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Commit 8b005aac authored by Mark Friedrichs's avatar Mark Friedrichs
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Adding z-bisect, 3-fold and z-only

parent 0d78f22f
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Showing with 290 additions and 5 deletions
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ 8b005aac
...@@ -424,7 +424,160 @@ void AmoebaReferenceMultipoleForce::checkChiral( MultipoleParticleData& particle ...@@ -424,7 +424,160 @@ void AmoebaReferenceMultipoleForce::checkChiral( MultipoleParticleData& particle
void AmoebaReferenceMultipoleForce::applyRotationMatrix( MultipoleParticleData& particleI, void AmoebaReferenceMultipoleForce::applyRotationMatrix( MultipoleParticleData& particleI,
const MultipoleParticleData& particleZ, const MultipoleParticleData& particleZ,
const MultipoleParticleData& particleX, int axisType ) const { const MultipoleParticleData& particleX,
MultipoleParticleData* particleY,
int axisType ) const {
// ---------------------------------------------------------------------------------------
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM two = 2.0;
static const std::string methodName = "AmoebaReferenceMultipoleForce::applyRotationMatrix";
static const int Y = 1;
static const int X = 0;
static const int Z = 2;
RealOpenMM* vector[3];
RealOpenMM rotationMatrix[3][3];
// ---------------------------------------------------------------------------------------
// handle case where rotation matrix is identity (e.g. single ion)
// get coordinates of this atom and the z & x axis atoms
// compute the vector between the atoms and 1/sqrt(d2), d2 is distance between
// this atom and the axis atom
vector[X] = rotationMatrix[0];
vector[Y] = rotationMatrix[1];
vector[Z] = rotationMatrix[2];
getDelta( particleI, particleZ, vector[Z] );
getDelta( particleI, particleX, vector[X] );
AmoebaReferenceForce::normalizeVector3( vector[Z] );
// branch based on axis type
if( axisType == AmoebaMultipoleForce::Bisector ){
// bisector
// dx = dx1 + dx2 (in Tinker code)
AmoebaReferenceForce::normalizeVector3( vector[X] );
vector[Z][0] += vector[X][0];
vector[Z][1] += vector[X][1];
vector[Z][2] += vector[X][2];
AmoebaReferenceForce::normalizeVector3( vector[Z] );
} else if( axisType == AmoebaMultipoleForce::ZBisect ){
// z-bisect
// dx = dx1 + dx2 (in Tinker code)
AmoebaReferenceForce::normalizeVector3( vector[X] );
getDelta( particleI, *particleY, vector[Y] );
AmoebaReferenceForce::normalizeVector3( vector[Y] );
vector[X][0] += vector[Y][0];
vector[X][1] += vector[Y][1];
vector[X][2] += vector[Y][2];
AmoebaReferenceForce::normalizeVector3( vector[X] );
} else if( axisType == AmoebaMultipoleForce::ThreeFold ){
// 3-fold
// dx = dx1 + dx2 + dx3 (in Tinker code)
AmoebaReferenceForce::normalizeVector3( vector[X] );
getDelta( particleI, *particleY, vector[Y] );
AmoebaReferenceForce::normalizeVector3( vector[Y] );
vector[Z][0] += vector[X][0] + vector[Y][0];
vector[Z][1] += vector[X][1] + vector[Y][1];
vector[Z][2] += vector[X][2] + vector[Y][2];
AmoebaReferenceForce::normalizeVector3( vector[Z] );
} else if( axisType == AmoebaMultipoleForce::ZOnly ){
// z-only
vector[X][0] = 0.1;
vector[X][1] = 0.1;
vector[X][2] = 0.1;
}
RealOpenMM dot = vector[Z][0]*vector[X][0] + vector[Z][1]*vector[X][1] + vector[Z][2]*vector[X][2];
vector[X][0] -= dot*vector[Z][0];
vector[X][1] -= dot*vector[Z][1];
vector[X][2] -= dot*vector[Z][2];
AmoebaReferenceForce::normalizeVector3( vector[X] );
