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Commit 82662e25 authored by peastman's avatar peastman
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Merge pull request #367 from leeping/master 

AMOEBA No Quadrupole Optimization
parents 31d02cdc be3f55f6
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Showing with 1142 additions and 36 deletions
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 82662e25
......@@ -921,6 +921,10 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
molecularQuadrupolesVec.push_back((float) quadrupole[4]);
molecularQuadrupolesVec.push_back((float) quadrupole[5]);
}
hasQuadrupoles = false;
for (int i = 0; i < (int) molecularQuadrupolesVec.size(); i++)
if (molecularQuadrupolesVec[i] != 0.0)
hasQuadrupoles = true;
int paddedNumAtoms = cu.getPaddedNumAtoms();
for (int i = numMultipoles; i < paddedNumAtoms; i++) {
dampingAndTholeVec.push_back(make_float2(0, 0));
......@@ -1040,6 +1044,8 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
defines["DIRECT_POLARIZATION"] = "";
if (useShuffle)
defines["USE_SHUFFLE"] = "";
if (hasQuadrupoles)
defines["INCLUDE_QUADRUPOLES"] = "";
defines["TILE_SIZE"] = cu.intToString(CudaContext::TileSize);
int numExclusionTiles = tilesWithExclusions.size();
defines["NUM_TILES_WITH_EXCLUSIONS"] = cu.intToString(numExclusionTiles);
......@@ -1104,9 +1110,9 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
if (usePME) {
electrostaticsSource << CudaKernelSources::vectorOps;
electrostaticsSource << CudaAmoebaKernelSources::pmeMultipoleElectrostatics;
electrostaticsSource << CudaAmoebaKernelSources::pmeElectrostaticPairForce;
electrostaticsSource << (hasQuadrupoles ? CudaAmoebaKernelSources::pmeElectrostaticPairForce : CudaAmoebaKernelSources::pmeElectrostaticPairForceNoQuadrupoles);
electrostaticsSource << "#define APPLY_SCALE\n";
electrostaticsSource << CudaAmoebaKernelSources::pmeElectrostaticPairForce;
electrostaticsSource << (hasQuadrupoles ? CudaAmoebaKernelSources::pmeElectrostaticPairForce : CudaAmoebaKernelSources::pmeElectrostaticPairForceNoQuadrupoles);
electrostaticsThreadMemory = 24*elementSize+3*sizeof(float)+3*sizeof(int)/(double) cu.TileSize;
if (!useShuffle)
electrostaticsThreadMemory += 3*elementSize;
......@@ -1115,13 +1121,13 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
electrostaticsSource << CudaKernelSources::vectorOps;
electrostaticsSource << CudaAmoebaKernelSources::multipoleElectrostatics;
electrostaticsSource << "#define F1\n";
electrostaticsSource << CudaAmoebaKernelSources::electrostaticPairForce;
electrostaticsSource << (hasQuadrupoles ? CudaAmoebaKernelSources::electrostaticPairForce : CudaAmoebaKernelSources::electrostaticPairForceNoQuadrupoles);
electrostaticsSource << "#undef F1\n";
electrostaticsSource << "#define T1\n";
electrostaticsSource << CudaAmoebaKernelSources::electrostaticPairForce;
electrostaticsSource << (hasQuadrupoles ? CudaAmoebaKernelSources::electrostaticPairForce : CudaAmoebaKernelSources::electrostaticPairForceNoQuadrupoles);
electrostaticsSource << "#undef T1\n";
electrostaticsSource << "#define T3\n";
electrostaticsSource << CudaAmoebaKernelSources::electrostaticPairForce;
electrostaticsSource << (hasQuadrupoles ? CudaAmoebaKernelSources::electrostaticPairForce : CudaAmoebaKernelSources::electrostaticPairForceNoQuadrupoles);
electrostaticsThreadMemory = 21*elementSize+2*sizeof(float)+3*sizeof(int)/(double) cu.TileSize;
if (!useShuffle)
electrostaticsThreadMemory += 3*elementSize;
......@@ -1851,6 +1857,11 @@ void CudaCalcAmoebaMultipoleForceKernel::copyParametersToContext(ContextImpl& co
molecularQuadrupolesVec.push_back((float) quadrupole[4]);
molecularQuadrupolesVec.push_back((float) quadrupole[5]);
}
if (!hasQuadrupoles) {
for (int i = 0; i < (int) molecularQuadrupolesVec.size(); i++)
if (molecularQuadrupolesVec[i] != 0.0)
throw OpenMMException("updateParametersInContext: Cannot set a non-zero quadrupole moment, because quadrupoles were excluded from the kernel");
}
for (int i = force.getNumMultipoles(); i < cu.getPaddedNumAtoms(); i++) {
dampingAndTholeVec.push_back(make_float2(0, 0));
polarizabilityVec.push_back(0);
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h
View file @ 82662e25
......@@ -380,7 +380,7 @@ private:
int numMultipoles, maxInducedIterations;
int fixedFieldThreads, inducedFieldThreads, electrostaticsThreads;
double inducedEpsilon;
bool hasInitializedScaleFactors, hasInitializedFFT, multipolesAreValid;
bool hasQuadrupoles, hasInitializedScaleFactors, hasInitializedFFT, multipolesAreValid;
CudaContext& cu;
const System& system;
std::vector<int3> covalentFlagValues;
......
plugins/amoeba/platforms/cuda/src/kernels/electrostaticPairForceNoQuadrupoles.cu 0 → 100644
View file @ 82662e25
/**
* This defines three different closely related functions, depending on which constant (F1, T1, or T3) is defined.
*/
#if defined F1
__device__ void computeOneInteractionF1(AtomData& atom1, volatile AtomData& atom2, float dScale, float pScale, float mScale, real& energy, real3& outputForce) {
#elif defined T1
__device__ void computeOneInteractionT1(AtomData& atom1, volatile AtomData& atom2, float dScale, float pScale, float mScale, real3& outputForce) {
#else
__device__ void computeOneInteractionT3(AtomData& atom1, volatile AtomData& atom2, float dScale, float pScale, float mScale, real3& outputForce) {
#endif
#ifdef F1
const float uScale = 1;
real ddsc3_0 = 0;
real ddsc3_1 = 0;
real ddsc3_2 = 0;
real ddsc5_0 = 0;
real ddsc5_1 = 0;
real ddsc5_2 = 0;
real ddsc7_0 = 0;
real ddsc7_1 = 0;
real ddsc7_2 = 0;
#endif
real xr = atom2.posq.x - atom1.posq.x;
real yr = atom2.posq.y - atom1.posq.y;
real zr = atom2.posq.z - atom1.posq.z;
real r2 = xr*xr + yr*yr + zr*zr;
real r = SQRT(r2);
real rr1 = RECIP(r);
real rr2 = rr1*rr1;
real rr3 = rr1*rr2;
real rr5 = 3*rr3*rr2;
real rr7 = 5*rr5*rr2;
real rr9 = 7*rr7*rr2;
#ifdef F1
real rr11 = 9*rr9*rr2;
#endif
real scale3 = 1;
real scale5 = 1;
real scale7 = 1;
