| 1 |
< |
#ifndef _MOLECULE_H_ |
| 2 |
< |
#define _MOLECULE_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 Molecule.hpp |
| 44 |
> |
* @author tlin |
| 45 |
> |
* @date 10/25/2004 |
| 46 |
> |
* @version 1.0 |
| 47 |
> |
*/ |
| 48 |
|
|
| 49 |
< |
#include <set> |
| 49 |
> |
#ifndef PRIMITIVES_MOLECULE_HPP |
| 50 |
> |
#define PRIMITIVES_MOLECULE_HPP |
| 51 |
|
#include <vector> |
| 52 |
+ |
#include <iostream> |
| 53 |
|
|
| 54 |
+ |
#include "constraints/ConstraintPair.hpp" |
| 55 |
+ |
#include "math/Vector3.hpp" |
| 56 |
|
#include "primitives/Atom.hpp" |
| 8 |
– |
#include "primitives/SRI.hpp" |
| 9 |
– |
#include "types/MoleculeStamp.hpp" |
| 57 |
|
#include "primitives/RigidBody.hpp" |
| 58 |
+ |
#include "primitives/Bond.hpp" |
| 59 |
+ |
#include "primitives/Bend.hpp" |
| 60 |
+ |
#include "primitives/Torsion.hpp" |
| 61 |
|
#include "primitives/CutoffGroup.hpp" |
| 62 |
|
|
| 63 |
< |
using namespace std; |
| 63 |
> |
namespace oopse{ |
| 64 |
|
|
| 65 |
< |
typedef struct{ |
| 16 |
< |
|
| 17 |
< |
int stampID; // the ID in the BASS component stamp array |
| 18 |
< |
int nAtoms; // the number of atoms in the molecule |
| 19 |
< |
int nBonds; // ... .. .. . .bonds .. .. . . . . |
| 20 |
< |
int nBends; // . . . . .. . .bends . . . . .. . |
| 21 |
< |
int nTorsions; // .. . . .. . . torsions . . .. . . |
| 22 |
< |
int nRigidBodies; // .. .. .. . rigid bodies ... .. |
| 23 |
< |
int nOriented; // .. . . . .. . oriented atoms . . . |
| 24 |
< |
|
| 25 |
< |
Atom** myAtoms; // the array of atoms |
| 26 |
< |
Bond** myBonds; // arrays of all the short range interactions |
| 27 |
< |
Bend** myBends; |
| 28 |
< |
Torsion** myTorsions; |
| 29 |
< |
vector<RigidBody*> myRigidBodies; |
| 30 |
< |
vector<StuntDouble*> myIntegrableObjects; |
| 31 |
< |
vector<CutoffGroup*> myCutoffGroups; |
| 32 |
< |
} molInit; |
| 65 |
> |
class Constraint; |
| 66 |
|
|
| 67 |
< |
class Molecule{ |
| 67 |
> |
/** |
| 68 |
> |
* @class Molecule Molecule.hpp "primitives/Molecule.hpp" |
| 69 |
> |
* @brief |
| 70 |
> |
*/ |
| 71 |
> |
class Molecule { |
| 72 |
> |
public: |
| 73 |
|
|
| 74 |
< |
public: |
| 75 |
< |
|
| 76 |
< |
Molecule( void ); |
| 77 |
< |
~Molecule( void ); |
| 74 |
> |
typedef std::vector<Atom*>::iterator AtomIterator; |
| 75 |
> |
typedef std::vector<Bond*>::iterator BondIterator; |
| 76 |
> |
typedef std::vector<Bend*>::iterator BendIterator; |
| 77 |
> |
typedef std::vector<Torsion*>::iterator TorsionIterator; |
| 78 |
> |
typedef std::vector<RigidBody*>::iterator RigidBodyIterator; |
| 79 |
> |
typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator; |
| 80 |
> |
typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator; |
| 81 |
> |
typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator; |
| 82 |
> |
typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator; |
| 83 |
> |
|
| 84 |
|
|
| 85 |
< |
void initialize( molInit &theInit ); |
| 85 |
> |
Molecule(int stampId, int globalIndex, const std::string& molName); |
| 86 |
> |
virtual ~Molecule(); |
| 87 |
|
|
| 88 |
< |
void setMyIndex( int theIndex ){ myIndex = theIndex;} |
| 89 |
< |
int getMyIndex( void ) { return myIndex; } |
| 88 |
> |
/** |
| 89 |
> |
* Returns the global index of this molecule. |
| 90 |
> |
* @return the global index of this molecule |
| 91 |
> |
*/ |
| 92 |
> |
int getGlobalIndex() { |
| 93 |
> |
return globalIndex_; |
| 94 |
> |
} |
| 95 |
|
|
| 96 |
< |
int getGlobalIndex( void ) { return globalIndex; } |
| 97 |
< |
void setGlobalIndex( int theIndex ) { globalIndex = theIndex; } |
| 96 |
> |
/** |
| 97 |
> |
* Returns the stamp id of this molecule |
| 98 |
> |
* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its |
| 99 |
> |
* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor. |
| 100 |
> |
*/ |
| 101 |
> |
int getStampId() { |
| 102 |
> |
return stampId_; |
| 103 |
> |
} |
| 104 |
|
|
| 105 |
< |
int getNAtoms ( void ) {return nAtoms;} |
| 106 |
< |
int getNBonds ( void ) {return nBonds;} |
| 107 |
< |
int getNBends ( void ) {return nBends;} |
| 108 |
< |
int getNTorsions( void ) {return nTorsions;} |
| 109 |
< |
int getNRigidBodies( void ) {return myRigidBodies.size();} |
| 110 |
< |
int getNOriented( void ) {return nOriented;} |
| 111 |
< |
int getNMembers ( void ) {return nMembers;} |
| 112 |
< |
int getStampID ( void ) {return stampID;} |
| 105 |
> |
/** Returns the name of the molecule */ |
| 106 |
> |
std::string getType() { |
| 107 |
> |
return moleculeName_; |
| 108 |
> |
} |
| 109 |
> |
|
| 110 |
> |
/** |
| 111 |
> |
* Sets the global index of this molecule. |
| 112 |
> |
* @param new global index to be set |
| 113 |
> |
*/ |
| 114 |
> |
int setGlobalIndex(int index) { |
| 115 |
> |
return globalIndex_; |
| 116 |
> |
} |
| 117 |
|
|
| 118 |
< |
Atom** getMyAtoms ( void ) {return myAtoms;} |
| 119 |
< |
Bond** getMyBonds ( void ) {return myBonds;} |
| 120 |
< |
Bend** getMyBends ( void ) {return myBends;} |
| 61 |
< |
Torsion** getMyTorsions( void ) {return myTorsions;} |
| 62 |
< |
vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;} |
| 63 |
< |
vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;} |
| 118 |
> |
|
| 119 |
> |
/** add an atom into this molecule */ |
| 120 |
> |
void addAtom(Atom* atom); |
| 121 |
|
|
| 122 |
< |
//beginCutoffGroup return the first group and initialize the iterator |
| 123 |
< |
CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){ |
| 67 |
< |
i = myCutoffGroups.begin(); |
| 68 |
< |
return i != myCutoffGroups.end()? *i : NULL; |
| 69 |
< |
} |
| 122 |
> |
/** add a bond into this molecule */ |
| 123 |
> |
void addBond(Bond* bond); |
| 124 |
|
|
| 125 |
< |
//nextCutoffGroup return next cutoff group based on the iterator |
| 126 |
< |
CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){ |
| 73 |
< |
i++; |
| 74 |
< |
return i != myCutoffGroups.end()? *i : NULL; |
