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#include <iostream> |
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#include <cstdlib> |
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#include <cmath> |
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#include "simError.h" |
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#include "MoLocator.hpp" |
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#include "MatVec3.h" |
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|
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MoLocator::MoLocator( MoleculeStamp* theStamp, ForceFields* theFF){ |
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|
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myStamp = theStamp; |
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myFF = theFF; |
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nIntegrableObjects = myStamp->getNIntegrable(); |
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calcRefCoords(); |
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} |
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|
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void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){ |
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Vector3d newCoor; |
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Vector3d velocity(0.0, 0.0, 0.0); |
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Vector3d angMomentum(0.0, 0.0, 0.0); |
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double quaternion[4]; |
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vector<StuntDouble*> myIntegrableObjects; |
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double rotMat[3][3]; |
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|
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quaternion[0] = 1.0; |
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quaternion[1] = 0.0; |
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quaternion[2] = 0.0; |
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quaternion[3] = 0.0; |
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|
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latVec2RotMat(ort, rotMat); |
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|
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myIntegrableObjects = mol->getIntegrableObjects(); |
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|
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if(myIntegrableObjects.size() != nIntegrableObjects){ |
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sprintf( painCave.errMsg, |
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"MoLocator error.\n" |
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" The number of integrable objects of MoleculeStamp is not the same as that of Molecule\n"); |
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painCave.isFatal = 1; |
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simError(); |
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|
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} |
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|
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for(int i=0; i<nIntegrableObjects; i++) { |
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|
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//calculate the reference coordinate for integrable objects after rotation |
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matVecMul3(rotMat, refCoords[i].vec, newCoor.vec); |
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newCoor += offset; |
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|
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myIntegrableObjects[i]->setPos( newCoor.vec); |
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myIntegrableObjects[i]->setVel(velocity.vec); |
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|
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if(myIntegrableObjects[i]->isDirectional()){ |
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myIntegrableObjects[i]->setA(rotMat); |
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myIntegrableObjects[i]->setJ(angMomentum.vec); |
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} |
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} |
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|
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} |
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|
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void MoLocator::calcRefCoords( void ){ |
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AtomStamp* currAtomStamp; |
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int nAtoms; |
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int nRigidBodies; |
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vector<double> mass; |
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Vector3d coor; |
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Vector3d refMolCom; |
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int nAtomsInRb; |
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double totMassInRb; |
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double currAtomMass; |
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double molMass; |
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|
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nAtoms= myStamp->getNAtoms(); |
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nRigidBodies = myStamp->getNRigidBodies(); |
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|
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for(size_t i=0; i<nAtoms; i++){ |
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currAtomStamp = myStamp->getAtom(i); |
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|
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if( !currAtomStamp->havePosition() ){ |
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sprintf( painCave.errMsg, |
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"MoLocator error.\n" |
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" Component %s, atom %s does not have a position specified.\n" |
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" This means MoLocator cannot initalize it's position.\n", |
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myStamp->getID(), |
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currAtomStamp->getType() ); |
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|
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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//if atom belongs to rigidbody, just skip it |
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if(myStamp->isAtomInRigidBody(i)) |
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continue; |
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//get mass and the reference coordinate |
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else{ |
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currAtomMass = myFF->getAtomTypeMass(currAtomStamp->getType()); |
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mass.push_back(currAtomMass); |
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coor.x = currAtomStamp->getPosX(); |
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coor.y = currAtomStamp->getPosY(); |
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coor.z = currAtomStamp->getPosZ(); |
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refCoords.push_back(coor); |
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|
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} |
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} |
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|
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for(int i = 0; i < nRigidBodies; i++){ |
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coor.x = 0; |
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coor.y = 0; |
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coor.z = 0; |
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totMassInRb = 0; |
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|
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for(int j = 0; j < nAtomsInRb; j++){ |
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currAtomMass = myFF->getAtomTypeMass(currAtomStamp->getType()); |
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totMassInRb += currAtomMass; |
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coor.x += currAtomStamp->getPosX() * currAtomMass; |
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coor.y += currAtomStamp->getPosY() * currAtomMass; |
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coor.z += currAtomStamp->getPosZ() * currAtomMass; |
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} |
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|
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mass.push_back(totMassInRb); |
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coor /= totMassInRb; |
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refCoords.push_back(coor); |
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} |
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|
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|
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//calculate the reference center of mass |
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molMass = 0; |
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refMolCom.x = 0; |
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refMolCom.y = 0; |
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refMolCom.z = 0; |
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|
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for(int i = 0; i < nIntegrableObjects; i++){ |
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refMolCom += refCoords[i] * mass[i]; |
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molMass += mass[i]; |
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} |
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|
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refMolCom /= molMass; |
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|
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//move the reference center of mass to (0,0,0) and adjust the reference coordinate |
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//of the integrabel objects |
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for(int i = 0; i < nIntegrableObjects; i++) |
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refCoords[i] -= refMolCom; |
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} |
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|
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|
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void latVec2RotMat(const Vector3d& lv, double rotMat[3][3]){ |
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|
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double theta, phi, psi; |
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|
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theta =acos(lv.z); |
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phi = atan2(lv.y, lv.x); |
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psi = 0; |
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|
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rotMat[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
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rotMat[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
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rotMat[0][2] = sin(theta) * sin(psi); |
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|
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rotMat[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
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rotMat[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
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rotMat[1][2] = sin(theta) * cos(psi); |
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|
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rotMat[2][0] = sin(phi) * sin(theta); |
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rotMat[2][1] = -cos(phi) * sin(theta); |
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rotMat[2][2] = cos(theta); |
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} |
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