
        for (int j = 3; j < PME_ORDER; j++) {
            real div = RECIP(j-1.0f);
            data[j-1] = div*dr*data[j-2];
            for (int k = 1; k < (j-1); k++)
                data[j-k-1] = div*((dr+(real4) k) *data[j-k-2] + (-dr+(real4) (j-k))*data[j-k-1]);
            data[0] = div*(- dr+1.0f)*data[0];
        }
        ddata[0] = -data[0];
        for (int j = 1; j < PME_ORDER; j++)
            ddata[j] = data[j-1]-data[j];
        data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2];
        for (int j = 1; j < (PME_ORDER-1); j++)
            data[PME_ORDER-j-1] = scale*((dr+(real4) j)*data[PME_ORDER-j-2] + (-dr+(real4) (PME_ORDER-j))*data[PME_ORDER-j-1]);
        data[0] = scale*(-dr+1.0f)*data[0];

        // Compute the force on this atom.

        for (int ix = 0; ix < PME_ORDER; ix++) {
            int xindex = gridIndex.x+ix;
            xindex -= (xindex >= GRID_SIZE_X ? GRID_SIZE_X : 0);
            for (int iy = 0; iy < PME_ORDER; iy++) {
                int yindex = gridIndex.y+iy;
                yindex -= (yindex >= GRID_SIZE_Y ? GRID_SIZE_Y : 0);
                for (int iz = 0; iz < PME_ORDER; iz++) {
                    int zindex = gridIndex.z+iz;
                    zindex -= (zindex >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
                    int index = xindex*GRID_SIZE_Y*GRID_SIZE_Z + yindex*GRID_SIZE_Z + zindex;
                    real gridvalue = pmeGrid[index];
                    force.x += ddata[ix].x*data[iy].y*data[iz].z*gridvalue;
                    force.y += data[ix].x*ddata[iy].y*data[iz].z*gridvalue;
                    force.z += data[ix].x*data[iy].y*ddata[iz].z*gridvalue;
                }
            }
        }
        real4 totalForce = forceBuffers[atom];
        real q = pos.w*EPSILON_FACTOR;
        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);
        totalForce.z -= q*(force.x*GRID_SIZE_X*recipBoxVecZ.x+force.y*GRID_SIZE_Y*recipBoxVecZ.y+force.z*GRID_SIZE_Z*recipBoxVecZ.z);
        forceBuffers[atom] = totalForce;
    }
}

__kernel void addForces(__global const real4* restrict forces, __global real4* restrict forceBuffers) {
    for (int atom = get_global_id(0); atom < NUM_ATOMS; atom += get_global_size(0))
        forceBuffers[atom] += forces[atom];
}