Changeset 056e70 for src/Thermostats

Timestamp:

Feb 24, 2011, 5:56:03 PM (14 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:

6b020f

Parents:

6625c3

Message:

Suffixed getters and setters for AtomInfo trajecories with AtStep.

• AtomInfo:: getters are now const members
• added lots of ASSERTS to getters with time step to assure no out-of-bounds access.

Location:

src/Thermostats

Files:

• Berendsen.cpp (modified) (1 diff)
• GaussianThermostat.cpp (modified) (2 diffs)
• Langevin.cpp (modified) (2 diffs)
• NoseHoover.cpp (modified) (2 diffs)
• Woodcock.cpp (modified) (1 diff)

src/Thermostats/Berendsen.cpp

@@ -63 +63 @@
   double ScaleTempFactor = getContainer().TargetTemp/ActualTemp;
   for(ForwardIterator iter=begin;iter!=end;++iter){
-    Vector &U = (*iter)->getAtomicVelocity(step);
+    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);
   }
   return ekin;

src/Thermostats/GaussianThermostat.cpp

@@ -70 +70 @@
   double ekin =0;
   for(ForwardIterator iter=begin;iter!=end;++iter){
-    Vector &U = (*iter)->getAtomicVelocity(step);
+    Vector U = (*iter)->getAtomicVelocityAtStep(step);
     if ((*iter)->getFixedIon() == 0) {// even FixedIon moves, only not by other's forces
       U += World::getInstance().getConfig()->Deltat * G_over_E * U;
       ekin += (*iter)->getType()->getMass() * U.NormSquared();
     }
+    (*iter)->setAtomicVelocityAtStep(step, U);
   }
   return ekin;
@@ -84 +85 @@
   G=0;
   for(ForwardIterator iter=begin;iter!=end;++iter){
-    const Vector &U = (*iter)->getAtomicVelocity(step);
-    const Vector &F = (*iter)->getAtomicForce(step);
+    const Vector &U = (*iter)->getAtomicVelocityAtStep(step);
+    const Vector &F = (*iter)->getAtomicForceAtStep(step);
     if ((*iter)->getFixedIon() == 0){ // even FixedIon moves, only not by other's forces
       G += U.ScalarProduct(F);

src/Thermostats/Langevin.cpp

@@ -89 +89 @@
     rng_distribution = new boost::normal_distribution<>(0,sigma);
     boost::variate_generator<boost::mt19937&, boost::normal_distribution<> > rng(*rng_engine, *rng_distribution);
-    Vector &U = (*iter)->getAtomicVelocity(step);
+    Vector U = (*iter)->getAtomicVelocityAtStep(step);
     if ((*iter)->getFixedIon() == 0) { // even FixedIon moves, only not by other's forces
       // throw a dice to determine whether it gets hit by a heat bath particle
@@ -102 +102 @@
       ekin += 0.5*(*iter)->getType()->getMass() * U.NormSquared();
     }
+    (*iter)->setAtomicVelocityAtStep(step, U);
     delete rng_distribution;
     rng_distribution = NULL;

src/Thermostats/NoseHoover.cpp

@@ -68 +68 @@
   double ekin =0;
   for(ForwardIterator iter=begin;iter!=end;++iter){
-    Vector &U = (*iter)->getAtomicVelocity(step);
+    Vector U = (*iter)->getAtomicVelocityAtStep(step);
     if ((*iter)->getFixedIon() == 0) { // even FixedIon moves, only not by other's forces
       U += World::getInstance().getConfig()->Deltat/(*iter)->getType()->getMass() * (alpha * (U * (*iter)->getType()->getMass()));
       ekin += (0.5*(*iter)->getType()->getMass()) * U.NormSquared();
     }
+    (*iter)->setAtomicVelocityAtStep(step, U);
   }
   return ekin;
@@ -82 +83 @@
   count=0;
   for(ForwardIterator iter = begin;iter!=end;++iter){
-    const Vector &U = (*iter)->getAtomicVelocity(step);
+    const Vector &U = (*iter)->getAtomicVelocityAtStep(step);
     if ((*iter)->getFixedIon() == 0) { // even FixedIon moves, only not by other's forces
       delta_alpha += U.NormSquared()*(*iter)->getType()->getMass();

src/Thermostats/Woodcock.cpp

@@ -67 +67 @@
     double ekin;
     for (ForwardIterator iter = begin; iter!=end;++iter){
-      Vector &U = (*iter)->getAtomicVelocity(step);
+      Vector U = (*iter)->getAtomicVelocityAtStep(step);
       if ((*iter)->getFixedIon() == 0){ // even FixedIon moves, only not by other's forces
         U *= ScaleTempFactor;
         ekin += 0.5*(*iter)->getType()->getMass() * U.NormSquared();
       }
+      (*iter)->setAtomicVelocityAtStep(step, U);
     }
   }