| 1 |
< |
#ifndef _ATOM_H_ |
| 2 |
< |
#define _ATOM_H_ |
| 1 |
> |
/* |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
> |
* |
| 4 |
> |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
> |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
> |
* redistribute this software in source and binary code form, provided |
| 7 |
> |
* that the following conditions are met: |
| 8 |
> |
* |
| 9 |
> |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
> |
* publication of scientific results based in part on use of the |
| 11 |
> |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
> |
* the article in which the program was described (Matthew |
| 13 |
> |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
> |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
> |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
> |
* |
| 18 |
> |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
> |
* notice, this list of conditions and the following disclaimer. |
| 20 |
> |
* |
| 21 |
> |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
> |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
> |
* documentation and/or other materials provided with the |
| 24 |
> |
* distribution. |
| 25 |
> |
* |
| 26 |
> |
* This software is provided "AS IS," without a warranty of any |
| 27 |
> |
* kind. All express or implied conditions, representations and |
| 28 |
> |
* warranties, including any implied warranty of merchantability, |
| 29 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
> |
* be liable for any damages suffered by licensee as a result of |
| 32 |
> |
* using, modifying or distributing the software or its |
| 33 |
> |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
> |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
> |
* damages, however caused and regardless of the theory of liability, |
| 37 |
> |
* arising out of the use of or inability to use software, even if the |
| 38 |
> |
* University of Notre Dame has been advised of the possibility of |
| 39 |
> |
* such damages. |
| 40 |
> |
*/ |
| 41 |
> |
|
| 42 |
> |
/** |
| 43 |
> |
* @file Atom.hpp |
| 44 |
> |
* @author tlin |
| 45 |
> |
* @date 10/22/2004 |
| 46 |
> |
* @version 1.0 |
| 47 |
> |
*/ |
| 48 |
|
|
| 49 |
< |
#include <string.h> |
| 50 |
< |
#include <stdlib.h> |
| 6 |
< |
#include <iostream> |
| 49 |
> |
#ifndef PRIMITIVES_ATOM_HPP |
| 50 |
> |
#define PRIMITIVES_ATOM_HPP |
| 51 |
|
|
| 52 |
< |
#include "SimState.hpp" |
| 53 |
< |
#include "StuntDouble.hpp" |
| 10 |
< |
#include "BaseVisitor.hpp" |
| 52 |
> |
#include "primitives/StuntDouble.hpp" |
| 53 |
> |
#include "types/AtomType.hpp" |
| 54 |
|
|
| 55 |
< |
class Atom : public StuntDouble { |
| 56 |
< |
public: |
| 55 |
> |
namespace oopse{ |
| 56 |
> |
class Atom : public StuntDouble { |
| 57 |
> |
public: |
| 58 |
> |
Atom(AtomType* at); |
| 59 |
|
|
| 60 |
< |
Atom(int theIndex, SimState* theConfig ); |
| 61 |
< |
virtual ~Atom() {} |
| 60 |
> |
virtual std::string getType() {return atomType_->getName();} |
| 61 |
> |
|
| 62 |
> |
/** |
| 63 |
> |
* Returns the inertia tensor of this stuntdouble |
| 64 |
> |
* @return the inertia tensor of this stuntdouble |
| 65 |
> |
*/ |
| 66 |
> |
virtual Mat3x3d getI(); |
| 67 |
|
|
| 68 |
< |
virtual void setCoords(void); |
| 68 |
> |
/** |
| 69 |
> |
* Returns the gradient of this stuntdouble |
| 70 |
> |
* @return the inertia tensor of this stuntdouble |
| 71 |
> |
*/ |
| 72 |
> |
virtual std::vector<double> getGrad(); |
| 73 |
|
|
| 74 |
< |
void getPos( double theP[3] ); |
| 21 |
< |
void setPos( double theP[3] ); |
| 74 |
> |
virtual void accept(BaseVisitor* v); |
| 75 |
|
|
| 76 |
< |
void getVel( double theV[3] ); |
| 77 |
< |
void setVel( double theV[3] ); |
| 76 |
> |
/** |
| 77 |
> |
* Returns the AtomType of this Atom. |
| 78 |
> |
