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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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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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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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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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#endif |
