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#include <stdlib.h> |
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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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|
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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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|
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Molecule::~Molecule( void ){ |
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int i; |
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|
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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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|
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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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|
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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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|
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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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|
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} |
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|
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void Molecule::initialize( molInit &theInit ){ |
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CutoffGroup* curCutoffGroup; |
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vector<CutoffGroup*>::iterator iterCutoff; |
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Atom* cutoffAtom; |
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vector<Atom*>::iterator iterAtom; |
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int atomIndex; |
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|
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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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nRigidBodies = theInit.nRigidBodies; |
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nOriented = theInit.nOriented; |
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nCutoffGroups = theInit.nCutoffGroups; |
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|
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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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myRigidBodies = theInit.myRigidBodies; |
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myIntegrableObjects = theInit.myIntegrableObjects; |
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|
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for (int i = 0; i < myRigidBodies.size(); i++) |
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myRigidBodies[i]->calcRefCoords(); |
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|
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myCutoffGroups = theInit.myCutoffGroups; |
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|
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//creat a global index set of atoms which belong to cutoff group. |
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//it will be use to speed up the query whether an atom belongs to cutoff group or not |
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cutoffAtomSet.clear(); |
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|
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for(curCutoffGroup = beginCutoffGroup(iterCutoff); curCutoffGroup != NULL; |
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curCutoffGroup = nextCutoffGroup(iterCutoff)){ |
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|
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for(cutoffAtom = curCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
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cutoffAtom = curCutoffGroup->beginAtom(iterAtom)){ |
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#ifdef IS_MPI |
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atomIndex = cutoffAtom->getGlobalIndex(); |
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#else |
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atomIndex = cutoffAtom->getIndex(); |
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#endif |
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cutoffAtomSet.insert(atomIndex); |
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}// end for(cutoffAtom) |
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}//end for(curCutoffGroup) |
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|
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} |
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|
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void Molecule::calcForces( void ){ |
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|
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int i; |
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double com[3]; |
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|
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for(i=0; i<myRigidBodies.size(); i++) { |
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myRigidBodies[i]->updateAtoms(); |
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} |
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|
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//calculate the center of mass of the molecule |
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//getCOM(com); |
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//for(int i = 0; i < nAtoms; i ++) |
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// myAtoms[i]->setRc(com); |
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|
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|
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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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|
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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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// Rigid Body forces and torques are done after the fortran force loop |
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|
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} |
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|
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double Molecule::getPotential( void ){ |
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|
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int i; |
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double myPot = 0.0; |
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for(i=0; i<myRigidBodies.size(); i++) { |
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myRigidBodies[i]->updateAtoms(); |
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} |
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|
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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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|
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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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|
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return myPot; |
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} |
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|
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void Molecule::printMe( void ){ |
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|
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int i; |
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|
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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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|
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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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|
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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 aPos[3]; |
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int i, j; |
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for(i=0; i<myIntegrableObjects.size(); i++) { |
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if(myIntegrableObjects[i] != NULL ) { |
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myIntegrableObjects[i]->getPos( aPos ); |
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for (j=0; j< 3; j++) |
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aPos[j] += delta[j]; |
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myIntegrableObjects[i]->setPos( aPos ); |
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} |
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} |
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|
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for(i=0; i<myRigidBodies.size(); i++) { |
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myRigidBodies[i]->getPos( aPos ); |
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|
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for (j=0; j< 3; j++) |
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aPos[j] += delta[j]; |
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myRigidBodies[i]->setPos( aPos ); |
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} |
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} |
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|
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void Molecule::atoms2rigidBodies( void ) { |
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int i; |
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for (i = 0; i < myRigidBodies.size(); i++) { |
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myRigidBodies[i]->calcForcesAndTorques(); |
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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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|
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double mass, mtot; |
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double aPos[3]; |
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int i, j; |
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|
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for (j=0; j<3; j++) |
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COM[j] = 0.0; |
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|
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mtot = 0.0; |
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|
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for (i=0; i < myIntegrableObjects.size(); i++) { |
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if (myIntegrableObjects[i] != NULL) { |
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|
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mass = myIntegrableObjects[i]->getMass(); |
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mtot += mass; |
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|
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myIntegrableObjects[i]->getPos( aPos ); |
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|
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for( j = 0; j < 3; j++) |
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COM[j] += aPos[j] * mass; |
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|
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} |
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} |
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for (j = 0; j < 3; j++) |
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COM[j] /= mtot; |
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} |
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|
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double Molecule::getCOMvel( double COMvel[3] ) { |
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|
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double mass, mtot; |
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double aVel[3]; |
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int i, j; |
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|
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|
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for (j=0; j<3; j++) |
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COMvel[j] = 0.0; |
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|
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mtot = 0.0; |
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|
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for (i=0; i < myIntegrableObjects.size(); i++) { |
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if (myIntegrableObjects[i] != NULL) { |
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mass = myIntegrableObjects[i]->getMass(); |
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mtot += mass; |
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|
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myIntegrableObjects[i]->getVel(aVel); |
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for (j=0; j<3; j++) |
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COMvel[j] += aVel[j]*mass; |
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|
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} |
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} |
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|
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for (j=0; j<3; j++) |
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COMvel[j] /= mtot; |
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|
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return mtot; |
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|
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} |
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|
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double Molecule::getTotalMass() |
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{ |
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|
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double totalMass; |
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|
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totalMass = 0; |
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for(int i =0; i < myIntegrableObjects.size(); i++){ |
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totalMass += myIntegrableObjects[i]->getMass(); |
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} |
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|
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return totalMass; |
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} |
