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135 lines
5.0 KiB
C++
135 lines
5.0 KiB
C++
// $Id$
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//
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// Created by Santosh Putta, Nov 2006
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//
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#include "ChiralViolationContrib.h"
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#include "ChiralSet.h"
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#include <ForceField/ForceField.h>
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#include <Geometry/point.h>
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namespace DistGeom {
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ChiralViolationContrib::ChiralViolationContrib(ForceFields::ForceField *owner, const ChiralSet* cset,
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double weight) {
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PRECONDITION(owner,"bad owner");
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PRECONDITION(cset, "bad chiral set")
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RANGE_CHECK(0,cset->d_idx1,owner->positions().size()-1);
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RANGE_CHECK(0,cset->d_idx2,owner->positions().size()-1);
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RANGE_CHECK(0,cset->d_idx3,owner->positions().size()-1);
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RANGE_CHECK(0,cset->d_idx4,owner->positions().size()-1);
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dp_forceField = owner;
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d_idx1 = cset->d_idx1;
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d_idx2 = cset->d_idx2;
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d_idx3 = cset->d_idx3;
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d_idx4 = cset->d_idx4;
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d_volLower = cset->getLowerVolumeBound();
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d_volUpper = cset->getUpperVolumeBound();
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d_weight = weight;
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}
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double ChiralViolationContrib::getEnergy(double *pos) const {
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PRECONDITION(dp_forceField,"no owner");
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PRECONDITION(pos,"bad vector");
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unsigned int dim = dp_forceField->dimension();
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// even if we are minimizing in higher dimension the chiral volume is
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// calculated using only the first 3 dimensions
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RDGeom::Point3D v1(pos[d_idx1*dim] - pos[d_idx4*dim],
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pos[d_idx1*dim+1] - pos[d_idx4*dim+1],
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pos[d_idx1*dim+2] - pos[d_idx4*dim+2]);
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RDGeom::Point3D v2(pos[d_idx2*dim] - pos[d_idx4*dim],
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pos[d_idx2*dim+1] - pos[d_idx4*dim+1],
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pos[d_idx2*dim+2] - pos[d_idx4*dim+2]);
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RDGeom::Point3D v3(pos[d_idx3*dim] - pos[d_idx4*dim],
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pos[d_idx3*dim+1] - pos[d_idx4*dim+1],
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pos[d_idx3*dim+2] - pos[d_idx4*dim+2]);
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RDGeom::Point3D v2xv3 = v2.crossProduct(v3);
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double vol = v1.dotProduct(v2xv3);
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double res=0.0;
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if (vol < d_volLower) {
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res=d_weight*(vol - d_volLower)*(vol - d_volLower);
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} else if (vol > d_volUpper) {
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res=d_weight*(vol - d_volUpper)*(vol - d_volUpper);
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}
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//std::cerr<<"Chiral Violation vol: "<<vol<<" E: "<<res<<std::endl;
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return res;
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}
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void ChiralViolationContrib::getGrad(double *pos, double *grad) const {
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PRECONDITION(dp_forceField,"no owner");
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PRECONDITION(pos,"bad vector");
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unsigned int dim = dp_forceField->dimension();
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// even if we are minimizing in higher dimension the chiral volume is
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// calculated using only the first 3 dimensions
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RDGeom::Point3D v1(pos[d_idx1*dim] - pos[d_idx4*dim],
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pos[d_idx1*dim+1] - pos[d_idx4*dim+1],
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pos[d_idx1*dim+2] - pos[d_idx4*dim+2]);
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RDGeom::Point3D v2(pos[d_idx2*dim] - pos[d_idx4*dim],
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pos[d_idx2*dim+1] - pos[d_idx4*dim+1],
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pos[d_idx2*dim+2] - pos[d_idx4*dim+2]);
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RDGeom::Point3D v3(pos[d_idx3*dim] - pos[d_idx4*dim],
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pos[d_idx3*dim+1] - pos[d_idx4*dim+1],
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pos[d_idx3*dim+2] - pos[d_idx4*dim+2]);
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RDGeom::Point3D v2xv3 = v2.crossProduct(v3);
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double vol = v1.dotProduct(v2xv3);
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double preFactor;
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if (vol < d_volLower) {
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preFactor = d_weight*(vol - d_volLower);
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} else if (vol > d_volUpper) {
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preFactor = d_weight*(vol - d_volUpper);
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} else {
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return;
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}
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// now comes the hard part - there are a total of 12 variables involved
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// 4 x 3 - four points and 3 dimensions
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//
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grad[dim*d_idx1] += preFactor*((v2.y)*(v3.z) - (v3.y)*(v2.z));
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grad[dim*d_idx1+1] += preFactor*((v3.x)*(v2.z) - (v2.x)*(v3.z));
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grad[dim*d_idx1+2] += preFactor*((v2.x)*(v3.y) - (v3.x)*(v2.y));
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grad[dim*d_idx2] += preFactor*((v3.y)*(v1.z) - (v3.z)*(v1.y));
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grad[dim*d_idx2 + 1] += preFactor*((v3.z)*(v1.x) - (v3.x)*(v1.z));
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grad[dim*d_idx2 + 2] += preFactor*((v3.x)*(v1.y) - (v3.y)*(v1.x));
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grad[dim*d_idx3] += preFactor*((v2.z)*(v1.y) - (v2.y)*(v1.z));
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grad[dim*d_idx3 + 1] += preFactor*((v2.x)*(v1.z) - (v2.z)*(v1.x));
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grad[dim*d_idx3 + 2] += preFactor*((v2.y)*(v1.x) - (v2.x)*(v1.y));
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grad[dim*d_idx4] += preFactor*(pos[d_idx1*dim+2]*(pos[d_idx2*dim+1] - pos[d_idx3*dim+1])
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+ pos[d_idx2*dim+2]*(pos[d_idx3*dim+1] - pos[d_idx1*dim+1])
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+ pos[d_idx3*dim+2]*(pos[d_idx1*dim+1] - pos[d_idx2*dim+1]));
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grad[dim*d_idx4+1] += preFactor*(pos[d_idx1*dim]*(pos[d_idx2*dim+2] - pos[d_idx3*dim+2])
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+ pos[d_idx2*dim]*(pos[d_idx3*dim+2] - pos[d_idx1*dim+2])
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+ pos[d_idx3*dim]*(pos[d_idx1*dim+2] - pos[d_idx2*dim+2]));
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grad[dim*d_idx4+2] += preFactor*(pos[d_idx1*dim+1]*(pos[d_idx2*dim] - pos[d_idx3*dim])
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+ pos[d_idx2*dim+1]*(pos[d_idx3*dim] - pos[d_idx1*dim])
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+ pos[d_idx3*dim+1]*(pos[d_idx1*dim] - pos[d_idx2*dim]));
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//std::cerr<<"Chiral Violation grad: "<<preFactor<<std::endl;
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}
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}
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