Changeset ddc85b

Timestamp:

Aug 18, 2010, 1:30:16 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

900402

Parents:

a19d73e

git-author:

Tillmann Crueger <crueger@…> (08/18/10 13:19:14)

git-committer:

Tillmann Crueger <crueger@…> (08/18/10 13:30:16)

Message:

Added a method that allows calculation of the total temperature of a set of atoms at a given time step

Location:

src

Files:

• AtomSet.hpp (modified) (5 diffs)
• atom_trajectoryparticle.cpp (modified) (1 diff)
• atom_trajectoryparticle.hpp (modified) (1 diff)

src/AtomSet.hpp

@@ -11 +11 @@
 
 #include <functional>
+#include <numeric>
 #include <algorithm>
 #include <boost/foreach.hpp>
@@ -22 +23 @@
 
 #include "atom.hpp"
-#include <list>
 
 // this tests, whether we actually have a Vector
@@ -59 +59 @@
   template<class Function>
   void transformNodes(Function f);
+  double totalTemperatureAtStep(unsigned int i) const;
 
 private:
@@ -68 +69 @@
     }
     Function &f;
+  };
+
+  struct temperatureSum {
+    temperatureSum(unsigned int _step) : step(_step),value(0) {}
+    double operator+(atom *atom){
+      return value + atom->getKineticEnergy(step);
+    }
+    double operator=(double _value){
+      value = _value;
+      return value;
+    }
+    unsigned int step;
+    double value;
   };
 };
@@ -86 +100 @@
 }
 
+template<class Set>
+inline double AtomSetMixin<Set>::totalTemperatureAtStep(unsigned int step) const{
+  return accumulate(this->begin(),this->end(),temperatureSum(step)).value;
+}
+
 // allows simpler definition of AtomSets
 #define ATOMSET(container_type) AtomSetMixin<container_type<atom*> >

src/atom_trajectoryparticle.cpp

@@ -46 +46 @@
 };
 
+double TrajectoryParticle::getKineticEnergy(unsigned int step){
+  return getType()->mass * Trajectory.U.at(step).NormSquared();
+}
+
 /** Evaluates some constraint potential if atom moves from \a startstep at once to \endstep in trajectory.
  * \param startstep trajectory begins at

src/atom_trajectoryparticle.hpp

@@ -53 +53 @@
   void VelocityVerletUpdate(int MDSteps, config *configuration, ForceMatrix *Force, const size_t offset);
   void SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity ) const;
+  double getKineticEnergy(unsigned int step);
 
   // thermostats