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Commit 065bc95f authored by Andy Simmonett's avatar Andy Simmonett
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Trivial refactoring and cleaning.

parent 98514cb9
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plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
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......@@ -322,24 +322,18 @@ void AmoebaReferenceMultipoleForce::loadParticleData(const vector<RealVec>& part
particleData[ii].quadrupole[QYZ] = quadrupoles[9*ii+5];
particleData[ii].quadrupole[QZZ] = quadrupoles[9*ii+8];
#if SPHERICAL_MULTIPOLES
// Form spherical harmonic dipoles from Cartesian moments.
particleData[ii].sphericalDipole[0] = dipoles[3*ii+2]; // z -> Q_10
particleData[ii].sphericalDipole[1] = dipoles[3*ii+0]; // x -> Q_11c
particleData[ii].sphericalDipole[2] = dipoles[3*ii+1]; // y -> Q_11s
const double S43 = 1.1547005383792515; // SQRT(FOUR/THREE)
const double S13 = 0.5773502691896257; // SQRT(ONE/THREE)
// Form spherical harmonic quadrupoles from Cartesian moments.
particleData[ii].sphericalQuadrupole[0] = quadrupoles[9*ii+8]*3.0; // zz -> Q_20
particleData[ii].sphericalQuadrupole[1] = S43 * quadrupoles[9*ii+2]*3.0; // xz -> Q_21c
particleData[ii].sphericalQuadrupole[2] = S43 * quadrupoles[9*ii+5]*3.0; // yz -> Q_21s
particleData[ii].sphericalQuadrupole[3] = S13 * (quadrupoles[9*ii+0] - quadrupoles[9*ii+4])*3.0; // xx-yy -> Q_22c
particleData[ii].sphericalQuadrupole[4] = S43 * quadrupoles[9*ii+1]*3.0; // xy -> Q_22s
// std::cout << "Body qpole " << ii <<std::endl;
// std::cout<< std::setprecision(10) << particleData[ii].sphericalQuadrupole[0] << "\t"
// << particleData[ii].sphericalQuadrupole[1] << "\t"
// << particleData[ii].sphericalQuadrupole[2] << "\t"
// << particleData[ii].sphericalQuadrupole[3] << "\t"
// << particleData[ii].sphericalQuadrupole[4] << std::endl;
#endif
particleData[ii].sphericalQuadrupole[1] = sqrtFourThirds * quadrupoles[9*ii+2]*3.0; // xz -> Q_21c
particleData[ii].sphericalQuadrupole[2] = sqrtFourThirds * quadrupoles[9*ii+5]*3.0; // yz -> Q_21s
particleData[ii].sphericalQuadrupole[3] = sqrtOneThird * (quadrupoles[9*ii+0] - quadrupoles[9*ii+4])*3.0; // xx-yy -> Q_22c
particleData[ii].sphericalQuadrupole[4] = sqrtFourThirds * quadrupoles[9*ii+1]*3.0; // xy -> Q_22s
#endif // SPHERICAL_MULTIPOLES
particleData[ii].thole = tholes[ii];
particleData[ii].dampingFactor = dampingFactors[ii];
particleData[ii].polarity = polarity[ii];
......@@ -531,7 +525,7 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrixToParticle( Multipol
dipoleRotationMatrix[2][2] = vectorY[1];
RealOpenMM quadrupoleRotationMatrix[5][5];
buildSphericalQuadrupoleMatrix(dipoleRotationMatrix, quadrupoleRotationMatrix);
buildSphericalQuadrupoleRotationMatrix(dipoleRotationMatrix, quadrupoleRotationMatrix);
// Rotate the dipoles
RealOpenMM rotatedDipole[3];
......@@ -555,11 +549,7 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrixToParticle( Multipol
}
for (int ii = 0; ii < 5; ii++)
particleI.sphericalQuadrupole[ii] = rotatedQuadrupole[ii];
// std::cout << std::setprecision(10) << std::endl;
// std::cout << "Atom\t" << particleI.particleIndex << std::endl;