AmoebaReferenceForce::getCrossProduct( vector[Z], vector[X], vector[Y] );
RealOpenMM labDipole[3];
for( int ii = 0; ii < 3; ii++ ){
labDipole[ii] = particleI.dipole[0]*rotationMatrix[0][ii];
for( int jj = 1; jj < 3; jj++ ){
labDipole[ii] += particleI.dipole[jj]*rotationMatrix[jj][ii];
}
}
particleI.dipole[0] = labDipole[0];
particleI.dipole[1] = labDipole[1];
particleI.dipole[2] = labDipole[2];
RealOpenMM mPole[3][3];
RealOpenMM rPole[3][3] = { { zero, zero, zero },
{ zero, zero, zero },
{ zero, zero, zero } };
mPole[0][0] = particleI.quadrupole[QXX];
mPole[0][1] = particleI.quadrupole[QXY];
mPole[0][2] = particleI.quadrupole[QXZ];
mPole[1][0] = particleI.quadrupole[QXY];
mPole[1][1] = particleI.quadrupole[QYY];
mPole[1][2] = particleI.quadrupole[QYZ];
mPole[2][0] = particleI.quadrupole[QXZ];
mPole[2][1] = particleI.quadrupole[QYZ];
mPole[2][2] = particleI.quadrupole[QZZ];
for( int ii = 0; ii < 3; ii++ ){
for( int jj = ii; jj < 3; jj++ ){
for( int kk = 0; kk < 3; kk++ ){
for( int mm = 0; mm < 3; mm++ ){
rPole[ii][jj] += rotationMatrix[kk][ii]*rotationMatrix[mm][jj]*mPole[kk][mm];
}
}
}
}
particleI.quadrupole[QXX] = rPole[0][0];
particleI.quadrupole[QXY] = rPole[0][1];
particleI.quadrupole[QXZ] = rPole[0][2];
particleI.quadrupole[QYY] = rPole[1][1];
particleI.quadrupole[QYZ] = rPole[1][2];
particleI.quadrupole[QZZ] = rPole[2][2];
return;
}
void AmoebaReferenceMultipoleForce::applyRotationMatrixOld( MultipoleParticleData& particleI,
const MultipoleParticleData& particleZ,
const MultipoleParticleData& particleX, int axisType ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -1388,15 +1541,131 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostaticPairIxn( ...@@ -1388,15 +1541,131 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostaticPairIxn(
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void AmoebaReferenceMultipoleForce::mapTorqueToForce( const MultipoleParticleData& particleI, /*
void AmoebaReferenceMultipoleForce::mapTorqueToForceOld( const MultipoleParticleData& particleI,
const MultipoleParticleData& particleU, const MultipoleParticleData& particleU,
const MultipoleParticleData& particleV, const MultipoleParticleData& particleV,
MultipoleParticleData* particleW,
int axisType, const Vec3& torque, RealOpenMM** forces ) const { int axisType, const Vec3& torque, RealOpenMM** forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
static const std::string methodName = "mapTorqueToForce"; static const std::string methodName = "mapTorqueToForce";
static const int U = 0;
static const int V = 1;
static const int W = 2;
static const int R = 3;
static const int S = 4;
static const int UV = 5;
static const int UW = 6;
static const int VW = 7;
static const int UR = 8;
static const int US = 9;
static const int VS = 10;
static const int WS = 11;
static const int LastVectorIndex = 12;
static const int X = 0;
static const int Y = 1;
static const int Z = 2;
static const int I = 3;
RealOpenMM norms[LastVectorIndex];
RealOpenMM vector[LastVectorIndex][3];
RealOpenMM angles[LastVectorIndex][2];
static const RealOpenMM one = 1.0;
static const RealOpenMM two = 2.0;
// ---------------------------------------------------------------------------------------
// get coordinates of this atom and the z & x axis atoms
// compute the vector between the atoms and 1/sqrt(d2), d2 is distance between
// this atom and the axis atom
getDelta( particleI, particleU, vector[U] );
norms[U] = AmoebaReferenceForce::normalizeVector3( vector[U] );