real pdamp = atom1.damp*atom2.damp;
if (pdamp != 0) {
real ratio = r/pdamp;
float pGamma = atom2.thole > atom1.thole ? atom1.thole : atom2.thole;
real damp = ratio*ratio*ratio*pGamma;
real dampExp = EXP(-damp);
real damp1 = damp + 1;
real damp2 = damp*damp;
scale3 = 1 - dampExp;
scale5 = 1 - damp1*dampExp;
scale7 = 1 - (damp1 + 0.6f*damp2)*dampExp;
#ifdef F1
real factor = 3*damp*dampExp*rr2;
real factor7 = -0.2f + 0.6f*damp;
ddsc3_0 = factor*xr;
ddsc5_0 = ddsc3_0*damp;
ddsc7_0 = ddsc5_0*factor7;
ddsc3_1 = factor*yr;
ddsc5_1 = ddsc3_1*damp;
ddsc7_1 = ddsc5_1*factor7;
ddsc3_2 = factor*zr;
ddsc5_2 = ddsc3_2*damp;
ddsc7_2 = ddsc5_2*factor7;
#endif
}
#if defined F1
real scale3i = rr3*scale3*uScale;
real scale5i = rr5*scale5*uScale;
#endif
real dsc3 = rr3*scale3*dScale;
real psc3 = rr3*scale3*pScale;
real dsc5 = rr5*scale5*dScale;
real psc5 = rr5*scale5*pScale;
real dsc7 = rr7*scale7*dScale;
real psc7 = rr7*scale7*pScale;
#if defined F1
real sc2 = atom1.dipole.x*atom2.dipole.x + atom1.dipole.y*atom2.dipole.y + atom1.dipole.z*atom2.dipole.z;
#endif
#if defined F1 || defined T1
real sc4 = atom2.dipole.x*xr + atom2.dipole.y*yr + atom2.dipole.z*zr;
#endif
#if defined F1 || defined T3
real sc3 = atom1.dipole.x*xr + atom1.dipole.y*yr + atom1.dipole.z*zr;
#endif
#if defined F1
real sci1 = atom1.inducedDipole.x*atom2.dipole.x + atom1.inducedDipole.y*atom2.dipole.y + atom1.inducedDipole.z*atom2.dipole.z +
atom2.inducedDipole.x*atom1.dipole.x + atom2.inducedDipole.y*atom1.dipole.y + atom2.inducedDipole.z*atom1.dipole.z;
#endif
#if defined F1 || defined T3
real sci3 = atom1.inducedDipole.x*xr + atom1.inducedDipole.y*yr + atom1.inducedDipole.z*zr;
#endif
#if defined F1 || defined T1
real sci4 = atom2.inducedDipole.x*xr + atom2.inducedDipole.y*yr + atom2.inducedDipole.z*zr;
#endif
#if defined F1
real scip1 = atom1.inducedDipolePolar.x*atom2.dipole.x + atom1.inducedDipolePolar.y*atom2.dipole.y + atom1.inducedDipolePolar.z*atom2.dipole.z +
atom2.inducedDipolePolar.x*atom1.dipole.x + atom2.inducedDipolePolar.y*atom1.dipole.y + atom2.inducedDipolePolar.z*atom1.dipole.z;
real scip2 = atom1.inducedDipole.x*atom2.inducedDipolePolar.x + atom1.inducedDipole.y*atom2.inducedDipolePolar.y + atom1.inducedDipole.z*atom2.inducedDipolePolar.z +
atom2.inducedDipole.x*atom1.inducedDipolePolar.x + atom2.inducedDipole.y*atom1.inducedDipolePolar.y + atom2.inducedDipole.z*atom1.inducedDipolePolar.z;
#endif
#if defined F1 || defined T3
real scip3 = ((atom1.inducedDipolePolar.x)*(xr) + (atom1.inducedDipolePolar.y)*(yr) + (atom1.inducedDipolePolar.z)*(zr));
#endif
#if defined F1 || defined T1
real scip4 = ((atom2.inducedDipolePolar.x)*(xr) + (atom2.inducedDipolePolar.y)*(yr) + (atom2.inducedDipolePolar.z)*(zr));
#endif
#ifdef F1
real gli1 = atom2.posq.w*sci3 - atom1.posq.w*sci4;
real gli6 = sci1;
real glip1 = atom2.posq.w*scip3 - atom1.posq.w*scip4;
real glip6 = scip1;
real gli2 = -sc3*sci4 - sci3*sc4;
real glip2 = -sc3*scip4 - scip3*sc4;
real factor3 = rr3*((gli1 + gli6)*pScale + (glip1 + glip6)*dScale);
real factor5 = rr5*(gli2*pScale + glip2*dScale);
real ftm2i_0 = -0.5f*(factor3*ddsc3_0 + factor5*ddsc5_0);
real ftm2i_1 = -0.5f*(factor3*ddsc3_1 + factor5*ddsc5_1);
real ftm2i_2 = -0.5f*(factor3*ddsc3_2 + factor5*ddsc5_2);
real gl0 = atom1.posq.w*atom2.posq.w;
real gl1 = atom2.posq.w*sc3 - atom1.posq.w*sc4;
real gl2 = -sc3*sc4;
real gl6 = sc2;
real gf1 = rr3*gl0 + rr5*(gl1+gl6) + rr7*gl2;
#endif
#if defined F1 || defined T1
real gf2 = -atom2.posq.w*rr3 + sc4*rr5;
real gf5 = 2*(-atom2.posq.w*rr5+sc4*rr7);
#endif
#if defined F1 || defined T3
real gf3 = atom1.posq.w*rr3 + sc3*rr5;
real gf6 = 2*(-atom1.posq.w*rr5-sc3*rr7);
#endif
#ifdef F1
real em = mScale*(rr1*gl0 + rr3*(gl1+gl6) + rr5*gl2);
real ei = 0.5f*((gli1+gli6)*psc3 + gli2*psc5);
energy = em+ei;
#endif
#ifdef F1
real ftm2_0 = mScale*(gf1*xr + gf2*atom1.dipole.x + gf3*atom2.dipole.x);
real ftm2_1 = mScale*(gf1*yr + gf2*atom1.dipole.y + gf3*atom2.dipole.y);
real ftm2_2 = mScale*(gf1*zr + gf2*atom1.dipole.z + gf3*atom2.dipole.z);
real gfi1 = rr2*(1.5f*((gli1+gli6)*psc3 + (glip1+glip6)*dsc3 + scip2*scale3i) + 2.5f*(gli2*psc5 + glip2*dsc5 - (sci3*scip4+scip3*sci4)*scale5i));
ftm2i_0 += gfi1*xr;
ftm2i_1 += gfi1*yr;
ftm2i_2 += gfi1*zr;
#endif
#if defined F1 || defined T1
real gfi5 = (sci4*psc7 + scip4*dsc7);
#endif
#if defined F1 || defined T3
real gfi6 = -(sci3*psc7 + scip3*dsc7);
#endif
#ifdef F1
ftm2i_0 += 0.5f*(-atom2.posq.w*(atom1.inducedDipole.x*psc3 + atom1.inducedDipolePolar.x*dsc3) +
sc4*(atom1.inducedDipole.x*psc5 + atom1.inducedDipolePolar.x*dsc5)) +
0.5f*(atom1.posq.w*(atom2.inducedDipole.x*psc3+atom2.inducedDipolePolar.x*dsc3) +
sc3*(atom2.inducedDipole.x*psc5 +atom2.inducedDipolePolar.x*dsc5)) +
scale5i*(sci4*atom1.inducedDipolePolar.x+scip4*atom1.inducedDipole.x +
sci3*atom2.inducedDipolePolar.x+scip3*atom2.inducedDipole.x)*0.5f +
0.5f*(sci4*psc5+scip4*dsc5)*atom1.dipole.x +
0.5f*(sci3*psc5+scip3*dsc5)*atom2.dipole.x;
ftm2i_1 += 0.5f*(-atom2.posq.w*(atom1.inducedDipole.y*psc3 + atom1.inducedDipolePolar.y*dsc3) +
sc4*(atom1.inducedDipole.y*psc5 + atom1.inducedDipolePolar.y*dsc5)) +
(atom1.posq.w*(atom2.inducedDipole.y*psc3+atom2.inducedDipolePolar.y*dsc3) +
sc3*(atom2.inducedDipole.y*psc5+atom2.inducedDipolePolar.y*dsc5))*0.5f +
scale5i*(sci4*atom1.inducedDipolePolar.y+scip4*atom1.inducedDipole.y + sci3*atom2.inducedDipolePolar.y+scip3*atom2.inducedDipole.y)*0.5f +
0.5f*(sci4*psc5+scip4*dsc5)*atom1.dipole.y +
0.5f*(sci3*psc5+scip3*dsc5)*atom2.dipole.y;
ftm2i_2 += 0.5f*(-atom2.posq.w*(atom1.inducedDipole.z*psc3 + atom1.inducedDipolePolar.z*dsc3) +
sc4*(atom1.inducedDipole.z*psc5 + atom1.inducedDipolePolar.z*dsc5)) +
(atom1.posq.w*(atom2.inducedDipole.z*psc3+atom2.inducedDipolePolar.z*dsc3) +
sc3*(atom2.inducedDipole.z*psc5+atom2.inducedDipolePolar.z*dsc5))*0.5f +
scale5i*(sci4*atom1.inducedDipolePolar.z+scip4*atom1.inducedDipole.z +
sci3*atom2.inducedDipolePolar.z+scip3*atom2.inducedDipole.z)*0.5f +
0.5f*(sci4*psc5+scip4*dsc5)*atom1.dipole.z +