// std::cout << "Atom\t" << rotatedDipole[0]<<"\t" << rotatedDipole[1]<<"\t" << rotatedDipole[2] << std::endl;
// std::cout << "Atom\t" << rotatedQuadrupole[0]<<"\t" << rotatedQuadrupole[1]<<"\t" << rotatedQuadrupole[2]<<"\t" << rotatedQuadrupole[3]<<"\t" << rotatedQuadrupole[4]<<"\t" << std::endl;
#endif
#endif // SPHERICAL_MULTIPOLES
}
......@@ -598,36 +588,35 @@ void AmoebaReferenceMultipoleForce::formQIRotationMatrix(const MultipoleParticle
}
void AmoebaReferenceMultipoleForce::buildSphericalQuadrupoleMatrix(const RealOpenMM (&D1)[3][3], RealOpenMM (&D2)[5][5]) const
void AmoebaReferenceMultipoleForce::buildSphericalQuadrupoleRotationMatrix(const RealOpenMM (&D1)[3][3], RealOpenMM (&D2)[5][5]) const
{
D2[0][0] = 0.5*(3.0*D1[0][0]*D1[0][0] - 1.0);
D2[1][0] = 1.732050807568877*D1[0][0]*D1[1][0];
D2[2][0] = 1.732050807568877*D1[0][0]*D1[2][0];
D2[3][0] = 0.8660254037844386*(D1[1][0]*D1[1][0] - D1[2][0]*D1[2][0]);
D2[4][0] = 1.732050807568877*D1[1][0]*D1[2][0];
D2[0][1] = 1.732050807568877*D1[0][0]*D1[0][1];
D2[1][0] = sqrtThree*D1[0][0]*D1[1][0];
D2[2][0] = sqrtThree*D1[0][0]*D1[2][0];
D2[3][0] = 0.5*sqrtThree*(D1[1][0]*D1[1][0] - D1[2][0]*D1[2][0]);
D2[4][0] = sqrtThree*D1[1][0]*D1[2][0];
D2[0][1] = sqrtThree*D1[0][0]*D1[0][1];
D2[1][1] = D1[1][0]*D1[0][1] + D1[0][0]*D1[1][1];
D2[2][1] = D1[2][0]*D1[0][1] + D1[0][0]*D1[2][1];
D2[3][1] = D1[1][0]*D1[1][1] - D1[2][0]*D1[2][1];
D2[4][1] = D1[2][0]*D1[1][1] + D1[1][0]*D1[2][1];
D2[0][2] = 1.732050807568877*D1[0][0]*D1[0][2];
D2[0][2] = sqrtThree*D1[0][0]*D1[0][2];
D2[1][2] = D1[1][0]*D1[0][2] + D1[0][0]*D1[1][2];
D2[2][2] = D1[2][0]*D1[0][2] + D1[0][0]*D1[2][2];
D2[3][2] = D1[1][0]*D1[1][2] - D1[2][0]*D1[2][2];
D2[4][2] = D1[2][0]*D1[1][2] + D1[1][0]*D1[2][2];
D2[0][3] = 0.8660254037844386*(D1[0][1]*D1[0][1] - D1[0][2]*D1[0][2]);
D2[0][3] = 0.5*sqrtThree*(D1[0][1]*D1[0][1] - D1[0][2]*D1[0][2]);
D2[1][3] = D1[0][1]*D1[1][1] - D1[0][2]*D1[1][2];
D2[2][3] = D1[0][1]*D1[2][1] - D1[0][2]*D1[2][2];
D2[3][3] = 0.5*(D1[1][1]*D1[1][1] - D1[2][1]*D1[2][1] - D1[1][2]*D1[1][2] + D1[2][2]*D1[2][2]);
D2[4][3] = D1[1][1]*D1[2][1] - D1[1][2]*D1[2][2];
D2[0][4] = 1.732050807568877*D1[0][1]*D1[0][2];
D2[0][4] = sqrtThree*D1[0][1]*D1[0][2];
D2[1][4] = D1[1][1]*D1[0][2] + D1[0][1]*D1[1][2];
D2[2][4] = D1[2][1]*D1[0][2] + D1[0][1]*D1[2][2];
D2[3][4] = D1[1][1]*D1[1][2] - D1[2][1]*D1[2][2];
D2[4][4] = D1[2][1]*D1[1][2] + D1[1][1]*D1[2][2];
}
#endif
#endif // SPHERICAL_MULTIPOLES
void AmoebaReferenceMultipoleForce::applyRotationMatrix(vector<MultipoleParticleData>& particleData,
const vector<int>& multipoleAtomXs,
......@@ -6048,7 +6037,7 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeDirectElectrostaticPair
RealOpenMM qiRotationMatrix1[3][3];
formQIRotationMatrix(particleI, particleJ, r, qiRotationMatrix1);
RealOpenMM qiRotationMatrix2[5][5];
buildSphericalQuadrupoleMatrix(qiRotationMatrix1, qiRotationMatrix2);
buildSphericalQuadrupoleRotationMatrix(qiRotationMatrix1, qiRotationMatrix2);
// The force rotation matrix rotates the QI forces into the lab
// frame, and makes sure the result is in {x,y,z} ordering. Its
// transpose is used to rotate the induced dipoles to the QI frame.
