Changeset 4b8630 for src/Analysis/analysis_correlation.cpp

Timestamp:

Oct 25, 2011, 3:31:54 PM (13 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:

be0c61

Parents:

4fc828

git-author:

Frederik Heber <heber@…> (02/19/11 00:09:43)

git-committer:

Frederik Heber <heber@…> (10/25/11 15:31:54)

Message:

World::setTime() now updates bond structure of system and related changes to DipoleAngularCorrelation.

• extended regression test Analysis/DipoleAngularCorrelation with xyz example whose bond structure is updated per time step.
• FIX: DepthFirstSearchAnalysis::operator() did not reset bonds to unused.
• FIX: DipoleAngularCorrelationAction has to work on atoms not molecules as the latter are subject to changes due to changing bond structure.
• FIX: DipoleAngularCorrelation() re-calculates current set of molecules from the select atoms and stores first atom in values file, not molecule name.

File:

• src/Analysis/analysis_correlation.cpp (modified) (6 diffs)

src/Analysis/analysis_correlation.cpp

@@ -31 +31 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "Descriptors/MoleculeOfAtomSelectionDescriptor.hpp"
 #include "Formula.hpp"
 #include "LinearAlgebra/Vector.hpp"
@@ -98 +99 @@
  * Note given element order is unimportant (i.e. g(Si, O) === g(O, Si))
  * Angles are given in degrees.
- * \param *molecules vector of molecules
+ * \param &atoms list of atoms of the molecules taking part (Note: molecules may
+ * change over time as bond structure is recalculated, hence we need the atoms)
  * \return Map of doubles with values the pair of the two atoms.
  */
-DipoleAngularCorrelationMap *DipoleAngularCorrelation(std::vector<molecule *> &molecules)
+DipoleAngularCorrelationMap *DipoleAngularCorrelation(std::vector<atom *> &atoms)
 {
   Info FunctionInfo(__func__);
   DipoleAngularCorrelationMap *outmap = new DipoleAngularCorrelationMap;
-//  double distance = 0.;
-//  Box &domain = World::getInstance().getDomain();
-//
-  if (molecules.empty()) {
-    DoeLog(1) && (eLog()<< Verbose(1) <<"No molecule given." << endl);
-    return outmap;
-  }
+  std::set<molecule *> molecules;
 
   // store original time step
   const unsigned int oldtime = WorldTime::getTime();
   World::getInstance().setTime(0);
+  // calculate molecules for this time step
+  BOOST_FOREACH(atom *_atom, atoms)
+    molecules.insert(_atom->getMolecule());
 
   BOOST_FOREACH(atom *_atom, World::getInstance().getAllAtoms())
@@ -155 +154 @@
   for (size_t step = 1; step < max_timesteps; ++step) {
     World::getInstance().setTime(step);
+    // recalculate molecules for this time step
+    molecules.clear();
+    BOOST_FOREACH(atom *_atom, atoms)
+      molecules.insert(_atom->getMolecule());
     size_t i=0;
     BOOST_FOREACH(molecule *_mol, molecules) {
@@ -161 +164 @@
       const double angle = Dipole.Angle(ZeroVector[i]) * (180./M_PI);
       LOG(1,"INFO: Resulting relative angle for molecule " << _mol->getId() << " is " << angle << ".");
-      outmap->insert ( make_pair (angle, _mol ) );
+      outmap->insert ( make_pair (angle, *_mol->begin() ) );
       ++i;
     }
@@ -591 +594 @@
 void OutputDipoleAngularCorrelation_Header( ofstream * const file )
 {
-  *file << "\tMolecule";
+  *file << "\tFirstAtomOfMolecule";
 };
 
@@ -601 +604 @@
 void OutputDipoleAngularCorrelation_Value( ofstream * const file, DipoleAngularCorrelationMap::const_iterator &runner )
 {
-  *file << runner->second->getId();
+  *file << runner->second->getName();
 };