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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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#include <iostream> |
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#include <cstdlib> |
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#include "utils/simError.h" |
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#include "applications/simpleBuilder/MoLocator.hpp" |
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#include "math/MatVec3.h" |
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#include "types/AtomType.hpp" |
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namespace oopse { |
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MoLocator::MoLocator( MoleculeStamp* theStamp, ForceField* theFF){ |
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MoLocator::MoLocator( MoleculeStamp* theStamp, ForceFields* theFF){ |
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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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calcRef(); |
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} |
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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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Vector3d newCoor; |
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Vector3d curRefCoor; |
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RotMat3x3d rotMat = latVec2RotMat(ort); |
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|
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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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latVec2RotMat(ort, rotMat); |
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myIntegrableObjects = mol->getIntegrableObjects(); |
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if(mol->getNIntegrableObjects() != 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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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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Molecule::IntegrableObjectIterator ii; |
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StuntDouble* integrableObject; |
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int i; |
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for (integrableObject = mol->beginIntegrableObject(ii), i = 0; integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii), ++i) { |
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} |
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for(int i=0; i<nIntegrableObjects; i++) { |
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newCoor = rotMat * refCoords[i]; |
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newCoor += offset; |
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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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matVecMul3(rotMat, curRefCoor, newCoor); |
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integrableObject->setPos( newCoor); |
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integrableObject->setVel(V3Zero); |
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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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myIntegrableObjects[i]->setPos( newCoor); |
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myIntegrableObjects[i]->setVel(zeroVector); |
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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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if(integrableObject->isDirectional()){ |
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integrableObject->setA(rotMat * integrableObject->getA()); |
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integrableObject->setJ(V3Zero); |
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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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void MoLocator::calcRef( 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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std::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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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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for(int j = 0; j < nAtomsInRb; j++){ |
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currAtomMass = myFF->getAtomTypeMass(currAtomStamp->getType()); |
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currAtomMass = getAtomMass(currAtomStamp->getType(), myFF); |
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totMassInRb += currAtomMass; |
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coor.x() += currAtomStamp->getPosX() * currAtomMass; |
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} |
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void latVec2RotMat(const Vector3d& lv, double rotMat[3][3]){ |
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double theta, phi, 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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double getAtomMass(const std::string& at, ForceField* myFF) { |
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double mass; |
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AtomType* atomType= myFF->getAtomType(at); |
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if (atomType != NULL) { |
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mass = atomType->getMass(); |
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} else { |
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mass = 0.0; |
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std::cerr << "Can not find AtomType: " << at << std::endl; |
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} |
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return mass; |
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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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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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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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double getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
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int nAtoms; |
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double totMass = 0; |
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nAtoms = molStamp->getNAtoms(); |
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for(size_t i = 0; i < nAtoms; i++) { |
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AtomStamp *currAtomStamp = molStamp->getAtom(i); |
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totMass += getAtomMass(currAtomStamp->getType(), myFF); |
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} |
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return totMass; |
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} |
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RotMat3x3d latVec2RotMat(const Vector3d& lv){ |
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double theta =acos(lv[2]); |
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double phi = atan2(lv[1], lv[0]); |
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double psi = 0; |
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return RotMat3x3d(phi, theta, psi); |
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|
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} |
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} |
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