Changeset 4882d5 for src/Atom

Timestamp:

Dec 14, 2012, 5:39:30 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:

5251af

Parents:

8b886f

git-author:

Frederik Heber <heber@…> (10/05/12 07:59:22)

git-committer:

Frederik Heber <heber@…> (12/14/12 17:39:30)

Message:

Rewrote VerletIntegrationAction to diminish dependence on ForceMatrix.

• atom::VelocityVerletUpdate() now works on the forces stored in AtomicForces.
• ThermoStatContainer::getActive() getter for the currently active thermostat.
• VerletForceIntegration::operator() split up into several smaller functions.

Location:

src/Atom

Files:

• atom_atominfo.cpp (modified) (2 diffs)
• atom_atominfo.hpp (modified) (1 diff)

src/Atom/atom_atominfo.cpp

@@ -584 +584 @@
  * \param Deltat time step width
  * \param IsAngstroem whether the force's underlying unit of length is angstroem or bohr radii
- * \param *Force matrix with forces
- */
-void AtomInfo::VelocityVerletUpdate(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem, ForceMatrix *Force, const size_t offset)
-{
+ */
+void AtomInfo::VelocityVerletUpdate(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="
@@ -593 +594 @@
   // update force
   // (F+F_old)/2m = a and thus: v = (F+F_old)/2m * t = (F + F_old) * a
-  Vector tempVector;
-  for (int d=0; d<NDIM; d++) {
-    ASSERT(Force->RowCounter[0] > nr,
-        "AtomInfo::VelocityVerletUpdate() - "+toString(nr)
-        +" out of bounds [0,"+toString(Force->RowCounter[0])
-        +"] access on force matrix.");
-    ASSERT(Force->ColumnCounter[0] > d+(int)offset,
-        "AtomInfo::VelocityVerletUpdate() - "+toString(d+offset)
-        +" out of bounds [0,"+toString(Force->ColumnCounter[0])
-        +"] access on force matrix.");
-    tempVector[d] = -Force->Matrix[0][nr][d+offset]*(IsAngstroem ? AtomicLengthToAngstroem : 1.);
-  }
-  LOG(3, "INFO: Force at step " << NextStep << " set to " << tempVector);
-  setAtomicForceAtStep(NextStep, tempVector);
+  LOG(3, "INFO: Force at step " << NextStep << " is " << getAtomicForceAtStep(NextStep));
 
   // update position
-  tempVector = getPositionAtStep(NextStep-1);
-  LOG(4, "INFO: initial position from last step " << setprecision(4) << tempVector);
-  tempVector += Deltat*(getAtomicVelocityAtStep(NextStep-1));     // s(t) = s(0) + v * deltat + 1/2 a * deltat^2
-  LOG(4, "INFO: position with velocity " << getAtomicVelocityAtStep(NextStep-1) << " from last step " << tempVector);
-  tempVector += 0.5*Deltat*Deltat*(getAtomicForceAtStep(NextStep))*(1./getMass());     // F = m * a and s =
-  LOG(4, "INFO: position with force " << getAtomicForceAtStep(NextStep) << " from last step " << tempVector);
-  setPositionAtStep(NextStep, tempVector);
-  LOG(3, "INFO: Position at step " << NextStep << " set to " << tempVector);
+  {
+    Vector tempVector = getPositionAtStep(LastStep);
+    LOG(4, "INFO: initial position from last step " << setprecision(4) << tempVector);
+    tempVector += Deltat*(getAtomicVelocityAtStep(LastStep));     // s(t) = s(0) + v * deltat + 1/2 a * deltat^2
+    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);
+    setPositionAtStep(NextStep, tempVector);
+    LOG(3, "INFO: Position at step " << NextStep << " set to " << tempVector);
+  }
 
   // Update U
-  tempVector = getAtomicVelocityAtStep(NextStep-1);
-  LOG(4, "INFO: initial velocity from last step " << tempVector);
-  tempVector += Deltat * (getAtomicForceAtStep(NextStep)+getAtomicForceAtStep(NextStep-1))*(1./getMass()); // v = F/m * t
-  LOG(4, "INFO: Velocity with force from last " << getAtomicForceAtStep(NextStep-1)
-      << " and present " << getAtomicForceAtStep(NextStep) << " step " << tempVector);
-  setAtomicVelocityAtStep(NextStep, tempVector);
-  LOG(3, "INFO: Velocity at step " << NextStep << " set to " << tempVector);
+  {
+    Vector tempVector = getAtomicVelocityAtStep(LastStep);
+    LOG(4, "INFO: initial velocity from last step " << tempVector);
+    tempVector += Deltat * .5*(getAtomicForceAtStep(LastStep)+getAtomicForceAtStep(NextStep))*(1./getMass()); // v = F/m * t
+    LOG(4, "INFO: Velocity with force from last " << getAtomicForceAtStep(LastStep)
+        << " and present " << getAtomicForceAtStep(NextStep) << " step " << tempVector);
+    setAtomicVelocityAtStep(NextStep, tempVector);
+    LOG(3, "INFO: Velocity at step " << NextStep << " set to " << tempVector);
+  }
 };
 

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, ForceMatrix *Force, const size_t offset);
+  void VelocityVerletUpdate(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem);
   double getKineticEnergy(const unsigned int step) const;
   Vector getMomentum(const unsigned int step) const;