Skip to content

GitLab

"vscode:/vscode.git/clone" did not exist on "3954264cfc444c2c7b61bc78e243c510dad6b5cd"
Commit 470c9b7f authored by Mark Friedrichs's avatar Mark Friedrichs
Browse files

Renamed math functions in Cuda kernels to single-precision equivalent [cos() -> cosf()]

parent fed50628
Hide whitespace changes
Inline Side-by-side
Showing with 195 additions and 195 deletions
platforms/cuda/src/kernels/kBrownianUpdate.cu
View file @ 470c9b7f
...@@ -72,7 +72,7 @@ void kBrownianUpdatePart1_kernel() ...@@ -72,7 +72,7 @@ void kBrownianUpdatePart1_kernel()
float4 force = cSim.pForce4[pos]; float4 force = cSim.pForce4[pos];
float invMass = cSim.pVelm4[pos].w; float invMass = cSim.pVelm4[pos].w;
float forceScale = cSim.tauDeltaT*invMass; float forceScale = cSim.tauDeltaT*invMass;
float noiseScale = cSim.noiseAmplitude*sqrt(invMass); float noiseScale = cSim.noiseAmplitude*sqrtf(invMass);
cSim.pOldPosq[pos] = apos; cSim.pOldPosq[pos] = apos;
apos.x = force.x*forceScale + noiseScale*random4a.x; apos.x = force.x*forceScale + noiseScale*random4a.x;
......
platforms/cuda/src/kernels/kCalculateAndersenThermostat.cu
View file @ 470c9b7f
...@@ -58,14 +58,14 @@ __global__ void kCalculateAndersenThermostat_kernel(int* atomGroups) ...@@ -58,14 +58,14 @@ __global__ void kCalculateAndersenThermostat_kernel(int* atomGroups)
__syncthreads(); __syncthreads();
float collisionProbability = 1.0f-exp(-cSim.collisionFrequency*cSim.pStepSize[0].y); float collisionProbability = 1.0f-exp(-cSim.collisionFrequency*cSim.pStepSize[0].y);
float randomRange = erf(collisionProbability/sqrt(2.0f)); float randomRange = erf(collisionProbability/sqrtf(2.0f));
while (pos < cSim.atoms) while (pos < cSim.atoms)
{ {
float4 velocity = cSim.pVelm4[pos]; float4 velocity = cSim.pVelm4[pos];
float4 selectRand = cSim.pRandom4[rpos + atomGroups[pos]]; float4 selectRand = cSim.pRandom4[rpos + atomGroups[pos]];
float4 velRand = cSim.pRandom4[rpos + pos]; float4 velRand = cSim.pRandom4[rpos + pos];
float scale = (selectRand.w > -randomRange && selectRand.w < randomRange ? 0.0f : 1.0f); float scale = (selectRand.w > -randomRange && selectRand.w < randomRange ? 0.0f : 1.0f);
float add = (1.0f-scale)*sqrt(cSim.kT*velocity.w); float add = (1.0f-scale)*sqrtf(cSim.kT*velocity.w);
velocity.x = scale*velocity.x + add*velRand.x; velocity.x = scale*velocity.x + add*velRand.x;
velocity.y = scale*velocity.y + add*velRand.y; velocity.y = scale*velocity.y + add*velRand.y;
velocity.z = scale*velocity.z + add*velRand.z; velocity.z = scale*velocity.z + add*velRand.z;
......
platforms/cuda/src/kernels/kCalculateCDLJEwaldFastReciprocal.h
View file @ 470c9b7f
...@@ -83,11 +83,11 @@ __global__ void kCalculateEwaldFastCosSinSums_kernel() ...@@ -83,11 +83,11 @@ __global__ void kCalculateEwaldFastCosSinSums_kernel()
{ {
float4 apos = cSim.pPosq[atom]; float4 apos = cSim.pPosq[atom];
float phase = apos.x*kx; float phase = apos.x*kx;
float2 structureFactor = make_float2(cos(phase), sin(phase)); float2 structureFactor = make_float2(cosf(phase), sinf(phase));
phase = apos.y*ky; phase = apos.y*ky;
structureFactor = MultofFloat2(structureFactor, make_float2(cos(phase), sin(phase))); structureFactor = MultofFloat2(structureFactor, make_float2(cosf(phase), sinf(phase)));
phase = apos.z*kz; phase = apos.z*kz;
structureFactor = MultofFloat2(structureFactor, make_float2(cos(phase), sin(phase))); structureFactor = MultofFloat2(structureFactor, make_float2(cosf(phase), sinf(phase)));
sum.x += apos.w*structureFactor.x; sum.x += apos.w*structureFactor.x;
sum.y += apos.w*structureFactor.y; sum.y += apos.w*structureFactor.y;
} }
...@@ -129,9 +129,9 @@ __global__ void kCalculateEwaldFastForces_kernel() ...@@ -129,9 +129,9 @@ __global__ void kCalculateEwaldFastForces_kernel()
for (int ry = lowry; ry < cSim.kmaxY; ry++) { for (int ry = lowry; ry < cSim.kmaxY; ry++) {
float ky = ry * cSim.recipBoxSizeY; float ky = ry * cSim.recipBoxSizeY;
float phase = apos.x*kx; float phase = apos.x*kx;
float2 tab_xy = make_float2(cos(phase), sin(phase)); float2 tab_xy = make_float2(cosf(phase), sinf(phase));
phase = apos.y*ky; phase = apos.y*ky;
tab_xy = MultofFloat2(tab_xy, make_float2(cos(phase), sin(phase))); tab_xy = MultofFloat2(tab_xy, make_float2(cosf(phase), sinf(phase)));
for (int rz = lowrz; rz < cSim.kmaxZ; rz++) { for (int rz = lowrz; rz < cSim.kmaxZ; rz++) {
float kz = rz * cSim.recipBoxSizeZ; float kz = rz * cSim.recipBoxSizeZ;
...@@ -141,7 +141,7 @@ __global__ void kCalculateEwaldFastForces_kernel() ...@@ -141,7 +141,7 @@ __global__ void kCalculateEwaldFastForces_kernel()
float k2 = kx*kx + ky*ky + kz*kz; float k2 = kx*kx + ky*ky + kz*kz;
float ak = exp(k2*cSim.factorEwald) / k2; float ak = exp(k2*cSim.factorEwald) / k2;
phase = apos.z*kz; phase = apos.z*kz;
float2 structureFactor = MultofFloat2(tab_xy, make_float2(cos(phase), sin(phase))); float2 structureFactor = MultofFloat2(tab_xy, make_float2(cosf(phase), sinf(phase)));
float2 cosSinSum = cSim.pEwaldCosSinSum[index]; float2 cosSinSum = cSim.pEwaldCosSinSum[index];
float dEdR = ak * apos.w * (cosSinSum.x*structureFactor.y - cosSinSum.y*structureFactor.x); float dEdR = ak * apos.w * (cosSinSum.x*structureFactor.y - cosSinSum.y*structureFactor.x);
force.x += 2 * recipCoeff * dEdR * kx; force.x += 2 * recipCoeff * dEdR * kx;
......
