Skip to content

GitLab

Commit f11d445b authored by Peter Eastman's avatar Peter Eastman
Browse files

Optimizations to KirkwoodEDiff kernel

parent 21ab511a
Show whitespace changes
Inline Side-by-side
Showing with 288 additions and 455 deletions
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwoodEDiff.cu
View file @ f11d445b
......@@ -89,56 +89,6 @@ __device__ void loadKirkwoodEDiffShared( struct KirkwoodEDiffParticle* sA, unsig
}
// load struct and arrays w/ shared data in sA
__device__ void loadKirkwoodEDiffData( struct KirkwoodEDiffParticle* sA,
float4* jCoord,
float* jDipole, float* jQuadrupole,
float* jInducedDipole, float* jInducedDipolePolar,
float* jInducedDipoleS, float* jInducedDipolePolarS )
{
// load coords, charge, ...
jCoord->x = sA->x;
jCoord->y = sA->y;
jCoord->z = sA->z;
jCoord->w = sA->q;
jDipole[0] = sA->labFrameDipole[0];
jDipole[1] = sA->labFrameDipole[1];
jDipole[2] = sA->labFrameDipole[2];
jQuadrupole[0] = sA->labFrameQuadrupole_XX;
jQuadrupole[1] = sA->labFrameQuadrupole_XY;
jQuadrupole[2] = sA->labFrameQuadrupole_XZ;
jQuadrupole[3] = sA->labFrameQuadrupole_XY;
jQuadrupole[4] = sA->labFrameQuadrupole_YY;
jQuadrupole[5] = sA->labFrameQuadrupole_YZ;
jQuadrupole[6] = sA->labFrameQuadrupole_XZ;
jQuadrupole[7] = sA->labFrameQuadrupole_YZ;
jQuadrupole[8] = sA->labFrameQuadrupole_ZZ;
jInducedDipole[0] = sA->inducedDipole[0];
jInducedDipole[1] = sA->inducedDipole[1];
jInducedDipole[2] = sA->inducedDipole[2];
jInducedDipolePolar[0] = sA->inducedDipoleP[0];
jInducedDipolePolar[1] = sA->inducedDipoleP[1];
jInducedDipolePolar[2] = sA->inducedDipoleP[2];
jInducedDipoleS[0] = sA->inducedDipoleS[0];
jInducedDipoleS[1] = sA->inducedDipoleS[1];
jInducedDipoleS[2] = sA->inducedDipoleS[2];
jInducedDipolePolarS[0] = sA->inducedDipolePS[0];
jInducedDipolePolarS[1] = sA->inducedDipolePS[1];
jInducedDipolePolarS[2] = sA->inducedDipolePS[2];
}
/*****************************************************************************
ediff1 correct vacuum to SCRF derivatives
......@@ -148,15 +98,7 @@ __device__ void loadKirkwoodEDiffData( struct KirkwoodEDiffParticle* sA,
******************************************************************************/
__device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI, float4 atomCoordinatesJ,
float dampingFactorI, float dampingFactorJ,
float tholeI, float tholeJ,
float* labFrameDipoleI, float* labFrameDipoleJ,
float* labFrameQuadrupoleI, float* labFrameQuadrupoleJ,
float* uindI, float* uindJ,
float* uinpI, float* uinpJ,
float* uindsI, float* uindsJ,
float* uinpsI, float* uinpsJ,
__device__ void calculateKirkwoodEDiffPairIxn_kernel( KirkwoodEDiffParticle& atomI, KirkwoodEDiffParticle& atomJ,
float pscale, float dscale,
float* outputEnergy, float* outputForce,
float* outputTorqueI, float* outputTorqueJ
......@@ -167,22 +109,18 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
//float f;
//float gfd;
float damp;
float scale3,scale5;
float scale7;
//float scale9;
float xr,yr,zr;
float psc3,psc5,psc7;
//float psc9;
float dsc3,dsc5,dsc7;
//float dsc9;
float scale3i,scale5i;
//float scale7i;
float r,r2,rr1,rr3;
float r,rr1,rr3;
float rr5,rr7,rr9;
float pdi,pgamma;
float ci,di[4],qi[10];
float ck,dk[4],qk[10];
float pgamma;
float fridmp[4],findmp[4];
float ftm2i[4];
float ttm2i[4],ttm3i[4];
......@@ -213,7 +151,7 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
float sc[11];
float sci[9],scip[9];
float gfi[7],gti[7];
float uscale;
const float uscale = 1.0f;
// float ftm1i(4,maxatm);
// float ttm1i(4,maxatm);
......@@ -223,53 +161,13 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
//f = cAmoebaSim.electric / cAmoebaSim.dwater;
pdi = dampingFactorI;
uscale = 1.0f;
// atom I
ci = atomCoordinatesI.w;
di[1] = labFrameDipoleI[0];
di[2] = labFrameDipoleI[1];
di[3] = labFrameDipoleI[2];
qi[1] = labFrameQuadrupoleI[0];
qi[2] = labFrameQuadrupoleI[1];
qi[3] = labFrameQuadrupoleI[2];
qi[4] = labFrameQuadrupoleI[3];
qi[5] = labFrameQuadrupoleI[4];
qi[6] = labFrameQuadrupoleI[5];
qi[7] = labFrameQuadrupoleI[6];
qi[8] = labFrameQuadrupoleI[7];
qi[9] = labFrameQuadrupoleI[8];
// atom J
ck = atomCoordinatesJ.w;
dk[1] = labFrameDipoleJ[0];
dk[2] = labFrameDipoleJ[1];
dk[3] = labFrameDipoleJ[2];
qk[1] = labFrameQuadrupoleJ[0];
qk[2] = labFrameQuadrupoleJ[1];
qk[3] = labFrameQuadrupoleJ[2];
qk[4] = labFrameQuadrupoleJ[3];
qk[5] = labFrameQuadrupoleJ[4];
qk[6] = labFrameQuadrupoleJ[5];
qk[7] = labFrameQuadrupoleJ[6];
qk[8] = labFrameQuadrupoleJ[7];
qk[9] = labFrameQuadrupoleJ[8];
// deltaR
xr = atomCoordinatesJ.x - atomCoordinatesI.x;
yr = atomCoordinatesJ.y - atomCoordinatesI.y;
zr = atomCoordinatesJ.z - atomCoordinatesI.z;
float xr = atomJ.x - atomI.x;
float yr = atomJ.y - atomI.y;
float zr = atomJ.z - atomI.z;
r2 = xr*xr + yr*yr + zr*zr;
float r2 = xr*xr + yr*yr + zr*zr;
if( r2 > cAmoebaSim.scalingDistanceCutoff ){
}
......@@ -299,9 +197,9 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
// apply Thole polarization damping to scale factors
damp = pdi * dampingFactorJ;
float damp = atomI.damp * atomJ.damp;
if( damp != 0.0f ){
pgamma = tholeJ > tholeI ? tholeI : tholeJ;
pgamma = atomJ.thole > atomI.thole ? atomI.thole : atomJ.thole;
float ratio = (r/damp);
damp = -pgamma * ratio*ratio*ratio;
if( damp > -50.0f){
......@@ -343,44 +241,44 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
// construct auxiliary vectors for permanent terms
#if 0
dixdk[1] = di[2]*dk[3] - di[3]*dk[2];
dixdk[2] = di[3]*dk[1] - di[1]*dk[3];
dixdk[3] = di[1]*dk[2] - di[2]*dk[1];
dixdk[1] = atomI.labFrameDipole[1]*atomJ.labFrameDipole[2] - atomI.labFrameDipole[2]*atomJ.labFrameDipole[1];
dixdk[2] = atomI.labFrameDipole[2]*atomJ.labFrameDipole[0] - atomI.labFrameDipole[0]*atomJ.labFrameDipole[2];
dixdk[3] = atomI.labFrameDipole[0]*atomJ.labFrameDipole[1] - atomI.labFrameDipole[1]*atomJ.labFrameDipole[0];
#endif
dixr[1] = di[2]*zr - di[3]*yr;
dixr[2] = di[3]*xr - di[1]*zr;
dixr[3] = di[1]*yr - di[2]*xr;
dixr[1] = atomI.labFrameDipole[1]*zr - atomI.labFrameDipole[2]*yr;
dixr[2] = atomI.labFrameDipole[2]*xr - atomI.labFrameDipole[0]*zr;
dixr[3] = atomI.labFrameDipole[0]*yr - atomI.labFrameDipole[1]*xr;
dkxr[1] = dk[2]*zr - dk[3]*yr;
dkxr[2] = dk[3]*xr - dk[1]*zr;
dkxr[3] = dk[1]*yr - dk[2]*xr;
dkxr[1] = atomJ.labFrameDipole[1]*zr - atomJ.labFrameDipole[2]*yr;
dkxr[2] = atomJ.labFrameDipole[2]*xr - atomJ.labFrameDipole[0]*zr;
