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Commit 5698a1fc authored by Peter Eastman's avatar Peter Eastman
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Fixing bugs in AMOEBA PME reciprocal space calculation

parent ad1b1ad1
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Showing with 101 additions and 75 deletions
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPME.cu
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......@@ -247,16 +247,16 @@ void kGridSpreadFixedMultipoles_kernel()
int atomIndex = atomData.x;
int z = atomData.y;
int iz = gridPoint.z-z+(gridPoint.z >= z ? 0 : cSim.pmeGridSize.z);
float atomCharge = 10*cSim.pPosq[atomIndex].w;
float atomDipoleX = 10*xscale*cAmoebaSim.pLabFrameDipole[atomIndex*3];
float atomDipoleY = 10*yscale*cAmoebaSim.pLabFrameDipole[atomIndex*3+1];
float atomDipoleZ = 10*zscale*cAmoebaSim.pLabFrameDipole[atomIndex*3+2];
float atomQuadrupoleXX = 10*xscale*xscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9];
float atomQuadrupoleXY = 20*xscale*yscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+1];
float atomQuadrupoleXZ = 20*xscale*zscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+2];
float atomQuadrupoleYY = 10*yscale*yscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+4];
float atomQuadrupoleYZ = 20*yscale*zscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+5];
float atomQuadrupoleZZ = 10*zscale*zscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+8];
float atomCharge = cSim.pPosq[atomIndex].w;
float atomDipoleX = xscale*cAmoebaSim.pLabFrameDipole[atomIndex*3];
float atomDipoleY = yscale*cAmoebaSim.pLabFrameDipole[atomIndex*3+1];
float atomDipoleZ = zscale*cAmoebaSim.pLabFrameDipole[atomIndex*3+2];
float atomQuadrupoleXX = xscale*xscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9];
float atomQuadrupoleXY = 2*xscale*yscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+1];
float atomQuadrupoleXZ = 2*xscale*zscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+2];
float atomQuadrupoleYY = yscale*yscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+4];
float atomQuadrupoleYZ = 2*yscale*zscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+5];
float atomQuadrupoleZZ = zscale*zscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+8];
float4 t = cAmoebaSim.pThetai1[atomIndex*AMOEBA_PME_ORDER+ix];
float4 u = cAmoebaSim.pThetai2[atomIndex*AMOEBA_PME_ORDER+iy];
float4 v = cAmoebaSim.pThetai3[atomIndex*AMOEBA_PME_ORDER+iz];
......@@ -277,16 +277,16 @@ void kGridSpreadFixedMultipoles_kernel()
int atomIndex = atomData.x;
int z = atomData.y;
int iz = gridPoint.z-z+(gridPoint.z >= z ? 0 : cSim.pmeGridSize.z);
float atomCharge = 10*cSim.pPosq[atomIndex].w;
float atomDipoleX = 10*xscale*cAmoebaSim.pLabFrameDipole[atomIndex*3];
float atomDipoleY = 10*yscale*cAmoebaSim.pLabFrameDipole[atomIndex*3+1];
float atomDipoleZ = 10*zscale*cAmoebaSim.pLabFrameDipole[atomIndex*3+2];
float atomQuadrupoleXX = 10*xscale*xscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9];
float atomQuadrupoleXY = 20*xscale*yscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+1];
float atomQuadrupoleXZ = 20*xscale*zscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+2];
float atomQuadrupoleYY = 10*yscale*yscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+4];
float atomQuadrupoleYZ = 20*yscale*zscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+5];
float atomQuadrupoleZZ = 10*zscale*zscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+8];
float atomCharge = cSim.pPosq[atomIndex].w;
float atomDipoleX = xscale*cAmoebaSim.pLabFrameDipole[atomIndex*3];
float atomDipoleY = yscale*cAmoebaSim.pLabFrameDipole[atomIndex*3+1];
float atomDipoleZ = zscale*cAmoebaSim.pLabFrameDipole[atomIndex*3+2];
float atomQuadrupoleXX = xscale*xscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9];
float atomQuadrupoleXY = 2*xscale*yscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+1];
float atomQuadrupoleXZ = 2*xscale*zscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+2];
float atomQuadrupoleYY = yscale*yscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+4];
float atomQuadrupoleYZ = 2*yscale*zscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+5];
float atomQuadrupoleZZ = zscale*zscale*cAmoebaSim.pLabFrameQuadrupole[atomIndex*9+8];
float4 t = cAmoebaSim.pThetai1[atomIndex*AMOEBA_PME_ORDER+ix];
float4 u = cAmoebaSim.pThetai2[atomIndex*AMOEBA_PME_ORDER+iy];
float4 v = cAmoebaSim.pThetai3[atomIndex*AMOEBA_PME_ORDER+iz];
......@@ -769,21 +769,48 @@ void kComputeFixedMultipoleForceAndEnergy_kernel()
const int deriv1[] = {1, 4, 7, 8, 10, 15, 17, 13, 14, 19};
const int deriv2[] = {2, 7, 5, 9, 13, 11, 18, 15, 19, 16};
const int deriv3[] = {3, 8, 9, 6, 14, 16, 12, 19, 17, 18};
const float xscale = cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX;
const float yscale = cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY;
const float zscale = cSim.pmeGridSize.z*cSim.invPeriodicBoxSizeZ;
float energy = 0.0f;
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < cSim.atoms; i += blockDim.x*gridDim.x) {
// Compute the force and energy.
