Context Navigation

source: src/boundary.hpp@ b8d4a3

Visit:

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 b8d4a3 was 9473f6, checked in by Frederik Heber <heber@…>, 15 years ago

FillBoxWithMolecule now allows boundary between filler molecules and the surface.

boundary.cpp:
- FillBoxWithMolecule() has additional parameter boundary and calls Tesselation::GetDistanceSquaredToSurface() to obtain distance to surface.
- FillBoxWithMolecule(*) verbosity states now inner point or within boundary.

builder.cpp:
- ParseCommandLineOptions() in case 'F' takes seven arguments instead of six and calls FillBoxWithMolecule() correctly.

tesselation.cpp:
- Make const what needs to be const: BoundaryPointSet, BoundaryLineSet, BoundaryTriangleSet
- added constructor BoundaryLineSet::BoundaryLineSet() that accept two endpoints instead of an array of two
- new function BoundaryTriangleSet::GetClosestPointInsideTriangle() calculates closest point in a given triangle to a reference point and returns squared distance.
- new function Tesselation::GetDistanceSquaredToSurface() that calculates the squared distance whose sign indicates whether reference is inside (-) or outside (+) and uses BoundaryTriangleSet::GetClosestPointInsideTriangle()
- function Tesselation::IsInnerPoint() renamed to Tesselation::GetDistanceSquaredToSurface().
- new function Tesselation::IsInnerPoint() just uses Tesselation::GetDistanceSquaredToSurface()

Property mode set to 100755

File size: 2.8 KB

Rev	Line
[8eb17a]	1	#ifndef BOUNDARY_HPP_
	2	#define BOUNDARY_HPP_
	3
[f66195]	4	using namespace std;
	5
	6	/********************************************* includes *********************************/
	7
[8eb17a]	8	// include config.h
	9	#ifdef HAVE_CONFIG_H
	10	#include <config.h>
	11	#endif
	12
[f66195]	13	#include <fstream>
	14	#include <iostream>
	15
[8eb17a]	16	// STL headers
	17	#include <map>
	18
[f66195]	19	#include "defs.hpp"
	20
	21	/**************************************** forward declarations ***************************/
	22
	23	class atom;
	24	class BoundaryPointSet;
	25	class BoundaryLineSet;
	26	class BoundaryTriangleSet;
	27	class config;
	28	class LinkedCell;
	29	class molecule;
	30	class MoleculeListClass;
	31	class Tesselation;
	32	class Vector;
	33
	34	/******************************************** definitions *******************************/
[357fba]	35
	36	#define DEBUG 1
[262bae]	37	#define DoSingleStepOutput 0
[b998c3]	38	#define SingleStepWidth 10
[8eb17a]	39
[edb93c]	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
[f66195]	48	/******************************************** declarations *****************************/
	49
[e138de]	50	double ConvexizeNonconvexEnvelope(class Tesselation &TesselStruct, const molecule const mol, const char * const filename);
[9473f6]	51	molecule * FillBoxWithMolecule(MoleculeListClass List, molecule filler, config &configuration, const double distance[NDIM], const double boundary, const double RandomAtomDisplacement, const double RandomMolDisplacement, const bool DoRandomRotation);
[e138de]	52	void FindConvexBorder(const molecule* const mol, Tesselation &TesselStruct, const LinkedCell LCList, const char *filename);
	53	Vector* FindEmbeddingHole(MoleculeListClass mols, molecule srcmol);
[776b64]	54	void FindNextSuitablePoint(class BoundaryTriangleSet BaseTriangle, class BoundaryLineSet BaseLine, atom& OptCandidate, Vector OptCandidateCenter, double ShortestAngle, const double RADIUS, LinkedCell LC);
[4fc93f]	55	bool FindNonConvexBorder(const molecule* const mol, Tesselation &TesselStruct, const LinkedCell &LC, const double RADIUS, const char *tempbasename);
[e138de]	56	Boundaries GetBoundaryPoints(const molecule mol, Tesselation *&TesselStruct);
	57	double * GetDiametersOfCluster(const Boundaries BoundaryPtr, const molecule mol, Tesselation *&TesselStruct, const bool IsAngstroem);
	58	void PrepareClustersinWater(config configuration, molecule mol, double ClusterVolume, double celldensity);
	59	bool RemoveAllBoundaryPoints(class Tesselation &TesselStruct, const molecule const mol, const char * const filename);
[71b20e]	60	void StoreTrianglesinFile(const molecule * const mol, const Tesselation * const TesselStruct, const char filename, const char extraSuffix);
[e138de]	61	double VolumeOfConvexEnvelope(class Tesselation TesselStruct, class config configuration);
[0077b5]	62
[8eb17a]	63
	64	#endif /BOUNDARY_HPP_/

Note: See TracBrowser for help on using the repository browser.

Context Navigation

source: src/boundary.hpp@ b8d4a3

Download in other formats: