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// $Id$
//
// Created by Santosh Putta, Nov 2006
//
#include "ChiralViolationContrib.h"
#include "ChiralSet.h"
#include <ForceField/ForceField.h>
#include <Geometry/point.h>
namespace DistGeom {
ChiralViolationContrib::ChiralViolationContrib(ForceFields::ForceField *owner, const ChiralSet* cset,
double weight) {
PRECONDITION(owner,"bad owner");
PRECONDITION(cset, "bad chiral set")
RANGE_CHECK(0,cset->d_idx1,owner->positions().size()-1);
RANGE_CHECK(0,cset->d_idx2,owner->positions().size()-1);
RANGE_CHECK(0,cset->d_idx3,owner->positions().size()-1);
RANGE_CHECK(0,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();
// 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 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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