......@@ -6123,13 +6112,12 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeDirectElectrostaticPair
}
// The Qtilde{x,y,z} torque intermediates for atoms I and J, which are used to obtain the torques on the permanent moments.
const RealOpenMM sqrt3 = sqrt(3.0);
RealOpenMM qiQIx[9] = {0.0, qiQI[3], 0.0, -qiQI[1], sqrt3*qiQI[6], qiQI[8], -sqrt3*qiQI[4] - qiQI[7], qiQI[6], -qiQI[5]};
RealOpenMM qiQIy[9] = {0.0, -qiQI[2], qiQI[1], 0.0, -sqrt3*qiQI[5], sqrt3*qiQI[4] - qiQI[7], -qiQI[8], qiQI[5], qiQI[6]};
RealOpenMM qiQIz[9] = {0.0, 0.0, -qiQI[3], qiQI[2], 0.0, -qiQI[6], qiQI[5], -2.0*qiQI[8], 2.0*qiQI[7]};
RealOpenMM qiQJx[9] = {0.0, qiQJ[3], 0.0, -qiQJ[1], sqrt3*qiQJ[6], qiQJ[8], -sqrt3*qiQJ[4] - qiQJ[7], qiQJ[6], -qiQJ[5]};
RealOpenMM qiQJy[9] = {0.0, -qiQJ[2], qiQJ[1], 0.0, -sqrt3*qiQJ[5], sqrt3*qiQJ[4] - qiQJ[7], -qiQJ[8], qiQJ[5], qiQJ[6]};
RealOpenMM qiQJz[9] = {0.0, 0.0, -qiQJ[3], qiQJ[2], 0.0, -qiQJ[6], qiQJ[5], -2.0*qiQJ[8], 2.0*qiQJ[7]};
RealOpenMM qiQIX[9] = {0.0, qiQI[3], 0.0, -qiQI[1], sqrtThree*qiQI[6], qiQI[8], -sqrtThree*qiQI[4] - qiQI[7], qiQI[6], -qiQI[5]};
RealOpenMM qiQIY[9] = {0.0, -qiQI[2], qiQI[1], 0.0, -sqrtThree*qiQI[5], sqrtThree*qiQI[4] - qiQI[7], -qiQI[8], qiQI[5], qiQI[6]};
RealOpenMM qiQIZ[9] = {0.0, 0.0, -qiQI[3], qiQI[2], 0.0, -qiQI[6], qiQI[5], -2.0*qiQI[8], 2.0*qiQI[7]};
RealOpenMM qiQJX[9] = {0.0, qiQJ[3], 0.0, -qiQJ[1], sqrtThree*qiQJ[6], qiQJ[8], -sqrtThree*qiQJ[4] - qiQJ[7], qiQJ[6], -qiQJ[5]};
RealOpenMM qiQJY[9] = {0.0, -qiQJ[2], qiQJ[1], 0.0, -sqrtThree*qiQJ[5], sqrtThree*qiQJ[4] - qiQJ[7], -qiQJ[8], qiQJ[5], qiQJ[6]};
RealOpenMM qiQJZ[9] = {0.0, 0.0, -qiQJ[3], qiQJ[2], 0.0, -qiQJ[6], qiQJ[5], -2.0*qiQJ[8], 2.0*qiQJ[7]};
// The field derivatives at I due to permanent and induced moments on J, and vice-versa.
