Changeset dde8ec for src

Timestamp:

Nov 12, 2012, 4:04:54 PM (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:

e06820

Parents:

1f66c7

git-author:

Frederik Heber <heber@…> (07/29/12 17:53:39)

git-committer:

Frederik Heber <heber@…> (11/12/12 16:04:54)

Message:

Histograms are now summed up, too.

• added Histogram cstor that just takes vector<double>.
• extracted Histogram::getMinMaxFromSamples().
• aded energy_eigenvalues key to MPQCDataEnergyVector_t.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (2 diffs)
• Fragmentation/Histogram/Histogram.cpp (modified) (3 diffs)
• Fragmentation/Histogram/Histogram.hpp (modified) (2 diffs)
• Jobs/MPQCDataMap.hpp (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -298 +298 @@
       boost::fusion::at_key<MPQCDataFused::energy_kinetic>(instance) = extractedData.energies.kinetic;
       boost::fusion::at_key<MPQCDataFused::energy_hcore>(instance) = extractedData.energies.hcore;
-  //    boost::fusion::at_key<MPQCDataFused::energy_eigenvalues>(instance) = extractedData.energies.eigenvalues;
+      boost::fusion::at_key<MPQCDataFused::energy_eigenvalues>(instance) = extractedData.energies.eigenvalues;
       MPQCData_Energy_fused.push_back(instance);
     }
@@ -343 +343 @@
             MatrixNrLookup)
         );
-    // TODO: Histogram still needs cstor taking just vector<double>
-
 
     // TODO: We need to put forces into specific class and implement operators

src/Fragmentation/Histogram/Histogram.cpp

@@ -98 +98 @@
 }
 
+Histogram::Histogram(const samples_t &samples) :
+  binwidth(0.5),
+  offset(0.)
+{
+  if (!samples.empty()) {
+    // set offset to first value
+    const_cast<BinLowerEnd &>(offset) = *samples.begin();
+    // set binwidth to statistical sensible value
+    MinMax_t MinMax = getMinMaxFromSamples(samples);
+    const_cast<double &>(binwidth) = (*(MinMax.second) - *(MinMax.first))/pow(samples.size(), 1./3.);
+    // and add all samples to these histogram bins
+    addSamples(samples);
+  }
+}
 
 Histogram::Histogram(const samples_t &samples, const BinLowerEnd _offset, const double _binwidth) :
@@ -106 +120 @@
 }
 
+Histogram::MinMax_t Histogram::getMinMaxFromSamples(const samples_t &samples) const
+{
+  std::pair<samples_t::const_iterator, samples_t::const_iterator> returnpair;
+  returnpair.first = min_element(samples.begin(), samples.end());
+  returnpair.second = max_element(samples.begin(), samples.end());
+  ASSERT((returnpair.second != samples.end()) || (returnpair.first != samples.end()),
+      "Histogram::Histogram() - cannot find min/max despite non-empty range.");
+  return returnpair;
+}
+
 void Histogram::addSamples(const samples_t &samples)
 {
@@ -111 +135 @@
   if (!samples.empty()) {
     // 1. get min and max and determine width
-    samples_t::const_iterator maxiter = max_element(samples.begin(), samples.end());
-    samples_t::const_iterator miniter = min_element(samples.begin(), samples.end());
-    ASSERT((maxiter != samples.end()) || (miniter != samples.end()),
-        "Histogram::Histogram() - cannot find min/max despite non-empty range.");
-//    LOG(1, "DEBUG: min is " << *miniter << " and max is " << *maxiter << ".");
+    MinMax_t MinMax = getMinMaxFromSamples(samples);
+//    LOG(1, "DEBUG: min is " << *(MinMax.first) << " and max is " << *(MinMax.second) << ".");
 
     // 2. create each bin
     {
       std::vector<Bin_t> vectorbins;
-      BinCreator_t BinCreator( getLowerEnd(*miniter), binwidth );
+      const BinLowerEnd HistogramStart = getLowerEnd(*(MinMax.first));
+      BinCreator_t BinCreator( HistogramStart, binwidth );
       // we need one extra bin for get...Bin()'s find to work properly
-      const int CountBins = ceil((*maxiter - getLowerEnd(*miniter))/binwidth)+1;
+      const int CountBins = ceil((*(MinMax.second) - HistogramStart)/binwidth)+1;
       vectorbins.resize(CountBins+1, Bin_t( make_pair(0., 0.) ) );
       std::generate( vectorbins.begin(), vectorbins.end(), BinCreator );

src/Fragmentation/Histogram/Histogram.hpp

@@ -49 +49 @@
   typedef std::map< BinLowerEnd, BinWeight > Bins_t;
 public:
+  /** Cpnstructor from a given set of sampled data.
+   *
+   * \param samples sampled data to construct histogram from
+   */
+  Histogram(const samples_t &samples);
+
+  /** Default constructor.
+   *
+   */
   Histogram() :
     binwidth(0.5),
@@ -165 +174 @@
    */
   std::string printBins() const;
+
+  //!> pair for min and max of given samples
+  typedef std::pair<samples_t::const_iterator, samples_t::const_iterator> MinMax_t;
+
+  /** Helper function that returns minimum and maximum in given \a samples
+   *
+   * @param samples sampled values
+   * @return pair of min and max value
+   */
+  MinMax_t getMinMaxFromSamples(const samples_t &samples) const;
 
 private:

src/Jobs/MPQCDataMap.hpp

@@ -51 +51 @@
     MPQCDataFused::energy_overlap,
     MPQCDataFused::energy_kinetic,
-    MPQCDataFused::energy_hcore /*,
-    MPQCDataFused::energy_eigenvalues */
+    MPQCDataFused::energy_hcore,
+    MPQCDataFused::energy_eigenvalues
 > MPQCDataEnergyVector_t;