kCalculateCustomNonbondedForces.h

/* -------------------------------------------------------------------------- *
 *                                   OpenMM                                   *
 * -------------------------------------------------------------------------- *
 * This is part of the OpenMM molecular simulation toolkit originating from   *
 * 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) 2009 Stanford University and the Authors.           *
 * Authors: Scott Le Grand, Peter Eastman                                     *
 * Contributors:                                                              *
 *                                                                            *
 * This program is free software: you can redistribute it and/or modify       *
 * it under the terms of the GNU Lesser General Public License as published   *
 * by the Free Software Foundation, either version 3 of the License, or       *
 * (at your option) any later version.                                        *
 *                                                                            *
 * This program is distributed in the hope that it will be useful,            *
 * but WITHOUT ANY WARRANTY; without even the implied warranty of             *
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
 * GNU Lesser General Public License for more details.                        *
 *                                                                            *
 * You should have received a copy of the GNU Lesser General Public License   *
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
 * -------------------------------------------------------------------------- */

/**
 * This file contains the kernels for evalauating custom nonbonded forces.  It is included
 * several times in kCalculateCustomNonbondedForces.cu with different #defines to generate
 * different versions of the kernels.
 */

__global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned int* workUnit)
{
    extern __shared__ float stack[];
    Atom* sA = (Atom*) &stack[cSim.customExpressionStackSize*blockDim.x];
    unsigned int totalWarps = cSim.nonbond_blocks*cSim.nonbond_threads_per_block/GRID;
    unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID;
    unsigned int numWorkUnits = cSim.pInteractionCount[0];
    unsigned int pos = warp*numWorkUnits/totalWarps;
    unsigned int end = (warp+1)*numWorkUnits/totalWarps;
    float totalEnergy = 0.0f;
#ifdef USE_CUTOFF
    float3* tempBuffer = (float3*) &sA[cSim.nonbond_threads_per_block];
#endif

    unsigned int lasty = 0xFFFFFFFF;
    while (pos < end)
    {

        // Extract cell coordinates from appropriate work unit
        unsigned int x = workUnit[pos];
        unsigned int y = ((x >> 2) & 0x7fff) << GRIDBITS;
        bool bExclusionFlag = (x & 0x1);
        x = (x >> 17) << GRIDBITS;
        float4      apos;   // Local atom x, y, z, q
        float3      af;     // Local atom fx, fy, fz
        unsigned int tgx = threadIdx.x & (GRID - 1);
        unsigned int tbx = threadIdx.x - tgx;
        unsigned int tj = tgx;
        Atom* psA = &sA[tbx];
        unsigned int i      = x + tgx;
        apos                = cSim.pPosq[i];
        float4 params       = cSim.pCustomParams[i];
        af.x                = 0.0f;
        af.y                = 0.0f;
        af.z                = 0.0f;
        if (x == y) // Handle diagonals uniquely at 50% efficiency
        {
            // Read fixed atom data into registers and GRF
            sA[threadIdx.x].x   = apos.x;
            sA[threadIdx.x].y   = apos.y;
            sA[threadIdx.x].z   = apos.z;
            sA[threadIdx.x].params = params;
            unsigned int xi   = x>>GRIDBITS;
            unsigned int cell = xi+xi*cSim.paddedNumberOfAtoms/GRID-xi*(xi+1)/2;
            unsigned int excl = cSim.pExclusion[cSim.pExclusionIndex[cell]+tgx];
            for (unsigned int j = 0; j < GRID; j++)
            {
                // Apply the combining rules to the parameters.

                float4 combinedParams = make_float4(0, 0, 0, 0);
                for (int k = 0; k < cSim.customParameters; k++)
                {
                    float value = kEvaluateExpression_kernel(&combiningRules[k], stack, 0.0f, params, psA[j].params);
                    switch (k)
                    {
                        case 0:
                            combinedParams.x = value;
                            break;
                        case 1:
                            combinedParams.y = value;
                            break;
                        case 2:
                            combinedParams.z = value;
                            break;
                        case 3:
                            combinedParams.w = value;
                            break;
                    }
                }

                // Compute the force.

