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#ifndef _DIRECTIONALATOM_H_ |
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#define _DIRECTIONALATOM_H_ |
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|
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#include <string.h> |
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#include <stdlib.h> |
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#include <iostream> |
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|
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#include "primitives/StuntDouble.hpp" |
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#include "primitives/Atom.hpp" |
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|
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class DirectionalAtom : public Atom { |
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|
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public: |
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DirectionalAtom(int theIndex, SimState* theConfig) : Atom(theIndex, |
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theConfig) |
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{ |
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objType = OT_DATOM; |
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|
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for (int i=0; i < 3; i++) |
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for (int j=0; j < 3; j++) |
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sU[i][j] = 0.0; |
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|
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} |
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virtual ~DirectionalAtom() {} |
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|
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virtual void setCoords(void); |
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|
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void printAmatIndex( void ); |
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|
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void setUnitFrameFromEuler(double phi, double theta, double psi); |
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void setEuler( double phi, double theta, double psi ); |
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|
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void zeroForces(); |
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|
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void getA( double the_A[3][3] ); // get the full rotation matrix |
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void setA( double the_A[3][3] ); |
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void rotateBy( double by_A[3][3] ); // rotate your frame using this matrix |
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|
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void getU( double the_u[3] ); // get the unit vetor |
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void updateU( void ); |
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|
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void getQ( double the_q[4] ); // get the quanternions |
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void setQ( double the_q[4] ); |
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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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void getJ( double theJ[3] ); |
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void setJ( double theJ[3] ); |
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/** |
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* @file DirectionalAtom.hpp |
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* @author tlin |
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* @date 10/23/2004 |
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* @version 1.0 |
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*/ |
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void getTrq( double theT[3] ); |
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void addTrq( double theT[3] ); |
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#ifndef PRIMITIVES_DIRECTIONALATOM_HPP |
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#define PRIMITIVES_DIRECTIONALATOM_HPP |
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|
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void setI( double the_I[3][3] ); |
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void getI( double the_I[3][3] ); |
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|
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void lab2Body( double r[3] ); |
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void body2Lab( double r[3] ); |
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|
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double getZangle( ); |
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void setZangle( double zAng ); |
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void addZangle( double zAng ); |
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|
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// Four functions added for derivatives with respect to Euler Angles: |
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// (Needed for minimization routines): |
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|
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void getGrad(double gradient[6] ); |
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void getEulerAngles( double myEuler[3] ); |
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|
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double max(double x, double y); |
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double min(double x, double y); |
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|
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virtual void accept(BaseVisitor* v) {v->visit(this);} |
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|
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private: |
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int dIndex; |
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|
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double sU[3][3]; // the standard unit vectors ( body fixed ) |
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|
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double jx, jy, jz; // the angular momentum vector ( body fixed ) |
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|
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double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed ) |
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double Iyx, Iyy, Iyz; |
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double Izx, Izy, Izz; |
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|
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}; |
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|
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#endif |
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#include "primitives/Atom.hpp" |
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#include "types/DirectionalAtomType.hpp" |
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namespace OpenMD{ |
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class DirectionalAtom : public Atom { |
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public: |
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DirectionalAtom(DirectionalAtomType* dAtomType); |
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/** |
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* Returns the inertia tensor of this stuntdouble |
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* @return the inertia tensor of this stuntdouble |
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*/ |
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virtual Mat3x3d getI(); |
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|
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/** |
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* Sets the previous rotation matrix of this stuntdouble |
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* @param a new rotation matrix |
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*/ |
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virtual void setPrevA(const RotMat3x3d& a); |
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|
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/** |
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* Sets the current rotation matrix of this stuntdouble |
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* @param a new rotation matrix |
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*/ |
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virtual void setA(const RotMat3x3d& a); |
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|
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/** |
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* Sets the rotation matrix of this stuntdouble in specified snapshot |
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* @param a rotation matrix to be set |
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* @param snapshotNo |
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* @see #getA |
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*/ |
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virtual void setA(const RotMat3x3d& a, int snapshotNo); |
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|
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/** |
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* Left multiple rotation matrix by another rotation matrix |
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* @param m a rotation matrix |
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*/ |
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void rotateBy(const RotMat3x3d& m); |
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|
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/** |
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* Returns the gradient of this stuntdouble |
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* @return the gradient of this stuntdouble |
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*/ |
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virtual std::vector<RealType> getGrad(); |
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|
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virtual void accept(BaseVisitor* v); |
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|
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protected: |
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RotMat3x3d electroBodyFrame_; // body fixed standard eletrostatic frame |
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}; |
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}//namespace OpenMD |
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#endif //PRIMITIVES_DIRECTIONALATOM_HPP |
