Changeset f73351 for src/Thermostats/Berendsen.cpp

Timestamp:

Jul 9, 2013, 6:21:28 AM (12 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:

11f0fa

Parents:

e5ebaf

git-author:

Frederik Heber <heber@…> (06/18/13 14:30:52)

git-committer:

Frederik Heber <heber@…> (07/09/13 06:21:28)

Message:

FIX: Some Thermostats would cause NaN on zero temperature.

• Berendsen and Woodcock divide through OldTemp which may be zero (because initial velocities are zero). This is now checked.
• also, default thermostat is now NoThermostat.
• NOTE: We lack an action to choose a thermostat but this needs some refactoring of the thermostats which are still based on being read from file.
• TESTFIX: Adapted three regression tests where pcp files were stored that contained still reference to old default Berendsen (with parameter 2.5).

File:

• src/Thermostats/Berendsen.cpp (modified) (1 diff)

src/Thermostats/Berendsen.cpp

@@ -85 +85 @@
   LOG(2,  "Applying Berendsen-VanGunsteren thermostat...");
   double ekin=0;
-  double ScaleTempFactor = getContainer().TargetTemp/ActualTemp;
-  for(ForwardIterator iter=begin;iter!=end;++iter){
-    Vector U = (*iter)->getAtomicVelocityAtStep(step);
-    if ((*iter)->getFixedIon() == 0) { // even FixedIon moves, only not by other's forces
-      U *= sqrt(1+(World::getInstance().getConfig()->Deltat/TempFrequency)*(ScaleTempFactor-1));
-      ekin += 0.5*(*iter)->getType()->getMass() * U.NormSquared();
+  if (fabs(ActualTemp) > MYEPSILON) {
+    double ScaleTempFactor = getContainer().TargetTemp/ActualTemp;
+    for(ForwardIterator iter=begin;iter!=end;++iter){
+      Vector U = (*iter)->getAtomicVelocityAtStep(step);
+      if ((*iter)->getFixedIon() == 0) { // even FixedIon moves, only not by other's forces
+        U *= sqrt(1+(World::getInstance().getConfig()->Deltat/TempFrequency)*(ScaleTempFactor-1));
+        ekin += 0.5*(*iter)->getType()->getMass() * U.NormSquared();
+      }
+      (*iter)->setAtomicVelocityAtStep(step, U);
     }
-    (*iter)->setAtomicVelocityAtStep(step, U);
   }
   return ekin;