Changeset 4fc828 for src/Analysis

Timestamp:

Oct 25, 2011, 3:28:27 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:

4b8630

Parents:

df8759

git-author:

Frederik Heber <heber@…> (02/16/11 12:56:48)

git-committer:

Frederik Heber <heber@…> (10/25/11 15:28:27)

Message:

DipoleAngularCorrelation working with multi-timestep PDBs with CONECT entries.

• new regression test Analysis/DipolarAngularCorrelation: testing rotated water dipole.

File:

• src/Analysis/analysis_correlation.cpp (modified) (9 diffs)

src/Analysis/analysis_correlation.cpp ¶

@@ -66 +66 @@
     // go through all bonds
     const BondList& ListOfBonds = (*atomiter)->getListOfBonds();
+    ASSERT(ListOfBonds.begin() != ListOfBonds.end(),
+        "getDipole() - no bonds in molecule!");
     for (BondList::const_iterator bonditer = ListOfBonds.begin();
         bonditer != ListOfBonds.end();
@@ -77 +79 @@
         BondDipoleVector.Normalize();
         BondDipoleVector *= DeltaEN;
+        LOG(3,"INFO: Dipole vector from bond " << **bonditer << " is " << BondDipoleVector);
         DipoleVector += BondDipoleVector;
         SumOfVectors++;
@@ -82 +85 @@
     }
   }
-  DipoleVector *= 1./(double)SumOfVectors;
+  LOG(3,"INFO: Sum over all bond dipole vectors is "
+      << DipoleVector << " with " << SumOfVectors << " in total.");
+  if (SumOfVectors != 0)
+    DipoleVector *= 1./(double)SumOfVectors;
   DoLog(1) && (Log() << Verbose(1) << "Resulting dipole vector is " << DipoleVector << std::endl);
 
@@ -111 +117 @@
   World::getInstance().setTime(0);
 
+  BOOST_FOREACH(atom *_atom, World::getInstance().getAllAtoms())
+    LOG(2, "INFO: Atom " << _atom->getId() << " "
+        << *dynamic_cast<AtomInfo *>(_atom) <<".");
+
   // get highest trajectory size
+  LOG(0,"STATUS: Retrieving maximum amount of time steps ...");
   size_t max_timesteps = 0;
+  size_t min_timesteps = -1;
   BOOST_FOREACH(molecule *_mol, molecules) {
     for(molecule::const_iterator iter = _mol->begin();
@@ -119 +131 @@
       if ((*iter)->getTrajectorySize() > max_timesteps)
         max_timesteps  = (*iter)->getTrajectorySize();
-    }
-  }
+      if (((*iter)->getTrajectorySize() <= max_timesteps) && (min_timesteps == (size_t)-1))
+        min_timesteps = (*iter)->getTrajectorySize();
+    }
+  }
+  LOG(1,"INFO: Minimum number of time steps found is " << min_timesteps);
+  LOG(1,"INFO: Maximum number of time steps found is " << max_timesteps);
+
   // get zero orientation for each molecule.
+  LOG(0,"STATUS: Calculating dipoles for first time step ...");
   std::vector<Vector> ZeroVector;
   ZeroVector.resize(molecules.size(), zeroVec);
@@ -128 +146 @@
     const Vector Dipole = getDipole(_mol->begin(), _mol->end());
     ZeroVector[i] = Dipole;
+    LOG(2,"INFO: Zero alignment for molecule " << _mol->getId() << " is " << ZeroVector[i]);
     ++i;
   }
+  LOG(1,"INFO: There is a total of " << i << " molecules.");
+
   // go through every time step
+  LOG(0,"STATUS: Calculating dipoles of following time steps ...");
   for (size_t step = 1; step < max_timesteps; ++step) {
     World::getInstance().setTime(step);
@@ -136 +158 @@
     BOOST_FOREACH(molecule *_mol, molecules) {
       const Vector Dipole = getDipole(_mol->begin(), _mol->end());
+      LOG(2,"INFO: Dipole vector at time step " << step << " for for molecule " << _mol->getId() << " is " << Dipole);
       const double angle = Dipole.Angle(ZeroVector[i]) * (180./M_PI);
-      DoLog(1) && (Log() << Verbose(1) << "Angle for molecule "
-          << _mol->getId() << " at time step " << step << " is " << angle << "." << endl);
+      LOG(1,"INFO: Resulting relative angle for molecule " << _mol->getId() << " is " << angle << ".");
       outmap->insert ( make_pair (angle, _mol ) );
       ++i;
@@ -147 +169 @@
   // set original time step again
   World::getInstance().setTime(oldtime);
+  LOG(0,"STATUS: Done.");
 
   // and return results
@@ -568 +591 @@
 void OutputDipoleAngularCorrelation_Header( ofstream * const file )
 {
-  *file << "\tMolecule1\tMolecule2";
+  *file << "\tMolecule";
 };