| 75 |
< |
} |
| 125 |
> |
/** add a bend into this molecule */ |
| 126 |
> |
void addBend(Bend* bend); |
| 127 |
|
|
| 128 |
< |
int getNCutoffGroups() {return nCutoffGroups;} |
| 128 |
> |
/** add a torsion into this molecule*/ |
| 129 |
> |
void addTorsion(Torsion* torsion); |
| 130 |
|
|
| 131 |
< |
void setStampID( int info ) {stampID = info;} |
| 131 |
> |
/** add a rigidbody into this molecule */ |
| 132 |
> |
void addRigidBody(RigidBody *rb); |
| 133 |
|
|
| 134 |
< |
void calcForces( void ); |
| 135 |
< |
void atoms2rigidBodies( void ); |
| 83 |
< |
double getPotential( void ); |
| 84 |
< |
|
| 85 |
< |
void printMe( void ); |
| 134 |
> |
/** add a cutoff group into this molecule */ |
| 135 |
> |
void addCutoffGroup(CutoffGroup* cp); |
| 136 |
|
|
| 137 |
< |
void getCOM( double COM[3] ); |
| 138 |
< |
void moveCOM( double delta[3] ); |
| 139 |
< |
double getCOMvel( double COMvel[3] ); |
| 90 |
< |
|
| 91 |
< |
double getTotalMass(); |
| 137 |
> |
void addConstraintPair(ConstraintPair* consPair); |
| 138 |
> |
|
| 139 |
> |
void addConstraintElem(ConstraintElem* consElem); |
| 140 |
|
|
| 141 |
< |
private: |
| 141 |
> |
/** */ |
| 142 |
> |
void complete(); |
| 143 |
|
|
| 144 |
< |
int stampID; // the ID in the BASS component stamp array |
| 145 |
< |
int nAtoms; // the number of atoms in the molecule |
| 146 |
< |
int nBonds; // ... .. .. . .bonds .. .. . . . . |
| 147 |
< |
int nBends; // . . . . .. . .bends . . . . .. . |
| 99 |
< |
int nTorsions; // .. . . .. . . torsions . . .. . . |
| 100 |
< |
int nRigidBodies; // .. . . .. .rigid bodies . . .. . . |
| 101 |
< |
int nOriented; // .. . . . .. . oriented atoms . . . |
| 102 |
< |
int nMembers; // .. . . . . . .atoms (legacy code) . . . |
| 103 |
< |
int nCutoffGroups; |
| 104 |
< |
|
| 105 |
< |
int myIndex; // mostly just for debug (and for making pressure calcs work) |
| 106 |
< |
int globalIndex; |
| 144 |
> |
/** Returns the total number of atoms in this molecule */ |
| 145 |
> |
unsigned int getNAtoms() { |
| 146 |
> |
return atoms_.size(); |
| 147 |
> |
} |
| 148 |
|
|
| 149 |
< |
Atom** myAtoms; // the array of atoms |
| 150 |
< |
Bond** myBonds; // arrays of all the short range interactions |
| 151 |
< |
Bend** myBends; |
| 152 |
< |
Torsion** myTorsions; |
| 153 |
< |
vector<RigidBody*> myRigidBodies; |
| 154 |
< |
vector<StuntDouble*> myIntegrableObjects; |
| 155 |
< |
vector<CutoffGroup*> myCutoffGroups; |
| 149 |
> |
/** Returns the total number of bonds in this molecule */ |
| 150 |
> |
unsigned int getNBonds(){ |
| 151 |
> |
return bonds_.size(); |
| 152 |
> |
} |
| 153 |
> |
|
| 154 |
> |
/** Returns the total number of bends in this molecule */ |
| 155 |
> |
unsigned int getNBends() { |
| 156 |
> |
return bends_.size(); |
| 157 |
> |
} |
| 158 |
> |
|
| 159 |
> |
/** Returns the total number of torsions in this molecule */ |
| 160 |
> |
unsigned int getNTorsions() { |
| 161 |
