--- trunk/OOPSE/libmdtools/SimInfo.hpp 2003/03/26 21:50:33 412 +++ trunk/OOPSE/libmdtools/SimInfo.hpp 2003/09/15 16:52:02 763 @@ -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" @@ -19,7 +23,7 @@ class SimInfo{ (public) public: SimInfo(); - ~SimInfo(){} + ~SimInfo(); int n_atoms; // the number of atoms Atom **atoms; // the array of atom objects @@ -30,33 +34,49 @@ class SimInfo{ (public) 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 + unsigned int nZconstraints; // the number of zConstraints unsigned int setTemp; // boolean to set the temperature at each sampleTime + unsigned 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_exclude; // the # of pairs excluded from long range forces - Exclude* excludes; // the pairs themselves + Exclude** excludes; // the pairs themselves int nGlobalExcludes; int* globalExcludes; // same as above, but these guys participate in // no long range forces. int* identArray; // array of unique identifiers for the atoms + int* molMembershipArray; // map of atom numbers onto molecule numbers int n_constraints; // the number of constraints on the system unsigned int n_SRI; // the number of short range interactions - SRI **sr_interactions;// the array of short range force objects 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; @@ -70,6 +90,8 @@ 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 @@ -82,13 +104,13 @@ class SimInfo{ (public) char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. ) char mixingRule[100]; // the mixing rules for Lennard jones/van der walls - Integrator *the_integrator; // the integrator of the simulation + BaseIntegrator *the_integrator; // the integrator of the simulation char finalName[300]; // the name of the eor file to be written 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.) @@ -98,17 +120,84 @@ class SimInfo{ (public) // sets the internal function pointer to fortran. void setInternal( void (*fSetup) setFortranSimList, - void (*fBox) setFortranBoxList ){ + void (*fBox) setFortranBoxList, + void (*fCut) notifyFortranCutOffList ){ setFsimulation = fSetup; setFortranBoxSize = fBox; + notifyFortranCutOffs = fCut; } + int getNDF(); + int getNDFraw(); + + void setBox( double newBox[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; } + + void setTime( double theTime ) { currentTime = theTime; } + void incrTime( double dt ) { currentTime += dt; } + void decrTime( double dt ) { currentTime -= 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]); + + 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; + void calcHmatInv( void ); + void calcBoxL(); + void checkCutOffs( void ); + // private function to initialize the fortran side of the simulation void (*setFsimulation) setFortranSimList; void (*setFortranBoxSize) setFortranBoxList; + + void (*notifyFortranCutOffs) notifyFortranCutOffList; + + //Addtional Properties of SimInfo + map properties; + };