--- trunk/OOPSE/libmdtools/SimInfo.hpp 2003/05/30 21:31:48 542 +++ trunk/OOPSE/libmdtools/SimInfo.hpp 2003/10/28 22:25:46 836 @@ -1,16 +1,20 @@ #ifndef __SIMINFO_H__ #define __SIMINFO_H__ +#include +#include +#include - #include "Atom.hpp" #include "Molecule.hpp" #include "AbstractClasses.hpp" #include "MakeStamps.hpp" +#include "SimState.hpp" #define __C #include "fSimulation.h" #include "fortranWrapDefines.hpp" +#include "GenericData.hpp" @@ -19,27 +23,28 @@ class SimInfo{ (public) public: SimInfo(); - ~SimInfo(){} + ~SimInfo(); int n_atoms; // the number of atoms Atom **atoms; // the array of atom objects double tau[9]; // the stress tensor - unsigned int n_bonds; // number of bends - unsigned int n_bends; // number of bends - unsigned int n_torsions; // number of torsions - unsigned int n_oriented; // number of of atoms with orientation - unsigned int ndf; // number of actual degrees of freedom - unsigned int ndfRaw; // number of settable degrees of freedom + int n_bonds; // number of bends + int n_bends; // number of bends + int n_torsions; // number of torsions + int n_oriented; // number of of atoms with orientation + int ndf; // number of actual degrees of freedom + int ndfRaw; // number of settable degrees of freedom + int ndfTrans; // number of translational degrees of freedom + int nZconstraints; // the number of zConstraints - unsigned int setTemp; // boolean to set the temperature at each sampleTime + int setTemp; // boolean to set the temperature at each sampleTime + int resetIntegrator; // boolean to reset the integrator - unsigned int n_dipoles; // number of dipoles - double ecr; // the electrostatic cutoff radius - double est; // the electrostatic skin thickness - double dielectric; // the dielectric of the medium for reaction field + int n_dipoles; // number of dipoles + int n_exclude; // the # of pairs excluded from long range forces Exclude** excludes; // the pairs themselves @@ -52,13 +57,27 @@ class SimInfo{ (public) int n_constraints; // the number of constraints on the system - unsigned int n_SRI; // the number of short range interactions + int n_SRI; // the number of short range interactions double lrPot; // the potential energy from the long range calculations. - double box_x, box_y, box_z; // the periodic boundry conditions - double rList, rCut; // variables for the neighborlist + double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the + // column vectors of the x, y, and z box vectors. + // h1 h2 h3 + // [ Xx Yx Zx ] + // [ Xy Yy Zy ] + // [ Xz Yz Zz ] + // + double HmatInv[3][3]; + + double boxL[3]; // The Lengths of the 3 column vectors of Hmat + double boxVol; + int orthoRhombic; + + double dielectric; // the dielectric of the medium for reaction field + + int usePBC; // whether we use periodic boundry conditions. int useLJ; int useSticky; @@ -72,11 +91,13 @@ class SimInfo{ (public) double sampleTime, statusTime; // the position and energy dump frequencies double target_temp; // the target temperature of the system double thermalTime; // the temp kick interval + double currentTime; // Used primarily for correlation Functions + double resetTime; // Use to reset the integrator periodically int n_mol; // n_molecules; Molecule* molecules; // the array of molecules - int nComponents; // the number of componentsin the system + int nComponents; // the number of components in the system int* componentsNmol; // the number of molecules of each component MoleculeStamp** compStamps;// the stamps matching the components LinkedMolStamp* headStamp; // list of stamps used in the simulation @@ -90,7 +111,7 @@ class SimInfo{ (public) char sampleName[300]; // the name of the dump file to be written char statusName[300]; // the name of the stat file to be written - + int seed; //seed for random number generator // refreshes the sim if things get changed (load balanceing, volume // adjustment, etc.) @@ -99,24 +120,96 @@ class SimInfo{ (public) // sets the internal function pointer to fortran. - void setInternal( void (*fSetup) setFortranSimList, - void (*fBox) setFortranBoxList ){ + void setInternal( setFortranSim_TD fSetup, + setFortranBox_TD fBox, + notifyFortranCutOff_TD fCut){ setFsimulation = fSetup; setFortranBoxSize = fBox; + notifyFortranCutOffs = fCut; } int getNDF(); int getNDFraw(); + int getNDFtranslational(); void setBox( double newBox[3] ); - void getBox( double theBox[3] ); + void setBoxM( double newBox[3][3] ); + void getBoxM( double theBox[3][3] ); + void scaleBox( double scale ); + + void setRcut( double theRcut ); + void setEcr( double theEcr ); + void setEcr( double theEcr, double theEst ); + double getRcut( void ) { return rCut; } + double getRlist( void ) { return rList; } + double getEcr( void ) { return ecr; } + double getEst( void ) { return est; } + double getMaxCutoff( void ) { return maxCutoff; } + + void setTime( double theTime ) { currentTime = theTime; } + void incrTime( double the_dt ) { currentTime += the_dt; } + void decrTime( double the_dt ) { currentTime -= the_dt; } + double getTime( void ) { return currentTime; } + + void wrapVector( double thePos[3] ); + + void matMul3(double a[3][3], double b[3][3], double out[3][3]); + void matVecMul3(double m[3][3], double inVec[3], double outVec[3]); + void invertMat3(double in[3][3], double out[3][3]); + void transposeMat3(double in[3][3], double out[3][3]); + void printMat3(double A[3][3]); + void printMat9(double A[9]); + double matDet3(double m[3][3]); + double matTrace3(double m[3][3]); + + void crossProduct3(double a[3],double b[3], double out[3]); + double dotProduct3(double a[3], double b[3]); + double length3(double a[3]); + + SimState* getConfiguration( void ) { return myConfiguration; } + + void addProperty(GenericData* prop); + GenericData* getProperty(const string& propName); + vector getProperties(); + + int getSeed(void) { return seed; } + void setSeed(int theSeed) { seed = theSeed;} + private: + + SimState* myConfiguration; + + double origRcut, origEcr; + int boxIsInit, haveOrigRcut, haveOrigEcr; + + double oldEcr; + double oldRcut; + + double rList, rCut; // variables for the neighborlist + double ecr; // the electrostatic cutoff radius + double est; // the electrostatic skin thickness + double maxCutoff; + + double distXY; + double distYZ; + double distZX; + void calcHmatInv( void ); + void calcBoxL(); + double calcMaxCutOff(); + void checkCutOffs( void ); + // private function to initialize the fortran side of the simulation - void (*setFsimulation) setFortranSimList; + setFortranSim_TD setFsimulation; - void (*setFortranBoxSize) setFortranBoxList; + setFortranBox_TD setFortranBoxSize; + + notifyFortranCutOff_TD notifyFortranCutOffs; + + //Addtional Properties of SimInfo + map properties; + };