getDelta( particleI, particleV, vector[V] );
norms[V] = AmoebaReferenceForce::normalizeVector3( vector[V] );
if( axisType == AmoebaMultipoleForce::ZBisect || axisType == AmoebaMultipoleForce::ThreeFold ){
getDelta( particleI, *particleW, vector[W] );
} else {
AmoebaReferenceForce::getCrossProduct( vector[U], vector[V], vector[W] );
}
norms[W] = AmoebaReferenceForce::normalizeVector3( vector[W] );
AmoebaReferenceForce::getCrossProduct( vector[V], vector[U], vector[UV] );
AmoebaReferenceForce::getCrossProduct( vector[W], vector[U], vector[UW] );
AmoebaReferenceForce::getCrossProduct( vector[W], vector[V], vector[VW] );
norms[UV] = normVector3( vector[UV] );
norms[UW] = normVector3( vector[UW] );
norms[VW] = normVector3( vector[VW] );
angles[UV][0] = DOT3( vector[U], vector[V] );
angles[UV][1] = sqrtf( 1.0f - angles[UV][0]*angles[UV][0]);
angles[UW][0] = DOT3( vector[U], vector[W] );
angles[UW][1] = sqrtf( 1.0f - angles[UW][0]*angles[UW][0]);
angles[VW][0] = DOT3( vector[V], vector[W] );
angles[VW][1] = sqrtf( 1.0f - angles[VW][0]*angles[VW][0]);
float dphi[3];
dphi[U] = DOT3( vector[U], (torque + threadId*3) );
dphi[V] = DOT3( vector[V], (torque + threadId*3) );
dphi[W] = DOT3( vector[W], (torque + threadId*3) );
dphi[U] *= -1.0f;
dphi[V] *= -1.0f;
dphi[W] *= -1.0f;
// branch based on axis type
if( axisType == AmoebaMultipoleForce::Bisector ){
// bisector
for( int ii = 0; ii < 3; ii++ ){
RealOpenMM du = -vector[W][ii]*dphi[V]/uvdis + up[ii]*dphi[W]/(two*norms[U]);
RealOpenMM dv = vector[W][ii]*dphi[U]/vudis + vp[ii]*dphi[W]/(two*norms[V]);
forces[particleU.particleIndex][ii] += du;
forces[particleV.particleIndex][ii] += dv;
forces[particleI.particleIndex][ii] -= (dv + du);
}
} else if( axisType == AmoebaMultipoleForce::ZThenX ){
for( int ii = 0; ii < 3; ii++ ){
RealOpenMM du = -vector[W][ii]*dphi[V]/uvdis + up[ii]*dphi[W]/norms[U];
RealOpenMM dv = vector[W][ii]*dphi[U]/vudis;
forces[particleU.particleIndex][ii] += du;
forces[particleV.particleIndex][ii] += dv;
forces[particleI.particleIndex][ii] -= (dv + du);
}
}
return;
}
*/
/**---------------------------------------------------------------------------------------
Map torques to forces
--------------------------------------------------------------------------------------- */
void AmoebaReferenceMultipoleForce::mapTorqueToForceOld( const MultipoleParticleData& particleI,
const MultipoleParticleData& particleU,
const MultipoleParticleData& particleV,
int axisType, const Vec3& torque, RealOpenMM** forces ) const {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "mapTorqueToForce";
static const int U = 0; static const int U = 0;
static const int V = 1; static const int V = 1;
static const int W = 2; static const int W = 2;
...@@ -1564,7 +1833,10 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostatic( std::v ...@@ -1564,7 +1833,10 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostatic( std::v
// map torques to forces // map torques to forces
for( unsigned int ii = 0; ii < particleData.size(); ii++ ){ for( unsigned int ii = 0; ii < particleData.size(); ii++ ){
mapTorqueToForce( particleData[ii], particleData[multipoleAtomZs[ii]], particleData[multipoleAtomXs[ii]], axisTypes[ii], torques[ii], forces ); // mapTorqueToForce( particleData[ii], particleData[multipoleAtomZs[ii]], particleData[multipoleAtomXs[ii]],
// multipoleAtomYs[ii] > -1 ? &particleData[multipoleAtomYs[ii]] : NULL, axisTypes[ii], torques[ii], forces );
mapTorqueToForceOld( particleData[ii], particleData[multipoleAtomZs[ii]], particleData[multipoleAtomXs[ii]],
