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#ifndef _MOLECULE_H_ |
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#define _MOLECULE_H_ |
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#include <set> |
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#include <vector> |
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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 "RigidBody.hpp" |
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#include "CutoffGroup.hpp" |
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using namespace std; |
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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; // .. . . . .. . oreineted atoms . . . |
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int nTorsions; // .. . . .. . . torsions . . .. . . |
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int nRigidBodies; // .. .. .. . rigid bodies ... .. |
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int nOriented; // .. . . . .. . oriented atoms . . . |
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int nCutoffGroups; |
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Atom** myAtoms; // the array of atoms |
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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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vector<RigidBody*> myRigidBodies; |
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vector<StuntDouble*> myIntegrableObjects; |
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vector<CutoffGroup*> myCutoffGroups; |
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} molInit; |
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class Molecule{ |
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void initialize( molInit &theInit ); |
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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 setMyIndex( int theIndex ){ myIndex = theIndex;} |
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int getMyIndex( void ) { return myIndex; } |
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int getGlobalIndex( void ) { return globalIndex; } |
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void setGlobalIndex( int theIndex ) { globalIndex = theIndex; } |
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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 getNRigidBodies( void ) {return myRigidBodies.size();} |
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int getNOriented( void ) {return nOriented;} |
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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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vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;} |
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vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;} |
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CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){ |
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i = myCutoffGroups.begin(); |
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return i != myCutoffGroups.end()? *i : NULL; |
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} |
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CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){ |
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i++; |
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return i != myCutoffGroups.end()? *i : NULL; |
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} |
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bool belongToCutoffGroup(int index){ |
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return cutoffAtomSet.find(index) != cutoffAtomSet.end()? true: false; |
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} |
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int getNCutoffGroups() {return nCutoffGroups;} |
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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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void atoms2rigidBodies( 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 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; // .. . . . .. . oreineted atoms . . . |
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int nTorsions; // .. . . .. . . torsions . . .. . . |
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int nRigidBodies; // .. . . .. .rigid bodies . . .. . . |
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int nOriented; // .. . . . .. . oriented atoms . . . |
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int nMembers; // .. . . . . . .atoms (legacy code) . . . |
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int nCutoffGroups; |
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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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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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int startAtom; |
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int endAtom; |
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vector<RigidBody*> myRigidBodies; |
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vector<StuntDouble*> myIntegrableObjects; |
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vector<CutoffGroup*> myCutoffGroups; |
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set<int> cutoffAtomSet; //global index of atoms belonging to cutoff group |
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}; |
