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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) ...@@ -147,19 +147,16 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float denominator = sqrt(denominator2); float denominator = sqrt(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);
af.w += dGpol_dalpha2_ij * psA[j].br;
dEdR += Gpol * (1.0f - 0.25f * expTerm); 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 #ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr) if (r2 > cSim.nonbondedCutoffSqr)
{ {
dEdR = 0.0f; dEdR = 0.0f;
/* E */ dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f; CDLJObcGbsa_energy = 0.0f;
} }
#endif #endif
/* E */
if (i < cSim.atoms) if (i < cSim.atoms)
{ {
energy += 0.5f*CDLJObcGbsa_energy; energy += 0.5f*CDLJObcGbsa_energy;
...@@ -171,6 +168,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -171,6 +168,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
af.x -= dx; af.x -= dx;
af.y -= dy; af.y -= dy;
af.z -= dz; af.z -= dz;
af.w += dGpol_dalpha2_ij * psA[j].br;
} }
} }
else // bExclusion else // bExclusion
...@@ -198,7 +196,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -198,7 +196,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float sig6 = sig2 * sig2 * sig2; float sig6 = sig2 * sig2 * sig2;
float eps = a.y * psA[j].eps; float eps = a.y * psA[j].eps;
float dEdR = eps * (12.0f * sig6 - 6.0f) * sig6; 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_CUTOFF
#ifdef USE_EWALD #ifdef USE_EWALD
...@@ -206,7 +203,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -206,7 +203,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
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);
/* E */
CDLJObcGbsa_energy += apos.w * psA[j].q * invR * erfcAlphaR; 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; bool needCorrection = !(excl & 0x1) && x+tgx != y+j && x+tgx < cSim.atoms && y+j < cSim.atoms;
if (needCorrection) if (needCorrection)
...@@ -218,14 +214,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -218,14 +214,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
} }
#else #else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2); 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); CDLJObcGbsa_energy += apos.w * psA[j].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif #endif
#else #else
float factorX = apos.w * psA[j].q * invR; float factorX = apos.w * psA[j].q * invR;
dEdR += factorX; dEdR += factorX;
/* E */
CDLJObcGbsa_energy += factorX; CDLJObcGbsa_energy += factorX;
#endif #endif
dEdR *= invR * invR; dEdR *= invR * invR;
...@@ -236,7 +230,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -236,7 +230,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
#endif #endif
{ {
dEdR = 0.0f; dEdR = 0.0f;
/* E */
CDLJObcGbsa_energy = 0.0f; CDLJObcGbsa_energy = 0.0f;
} }
...@@ -248,22 +241,20 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -248,22 +241,20 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float denominator = sqrt(denominator2); float denominator = sqrt(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);
af.w += dGpol_dalpha2_ij * psA[j].br;
dEdR += Gpol * (1.0f - 0.25f * expTerm); 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 defined USE_PERIODIC
if (i >= cSim.atoms || x+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr) if (i >= cSim.atoms || x+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
{ {
dEdR = 0.0f; dEdR = 0.0f;
/* E */ dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f; CDLJObcGbsa_energy = 0.0f;
} }
#elif defined USE_CUTOFF #elif defined USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr) if (r2 > cSim.nonbondedCutoffSqr)
{ {
dEdR = 0.0f; dEdR = 0.0f;
/* E */ dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f; CDLJObcGbsa_energy = 0.0f;
} }
#endif #endif
...@@ -279,6 +270,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -279,6 +270,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
af.x -= dx; af.x -= dx;
af.y -= dy; af.y -= dy;
af.z -= dz; af.z -= dz;
af.w += dGpol_dalpha2_ij * psA[j].br;
excl >>= 1; excl >>= 1;
} }
} }
...@@ -352,7 +344,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -352,7 +344,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float sig6 = sig2 * sig2 * sig2; float sig6 = sig2 * sig2 * sig2;
float eps = a.y * psA[tj].eps; float eps = a.y * psA[tj].eps;
float dEdR = eps * (12.0f * sig6 - 6.0f) * sig6; 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_CUTOFF
#ifdef USE_EWALD #ifdef USE_EWALD
...@@ -360,18 +351,15 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -360,18 +351,15 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
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);
/* E */
CDLJObcGbsa_energy += apos.w * psA[tj].q * invR * erfcAlphaR; CDLJObcGbsa_energy += apos.w * psA[tj].q * invR * erfcAlphaR;
#else #else
dEdR += apos.w * psA[tj].q * (invR - 2.0f * cSim.reactionFieldK * r2); 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); CDLJObcGbsa_energy += apos.w * psA[tj].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif #endif
#else #else
float factorX = apos.w * psA[tj].q * invR; float factorX = apos.w * psA[tj].q * invR;
dEdR += factorX; dEdR += factorX;
/* E */
CDLJObcGbsa_energy += factorX; CDLJObcGbsa_energy += factorX;
#endif #endif
dEdR *= invR * invR; dEdR *= invR * invR;
...@@ -384,16 +372,13 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -384,16 +372,13 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float denominator = sqrt(denominator2); float denominator = sqrt(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);
af.w += dGpol_dalpha2_ij * psA[tj].br;
psA[tj].fb += dGpol_dalpha2_ij * br;
dEdR += Gpol * (1.0f - 0.25f * expTerm); dEdR += Gpol * (1.0f - 0.25f * expTerm);
/* E */
CDLJObcGbsa_energy += (q2 * psA[tj].q) / denominator; CDLJObcGbsa_energy += (q2 * psA[tj].q) / denominator;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr) if (r2 > cSim.nonbondedCutoffSqr)
{ {
dEdR = 0.0f; dEdR = 0.0f;
/* E */ dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f; CDLJObcGbsa_energy = 0.0f;
} }
#endif #endif
...@@ -409,9 +394,11 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -409,9 +394,11 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
af.x -= dx; af.x -= dx;
af.y -= dy; af.y -= dy;
af.z -= dz; af.z -= dz;
af.w += dGpol_dalpha2_ij * psA[tj].br;
psA[tj].fx += dx; psA[tj].fx += dx;
psA[tj].fy += dy; psA[tj].fy += dy;
psA[tj].fz += dz; psA[tj].fz += dz;
psA[tj].fb += dGpol_dalpha2_ij * br;
tj = (tj + 1) & (GRID - 1); tj = (tj + 1) & (GRID - 1);
} }
} }
...@@ -442,7 +429,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -442,7 +429,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float sig6 = sig2 * sig2 * sig2; float sig6 = sig2 * sig2 * sig2;
float eps = a.y * psA[j].eps; float eps = a.y * psA[j].eps;
float dEdR = eps * (12.0f * sig6 - 6.0f) * sig6; 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_CUTOFF
#ifdef USE_EWALD #ifdef USE_EWALD
...@@ -453,14 +439,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -453,14 +439,12 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
CDLJObcGbsa_energy += apos.w * psA[j].q * invR * erfcAlphaR; CDLJObcGbsa_energy += apos.w * psA[j].q * invR * erfcAlphaR;
#else #else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2); 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); CDLJObcGbsa_energy += apos.w * psA[j].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif #endif
#else #else
float factorX = apos.w * psA[j].q * invR; float factorX = apos.w * psA[j].q * invR;
dEdR += factorX; dEdR += factorX;
/* E */
CDLJObcGbsa_energy += factorX; CDLJObcGbsa_energy += factorX;
#endif #endif
dEdR *= invR * invR; dEdR *= invR * invR;
...@@ -473,33 +457,17 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -473,33 +457,17 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float denominator = sqrt(denominator2); float denominator = sqrt(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);
af.w += dGpol_dalpha2_ij * psA[j].br;
dEdR += Gpol * (1.0f - 0.25f * expTerm); dEdR += Gpol * (1.0f - 0.25f * expTerm);
/* E */
CDLJObcGbsa_energy += (q2 * psA[j].q) / denominator; 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 #ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr) if (r2 > cSim.nonbondedCutoffSqr)
{ {
dEdR = 0.0f; dEdR = 0.0f;
/* E */ dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f; CDLJObcGbsa_energy = 0.0f;
} }
#endif #endif
/* E */
if (i < cSim.atoms) if (i < cSim.atoms)
{ {
energy += CDLJObcGbsa_energy; energy += CDLJObcGbsa_energy;
...@@ -511,6 +479,8 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -511,6 +479,8 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
af.x -= dx; af.x -= dx;
af.y -= dy; af.y -= dy;
af.z -= dz; af.z -= dz;
af.w += dGpol_dalpha2_ij * psA[j].br;
tempBuffer[threadIdx.x] = dx; tempBuffer[threadIdx.x] = dx;
if (tgx % 2 == 0) if (tgx % 2 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+1]; tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+1];
...@@ -522,6 +492,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -522,6 +492,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8]; tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8];
if (tgx == 0) if (tgx == 0)
