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Commit 770f7abc authored by Peter Eastman's avatar Peter Eastman
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Correctly record fields from PME

parent bd4fb844
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Showing with 77 additions and 32 deletions
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPME.cu
View file @ 770f7abc
...@@ -729,12 +729,13 @@ void kComputeFixedMultipoleForceAndEnergy_kernel() ...@@ -729,12 +729,13 @@ void kComputeFixedMultipoleForceAndEnergy_kernel()
multipole[7] = cAmoebaSim.pLabFrameQuadrupole[i*9+4]; multipole[7] = cAmoebaSim.pLabFrameQuadrupole[i*9+4];
multipole[8] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+5]; multipole[8] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+5];
multipole[9] = cAmoebaSim.pLabFrameQuadrupole[i*9+8]; multipole[9] = cAmoebaSim.pLabFrameQuadrupole[i*9+8];
float* phi = &cAmoebaSim.pPhi[20*i];
float4 f = make_float4(0.0f, 0.0f, 0.0f, 0.0f); float4 f = make_float4(0.0f, 0.0f, 0.0f, 0.0f);
for (int k = 0; k < 10; k++) { for (int k = 0; k < 10; k++) {
energy += multipole[k]*cAmoebaSim.pPhi[20*i+k]; energy += multipole[k]*phi[k];
f.x += multipole[k]*cAmoebaSim.pPhi[20*i+deriv1[k]]; f.x += multipole[k]*phi[deriv1[k]];
f.y += multipole[k]*cAmoebaSim.pPhi[20*i+deriv2[k]]; f.y += multipole[k]*phi[deriv2[k]];
f.z += multipole[k]*cAmoebaSim.pPhi[20*i+deriv3[k]]; f.z += multipole[k]*phi[deriv3[k]];
} }
f.x *= cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX; f.x *= cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX;
f.y *= cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY; f.y *= cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY;
...@@ -747,18 +748,18 @@ void kComputeFixedMultipoleForceAndEnergy_kernel() ...@@ -747,18 +748,18 @@ void kComputeFixedMultipoleForceAndEnergy_kernel()
// Compute the torque. // Compute the torque.
cAmoebaSim.pTorque[3*i] = multipole[3]*cAmoebaSim.pPhi[2] - multipole[2]*cAmoebaSim.pPhi[3] cAmoebaSim.pTorque[3*i] = multipole[3]*phi[2] - multipole[2]*phi[3]
+ 2.0f*(multipole[6]-multipole[5])*cAmoebaSim.pPhi[9] + 2.0f*(multipole[6]-multipole[5])*phi[9]
+ multipole[8]*cAmoebaSim.pPhi[7] + multipole[9]*cAmoebaSim.pPhi[5] + multipole[8]*phi[7] + multipole[9]*phi[5]
- multipole[7]*cAmoebaSim.pPhi[8] - multipole[9]*cAmoebaSim.pPhi[6]; - multipole[7]*phi[8] - multipole[9]*phi[6];
cAmoebaSim.pTorque[3*i+1] = multipole[1]*cAmoebaSim.pPhi[3] - multipole[3]*cAmoebaSim.pPhi[1] cAmoebaSim.pTorque[3*i+1] = multipole[1]*phi[3] - multipole[3]*phi[1]
+ 2.0f*(multipole[4]-multipole[6])*cAmoebaSim.pPhi[9] + 2.0f*(multipole[4]-multipole[6])*phi[9]
+ multipole[7]*cAmoebaSim.pPhi[9] + multipole[8]*cAmoebaSim.pPhi[6] + multipole[7]*phi[9] + multipole[8]*phi[6]
- multipole[8]*cAmoebaSim.pPhi[4] - multipole[9]*cAmoebaSim.pPhi[7]; - multipole[8]*phi[4] - multipole[9]*phi[7];
