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Commit 470c9b7f authored by Mark Friedrichs's avatar Mark Friedrichs
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Renamed math functions in Cuda kernels to single-precision equivalent [cos() -> cosf()]

parent fed50628
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Showing with 84 additions and 84 deletions
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateGBVISoftcoreBornSum.h
View file @ 470c9b7f
...@@ -99,9 +99,9 @@ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit) ...@@ -99,9 +99,9 @@ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit)
dy = psA[j].y - apos.y; dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z; dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
#if defined USE_CUTOFF #if defined USE_CUTOFF
...@@ -110,7 +110,7 @@ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit) ...@@ -110,7 +110,7 @@ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit)
if (i < cSim.atoms && x+j < cSim.atoms && j != tgx ) if (i < cSim.atoms && x+j < cSim.atoms && j != tgx )
#endif #endif
{ {
bSum += psA[j].bornRadiusScaleFactor*getGBVI_Volume( sqrt(r2), ar.x, psA[j].sr ); bSum += psA[j].bornRadiusScaleFactor*getGBVI_Volume( sqrtf(r2), ar.x, psA[j].sr );
} }
} }
...@@ -166,9 +166,9 @@ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit) ...@@ -166,9 +166,9 @@ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit)
dy = psA[tj].y - apos.y; dy = psA[tj].y - apos.y;
dz = psA[tj].z - apos.z; dz = psA[tj].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
...@@ -177,7 +177,7 @@ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit) ...@@ -177,7 +177,7 @@ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit)
if (i < cSim.atoms && y+tj < cSim.atoms ) if (i < cSim.atoms && y+tj < cSim.atoms )
#endif #endif
{ {
r = sqrt(r2); r = sqrtf(r2);
// psA[tj].sr = Sj // psA[tj].sr = Sj
// ar.x = Ri // ar.x = Ri
...@@ -204,9 +204,9 @@ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit) ...@@ -204,9 +204,9 @@ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit)
dy = psA[j].y - apos.y; dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z; dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
...@@ -215,7 +215,7 @@ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit) ...@@ -215,7 +215,7 @@ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit)
if (i < cSim.atoms && y+j < cSim.atoms) if (i < cSim.atoms && y+j < cSim.atoms)
#endif #endif
{ {
r = sqrt(r2); r = sqrtf(r2);
tempBuffer[threadIdx.x] = ar.w*getGBVI_Volume( r, psA[j].r, ar.y ); tempBuffer[threadIdx.x] = ar.w*getGBVI_Volume( r, psA[j].r, ar.y );
apos.w += psA[j].bornRadiusScaleFactor*getGBVI_Volume( r, ar.x, psA[j].sr ); apos.w += psA[j].bornRadiusScaleFactor*getGBVI_Volume( r, ar.x, psA[j].sr );
} }
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateGBVISoftcoreForces2.h
View file @ 470c9b7f
...@@ -104,12 +104,12 @@ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int* workUnit ...@@ -104,12 +104,12 @@ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int* workUnit
float dz = psA[j].z - apos.z; float dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r2 = dx * dx + dy * dy + dz * dz; float r2 = dx * dx + dy * dy + dz * dz;
float r = sqrt(r2); float r = sqrtf(r2);
// Atom I Born forces and sum // Atom I Born forces and sum
float dE = psA[j].bornRadiusScaleFactor*getGBVI_dE2( r, ar.x, psA[j].sr, fb ); float dE = psA[j].bornRadiusScaleFactor*getGBVI_dE2( r, ar.x, psA[j].sr, fb );
...@@ -190,12 +190,12 @@ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int* workUnit ...@@ -190,12 +190,12 @@ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int* workUnit
float dy = psA[tj].y - apos.y; float dy = psA[tj].y - apos.y;
