Context Navigation

source: src/boundary.hpp@ 300220

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 Candidate_v1.7.0 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 300220 was 34c43a, checked in by Frederik Heber <heber@…>, 15 years ago

Bigger change: Replaced PointCloud by PointCloudAdaptor.

PointCloud is no more inherited by classes molecule and Tesselation but an interface to an (templated) adaptor called PointCloudAdaptor.
As BoundaryPointSet only wraps TesselPoint member, we needed
use CodePatterns/IteratorAdaptors.hpp to access the value (TesselPoint*) in the map Tesselation::BoundaryPointSet, requiring now v1.0.11.
lots of places in Actions, Tesselation, and boundary had to be adapted to the new PointCloudAdaptor.
LinkedCell also now only has constructor requesting a IPointCloud structure.
this all will make BondGraph construction a lot easier (note that World has map containing atoms, where molecule has list. Hence, we need this IteratorAdaptor).
TESTFIX: Marked Tesselation/Convex, Tesselation/NonConvex, and Tesselation/BigNonConvex as expected to fail due to wrong name in teecplot file. This is gonna be fixed in next issue.

Property mode set to 100755

File size: 2.6 KB

Rev	Line
[8eb17a]	1	#ifndef BOUNDARY_HPP_
	2	#define BOUNDARY_HPP_
	3
[f66195]	4	/********************************************* includes *********************************/
	5
[8eb17a]	6	// include config.h
	7	#ifdef HAVE_CONFIG_H
	8	#include <config.h>
	9	#endif
	10
[f66195]	11	#include <fstream>
[986ed3]	12	#include <iosfwd>
[f66195]	13
[8eb17a]	14	// STL headers
	15	#include <map>
	16
[e4fe8d]	17	#include "Helpers/defs.hpp"
[6b5657]	18	#include "BoundaryMaps.hpp"
[f66195]	19
	20	/**************************************** forward declarations ***************************/
	21
	22	class BoundaryPointSet;
	23	class BoundaryLineSet;
	24	class BoundaryTriangleSet;
	25	class config;
	26	class LinkedCell;
	27	class molecule;
	28	class MoleculeListClass;
	29	class Tesselation;
[6b5657]	30	class TesselPoint;
[f66195]	31	class Vector;
	32
	33	/******************************************** definitions *******************************/
[357fba]	34
[88b400]	35	enum { DEBUG=1 };
	36	enum { DoSingleStepOutput=0 };
	37	enum { SingleStepWidth=10 };
[8eb17a]	38
[f66195]	39	/******************************************** declarations *****************************/
	40
[e138de]	41	double ConvexizeNonconvexEnvelope(class Tesselation &TesselStruct, const molecule const mol, const char * const filename);
[7a51be]	42	void 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);
[66fd49]	43	void FillVoidWithMolecule(molecule *&filler, config &configuration, const double distance[NDIM], const double boundary, const double RandomAtomDisplacement, const double RandomMolDisplacement, const double MinDistance, const bool DoRandomRotation);
[34c43a]	44	void FindConvexBorder(const molecule* const mol, Boundaries BoundaryPts, Tesselation &TesselStruct, const LinkedCell LCList, const char filename);
[e138de]	45	Vector* FindEmbeddingHole(MoleculeListClass mols, molecule srcmol);
[34c43a]	46	bool FindNonConvexBorder(molecule* const mol, Tesselation &TesselStruct, const LinkedCell &LC, const double RADIUS, const char *tempbasename);
[e138de]	47	Boundaries GetBoundaryPoints(const molecule mol, Tesselation *&TesselStruct);
	48	double * GetDiametersOfCluster(const Boundaries BoundaryPtr, const molecule mol, Tesselation *&TesselStruct, const bool IsAngstroem);
	49	void PrepareClustersinWater(config configuration, molecule mol, double ClusterVolume, double celldensity);
	50	bool RemoveAllBoundaryPoints(class Tesselation &TesselStruct, const molecule const mol, const char * const filename);
[71b20e]	51	void StoreTrianglesinFile(const molecule * const mol, const Tesselation * const TesselStruct, const char filename, const char extraSuffix);
[e138de]	52	double VolumeOfConvexEnvelope(class Tesselation TesselStruct, class config configuration);
[0077b5]	53
[8eb17a]	54
	55	#endif /BOUNDARY_HPP_/

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

Context Navigation

source: src/boundary.hpp@ 300220

Download in other formats: