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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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MoLocator::MoLocator( MoleculeStamp* theStamp, ForceFields* theFF){ |
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MoLocator::MoLocator( MoleculeStamp* theStamp ){ |
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myStamp = theStamp; |
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nAtoms = myStamp->getNAtoms(); |
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myCoords = NULL; |
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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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MoLocator::~MoLocator(){ |
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void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){ |
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double newCoor[3]; |
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double curRefCoor[3]; |
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double zeroVector[3]; |
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vector<StuntDouble*> myIntegrableObjects; |
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double rotMat[3][3]; |
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if( myCoords != NULL ) delete[] myCoords; |
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} |
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void MoLocator::placeMol( double pos[3], double A[3][3], Atom** atomArray, |
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int atomIndex, SimState* myConfig ){ |
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int i,j,k; |
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double r[3], ji[3]; |
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double phi, theta, psi; |
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double sux, suy, suz; |
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double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz; |
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double ux, uy, uz, u, uSqr; |
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zeroVector[0] = 0.0; |
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zeroVector[1] = 0.0; |
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zeroVector[2] = 0.0; |
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AtomStamp* currAtom; |
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DirectionalAtom* dAtom; |
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double vel[3]; |
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for(i=0;i<3;i++)vel[i]=0.0; |
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for(i=0; i<nAtoms; i++){ |
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currAtom = myStamp->getAtom( i ); |
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j = atomIndex+i; |
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if( currAtom->haveOrientation()){ |
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dAtom = new DirectionalAtom( j, myConfig); |
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atomArray[j] = dAtom; |
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atomArray[j]->setCoords(); |
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// Directional Atoms have standard unit vectors which are oriented |
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// in space using the three Euler angles. |
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phi = currAtom->getEulerPhi() * M_PI / 180.0; |
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theta = currAtom->getEulerTheta() * M_PI / 180.0; |
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psi = currAtom->getEulerPsi()* M_PI / 180.0; |
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dAtom->setUnitFrameFromEuler(phi, theta, psi); |
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dAtom->setA( A ); |
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ji[0] = 0.0; |
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ji[1] = 0.0; |
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ji[2] = 0.0; |
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dAtom->setJ( ji ); |
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} |
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else{ |
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atomArray[j] = new Atom( j, myConfig); |
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atomArray[j]->setCoords(); |
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} |
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atomArray[j]->setType( currAtom->getType() ); |
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for(k=0; k<3; k++) r[k] = myCoords[(i*3)+k]; |
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rotMe( r, A ); |
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for(k=0; k<3; k++) r[k] += pos[k]; |
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atomArray[j]->setPos( r ); |
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atomArray[j]->setVel( vel );; |
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} |
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} |
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void MoLocator::calcRefCoords( void ){ |
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int i,j,k; |
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AtomStamp* currAtom; |
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double centerX, centerY, centerZ; |
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double smallX, smallY, smallZ; |
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double bigX, bigY, bigZ; |
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double dx, dy, dz; |
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double dsqr; |
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latVec2RotMat(ort, rotMat); |
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centerX = 0.0; |
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centerY = 0.0; |
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centerZ = 0.0; |
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myIntegrableObjects = mol->getIntegrableObjects(); |
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for(i=0; i<nAtoms; i++){ |
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currAtom = myStamp->getAtom(i); |
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if( !currAtom->havePosition() ){ |
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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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" 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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currAtom->getType() ); |
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painCave.isFatal = 1; |
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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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centerX += currAtom->getPosX(); |
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centerY += currAtom->getPosY(); |
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centerZ += currAtom->getPosZ(); |
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} |
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for(int i=0; i<nIntegrableObjects; i++) { |
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centerX /= nAtoms; |
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centerY /= nAtoms; |
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centerZ /= nAtoms; |
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myCoords = new double[nAtoms*3]; |
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j = 0; |
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for(i=0; i<nAtoms; i++){ |
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//calculate the reference coordinate for integrable objects after rotation |
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curRefCoor[0] = refCoords[i][0]; |