float dz = psA[tj].z - apos.z; float dz = psA[tj].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r2 = dx * dx + dy * dy + dz * dz; float r2 = dx * dx + dy * dy + dz * dz;
float r = sqrt(r2); float r = sqrtf(r2);
float dE = psA[tj].bornRadiusScaleFactor*getGBVI_dE2( r, ar.x, psA[tj].sr, fb ); float dE = psA[tj].bornRadiusScaleFactor*getGBVI_dE2( r, ar.x, psA[tj].sr, fb );
...@@ -256,12 +256,12 @@ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int* workUnit ...@@ -256,12 +256,12 @@ void METHOD_NAME(kCalculateGBVISoftcore, Forces2_kernel)(unsigned int* workUnit
float dy = psA[j].y - apos.y; float dy = psA[j].y - apos.y;
float dz = psA[j].z - apos.z; float dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r2 = dx * dx + dy * dy + dz * dz; float r2 = dx * dx + dy * dy + dz * dz;
float r = sqrt(r2); float r = sqrtf(r2);
// Interleaved Atom I and J Born Forces and sum components // Interleaved Atom I and J Born Forces and sum components
float dE = psA[j].bornRadiusScaleFactor*getGBVI_dE2( r, ar.x, psA[j].sr, fb ); float dE = psA[j].bornRadiusScaleFactor*getGBVI_dE2( r, ar.x, psA[j].sr, fb );
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateLocalSoftcoreForces.cu
View file @ 470c9b7f
...@@ -142,7 +142,7 @@ __global__ void kCalculateLocalSoftcoreForces_kernel() ...@@ -142,7 +142,7 @@ __global__ void kCalculateLocalSoftcoreForces_kernel()
d.z = a1.z - a2.z; d.z = a1.z - a2.z;
float r2 = DOT3(d, d); float r2 = DOT3(d, d);
float inverseR = 1.0f / sqrt(r2); float inverseR = 1.0f / sqrtf(r2);
#ifdef USE_SOFTCORE_LJ #ifdef USE_SOFTCORE_LJ
float CDLJ_energy = 0.0f; float CDLJ_energy = 0.0f;
float dEdR = getSoftCoreLJ( r2, LJ14.y, LJ14.x, LJ14.w, LJ14.w, &CDLJ_energy ); float dEdR = getSoftCoreLJ( r2, LJ14.y, LJ14.x, LJ14.w, LJ14.w, &CDLJ_energy );
...@@ -187,7 +187,7 @@ __global__ void kCalculateLocalSoftcoreForces_kernel() ...@@ -187,7 +187,7 @@ __global__ void kCalculateLocalSoftcoreForces_kernel()
d.y = a1.y - a2.y; d.y = a1.y - a2.y;
d.z = a1.z - a2.z; d.z = a1.z - a2.z;
float r2 = DOT3(d, d); float r2 = DOT3(d, d);
float inverseR = 1.0f / sqrt(r2); float inverseR = 1.0f / sqrtf(r2);
#ifdef USE_SOFTCORE_LJ #ifdef USE_SOFTCORE_LJ
float dEdR = getSoftCoreLJ( r2, LJ14.y, LJ14.x, LJ14.w, LJ14.w, &LJ14_energy); float dEdR = getSoftCoreLJ( r2, LJ14.y, LJ14.x, LJ14.w, LJ14.w, &LJ14_energy);
#else #else
...@@ -235,11 +235,11 @@ __global__ void kCalculateLocalSoftcoreForces_kernel() ...@@ -235,11 +235,11 @@ __global__ void kCalculateLocalSoftcoreForces_kernel()
d.x = a1.x - a2.x; d.x = a1.x - a2.x;
d.y = a1.y - a2.y; d.y = a1.y - a2.y;
d.z = a1.z - a2.z; d.z = a1.z - a2.z;
d.x -= floor(d.x/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; d.x -= floorf(d.x/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
d.y -= floor(d.y/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; d.y -= floorf(d.y/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
d.z -= floor(d.z/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; d.z -= floorf(d.z/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
float r2 = DOT3(d, d); float r2 = DOT3(d, d);
float inverseR = 1.0f / sqrt(r2); float inverseR = 1.0f / sqrtf(r2);
#ifdef USE_SOFTCORE_LJ #ifdef USE_SOFTCORE_LJ
float dEdR = getSoftCoreLJ( r2, LJ14.y, LJ14.x, LJ14.w, LJ14.w, &LJ14_energy); float dEdR = getSoftCoreLJ( r2, LJ14.y, LJ14.x, LJ14.w, LJ14.w, &LJ14_energy);
#else #else
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateNonbondedSoftcore.h
View file @ 470c9b7f
...@@ -104,12 +104,12 @@ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit ) ...@@ -104,12 +104,12 @@ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit )
dy = psA[j].y - apos.y; dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z; dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