dkxr[3] = atomJ.labFrameDipole[0]*yr - atomJ.labFrameDipole[1]*xr;
qir[1] = qi[1]*xr + qi[4]*yr + qi[7]*zr;
qir[2] = qi[2]*xr + qi[5]*yr + qi[8]*zr;
qir[3] = qi[3]*xr + qi[6]*yr + qi[9]*zr;
qir[1] = atomI.labFrameQuadrupole_XX*xr + atomI.labFrameQuadrupole_XY*yr + atomI.labFrameQuadrupole_XZ*zr;
qir[2] = atomI.labFrameQuadrupole_XY*xr + atomI.labFrameQuadrupole_YY*yr + atomI.labFrameQuadrupole_YZ*zr;
qir[3] = atomI.labFrameQuadrupole_XZ*xr + atomI.labFrameQuadrupole_YZ*yr + atomI.labFrameQuadrupole_ZZ*zr;
qkr[1] = qk[1]*xr + qk[4]*yr + qk[7]*zr;
qkr[2] = qk[2]*xr + qk[5]*yr + qk[8]*zr;
qkr[3] = qk[3]*xr + qk[6]*yr + qk[9]*zr;
qkr[1] = atomJ.labFrameQuadrupole_XX*xr + atomJ.labFrameQuadrupole_XY*yr + atomJ.labFrameQuadrupole_XZ*zr;
qkr[2] = atomJ.labFrameQuadrupole_XY*xr + atomJ.labFrameQuadrupole_YY*yr + atomJ.labFrameQuadrupole_YZ*zr;
qkr[3] = atomJ.labFrameQuadrupole_XZ*xr + atomJ.labFrameQuadrupole_YZ*yr + atomJ.labFrameQuadrupole_ZZ*zr;
#if 0
qiqkr[1] = qi[1]*qkr[1] + qi[4]*qkr[2] + qi[7]*qkr[3];
qiqkr[2] = qi[2]*qkr[1] + qi[5]*qkr[2] + qi[8]*qkr[3];
qiqkr[3] = qi[3]*qkr[1] + qi[6]*qkr[2] + qi[9]*qkr[3];
qiqkr[1] = atomI.labFrameQuadrupole_XX*qkr[1] + atomI.labFrameQuadrupole_XY*qkr[2] + atomI.labFrameQuadrupole_XZ*qkr[3];
qiqkr[2] = atomI.labFrameQuadrupole_XY*qkr[1] + atomI.labFrameQuadrupole_YY*qkr[2] + atomI.labFrameQuadrupole_YZ*qkr[3];
qiqkr[3] = atomI.labFrameQuadrupole_XZ*qkr[1] + atomI.labFrameQuadrupole_YZ*qkr[2] + atomI.labFrameQuadrupole_ZZ*qkr[3];
qkqir[1] = qk[1]*qir[1] + qk[4]*qir[2] + qk[7]*qir[3];
qkqir[2] = qk[2]*qir[1] + qk[5]*qir[2] + qk[8]*qir[3];
qkqir[3] = qk[3]*qir[1] + qk[6]*qir[2] + qk[9]*qir[3];
qkqir[1] = atomJ.labFrameQuadrupole_XX*qir[1] + atomJ.labFrameQuadrupole_XY*qir[2] + atomJ.labFrameQuadrupole_XZ*qir[3];
qkqir[2] = atomJ.labFrameQuadrupole_XY*qir[1] + atomJ.labFrameQuadrupole_YY*qir[2] + atomJ.labFrameQuadrupole_YZ*qir[3];
qkqir[3] = atomJ.labFrameQuadrupole_XZ*qir[1] + atomJ.labFrameQuadrupole_YZ*qir[2] + atomJ.labFrameQuadrupole_ZZ*qir[3];
qixqk[1] = qi[2]*qk[3] + qi[5]*qk[6] + qi[8]*qk[9] -
qi[3]*qk[2] - qi[6]*qk[5] - qi[9]*qk[8];
qixqk[1] = atomI.labFrameQuadrupole_XY*atomJ.labFrameQuadrupole_XZ + atomI.labFrameQuadrupole_YY*atomJ.labFrameQuadrupole_YZ + atomI.labFrameQuadrupole_YZ*atomJ.labFrameQuadrupole_ZZ -
atomI.labFrameQuadrupole_XZ*atomJ.labFrameQuadrupole_XY - atomI.labFrameQuadrupole_YZ*atomJ.labFrameQuadrupole_YY - atomI.labFrameQuadrupole_ZZ*atomJ.labFrameQuadrupole_YZ;
qixqk[2] = qi[3]*qk[1] + qi[6]*qk[4] + qi[9]*qk[7] -
qi[1]*qk[3] - qi[4]*qk[6] - qi[7]*qk[9];
qixqk[2] = atomI.labFrameQuadrupole_XZ*atomJ.labFrameQuadrupole_XX + atomI.labFrameQuadrupole_YZ*atomJ.labFrameQuadrupole_XY + atomI.labFrameQuadrupole_ZZ*atomJ.labFrameQuadrupole_XZ -
atomI.labFrameQuadrupole_XX*atomJ.labFrameQuadrupole_XZ - atomI.labFrameQuadrupole_XY*atomJ.labFrameQuadrupole_YZ - atomI.labFrameQuadrupole_XZ*atomJ.labFrameQuadrupole_ZZ;
qixqk[3] = qi[1]*qk[2] + qi[4]*qk[5] + qi[7]*qk[8] -
qi[2]*qk[1] - qi[5]*qk[4] - qi[8]*qk[7];
qixqk[3] = atomI.labFrameQuadrupole_XX*atomJ.labFrameQuadrupole_XY + atomI.labFrameQuadrupole_XY*atomJ.labFrameQuadrupole_YY + atomI.labFrameQuadrupole_XZ*atomJ.labFrameQuadrupole_YZ -
atomI.labFrameQuadrupole_XY*atomJ.labFrameQuadrupole_XX - atomI.labFrameQuadrupole_YY*atomJ.labFrameQuadrupole_XY - atomI.labFrameQuadrupole_YZ*atomJ.labFrameQuadrupole_XZ;
#endif
rxqir[1] = yr*qir[3] - zr*qir[2];
......@@ -404,21 +302,21 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
qkrxqir[2] = qkr[3]*qir[1] - qkr[1]*qir[3];
qkrxqir[3] = qkr[1]*qir[2] - qkr[2]*qir[1];
qidk[1] = qi[1]*dk[1] + qi[4]*dk[2] + qi[7]*dk[3];
qidk[2] = qi[2]*dk[1] + qi[5]*dk[2] + qi[8]*dk[3];
qidk[3] = qi[3]*dk[1] + qi[6]*dk[2] + qi[9]*dk[3];
qidk[1] = atomI.labFrameQuadrupole_XX*atomJ.labFrameDipole[0] + atomI.labFrameQuadrupole_XY*atomJ.labFrameDipole[1] + atomI.labFrameQuadrupole_XZ*atomJ.labFrameDipole[2];
qidk[2] = atomI.labFrameQuadrupole_XY*atomJ.labFrameDipole[0] + atomI.labFrameQuadrupole_YY*atomJ.labFrameDipole[1] + atomI.labFrameQuadrupole_YZ*atomJ.labFrameDipole[2];
qidk[3] = atomI.labFrameQuadrupole_XZ*atomJ.labFrameDipole[0] + atomI.labFrameQuadrupole_YZ*atomJ.labFrameDipole[1] + atomI.labFrameQuadrupole_ZZ*atomJ.labFrameDipole[2];
qkdi[1] = qk[1]*di[1] + qk[4]*di[2] + qk[7]*di[3];
qkdi[2] = qk[2]*di[1] + qk[5]*di[2] + qk[8]*di[3];
qkdi[3] = qk[3]*di[1] + qk[6]*di[2] + qk[9]*di[3];
qkdi[1] = atomJ.labFrameQuadrupole_XX*atomI.labFrameDipole[0] + atomJ.labFrameQuadrupole_XY*atomI.labFrameDipole[1] + atomJ.labFrameQuadrupole_XZ*atomI.labFrameDipole[2];
qkdi[2] = atomJ.labFrameQuadrupole_XY*atomI.labFrameDipole[0] + atomJ.labFrameQuadrupole_YY*atomI.labFrameDipole[1] + atomJ.labFrameQuadrupole_YZ*atomI.labFrameDipole[2];
qkdi[3] = atomJ.labFrameQuadrupole_XZ*atomI.labFrameDipole[0] + atomJ.labFrameQuadrupole_YZ*atomI.labFrameDipole[1] + atomJ.labFrameQuadrupole_ZZ*atomI.labFrameDipole[2];
dixqkr[1] = di[2]*qkr[3] - di[3]*qkr[2];
dixqkr[2] = di[3]*qkr[1] - di[1]*qkr[3];
dixqkr[3] = di[1]*qkr[2] - di[2]*qkr[1];
dixqkr[1] = atomI.labFrameDipole[1]*qkr[3] - atomI.labFrameDipole[2]*qkr[2];
dixqkr[2] = atomI.labFrameDipole[2]*qkr[1] - atomI.labFrameDipole[0]*qkr[3];
dixqkr[3] = atomI.labFrameDipole[0]*qkr[2] - atomI.labFrameDipole[1]*qkr[1];
dkxqir[1] = dk[2]*qir[3] - dk[3]*qir[2];
dkxqir[2] = dk[3]*qir[1] - dk[1]*qir[3];
dkxqir[3] = dk[1]*qir[2] - dk[2]*qir[1];
dkxqir[1] = atomJ.labFrameDipole[1]*qir[3] - atomJ.labFrameDipole[2]*qir[2];
dkxqir[2] = atomJ.labFrameDipole[2]*qir[1] - atomJ.labFrameDipole[0]*qir[3];
dkxqir[3] = atomJ.labFrameDipole[0]*qir[2] - atomJ.labFrameDipole[1]*qir[1];
rxqidk[1] = yr*qidk[3] - zr*qidk[2];
rxqidk[2] = zr*qidk[1] - xr*qidk[3];
......@@ -431,60 +329,60 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
// get intermediate variables for permanent energy terms
sc[3] = di[1]*xr + di[2]*yr + di[3]*zr;
sc[4] = dk[1]*xr + dk[2]*yr + dk[3]*zr;
sc[3] = atomI.labFrameDipole[0]*xr + atomI.labFrameDipole[1]*yr + atomI.labFrameDipole[2]*zr;
sc[4] = atomJ.labFrameDipole[0]*xr + atomJ.labFrameDipole[1]*yr + atomJ.labFrameDipole[2]*zr;
sc[5] = qir[1]*xr + qir[2]*yr + qir[3]*zr;
sc[6] = qkr[1]*xr + qkr[2]*yr + qkr[3]*zr;
// construct auxiliary vectors for induced terms
dixuk[1] = di[2]*uindsJ[2] - di[3]*uindsJ[1];
dixuk[2] = di[3]*uindsJ[0] - di[1]*uindsJ[2];
dixuk[3] = di[1]*uindsJ[1] - di[2]*uindsJ[0];