platforms/cuda/src/kernels/kCalculateCDLJEwaldReciprocal.h
View file @ 470c9b7f
...@@ -63,10 +63,10 @@ __global__ void kCalculateCDLJEwaldReciprocalForces_kernel() ...@@ -63,10 +63,10 @@ __global__ void kCalculateCDLJEwaldReciprocalForces_kernel()
float arg1 = kx*apos1.x + ky*apos1.y + kz*apos1.z; float arg1 = kx*apos1.x + ky*apos1.y + kz*apos1.z;
float arg2 = kx*apos2.x + ky*apos2.y + kz*apos2.z; float arg2 = kx*apos2.x + ky*apos2.y + kz*apos2.z;
float sinI = sin(arg1); float sinI = sinf(arg1);
float sinJ = sin(arg2); float sinJ = sinf(arg2);
float cosI = cos(arg1); float cosI = cosf(arg1);
float cosJ = cos(arg2); float cosJ = cosf(arg2);
float f = scale * ek * (-sinI*cosJ + cosI*sinJ) / k2; float f = scale * ek * (-sinI*cosJ + cosI*sinJ) / k2;
af.x -= kx*f; af.x -= kx*f;
......
platforms/cuda/src/kernels/kCalculateCDLJForces.h
View file @ 470c9b7f
...@@ -56,7 +56,7 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit) ...@@ -56,7 +56,7 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit)
#endif #endif
#ifdef USE_EWALD #ifdef USE_EWALD
const float TWO_OVER_SQRT_PI = 2.0f/sqrt(LOCAL_HACK_PI); const float TWO_OVER_SQRT_PI = 2.0f/sqrtf(LOCAL_HACK_PI);
#endif #endif
unsigned int lasty = 0xFFFFFFFF; unsigned int lasty = 0xFFFFFFFF;
...@@ -108,12 +108,12 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit) ...@@ -108,12 +108,12 @@ void METHOD_NAME(kCalculateCDLJ, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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;
sig2 = invR * sig; sig2 = invR * sig;
sig2 *= sig2; sig2 *= sig2;
...@@ -124,7 +124,7 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit) ...@@ -124,7 +124,7 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit)
CDLJ_energy = eps * (sig6 - 1.0f) * sig6; CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
#ifdef USE_EWALD #ifdef USE_EWALD
float r = sqrt(r2); float r = sqrtf(r2);
float alphaR = cSim.alphaEwald * r; float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR); float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI ); dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI );
...@@ -170,12 +170,12 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit) ...@@ -170,12 +170,12 @@ void METHOD_NAME(kCalculateCDLJ, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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;
sig2 = invR * sig; sig2 = invR * sig;
sig2 *= sig2; sig2 *= sig2;
...@@ -186,7 +186,7 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit) ...@@ -186,7 +186,7 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit)
CDLJ_energy = eps * (sig6 - 1.0f) * sig6; CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
#ifdef USE_EWALD #ifdef USE_EWALD
float r = sqrt(r2); float r = sqrtf(r2);
float alphaR = cSim.alphaEwald * r; float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR); float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI); dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
...@@ -287,12 +287,12 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit) ...@@ -287,12 +287,12 @@ void METHOD_NAME(kCalculateCDLJ, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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;
sig2 = invR * sig; sig2 = invR * sig;
sig2 *= sig2; sig2 *= sig2;
...@@ -303,7 +303,7 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit) ...@@ -303,7 +303,7 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit)
CDLJ_energy = eps * (sig6 - 1.0f) * sig6; CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
#ifdef USE_EWALD #ifdef USE_EWALD
float r = sqrt(r2); float r = sqrtf(r2);
float alphaR = cSim.alphaEwald * r; float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR); float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[tj].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI); dEdR += apos.w * psA[tj].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
...@@ -355,12 +355,12 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit) ...@@ -355,12 +355,12 @@ void METHOD_NAME(kCalculateCDLJ, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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;
sig2 = invR * sig; sig2 = invR * sig;
sig2 *= sig2; sig2 *= sig2;
...@@ -371,7 +371,7 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit) ...@@ -371,7 +371,7 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit)
CDLJ_energy = eps * (sig6 - 1.0f) * sig6; CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
#ifdef USE_EWALD #ifdef USE_EWALD
float r = sqrt(r2); float r = sqrtf(r2);
float alphaR = cSim.alphaEwald * r; float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR); float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI); dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
...@@ -458,12 +458,12 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit) ...@@ -458,12 +458,12 @@ void METHOD_NAME(kCalculateCDLJ, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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;
sig2 = invR * sig; sig2 = invR * sig;
sig2 *= sig2; sig2 *= sig2;
...@@ -474,7 +474,7 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit) ...@@ -474,7 +474,7 @@ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUnit)
CDLJ_energy = eps * (sig6 - 1.0f) * sig6; CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
#ifdef USE_EWALD #ifdef USE_EWALD
float r = sqrt(r2); float r = sqrtf(r2);
float alphaR = cSim.alphaEwald * r; float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR); float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[tj].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI); dEdR += apos.w * psA[tj].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
......
platforms/cuda/src/kernels/kCalculateCDLJObcGbsaForces1.h
View file @ 470c9b7f
...@@ -94,14 +94,14 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit ) ...@@ -94,14 +94,14 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r2 = dx * dx + dy * dy + dz * dz; float r2 = dx * dx + dy * dy + dz * dz;
// CDLJ part // CDLJ part
float invR = 1.0f / sqrt(r2); float invR = 1.0f / sqrtf(r2);
float sig = a.x + psA[j].sig; float sig = a.x + psA[j].sig;
float sig2 = invR * sig; float sig2 = invR * sig;
sig2 *= sig2; sig2 *= sig2;
...@@ -123,9 +123,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit ) ...@@ -123,9 +123,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit )
// ObcGbsaForce1 part // ObcGbsaForce1 part
float alpha2_ij = br * psA[j].br; float alpha2_ij = br * psA[j].br;
float D_ij = r2 / (4.0f * alpha2_ij); float D_ij = r2 / (4.0f * alpha2_ij);
float expTerm = exp(-D_ij); float expTerm = expf(-D_ij);
float denominator2 = r2 + alpha2_ij * expTerm; float denominator2 = r2 + alpha2_ij * expTerm;
float denominator = sqrt(denominator2); float denominator = sqrtf(denominator2);
float Gpol = (q2 * psA[j].q) / (denominator * denominator2); float Gpol = (q2 * psA[j].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij); float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
dEdR += Gpol * (1.0f - 0.25f * expTerm); dEdR += Gpol * (1.0f - 0.25f * expTerm);
...@@ -164,14 +164,14 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit ) ...@@ -164,14 +164,14 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r2 = dx * dx + dy * dy + dz * dz; float r2 = dx * dx + dy * dy + dz * dz;
// CDLJ part // CDLJ part
float invR = 1.0f / sqrt(r2); float invR = 1.0f / sqrtf(r2);
float sig = a.x + psA[j].sig; float sig = a.x + psA[j].sig;