* @return the atom type of this atom |
| 79 |
> |
*/ |
| 80 |
> |
AtomType* getAtomType() { |
| 81 |
> |
return atomType_; |
| 82 |
> |
} |
| 83 |
> |
|
| 84 |
> |
//forward functions of AtomType class |
| 85 |
> |
bool isCharge() { |
| 86 |
> |
return atomType_->isCharge(); |
| 87 |
> |
} |
| 88 |
> |
|
| 89 |
> |
bool isDirectional() { |
| 90 |
> |
return atomType_->isDirectional(); |
| 91 |
> |
} |
| 92 |
|
|
| 93 |
< |
void getFrc( double theF[3] ); |
| 94 |
< |
void addFrc( double theF[3] ); |
| 93 |
> |
bool isDipole() { |
| 94 |
> |
return atomType_->isDipole(); |
| 95 |
> |
} |
| 96 |
|
|
| 97 |
< |
virtual void zeroForces(); |
| 97 |
> |
bool isQudrapole() { |
| 98 |
> |
return atomType_->isQuadrupole(); |
| 99 |
> |
} |
| 100 |
> |
|
| 101 |
> |
bool isMultipole() { |
| 102 |
> |
return atomType_->isMultipole(); |
| 103 |
> |
} |
| 104 |
> |
|
| 105 |
> |
bool isGayBerne() { |
| 106 |
> |
return atomType_->isGayBerne(); |
| 107 |
> |
} |
| 108 |
> |
|
| 109 |
> |
bool isSticky() { |
| 110 |
> |
return atomType_->isSticky(); |
| 111 |
> |
} |
| 112 |
|
|
| 113 |
< |
double getMass() {return c_mass;} |
| 114 |
< |
void setMass(double mass) {c_mass = mass;} |
| 115 |
< |
|
| 34 |
< |
int getIndex() const {return index;} |
| 35 |
< |
void setIndex(int theIndex); |
| 113 |
> |
bool isShape() { |
| 114 |
> |
return atomType_->isShape(); |
| 115 |
> |
} |
| 116 |
|
|
| 117 |
< |
char *getType() {return c_name;} |
| 118 |
< |
void setType(char * name) {strcpy(c_name,name);} |
| 119 |
< |
|
| 120 |
< |
int getIdent( void ) { return ident; } |
| 121 |
< |
void setIdent( int info ) { ident = info; } |
| 117 |
> |
int getIdent() { |
| 118 |
> |
return atomType_->getIdent(); |
| 119 |
> |
} |
| 120 |
> |
|
| 121 |
> |
protected: |
| 122 |
> |
AtomType* atomType_; |
| 123 |
> |
}; |
| 124 |
|
|
| 125 |
< |
#ifdef IS_MPI |
| 44 |
< |
int getGlobalIndex( void ) { return myGlobalIndex; } |
| 45 |
< |
void setGlobalIndex( int info ) { myGlobalIndex = info; } |
| 46 |
< |
#endif // is_mpi |
| 125 |
> |
}//namepace oopse |
| 126 |
|
|
| 127 |
< |
void setHasDipole( int value ) { has_dipole = value; } |
| 49 |
< |
int hasDipole( void ) { return has_dipole; } |
| 50 |
< |
|
| 51 |
< |
void setHasCharge(int value) {has_charge = value;} |
| 52 |
< |
int hasCharge(void) {return has_charge;} |
| 53 |
< |
|
| 54 |
< |
|
| 55 |
< |
virtual void accept(BaseVisitor* v) {v->visit(this);} |
| 56 |
< |
|
| 57 |
< |
protected: |
| 58 |
< |
|
| 59 |
< |
SimState* myConfig; |
| 60 |
< |
|
| 61 |
< |
double* pos; // the position array |
| 62 |
< |
double* vel; // the velocity array |
| 63 |
< |
double* frc; // the forc array |
| 64 |
< |
double* trq; // the torque vector ( space fixed ) |
| 65 |
< |
double* Amat; // the rotation matrix |
| 66 |
< |
double* mu; // the array of dipole moments |
| 67 |
< |
double* ul; // the lab frame unit directional vector |
| 68 |
< |
|
| 69 |
< |
double zAngle; // the rotation about the z-axis ( body-fixed ) |
| 70 |
< |
|
| 71 |
< |
double c_mass; /* the mass of the atom in amu */ |
| 72 |
< |
|
| 73 |
< |
int index; /* set the atom's index */ |
| 74 |
< |
int offset; // the atom's offset in the storage array |
| 75 |
< |
int offsetX, offsetY, offsetZ; |
| 76 |
< |
|
| 77 |
< |
int Axx, Axy, Axz; // the rotational matrix indices |
| 78 |
< |
int Ayx, Ayy, Ayz; |
| 79 |
< |
int Azx, Azy, Azz; |
| 80 |
< |
|
| 81 |
< |
char c_name[100]; /* it's name */ |
| 82 |
< |
int ident; // it's unique numeric identity. |
| 83 |
< |
|
| 84 |
< |
int has_dipole; // dipole boolean |
| 85 |
< |
int has_charge; // charge boolean |
| 86 |
< |
|
| 87 |
< |
bool hasCoords; |
| 88 |
< |
|
| 89 |
< |
#ifdef IS_MPI |
| 90 |
< |
int myGlobalIndex; |
| 91 |
< |
#endif |
| 92 |
< |
|
| 93 |
< |
}; |
| 94 |
< |
|
| 95 |
< |
#endif |
| 127 |
> |
#endif //PRIMITIVES_ATOM_HPP |
