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#ifndef __SIMINFO_H__ |
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#define __SIMINFO_H__ |
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#include <map> |
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#include <string> |
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#include <vector> |
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#include "Atom.hpp" |
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#include "RigidBody.hpp" |
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#include "Molecule.hpp" |
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#include "Exclude.hpp" |
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#include "SkipList.hpp" |
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#include "AbstractClasses.hpp" |
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#include "MakeStamps.hpp" |
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#include "SimState.hpp" |
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#include "Restraints.hpp" |
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#define __C |
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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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double roundMe( double x ); |
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class OOPSEMinimizer; |
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class SimInfo{ |
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public: |
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SimInfo(); |
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~SimInfo(){} |
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~SimInfo(); |
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int n_atoms; // the number of atoms |
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Atom **atoms; // the array of atom objects |
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vector<RigidBody*> rigidBodies; // A vector of rigid bodies |
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vector<StuntDouble*> integrableObjects; |
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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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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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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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double ecr; // the electrostatic cutoff radius |
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double est; // the electrostatic skin thickness |
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double dielectric; // the dielectric of the medium for reaction field |
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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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Exclude** excludes; // the pairs themselves |
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int n_exclude; |
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Exclude* excludes; // the exclude list for ignoring pairs in fortran |
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int nGlobalExcludes; |
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int* globalExcludes; // same as above, but these guys participate in |
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// no 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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double Hmat[9]; // the periodic boundry conditions. The Hmat is the |
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// column vectors of the x, y, and z box vectors. |
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// |
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// h1 h2 h3 |
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// [ Xx Yx Zx ] |
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// [ Xy Yy Zy ] |
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// [ Xz Yz Zz ] |
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// |
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// to preserve compatibility with Fortran the |
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// ordering in the array is as follows: |
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// |
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// [ 0 3 6 ] |
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// [ 1 4 7 ] |
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// [ 2 5 8 ] |
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double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the |
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// column vectors of the x, y, and z box vectors. |
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// h1 h2 h3 |
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// [ Xx Yx Zx ] |
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// [ Xy Yy Zy ] |
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// [ Xz Yz Zz ] |
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// |
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double HmatInv[3][3]; |
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double HmatI[9]; // the inverted Hmat; |
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double boxLx, boxLy, boxLz; // the box Lengths |
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double boxVol, orthoRhombic; |
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double boxL[3]; // The Lengths of the 3 column vectors of Hmat |
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double boxVol; |
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int orthoRhombic; |
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double dielectric; // the dielectric of the medium for reaction field |
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double rList, rCut; // variables for the neighborlist |
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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 haveCutoffGroups; |
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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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double target_temp; // the target temperature of the system |
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double thermalTime; // the temp kick interval |
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double currentTime; // Used primarily for correlation Functions |
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double resetTime; // Use to reset the integrator periodically |
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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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Restraints* restraint; |
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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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char rawPotName[300]; // the name of the raw file to be written |
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int seed; //seed for random number generator |
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int useSolidThermInt; // is solid-state thermodynamic integration being used |
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int useLiquidThermInt; // is liquid thermodynamic integration being used |
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double thermIntLambda; // lambda for TI |
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double thermIntK; // power of lambda for TI |
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double vRaw; // unperturbed potential for TI |
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double vHarm; // harmonic potential for TI |
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int i; // just an int |
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vector<double> mfact; |
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vector<int> FglobalGroupMembership; |
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int ngroup; |
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int* globalGroupMembership; |
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// refreshes the sim if things get changed (load balanceing, volume |
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// adjustment, etc.) |
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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 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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} |
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int getNDF(); |
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int getNDFraw(); |
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int getNDFtranslational(); |
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int getTotIntegrableObjects(); |
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void setBox( double newBox[3] ); |
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void setBoxM( double newBox[9] ); |
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void getBoxM( double theBox[9] ); |
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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 setDefaultRcut( double theRcut ); |
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void setDefaultRcut( double theRcut, double theRsw ); |
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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 getRsw( void ) { return rSw; } |
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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 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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SimState* getConfiguration( void ) { return myConfiguration; } |
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void addProperty(GenericData* prop); |
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GenericData* getProperty(const string& propName); |
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//vector<GenericData*>& getProperties() {return properties;} |
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int getSeed(void) { return seed; } |
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void setSeed(int theSeed) { seed = theSeed;} |
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private: |
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SimState* myConfiguration; |
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int boxIsInit, haveRcut, haveRsw; |
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double rList, rCut; // variables for the neighborlist |
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double rSw; // the switching radius |
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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 calcHmatI( void ); |
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void calcHmatInv( void ); |
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void calcBoxL(); |
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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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}; |
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setFortranBox_TD setFortranBoxSize; |
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notifyFortranCutOff_TD notifyFortranCutOffs; |
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//Addtional Properties of SimInfo |
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map<string, GenericData*> properties; |
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void getFortranGroupArrays(SimInfo* info, |
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vector<int>& FglobalGroupMembership, |
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vector<double>& mfact); |
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}; |
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#endif |