0.5f*(sci3*psc5+scip3*dsc5)*atom2.dipole.z;
#ifdef DIRECT_POLARIZATION
real gfd = 0.5*(3*rr2*scip2*scale3i - 5*rr2*(scip3*sci4+sci3*scip4)*scale5i);
real temp5 = 0.5*scale5i;
real fdir_0 = gfd*xr + temp5*(sci4*atom1.inducedDipolePolar.x + scip4*atom1.inducedDipole.x + sci3*atom2.inducedDipolePolar.x + scip3*atom2.inducedDipole.x);
real fdir_1 = gfd*yr + temp5*(sci4*atom1.inducedDipolePolar.y + scip4*atom1.inducedDipole.y + sci3*atom2.inducedDipolePolar.y + scip3*atom2.inducedDipole.y);
real fdir_2 = gfd*zr + temp5*(sci4*atom1.inducedDipolePolar.z + scip4*atom1.inducedDipole.z + sci3*atom2.inducedDipolePolar.z + scip3*atom2.inducedDipole.z);
ftm2i_0 -= fdir_0;
ftm2i_1 -= fdir_1;
ftm2i_2 -= fdir_2;
#else
real scaleF = 0.5f*uScale;
real inducedFactor3 = scip2*rr3*scaleF;
real inducedFactor5 = (sci3*scip4+scip3*sci4)*rr5*scaleF;
real findmp_0 = inducedFactor3*ddsc3_0 - inducedFactor5*ddsc5_0;
real findmp_1 = inducedFactor3*ddsc3_1 - inducedFactor5*ddsc5_1;
real findmp_2 = inducedFactor3*ddsc3_2 - inducedFactor5*ddsc5_2;
ftm2i_0 -= findmp_0;
ftm2i_1 -= findmp_1;
ftm2i_2 -= findmp_2;
#endif
#endif
#if defined T1
real gti2 = 0.5f*(sci4*psc5+scip4*dsc5);
real gti5 = gfi5;
#endif
#if defined T3
real gti3 = 0.5f*(sci3*psc5+scip3*dsc5);
real gti6 = gfi6;
#endif
#if defined T1 || defined T3
real dixdk_0 = atom1.dipole.y*atom2.dipole.z - atom1.dipole.z*atom2.dipole.y;
real dixdk_1 = atom1.dipole.z*atom2.dipole.x - atom1.dipole.x*atom2.dipole.z;
real dixdk_2 = atom1.dipole.x*atom2.dipole.y - atom1.dipole.y*atom2.dipole.x;
#if defined T1
real dixuk_0 = atom1.dipole.y*atom2.inducedDipole.z - atom1.dipole.z*atom2.inducedDipole.y;
real dixuk_1 = atom1.dipole.z*atom2.inducedDipole.x - atom1.dipole.x*atom2.inducedDipole.z;
real dixuk_2 = atom1.dipole.x*atom2.inducedDipole.y - atom1.dipole.y*atom2.inducedDipole.x;
#endif
#endif
#ifdef T1
real dixukp_0 = atom1.dipole.y*atom2.inducedDipolePolar.z - atom1.dipole.z*atom2.inducedDipolePolar.y;
real dixukp_1 = atom1.dipole.z*atom2.inducedDipolePolar.x - atom1.dipole.x*atom2.inducedDipolePolar.z;
real dixukp_2 = atom1.dipole.x*atom2.inducedDipolePolar.y - atom1.dipole.y*atom2.inducedDipolePolar.x;
#endif
#ifdef T1
real dixr_0 = atom1.dipole.y*zr - atom1.dipole.z*yr;
real dixr_1 = atom1.dipole.z*xr - atom1.dipole.x*zr;
real dixr_2 = atom1.dipole.x*yr - atom1.dipole.y*xr;
#endif
#ifdef T1
real ttm2_0 = -rr3*dixdk_0 + gf2*dixr_0;
real ttm2_1 = -rr3*dixdk_1 + gf2*dixr_1;
real ttm2_2 = -rr3*dixdk_2 + gf2*dixr_2;
real ttm2i_0 = -(dixuk_0*psc3+dixukp_0*dsc3)*0.5f + gti2*dixr_0;
real ttm2i_1 = -(dixuk_1*psc3+dixukp_1*dsc3)*0.5f + gti2*dixr_1;
real ttm2i_2 = -(dixuk_2*psc3+dixukp_2*dsc3)*0.5f + gti2*dixr_2;
#endif
#ifdef T3
real dkxr_0 = atom2.dipole.y*zr - atom2.dipole.z*yr;
real dkxr_1 = atom2.dipole.z*xr - atom2.dipole.x*zr;
real dkxr_2 = atom2.dipole.x*yr - atom2.dipole.y*xr;
real dkxui_0 = atom2.dipole.y*atom1.inducedDipole.z - atom2.dipole.z*atom1.inducedDipole.y;
real dkxui_1 = atom2.dipole.z*atom1.inducedDipole.x - atom2.dipole.x*atom1.inducedDipole.z;
real dkxui_2 = atom2.dipole.x*atom1.inducedDipole.y - atom2.dipole.y*atom1.inducedDipole.x;
real dkxuip_0 = atom2.dipole.y*atom1.inducedDipolePolar.z - atom2.dipole.z*atom1.inducedDipolePolar.y;
real dkxuip_1 = atom2.dipole.z*atom1.inducedDipolePolar.x - atom2.dipole.x*atom1.inducedDipolePolar.z;
real dkxuip_2 = atom2.dipole.x*atom1.inducedDipolePolar.y - atom2.dipole.y*atom1.inducedDipolePolar.x;
real ttm3_0 = rr3*dixdk_0 + gf3*dkxr_0;
real ttm3_1 = rr3*dixdk_1 + gf3*dkxr_1;
real ttm3_2 = rr3*dixdk_2 + gf3*dkxr_2;
real ttm3i_0 = -(dkxui_0*psc3+ dkxuip_0*dsc3)*0.5f + gti3*dkxr_0;
real ttm3i_1 = -(dkxui_1*psc3+ dkxuip_1*dsc3)*0.5f + gti3*dkxr_1;
real ttm3i_2 = -(dkxui_2*psc3+ dkxuip_2*dsc3)*0.5f + gti3*dkxr_2;
#endif
if (mScale < 1) {
#ifdef T1
ttm2_0 *= mScale;
ttm2_1 *= mScale;
ttm2_2 *= mScale;
#endif
#ifdef T3
ttm3_0 *= mScale;
ttm3_1 *= mScale;
ttm3_2 *= mScale;
#endif
}
#ifdef F1
outputForce.x = -(ftm2_0+ftm2i_0);
outputForce.y = -(ftm2_1+ftm2i_1);
outputForce.z = -(ftm2_2+ftm2i_2);
#endif
#ifdef T1
outputForce.x = (ttm2_0 + ttm2i_0);
outputForce.y = (ttm2_1 + ttm2i_1);
outputForce.z = (ttm2_2 + ttm2i_2);
#endif
#ifdef T3
outputForce.x = (ttm3_0 + ttm3i_0);
outputForce.y = (ttm3_1 + ttm3i_1);
outputForce.z = (ttm3_2 + ttm3i_2);
#endif
}
plugins/amoeba/platforms/cuda/src/kernels/multipoleElectrostatics.cu
View file @ 82662e25
......@@ -3,8 +3,10 @@
typedef struct {
real4 posq;
real3 force, dipole, inducedDipole, inducedDipolePolar;
#ifdef INCLUDE_QUADRUPOLES
real quadrupoleXX, quadrupoleXY, quadrupoleXZ;
real quadrupoleYY, quadrupoleYZ;
#endif
float thole, damp;
} AtomData;
......@@ -18,11 +20,13 @@ inline __device__ void loadAtomData(AtomData& data, int atom, const real4* __res
data.dipole.x = labFrameDipole[atom*3];
data.dipole.y = labFrameDipole[atom*3+1];
data.dipole.z = labFrameDipole[atom*3+2];
#ifdef INCLUDE_QUADRUPOLES
data.quadrupoleXX = labFrameQuadrupole[atom*5];
data.quadrupoleXY = labFrameQuadrupole[atom*5+1];
data.quadrupoleXZ = labFrameQuadrupole[atom*5+2];
data.quadrupoleYY = labFrameQuadrupole[atom*5+3];
data.quadrupoleYZ = labFrameQuadrupole[atom*5+4];
#endif
data.inducedDipole.x = inducedDipole[atom*3];
data.inducedDipole.y = inducedDipole[atom*3+1];
data.inducedDipole.z = inducedDipole[atom*3+2];
......@@ -92,11 +96,13 @@ extern "C" __global__ void computeElectrostatics(
localData[threadIdx.x].posq = data.posq;
localData[threadIdx.x].dipole = data.dipole;
#ifdef INCLUDE_QUADRUPOLES
localData[threadIdx.x].quadrupoleXX = data.quadrupoleXX;
localData[threadIdx.x].quadrupoleXY = data.quadrupoleXY;
localData[threadIdx.x].quadrupoleXZ = data.quadrupoleXZ;
localData[threadIdx.x].quadrupoleYY = data.quadrupoleYY;
localData[threadIdx.x].quadrupoleYZ = data.quadrupoleYZ;
#endif
localData[threadIdx.x].inducedDipole = data.inducedDipole;
localData[threadIdx.x].inducedDipolePolar = data.inducedDipolePolar;
localData[threadIdx.x].thole = data.thole;
......