// Also, their derivatives w.r.t. R, which are needed for force calculations
......@@ -6300,9 +6288,9 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeDirectElectrostaticPair
Vjid[0] += -(eUIndCoef*qiQI[4]);
// D-Q and Uind-Q terms (m=1)
ePermCoef = -sqrt3*rInvVec[4]*(mScale + bVec[3]);
eUIndCoef = -sqrt3*rInvVec[4]*(dScale*thole_q1 + bVec[3]);
eUInpCoef = -sqrt3*rInvVec[4]*(pScale*thole_q1 + bVec[3]);
ePermCoef = -sqrtThree*rInvVec[4]*(mScale + bVec[3]);
eUIndCoef = -sqrtThree*rInvVec[4]*(dScale*thole_q1 + bVec[3]);
eUInpCoef = -sqrtThree*rInvVec[4]*(pScale*thole_q1 + bVec[3]);
dPermCoef = fourSqrtOneThird*rInvVec[5]*(1.5*(mScale + bVec[3]) + 0.5*alphaRVec[5]*X);
dUIndCoef = fourSqrtOneThird*rInvVec[5]*(3.0*(dScale*dthole_q1 + bVec[3]) + alphaRVec[5]*X);
dUInpCoef = fourSqrtOneThird*rInvVec[5]*(3.0*(pScale*dthole_q1 + bVec[3]) + alphaRVec[5]*X);
......@@ -6362,72 +6350,66 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeDirectElectrostaticPair
VijR[8] = dPermCoef*qiQJ[8];
VjiR[8] = dPermCoef*qiQI[8];
// Define the torque intermediates for the induced dipoles. These are simply the induced dipole torque
// intermediates dotted with the dipole field at each center. We inline the induced dipole torque
// intermediates here, for simplicity.
// Evaluate the energies, forces and torques due to permanent+induced moments
// interacting with just the permanent moments.
energy = 0.5*(qiQI[0]*Vij[0] + qiQJ[0]*Vji[0]);
RealOpenMM fIZ = qiQI[0]*VijR[0];
RealOpenMM fJZ = qiQJ[0]*VjiR[0];
RealOpenMM EIX = 0.0, EIY = 0.0, EIZ = 0.0, EJX = 0.0, EJY = 0.0, EJZ = 0.0;
for(int i = 1; i < 9; ++i){
energy += 0.5*(qiQI[i]*Vij[i] + qiQJ[i]*Vji[i]);
fIZ += qiQI[i]*VijR[i];
fJZ += qiQJ[i]*VjiR[i];
EIX += qiQIX[i]*Vij[i];
EIY += qiQIY[i]*Vij[i];
EIZ += qiQIZ[i]*Vij[i];
EJX += qiQJX[i]*Vji[i];
EJY += qiQJY[i]*Vji[i];
EJZ += qiQJZ[i]*Vji[i];
}
// Define the torque intermediates for the induced dipoles. These are simply the induced dipole torque
// intermediates dotted with the field due to permanent moments only, at each center. We inline the
// induced dipole torque intermediates here, for simplicity. N.B. There are no torques on the dipoles
// themselves, so we accumulate the torque intermediates into separate variables to allow them to be
// used only in the force calculation.
