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// $Id$
//
// Created by Santosh Putta, Nov 2006
//
#include "ChiralViolationContrib.h"
#include "ChiralSet.h"
#include <ForceField/ForceField.h>
namespace DistGeom {
ChiralViolationContrib::ChiralViolationContrib(ForceFields::ForceField *owner,
const ChiralSet *cset,
double weight) {
PRECONDITION(owner, "bad owner");
PRECONDITION(cset, "bad chiral set")
URANGE_CHECK(cset->d_idx1, owner->positions().size() - 1);
URANGE_CHECK(cset->d_idx2, owner->positions().size() - 1);
URANGE_CHECK(cset->d_idx3, owner->positions().size() - 1);
URANGE_CHECK(cset->d_idx4, owner->positions().size() - 1);
dp_forceField = owner;
d_idx1 = cset->d_idx1;
d_idx2 = cset->d_idx2;
d_idx3 = cset->d_idx3;
d_idx4 = cset->d_idx4;
d_volLower = cset->getLowerVolumeBound();
d_volUpper = cset->getUpperVolumeBound();
d_weight = weight;
}
double ChiralViolationContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
unsigned int dim = dp_forceField->dimension();
double vol = calcChiralVolume(d_idx1, d_idx2, d_idx3, d_idx4, pos, dim);
double res = 0.0;
if (vol < d_volLower) {
res = d_weight * (vol - d_volLower) * (vol - d_volLower);
} else if (vol > d_volUpper) {
res = d_weight * (vol - d_volUpper) * (vol - d_volUpper);
}
// std::cerr<<"Chiral Violation vol: "<<vol<<" E: "<<res<<std::endl;
return res;
}
void ChiralViolationContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
unsigned int dim = dp_forceField->dimension();
// even if we are minimizing in higher dimension the chiral volume is
// calculated using only the first 3 dimensions
RDGeom::Point3D v1(pos[d_idx1 * dim] - pos[d_idx4 * dim],
pos[d_idx1 * dim + 1] - pos[d_idx4 * dim + 1],
pos[d_idx1 * dim + 2] - pos[d_idx4 * dim + 2]);
RDGeom::Point3D v2(pos[d_idx2 * dim] - pos[d_idx4 * dim],
pos[d_idx2 * dim + 1] - pos[d_idx4 * dim + 1],
pos[d_idx2 * dim + 2] - pos[d_idx4 * dim + 2]);
RDGeom::Point3D v3(pos[d_idx3 * dim] - pos[d_idx4 * dim],
pos[d_idx3 * dim + 1] - pos[d_idx4 * dim + 1],
pos[d_idx3 * dim + 2] - pos[d_idx4 * dim + 2]);
RDGeom::Point3D v2xv3 = v2.crossProduct(v3);
double vol = v1.dotProduct(v2xv3);
double preFactor;
if (vol < d_volLower) {
preFactor = d_weight * (vol - d_volLower);
} else if (vol > d_volUpper) {
preFactor = d_weight * (vol - d_volUpper);
} else {
return;
}
// now comes the hard part - there are a total of 12 variables involved
// 4 x 3 - four points and 3 dimensions
//
grad[dim * d_idx1] += preFactor * ((v2.y) * (v3.z) - (v3.y) * (v2.z));
grad[dim * d_idx1 + 1] += preFactor * ((v3.x) * (v2.z) - (v2.x) * (v3.z));
grad[dim * d_idx1 + 2] += preFactor * ((v2.x) * (v3.y) - (v3.x) * (v2.y));
grad[dim * d_idx2] += preFactor * ((v3.y) * (v1.z) - (v3.z) * (v1.y));
grad[dim * d_idx2 + 1] += preFactor * ((v3.z) * (v1.x) - (v3.x) * (v1.z));
grad[dim * d_idx2 + 2] += preFactor * ((v3.x) * (v1.y) - (v3.y) * (v1.x));
grad[dim * d_idx3] += preFactor * ((v2.z) * (v1.y) - (v2.y) * (v1.z));
grad[dim * d_idx3 + 1] += preFactor * ((v2.x) * (v1.z) - (v2.z) * (v1.x));
grad[dim * d_idx3 + 2] += preFactor * ((v2.y) * (v1.x) - (v2.x) * (v1.y));
grad[dim * d_idx4] +=
preFactor *
(pos[d_idx1 * dim + 2] * (pos[d_idx2 * dim + 1] - pos[d_idx3 * dim + 1]) +
pos[d_idx2 * dim + 2] * (pos[d_idx3 * dim + 1] - pos[d_idx1 * dim + 1]) +
pos[d_idx3 * dim + 2] * (pos[d_idx1 * dim + 1] - pos[d_idx2 * dim + 1]));
grad[dim * d_idx4 + 1] +=
preFactor *
(pos[d_idx1 * dim] * (pos[d_idx2 * dim + 2] - pos[d_idx3 * dim + 2]) +
pos[d_idx2 * dim] * (pos[d_idx3 * dim + 2] - pos[d_idx1 * dim + 2]) +
pos[d_idx3 * dim] * (pos[d_idx1 * dim + 2] - pos[d_idx2 * dim + 2]));
grad[dim * d_idx4 + 2] +=
preFactor *
(pos[d_idx1 * dim + 1] * (pos[d_idx2 * dim] - pos[d_idx3 * dim]) +
pos[d_idx2 * dim + 1] * (pos[d_idx3 * dim] - pos[d_idx1 * dim]) +
pos[d_idx3 * dim + 1] * (pos[d_idx1 * dim] - pos[d_idx2 * dim]));
// std::cerr<<"Chiral Violation grad: "<<preFactor<<std::endl;
}
}
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