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#include <cstdlib> |
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#include <stdlib.h> |
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#include "Molecule.hpp" |
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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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double aPos[3]; |
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int i, j; |
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for(i=0; i<nAtoms; i++) { |
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if(myAtoms[i] != NULL ) { |
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myAtoms[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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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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myAtoms[i]->setPos( aPos ); |
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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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double aPos[3]; |
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int i, j; |
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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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for (j=0; j<3; j++) |
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COM[j] = 0.0; |
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mtot = 0.0; |
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for (i=0; i < nAtoms; i++) { |
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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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myAtoms[i]->getPos( aPos ); |
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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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COM[0] /= mtot; |
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COM[1] /= mtot; |
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COM[2] /= mtot; |
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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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void Molecule::getCOMvel( double mtot, double COMvel[3] ) { |
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double Molecule::getCOMvel( double COMvel[3] ) { |
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double mass; |
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int i; |
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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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COMvel[0] = 0.0; |
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COMvel[1] = 0.0; |
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COMvel[2] = 0.0; |
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for (j=0; j<3; j++) |
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COMvel[j] = 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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myAtoms[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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COMvel[0] /= mtot; |
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COMvel[1] /= mtot; |
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COMvel[2] /= mtot; |
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for (j=0; j<3; j++) |
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COMvel[j] /= mtot; |
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return mtot; |
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} |
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double Molecule::getTotalMass() |
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{ |
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int natoms; |
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Atom** atoms; |
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double totalMass; |
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natoms = getNAtoms(); |
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atoms = getMyAtoms(); |
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totalMass = 0; |
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for(int i =0; i < natoms; i++){ |
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totalMass += atoms[i]->getMass(); |
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} |
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return totalMass; |
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} |
