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root/group/trunk/OOPSE/libmdtools/Molecule.hpp
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Comparing trunk/OOPSE/libmdtools/Molecule.hpp (file contents):
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 4 | Line 4
4   #include "Atom.hpp"
5   #include "SRI.hpp"
6   #include "MoleculeStamp.hpp"
7 < #include "Exclude.hpp"
7 > #include "RigidBody.hpp"
8  
9   typedef struct{
10    
# Line 13 | Line 13 | typedef struct{
13    int nBonds;    // ... .. ..  . .bonds .. .. . . . .
14    int nBends;    // . . . . .. . .bends . . . . .. .
15    int nTorsions; // .. . . .. . . torsions . . .. . .
16 +  int nRigidBodies; // .. .. .. . rigid bodies ... ..
17    int nOriented; // .. . . . .. . oriented atoms . . .
17 –  int nExcludes; // . . .. . . . .exclude pairs.. . . .
18  
19    Atom** myAtoms;      // the array of atoms
20 –  Exclude** myExcludes;// the array of Excluded pairs
20    Bond** myBonds;      // arrays of all the short range interactions
21    Bend** myBends;
22    Torsion** myTorsions;
23 <
25 <
23 >  RigidBody** myRigidBodies;
24   } molInit;
25  
26   class Molecule{
# Line 40 | Line 38 | class Molecule{ (public)
38    int getMyIndex( void ) { return myIndex; }
39    int getGlobalIndex( void ) { return globalIndex; }
40  
41 <  int getNAtoms   ( void ) {return nAtoms;}
42 <  int getNBonds   ( void ) {return nBonds;}
43 <  int getNBends   ( void ) {return nBends;}
44 <  int getNTorsions( void ) {return nTorsions;}
45 <  int getNOriented( void ) {return nOriented;}
46 <  int getNExcludes( void ) {return nExcludes;}
47 <  int getNMembers ( void ) {return nMembers;}
48 <  int getStampID  ( void ) {return stampID;}
41 >  int getNAtoms   ( void )    {return nAtoms;}
42 >  int getNBonds   ( void )    {return nBonds;}
43 >  int getNBends   ( void )    {return nBends;}
44 >  int getNTorsions( void )    {return nTorsions;}
45 >  int getNRigidBodies( void ) {return nRigidBodies;}
46 >  int getNOriented( void )    {return nOriented;}
47 >  int getNMembers ( void )    {return nMembers;}
48 >  int getStampID  ( void )    {return stampID;}
49  
50 <  Atom**     getMyAtoms   ( void ) {return myAtoms;}
51 <  Bond**     getMyBonds   ( void ) {return myBonds;}
52 <  Bend**     getMyBends   ( void ) {return myBends;}
53 <  Torsion**  getMyTorsions( void ) {return myTorsions;}
54 <  Exclude**  getMyExcludes( void ) {return myExcludes;}
50 >  Atom**      getMyAtoms   ( void )    {return myAtoms;}
51 >  Bond**      getMyBonds   ( void )    {return myBonds;}
52 >  Bend**      getMyBends   ( void )    {return myBends;}
53 >  Torsion**   getMyTorsions( void )    {return myTorsions;}
54 >  RigidBody** getMyRigidBodies( void ) {return myRigidBodies;}
55    
56 <  void setStampID( int info ) {stampID = info;}
59 <  
56 >  void setStampID( int info ) {stampID = info;}
57  
61 –
62 –
58    void calcForces( void );
59 +  void atoms2rigidBodies( void );
60    double getPotential( void );
61    
62    void printMe( void );
# Line 78 | Line 74 | class Molecule{ (public)
74    int nBonds;    // ... .. ..  . .bonds .. .. . . . .
75    int nBends;    // . . . . .. . .bends . . . . .. .
76    int nTorsions; // .. . . .. . . torsions . . .. . .
77 +  int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
78    int nOriented; // .. . . . .. . oriented atoms . . .
79    int nMembers;  // .. . . . . . .atoms (legacy code) . . .
83 –  int nExcludes; // . . . . .. .. excludes .. . .
80  
81    int myIndex; // mostly just for debug (and for making pressure calcs work)
82    int globalIndex;
# Line 89 | Line 85 | class Molecule{ (public)
85    Bond** myBonds;     // arrays of all the short range interactions
86    Bend** myBends;
87    Torsion** myTorsions;
88 <  Exclude** myExcludes; // array of the excluded pairs of long range forces
88 >  RigidBody** myRigidBodies;
89    
90   };
91  

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