float sig2 = invR * sig; float sig2 = invR * sig;
sig2 *= sig2; sig2 *= sig2;
...@@ -198,9 +198,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit ) ...@@ -198,9 +198,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit )
// ObcGbsaForce1 part // ObcGbsaForce1 part
float alpha2_ij = br * psA[j].br; float alpha2_ij = br * psA[j].br;
float D_ij = r2 / (4.0f * alpha2_ij); float D_ij = r2 / (4.0f * alpha2_ij);
float expTerm = exp(-D_ij); float expTerm = expf(-D_ij);
float denominator2 = r2 + alpha2_ij * expTerm; float denominator2 = r2 + alpha2_ij * expTerm;
float denominator = sqrt(denominator2); float denominator = sqrtf(denominator2);
float Gpol = (q2 * psA[j].q) / (denominator * denominator2); float Gpol = (q2 * psA[j].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij); float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
dEdR += Gpol * (1.0f - 0.25f * expTerm); dEdR += Gpol * (1.0f - 0.25f * expTerm);
...@@ -283,14 +283,14 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit ) ...@@ -283,14 +283,14 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r2 = dx * dx + dy * dy + dz * dz; float r2 = dx * dx + dy * dy + dz * dz;
// CDLJ part // CDLJ part
float invR = 1.0f / sqrt(r2); float invR = 1.0f / sqrtf(r2);
float sig = a.x + psA[tj].sig; float sig = a.x + psA[tj].sig;
float sig2 = invR * sig; float sig2 = invR * sig;
sig2 *= sig2; sig2 *= sig2;
...@@ -312,9 +312,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit ) ...@@ -312,9 +312,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit )
// ObcGbsaForce1 part // ObcGbsaForce1 part
float alpha2_ij = br * psA[tj].br; float alpha2_ij = br * psA[tj].br;
float D_ij = r2 / (4.0f * alpha2_ij); float D_ij = r2 / (4.0f * alpha2_ij);
float expTerm = exp(-D_ij); float expTerm = expf(-D_ij);
float denominator2 = r2 + alpha2_ij * expTerm; float denominator2 = r2 + alpha2_ij * expTerm;
float denominator = sqrt(denominator2); float denominator = sqrtf(denominator2);
float Gpol = (q2 * psA[tj].q) / (denominator * denominator2); float Gpol = (q2 * psA[tj].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij); float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
dEdR += Gpol * (1.0f - 0.25f * expTerm); dEdR += Gpol * (1.0f - 0.25f * expTerm);
...@@ -362,14 +362,14 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit ) ...@@ -362,14 +362,14 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r2 = dx * dx + dy * dy + dz * dz; float r2 = dx * dx + dy * dy + dz * dz;
// CDLJ part // CDLJ part
float invR = 1.0f / sqrt(r2); float invR = 1.0f / sqrtf(r2);
float sig = a.x + psA[j].sig; float sig = a.x + psA[j].sig;
float sig2 = invR * sig; float sig2 = invR * sig;
sig2 *= sig2; sig2 *= sig2;
...@@ -391,9 +391,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit ) ...@@ -391,9 +391,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit )
// ObcGbsaForce1 part // ObcGbsaForce1 part
float alpha2_ij = br * psA[j].br; float alpha2_ij = br * psA[j].br;
float D_ij = r2 / (4.0f * alpha2_ij); float D_ij = r2 / (4.0f * alpha2_ij);
float expTerm = exp(-D_ij); float expTerm = expf(-D_ij);
float denominator2 = r2 + alpha2_ij * expTerm; float denominator2 = r2 + alpha2_ij * expTerm;
float denominator = sqrt(denominator2); float denominator = sqrtf(denominator2);
float Gpol = (q2 * psA[j].q) / (denominator * denominator2); float Gpol = (q2 * psA[j].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij); float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
dEdR += Gpol * (1.0f - 0.25f * expTerm); dEdR += Gpol * (1.0f - 0.25f * expTerm);
...@@ -486,14 +486,14 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit ) ...@@ -486,14 +486,14 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r2 = dx * dx + dy * dy + dz * dz; float r2 = dx * dx + dy * dy + dz * dz;
// CDLJ part // CDLJ part
float invR = 1.0f / sqrt(r2); float invR = 1.0f / sqrtf(r2);
float sig = a.x + psA[tj].sig; float sig = a.x + psA[tj].sig;
float sig2 = invR * sig; float sig2 = invR * sig;
sig2 *= sig2; sig2 *= sig2;
...@@ -519,9 +519,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit ) ...@@ -519,9 +519,9 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit )
// ObcGbsaForce1 part // ObcGbsaForce1 part
float alpha2_ij = br * psA[tj].br; float alpha2_ij = br * psA[tj].br;
float D_ij = r2 / (4.0f * alpha2_ij); float D_ij = r2 / (4.0f * alpha2_ij);
float expTerm = exp(-D_ij); float expTerm = expf(-D_ij);
float denominator2 = r2 + alpha2_ij * expTerm; float denominator2 = r2 + alpha2_ij * expTerm;
float denominator = sqrt(denominator2); float denominator = sqrtf(denominator2);
float Gpol = (q2 * psA[tj].q) / (denominator * denominator2); float Gpol = (q2 * psA[tj].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij); float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
dEdR += Gpol * (1.0f - 0.25f * expTerm); dEdR += Gpol * (1.0f - 0.25f * expTerm);
......
platforms/cuda/src/kernels/kCalculateCMAPTorsionForces.cu
View file @ 470c9b7f
...@@ -48,7 +48,7 @@ using namespace std; ...@@ -48,7 +48,7 @@ using namespace std;
dp = DOT3(v1, v2); \ dp = DOT3(v1, v2); \
float norm1 = DOT3(v1, v1); \ float norm1 = DOT3(v1, v1); \
float norm2 = DOT3(v2, v2); \ float norm2 = DOT3(v2, v2); \
dp /= sqrt(norm1 * norm2); \ dp /= sqrtf(norm1 * norm2); \
dp = min(dp, 1.0f); \ dp = min(dp, 1.0f); \
dp = max(dp, -1.0f); \ dp = max(dp, -1.0f); \
} }
...@@ -60,12 +60,12 @@ using namespace std; ...@@ -60,12 +60,12 @@ using namespace std;
if (dp > 0.99f || dp < -0.99f) { \ if (dp > 0.99f || dp < -0.99f) { \
float3 cross = CROSS_PRODUCT(v1, v2); \ float3 cross = CROSS_PRODUCT(v1, v2); \
float scale = DOT3(v1, v1)*DOT3(v2, v2); \ float scale = DOT3(v1, v1)*DOT3(v2, v2); \
angle = asin(sqrt(DOT3(cross, cross)/scale)); \ angle = asinf(sqrtf(DOT3(cross, cross)/scale)); \
if (dp < 0.0f) \ if (dp < 0.0f) \
angle = LOCAL_HACK_PI-angle; \ angle = LOCAL_HACK_PI-angle; \
} \ } \
else { \ else { \
angle = acos(dp); \ angle = acosf(dp); \
} \ } \
} }
...@@ -166,7 +166,7 @@ void kCalculateCMAPTorsionForces_kernel(int numAtoms, int numTorsions, float4* f ...@@ -166,7 +166,7 @@ void kCalculateCMAPTorsionForces_kernel(int numAtoms, int numTorsions, float4* f
float normCross1 = DOT3(cp0a, cp0a); float normCross1 = DOT3(cp0a, cp0a);
float normSqrBC = DOT3(v1a, v1a); float normSqrBC = DOT3(v1a, v1a);
float normBC = sqrt(normSqrBC); float normBC = sqrtf(normSqrBC);
float normCross2 = DOT3(cp1a, cp1a); float normCross2 = DOT3(cp1a, cp1a);
float dp = 1.0f/normSqrBC; float dp = 1.0f/normSqrBC;
float4 ff = make_float4((-dEdA*normBC)/normCross1, DOT3(v0a, v1a)*dp, DOT3(v2a, v1a)*dp, (dEdA*normBC)/normCross2); float4 ff = make_float4((-dEdA*normBC)/normCross1, DOT3(v0a, v1a)*dp, DOT3(v2a, v1a)*dp, (dEdA*normBC)/normCross2);
...@@ -204,7 +204,7 @@ void kCalculateCMAPTorsionForces_kernel(int numAtoms, int numTorsions, float4* f ...@@ -204,7 +204,7 @@ void kCalculateCMAPTorsionForces_kernel(int numAtoms, int numTorsions, float4* f
normCross1 = DOT3(cp0b, cp0b); normCross1 = DOT3(cp0b, cp0b);
normSqrBC = DOT3(v1b, v1b); normSqrBC = DOT3(v1b, v1b);
normBC = sqrt(normSqrBC); normBC = sqrtf(normSqrBC);
normCross2 = DOT3(cp1b, cp1b); normCross2 = DOT3(cp1b, cp1b);
dp = 1.0f/normSqrBC; dp = 1.0f/normSqrBC;
ff = make_float4((-dEdB*normBC)/normCross1, DOT3(v0b, v1b)*dp, DOT3(v2b, v1b)*dp, (dEdB*normBC)/normCross2); ff = make_float4((-dEdB*normBC)/normCross1, DOT3(v0b, v1b)*dp, DOT3(v2b, v1b)*dp, (dEdB*normBC)/normCross2);
......
