Changeset bd6e5c for src/Fragmentation

Timestamp:

May 18, 2016, 10:02:06 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, 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_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, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, 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:

d713ce

Parents:

d45ed9

git-author:

Frederik Heber <heber@…> (03/07/16 13:44:02)

git-committer:

Frederik Heber <heber@…> (05/18/16 22:02:06)

Message:

Prepared AtomFragmentsMap to work in ids, not instances.

• no more ptrs such that we may convert it into a serializable singleton container.

Location:

src/Fragmentation

Files:

• AtomFragmentsMap.cpp (modified) (2 diffs)
• AtomFragmentsMap.hpp (modified) (2 diffs)
• Interfragmenter.cpp (modified) (4 diffs)
• Interfragmenter.hpp (modified) (1 diff)

src/Fragmentation/AtomFragmentsMap.cpp

@@ -54 +54 @@
     const KeySet &keyset = keysetiter->first;
     LOG(2, "DEBUG: Current keyset is " << keyset);
-    const AtomIdSet atoms(keyset);
-    const size_t atoms_size = atoms.getAtomIds().size();
-    if ((atoms_size > _MaxOrder) || (atoms_size == 0))
+    if ((keyset.size() > _MaxOrder) || (keyset.empty()))
       continue;
-    for (AtomIdSet::const_iterator atomiter = atoms.begin();
-        atomiter != atoms.end(); ++atomiter) {
+    for (KeySet::const_iterator keyiter = keyset.begin();
+        keyiter != keyset.end(); ++keyiter) {
       // either create new list ...
       std::pair<AtomFragmentsMap_t::iterator, bool> inserter =
-          atommap.insert( std::make_pair(*atomiter, keysets_t(1, &keyset) ));
+          atommap.insert( std::make_pair(*keyiter, keysets_t(1, keyset) ));
       // ... or push to end
       if (inserter.second) {
@@ -68 +66 @@
       } else {
         LOG(3, "DEBUG: Added keyset to present entry.");
-        inserter.first->second.push_back(&keyset);
+        inserter.first->second.push_back(keyset);
       }
     }

src/Fragmentation/AtomFragmentsMap.hpp

@@ -18 +18 @@
 #include <map>
 
-class atom;
+#include "types.hpp"
+
 class KeySet;
 class Graph;
@@ -33 +34 @@
       size_t _MaxOrder);
 
-  typedef std::list<const KeySet *> keysets_t;
+  typedef std::list<KeySet> keysets_t;
   //!> typedef for the internal map
-  typedef std::map<const atom *, keysets_t> AtomFragmentsMap_t;
+  typedef std::map<atomId_t, keysets_t> AtomFragmentsMap_t;
 
   const AtomFragmentsMap_t& getMap() const

src/Fragmentation/Interfragmenter.cpp

@@ -107 +107 @@
   for (candidates_t::const_iterator candidateiter = _candidates.begin();
       candidateiter != _candidates.end(); ++candidateiter) {
-    const atom * _atom = *candidateiter;
-    atomkeyset_t::const_iterator iter = _atomkeyset.find(_atom);
+    const atomId_t atomid = (*candidateiter)->getId();
+    atomkeyset_t::const_iterator iter = _atomkeyset.find(atomid);
     ASSERT( iter != _atomkeyset.end(),
         "Interfragmenter::getAtomSpecificKeySetMap() - could not find atom "
-        +toString(_atom->getId())+" in lookup.");
-    fragmentmap.insert( std::make_pair( _atom, iter->second) );
+        +toString(atomid)+" in lookup.");
+    fragmentmap.insert( std::make_pair( atomid, iter->second) );
   }
   LOG(4, "DEBUG: Copied part of lookup map contains " << fragmentmap.size() << " keys.");
@@ -122 +122 @@
     const size_t _MaxOrder,
     const candidates_t &_candidates,
-    atomkeyset_t &_fragmentmap,
+    const atomkeyset_t &_fragmentmap,
     const KeySet &_keyset,
     Graph &_InterFragments,
@@ -131 +131 @@
     const atom *_atom = *candidateiter;
     LOG(3, "DEBUG: Current candidate is " << *_atom << ".");
-    atomkeyset_t::iterator finditer = _fragmentmap.find(_atom);
+    atomkeyset_t::const_iterator finditer = _fragmentmap.find(_atom->getId());
     ASSERT( finditer != _fragmentmap.end(),
         "Interfragmenter::combineFragments() - could not find atom "
         +toString(_atom->getId())+" in fragment specific lookup.");
-    keysets_t &othersets = finditer->second;
+    // copy set to allow erase
+    keysets_t othersets(finditer->second);
     ASSERT( !othersets.empty(),
         "Interfragmenter::combineFragments() - keysets to "+toString(_atom->getId())+
@@ -141 +142 @@
     keysets_t::iterator otheriter = othersets.begin();
     while (otheriter != othersets.end()) {
-      const KeySet &otherset = **otheriter;
+      const KeySet &otherset = *otheriter;
       LOG(3, "DEBUG: Current keyset is " << otherset << ".");
       // only add them one way round and not the other

src/Fragmentation/Interfragmenter.hpp

@@ -114 +114 @@
       const size_t _MaxOrder,
       const candidates_t &_candidates,
-      atomkeyset_t &_fragmentmap,
+      const atomkeyset_t &_fragmentmap,
       const KeySet &_keyset,
       Graph &_InterFragments,