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#ifndef _ATOM_H_ |
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#define _ATOM_H_ |
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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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|
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/** |
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* @file Atom.hpp |
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* @author tlin |
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* @date 10/22/2004 |
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* @version 1.0 |
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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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#ifndef PRIMITIVES_ATOM_HPP |
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#define PRIMITIVES_ATOM_HPP |
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#include "brains/SimState.hpp" |
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#include "primitives/StuntDouble.hpp" |
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#include "visitors/BaseVisitor.hpp" |
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#include "types/AtomType.hpp" |
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class Atom : public StuntDouble { |
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public: |
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namespace oopse{ |
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class Atom : public StuntDouble { |
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public: |
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Atom(AtomType* at); |
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Atom(int theIndex, SimState* theConfig ); |
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virtual ~Atom() {} |
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virtual std::string getType() {return atomType_->getName();} |
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|
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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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virtual void setCoords(void); |
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/** |
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* Returns the gradient of this stuntdouble |
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* @return the inertia tensor of this stuntdouble |
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*/ |
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virtual std::vector<double> getGrad(); |
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void getPos( double theP[3] ); |
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void setPos( double theP[3] ); |
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virtual void accept(BaseVisitor* v); |
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void getVel( double theV[3] ); |
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void setVel( double theV[3] ); |
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/** |
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* Returns the AtomType of this Atom. |
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* @return the atom type of this atom |
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*/ |
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AtomType* getAtomType() { |
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return atomType_; |
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} |
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|
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//forward functions of AtomType class |
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bool isCharge() { |
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return atomType_->isCharge(); |
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} |
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bool isDirectional() { |
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return atomType_->isDirectional(); |
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} |
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void getFrc( double theF[3] ); |
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void addFrc( double theF[3] ); |
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bool isDipole() { |
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return atomType_->isDipole(); |
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} |
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virtual void zeroForces(); |
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bool isQudrapole() { |
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return atomType_->isQuadrupole(); |
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} |
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|
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bool isMultipole() { |
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return atomType_->isMultipole(); |
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} |
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bool isGayBerne() { |
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return atomType_->isGayBerne(); |
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} |
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bool isSticky() { |
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return atomType_->isSticky(); |
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} |
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double getMass() {return c_mass;} |
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void setMass(double mass) {c_mass = mass;} |
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int getIndex() const {return index;} |
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void setIndex(int theIndex); |
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bool isShape() { |
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return atomType_->isShape(); |
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} |
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char *getType() {return c_name;} |
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void setType(char * name) {strcpy(c_name,name);} |
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int getIdent( void ) { return ident; } |
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void setIdent( int info ) { ident = info; } |
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int getIdent() { |
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return atomType_->getIdent(); |
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} |
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protected: |
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AtomType* atomType_; |
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}; |
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#ifdef IS_MPI |
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int getGlobalIndex( void ) { return myGlobalIndex; } |
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void setGlobalIndex( int info ) { myGlobalIndex = info; } |
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#endif // is_mpi |
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}//namepace oopse |
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void setHasDipole( int value ) { has_dipole = value; } |
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int hasDipole( void ) { return has_dipole; } |
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void setHasCharge(int value) {has_charge = value;} |
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int hasCharge(void) {return has_charge;} |
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virtual void accept(BaseVisitor* v) {v->visit(this);} |
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protected: |
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SimState* myConfig; |
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double* pos; // the position array |
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double* vel; // the velocity array |
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double* frc; // the forc array |
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double* trq; // the torque vector ( space fixed ) |
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double* Amat; // the rotation matrix |
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double* mu; // the array of dipole moments |
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double* ul; // the lab frame unit directional vector |
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double zAngle; // the rotation about the z-axis ( body-fixed ) |
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double c_mass; /* the mass of the atom in amu */ |
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int index; /* set the atom's index */ |
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int offset; // the atom's offset in the storage array |
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int offsetX, offsetY, offsetZ; |
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int Axx, Axy, Axz; // the rotational matrix indices |
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int Ayx, Ayy, Ayz; |
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int Azx, Azy, Azz; |
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char c_name[100]; /* it's name */ |
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int ident; // it's unique numeric identity. |
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int has_dipole; // dipole boolean |
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int has_charge; // charge boolean |
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bool hasCoords; |
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#ifdef IS_MPI |
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int myGlobalIndex; |
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#endif |
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}; |
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#endif |
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#endif //PRIMITIVES_ATOM_HPP |
