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;
}
/** Calculate non-bonded energy using the nonbondParm array. The total
* LJ (vdw) energy is put in ELJ, and the total Coulomb (elec) energy
* is put in Eelec. Depending on the value of nb_calcType, each pair
* energy is either compared to a reference, distributed over both atoms
* evenly in the cumulative array, or reference values are set. If comparing
* to a reference structure, pairs for which the energy difference exceeds
* the cutoffs are printed.
*/
void Action_Pairwise::NonbondEnergy(Frame const& frameIn, Topology const& parmIn,
AtomMask const& maskIn)
{
double delta2;
NonbondEnergyType refE;
ELJ_ = 0.0;
Eelec_ = 0.0;
std::vector<NonbondEnergyType>::const_iterator refpair = ref_nonbondEnergy_.begin();
// Loop over all atom pairs and set information
// Outer loop
for (AtomMask::const_iterator maskatom1 = maskIn.begin();
maskatom1 != maskIn.end(); ++maskatom1)
{
// Get coordinates for first atom.
Vec3 coord1 = frameIn.XYZ( *maskatom1 );
// Set up exclusion list for this atom
Atom::excluded_iterator excluded_atom = parmIn[*maskatom1].excludedbegin();
// Inner loop
for (AtomMask::const_iterator maskatom2 = maskatom1 + 1;
maskatom2 != maskIn.end(); ++maskatom2)
{
// If atom is excluded, just increment to next excluded atom;
// otherwise perform energy calc.
if ( excluded_atom != parmIn[*maskatom1].excludedend() && *maskatom2 == *excluded_atom )
++excluded_atom;
else {
// Calculate the vector pointing from atom2 to atom1
Vec3 JI = coord1 - Vec3(frameIn.XYZ( *maskatom2 ));
double rij2 = JI.Magnitude2();
// Normalize
double rij = sqrt(rij2);
JI /= rij;
// LJ energy
NonbondType const& LJ = parmIn.GetLJparam(*maskatom1, *maskatom2);
double r2 = 1.0 / rij2;
double r6 = r2 * r2 * r2;
double r12 = r6 * r6;
double f12 = LJ.A() * r12; // A/r^12
double f6 = LJ.B() * r6; // B/r^6
double e_vdw = f12 - f6; // (A/r^12)-(B/r^6)
ELJ_ += e_vdw;
// LJ Force
//force=((12*f12)-(6*f6))*r2; // (12A/r^13)-(6B/r^7)
//scalarmult(f,JI,F);
// Coulomb energy
double qiqj = QFAC * parmIn[*maskatom1].Charge() * parmIn[*maskatom2].Charge();
double e_elec = qiqj / rij;
Eelec_ += e_elec;
// Coulomb Force
//force=e_elec/rij; // kes_*(qiqj/r)*(1/r)
//scalarmult(f,JI,F);
// ----------------------------------------
int atom1 = *maskatom1;
int atom2 = *maskatom2;
if (nb_calcType_ == COMPARE_REF) {
// 1 - Comparison to reference, cumulative dEnergy on atoms
// dEvdw
double delta_vdw = refpair->evdw - e_vdw;
// dEelec
double delta_eelec = refpair->eelec - e_elec;
// Output
if (Eout_ != 0)
WriteEnergies(parmIn, atom1, atom2, delta_vdw, delta_eelec, "d");
vdwMat_->Element(atom1, atom2) += delta_vdw;
eleMat_->Element(atom1, atom2) += delta_eelec;
// Divide the total pair dEvdw between both atoms.
delta2 = delta_vdw * 0.5;
atom_evdw_[atom1] += delta2;
atom_evdw_[atom2] += delta2;
// Divide the total pair dEelec between both atoms.
delta2 = delta_eelec * 0.5;
atom_eelec_[atom1] += delta2;
atom_eelec_[atom2] += delta2;
} else if (nb_calcType_ == NORMAL) {
// 2 - No reference, just cumulative Energy on atoms
if (Eout_ != 0)
WriteEnergies(parmIn, atom1, atom2, e_vdw, e_elec, "");
vdwMat_->Element(atom1, atom2) += e_vdw;
eleMat_->Element(atom1, atom2) += e_elec;
// Cumulative evdw - divide between both atoms
delta2 = e_vdw * 0.5;
atom_evdw_[atom1] += delta2;
atom_evdw_[atom2] += delta2;
// Cumulative eelec - divide between both atoms
delta2 = e_elec * 0.5;
atom_eelec_[atom1] += delta2;
atom_eelec_[atom2] += delta2;
} else { // if nb_calcType_ == SET_REF
// 3 - Store the reference nonbond energy for this pair
refE.evdw = e_vdw;
refE.eelec = e_elec;
ref_nonbondEnergy_.push_back( refE );
}
++refpair;
// ----------------------------------------
} // END pair not excluded
} // END Inner loop
} // END Outer loop
}
