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root/group/trunk/OOPSE/libmdtools/Molecule.hpp
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Comparing trunk/OOPSE/libmdtools/Molecule.hpp (file contents):
Revision 438 by chuckv, Mon Mar 31 21:50:59 2003 UTC vs.
Revision 1167 by tim, Wed May 12 16:38:45 2004 UTC

# Line 1 | Line 1
1   #ifndef _MOLECULE_H_
2   #define _MOLECULE_H_
3  
4 + #include <set>
5 + #include <vector>
6 +
7   #include "Atom.hpp"
8   #include "SRI.hpp"
9   #include "MoleculeStamp.hpp"
10 < #include "Exclude.hpp"
10 > #include "RigidBody.hpp"
11 > #include "CutoffGroup.hpp"
12  
13 + using namespace std;
14 +
15   typedef struct{
16    
17    int stampID;   // the ID in the BASS component stamp array
# Line 13 | Line 19 | typedef struct{
19    int nBonds;    // ... .. ..  . .bonds .. .. . . . .
20    int nBends;    // . . . . .. . .bends . . . . .. .
21    int nTorsions; // .. . . .. . . torsions . . .. . .
22 +  int nRigidBodies; // .. .. .. . rigid bodies ... ..
23    int nOriented; // .. . . . .. . oriented atoms . . .
17 –  int nExcludes; // . . .. . . . .exclude pairs.. . . .
24    
25    Atom** myAtoms;      // the array of atoms
20 –  Exclude** myExcludes;// the array of Excluded pairs
26    Bond** myBonds;      // arrays of all the short range interactions
27    Bend** myBends;
28    Torsion** myTorsions;
29 <
30 <
29 >  vector<RigidBody*>   myRigidBodies;
30 >  vector<StuntDouble*> myIntegrableObjects;
31 >  vector<CutoffGroup*> myCutoffGroups;
32   } molInit;
33  
34   class Molecule{
# Line 35 | Line 41 | class Molecule{ (public)
41    void initialize( molInit &theInit );
42  
43    void setMyIndex( int theIndex ){ myIndex = theIndex;}
44 <
39 <  int getNAtoms   ( void ) {return nAtoms;}
40 <  int getNBonds   ( void ) {return nBonds;}
41 <  int getNBends   ( void ) {return nBends;}
42 <  int getNTorsions( void ) {return nTorsions;}
43 <  int getNOriented( void ) {return nOriented;}
44 <  int getNExcludes( void ) {return nExcludes;}
45 <  int getNMembers ( void ) {return nMembers;}
46 <  int getStampID  ( void ) {return stampID;}
44 >  int getMyIndex( void ) { return myIndex; }
45  
46 <  Atom**     getMyAtoms   ( void ) {return myAtoms;}
47 <  Bond**     getMyBonds   ( void ) {return myBonds;}
48 <  Bend**     getMyBends   ( void ) {return myBends;}
49 <  Torsion**  getMyTorsions( void ) {return myTorsions;}
50 <  Exclude**  getMyExcludes( void ) {return myExcludes;}
46 >  int getGlobalIndex( void ) { return globalIndex; }
47 >  void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
48 >
49 >  int getNAtoms   ( void )    {return nAtoms;}
50 >  int getNBonds   ( void )    {return nBonds;}
51 >  int getNBends   ( void )    {return nBends;}
52 >  int getNTorsions( void )    {return nTorsions;}
53 >  int getNRigidBodies( void ) {return myRigidBodies.size();}
54 >  int getNOriented( void )    {return nOriented;}
55 >  int getNMembers ( void )    {return nMembers;}
56 >  int getStampID  ( void )    {return stampID;}
57 >
58 >  Atom**      getMyAtoms   ( void )    {return myAtoms;}
59 >  Bond**      getMyBonds   ( void )    {return myBonds;}
60 >  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;}
64 >
65 >  CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
66 >    i = myCutoffGroups.begin();
67 >    return i != myCutoffGroups.end()? *i : NULL;
68 >  }
69 >
70 >  CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){
71 >    i++;
72 >    return i != myCutoffGroups.end()? *i : NULL;
73 >  }
74 >
75 >  int getNCutoffGroups() {return nCutoffGroups;}
76    
77 <  void setStampID( int info ) {stampID = info;}
77 >  void setStampID( int info ) {stampID = info;}
78  
79    void calcForces( void );
80 +  void atoms2rigidBodies( void );
81    double getPotential( void );
82    
83    void printMe( void );
84 +
85 +  void getCOM( double COM[3] );
86 +  void moveCOM( double delta[3] );
87 +  double getCOMvel( double COMvel[3] );
88    
89 +  double getTotalMass();
90  
91   private:
92  
# Line 66 | Line 95 | class Molecule{ (public)
95    int nBonds;    // ... .. ..  . .bonds .. .. . . . .
96    int nBends;    // . . . . .. . .bends . . . . .. .
97    int nTorsions; // .. . . .. . . torsions . . .. . .
98 +  int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
99    int nOriented; // .. . . . .. . oriented atoms . . .
100    int nMembers;  // .. . . . . . .atoms (legacy code) . . .
101 <  int nExcludes; // . . . . .. .. excludes .. . .
101 >  int nCutoffGroups;
102 >  
103 >  int myIndex; // mostly just for debug (and for making pressure calcs work)
104 >  int globalIndex;
105  
73 –  int myIndex; // mostly just for debug
74 –
106    Atom** myAtoms;     // the array of atoms
107    Bond** myBonds;     // arrays of all the short range interactions
108    Bend** myBends;
109    Torsion** myTorsions;
110 <  Exclude** myExcludes; // array of the excluded pairs of long range forces
111 <  
110 >  vector<RigidBody*>   myRigidBodies;
111 >  vector<StuntDouble*> myIntegrableObjects;
112 >  vector<CutoffGroup*> myCutoffGroups;
113 >
114 >
115   };
116  
117   #endif

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