// Compute the torque.
multipole[0] = cSim.pPosq[i].w;
multipole[1] = cAmoebaSim.pLabFrameDipole[i*3];
multipole[2] = cAmoebaSim.pLabFrameDipole[i*3+1];
multipole[3] = cAmoebaSim.pLabFrameDipole[i*3+2];
multipole[4] = cAmoebaSim.pLabFrameQuadrupole[i*9];
multipole[5] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+1];
multipole[6] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+2];
multipole[7] = cAmoebaSim.pLabFrameQuadrupole[i*9+4];
multipole[8] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+5];
multipole[9] = cAmoebaSim.pLabFrameQuadrupole[i*9+8];
multipole[5] = cAmoebaSim.pLabFrameQuadrupole[i*9+4];
multipole[6] = cAmoebaSim.pLabFrameQuadrupole[i*9+8];
multipole[7] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+1];
multipole[8] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+2];
multipole[9] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+5];
float* phi = &cAmoebaSim.pPhi[20*i];
cAmoebaSim.pTorque[3*i] = -cAmoebaSim.electric*(multipole[3]*yscale*phi[2] - multipole[2]*zscale*phi[3]
+ 2.0f*(multipole[6]-multipole[5])*zscale*zscale*phi[9]
+ multipole[8]*yscale*yscale*phi[7] + multipole[9]*xscale*yscale*phi[5]
- multipole[7]*yscale*zscale*phi[8] - multipole[9]*xscale*zscale*phi[6]);
cAmoebaSim.pTorque[3*i+1] = -cAmoebaSim.electric*(multipole[1]*zscale*phi[3] - multipole[3]*xscale*phi[1]
+ 2.0f*(multipole[4]-multipole[6])*zscale*zscale*phi[8]
+ multipole[7]*zscale*zscale*phi[9] + multipole[8]*xscale*zscale*phi[6]
- multipole[8]*xscale*xscale*phi[4] - multipole[9]*yscale*yscale*phi[7]);
cAmoebaSim.pTorque[3*i+2] = -cAmoebaSim.electric*(multipole[2]*xscale*phi[1] - multipole[1]*yscale*phi[2]
+ 2.0f*(multipole[5]-multipole[4])*yscale*yscale*phi[7]
+ multipole[7]*xscale*xscale*phi[4] + multipole[9]*yscale*zscale*phi[8]
- multipole[7]*xscale*yscale*phi[5] - multipole[8]*zscale*zscale*phi[9]);
// Compute the force and energy.
multipole[1] *= xscale;
multipole[2] *= yscale;
multipole[3] *= zscale;
multipole[4] *= xscale*xscale;
multipole[5] *= xscale*yscale;
multipole[6] *= xscale*zscale;
multipole[7] *= yscale*yscale;
multipole[8] *= yscale*zscale;
multipole[9] *= zscale*zscale;
float4 f = make_float4(0.0f, 0.0f, 0.0f, 0.0f);
for (int k = 0; k < 10; k++) {
energy += multipole[k]*phi[k];
......@@ -791,31 +818,18 @@ void kComputeFixedMultipoleForceAndEnergy_kernel()
f.y += multipole[k]*phi[deriv2[k]];
f.z += multipole[k]*phi[deriv3[k]];
}
f.x *= cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX;
f.y *= cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY;
f.z *= cSim.pmeGridSize.z*cSim.invPeriodicBoxSizeZ;
f.x *= cAmoebaSim.electric*cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX;
f.y *= cAmoebaSim.electric*cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY;
f.z *= cAmoebaSim.electric*cSim.pmeGridSize.z*cSim.invPeriodicBoxSizeZ;
float4 force = cSim.pForce4[i];
force.x += f.x;
force.y += f.y;
force.z += f.z;
cSim.pForce4[i] = force;
// Compute the torque.
