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#include <cstdlib> |
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#include "Molecule.hpp" |
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#include "simError.h" |
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Molecule::Molecule( void ){ |
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myAtoms = NULL; |
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myBonds = NULL; |
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myBends = NULL; |
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myTorsions = NULL; |
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} |
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Molecule::~Molecule( void ){ |
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int i; |
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if( myAtoms != NULL ){ |
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for(i=0; i<nAtoms; i++) if(myAtoms[i] != NULL ) delete myAtoms[i]; |
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delete[] myAtoms; |
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} |
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if( myBonds != NULL ){ |
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for(i=0; i<nBonds; i++) if(myBonds[i] != NULL ) delete myBonds[i]; |
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delete[] myBonds; |
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} |
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if( myBends != NULL ){ |
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for(i=0; i<nBends; i++) if(myBends[i] != NULL ) delete myBends[i]; |
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delete[] myBends; |
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} |
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if( myTorsions != NULL ){ |
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for(i=0; i<nTorsions; i++) if(myTorsions[i] != NULL ) delete myTorsions[i]; |
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delete[] myTorsions; |
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} |
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if( myExcludes != NULL ){ |
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for(i=0; i<nExcludes; i++) if(myExcludes[i] != NULL ) delete myExcludes[i]; |
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delete[] myExcludes; |
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} |
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} |
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void Molecule::initialize( molInit &theInit ){ |
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nAtoms = theInit.nAtoms; |
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nMembers = nAtoms; |
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nBonds = theInit.nBonds; |
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nBends = theInit.nBends; |
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nTorsions = theInit.nTorsions; |
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nExcludes = theInit.nExcludes; |
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nOriented = theInit.nOriented; |
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myAtoms = theInit.myAtoms; |
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myBonds = theInit.myBonds; |
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myBends = theInit.myBends; |
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myTorsions = theInit.myTorsions; |
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myExcludes = theInit.myExcludes; |
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} |
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void Molecule::calcForces( void ){ |
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int i; |
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for(i=0; i<nBonds; i++){ |
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myBonds[i]->calc_forces(); |
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} |
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for(i=0; i<nBends; i++){ |
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myBends[i]->calc_forces(); |
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} |
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for(i=0; i<nTorsions; i++){ |
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myTorsions[i]->calc_forces(); |
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} |
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} |
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double Molecule::getPotential( void ){ |
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int i; |
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double myPot = 0.0; |
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for(i=0; i<nBonds; i++){ |
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myPot += myBonds[i]->get_potential(); |
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} |
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for(i=0; i<nBends; i++){ |
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myPot += myBends[i]->get_potential(); |
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} |
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for(i=0; i<nTorsions; i++){ |
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myPot += myTorsions[i]->get_potential(); |
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} |
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return myPot; |
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} |
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void Molecule::printMe( void ){ |
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int i; |
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for(i=0; i<nBonds; i++){ |
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myBonds[i]->printMe(); |
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} |
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for(i=0; i<nBends; i++){ |
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myBends[i]->printMe(); |
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} |
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for(i=0; i<nTorsions; i++){ |
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myTorsions[i]->printMe(); |
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} |
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} |
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void Molecule::moveCOM(double delta[3]){ |
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double x, y, z; |
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int i; |
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for(i=0; i<nAtoms; i++) { |
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if(myAtoms[i] != NULL ) { |
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x = myAtoms[i]->getX() + delta[0]; |
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y = myAtoms[i]->getY() + delta[1]; |
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z = myAtoms[i]->getZ() + delta[2]; |
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myAtoms[i]->setX(x); |
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myAtoms[i]->setY(y); |
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myAtoms[i]->setZ(z); |
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} |
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} |
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} |
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void Molecule::getCOM( double COM[3] ) { |
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double mass, mtot; |
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int i; |
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COM[0] = 0.0; |
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COM[1] = 0.0; |
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COM[2] = 0.0; |
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mtot = 0.0; |
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for (i=0; i < nAtoms; i++) { |
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if (myAtoms[i] != NULL) { |
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mass = myAtoms[i]->getMass(); |
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mtot += mass; |
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COM[0] += myAtoms[i]->getX() * mass; |
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COM[1] += myAtoms[i]->getY() * mass; |
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COM[2] += myAtoms[i]->getZ() * mass; |
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} |
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} |
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COM[0] /= mtot; |
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COM[1] /= mtot; |
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COM[2] /= mtot; |
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} |
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double Molecule::getCOMvel( double COMvel[3] ) { |
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double mass, mtot; |
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int i; |
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COMvel[0] = 0.0; |
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COMvel[1] = 0.0; |
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COMvel[2] = 0.0; |
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mtot = 0.0; |
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for (i=0; i < nAtoms; i++) { |
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if (myAtoms[i] != NULL) { |
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mass = myAtoms[i]->getMass(); |
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mtot += mass; |
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COMvel[0] += myAtoms[i]->get_vx() * mass; |
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COMvel[1] += myAtoms[i]->get_vy() * mass; |
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COMvel[2] += myAtoms[i]->get_vz() * mass; |
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} |
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} |
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COMvel[0] /= mtot; |
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COMvel[1] /= mtot; |
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COMvel[2] /= mtot; |
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return mtot; |
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} |
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void Molecule::atomicRollCall(int* molMembership) { |
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int i, which; |
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for (i=0; i < nAtoms; i++) { |
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if (myAtoms[i] != NULL) { |
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which = myAtoms[i]->getIndex(); |
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molMembership[which] = globalIndex; |
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} |
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} |
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} |
