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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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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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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 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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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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int ngroup; |
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vector<int> groupList; |
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vector<int> groupStart; |
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// refreshes the sim if things get changed (load balanceing, volume |
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// adjustment, etc.) |
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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[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 setDefaultRcut( double theRcut ); |
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void setEcr( double theEcr ); |
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void setDefaultEcr( double theEcr ); |
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void setEcr( double theEcr, double theEst ); |
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void setDefaultEcr( double theEcr, double theEst ); |
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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 getEcr( void ) { return ecr; } |
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double getEst( void ) { return est; } |
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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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void wrapVector( double thePos[3] ); |
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void matMul3(double a[3][3], double b[3][3], double out[3][3]); |
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void matVecMul3(double m[3][3], double inVec[3], double outVec[3]); |
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void invertMat3(double in[3][3], double out[3][3]); |
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void transposeMat3(double in[3][3], double out[3][3]); |
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void printMat3(double A[3][3]); |
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void printMat9(double A[9]); |
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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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GenericData* getProperty(const string& propName); |
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vector<GenericData*> getProperties(); |
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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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SimState* myConfiguration; |
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double origRcut, origEcr; |
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int boxIsInit, haveOrigRcut, haveOrigEcr; |
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int boxIsInit, haveRcut, haveRsw; |
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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 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 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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setFortranSim_TD setFsimulation; |
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}; |
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void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, |
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vector<int>& groupList, vector<int>& groupStart); |
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#endif |