axisTypes[ii], torques[ii], forces );
} }
// diagnostics // diagnostics
...@@ -1632,7 +1904,8 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsig ...@@ -1632,7 +1904,8 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsig
for( unsigned int ii = 0; ii < numParticles; ii++ ){ for( unsigned int ii = 0; ii < numParticles; ii++ ){
if( multipoleAtomZs[ii] >= 0 && multipoleAtomXs[ii] >= 0 ){ if( multipoleAtomZs[ii] >= 0 && multipoleAtomXs[ii] >= 0 ){
applyRotationMatrix( particleData[ii], particleData[multipoleAtomZs[ii]], particleData[multipoleAtomXs[ii]], axisTypes[ii] ); applyRotationMatrix( particleData[ii], particleData[multipoleAtomZs[ii]], particleData[multipoleAtomXs[ii]],
multipoleAtomYs[ii] > -1 ? &particleData[multipoleAtomYs[ii]] : NULL, axisTypes[ii] );
} }
} }
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ 8b005aac
...@@ -438,7 +438,12 @@ private: ...@@ -438,7 +438,12 @@ private:
void applyRotationMatrix( MultipoleParticleData& particleI, void applyRotationMatrix( MultipoleParticleData& particleI,
const MultipoleParticleData& particleZ, const MultipoleParticleData& particleZ,
const MultipoleParticleData& particleX, int axisType ) const; const MultipoleParticleData& particleX,
MultipoleParticleData* particleY, int axisType ) const;
void applyRotationMatrixOld( MultipoleParticleData& particleI,
const MultipoleParticleData& particleZ,
const MultipoleParticleData& particleX, int axisType ) const;
void calculateFixedEFieldPairIxn( MultipoleParticleData& particleI, MultipoleParticleData& particleJ, void calculateFixedEFieldPairIxn( MultipoleParticleData& particleI, MultipoleParticleData& particleJ,
RealOpenMM dScale, RealOpenMM pScale ) const; RealOpenMM dScale, RealOpenMM pScale ) const;
...@@ -468,6 +473,7 @@ private: ...@@ -468,6 +473,7 @@ private:
@param particleI particle whose torque is to be mapped @param particleI particle whose torque is to be mapped
@param particleU particle1 of lab frame for particleI @param particleU particle1 of lab frame for particleI
@param particleV particle2 of lab frame for particleI @param particleV particle2 of lab frame for particleI
@param particleW particle3 of lab frame for particleI
@param axisType axis type (Bisector/Z-then-X, ...) @param axisType axis type (Bisector/Z-then-X, ...)
@param torque torque on particle I @param torque torque on particle I
...@@ -476,8 +482,14 @@ private: ...@@ -476,8 +482,14 @@ private:
void mapTorqueToForce( const MultipoleParticleData& particleI, void mapTorqueToForce( const MultipoleParticleData& particleI,
const MultipoleParticleData& particleU, const MultipoleParticleData& particleU,
const MultipoleParticleData& particleV, const MultipoleParticleData& particleV,
MultipoleParticleData* particleW,
int axisType, const Vec3& torque, RealOpenMM** forces ) const; int axisType, const Vec3& torque, RealOpenMM** forces ) const;
void mapTorqueToForceOld( const MultipoleParticleData& particleI,
const MultipoleParticleData& particleU,
const MultipoleParticleData& particleV,
int axisType, const Vec3& torque, RealOpenMM** forces ) const;
RealOpenMM calculateNoCutoffElectrostatic( std::vector<MultipoleParticleData>& particleData, RealOpenMM calculateNoCutoffElectrostatic( std::vector<MultipoleParticleData>& particleData,
const std::vector<int>& axisTypes, const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomZs, const std::vector<int>& multipoleAtomZs,
......
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