Changeset bcb593 for src/Dynamics

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/Dynamics/VerletForceIntegration.hpp (modified) (3 diffs)

src/Dynamics/VerletForceIntegration.hpp

@@ -78 +78 @@
 
   /** Performs Verlet integration.
-   * Note that we assume the parsed forces to be in atomic units (hence, if coordinates are in angstroem, we
-   * have to transform them).
-   * This adds a new MD step \f$ t + \Delta t \f$ to the config file.
+   *
+   * We assume that forces have just been calculated. Then, we perform the velocity
+   * and the position calculation for \f$ t + \Delta t \f$, such that forces may be
+   * again calculated with respect to the new position.
+   *
    * \param NextStep current time step (i.e. \f$ t + \Delta t \f$ in the sense of the velocity verlet)
    * \param offset offset in matrix file to the first force component
@@ -100 +102 @@
     // make sum of forces equal zero
     if (FixedCenterOfMass)
-      correctForceMatrixForFixedCenterOfMass(offset,NextStep);
+      correctForceMatrixForFixedCenterOfMass(offset,NextStep-1);
 
     // solve a constrained potential if we are meant to
-    if (DoConstrainedMD) {
-      performConstraintMinimization(DoConstrainedMD,NextStep);
+    if (DoConstrainedMD)
+      performConstraintMinimization(DoConstrainedMD,NextStep-1);
+
+    if (NextStep > 0) {
+      for(typename AtomSetMixin<T>::iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+        //std::cout << "Id of atom is " << (*iter)->getId() << std::endl;
+        (*iter)->VelocityVerletUpdateU((*iter)->getId(), NextStep-1, Deltat, IsAngstroem);
+      }
+
+      // make sum of velocities equal zero
+      if (FixedCenterOfMass)
+        correctVelocitiesForFixedCenterOfMass(NextStep-1);
+
+      // thermostat
+      performThermostatControl(NextStep-1);
     }
 
@@ -112 +127 @@
     for(typename AtomSetMixin<T>::iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
       //std::cout << "Id of atom is " << (*iter)->getId() << std::endl;
-      (*iter)->VelocityVerletUpdate((*iter)->getId(), NextStep, Deltat, IsAngstroem);
-    }
-
-    // make sum of velocities equal zero
-    if (FixedCenterOfMass)
-      correctVelocitiesForFixedCenterOfMass(NextStep);
-
-    // thermostat
-    performThermostatControl(NextStep);
+      (*iter)->VelocityVerletUpdateX((*iter)->getId(), NextStep, Deltat, IsAngstroem);
+    }
 
     // exit