Changeset 184943 for src/Fragmentation/SetValues

Timestamp:

Nov 21, 2012, 10:03:24 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:

f3bc5f

Parents:

c74fdb

git-author:

Frederik Heber <heber@…> (08/08/12 13:36:24)

git-committer:

Frederik Heber <heber@…> (11/21/12 10:03:24)

Message:

Added Fragment to MPQCData fusion maps and is used in FragmentationAutomationAction.

• new helpers Fragment::getPositions() and ::getCharges().
• SumUpChargeDensity() now also sums up a full Fragment.
• the Fragment is used by createLongRangeJobs to extract required posittions and charges from.

Location:

src/Fragmentation/SetValues

Files:

• Fragment.cpp (modified) (3 diffs)
• Fragment.hpp (modified) (4 diffs)

src/Fragmentation/SetValues/Fragment.cpp

@@ -38 +38 @@
 #include "Fragment.hpp"
 
+#include <iostream>
+
 #include "CodePatterns/Assert.hpp"
 
@@ -43 +45 @@
 {}
 
-Fragment::Fragment(positions_t &_positions, charges_t &_charges)
+Fragment::Fragment(const positions_t &_positions, const charges_t &_charges)
 {
   ASSERT( _positions.size() == _charges.size(),
@@ -101 +103 @@
 }
 
+Fragment::positions_t Fragment::getPositions() const
+{
+  positions_t positions;
+  for (nuclei_t::const_iterator iter = nuclei.begin();
+      iter != nuclei.end(); ++iter)
+    positions.push_back(iter->first);
+  return positions;
+}
+
+Fragment::charges_t Fragment::getCharges() const
+{
+  charges_t charges;
+  for (nuclei_t::const_iterator iter = nuclei.begin();
+      iter != nuclei.end(); ++iter)
+    charges.push_back(iter->second);
+  return charges;
+}
+
+std::ostream & operator<<(std::ostream &ost, const Fragment &f)
+{
+  size_t NucleiCounter = 1;
+  for (Fragment::nuclei_t::const_iterator iter = f.nuclei.begin();
+      iter != f.nuclei.end(); ++iter)
+    ost << NucleiCounter++ << "\t" << iter->first << " with charge " << iter->second << std::endl;
+  return ost;
+}
+
 template<> Fragment ZeroInstance<Fragment>()
 {

src/Fragmentation/SetValues/Fragment.hpp

@@ -15 +15 @@
 #endif
 
+#include <iosfwd>
 #include <vector>
 
 class Fragment {
+  //!> grant ostream operator access
+  friend std::ostream & operator<<(std::ostream &ost, const Fragment &f);
 public:
   typedef std::vector< std::vector<double> > positions_t;
@@ -41 +44 @@
    * @param _charges given charges
    */
-  Fragment(std::vector< std::vector<double> > &_positions, std::vector< double > &_charges);
+  Fragment(const std::vector< std::vector<double> > &_positions, const std::vector< double > &_charges);
 
   /** Adding another fragment onto this one.
@@ -67 +70 @@
   Fragment& operator-=(const Fragment &other);
 
+  /** Getter for all stored positions.
+   *
+   * @return vector of positions
+   */
+  positions_t getPositions() const;
+
+  /** Getter for all stored charges.
+   *
+   * @return vector of charges
+   */
+  charges_t getCharges() const;
+
 private:
   /** Helper function that checks whether this nuclei is present.
@@ -87 +102 @@
 };
 
+std::ostream & operator<<(std::ostream &ost, const Fragment &f);
+
 template<typename T> T ZeroInstance();
 template<> Fragment ZeroInstance<Fragment>();