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Commit 761d7e17 authored by Mark Friedrichs's avatar Mark Friedrichs
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Removal of limitation for 'long-range in sequence' covalent bonds 

Reduced memory footprint
parent 80c4976e
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Showing with 524 additions and 1034 deletions
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaMutualInducedAndGkFields.h
View file @ 761d7e17
......@@ -118,7 +118,7 @@ void METHOD_NAME(kCalculateAmoebaMutualInducedAndGkFields, _kernel)(
#endif
);
unsigned int mask = ( (atomI == (y + j)) || (atomI >= cAmoebaSim.numberOfAtoms) || ((y+j) >= cAmoebaSim.numberOfAtoms) ) ? 0 : 1;
unsigned int mask = ( (atomI == (y + j)) || (atomI >= cSim.atoms) || ((y+j) >= cSim.atoms) ) ? 0 : 1;
// add to field at atomI the field due atomJ's dipole
......@@ -162,7 +162,7 @@ if( atomI == targetAtom ){
// atomI == atomJ contribution included
mask = ( (atomI >= cAmoebaSim.numberOfAtoms) || ((y+j) >= cAmoebaSim.numberOfAtoms) ) ? 0 : 1;
mask = ( (atomI >= cSim.atoms) || ((y+j) >= cSim.atoms) ) ? 0 : 1;
fieldSumS[0] += mask ? ijField[0][0] : 0.0f;
fieldSumS[1] += mask ? ijField[0][1] : 0.0f;
fieldSumS[2] += mask ? ijField[0][2] : 0.0f;
......@@ -181,7 +181,7 @@ if( atomI == targetAtom ){
index = debugAccumulate( index, debugArray, jDipoleS, 1, 7.0f );
index = debugAccumulate( index, debugArray, jDipolePolarS, 1, 8.0f );
index += cAmoebaSim.paddedNumberOfAtoms;
index += cSim.paddedNumberOfAtoms;
debugArray[index].x = bornRadii[atomI];
debugArray[index].y = jBornRadius;
debugArray[index].w = 9.0f;
......@@ -195,7 +195,7 @@ if( atomI == targetAtom ){
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = 3*(x + tgx + warp*cAmoebaSim.paddedNumberOfAtoms);
unsigned int offset = 3*(x + tgx + warp*cSim.paddedNumberOfAtoms);
load3dArrayBufferPerWarp( offset, fieldSum, outputField );
load3dArrayBufferPerWarp( offset, fieldPolarSum, outputFieldPolar );
......@@ -204,7 +204,7 @@ if( atomI == targetAtom ){
load3dArrayBufferPerWarp( offset, fieldPolarSumS, outputFieldPolarS );
#else
unsigned int offset = 3*(x + tgx + (x >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms);
unsigned int offset = 3*(x + tgx + (x >> GRIDBITS) * cSim.paddedNumberOfAtoms);
load3dArray( offset, fieldSum, outputField );
load3dArray( offset, fieldPolarSum, outputFieldPolar);
......@@ -241,7 +241,7 @@ if( atomI == targetAtom ){
#endif
);
if( (atomI < cAmoebaSim.numberOfAtoms) && ((y+tj) < cAmoebaSim.numberOfAtoms) ){
if( (atomI < cSim.atoms) && ((y+tj) < cSim.atoms) ){
// add to field at atomI the field due atomJ's dipole
......@@ -294,7 +294,7 @@ if( atomI == targetAtom ){
unsigned int index = (atomI == targetAtom) ? (y + tj) : atomI;
if( atomI == targetAtom || (y + tj) == targetAtom ){
unsigned int indexI = (atomI == targetAtom) ? 0 : 2;
unsigned int maskD = (atomI < cAmoebaSim.numberOfAtoms) && ((y+tj) < cAmoebaSim.numberOfAtoms);
unsigned int maskD = (atomI < cSim.atoms) && ((y+tj) < cSim.atoms);
debugArray[index].x = (float) atomI;
debugArray[index].y = (float) (y + tj);
......@@ -314,7 +314,7 @@ if( atomI == targetAtom || (y + tj) == targetAtom ){
);
if( (atomI < cAmoebaSim.numberOfAtoms) && ((y+tj) < cAmoebaSim.numberOfAtoms) ){
if( (atomI < cSim.atoms) && ((y+tj) < cSim.atoms) ){
fieldSumS[0] += ijField[0][0];
fieldSumS[1] += ijField[0][1];
......@@ -341,14 +341,14 @@ if( atomI == targetAtom || (y + tj) == targetAtom ){
#if 0
if( atomI == targetAtom || (y + tj) == targetAtom ){
unsigned int indexI = (atomI == targetAtom) ? 0 : 1;
unsigned int maskD = (atomI < cAmoebaSim.numberOfAtoms) && ((y+tj) < cAmoebaSim.numberOfAtoms);
unsigned int maskD = (atomI < cSim.atoms) && ((y+tj) < cSim.atoms);
index = debugAccumulate( index, debugArray, ijField[indexI], maskD, -5.0f );
index = debugAccumulate( index, debugArray, ijField[indexI+2], maskD, -6.0f );
index = debugAccumulate( index, debugArray, jDipoleS, 1, -7.0f );
index = debugAccumulate( index, debugArray, jDipolePolarS, 1, -8.0f );
index += cAmoebaSim.paddedNumberOfAtoms;
index += cSim.paddedNumberOfAtoms;
debugArray[index].x = bornRadii[atomI];
debugArray[index].y = jBornRadius;
debugArray[index].w = -9.0f;
......@@ -362,13 +362,13 @@ if( atomI == targetAtom || (y + tj) == targetAtom ){
// Write results
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = 3*(x + tgx + warp*cAmoebaSim.paddedNumberOfAtoms);
unsigned int offset = 3*(x + tgx + warp*cSim.paddedNumberOfAtoms);
load3dArrayBufferPerWarp( offset, fieldSum, outputField );
load3dArrayBufferPerWarp( offset, fieldPolarSum, outputFieldPolar);
load3dArrayBufferPerWarp( offset, fieldSumS, outputFieldS );
load3dArrayBufferPerWarp( offset, fieldPolarSumS, outputFieldPolarS );
offset = 3*(y + tgx + warp*cAmoebaSim.paddedNumberOfAtoms);
offset = 3*(y + tgx + warp*cSim.paddedNumberOfAtoms);
load3dArrayBufferPerWarp( offset, sA[threadIdx.x].field, outputField );
load3dArrayBufferPerWarp( offset, sA[threadIdx.x].fieldPolar, outputFieldPolar);
......@@ -376,13 +376,13 @@ if( atomI == targetAtom || (y + tj) == targetAtom ){
load3dArrayBufferPerWarp( offset, sA[threadIdx.x].fieldPolarS, outputFieldPolarS);
#else
unsigned int offset = 3*(x + tgx + (y >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms);
unsigned int offset = 3*(x + tgx + (y >> GRIDBITS) * cSim.paddedNumberOfAtoms);
load3dArray( offset, fieldSum, outputField );
load3dArray( offset, fieldPolarSum, outputFieldPolar);
load3dArray( offset, fieldSumS, outputFieldS );
load3dArray( offset, fieldPolarSumS, outputFieldPolarS);
offset = 3*(y + tgx + (x >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms);
offset = 3*(y + tgx + (x >> GRIDBITS) * cSim.paddedNumberOfAtoms);
load3dArray( offset, sA[threadIdx.x].field, outputField );
load3dArray( offset, sA[threadIdx.x].fieldPolar, outputFieldPolar);
load3dArray( offset, sA[threadIdx.x].fieldS, outputFieldS );
......
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