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Commit a161d091 authored by Mark Friedrichs's avatar Mark Friedrichs
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Fix for Born force calculation when cutoffs are applied

parent e772c611
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Showing with 53 additions and 72 deletions
platforms/cuda/src/kernels/kCalculateCDLJObcGbsaForces1.h
View file @ a161d091
......@@ -147,19 +147,16 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float denominator = sqrt(denominator2);
float Gpol = (q2 * psA[j].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
af.w += dGpol_dalpha2_ij * psA[j].br;
dEdR += Gpol * (1.0f - 0.25f * expTerm);
/* E */
CDLJObcGbsa_energy += (q2 * psA[j].q) / denominator;
CDLJObcGbsa_energy += (q2 * psA[j].q) / denominator;
#ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
CDLJObcGbsa_energy = 0.0f;
dEdR = 0.0f;
dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
#endif
/* E */
if (i < cSim.atoms)
{
energy += 0.5f*CDLJObcGbsa_energy;
......@@ -171,6 +168,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
af.x -= dx;
af.y -= dy;
af.z -= dz;
af.w += dGpol_dalpha2_ij * psA[j].br;
}
}
else // bExclusion
......@@ -198,15 +196,13 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float sig6 = sig2 * sig2 * sig2;
float eps = a.y * psA[j].eps;
float dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJObcGbsa_energy = eps * (sig6 - 1.0f) * sig6;
CDLJObcGbsa_energy = eps * (sig6 - 1.0f) * sig6;
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
/* E */
CDLJObcGbsa_energy += apos.w * psA[j].q * invR * erfcAlphaR;
bool needCorrection = !(excl & 0x1) && x+tgx != y+j && x+tgx < cSim.atoms && y+j < cSim.atoms;
if (needCorrection)
......@@ -218,14 +214,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
}
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJObcGbsa_energy += apos.w * psA[j].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
#else
float factorX = apos.w * psA[j].q * invR;
dEdR += factorX;
/* E */
CDLJObcGbsa_energy += factorX;
#endif
dEdR *= invR * invR;
......@@ -236,8 +230,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
#endif
{
dEdR = 0.0f;
/* E */
CDLJObcGbsa_energy = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
// ObcGbsaForce1 part
......@@ -248,23 +241,21 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float denominator = sqrt(denominator2);
float Gpol = (q2 * psA[j].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
af.w += dGpol_dalpha2_ij * psA[j].br;
dEdR += Gpol * (1.0f - 0.25f * expTerm);
/* E */
CDLJObcGbsa_energy += (q2 * psA[j].q) / denominator;
CDLJObcGbsa_energy += (q2 * psA[j].q) / denominator;
#if defined USE_PERIODIC
if (i >= cSim.atoms || x+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
CDLJObcGbsa_energy = 0.0f;
dEdR = 0.0f;
dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
#elif defined USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
CDLJObcGbsa_energy = 0.0f;
dEdR = 0.0f;
dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
#endif
/* E */
......@@ -279,6 +270,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
af.x -= dx;
af.y -= dy;
af.z -= dz;
af.w += dGpol_dalpha2_ij * psA[j].br;
excl >>= 1;
}
}
......@@ -352,7 +344,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float sig6 = sig2 * sig2 * sig2;
float eps = a.y * psA[tj].eps;
float dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJObcGbsa_energy = eps * (sig6 - 1.0f) * sig6;
#ifdef USE_CUTOFF
#ifdef USE_EWALD
......@@ -360,18 +351,15 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[tj].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
/* E */
CDLJObcGbsa_energy += apos.w * psA[tj].q * invR * erfcAlphaR;
#else
dEdR += apos.w * psA[tj].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJObcGbsa_energy += apos.w * psA[tj].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
#else
float factorX = apos.w * psA[tj].q * invR;
dEdR += factorX;
/* E */
CDLJObcGbsa_energy += factorX;
#endif
dEdR *= invR * invR;
......@@ -384,17 +372,14 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float denominator = sqrt(denominator2);
float Gpol = (q2 * psA[tj].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
af.w += dGpol_dalpha2_ij * psA[tj].br;
psA[tj].fb += dGpol_dalpha2_ij * br;
dEdR += Gpol * (1.0f - 0.25f * expTerm);
/* E */
CDLJObcGbsa_energy += (q2 * psA[tj].q) / denominator;
#ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
CDLJObcGbsa_energy = 0.0f;
dEdR = 0.0f;
dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
#endif
/* E */
......@@ -409,9 +394,11 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
af.x -= dx;
af.y -= dy;
af.z -= dz;
af.w += dGpol_dalpha2_ij * psA[tj].br;
psA[tj].fx += dx;
psA[tj].fy += dy;
psA[tj].fz += dz;
psA[tj].fb += dGpol_dalpha2_ij * br;
tj = (tj + 1) & (GRID - 1);
}
}
......@@ -442,7 +429,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float sig6 = sig2 * sig2 * sig2;
float eps = a.y * psA[j].eps;
float dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJObcGbsa_energy = eps * (sig6 - 1.0f) * sig6;
#ifdef USE_CUTOFF
#ifdef USE_EWALD
......@@ -453,14 +439,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
CDLJObcGbsa_energy += apos.w * psA[j].q * invR * erfcAlphaR;
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJObcGbsa_energy += apos.w * psA[j].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
#else
float factorX = apos.w * psA[j].q * invR;
dEdR += factorX;
/* E */
CDLJObcGbsa_energy += factorX;
#endif
dEdR *= invR * invR;
......@@ -473,36 +457,20 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float denominator = sqrt(denominator2);
float Gpol = (q2 * psA[j].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
af.w += dGpol_dalpha2_ij * psA[j].br;
dEdR += Gpol * (1.0f - 0.25f * expTerm);
/* E */
CDLJObcGbsa_energy += (q2 * psA[j].q) / denominator;
// Sum the Born forces.