plugins/amoeba/platforms/cuda/src/kernels/multipoleFixedField.cu
View file @ 82662e25
......@@ -3,8 +3,10 @@
typedef struct {
real4 posq;
real3 field, fieldPolar, dipole;
#ifdef INCLUDE_QUADRUPOLES
real quadrupoleXX, quadrupoleXY, quadrupoleXZ;
real quadrupoleYY, quadrupoleYZ, quadrupoleZZ;
#endif
float thole, damp;
#ifdef USE_GK
real3 gkField;
......@@ -17,12 +19,14 @@ inline __device__ void loadAtomData(AtomData& data, int atom, const real4* __res
data.dipole.x = labFrameDipole[atom*3];
data.dipole.y = labFrameDipole[atom*3+1];
data.dipole.z = labFrameDipole[atom*3+2];
#ifdef INCLUDE_QUADRUPOLES
data.quadrupoleXX = labFrameQuadrupole[atom*5];
data.quadrupoleXY = labFrameQuadrupole[atom*5+1];
data.quadrupoleXZ = labFrameQuadrupole[atom*5+2];
data.quadrupoleYY = labFrameQuadrupole[atom*5+3];
data.quadrupoleYZ = labFrameQuadrupole[atom*5+4];
data.quadrupoleZZ = -(data.quadrupoleXX+data.quadrupoleYY);
#endif
float2 temp = dampingAndThole[atom];
data.damp = temp.x;
data.thole = temp.y;
......@@ -85,15 +89,15 @@ __device__ void computeOneInteraction(AtomData& atom1, AtomData& atom2, real3 de
real prr7 = 15*(1-psc7)/r7;
real dir = dot(atom1.dipole, deltaR);
real dkr = dot(atom2.dipole, deltaR);
#ifdef INCLUDE_QUADRUPOLES
real3 qi;
qi.x = atom1.quadrupoleXX*deltaR.x + atom1.quadrupoleXY*deltaR.y + atom1.quadrupoleXZ*deltaR.z;
qi.y = atom1.quadrupoleXY*deltaR.x + atom1.quadrupoleYY*deltaR.y + atom1.quadrupoleYZ*deltaR.z;
qi.z = atom1.quadrupoleXZ*deltaR.x + atom1.quadrupoleYZ*deltaR.y + atom1.quadrupoleZZ*deltaR.z;
real qir = dot(qi, deltaR);
real dkr = dot(atom2.dipole, deltaR);
real3 qk;
qk.x = atom2.quadrupoleXX*deltaR.x + atom2.quadrupoleXY*deltaR.y + atom2.quadrupoleXZ*deltaR.z;
qk.y = atom2.quadrupoleXY*deltaR.x + atom2.quadrupoleYY*deltaR.y + atom2.quadrupoleYZ*deltaR.z;
......@@ -106,7 +110,14 @@ __device__ void computeOneInteraction(AtomData& atom1, AtomData& atom2, real3 de
real3 fkd = deltaR*(drr3*atom1.posq.w+drr5*dir+drr7*qir) - drr3*atom1.dipole - 2*drr5*qi;
real3 fip = -deltaR*(prr3*atom2.posq.w-prr5*dkr+prr7*qkr) - prr3*atom2.dipole + 2*prr5*qk;
real3 fkp = deltaR*(prr3*atom1.posq.w+prr5*dir+prr7*qir) - prr3*atom1.dipole - 2*prr5*qi;
#else
real3 fim = -deltaR*(bn1*atom2.posq.w-bn2*dkr) - bn1*atom2.dipole;
real3 fkm = deltaR*(bn1*atom1.posq.w+bn2*dir) - bn1*atom1.dipole;
real3 fid = -deltaR*(drr3*atom2.posq.w-drr5*dkr) - drr3*atom2.dipole;
real3 fkd = deltaR*(drr3*atom1.posq.w+drr5*dir) - drr3*atom1.dipole;
real3 fip = -deltaR*(prr3*atom2.posq.w-prr5*dkr) - prr3*atom2.dipole;
real3 fkp = deltaR*(prr3*atom1.posq.w+prr5*dir) - prr3*atom1.dipole;
#endif
// increment the field at each site due to this interaction
fields[0] = fim-fid;
......@@ -153,29 +164,34 @@ __device__ void computeOneInteraction(AtomData& atom1, AtomData& atom2, real3 de
real rr5_2 = 2*rr5;
real3 qDotDelta;
qDotDelta.x = deltaR.x*atom2.quadrupoleXX + deltaR.y*atom2.quadrupoleXY + deltaR.z*atom2.quadrupoleXZ;
qDotDelta.y = deltaR.x*atom2.quadrupoleXY + deltaR.y*atom2.quadrupoleYY + deltaR.z*atom2.quadrupoleYZ;
qDotDelta.z = deltaR.x*atom2.quadrupoleXZ + deltaR.y*atom2.quadrupoleYZ + deltaR.z*atom2.quadrupoleZZ;
real dotdd = dot(deltaR, atom2.dipole);
real dotqd = dot(deltaR, qDotDelta);
real factor = -rr3*atom2.posq.w + rr5*dotdd - rr7*dotqd;
real3 field1 = deltaR*factor - rr3*atom2.dipole + rr5_2*qDotDelta;
real dir = dot(atom1.dipole, deltaR);
real dkr = dot(atom2.dipole, deltaR);
#ifdef INCLUDE_QUADRUPOLES
real3 qi;
qi.x = atom1.quadrupoleXX*deltaR.x + atom1.quadrupoleXY*deltaR.y + atom1.quadrupoleXZ*deltaR.z;
qi.y = atom1.quadrupoleXY*deltaR.x + atom1.quadrupoleYY*deltaR.y + atom1.quadrupoleYZ*deltaR.z;
qi.z = atom1.quadrupoleXZ*deltaR.x + atom1.quadrupoleYZ*deltaR.y + atom1.quadrupoleZZ*deltaR.z;
real qir = dot(qi, deltaR);
real3 qk;
qk.x = atom2.quadrupoleXX*deltaR.x + atom2.quadrupoleXY*deltaR.y + atom2.quadrupoleXZ*deltaR.z;
qk.y = atom2.quadrupoleXY*deltaR.x + atom2.quadrupoleYY*deltaR.y + atom2.quadrupoleYZ*deltaR.z;
qk.z = atom2.quadrupoleXZ*deltaR.x + atom2.quadrupoleYZ*deltaR.y + atom2.quadrupoleZZ*deltaR.z;
real qkr = dot(qk, deltaR);
real factor = -rr3*atom2.posq.w + rr5*dkr - rr7*qkr;
real3 field1 = deltaR*factor - rr3*atom2.dipole + rr5_2*qk;
factor = rr3*atom1.posq.w + rr5*dir + rr7*qir;
real3 field2 = deltaR*factor - rr3*atom1.dipole - rr5_2*qi;
#else
real factor = -rr3*atom2.posq.w + rr5*dkr;
real3 field1 = deltaR*factor - rr3*atom2.dipole;
factor = rr3*atom1.posq.w + rr5*dir;
real3 field2 = deltaR*factor - rr3*atom1.dipole;
#endif
fields[0] = dScale*field1;
fields[1] = pScale*field1;
qDotDelta.x = deltaR.x*atom1.quadrupoleXX + deltaR.y*atom1.quadrupoleXY + deltaR.z*atom1.quadrupoleXZ;
qDotDelta.y = deltaR.x*atom1.quadrupoleXY + deltaR.y*atom1.quadrupoleYY + deltaR.z*atom1.quadrupoleYZ;
qDotDelta.z = deltaR.x*atom1.quadrupoleXZ + deltaR.y*atom1.quadrupoleYZ + deltaR.z*atom1.quadrupoleZZ;
dotdd = dot(deltaR, atom1.dipole);
dotqd = dot(deltaR, qDotDelta);
factor = rr3*atom1.posq.w + rr5*dotdd + rr7*dotqd;
real3 field2 = deltaR*factor - rr3*atom1.dipole - rr5_2*qDotDelta;
fields[2] = dScale*field2;
fields[3] = pScale*field2;
}
......@@ -200,6 +216,7 @@ __device__ void computeOneGkInteraction(AtomData& atom1, AtomData& atom2, real3
real uyk = atom2.dipole.y;
real uzk = atom2.dipole.z;
#ifdef INCLUDE_QUADRUPOLES
real qxxi = atom1.quadrupoleXX;
real qxyi = atom1.quadrupoleXY;
real qxzi = atom1.quadrupoleXZ;
......@@ -212,7 +229,20 @@ __device__ void computeOneGkInteraction(AtomData& atom1, AtomData& atom2, real3
real qyyk = atom2.quadrupoleYY;
real qyzk = atom2.quadrupoleYZ;
real qzzk = atom2.quadrupoleZZ;
#else
real qxxi = 0;
real qxyi = 0;
real qxzi = 0;
real qyyi = 0;
real qyzi = 0;
real qzzi = 0;
real qxxk = 0;
real qxyk = 0;
real qxzk = 0;
real qyyk = 0;
real qyzk = 0;
real qzzk = 0;
#endif
real xr2 = delta.x*delta.x;
real yr2 = delta.y*delta.y;
real zr2 = delta.z*delta.z;
......@@ -438,12 +468,14 @@ extern "C" __global__ void computeFixedField(
const unsigned int localAtomIndex = threadIdx.x;
localData[localAtomIndex].posq = data.posq;
localData[localAtomIndex].dipole = data.dipole;
#ifdef INCLUDE_QUADRUPOLES
localData[localAtomIndex].quadrupoleXX = data.quadrupoleXX;
localData[localAtomIndex].quadrupoleXY = data.quadrupoleXY;
localData[localAtomIndex].quadrupoleXZ = data.quadrupoleXZ;
localData[localAtomIndex].quadrupoleYY = data.quadrupoleYY;
localData[localAtomIndex].quadrupoleYZ = data.quadrupoleYZ;
localData[localAtomIndex].quadrupoleZZ = data.quadrupoleZZ;
#endif
localData[localAtomIndex].thole = data.thole;
localData[localAtomIndex].damp = data.damp;
#ifdef USE_GK
......
