--- trunk/OOPSE/libmdtools/SimInfo.hpp 2003/09/16 20:02:11 767 +++ trunk/OOPSE/libmdtools/SimInfo.hpp 2004/04/19 03:52:27 1118 @@ -6,7 +6,10 @@ #include #include "Atom.hpp" +#include "RigidBody.hpp" #include "Molecule.hpp" +#include "Exclude.hpp" +#include "SkipList.hpp" #include "AbstractClasses.hpp" #include "MakeStamps.hpp" #include "SimState.hpp" @@ -15,9 +18,10 @@ #include "fSimulation.h" #include "fortranWrapDefines.hpp" #include "GenericData.hpp" +//#include "Minimizer.hpp" +//#include "OOPSEMinimizer.hpp" - - +class OOPSEMinimizer; class SimInfo{ public: @@ -27,27 +31,28 @@ class SimInfo{ (public) int n_atoms; // the number of atoms Atom **atoms; // the array of atom objects + + vector rigidBodies; // A vector of rigid bodies + vector integrableObjects; 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 - unsigned int ndfTrans; // number of translational degrees of freedom - unsigned int nZconstraints; // the number of zConstraints + 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 - unsigned int resetIntegrator; // boolean to reset the integrator + int setTemp; // boolean to set the temperature at each sampleTime + int resetIntegrator; // boolean to reset the integrator - unsigned int n_dipoles; // number of dipoles + int n_dipoles; // number of dipoles - - int n_exclude; // the # of pairs excluded from long range forces - Exclude** excludes; // the pairs themselves - + int n_exclude; + Exclude* excludes; // the exclude list for ignoring pairs in fortran int nGlobalExcludes; int* globalExcludes; // same as above, but these guys participate in // no long range forces. @@ -57,7 +62,7 @@ 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. @@ -81,11 +86,14 @@ class SimInfo{ (public) int usePBC; // whether we use periodic boundry conditions. int useLJ; int useSticky; - int useDipole; + int useCharges; + int useDipoles; int useReactionField; int useGB; int useEAM; + bool useInitXSstate; + double orthoTolerance; double dt, run_time; // the time step and total time double sampleTime, statusTime; // the position and energy dump frequencies @@ -97,7 +105,7 @@ class SimInfo{ (public) 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 @@ -107,6 +115,9 @@ class SimInfo{ (public) char mixingRule[100]; // the mixing rules for Lennard jones/van der walls BaseIntegrator *the_integrator; // the integrator of the simulation + OOPSEMinimizer* the_minimizer; // the energy minimizer + bool has_minimizer; + 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 @@ -120,9 +131,9 @@ class SimInfo{ (public) // sets the internal function pointer to fortran. - void setInternal( void (*fSetup) setFortranSimList, - void (*fBox) setFortranBoxList, - void (*fCut) notifyFortranCutOffList ){ + void setInternal( setFortranSim_TD fSetup, + setFortranBox_TD fBox, + notifyFortranCutOff_TD fCut){ setFsimulation = fSetup; setFortranBoxSize = fBox; notifyFortranCutOffs = fCut; @@ -131,42 +142,35 @@ class SimInfo{ (public) int getNDF(); int getNDFraw(); int getNDFtranslational(); - + int getTotIntegrableObjects(); 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 ); + void setDefaultRcut( double theRcut ); + void setDefaultEcr( double theEcr ); + void setDefaultEcr( double theEcr, double theEst ); + void checkCutOffs( void ); 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 dt ) { currentTime += dt; } - void decrTime( double dt ) { currentTime -= dt; } + 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]); - SimState* getConfiguration( void ) { return myConfiguration; } void addProperty(GenericData* prop); GenericData* getProperty(const string& propName); - vector getProperties(); + //vector& getProperties() {return properties;} int getSeed(void) { return seed; } void setSeed(int theSeed) { seed = theSeed;} @@ -175,33 +179,31 @@ class SimInfo{ (public) SimState* myConfiguration; - double origRcut, origEcr; - int boxIsInit, haveOrigRcut, haveOrigEcr; + int boxIsInit, haveRcut, haveEcr; - 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(); - void checkCutOffs( void ); + double calcMaxCutOff(); // private function to initialize the fortran side of the simulation - void (*setFsimulation) setFortranSimList; + setFortranSim_TD setFsimulation; - void (*setFortranBoxSize) setFortranBoxList; + setFortranBox_TD setFortranBoxSize; - void (*notifyFortranCutOffs) notifyFortranCutOffList; + notifyFortranCutOff_TD notifyFortranCutOffs; //Addtional Properties of SimInfo map properties; }; - - #endif