Changeset bcb593 for src/Actions/MoleculeAction/VerletIntegrationAction.cpp

Timestamp:

Jul 11, 2013, 9:43:31 PM (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:

9c1324

Parents:

11f0fa

git-author:

Frederik Heber <heber@…> (06/18/13 14:35:36)

git-committer:

Frederik Heber <heber@…> (07/11/13 21:43:31)

Message:

FIX: VerletIntegrationAction now assumes forces have just been calculated.

• according to Wikipedia's Velocity_Verlet info, we first integrate position, then calculate forces, then integrate velocity. This assumes that forces based on next time step's position are already known. This is possible when parsed from file but not if they are calculated dynamically via fragmentation. Hence, we now integrate velocity from last time step to current, then integrate position from current time step to next. Then we are in the position to calculate forces and do this cycle again.
• for this, VelocityVerletUpdate was split into ..X() and ..U() for independent integration of position and velocity.
• VelocityVerletIntegration::operator() now first corrects forces, then integrates velocites, corrects them too and finally integrates positions according to the above new scheme.
• removed option MDSteps from VerletIntegrationAction.
• TESTFIX: Had to change regression rest on VerletIntegration since the cycle sequence has changed. It was nonsense before to have the forces already in some file respective to future position that actually first need to come out of the time integration.

File:

• src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) (2 diffs)

src/Actions/MoleculeAction/VerletIntegrationAction.cpp

@@ -42 +42 @@
 #include "molecule.hpp"
 #include "World.hpp"
+#include "WorldTime.hpp"
 
 #include <vector>
@@ -59 +60 @@
   // TODO: sollte besser stream nutzen, nicht filename direkt (es sei denn, ist prefix), besser fuer unit test
   AtomSetMixin<std::vector<atom *> > set(World::getInstance().getSelectedAtoms());
-  for (unsigned int step = 0; step < params.MDSteps.get(); ++step) {
-    VerletForceIntegration<std::vector<atom *> > Verlet(set, params.Deltat.get(), false);
-    // parse forces into next step
-    if (!params.forcesfile.get().string().empty()) {
-      LOG(1, "Parsing forces file.");
-      if (!Verlet.parseForcesFile(params.forcesfile.get().string().c_str(), step))
-        LOG(2, "File " << params.forcesfile.get() << " not found.");
-      else
-        LOG(2, "File " << params.forcesfile.get() << " found and parsed.");
-    }
-    // perform velocity verlet update
-    LOG(1, "Verlet integrating.");
-    if (!Verlet(step+1, 1, 0, params.FixedCenterOfMass.get()))
+  // we always operate relative to current time step
+  size_t CurrentStep = WorldTime::getInstance().getTime();
+  VerletForceIntegration<std::vector<atom *> > Verlet(set, params.Deltat.get(), true);
+  // parse forces into next step
+  if (!params.forcesfile.get().string().empty()) {
+    LOG(1, "Parsing forces file.");
+    if (!Verlet.parseForcesFile(params.forcesfile.get().string().c_str(), CurrentStep))
       LOG(2, "File " << params.forcesfile.get() << " not found.");
     else
       LOG(2, "File " << params.forcesfile.get() << " found and parsed.");
   }
+  // perform velocity verlet update
+  LOG(1, "Verlet integrating.");
+  if (!Verlet(CurrentStep+1, 1, 0, params.FixedCenterOfMass.get()))
+    ELOG(1, "Velocity verlet failed.");
+  else
+    LOG(2, "DEBUG: Successfully performed updates on velocity and position.");
+  // increment to next time step
+  World::getInstance().setTime(CurrentStep+1);
 
   return Action::success;