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#include "Atom.hpp" |
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#include "SRI.hpp" |
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#include "MoleculeStamp.hpp" |
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#include "Exclude.hpp" |
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typedef struct{ |
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int stampID; // the ID in the BASS component stamp array |
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int nAtoms; // the number of atoms in the molecule |
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int nBonds; // ... .. .. . .bonds .. .. . . . . |
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int nBends; // . . . . .. . .bends . . . . .. . |
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int nTorsions; // .. . . .. . . torsions . . .. . . |
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int nOriented; // .. . . . .. . oriented atoms . . . |
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int nExcludes; // . . .. . . . .exclude pairs.. . . . |
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|
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Atom** myAtoms; // the array of atoms |
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Exclude** myExcludes;// the array of Excluded pairs |
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Bond** myBonds; // arrays of all the short range interactions |
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Bend** myBends; |
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Torsion** myTorsions; |
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|
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} molInit; |
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class Molecule{ |
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public: |
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Molecule() {} |
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~Molecule() {} |
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Molecule( void ); |
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~Molecule( void ); |
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int getNMembers( void ) { return nMembers; } |
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int getStartAtom( void ) { return startAtom; } |
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int getEndAtom( void ) { return endAtom; } |
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int getStampID( void ) { return stampID; } |
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void initialize( molInit &theInit ); |
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void setMyIndex( int theIndex ){ myIndex = theIndex;} |
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void setGlobalIndex( int theIndex ) { globalIndex = theIndex; } |
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int getMyIndex( void ) { return myIndex; } |
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int getGlobalIndex( void ) { return globalIndex; } |
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int getNAtoms ( void ) {return nAtoms;} |
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int getNBonds ( void ) {return nBonds;} |
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int getNBends ( void ) {return nBends;} |
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int getNTorsions( void ) {return nTorsions;} |
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int getNOriented( void ) {return nOriented;} |
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int getNExcludes( void ) {return nExcludes;} |
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int getNMembers ( void ) {return nMembers;} |
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int getStampID ( void ) {return stampID;} |
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Atom** getMyAtoms ( void ) {return myAtoms;} |
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Bond** getMyBonds ( void ) {return myBonds;} |
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Bend** getMyBends ( void ) {return myBends;} |
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Torsion** getMyTorsions( void ) {return myTorsions;} |
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Exclude** getMyExcludes( void ) {return myExcludes;} |
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< |
void setNMembers( int info ) { nMembers = info; } |
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void setStartAtom( int info ) { startAtom = info; } |
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void setEndAtom( int info ) { endAtom = info; } |
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void setStampID( int info ) { stampID = info; } |
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void setStampID( int info ) {stampID = info;} |
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void calcForces( void ); |
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double getPotential( void ); |
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void printMe( void ); |
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void getCOM( double COM[3] ); |
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void moveCOM( double delta[3] ); |
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double getCOMvel( double COMvel[3] ); |
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double getTotalMass(); |
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private: |
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< |
int nMembers; |
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< |
int startAtom; |
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< |
int endAtom; |
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> |
int stampID; // the ID in the BASS component stamp array |
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> |
int nAtoms; // the number of atoms in the molecule |
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> |
int nBonds; // ... .. .. . .bonds .. .. . . . . |
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int nBends; // . . . . .. . .bends . . . . .. . |
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int nTorsions; // .. . . .. . . torsions . . .. . . |
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int nOriented; // .. . . . .. . oriented atoms . . . |
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int nMembers; // .. . . . . . .atoms (legacy code) . . . |
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int nExcludes; // . . . . .. .. excludes .. . . |
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< |
int stampID; |
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> |
int myIndex; // mostly just for debug (and for making pressure calcs work) |
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int globalIndex; |
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Atom** myAtoms; // the array of atoms |
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Bond** myBonds; // arrays of all the short range interactions |
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Bend** myBends; |
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Torsion** myTorsions; |
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Exclude** myExcludes; // array of the excluded pairs of long range forces |
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}; |
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#endif |