> |
return torsions_.size(); |
| 162 |
> |
} |
| 163 |
> |
|
| 164 |
> |
/** Returns the total number of rigid bodies in this molecule */ |
| 165 |
> |
unsigned int getNRigidBodies() { |
| 166 |
> |
return rigidBodies_.size(); |
| 167 |
> |
} |
| 168 |
> |
|
| 169 |
> |
/** Returns the total number of integrable objects in this molecule */ |
| 170 |
> |
unsigned int getNIntegrableObjects() { |
| 171 |
> |
return integrableObjects_.size(); |
| 172 |
> |
} |
| 173 |
> |
|
| 174 |
> |
/** Returns the total number of cutoff groups in this molecule */ |
| 175 |
> |
unsigned int getNCutoffGroups() { |
| 176 |
> |
return cutoffGroups_.size(); |
| 177 |
> |
} |
| 178 |
> |
|
| 179 |
> |
/** Returns the total number of constraints in this molecule */ |
| 180 |
> |
unsigned int getNConstraintPairs() { |
| 181 |
> |
return constraintPairs_.size(); |
| 182 |
> |
} |
| 183 |
> |
|
| 184 |
> |
Atom* getAtomAt(unsigned int i) { |
| 185 |
> |
assert(i < atoms_.size()); |
| 186 |
> |
return atoms_[i]; |
| 187 |
> |
} |
| 188 |
> |
|
| 189 |
> |
Atom* beginAtom(std::vector<Atom*>::iterator& i) { |
| 190 |
> |
i = atoms_.begin(); |
| 191 |
> |
return (i == atoms_.end()) ? NULL : *i; |
| 192 |
> |
} |
| 193 |
> |
|
| 194 |
> |
Atom* nextAtom(std::vector<Atom*>::iterator& i) { |
| 195 |
> |
++i; |
| 196 |
> |
return (i == atoms_.end()) ? NULL : *i; |
| 197 |
> |
} |
| 198 |
> |
|
| 199 |
> |
Bond* beginBond(std::vector<Bond*>::iterator& i) { |
| 200 |
> |
i = bonds_.begin(); |
| 201 |
> |
return (i == bonds_.end()) ? NULL : *i; |
| 202 |
> |
} |
| 203 |
> |
|
| 204 |
> |
Bond* nextBond(std::vector<Bond*>::iterator& i) { |
| 205 |
> |
++i; |
| 206 |
> |
return (i == bonds_.end()) ? NULL : *i; |
| 207 |
> |
|
| 208 |
> |
} |
| 209 |
> |
|
| 210 |
> |
Bend* beginBend(std::vector<Bend*>::iterator& i) { |
| 211 |
> |
i = bends_.begin(); |
| 212 |
> |
return (i == bends_.end()) ? NULL : *i; |
| 213 |
> |
} |
| 214 |
> |
|
| 215 |
> |
Bend* nextBend(std::vector<Bend*>::iterator& i) { |
| 216 |
> |
++i; |
| 217 |
> |
return (i == bends_.end()) ? NULL : *i; |
| 218 |
> |
} |
| 219 |
> |
|
| 220 |
> |
Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) { |
| 221 |
> |
i = torsions_.begin(); |
| 222 |
> |
return (i == torsions_.end()) ? NULL : *i; |
| 223 |
> |
} |
| 224 |
> |
|
| 225 |
> |
Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) { |
| 226 |
> |
++i; |
| 227 |
> |
return (i == torsions_.end()) ? NULL : *i; |
| 228 |
> |
} |
| 229 |
> |
|
| 230 |
> |
RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) { |
| 231 |
> |
i = rigidBodies_.begin(); |
| 232 |
> |
return (i == rigidBodies_.end()) ? NULL : *i; |
| 233 |
> |
} |
| 234 |
> |
|
| 235 |
> |
RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) { |
| 236 |
> |
++i; |
| 237 |
> |
return (i == rigidBodies_.end()) ? NULL : *i; |
| 238 |
> |
} |
| 239 |
> |
|
| 240 |
> |
StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) { |