//
// The torque about the x axis (needed to obtain the y force on the induced dipoles, below)
// qiUindIx[0] = qiQUindI[2]; qiUindIx[1] = 0; qiUindIx[2] = -qiQUindI[0]
RealOpenMM iEix = qiUinpI[2]*Vijp[0] + qiUindI[2]*Vijd[0] - qiUinpI[0]*Vijp[2] - qiUindI[0]*Vijd[2];
RealOpenMM iEjx = qiUinpJ[2]*Vjip[0] + qiUindJ[2]*Vjid[0] - qiUinpJ[0]*Vjip[2] - qiUindJ[0]*Vjid[2];
RealOpenMM iEIX = qiUinpI[2]*Vijp[0] + qiUindI[2]*Vijd[0] - qiUinpI[0]*Vijp[2] - qiUindI[0]*Vijd[2];
RealOpenMM iEJX = qiUinpJ[2]*Vjip[0] + qiUindJ[2]*Vjid[0] - qiUinpJ[0]*Vjip[2] - qiUindJ[0]*Vjid[2];
// The torque about the y axis (needed to obtain the x force on the induced dipoles, below)
// qiUindIy[0] = -qiQUindI[1]; qiUindIy[1] = qiQUindI[0]; qiUindIy[2] = 0
RealOpenMM iEiy = qiUinpI[0]*Vijp[1] + qiUindI[0]*Vijd[1] - qiUinpI[1]*Vijp[0] - qiUindI[1]*Vijd[0];
RealOpenMM iEjy = qiUinpJ[0]*Vjip[1] + qiUindJ[0]*Vjid[1] - qiUinpJ[1]*Vjip[0] - qiUindJ[1]*Vjid[0];
RealOpenMM iEIY = qiUinpI[0]*Vijp[1] + qiUindI[0]*Vijd[1] - qiUinpI[1]*Vijp[0] - qiUindI[1]*Vijd[0];
RealOpenMM iEJY = qiUinpJ[0]*Vjip[1] + qiUindJ[0]*Vjid[1] - qiUinpJ[1]*Vjip[0] - qiUindJ[1]*Vjid[0];
// Add in the induced-induced terms, if needed. N.B. No torques here.
RealOpenMM iFiZ = 0.0;
RealOpenMM iFjz = 0.0;
// Add in the induced-induced terms, if needed.
if(getPolarizationType() == AmoebaReferenceMultipoleForce::Mutual){
// Uind-Uind terms (m=0)
RealOpenMM eCoef = -fourThirds*rInvVec[3]*(3.0*(uScale*thole_d0 + bVec[3]) + alphaRVec[3]*X);
RealOpenMM dCoef = rInvVec[4]*(6.0*(uScale*dthole_d0 + bVec[3]) + 4.0*alphaRVec[5]*X);
iEix += eCoef*(qiUinpI[2]*qiUindJ[0] + qiUindI[2]*qiUinpJ[0]);
iEjx += eCoef*(qiUinpJ[2]*qiUindI[0] + qiUindJ[2]*qiUinpI[0]);
iEiy -= eCoef*(qiUinpI[1]*qiUindJ[0] + qiUindI[1]*qiUinpJ[0]);
iEjy -= eCoef*(qiUinpJ[1]*qiUindI[0] + qiUindJ[1]*qiUinpI[0]);
iFiZ += dCoef*(qiUinpI[0]*qiUindJ[0] + qiUindI[0]*qiUinpJ[0]);
iFjz += dCoef*(qiUinpJ[0]*qiUindI[0] + qiUindJ[0]*qiUinpI[0]);
iEIX += eCoef*(qiUinpI[2]*qiUindJ[0] + qiUindI[2]*qiUinpJ[0]);
iEJX += eCoef*(qiUinpJ[2]*qiUindI[0] + qiUindJ[2]*qiUinpI[0]);
iEIY -= eCoef*(qiUinpI[1]*qiUindJ[0] + qiUindI[1]*qiUinpJ[0]);
iEJY -= eCoef*(qiUinpJ[1]*qiUindI[0] + qiUindJ[1]*qiUinpI[0]);
fIZ += dCoef*(qiUinpI[0]*qiUindJ[0] + qiUindI[0]*qiUinpJ[0]);
fIZ += dCoef*(qiUinpJ[0]*qiUindI[0] + qiUindJ[0]*qiUinpI[0]);
