/* -------------------------------------------------------------------------- *
* 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: Erik Lindahl, Rossen Apostolov, Szilard Pall, 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 . *
* -------------------------------------------------------------------------- */
#include "gputypes.h"
#include "bbsort.h"
#include
using namespace std;
static __constant__ cudaGmxSimulation cSim;
void SetCalculatePMESim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetSim copy to cSim failed");
}
void GetCalculatePMESim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyFromSymbol: SetSim copy from cSim failed");
}
inline __host__ __device__ int fast_mod(int a, int b)
{
return (b & (b - 1)) ? a % b : a & (b - 1);
}
inline __host__ __device__ float4 make_float4(float s)
{
return make_float4(s, s, s, s);
}
inline __host__ __device__ float4 operator-(float4 &a)
{
return make_float4(-a.x, -a.y, -a.z, -a.w);
}
inline __host__ __device__ float4 operator-(float4 a, float4 b)
{
return make_float4(a.x - b.x, a.y - b.y, a.z - b.z, a.w - b.w);
}
inline __host__ __device__ float4 operator+(float4 a, float4 b)
{
return make_float4(a.x + b.x, a.y + b.y, a.z + b.z, a.w + b.w);
}
inline __host__ __device__ float4 operator+(float4 a, float b)
{
return make_float4(a.x + b, a.y + b, a.z + b, a.w + b);
}
inline __host__ __device__ float4 operator+(float a, float4 b)
{
return make_float4(a + b.x, a + b.y, a + b.z, a + b.w);
}
inline __host__ __device__ float4 operator*(float s, float4 a)
{
return make_float4(a.x * s, a.y * s, a.z * s, a.w * s);
}
inline __host__ __device__ float4 operator*(float4 a, float4 b)
{
return make_float4(a.x * b.x, a.y * b.y, a.z * b.z, a.w + b.w);
}
inline __host__ __device__ float4 make_float4(int3 a)
{
return make_float4(a.x, a.y, a.z, 0);
}
__global__ void kUpdateGridIndexAndFraction_kernel()
{
unsigned int tnb = blockDim.x * gridDim.x;
unsigned int tid = blockIdx.x * blockDim.x + threadIdx.x;
for (int i = tid; i < cSim.atoms; i += tnb)
{
float4 ftmp = cSim.pPosq[i];
float3 t = make_float3((ftmp.x/cSim.periodicBoxSizeX+1.0f)*cSim.pmeGridSize.x,
(ftmp.y/cSim.periodicBoxSizeY+1.0f)*cSim.pmeGridSize.y,
(ftmp.z/cSim.periodicBoxSizeZ+1.0f)*cSim.pmeGridSize.z);
float3 tix;
ftmp.x = modff(t.x, &tix.x);
ftmp.y = modff(t.y, &tix.y);
ftmp.z = modff(t.z, &tix.z);
cSim.pPmeParticleFraction[i] = ftmp;
int4 itmp = make_int4(fast_mod(__float2int_rd(tix.x), cSim.pmeGridSize.x),
fast_mod(__float2int_rd(tix.y), cSim.pmeGridSize.y),
fast_mod(__float2int_rd(tix.z), cSim.pmeGridSize.z), 0);
cSim.pPmeParticleIndex[i] = itmp;
cSim.pPmeAtomGridIndex[i] = make_float2(i, itmp.x*cSim.pmeGridSize.y*cSim.pmeGridSize.z+itmp.y*cSim.pmeGridSize.z+itmp.z);
}
//
// // Compute flags for which atoms affect which groups of grid points.
//
// const int3 numGroups = make_int3((cSim.pmeGridSize.x+cSim.pmeGroupSize.x-1)/cSim.pmeGroupSize.x, (cSim.pmeGridSize.y+cSim.pmeGroupSize.y-1)/cSim.pmeGroupSize.y, (cSim.pmeGridSize.z+cSim.pmeGroupSize.z-1)/cSim.pmeGroupSize.z);
// const unsigned int totalGroups = numGroups.x*numGroups.y*numGroups.z;
// const float3 gridScale = make_float3(cSim.pmeGridSize.x/cSim.periodicBoxSizeX, cSim.pmeGridSize.y/cSim.periodicBoxSizeY, cSim.pmeGridSize.z/cSim.periodicBoxSizeZ);
// for (int group = tid; group < totalGroups; group += tnb)
// {
// int3 gridBase;
// gridBase.x = group/(numGroups.y*numGroups.z);
// int remainder = group-gridBase.x*numGroups.y*numGroups.z;
// gridBase.y = remainder/numGroups.z;
// gridBase.z = remainder-gridBase.y*numGroups.z;
// gridBase.x *= cSim.pmeGroupSize.x;
// gridBase.y *= cSim.pmeGroupSize.y;
// gridBase.z *= cSim.pmeGroupSize.z;
// unsigned int flags = 0;
// unsigned int baseIndex = group*(cSim.paddedNumberOfAtoms/32);
// for (int atomBlock = 0; atomBlock < cSim.paddedNumberOfAtoms>>GRIDBITS; atomBlock++)
// {
// // Decide if this block actually needs to be processed.
