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Commit 21ab511a authored by Peter Eastman's avatar Peter Eastman
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Optimizations to Kirkwood kernel

parent f08750f2
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plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwood.h
View file @ 21ab511a
...@@ -60,13 +60,6 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwood, Forces_kernel)( ...@@ -60,13 +60,6 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwood, Forces_kernel)(
// pWorkArray_1_1 == dBorn // pWorkArray_1_1 == dBorn
// pWorkArray_1_2 == dBornPolar // pWorkArray_1_2 == dBornPolar
float4 jCoord;
float jDipole[3];
float jQuadrupole[9];
float jInducedDipole[3];
float jInducedDipolePolar[3];
float jBornRadius;
float energySum = 0.0f; float energySum = 0.0f;
while (pos < end) while (pos < end)
...@@ -87,20 +80,21 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwood, Forces_kernel)( ...@@ -87,20 +80,21 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwood, Forces_kernel)(
KirkwoodParticle* psA = &sA[tbx]; KirkwoodParticle* psA = &sA[tbx];
unsigned int atomI = x + tgx; unsigned int atomI = x + tgx;
float4 iCoord = cSim.pPosq[atomI]; KirkwoodParticle localParticle;
loadKirkwoodShared(&localParticle, atomI,
cSim.pPosq, cAmoebaSim.pLabFrameDipole, cAmoebaSim.pLabFrameQuadrupole,
cAmoebaSim.pInducedDipoleS, cAmoebaSim.pInducedDipolePolarS, cSim.pBornRadii );
float forceSum[3];
float torqueSum[3];
float dBornSum; float dBornSum;
float dBornPolarSum; float dBornPolarSum;
forceSum[0] = 0.0f; localParticle.force[0] = 0.0f;
forceSum[1] = 0.0f; localParticle.force[1] = 0.0f;
forceSum[2] = 0.0f; localParticle.force[2] = 0.0f;
torqueSum[0] = 0.0f; localParticle.torque[0] = 0.0f;
torqueSum[1] = 0.0f; localParticle.torque[1] = 0.0f;
torqueSum[2] = 0.0f; localParticle.torque[2] = 0.0f;
dBornSum = 0.0f; dBornSum = 0.0f;
dBornPolarSum = 0.0f; dBornPolarSum = 0.0f;
...@@ -131,18 +125,8 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwood, Forces_kernel)( ...@@ -131,18 +125,8 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwood, Forces_kernel)(
unsigned int atomJ = y + j; unsigned int atomJ = y + j;
unsigned int sameAtom = atomI == atomJ ? 1 : 0; unsigned int sameAtom = atomI == atomJ ? 1 : 0;
// load coords, charge, ... calculateKirkwoodPairIxn_kernel( localParticle, psA[j],
sameAtom,
loadKirkwoodData( &(psA[j]), &jCoord, jDipole, jQuadrupole,
jInducedDipole, jInducedDipolePolar, &jBornRadius );
calculateKirkwoodPairIxn_kernel( sameAtom,
iCoord, jCoord,
&(cAmoebaSim.pLabFrameDipole[3*atomI]), jDipole,
&(cAmoebaSim.pLabFrameQuadrupole[9*atomI]), jQuadrupole,
&(cAmoebaSim.pInducedDipoleS[3*atomI]), jInducedDipole,
&(cAmoebaSim.pInducedDipolePolarS[3*atomI]),jInducedDipolePolar,
cSim.pBornRadii[atomI], jBornRadius,
force, torque, dBorn, dBornPolar, &energy force, torque, dBorn, dBornPolar, &energy
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
, pullBack , pullBack
...@@ -153,9 +137,9 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwood, Forces_kernel)( ...@@ -153,9 +137,9 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwood, Forces_kernel)(
// torques include i == j contribution // torques include i == j contribution
torqueSum[0] += mask ? torque[0][0] : 0.0f; localParticle.torque[0] += mask ? torque[0][0] : 0.0f;
torqueSum[1] += mask ? torque[0][1] : 0.0f; localParticle.torque[1] += mask ? torque[0][1] : 0.0f;
torqueSum[2] += mask ? torque[0][2] : 0.0f; localParticle.torque[2] += mask ? torque[0][2] : 0.0f;
dBornSum += mask ? dBorn[0] : 0.0f; dBornSum += mask ? dBorn[0] : 0.0f;
dBornPolarSum += mask ? dBornPolar[0] : 0.0f; dBornPolarSum += mask ? dBornPolar[0] : 0.0f;
...@@ -165,9 +149,9 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwood, Forces_kernel)( ...@@ -165,9 +149,9 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwood, Forces_kernel)(
mask = (atomI == atomJ) ? 0 : mask; mask = (atomI == atomJ) ? 0 : mask;
forceSum[0] += mask ? force[0] : 0.0f; localParticle.force[0] += mask ? force[0] : 0.0f;
forceSum[1] += mask ? force[1] : 0.0f; localParticle.force[1] += mask ? force[1] : 0.0f;
forceSum[2] += mask ? force[2] : 0.0f; localParticle.force[2] += mask ? force[2] : 0.0f;