cAmoebaSim.pTorque[3*i] = multipole[3]*phi[2] - multipole[2]*phi[3]
+ 2.0f*(multipole[6]-multipole[5])*phi[9]
+ multipole[8]*phi[7] + multipole[9]*phi[5]
- multipole[7]*phi[8] - multipole[9]*phi[6];
cAmoebaSim.pTorque[3*i+1] = multipole[1]*phi[3] - multipole[3]*phi[1]
+ 2.0f*(multipole[4]-multipole[6])*phi[9]
+ multipole[7]*phi[9] + multipole[8]*phi[6]
- multipole[8]*phi[4] - multipole[9]*phi[7];
cAmoebaSim.pTorque[3*i+2] = multipole[2]*phi[1] - multipole[1]*phi[2]
+ 2.0f*(multipole[5]-multipole[4])*phi[7]
+ multipole[7]*phi[4] + multipole[9]*phi[8]
- 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*cAmoebaSim.electric*energy;
}
__global__
......@@ -834,20 +848,48 @@ void kComputeInducedDipoleForceAndEnergy_kernel()
const int deriv1[] = {1, 4, 7, 8, 10, 15, 17, 13, 14, 19};
const int deriv2[] = {2, 7, 5, 9, 13, 11, 18, 15, 19, 16};
const int deriv3[] = {3, 8, 9, 6, 14, 16, 12, 19, 17, 18};
const float xscale = cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX;
const float yscale = cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY;
const float zscale = cSim.pmeGridSize.z*cSim.invPeriodicBoxSizeZ;
float energy = 0.0f;
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < cSim.atoms; i += blockDim.x*gridDim.x) {
// Compute the force and energy.
// Compute the torque.
multipole[0] = cSim.pPosq[i].w;
multipole[1] = cAmoebaSim.pLabFrameDipole[i*3];
multipole[2] = cAmoebaSim.pLabFrameDipole[i*3+1];
multipole[3] = cAmoebaSim.pLabFrameDipole[i*3+2];
multipole[4] = cAmoebaSim.pLabFrameQuadrupole[i*9];
multipole[5] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+1];
multipole[6] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+2];
multipole[7] = cAmoebaSim.pLabFrameQuadrupole[i*9+4];
multipole[8] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+5];
multipole[9] = cAmoebaSim.pLabFrameQuadrupole[i*9+8];
multipole[5] = cAmoebaSim.pLabFrameQuadrupole[i*9+4];
multipole[6] = cAmoebaSim.pLabFrameQuadrupole[i*9+8];
multipole[7] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+1];
multipole[8] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+2];
multipole[9] = 2*cAmoebaSim.pLabFrameQuadrupole[i*9+5];
float* phidp = &cAmoebaSim.pPhidp[20*i];
cAmoebaSim.pTorque[3*i] = -0.5f*cAmoebaSim.electric*(multipole[3]*yscale*phidp[2] - multipole[2]*zscale*phidp[3]
+ 2.0f*(multipole[6]-multipole[5])*zscale*zscale*phidp[9]
+ multipole[8]*yscale*yscale*phidp[7] + multipole[9]*xscale*yscale*phidp[5]
- multipole[7]*yscale*zscale*phidp[8] - multipole[9]*xscale*zscale*phidp[6]);
cAmoebaSim.pTorque[3*i+1] = -0.5f*cAmoebaSim.electric*(multipole[1]*zscale*phidp[3] - multipole[3]*xscale*phidp[1]
+ 2.0f*(multipole[4]-multipole[6])*zscale*zscale*phidp[8]
+ multipole[7]*zscale*zscale*phidp[9] + multipole[8]*xscale*zscale*phidp[6]
- multipole[8]*xscale*xscale*phidp[4] - multipole[9]*yscale*yscale*phidp[7]);
cAmoebaSim.pTorque[3*i+2] = -0.5f*cAmoebaSim.electric*(multipole[2]*xscale*phidp[1] - multipole[1]*yscale*phidp[2]
+ 2.0f*(multipole[5]-multipole[4])*yscale*yscale*phidp[7]
+ multipole[7]*xscale*xscale*phidp[4] + multipole[9]*yscale*zscale*phidp[8]
- multipole[7]*xscale*yscale*phidp[5] - multipole[8]*zscale*zscale*phidp[9]);
// Compute the force and energy.
