kCalculateAndersenThermostat.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:                                                              *
 *                                                                            *
 * Permission is hereby granted, free of charge, to any person obtaining a    *
 * copy of this software and associated documentation files (the "Software"), *
 * to deal in the Software without restriction, including without limitation  *
 * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
 * and/or sell copies of the Software, and to permit persons to whom the      *
 * Software is furnished to do so, subject to the following conditions:       *
 *                                                                            *
 * The above copyright notice and this permission notice shall be included in *
 * all copies or substantial portions of the Software.                        *
 *                                                                            *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
 * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
 * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
 * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
 * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
 * -------------------------------------------------------------------------- */

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

#include "gputypes.h"

static __constant__ cudaGmxSimulation cSim;

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

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

__global__ void kCalculateAndersenThermostat_kernel()
{
    unsigned int pos            = threadIdx.x + blockIdx.x * blockDim.x;
    unsigned int rpos           = cSim.pRandomPosition[blockIdx.x];
    __syncthreads();
    
    while (pos < cSim.atoms)
    {
        float4 velocity         = cSim.pVelm4[pos];
        float4 random4a         = cSim.pRandom4a[rpos + pos];
        float scale = (random4a.w < cSim.collisionProbability ? 0.0 : 1.0);
        float add = (1.0-scale)*sqrt(cSim.kT*velocity.w);
        velocity.x = scale*velocity.x + add*random4a.x;
        velocity.y = scale*velocity.y + add*random4a.y;
        velocity.z = scale*velocity.z + add*random4a.z;
        cSim.pVelm4[pos]        = velocity;
         
        pos                    += blockDim.x * gridDim.x;    
    }

    // Update random position pointer
    if (threadIdx.x == 0)
    {
        rpos                   += cSim.paddedNumberOfAtoms;
        if (rpos > cSim.randoms)
            rpos               -= cSim.randoms;
        cSim.pRandomPosition[blockIdx.x] = rpos;
    }
}

extern void kGenerateRandoms(gpuContext gpu);
void kCalculateAndersenThermostat(gpuContext gpu)
{
//    printf("kCalculateAndersenThermostat\n");
    kCalculateAndersenThermostat_kernel<<<gpu->sim.blocks, gpu->sim.update_threads_per_block>>>();
    LAUNCHERROR("kCalculateAndersenThermostat");
    
    // Update randoms if necessary
    static int iteration = 0;
    iteration++;
    if (iteration == gpu->sim.randomIterations)
    {
        kGenerateRandoms(gpu);
        iteration = 0;
    }
}