Changeset 579a81 for src/Thermostats

Timestamp:

Aug 20, 2010, 1:54:23 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:

0b882a

Parents:

194649

Message:

Added a basic self-descriptive structure for Thermostats

Location:

src/Thermostats

Files:

• Berendsen.cpp (modified) (3 diffs)
• Berendsen.hpp (modified) (1 diff)
• GaussianThermostat.cpp (modified) (4 diffs)
• GaussianThermostat.hpp (modified) (1 diff)
• Langevin.cpp (modified) (2 diffs)
• Langevin.hpp (modified) (1 diff)
• NoThermostat.cpp (modified) (1 diff)
• NoThermostat.hpp (modified) (1 diff)
• NoseHoover.cpp (modified) (3 diffs)
• NoseHoover.hpp (modified) (2 diffs)
• Thermostat.cpp (modified) (1 diff)
• Thermostat.hpp (modified) (1 diff)
• Woodcock.cpp (modified) (3 diffs)
• Woodcock.hpp (modified) (1 diff)

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();
+}

src/Thermostats/Berendsen.hpp

@@ -17 +17 @@
   virtual ~Berendsen();
 
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::list));
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::vector));
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::set));
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms);
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms);
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms);
 
-  virtual std::string name() { return "Berendsen";}
+  virtual std::string name();
+
+  virtual std::string writeParam();
+
 private:
   template <class ForwardIterator>
-  double doScaleAtoms(config &configuration,unsigned int step,ForwardIterator begin, ForwardIterator end);
+  double doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin, ForwardIterator end);
 
-  double ActualTemp;
+  double TempFrequency;
+};
+
+template <>
+struct ThermostatTraits<class Berendsen>{
+  ThermostatTraits();
+  const char* name;
 };
 

src/Thermostats/GaussianThermostat.cpp

@@ -13 +13 @@
 #include "element.hpp"
 #include "config.hpp"
+#include "World.hpp"
+
 #include <set>
 
-GaussianThermostat::GaussianThermostat() : E(0),G(0)
+GaussianThermostat::GaussianThermostat(int _ScaleTempStep) :
+  E(0),G(0),
+  ScaleTempStep(_ScaleTempStep)
 {}
 
@@ -21 +25 @@
 {}
 
-double GaussianThermostat::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::list) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+ThermostatTraits<GaussianThermostat>::ThermostatTraits() :
+  name("Gaussian")
+{}
+
+double GaussianThermostat::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
-double GaussianThermostat::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::vector) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+double GaussianThermostat::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
-double GaussianThermostat::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::set) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+double GaussianThermostat::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
 template <class ForwardIterator>
-double GaussianThermostat::doScaleAtoms(config &configuration,unsigned int step,ForwardIterator begin, ForwardIterator end){
+double GaussianThermostat::doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin, ForwardIterator end){
   DoLog(2) && (Log() << Verbose(2) <<  "Applying Gaussian thermostat..." << endl);
   init(step,begin,end);
@@ -43 +51 @@
     Vector &U = (*iter)->Trajectory.U.at(step);
     if ((*iter)->FixedIon == 0) {// even FixedIon moves, only not by other's forces
-      U += configuration.Deltat * G_over_E * U;
+      U += World::getInstance().getConfig()->Deltat * G_over_E * U;
       ekin += (*iter)->getType()->mass * U.NormSquared();
     }
@@ -71 +79 @@
   return G;
 }
+
+std::string GaussianThermostat::name(){
+  return ThermostatTraits<GaussianThermostat>().name;
+}
+
+std::string GaussianThermostat::writeParams(){
+  std::stringstream sstr;
+  sstr << ScaleTempStep;
+  return sstr.str();
+}

src/Thermostats/GaussianThermostat.hpp

@@ -16 +16 @@
 {
 public:
-  GaussianThermostat();
+  GaussianThermostat(int ScaleTempStep);
   virtual ~GaussianThermostat();
 
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::list));
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::vector));
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::set));
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms);
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms);
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms);
 
