double Action_LIE::Calculate_LJ(Frame const& frameIn, Topology const& parmIn) const {
double result = 0;
// Loop over ligand atoms
AtomMask::const_iterator mask1_end = Mask1_.end();
AtomMask::const_iterator mask2_end = Mask2_.end();
for (AtomMask::const_iterator maskatom1 = Mask1_.begin();
maskatom1 != mask1_end; maskatom1++) {
int crdidx1 = (*maskatom1) * 3; // index into coordinate array
Vec3 atm1 = Vec3(frameIn.CRD(crdidx1));
for (AtomMask::const_iterator maskatom2 = Mask2_.begin();
maskatom2 != mask2_end; maskatom2++) {
int crdidx2 = (*maskatom2) * 3; // index into coordinate array
Vec3 atm2 = Vec3(frameIn.CRD(crdidx2));
double dist2;
// Get imaged distance
Matrix_3x3 ucell, recip;
switch( ImageType() ) {
case NONORTHO:
frameIn.BoxCrd().ToRecip(ucell, recip);
dist2 = DIST2_ImageNonOrtho(atm1, atm2, ucell, recip);
break;
case ORTHO:
dist2 = DIST2_ImageOrtho(atm1, atm2, frameIn.BoxCrd());
break;
default:
dist2 = DIST2_NoImage(atm1, atm2);
}
if (dist2 > cut2vdw_) continue;
// Here we add to our nonbonded (VDW) energy
NonbondType const& LJ = parmIn.GetLJparam(*maskatom1, *maskatom2);
double r2 = 1 / dist2;
double r6 = r2 * r2 * r2;
result += LJ.A() * r6 * r6 - LJ.B() * r6;
}
}
return result;
}
double Action_LIE::Calculate_Elec(Frame const& frameIn) const {
double result = 0;
// Loop over ligand atoms
AtomMask::const_iterator mask1_end = Mask1_.end();
AtomMask::const_iterator mask2_end = Mask2_.end();
for (AtomMask::const_iterator maskatom1 = Mask1_.begin();
maskatom1 != mask1_end; maskatom1++) {
int crdidx1 = (*maskatom1) * 3; // index into coordinate array
Vec3 atm1 = Vec3(frameIn.CRD(crdidx1));
for (AtomMask::const_iterator maskatom2 = Mask2_.begin();
maskatom2 != mask2_end; maskatom2++) {
int crdidx2 = (*maskatom2) * 3; // index into coordinate array
Vec3 atm2 = Vec3(frameIn.CRD(crdidx2));
double dist2;
// Get imaged distance
Matrix_3x3 ucell, recip;
switch( ImageType() ) {
case NONORTHO:
frameIn.BoxCrd().ToRecip(ucell, recip);
dist2 = DIST2_ImageNonOrtho(atm1, atm2, ucell, recip);
break;
case ORTHO:
dist2 = DIST2_ImageOrtho(atm1, atm2, frameIn.BoxCrd());
break;
default:
dist2 = DIST2_NoImage(atm1, atm2);
}
if (dist2 > cut2elec_) continue;
// Here we add to our electrostatic energy
double qiqj = atom_charge_[*maskatom1] * atom_charge_[*maskatom2];
double shift = (1 - dist2 * onecut2_);
result += qiqj / sqrt(dist2) * shift * shift;
}
}
return result;
}
/** Calc Covariance Matrix */
void Action_Matrix::CalcCovarianceMatrix(Frame const& currentFrame) {
# ifdef _OPENMP
#ifdef NEW_MATRIX_PARA /* New matrix parallelization */
//int idx2, atomCrd2, offset2, midx, idx1, atomCrd1, offset1;
int idx2, midx, idx1;
double Mj;
if (useMask2_) { // FULL MATRIX TODO
return;
} else { // HALF MATRIX
DataSet_MatrixDbl& matrix = *Mat_;
Darray& vect1 = Mat_->V1();
//int Ncoords = mask1_.Nselected() * 3;
int Ncoords = (int)crd_indices_.size();
//# pragma omp parallel private(idx2, atomCrd2, offset2, midx, idx1, atomCrd1, offset1, Mj)
# pragma omp parallel private(idx2, midx, idx1, Mj)
{
# pragma omp for schedule(dynamic)
for (idx2 = 0; idx2 < Ncoords; idx2++)
{
//atomCrd2 = mask1_[idx2 / 3] * 3;
//offset2 = idx2 % 3;
//Mj = currentFrame[atomCrd2 + offset2];
Mj = currentFrame[ crd_indices_[idx2] ];
vect1[idx2] += Mj;
vect2_[idx2] += (Mj * Mj);
midx = (idx2 * (int)matrix.Ncols() - (idx2 * (idx2-1) / 2));
for (idx1 = idx2; idx1 < Ncoords; idx1++, midx++)
{
//atomCrd1 = mask1_[idx1 / 3] * 3;
//offset1 = idx1 % 3;
//matrix[midx] += (currentFrame[atomCrd1 + offset1] * Mj);
matrix[midx] += (currentFrame[ crd_indices_[idx1] ] * Mj);
}
} // END for loop
} // END openmp pragma
}
#else /* Original matrix parallelization */
int m1_idx, m2_idx;