| 241 |
> |
i = integrableObjects_.begin(); |
| 242 |
> |
return (i == integrableObjects_.end()) ? NULL : *i; |
| 243 |
> |
} |
| 244 |
> |
|
| 245 |
> |
StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) { |
| 246 |
> |
++i; |
| 247 |
> |
return (i == integrableObjects_.end()) ? NULL : *i; |
| 248 |
> |
} |
| 249 |
> |
|
| 250 |
> |
CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
| 251 |
> |
i = cutoffGroups_.begin(); |
| 252 |
> |
return (i == cutoffGroups_.end()) ? NULL : *i; |
| 253 |
> |
} |
| 254 |
> |
|
| 255 |
> |
CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
| 256 |
> |
++i; |
| 257 |
> |
return (i == cutoffGroups_.end()) ? NULL : *i; |
| 258 |
> |
} |
| 259 |
> |
|
| 260 |
> |
ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) { |
| 261 |
> |
i = constraintPairs_.begin(); |
| 262 |
> |
return (i == constraintPairs_.end()) ? NULL : *i; |
| 263 |
> |
} |
| 264 |
> |
|
| 265 |
> |
ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) { |
| 266 |
> |
++i; |
| 267 |
> |
return (i == constraintPairs_.end()) ? NULL : *i; |
| 268 |
> |
} |
| 269 |
> |
|
| 270 |
> |
ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) { |
| 271 |
> |
i = constraintElems_.begin(); |
| 272 |
> |
return (i == constraintElems_.end()) ? NULL : *i; |
| 273 |
> |
} |
| 274 |
> |
|
| 275 |
> |
ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) { |
| 276 |
> |
++i; |
| 277 |
> |
return (i == constraintElems_.end()) ? NULL : *i; |
| 278 |
> |
} |
| 279 |
> |
|
| 280 |
> |
/** return the total potential energy of short range interaction of this molecule */ |
| 281 |
> |
double getPotential(); |
| 282 |
> |
|
| 283 |
> |
/** get total mass of this molecule */ |
| 284 |
> |
double getMass(); |
| 285 |
> |
|
| 286 |
> |
/** return the center of mass of this molecule */ |
| 287 |
> |
Vector3d getCom(); |
| 288 |
> |
|
| 289 |
> |
/** Moves the center of this molecule */ |
| 290 |
> |
void moveCom(const Vector3d& delta); |
| 291 |
> |
|
| 292 |
> |
/** Returns the velocity of center of mass of this molecule */ |
| 293 |
> |
Vector3d getComVel(); |
| 294 |
> |
|
| 295 |
> |
friend std::ostream& operator <<(std::ostream& o, Molecule& mol); |
| 296 |
> |
|
| 297 |
> |
private: |
| 298 |
> |
|
| 299 |
> |
int globalIndex_; |
| 300 |
> |
|
| 301 |
> |
std::vector<Atom*> atoms_; |
| 302 |
> |
std::vector<Bond*> bonds_; |
| 303 |
> |
std::vector<Bend*> bends_; |
| 304 |
> |
std::vector<Torsion*> torsions_; |
| 305 |
> |
std::vector<RigidBody*> rigidBodies_; |
| 306 |
> |
std::vector<StuntDouble*> integrableObjects_; |
| 307 |
> |
std::vector<CutoffGroup*> cutoffGroups_; |
| 308 |
> |
std::vector<ConstraintPair*> constraintPairs_; |
| 309 |
> |
std::vector<ConstraintElem*> constraintElems_; |
| 310 |
> |
int stampId_; |
| 311 |
> |
std::string moleculeName_; |
| 312 |
|
}; |
| 313 |
|
|
| 314 |
< |
#endif |
| 314 |
> |
} //namespace oopse |
| 315 |
> |
#endif // |