dixuk[1] = atomI.labFrameDipole[1]*atomJ.inducedDipoleS[2] - atomI.labFrameDipole[2]*atomJ.inducedDipoleS[1];
dixuk[2] = atomI.labFrameDipole[2]*atomJ.inducedDipoleS[0] - atomI.labFrameDipole[0]*atomJ.inducedDipoleS[2];
dixuk[3] = atomI.labFrameDipole[0]*atomJ.inducedDipoleS[1] - atomI.labFrameDipole[1]*atomJ.inducedDipoleS[0];
dkxui[1] = dk[2]*uindsI[2] - dk[3]*uindsI[1];
dkxui[2] = dk[3]*uindsI[0] - dk[1]*uindsI[2];
dkxui[3] = dk[1]*uindsI[1] - dk[2]*uindsI[0];
dkxui[1] = atomJ.labFrameDipole[1]*atomI.inducedDipoleS[2] - atomJ.labFrameDipole[2]*atomI.inducedDipoleS[1];
dkxui[2] = atomJ.labFrameDipole[2]*atomI.inducedDipoleS[0] - atomJ.labFrameDipole[0]*atomI.inducedDipoleS[2];
dkxui[3] = atomJ.labFrameDipole[0]*atomI.inducedDipoleS[1] - atomJ.labFrameDipole[1]*atomI.inducedDipoleS[0];
dixukp[1] = di[2]*uinpsJ[2] - di[3]*uinpsJ[1];
dixukp[2] = di[3]*uinpsJ[0] - di[1]*uinpsJ[2];
dixukp[3] = di[1]*uinpsJ[1] - di[2]*uinpsJ[0];
dixukp[1] = atomI.labFrameDipole[1]*atomJ.inducedDipolePS[2] - atomI.labFrameDipole[2]*atomJ.inducedDipolePS[1];
dixukp[2] = atomI.labFrameDipole[2]*atomJ.inducedDipolePS[0] - atomI.labFrameDipole[0]*atomJ.inducedDipolePS[2];
dixukp[3] = atomI.labFrameDipole[0]*atomJ.inducedDipolePS[1] - atomI.labFrameDipole[1]*atomJ.inducedDipolePS[0];
dkxuip[1] = dk[2]*uinpsI[2] - dk[3]*uinpsI[1];
dkxuip[2] = dk[3]*uinpsI[0] - dk[1]*uinpsI[2];
dkxuip[3] = dk[1]*uinpsI[1] - dk[2]*uinpsI[0];
dkxuip[1] = atomJ.labFrameDipole[1]*atomI.inducedDipolePS[2] - atomJ.labFrameDipole[2]*atomI.inducedDipolePS[1];
dkxuip[2] = atomJ.labFrameDipole[2]*atomI.inducedDipolePS[0] - atomJ.labFrameDipole[0]*atomI.inducedDipolePS[2];
dkxuip[3] = atomJ.labFrameDipole[0]*atomI.inducedDipolePS[1] - atomJ.labFrameDipole[1]*atomI.inducedDipolePS[0];
qiuk[1] = qi[1]*uindsJ[0] + qi[4]*uindsJ[1] + qi[7]*uindsJ[2];
qiuk[2] = qi[2]*uindsJ[0] + qi[5]*uindsJ[1] + qi[8]*uindsJ[2];
qiuk[3] = qi[3]*uindsJ[0] + qi[6]*uindsJ[1] + qi[9]*uindsJ[2];
qiuk[1] = atomI.labFrameQuadrupole_XX*atomJ.inducedDipoleS[0] + atomI.labFrameQuadrupole_XY*atomJ.inducedDipoleS[1] + atomI.labFrameQuadrupole_XZ*atomJ.inducedDipoleS[2];
qiuk[2] = atomI.labFrameQuadrupole_XY*atomJ.inducedDipoleS[0] + atomI.labFrameQuadrupole_YY*atomJ.inducedDipoleS[1] + atomI.labFrameQuadrupole_YZ*atomJ.inducedDipoleS[2];
qiuk[3] = atomI.labFrameQuadrupole_XZ*atomJ.inducedDipoleS[0] + atomI.labFrameQuadrupole_YZ*atomJ.inducedDipoleS[1] + atomI.labFrameQuadrupole_ZZ*atomJ.inducedDipoleS[2];
qkui[1] = qk[1]*uindsI[0] + qk[4]*uindsI[1] + qk[7]*uindsI[2];
qkui[2] = qk[2]*uindsI[0] + qk[5]*uindsI[1] + qk[8]*uindsI[2];
qkui[3] = qk[3]*uindsI[0] + qk[6]*uindsI[1] + qk[9]*uindsI[2];
qkui[1] = atomJ.labFrameQuadrupole_XX*atomI.inducedDipoleS[0] + atomJ.labFrameQuadrupole_XY*atomI.inducedDipoleS[1] + atomJ.labFrameQuadrupole_XZ*atomI.inducedDipoleS[2];
qkui[2] = atomJ.labFrameQuadrupole_XY*atomI.inducedDipoleS[0] + atomJ.labFrameQuadrupole_YY*atomI.inducedDipoleS[1] + atomJ.labFrameQuadrupole_YZ*atomI.inducedDipoleS[2];
qkui[3] = atomJ.labFrameQuadrupole_XZ*atomI.inducedDipoleS[0] + atomJ.labFrameQuadrupole_YZ*atomI.inducedDipoleS[1] + atomJ.labFrameQuadrupole_ZZ*atomI.inducedDipoleS[2];
qiukp[1] = qi[1]*uinpsJ[0] + qi[4]*uinpsJ[1] + qi[7]*uinpsJ[2];
qiukp[2] = qi[2]*uinpsJ[0] + qi[5]*uinpsJ[1] + qi[8]*uinpsJ[2];
qiukp[3] = qi[3]*uinpsJ[0] + qi[6]*uinpsJ[1] + qi[9]*uinpsJ[2];
qiukp[1] = atomI.labFrameQuadrupole_XX*atomJ.inducedDipolePS[0] + atomI.labFrameQuadrupole_XY*atomJ.inducedDipolePS[1] + atomI.labFrameQuadrupole_XZ*atomJ.inducedDipolePS[2];
qiukp[2] = atomI.labFrameQuadrupole_XY*atomJ.inducedDipolePS[0] + atomI.labFrameQuadrupole_YY*atomJ.inducedDipolePS[1] + atomI.labFrameQuadrupole_YZ*atomJ.inducedDipolePS[2];
qiukp[3] = atomI.labFrameQuadrupole_XZ*atomJ.inducedDipolePS[0] + atomI.labFrameQuadrupole_YZ*atomJ.inducedDipolePS[1] + atomI.labFrameQuadrupole_ZZ*atomJ.inducedDipolePS[2];
qkuip[1] = qk[1]*uinpsI[0] + qk[4]*uinpsI[1] + qk[7]*uinpsI[2];
qkuip[2] = qk[2]*uinpsI[0] + qk[5]*uinpsI[1] + qk[8]*uinpsI[2];
qkuip[3] = qk[3]*uinpsI[0] + qk[6]*uinpsI[1] + qk[9]*uinpsI[2];
qkuip[1] = atomJ.labFrameQuadrupole_XX*atomI.inducedDipolePS[0] + atomJ.labFrameQuadrupole_XY*atomI.inducedDipolePS[1] + atomJ.labFrameQuadrupole_XZ*atomI.inducedDipolePS[2];
qkuip[2] = atomJ.labFrameQuadrupole_XY*atomI.inducedDipolePS[0] + atomJ.labFrameQuadrupole_YY*atomI.inducedDipolePS[1] + atomJ.labFrameQuadrupole_YZ*atomI.inducedDipolePS[2];
qkuip[3] = atomJ.labFrameQuadrupole_XZ*atomI.inducedDipolePS[0] + atomJ.labFrameQuadrupole_YZ*atomI.inducedDipolePS[1] + atomJ.labFrameQuadrupole_ZZ*atomI.inducedDipolePS[2];
uixqkr[1] = uindsI[1]*qkr[3] - uindsI[2]*qkr[2];
uixqkr[2] = uindsI[2]*qkr[1] - uindsI[0]*qkr[3];
uixqkr[3] = uindsI[0]*qkr[2] - uindsI[1]*qkr[1];
uixqkr[1] = atomI.inducedDipoleS[1]*qkr[3] - atomI.inducedDipoleS[2]*qkr[2];
uixqkr[2] = atomI.inducedDipoleS[2]*qkr[1] - atomI.inducedDipoleS[0]*qkr[3];
uixqkr[3] = atomI.inducedDipoleS[0]*qkr[2] - atomI.inducedDipoleS[1]*qkr[1];
ukxqir[1] = uindsJ[1]*qir[3] - uindsJ[2]*qir[2];
ukxqir[2] = uindsJ[2]*qir[1] - uindsJ[0]*qir[3];
ukxqir[3] = uindsJ[0]*qir[2] - uindsJ[1]*qir[1];
ukxqir[1] = atomJ.inducedDipoleS[1]*qir[3] - atomJ.inducedDipoleS[2]*qir[2];
ukxqir[2] = atomJ.inducedDipoleS[2]*qir[1] - atomJ.inducedDipoleS[0]*qir[3];
ukxqir[3] = atomJ.inducedDipoleS[0]*qir[2] - atomJ.inducedDipoleS[1]*qir[1];
uixqkrp[1] = uinpsI[1]*qkr[3] - uinpsI[2]*qkr[2];
uixqkrp[2] = uinpsI[2]*qkr[1] - uinpsI[0]*qkr[3];
uixqkrp[3] = uinpsI[0]*qkr[2] - uinpsI[1]*qkr[1];
uixqkrp[1] = atomI.inducedDipolePS[1]*qkr[3] - atomI.inducedDipolePS[2]*qkr[2];
uixqkrp[2] = atomI.inducedDipolePS[2]*qkr[1] - atomI.inducedDipolePS[0]*qkr[3];
uixqkrp[3] = atomI.inducedDipolePS[0]*qkr[2] - atomI.inducedDipolePS[1]*qkr[1];
ukxqirp[1] = uinpsJ[1]*qir[3] - uinpsJ[2]*qir[2];
ukxqirp[2] = uinpsJ[2]*qir[1] - uinpsJ[0]*qir[3];
ukxqirp[3] = uinpsJ[0]*qir[2] - uinpsJ[1]*qir[1];
ukxqirp[1] = atomJ.inducedDipolePS[1]*qir[3] - atomJ.inducedDipolePS[2]*qir[2];
ukxqirp[2] = atomJ.inducedDipolePS[2]*qir[1] - atomJ.inducedDipolePS[0]*qir[3];
ukxqirp[3] = atomJ.inducedDipolePS[0]*qir[2] - atomJ.inducedDipolePS[1]*qir[1];
rxqiuk[1] = yr*qiuk[3] - zr*qiuk[2];
rxqiuk[2] = zr*qiuk[1] - xr*qiuk[3];
......@@ -504,41 +402,41 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
// get intermediate variables for induction energy terms
sci[1] = uindsI[0]*dk[1] + uindsI[1]*dk[2] +