platforms/cuda/src/kernels/kCalculateCustomAngleForces.cu
View file @ 470c9b7f
...@@ -108,12 +108,12 @@ void kCalculateCustomAngleForces_kernel() ...@@ -108,12 +108,12 @@ void kCalculateCustomAngleForces_kernel()
float3 v1 = make_float3(a2.x-a3.x, a2.y-a3.y, a2.z-a3.z); float3 v1 = make_float3(a2.x-a3.x, a2.y-a3.y, a2.z-a3.z);
float3 cp = CROSS_PRODUCT(v0, v1); float3 cp = CROSS_PRODUCT(v0, v1);
float rp = DOT3(cp, cp); float rp = DOT3(cp, cp);
rp = max(sqrt(rp), 1.0e-06f); rp = max(sqrtf(rp), 1.0e-06f);
float r21 = DOT3(v0, v0); float r21 = DOT3(v0, v0);
float r23 = DOT3(v1, v1); float r23 = DOT3(v1, v1);
float dot = DOT3(v0, v1); float dot = DOT3(v0, v1);
float cosine = max(-1.0f, min(1.0f, dot/sqrt(r21*r23))); float cosine = max(-1.0f, min(1.0f, dot/sqrtf(r21*r23)));
VARIABLE(0) = acos(cosine); VARIABLE(0) = acosf(cosine);
VARIABLE(1) = params.x; VARIABLE(1) = params.x;
VARIABLE(2) = params.y; VARIABLE(2) = params.y;
VARIABLE(3) = params.z; VARIABLE(3) = params.z;
......
platforms/cuda/src/kernels/kCalculateCustomBondForces.cu
View file @ 470c9b7f
...@@ -102,7 +102,7 @@ void kCalculateCustomBondForces_kernel() ...@@ -102,7 +102,7 @@ void kCalculateCustomBondForces_kernel()
float dx = a1.x - a2.x; float dx = a1.x - a2.x;
float dy = a1.y - a2.y; float dy = a1.y - a2.y;
float dz = a1.z - a2.z; float dz = a1.z - a2.z;
float r = sqrt(dx*dx + dy*dy + dz*dz); float r = sqrtf(dx*dx + dy*dy + dz*dz);
float invR = 1.0f/r; float invR = 1.0f/r;
VARIABLE(0) = r; VARIABLE(0) = r;
VARIABLE(1) = params.x; VARIABLE(1) = params.x;
......
platforms/cuda/src/kernels/kCalculateCustomNonbondedForces.h
View file @ 470c9b7f
...@@ -97,11 +97,11 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i ...@@ -97,11 +97,11 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i
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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r = sqrt(dx*dx + dy*dy + dz*dz); float r = sqrtf(dx*dx + dy*dy + dz*dz);
float invR = 1.0f/r; float invR = 1.0f/r;
VARIABLE(8) = r; VARIABLE(8) = r;
float dEdR = -kEvaluateExpression_kernel(&forceExp, stack, variables)*invR; float dEdR = -kEvaluateExpression_kernel(&forceExp, stack, variables)*invR;
...@@ -188,11 +188,11 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i ...@@ -188,11 +188,11 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i
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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r = sqrt(dx*dx + dy*dy + dz*dz); float r = sqrtf(dx*dx + dy*dy + dz*dz);
float invR = 1.0f/r; float invR = 1.0f/r;
VARIABLE(8) = r; VARIABLE(8) = r;
float dEdR = -kEvaluateExpression_kernel(&forceExp, stack, variables)*invR; float dEdR = -kEvaluateExpression_kernel(&forceExp, stack, variables)*invR;
...@@ -243,11 +243,11 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i ...@@ -243,11 +243,11 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i
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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r = sqrt(dx*dx + dy*dy + dz*dz); float r = sqrtf(dx*dx + dy*dy + dz*dz);
float invR = 1.0f/r; float invR = 1.0f/r;
VARIABLE(8) = r; VARIABLE(8) = r;
float dEdR = -kEvaluateExpression_kernel(&forceExp, stack, variables)*invR; float dEdR = -kEvaluateExpression_kernel(&forceExp, stack, variables)*invR;
...@@ -334,11 +334,11 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i ...@@ -334,11 +334,11 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i
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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float r = sqrt(dx*dx + dy*dy + dz*dz); float r = sqrtf(dx*dx + dy*dy + dz*dz);
float invR = 1.0f/r; float invR = 1.0f/r;
VARIABLE(8) = r; VARIABLE(8) = r;
float dEdR = -kEvaluateExpression_kernel(&forceExp, stack, variables)*invR; float dEdR = -kEvaluateExpression_kernel(&forceExp, stack, variables)*invR;
......
platforms/cuda/src/kernels/kCalculateCustomTorsionForces.cu
View file @ 470c9b7f
...@@ -88,7 +88,7 @@ void SetCustomTorsionGlobalParams(const vector<float>& paramValues) ...@@ -88,7 +88,7 @@ void SetCustomTorsionGlobalParams(const vector<float>& paramValues)
dp = DOT3(v1, v2); \ dp = DOT3(v1, v2); \
float norm1 = DOT3(v1, v1); \ float norm1 = DOT3(v1, v1); \
float norm2 = DOT3(v2, v2); \ float norm2 = DOT3(v2, v2); \
dp /= sqrt(norm1 * norm2); \ dp /= sqrtf(norm1 * norm2); \
dp = min(dp, 1.0f); \ dp = min(dp, 1.0f); \
dp = max(dp, -1.0f); \ dp = max(dp, -1.0f); \
} }
...@@ -100,12 +100,12 @@ void SetCustomTorsionGlobalParams(const vector<float>& paramValues) ...@@ -100,12 +100,12 @@ void SetCustomTorsionGlobalParams(const vector<float>& paramValues)
if (dp > 0.99f || dp < -0.99f) { \ if (dp > 0.99f || dp < -0.99f) { \
float3 cross = CROSS_PRODUCT(v1, v2); \ float3 cross = CROSS_PRODUCT(v1, v2); \
float scale = DOT3(v1, v1)*DOT3(v2, v2); \ float scale = DOT3(v1, v1)*DOT3(v2, v2); \
angle = asin(sqrt(DOT3(cross, cross)/scale)); \ angle = asinf(sqrtf(DOT3(cross, cross)/scale)); \
if (dp < 0.0f) \ if (dp < 0.0f) \
angle = LOCAL_HACK_PI-angle; \ angle = LOCAL_HACK_PI-angle; \
} \ } \
else { \ else { \
angle = acos(dp); \ angle = acosf(dp); \
} \ } \
} }
...@@ -155,7 +155,7 @@ void kCalculateCustomTorsionForces_kernel() ...@@ -155,7 +155,7 @@ void kCalculateCustomTorsionForces_kernel()
VARIABLE(4) = params.w; VARIABLE(4) = params.w;
float dEdAngle = kEvaluateExpression_kernel(&forceExp, stack, variables); float dEdAngle = kEvaluateExpression_kernel(&forceExp, stack, variables);
totalEnergy += kEvaluateExpression_kernel(&energyExp, stack, variables); totalEnergy += kEvaluateExpression_kernel(&energyExp, stack, variables);
float normBC = sqrt(DOT3(v1, v1)); float normBC = sqrtf(DOT3(v1, v1));
float dp = 1.0f / DOT3(v1, v1); float dp = 1.0f / DOT3(v1, v1);
float4 ff = make_float4((-dEdAngle*normBC)/DOT3(cp0, cp0), DOT3(v0, v1)*dp, DOT3(v2, v1)*dp, (dEdAngle*normBC)/DOT3(cp1, cp1)); float4 ff = make_float4((-dEdAngle*normBC)/DOT3(cp0, cp0), DOT3(v0, v1)*dp, DOT3(v2, v1)*dp, (dEdAngle*normBC)/DOT3(cp1, cp1));
float3 internalF0 = make_float3(ff.x*cp0.x, ff.x*cp0.y, ff.x*cp0.z); float3 internalF0 = make_float3(ff.x*cp0.x, ff.x*cp0.y, ff.x*cp0.z);
......
