Changeset c864a8

Timestamp:

Feb 24, 2011, 4:27:00 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:

bce72c

Parents:

76163d

git-author:

Frederik Heber <heber@…> (02/07/11 17:58:50)

git-committer:

Frederik Heber <heber@…> (02/24/11 16:27:00)

Message:

Moved TrajectoryParticle::EvaluateConstrainedForce() into molecule::EvaluateConstrainedForces().

Location:

src

Files:

• atom_trajectoryparticle.cpp (modified) (1 diff)
• atom_trajectoryparticle.hpp (modified) (1 diff)
• molecule_dynamics.cpp (modified) (1 diff)

src/atom_trajectoryparticle.cpp

@@ -52 +52 @@
   return getType()->getMass()*Trajectory.U.at(step);
 }
-
-/** Evaluates some constraint potential if atom moves from \a startstep at once to \endstep in trajectory.
- * \param startstep trajectory begins at
- * \param endstep trajectory ends at
- * \param **PermutationMap if atom switches places with some other atom, there is no translation but a permutaton noted here (not in the trajectories of ea
- * \param *Force Force matrix to store result in
- */
-void TrajectoryParticle::EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force) const
-{
-  double constant = 10.;
-  TrajectoryParticle *Sprinter = PermutationMap[nr];
-  // set forces
-  for (int i=NDIM;i++;)
-    Force->Matrix[0][nr][5+i] += 2.*constant*sqrt(Trajectory.R.at(startstep).distance(Sprinter->Trajectory.R.at(endstep)));
-};
 
 /** Extends the trajectory STL vector to the new size.

src/atom_trajectoryparticle.hpp

@@ -42 +42 @@
   virtual ~TrajectoryParticle();
 
-  // constraint potential and dynamics stuff
-  void EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force) const;
-
-  // trajectory stuff
   void ResizeTrajectory(int MaxSteps);
   void CopyStepOnStep(int dest, int src);

src/molecule_dynamics.cpp

@@ -481 +481 @@
 void molecule::EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force)
 {
+  double constant = 10.;
+
   /// evaluate forces (only the distance to target dependent part) with the final PermutationMap
   DoLog(1) && (Log() << Verbose(1) << "Calculating forces and adding onto ForceMatrix ... " << endl);
-  for_each(atoms.begin(),
-           atoms.end(),
-           boost::bind(&atom::EvaluateConstrainedForce,_1,startstep,endstep,PermutationMap,Force));
+  BOOST_FOREACH(atom *_atom, atoms) {
+    atom *Sprinter = PermutationMap[_atom->nr];
+    // set forces
+    for (int i=NDIM;i++;)
+      Force->Matrix[0][_atom->nr][5+i] += 2.*constant*sqrt(_atom->Trajectory.R.at(startstep).distance(Sprinter->Trajectory.R.at(endstep)));
+  }
   DoLog(1) && (Log() << Verbose(1) << "done." << endl);
 };