| 1 | #ifndef BOUNDARY_HPP_
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| 2 | #define BOUNDARY_HPP_
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| 3 |
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| 4 | using namespace std;
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| 5 |
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| 6 | /*********************************************** includes ***********************************/
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| 7 |
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| 8 | // include config.h
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| 9 | #ifdef HAVE_CONFIG_H
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| 10 | #include <config.h>
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| 11 | #endif
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| 12 |
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| 13 | #include <fstream>
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| 14 | #include <iostream>
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| 15 |
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| 16 | // STL headers
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| 17 | #include <map>
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| 18 |
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| 19 | #include "defs.hpp"
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| 20 |
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| 21 | /****************************************** forward declarations *****************************/
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| 22 |
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| 23 | class atom;
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| 24 | class BoundaryPointSet;
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| 25 | class BoundaryLineSet;
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| 26 | class BoundaryTriangleSet;
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| 27 | class config;
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| 28 | class LinkedCell;
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| 29 | class molecule;
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| 30 | class MoleculeListClass;
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| 31 | class Tesselation;
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| 32 | class Vector;
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| 33 |
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| 34 | /********************************************** definitions *********************************/
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| 35 |
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| 36 | #define DEBUG 1
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| 37 | #define DoSingleStepOutput 0
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| 38 | #define SingleStepWidth 10
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| 39 |
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| 40 | #define DistancePair pair < double, atom* >
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| 41 | #define DistanceMap multimap < double, atom* >
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| 42 | #define DistanceTestPair pair < DistanceMap::iterator, bool>
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| 43 |
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| 44 | #define Boundaries map <double, DistancePair >
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| 45 | #define BoundariesPair pair<double, DistancePair >
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| 46 | #define BoundariesTestPair pair< Boundaries::iterator, bool>
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| 47 |
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| 48 | /********************************************** declarations *******************************/
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| 49 |
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| 50 | double ConvexizeNonconvexEnvelope(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename);
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| 51 | molecule * FillBoxWithMolecule(MoleculeListClass *List, molecule *filler, config &configuration, const double distance[NDIM], const double epsilon, const double RandomAtomDisplacement, const double RandomMolDisplacement, const bool DoRandomRotation);
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| 52 | void FindConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *LCList, const char *filename);
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| 53 | Vector* FindEmbeddingHole(MoleculeListClass *mols, molecule *srcmol);
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| 54 | void FindNextSuitablePoint(class BoundaryTriangleSet *BaseTriangle, class BoundaryLineSet *BaseLine, atom*& OptCandidate, Vector *OptCandidateCenter, double *ShortestAngle, const double RADIUS, LinkedCell *LC);
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| 55 | bool FindNonConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LC, const double RADIUS, const char *tempbasename);
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| 56 | Boundaries *GetBoundaryPoints(const molecule *mol, Tesselation *&TesselStruct);
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| 57 | double * GetDiametersOfCluster(const Boundaries *BoundaryPtr, const molecule *mol, Tesselation *&TesselStruct, const bool IsAngstroem);
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| 58 | void PrepareClustersinWater(config *configuration, molecule *mol, double ClusterVolume, double celldensity);
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| 59 | bool RemoveAllBoundaryPoints(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename);
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| 60 | void StoreTrianglesinFile(const molecule * const mol, const Tesselation * const TesselStruct, const char *filename, const char *extraSuffix);
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| 61 | double VolumeOfConvexEnvelope(class Tesselation *TesselStruct, class config *configuration);
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| 62 |
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| 63 |
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| 64 | #endif /*BOUNDARY_HPP_*/
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