Changeset 957c42 for src/molecule.cpp

Timestamp:

Feb 25, 2010, 11:15:22 AM (16 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

5a7243

Parents:

0188ea (diff), 244d26 (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 'StructureRefactoring' into MenuRefactoring

File:

• src/molecule.cpp (modified) (8 diffs)

src/molecule.cpp

@@ -8 +8 @@
 #include <boost/bind.hpp>
 
+#include "World.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
@@ -30 +31 @@
  * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
  */
-molecule::molecule(const periodentafel * const teil) : elemente(teil), start(new atom), end(new atom), 
+molecule::molecule(const periodentafel * const teil) : elemente(teil), start(World::get()->createAtom()), end(World::get()->createAtom()),
   first(new bond(start, end, 1, -1)), last(new bond(start, end, 1, -1)), MDSteps(0), AtomCount(0), 
   BondCount(0), ElementCount(0), NoNonHydrogen(0), NoNonBonds(0), NoCyclicBonds(0), BondDistance(0.), 
@@ -60 +61 @@
   delete(first);
   delete(last);
-  delete(end);
-  delete(start);
+  end->getWorld()->destroyAtom(end);
+  start->getWorld()->destroyAtom(start);
 };
 
@@ -135 +136 @@
   OBSERVE;
   if (pointer != NULL) {
-    atom *walker = new atom(pointer);
+    atom *walker = pointer->clone();
     walker->Name = Malloc<char>(strlen(pointer->Name) + 1, "atom::atom: *Name");
     strcpy (walker->Name, pointer->Name);
@@ -242 +243 @@
   switch(TopBond->BondDegree) {
     case 1:
-      FirstOtherAtom = new atom();    // new atom
+      FirstOtherAtom = World::get()->createAtom();    // new atom
       FirstOtherAtom->type = elemente->FindElement(1);  // element is Hydrogen
       FirstOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
@@ -299 +300 @@
 
       // create the two Hydrogens ...
-      FirstOtherAtom = new atom();
-      SecondOtherAtom = new atom();
+      FirstOtherAtom = World::get()->createAtom();
+      SecondOtherAtom = World::get()->createAtom();
       FirstOtherAtom->type = elemente->FindElement(1);
       SecondOtherAtom->type = elemente->FindElement(1);
@@ -354 +355 @@
     case 3:
       // take the "usual" tetraoidal angle and add the three Hydrogen in direction of the bond (height of the tetraoid)
-      FirstOtherAtom = new atom();
-      SecondOtherAtom = new atom();
-      ThirdOtherAtom = new atom();
+      FirstOtherAtom = World::get()->createAtom();
+      SecondOtherAtom = World::get()->createAtom();
+      ThirdOtherAtom = World::get()->createAtom();
       FirstOtherAtom->type = elemente->FindElement(1);
       SecondOtherAtom->type = elemente->FindElement(1);
@@ -475 +476 @@
     MDSteps++;
   for(i=0;i<NumberOfAtoms;i++){
-    Walker = new atom;
+    Walker = World::get()->createAtom();
     getline(xyzfile,line,'\n');
     istringstream *item = new istringstream(line);