invR = 1.0f / sqrt(r2); invR = 1.0f / sqrtf(r2);
sig = a.x + psA[j].sig; sig = a.x + psA[j].sig;
eps = a.y * psA[j].eps; eps = a.y * psA[j].eps;
#ifdef USE_SOFTCORE_LJ #ifdef USE_SOFTCORE_LJ
...@@ -158,12 +158,12 @@ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit ) ...@@ -158,12 +158,12 @@ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit )
dy = psA[j].y - apos.y; dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z; dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
invR = 1.0f / sqrt(r2); invR = 1.0f / sqrtf(r2);
sig = a.x + psA[j].sig; sig = a.x + psA[j].sig;
eps = a.y * psA[j].eps; eps = a.y * psA[j].eps;
#ifdef USE_SOFTCORE_LJ #ifdef USE_SOFTCORE_LJ
...@@ -266,12 +266,12 @@ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit ) ...@@ -266,12 +266,12 @@ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit )
dy = psA[tj].y - apos.y; dy = psA[tj].y - apos.y;
dz = psA[tj].z - apos.z; dz = psA[tj].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
invR = 1.0f / sqrt(r2); invR = 1.0f / sqrtf(r2);
sig = a.x + psA[tj].sig; sig = a.x + psA[tj].sig;
eps = a.y * psA[tj].eps; eps = a.y * psA[tj].eps;
#ifdef USE_SOFTCORE_LJ #ifdef USE_SOFTCORE_LJ
...@@ -325,12 +325,12 @@ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit ) ...@@ -325,12 +325,12 @@ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit )
dy = psA[j].y - apos.y; dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z; dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
invR = 1.0f / sqrt(r2); invR = 1.0f / sqrtf(r2);
sig = a.x + psA[j].sig; sig = a.x + psA[j].sig;
eps = a.y * psA[j].eps; eps = a.y * psA[j].eps;
#ifdef USE_SOFTCORE_LJ #ifdef USE_SOFTCORE_LJ
...@@ -419,12 +419,12 @@ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit ) ...@@ -419,12 +419,12 @@ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit )
dy = psA[tj].y - apos.y; dy = psA[tj].y - apos.y;
dz = psA[tj].z - apos.z; dz = psA[tj].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
invR = 1.0f / sqrt(r2); invR = 1.0f / sqrtf(r2);
sig = a.x + psA[tj].sig; sig = a.x + psA[tj].sig;
eps = a.y * psA[tj].eps; eps = a.y * psA[tj].eps;
#ifdef USE_SOFTCORE_LJ #ifdef USE_SOFTCORE_LJ
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreBornSum.h
View file @ 470c9b7f
...@@ -99,9 +99,9 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn ...@@ -99,9 +99,9 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn
dy = psA[j].y - apos.y; dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z; dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
...@@ -112,7 +112,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn ...@@ -112,7 +112,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn
if (i < cSim.atoms && x+j < cSim.atoms ) if (i < cSim.atoms && x+j < cSim.atoms )
#endif #endif
{ {
r = sqrt(r2); r = sqrtf(r2);
float rInverse = 1.0f/r; float rInverse = 1.0f/r;
float rScaledRadiusJ = r + psA[j].sr; float rScaledRadiusJ = r + psA[j].sr;
if( (j != tgx) && (ar.x < rScaledRadiusJ) ){ if( (j != tgx) && (ar.x < rScaledRadiusJ) ){
...@@ -120,7 +120,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn ...@@ -120,7 +120,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn
float u_ij = 1.0f / rScaledRadiusJ; float u_ij = 1.0f / rScaledRadiusJ;
float l_ij2 = l_ij * l_ij; float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij; float u_ij2 = u_ij * u_ij;
float ratio = log(u_ij / l_ij); float ratio = logf(u_ij / l_ij);
float term = l_ij - u_ij + float term = l_ij - u_ij +
0.25f * r * (u_ij2 - l_ij2) + 0.25f * r * (u_ij2 - l_ij2) +
(0.50f * rInverse * ratio) + (0.50f * rInverse * ratio) +