psA[j].fx += tempBuffer[threadIdx.x] + tempBuffer[threadIdx.x+16]; psA[j].fx += tempBuffer[threadIdx.x] + tempBuffer[threadIdx.x+16];
tempBuffer[threadIdx.x] = dy; tempBuffer[threadIdx.x] = dy;
if (tgx % 2 == 0) if (tgx % 2 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+1]; tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+1];
...@@ -533,6 +504,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -533,6 +504,7 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8]; tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8];
if (tgx == 0) if (tgx == 0)
psA[j].fy += tempBuffer[threadIdx.x] + tempBuffer[threadIdx.x+16]; psA[j].fy += tempBuffer[threadIdx.x] + tempBuffer[threadIdx.x+16];
tempBuffer[threadIdx.x] = dz; tempBuffer[threadIdx.x] = dz;
if (tgx % 2 == 0) if (tgx % 2 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+1]; tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+1];
...@@ -544,6 +516,21 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -544,6 +516,21 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8]; tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8];
if (tgx == 0) if (tgx == 0)
psA[j].fz += tempBuffer[threadIdx.x] + tempBuffer[threadIdx.x+16]; 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];
} }
} }
} }
...@@ -576,7 +563,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -576,7 +563,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float sig6 = sig2 * sig2 * sig2; float sig6 = sig2 * sig2 * sig2;
float eps = a.y * psA[tj].eps; float eps = a.y * psA[tj].eps;
float dEdR = eps * (12.0f * sig6 - 6.0f) * sig6; 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_CUTOFF
#ifdef USE_EWALD #ifdef USE_EWALD
...@@ -584,7 +570,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -584,7 +570,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
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);
/* E */
CDLJObcGbsa_energy += apos.w * psA[tj].q * invR * erfcAlphaR; 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; bool needCorrection = !(excl & 0x1) && x+tgx != y+tj && x+tgx < cSim.atoms && y+tj < cSim.atoms;
if (needCorrection) if (needCorrection)
...@@ -596,13 +581,11 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -596,13 +581,11 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
} }
#else #else
dEdR += apos.w * psA[tj].q * (invR - 2.0f * cSim.reactionFieldK * r2); 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); CDLJObcGbsa_energy += apos.w * psA[tj].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif #endif
#else #else
float factorX = apos.w * psA[tj].q * invR; float factorX = apos.w * psA[tj].q * invR;
dEdR += factorX; dEdR += factorX;
/* E */
CDLJObcGbsa_energy += factorX; CDLJObcGbsa_energy += factorX;
#endif #endif
dEdR *= invR * invR; dEdR *= invR * invR;
...@@ -613,7 +596,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -613,7 +596,6 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
#endif #endif
{ {
dEdR = 0.0f; dEdR = 0.0f;
/* E */
CDLJObcGbsa_energy = 0.0f; CDLJObcGbsa_energy = 0.0f;
} }
...@@ -625,23 +607,20 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -625,23 +607,20 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
float denominator = sqrt(denominator2); float denominator = sqrt(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);
af.w += dGpol_dalpha2_ij * psA[tj].br;
psA[tj].fb += dGpol_dalpha2_ij * br;
dEdR += Gpol * (1.0f - 0.25f * expTerm); 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 defined USE_PERIODIC
if (i >= cSim.atoms || y+tj >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr) if (i >= cSim.atoms || y+tj >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
{ {
dEdR = 0.0f; dEdR = 0.0f;
/* E */ dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f; CDLJObcGbsa_energy = 0.0f;
} }
#elif defined USE_CUTOFF #elif defined USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr) if (r2 > cSim.nonbondedCutoffSqr)
{ {
dEdR = 0.0f; dEdR = 0.0f;
/* E */ dGpol_dalpha2_ij = 0.0f;
CDLJObcGbsa_energy = 0.0f; CDLJObcGbsa_energy = 0.0f;
} }
#endif #endif
...@@ -657,9 +636,11 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit) ...@@ -657,9 +636,11 @@ void METHOD_NAME(kCalculateCDLJObcGbsa, Forces1_kernel)(unsigned int* workUnit)
af.x -= dx; af.x -= dx;
af.y -= dy; af.y -= dy;
af.z -= dz; af.z -= dz;
af.w += dGpol_dalpha2_ij * psA[tj].br;
psA[tj].fx += dx; psA[tj].fx += dx;
psA[tj].fy += dy; psA[tj].fy += dy;
psA[tj].fz += dz; psA[tj].fz += dz;
psA[tj].fb += dGpol_dalpha2_ij * br;
excl >>= 1; excl >>= 1;
tj = (tj + 1) & (GRID - 1); tj = (tj + 1) & (GRID - 1);
} }
......
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