// Uind-Uind terms (m=1)
eCoef = 2.0*rInvVec[3]*(uScale*thole_d1 + bVec[3] - twoThirds*alphaRVec[3]*X);
dCoef = -3.0*rInvVec[4]*(uScale*dthole_d1 + bVec[3]);
iEix -= eCoef*(qiUinpI[0]*qiUindJ[2] + qiUindI[0]*qiUinpJ[2]);
iEjx -= eCoef*(qiUinpJ[0]*qiUindI[2] + qiUindJ[0]*qiUinpI[2]);
iEiy += eCoef*(qiUinpI[0]*qiUindJ[1] + qiUindI[0]*qiUinpJ[1]);
iEjy += eCoef*(qiUinpJ[0]*qiUindI[1] + qiUindJ[0]*qiUinpI[1]);
iFiZ += dCoef*(qiUinpI[1]*qiUindJ[1] + qiUindI[1]*qiUinpJ[1] + qiUinpI[2]*qiUindJ[2] + qiUindI[2]*qiUinpJ[2]);
iFjz += dCoef*(qiUinpJ[1]*qiUindI[1] + qiUindJ[1]*qiUinpI[1] + qiUinpJ[2]*qiUindI[2] + qiUindJ[2]*qiUinpI[2]);
iEIX -= eCoef*(qiUinpI[0]*qiUindJ[2] + qiUindI[0]*qiUinpJ[2]);
iEJX -= eCoef*(qiUinpJ[0]*qiUindI[2] + qiUindJ[0]*qiUinpI[2]);
iEIY += eCoef*(qiUinpI[0]*qiUindJ[1] + qiUindI[0]*qiUinpJ[1]);
iEJY += eCoef*(qiUinpJ[0]*qiUindI[1] + qiUindJ[0]*qiUinpI[1]);
fIZ += dCoef*(qiUinpI[1]*qiUindJ[1] + qiUindI[1]*qiUinpJ[1] + qiUinpI[2]*qiUindJ[2] + qiUindI[2]*qiUinpJ[2]);
fIZ += dCoef*(qiUinpJ[1]*qiUindI[1] + qiUindJ[1]*qiUinpI[1] + qiUinpJ[2]*qiUindI[2] + qiUindJ[2]*qiUinpI[2]);
}
energy = 0.5*(qiQI[0]*Vij[0] + qiQJ[0]*Vji[0]);
RealOpenMM fiZ = qiQI[0]*VijR[0];
RealOpenMM fjZ = qiQJ[0]*VjiR[0];
RealOpenMM Eix = 0.0, Eiy = 0.0, Eiz = 0.0, Ejx = 0.0, Ejy = 0.0, Ejz = 0.0;
for(int i = 1; i < 9; ++i){
energy += 0.5*(qiQI[i]*Vij[i] + qiQJ[i]*Vji[i]);
fiZ += qiQI[i]*VijR[i];
fjZ += qiQJ[i]*VjiR[i];
Eix += qiQIx[i]*Vij[i];
Eiy += qiQIy[i]*Vij[i];
Eiz += qiQIz[i]*Vij[i];
Ejx += qiQJx[i]*Vji[i];
Ejy += qiQJy[i]*Vji[i];
Ejz += qiQJz[i]*Vji[i];
}
// The quasi-internal frame forces and torques
RealOpenMM qiForce[3], qiTorqueI[3], qiTorqueJ[3];
qiForce[0] = (Eiy + Ejy + iEiy + iEjy) * rInv;
qiForce[1] = -(Eix + Ejx + iEix + iEjx) * rInv;
qiForce[2] = -(fjZ + fiZ + iFiZ + iFjz);
// Note that the induced torque intermediates are used in the force expression above,
// but not in the actual torques below; the induced dipoles are isotropic.
qiTorqueI[0] = -Eix;
qiTorqueI[1] = -Eiy;
qiTorqueI[2] = -Eiz;
qiTorqueJ[0] = -Ejx;
qiTorqueJ[1] = -Ejy;
qiTorqueJ[2] = -Ejz;
// The quasi-internal frame forces and torques. Note that the induced torque intermediates are
// used in the force expression, but not in the torques; the induced dipoles are isotropic.