...@@ -190,9 +190,9 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn ...@@ -190,9 +190,9 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn
dy = psA[tj].y - apos.y; dy = psA[tj].y - apos.y;
dz = psA[tj].z - apos.z; dz = psA[tj].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
...@@ -201,7 +201,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn ...@@ -201,7 +201,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn
if (i < cSim.atoms && y+tj < cSim.atoms ) if (i < cSim.atoms && y+tj < cSim.atoms )
#endif #endif
{ {
r = sqrt(r2); r = sqrtf(r2);
float rInverse = 1.0f / r; float rInverse = 1.0f / r;
float rScaledRadiusJ = r + psA[tj].sr; float rScaledRadiusJ = r + psA[tj].sr;
if (ar.x < rScaledRadiusJ) if (ar.x < rScaledRadiusJ)
...@@ -210,7 +210,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn ...@@ -210,7 +210,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn
float u_ij = 1.0f / rScaledRadiusJ; float u_ij = 1.0f / rScaledRadiusJ;
float l_ij2 = l_ij * l_ij; float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij; float u_ij2 = u_ij * u_ij;
float ratio = log(u_ij / l_ij); float ratio = logf(u_ij / l_ij);
float term = l_ij - u_ij + float term = l_ij - u_ij +
0.25f * r * (u_ij2 - l_ij2) + 0.25f * r * (u_ij2 - l_ij2) +
(0.50f * rInverse * ratio) + (0.50f * rInverse * ratio) +
...@@ -232,7 +232,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn ...@@ -232,7 +232,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn
float u_ij = 1.0f / rScaledRadiusI; float u_ij = 1.0f / rScaledRadiusI;
float l_ij2 = l_ij * l_ij; float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij; float u_ij2 = u_ij * u_ij;
float ratio = log(u_ij / l_ij); float ratio = logf(u_ij / l_ij);
float term = l_ij - u_ij + float term = l_ij - u_ij +
0.25f * r * (u_ij2 - l_ij2) + 0.25f * r * (u_ij2 - l_ij2) +
(0.50f * rInverse * ratio) + (0.50f * rInverse * ratio) +
...@@ -265,9 +265,9 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn ...@@ -265,9 +265,9 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn
dy = psA[j].y - apos.y; dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z; dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
r2 = dx * dx + dy * dy + dz * dz; r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
...@@ -276,7 +276,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn ...@@ -276,7 +276,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn
if (i < cSim.atoms && y+j < cSim.atoms ) if (i < cSim.atoms && y+j < cSim.atoms )
#endif #endif
{ {
r = sqrt(r2); r = sqrtf(r2);
float rInverse = 1.0f / r; float rInverse = 1.0f / r;
float rScaledRadiusJ = r + psA[j].sr; float rScaledRadiusJ = r + psA[j].sr;
if (ar.x < rScaledRadiusJ) if (ar.x < rScaledRadiusJ)
...@@ -285,7 +285,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn ...@@ -285,7 +285,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn
float u_ij = 1.0f / rScaledRadiusJ; float u_ij = 1.0f / rScaledRadiusJ;
float l_ij2 = l_ij * l_ij; float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij; float u_ij2 = u_ij * u_ij;
float ratio = log(u_ij / l_ij); float ratio = logf(u_ij / l_ij);
float term = l_ij - float term = l_ij -
u_ij + u_ij +
0.25f * r * (u_ij2 - l_ij2) + 0.25f * r * (u_ij2 - l_ij2) +
...@@ -306,7 +306,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn ...@@ -306,7 +306,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, BornSum_kernel)(unsigned int* workUn
float u_ij = 1.0f / rScaledRadiusI; float u_ij = 1.0f / rScaledRadiusI;
float l_ij2 = l_ij * l_ij; float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij; float u_ij2 = u_ij * u_ij;
float ratio = log(u_ij / l_ij); float ratio = logf(u_ij / l_ij);
float term = l_ij - float term = l_ij -
u_ij + u_ij +
0.25f * r * (u_ij2 - l_ij2) + 0.25f * r * (u_ij2 - l_ij2) +
......
