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Commit 49173b75 authored by Peter Eastman's avatar Peter Eastman
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Continuing implementation of PME reciprocal space calculation

parent fb62fecb
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Showing with 351 additions and 4 deletions
plugins/amoeba/platforms/cuda/src/kernels/AmoebaGpu.cpp
View file @ 49173b75
......@@ -80,6 +80,10 @@ amoebaGpuContext amoebaGpuInit( _gpuContext* gpu )
amoebaGpu->psThetai3 = NULL;
amoebaGpu->psQfac = NULL;
amoebaGpu->psIgrid = NULL;
amoebaGpu->psPhi = NULL;
amoebaGpu->psPhid = NULL;
amoebaGpu->psPhip = NULL;
amoebaGpu->psPhidp = NULL;
return amoebaGpu;
}
......@@ -2219,6 +2223,14 @@ void gpuSetAmoebaPMEParameters(amoebaGpuContext amoebaGpu, float alpha, int grid
amoebaGpu->amoebaSim.pThetai3 = amoebaGpu->psThetai3->_pDevData;
amoebaGpu->psIgrid = new CUDAStream<int4>(gpu->natoms, 1, "igrid");
amoebaGpu->amoebaSim.pIgrid = amoebaGpu->psIgrid->_pDevData;
amoebaGpu->psPhi = new CUDAStream<float>(20*gpu->natoms, 1, "phi");
amoebaGpu->amoebaSim.pPhi = amoebaGpu->psPhi->_pDevData;
amoebaGpu->psPhid = new CUDAStream<float>(10*gpu->natoms, 1, "phid");
amoebaGpu->amoebaSim.pPhid = amoebaGpu->psPhid->_pDevData;
amoebaGpu->psPhip = new CUDAStream<float>(10*gpu->natoms, 1, "phip");
amoebaGpu->amoebaSim.pPhip = amoebaGpu->psPhip->_pDevData;
amoebaGpu->psPhidp = new CUDAStream<float>(20*gpu->natoms, 1, "phidp");
amoebaGpu->amoebaSim.pPhidp = amoebaGpu->psPhidp->_pDevData;
gpu->psPmeAtomGridIndex = new CUDAStream<int2>(gpu->natoms, 1, "PmeAtomGridIndex");
gpu->sim.pPmeAtomGridIndex = gpu->psPmeAtomGridIndex->_pDevData;
gpu->psPmeBsplineTheta = new CUDAStream<float4>(1, 1, "PmeBsplineTheta"); // Not actually uesd
......@@ -2704,6 +2716,10 @@ void amoebaGpuShutDown(amoebaGpuContext gpu)
delete gpu->psThetai3;
delete gpu->psQfac;
delete gpu->psIgrid;
delete gpu->psPhi;
delete gpu->psPhid;
delete gpu->psPhip;
delete gpu->psPhidp;
}
if( gpu->pMapArray ){
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaTypes.h
View file @ 49173b75
......@@ -186,6 +186,10 @@ struct cudaAmoebaGmxSimulation {
float4* pThetai2;
float4* pThetai3;
int4* pIgrid;
float* pPhi;
float* pPhid;
float* pPhip;
float* pPhidp;
};
#endif
plugins/amoeba/platforms/cuda/src/kernels/amoebaGpuTypes.h
View file @ 49173b75
......@@ -227,6 +227,10 @@ struct _amoebaGpuContext {
CUDAStream<float4>* psThetai2;
CUDAStream<float4>* psThetai3;
CUDAStream<int4>* psIgrid;
CUDAStream<float>* psPhi;
CUDAStream<float>* psPhid;
CUDAStream<float>* psPhip;
CUDAStream<float>* psPhidp;
};
typedef struct _amoebaGpuContext *amoebaGpuContext;
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPME.cu
View file @ 49173b75
......@@ -106,7 +106,7 @@ __launch_bounds__(256, 1)
#else
__launch_bounds__(128, 1)
#endif
void computeBsplines_kernel()
void kComputeBsplines_kernel()
{
extern __shared__ float bsplines_cache[]; // size = block_size*pme_order*pme_order
float* array = &bsplines_cache[threadIdx.x*AMOEBA_PME_ORDER*AMOEBA_PME_ORDER];
......@@ -149,16 +149,17 @@ void computeBsplines_kernel()
int igrid3 = ifr - AMOEBA_PME_ORDER;
computeBSplinePoint(&cAmoebaSim.pThetai3[i*AMOEBA_PME_ORDER], w, array);
// Record the grid point.