//
// int flagIndex = atomBlock%32;
// if (flagIndex == 0)
// flags = 0;
// float4 boxSize = cSim.pGridBoundingBox[atomBlock];
// float4 center = cSim.pGridCenter[atomBlock];
// int maxx = (int) ceil((center.x+boxSize.x)*gridScale.x)+cSim.pmeGroupSize.x+PME_ORDER;
// int maxy = (int) ceil((center.y+boxSize.y)*gridScale.y)+cSim.pmeGroupSize.y+PME_ORDER;
// int maxz = (int) ceil((center.z+boxSize.z)*gridScale.z)+cSim.pmeGroupSize.z+PME_ORDER;
// int minx = (int) floor((center.x-boxSize.x)*gridScale.x);
// int miny = (int) floor((center.y-boxSize.y)*gridScale.y);
// int minz = (int) floor((center.z-boxSize.z)*gridScale.z);
// int x = minx+(gridBase.x-minx)%cSim.pmeGridSize.x;
// int y = miny+(gridBase.y-miny)%cSim.pmeGridSize.y;
// int z = minz+(gridBase.z-minz)%cSim.pmeGridSize.z;
// if (maxx < x || maxy < y || maxz < z)
// flags += 1<>GRIDBITS)
// cSim.pPmeInteractionFlags[baseIndex+atomBlock/32] = flags;
// }
// }
}
/**
* For each grid point, find the range of sorted atoms associated with that point.
*/
__global__ void kFindAtomRangeForGrid_kernel()
{
int thread = blockIdx.x*blockDim.x+threadIdx.x;
int start = (cSim.atoms*thread)/(blockDim.x*gridDim.x);
int end = (cSim.atoms*(thread+1))/(blockDim.x*gridDim.x);
int last = (thread == 0 ? -1 : cSim.pPmeAtomGridIndex[start-1].y);
for (int i = start; i < end; ++i)
{
float2 atomData = cSim.pPmeAtomGridIndex[i];
int gridIndex = atomData.y;
if (gridIndex != last)
{
for (int j = last+1; j <= gridIndex; ++j)
cSim.pPmeAtomRange[j] = i;
last = gridIndex;
}
// The grid index won't be needed again. Reuse that component to hold the atom charge, thus saving
// an extra load operation in the charge spreading kernel.
cSim.pPmeAtomGridIndex[i].y = cSim.pPosq[(int) atomData.x].w;
}
// Fill in values beyond the last atom.
if (thread == blockDim.x*gridDim.x-1)
{
int gridSize = cSim.pmeGridSize.x*cSim.pmeGridSize.y*cSim.pmeGridSize.z;
for (int j = last+1; j <= gridSize; ++j)
cSim.pPmeAtomRange[j] = cSim.atoms;
}
}
__global__ void kUpdateBsplines_kernel()
{
unsigned int tnb = blockDim.x * gridDim.x;
unsigned int tid = blockIdx.x * blockDim.x + threadIdx.x;
extern __shared__ float4 bsplines_cache[]; // size = 2 * block_size * pme_order
const float4 div_o = make_float4(1.0f/(PME_ORDER - 1));
for (int i = tid; i < cSim.atoms; i += tnb)
{
float4* data = &bsplines_cache[threadIdx.x*PME_ORDER];
float4* ddata = &bsplines_cache[threadIdx.x*PME_ORDER + blockDim.x*PME_ORDER];
for (int j = 0; j < PME_ORDER; j++)
{
data[j] = make_float4(0.0f);
ddata[j] = make_float4(0.0f);
}
float4 dr = cSim.pPmeParticleFraction[i];
data[PME_ORDER - 1] = make_float4(0.0f);
data[1] = dr;
data[0] = make_float4(1.0f) - dr;
for (int j = 3; j < PME_ORDER; j++)
{
float div = 1.0f / ((float)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 + float(k)) * data[j - k - 2] +
(-dr + ((float)(j - k))) * data[j - k - 1]);
}
data[0] = div * (- dr + 1) * 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] = div_o * dr * data[PME_ORDER - 2];
for (int j = 1; j < (PME_ORDER - 1); j++)
{
data[PME_ORDER - j - 1] =
div_o * (
(dr + (float)j) * data[PME_ORDER - j - 2] +
(-dr + ((float)(PME_ORDER - j))) * data[PME_ORDER - j - 1]
);
}
data[0] = div_o * (-dr + 1.0f) * data[0];
for (int j = 0; j < PME_ORDER; j++)
{
cSim.pPmeBsplineTheta[i + j*cSim.atoms] = data[j];
cSim.pPmeBsplineDtheta[i + j*cSim.atoms] = ddata[j];
}
}
}
//__global__ void kGridSpreadCharge_kernel()
//{
// extern __shared__ float atomCharge[];
// int4* atomGridIndex = (int4*) &atomCharge[blockDim.x];
// const unsigned int totalWarps = gridDim.x*blockDim.x/GRID;
// const unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID;
// const int3 numGroups = make_int3((cSim.pmeGridSize.x+cSim.pmeGroupSize.x-1)/cSim.pmeGroupSize.x, (cSim.pmeGridSize.y+cSim.pmeGroupSize.y-1)/cSim.pmeGroupSize.y, (cSim.pmeGridSize.z+cSim.pmeGroupSize.z-1)/cSim.pmeGroupSize.z);
// const unsigned int totalGroups = numGroups.x*numGroups.y*numGroups.z;
// unsigned int group = warp*totalGroups/totalWarps;
// const unsigned int end = (warp+1)*totalGroups/totalWarps;
// const unsigned int index = threadIdx.x & (GRID - 1);
//
// while (group < end)
// {
// // Process a group of grid points of size cSim.pmeGroupSize. First figure out the base index for the group,
// // and the index of the specific point this thread will handle.