cAmoebaSim.pTorque[3*i+2] = multipole[2]*cAmoebaSim.pPhi[1] - multipole[1]*cAmoebaSim.pPhi[2] cAmoebaSim.pTorque[3*i+2] = multipole[2]*phi[1] - multipole[1]*phi[2]
+ 2.0f*(multipole[5]-multipole[4])*cAmoebaSim.pPhi[7] + 2.0f*(multipole[5]-multipole[4])*phi[7]
+ multipole[7]*cAmoebaSim.pPhi[4] + multipole[9]*cAmoebaSim.pPhi[8] + multipole[7]*phi[4] + multipole[9]*phi[8]
- multipole[7]*cAmoebaSim.pPhi[5] - multipole[8]*cAmoebaSim.pPhi[9]; - multipole[7]*phi[5] - multipole[8]*phi[9];
} }
cSim.pEnergy[blockIdx.x*blockDim.x+threadIdx.x] += 0.5f*energy; cSim.pEnergy[blockIdx.x*blockDim.x+threadIdx.x] += 0.5f*energy;
} }
...@@ -799,15 +800,18 @@ void kComputeInducedDipoleForceAndEnergy_kernel() ...@@ -799,15 +800,18 @@ void kComputeInducedDipoleForceAndEnergy_kernel()
inducedDipolePolar[0] = cAmoebaSim.pInducedDipolePolar[i*3]; inducedDipolePolar[0] = cAmoebaSim.pInducedDipolePolar[i*3];
inducedDipolePolar[1] = cAmoebaSim.pInducedDipolePolar[i*3+1]; inducedDipolePolar[1] = cAmoebaSim.pInducedDipolePolar[i*3+1];
inducedDipolePolar[2] = cAmoebaSim.pInducedDipolePolar[i*3+2]; inducedDipolePolar[2] = cAmoebaSim.pInducedDipolePolar[i*3+2];
float* phi = &cAmoebaSim.pPhi[20*i];
float* phip = &cAmoebaSim.pPhip[20*i];
float* phid = &cAmoebaSim.pPhid[20*i];
float4 f = make_float4(0.0f, 0.0f, 0.0f, 0.0f); float4 f = make_float4(0.0f, 0.0f, 0.0f, 0.0f);
for (int k = 0; k < 3; k++) { for (int k = 0; k < 3; k++) {
int j1 = deriv1[k+1]; int j1 = deriv1[k+1];
int j2 = deriv1[k+2]; int j2 = deriv1[k+2];
int j3 = deriv1[k+3]; int j3 = deriv1[k+3];
energy += inducedDipole[k]*cAmoebaSim.pPhi[20*i+k+1]; energy += inducedDipole[k]*phi[k+1];
f.x += (inducedDipole[k]+inducedDipolePolar[k])*cAmoebaSim.pPhi[20*i+j1] + inducedDipole[k]*cAmoebaSim.pPhip[20*i+j1] + inducedDipolePolar[k]*cAmoebaSim.pPhid[20*i+j1]; f.x += (inducedDipole[k]+inducedDipolePolar[k])*phi[j1] + inducedDipole[k]*phip[j1] + inducedDipolePolar[k]*phid[j1];
f.y += (inducedDipole[k]+inducedDipolePolar[k])*cAmoebaSim.pPhi[20*i+j2] + inducedDipole[k]*cAmoebaSim.pPhip[20*i+j2] + inducedDipolePolar[k]*cAmoebaSim.pPhid[20*i+j2]; f.y += (inducedDipole[k]+inducedDipolePolar[k])*phi[j2] + inducedDipole[k]*phip[j2] + inducedDipolePolar[k]*phid[j2];
f.z += (inducedDipole[k]+inducedDipolePolar[k])*cAmoebaSim.pPhi[20*i+j3] + inducedDipole[k]*cAmoebaSim.pPhip[20*i+j3] + inducedDipolePolar[k]*cAmoebaSim.pPhid[20*i+j3]; f.z += (inducedDipole[k]+inducedDipolePolar[k])*phi[j3] + inducedDipole[k]*phip[j3] + inducedDipolePolar[k]*phid[j3];
} }
for (int k = 0; k < 10; k++) { for (int k = 0; k < 10; k++) {
f.x += multipole[k]*cAmoebaSim.pPhidp[20*i+deriv1[k]]; f.x += multipole[k]*cAmoebaSim.pPhidp[20*i+deriv1[k]];
...@@ -825,22 +829,59 @@ void kComputeInducedDipoleForceAndEnergy_kernel() ...@@ -825,22 +829,59 @@ void kComputeInducedDipoleForceAndEnergy_kernel()
// Compute the torque. // Compute the torque.