uindsI[2]*dk[3] + di[1]*uindsJ[0] +
di[2]*uindsJ[1] + di[3]*uindsJ[2];
sci[1] = atomI.inducedDipoleS[0]*atomJ.labFrameDipole[0] + atomI.inducedDipoleS[1]*atomJ.labFrameDipole[1] +
atomI.inducedDipoleS[2]*atomJ.labFrameDipole[2] + atomI.labFrameDipole[0]*atomJ.inducedDipoleS[0] +
atomI.labFrameDipole[1]*atomJ.inducedDipoleS[1] + atomI.labFrameDipole[2]*atomJ.inducedDipoleS[2];
sci[2] = uindsI[0]*uindsJ[0] + uindsI[1]*uindsJ[1] + uindsI[2]*uindsJ[2];
sci[2] = atomI.inducedDipoleS[0]*atomJ.inducedDipoleS[0] + atomI.inducedDipoleS[1]*atomJ.inducedDipoleS[1] + atomI.inducedDipoleS[2]*atomJ.inducedDipoleS[2];
sci[3] = uindsI[0]*xr + uindsI[1]*yr + uindsI[2]*zr;
sci[4] = uindsJ[0]*xr + uindsJ[1]*yr + uindsJ[2]*zr;
sci[3] = atomI.inducedDipoleS[0]*xr + atomI.inducedDipoleS[1]*yr + atomI.inducedDipoleS[2]*zr;
sci[4] = atomJ.inducedDipoleS[0]*xr + atomJ.inducedDipoleS[1]*yr + atomJ.inducedDipoleS[2]*zr;
sci[7] = qir[1]*uindsJ[0] + qir[2]*uindsJ[1] + qir[3]*uindsJ[2];
sci[8] = qkr[1]*uindsI[0] + qkr[2]*uindsI[1] + qkr[3]*uindsI[2];
sci[7] = qir[1]*atomJ.inducedDipoleS[0] + qir[2]*atomJ.inducedDipoleS[1] + qir[3]*atomJ.inducedDipoleS[2];
sci[8] = qkr[1]*atomI.inducedDipoleS[0] + qkr[2]*atomI.inducedDipoleS[1] + qkr[3]*atomI.inducedDipoleS[2];
scip[1] = uinpsI[0]*dk[1] + uinpsI[1]*dk[2] +
uinpsI[2]*dk[3] + di[1]*uinpsJ[0] +
di[2]*uinpsJ[1] + di[3]*uinpsJ[2];
scip[1] = atomI.inducedDipolePS[0]*atomJ.labFrameDipole[0] + atomI.inducedDipolePS[1]*atomJ.labFrameDipole[1] +
atomI.inducedDipolePS[2]*atomJ.labFrameDipole[2] + atomI.labFrameDipole[0]*atomJ.inducedDipolePS[0] +
atomI.labFrameDipole[1]*atomJ.inducedDipolePS[1] + atomI.labFrameDipole[2]*atomJ.inducedDipolePS[2];
scip[2] = uindsI[0]*uinpsJ[0] + uindsI[1]*uinpsJ[1] +
uindsI[2]*uinpsJ[2] + uinpsI[0]*uindsJ[0] +
uinpsI[1]*uindsJ[1] + uinpsI[2]*uindsJ[2];
scip[2] = atomI.inducedDipoleS[0]*atomJ.inducedDipolePS[0] + atomI.inducedDipoleS[1]*atomJ.inducedDipolePS[1] +
atomI.inducedDipoleS[2]*atomJ.inducedDipolePS[2] + atomI.inducedDipolePS[0]*atomJ.inducedDipoleS[0] +
atomI.inducedDipolePS[1]*atomJ.inducedDipoleS[1] + atomI.inducedDipolePS[2]*atomJ.inducedDipoleS[2];
scip[3] = uinpsI[0]*xr + uinpsI[1]*yr + uinpsI[2]*zr;
scip[4] = uinpsJ[0]*xr + uinpsJ[1]*yr + uinpsJ[2]*zr;
scip[3] = atomI.inducedDipolePS[0]*xr + atomI.inducedDipolePS[1]*yr + atomI.inducedDipolePS[2]*zr;
scip[4] = atomJ.inducedDipolePS[0]*xr + atomJ.inducedDipolePS[1]*yr + atomJ.inducedDipolePS[2]*zr;
scip[7] = qir[1]*uinpsJ[0] + qir[2]*uinpsJ[1] + qir[3]*uinpsJ[2];
scip[8] = qkr[1]*uinpsI[0] + qkr[2]*uinpsI[1] + qkr[3]*uinpsI[2];
scip[7] = qir[1]*atomJ.inducedDipolePS[0] + qir[2]*atomJ.inducedDipolePS[1] + qir[3]*atomJ.inducedDipolePS[2];
scip[8] = qkr[1]*atomI.inducedDipolePS[0] + qkr[2]*atomI.inducedDipolePS[1] + qkr[3]*atomI.inducedDipolePS[2];
// calculate the gl functions for potential energy
gli[1] = ck*sci[3] - ci*sci[4];
gli[1] = atomJ.q*sci[3] - atomI.q*sci[4];
gli[2] = -sc[3]*sci[4] - sci[3]*sc[4];
gli[3] = sci[3]*sc[6] - sci[4]*sc[5];
gli[6] = sci[1];
gli[7] = 2.0f * (sci[7]-sci[8]);
glip[1] = ck*scip[3] - ci*scip[4];
glip[1] = atomJ.q*scip[3] - atomI.q*scip[4];
glip[2] = -sc[3]*scip[4] - scip[3]*sc[4];
glip[3] = scip[3]*sc[6] - scip[4]*sc[5];
glip[6] = scip[1];
......@@ -559,8 +457,8 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
(sci[3]*scip[4]+scip[3]*sci[4])*scale5i) +
0.5f*rr9*(gli[3]*psc7+glip[3]*dsc7);
gfi[2] = -rr3*ck + rr5*sc[4] - rr7*sc[6];
gfi[3] = rr3*ci + rr5*sc[3] + rr7*sc[5];
gfi[2] = -rr3*atomJ.q + rr5*sc[4] - rr7*sc[6];
gfi[3] = rr3*atomI.q + rr5*sc[3] + rr7*sc[5];
gfi[4] = 2.0f * rr5;
gfi[5] = rr7 * (sci[4]*psc7+scip[4]*dsc7);
gfi[6] = -rr7 * (sci[3]*psc7+scip[3]*dsc7);
......@@ -568,46 +466,46 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
// get the induced force;
ftm2i[1] = gfi[1]*xr + 0.5f*
(- rr3*ck*(uindsI[0]*psc3+uinpsI[0]*dsc3)
+ rr5*sc[4]*(uindsI[0]*psc5+uinpsI[0]*dsc5)
- rr7*sc[6]*(uindsI[0]*psc7+uinpsI[0]*dsc7))
+(rr3*ci*(uindsJ[0]*psc3+uinpsJ[0]*dsc3)
+ rr5*sc[3]*(uindsJ[0]*psc5+uinpsJ[0]*dsc5)
+ rr7*sc[5]*(uindsJ[0]*psc7+uinpsJ[0]*dsc7))*0.5f
+ rr5*scale5i*(sci[4]*uinpsI[0]+scip[4]*uindsI[0]
+ sci[3]*uinpsJ[0]+scip[3]*uindsJ[0])*0.5f
+ 0.5f*(sci[4]*psc5+scip[4]*dsc5)*rr5*di[1]
+ 0.5f*(sci[3]*psc5+scip[3]*dsc5)*rr5*dk[1]
(- rr3*atomJ.q*(atomI.inducedDipoleS[0]*psc3+atomI.inducedDipolePS[0]*dsc3)
+ rr5*sc[4]*(atomI.inducedDipoleS[0]*psc5+atomI.inducedDipolePS[0]*dsc5)
- rr7*sc[6]*(atomI.inducedDipoleS[0]*psc7+atomI.inducedDipolePS[0]*dsc7))
+(rr3*atomI.q*(atomJ.inducedDipoleS[0]*psc3+atomJ.inducedDipolePS[0]*dsc3)
+ rr5*sc[3]*(atomJ.inducedDipoleS[0]*psc5+atomJ.inducedDipolePS[0]*dsc5)
+ rr7*sc[5]*(atomJ.inducedDipoleS[0]*psc7+atomJ.inducedDipolePS[0]*dsc7))*0.5f
+ rr5*scale5i*(sci[4]*atomI.inducedDipolePS[0]+scip[4]*atomI.inducedDipoleS[0]
+ sci[3]*atomJ.inducedDipolePS[0]+scip[3]*atomJ.inducedDipoleS[0])*0.5f
+ 0.5f*(sci[4]*psc5+scip[4]*dsc5)*rr5*atomI.labFrameDipole[0]
+ 0.5f*(sci[3]*psc5+scip[3]*dsc5)*rr5*atomJ.labFrameDipole[0]
+ 0.5f*gfi[4]*((qkui[1]-qiuk[1])*psc5
+ (qkuip[1]-qiukp[1])*dsc5)
+ gfi[5]*qir[1] + gfi[6]*qkr[1];
ftm2i[2] = gfi[1]*yr + 0.5f*
(- rr3*ck*(uindsI[1]*psc3+uinpsI[1]*dsc3)
+ rr5*sc[4]*(uindsI[1]*psc5+uinpsI[1]*dsc5)
- rr7*sc[6]*(uindsI[1]*psc7+uinpsI[1]*dsc7))
+(rr3*ci*(uindsJ[1]*psc3+uinpsJ[1]*dsc3)
+ rr5*sc[3]*(uindsJ[1]*psc5+uinpsJ[1]*dsc5)
+ rr7*sc[5]*(uindsJ[1]*psc7+uinpsJ[1]*dsc7))*0.5f
+ rr5*scale5i*(sci[4]*uinpsI[1]+scip[4]*uindsI[1]
+ sci[3]*uinpsJ[1]+scip[3]*uindsJ[1])*0.5f
+ 0.5f*(sci[4]*psc5+scip[4]*dsc5)*rr5*di[2]
+ 0.5f*(sci[3]*psc5+scip[3]*dsc5)*rr5*dk[2]
(- rr3*atomJ.q*(atomI.inducedDipoleS[1]*psc3+atomI.inducedDipolePS[1]*dsc3)
+ rr5*sc[4]*(atomI.inducedDipoleS[1]*psc5+atomI.inducedDipolePS[1]*dsc5)
- rr7*sc[6]*(atomI.inducedDipoleS[1]*psc7+atomI.inducedDipolePS[1]*dsc7))
+(rr3*atomI.q*(atomJ.inducedDipoleS[1]*psc3+atomJ.inducedDipolePS[1]*dsc3)
+ rr5*sc[3]*(atomJ.inducedDipoleS[1]*psc5+atomJ.inducedDipolePS[1]*dsc5)
+ rr7*sc[5]*(atomJ.inducedDipoleS[1]*psc7+atomJ.inducedDipolePS[1]*dsc7))*0.5f
+ rr5*scale5i*(sci[4]*atomI.inducedDipolePS[1]+scip[4]*atomI.inducedDipoleS[1]
+ sci[3]*atomJ.inducedDipolePS[1]+scip[3]*atomJ.inducedDipoleS[1])*0.5f
+ 0.5f*(sci[4]*psc5+scip[4]*dsc5)*rr5*atomI.labFrameDipole[1]
+ 0.5f*(sci[3]*psc5+scip[3]*dsc5)*rr5*atomJ.labFrameDipole[1]
+ 0.5f*gfi[4]*((qkui[2]-qiuk[2])*psc5
+ (qkuip[2]-qiukp[2])*dsc5)
