kCalculateCustomNonbondedForces.cu

/* -------------------------------------------------------------------------- *
 *                                   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/>.      *
 * -------------------------------------------------------------------------- */

#include <stdio.h>
#include <cuda.h>
#include <vector_functions.h>
#include <cstdlib>
#include <string>
#include <iostream>
#include <fstream>
using namespace std;

#include "gputypes.h"
#include "cudatypes.h"

#define UNROLLXX 0
#define UNROLLXY 0

struct Atom {
    float x;
    float y;
    float z;
    float4 params;
    float fx;
    float fy;
    float fz;
};

static __constant__ cudaGmxSimulation cSim;
static __constant__ Expression<128> forceExp;
static __constant__ Expression<128> energyExp;
static __constant__ Expression<64> combiningRules[4];
static __constant__ float globalParams[8];

texture<float4, 1, cudaReadModeElementType> texRef0;
texture<float4, 1, cudaReadModeElementType> texRef1;
texture<float4, 1, cudaReadModeElementType> texRef2;
texture<float4, 1, cudaReadModeElementType> texRef3;

void SetCalculateCustomNonbondedForcesSim(gpuContext gpu)
{
    cudaError_t status;
    status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
    RTERROR(status, "cudaMemcpyToSymbol: SetSim copy to cSim failed");
}

void GetCalculateCustomNonbondedForcesSim(gpuContext gpu)
{
    cudaError_t status;
    status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
    RTERROR(status, "cudaMemcpyFromSymbol: SetSim copy from cSim failed");
}

void SetCustomNonbondedForceExpression(const Expression<128>& expression)
{
    cudaError_t status;
    status = cudaMemcpyToSymbol(forceExp, &expression, sizeof(forceExp));
    RTERROR(status, "SetCustomNonbondedForceExpression: cudaMemcpyToSymbol failed");
}

void SetCustomNonbondedEnergyExpression(const Expression<128>& expression)
{
    cudaError_t status;
    status = cudaMemcpyToSymbol(energyExp, &expression, sizeof(energyExp));
    RTERROR(status, "SetCustomNonbondedEnergyExpression: cudaMemcpyToSymbol failed");
}

void SetCustomNonbondedCombiningRules(const Expression<64>* expressions)
{
    cudaError_t status;
    status = cudaMemcpyToSymbol(combiningRules, expressions, sizeof(combiningRules));
    RTERROR(status, "SetCustomNonbondedCombiningRules: cudaMemcpyToSymbol failed");
}

void SetCustomNonbondedGlobalParams(float* paramValues)
{
    cudaError_t status;
    status = cudaMemcpyToSymbol(globalParams, paramValues, sizeof(globalParams));
    RTERROR(status, "SetCustomNonbondedGlobalParams: cudaMemcpyToSymbol failed");
}

#define STACK(y) stack[(y)*blockDim.x+threadIdx.x]
#define VARIABLE(y) variables[(y)*blockDim.x+threadIdx.x]

