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lj_force.cu
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lj_force.cu
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#include <stdio.h>
//////////////////////////float3////////////////////////////////
inline __device__ float3 operator+(float3 a, float b)
{
return make_float3(a.x + b, a.y + b, a.z + b);
}
inline __device__ float3 operator-(float3 a, float b)
{
return make_float3(a.x - b, a.y - b, a.z - b);
}
inline __device__ float3 operator+(float3 a, float3 b)
{
return make_float3(a.x + b.x, a.y + b.y, a.z + b.z);
}
inline __device__ float3 operator-(float3 a, float3 b)
{
return make_float3(a.x - b.x, a.y - b.y, a.z - b.z);
}
inline __device__ void operator+=(float3 &a, float3 b)
{
a.x += b.x;
a.y += b.y;
a.z += b.z;
}
inline __device__ void operator-=(float3 &a, float3 b)
{
a.x -= b.x;
a.y -= b.y;
a.z -= b.z;
}
inline __device__ float3 operator/(float3 a, float3 b)
{
return make_float3(a.x/b.x, a.y/b.y, a.z/b.z);
}
inline __device__ float3 operator*(float3 a, float b)
{
return make_float3(a.x*b, a.y*b, a.z*b);
}
inline __device__ float3 operator*(float a, float3 b)
{
return make_float3(a*b.x, a*b.y, a*b.z);
}
inline __device__ float3 operator*(float3 a, float3 b)
{
return make_float3(a.x*b.x, a.y*b.y, a.z*b.z);
}
inline __device__ float3 operator*(float3 a, int3 b)
{
return make_float3(a.x*b.x, a.y*b.y, a.z*b.z);
}
///////////////////////////int3/////////////////////////////////
inline __device__ int3 operator+(int3 a, int3 b)
{
return make_int3(a.x + b.x, a.y + b.y, a.z + b.z);
}
inline __device__ int3 operator-(int3 a, int3 b)
{
return make_int3(a.x - b.x, a.y - b.y, a.z - b.z);
}
inline __device__ int3 operator+(int3 a, int b)
{
return make_int3(a.x + b, a.y + b, a.z + b);
}
inline __device__ int3 operator-(int3 a, int b)
{
return make_int3(a.x - b, a.y - b, a.z - b);
}
inline __device__ int3 operator+(int a, int3 b)
{
return make_int3(a + b.x, a + b.y, a + b.z);
}
inline __device__ int3 operator-(int a, int3 b)
{
return make_int3(a - b.x, a - b.y, a - b.z);
}
////////////////////////////////////////////////////////////////
inline __device__ int3 clamp(int3 x, int a, int3 b)
{
return make_int3(max(a, min(x.x, b.x)), max(a, min(x.y, b.y)), max(a, min(x.z, b.z)));
}
inline __device__ int3 clamp(int3 x, int3 a, int b)
{
return make_int3(max(a.x, min(x.x, b)), max(a.y, min(x.y, b)), max(a.z, min(x.z, b)));
}
inline __device__ int3 floorf(float3 v)
{
return make_int3(floorf(v.x), floorf(v.y), floorf(v.z));
}
inline __device__ float3 round(float3 v)
{
return make_float3(round(v.x), round(v.y), round(v.z));
}
inline __device__ int dot(int3 a, int3 b)
{
return a.x*b.x + a.y*b.y + a.z*b.z;
}
inline __device__ float dot(float3 a, float3 b)
{
return a.x*b.x + a.y*b.y + a.z*b.z;
}
inline __device__ int mod(int a, int b)
{
int k = a % b;
return (k < 0) ? (k + b) : k;
}
inline __device__ int3 mod(int3 a, int3 b)
{
return make_int3(mod(a.x,b.x), mod(a.y,b.y), mod(a.z,b.z));
}
////////////////////////////////////////////////////////////////
struct BinStep
{
int3 positive, negative;
};
inline __device__ int3 getLocalBinIndex(float3 coordinate, float3 binLength, int3 binDim)
{
return clamp(floorf(coordinate/binLength), 0, binDim - 1);
}
inline __device__ int getBinIndex(int3 localBinIndex, int3 binDim)
{
return dot(localBinIndex, make_int3(1, binDim.x, binDim.x*binDim.y));
}
inline __device__ void stepLimit(int &positive, int &negative, int binDim)
{
if (positive - negative > binDim - 1)
{
if (positive > -negative)
{
positive = negative + binDim - 1;
}
else
{
negative = positive - binDim + 1;
}
}
}
inline __device__ void lennardJones(float3 &ljF, float &ljU, float3 R, float r2, float eps, float sig)
{
float sr = sig*sig/r2;
sr = sr*sr*sr;
ljF += eps/r2*(2.0f*sr*sr - sr)*R;
ljU += eps*(sr*sr - sr);
}