+ gfi[5]*qir[2] + gfi[6]*qkr[2];
ftm2i[3] = gfi[1]*zr + 0.5f*
(- rr3*ck*(uindsI[2]*psc3+uinpsI[2]*dsc3)
+ rr5*sc[4]*(uindsI[2]*psc5+uinpsI[2]*dsc5)
- rr7*sc[6]*(uindsI[2]*psc7+uinpsI[2]*dsc7))
+(rr3*ci*(uindsJ[2]*psc3+uinpsJ[2]*dsc3)
+ rr5*sc[3]*(uindsJ[2]*psc5+uinpsJ[2]*dsc5)
+ rr7*sc[5]*(uindsJ[2]*psc7+uinpsJ[2]*dsc7))*0.5f
+ rr5*scale5i*(sci[4]*uinpsI[2]+scip[4]*uindsI[2]
+ sci[3]*uinpsJ[2]+scip[3]*uindsJ[2])*0.5f
+ 0.5f*(sci[4]*psc5+scip[4]*dsc5)*rr5*di[3]
+ 0.5f*(sci[3]*psc5+scip[3]*dsc5)*rr5*dk[3]
(- rr3*atomJ.q*(atomI.inducedDipoleS[2]*psc3+atomI.inducedDipolePS[2]*dsc3)
+ rr5*sc[4]*(atomI.inducedDipoleS[2]*psc5+atomI.inducedDipolePS[2]*dsc5)
- rr7*sc[6]*(atomI.inducedDipoleS[2]*psc7+atomI.inducedDipolePS[2]*dsc7))
+(rr3*atomI.q*(atomJ.inducedDipoleS[2]*psc3+atomJ.inducedDipolePS[2]*dsc3)
+ rr5*sc[3]*(atomJ.inducedDipoleS[2]*psc5+atomJ.inducedDipolePS[2]*dsc5)
+ rr7*sc[5]*(atomJ.inducedDipoleS[2]*psc7+atomJ.inducedDipolePS[2]*dsc7))*0.5f
+ rr5*scale5i*(sci[4]*atomI.inducedDipolePS[2]+scip[4]*atomI.inducedDipoleS[2]
+ sci[3]*atomJ.inducedDipolePS[2]+scip[3]*atomJ.inducedDipoleS[2])*0.5f
+ 0.5f*(sci[4]*psc5+scip[4]*dsc5)*rr5*atomI.labFrameDipole[2]
+ 0.5f*(sci[3]*psc5+scip[3]*dsc5)*rr5*atomJ.labFrameDipole[2]
+ 0.5f*gfi[4]*((qkui[3]-qiuk[3])*psc5
+ (qkuip[3]-qiukp[3])*dsc5)
+ gfi[5]*qir[3] + gfi[6]*qkr[3];
......@@ -656,14 +554,14 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
gfd = 0.5f * (rr5*scip[2]*scale3i;
& - rr7*(scip[3]*sci[4]+sci[3]*scip[4])*scale5i);
fdir[1] = gfd*xr + 0.5f*rr5*scale5i;
& * (sci[4]*uinpsI[0]+scip[4]*uindsI[0];
& +sci[3]*uinpsJ[0]+scip[3]*uindsJ[0]);
& * (sci[4]*atomI.inducedDipolePS[0]+scip[4]*atomI.inducedDipoleS[0];
& +sci[3]*atomJ.inducedDipolePS[0]+scip[3]*atomJ.inducedDipoleS[0]);
fdir[2] = gfd*yr + 0.5f*rr5*scale5i;
& * (sci[4]*uinpsI[1]+scip[4]*uindsI[1];
& +sci[3]*uinpsJ[1]+scip[3]*uindsJ[1]);
& * (sci[4]*atomI.inducedDipolePS[1]+scip[4]*atomI.inducedDipoleS[1];
& +sci[3]*atomJ.inducedDipolePS[1]+scip[3]*atomJ.inducedDipoleS[1]);
fdir[3] = gfd*zr + 0.5f*rr5*scale5i;
& * (sci[4]*uinpsI[2]+scip[4]*uindsI[2];
& +sci[3]*uinpsJ[2]+scip[3]*uindsJ[2]);
& * (sci[4]*atomI.inducedDipolePS[2]+scip[4]*atomI.inducedDipoleS[2];
& +sci[3]*atomJ.inducedDipolePS[2]+scip[3]*atomJ.inducedDipoleS[2]);
ftm2i[1] = ftm2i[1] - fdir[1] + findmp[1];
ftm2i[2] = ftm2i[2] - fdir[2] + findmp[2];
ftm2i[3] = ftm2i[3] - fdir[3] + findmp[3];
......@@ -739,53 +637,53 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
// construct auxiliary vectors for induced terms
dixuk[1] = di[2]*uindJ[2] - di[3]*uindJ[1];
dixuk[2] = di[3]*uindJ[0] - di[1]*uindJ[2];
dixuk[3] = di[1]*uindJ[1] - di[2]*uindJ[0];
dixuk[1] = atomI.labFrameDipole[1]*atomJ.inducedDipole[2] - atomI.labFrameDipole[2]*atomJ.inducedDipole[1];
dixuk[2] = atomI.labFrameDipole[2]*atomJ.inducedDipole[0] - atomI.labFrameDipole[0]*atomJ.inducedDipole[2];
dixuk[3] = atomI.labFrameDipole[0]*atomJ.inducedDipole[1] - atomI.labFrameDipole[1]*atomJ.inducedDipole[0];
dkxui[1] = dk[2]*uindI[2] - dk[3]*uindI[1];
dkxui[2] = dk[3]*uindI[0] - dk[1]*uindI[2];
dkxui[3] = dk[1]*uindI[1] - dk[2]*uindI[0];
dkxui[1] = atomJ.labFrameDipole[1]*atomI.inducedDipole[2] - atomJ.labFrameDipole[2]*atomI.inducedDipole[1];
dkxui[2] = atomJ.labFrameDipole[2]*atomI.inducedDipole[0] - atomJ.labFrameDipole[0]*atomI.inducedDipole[2];
dkxui[3] = atomJ.labFrameDipole[0]*atomI.inducedDipole[1] - atomJ.labFrameDipole[1]*atomI.inducedDipole[0];
dixukp[1] = di[2]*uinpJ[2] - di[3]*uinpJ[1];
dixukp[2] = di[3]*uinpJ[0] - di[1]*uinpJ[2];
dixukp[3] = di[1]*uinpJ[1] - di[2]*uinpJ[0];
dixukp[1] = atomI.labFrameDipole[1]*atomJ.inducedDipoleP[2] - atomI.labFrameDipole[2]*atomJ.inducedDipoleP[1];
dixukp[2] = atomI.labFrameDipole[2]*atomJ.inducedDipoleP[0] - atomI.labFrameDipole[0]*atomJ.inducedDipoleP[2];
dixukp[3] = atomI.labFrameDipole[0]*atomJ.inducedDipoleP[1] - atomI.labFrameDipole[1]*atomJ.inducedDipoleP[0];
dkxuip[1] = dk[2]*uinpI[2] - dk[3]*uinpI[1];
dkxuip[2] = dk[3]*uinpI[0] - dk[1]*uinpI[2];
dkxuip[3] = dk[1]*uinpI[1] - dk[2]*uinpI[0];
dkxuip[1] = atomJ.labFrameDipole[1]*atomI.inducedDipoleP[2] - atomJ.labFrameDipole[2]*atomI.inducedDipoleP[1];
dkxuip[2] = atomJ.labFrameDipole[2]*atomI.inducedDipoleP[0] - atomJ.labFrameDipole[0]*atomI.inducedDipoleP[2];
dkxuip[3] = atomJ.labFrameDipole[0]*atomI.inducedDipoleP[1] - atomJ.labFrameDipole[1]*atomI.inducedDipoleP[0];
qiuk[1] = qi[1]*uindJ[0] + qi[4]*uindJ[1] + qi[7]*uindJ[2];
qiuk[2] = qi[2]*uindJ[0] + qi[5]*uindJ[1] + qi[8]*uindJ[2];
qiuk[3] = qi[3]*uindJ[0] + qi[6]*uindJ[1] + qi[9]*uindJ[2];
qiuk[1] = atomI.labFrameQuadrupole_XX*atomJ.inducedDipole[0] + atomI.labFrameQuadrupole_XY*atomJ.inducedDipole[1] + atomI.labFrameQuadrupole_XZ*atomJ.inducedDipole[2];
qiuk[2] = atomI.labFrameQuadrupole_XY*atomJ.inducedDipole[0] + atomI.labFrameQuadrupole_YY*atomJ.inducedDipole[1] + atomI.labFrameQuadrupole_YZ*atomJ.inducedDipole[2];
qiuk[3] = atomI.labFrameQuadrupole_XZ*atomJ.inducedDipole[0] + atomI.labFrameQuadrupole_YZ*atomJ.inducedDipole[1] + atomI.labFrameQuadrupole_ZZ*atomJ.inducedDipole[2];
qkui[1] = qk[1]*uindI[0] + qk[4]*uindI[1] + qk[7]*uindI[2];
qkui[2] = qk[2]*uindI[0] + qk[5]*uindI[1] + qk[8]*uindI[2];
qkui[3] = qk[3]*uindI[0] + qk[6]*uindI[1] + qk[9]*uindI[2];
qkui[1] = atomJ.labFrameQuadrupole_XX*atomI.inducedDipole[0] + atomJ.labFrameQuadrupole_XY*atomI.inducedDipole[1] + atomJ.labFrameQuadrupole_XZ*atomI.inducedDipole[2];
qkui[2] = atomJ.labFrameQuadrupole_XY*atomI.inducedDipole[0] + atomJ.labFrameQuadrupole_YY*atomI.inducedDipole[1] + atomJ.labFrameQuadrupole_YZ*atomI.inducedDipole[2];
qkui[3] = atomJ.labFrameQuadrupole_XZ*atomI.inducedDipole[0] + atomJ.labFrameQuadrupole_YZ*atomI.inducedDipole[1] + atomJ.labFrameQuadrupole_ZZ*atomI.inducedDipole[2];
qiukp[1] = qi[1]*uinpJ[0] + qi[4]*uinpJ[1] + qi[7]*uinpJ[2];
qiukp[2] = qi[2]*uinpJ[0] + qi[5]*uinpJ[1] + qi[8]*uinpJ[2];
qiukp[3] = qi[3]*uinpJ[0] + qi[6]*uinpJ[1] + qi[9]*uinpJ[2];
qiukp[1] = atomI.labFrameQuadrupole_XX*atomJ.inducedDipoleP[0] + atomI.labFrameQuadrupole_XY*atomJ.inducedDipoleP[1] + atomI.labFrameQuadrupole_XZ*atomJ.inducedDipoleP[2];
qiukp[2] = atomI.labFrameQuadrupole_XY*atomJ.inducedDipoleP[0] + atomI.labFrameQuadrupole_YY*atomJ.inducedDipoleP[1] + atomI.labFrameQuadrupole_YZ*atomJ.inducedDipoleP[2];
qiukp[3] = atomI.labFrameQuadrupole_XZ*atomJ.inducedDipoleP[0] + atomI.labFrameQuadrupole_YZ*atomJ.inducedDipoleP[1] + atomI.labFrameQuadrupole_ZZ*atomJ.inducedDipoleP[2];