template<int SIZE>
__device__ float kEvaluateExpression_kernel(Expression<SIZE>* expression, float* stack, float* variables)
{
    int stackPointer = -1;
    for (int i = 0; i < expression->length; i++)
    {
        int op = expression->op[i];
        if (op < MULTIPLY) {
            STACK(++stackPointer) = VARIABLE(op-VARIABLE0);
        }
        else if (op < NEGATE) {
            if (op < MULTIPLY_CONSTANT) {
                if (op == MULTIPLY) {
                    float temp = STACK(stackPointer);
                    STACK(--stackPointer) *= temp;
                }
                else if (op == DIVIDE) {
                    float temp = STACK(stackPointer);
                    STACK(stackPointer) = temp/STACK(--stackPointer);
                }
                else if (op == ADD) {
                    float temp = STACK(stackPointer);
                    STACK(--stackPointer) += temp;
                }
                else if (op == SUBTRACT) {
                    float temp = STACK(stackPointer);
                    STACK(stackPointer) = temp-STACK(--stackPointer);
                }
                else /*if (op == POWER)*/ {
                    float temp = STACK(stackPointer);
                    STACK(stackPointer) = pow(temp, STACK(--stackPointer));
                }
            }
            else if (op < GLOBAL) {
                if (op == MULTIPLY_CONSTANT) {
                    STACK(stackPointer) *= expression->arg[i];
                }
                else if (op == POWER_CONSTANT) {
                    STACK(stackPointer) = pow(STACK(stackPointer), expression->arg[i]);
                }
                else /*if (op == ADD_CONSTANT)*/ {
                    STACK(stackPointer) += expression->arg[i];
                }
            }
            else {
                if (op == GLOBAL) {
                    STACK(++stackPointer) = globalParams[(int) expression->arg[i]];
                }
                else if (op == CONSTANT) {
                    STACK(++stackPointer) = expression->arg[i];
                }
                else /*if (op == CUSTOM || op == CUSTOM_DERIV)*/ {
                    int function = (int) expression->arg[i];
                    float x = STACK(stackPointer);
                    float4 params = cSim.pTabulatedFunctionParams[function];
                    if (x < params.x || x > params.y)
                        STACK(stackPointer) = 0.0f;
                    else
                    {
                        int index = floor((x-params.x)*params.z);
                        float4 coeff;
                        if (function == 0)
                            coeff = tex1Dfetch(texRef0, index);
                        else if (function == 1)
                            coeff = tex1Dfetch(texRef1, index);
                        else if (function == 2)
                            coeff = tex1Dfetch(texRef2, index);
                        else
                            coeff = tex1Dfetch(texRef3, index);
                        x = (x-params.x)*params.z-index;
                        if (op == CUSTOM)
                            STACK(stackPointer) = coeff.x+x*(coeff.y+x*(coeff.z+x*coeff.w));
                        else
                            STACK(stackPointer) = (coeff.y+x*(2.0f*coeff.z+x*3.0f*coeff.w))*params.z;
                    }
                }
            }
        }
        else {
            if (op < SIN) {
                if (op == NEGATE) {
                    STACK(stackPointer) *= -1.0f;
                }
                else if (op == RECIPROCAL) {
                    STACK(stackPointer) = 1.0f/STACK(stackPointer);
                }
                else if (op == SQRT) {
                    STACK(stackPointer) = sqrt(STACK(stackPointer));
                }
                else if (op == EXP) {
                    STACK(stackPointer) = exp(STACK(stackPointer));
                }
                else if (op == LOG) {
                    STACK(stackPointer) = log(STACK(stackPointer));
                }
                else if (op == SQUARE) {
                    float temp = STACK(stackPointer);
                    STACK(stackPointer) *= temp;
                }
                else /*if (op == CUBE)*/ {
                    float temp = STACK(stackPointer);
                    STACK(stackPointer) *= temp*temp;
                }
            }
            else {
                if (op == SIN) {
                    STACK(stackPointer) = sin(STACK(stackPointer));
                }
                else if (op == COS) {
                    STACK(stackPointer) = cos(STACK(stackPointer));
                }
                else if (op == SEC) {
                    STACK(stackPointer) = 1.0f/cos(STACK(stackPointer));
                }
                else if (op == CSC) {
                    STACK(stackPointer) = 1.0f/sin(STACK(stackPointer));
                }
                else if (op == TAN) {
                    STACK(stackPointer) = tan(STACK(stackPointer));
                }
                else if (op == COT) {
                    STACK(stackPointer) = 1.0f/tan(STACK(stackPointer));
                }
                else if (op == ASIN) {
                    STACK(stackPointer) = asin(STACK(stackPointer));
                }
                else if (op == ACOS) {
                    STACK(stackPointer) = acos(STACK(stackPointer));
                }
                else if (op == ATAN) {
                    STACK(stackPointer) = atan(STACK(stackPointer));
                }
                else if (op == SINH) {
                    STACK(stackPointer) = sinh(STACK(stackPointer));
                }
                else if (op == COSH) {
                    STACK(stackPointer) = cosh(STACK(stackPointer));
                }
                else /*if (op == TANH)*/ {
                    STACK(stackPointer) = tanh(STACK(stackPointer));
                }
            }
        }
    }
    return STACK(stackPointer);
}

// Include versions of the kernels for N^2 calculations.

