Changeset e7350d4


Ignore:
Timestamp:
Mar 1, 2011, 10:16:39 AM (14 years ago)
Author:
Frederik Heber <heber@…>
Branches:
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
Children:
7adf0f
Parents:
72d90e
git-author:
Frederik Heber <heber@…> (02/18/11 14:27:56)
git-committer:
Frederik Heber <heber@…> (03/01/11 10:16:39)
Message:

DOCUFIX: BondGraph - moved doxygen comments from cpp to header.

Location:
src
Files:
2 edited

Legend:

Unmodified
Added
Removed

  • src/bondgraph.cpp

    r72d90e re7350d4  
    3636const double BondGraph::BondThreshold = 0.4;   //!< CSD threshold in bond check which is the width of the interval whose center is the sum of the covalent radii
    3737
    38 /** Constructor of class BondGraph.
    39  * This classes contains typical bond lengths and thus may be used to construct a bond graph for a given molecule.
    40  */
    4138BondGraph::BondGraph(bool IsA) :
    4239    BondLengthMatrix(NULL),
    … …  
    4542{};
    4643
    47 /** Destructor of class BondGraph.
    48  */
    4944BondGraph::~BondGraph()
    5045{
    … …  
    5449};
    5550
    56 /** Parses the bond lengths in a given file and puts them int a matrix form.
    57  * Allocates \a MatrixContainer for BondGraph::BondLengthMatrix, using MatrixContainer::ParseMatrix(),
    58  * but only if parsing is successful. Otherwise variable is left as NULL.
    59  * \param &input input stream to parse table from
    60  * \return true - success in parsing file, false - failed to parse the file
    61  */
    6251bool BondGraph::LoadBondLengthTable(std::istream &input)
    6352{
    … …  
    10089};
    10190
    102 /** Parses the bond lengths in a given file and puts them int a matrix form.
    103  * \param *out output stream for debugging
    104  * \param *mol molecule with atoms
    105  * \return true - success, false - failed to construct bond structure
    106  */
    10791bool BondGraph::ConstructBondGraph(molecule * const mol)
    10892{
    … …  
    119103};
    120104
    121 /** Returns the entry for a given index pair.
    122  * \param firstelement index/atom number of first element (row index)
    123  * \param secondelement index/atom number of second element (column index)
    124  * \note matrix is of course symmetric.
    125  */
    126105double BondGraph::GetBondLength(int firstZ, int secondZ)
    127106{
    … …  
    136115};
    137116
    138 /** Determines the maximum of all element::CovalentRadius for elements present in \a *mol.
    139  * \param *out output stream for debugging
    140  * \param *mol molecule with all atoms and their respective elements.
    141  */
    142117double BondGraph::SetMaxDistanceToMaxOfCovalentRadii(const molecule * const mol)
    143118{
    … …  
    155130};
    156131
    157 /** Returns the maximum distance (e.g. necessary for LinkedCell).
    158  * \return BondGraph::max_distance
    159  */
    160132double BondGraph::getMaxDistance() const
    161133{
    … …  
    164136
    165137
    166 /** Returns bond criterion for given pair based on covalent radius.
    167  * \param *Walker first BondedParticle
    168  * \param *OtherWalker second BondedParticle
    169  * \param &MinDistance lower bond bound on return
    170  * \param &MaxDistance upper bond bound on return
    171  * \param IsAngstroem whether units are in angstroem or bohr radii
    172  */
    173138void BondGraph::CovalentMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
    174139{
    … …  
    179144};
    180145
    181 /** Returns bond criterion for given pair based on a bond length matrix.
    182  * The matrix should be contained in \a this BondGraph and contain an element-
    183  * to-element length.
    184  * \param *Walker first BondedParticle
    185  * \param *OtherWalker second BondedParticle
    186  * \param &MinDistance lower bond bound on return
    187  * \param &MaxDistance upper bond bound on return
    188  * \param IsAngstroem whether units are in angstroem or bohr radii
    189  */
    190146void BondGraph::BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
    191147{

  • src/bondgraph.hpp

    r72d90e re7350d4  
    3434class BondGraph {
    3535public:
     36  /** Constructor of class BondGraph.
     37   * This classes contains typical bond lengths and thus may be used to construct a bond graph for a given molecule.
     38   */
    3639  BondGraph(bool IsA);
     40
     41  /** Destructor of class BondGraph.
     42   */
    3743  ~BondGraph();
     44
     45  /** Parses the bond lengths in a given file and puts them int a matrix form.
     46   * Allocates \a MatrixContainer for BondGraph::BondLengthMatrix, using MatrixContainer::ParseMatrix(),
     47   * but only if parsing is successful. Otherwise variable is left as NULL.
     48   * \param &input input stream to parse table from
     49   * \return true - success in parsing file, false - failed to parse the file
     50   */
    3851  bool LoadBondLengthTable(std::istream &input);
     52
     53  /** Parses the bond lengths in a given file and puts them int a matrix form.
     54   * \param *out output stream for debugging
     55   * \param *mol molecule with atoms
     56   * \return true - success, false - failed to construct bond structure
     57   */
    3958  bool ConstructBondGraph(molecule * const mol);
     59
     60  /** Returns the entry for a given index pair.
     61   * \param firstelement index/atom number of first element (row index)
     62   * \param secondelement index/atom number of second element (column index)
     63   * \note matrix is of course symmetric.
     64   */
    4065  double GetBondLength(int firstelement, int secondelement);
     66
     67  /** Determines the maximum of all element::CovalentRadius for elements present in \a *mol.
     68   * \param *out output stream for debugging
     69   * \param *mol molecule with all atoms and their respective elements.
     70   */
    4171  double SetMaxDistanceToMaxOfCovalentRadii(const molecule * const mol);
    42 
    4372
    4473  /** Returns bond criterion for given pair based on a bond length matrix.
    … …  
    5281  void getMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);
    5382
     83  /** Returns the maximum distance (e.g. necessary for LinkedCell).
     84   * \return BondGraph::max_distance
     85   */
    5486  double getMaxDistance() const;
    5587
    … …  
    5789  static const double BondThreshold;
    5890
     91  /** Returns bond criterion for given pair based on a bond length matrix.
     92   * The matrix should be contained in \a this BondGraph and contain an element-
     93   * to-element length.
     94   * \param *Walker first BondedParticle
     95   * \param *OtherWalker second BondedParticle
     96   * \param &MinDistance lower bond bound on return
     97   * \param &MaxDistance upper bond bound on return
     98   * \param IsAngstroem whether units are in angstroem or bohr radii
     99   */
    59100  void BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);
    60101
     102  /** Returns bond criterion for given pair based on covalent radius.
     103   * \param *Walker first BondedParticle
     104   * \param *OtherWalker second BondedParticle
     105   * \param &MinDistance lower bond bound on return
     106   * \param &MaxDistance upper bond bound on return
     107   * \param IsAngstroem whether units are in angstroem or bohr radii
     108   */
    61109  void CovalentMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);
    62110
     111  //!> Matrix with bond lenth per two elements
    63112  MatrixContainer *BondLengthMatrix;
     113  //!> maximum distance over all bonds possible
    64114  double max_distance;
     115  //!> distance units are angstroem (true), bohr radii (false)
    65116  bool IsAngstroem;
    66117};
Note: See TracChangeset for help on using the changeset viewer.