qkuip[1] = qk[1]*uinpI[0] + qk[4]*uinpI[1] + qk[7]*uinpI[2];
qkuip[2] = qk[2]*uinpI[0] + qk[5]*uinpI[1] + qk[8]*uinpI[2];
qkuip[3] = qk[3]*uinpI[0] + qk[6]*uinpI[1] + qk[9]*uinpI[2];
qkuip[1] = atomJ.labFrameQuadrupole_XX*atomI.inducedDipoleP[0] + atomJ.labFrameQuadrupole_XY*atomI.inducedDipoleP[1] + atomJ.labFrameQuadrupole_XZ*atomI.inducedDipoleP[2];
qkuip[2] = atomJ.labFrameQuadrupole_XY*atomI.inducedDipoleP[0] + atomJ.labFrameQuadrupole_YY*atomI.inducedDipoleP[1] + atomJ.labFrameQuadrupole_YZ*atomI.inducedDipoleP[2];
qkuip[3] = atomJ.labFrameQuadrupole_XZ*atomI.inducedDipoleP[0] + atomJ.labFrameQuadrupole_YZ*atomI.inducedDipoleP[1] + atomJ.labFrameQuadrupole_ZZ*atomI.inducedDipoleP[2];
uixqkr[1] = uindI[1]*qkr[3] - uindI[2]*qkr[2];
uixqkr[2] = uindI[2]*qkr[1] - uindI[0]*qkr[3];
uixqkr[3] = uindI[0]*qkr[2] - uindI[1]*qkr[1];
uixqkr[1] = atomI.inducedDipole[1]*qkr[3] - atomI.inducedDipole[2]*qkr[2];
uixqkr[2] = atomI.inducedDipole[2]*qkr[1] - atomI.inducedDipole[0]*qkr[3];
uixqkr[3] = atomI.inducedDipole[0]*qkr[2] - atomI.inducedDipole[1]*qkr[1];
ukxqir[1] = uindJ[1]*qir[3] - uindJ[2]*qir[2];
ukxqir[2] = uindJ[2]*qir[1] - uindJ[0]*qir[3];
ukxqir[3] = uindJ[0]*qir[2] - uindJ[1]*qir[1];
ukxqir[1] = atomJ.inducedDipole[1]*qir[3] - atomJ.inducedDipole[2]*qir[2];
ukxqir[2] = atomJ.inducedDipole[2]*qir[1] - atomJ.inducedDipole[0]*qir[3];
ukxqir[3] = atomJ.inducedDipole[0]*qir[2] - atomJ.inducedDipole[1]*qir[1];
uixqkrp[1] = uinpI[1]*qkr[3] - uinpI[2]*qkr[2];
uixqkrp[2] = uinpI[2]*qkr[1] - uinpI[0]*qkr[3];
uixqkrp[3] = uinpI[0]*qkr[2] - uinpI[1]*qkr[1];
uixqkrp[1] = atomI.inducedDipoleP[1]*qkr[3] - atomI.inducedDipoleP[2]*qkr[2];
uixqkrp[2] = atomI.inducedDipoleP[2]*qkr[1] - atomI.inducedDipoleP[0]*qkr[3];
uixqkrp[3] = atomI.inducedDipoleP[0]*qkr[2] - atomI.inducedDipoleP[1]*qkr[1];
ukxqirp[1] = uinpJ[1]*qir[3] - uinpJ[2]*qir[2];
ukxqirp[2] = uinpJ[2]*qir[1] - uinpJ[0]*qir[3];
ukxqirp[3] = uinpJ[0]*qir[2] - uinpJ[1]*qir[1];
ukxqirp[1] = atomJ.inducedDipoleP[1]*qir[3] - atomJ.inducedDipoleP[2]*qir[2];
ukxqirp[2] = atomJ.inducedDipoleP[2]*qir[1] - atomJ.inducedDipoleP[0]*qir[3];
ukxqirp[3] = atomJ.inducedDipoleP[0]*qir[2] - atomJ.inducedDipoleP[1]*qir[1];
rxqiuk[1] = yr*qiuk[3] - zr*qiuk[2];
rxqiuk[2] = zr*qiuk[1] - xr*qiuk[3];
......@@ -805,36 +703,36 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
// get intermediate variables for induction energy terms
sci[1] = uindI[0]*dk[1] + uindI[1]*dk[2]
+ uindI[2]*dk[3] + di[1]*uindJ[0]
+ di[2]*uindJ[1] + di[3]*uindJ[2];
sci[1] = atomI.inducedDipole[0]*atomJ.labFrameDipole[0] + atomI.inducedDipole[1]*atomJ.labFrameDipole[1]
+ atomI.inducedDipole[2]*atomJ.labFrameDipole[2] + atomI.labFrameDipole[0]*atomJ.inducedDipole[0]
+ atomI.labFrameDipole[1]*atomJ.inducedDipole[1] + atomI.labFrameDipole[2]*atomJ.inducedDipole[2];
sci[2] = uindI[0]*uindJ[0] + uindI[1]*uindJ[1] + uindI[2]*uindJ[2];
sci[2] = atomI.inducedDipole[0]*atomJ.inducedDipole[0] + atomI.inducedDipole[1]*atomJ.inducedDipole[1] + atomI.inducedDipole[2]*atomJ.inducedDipole[2];
sci[3] = uindI[0]*xr + uindI[1]*yr + uindI[2]*zr;
sci[4] = uindJ[0]*xr + uindJ[1]*yr + uindJ[2]*zr;
sci[3] = atomI.inducedDipole[0]*xr + atomI.inducedDipole[1]*yr + atomI.inducedDipole[2]*zr;
sci[4] = atomJ.inducedDipole[0]*xr + atomJ.inducedDipole[1]*yr + atomJ.inducedDipole[2]*zr;
sci[7] = qir[1]*uindJ[0] + qir[2]*uindJ[1] + qir[3]*uindJ[2];
sci[8] = qkr[1]*uindI[0] + qkr[2]*uindI[1] + qkr[3]*uindI[2];
sci[7] = qir[1]*atomJ.inducedDipole[0] + qir[2]*atomJ.inducedDipole[1] + qir[3]*atomJ.inducedDipole[2];
sci[8] = qkr[1]*atomI.inducedDipole[0] + qkr[2]*atomI.inducedDipole[1] + qkr[3]*atomI.inducedDipole[2];
scip[1] = uinpI[0]*dk[1] + uinpI[1]*dk[2] + uinpI[2]*dk[3] + di[1]*uinpJ[0] + di[2]*uinpJ[1] + di[3]*uinpJ[2];
scip[2] = uindI[0]*uinpJ[0]+uindI[1]*uinpJ[1] + uindI[2]*uinpJ[2]+uinpI[0]*uindJ[0] + uinpI[1]*uindJ[1]+uinpI[2]*uindJ[2];
scip[1] = atomI.inducedDipoleP[0]*atomJ.labFrameDipole[0] + atomI.inducedDipoleP[1]*atomJ.labFrameDipole[1] + atomI.inducedDipoleP[2]*atomJ.labFrameDipole[2] + atomI.labFrameDipole[0]*atomJ.inducedDipoleP[0] + atomI.labFrameDipole[1]*atomJ.inducedDipoleP[1] + atomI.labFrameDipole[2]*atomJ.inducedDipoleP[2];
scip[2] = atomI.inducedDipole[0]*atomJ.inducedDipoleP[0]+atomI.inducedDipole[1]*atomJ.inducedDipoleP[1] + atomI.inducedDipole[2]*atomJ.inducedDipoleP[2]+atomI.inducedDipoleP[0]*atomJ.inducedDipole[0] + atomI.inducedDipoleP[1]*atomJ.inducedDipole[1]+atomI.inducedDipoleP[2]*atomJ.inducedDipole[2];
scip[3] = uinpI[0]*xr + uinpI[1]*yr + uinpI[2]*zr;
scip[4] = uinpJ[0]*xr + uinpJ[1]*yr + uinpJ[2]*zr;
scip[3] = atomI.inducedDipoleP[0]*xr + atomI.inducedDipoleP[1]*yr + atomI.inducedDipoleP[2]*zr;
scip[4] = atomJ.inducedDipoleP[0]*xr + atomJ.inducedDipoleP[1]*yr + atomJ.inducedDipoleP[2]*zr;
scip[7] = qir[1]*uinpJ[0] + qir[2]*uinpJ[1] + qir[3]*uinpJ[2];
scip[8] = qkr[1]*uinpI[0] + qkr[2]*uinpI[1] + qkr[3]*uinpI[2];
scip[7] = qir[1]*atomJ.inducedDipoleP[0] + qir[2]*atomJ.inducedDipoleP[1] + qir[3]*atomJ.inducedDipoleP[2];
scip[8] = qkr[1]*atomI.inducedDipoleP[0] + qkr[2]*atomI.inducedDipoleP[1] + qkr[3]*atomI.inducedDipoleP[2];
// calculate the gl functions for potential energy
gli[1] = ck*sci[3] - ci*sci[4];
gli[1] = atomJ.q*sci[3] - atomI.q*sci[4];
gli[2] = -sc[3]*sci[4] - sci[3]*sc[4];
gli[3] = sci[3]*sc[6] - sci[4]*sc[5];
gli[6] = sci[1];
gli[7] = 2.0f * (sci[7]-sci[8]);
glip[1] = ck*scip[3] - ci*scip[4];
glip[1] = atomJ.q*scip[3] - atomI.q*scip[4];
glip[2] = -sc[3]*scip[4] - scip[3]*sc[4];
glip[3] = scip[3]*sc[6] - scip[4]*sc[5];
glip[6] = scip[1];
......@@ -851,8 +749,8 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
-(sci[3]*scip[4]+scip[3]*sci[4])*scale5i)
+ 0.5f*rr9*(gli[3]*psc7+glip[3]*dsc7);
gfi[2] = -rr3*ck + rr5*sc[4] - rr7*sc[6];
gfi[3] = rr3*ci + rr5*sc[3] + rr7*sc[5];
gfi[2] = -rr3*atomJ.q + rr5*sc[4] - rr7*sc[6];
gfi[3] = rr3*atomI.q + rr5*sc[3] + rr7*sc[5];
gfi[4] = 2.0f * rr5;
gfi[5] = rr7 * (sci[4]*psc7+scip[4]*dsc7);
gfi[6] = -rr7 * (sci[3]*psc7+scip[3]*dsc7);
......@@ -860,46 +758,46 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
// get the induced force
ftm2i[1] = gfi[1]*xr + 0.5f*
(- rr3*ck*(uindI[0]*psc3+uinpI[0]*dsc3)
+ rr5*sc[4]*(uindI[0]*psc5+uinpI[0]*dsc5)
- rr7*sc[6]*(uindI[0]*psc7+uinpI[0]*dsc7))
+(rr3*ci*(uindJ[0]*psc3+uinpJ[0]*dsc3)