platforms/cuda/src/kernels/kCalculateGBVIBornSum.cu
View file @ 470c9b7f
...@@ -195,7 +195,7 @@ __device__ void computeBornRadiiUsingQuinticSpline( float atomicRadius3, float b ...@@ -195,7 +195,7 @@ __device__ void computeBornRadiiUsingQuinticSpline( float atomicRadius3, float b
sum = atomicRadius3 - bornSum; sum = atomicRadius3 - bornSum;
*switchDeriviative = one; *switchDeriviative = one;
} }
*bornRadius = pow( sum, minusOneThird ); *bornRadius = powf( sum, minusOneThird );
} }
__global__ void kReduceGBVIBornSum_kernel() __global__ void kReduceGBVIBornSum_kernel()
...@@ -221,7 +221,7 @@ __global__ void kReduceGBVIBornSum_kernel() ...@@ -221,7 +221,7 @@ __global__ void kReduceGBVIBornSum_kernel()
Rinv = Rinv*Rinv*Rinv; Rinv = Rinv*Rinv*Rinv;
if( cSim.gbviBornRadiusScalingMethod == 0 ){ if( cSim.gbviBornRadiusScalingMethod == 0 ){
sum = Rinv - sum; sum = Rinv - sum;
cSim.pBornRadii[pos] = pow( sum, (-1.0f/3.0f) ); cSim.pBornRadii[pos] = powf( sum, (-1.0f/3.0f) );
cSim.pGBVISwitchDerivative[pos] = 1.0f; cSim.pGBVISwitchDerivative[pos] = 1.0f;
} else { } else {
float bornRadius; float bornRadius;
......
platforms/cuda/src/kernels/kCalculateGBVIBornSum.h
View file @ 470c9b7f
...@@ -98,9 +98,9 @@ void METHOD_NAME(kCalculateGBVI, BornSum_kernel)(unsigned int* workUnit) ...@@ -98,9 +98,9 @@ void METHOD_NAME(kCalculateGBVI, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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
...@@ -109,7 +109,7 @@ void METHOD_NAME(kCalculateGBVI, BornSum_kernel)(unsigned int* workUnit) ...@@ -109,7 +109,7 @@ void METHOD_NAME(kCalculateGBVI, 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
{ {
r = sqrt(r2); r = sqrtf(r2);
apos.w += getGBVI_Volume( r, ar.x, psA[j].sr ); apos.w += getGBVI_Volume( r, ar.x, psA[j].sr );
} }
} }
...@@ -161,9 +161,9 @@ void METHOD_NAME(kCalculateGBVI, BornSum_kernel)(unsigned int* workUnit) ...@@ -161,9 +161,9 @@ void METHOD_NAME(kCalculateGBVI, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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
...@@ -173,7 +173,7 @@ void METHOD_NAME(kCalculateGBVI, BornSum_kernel)(unsigned int* workUnit) ...@@ -173,7 +173,7 @@ void METHOD_NAME(kCalculateGBVI, BornSum_kernel)(unsigned int* workUnit)
#endif #endif
{ {
r = sqrt(r2); r = sqrtf(r2);
apos.w += getGBVI_Volume( r, ar.x, psA[tj].sr ); apos.w += getGBVI_Volume( r, ar.x, psA[tj].sr );
psA[tj].sum += getGBVI_Volume( r, psA[tj].r, ar.y ); psA[tj].sum += getGBVI_Volume( r, psA[tj].r, ar.y );
} }
...@@ -194,9 +194,9 @@ void METHOD_NAME(kCalculateGBVI, BornSum_kernel)(unsigned int* workUnit) ...@@ -194,9 +194,9 @@ void METHOD_NAME(kCalculateGBVI, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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
...@@ -205,7 +205,7 @@ void METHOD_NAME(kCalculateGBVI, BornSum_kernel)(unsigned int* workUnit) ...@@ -205,7 +205,7 @@ void METHOD_NAME(kCalculateGBVI, 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);
apos.w += getGBVI_Volume( r, ar.x, psA[j].sr ); apos.w += getGBVI_Volume( r, ar.x, psA[j].sr );
tempBuffer[threadIdx.x] = getGBVI_Volume( r, psA[j].r, ar.y ); tempBuffer[threadIdx.x] = getGBVI_Volume( r, psA[j].r, ar.y );
} }
......
platforms/cuda/src/kernels/kCalculateGBVIForces2.h
View file @ 470c9b7f
...@@ -94,12 +94,12 @@ METHOD_NAME(kCalculateGBVI, Forces2_kernel)(unsigned int* workUnit ) ...@@ -94,12 +94,12 @@ METHOD_NAME(kCalculateGBVI, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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 = getGBVI_dE2( r, ar.x, psA[j].sr, fb ); float dE = getGBVI_dE2( r, ar.x, psA[j].sr, fb );
...@@ -171,12 +171,12 @@ METHOD_NAME(kCalculateGBVI, Forces2_kernel)(unsigned int* workUnit ) ...@@ -171,12 +171,12 @@ METHOD_NAME(kCalculateGBVI, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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 = getGBVI_dE2( r, ar.x, psA[tj].sr, fb ); float dE = getGBVI_dE2( r, ar.x, psA[tj].sr, fb );
...@@ -236,12 +236,12 @@ METHOD_NAME(kCalculateGBVI, Forces2_kernel)(unsigned int* workUnit ) ...@@ -236,12 +236,12 @@ METHOD_NAME(kCalculateGBVI, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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 = getGBVI_dE2( r, ar.x, psA[j].sr, fb ); float dE = getGBVI_dE2( r, ar.x, psA[j].sr, fb );
......