#define METHOD_NAME(a, b) a##N2##b
#include "kCalculateCustomNonbondedForces.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##N2ByWarp##b
#include "kCalculateCustomNonbondedForces.h"

// Include versions of the kernels with cutoffs.

#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_CUTOFF
#define METHOD_NAME(a, b) a##Cutoff##b
#include "kCalculateCustomNonbondedForces.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##CutoffByWarp##b
#include "kCalculateCustomNonbondedForces.h"

// Include versions of the kernels with periodic boundary conditions.

#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_PERIODIC
#define METHOD_NAME(a, b) a##Periodic##b
#include "kCalculateCustomNonbondedForces.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##PeriodicByWarp##b
#include "kCalculateCustomNonbondedForces.h"

__global__ void kFindBlockBoundsCutoff_kernel();
__global__ void kFindBlocksWithInteractionsCutoff_kernel();
__global__ void kFindInteractionsWithinBlocksCutoff_kernel(unsigned int* workUnit);
__global__ void kFindBlockBoundsPeriodic_kernel();
__global__ void kFindBlocksWithInteractionsPeriodic_kernel();
__global__ void kFindInteractionsWithinBlocksPeriodic_kernel(unsigned int* workUnit);

void kCalculateCustomNonbondedForces(gpuContext gpu, bool neighborListValid)
{
//    printf("kCalculateCustomNonbondedCutoffForces\n");
    if (gpu->tabulatedFunctionsChanged)
    {
        cudaChannelFormatDesc channelDesc = cudaCreateChannelDesc<float4>();
        if (gpu->tabulatedFunctions[0].coefficients != NULL)
            cudaBindTexture(NULL, &texRef0, gpu->tabulatedFunctions[0].coefficients->_pDevData, &channelDesc, gpu->tabulatedFunctions[0].coefficients->_length*sizeof(float4));
        if (gpu->tabulatedFunctions[1].coefficients != NULL)
            cudaBindTexture(NULL, &texRef1, gpu->tabulatedFunctions[1].coefficients->_pDevData, &channelDesc, gpu->tabulatedFunctions[1].coefficients->_length*sizeof(float4));
        if (gpu->tabulatedFunctions[2].coefficients != NULL)
            cudaBindTexture(NULL, &texRef2, gpu->tabulatedFunctions[2].coefficients->_pDevData, &channelDesc, gpu->tabulatedFunctions[2].coefficients->_length*sizeof(float4));
        if (gpu->tabulatedFunctions[3].coefficients != NULL)
            cudaBindTexture(NULL, &texRef3, gpu->tabulatedFunctions[3].coefficients->_pDevData, &channelDesc, gpu->tabulatedFunctions[3].coefficients->_length*sizeof(float4));
        gpu->tabulatedFunctionsChanged = false;
    }
    int sharedPerThread = sizeof(Atom)+gpu->sim.customExpressionStackSize*sizeof(float)+8*sizeof(float);
    if (gpu->sim.customNonbondedMethod != NO_CUTOFF)
        sharedPerThread += sizeof(float3);
    int threads = gpu->sim.nonbond_threads_per_block;
    int maxThreads = 16380/sharedPerThread;
    if (threads > maxThreads)
        threads = (maxThreads/32)*32;
    switch (gpu->sim.customNonbondedMethod)
    {
        case NO_CUTOFF:
            if (gpu->bOutputBufferPerWarp)
                kCalculateCustomNonbondedN2ByWarpForces_kernel<<<gpu->sim.nonbond_blocks, threads, sharedPerThread*threads>>>(gpu->sim.pWorkUnit);
            else
                kCalculateCustomNonbondedN2Forces_kernel<<<gpu->sim.nonbond_blocks, threads, sharedPerThread*threads>>>(gpu->sim.pWorkUnit);
            LAUNCHERROR("kCalculateCustomNonbondedN2Forces");
            kCalculateCustomNonbondedN2Exceptions_kernel<<<gpu->sim.blocks, gpu->sim.custom_exception_threads_per_block,
                    gpu->sim.customExpressionStackSize*sizeof(float)*gpu->sim.custom_exception_threads_per_block>>>();
            LAUNCHERROR("kCalculateCustomNonbondedN2Exceptions");
            break;
        case CUTOFF:
            if (!neighborListValid)
            {
                kFindBlockBoundsCutoff_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
                LAUNCHERROR("kFindBlockBoundsCutoff");
                kFindBlocksWithInteractionsCutoff_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
                LAUNCHERROR("kFindBlocksWithInteractionsCutoff");
                compactStream(gpu->compactPlan, gpu->sim.pInteractingWorkUnit, gpu->sim.pWorkUnit, gpu->sim.pInteractionFlag, gpu->sim.workUnits, gpu->sim.pInteractionCount);
                kFindInteractionsWithinBlocksCutoff_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
                        sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
            }
            if (gpu->bOutputBufferPerWarp)
                kCalculateCustomNonbondedCutoffByWarpForces_kernel<<<gpu->sim.nonbond_blocks, threads, sharedPerThread*threads>>>(gpu->sim.pInteractingWorkUnit);
            else
                kCalculateCustomNonbondedCutoffForces_kernel<<<gpu->sim.nonbond_blocks, threads, sharedPerThread*threads>>>(gpu->sim.pInteractingWorkUnit);
            LAUNCHERROR("kCalculateCustomNonbondedCutoffForces");
            kCalculateCustomNonbondedCutoffExceptions_kernel<<<gpu->sim.blocks, gpu->sim.custom_exception_threads_per_block,
                    gpu->sim.customExpressionStackSize*sizeof(float)*gpu->sim.custom_exception_threads_per_block>>>();
            LAUNCHERROR("kCalculateCustomNonbondedCutoffExceptions");
            break;
        case PERIODIC:
            if (!neighborListValid)
            {
                kFindBlockBoundsPeriodic_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
                LAUNCHERROR("kFindBlockBoundsPeriodic");
                kFindBlocksWithInteractionsPeriodic_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
                LAUNCHERROR("kFindBlocksWithInteractionsPeriodic");
                compactStream(gpu->compactPlan, gpu->sim.pInteractingWorkUnit, gpu->sim.pWorkUnit, gpu->sim.pInteractionFlag, gpu->sim.workUnits, gpu->sim.pInteractionCount);
                kFindInteractionsWithinBlocksPeriodic_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
                        sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
            }
            if (gpu->bOutputBufferPerWarp)
                kCalculateCustomNonbondedPeriodicByWarpForces_kernel<<<gpu->sim.nonbond_blocks, threads, sharedPerThread*threads>>>(gpu->sim.pInteractingWorkUnit);
            else
                kCalculateCustomNonbondedPeriodicForces_kernel<<<gpu->sim.nonbond_blocks, threads, sharedPerThread*threads>>>(gpu->sim.pInteractingWorkUnit);
            LAUNCHERROR("kCalculateCustomNonbondedPeriodicForces");
            kCalculateCustomNonbondedPeriodicExceptions_kernel<<<gpu->sim.blocks, gpu->sim.custom_exception_threads_per_block,
                    (gpu->sim.customExpressionStackSize+8)*sizeof(float)*gpu->sim.custom_exception_threads_per_block>>>();
            LAUNCHERROR("kCalculateCustomNonbondedPeriodicExceptions");
            break;
    }
}