Changeset abd8f7 for src

Timestamp:

Jul 2, 2010, 9:12:10 AM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

a630fd

Parents:

cd82ec

Message:

Added comments for Box class

File:

• src/Box.hpp (modified) (3 diffs)

src/Box.hpp

@@ -15 +15 @@
 #include "VectorSet.hpp"
 
+/**
+ * A simple class that can be used to store periodic Boxes
+ * in the form of a parallelepiped.
+ *
+ * Stores a matrix that can be used to translate from periodic
+ * [0,1) space as well as the inverse that is needed to
+ * translate back to that space.
+ */
 class Box
 {
@@ -22 +30 @@
   virtual ~Box();
 
+  /**
+   * Get the matrix describing the form of the parallelepiped
+   */
   const Matrix &getM() const;
+
+  /**
+   * Get the inverse of the matrix M (see above).
+   */
   const Matrix &getMinv() const;
+
+  /**
+   * Set the form of the parallelepiped.
+   */
   void setM(Matrix);
 
@@ -29 +48 @@
   Box &operator=(const Matrix&);
 
+  /**
+   * Translate a point from [0,1) to the boxed space.
+   */
   Vector translateIn(const Vector &point) const;
+
+  /**
+   * Translate a point from the boxed space to the [0,1) space.
+   */
   Vector translateOut(const Vector &point) const;
 
+  /**
+   * Wrap a point so that it will lie within the space defined by the box.
+   */
   Vector WrapPeriodically(const Vector &point) const;
+
+  /**
+   * Produce corresponding points in several adjacent boxes.
+   */
   VECTORSET(std::list) explode(const Vector &point) const;
 
+  /**
+   * Calculate the distance of two points in the periodic space
+   * defined by this box
+   */
   double periodicDistanceSquared(const Vector &point1,const Vector &point2) const;
+
+  /**
+   * Calculate the distance of two points in the periodic space
+   * defined by this box
+   */
   double periodicDistance(const Vector &point1,const Vector &point2) const;