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curRefCoor[1] = refCoords[i][1]; |
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curRefCoor[2] = refCoords[i][2]; |
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currAtom = myStamp->getAtom(i); |
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j = i*3; |
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myCoords[j] = currAtom->getPosX() - centerX; |
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myCoords[j+1] = currAtom->getPosY() - centerY; |
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myCoords[j+2] = currAtom->getPosZ() - centerZ; |
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} |
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smallX = myCoords[0]; |
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smallY = myCoords[1]; |
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smallZ = myCoords[2]; |
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matVecMul3(rotMat, curRefCoor, newCoor); |
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bigX = myCoords[0]; |
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bigY = myCoords[1]; |
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bigZ = myCoords[2]; |
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newCoor[0] += offset[0]; |
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newCoor[1] += offset[1]; |
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newCoor[2] += offset[2]; |
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j=0; |
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for(i=1; i<nAtoms; i++){ |
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j= i*3; |
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if( myCoords[j] < smallX ) smallX = myCoords[j]; |
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if( myCoords[j+1] < smallY ) smallY = myCoords[j+1]; |
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if( myCoords[j+2] < smallZ ) smallZ = myCoords[j+2]; |
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myIntegrableObjects[i]->setPos( newCoor); |
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myIntegrableObjects[i]->setVel(zeroVector); |
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if( myCoords[j] > bigX ) bigX = myCoords[j]; |
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if( myCoords[j+1] > bigY ) bigY = myCoords[j+1]; |
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if( myCoords[j+2] > bigZ ) bigZ = myCoords[j+2]; |
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if(myIntegrableObjects[i]->isDirectional()){ |
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myIntegrableObjects[i]->setA(rotMat); |
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myIntegrableObjects[i]->setJ(zeroVector); |
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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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nAtoms= myStamp->getNAtoms(); |
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nRigidBodies = myStamp->getNRigidBodies(); |
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dx = bigX - smallX; |
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dy = bigY - smallY; |
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dz = bigZ - smallZ; |
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for(size_t i=0; i<nAtoms; i++){ |
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dsqr = (dx * dx) + (dy * dy) + (dz * dz); |
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maxLength = sqrt( dsqr ); |
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} |
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currAtomStamp = myStamp->getAtom(i); |
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void MoLocator::rotMe( double r[3], double A[3][3] ){ |
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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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double rt[3]; |
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int i,j; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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for(i=0; i<3; i++) rt[i] = r[i]; |
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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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for(i=0; i<3; i++){ |
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r[i] = 0.0; |
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for(j=0; j<3; j++){ |
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r[i] += A[i][j] * rt[j]; |
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} |
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} |
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} |
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void getRandomRot( double rot[3][3] ){ |
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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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double theta, phi, psi; |
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double cosTheta; |
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for(int j = 0; j < nAtomsInRb; j++){ |
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// select random phi, psi, and cosTheta |
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currAtomMass = myFF->getAtomTypeMass(currAtomStamp->getType()); |
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totMassInRb += currAtomMass; |
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|
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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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phi = 2.0 * M_PI * drand48(); |
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psi = 2.0 * M_PI * drand48(); |
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cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1 |
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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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theta = acos( cosTheta ); |
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getEulerRot( theta, phi, psi, rot ); |
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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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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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refMolCom /= molMass; |
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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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void getEulerRot( double theta, double phi, double psi, double rot[3][3] ){ |
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void latVec2RotMat(const Vector3d& lv, double rotMat[3][3]){ |
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rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
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rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
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rot[0][2] = sin(theta) * sin(psi); |
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double theta, phi, psi; |
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rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
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rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
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rot[1][2] = sin(theta) * cos(psi); |
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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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rot[2][0] = sin(phi) * sin(theta); |
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rot[2][1] = -cos(phi) * sin(theta); |
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rot[2][2] = cos(theta); |
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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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