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreForces2.h
View file @ 470c9b7f
...@@ -95,12 +95,12 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUn ...@@ -95,12 +95,12 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUn
float dy = psA[j].y - apos.y; float dy = psA[j].y - apos.y;
float dz = psA[j].z - apos.z; float dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r2 = dx * dx + dy * dy + dz * dz; float r2 = dx * dx + dy * dy + dz * dz;
float r = sqrt(r2); float r = sqrtf(r2);
// Atom I Born forces and sum // Atom I Born forces and sum
...@@ -112,7 +112,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUn ...@@ -112,7 +112,7 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUn
float l_ij2 = l_ij * l_ij; float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij; float u_ij2 = u_ij * u_ij;
float r2Inverse = rInverse * rInverse; float r2Inverse = rInverse * rInverse;
float t1 = log (u_ij / l_ij); float t1 = logf(u_ij / l_ij);
float t2 = (l_ij2 - u_ij2); float t2 = (l_ij2 - u_ij2);
float t3 = t2 * rInverse; float t3 = t2 * rInverse;
t1 *= rInverse; t1 *= rInverse;
...@@ -194,12 +194,12 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUn ...@@ -194,12 +194,12 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUn
float dy = psA[tj].y - apos.y; float dy = psA[tj].y - apos.y;
float dz = psA[tj].z - apos.z; float dz = psA[tj].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r2 = dx * dx + dy * dy + dz * dz; float r2 = dx * dx + dy * dy + dz * dz;
float r = sqrt(r2); float r = sqrtf(r2);
// Interleaved Atom I and J Born Forces and sum components // Interleaved Atom I and J Born Forces and sum components
float r2Inverse = 1.0f / r2; float r2Inverse = 1.0f / r2;
...@@ -214,8 +214,8 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUn ...@@ -214,8 +214,8 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUn
float l_ij2I = l_ijI * l_ijI; float l_ij2I = l_ijI * l_ijI;
float u_ij2J = u_ijJ * u_ijJ; float u_ij2J = u_ijJ * u_ijJ;
float u_ij2I = u_ijI * u_ijI; float u_ij2I = u_ijI * u_ijI;
float t1J = log (u_ijJ / l_ijJ); float t1J = logf(u_ijJ / l_ijJ);
float t1I = log (u_ijI / l_ijI); float t1I = logf(u_ijI / l_ijI);
float t2J = (l_ij2J - u_ij2J); float t2J = (l_ij2J - u_ij2J);
float t2I = (l_ij2I - u_ij2I); float t2I = (l_ij2I - u_ij2I);
float t3J = t2J * rInverse; float t3J = t2J * rInverse;
...@@ -290,12 +290,12 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUn ...@@ -290,12 +290,12 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUn
float dy = psA[j].y - apos.y; float dy = psA[j].y - apos.y;
float dz = psA[j].z - apos.z; float dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r2 = dx * dx + dy * dy + dz * dz; float r2 = dx * dx + dy * dy + dz * dz;
float r = sqrt(r2); float r = sqrtf(r2);
// Interleaved Atom I and J Born Forces and sum components // Interleaved Atom I and J Born Forces and sum components
float r2Inverse = 1.0f / r2; float r2Inverse = 1.0f / r2;
...@@ -310,8 +310,8 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUn ...@@ -310,8 +310,8 @@ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUn
float l_ij2I = l_ijI * l_ijI; float l_ij2I = l_ijI * l_ijI;
float u_ij2J = u_ijJ * u_ijJ; float u_ij2J = u_ijJ * u_ijJ;
float u_ij2I = u_ijI * u_ijI; float u_ij2I = u_ijI * u_ijI;
float t1J = log (u_ijJ / l_ijJ); float t1J = logf(u_ijJ / l_ijJ);
float t1I = log (u_ijI / l_ijI); float t1I = logf(u_ijI / l_ijI);
float t2J = (l_ij2J - u_ij2J); float t2J = (l_ij2J - u_ij2J);
float t2I = (l_ij2I - u_ij2I); float t2I = (l_ij2I - u_ij2I);
float t3J = t2J * rInverse; float t3J = t2J * rInverse;
......
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