-  virtual std::string name() { return "Gaussian";}
   double getE() const;
   double getG() const;
+
+  virtual std::string name();
+  virtual std::string writeParams();
 private:
   template <class ForwardIterator>
   void init(unsigned int step,ForwardIterator begin, ForwardIterator end);
   template <class ForwardIterator>
-  double doScaleAtoms(config &configuration,unsigned int step,ForwardIterator begin, ForwardIterator end);
+  double doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin, ForwardIterator end);
   double E,G;
+  int ScaleTempStep;
+};
+
+template <>
+struct ThermostatTraits<GaussianThermostat>{
+  ThermostatTraits();
+  const char* name;
 };
 

src/Thermostats/Langevin.cpp

@@ -25 +25 @@
 }
 
-double Langevin::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::list) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+ThermostatTraits<class Langevin>::ThermostatTraits() :
+  name("Langevin")
+{}
+
+double Langevin::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
-double Langevin::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::vector) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+double Langevin::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
-double Langevin::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::set) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+double Langevin::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
 template <class ForwardIterator>
-double Langevin::doScaleAtoms(config &configuration,unsigned int step,ForwardIterator begin, ForwardIterator end){
+double Langevin::doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin, ForwardIterator end){
   DoLog(2) && (Log() << Verbose(2) <<  "Applying Langevin thermostat..." << endl);
   double ekin=0;
   for(ForwardIterator iter=begin;iter!=end;++iter){
-    double sigma  = sqrt(configuration.Thermostats->TargetTemp/(*iter)->getType()->mass); // sigma = (k_b T)/m (Hartree/atomicmass = atomiclength/atomictime)
+    double sigma  = sqrt(getContainer().TargetTemp/(*iter)->getType()->mass); // sigma = (k_b T)/m (Hartree/atomicmass = atomiclength/atomictime)
     Vector &U = (*iter)->Trajectory.U.at(step);
     if ((*iter)->FixedIon == 0) { // even FixedIon moves, only not by other's forces
       // throw a dice to determine whether it gets hit by a heat bath particle
-      if (((((rand()/(double)RAND_MAX))*configuration.Thermostats->TempFrequency) < 1.)) {
+      if (((((rand()/(double)RAND_MAX))*TempFrequency) < 1.)) {
         DoLog(3) && (Log() << Verbose(3) << "Particle " << (**iter) << " was hit (sigma " << sigma << "): " << sqrt(U[0]*U[0]+U[1]*U[1]+U[2]*U[2]) << " -> ");
         // pick three random numbers from a Boltzmann distribution around the desired temperature T for each momenta axis
@@ -59 +63 @@
   return ekin;
 }
+
+std::string Langevin::name(){
+  return ThermostatTraits<Langevin>().name;
+}
+
+std::string Langevin::writeParams(){
+  stringstream sstr;
+  sstr << TempFrequency << "\t" << alpha;
+  return sstr.str();
+}

src/Thermostats/Langevin.hpp

@@ -17 +17 @@
   virtual ~Langevin();
 
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::list))=0;
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::vector))=0;
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::set))=0;
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms);
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms);
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms);
 
-  virtual std::string name(){return "Langevin";}
+  virtual std::string name();
+  virtual std::string writeParams();
 
 private:
   template <class ForwardIterator>
-  double doScaleAtoms(config &configuration,unsigned int step,ForwardIterator begin, ForwardIterator end);
+  double doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin, ForwardIterator end);
 
+
+  double TempFrequency;
+  double alpha;
   gsl_rng * r;
   const gsl_rng_type * T;
 };
 
+template <>
+struct ThermostatTraits<class Langevin>{
+  ThermostatTraits();
+  const char* name;
+};
+
 #endif /* LANGEVIN_HPP_ */

src/Thermostats/NoThermostat.cpp

@@ -14 +14 @@
 {}
 
-double NoThermostat::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::list) atoms){
+ThermostatTraits<class NoThermostat>::ThermostatTraits() :
+  name("None")
+{}
+
+double NoThermostat::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms){
   return 0;
 }
 
-double NoThermostat::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::vector) atoms){
+double NoThermostat::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms){
   return 0;
 }
 
-double NoThermostat::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::set) atoms){
+double NoThermostat::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms){
   return 0;
 }
+
+std::string NoThermostat::name(){
+  return ThermostatTraits<NoThermostat>().name;
+}
+
+std::string NoThermostat::writeParams(){
+  return "";
+}

src/Thermostats/NoThermostat.hpp

@@ -17 +17 @@
   virtual ~NoThermostat();
 
