Changeset 1cc661 for src/Analysis

Timestamp:

Oct 25, 2011, 3:33:14 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:

0a7fad

Parents:

be0c61

git-author:

Frederik Heber <heber@…> (05/11/11 07:37:35)

git-committer:

Frederik Heber <heber@…> (10/25/11 15:33:14)

Message:

Refactored part of DipoleAngularCorrelation into method getTrajectoryBounds().

Location:

src/Analysis

Files:

• analysis_correlation.cpp (modified) (3 diffs)
• analysis_correlation.hpp (modified) (2 diffs)

src/Analysis/analysis_correlation.cpp

@@ -95 +95 @@
 };
 
+/** Calculate minimum and maximum amount of trajectory steps by going through given atomic trajectories.
+ * \param vector of atoms whose trajectories to check for [min,max]
+ * \return range with [min, max]
+ */
+range<size_t> getMaximumTrajectoryBounds(std::vector<atom *> &atoms)
+{
+  // 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(atom *_atom, atoms) {
+    if (_atom->getTrajectorySize() > max_timesteps)
+      max_timesteps  = _atom->getTrajectorySize();
+    if ((_atom->getTrajectorySize() <= max_timesteps) && (min_timesteps == (size_t)-1))
+      min_timesteps = _atom->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);
+
+  return range<size_t>(min_timesteps, max_timesteps);
+}
+
+
 /** Calculates the dipole angular correlation for given molecule type.
  * Calculate the change of the dipole orientation angle over time.
@@ -120 +143 @@
         << *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();
-        iter != _mol->end();
-        ++iter) {
-      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.
@@ -150 +157 @@
   // go through every time step
   LOG(0,"STATUS: Calculating dipoles of following time steps ...");
-  for (size_t step = 1; step < max_timesteps; ++step) {
+  range<size_t> timesteps = getMaximumTrajectoryBounds(atoms);
+  for (size_t step = 1; step < timesteps.first; ++step) {
     World::getInstance().setTime(step);
     // recalculate molecules for this time step

src/Analysis/analysis_correlation.hpp

@@ -31 +31 @@
 #include "CodePatterns/Info.hpp"
 #include "CodePatterns/Log.hpp"
+#include "CodePatterns/Range.hpp"
 #include "CodePatterns/Verbose.hpp"
 #include "Helpers/helpers.hpp"
@@ -53 +54 @@
 
 /********************************************** declarations *******************************/
+
+range<size_t> getMaximumTrajectoryBounds(std::vector<atom *> &atoms);
 
 DipoleAngularCorrelationMap *DipoleAngularCorrelation(std::vector<atom *> &atoms);