platforms/cuda/src/kernels/kCalculateLocalForces.cu
View file @ 470c9b7f
...@@ -48,7 +48,7 @@ static __constant__ cudaGmxSimulation cSim; ...@@ -48,7 +48,7 @@ static __constant__ cudaGmxSimulation cSim;
dp = DOT3(v1, v2); \ dp = DOT3(v1, v2); \
float norm1 = DOT3(v1, v1); \ float norm1 = DOT3(v1, v1); \
float norm2 = DOT3(v2, v2); \ float norm2 = DOT3(v2, v2); \
dp /= sqrt(norm1 * norm2); \ dp /= sqrtf(norm1 * norm2); \
dp = min(dp, 1.0f); \ dp = min(dp, 1.0f); \
dp = max(dp, -1.0f); \ dp = max(dp, -1.0f); \
} }
...@@ -60,14 +60,14 @@ static __constant__ cudaGmxSimulation cSim; ...@@ -60,14 +60,14 @@ static __constant__ cudaGmxSimulation cSim;
#define GETPREFACTORSGIVENANGLECOSINE(cosine, param, dEdR) \ #define GETPREFACTORSGIVENANGLECOSINE(cosine, param, dEdR) \
{ \ { \
float angle = acos(cosine); \ float angle = acosf(cosine); \
float deltaIdeal = angle - (param.x * (LOCAL_HACK_PI / 180.0f)); \ float deltaIdeal = angle - (param.x * (LOCAL_HACK_PI / 180.0f)); \
dEdR = param.y * deltaIdeal; \ dEdR = param.y * deltaIdeal; \
} }
#define GETENERGYGIVENANGLECOSINE(cosine, param, dEdR) \ #define GETENERGYGIVENANGLECOSINE(cosine, param, dEdR) \
{ \ { \
float angle = acos(cosine); \ float angle = acosf(cosine); \
float deltaIdeal = angle - (param.x * (LOCAL_HACK_PI / 180.0f)); \ float deltaIdeal = angle - (param.x * (LOCAL_HACK_PI / 180.0f)); \
dEdR = param.y * deltaIdeal * deltaIdeal; \ dEdR = param.y * deltaIdeal * deltaIdeal; \
} }
...@@ -80,12 +80,12 @@ static __constant__ cudaGmxSimulation cSim; ...@@ -80,12 +80,12 @@ static __constant__ cudaGmxSimulation cSim;
float4 cross; \ float4 cross; \
CROSS_PRODUCT(v1, v2, cross); \ CROSS_PRODUCT(v1, v2, cross); \
float scale = DOT3(v1, v1)*DOT3(v2, v2); \ float scale = DOT3(v1, v1)*DOT3(v2, v2); \
angle = asin(sqrt(DOT3(cross, cross)/scale)); \ angle = asinf(sqrtf(DOT3(cross, cross)/scale)); \
if (dp < 0.0f) \ if (dp < 0.0f) \
angle = LOCAL_HACK_PI-angle; \ angle = LOCAL_HACK_PI-angle; \
} \ } \
else { \ else { \
angle = acos(dp); \ angle = acosf(dp); \
} \ } \
} }
...@@ -105,7 +105,7 @@ static __constant__ cudaGmxSimulation cSim; ...@@ -105,7 +105,7 @@ static __constant__ cudaGmxSimulation cSim;
GETANGLEBETWEENTWOVECTORS(cp0, cp1, angle); \ GETANGLEBETWEENTWOVECTORS(cp0, cp1, angle); \
float dp = DOT3(signVector, cp1); \ float dp = DOT3(signVector, cp1); \
angle = (dp >= 0) ? angle : -angle; \ angle = (dp >= 0) ? angle : -angle; \
cosine = cos(angle); \ cosine = cosf(angle); \
} }
void SetCalculateLocalForcesSim(gpuContext gpu) void SetCalculateLocalForcesSim(gpuContext gpu)
...@@ -150,7 +150,7 @@ void kCalculateLocalForces_kernel() ...@@ -150,7 +150,7 @@ void kCalculateLocalForces_kernel()
float dy = atomB.y - atomA.y; float dy = atomB.y - atomA.y;
float dz = atomB.z - atomA.z; float dz = atomB.z - atomA.z;
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 deltaIdeal = r - bond.x; float deltaIdeal = r - bond.x;
/* E */ energy += 0.5f * bond.y * deltaIdeal * deltaIdeal; /* E */ energy += 0.5f * bond.y * deltaIdeal * deltaIdeal;
float dEdR = bond.y * deltaIdeal; float dEdR = bond.y * deltaIdeal;
...@@ -194,11 +194,11 @@ void kCalculateLocalForces_kernel() ...@@ -194,11 +194,11 @@ void kCalculateLocalForces_kernel()
float3 cp; float3 cp;
CROSS_PRODUCT(A->v0, A->v1, cp); CROSS_PRODUCT(A->v0, A->v1, cp);
float rp = DOT3(cp, cp); //cx * cx + cy * cy + cz * cz; float rp = DOT3(cp, cp); //cx * cx + cy * cy + cz * cz;
rp = max(sqrt(rp), 1.0e-06f); rp = max(sqrtf(rp), 1.0e-06f);
float r21 = DOT3(A->v0, A->v0); // dx1 * dx1 + dy1 * dy1 + dz1 * dz1; float r21 = DOT3(A->v0, A->v0); // dx1 * dx1 + dy1 * dy1 + dz1 * dz1;
float r23 = DOT3(A->v1, A->v1); // dx2 * dx2 + dy2 * dy2 + dz2 * dz2; float r23 = DOT3(A->v1, A->v1); // dx2 * dx2 + dy2 * dy2 + dz2 * dz2;
float dot = DOT3(A->v0, A->v1); // dx1 * dx2 + dy1 * dy2 + dz1 * dz2; float dot = DOT3(A->v0, A->v1); // dx1 * dx2 + dy1 * dy2 + dz1 * dz2;
float cosine = max(-1.0f, min(1.0f, dot / sqrt(r21 * r23))); float cosine = max(-1.0f, min(1.0f, dot / sqrtf(r21 * r23)));
float angle_energy; float angle_energy;
/* E */ GETENERGYGIVENANGLECOSINE(cosine, bond_angle, angle_energy); /* E */ GETENERGYGIVENANGLECOSINE(cosine, bond_angle, angle_energy);
...@@ -270,7 +270,7 @@ void kCalculateLocalForces_kernel() ...@@ -270,7 +270,7 @@ void kCalculateLocalForces_kernel()
// ATTENTION: This section leads to a divergent deltaAngle values wrt // ATTENTION: This section leads to a divergent deltaAngle values wrt
// forces and energies. We separate the case dihedral.z = n = 0, which // forces and energies. We separate the case dihedral.z = n = 0, which
// is treated by the calculation of energies via a harmonic potential // is treated by the calculation of energies via a harmonic potential
/* E */ if (dihedral.z) energy += dihedral.x * (1.0f + cos(deltaAngle)); /* E */ if (dihedral.z) energy += dihedral.x * (1.0f + cosf(deltaAngle));
/* E */ else /* E */ else
{ {
float deltaAngle = dihedralAngle - dihedral.y; float deltaAngle = dihedralAngle - dihedral.y;
...@@ -279,10 +279,10 @@ void kCalculateLocalForces_kernel() ...@@ -279,10 +279,10 @@ void kCalculateLocalForces_kernel()
energy += dihedral.x * deltaAngle * deltaAngle; energy += dihedral.x * deltaAngle * deltaAngle;
} }
float sinDeltaAngle = sin(deltaAngle); float sinDeltaAngle = sinf(deltaAngle);
float dEdAngle = -dihedral.x * dihedral.z * sinDeltaAngle; float dEdAngle = -dihedral.x * dihedral.z * sinDeltaAngle;
float normCross1 = DOT3(cp0, cp0); float normCross1 = DOT3(cp0, cp0);
float normBC = sqrt(DOT3(A->v1, A->v1)); float normBC = sqrtf(DOT3(A->v1, A->v1));
float4 ff; float4 ff;
ff.x = (-dEdAngle * normBC) / normCross1; ff.x = (-dEdAngle * normBC) / normCross1;
float normCross2 = DOT3(cp1, cp1); float normCross2 = DOT3(cp1, cp1);
...@@ -400,11 +400,11 @@ void kCalculateLocalForces_kernel() ...@@ -400,11 +400,11 @@ void kCalculateLocalForces_kernel()
rb_energy += dihedral2.y * cosFactor * cosPhi; rb_energy += dihedral2.y * cosFactor * cosPhi;
/* E */ energy += rb_energy; /* E */ energy += rb_energy;
// printf("%4d - 5: %9.4f %9.4f\n", pos1, dEdAngle, cosFactor); // printf("%4d - 5: %9.4f %9.4f\n", pos1, dEdAngle, cosFactor);
dEdAngle *= sin(dihedralAngle); dEdAngle *= sinf(dihedralAngle);
// printf("%4d - f: %9.4f\n", pos1, dEdAngle); // printf("%4d - f: %9.4f\n", pos1, dEdAngle);
float normCross1 = DOT3(cp0, cp0); float normCross1 = DOT3(cp0, cp0);
float normBC = sqrt(DOT3(A->v1, A->v1)); float normBC = sqrtf(DOT3(A->v1, A->v1));
float4 ff; float4 ff;
ff.x = (-dEdAngle * normBC) / normCross1; ff.x = (-dEdAngle * normBC) / normCross1;
float normCross2 = DOT3(cp1, cp1); float normCross2 = DOT3(cp1, cp1);
...@@ -475,7 +475,7 @@ void kCalculateLocalForces_kernel() ...@@ -475,7 +475,7 @@ void kCalculateLocalForces_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);
float sig2 = inverseR * LJ14.y; float sig2 = inverseR * LJ14.y;
sig2 *= sig2; sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2; float sig6 = sig2 * sig2 * sig2;
......