+ rr5*sc[3]*(uindJ[0]*psc5+uinpJ[0]*dsc5)
+ rr7*sc[5]*(uindJ[0]*psc7+uinpJ[0]*dsc7))*0.5f
+ rr5*scale5i*(sci[4]*uinpI[0]+scip[4]*uindI[0]
+ sci[3]*uinpJ[0]+scip[3]*uindJ[0])*0.5f
+ 0.5f*(sci[4]*psc5+scip[4]*dsc5)*rr5*di[1]
+ 0.5f*(sci[3]*psc5+scip[3]*dsc5)*rr5*dk[1]
(- rr3*atomJ.q*(atomI.inducedDipole[0]*psc3+atomI.inducedDipoleP[0]*dsc3)
+ rr5*sc[4]*(atomI.inducedDipole[0]*psc5+atomI.inducedDipoleP[0]*dsc5)
- rr7*sc[6]*(atomI.inducedDipole[0]*psc7+atomI.inducedDipoleP[0]*dsc7))
+(rr3*atomI.q*(atomJ.inducedDipole[0]*psc3+atomJ.inducedDipoleP[0]*dsc3)
+ rr5*sc[3]*(atomJ.inducedDipole[0]*psc5+atomJ.inducedDipoleP[0]*dsc5)
+ rr7*sc[5]*(atomJ.inducedDipole[0]*psc7+atomJ.inducedDipoleP[0]*dsc7))*0.5f
+ rr5*scale5i*(sci[4]*atomI.inducedDipoleP[0]+scip[4]*atomI.inducedDipole[0]
+ sci[3]*atomJ.inducedDipoleP[0]+scip[3]*atomJ.inducedDipole[0])*0.5f
+ 0.5f*(sci[4]*psc5+scip[4]*dsc5)*rr5*atomI.labFrameDipole[0]
+ 0.5f*(sci[3]*psc5+scip[3]*dsc5)*rr5*atomJ.labFrameDipole[0]
+ 0.5f*gfi[4]*((qkui[1]-qiuk[1])*psc5
+ (qkuip[1]-qiukp[1])*dsc5)
+ gfi[5]*qir[1] + gfi[6]*qkr[1];
ftm2i[2] = gfi[1]*yr + 0.5f*
(- rr3*ck*(uindI[1]*psc3+uinpI[1]*dsc3)
+ rr5*sc[4]*(uindI[1]*psc5+uinpI[1]*dsc5)
- rr7*sc[6]*(uindI[1]*psc7+uinpI[1]*dsc7))
+(rr3*ci*(uindJ[1]*psc3+uinpJ[1]*dsc3)
+ rr5*sc[3]*(uindJ[1]*psc5+uinpJ[1]*dsc5)
+ rr7*sc[5]*(uindJ[1]*psc7+uinpJ[1]*dsc7))*0.5f
+ rr5*scale5i*(sci[4]*uinpI[1]+scip[4]*uindI[1]
+ sci[3]*uinpJ[1]+scip[3]*uindJ[1])*0.5f
+ 0.5f*(sci[4]*psc5+scip[4]*dsc5)*rr5*di[2]
+ 0.5f*(sci[3]*psc5+scip[3]*dsc5)*rr5*dk[2]
(- rr3*atomJ.q*(atomI.inducedDipole[1]*psc3+atomI.inducedDipoleP[1]*dsc3)
+ rr5*sc[4]*(atomI.inducedDipole[1]*psc5+atomI.inducedDipoleP[1]*dsc5)
- rr7*sc[6]*(atomI.inducedDipole[1]*psc7+atomI.inducedDipoleP[1]*dsc7))
+(rr3*atomI.q*(atomJ.inducedDipole[1]*psc3+atomJ.inducedDipoleP[1]*dsc3)
+ rr5*sc[3]*(atomJ.inducedDipole[1]*psc5+atomJ.inducedDipoleP[1]*dsc5)
+ rr7*sc[5]*(atomJ.inducedDipole[1]*psc7+atomJ.inducedDipoleP[1]*dsc7))*0.5f
+ rr5*scale5i*(sci[4]*atomI.inducedDipoleP[1]+scip[4]*atomI.inducedDipole[1]
+ sci[3]*atomJ.inducedDipoleP[1]+scip[3]*atomJ.inducedDipole[1])*0.5f
+ 0.5f*(sci[4]*psc5+scip[4]*dsc5)*rr5*atomI.labFrameDipole[1]
+ 0.5f*(sci[3]*psc5+scip[3]*dsc5)*rr5*atomJ.labFrameDipole[1]
+ 0.5f*gfi[4]*((qkui[2]-qiuk[2])*psc5
+ (qkuip[2]-qiukp[2])*dsc5)
+ gfi[5]*qir[2] + gfi[6]*qkr[2];
ftm2i[3] = gfi[1]*zr + 0.5f*
(- rr3*ck*(uindI[2]*psc3+uinpI[2]*dsc3)
+ rr5*sc[4]*(uindI[2]*psc5+uinpI[2]*dsc5)
- rr7*sc[6]*(uindI[2]*psc7+uinpI[2]*dsc7))
+(rr3*ci*(uindJ[2]*psc3+uinpJ[2]*dsc3)
+ rr5*sc[3]*(uindJ[2]*psc5+uinpJ[2]*dsc5)
+ rr7*sc[5]*(uindJ[2]*psc7+uinpJ[2]*dsc7))*0.5f
+ rr5*scale5i*(sci[4]*uinpI[2]+scip[4]*uindI[2]
+ sci[3]*uinpJ[2]+scip[3]*uindJ[2])*0.5f
+ 0.5f*(sci[4]*psc5+scip[4]*dsc5)*rr5*di[3]
+ 0.5f*(sci[3]*psc5+scip[3]*dsc5)*rr5*dk[3]
(- rr3*atomJ.q*(atomI.inducedDipole[2]*psc3+atomI.inducedDipoleP[2]*dsc3)
+ rr5*sc[4]*(atomI.inducedDipole[2]*psc5+atomI.inducedDipoleP[2]*dsc5)
- rr7*sc[6]*(atomI.inducedDipole[2]*psc7+atomI.inducedDipoleP[2]*dsc7))
+(rr3*atomI.q*(atomJ.inducedDipole[2]*psc3+atomJ.inducedDipoleP[2]*dsc3)
+ rr5*sc[3]*(atomJ.inducedDipole[2]*psc5+atomJ.inducedDipoleP[2]*dsc5)
+ rr7*sc[5]*(atomJ.inducedDipole[2]*psc7+atomJ.inducedDipoleP[2]*dsc7))*0.5f
+ rr5*scale5i*(sci[4]*atomI.inducedDipoleP[2]+scip[4]*atomI.inducedDipole[2]
+ sci[3]*atomJ.inducedDipoleP[2]+scip[3]*atomJ.inducedDipole[2])*0.5f
+ 0.5f*(sci[4]*psc5+scip[4]*dsc5)*rr5*atomI.labFrameDipole[2]
+ 0.5f*(sci[3]*psc5+scip[3]*dsc5)*rr5*atomJ.labFrameDipole[2]
+ 0.5f*gfi[4]*((qkui[3]-qiuk[3])*psc5
+ (qkuip[3]-qiukp[3])*dsc5)
+ gfi[5]*qir[3] + gfi[6]*qkr[3];
......@@ -948,14 +846,14 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
gfd = 0.5f * (rr5*scip[2]*scale3i;
& - rr7*(scip[3]*sci[4]+sci[3]*scip[4])*scale5i);
fdir[1] = gfd*xr + 0.5f*rr5*scale5i;
& * (sci[4]*uinpI[0]+scip[4]*uindI[0];
& +sci[3]*uinpJ[0]+scip[3]*uindJ[0]);
& * (sci[4]*atomI.inducedDipoleP[0]+scip[4]*atomI.inducedDipole[0];
& +sci[3]*atomJ.inducedDipoleP[0]+scip[3]*atomJ.inducedDipole[0]);
fdir[2] = gfd*yr + 0.5f*rr5*scale5i;
& * (sci[4]*uinpI[1]+scip[4]*uindI[1];
& +sci[3]*uinpJ[1]+scip[3]*uindJ[1]);
& * (sci[4]*atomI.inducedDipoleP[1]+scip[4]*atomI.inducedDipole[1];
& +sci[3]*atomJ.inducedDipoleP[1]+scip[3]*atomJ.inducedDipole[1]);
fdir[3] = gfd*zr + 0.5f*rr5*scale5i;
& * (sci[4]*uinpI[2]+scip[4]*uindI[2];
& +sci[3]*uinpJ[2]+scip[3]*uindJ[2]);
& * (sci[4]*atomI.inducedDipoleP[2]+scip[4]*atomI.inducedDipole[2];
& +sci[3]*atomJ.inducedDipoleP[2]+scip[3]*atomJ.inducedDipole[2]);
ftm2i[1] = ftm2i[1] - fdir[1] + findmp[1];
ftm2i[2] = ftm2i[2] - fdir[2] + findmp[2];
ftm2i[3] = ftm2i[3] - fdir[3] + findmp[3];
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwoodEDiff.h
View file @ f11d445b
......@@ -63,14 +63,6 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwoodEDiff, Forces_kernel)(
unsigned int end = (warp+1)*numWorkUnits/totalWarps;
unsigned int lasty = 0xFFFFFFFF;
float4 jCoord;
float jDipole[3];
float jQuadrupole[9];
float jInducedDipole[3];
float jInducedDipolePolar[3];
float jInducedDipoleS[3];
float jInducedDipolePolarS[3];
float totalEnergy = 0.0f;
float tinker_f = (cAmoebaSim.electric/cAmoebaSim.dielec);
......@@ -81,9 +73,6 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwoodEDiff, Forces_kernel)(
unsigned int y;
bool bExclusionFlag;
float forceSum[3];
float torqueSum[3];
float force[3];
float torqueI[3];
float torqueJ[3];
......@@ -100,15 +89,20 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwoodEDiff, Forces_kernel)(
KirkwoodEDiffParticle* psA = &sA[tbx];
unsigned int atomI = x + tgx;
float4 iCoord = atomCoord[atomI];
KirkwoodEDiffParticle localParticle;
loadKirkwoodEDiffShared(&localParticle, atomI,
atomCoord,
labFrameDipole, labFrameQuadrupole,
inducedDipole, inducedDipolePolar,
inducedDipoleS, inducedDipolePolarS );
forceSum[0] = 0.0f;
forceSum[1] = 0.0f;
forceSum[2] = 0.0f;
localParticle.force[0] = 0.0f;
localParticle.force[1] = 0.0f;
localParticle.force[2] = 0.0f;
torqueSum[0] = 0.0f;
torqueSum[1] = 0.0f;
torqueSum[2] = 0.0f;
localParticle.torque[0] = 0.0f;
localParticle.torque[1] = 0.0f;
localParticle.torque[2] = 0.0f;
if (x == y) // Handle diagonals uniquely at 50% efficiency
{
......@@ -135,22 +129,8 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwoodEDiff, Forces_kernel)(
unsigned int atomJ = (y + j);
// load coords, charge, ...