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::list));
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::vector));
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::set));
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms);
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms);
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms);
 
-  virtual std::string name() { return "None";}
+  virtual std::string name();
+  virtual std::string writeParams();
+};
+
+template <>
+struct ThermostatTraits<class NoThermostat>{
+  ThermostatTraits();
+  const char* name;
 };
 

src/Thermostats/NoseHoover.cpp

@@ -13 +13 @@
 #include "Helpers/Log.hpp"
 #include "ThermoStatContainer.hpp"
+#include "World.hpp"
 
-NoseHoover::NoseHoover()
+NoseHoover::NoseHoover(double _HooverMass) :
+  HooverMass(_HooverMass)
 {}
 
@@ -20 +22 @@
 {}
 
+ThermostatTraits<class NoseHoover>::ThermostatTraits() :
+  name("NoseHoover")
+{}
 
-double NoseHoover::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::list) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+
+double NoseHoover::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
-double NoseHoover::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::vector) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+double NoseHoover::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
-double NoseHoover::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::set) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+double NoseHoover::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
 template <class ForwardIterator>
-double NoseHoover::doScaleAtoms(config &configuration,unsigned int step,ForwardIterator begin, ForwardIterator end){
+double NoseHoover::doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin, ForwardIterator end){
   DoLog(2) && (Log() << Verbose(2) <<  "Applying Nose-Hoover thermostat..." << endl);
   init(step,begin,end);
-  delta_alpha = (delta_alpha - (3.*count+1.) * configuration.Thermostats->TargetTemp)/(configuration.Thermostats->HooverMass*Units2Electronmass);
-  configuration.Thermostats->alpha += delta_alpha*configuration.Deltat;
-  DoLog(3) && (Log() << Verbose(3) << "alpha = " << delta_alpha << " * " << configuration.Deltat << " = " << configuration.Thermostats->alpha << "." << endl);
+  delta_alpha = (delta_alpha - (3.*count+1.) * getContainer().TargetTemp)/(HooverMass*Units2Electronmass);
+  getContainer().alpha += delta_alpha*World::getInstance().getConfig()->Deltat;
+  DoLog(3) && (Log() << Verbose(3) << "alpha = " << delta_alpha << " * " << World::getInstance().getConfig()->Deltat << " = " << getContainer().alpha << "." << endl);
   double ekin =0;
   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 += configuration.Deltat/(*iter)->getType()->mass * (configuration.Thermostats->alpha * (U * (*iter)->getType()->mass));
+      U += World::getInstance().getConfig()->Deltat/(*iter)->getType()->mass * (getContainer().alpha * (U * (*iter)->getType()->mass));
       ekin += (0.5*(*iter)->getType()->mass) * U.NormSquared();
     }
@@ -63 +69 @@
   }
 }
+
+std::string NoseHoover::name(){
+  return ThermostatTraits<NoseHoover>().name;
+}
+
+std::string NoseHoover::writeParams(){
+  std::stringstream sstr;
+  sstr << HooverMass;
+  return sstr.str();
+}

src/Thermostats/NoseHoover.hpp

@@ -14 +14 @@
 {
 public:
-  NoseHoover();
+  NoseHoover(double _HooverMass);
   virtual ~NoseHoover();
 
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::list));
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::vector));
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::set));
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms);
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms);
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms);
 
-  virtual std::string name() { return "Nose-Hoover";}
+  virtual std::string name();
+  virtual std::string writeParams();
 
 private:
@@ -27 +28 @@
   void init(unsigned int step,ForwardIterator begin, ForwardIterator end);
   template <class ForwardIterator>
-  double doScaleAtoms(config &configuration,unsigned int step,ForwardIterator begin, ForwardIterator end);
+  double doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin, ForwardIterator end);
 
+  double HooverMass;
   double delta_alpha;
   int count;
 };
 
+template <>
+struct ThermostatTraits<class NoseHoover>{
+  ThermostatTraits();
+  const char* name;
+};
+
+
 #endif /* NOSEHOOVER_HPP_ */

src/Thermostats/Thermostat.cpp

@@ -8 +8 @@
 #include "Thermostat.hpp"
 
-Thermostat::Thermostat()
+#include "Helpers/Assert.hpp"
+
+Thermostat::Thermostat() :
+  container(0)
 {}
 
