Changeset 776b64 for src/moleculelist.cpp

Timestamp:

Oct 27, 2009, 4:11:22 PM (16 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, Candidate_v1.7.1, 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:

fb73b8

Parents:

ad37ab

Message:

Huge refactoring to make const what is const (ticket #38), continued.

• too many changes because of too many cross-references to be able to list them up here.
• NOTE that "make check" runs fine and did catch several error.
• note that we had to use const_iterator several times when the map, ... was declared const.
• at times we changed an allocated LinkedCell LCList(...) into

const LinkedCell *LCList;
LCList = new LinkedCell(...);

• also mutable (see ticket #5) was used, e.g. for molecule::InternalPointer (PointCloud changes are allowed, because they are just accounting).

Signed-off-by: Frederik Heber <heber@…>

File:

• src/moleculelist.cpp (modified) (3 diffs)

src/moleculelist.cpp

@@ -306 +306 @@
 bool MoleculeListClass::EmbedMerge(molecule *mol, molecule *srcmol)
 {
+  LinkedCell *LCList = NULL;
+  Tesselation *TesselStruct = NULL;
   if ((srcmol == NULL) || (mol == NULL)) {
     cout << Verbose(1) << "ERROR: Either fixed or variable molecule is given as NULL." << endl;
@@ -312 +314 @@
 
   // calculate envelope for *mol
-  LinkedCell *LCList = new LinkedCell(mol, 8.);
-  FindNonConvexBorder((ofstream *)&cout, mol, LCList, 4., NULL);
-  if (mol->TesselStruct == NULL) {
+  LCList = new LinkedCell(mol, 8.);
+  FindNonConvexBorder((ofstream *)&cout, mol, TesselStruct, (const LinkedCell *&)LCList, 4., NULL);
+  if (TesselStruct == NULL) {
     cout << Verbose(1) << "ERROR: Could not tesselate the fixed molecule." << endl;
     return false;
   }
   delete(LCList);
-  LCList = new LinkedCell(mol->TesselStruct, 8.);  // re-create with boundary points only!
+  LCList = new LinkedCell(TesselStruct, 8.);  // re-create with boundary points only!
 
   // prepare index list for bonds
@@ -333 +335 @@
     Walker = Walker->next;
     cout << Verbose(2) << "INFO: Current Walker is " << *Walker << "." << endl;
-    if (!mol->TesselStruct->IsInnerPoint((ofstream *)&cout, Walker->x, LCList)) {
+    if (!TesselStruct->IsInnerPoint((ofstream *)&cout, Walker->x, LCList)) {
       CopyAtoms[Walker->nr] = new atom(Walker);
       mol->AddAtom(CopyAtoms[Walker->nr]);