Changeset 20943b for src/molecule_dynamics.cpp

Timestamp:

Mar 1, 2011, 1:17:09 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:

8009ce

Parents:

9e23a3

git-author:

Frederik Heber <heber@…> (02/25/11 09:39:10)

git-committer:

Frederik Heber <heber@…> (03/01/11 13:17:09)

Message:

Rewrote LinearInterpolationBetweenSteps into a functor in Dynamics/

• formerly called molecule::LinearInterpolationBetweenConfigurations().

File:

• src/molecule_dynamics.cpp (modified) (1 diff)

src/molecule_dynamics.cpp

@@ -38 +38 @@
 /************************************* Functions for class molecule *********************************/
 
-
-/** Performs a linear interpolation between two desired atomic configurations with a given number of steps.
- * Note, step number is config::MaxOuterStep
- * \param *out output stream for debugging
- * \param startstep stating initial configuration in molecule::Trajectories
- * \param endstep stating final configuration in molecule::Trajectories
- * \param &prefix path and prefix
- * \param &config configuration structure
- * \param MapByIdentity if true we just use the identity to map atoms in start config to end config, if not we find mapping by \sa MinimiseConstrainedPotential()
- * \return true - success in writing step files, false - error writing files or only one step in molecule::Trajectories
- */
-bool molecule::LinearInterpolationBetweenConfiguration(int startstep, int endstep, std::string prefix, config &configuration, bool MapByIdentity)
-{
-  // TODO: rewrite permutationMaps using enumeration objects
-  molecule *mol = NULL;
-  bool status = true;
-  int MaxSteps = configuration.MaxOuterStep;
-  MoleculeListClass *MoleculePerStep = new MoleculeListClass(World::getPointer());
-  // Get the Permutation Map by MinimiseConstrainedPotential
-  atom **PermutationMap = NULL;
-  atom *Sprinter = NULL;
-  if (!MapByIdentity) {
-    MinimiseConstrainedPotential Minimiser(atoms);
-    Minimiser(PermutationMap, startstep, endstep, configuration.GetIsAngstroem());
-  } else {
-    // TODO: construction of enumeration goes here
-    PermutationMap = new atom *[getAtomCount()];
-    for(internal_iterator iter = atoms.begin(); iter != atoms.end();++iter){
-      PermutationMap[(*iter)->getNr()] = (*iter);
-    }
-  }
-
-  // check whether we have sufficient space in Trajectories for each atom
-  LOG(1, "STATUS: Extending each trajectory size to " << MaxSteps+1 << ".");
-  for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::ResizeTrajectory),MaxSteps+1));
-  // push endstep to last one
-  for_each(atoms.begin(),atoms.end(),boost::bind(&atom::CopyStepOnStep,_1,MaxSteps,endstep));
-  endstep = MaxSteps;
-
-  // go through all steps and add the molecular configuration to the list and to the Trajectories of \a this molecule
-  DoLog(1) && (Log() << Verbose(1) << "Filling intermediate " << MaxSteps << " steps with MDSteps of " << MDSteps << "." << endl);
-  for (int step = 0; step <= MaxSteps; step++) {
-    mol = World::getInstance().createMolecule();
-    MoleculePerStep->insert(mol);
-    for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
-      // add to molecule list
-      Sprinter = mol->AddCopyAtom((*iter));
-      // add to Trajectories
-      Vector temp = (*iter)->getPositionAtStep(startstep) + (PermutationMap[(*iter)->getNr()]->getPositionAtStep(endstep) - (*iter)->getPositionAtStep(startstep))*((double)step/(double)MaxSteps);
-      Sprinter->setPosition(temp);
-      (*iter)->setAtomicVelocityAtStep(step, zeroVec);
-      (*iter)->setAtomicForceAtStep(step, zeroVec);
-      //Log() << Verbose(3) << step << ">=" << MDSteps-1 << endl;
-    }
-  }
-  MDSteps = MaxSteps+1;   // otherwise new Trajectories' points aren't stored on save&exit
-
-  // store the list to single step files
-  int *SortIndex = new int[getAtomCount()];
-  for (int i=getAtomCount(); i--; )
-    SortIndex[i] = i;
-
-  status = MoleculePerStep->OutputConfigForListOfFragments(prefix, SortIndex);
-  delete[](SortIndex);
-
-  // free and return
-  delete[](PermutationMap);
-  delete(MoleculePerStep);
-  return status;
-};
 
 /** Parses nuclear forces from file and performs Verlet integration.