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root/group/trunk/OOPSE/libmdtools/Molecule.hpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/Molecule.hpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/Molecule.hpp (file contents), 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 "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
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;
33 +
34   class Molecule{
35  
36   public:
37    
38 <  Molecule() {}
39 <  ~Molecule() {}
38 >  Molecule( void );
39 >  ~Molecule( void );
40  
41 <  int   getNMembers( void )  { return nMembers; }
42 <  int   getStartAtom( void ) { return startAtom; }
43 <  int   getEndAtom( void )   { return endAtom; }
44 <  int   getStampID( void )   { return stampID; }
41 >  void initialize( molInit &theInit );
42 >
43 >  void setMyIndex( int theIndex ){ myIndex = theIndex;}
44 >  int getMyIndex( void ) { return myIndex; }
45 >
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   setNMembers( int info )  { nMembers = info; }
78 <  void   setStartAtom( int info ) { startAtom = info; }
79 <  void   setEndAtom( int info )   { endAtom = info; }
80 <  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  
93 <  int nMembers;
94 <  int startAtom;
95 <  int endAtom;
93 >  int stampID;   // the ID in the BASS component stamp array
94 >  int nAtoms;    // the number of atoms in the molecule
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 nCutoffGroups;
102 >  
103 >  int myIndex; // mostly just for debug (and for making pressure calcs work)
104 >  int globalIndex;
105  
106 <  int stampID;
106 >  Atom** myAtoms;     // the array of atoms
107 >  Bond** myBonds;     // arrays of all the short range interactions
108 >  Bend** myBends;
109 >  Torsion** myTorsions;
110 >  vector<RigidBody*>   myRigidBodies;
111 >  vector<StuntDouble*> myIntegrableObjects;
112 >  vector<CutoffGroup*> myCutoffGroups;
113 >
114 >
115   };
116  
117   #endif

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