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
...@@ -238,8 +222,8 @@ if( atomI == targetAtom || atomJ == targetAtom ){ ...@@ -238,8 +222,8 @@ if( atomI == targetAtom || atomJ == targetAtom ){
offset *= 3; offset *= 3;
load3dArrayBufferPerWarp( offset, forceSum, cAmoebaSim.pWorkArray_3_1 ); load3dArrayBufferPerWarp( offset, localParticle.force, cAmoebaSim.pWorkArray_3_1 );
load3dArrayBufferPerWarp( offset, torqueSum, cAmoebaSim.pWorkArray_3_2 ); load3dArrayBufferPerWarp( offset, localParticle.torque, cAmoebaSim.pWorkArray_3_2 );
#else #else
unsigned int offset = x + tgx + (x >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms; unsigned int offset = x + tgx + (x >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms;
...@@ -249,8 +233,8 @@ if( atomI == targetAtom || atomJ == targetAtom ){ ...@@ -249,8 +233,8 @@ if( atomI == targetAtom || atomJ == targetAtom ){
offset *= 3; offset *= 3;
load3dArray( offset, forceSum, cAmoebaSim.pWorkArray_3_1 ); load3dArray( offset, localParticle.force, cAmoebaSim.pWorkArray_3_1 );
load3dArray( offset, torqueSum, cAmoebaSim.pWorkArray_3_2 ); load3dArray( offset, localParticle.torque, cAmoebaSim.pWorkArray_3_2 );
#endif #endif
...@@ -286,18 +270,8 @@ if( atomI == targetAtom || atomJ == targetAtom ){ ...@@ -286,18 +270,8 @@ if( atomI == targetAtom || atomJ == targetAtom ){
unsigned int atomJ = y + tj; unsigned int atomJ = y + tj;
unsigned int sameAtom = 0; unsigned int sameAtom = 0;
// load coords, charge, ... calculateKirkwoodPairIxn_kernel( localParticle, psA[tj],
sameAtom,
loadKirkwoodData( &(psA[tj]), &jCoord, jDipole, jQuadrupole,
jInducedDipole, jInducedDipolePolar, &jBornRadius );
calculateKirkwoodPairIxn_kernel( sameAtom,
iCoord, jCoord,
&(cAmoebaSim.pLabFrameDipole[3*atomI]), jDipole,
&(cAmoebaSim.pLabFrameQuadrupole[9*atomI]), jQuadrupole,
&(cAmoebaSim.pInducedDipoleS[3*atomI]), jInducedDipole,
&(cAmoebaSim.pInducedDipolePolarS[3*atomI]), jInducedDipolePolar,
cSim.pBornRadii[atomI], jBornRadius,
force, torque, dBorn, dBornPolar, &energy force, torque, dBorn, dBornPolar, &energy
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
, pullBack , pullBack
...@@ -308,13 +282,13 @@ if( atomI == targetAtom || atomJ == targetAtom ){ ...@@ -308,13 +282,13 @@ if( atomI == targetAtom || atomJ == targetAtom ){
// add force and torque to atom I due atom J // add force and torque to atom I due atom J
forceSum[0] += mask ? force[0] : 0.0f; localParticle.force[0] += mask ? force[0] : 0.0f;
forceSum[1] += mask ? force[1] : 0.0f; localParticle.force[1] += mask ? force[1] : 0.0f;
forceSum[2] += mask ? force[2] : 0.0f; localParticle.force[2] += mask ? force[2] : 0.0f;
torqueSum[0] += mask ? torque[0][0] : 0.0f; localParticle.torque[0] += mask ? torque[0][0] : 0.0f;
torqueSum[1] += mask ? torque[0][1] : 0.0f; localParticle.torque[1] += mask ? torque[0][1] : 0.0f;
torqueSum[2] += mask ? torque[0][2] : 0.0f; localParticle.torque[2] += mask ? torque[0][2] : 0.0f;
dBornSum += mask ? dBorn[0] : 0.0f; dBornSum += mask ? dBorn[0] : 0.0f;
dBornPolarSum += mask ? dBornPolar[0] : 0.0f; dBornPolarSum += mask ? dBornPolar[0] : 0.0f;
...@@ -410,8 +384,8 @@ if( mask || !mask ){ ...@@ -410,8 +384,8 @@ if( mask || !mask ){
offset *= 3; offset *= 3;
load3dArrayBufferPerWarp( offset, forceSum, cAmoebaSim.pWorkArray_3_1 ); load3dArrayBufferPerWarp( offset, localParticle.force, cAmoebaSim.pWorkArray_3_1 );
load3dArrayBufferPerWarp( offset, torqueSum, cAmoebaSim.pWorkArray_3_2 ); load3dArrayBufferPerWarp( offset, localParticle.torque, cAmoebaSim.pWorkArray_3_2 );
offset = y + tgx + warp*cAmoebaSim.paddedNumberOfAtoms; offset = y + tgx + warp*cAmoebaSim.paddedNumberOfAtoms;
...@@ -435,8 +409,8 @@ if( mask || !mask ){ ...@@ -435,8 +409,8 @@ if( mask || !mask ){
offset *= 3; offset *= 3;
load3dArray( offset, forceSum, cAmoebaSim.pWorkArray_3_1 ); load3dArray( offset, localParticle.force, cAmoebaSim.pWorkArray_3_1 );
load3dArray( offset, torqueSum, cAmoebaSim.pWorkArray_3_2 ); load3dArray( offset, localParticle.torque, cAmoebaSim.pWorkArray_3_2 );
offset = y + tgx + (x >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms; offset = y + tgx + (x >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms;
......
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