source: src/boundary.hpp@ 1513a74

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since 1513a74 was 775d133, checked in by Frederik Heber <heber@…>, 15 years ago

Filling has a MaxDistance, somes changes to the Correlation Analysis.

Correlation:

  • OutputCorrelation() have setprecision(8), as irregularities appeared in the output files with regard to the number of digits.
  • ParseCommandLineOptions() for case 'C' now needs BinStart and BinEnd. However, may be set to 0,0 (search for yourself), or (0,-1) (start at 0, but search end for yourself).
  • BUGFIX: argument index of element parameter was wrong from the change [E/P/S].

Filling:
  • Property mode set to 100755
File size: 2.8 KB
Line 
1#ifndef BOUNDARY_HPP_
2#define BOUNDARY_HPP_
3
4using namespace std;
5
6/*********************************************** includes ***********************************/
7
8// include config.h
9#ifdef HAVE_CONFIG_H
10#include <config.h>
11#endif
12
13#include <fstream>
14#include <iostream>
15
16// STL headers
17#include <map>
18
19#include "defs.hpp"
20
21/****************************************** forward declarations *****************************/
22
23class atom;
24class BoundaryPointSet;
25class BoundaryLineSet;
26class BoundaryTriangleSet;
27class config;
28class LinkedCell;
29class molecule;
30class MoleculeListClass;
31class Tesselation;
32class Vector;
33
34/********************************************** definitions *********************************/
35
36#define DEBUG 1
37#define DoSingleStepOutput 0
38#define SingleStepWidth 10
39
40#define DistancePair pair < double, atom* >
41#define DistanceMap multimap < double, atom* >
42#define DistanceTestPair pair < DistanceMap::iterator, bool>
43
44#define Boundaries map <double, DistancePair >
45#define BoundariesPair pair<double, DistancePair >
46#define BoundariesTestPair pair< Boundaries::iterator, bool>
47
48/********************************************** declarations *******************************/
49
50double ConvexizeNonconvexEnvelope(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename);
51molecule * FillBoxWithMolecule(MoleculeListClass *List, molecule *filler, config &configuration, const double MaxDistance, const double distance[NDIM], const double boundary, const double RandomAtomDisplacement, const double RandomMolDisplacement, const bool DoRandomRotation);
52void FindConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *LCList, const char *filename);
53Vector* FindEmbeddingHole(MoleculeListClass *mols, molecule *srcmol);
54void FindNextSuitablePoint(class BoundaryTriangleSet *BaseTriangle, class BoundaryLineSet *BaseLine, atom*& OptCandidate, Vector *OptCandidateCenter, double *ShortestAngle, const double RADIUS, LinkedCell *LC);
55bool FindNonConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LC, const double RADIUS, const char *tempbasename);
56Boundaries *GetBoundaryPoints(const molecule *mol, Tesselation *&TesselStruct);
57double * GetDiametersOfCluster(const Boundaries *BoundaryPtr, const molecule *mol, Tesselation *&TesselStruct, const bool IsAngstroem);
58void PrepareClustersinWater(config *configuration, molecule *mol, double ClusterVolume, double celldensity);
59bool RemoveAllBoundaryPoints(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename);
60void StoreTrianglesinFile(const molecule * const mol, const Tesselation * const TesselStruct, const char *filename, const char *extraSuffix);
61double VolumeOfConvexEnvelope(class Tesselation *TesselStruct, class config *configuration);
62
63
64#endif /*BOUNDARY_HPP_*/
Note: See TracBrowser for help on using the repository browser.