loadKirkwoodEDiffData( &(psA[j]), &jCoord,
jDipole, jQuadrupole,
jInducedDipole, jInducedDipolePolar,
jInducedDipoleS, jInducedDipolePolarS );
calculateKirkwoodEDiffPairIxn_kernel( iCoord, jCoord,
cAmoebaSim.pDampingFactorAndThole[atomI].x, psA[j].damp,
cAmoebaSim.pDampingFactorAndThole[atomI].y, psA[j].thole,
&(labFrameDipole[3*atomI]), jDipole,
&(labFrameQuadrupole[9*atomI]), jQuadrupole,
&(inducedDipole[3*atomI]), jInducedDipole,
&(inducedDipolePolar[3*atomI]), jInducedDipolePolar,
&(inducedDipoleS[3*atomI]), jInducedDipoleS,
&(inducedDipolePolarS[3*atomI]), jInducedDipolePolarS,
calculateKirkwoodEDiffPairIxn_kernel( localParticle, psA[j],
pScale, dScale,
&energy, force, torqueI, torqueJ
#ifdef AMOEBA_DEBUG
......@@ -162,9 +142,9 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwoodEDiff, Forces_kernel)(
// torques include i == j contribution
torqueSum[0] += mask ? torqueI[0] : 0.0f;
torqueSum[1] += mask ? torqueI[1] : 0.0f;
torqueSum[2] += mask ? torqueI[2] : 0.0f;
localParticle.torque[0] += mask ? torqueI[0] : 0.0f;
localParticle.torque[1] += mask ? torqueI[1] : 0.0f;
localParticle.torque[2] += mask ? torqueI[2] : 0.0f;
totalEnergy += mask ? 0.5f*energy : 0.0f;
......@@ -172,9 +152,9 @@ void METHOD_NAME(kCalculateAmoebaCudaKirkwoodEDiff, Forces_kernel)(
mask = (atomI == atomJ) ? 0 : mask;
forceSum[0] += mask ? force[0] : 0.0f;
forceSum[1] += mask ? force[1] : 0.0f;
forceSum[2] += mask ? force[2] : 0.0f;
localParticle.force[0] += mask ? force[0] : 0.0f;
localParticle.force[1] += mask ? force[1] : 0.0f;
localParticle.force[2] += mask ? force[2] : 0.0f;
#ifdef AMOEBA_DEBUG
......@@ -210,27 +190,12 @@ if( atomI == targetAtom || atomJ == targetAtom ){
unsigned int atomJ = (y + j);
// load coords, charge, ...
loadKirkwoodEDiffData( &(psA[j]), &jCoord,
jDipole, jQuadrupole,
jInducedDipole, jInducedDipolePolar,
jInducedDipoleS, jInducedDipolePolarS );
float pScale;
float dScale;
getMaskedDScaleFactor( j, dScaleMask, &dScale );
getMaskedPScaleFactor( j, pScaleMask, &pScale );
calculateKirkwoodEDiffPairIxn_kernel( iCoord, jCoord,
cAmoebaSim.pDampingFactorAndThole[atomI].x, psA[j].damp,
cAmoebaSim.pDampingFactorAndThole[atomI].y, psA[j].thole,
&(labFrameDipole[3*atomI]), jDipole,
&(labFrameQuadrupole[9*atomI]), jQuadrupole,
&(inducedDipole[3*atomI]), jInducedDipole,
&(inducedDipolePolar[3*atomI]), jInducedDipolePolar,
&(inducedDipoleS[3*atomI]), jInducedDipoleS,
&(inducedDipolePolarS[3*atomI]), jInducedDipolePolarS,
calculateKirkwoodEDiffPairIxn_kernel( localParticle, psA[j],
pScale, dScale,
&energy, force, torqueI, torqueJ
#ifdef AMOEBA_DEBUG
......@@ -242,17 +207,17 @@ if( atomI == targetAtom || atomJ == targetAtom ){
// torques include i == j contribution
torqueSum[0] += mask ? torqueI[0] : 0.0f;
torqueSum[1] += mask ? torqueI[1] : 0.0f;
torqueSum[2] += mask ? torqueI[2] : 0.0f;
localParticle.torque[0] += mask ? torqueI[0] : 0.0f;
localParticle.torque[1] += mask ? torqueI[1] : 0.0f;
localParticle.torque[2] += mask ? torqueI[2] : 0.0f;
totalEnergy += mask ? 0.5f*energy : 0.0f;
// add to field at atomI the field due atomJ's charge/dipole/quadrupole
forceSum[0] += mask ? force[0] : 0.0f;
forceSum[1] += mask ? force[1] : 0.0f;
forceSum[2] += mask ? force[2] : 0.0f;
localParticle.force[0] += mask ? force[0] : 0.0f;
localParticle.force[1] += mask ? force[1] : 0.0f;
localParticle.force[2] += mask ? force[2] : 0.0f;
#ifdef AMOEBA_DEBUG
......@@ -280,19 +245,19 @@ if( atomI == targetAtom || atomJ == targetAtom ){
// scale and write results
scale3dArray( tinker_f, forceSum );
scale3dArray( tinker_f, torqueSum );
scale3dArray( tinker_f, localParticle.force );
scale3dArray( tinker_f, localParticle.torque );
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = 3*(x + tgx + warp*cAmoebaSim.paddedNumberOfAtoms);
load3dArrayBufferPerWarp( offset, forceSum, outputForce );
load3dArrayBufferPerWarp( offset, torqueSum, outputTorque );
load3dArrayBufferPerWarp( offset, localParticle.force, outputForce );
load3dArrayBufferPerWarp( offset, localParticle.torque, outputTorque );
#else
unsigned int offset = 3*(x + tgx + (x >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms);
load3dArray( offset, forceSum, outputForce );
load3dArray( offset, torqueSum, outputTorque );
load3dArray( offset, localParticle.force, outputForce );
load3dArray( offset, localParticle.torque, outputTorque );
#endif
......@@ -329,22 +294,7 @@ if( atomI == targetAtom || atomJ == targetAtom ){
unsigned int atomJ = y + tj;
// load coords, charge, ...
loadKirkwoodEDiffData( &(psA[tj]), &jCoord,
jDipole, jQuadrupole,
jInducedDipole, jInducedDipolePolar,
jInducedDipoleS, jInducedDipolePolarS );
calculateKirkwoodEDiffPairIxn_kernel( iCoord, jCoord,
cAmoebaSim.pDampingFactorAndThole[atomI].x, psA[tj].damp,
cAmoebaSim.pDampingFactorAndThole[atomI].y, psA[tj].thole,
&(labFrameDipole[3*atomI]), jDipole,
&(labFrameQuadrupole[9*atomI]), jQuadrupole,
&(inducedDipole[3*atomI]), jInducedDipole,
&(inducedDipolePolar[3*atomI]), jInducedDipolePolar,
&(inducedDipoleS[3*atomI]), jInducedDipoleS,
&(inducedDipolePolarS[3*atomI]), jInducedDipolePolarS,
calculateKirkwoodEDiffPairIxn_kernel( localParticle, psA[tj],
pScale, dScale,
&energy, force,
torqueI, torqueJ
......@@ -358,13 +308,13 @@ if( atomI == targetAtom || atomJ == targetAtom ){
// add force and torque to atom I due atom J
forceSum[0] += mask ? force[0] : 0.0f;
forceSum[1] += mask ? force[1] : 0.0f;
forceSum[2] += mask ? force[2] : 0.0f;
localParticle.force[0] += mask ? force[0] : 0.0f;
localParticle.force[1] += mask ? force[1] : 0.0f;
localParticle.force[2] += mask ? force[2] : 0.0f;
torqueSum[0] += mask ? torqueI[0] : 0.0f;
torqueSum[1] += mask ? torqueI[1] : 0.0f;
torqueSum[2] += mask ? torqueI[2] : 0.0f;
localParticle.torque[0] += mask ? torqueI[0] : 0.0f;
localParticle.torque[1] += mask ? torqueI[1] : 0.0f;
localParticle.torque[2] += mask ? torqueI[2] : 0.0f;
totalEnergy += mask ? energy : 0.0f;
......@@ -413,27 +363,12 @@ if( atomI == targetAtom || atomJ == targetAtom ){
{
unsigned int atomJ = y + tj;
// load coords, charge, ...
loadKirkwoodEDiffData( &(psA[tj]), &jCoord,
jDipole, jQuadrupole,
jInducedDipole, jInducedDipolePolar,
jInducedDipoleS, jInducedDipolePolarS );
float dScale;
float pScale;
getMaskedDScaleFactor( tj, dScaleMask, &dScale );
getMaskedPScaleFactor( tj, pScaleMask, &pScale );
calculateKirkwoodEDiffPairIxn_kernel( iCoord, jCoord,
cAmoebaSim.pDampingFactorAndThole[atomI].x, psA[tj].damp,
cAmoebaSim.pDampingFactorAndThole[atomI].y, psA[tj].thole,
&(labFrameDipole[3*atomI]), jDipole,
&(labFrameQuadrupole[9*atomI]), jQuadrupole,
&(inducedDipole[3*atomI]), jInducedDipole,
&(inducedDipolePolar[3*atomI]), jInducedDipolePolar,
&(inducedDipoleS[3*atomI]), jInducedDipoleS,
&(inducedDipolePolarS[3*atomI]), jInducedDipolePolarS,
calculateKirkwoodEDiffPairIxn_kernel( localParticle, psA[tj],
pScale, dScale,
&energy, force,
torqueI, torqueJ
......@@ -447,13 +382,13 @@ if( atomI == targetAtom || atomJ == targetAtom ){
// add force and torque to atom I due atom J
forceSum[0] += mask ? force[0] : 0.0f;
forceSum[1] += mask ? force[1] : 0.0f;
forceSum[2] += mask ? force[2] : 0.0f;
localParticle.force[0] += mask ? force[0] : 0.0f;
localParticle.force[1] += mask ? force[1] : 0.0f;
localParticle.force[2] += mask ? force[2] : 0.0f;
torqueSum[0] += mask ? torqueI[0] : 0.0f;
torqueSum[1] += mask ? torqueI[1] : 0.0f;
torqueSum[2] += mask ? torqueI[2] : 0.0f;
localParticle.torque[0] += mask ? torqueI[0] : 0.0f;
localParticle.torque[1] += mask ? torqueI[1] : 0.0f;
localParticle.torque[2] += mask ? torqueI[2] : 0.0f;
totalEnergy += mask ? energy : 0.0f;
......@@ -492,8 +427,8 @@ if( atomI == targetAtom || atomJ == targetAtom ){
// scale and write results
scale3dArray( tinker_f, forceSum );
scale3dArray( tinker_f, torqueSum );
scale3dArray( tinker_f, localParticle.force );
scale3dArray( tinker_f, localParticle.torque );
scale3dArray( tinker_f, sA[threadIdx.x].force );
scale3dArray( tinker_f, sA[threadIdx.x].torque );
......@@ -502,8 +437,8 @@ if( atomI == targetAtom || atomJ == targetAtom ){
unsigned int offset = 3*(x + tgx + warp*cAmoebaSim.paddedNumberOfAtoms);
load3dArrayBufferPerWarp( offset, forceSum, outputForce );
load3dArrayBufferPerWarp( offset, torqueSum, outputTorque );
load3dArrayBufferPerWarp( offset, localParticle.force, outputForce );
load3dArrayBufferPerWarp( offset, localParticle.torque, outputTorque );
offset = 3*(y + tgx + warp*cAmoebaSim.paddedNumberOfAtoms);
......@@ -512,8 +447,8 @@ if( atomI == targetAtom || atomJ == targetAtom ){
#else
unsigned int offset = 3*(x + tgx + (y >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms);
load3dArray( offset, forceSum, outputForce );
load3dArray( offset, torqueSum, outputTorque );
load3dArray( offset, localParticle.force, outputForce );
load3dArray( offset, localParticle.torque, outputTorque );
offset = 3*(y + tgx + (x >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms);
......
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