__device__ BinStep getBinStep(float3 coordinate, float3 binLength, int3 binDim, int3 localBinIndex, float cutoff)
{
struct BinStep binStep;
binStep.positive = clamp(floorf((coordinate + cutoff)/binLength) - localBinIndex, 0, binDim - 1);
binStep.negative = clamp(floorf((coordinate - cutoff)/binLength) - localBinIndex, 1 - binDim, 0);
stepLimit(binStep.positive.x, binStep.negative.x, binDim.x);
stepLimit(binStep.positive.y, binStep.negative.y, binDim.y);
stepLimit(binStep.positive.z, binStep.negative.z, binDim.z);
return binStep;
}
////////////////////////////////////////////////////////////////
extern "C"
__global__ void fillBins(float3 *coordinate, int *binIndex, unsigned int *binCount,
float3 binLength, int3 binDim, unsigned int arraySize)
{
unsigned int idg = blockIdx.x*blockDim.x + threadIdx.x;
if (idg < arraySize)
{
int idB = getBinIndex(getLocalBinIndex(coordinate[idg], binLength, binDim), binDim);
binIndex[idg] = idB;
atomicInc(&binCount[idB], arraySize);
}
}
extern "C"
__global__ void countingSort(int *binIndex, unsigned int *prefixSum,
float3 *coordinate, float3 *velocity,
float3 *coordinateSorted, float3 *velocitySorted,
unsigned int arraySize)
{
unsigned int idg = blockIdx.x*blockDim.x + threadIdx.x;
if (idg < arraySize)
{
unsigned int idgSorted = atomicDec(&prefixSum[binIndex[idg]], arraySize) - 1u;
coordinateSorted[idgSorted] = coordinate[idg];
velocitySorted[idgSorted] = velocity[idg];
}
}
extern "C"
__global__ void ljForce(float3 *coordinateSorted, float3 *force,
float *potentialEnergy, unsigned int *binCount, unsigned int *prefixSum,
float3 boxSize, float3 binLength, int3 binDim, float cutoff, float eps, float sig,
unsigned int arraySize)
{
unsigned int idg = blockIdx.x*blockDim.x + threadIdx.x;
if (idg < arraySize)
{
float3 R;
float r2;
int binIndexNeighbour;
unsigned int ionCount, offset;
float3 coordinate = coordinateSorted[idg];
int3 localBinIndex = getLocalBinIndex(coordinate, binLength, binDim);
struct BinStep binStep = getBinStep(coordinate, binLength, binDim, localBinIndex, cutoff);
float3 ljF = make_float3(0.0f,0.0f,0.0f);
float cutoff2 = cutoff*cutoff;
float ljU = 0.0f;
for (int dz = binStep.negative.z; dz <= binStep.positive.z; ++dz)
{
for (int dy = binStep.negative.y; dy <= binStep.positive.y; ++dy)
{
for (int dx = binStep.negative.x; dx <= binStep.positive.x; ++dx)
{
binIndexNeighbour = getBinIndex(mod(localBinIndex + make_int3(dx,dy,dz), binDim), binDim);
ionCount = binCount[binIndexNeighbour];
if (ionCount == 0u)
{
continue;
}
offset = prefixSum[binIndexNeighbour];
for (unsigned int i = offset; i < offset + ionCount; ++i)
{
if (i == idg)
{
continue;
}
R = coordinate - coordinateSorted[i];
r2 = dot(R, R);
if (r2 < cutoff2)
{
lennardJones(ljF, ljU, R, r2, eps, sig);
continue;
}
R -= boxSize*round(R/boxSize);
r2 = dot(R, R);
if (r2 < cutoff2)
{
lennardJones(ljF, ljU, R, r2, eps, sig);
}
}
}
}
}
force[idg] = 24.0f*ljF;
potentialEnergy[idg] = 2.0f*ljU;
}
}
extern "C"
__global__ void verletPre(float3 *coordinate, float3 *velocity,
float3 *coordinateSorted, float3 *velocitySorted,
float3 *force, float3 boxSize, float mass, float dt, unsigned int arraySize)
{
unsigned int idg = blockIdx.x*blockDim.x + threadIdx.x;
if (idg < arraySize)
{
float3 coord, vel;
vel = velocitySorted[idg];
coord = coordinateSorted[idg];
vel += 0.00482426665f*dt/mass*force[idg]; // 0.00964853329 * 0.5
coord += dt*vel;
velocity[idg] = vel;
coordinate[idg] = coord - boxSize*floorf(coord/boxSize);
}
}
extern "C"
__global__ void verletPos(float3 *velocitySorted, float3 *force, float *kineticEnergy,
float mass, float dt, unsigned int arraySize)
{
unsigned int idg = blockIdx.x*blockDim.x + threadIdx.x;
if (idg < arraySize)
{
float3 vel = velocitySorted[idg];
vel += 0.00482426665f*dt/mass*force[idg]; // 0.00964853329 * 0.5
kineticEnergy[idg] = 51.8213479f*mass*dot(vel, vel);
velocitySorted[idg] = vel;
}
}