Changeset 1363de for src/atom.hpp

Timestamp:

Mar 2, 2011, 9:53:08 PM (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:

0d9546

Parents:

09ac12

git-author:

Frederik Heber <heber@…> (02/25/11 20:35:17)

git-committer:

Frederik Heber <heber@…> (03/02/11 21:53:08)

Message:

DOCUFIX: atom - Moved all doxygen documentation to header file.

File:

• src/atom.hpp (modified) (3 diffs)

src/atom.hpp

@@ -47 +47 @@
   friend atom* NewAtom(atomId_t);
   friend void  DeleteAtom(atom*);
-  public:
+public:
     atom *father;   //!< In many-body bond order fragmentations points to originating atom
     int *sort;      //!< sort criteria
 
+  /** Clones this atom.
+   *
+   * Does not clone the bonds!
+   *
+   * @return reference to atom
+   */
   virtual atom *clone();
 
@@ -61 +67 @@
   virtual void UpdateSteps();
 
+  /** Output of a single atom with given numbering.
+   * \param ElementNo cardinal number of the element
+   * \param AtomNo cardinal number among these atoms of the same element
+   * \param *out stream to output to
+   * \param *comment commentary after '#' sign
+   * \return true - \a *out present, false - \a *out is NULL
+   */
   bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
+
+  /** Output of a single atom with numbering from array according to atom::type.
+   * \param *ElementNo cardinal number of the element
+   * \param *AtomNo cardinal number among these atoms of the same element
+   * \param *out stream to output to
+   * \param *comment commentary after '#' sign
+   * \return true - \a *out present, false - \a *out is NULL
+   */
   bool OutputArrayIndexed(ostream * const out,const enumeration<const element*>&, int *AtomNo, const char *comment = NULL) const;
+
+  /** Output of a single atom as one line in xyz file.
+   * \param *out stream to output to
+   * \return true - \a *out present, false - \a *out is NULL
+   */
   bool OutputXYZLine(ofstream *out) const;
+
+  /** Output of a single atom as one line in xyz file.
+   * \param *out stream to output to
+   * \param *ElementNo array with ion type number in the config file this atom's element shall have
+   * \param *AtomNo array with atom number in the config file this atom shall have, is increase by one automatically
+   * \param step Trajectory time step to output
+   * \return true - \a *out present, false - \a *out is NULL
+   */
   bool OutputTrajectory(ofstream * const out, const enumeration<const element*>&, int *AtomNo, const int step) const;
+
+  /** Output of a single atom as one lin in xyz file.
+   * \param *out stream to output to
+   * \param step Trajectory time step to output
+   * \return true - \a *out present, false - \a *out is NULL
+   */
   bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
+
+  /** Outputs the MPQC configuration line for this atom.
+   * \param *out output stream
+   * \param *center center of molecule subtracted from position
+   * \param *AtomNo pointer to atom counter that is increased by one
+   */
   void OutputMPQCLine(ostream * const out, const Vector *center) const;
 
+  /** Initialises the component number array.
+   * Size is set to atom::ListOfBonds.size()+1 (last is th encode end by -1)
+   */
   void InitComponentNr();
+
+  /** Resets GraphNr to -1.
+   *
+   */
   void resetGraphNr();
 
+  /** Check whether father is equal to given atom.
+   * \param *ptr atom to compare father to
+   * \param **res return value (only set if atom::father is equal to \a *ptr)
+   */
   void EqualsFather ( const atom *ptr, const atom **res ) const;
+
+  /** States whether the given \a *ptr is our father.
+   *
+   * @param ptr atom to compare atom::Father with
+   * @return true - \a *ptr is father, false - not
+   */
   bool isFather(const atom *ptr);
+
+  /** If we are copy of copy, we are linked to be just a copy.
+   *
+   */
   void CorrectFather();
+
+  /** Climbs up the father list until NULL, last is returned.
+   * \return true father, i.e. whose father points to itself, NULL if it could not be found or has none (added hydrogen)
+   */
   atom *GetTrueFather();
+
+  /** Compares the indices of \a this atom with a given \a ptr.
+   * \param ptr atom to compare index against
+   * \return true - this one's is smaller, false - not
+   */
   bool Compare(const atom &ptr) const;
 
+  /** Returns distance to a given vector.
+   * \param origin vector to calculate distance to
+   * \return distance
+   */
   double DistanceToVector(const Vector &origin) const;
+
+  /** Returns squared distance to a given vector.
+   * \param origin vector to calculate distance to
+   * \return distance squared
+   */
   double DistanceSquaredToVector(const Vector &origin) const;
+  /** Checks whether atom is within the given box.
+   * \param offset offset to box origin
+   * \param *parallelepiped box matrix
+   * \return true - is inside, false - is not
+   */
   bool IsInShape(const Shape&) const;
 
@@ -101 +191 @@
    virtual void setId(atomId_t);
 
+   /** Makes the atom be contained in the new molecule \a *_mol.
+    * Uses atom::removeFromMolecule() to delist from old molecule.
+    * \param *_mol pointer to new molecule
+    */
    void setMolecule(molecule*);
+
+   /** Returns pointer to the molecule which atom belongs to.
+    * \return containing molecule
+    */
    molecule* getMolecule() const;
+
+   /** Erases the atom in atom::mol's list of atoms and sets it to zero.
+    */
    void removeFromMolecule();
 
+   /** Getter for ParticleInfo::Nr of the atom.
+    *
+    * @return index
+    */
    int getNr() const;