cAmoebaSim.pTorque[3*i] = multipole[3]*cAmoebaSim.pPhi[2] - multipole[2]*cAmoebaSim.pPhi[3] cAmoebaSim.pTorque[3*i] = multipole[3]*phi[2] - multipole[2]*phi[3]
+ 2.0f*(multipole[6]-multipole[5])*cAmoebaSim.pPhi[9] + 2.0f*(multipole[6]-multipole[5])*phi[9]
+ multipole[8]*cAmoebaSim.pPhi[7] + multipole[9]*cAmoebaSim.pPhi[5] + multipole[8]*phi[7] + multipole[9]*phi[5]
- multipole[7]*cAmoebaSim.pPhi[8] - multipole[9]*cAmoebaSim.pPhi[6]; - multipole[7]*phi[8] - multipole[9]*phi[6];
cAmoebaSim.pTorque[3*i+1] = multipole[1]*cAmoebaSim.pPhi[3] - multipole[3]*cAmoebaSim.pPhi[1] cAmoebaSim.pTorque[3*i+1] = multipole[1]*phi[3] - multipole[3]*phi[1]
+ 2.0f*(multipole[4]-multipole[6])*cAmoebaSim.pPhi[9] + 2.0f*(multipole[4]-multipole[6])*phi[9]
+ multipole[7]*cAmoebaSim.pPhi[9] + multipole[8]*cAmoebaSim.pPhi[6] + multipole[7]*phi[9] + multipole[8]*phi[6]
- multipole[8]*cAmoebaSim.pPhi[4] - multipole[9]*cAmoebaSim.pPhi[7]; - multipole[8]*phi[4] - multipole[9]*phi[7];
cAmoebaSim.pTorque[3*i+2] = multipole[2]*cAmoebaSim.pPhi[1] - multipole[1]*cAmoebaSim.pPhi[2] cAmoebaSim.pTorque[3*i+2] = multipole[2]*phi[1] - multipole[1]*phi[2]
+ 2.0f*(multipole[5]-multipole[4])*cAmoebaSim.pPhi[7] + 2.0f*(multipole[5]-multipole[4])*phi[7]
+ multipole[7]*cAmoebaSim.pPhi[4] + multipole[9]*cAmoebaSim.pPhi[8] + multipole[7]*phi[4] + multipole[9]*phi[8]
- multipole[7]*cAmoebaSim.pPhi[5] - multipole[8]*cAmoebaSim.pPhi[9]; - multipole[7]*phi[5] - multipole[8]*phi[9];
} }
cSim.pEnergy[blockIdx.x*blockDim.x+threadIdx.x] += 0.5f*energy; cSim.pEnergy[blockIdx.x*blockDim.x+threadIdx.x] += 0.5f*energy;
} }
__global__
#if (__CUDA_ARCH__ >= 200)
__launch_bounds__(768, 1)
#elif (__CUDA_ARCH__ >= 120)
__launch_bounds__(384, 1)
#else
__launch_bounds__(192, 1)
#endif
void kRecordFixedMultipoleField_kernel(float* output)
{
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < cSim.atoms; i += blockDim.x*gridDim.x) {
output[3*i] -= cAmoebaSim.pPhi[20*i];
output[3*i+1] -= cAmoebaSim.pPhi[20*i+1];
output[3*i+2] -= cAmoebaSim.pPhi[20*i+2];
}
}
__global__
#if (__CUDA_ARCH__ >= 200)
__launch_bounds__(768, 1)
#elif (__CUDA_ARCH__ >= 120)
__launch_bounds__(384, 1)
#else
__launch_bounds__(192, 1)
#endif
void kRecordInducedDipoleField_kernel(float* output, float* outputPolar)
{
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < cSim.atoms; i += blockDim.x*gridDim.x) {
output[3*i] -= cAmoebaSim.pPhid[20*i];