cAmoebaSim.pIgrid[i] = make_int4(igrid1, igrid2, igrid3, 0);
cSim.pPmeAtomGridIndex[i] = make_int2(i, igrid1*cSim.pmeGridSize.y*cSim.pmeGridSize.z+igrid2*cSim.pmeGridSize.z+igrid3);
}
}
__global__
#if (__CUDA_ARCH__ >= 200)
__launch_bounds__(1024, 1)
#elif (__CUDA_ARCH__ >= 130)
#elif (__CUDA_ARCH__ >= 120)
__launch_bounds__(512, 1)
#else
__launch_bounds__(256, 1)
......@@ -245,6 +246,328 @@ void kGridSpreadMultipoles_kernel()
}
}
}
cSim.pPmeGrid[gridIndex] = make_cuComplex(result*sqrt(cSim.epsfac), 0.0f);
cSim.pPmeGrid[gridIndex] = make_cuComplex(result, 0.0f);
}
}
__global__
#if (__CUDA_ARCH__ >= 200)
__launch_bounds__(1024, 1)
#elif (__CUDA_ARCH__ >= 120)
__launch_bounds__(512, 1)
#else
__launch_bounds__(256, 1)
#endif
void kComputeFixedPotentialFromGrid_kernel()
{
// extract the permanent multipole field at each site
for (int m = blockIdx.x*blockDim.x+threadIdx.x; m < cSim.atoms; m += blockDim.x*gridDim.x) {
int4 grid = cAmoebaSim.pIgrid[m];
float tuv000 = 0.0f;
float tuv001 = 0.0f;
float tuv010 = 0.0f;
float tuv100 = 0.0f;
float tuv200 = 0.0f;
float tuv020 = 0.0f;
float tuv002 = 0.0f;
float tuv110 = 0.0f;
float tuv101 = 0.0f;
float tuv011 = 0.0f;
float tuv300 = 0.0f;
float tuv030 = 0.0f;
float tuv003 = 0.0f;
float tuv210 = 0.0f;
float tuv201 = 0.0f;
float tuv120 = 0.0f;
float tuv021 = 0.0f;
float tuv102 = 0.0f;
float tuv012 = 0.0f;
float tuv111 = 0.0f;
for (int it3 = 0; it3 < AMOEBA_PME_ORDER; it3++) {
int k = grid.z+it3-(grid.z+it3 >= cSim.pmeGridSize.z ? cSim.pmeGridSize.z : 0);
float4 v = cAmoebaSim.pThetai3[m*AMOEBA_PME_ORDER+it3];
float tu00 = 0.0f;
float tu10 = 0.0f;
float tu01 = 0.0f;
float tu20 = 0.0f;
float tu11 = 0.0f;
float tu02 = 0.0f;
float tu30 = 0.0f;
float tu21 = 0.0f;
float tu12 = 0.0f;
float tu03 = 0.0f;
for (int it2 = 0; it2 < AMOEBA_PME_ORDER; it2++) {
int j = grid.y+it2-(grid.y+it2 >= cSim.pmeGridSize.y ? cSim.pmeGridSize.y : 0);
float4 u = cAmoebaSim.pThetai2[m*AMOEBA_PME_ORDER+it2];
float4 t = make_float4(0.0f, 0.0f, 0.0f, 0.0f);
for (int it1 = 0; it1 < AMOEBA_PME_ORDER; it1++) {
int i = grid.x+it1-(grid.x+it1 >= cSim.pmeGridSize.x ? cSim.pmeGridSize.x : 0);
int gridIndex = i*cSim.pmeGridSize.y*cSim.pmeGridSize.z + j*cSim.pmeGridSize.z + k;
float tq = cSim.pPmeGrid[gridIndex].x;
