Changeset 6625c3 for src/AtomSet.hpp

Timestamp:

Feb 24, 2011, 5:46:46 PM (14 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:

056e70

Parents:

54b42e

git-author:

Frederik Heber <heber@…> (02/24/11 11:18:59)

git-committer:

Frederik Heber <heber@…> (02/24/11 17:46:46)

Message:

Removed atom_trajectoryparticle*, replaced by AtomInfo class now having std::vector<> for trajectories.

AtomInfo:

• AtomInfo stores position, velocity, and force in vectors.
• getter and setter implemented for velocity and force.
• all functions from TrajectoryParticle put into AtomInfo.
• Direct access to velocity and force exchanged by getter/setter everywhere.
• FIX: molecule::LinearInterpolationBetweenConfiguration() extends trajectory to MaxSteps+1 (for endstep).

Other changes:

• gsl_rng_gaussian() exchanged by boost::random specific type.

File:

• src/AtomSet.hpp (modified) (7 diffs)

src/AtomSet.hpp

@@ -82 +82 @@
   template<class T>
   struct valueSum {
-    valueSum(T (atom::*_f)() const,T startValue) :
+    valueSum(T (AtomInfo::*_f)() const,T startValue) :
       f(_f),
       value(startValue)
     {}
-    T operator+(atom *atom){
+    T operator+(AtomInfo *atom){
       return value + (atom->*f)();
     }
@@ -93 +93 @@
       return value;
     }
-    T (atom::*f)() const;
+    T (AtomInfo::*f)() const;
     T value;
   };
@@ -99 +99 @@
   template<class T>
   struct stepValueSum {
-    stepValueSum(unsigned int _step, T (atom::*_f)(unsigned int) const,T startValue) :
+    stepValueSum(unsigned int _step, T (AtomInfo::*_f)(unsigned int) const,T startValue) :
       step(_step),
       f(_f),
       value(startValue)
     {}
-    T operator+(atom *atom){
+    T operator+(AtomInfo *atom){
       return value + (atom->*f)(step);
     }
@@ -112 +112 @@
     }
     unsigned int step;
-    T (atom::*f)(unsigned int) const;
+    T (AtomInfo::*f)(unsigned int) const;
     T value;
   };
@@ -119 +119 @@
 template<class Set>
 inline void AtomSetMixin<Set>::translate(const Vector &translater){
-  BOOST_FOREACH(atom *atom,*this){
+  BOOST_FOREACH(AtomInfo *atom,*this){
     *(atom) += translater;
   }
@@ -126 +126 @@
 template<class Set>
 inline void AtomSetMixin<Set>::addVelocityAtStep(const Vector velocity, unsigned int step){
-  BOOST_FOREACH(atom *atom,*this){
-    atom->Trajectory.U.at(step) += velocity;
+  BOOST_FOREACH(AtomInfo *atom,*this){
+    atom->getAtomicVelocity(step) += velocity;
   }
 }
@@ -141 +141 @@
 template<class Set>
 inline double AtomSetMixin<Set>::totalMass() const{
-  return accumulate(this->begin(),this->end(),valueSum<double>(&atom::getMass,0)).value;
+  return accumulate(this->begin(),this->end(),valueSum<double>(&AtomInfo::getMass,0)).value;
 }
 
 template<class Set>
 inline double AtomSetMixin<Set>::totalTemperatureAtStep(unsigned int step) const{
-  return accumulate(this->begin(),this->end(),stepValueSum<double>(step,&atom::getKineticEnergy,0)).value;
+  return accumulate(this->begin(),this->end(),stepValueSum<double>(step,&AtomInfo::getKineticEnergy,0)).value;
 }
 
 template<class Set>
 inline Vector AtomSetMixin<Set>::totalMomentumAtStep(unsigned int step) const{
-  return accumulate(this->begin(),this->end(),stepValueSum<Vector>(step,&atom::getMomentum,Vector())).value;
+  return accumulate(this->begin(),this->end(),stepValueSum<Vector>(step,&AtomInfo::getMomentum,Vector())).value;
 }