Changeset 1a00bb for src/Jobs/Grid/SamplingGrid.hpp

Timestamp:

Feb 15, 2013, 9:51:48 AM (12 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:

e2404f

Parents:

98f8fe

git-author:

Frederik Heber <heber@…> (12/03/12 09:02:23)

git-committer:

Frederik Heber <heber@…> (02/15/13 09:51:48)

Message:

Rewrote parts of SampingGrid such that a window of non-zero entries is used.

• this makes the last part final O(N) as so far for the sampled_grid the whole domain has to be used instead of a tiny region around the specific fragment.
• for this we added extendWindow() and addOntoWindow() including some new member variables that hold the window size.
• added default cstor that correctly used SampingGridProperties default cstor. Otherwise we got the funny behavior that on some systems the very first job of q MPQCCommandJob (tests/JobMarket/2) is not re-instantiated.
• unit test extended to cover the new functionality but marked as expected to fail because it is not yet working correctly.

File:

• src/Jobs/Grid/SamplingGrid.hpp (modified) (4 diffs)

src/Jobs/Grid/SamplingGrid.hpp

@@ -75 +75 @@
   /** default cstor.
    */
-  SamplingGrid()
-  {}
+  SamplingGrid();
 
   virtual ~SamplingGrid();
@@ -128 +127 @@
   double integral(const SamplingGrid &weight) const;
 
+  /** Returns the volume of the domain for this sampled function.
+   *
+   * @return volume
+   */
+  const double getVolume() const;
+
+  /** Returns the total number of gridpoints of the discrete mesh covering the (window) volume.
+   *
+   * @return number of gridpoints sampled_values should have
+   */
+  const size_t getWindowGridPoints() const;
+
+  /** Returns the total number of gridpoints of the discrete mesh covering the volume.
+   *
+   * @return number of gridpoints sampled_values should have
+   */
+  const size_t getTotalGridPoints() const;
+
+  /** Returns the number of grid points per axis.
+   *
+   * @return number of grid points per unit length
+   */
+  const size_t getGridPointsPerAxis() const;
+
+  /** Returns the volume of the domain covered by the current window.
+   *
+   * @return volume of window
+   */
+  const double getWindowVolume() const;
+
+  /** Sets the size of the window.
+   *
+   * \note also resets the sampled points so far.
+   *
+   * \param _begin_window start of new window
+   * \param _end_window end of window
+   */
+  void setWindow(const double _begin_window[3], const double _end_window[3]);
+
 private:
-  /** Returns the volume of the domain for this sampled function.
-   *
-   * @return volume
-   */
-  double getVolume() const;
-
-  /** Returns the total number of gridpoints of the discrete mesh covering the (window) volume.
-   *
-   * @return number of gridpoints sampled_values should have
-   */
-  const size_t getTotalGridPoints() const;
-
-  /** Returns the number of grid points per axis.
-   *
-   * @return number of grid points per unit length
-   */
-  const size_t getGridPointsPerAxis() const;
-
+  /** Extends the window while keeping the values.
+   *
+   * \param _begin_window new start of window
+   * \param _end_window new end of window
+   */
+  void extendWindow(const double _begin_window[3], const double _end_window[3]);
+
+  /** Adds another window onto the one in this instance.
+   *
+   * \note We assume here that the given window fits on the this one.
+   *
+   * \param _begin_window start of other window
+   * \param _end_window end of other window
+   * \param _sampled_grid other set of sampled values
+   */
+  void addOntoWindow(
+      const double _begin_window[3],
+      const double _end_window[3],
+      const sampledvalues_t &_sampled_grid);
 
   /** Helper function that contains all the logic of how to superpose two
@@ -158 +197 @@
   void superposeOtherGrids(const SamplingGrid &other, const double prefactor);
 
+  /** Sets the size of the window.
+   *
+   * \note also resets the sampled points so far.
+   *
+   * \param _begin_window start of new window
+   * \param _size size of the window
+   */
+  void setWindowSize(const double _begin_window[3], const double _size);
+
+  /** Sets the size of the window.
+   *
+   * \note also resets the sampled points so far.
+   *
+   * \param _begin_window start of new window
+   * \param _end_window end of window
+   */
+  void setWindowSize(const double _begin_window[3], const double _end_window[3]);
+
 public:
-  //!> sample points
+  /// We do not store the whole grid if many entries are actually zero
+  /// but only a window wherein the sampled function is non-zero.
+
+  //!> sample points of the window
   sampledvalues_t sampled_grid;
+
+  //!> start of the window relative to SamplingGridProperties::begin and SamplingGridProperties::size
+  double begin_window[3];
+  //!> end of the window relative to SamplingGridProperties::begin and SamplingGridProperties::size
+  double end_window[3];
 
 private:
@@ -172 +237 @@
     ar & boost::serialization::base_object<SamplingGridProperties>(*this);
     ar & const_cast< sampledvalues_t &>(sampled_grid);
+    for(size_t i=0;i<3;++i) {
+      ar & begin_window[i];
+      ar & end_window[i];
+    }
   }
+
+  //!> static typedef to use in cstor when no initial values are given
+  static const double zeroOffset[3];
 };