float4 tadd = cAmoebaSim.pThetai1[m*AMOEBA_PME_ORDER+it1];
t.x += tq*tadd.x;
t.y += tq*tadd.y;
t.z += tq*tadd.z;
t.w += tq*tadd.w;
}
tu00 += t.x*u.x;
tu10 += t.y*u.x;
tu01 += t.x*u.y;
tu20 += t.z*u.x;
tu11 += t.y*u.y;
tu02 += t.x*u.z;
tu30 += t.w*u.x;
tu21 += t.z*u.y;
tu12 += t.y*u.z;
tu03 += t.x*u.w;
}
tuv000 += tu00*v.x;
tuv100 += tu10*v.x;
tuv010 += tu01*v.x;
tuv001 += tu00*v.y;
tuv200 += tu20*v.x;
tuv020 += tu02*v.x;
tuv002 += tu00*v.z;
tuv110 += tu11*v.x;
tuv101 += tu10*v.y;
tuv011 += tu01*v.y;
tuv300 += tu30*v.x;
tuv030 += tu03*v.x;
tuv003 += tu00*v.w;
tuv210 += tu21*v.x;
tuv201 += tu20*v.y;
tuv120 += tu12*v.x;
tuv021 += tu02*v.y;
tuv102 += tu10*v.z;
tuv012 += tu01*v.z;
tuv111 += tu11*v.y;
}
cAmoebaSim.pPhi[20*m] = tuv000;
cAmoebaSim.pPhi[20*m+1] = tuv100;
cAmoebaSim.pPhi[20*m+2] = tuv010;
cAmoebaSim.pPhi[20*m+3] = tuv001;
cAmoebaSim.pPhi[20*m+4] = tuv200;
cAmoebaSim.pPhi[20*m+5] = tuv020;
cAmoebaSim.pPhi[20*m+6] = tuv002;
cAmoebaSim.pPhi[20*m+7] = tuv110;
cAmoebaSim.pPhi[20*m+8] = tuv101;
cAmoebaSim.pPhi[20*m+9] = tuv011;
cAmoebaSim.pPhi[20*m+10] = tuv300;
cAmoebaSim.pPhi[20*m+11] = tuv030;
cAmoebaSim.pPhi[20*m+12] = tuv003;
cAmoebaSim.pPhi[20*m+13] = tuv210;
cAmoebaSim.pPhi[20*m+14] = tuv201;
cAmoebaSim.pPhi[20*m+15] = tuv120;
cAmoebaSim.pPhi[20*m+16] = tuv021;
cAmoebaSim.pPhi[20*m+17] = tuv102;
cAmoebaSim.pPhi[20*m+18] = tuv012;
cAmoebaSim.pPhi[20*m+19] = tuv111;
}
}
__global__
#if (__CUDA_ARCH__ >= 200)
__launch_bounds__(1024, 1)
#elif (__CUDA_ARCH__ >= 120)
__launch_bounds__(512, 1)
#else
__launch_bounds__(256, 1)
#endif
void kComputeInducedPotentialFromGrid_kernel()
{
// extract the induced dipole field at each site
for (int m = blockIdx.x*blockDim.x+threadIdx.x; m < cSim.atoms; m += blockDim.x*gridDim.x) {
int4 grid = cAmoebaSim.pIgrid[m];
float tuv100_1 = 0.0f;
float tuv010_1 = 0.0f;
float tuv001_1 = 0.0f;
float tuv200_1 = 0.0f;
float tuv020_1 = 0.0f;
float tuv002_1 = 0.0f;
float tuv110_1 = 0.0f;
float tuv101_1 = 0.0f;
float tuv011_1 = 0.0f;
float tuv100_2 = 0.0f;
float tuv010_2 = 0.0f;
float tuv001_2 = 0.0f;
float tuv200_2 = 0.0f;
float tuv020_2 = 0.0f;
float tuv002_2 = 0.0f;
float tuv110_2 = 0.0f;
float tuv101_2 = 0.0f;
float tuv011_2 = 0.0f;
float tuv000 = 0.0f;
float tuv001 = 0.0f;
float tuv010 = 0.0f;
float tuv100 = 0.0f;
