Changeset af9be32

Timestamp:

Apr 6, 2012, 11:44:51 AM (13 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:

72e4c95

Parents:

06070b

git-author:

Frederik Heber <heber@…> (04/05/12 14:09:17)

git-committer:

Frederik Heber <heber@…> (04/06/12 11:44:51)

Message:

Added BondInfo to store bond's state information for later re-instantiation.

• also added StoreBondInformationFromAtoms() and AddBondsFromBondInfo() to UndoRedoHelpers.

Location:

src

Files:

• Actions/UndoRedoHelpers.cpp (modified) (2 diffs)
• Actions/UndoRedoHelpers.hpp (modified) (2 diffs)
• Bond/BondInfo.cpp (added)
• Bond/BondInfo.hpp (added)
• Makefile.am (modified) (2 diffs)

src/Actions/UndoRedoHelpers.cpp

@@ -36 +36 @@
   for (; i<atoms.size(); ++i) {
     // re-create the atom
-    LOG(1, "Re-adding atom " << atoms[i].getId() << ".");
+    LOG(3, "DEBUG: Re-adding atom " << atoms[i].getId() << ".");
     atom *Walker = World::getInstance().createAtom();
     if (!atoms[i].setAtom(*Walker)) {
@@ -59 +59 @@
     World::getInstance().destroyAtom(_atom.getId());
   }
+}
+
+void MoleCuilder::StoreBondInformationFromAtoms(
+    const std::vector<const atom*> &atoms,
+    std::vector< BondInfo > &bonds)
+{
+  ASSERT( bonds.empty(),
+      "StoreBondInformationFromAtoms() - give bonds vector is not empty.");
+  bonds.reserve(atoms.size()*4);
+  for (std::vector<const atom*>::const_iterator atomiter = atoms.begin();
+      atomiter != atoms.end(); ++atomiter) {
+    const BondList & _atom_bonds = (*atomiter)->getListOfBonds();
+    for(BondList::const_iterator iter = _atom_bonds.begin(); iter != _atom_bonds.end(); ++iter)
+      bonds.push_back( BondInfo(*iter) );
+  }
+}
+
+bool MoleCuilder::AddBondsFromBondInfo(const std::vector< BondInfo > &bonds)
+{
+  bool status = true;
+  for(std::vector< BondInfo >::const_iterator iter = bonds.begin();
+      iter != bonds.end(); ++iter)
+    if (!(*iter).RecreateBond())
+      status = false;
+  return status;
 }
 

src/Actions/UndoRedoHelpers.hpp

@@ -18 +18 @@
 
 #include "Atom/AtomicInfo.hpp"
+#include "Bond/BondInfo.hpp"
 
 namespace MoleCuilder {
@@ -33 +34 @@
    */
   void RemoveAtomsFromAtomicInfo(std::vector<AtomicInfo> &atoms);
+
+  /** Stores the required bond information in for all \a atoms in \a bonds.
+   *
+   * @param atoms atoms whose bonds to store
+   * @param bonds vector with bond information on return
+   */
+  void StoreBondInformationFromAtoms(
+      const std::vector<const atom*> &atoms,
+      std::vector<BondInfo> &bonds);
+
+  /** Recreates bonds from information stored in \a bonds.
+   *
+   * @param bonds bond state information
+   * @return true - all bonds restored, false - at least one bond could not be restored
+   */
+  bool AddBondsFromBondInfo(const std::vector< BondInfo > &bonds);
 
   /** Sets atoms to state information stored as AtomicInfo.

src/Makefile.am

@@ -29 +29 @@
         Bond/bond.cpp \
         Bond/bond_observable.cpp \
+        Bond/BondInfo.cpp \
         Bond/GraphEdge.cpp
 
@@ -34 +35 @@
         Bond/bond.hpp \
         Bond/bond_observable.hpp \
+        Bond/BondInfo.hpp \
         Bond/GraphEdge.hpp