Action_Thermostats
Add_AtomRandomPerturbation
Add_FitFragmentPartialChargesAction
Add_RotateAroundBondAction
Add_SelectAtomByNameAction
Added_ParseSaveFragmentResults
Adding_Graph_to_ChangeBondActions
Adding_MD_integration_tests
Adding_StructOpt_integration_tests
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_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
FragmentMolecule_checks_bonddegrees
GeometryObjects
Gui_Fixes
Gui_displays_atomic_force_velocity
IndependentFragmentGrids
IndependentFragmentGrids_IndividualZeroInstances
IndependentFragmentGrids_IntegrationTest
IndependentFragmentGrids_Sole_NN_Calculation
JobMarket_RobustOnKillsSegFaults
JobMarket_StableWorkerPool
JobMarket_unresolvable_hostname_fix
ODR_violation_mpqc_open
PartialCharges_OrthogonalSummation
PythonUI_with_named_parameters
QtGui_reactivate_TimeChanged_changes
Recreated_GuiChecks
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
| Line | |
|---|
| 1 | #ifndef BOUNDARY_HPP_
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|---|
| 2 | #define BOUNDARY_HPP_
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|---|
| 3 |
|
|---|
| 4 | /*********************************************** includes ***********************************/
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| 5 |
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| 6 | // include config.h
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| 7 | #ifdef HAVE_CONFIG_H
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|---|
| 8 | #include <config.h>
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|---|
| 9 | #endif
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| 10 |
|
|---|
| 11 | #include <fstream>
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|---|
| 12 | #include <iosfwd>
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| 13 |
|
|---|
| 14 | // STL headers
|
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| 15 | #include <map>
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|---|
| 16 |
|
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| 17 | #include "LinearAlgebra/defs.hpp"
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|---|
| 18 | #include "BoundaryMaps.hpp"
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| 19 |
|
|---|
| 20 | /****************************************** forward declarations *****************************/
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| 21 |
|
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| 22 | class BoundaryPointSet;
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| 23 | class BoundaryLineSet;
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|---|
| 24 | class BoundaryTriangleSet;
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|---|
| 25 | class config;
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|---|
| 26 | class LinkedCell_deprecated;
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| 27 | class molecule;
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| 28 | class Tesselation;
|
|---|
| 29 | class TesselPoint;
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| 30 | class Vector;
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|---|
| 31 |
|
|---|
| 32 | /********************************************** definitions *********************************/
|
|---|
| 33 |
|
|---|
| 34 | enum { DEBUG=1 };
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|---|
| 35 | enum { DoSingleStepOutput=0 };
|
|---|
| 36 | enum { SingleStepWidth=10 };
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|---|
| 37 |
|
|---|
| 38 | /********************************************** declarations *******************************/
|
|---|
| 39 |
|
|---|
| 40 | double ConvexizeNonconvexEnvelope(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename, bool DebugOutputEveryStep = false);
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| 41 | void FindConvexBorder(const molecule* const mol, Boundaries *BoundaryPts, Tesselation *&TesselStruct, const LinkedCell_deprecated *LCList, const char *filename);
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| 42 | bool FindNonConvexBorder(molecule* const mol, Tesselation *&TesselStruct, const LinkedCell_deprecated *&LC, const double RADIUS, const char *tempbasename);
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| 43 | Boundaries *GetBoundaryPoints(const molecule *mol, Tesselation *&TesselStruct);
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|---|
| 44 | double * GetDiametersOfCluster(const Boundaries *BoundaryPtr, const molecule *mol, Tesselation *&TesselStruct, const bool IsAngstroem);
|
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| 45 | bool RemoveAllBoundaryPoints(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename);
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| 46 | void StoreTrianglesinFile(const molecule * const mol, const Tesselation * const TesselStruct, const char *filename, const char *extraSuffix);
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| 47 |
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| 48 |
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| 49 | #endif /*BOUNDARY_HPP_*/
|
|---|
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