//
// int3 gridBase;
// gridBase.x = group/(numGroups.y*numGroups.z);
// int remainder = group-gridBase.x*numGroups.y*numGroups.z;
// gridBase.y = remainder/numGroups.z;
// gridBase.z = remainder-gridBase.y*numGroups.z;
// gridBase.x *= cSim.pmeGroupSize.x;
// gridBase.y *= cSim.pmeGroupSize.y;
// gridBase.z *= cSim.pmeGroupSize.z;
// int3 gridPoint;
// gridPoint.x = index/(cSim.pmeGroupSize.y*cSim.pmeGroupSize.z);
// remainder = index-gridPoint.x*cSim.pmeGroupSize.y*cSim.pmeGroupSize.z;
// gridPoint.y = remainder/cSim.pmeGroupSize.z;
// gridPoint.z = remainder-gridPoint.y*cSim.pmeGroupSize.z;
// gridPoint.x += gridBase.x;
// gridPoint.y += gridBase.y;
// gridPoint.z += gridBase.z;
//
// // Loop over blocks of atoms.
//
// float result = 0.0f;
// int flags = 0;
// unsigned int baseIndex = group*(cSim.paddedNumberOfAtoms/32);
// for (int atomBlock = 0; atomBlock < cSim.paddedNumberOfAtoms>>GRIDBITS; atomBlock++)
// {
// // Decide if this block actually needs to be processed.
//
// int flagIndex = atomBlock%32;
// if (flagIndex == 0)
// flags = cSim.pPmeInteractionFlags[baseIndex+atomBlock/32];
// if ((flags & (1<sim.blocks, gpu->sim.update_threads_per_block>>>();
LAUNCHERROR("kUpdateGridIndexAndFraction");
bbSort(gpu->psPmeAtomGridIndex->_pDevData, gpu->natoms);
kFindAtomRangeForGrid_kernel<<sim.blocks, gpu->sim.update_threads_per_block>>>();
LAUNCHERROR("kFindAtomRangeForGrid");
unsigned int threads = 16380/(2*PME_ORDER*sizeof(float4));
kUpdateBsplines_kernel<<sim.blocks, threads, 2*threads*PME_ORDER*sizeof(float4)>>>();
LAUNCHERROR("kUpdateBsplines");
kGridSpreadCharge_kernel<<sim.blocks, 64, 64*(sizeof(float)+sizeof(int4))>>>();
LAUNCHERROR("kGridSpreadCharge");
// gpu->psPmeGrid->Download();
// for (int i = 0; i < gpu->psPmeGrid->_length; i += 100)
// printf("%d %f %f\n", i, (*gpu->psPmeGrid)[i].x, (*gpu->psPmeGrid)[i].y);
cufftExecC2C(gpu->fftplan, gpu->psPmeGrid->_pDevData, gpu->psPmeGrid->_pDevData, CUFFT_FORWARD);
kReciprocalConvolution_kernel<<sim.blocks, gpu->sim.nonbond_threads_per_block>>>();
LAUNCHERROR("kReciprocalConvolution");
cufftExecC2C(gpu->fftplan, gpu->psPmeGrid->_pDevData, gpu->psPmeGrid->_pDevData, CUFFT_INVERSE);
kGridInterpolateForce_kernel<<sim.blocks, gpu->sim.update_threads_per_block>>>();
LAUNCHERROR("kGridInterpolateForce");
}