                float dx        = psA[j].x - apos.x;
                float dy        = psA[j].y - apos.y;
                float dz        = psA[j].z - apos.z;
#ifdef USE_PERIODIC
                dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
                dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
                dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
                float r         = sqrt(dx*dx + dy*dy + dz*dz);
                float invR      = 1.0f/r;
                float dEdR      = -kEvaluateExpression_kernel(&forceExp, stack, r, combinedParams, combinedParams)*invR;
                float energy    = kEvaluateExpression_kernel(&energyExp, stack, r, combinedParams, combinedParams);
#ifdef USE_CUTOFF
                if (!(excl & 0x1) || r > cSim.nonbondedCutoff)
#else
                if (!(excl & 0x1))
#endif
                {
                    dEdR = 0.0f;
                    energy = 0.0f;
                }
                totalEnergy    += 0.5f*energy;
                dx             *= dEdR;
                dy             *= dEdR;
                dz             *= dEdR;
                af.x           -= dx;
                af.y           -= dy;
                af.z           -= dz;
                excl          >>= 1;
            }

            // Write results
            float4 of;
#ifdef USE_OUTPUT_BUFFER_PER_WARP
            unsigned int offset                          = x + tgx + warp*cSim.stride;
            of                                  = cSim.pForce4a[offset];
            of.x                               += af.x;
            of.y                               += af.y;
            of.z                               += af.z;
            cSim.pForce4a[offset]               = of;
#else
            of.x                                = af.x;
            of.y                                = af.y;
            of.z                                = af.z;
            of.w                                = 0.0f;
            unsigned int offset                          = x + tgx + (x >> GRIDBITS) * cSim.stride;
            cSim.pForce4a[offset]               = of;
#endif
        }
        else        // 100% utilization
        {
            // Read fixed atom data into registers and GRF
            if (lasty != y)
            {
                unsigned int j                   = y + tgx;
                float4 temp             = cSim.pPosq[j];
                sA[threadIdx.x].x       = temp.x;
                sA[threadIdx.x].y       = temp.y;
                sA[threadIdx.x].z       = temp.z;
                sA[threadIdx.x].params  = cSim.pCustomParams[j];
            }
            sA[threadIdx.x].fx      = 0.0f;
            sA[threadIdx.x].fy      = 0.0f;
            sA[threadIdx.x].fz      = 0.0f;
            if (!bExclusionFlag)
            {
#ifdef USE_CUTOFF
                unsigned int flags = cSim.pInteractionFlag[pos];
                if (flags == 0)
                {
                    // No interactions in this block.
                }
                else if (flags == 0xFFFFFFFF)
#endif
                {
                    // Compute all interactions within this block.

                    for (unsigned int j = 0; j < GRID; j++)
                    {
                        // Apply the combining rules to the parameters.

                        float4 combinedParams = make_float4(0, 0, 0, 0);
                        for (int k = 0; k < cSim.customParameters; k++)
                        {
                            float value = kEvaluateExpression_kernel(&combiningRules[k], stack, 0.0f, params, psA[tj].params);
                            switch (k)
                            {
                                case 0:
                                    combinedParams.x = value;
                                    break;
                                case 1:
                                    combinedParams.y = value;
                                    break;
                                case 2:
                                    combinedParams.z = value;
                                    break;
                                case 3:
                                    combinedParams.w = value;
                                    break;
                            }
                        }

                        // Compute the force.

                        float dx        = psA[tj].x - apos.x;
                        float dy        = psA[tj].y - apos.y;
                        float dz        = psA[tj].z - apos.z;
#ifdef USE_PERIODIC
                        dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
                        dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
                        dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
                        float r         = sqrt(dx*dx + dy*dy + dz*dz);
                        float invR      = 1.0f/r;
                        float dEdR      = -kEvaluateExpression_kernel(&forceExp, stack, r, combinedParams, combinedParams)*invR;
                        float energy    = kEvaluateExpression_kernel(&energyExp, stack, r, combinedParams, combinedParams);
#ifdef USE_CUTOFF
                        if (r > cSim.nonbondedCutoff)
                        {
                            dEdR = 0.0f;
                            energy = 0.0f;
                        }
#endif
                        totalEnergy    += energy;
                        dx             *= dEdR;
                        dy             *= dEdR;
                        dz             *= dEdR;
                        af.x           -= dx;
                        af.y           -= dy;
                        af.z           -= dz;
                        psA[tj].fx     += dx;
                        psA[tj].fy     += dy;
                        psA[tj].fz     += dz;
                        tj              = (tj + 1) & (GRID - 1);
                    }
                }
#ifdef USE_CUTOFF
                else
                {
                    // Compute only a subset of the interactions in this block.

                    for (unsigned int j = 0; j < GRID; j++)
                    {
                        if ((flags&(1<<j)) != 0)
                        {
                            // Apply the combining rules to the parameters.

