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#include "fSimulation.h" |
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#include "fortranWrapDefines.hpp" |
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#include "GenericData.hpp" |
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//#include "Minimizer.hpp" |
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//#include "OOPSEMinimizer.hpp" |
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class OOPSEMinimizer; |
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class SimInfo{ |
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public: |
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double tau[9]; // the stress tensor |
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unsigned int n_bonds; // number of bends |
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unsigned int n_bends; // number of bends |
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unsigned int n_torsions; // number of torsions |
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unsigned int n_oriented; // number of of atoms with orientation |
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unsigned int ndf; // number of actual degrees of freedom |
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unsigned int ndfRaw; // number of settable degrees of freedom |
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unsigned int nZconstraints; // the number of zConstraints |
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int n_bonds; // number of bends |
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int n_bends; // number of bends |
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int n_torsions; // number of torsions |
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int n_oriented; // number of of atoms with orientation |
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int ndf; // number of actual degrees of freedom |
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int ndfRaw; // number of settable degrees of freedom |
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int ndfTrans; // number of translational degrees of freedom |
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int nZconstraints; // the number of zConstraints |
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unsigned int setTemp; // boolean to set the temperature at each sampleTime |
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unsigned int resetIntegrator; // boolean to reset the integrator |
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int setTemp; // boolean to set the temperature at each sampleTime |
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int resetIntegrator; // boolean to reset the integrator |
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unsigned int n_dipoles; // number of dipoles |
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int n_dipoles; // number of dipoles |
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int n_exclude; // the # of pairs excluded from long range forces |
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int n_constraints; // the number of constraints on the system |
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unsigned int n_SRI; // the number of short range interactions |
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int n_SRI; // the number of short range interactions |
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double lrPot; // the potential energy from the long range calculations. |
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int usePBC; // whether we use periodic boundry conditions. |
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int useLJ; |
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int useSticky; |
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int useDipole; |
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int useCharges; |
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int useDipoles; |
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int useReactionField; |
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int useGB; |
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int useEAM; |
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bool useInitXSstate; |
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double orthoTolerance; |
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double dt, run_time; // the time step and total time |
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double sampleTime, statusTime; // the position and energy dump frequencies |
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int n_mol; // n_molecules; |
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Molecule* molecules; // the array of molecules |
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int nComponents; // the number of componentsin the system |
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int nComponents; // the number of components in the system |
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int* componentsNmol; // the number of molecules of each component |
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MoleculeStamp** compStamps;// the stamps matching the components |
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LinkedMolStamp* headStamp; // list of stamps used in the simulation |
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char mixingRule[100]; // the mixing rules for Lennard jones/van der walls |
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BaseIntegrator *the_integrator; // the integrator of the simulation |
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OOPSEMinimizer* the_minimizer; // the energy minimizer |
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bool has_minimizer; |
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char finalName[300]; // the name of the eor file to be written |
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char sampleName[300]; // the name of the dump file to be written |
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char statusName[300]; // the name of the stat file to be written |
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// sets the internal function pointer to fortran. |
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void setInternal( void (*fSetup) setFortranSimList, |
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void (*fBox) setFortranBoxList, |
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void (*fCut) notifyFortranCutOffList ){ |
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void setInternal( setFortranSim_TD fSetup, |
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setFortranBox_TD fBox, |
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notifyFortranCutOff_TD fCut){ |
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setFsimulation = fSetup; |
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setFortranBoxSize = fBox; |
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notifyFortranCutOffs = fCut; |
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int getNDF(); |
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int getNDFraw(); |
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int getNDFtranslational(); |
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void setBox( double newBox[3] ); |
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void setBoxM( double newBox[3][3] ); |
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void getBoxM( double theBox[3][3] ); |
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void scaleBox( double scale ); |
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void setRcut( double theRcut ); |
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void setEcr( double theEcr ); |
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void setEcr( double theEcr, double theEst ); |
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void setDefaultRcut( double theRcut ); |
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void setDefaultEcr( double theEcr ); |
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void setDefaultEcr( double theEcr, double theEst ); |
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void checkCutOffs( void ); |
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double getRcut( void ) { return rCut; } |
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double getRlist( void ) { return rList; } |
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double getEcr( void ) { return ecr; } |
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double getEst( void ) { return est; } |
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double getMaxCutoff( void ) { return maxCutoff; } |
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void setTime( double theTime ) { currentTime = theTime; } |
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void incrTime( double dt ) { currentTime += dt; } |
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void decrTime( double dt ) { currentTime -= dt; } |
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void incrTime( double the_dt ) { currentTime += the_dt; } |
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void decrTime( double the_dt ) { currentTime -= the_dt; } |
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double getTime( void ) { return currentTime; } |
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void wrapVector( double thePos[3] ); |
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double matDet3(double m[3][3]); |
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double matTrace3(double m[3][3]); |
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void crossProduct3(double a[3],double b[3], double out[3]); |
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double dotProduct3(double a[3], double b[3]); |
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double length3(double a[3]); |
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SimState* getConfiguration( void ) { return myConfiguration; } |
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void addProperty(GenericData* prop); |
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SimState* myConfiguration; |
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double origRcut, origEcr; |
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int boxIsInit, haveOrigRcut, haveOrigEcr; |
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int boxIsInit, haveRcut, haveEcr; |
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double oldEcr; |
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double oldRcut; |
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double rList, rCut; // variables for the neighborlist |
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double ecr; // the electrostatic cutoff radius |
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double est; // the electrostatic skin thickness |
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double maxCutoff; |
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double distXY; |
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double distYZ; |
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double distZX; |
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void calcHmatInv( void ); |
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void calcBoxL(); |
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void checkCutOffs( void ); |
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double calcMaxCutOff(); |
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// private function to initialize the fortran side of the simulation |
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void (*setFsimulation) setFortranSimList; |
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setFortranSim_TD setFsimulation; |
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void (*setFortranBoxSize) setFortranBoxList; |
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setFortranBox_TD setFortranBoxSize; |
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void (*notifyFortranCutOffs) notifyFortranCutOffList; |
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notifyFortranCutOff_TD notifyFortranCutOffs; |
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//Addtional Properties of SimInfo |
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map<string, GenericData*> properties; |