float tuv200 = 0.0f;
float tuv020 = 0.0f;
float tuv002 = 0.0f;
float tuv110 = 0.0f;
float tuv101 = 0.0f;
float tuv011 = 0.0f;
float tuv300 = 0.0f;
float tuv030 = 0.0f;
float tuv003 = 0.0f;
float tuv210 = 0.0f;
float tuv201 = 0.0f;
float tuv120 = 0.0f;
float tuv021 = 0.0f;
float tuv102 = 0.0f;
float tuv012 = 0.0f;
float tuv111 = 0.0f;
for (int it3 = 0; it3 < AMOEBA_PME_ORDER; it3++) {
int k = grid.z+it3-(grid.z+it3 >= cSim.pmeGridSize.z ? cSim.pmeGridSize.z : 0);
float4 v = cAmoebaSim.pThetai3[m*AMOEBA_PME_ORDER+it3];
float tu00_1 = 0.0f;
float tu01_1 = 0.0f;
float tu10_1 = 0.0f;
float tu20_1 = 0.0f;
float tu11_1 = 0.0f;
float tu02_1 = 0.0f;
float tu00_2 = 0.0f;
float tu01_2 = 0.0f;
float tu10_2 = 0.0f;
float tu20_2 = 0.0f;
float tu11_2 = 0.0f;
float tu02_2 = 0.0f;
float tu00 = 0.0f;
float tu10 = 0.0f;
float tu01 = 0.0f;
float tu20 = 0.0f;
float tu11 = 0.0f;
float tu02 = 0.0f;
float tu30 = 0.0f;
float tu21 = 0.0f;
float tu12 = 0.0f;
float tu03 = 0.0f;
for (int it2 = 0; it2 < AMOEBA_PME_ORDER; it2++) {
int j = grid.y+it2-(grid.y+it2 >= cSim.pmeGridSize.y ? cSim.pmeGridSize.y : 0);
float4 u = cAmoebaSim.pThetai2[m*AMOEBA_PME_ORDER+it2];
float t0_1 = 0.0f;
float t1_1 = 0.0f;
float t2_1 = 0.0f;
float t0_2 = 0.0f;
float t1_2 = 0.0f;
float t2_2 = 0.0f;
float t3 = 0.0f;
for (int it1 = 0; it1 < AMOEBA_PME_ORDER; it1++) {
int i = grid.x+it1-(grid.x+it1 >= cSim.pmeGridSize.x ? cSim.pmeGridSize.x : 0);
int gridIndex = i*cSim.pmeGridSize.y*cSim.pmeGridSize.z + j*cSim.pmeGridSize.z + k;
cufftComplex tq = cSim.pPmeGrid[gridIndex];
float4 tadd = cAmoebaSim.pThetai1[m*AMOEBA_PME_ORDER+it1];
t0_1 += tq.x*tadd.x;
t1_1 += tq.x*tadd.y;
t2_1 += tq.x*tadd.z;
t0_2 += tq.y*tadd.x;
t1_2 += tq.y*tadd.y;
t2_2 += tq.y*tadd.z;
t3 += (tq.x+tq.x)*tadd.w;
}
tu00_1 += t0_1*u.x;
tu10_1 += t1_1*u.x;
tu01_1 += t0_1*u.y;
tu20_1 += t2_1*u.x;
tu11_1 += t1_1*u.y;
tu02_1 += t0_1*u.z;
tu00_2 += t0_2*u.x;
tu10_2 += t1_2*u.x;
tu01_2 += t0_2*u.y;
tu20_2 += t2_2*u.x;
tu11_2 += t1_2*u.y;
tu02_2 += t0_2*u.z;
float t0 = t0_1 + t0_2;
float t1 = t1_1 + t1_2;
float t2 = t2_1 + t2_2;
tu00 += t0*u.x;
tu10 += t1*u.x;
tu01 += t0*u.y;
tu20 += t2*u.x;
tu11 += t1*u.y;
tu02 += t0*u.z;
tu30 += t3*u.x;
tu21 += t2*u.y;
tu12 += t1*u.z;
tu03 += t0*u.w;
}
tuv100_1 += tu10_1*v.x;
