Changeset 9879f6 for src/Legacy/oldmenu.cpp

Timestamp:

Mar 5, 2010, 10:16:47 AM (15 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:

d3347e

Parents:

e87acf

git-author:

Frederik Heber <heber@…> (03/05/10 10:08:44)

git-committer:

Frederik Heber <heber@…> (03/05/10 10:16:47)

Message:

Huge Refactoring due to class molecule now being an STL container.

• molecule::start and molecule::end were dropped. Hence, the usual construct Walker = start while (Walker->next != end) {

Walker = walker->next
...

}
was changed to
for (molecule::iterator iter = begin(); iter != end(); ++iter) {

...

}
and (*iter) used instead of Walker.

• Two build errors remain (beside some more in folder Actions, Patterns and unittest) in molecule_pointcloud.cpp and molecule.cpp
• lists.cpp was deleted as specialization of atom* was not needed anymore
• link, unlink, add, remove, removewithoutcheck all are not needed for atoms anymore, just for bonds (where first, last entries remain in molecule)
• CreateFatherLookupTable() was put back into class molecule.
• molecule::InternalPointer is now an iterator
• class PointCloud: GoToPrevious() and GetTerminalPoint() were dropped as not needed.
• some new STL functions in class molecule: size(), empty(), erase(), find() and insert()

File:

• src/Legacy/oldmenu.cpp (modified) (7 diffs)

src/Legacy/oldmenu.cpp

@@ -447 +447 @@
       break;
     case 'b':
-      second = mol->AskAtom("Enter number of atom as reference point: ");
-      Log() << Verbose(0) << "Enter radius: ";
-      cin >> tmp1;
-      first = mol->start;
-      second = first->next;
-      while(second != mol->end) {
-        first = second;
-        second = first->next;
-        if (first->x.DistanceSquared((const Vector *)&second->x) > tmp1*tmp1) // distance to first above radius ...
-          mol->RemoveAtom(first);
+      {
+        second = mol->AskAtom("Enter number of atom as reference point: ");
+        Log() << Verbose(0) << "Enter radius: ";
+        cin >> tmp1;
+        molecule::iterator runner;
+        for (molecule::iterator iter = mol->begin(); iter != mol->end(); ) {
+          runner = iter++;
+          if ((*runner)->x.DistanceSquared((const Vector *)&(*runner)->x) > tmp1*tmp1) // distance to first above radius ...
+            mol->RemoveAtom((*runner));
+        }
       }
       break;
@@ -466 +466 @@
       Log() << Verbose(0) << "Upper boundary: ";
       cin >> tmp2;
-      first = mol->start;
-      second = first->next;
-      while(second != mol->end) {
-        first = second;
-        second = first->next;
-        if ((first->x.x[axis] < tmp1) || (first->x.x[axis] > tmp2)) {// out of boundary ...
-          //Log() << Verbose(0) << "Atom " << *first << " with " << first->x.x[axis] << " on axis " << axis << " is out of bounds [" << tmp1 << "," << tmp2 << "]." << endl;
-          mol->RemoveAtom(first);
+      molecule::iterator runner;
+      for (molecule::iterator iter = mol->begin(); iter != mol->end(); ) {
+        runner = iter++;
+        if (((*runner)->x.x[axis] < tmp1) || ((*runner)->x.x[axis] > tmp2)) {// out of boundary ...
+          //Log() << Verbose(0) << "Atom " << *(*runner) << " with " << (*runner)->x.x[axis] << " on axis " << axis << " is out of bounds [" << tmp1 << "," << tmp2 << "]." << endl;
+          mol->RemoveAtom((*runner));
         }
       }
@@ -516 +514 @@
         min[i] = 0.;
 
-      second = mol->start;
-      while ((second->next != mol->end)) {
-        second = second->next; // advance
-        Z = second->type->Z;
+      for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+        Z = (*iter)->type->Z;
         tmp1 = 0.;
-        if (first != second) {
+        if (first != (*iter)) {
           x.CopyVector((const Vector *)&first->x);
-          x.SubtractVector((const Vector *)&second->x);
+          x.SubtractVector((const Vector *)&(*iter)->x);
           tmp1 = x.Norm();
         }
         if ((tmp1 != 0.) && ((min[Z] == 0.) || (tmp1 < min[Z]))) min[Z] = tmp1;
-        //Log() << Verbose(0) << "Bond length between Atom " << first->nr << " and " << second->nr << ": " << tmp1 << " a.u." << endl;
+        //Log() << Verbose(0) << "Bond length between Atom " << first->nr << " and " << ((*iter)->nr << ": " << tmp1 << " a.u." << endl;
       }
       for (int i=MAX_ELEMENTS;i--;)
@@ -767 +763 @@
       vectors = new Vector *[count];
       j = 0;
-      first = mol->start;
-      while (first->next != mol->end) { // make a list of all atoms with coordinates and element
-        first = first->next;
-        Elements[j] = first->type;
-        vectors[j] = &first->x;
+      for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+        Elements[j] = (*iter)->type;
+        vectors[j] = &(*iter)->x;
         j++;
       }
@@ -1029 +1023 @@
     return;
   }
-  atom *Walker = mol->start;
 
   // generate some KeySets
@@ -1035 +1028 @@
   KeySet TestSets[mol->AtomCount+1];
   i=1;
-  while (Walker->next != mol->end) {
-    Walker = Walker->next;
+  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
     for (int j=0;j<i;j++) {
-      TestSets[j].insert(Walker->nr);
+      TestSets[j].insert((*iter)->nr);
     }
     i++;
@@ -1044 +1036 @@
   Log() << Verbose(0) << "Testing insertion of already present item in KeySets." << endl;
   KeySetTestPair test;
-  test = TestSets[mol->AtomCount-1].insert(Walker->nr);
-  if (test.second) {
-    Log() << Verbose(1) << "Insertion worked?!" << endl;
+  molecule::const_iterator iter = mol->begin();
+  if (iter != mol->end()) {
+    test = TestSets[mol->AtomCount-1].insert((*iter)->nr);
+    if (test.second) {
+      Log() << Verbose(1) << "Insertion worked?!" << endl;
+    } else {
+      Log() << Verbose(1) << "Insertion rejected: Present object is " << (*test.first) << "." << endl;
+    }
   } else {
-    Log() << Verbose(1) << "Insertion rejected: Present object is " << (*test.first) << "." << endl;
-  }
-  TestSets[mol->AtomCount].insert(mol->end->previous->nr);
-  TestSets[mol->AtomCount].insert(mol->end->previous->previous->previous->nr);
+    eLog() << Verbose(1) << "No atoms to test double insertion." << endl;
+  }
 
   // constructing Graph structure