platforms/cuda/src/kernels/kCalculateObcGbsaBornSum.h
View file @ 470c9b7f
...@@ -88,9 +88,9 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit) ...@@ -88,9 +88,9 @@ void METHOD_NAME(kCalculateObcGbsa, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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
...@@ -99,7 +99,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit) ...@@ -99,7 +99,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit)
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))
...@@ -108,7 +108,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit) ...@@ -108,7 +108,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit)
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);
apos.w += l_ij - apos.w += l_ij -
u_ij + u_ij +
0.25f * r * (u_ij2 - l_ij2) + 0.25f * r * (u_ij2 - l_ij2) +
...@@ -167,9 +167,9 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit) ...@@ -167,9 +167,9 @@ void METHOD_NAME(kCalculateObcGbsa, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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
...@@ -178,7 +178,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit) ...@@ -178,7 +178,7 @@ void METHOD_NAME(kCalculateObcGbsa, 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);
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)
...@@ -187,7 +187,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit) ...@@ -187,7 +187,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit)
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) +
...@@ -208,7 +208,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit) ...@@ -208,7 +208,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit)
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) +
...@@ -240,9 +240,9 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit) ...@@ -240,9 +240,9 @@ void METHOD_NAME(kCalculateObcGbsa, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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
...@@ -251,7 +251,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit) ...@@ -251,7 +251,7 @@ void METHOD_NAME(kCalculateObcGbsa, 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);
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)
...@@ -260,7 +260,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit) ...@@ -260,7 +260,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit)
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) +
...@@ -281,7 +281,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit) ...@@ -281,7 +281,7 @@ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit)
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) +
......
platforms/cuda/src/kernels/kCalculateObcGbsaForces2.h
View file @ 470c9b7f
...@@ -87,12 +87,12 @@ void METHOD_NAME(kCalculateObcGbsa, Forces2_kernel)(unsigned int* workUnit) ...@@ -87,12 +87,12 @@ void METHOD_NAME(kCalculateObcGbsa, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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
...@@ -104,7 +104,7 @@ void METHOD_NAME(kCalculateObcGbsa, Forces2_kernel)(unsigned int* workUnit) ...@@ -104,7 +104,7 @@ void METHOD_NAME(kCalculateObcGbsa, Forces2_kernel)(unsigned int* workUnit)
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;
...@@ -182,12 +182,12 @@ void METHOD_NAME(kCalculateObcGbsa, Forces2_kernel)(unsigned int* workUnit) ...@@ -182,12 +182,12 @@ void METHOD_NAME(kCalculateObcGbsa, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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;
...@@ -202,8 +202,8 @@ void METHOD_NAME(kCalculateObcGbsa, Forces2_kernel)(unsigned int* workUnit) ...@@ -202,8 +202,8 @@ void METHOD_NAME(kCalculateObcGbsa, Forces2_kernel)(unsigned int* workUnit)
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;
...@@ -280,12 +280,12 @@ void METHOD_NAME(kCalculateObcGbsa, Forces2_kernel)(unsigned int* workUnit) ...@@ -280,12 +280,12 @@ void METHOD_NAME(kCalculateObcGbsa, 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.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+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;
...@@ -300,8 +300,8 @@ void METHOD_NAME(kCalculateObcGbsa, Forces2_kernel)(unsigned int* workUnit) ...@@ -300,8 +300,8 @@ void METHOD_NAME(kCalculateObcGbsa, Forces2_kernel)(unsigned int* workUnit)
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;
......
platforms/cuda/src/kernels/kCalculatePME.cu
View file @ 470c9b7f
...@@ -121,9 +121,9 @@ void kUpdateBsplines_kernel() ...@@ -121,9 +121,9 @@ void kUpdateBsplines_kernel()
} }
float4 posq = cSim.pPosq[i]; float4 posq = cSim.pPosq[i];
posq.x -= floor(posq.x*cSim.invPeriodicBoxSizeX)*cSim.periodicBoxSizeX; posq.x -= floorf(posq.x*cSim.invPeriodicBoxSizeX)*cSim.periodicBoxSizeX;
posq.y -= floor(posq.y*cSim.invPeriodicBoxSizeY)*cSim.periodicBoxSizeY; posq.y -= floorf(posq.y*cSim.invPeriodicBoxSizeY)*cSim.periodicBoxSizeY;
posq.z -= floor(posq.z*cSim.invPeriodicBoxSizeZ)*cSim.periodicBoxSizeZ; posq.z -= floorf(posq.z*cSim.invPeriodicBoxSizeZ)*cSim.periodicBoxSizeZ;
float3 t = make_float3((posq.x*cSim.invPeriodicBoxSizeX)*cSim.pmeGridSize.x, float3 t = make_float3((posq.x*cSim.invPeriodicBoxSizeX)*cSim.pmeGridSize.x,
(posq.y*cSim.invPeriodicBoxSizeY)*cSim.pmeGridSize.y, (posq.y*cSim.invPeriodicBoxSizeY)*cSim.pmeGridSize.y,
(posq.z*cSim.invPeriodicBoxSizeZ)*cSim.pmeGridSize.z); (posq.z*cSim.invPeriodicBoxSizeZ)*cSim.pmeGridSize.z);
...@@ -210,7 +210,7 @@ void kFindAtomRangeForGrid_kernel() ...@@ -210,7 +210,7 @@ void kFindAtomRangeForGrid_kernel()
// some work in the charge spreading kernel. // some work in the charge spreading kernel.
