Changeset bcb593 for src/Atom

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.

Location:

src/Atom

Files:

• atom_atominfo.cpp (modified) (4 diffs)
• atom_atominfo.hpp (modified) (1 diff)

src/Atom/atom_atominfo.cpp

@@ -279 +279 @@
 {
   OBSERVE;
-  NOTIFY(AtomObservable::VelocityChanged);
+  NOTIFY(AtomObservable::ForceChanged);
   ASSERT(WorldTime::getTime() < AtomicForce.size(),
       "AtomInfo::setAtomicForce() - Access out of range: "
@@ -291 +291 @@
   OBSERVE;
   if (WorldTime::getTime() == _step)
-    NOTIFY(AtomObservable::VelocityChanged);
+    NOTIFY(AtomObservable::ForceChanged);
   const unsigned int size = AtomicForce.size();
   ASSERT(_step <= size,
@@ -579 +579 @@
 };
 
-/** Performs a velocity verlet update of the trajectory.
- * Parameters are according to those in configuration class.
+/** Performs a velocity verlet update of the position at \a NextStep from \a LastStep information only.
+ *
+ * We calculate \f$x(t + \delta t) = x(t) + v(t)* \delta t + .5 * \delta t * \delta t * F(t)/m \f$.
+ *
+ *
  * \param NextStep index of sequential step to set
  * \param Deltat time step width
  * \param IsAngstroem whether the force's underlying unit of length is angstroem or bohr radii
  */
-void AtomInfo::VelocityVerletUpdate(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem)
+void AtomInfo::VelocityVerletUpdateX(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem)
 {
   const unsigned int LastStep = NextStep == 0 ? 0 : NextStep-1;
 
   LOG(2, "INFO: Particle that currently " << *this);
-  LOG(2, "INFO: Integrating with mass=" << getMass() << " and Deltat="
+  LOG(2, "INFO: Integrating position with mass=" << getMass() << " and Deltat="
       << Deltat << " at NextStep=" << NextStep);
-  // update force
-  // (F+F_old)/2m = a and thus: v = (F+F_old)/2m * t = (F + F_old) * a
-  LOG(3, "INFO: Force at step " << NextStep << " is " << getAtomicForceAtStep(NextStep));
 
   // update position
@@ -603 +603 @@
     LOG(4, "INFO: position with velocity " << getAtomicVelocityAtStep(LastStep) << " from last step " << tempVector);
     tempVector += .5*Deltat*Deltat*(getAtomicForceAtStep(LastStep))*(1./getMass());     // F = m * a and s =
-    LOG(4, "INFO: position with force " << getAtomicForceAtStep(NextStep) << " from last step " << tempVector);
+    LOG(4, "INFO: position with force " << getAtomicForceAtStep(LastStep) << " from last step " << tempVector);
     setPositionAtStep(NextStep, tempVector);
     LOG(3, "INFO: Position at step " << NextStep << " set to " << tempVector);
   }
+};
+
+/** Performs a velocity verlet update of the velocity at \a NextStep.
+ *
+ * \note forces at NextStep should have been calculated based on position at NextStep prior
+ * to calling this function.
+ *
+ * We calculate \f$v(t) = v(t - \delta t) + \delta _t * .5 * (F(t - \delta t) + F(t))/m \f$.
+ *
+ * Parameters are according to those in configuration class.
+ * \param NextStep index of sequential step to set
+ * \param Deltat time step width
+ * \param IsAngstroem whether the force's underlying unit of length is angstroem or bohr radii
+ */
+void AtomInfo::VelocityVerletUpdateU(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem)
+{
+  const unsigned int LastStep = NextStep == 0 ? 0 : NextStep-1;
+
+  LOG(2, "INFO: Particle that currently " << *this);
+  LOG(2, "INFO: Integrating velocity with mass=" << getMass() << " and Deltat="
+      << Deltat << " at NextStep=" << NextStep);
 
   // Update U

src/Atom/atom_atominfo.hpp

@@ -267 +267 @@
   size_t getTrajectorySize() const;
   void CopyStepOnStep(const unsigned int dest, const unsigned int src);
-  void VelocityVerletUpdate(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem);
+  void VelocityVerletUpdateX(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem);
+  void VelocityVerletUpdateU(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem);
   double getKineticEnergy(const unsigned int step) const;
   Vector getMomentum(const unsigned int step) const;