source: src/bondgraph.hpp@ ff3c40

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 ff3c40 was af2c424, checked in by Frederik Heber <heber@…>, 14 years ago

LinkedCell constructor rewritten.

  • had to introduce getValue(iterator) to: molecule, tesselation, LinkedCell::LinkedNodes
  • LinkedCell::LinkedNodes is not a typedef anymore
  • new class LinkedCell::LinkedNodes derived from stl::list<TesselPoint *> to add getValue(iterator).
  • LinkedCell constructors changed:
    • use template for all classes that have begin(), end() and ... sigh ... getValue()
    • Argh! STL containers do all have begin() and end() but no consistent operator* (maps return pair<> ...)
    • specialized version for PointCloud derivatives
    • various functions had to be changed due to changed signature of LinkedCell constructor
  • Property mode set to 100644
File size: 1.5 KB
Line 
1/*
2 * bondgraph.hpp
3 *
4 * Created on: Oct 29, 2009
5 * Author: heber
6 */
7
8#ifndef BONDGRAPH_HPP_
9#define BONDGRAPH_HPP_
10
11using namespace std;
12
13/*********************************************** includes ***********************************/
14
15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19
20#include <iosfwd>
21
22
23/****************************************** forward declarations *****************************/
24
25class molecule;
26class BondedParticle;
27class MatrixContainer;
28
29/********************************************** definitions *********************************/
30
31/********************************************** declarations *******************************/
32
33
34class BondGraph {
35public:
36 BondGraph(bool IsA);
37 ~BondGraph();
38 bool LoadBondLengthTable(const string &filename);
39 bool ConstructBondGraph(molecule * const mol);
40 double GetBondLength(int firstelement, int secondelement);
41 double SetMaxDistanceToMaxOfCovalentRadii(const molecule * const mol);
42
43 void BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);
44 void CovalentMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);
45
46 double getMaxDistance() const;
47
48private:
49 static const double BondThreshold;
50
51 MatrixContainer *BondLengthMatrix;
52 double max_distance;
53 bool IsAngstroem;
54};
55
56#endif /* BONDGRAPH_HPP_ */
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