                            float4 combinedParams = make_float4(0, 0, 0, 0);
                            for (int k = 0; k < cSim.customParameters; k++)
                            {
                                float value = kEvaluateExpression_kernel(&combiningRules[k], stack, 0.0f, params, psA[j].params);
                                switch (k)
                                {
                                    case 0:
                                        combinedParams.x = value;
                                        break;
                                    case 1:
                                        combinedParams.y = value;
                                        break;
                                    case 2:
                                        combinedParams.z = value;
                                        break;
                                    case 3:
                                        combinedParams.w = value;
                                        break;
                                }
                            }

                            // Compute the force.

                            float dx        = psA[j].x - apos.x;
                            float dy        = psA[j].y - apos.y;
                            float dz        = psA[j].z - apos.z;
#ifdef USE_PERIODIC
                            dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
                            dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
                            dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
                            float r         = sqrt(dx*dx + dy*dy + dz*dz);
                            float invR      = 1.0f/r;
                            float dEdR      = -kEvaluateExpression_kernel(&forceExp, stack, r, combinedParams, combinedParams)*invR;
                            float energy    = kEvaluateExpression_kernel(&energyExp, stack, r, combinedParams, combinedParams);
#ifdef USE_CUTOFF
                            if (r > cSim.nonbondedCutoff)
                            {
                                dEdR = 0.0f;
                                energy = 0.0f;
                            }
#endif
                            totalEnergy    += energy;
                            dx             *= dEdR;
                            dy             *= dEdR;
                            dz             *= dEdR;
                            af.x           -= dx;
                            af.y           -= dy;
                            af.z           -= dz;
                            tempBuffer[threadIdx.x].x = dx;
                            tempBuffer[threadIdx.x].y = dy;
                            tempBuffer[threadIdx.x].z = dz;

                            // Sum the forces on atom j.

                            if (tgx % 2 == 0)
                            {
                                tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+1].x;
                                tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+1].y;
                                tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+1].z;
                            }
                            if (tgx % 4 == 0)
                            {
                                tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+2].x;
                                tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+2].y;
                                tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+2].z;
                            }
                            if (tgx % 8 == 0)
                            {
                                tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+4].x;
                                tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+4].y;
                                tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+4].z;
                            }
                            if (tgx % 16 == 0)
                            {
                                tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+8].x;
                                tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+8].y;
                                tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+8].z;
                            }
                            if (tgx == 0)
                            {
                                psA[j].fx += tempBuffer[threadIdx.x].x + tempBuffer[threadIdx.x+16].x;
                                psA[j].fy += tempBuffer[threadIdx.x].y + tempBuffer[threadIdx.x+16].y;
                                psA[j].fz += tempBuffer[threadIdx.x].z + tempBuffer[threadIdx.x+16].z;
                            }
                        }
                    }
                }
#endif
            }
            else  // bExclusion
            {
                // Read fixed atom data into registers and GRF
                unsigned int xi   = x>>GRIDBITS;
                unsigned int yi   = y>>GRIDBITS;
                unsigned int cell          = xi+yi*cSim.paddedNumberOfAtoms/GRID-yi*(yi+1)/2;
                unsigned int excl = cSim.pExclusion[cSim.pExclusionIndex[cell]+tgx];
                excl              = (excl >> tgx) | (excl << (GRID - tgx));
                for (unsigned int j = 0; j < GRID; j++)
                {
                    // Apply the combining rules to the parameters.

                    float4 combinedParams = make_float4(0, 0, 0, 0);
                    for (int k = 0; k < cSim.customParameters; k++)
                    {
                        float value = kEvaluateExpression_kernel(&combiningRules[k], stack, 0.0f, params, psA[tj].params);
                        switch (k)
                        {
                            case 0:
                                combinedParams.x = value;
                                break;
                            case 1:
                                combinedParams.y = value;
                                break;
                            case 2:
                                combinedParams.z = value;
                                break;
                            case 3:
                                combinedParams.w = value;
                                break;
                        }
                    }

                    // Compute the force.

                    float dx        = psA[tj].x - apos.x;
                    float dy        = psA[tj].y - apos.y;
                    float dz        = psA[tj].z - apos.z;
#ifdef USE_PERIODIC
                    dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
                    dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
                    dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
                    float r         = sqrt(dx*dx + dy*dy + dz*dz);
                    float invR      = 1.0f/r;
                    float dEdR      = -kEvaluateExpression_kernel(&forceExp, stack, r, combinedParams, combinedParams)*invR;
                    float energy    = kEvaluateExpression_kernel(&energyExp, stack, r, combinedParams, combinedParams);
#ifdef USE_CUTOFF
                    if (!(excl & 0x1) || r > cSim.nonbondedCutoff)
#else
                    if (!(excl & 0x1))
#endif
                    {
                        dEdR = 0.0f;
                        energy = 0.0f;
                    }
                    totalEnergy    += energy;
                    dx             *= dEdR;
                    dy             *= dEdR;
                    dz             *= dEdR;
                    af.x           -= dx;
                    af.y           -= dy;
                    af.z           -= dz;
                    psA[tj].fx     += dx;
                    psA[tj].fy     += dy;
                    psA[tj].fz     += dz;
                    excl          >>= 1;
                    tj              = (tj + 1) & (GRID - 1);
                }
            }

            // Write results
            float4 of;
#ifdef USE_OUTPUT_BUFFER_PER_WARP
            unsigned int offset                 = x + tgx + warp*cSim.stride;
            of                                  = cSim.pForce4a[offset];
            of.x                               += af.x;
            of.y                               += af.y;
            of.z                               += af.z;
            cSim.pForce4a[offset]               = of;
            offset                              = y + tgx + warp*cSim.stride;
            of                                  = cSim.pForce4a[offset];
            of.x                               += sA[threadIdx.x].fx;
            of.y                               += sA[threadIdx.x].fy;
            of.z                               += sA[threadIdx.x].fz;
            cSim.pForce4a[offset]               = of;
#else
            of.x                                = af.x;
            of.y                                = af.y;
            of.z                                = af.z;
            of.w                                = 0.0f;
            unsigned int offset                 = x + tgx + (y >> GRIDBITS) * cSim.stride;
            cSim.pForce4a[offset]               = of;
            of.x                                = sA[threadIdx.x].fx;
            of.y                                = sA[threadIdx.x].fy;
            of.z                                = sA[threadIdx.x].fz;
            offset                              = y + tgx + (x >> GRIDBITS) * cSim.stride;
            cSim.pForce4a[offset]               = of;
#endif
            lasty = y;
        }

        pos++;
    }
    cSim.pEnergy[blockIdx.x*blockDim.x+threadIdx.x] += totalEnergy;
}


__global__ void METHOD_NAME(kCalculateCustomNonbonded, Exceptions_kernel)()
{
    extern __shared__ float stack[];
    unsigned int pos = blockIdx.x * blockDim.x + threadIdx.x;
    float totalEnergy = 0.0f;

    while (pos < cSim.customExceptions)
    {
        int4 atom       = cSim.pCustomExceptionID[pos];
        float4 params   = cSim.pCustomExceptionParams[pos];
        float4 a1       = cSim.pPosq[atom.x];
        float4 a2       = cSim.pPosq[atom.y];
        float dx        = a1.x - a2.x;
        float dy        = a1.y - a2.y;
        float dz        = a1.z - a2.z;
#ifdef USE_PERIODIC
        dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
        dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
        dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
        float r         = sqrt(dx*dx + dy*dy + dz*dz);
        float invR      = 1.0f/r;
        float dEdR      = -kEvaluateExpression_kernel(&forceExp, stack, r, params, params)*invR;
        float energy    = kEvaluateExpression_kernel(&energyExp, stack, r, params, params);
#ifdef USE_CUTOFF
        if (r > cSim.nonbondedCutoff)
        {
            dEdR = 0.0f;
            energy = 0.0f;
        }
#endif
        totalEnergy          += energy;
        dx                   *= dEdR;
        dy                   *= dEdR;
        dz                   *= dEdR;
        unsigned int offsetA  = atom.x + atom.z * cSim.stride;
        unsigned int offsetB  = atom.y + atom.w * cSim.stride;
        float4 forceA         = cSim.pForce4[offsetA];
        float4 forceB         = cSim.pForce4[offsetB];
        forceA.x             += dx;
        forceA.y             += dy;
        forceA.z             += dz;
        forceB.x             -= dx;
        forceB.y             -= dy;
        forceB.z             -= dz;
        cSim.pForce4[offsetA] = forceA;
        cSim.pForce4[offsetB] = forceB;
        pos                  += blockDim.x * gridDim.x;
    }
    cSim.pEnergy[blockIdx.x * blockDim.x + threadIdx.x] += totalEnergy;
}