double Vj;
const double* XYZi;
const double* XYZj;
unsigned int ny;
DataSet_MatrixDbl::iterator mat;
v_iterator v1, v2;
if (useMask2_) { // FULL MATRIX
int NX = (int)Mat_->Ncols();
int crd_max = (int)crd_indices_.size();
# pragma omp parallel private(m1_idx, m2_idx, XYZi, XYZj, Vj, mat, v1, v2, ny)
{
#pragma omp for
for (m2_idx = 0; m2_idx < mask2_.Nselected(); m2_idx++) {
mat = Mat_->begin() + ((m2_idx*3)*NX);
XYZj = currentFrame.XYZ( mask2_[m2_idx] );
for (ny = 0; ny < 3; ny++) {
Vj = XYZj[ny];
for (m1_idx = 0; m1_idx < mask1_.Nselected(); m1_idx++) {
XYZi = currentFrame.XYZ( mask1_[m1_idx] );
*(mat++) += Vj * XYZi[0];
*(mat++) += Vj * XYZi[1];
*(mat++) += Vj * XYZi[2];
}
}
}
// Mask1/Mask2 diagonal
# pragma omp for
for (m1_idx = 0; m1_idx < crd_max; m1_idx++) {
v1 = Mat_->v1begin() + (m1_idx * 3); // Index into vect/vect2
v2 = vect2_.begin() + (m1_idx * 3);
StoreVec(v1, v2, currentFrame.CRD( crd_indices_[m1_idx] ));
}
} // END PARALLEL BLOCK FULL
return;
} else { // HALF MATRIX
int v_idx;
unsigned int nx;
double d_m2_idx;
double TwoN = (double)( Mat_->Ncols() * 2 );
# pragma omp parallel private(m1_idx, m2_idx, d_m2_idx, v_idx, XYZi, XYZj, Vj, mat, v1, v2, ny, nx)
{
#pragma omp for schedule(dynamic)
for (m2_idx = 0; m2_idx < mask1_.Nselected(); m2_idx++) {
v_idx = m2_idx * 3;
d_m2_idx = (double)v_idx;
mat = Mat_->begin() + (int)(0.5*d_m2_idx*(TwoN-d_m2_idx-1.0)+d_m2_idx);
v1 = Mat_->v1begin() + v_idx;
v2 = vect2_.begin() + v_idx;
XYZj = currentFrame.XYZ( mask1_[m2_idx] );
StoreVec(v1, v2, XYZj);
for (ny = 0; ny < 3; ny++) {
Vj = XYZj[ny];
// m1_idx = m2_idx, diagonal
for (nx = ny; nx < 3; nx++)
*(mat++) += Vj * XYZj[nx]; // Vj * i{0,1,2}, Vj * i{1,2}, Vj * i{2}
for (m1_idx = m2_idx+1; m1_idx < mask1_.Nselected(); m1_idx++) {
XYZi = currentFrame.XYZ( mask1_[m1_idx] );
*(mat++) += Vj * XYZi[0];
*(mat++) += Vj * XYZi[1];
*(mat++) += Vj * XYZi[2];
}
}
}
} // END PARALLEL BLOCK HALF
}
#endif
# else
DataSet_MatrixDbl::iterator mat = Mat_->begin();
v_iterator v1idx1 = Mat_->v1begin();
v_iterator v2idx1 = vect2_.begin();
if (useMask2_) {
// Full Matrix
// Position for mask2 halfway through vect/vect2
v_iterator v1idx2 = Mat_->v1begin() + (mask1_.Nselected() * 3);
v_iterator v2idx2 = vect2_.begin() + (mask1_.Nselected() * 3);
bool storeVecj = true; // Only store vecj|vecj^2 first time through inner loop
// OUTER LOOP
for (AtomMask::const_iterator atom2 = mask2_.begin(); atom2 != mask2_.end(); ++atom2)
{
const double* XYZi = currentFrame.XYZ( *atom2 );
// Store veci and veci^2
StoreVec(v1idx2, v2idx2, XYZi);
// Loop over X, Y, and Z of veci
for (int iidx = 0; iidx < 3; ++iidx) {
double Vi = XYZi[iidx];
// INNER LOOP
for (AtomMask::const_iterator atom1 = mask1_.begin(); atom1 != mask1_.end(); ++atom1)
{
const double* XYZj = currentFrame.XYZ( *atom1 );
// Store vecj and vecj^2, first time through only
if (storeVecj)
StoreVec(v1idx1, v2idx1, XYZj);
*(mat++) += Vi * XYZj[0];
*(mat++) += Vi * XYZj[1];
*(mat++) += Vi * XYZj[2];
}
storeVecj = false;
}
}
} else {
// Half Matrix
// OUTER LOOP
for (AtomMask::const_iterator atom2 = mask1_.begin(); atom2 != mask1_.end(); ++atom2)
{
const double* XYZi = currentFrame.XYZ( *atom2 );
// Store veci and veci^2
StoreVec(v1idx1, v2idx1, XYZi);
// Loop over X, Y, and Z of veci
for (int iidx = 0; iidx < 3; ++iidx) {
double Vi = XYZi[iidx];
// Diagonal
for (int jidx = iidx; jidx < 3; jidx++)
*(mat++) += Vi * XYZi[jidx]; // Vi * j{0,1,2}, Vi * j{1,2}, Vi * j{2}
// INNER LOOP
for (AtomMask::const_iterator atom1 = atom2 + 1; atom1 != mask1_.end(); ++atom1)
{
const double* XYZj = currentFrame.XYZ( *atom1 );
*(mat++) += Vi * XYZj[0];
*(mat++) += Vi * XYZj[1];
*(mat++) += Vi * XYZj[2];
}
}
}
}
# endif
}
