1 |
mmeineke |
377 |
#ifndef _MOLECULE_H_ |
2 |
|
|
#define _MOLECULE_H_ |
3 |
|
|
|
4 |
|
|
#include "Atom.hpp" |
5 |
|
|
#include "SRI.hpp" |
6 |
mmeineke |
407 |
#include "MoleculeStamp.hpp" |
7 |
gezelter |
1097 |
#include "RigidBody.hpp" |
8 |
mmeineke |
377 |
|
9 |
mmeineke |
407 |
typedef struct{ |
10 |
|
|
|
11 |
|
|
int stampID; // the ID in the BASS component stamp array |
12 |
|
|
int nAtoms; // the number of atoms in the molecule |
13 |
|
|
int nBonds; // ... .. .. . .bonds .. .. . . . . |
14 |
|
|
int nBends; // . . . . .. . .bends . . . . .. . |
15 |
gezelter |
416 |
int nTorsions; // .. . . .. . . torsions . . .. . . |
16 |
gezelter |
1097 |
int nRigidBodies; // .. .. .. . rigid bodies ... .. |
17 |
gezelter |
416 |
int nOriented; // .. . . . .. . oriented atoms . . . |
18 |
gezelter |
446 |
|
19 |
mmeineke |
412 |
Atom** myAtoms; // the array of atoms |
20 |
mmeineke |
407 |
Bond** myBonds; // arrays of all the short range interactions |
21 |
|
|
Bend** myBends; |
22 |
|
|
Torsion** myTorsions; |
23 |
gezelter |
1104 |
vector<RigidBody*> myRigidBodies; |
24 |
|
|
vector<StuntDouble*> myIntegrableObjects; |
25 |
mmeineke |
407 |
} molInit; |
26 |
|
|
|
27 |
mmeineke |
377 |
class Molecule{ |
28 |
|
|
|
29 |
|
|
public: |
30 |
|
|
|
31 |
mmeineke |
407 |
Molecule( void ); |
32 |
|
|
~Molecule( void ); |
33 |
mmeineke |
377 |
|
34 |
mmeineke |
407 |
void initialize( molInit &theInit ); |
35 |
chuckv |
438 |
|
36 |
|
|
void setMyIndex( int theIndex ){ myIndex = theIndex;} |
37 |
tim |
1108 |
int getMyIndex( void ) { return myIndex; } |
38 |
|
|
|
39 |
|
|
int getGlobalIndex( void ) { return globalIndex; } |
40 |
gezelter |
490 |
void setGlobalIndex( int theIndex ) { globalIndex = theIndex; } |
41 |
mmeineke |
489 |
|
42 |
gezelter |
1097 |
int getNAtoms ( void ) {return nAtoms;} |
43 |
|
|
int getNBonds ( void ) {return nBonds;} |
44 |
|
|
int getNBends ( void ) {return nBends;} |
45 |
|
|
int getNTorsions( void ) {return nTorsions;} |
46 |
gezelter |
1104 |
int getNRigidBodies( void ) {return myRigidBodies.size();} |
47 |
gezelter |
1097 |
int getNOriented( void ) {return nOriented;} |
48 |
|
|
int getNMembers ( void ) {return nMembers;} |
49 |
|
|
int getStampID ( void ) {return stampID;} |
50 |
mmeineke |
407 |
|
51 |
gezelter |
1097 |
Atom** getMyAtoms ( void ) {return myAtoms;} |
52 |
|
|
Bond** getMyBonds ( void ) {return myBonds;} |
53 |
|
|
Bend** getMyBends ( void ) {return myBends;} |
54 |
|
|
Torsion** getMyTorsions( void ) {return myTorsions;} |
55 |
gezelter |
1104 |
vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;} |
56 |
tim |
1108 |
vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;} |
57 |
mmeineke |
377 |
|
58 |
gezelter |
1097 |
void setStampID( int info ) {stampID = info;} |
59 |
mmeineke |
423 |
|
60 |
|
|
void calcForces( void ); |
61 |
gezelter |
1097 |
void atoms2rigidBodies( void ); |
62 |
mmeineke |
423 |
double getPotential( void ); |
63 |
mmeineke |
377 |
|
64 |
mmeineke |
435 |
void printMe( void ); |
65 |
mmeineke |
377 |
|
66 |
mmeineke |
449 |
void getCOM( double COM[3] ); |
67 |
mmeineke |
452 |
void moveCOM( double delta[3] ); |
68 |
gezelter |
475 |
double getCOMvel( double COMvel[3] ); |
69 |
tim |
658 |
|
70 |
|
|
double getTotalMass(); |
71 |
gezelter |
446 |
|
72 |
mmeineke |
377 |
private: |
73 |
|
|
|
74 |
mmeineke |
407 |
int stampID; // the ID in the BASS component stamp array |
75 |
|
|
int nAtoms; // the number of atoms in the molecule |
76 |
|
|
int nBonds; // ... .. .. . .bonds .. .. . . . . |
77 |
|
|
int nBends; // . . . . .. . .bends . . . . .. . |
78 |
gezelter |
416 |
int nTorsions; // .. . . .. . . torsions . . .. . . |
79 |
gezelter |
1097 |
int nRigidBodies; // .. . . .. .rigid bodies . . .. . . |
80 |
gezelter |
416 |
int nOriented; // .. . . . .. . oriented atoms . . . |
81 |
mmeineke |
423 |
int nMembers; // .. . . . . . .atoms (legacy code) . . . |
82 |
mmeineke |
407 |
|
83 |
gezelter |
483 |
int myIndex; // mostly just for debug (and for making pressure calcs work) |
84 |
mmeineke |
489 |
int globalIndex; |
85 |
chuckv |
438 |
|
86 |
mmeineke |
407 |
Atom** myAtoms; // the array of atoms |
87 |
mmeineke |
423 |
Bond** myBonds; // arrays of all the short range interactions |
88 |
mmeineke |
407 |
Bend** myBends; |
89 |
|
|
Torsion** myTorsions; |
90 |
gezelter |
1104 |
vector<RigidBody*> myRigidBodies; |
91 |
|
|
vector<StuntDouble*> myIntegrableObjects; |
92 |
|
|
|
93 |
mmeineke |
377 |
}; |
94 |
|
|
|
95 |
|
|
#endif |