output[3*i+1] -= cAmoebaSim.pPhid[20*i+1];
output[3*i+2] -= cAmoebaSim.pPhid[20*i+2];
outputPolar[3*i] -= cAmoebaSim.pPhip[20*i];
outputPolar[3*i+1] -= cAmoebaSim.pPhip[20*i+1];
outputPolar[3*i+2] -= cAmoebaSim.pPhip[20*i+2];
}
}
extern void cudaComputeAmoebaMapTorquesAndAddTotalForce2(amoebaGpuContext gpu, CUDAStream<float>* psTorque, CUDAStream<float4>* psOutputForce); extern void cudaComputeAmoebaMapTorquesAndAddTotalForce2(amoebaGpuContext gpu, CUDAStream<float>* psTorque, CUDAStream<float4>* psOutputForce);
__global__ void kFindAtomRangeForGrid_kernel(); __global__ void kFindAtomRangeForGrid_kernel();
...@@ -875,6 +916,8 @@ void kCalculateAmoebaPMEFixedMultipoleField(amoebaGpuContext amoebaGpu) ...@@ -875,6 +916,8 @@ void kCalculateAmoebaPMEFixedMultipoleField(amoebaGpuContext amoebaGpu)
cufftExecC2C(gpu->fftplan, gpu->psPmeGrid->_pDevData, gpu->psPmeGrid->_pDevData, CUFFT_INVERSE); cufftExecC2C(gpu->fftplan, gpu->psPmeGrid->_pDevData, gpu->psPmeGrid->_pDevData, CUFFT_INVERSE);
kComputeFixedPotentialFromGrid_kernel<<<gpu->sim.blocks, gpu->sim.update_threads_per_block>>>(); kComputeFixedPotentialFromGrid_kernel<<<gpu->sim.blocks, gpu->sim.update_threads_per_block>>>();
LAUNCHERROR("kComputeFixedPotentialFromGrid"); LAUNCHERROR("kComputeFixedPotentialFromGrid");
kRecordFixedMultipoleField_kernel<<<gpu->sim.blocks, gpu->sim.update_threads_per_block>>>(amoebaGpu->psE_Field->_pDevData);
LAUNCHERROR("kRecordFixedMultipoleField");
} }
/** /**
...@@ -893,6 +936,8 @@ void kCalculateAmoebaPMEInducedDipoleField(amoebaGpuContext amoebaGpu) ...@@ -893,6 +936,8 @@ void kCalculateAmoebaPMEInducedDipoleField(amoebaGpuContext amoebaGpu)
cufftExecC2C(gpu->fftplan, gpu->psPmeGrid->_pDevData, gpu->psPmeGrid->_pDevData, CUFFT_INVERSE); cufftExecC2C(gpu->fftplan, gpu->psPmeGrid->_pDevData, gpu->psPmeGrid->_pDevData, CUFFT_INVERSE);
kComputeInducedPotentialFromGrid_kernel<<<gpu->sim.blocks, gpu->sim.update_threads_per_block>>>(); kComputeInducedPotentialFromGrid_kernel<<<gpu->sim.blocks, gpu->sim.update_threads_per_block>>>();
LAUNCHERROR("kComputeInducedPotentialFromGrid"); LAUNCHERROR("kComputeInducedPotentialFromGrid");
kRecordInducedDipoleField_kernel<<<gpu->sim.blocks, gpu->sim.update_threads_per_block>>>(amoebaGpu->psE_Field->_pDevData, amoebaGpu->psE_FieldPolar->_pDevData);
LAUNCHERROR("kRecordInducedDipoleField");
} }
/** /**
......
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