 Thermostat::~Thermostat()
 {}
+
+ThermostatTraits<Thermostat>::ThermostatTraits() :
+  name("Base")
+{}
+
+void Thermostat::addToContainer(ThermoStatContainer &_container){
+  container = &_container;
+}
+
+ThermoStatContainer &Thermostat::getContainer(){
+  ASSERT(container,"No container used for this Thermostat");
+  return *container;
+}

src/Thermostats/Thermostat.hpp

@@ -17 +17 @@
 #include "AtomSet.hpp"
 
+class ThermoStatContainer;
+
 class Thermostat
 {
 public:
   Thermostat();
-  virtual  ~Thermostat();
+  virtual ~Thermostat();
 
   // cannot template this, because we need virtual functions
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::list))=0;
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::vector))=0;
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::set))=0;
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms)=0;
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms)=0;
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms)=0;
 
   virtual std::string name()=0;
+
+  virtual std::string writeParams()=0;
+protected:
+  void addToContainer(ThermoStatContainer &);
+  ThermoStatContainer &getContainer();
+private:
+  ThermoStatContainer* container;
+};
+
+template <class Thermostat>
+struct ThermostatTraits;
+
+template <>
+struct ThermostatTraits<Thermostat>{
+  ThermostatTraits();
+  const char* name;
 };
 

src/Thermostats/Woodcock.cpp

@@ -14 +14 @@
 #include "ThermoStatContainer.hpp"
 
-Woodcock::Woodcock(int _MDSteps, double _ActualTemp) :
-  MDSteps(_MDSteps),
-  ActualTemp(_ActualTemp)
+#include <sstream>
+
+Woodcock::Woodcock(int _ScaleTempStep) :
+  ScaleTempStep(_ScaleTempStep)
 {}
 
@@ -22 +23 @@
 {}
 
-double Woodcock::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::list) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+ThermostatTraits<class Woodcock>::ThermostatTraits() :
+  name("Woodcock")
+{}
+
+double Woodcock::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
-double Woodcock::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::vector) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+double Woodcock::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
-double Woodcock::scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::set) atoms){
-  return doScaleAtoms(configuration,step,atoms.begin(),atoms.end());
+double Woodcock::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms){
+  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
 }
 
 template <class ForwardIterator>
-double Woodcock::doScaleAtoms(config &configuration,unsigned int step,ForwardIterator begin,ForwardIterator end){
+double Woodcock::doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin,ForwardIterator end){
   double ekin=0;
-  if ((configuration.Thermostats->ScaleTempStep > 0) && ((MDSteps-1) % configuration.Thermostats->ScaleTempStep == 0)) {
-    double ScaleTempFactor = sqrt(configuration.Thermostats->TargetTemp/ActualTemp);
+  if ((ScaleTempStep > 0) && ((step-1) % ScaleTempStep == 0)) {
+    double ScaleTempFactor = sqrt(getContainer().TargetTemp/ActualTemp);
     DoLog(2) && (Log() << Verbose(2) <<  "Applying Woodcock thermostat..." << endl);
     double ekin;
@@ -51 +56 @@
   return ekin;
 }
+
+std::string Woodcock::name(){
+  return ThermostatTraits<Woodcock>().name;
+}
+
+std::string Woodcock::writeParams(){
+  std::stringstream sstr;
+  sstr << ScaleTempStep;
+  return sstr.str();
+}

src/Thermostats/Woodcock.hpp

@@ -14 +14 @@
 {
 public:
-  Woodcock(int,double);
+  Woodcock(int);
   virtual ~Woodcock();
 
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::list));
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::vector));
-  virtual double scaleAtoms(config &configuration,unsigned int step,ATOMSET(std::set));
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms);
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms);
+  virtual double scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms);
 
-  virtual std::string name(){return "Woodcock";}
+  virtual std::string name();
+
+  virtual std::string writeParams();
 
 private:
   template <class ForwardIterator>
-  double doScaleAtoms(config &configuration,unsigned int step,ForwardIterator begin,ForwardIterator end);
+  double doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin,ForwardIterator end);
 
-  int MDSteps;
-  double ActualTemp;
+  int ScaleTempStep;
+};
+
+template <>
+struct ThermostatTraits<class Woodcock>{
+  ThermostatTraits();
+  const char* name;
 };