plugins/amoeba/platforms/cuda/src/kernels/pmeElectrostaticPairForceNoQuadrupoles.cu 0 → 100644
View file @ 82662e25
__device__ void
#ifdef APPLY_SCALE
computeOneInteractionF1(
#else
computeOneInteractionF1NoScale(
#endif
AtomData& atom1, volatile AtomData& atom2, real4 delta, real4 bn, real bn5, float forceFactor,
#ifdef APPLY_SCALE
float dScale, float pScale, float mScale,
#endif
real3& force, real& energy) {
real xr = delta.x;
real yr = delta.y;
real zr = delta.z;
#ifdef APPLY_SCALE
real rr1 = delta.w;
#endif
// set the permanent multipole and induced dipole values;
real ci = atom1.q;
real di1 = atom1.dipole.x;
real di2 = atom1.dipole.y;
real di3 = atom1.dipole.z;
real ck = atom2.q;
real dk1 = atom2.dipole.x;
real dk2 = atom2.dipole.y;
real dk3 = atom2.dipole.z;
real bn1 = bn.x;
real bn2 = bn.y;
real bn3 = bn.z;
real bn4 = bn.w;
#ifdef APPLY_SCALE
real offset = 1-mScale;
real rr3 = rr1*rr1*rr1;
real gf4 = 2*(bn2 - 3*offset*rr3*rr1*rr1);
#else
real gf4 = 2*bn2;
#endif
real ftm21 = 0;
real ftm22 = 0;
real ftm23 = 0;
// calculate the scalar products for permanent components
real gl6 = di1*dk1 + di2*dk2 + di3*dk3;
real sc3 = di1*xr + di2*yr + di3*zr;
real sc4 = dk1*xr + dk2*yr + dk3*zr;
real gl0 = ci*ck;
real gl1 = ck*sc3 - ci*sc4;
real gl2 = -sc3*sc4;
#ifdef APPLY_SCALE
energy += forceFactor*(-offset*rr1*gl0 + (bn1-offset*rr3)*(gl1+gl6) + (bn2-offset*(3*rr3*rr1*rr1))*gl2);
#else
energy += forceFactor*(bn1*(gl1+gl6) + bn2*gl2);
#endif
real gf1 = bn1*gl0 + bn2*(gl1+gl6) + bn3*gl2;
#ifdef APPLY_SCALE
gf1 -= offset*(rr3*gl0 + (3*rr3*rr1*rr1)*(gl1+gl6) + (15*rr3*rr3*rr1)*gl2);
#endif
ftm21 += gf1*xr;
ftm22 += gf1*yr;
ftm23 += gf1*zr;
#ifdef APPLY_SCALE
real gf2 = -ck*bn1 + sc4*bn2 - offset*(-ck*rr3 + sc4*(3*rr3*rr1*rr1));
#else
real gf2 = -ck*bn1 + sc4*bn2;
#endif
ftm21 += gf2*di1;
ftm22 += gf2*di2;
ftm23 += gf2*di3;
#ifdef APPLY_SCALE
real gf3 = ci*bn1 + sc3*bn2 - offset*(ci*rr3 + sc3*(3*rr3*rr1*rr1));
#else
real gf3 = ci*bn1 + sc3*bn2;
#endif
ftm21 += gf3*dk1;
ftm22 += gf3*dk2;
ftm23 += gf3*dk3;
force.x = ftm21;
force.y = ftm22;
force.z = ftm23;
}
__device__ void
#ifdef APPLY_SCALE
computeOneInteractionF2(
#else
computeOneInteractionF2NoScale(
#endif
AtomData& atom1, volatile AtomData& atom2, real4 delta, real4 bn, float forceFactor,
#ifdef APPLY_SCALE
float dScale, float pScale, float mScale,
#endif
real3& force, real& energy) {
const float uScale = 1;
real xr = delta.x;
real yr = delta.y;
real zr = delta.z;
real rr1 = delta.w;
// set the permanent multipole and induced dipole values;
real ci = atom1.q;
real di1 = atom1.dipole.x;
real di2 = atom1.dipole.y;
real di3 = atom1.dipole.z;
real bn1 = bn.x;
real bn2 = bn.y;
real bn3 = bn.z;
real bn4 = bn.w;
real damp = atom1.damp*atom2.damp;
if (damp != 0) {
real pgamma = atom1.thole < atom2.thole ? atom1.thole : atom2.thole;
real ratio = RECIP(rr1*damp);
damp = -pgamma*ratio*ratio*ratio;
damp = damp < -50 ? 0 : damp;
}
real scale5 = (damp == 0) ? 1 : (1 - (1-damp)*EXP(damp));
real rr5 = rr1*rr1;
rr5 = 3*rr1*rr5*rr5;
#ifdef APPLY_SCALE
real psc5 = rr5*(1 - scale5*pScale);
real dsc5 = rr5*(1 - scale5*dScale);
real usc5 = rr5*(1 - scale5*uScale);
#else
real psc5 = rr5*(1 - scale5);
#endif
real ftm21 = 0;
real ftm22 = 0;
real ftm23 = 0;
real expdamp = EXP(damp);
real scale3 = (damp == 0) ? 1 : (1 - expdamp);
real rr3 = rr1*rr1*rr1;
#ifdef APPLY_SCALE
real psc3 = rr3*(1 - scale3*pScale);
real dsc3 = rr3*(1 - scale3*dScale);
real usc3 = rr3*(1 - scale3*uScale);
#else
real psc3 = rr3*(1 - scale3);
#endif
real scale7 = (damp == 0) ? 1 : (1 - (1-damp+0.6f*damp*damp)*expdamp);
#ifdef APPLY_SCALE
real psc7 = (15*rr3*rr3*rr1)*(1 - scale7*pScale);
real dsc7 = (15*rr3*rr3*rr1)*(1 - scale7*dScale);
#else
real psc7 = (15*rr3*rr3*rr1)*(1 - scale7);
#endif
real sc3 = di1*xr + di2*yr + di3*zr;
real gfi3 = ci*bn1 + sc3*bn2;
real prefactor1;
prefactor1 = 0.5f*(ci*psc3 + sc3*psc5 - gfi3);
ftm21 -= prefactor1*atom2.inducedDipole.x;
ftm22 -= prefactor1*atom2.inducedDipole.y;
ftm23 -= prefactor1*atom2.inducedDipole.z;
#ifdef APPLY_SCALE
prefactor1 = 0.5f*(ci*dsc3 + sc3*dsc5 - gfi3);
#endif
ftm21 -= prefactor1*atom2.inducedDipolePolar.x;
ftm22 -= prefactor1*atom2.inducedDipolePolar.y;
ftm23 -= prefactor1*atom2.inducedDipolePolar.z;
real sci4 = atom2.inducedDipole.x*xr + atom2.inducedDipole.y*yr + atom2.inducedDipole.z*zr;
energy += forceFactor*0.5f*sci4*((psc3-bn1)*ci + (psc5-bn2)*sc3);
real scip4 = atom2.inducedDipolePolar.x*xr + atom2.inducedDipolePolar.y*yr + atom2.inducedDipolePolar.z*zr;
#ifndef DIRECT_POLARIZATION
#ifdef APPLY_SCALE
prefactor1 = 0.5f*(bn2 - usc5);
#else
prefactor1 = 0.5f*(bn2 - psc5);
#endif
ftm21 += prefactor1*((sci4*atom1.inducedDipolePolar.x + scip4*atom1.inducedDipole.x));
ftm22 += prefactor1*((sci4*atom1.inducedDipolePolar.y + scip4*atom1.inducedDipole.y));
ftm23 += prefactor1*((sci4*atom1.inducedDipolePolar.z + scip4*atom1.inducedDipole.z));
#endif
#ifdef APPLY_SCALE
prefactor1 = 0.5f*(bn2*(sci4+scip4) - (sci4*psc5+scip4*dsc5));
#else
sci4 += scip4;
prefactor1 = 0.5f*sci4*(bn2 - psc5);
#endif
ftm21 += prefactor1*di1;
ftm22 += prefactor1*di2;
ftm23 += prefactor1*di3;
#ifdef APPLY_SCALE
real gli1 = -ci*sci4;
real gli2 = -sc3*sci4;
real glip1 = -ci*scip4;
real glip2 = -sc3*scip4;
#else
real gli1 = -ci*sci4;
real gli2 = -sc3*sci4;
#endif
#ifdef APPLY_SCALE
real gfi1 = (bn2*(gli1+glip1) + bn3*(gli2+glip2));
gfi1 -= (rr1*rr1)*(3*(gli1*psc3 + glip1*dsc3) + 5*(gli2*psc5 + glip2*dsc5));
#else
real gfi1 = bn2*gli1 + bn3*gli2;
