Changeset 7ba268 for src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp

Timestamp:

Nov 3, 2011, 9:52:29 AM (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:

bbff92

Parents:

13510b (diff), 5837dd (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'DipoleAngularCorrelation' into mergeMaster

Conflicts:

src/World.cpp

• tiny conflict in World.cpp

File:

• src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) (3 diffs)

src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp

@@ -9 +9 @@
  * DipoleAngularCorrelationAction.cpp
  *
- *  Created on: May 9, 2010
+ *  Created on: Feb 11, 2011
  *      Author: heber
  */
@@ -23 +23 @@
 #include "Tesselation/boundary.hpp"
 #include "linkedcell.hpp"
-#include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Descriptors/AtomOfMoleculeSelectionDescriptor.hpp"
+#include "Descriptors/MoleculeFormulaDescriptor.hpp"
 #include "Element/element.hpp"
-#include "molecule.hpp"
 #include "Element/periodentafel.hpp"
 #include "LinearAlgebra/Vector.hpp"
+#include "molecule.hpp"
 #include "World.hpp"
+#include "WorldTime.hpp"
 
 #include <iostream>
+#include <map>
 #include <string>
 
@@ -45 +48 @@
 Action::state_ptr AnalysisDipoleAngularCorrelationAction::performCall() {
   //int ranges[3] = {1, 1, 1};
-  ofstream output;
-  ofstream binoutput;
   string type;
-  BinPairMap *binmap = NULL;
 
   // obtain information
   getParametersfromValueStorage();
+  ASSERT(!params.periodic, "AnalysisDipoleAngularCorrelationAction() - periodic case not implemented.");
 
-  // execute action
-  output.open(params.outputname.string().c_str());
-  binoutput.open(params.binoutputname.string().c_str());
-  DipoleAngularCorrelationMap *correlationmap = NULL;
-  std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
-  DoLog(0) && (Log() << Verbose(0) << "There are " << molecules.size() << " selected molecules." << std::endl);
-  ASSERT(!params.periodic, "AnalysisDipoleAngularCorrelationAction() - periodic case not implemented.");
-  correlationmap = DipoleAngularCorrelation(molecules);
-  OutputCorrelationMap<DipoleAngularCorrelationMap>(&output, correlationmap, OutputDipoleAngularCorrelation_Header, OutputDipoleAngularCorrelation_Value);
-  binmap = BinData( correlationmap, params.BinWidth, params.BinStart, params.BinEnd );
-  OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
-  delete(binmap);
-  delete(correlationmap);
-  output.close();
-  binoutput.close();
+  // get selected atoms
+  std::vector<atom*> old_atom_selection = World::getInstance().getSelectedAtoms();
+  std::vector<molecule*> old_molecule_selection = World::getInstance().getSelectedMolecules();
+
+  // get current time step
+  const unsigned int oldtime = WorldTime::getTime();
+
+  // select atoms and obtain zero dipole orientation
+  Formula DipoleFormula(params.DipoleFormula);
+  World::getInstance().setTime(params.timestepzero);
+  World::getInstance().clearMoleculeSelection(); // TODO: This should be done in setTime or where molecules are re-done
+  World::getInstance().selectAllMolecules(MoleculeByFormula(DipoleFormula));
+  std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
+  std::map<atomId_t, Vector> ZeroVector = CalculateZeroAngularDipole(molecules);
+
+  // go through each step of common trajectory of all atoms in set
+  World::getInstance().clearAtomSelection();
+  World::getInstance().selectAllAtoms(AtomsByMoleculeSelection());
+  std::vector<atom *> atoms = World::getInstance().getSelectedAtoms();
+  ASSERT(!atoms.empty(),
+      "AnalysisDipoleAngularCorrelationAction::performCall() - "
+      +toString(DipoleFormula)+" selects no atoms.");
+  range<size_t> timesteps = getMaximumTrajectoryBounds(atoms);
+  ASSERT(params.timestepzero < timesteps.first,
+    "AnalysisDipoleAngularCorrelationAction::performCall() - time step zero "
+    +toString(params.timestepzero)+" is beyond trajectory range ("
+    +toString(timesteps.first)+") of some atoms.");
+  for (size_t step = params.timestepzero; step < timesteps.first; ++step) {
+    // calculate dipoles relative to zero orientation
+    DipoleAngularCorrelationMap *correlationmap = NULL;
+    correlationmap = DipoleAngularCorrelation(DipoleFormula, step, ZeroVector, DontResetTime);
+
+    // prepare step string in filename
+    std::stringstream stepstream;
+    stepstream << std::setw(4) << std::setfill('0') << step;
+    const std::string stepname(stepstream.str());
+
+    // output correlation map
+    ofstream output;
+    std::string filename = params.outputname.string()+"."+stepname+".dat";
+    output.open(filename.c_str());
+    OutputCorrelationMap<DipoleAngularCorrelationMap>(&output, correlationmap, OutputDipoleAngularCorrelation_Header, OutputDipoleAngularCorrelation_Value);
+    output.close();
+
+    // bin map
+    BinPairMap *binmap = BinData( correlationmap, params.BinWidth, params.BinStart, params.BinEnd );
+
+    // free correlation map
+    delete(correlationmap);
+
+    // output binned map
+    ofstream binoutput;
+    std::string binfilename = params.binoutputname.string()+"."+stepname+".dat";
+    binoutput.open(binfilename.c_str());
+    OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
+    binoutput.close();
+
+    // free binned map
+    delete(binmap);
+  }
+
+  // reset to old time step
+  World::getInstance().setTime(oldtime);
+
+  // reset to old selections
+  World::getInstance().clearAtomSelection();
+  BOOST_FOREACH(atom *_atom, old_atom_selection) {
+    World::getInstance().selectAtom(_atom);
+  }
+  World::getInstance().clearMoleculeSelection();
+  BOOST_FOREACH(molecule *_mol, old_molecule_selection) {
+    World::getInstance().selectMolecule(_mol);
+  }
+
+  // exit
   return Action::success;
 }