Changeset f01769 for src/Fragmentation

Timestamp:

Jul 24, 2015, 4:44:34 PM (10 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:

a58c16

Parents:

1259df

git-author:

Frederik Heber <heber@…> (06/01/15 16:57:36)

git-committer:

Frederik Heber <heber@…> (07/24/15 16:44:34)

Message:

Replaced World::getAtom() wherever possible by const version.

• some AtomSet member functions now have const atom ptr instead of atom ptr.
• molecule can return const and non-const AtomSet.
• added FromIdToConstAtom to allow iterate through atoms in molecule (which are stored by id, not by ptr) in const fashion.
• in molecule::isInMolecule() is now const, ::CopyMolecule..() is non-const (because copying involves father atom who is stored non-const).

Location:

src/Fragmentation

Files:

• Fragmentation.cpp (modified) (5 diffs)
• Graph.cpp (modified) (1 diff)
• Homology/HomologyGraph_getFromKeyset.cpp (modified) (3 diffs)

src/Fragmentation/Fragmentation.cpp

@@ -169 +169 @@
   // ===== 2. create AtomMask that takes Saturation condition into account
   AtomMask_t AtomMask(atomids);
-  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+  for (molecule::const_iterator iter = const_cast<const molecule *>(mol)->begin();
+      iter != const_cast<const molecule *>(mol)->end();
+      ++iter) {
     // remove in hydrogen and we do saturate
     if ((treatment == ExcludeHydrogen) && ((*iter)->getType()->getAtomicNumber() == 1)) // skip hydrogen
@@ -269 +271 @@
   // Construct the complete KeySet which we need for topmost level only (but for all Roots)
   KeySet CompleteMolecule;
-  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+  for (molecule::const_iterator iter = const_cast<const molecule *>(mol)->begin();
+      iter != const_cast<const molecule *>(mol)->end();
+      ++iter) {
     CompleteMolecule.insert((*iter)->GetTrueFather()->getNr());
   }
@@ -353 +357 @@
   int FragmentCount;
   // get maximum bond degree
-  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+  for (molecule::const_iterator iter = const_cast<const molecule *>(mol)->begin();
+      iter != const_cast<const molecule *>(mol)->end();
+      ++iter) {
     const BondList& ListOfBonds = (*iter)->getListOfBonds();
     c = (ListOfBonds.size() > c) ? ListOfBonds.size() : c;
@@ -442 +448 @@
   output << "INFO: Writing OrderAtSite " << ORDERATSITEFILE << " ... ";
   if (file.good()) {
-    for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+    for (molecule::const_iterator iter = const_cast<const molecule *>(mol)->begin();
+        iter != const_cast<const molecule *>(mol)->end();
+        ++iter) {
       file << (*iter)->getId()
           << "\t" << (int)(*iter)->AdaptiveOrder
@@ -529 +537 @@
 void Fragmentation::FillRootStackForSubgraphs(KeyStack &RootStack, const AtomMask_t &AtomMask)
 {
-  for(molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+  for(molecule::const_iterator iter = const_cast<const molecule *>(mol)->begin();
+      iter != const_cast<const molecule *>(mol)->end();
+      ++iter) {
     const atom * const Father = (*iter)->GetTrueFather();
     if (AtomMask.isTrue(Father->getNr())) // apply mask

src/Fragmentation/Graph.cpp

@@ -265 +265 @@
         keyiter != iter->first.end(); ++keyiter) {
       const size_t globalid = *keyiter;
-      const atom *Walker = World::getInstance().getAtom(AtomById(globalid));
+      const atom * const Walker = const_cast<const World &>(World::getInstance()).
+          getAtom(AtomById(globalid));
       if (Walker != NULL) {
         if (Walker->getMolecule() != mol) {

src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp

@@ -59 +59 @@
       iter != keyset.end(); ++iter) {
 //    LOG(2, "DEBUG: Current global id is " << *iter << ".");
-    const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
+    const atom * const Walker = const_cast<const World &>(World::getInstance()).
+        getAtom(AtomById(*iter));
     if (Walker != NULL) {
       size_t NoBonds = 0;
@@ -65 +66 @@
       for (BondList::const_iterator bonditer = ListOfBonds.begin();
           bonditer != ListOfBonds.end(); ++bonditer) {
-        const atom *OtherWalker = (*bonditer)->GetOtherAtom(Walker);
+        const atom * const OtherWalker = (*bonditer)->GetOtherAtom(Walker);
         if (keyset.count(OtherWalker->getId()))
           ++NoBonds;
@@ -89 +90 @@
       iter != keyset.end(); ++iter) {
 //    LOG(2, "DEBUG: Current global id is " << *iter << ".");
-    const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
+    const atom * const Walker = const_cast<const World &>(World::getInstance()).
+        getAtom(AtomById(*iter));
     if (Walker != NULL) {
       const BondList& ListOfBonds = Walker->getListOfBonds();
       for (BondList::const_iterator bonditer = ListOfBonds.begin();
           bonditer != ListOfBonds.end(); ++bonditer) {
-        const atom *OtherWalker = (*bonditer)->GetOtherAtom(Walker);
+        const atom * const OtherWalker = (*bonditer)->GetOtherAtom(Walker);
 //        LOG(2, "DEBUG: Neighbor is " << OtherWalker->getId() << ".");
         if ((keyset.count(OtherWalker->getId())) && (Walker->getId() < OtherWalker->getId())) {