gfi1 -= (rr1*rr1)*(3*gli1*psc3 + 5*gli2*psc5);
#endif
gfi1 *= 0.5f;
ftm21 += gfi1*xr;
ftm22 += gfi1*yr;
ftm23 += gfi1*zr;
if (damp != 0) {
real expdamp = EXP(damp);
real temp3 = -1.5f*damp*expdamp*rr1*rr1;
real temp5 = -damp;
real temp7 = -0.2f - 0.6f*damp;
real ddsc31 = temp3*xr;
real ddsc32 = temp3*yr;
real ddsc33 = temp3*zr;
real ddsc51 = temp5*ddsc31;
real ddsc52 = temp5*ddsc32;
real ddsc53 = temp5*ddsc33;
real ddsc71 = temp7*ddsc51;
real ddsc72 = temp7*ddsc52;
real ddsc73 = temp7*ddsc53;
real rr3 = rr1*rr1*rr1;
#ifdef APPLY_SCALE
temp3 = (gli1*pScale + glip1*dScale);
temp5 = (3*rr1*rr1)*(gli2*pScale + glip2*dScale);
#else
temp3 = gli1;
temp5 = (3*rr1*rr1)*gli2;
#endif
ftm21 -= rr3*(temp3*ddsc31 + temp5*ddsc51);
ftm22 -= rr3*(temp3*ddsc32 + temp5*ddsc52);
ftm23 -= rr3*(temp3*ddsc33 + temp5*ddsc53);
}
//K
real dk1 = atom2.dipole.x;
real dk2 = atom2.dipole.y;
real dk3 = atom2.dipole.z;
real sc4 = dk1*xr + dk2*yr + dk3*zr;
real ck = atom2.q;
real gfi2 = (-ck*bn1 + sc4*bn2);
prefactor1 = 0.5f*(ck*psc3 - sc4*psc5 + gfi2);
ftm21 += prefactor1*atom1.inducedDipole.x;
ftm22 += prefactor1*atom1.inducedDipole.y;
ftm23 += prefactor1*atom1.inducedDipole.z;
#ifdef APPLY_SCALE
prefactor1 = 0.5f*(ck*dsc3 - sc4*dsc5 + gfi2);
#endif
ftm21 += prefactor1*atom1.inducedDipolePolar.x;
ftm22 += prefactor1*atom1.inducedDipolePolar.y;
ftm23 += prefactor1*atom1.inducedDipolePolar.z;
real sci3 = atom1.inducedDipole.x*xr + atom1.inducedDipole.y*yr + atom1.inducedDipole.z*zr;
energy += forceFactor*0.5f*sci3*(ck*(bn1-psc3) - sc4*(bn2-psc5));
real scip3 = atom1.inducedDipolePolar.x*xr + atom1.inducedDipolePolar.y*yr + atom1.inducedDipolePolar.z*zr;
#ifndef DIRECT_POLARIZATION
#ifdef APPLY_SCALE
prefactor1 = 0.5f*(bn2 - usc5);
#else
prefactor1 = 0.5f*(bn2 - psc5);
#endif
ftm21 += prefactor1*(sci3*atom2.inducedDipolePolar.x + scip3*atom2.inducedDipole.x);
ftm22 += prefactor1*(sci3*atom2.inducedDipolePolar.y + scip3*atom2.inducedDipole.y);
ftm23 += prefactor1*(sci3*atom2.inducedDipolePolar.z + scip3*atom2.inducedDipole.z);
real sci34;
sci4 = atom2.inducedDipole.x*xr + atom2.inducedDipole.y*yr + atom2.inducedDipole.z*zr;
scip4 = atom2.inducedDipolePolar.x*xr + atom2.inducedDipolePolar.y*yr + atom2.inducedDipolePolar.z*zr;
sci34 = (sci3*scip4+scip3*sci4);
#ifdef APPLY_SCALE
gfi1 = sci34*(usc5*(5*rr1*rr1) -bn3);
#else
gfi1 = sci34*(psc5*(5*rr1*rr1) -bn3);
#endif
#else
gfi1 = 0;
#endif
#ifdef APPLY_SCALE
prefactor1 = 0.5f*(bn2*(sci3+scip3) - (sci3*psc5+scip3*dsc5));
#else
sci3 += scip3;
prefactor1 = 0.5f*sci3*(bn2 - psc5);
#endif
ftm21 += prefactor1*dk1;
ftm22 += prefactor1*dk2;
ftm23 += prefactor1*dk3;
#ifdef APPLY_SCALE
real gfi6 = -bn3*(sci3+scip3) + (sci3*psc7+scip3*dsc7);
#else
real gfi6 = sci3*(psc7 - bn3);
#endif
real sci1 = atom1.inducedDipole.x*dk1 + atom1.inducedDipole.y*dk2 + atom1.inducedDipole.z*dk3 + di1*atom2.inducedDipole.x + di2*atom2.inducedDipole.y + di3*atom2.inducedDipole.z;
energy += forceFactor*0.5f*(sci1*(bn1-psc3));
real scip1 = atom1.inducedDipolePolar.x*dk1 + atom1.inducedDipolePolar.y*dk2 + atom1.inducedDipolePolar.z*dk3 + di1*atom2.inducedDipolePolar.x + di2*atom2.inducedDipolePolar.y + di3*atom2.inducedDipolePolar.z;
#ifndef APPLY_SCALE
sci1 += scip1;
#endif
real scip2 = atom1.inducedDipole.x*atom2.inducedDipolePolar.x +
atom1.inducedDipole.y*atom2.inducedDipolePolar.y +
atom1.inducedDipole.z*atom2.inducedDipolePolar.z +
atom2.inducedDipole.x*atom1.inducedDipolePolar.x +
atom2.inducedDipole.y*atom1.inducedDipolePolar.y +
atom2.inducedDipole.z*atom1.inducedDipolePolar.z;
gli1 = ck*sci3 + sci1;
gli2 = -sci3*sc4;
#ifdef APPLY_SCALE
glip1 = ck*scip3 + scip1;
glip2 = -scip3*sc4;
#endif
#ifdef APPLY_SCALE
gfi1 += (bn2*(gli1+glip1) + bn3*(gli2+glip2));
gfi1 -= (rr1*rr1)*(3*(gli1*psc3 + glip1*dsc3) + 5*(gli2*psc5 + glip2*dsc5));
#else
gfi1 += (bn2*gli1 + bn3*gli2);
gfi1 -= (rr1*rr1)*(3*gli1*psc3 + 5*gli2*psc5);
#endif
#ifndef DIRECT_POLARIZATION
#ifdef APPLY_SCALE
gfi1 += scip2*(bn2 - (3*rr1*rr1)*usc3);
#else
gfi1 += scip2*(bn2 - (3*rr1*rr1)*psc3);
#endif
#endif
gfi1 *= 0.5f;
ftm21 += gfi1*xr;
ftm22 += gfi1*yr;
ftm23 += gfi1*zr;
if (damp != 0) {
real expdamp = EXP(damp);
real temp3 = -1.5f*damp*expdamp*rr1*rr1;
real temp5 = -damp;
real temp7 = -0.2f - 0.6f*damp;
real ddsc31 = temp3*xr;
real ddsc32 = temp3*yr;
real ddsc33 = temp3*zr;
real ddsc51 = temp5*ddsc31;
real ddsc52 = temp5*ddsc32;
real ddsc53 = temp5*ddsc33;
real ddsc71 = temp7*ddsc51;
real ddsc72 = temp7*ddsc52;
real ddsc73 = temp7*ddsc53;
real rr3 = rr1*rr1*rr1;
#ifdef APPLY_SCALE
temp3 = gli1*pScale + glip1*dScale;
temp5 = (3*rr1*rr1)*(gli2*pScale + glip2*dScale);
#else
temp3 = gli1;
temp5 = (3*rr1*rr1)*gli2;
#endif
ftm21 -= rr3*(temp3*ddsc31 + temp5*ddsc51);
ftm22 -= rr3*(temp3*ddsc32 + temp5*ddsc52);
ftm23 -= rr3*(temp3*ddsc33 + temp5*ddsc53);
#ifndef DIRECT_POLARIZATION
#ifdef APPLY_SCALE
temp3 = uScale*scip2;
temp5 = -(3*rr1*rr1)*uScale*sci34;
#else
temp3 = scip2;
temp5 = -(3*rr1*rr1)*sci34;
#endif
ftm21 -= rr3*(temp3*ddsc31 + temp5*ddsc51);
ftm22 -= rr3*(temp3*ddsc32 + temp5*ddsc52);
ftm23 -= rr3*(temp3*ddsc33 + temp5*ddsc53);
#endif
}
force.x += ftm21;
force.y += ftm22;
force.z += ftm23;
}
__device__ void
#ifdef APPLY_SCALE
computeOneInteractionT1(
#else
computeOneInteractionT1NoScale(
#endif
AtomData& atom1, volatile AtomData& atom2, const real4 delta, const real4 bn
#ifdef APPLY_SCALE
, float dScale, float pScale, float mScale
#endif
) {
real xr = delta.x;
real yr = delta.y;
real zr = delta.z;
#ifdef APPLY_SCALE
