Changeset a33931 for src/moleculelist.cpp

Timestamp:

Oct 5, 2009, 4:05:53 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, 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:

c26f44

Parents:

7dea7c (diff), c0917c (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'ConcaveHull' into ConvexHull

Conflicts:

.gitignore
molecuilder/src/Makefile.am
molecuilder/src/atom.cpp
molecuilder/src/tesselation.cpp

no serious overlaps, just a free Frees that were not present in ConcaveHull were MemoryAllocator class was added.

File:

• src/moleculelist.cpp (modified) (9 diffs)

src/moleculelist.cpp

@@ -8 +8 @@
 #include "config.hpp"
 #include "molecules.hpp"
+#include "memoryallocator.hpp"
 
 /*********************************** Functions for class MoleculeListClass *************************/
@@ -412 +413 @@
 
   // 0b. allocate memory for constants
-  FitConstant = (double ***) Malloc(sizeof(double **) * 3, "MoleculeListClass::AddHydrogenCorrection: ***FitConstant");
+  FitConstant = Malloc<double**>(3, "MoleculeListClass::AddHydrogenCorrection: ***FitConstant");
   for (int k = 0; k < 3; k++) {
-    FitConstant[k] = (double **) Malloc(sizeof(double *) * a, "MoleculeListClass::AddHydrogenCorrection: **FitConstant[]");
+    FitConstant[k] = Malloc<double*>(a, "MoleculeListClass::AddHydrogenCorrection: **FitConstant[]");
     for (int i = a; i--;) {
-      FitConstant[k][i] = (double *) Malloc(sizeof(double) * b, "MoleculeListClass::AddHydrogenCorrection: *FitConstant[][]");
+      FitConstant[k][i] = Malloc<double>(b, "MoleculeListClass::AddHydrogenCorrection: *FitConstant[][]");
     }
   }
@@ -461 +462 @@
 
   // 0d. allocate final correction matrix
-  correction = (double **) Malloc(sizeof(double *) * a, "MoleculeListClass::AddHydrogenCorrection: **correction");
+  correction = Malloc<double*>(a, "MoleculeListClass::AddHydrogenCorrection: **correction");
   for (int i = a; i--;)
-    correction[i] = (double *) Malloc(sizeof(double) * b, "MoleculeListClass::AddHydrogenCorrection: *correction[]");
+    correction[i] = Malloc<double>(b, "MoleculeListClass::AddHydrogenCorrection: *correction[]");
 
   // 1a. go through every molecule in the list
@@ -537 +538 @@
   output.close();
   // 6. free memory of parsed matrices
-  FitConstant = (double ***) Malloc(sizeof(double **) * a, "MoleculeListClass::AddHydrogenCorrection: ***FitConstant");
+  FitConstant = Malloc<double**>(a, "MoleculeListClass::AddHydrogenCorrection: ***FitConstant");
   for (int k = 0; k < 3; k++) {
-    FitConstant[k] = (double **) Malloc(sizeof(double *) * a, "MoleculeListClass::AddHydrogenCorrection: **FitConstant[]");
+    FitConstant[k] = Malloc<double*>(a, "MoleculeListClass::AddHydrogenCorrection: **FitConstant[]");
     for (int i = a; i--;) {
-      FitConstant[k][i] = (double *) Malloc(sizeof(double) * b, "MoleculeListClass::AddHydrogenCorrection: *FitConstant[][]");
+      FitConstant[k][i] = Malloc<double>(b, "MoleculeListClass::AddHydrogenCorrection: *FitConstant[][]");
     }
   }
@@ -702 +703 @@
     //outputFragment.clear();
     delete (FragmentNumber);
-    //Free((void **)&FragmentNumber, "MoleculeListClass::OutputConfigForListOfFragments: *FragmentNumber");
+    //Free(&FragmentNumber);
   }
   cout << " done." << endl;
@@ -845 +846 @@
   if ((FreeList) && (ListOfLocalAtoms != NULL)) {
     // free the index lookup list
-    Free((void **) &ListOfLocalAtoms[FragmentCounter], "MoleculeLeafClass::FillBondStructureFromReference - **ListOfLocalAtoms[]");
+    Free(&ListOfLocalAtoms[FragmentCounter]);
     if (FragmentCounter == 0) // first fragments frees the initial pointer to list
-      Free((void **) &ListOfLocalAtoms, "MoleculeLeafClass::FillBondStructureFromReference - ***ListOfLocalAtoms");
+      Free(&ListOfLocalAtoms);
   }
   FragmentCounter--;
@@ -910 +911 @@
   if (ListOfLocalAtoms == NULL) { // allocated initial pointer
     // allocate and set each field to NULL
-    ListOfLocalAtoms = (atom ***) Malloc(sizeof(atom **) * Counter, "MoleculeLeafClass::FillBondStructureFromReference - ***ListOfLocalAtoms");
+    ListOfLocalAtoms = Malloc<atom**>(Counter, "MoleculeLeafClass::FillBondStructureFromReference - ***ListOfLocalAtoms");
     if (ListOfLocalAtoms != NULL) {
       for (int i = Counter; i--;)
@@ -954 +955 @@
   if (FragmentList == NULL) {
     KeySetCounter = Count();
-    FragmentList = (Graph **) Malloc(sizeof(Graph *) * KeySetCounter, "MoleculeLeafClass::AssignKeySetsToFragment - **FragmentList");
+    FragmentList = Malloc<Graph*>(KeySetCounter, "MoleculeLeafClass::AssignKeySetsToFragment - **FragmentList");
     for (int i = KeySetCounter; i--;)
       FragmentList[i] = NULL;
@@ -990 +991 @@
   if ((FreeList) && (ListOfLocalAtoms != NULL)) {
     // free the index lookup list
-    Free((void **) &ListOfLocalAtoms[FragmentCounter], "MoleculeLeafClass::AssignKeySetsToFragment - **ListOfLocalAtoms[]");
+    Free(&ListOfLocalAtoms[FragmentCounter]);
     if (FragmentCounter == 0) // first fragments frees the initial pointer to list
-      Free((void **) &ListOfLocalAtoms, "MoleculeLeafClass::AssignKeySetsToFragment - ***ListOfLocalAtoms");
+      Free(&ListOfLocalAtoms);
   }
   *out << Verbose(1) << "End of AssignKeySetsToFragment." << endl;