Changeset c0c650 for src/Thermostats

Timestamp:

Aug 25, 2010, 9:24:25 AM (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:

3e4162

Parents:

0b882a

Message:

Added structure that allows construction of thermostats from parameters in a configfile

Location:

src/Thermostats

Files:

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

src/Thermostats/Berendsen.cpp

@@ -25 +25 @@
 {}
 
+Thermostat *ThermostatTraits<class Berendsen>::make(class ConfigFileBuffer * const fb){
+  double TempFrequency;
+  const int verbose = 0;
+  ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read \tau_T
+  return new class Berendsen(TempFrequency);
+}
 
 double Berendsen::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms){
@@ -57 +63 @@
 }
 
-std::string Berendsen::writeParam(){
+std::string Berendsen::writeParams(){
   stringstream sstr;
   sstr << TempFrequency;

src/Thermostats/Berendsen.hpp

@@ -23 +23 @@
   virtual std::string name();
 
-  virtual std::string writeParam();
+  virtual std::string writeParams();
 
 private:
@@ -36 +36 @@
 {
   ThermostatTraits();
+  virtual Thermostat *make(class ConfigFileBuffer * const fb);
   const char* name;
 };

src/Thermostats/GaussianThermostat.cpp

@@ -28 +28 @@
   name("Gaussian")
 {}
+
+Thermostat *ThermostatTraits<GaussianThermostat>::make(class ConfigFileBuffer * const fb){
+  int ScaleTempStep;
+  const int verbose = 0;
+  ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read collision rate
+  return new class GaussianThermostat(ScaleTempStep);
+}
 
 double GaussianThermostat::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms){

src/Thermostats/GaussianThermostat.hpp

@@ -41 +41 @@
 {
   ThermostatTraits();
+  virtual Thermostat *make(class ConfigFileBuffer * const fb);
   const char* name;
 };

src/Thermostats/Langevin.cpp

@@ -13 +13 @@
 #include "ThermoStatContainer.hpp"
 
-Langevin::Langevin()
+Langevin::Langevin(double _TempFrequency,double _alpha) :
+  TempFrequency(_TempFrequency),
+  alpha(_alpha)
 {
   gsl_rng_env_setup();
@@ -28 +30 @@
   name("Langevin")
 {}
+
+Thermostat *ThermostatTraits<class Langevin>::make(class ConfigFileBuffer * const fb){
+  double TempFrequency;
+  double alpha;
+  const int verbose = 0;
+  ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read gamma
+  if (ParseForParameter(verbose,fb,"Thermostat", 0, 3, 1, double_type, &alpha, 1, optional)) {
+    DoLog(2) && (Log() << Verbose(2) << "Extended Stochastic Thermostat detected with interpolation coefficient " << alpha << "." << endl);
+  } else {
+    alpha = 1.;
+  }
+  return new class Langevin(TempFrequency,alpha);
+}
 
 double Langevin::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms){
@@ -51 +66 @@
       // throw a dice to determine whether it gets hit by a heat bath particle
       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]) << " -> ");
+        DoLog(3) && (Log() << Verbose(3) << "Particle " << (**iter) << " was hit (sigma " << sigma << "): " << U.Norm() << " -> ");
         // pick three random numbers from a Boltzmann distribution around the desired temperature T for each momenta axis
         for (int d=0; d<NDIM; d++) {
           U[d] = gsl_ran_gaussian (r, sigma);
         }
-        DoLog(2) && (Log() << Verbose(2) << sqrt(U[0]*U[0]+U[1]*U[1]+U[2]*U[2]) << endl);
+        DoLog(2) && (Log() << Verbose(2) << U.Norm() << endl);
       }
       ekin += 0.5*(*iter)->getType()->mass * U.NormSquared();

src/Thermostats/Langevin.hpp

@@ -14 +14 @@
 {
 public:
-  Langevin();
+  Langevin(double,double);
   virtual ~Langevin();
 
@@ -39 +39 @@
 {
   ThermostatTraits();
+  virtual Thermostat *make(class ConfigFileBuffer * const fb);
   const char* name;
 };

src/Thermostats/NoThermostat.cpp

@@ -17 +17 @@
   name("None")
 {}
+
+Thermostat *ThermostatTraits<class NoThermostat>::make(class ConfigFileBuffer * const fb){
+  return new class NoThermostat();
+}
 
 double NoThermostat::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms){

src/Thermostats/NoThermostat.hpp

@@ -29 +29 @@
 {
   ThermostatTraits();
+  virtual Thermostat *make(class ConfigFileBuffer * const fb);
   const char* name;
 };

src/Thermostats/NoseHoover.cpp

@@ -16 +16 @@
 
 NoseHoover::NoseHoover(double _HooverMass) :
-  HooverMass(_HooverMass)
+  HooverMass(_HooverMass),
+  alpha(0)
 {}
 
@@ -26 +27 @@
 {}
 
+Thermostat *ThermostatTraits<class NoseHoover>::make(class ConfigFileBuffer * const fb){
+  double HooverMass;
+  const int verbose = 0;
+  ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &HooverMass, 1, critical); // read Hoovermass
+  return new class NoseHoover(HooverMass);
+}
 
 double NoseHoover::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms){
@@ -44 +51 @@
   init(step,begin,end);
   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);
+  alpha += delta_alpha*World::getInstance().getConfig()->Deltat;
+  DoLog(3) && (Log() << Verbose(3) << "alpha = " << delta_alpha << " * " << World::getInstance().getConfig()->Deltat << " = " << 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 += World::getInstance().getConfig()->Deltat/(*iter)->getType()->mass * (getContainer().alpha * (U * (*iter)->getType()->mass));
+      U += World::getInstance().getConfig()->Deltat/(*iter)->getType()->mass * (alpha * (U * (*iter)->getType()->mass));
       ekin += (0.5*(*iter)->getType()->mass) * U.NormSquared();
     }

src/Thermostats/NoseHoover.hpp

@@ -32 +32 @@
   double HooverMass;
   double delta_alpha;
+  double alpha;
   int count;
 };
@@ -39 +40 @@
 {
   ThermostatTraits();
+  virtual Thermostat *make(class ConfigFileBuffer * const fb);
   const char* name;
 };

src/Thermostats/Thermostat.hpp

@@ -46 +46 @@
 struct ThermostatTraits<Thermostat>{
   ThermostatTraits();
+  virtual Thermostat *make(class ConfigFileBuffer * const fb)=0;
   const char* name;
 };

src/Thermostats/Woodcock.cpp

@@ -26 +26 @@
   name("Woodcock")
 {}
+
+Thermostat *ThermostatTraits<class Woodcock>::make(class ConfigFileBuffer * const fb){
+  int ScaleTempStep;
+  const int verbose = 0;
+  ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read scaling frequency
+  return new class Woodcock(ScaleTempStep);
+}
 
 double Woodcock::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms){

src/Thermostats/Woodcock.hpp

@@ -36 +36 @@
 {
   ThermostatTraits();
+  virtual Thermostat *make(class ConfigFileBuffer * const fb);
   const char* name;
 };