tuv010_1 += tu01_1*v.x;
tuv001_1 += tu00_1*v.y;
tuv200_1 += tu20_1*v.x;
tuv020_1 += tu02_1*v.x;
tuv002_1 += tu00_1*v.z;
tuv110_1 += tu11_1*v.x;
tuv101_1 += tu10_1*v.y;
tuv011_1 += tu01_1*v.y;
tuv100_2 += tu10_2*v.x;
tuv010_2 += tu01_2*v.x;
tuv001_2 += tu00_2*v.y;
tuv200_2 += tu20_2*v.x;
tuv020_2 += tu02_2*v.x;
tuv002_2 += tu00_2*v.z;
tuv110_2 += tu11_2*v.x;
tuv101_2 += tu10_2*v.y;
tuv011_2 += tu01_2*v.y;
tuv000 += tu00*v.x;
tuv100 += tu10*v.x;
tuv010 += tu01*v.x;
tuv001 += tu00*v.y;
tuv200 += tu20*v.x;
tuv020 += tu02*v.x;
tuv002 += tu00*v.z;
tuv110 += tu11*v.x;
tuv101 += tu10*v.y;
tuv011 += tu01*v.y;
tuv300 += tu30*v.x;
tuv030 += tu03*v.x;
tuv003 += tu00*v.w;
tuv210 += tu21*v.x;
tuv201 += tu20*v.y;
tuv120 += tu12*v.x;
tuv021 += tu02*v.y;
tuv102 += tu10*v.z;
tuv012 += tu01*v.z;
tuv111 += tu11*v.y;
}
cAmoebaSim.pPhid[20*m+1] = tuv100_1;
cAmoebaSim.pPhid[20*m+2] = tuv010_1;
cAmoebaSim.pPhid[20*m+3] = tuv001_1;
cAmoebaSim.pPhid[20*m+4] = tuv200_1;
cAmoebaSim.pPhid[20*m+5] = tuv020_1;
cAmoebaSim.pPhid[20*m+6] = tuv002_1;
cAmoebaSim.pPhid[20*m+7] = tuv110_1;
cAmoebaSim.pPhid[20*m+8] = tuv101_1;
cAmoebaSim.pPhid[20*m+9] = tuv011_1;
cAmoebaSim.pPhip[20*m+1] = tuv100_2;
cAmoebaSim.pPhip[20*m+2] = tuv010_2;
cAmoebaSim.pPhip[20*m+3] = tuv001_2;
cAmoebaSim.pPhip[20*m+4] = tuv200_2;
cAmoebaSim.pPhip[20*m+5] = tuv020_2;
cAmoebaSim.pPhip[20*m+6] = tuv002_2;
cAmoebaSim.pPhip[20*m+7] = tuv110_2;
cAmoebaSim.pPhip[20*m+8] = tuv101_2;
cAmoebaSim.pPhip[20*m+9] = tuv011_2;
cAmoebaSim.pPhidp[20*m] = tuv000;
cAmoebaSim.pPhidp[20*m+1] = tuv100;
cAmoebaSim.pPhidp[20*m+2] = tuv010;
cAmoebaSim.pPhidp[20*m+3] = tuv001;
cAmoebaSim.pPhidp[20*m+4] = tuv200;
cAmoebaSim.pPhidp[20*m+5] = tuv020;
cAmoebaSim.pPhidp[20*m+6] = tuv002;
cAmoebaSim.pPhidp[20*m+7] = tuv110;
cAmoebaSim.pPhidp[20*m+8] = tuv101;
cAmoebaSim.pPhidp[20*m+9] = tuv011;
cAmoebaSim.pPhidp[20*m+10] = tuv300;
cAmoebaSim.pPhidp[20*m+11] = tuv030;
cAmoebaSim.pPhidp[20*m+12] = tuv003;
cAmoebaSim.pPhidp[20*m+13] = tuv210;
cAmoebaSim.pPhidp[20*m+14] = tuv201;
cAmoebaSim.pPhidp[20*m+15] = tuv120;
cAmoebaSim.pPhidp[20*m+16] = tuv021;
cAmoebaSim.pPhidp[20*m+17] = tuv102;
cAmoebaSim.pPhidp[20*m+18] = tuv012;
cAmoebaSim.pPhidp[20*m+19] = tuv111;
}
}
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