tempBuffer[threadIdx.x] = dGpol_dalpha2_ij * br;
if (tgx % 2 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+1];
if (tgx % 4 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+2];
if (tgx % 8 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+4];
if (tgx % 16 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8];
if (tgx == 0)
psA[j].fb += tempBuffer[threadIdx.x] + tempBuffer[threadIdx.x+16];
#ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
CDLJObcGbsa_energy = 0.0f;
dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
#endif
/* E */
if (i < cSim.atoms)
{
energy += CDLJObcGbsa_energy;
energy += CDLJObcGbsa_energy;
}
// Add forces
dx *= dEdR;
......@@ -511,6 +479,8 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
af.x -= dx;
af.y -= dy;
af.z -= dz;
af.w += dGpol_dalpha2_ij * psA[j].br;
tempBuffer[threadIdx.x] = dx;
if (tgx % 2 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+1];
......@@ -522,6 +492,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8];
if (tgx == 0)
psA[j].fx += tempBuffer[threadIdx.x] + tempBuffer[threadIdx.x+16];
tempBuffer[threadIdx.x] = dy;
if (tgx % 2 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+1];
......@@ -533,6 +504,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8];
if (tgx == 0)
psA[j].fy += tempBuffer[threadIdx.x] + tempBuffer[threadIdx.x+16];
tempBuffer[threadIdx.x] = dz;
if (tgx % 2 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+1];
......@@ -544,6 +516,21 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8];
if (tgx == 0)
psA[j].fz += tempBuffer[threadIdx.x] + tempBuffer[threadIdx.x+16];
// Sum the Born forces.
tempBuffer[threadIdx.x] = dGpol_dalpha2_ij * br;
if (tgx % 2 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+1];
if (tgx % 4 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+2];
if (tgx % 8 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+4];
if (tgx % 16 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8];
if (tgx == 0)
psA[j].fb += tempBuffer[threadIdx.x] + tempBuffer[threadIdx.x+16];
}
}
}
......@@ -576,15 +563,13 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float sig6 = sig2 * sig2 * sig2;
float eps = a.y * psA[tj].eps;
float dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJObcGbsa_energy = eps * (sig6 - 1.0f) * sig6;
CDLJObcGbsa_energy = eps * (sig6 - 1.0f) * sig6;
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[tj].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
/* E */
CDLJObcGbsa_energy += apos.w * psA[tj].q * invR * erfcAlphaR;
bool needCorrection = !(excl & 0x1) && x+tgx != y+tj && x+tgx < cSim.atoms && y+tj < cSim.atoms;
if (needCorrection)
......@@ -596,13 +581,11 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
}
#else
dEdR += apos.w * psA[tj].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJObcGbsa_energy += apos.w * psA[tj].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
#else
float factorX = apos.w * psA[tj].q * invR;
dEdR += factorX;
/* E */
CDLJObcGbsa_energy += factorX;
#endif
dEdR *= invR * invR;
......@@ -613,8 +596,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
#endif
{
dEdR = 0.0f;
/* E */
CDLJObcGbsa_energy = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
// ObcGbsaForce1 part
......@@ -625,24 +607,21 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float denominator = sqrt(denominator2);
float Gpol = (q2 * psA[tj].q) / (denominator * denominator2);
float dGpol_dalpha2_ij = -0.5f * Gpol * expTerm * (1.0f + D_ij);
af.w += dGpol_dalpha2_ij * psA[tj].br;
psA[tj].fb += dGpol_dalpha2_ij * br;
dEdR += Gpol * (1.0f - 0.25f * expTerm);
/* E */
CDLJObcGbsa_energy += (q2 * psA[tj].q) / denominator;
CDLJObcGbsa_energy += (q2 * psA[tj].q) / denominator;
#if defined USE_PERIODIC
if (i >= cSim.atoms || y+tj >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
CDLJObcGbsa_energy = 0.0f;
dEdR = 0.0f;
dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
#elif defined USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
CDLJObcGbsa_energy = 0.0f;
dEdR = 0.0f;
dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f;
}
#endif
/* E */
......@@ -657,9 +636,11 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
af.x -= dx;
af.y -= dy;
af.z -= dz;
af.w += dGpol_dalpha2_ij * psA[tj].br;
psA[tj].fx += dx;
psA[tj].fy += dy;
psA[tj].fz += dz;
psA[tj].fb += dGpol_dalpha2_ij * br;
excl >>= 1;
tj = (tj + 1) & (GRID - 1);
}
......
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