Changeset f01769 for src/moleculelist.cpp

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, Candidate_v1.7.0, 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).

File:

• src/moleculelist.cpp (modified) (12 diffs)

src/moleculelist.cpp

@@ -129 +129 @@
   //LOG(0, "Comparing fragment no. " << *(molecule **)a << " to " << *(molecule **)b << ".");
   // Yes those types are awkward... but check it for yourself it checks out this way
-  molecule *const *mol1_ptr= static_cast<molecule *const *>(a);
-  molecule *mol1 = *mol1_ptr;
-  molecule *const *mol2_ptr= static_cast<molecule *const *>(b);
-  molecule *mol2 = *mol2_ptr;
+  const molecule *const *mol1_ptr= static_cast<molecule *const *>(a);
+  const molecule *mol1 = *mol1_ptr;
+  const molecule *const *mol2_ptr= static_cast<molecule *const *>(b);
+  const molecule *mol2 = *mol2_ptr;
   if (mol1->getAtomCount() < mol2->getAtomCount()) {
     return -1;
@@ -212 +212 @@
   else {
     Origin.Zero();
-    for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
+    for (MoleculeList::const_iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
       // count atoms per element and determine size of bounding sphere
       size=0.;
-      for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
+      const molecule *MolRunner = *ListRunner;
+      for (molecule::const_iterator iter = MolRunner->begin(); iter != MolRunner->end(); ++iter) {
         counts[(*iter)->getType()->getAtomicNumber()]++;
         if ((*iter)->DistanceSquared(Origin) > size)
@@ -221 +222 @@
       }
       // output Index, Name, number of atoms, chemical formula
-      (*out) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->getAtomCount() << "\t";
+      (*out) << (MolRunner->ActiveFlag ? "*" : " ") << MolRunner->IndexNr << "\t" << MolRunner->name << "\t\t" << MolRunner->getAtomCount() << "\t";
 
       std::map<atomicNumber_t,unsigned int>::reverse_iterator iter;
@@ -229 +230 @@
       }
       // Center and size
-      Vector Center = (*ListRunner)->DetermineCenterOfAll();
+      Vector Center = MolRunner->DetermineCenterOfAll();
       (*out) << "\t" << Center << "\t" << sqrt(size) << endl;
     }
@@ -407 +408 @@
         correction[k][j] = 0.;
     // 2. take every hydrogen that is a saturated one
-    for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
+    const molecule *MolRunner = *ListRunner;
+    for (molecule::const_iterator iter = MolRunner->begin(); iter != MolRunner->end(); ++iter) {
       //LOG(1, "(*iter): " << *(*iter) << " with first bond " << *((*iter)->getListOfBonds().begin()) << ".");
       if (((*iter)->getType()->getAtomicNumber() == 1) && (((*iter)->getFather() == NULL)
           || ((*iter)->getFather()->getType()->getAtomicNumber() != 1))) { // if it's a hydrogen
-        for (molecule::const_iterator runner = (*ListRunner)->begin(); runner != (*ListRunner)->end(); ++runner) {
+        for (molecule::const_iterator runner = MolRunner->begin(); runner != MolRunner->end(); ++runner) {
           //LOG(2, "Runner: " << *(*runner) << " with first bond " << *((*iter)->getListOfBonds().begin()) << ".");
           // 3. take every other hydrogen that is the not the first and not bound to same bonding partner
@@ -420 +422 @@
             distance = (*runner)->distance(*(*iter));
             //std::stringstream output;
-            //output << "Fragment " << (*ListRunner)->name << ": " << *(*runner) << "<= " << distance << "=>" << *(*iter) << ":";
+            //output << "Fragment " << MolRunner->name << ": " << *(*runner) << "<= " << distance << "=>" << *(*iter) << ":";
             for (int k = 0; k < a; k++) {
               for (int j = 0; j < b; j++) {
@@ -447 +449 @@
     line.append("/");
     line += FRAGMENTPREFIX;
-    FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), (*ListRunner)->IndexNr);
+    FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), MolRunner->IndexNr);
     line += FragmentNumber;
     delete[] (FragmentNumber);
@@ -506 +508 @@
     for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
       periodentafel::const_iterator elemIter;
+      const molecule *MolRunner = *ListRunner;
       for(elemIter=periode->begin();elemIter!=periode->end();++elemIter){
-        if ((*ListRunner)->hasElement((*elemIter).first)) { // if this element got atoms
-          for(molecule::iterator atomIter = (*ListRunner)->begin(); atomIter !=(*ListRunner)->end();++atomIter){
+        if (MolRunner->hasElement((*elemIter).first)) { // if this element got atoms
+          for(molecule::const_iterator atomIter = MolRunner->begin(); atomIter !=MolRunner->end();++atomIter){
             if ((*atomIter)->getType()->getAtomicNumber() == (*elemIter).first) {
               if (((*atomIter)->GetTrueFather() != NULL) && ((*atomIter)->GetTrueFather() != (*atomIter))) {// if there is a rea
@@ -557 +560 @@
   for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
     // correct periodic
+    const molecule *MolRunner = *ListRunner;
     if ((*ListRunner)->ScanForPeriodicCorrection()) {
       count++;
@@ -565 +569 @@
       std::stringstream output;
       output << "Contained atoms: ";
-      for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
+      for (molecule::const_iterator iter = MolRunner->begin(); iter != MolRunner->end(); ++iter) {
         output << (*iter)->getName() << " ";
       }
@@ -573 +577 @@
     {
 //      // center on edge
-//      (*ListRunner)->CenterEdge(&BoxDimension);
+//      MolRunner->CenterEdge(&BoxDimension);
 //      for (int k = 0; k < NDIM; k++)  // if one edge is to small, set at least to 1 angstroem
 //        if (BoxDimension[k] < 1.)
@@ -588 +592 @@
 //      }
 //      World::getInstance().setDomain(cell_size);
-//      (*ListRunner)->Translate(&BoxDimension);
+//      MolRunner->Translate(&BoxDimension);
 
       // output file