Changeset 7ba268 for src/Actions

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

Location:

src/Actions

Files:

• AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) (3 diffs)
• AnalysisAction/DipoleAngularCorrelationAction.def (modified) (3 diffs)
• AnalysisAction/DipoleAngularCorrelationAction.hpp (modified) (1 diff)
• AnalysisAction/DipoleCorrelationAction.cpp (added)
• AnalysisAction/DipoleCorrelationAction.def (added)
• AnalysisAction/DipoleCorrelationAction.hpp (added)
• Makefile.am (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;
 }

src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def

@@ -2 +2 @@
  * DipoleAngularCorrelationAction.def
  *
- *  Created on: Aug 25, 2010
+ *  Created on: Feb 11, 2011
  *      Author: heber
  */
@@ -13 +13 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
-#define paramtypes (double)(double)(double)(boost::filesystem::path)(boost::filesystem::path)(bool)
-#define paramreferences (BinStart)(BinWidth)(BinEnd)(outputname)(binoutputname)(periodic)
-#define paramtokens ("bin-start")("bin-width")("bin-end")("output-file")("bin-output-file")("periodic")
-#define paramdescriptions ("start of the first bin")("width of the bins")("start of the last bin")("name of the output file")("name of the bin output file")("system is constraint to periodic boundary conditions")
-#define paramdefaults (NODEFAULT)("0.5")(NODEFAULT)(NODEFAULT)(NODEFAULT)("0")
+#define paramtypes (std::string)(double)(double)(double)(boost::filesystem::path)(boost::filesystem::path)(bool)(unsigned int)
+#define paramreferences (DipoleFormula)(BinStart)(BinWidth)(BinEnd)(outputname)(binoutputname)(periodic)(timestepzero)
+#define paramtokens ("dipole-angular-correlation")("bin-start")("bin-width")("bin-end")("output-file")("bin-output-file")("periodic")("time-step-zero")
+#define paramdescriptions ("formula of molecules to calculate dipole of")("start of the first bin")("width of the bins")("start of the last bin")("name of the output file")("name of the bin output file")("system is constraint to periodic boundary conditions")("initial time step to correlate following ones against")
+#define paramdefaults (NODEFAULT)(NODEFAULT)("0.5")(NODEFAULT)(NODEFAULT)(NODEFAULT)("0")("0")
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS
@@ -24 +24 @@
 #define MENUPOSITION 3
 #define ACTIONNAME DipoleAngularCorrelation
-#define TOKEN "dipole-correlation"
+#define TOKEN "dipole-angular-correlation"
 
 // finally the information stored in the ActionTrait specialization

src/Actions/AnalysisAction/DipoleAngularCorrelationAction.hpp

@@ -2 +2 @@
  * DipoleAngularCorrelationAction.hpp
  *
- *  Created on: May 9, 2010
+ *  Created on: Feb 11, 2011
  *      Author: heber
  */

src/Actions/Makefile.am

@@ -88 +88 @@
 ANALYSISACTIONSOURCE = \
   Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp \
+  Actions/AnalysisAction/DipoleCorrelationAction.cpp \
   Actions/AnalysisAction/MolecularVolumeAction.cpp \
   Actions/AnalysisAction/PairCorrelationAction.cpp \
@@ -95 +96 @@
 ANALYSISACTIONHEADER = \
   Actions/AnalysisAction/DipoleAngularCorrelationAction.hpp \
+  Actions/AnalysisAction/DipoleCorrelationAction.hpp \
   Actions/AnalysisAction/MolecularVolumeAction.hpp \
   Actions/AnalysisAction/PairCorrelationAction.hpp \
@@ -102 +104 @@
 ANALYSISACTIONDEFS = \
   Actions/AnalysisAction/DipoleAngularCorrelationAction.def \
+  Actions/AnalysisAction/DipoleCorrelationAction.def \
   Actions/AnalysisAction/MolecularVolumeAction.def \
   Actions/AnalysisAction/PairCorrelationAction.def \