real rr1 = delta.w;
#endif
// set the permanent multipole and induced dipole values;
real di1 = atom1.dipole.x;
real di2 = atom1.dipole.y;
real di3 = atom1.dipole.z;
real ck = atom2.q;
real dk1 = atom2.dipole.x;
real dk2 = atom2.dipole.y;
real dk3 = atom2.dipole.z;
real bn1 = bn.x;
real bn2 = bn.y;
real bn3 = bn.z;
real bn4 = bn.w;
// apply Thole polarization damping to scale factors
#ifdef APPLY_SCALE
real rr2 = rr1*rr1;
real rr3 = rr1*rr2;
real rr5 = 3*rr3*rr2;
real rr7 = 5*rr5*rr2;
real rr9 = 7*rr7*rr2;
real scale = 1-mScale;
real prefactor = scale*rr3 - bn1;
#else
real prefactor = -bn1;
#endif
real dixdk1 = di2*dk3 - di3*dk2;
real ttm21 = prefactor*dixdk1;
real dixdk2 = di3*dk1 - di1*dk3;
real ttm22 = prefactor*dixdk2;
real dixdk3 = di1*dk2 - di2*dk1;
real ttm23 = prefactor*dixdk3;
real sc4 = dk1*xr + dk2*yr + dk3*zr;
real sc6 = 0;
real gf2 = -ck*bn1 + sc4*bn2;
#ifdef APPLY_SCALE
real gfr2 = -ck*rr3 + sc4*rr5;
prefactor = (gf2 - scale*gfr2);
#else
prefactor = gf2;
#endif
ttm21 += prefactor*(di2*zr - di3*yr);
ttm22 += prefactor*(di3*xr - di1*zr);
ttm23 += prefactor*(di1*yr - di2*xr);
atom1.torque.x += ttm21;
atom1.torque.y += ttm22;
atom1.torque.z += ttm23;
}
__device__ void
#ifdef APPLY_SCALE
computeOneInteractionT2(
#else
computeOneInteractionT2NoScale(
#endif
AtomData& atom1, volatile AtomData& atom2, const real4 delta, const real4 bn
#ifdef APPLY_SCALE
, float dScale, float pScale, float mScale
#endif
) {
real xr = delta.x;
real yr = delta.y;
real zr = delta.z;
real rr1 = delta.w;
// set the permanent multipole and induced dipole values;
real di1 = atom1.dipole.x;
real di2 = atom1.dipole.y;
real di3 = atom1.dipole.z;
real bn1 = bn.x;
real bn2 = bn.y;
real bn3 = bn.z;
// apply Thole polarization damping to scale factors
real scale3 = 1;
real scale5 = 1;
real scale7 = 1;
real damp = atom1.damp*atom2.damp;
if (damp != 0) {
real pgamma = atom1.thole < atom2.thole ? atom1.thole : atom2.thole;
real ratio = RECIP(rr1*damp);
damp = -pgamma*ratio*ratio*ratio;
real expdamp = EXP(damp);
scale3 = 1 - expdamp;
scale5 = 1 - (1-damp)*expdamp;
scale7 = 1 - (1-damp+0.6f*damp*damp)*expdamp;
}
real rr3 = rr1*rr1*rr1;
#ifdef APPLY_SCALE
real dsc3 = rr3*(1 - scale3*dScale);
real dsc5 = (3*rr3*rr1*rr1)* (1 - scale5*dScale);
real dsc7 = (15*rr3*rr3*rr1)*(1 - scale7*dScale);
real psc3 = rr3*(1 - scale3*pScale);
real psc5 = (3*rr3*rr1*rr1)*(1 - scale5*pScale);
real psc7 = (15*rr3*rr3*rr1)*(1 - scale7*pScale);
#else
real psc3 = rr3*(1 - scale3);
real psc5 = (3*rr3*rr1*rr1)*(1 - scale5);
real psc7 = (15*rr3*rr3*rr1)*(1 - scale7);
#endif
real prefactor1 = 0.5f*(psc3 - bn1);
#ifdef APPLY_SCALE
real prefactor2 = 0.5f*(dsc3 - bn1);
#endif
real dixuk1 = di2*atom2.inducedDipole.z - di3*atom2.inducedDipole.y;
real dixukp1 = di2*atom2.inducedDipolePolar.z - di3*atom2.inducedDipolePolar.y;
#ifdef APPLY_SCALE
real ttm2i1 = prefactor1*dixuk1 + prefactor2*dixukp1;
#else
real ttm2i1 = prefactor1*(dixuk1 + dixukp1);
#endif
real dixuk2 = di3*atom2.inducedDipole.x - di1*atom2.inducedDipole.z;
real dixukp2 = di3*atom2.inducedDipolePolar.x - di1*atom2.inducedDipolePolar.z;
#ifdef APPLY_SCALE
real ttm2i2 = prefactor1*dixuk2 + prefactor2*dixukp2;
#else
real ttm2i2 = prefactor1*(dixuk2 + dixukp2);
#endif
real dixuk3 = di1*atom2.inducedDipole.y - di2*atom2.inducedDipole.x;
real dixukp3 = di1*atom2.inducedDipolePolar.y - di2*atom2.inducedDipolePolar.x;
#ifdef APPLY_SCALE
real ttm2i3 = prefactor1*dixuk3 + prefactor2*dixukp3;
#else
real ttm2i3 = prefactor1*(dixuk3 + dixukp3);
#endif
real sci4 = atom2.inducedDipole.x*xr + atom2.inducedDipole.y*yr + atom2.inducedDipole.z*zr;
real scip4 = atom2.inducedDipolePolar.x*xr + atom2.inducedDipolePolar.y*yr + atom2.inducedDipolePolar.z*zr;
real gti2 = bn2*(sci4+scip4);
#ifdef APPLY_SCALE
real gtri2 = (sci4*psc5+scip4*dsc5);
#else
real gtri2 = psc5*(sci4+scip4);
#endif
prefactor1 = 0.5f*(gti2 - gtri2);
ttm2i1 += prefactor1*(di2*zr - di3*yr);
ttm2i2 += prefactor1*(di3*xr - di1*zr);
ttm2i3 += prefactor1*(di1*yr - di2*xr);
atom1.torque.x += ttm2i1;
atom1.torque.y += ttm2i2;
atom1.torque.z += ttm2i3;
}
plugins/amoeba/platforms/cuda/src/kernels/pmeMultipoleElectrostatics.cu
View file @ 82662e25
......@@ -2,9 +2,12 @@
typedef struct {
real3 pos, force, torque, dipole, inducedDipole, inducedDipolePolar;
real q, quadrupoleXX, quadrupoleXY, quadrupoleXZ;
real quadrupoleYY, quadrupoleYZ;
float thole, damp, padding;
real q;
float thole, damp;
#ifdef INCLUDE_QUADRUPOLES
real quadrupoleXX, quadrupoleXY, quadrupoleXZ, quadrupoleYY, quadrupoleYZ;
float padding;
#endif
} AtomData;
__device__ void computeOneInteractionF1(AtomData& atom1, volatile AtomData& atom2, real4 delta, real4 bn, real bn5, float forceFactor, float dScale, float pScale, float mScale, real3& force, real& energy);
......@@ -24,11 +27,13 @@ inline __device__ void loadAtomData(AtomData& data, int atom, const real4* __res
data.dipole.x = labFrameDipole[atom*3];
data.dipole.y = labFrameDipole[atom*3+1];
data.dipole.z = labFrameDipole[atom*3+2];
#ifdef INCLUDE_QUADRUPOLES
data.quadrupoleXX = labFrameQuadrupole[atom*5];
data.quadrupoleXY = labFrameQuadrupole[atom*5+1];
data.quadrupoleXZ = labFrameQuadrupole[atom*5+2];
data.quadrupoleYY = labFrameQuadrupole[atom*5+3];
data.quadrupoleYZ = labFrameQuadrupole[atom*5+4];
#endif
data.inducedDipole.x = inducedDipole[atom*3];
data.inducedDipole.y = inducedDipole[atom*3+1];
data.inducedDipole.z = inducedDipole[atom*3+2];
......@@ -158,12 +163,16 @@ __device__ void computeSelfEnergyAndTorque(AtomData& atom1, real& energy) {
