Changeset 579a81 for src/Thermostats/Berendsen.cpp

Timestamp:

Aug 20, 2010, 1:54:23 PM (14 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:

0b882a

Parents:

194649

Message:

Added a basic self-descriptive structure for Thermostats

File:

• src/Thermostats/Berendsen.cpp (modified) (3 diffs)

src/Thermostats/Berendsen.cpp

@@ -12 +12 @@
 #include "Helpers/Log.hpp"
 #include "ThermoStatContainer.hpp"
+#include "World.hpp"
 
-Berendsen::Berendsen(double _ActualTemp) :
-  ActualTemp(_ActualTemp)
+Berendsen::Berendsen(double _TempFrequency) :
+  TempFrequency(_TempFrequency)
 {}
 
@@ -20 +21 @@
 {}
 
-double Berendsen::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::list) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+ThermostatTraits<class Berendsen>::ThermostatTraits() :
+  name("Berendsen")
+{}
+
+
+double Berendsen::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
-double Berendsen::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::vector) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+double Berendsen::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
-double Berendsen::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::set) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+double Berendsen::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
 template <class ForwardIterator>
-double Berendsen::doScaleAtoms(config &configuration,unsigned int step,ForwardIterator begin, ForwardIterator end){
+double Berendsen::doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin, ForwardIterator end){
   DoLog(2) && (Log() << Verbose(2) <<  "Applying Berendsen-VanGunsteren thermostat..." << endl);
   double ekin;
-  double ScaleTempFactor = configuration.Thermostats->TargetTemp/ActualTemp;
+  double ScaleTempFactor = getContainer().TargetTemp/ActualTemp;
   for(ForwardIterator iter=begin;iter!=end;++iter){
     Vector &U = (*iter)->Trajectory.U.at(step);
     if ((*iter)->FixedIon == 0) { // even FixedIon moves, only not by other's forces
-      U *= sqrt(1+(configuration.Deltat/configuration.Thermostats->TempFrequency)*(ScaleTempFactor-1));
+      U *= sqrt(1+(World::getInstance().getConfig()->Deltat/TempFrequency)*(ScaleTempFactor-1));
       ekin += 0.5*(*iter)->getType()->mass * U.NormSquared();
     }
@@ -46 +52 @@
   return ekin;
 }
+
+std::string Berendsen::name(){
+  return ThermostatTraits<Berendsen>().name;
+}
+
+std::string Berendsen::writeParam(){
+  stringstream sstr;
+  sstr << TempFrequency;
+  return sstr.str();
+}