RealOpenMM qiForce[3] = {rInv*(EIY+EJY+iEIY+iEJY), -rInv*(EIX+EJX+iEIX+iEJX), -(fJZ+fIZ)};
RealOpenMM qiTorqueI[3] = {-EIX, -EIY, -EIZ};
RealOpenMM qiTorqueJ[3] = {-EJX, -EJY, -EJZ};
// Rotate the forces and torques back to the lab frame
for (int ii = 0; ii < 3; ii++) {
......@@ -6435,7 +6417,7 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeDirectElectrostaticPair
RealOpenMM torqueIVal = 0.0;
RealOpenMM torqueJVal = 0.0;
for (int jj = 0; jj < 3; jj++) {
forceVal += forceRotationMatrix[ii][jj] * qiForce[jj];
forceVal += forceRotationMatrix[ii][jj] * qiForce[jj];
torqueIVal += forceRotationMatrix[ii][jj] * qiTorqueI[jj];
torqueJVal += forceRotationMatrix[ii][jj] * qiTorqueJ[jj];
}
......@@ -6445,7 +6427,7 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeDirectElectrostaticPair
forces[jIndex][ii] += forceVal;
}
#else // If SPHERICAL_MULTIPOLES
#else // SPHERICAL_MULTIPOLES
RealOpenMM xr = deltaR[0];
RealOpenMM yr = deltaR[1];
......@@ -7121,7 +7103,7 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeDirectElectrostaticPair
torques[jIndex][1] += (ttm32 + ttm3i2)*conversionFactor;
torques[jIndex][2] += (ttm33 + ttm3i3)*conversionFactor;
#endif // If SPHERICAL_MULTIPOLES
#endif // SPHERICAL_MULTIPOLES
#if DEBUG_MULTIPOLES
std::cout << "Pair\t" << iIndex+1 << "\t" << jIndex+1 << std::endl;
......@@ -7130,7 +7112,7 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeDirectElectrostaticPair
std::cout << "\tForceJ: " << FMT(forces[jIndex][0]) << FMT(forces[jIndex][1]) << FMT(forces[jIndex][2]) << std::endl;
std::cout << "\tTorqueI: " << FMT(torques[iIndex][0]) << FMT(torques[iIndex][1]) << FMT(torques[iIndex][2]) << std::endl;
std::cout << "\tTorqueJ: " << FMT(torques[jIndex][0]) << FMT(torques[jIndex][1]) << FMT(torques[jIndex][2]) << std::endl;
#endif
#endif // DEBUG_MULTIPOLES
return energy;
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ 065bc95f
......@@ -47,10 +47,13 @@ const RealOpenMM oneThird = 1.0/3.0;
const RealOpenMM twoThirds = 2.0/3.0;
const RealOpenMM fourThirds = 4.0/3.0;
const RealOpenMM fourSqrtOneThird = 4.0/sqrt(3.0);
const RealOpenMM sqrtFourThirds = 2.0/sqrt(3.0);
const RealOpenMM sqrtOneThird = 1.0/sqrt(3.0);
const RealOpenMM sqrtThree = sqrt(3.0);
const RealOpenMM oneNinth = 1.0/9.0;
const RealOpenMM fourOverFortyFive = 4.0/45.0;
const RealOpenMM fourOverFifteen = 4.0/15.0;
#endif
#endif // SPHERICAL_MULTIPOLES
/**
......@@ -837,7 +840,7 @@ protected:
* @param D1 The input spherical harmonic dipole rotation matrix
* @param D2 The output spherical harmonic quadrupole rotation matrix
*/
void buildSphericalQuadrupoleMatrix(const RealOpenMM (&D1)[3][3], RealOpenMM (&D2)[5][5]) const;
void buildSphericalQuadrupoleRotationMatrix(const RealOpenMM (&D1)[3][3], RealOpenMM (&D2)[5][5]) const;
#endif
/**
......
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