real fterm = -EWALD_ALPHA/SQRT_PI;
real cii = atom1.q*atom1.q;
real dii = dot(atom1.dipole, atom1.dipole);
#ifdef INCLUDE_QUADRUPOLES
real qii = 2*(atom1.quadrupoleXX*atom1.quadrupoleXX +
atom1.quadrupoleYY*atom1.quadrupoleYY +
atom1.quadrupoleXX*atom1.quadrupoleYY +
atom1.quadrupoleXY*atom1.quadrupoleXY +
atom1.quadrupoleXZ*atom1.quadrupoleXZ +
atom1.quadrupoleYZ*atom1.quadrupoleYZ);
#else
real qii = 0;
#endif
real uii = dot(atom1.dipole, atom1.inducedDipole);
real selfEnergy = (cii + term*(dii/3 + 2*term*qii/5));
selfEnergy += term*uii/3;
......@@ -216,11 +225,13 @@ extern "C" __global__ void computeElectrostatics(
localData[threadIdx.x].pos = data.pos;
localData[threadIdx.x].q = data.q;
localData[threadIdx.x].dipole = data.dipole;
#ifdef INCLUDE_QUADRUPOLES
localData[threadIdx.x].quadrupoleXX = data.quadrupoleXX;
localData[threadIdx.x].quadrupoleXY = data.quadrupoleXY;
localData[threadIdx.x].quadrupoleXZ = data.quadrupoleXZ;
localData[threadIdx.x].quadrupoleYY = data.quadrupoleYY;
localData[threadIdx.x].quadrupoleYZ = data.quadrupoleYZ;
#endif
localData[threadIdx.x].inducedDipole = data.inducedDipole;
localData[threadIdx.x].inducedDipolePolar = data.inducedDipolePolar;
localData[threadIdx.x].thole = data.thole;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaMultipoleForce.cpp
View file @ 82662e25
......@@ -50,6 +50,8 @@
using namespace OpenMM;
using namespace std;
const double TOL = 1e-4;
extern "C" void registerAmoebaCudaKernelFactories();
......@@ -2893,6 +2895,75 @@ static void testMultipoleGridPotential( FILE* log ) {
}
/**
* Test whether the alternate kernels with no quadrupoles work correctly.
*/
static void testNoQuadrupoles(bool usePme) {
string testName = "testNoQuadrupoles";
int inputPmeGridDimension = 10;
double cutoff = 0.3;
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
setupMultipoleAmmonia(system, amoebaMultipoleForce, usePme ? AmoebaMultipoleForce::PME : AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Direct,
cutoff, inputPmeGridDimension);
// First compute forces with quadrupoles. This ensures they will be included in the kernel.
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("CUDA"));
vector<Vec3> forces1;
double energy1;
getForcesEnergyMultipoleAmmonia(context, forces1, energy1);
// Now set all quadrupoles to zero and recalculate.
for (int i = 0; i < system.getNumParticles(); i++) {
double charge, thole, damping, polarity;
int axisType, atomX, atomY, atomZ;
vector<double> dipole, quadrupole;
amoebaMultipoleForce->getMultipoleParameters(i, charge, dipole, quadrupole, axisType, atomZ, atomX, atomY, thole, damping, polarity);
for (int j = 0; j < (int) quadrupole.size(); j++)
quadrupole[j] = 0;
amoebaMultipoleForce->setMultipoleParameters(i, charge, dipole, quadrupole, axisType, atomZ, atomX, atomY, thole, damping, polarity);
}
amoebaMultipoleForce->updateParametersInContext(context);
vector<Vec3> forces2;
double energy2;
getForcesEnergyMultipoleAmmonia(context, forces2, energy2);
ASSERT(energy1 != energy2);
// Create a new context with no quadrupoles from the beginning.
LangevinIntegrator integrator2(0.0, 0.1, 0.01);
Context context2(system, integrator2, Platform::getPlatformByName("CUDA"));
vector<Vec3> forces3;
double energy3;
getForcesEnergyMultipoleAmmonia(context2, forces3, energy3);
double tolerance = 1e-5;
compareForcesEnergy(testName, energy2, energy3, forces2, forces3, tolerance, NULL);
// If we try to set a quadrupole, that should produce and exception.
double charge, thole, damping, polarity;
int axisType, atomX, atomY, atomZ;
vector<double> dipole, quadrupole;
amoebaMultipoleForce->getMultipoleParameters(0, charge, dipole, quadrupole, axisType, atomZ, atomX, atomY, thole, damping, polarity);
quadrupole[0] = 1.0;
amoebaMultipoleForce->setMultipoleParameters(0, charge, dipole, quadrupole, axisType, atomZ, atomX, atomY, thole, damping, polarity);
bool threwException = false;
try {
amoebaMultipoleForce->updateParametersInContext(context2);
}
catch (OpenMMException& ex) {
threwException = true;
}
ASSERT(threwException);
}
int main(int argc, char* argv[]) {
try {
std::cout << "TestCudaAmoebaMultipoleForce running test..." << std::endl;
......@@ -2940,6 +3011,9 @@ int main(int argc, char* argv[]) {
// large box of water
testPMEMutualPolarizationLargeWater( log );
testNoQuadrupoles(false);
testNoQuadrupoles(true);
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
wrappers/python/simtk/openmm/app/statedatareporter.py
View file @ 82662e25
......@@ -31,8 +31,16 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
__author__ = "Peter Eastman"
__version__ = "1.0"
import bz2
import gzip
try:
import bz2
have_bz2 = True
except: have_bz2 = False
try:
import gzip
have_gzip = True
except: have_gzip = False
import simtk.openmm as mm
import simtk.unit as unit
import math
......@@ -83,8 +91,12 @@ class StateDataReporter(object):
# Detect the desired compression scheme from the filename extension
# and open all files unbuffered
if file.endswith('.gz'):
if not have_gzip:
raise RuntimeError("Cannot write .gz file because Python could not import gzip library")
self._out = gzip.GzipFile(fileobj=open(file, 'wb', 0))
elif file.endswith('.bz2'):
if not have_bz2:
raise RuntimeError("Cannot write .bz2 file because Python could not import bz2 library")
self._out = bz2.BZ2File(file, 'w', 0)
else:
self._out = open(file, 'w', 0)
......
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