Changeset 4b8630

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.

Files:

• src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) (1 diff)
• src/Analysis/analysis_correlation.cpp (modified) (6 diffs)
• src/Analysis/analysis_correlation.hpp (modified) (2 diffs)
• src/World.cpp (modified) (3 diffs)
• tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.xyz (added)
• tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.xyz (added)
• tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) (1 diff)

src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp

@@ -56 +56 @@
   binoutput.open(params.binoutputname.string().c_str());
   DipoleAngularCorrelationMap *correlationmap = NULL;
-  std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
-  LOG(0, "STATUS: There are " << molecules.size() << " selected molecules.");
+  std::vector<atom*> atoms = World::getInstance().getSelectedAtoms();
+  LOG(0, "STATUS: There are " << atoms.size() << " selected atoms.");
   ASSERT(!params.periodic, "AnalysisDipoleAngularCorrelationAction() - periodic case not implemented.");
-  correlationmap = DipoleAngularCorrelation(molecules);
+  correlationmap = DipoleAngularCorrelation(atoms);
   OutputCorrelationMap<DipoleAngularCorrelationMap>(&output, correlationmap, OutputDipoleAngularCorrelation_Header, OutputDipoleAngularCorrelation_Value);
   binmap = BinData( correlationmap, params.BinWidth, params.BinStart, params.BinEnd );

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();
 };
 

src/Analysis/analysis_correlation.hpp

@@ -46 +46 @@
 
 typedef multimap<double, pair<atom *, atom *> > PairCorrelationMap;
-typedef multimap<double, molecule * > DipoleAngularCorrelationMap;
+typedef multimap<double, atom * > DipoleAngularCorrelationMap;
 typedef multimap<double, pair<molecule *, molecule *> > DipoleCorrelationMap;
 typedef multimap<double, pair<atom *, const Vector *> > CorrelationToPointMap;
@@ -54 +54 @@
 /********************************************** declarations *******************************/
 
-DipoleAngularCorrelationMap *DipoleAngularCorrelation(std::vector<molecule *> &molecules);
+DipoleAngularCorrelationMap *DipoleAngularCorrelation(std::vector<atom *> &atoms);
 DipoleCorrelationMap *DipoleCorrelation(std::vector<molecule *> &molecules);
 PairCorrelationMap *PairCorrelation(std::vector<molecule *> &molecules, const std::vector<const element *> &elements);

src/World.cpp

@@ -25 +25 @@
 
 #include "Actions/ActionTraits.hpp"
-//#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
 #include "Actions/ManipulateAtomsProcess.hpp"
 #include "atom.hpp"
@@ -37 +36 @@
 #include "Descriptors/MoleculeDescriptor_impl.hpp"
 #include "Descriptors/SelectiveIterator_impl.hpp"
+#include "Graph/DepthFirstSearchAnalysis.hpp"
 #include "Helpers/defs.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
@@ -137 +137 @@
     // set new time
     WorldTime::setTime(_step);
-    // re-instantiate bond structure
-    //FragmentationSubgraphDissection();
+    // TODO: removed when BondGraph creates the adjacency
+    // 1. remove all of World's molecules
+    for (MoleculeIterator iter = getMoleculeIter();
+        getMoleculeIter() != moleculeEnd();
+        iter = getMoleculeIter()) {
+      getMolecules()->erase(*iter);
+      destroyMolecule(*iter);
+    }
+    // 2. (re-)create bondgraph
+    AtomComposite Set = getAllAtoms();
+    BG->CreateAdjacency(Set);
+
+    // 3. scan for connected subgraphs => molecules
+    DepthFirstSearchAnalysis DFS;
+    DFS();
+    DFS.UpdateMoleculeStructure();
   }
 }

tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at

@@ -4 +4 @@
 AT_KEYWORDS([analysis dipole correlation pdb dipole-angular-correlation])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.pdb .], 0)
-AT_CHECK([../../molecuilder -v 4 -i watermulti_X.pdb -o pdb --select-molecules-by-formula H2O --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values_X.dat --bin-output-file water_histogram_X.dat], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -v 4 -i watermulti_X.pdb -o pdb --select-molecules-by-formula H2O --select-molecules-atoms --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values_X.dat --bin-output-file water_histogram_X.dat], 0, [stdout], [stderr])
 AT_CHECK([file=water_histogram_X.dat; diff $file ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/post/$file], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.pdb .], 0)
-AT_CHECK([../../molecuilder -v 4 -i watermulti_Y.pdb -o pdb --select-molecules-by-formula H2O --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values_Y.dat --bin-output-file water_histogram_Y.dat], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -v 4 -i watermulti_Y.pdb -o pdb --select-molecules-by-formula H2O --select-molecules-atoms --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values_Y.dat --bin-output-file water_histogram_Y.dat], 0, [stdout], [stderr])
 AT_CHECK([file=water_histogram_Y.dat; diff $file ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
 
+AT_SETUP([Analysis - dipole angular correlation on XYZs])
+AT_KEYWORDS([analysis dipole correlation xyz dipole-angular-correlation])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.xyz .], 0)
+AT_CHECK([../../molecuilder -v 4 -i watermulti_X.xyz -o xyz -I --select-molecules-by-formula H2O --select-molecules-atoms --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values_X.dat --bin-output-file water_histogram_X.dat], 0, [stdout], [stderr])
+AT_CHECK([file=water_histogram_X.dat; diff $file ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/post/$file], 0, [ignore], [ignore])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.xyz .], 0)
+AT_CHECK([../../molecuilder -v 4 -i watermulti_Y.xyz -o xyz -I --select-molecules-by-formula H2O --select-molecules-atoms --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values_Y.dat --bin-output-file water_histogram_Y.dat], 0, [stdout], [stderr])
+AT_CHECK([file=water_histogram_Y.dat; diff $file ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/post/$file], 0, [ignore], [ignore])
+AT_CLEANUP
+