float posz = cSim.pPosq[atomData.x].z; float posz = cSim.pPosq[atomData.x].z;
posz -= floor(posz*cSim.invPeriodicBoxSizeZ)*cSim.periodicBoxSizeZ; posz -= floorf(posz*cSim.invPeriodicBoxSizeZ)*cSim.periodicBoxSizeZ;
int z = ((int) ((posz*cSim.invPeriodicBoxSizeZ)*cSim.pmeGridSize.z)) % cSim.pmeGridSize.z; int z = ((int) ((posz*cSim.invPeriodicBoxSizeZ)*cSim.pmeGridSize.z)) % cSim.pmeGridSize.z;
cSim.pPmeAtomGridIndex[i].y = z; cSim.pPmeAtomGridIndex[i].y = z;
} }
...@@ -278,7 +278,7 @@ void kGridSpreadCharge_kernel() ...@@ -278,7 +278,7 @@ void kGridSpreadCharge_kernel()
} }
} }
} }
cSim.pPmeGrid[gridIndex] = make_cuComplex(result*sqrt(cSim.epsfac), 0.0f); cSim.pPmeGrid[gridIndex] = make_cuComplex(result*sqrtf(cSim.epsfac), 0.0f);
} }
} }
...@@ -337,9 +337,9 @@ void kGridInterpolateForce_kernel() ...@@ -337,9 +337,9 @@ void kGridInterpolateForce_kernel()
{ {
float3 force = make_float3(0.0f, 0.0f, 0.0f); float3 force = make_float3(0.0f, 0.0f, 0.0f);
float4 posq = cSim.pPosq[atom]; float4 posq = cSim.pPosq[atom];
posq.x -= floor(posq.x*cSim.invPeriodicBoxSizeX)*cSim.periodicBoxSizeX; posq.x -= floorf(posq.x*cSim.invPeriodicBoxSizeX)*cSim.periodicBoxSizeX;
posq.y -= floor(posq.y*cSim.invPeriodicBoxSizeY)*cSim.periodicBoxSizeY; posq.y -= floorf(posq.y*cSim.invPeriodicBoxSizeY)*cSim.periodicBoxSizeY;
posq.z -= floor(posq.z*cSim.invPeriodicBoxSizeZ)*cSim.periodicBoxSizeZ; posq.z -= floorf(posq.z*cSim.invPeriodicBoxSizeZ)*cSim.periodicBoxSizeZ;
float3 t = make_float3((posq.x*cSim.invPeriodicBoxSizeX)*cSim.pmeGridSize.x, float3 t = make_float3((posq.x*cSim.invPeriodicBoxSizeX)*cSim.pmeGridSize.x,
(posq.y*cSim.invPeriodicBoxSizeY)*cSim.pmeGridSize.y, (posq.y*cSim.invPeriodicBoxSizeY)*cSim.pmeGridSize.y,
(posq.z*cSim.invPeriodicBoxSizeZ)*cSim.pmeGridSize.z); (posq.z*cSim.invPeriodicBoxSizeZ)*cSim.pmeGridSize.z);
...@@ -373,7 +373,7 @@ void kGridInterpolateForce_kernel() ...@@ -373,7 +373,7 @@ void kGridInterpolateForce_kernel()
} }
} }
float4 totalForce = cSim.pForce4[atom]; float4 totalForce = cSim.pForce4[atom];
float q = posq.w*sqrt(cSim.epsfac); float q = posq.w*sqrtf(cSim.epsfac);
totalForce.x -= q*force.x*cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX; totalForce.x -= q*force.x*cSim.pmeGridSize.x*cSim.invPeriodicBoxSizeX;
totalForce.y -= q*force.y*cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY; totalForce.y -= q*force.y*cSim.pmeGridSize.y*cSim.invPeriodicBoxSizeY;
totalForce.z -= q*force.z*cSim.pmeGridSize.z*cSim.invPeriodicBoxSizeZ; totalForce.z -= q*force.z*cSim.pmeGridSize.z*cSim.invPeriodicBoxSizeZ;
......
platforms/cuda/src/kernels/kFindInteractingBlocks.h
View file @ 470c9b7f
...@@ -41,9 +41,9 @@ __global__ void METHOD_NAME(kFindBlockBounds, _kernel)() ...@@ -41,9 +41,9 @@ __global__ void METHOD_NAME(kFindBlockBounds, _kernel)()
{ {
float4 apos = cSim.pPosq[base]; float4 apos = cSim.pPosq[base];
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
apos.x -= floor(apos.x*cSim.invPeriodicBoxSizeX)*cSim.periodicBoxSizeX; apos.x -= floorf(apos.x*cSim.invPeriodicBoxSizeX)*cSim.periodicBoxSizeX;
apos.y -= floor(apos.y*cSim.invPeriodicBoxSizeY)*cSim.periodicBoxSizeY; apos.y -= floorf(apos.y*cSim.invPeriodicBoxSizeY)*cSim.periodicBoxSizeY;
apos.z -= floor(apos.z*cSim.invPeriodicBoxSizeZ)*cSim.periodicBoxSizeZ; apos.z -= floorf(apos.z*cSim.invPeriodicBoxSizeZ)*cSim.periodicBoxSizeZ;
float4 firstPoint = apos; float4 firstPoint = apos;
#endif #endif
float minx = apos.x; float minx = apos.x;
...@@ -56,9 +56,9 @@ __global__ void METHOD_NAME(kFindBlockBounds, _kernel)() ...@@ -56,9 +56,9 @@ __global__ void METHOD_NAME(kFindBlockBounds, _kernel)()
{ {
apos = cSim.pPosq[base+i]; apos = cSim.pPosq[base+i];
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
apos.x -= floor((apos.x-firstPoint.x)*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; apos.x -= floorf((apos.x-firstPoint.x)*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
apos.y -= floor((apos.y-firstPoint.y)*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; apos.y -= floorf((apos.y-firstPoint.y)*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
apos.z -= floor((apos.z-firstPoint.z)*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; apos.z -= floorf((apos.z-firstPoint.z)*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
minx = min(minx, apos.x); minx = min(minx, apos.x);
maxx = max(maxx, apos.x); maxx = max(maxx, apos.x);
...@@ -95,9 +95,9 @@ __global__ void METHOD_NAME(kFindBlocksWithInteractions, _kernel)() ...@@ -95,9 +95,9 @@ __global__ void METHOD_NAME(kFindBlocksWithInteractions, _kernel)()
float dy = centera.y-centerb.y; float dy = centera.y-centerb.y;
float dz = centera.z-centerb.z; float dz = centera.z-centerb.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
float4 boxSizea = cSim.pGridBoundingBox[x]; float4 boxSizea = cSim.pGridBoundingBox[x];
float4 boxSizeb = cSim.pGridBoundingBox[y]; float4 boxSizeb = cSim.pGridBoundingBox[y];
...@@ -156,9 +156,9 @@ __global__ void METHOD_NAME(kFindInteractionsWithinBlocks, _kernel)(unsigned int ...@@ -156,9 +156,9 @@ __global__ void METHOD_NAME(kFindInteractionsWithinBlocks, _kernel)(unsigned int
float dy = apos.y-center.y; float dy = apos.y-center.y;
float dz = apos.z-center.z; float dz = apos.z-center.z;
#ifdef USE_PERIODIC #ifdef USE_PERIODIC
dx -= floor(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif #endif
dx = max(0.0f, abs(dx)-boxSize.x); dx = max(0.0f, abs(dx)-boxSize.x);
dy = max(0.0f, abs(dy)-boxSize.y); dy = max(0.0f, abs(dy)-boxSize.y);
......
platforms/cuda/src/kernels/kForces.cu
View file @ 470c9b7f
...@@ -346,7 +346,7 @@ void kReduceObcGbsaBornForces_kernel() ...@@ -346,7 +346,7 @@ void kReduceObcGbsaBornForces_kernel()
totalForce += *pFt; totalForce += *pFt;
} }
float r = (obcData.x + cSim.dielectricOffset + cSim.probeRadius); float r = (obcData.x + cSim.dielectricOffset + cSim.probeRadius);
float ratio6 = pow((obcData.x + cSim.dielectricOffset) / bornRadius, 6.0f); float ratio6 = powf((obcData.x + cSim.dielectricOffset) / bornRadius, 6.0f);
float saTerm = cSim.surfaceAreaFactor * r * r * ratio6; float saTerm = cSim.surfaceAreaFactor * r * r * ratio6;
totalForce += saTerm / bornRadius; totalForce += saTerm / bornRadius;
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment