Changeset c0c650 for src/Thermostats/NoseHoover.cpp

Timestamp:

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

3e4162

Parents:

0b882a

Message:

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

File:

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

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();
     }