multipole[1] *= xscale;
multipole[2] *= yscale;
multipole[3] *= zscale;
multipole[4] *= xscale*xscale;
multipole[5] *= xscale*yscale;
multipole[6] *= xscale*zscale;
multipole[7] *= yscale*yscale;
multipole[8] *= yscale*zscale;
multipole[9] *= zscale*zscale;
inducedDipole[0] = cAmoebaSim.pInducedDipole[i*3];
inducedDipole[1] = cAmoebaSim.pInducedDipole[i*3+1];
inducedDipole[2] = cAmoebaSim.pInducedDipole[i*3+2];
......@@ -867,37 +909,21 @@ void kComputeInducedDipoleForceAndEnergy_kernel()
f.y += (inducedDipole[k]+inducedDipolePolar[k])*phi[j2] + inducedDipole[k]*phip[j2] + inducedDipolePolar[k]*phid[j2];
f.z += (inducedDipole[k]+inducedDipolePolar[k])*phi[j3] + inducedDipole[k]*phip[j3] + inducedDipolePolar[k]*phid[j3];
}
float* phidp = &cAmoebaSim.pPhidp[20*i];
for (int k = 0; k < 10; k++) {
f.x += multipole[k]*phidp[deriv1[k]];
f.y += multipole[k]*phidp[deriv2[k]];
f.z += multipole[k]*phidp[deriv3[k]];
}
f.x *= cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX;
f.y *= cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY;
f.z *= cSim.pmeGridSize.z*cSim.invPeriodicBoxSizeZ;
f.x *= 0.5f*cAmoebaSim.electric*cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX;
f.y *= 0.5f*cAmoebaSim.electric*cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY;
f.z *= 0.5f*cAmoebaSim.electric*cSim.pmeGridSize.z*cSim.invPeriodicBoxSizeZ;
float4 force = cSim.pForce4[i];
force.x += f.x;
force.y += f.y;
force.z += f.z;
cSim.pForce4[i] = force;
// Compute the torque.
cAmoebaSim.pTorque[3*i] = multipole[3]*phi[2] - multipole[2]*phi[3]
+ 2.0f*(multipole[6]-multipole[5])*phi[9]
+ multipole[8]*phi[7] + multipole[9]*phi[5]
- multipole[7]*phi[8] - multipole[9]*phi[6];
cAmoebaSim.pTorque[3*i+1] = multipole[1]*phi[3] - multipole[3]*phi[1]
+ 2.0f*(multipole[4]-multipole[6])*phi[9]
+ multipole[7]*phi[9] + multipole[8]*phi[6]
- multipole[8]*phi[4] - multipole[9]*phi[7];
cAmoebaSim.pTorque[3*i+2] = multipole[2]*phi[1] - multipole[1]*phi[2]
+ 2.0f*(multipole[5]-multipole[4])*phi[7]
+ multipole[7]*phi[4] + multipole[9]*phi[8]
- 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*cAmoebaSim.electric*energy;
}
__global__
......@@ -910,9 +936,9 @@ __launch_bounds__(192, 1)
#endif
void kRecordFixedMultipoleField_kernel(float* output)
{
const float xscale = 0.1f*cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX;
const float yscale = 0.1f*cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY;
const float zscale = 0.1f*cSim.pmeGridSize.z*cSim.invPeriodicBoxSizeZ;
const float xscale = cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX;
const float yscale = cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY;
const float zscale = cSim.pmeGridSize.z*cSim.invPeriodicBoxSizeZ;
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < cSim.atoms; i += blockDim.x*gridDim.x) {
output[3*i] = -xscale*cAmoebaSim.pPhi[20*i+1];
output[3*i+1] = -yscale*cAmoebaSim.pPhi[20*i+2];
......@@ -930,9 +956,9 @@ __launch_bounds__(192, 1)
#endif
void kRecordInducedDipoleField_kernel(float* output, float* outputPolar)
{
const float xscale = 0.1f*cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX;
const float yscale = 0.1f*cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY;
const float zscale = 0.1f*cSim.pmeGridSize.z*cSim.invPeriodicBoxSizeZ;
const float xscale = cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX;
const float yscale = cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY;
const float zscale = cSim.pmeGridSize.z*cSim.invPeriodicBoxSizeZ;
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < cSim.atoms; i += blockDim.x*gridDim.x) {
output[3*i] -= xscale*cAmoebaSim.pPhid[10*i+1];
output[3*i+1] -= yscale*cAmoebaSim.pPhid[10*i+2];
......
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