Changeset 9879f6 for src/molecule.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/molecule.cpp (modified) (16 diffs)

src/molecule.cpp

@@ -37 +37 @@
   formula(this,boost::bind(&molecule::calcFormula,this)),
   last_atom(0),
-  InternalPointer(start)
-{
-  // init atom chain list
-  //start->father = NULL;
-  //end->father = NULL;
-  //link(start,end);
-
+  InternalPointer(begin())
+{
   // init bond chain list
   link(first,last);
@@ -67 +62 @@
   delete(first);
   delete(last);
-  end->getWorld()->destroyAtom(end);
-  start->getWorld()->destroyAtom(start);
 };
 
@@ -103 +96 @@
   for (int j = 0; j<MAX_ELEMENTS;j++)
     Counts[j] = 0;
-  for(atom *Walker = start; Walker != end; Walker = Walker->next) {
-    Counts[Walker->type->Z]++;
+  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+    Counts[(*iter)->type->Z]++;
   }
   for(element* Elemental = elemente->end; Elemental != elemente->start; Elemental = Elemental->previous) {
@@ -124 +117 @@
 }
 
-molecule::iterator molecule::ende(){
+molecule::iterator molecule::end(){
   return molecule::iterator(atoms.end(),this);
 }
 
-molecule::const_iterator molecule::ende() const{
+molecule::const_iterator molecule::end() const{
   return atoms.end();
+}
+
+bool molecule::empty() const
+{
+  return (begin() == end());
+}
+
+size_t molecule::size() const
+{
+  size_t counter = 0;
+  for (molecule::const_iterator iter = begin(); iter != end (); ++iter)
+    counter++;
+  return counter;
+}
+
+molecule::const_iterator molecule::erase( const_iterator loc )
+{
+  molecule::const_iterator iter = loc;
+  iter--;
+  atoms.erase( loc );
+  return iter;
+}
+
+molecule::const_iterator molecule::erase( atom *& key )
+{
+  molecule::const_iterator iter = find(key);
+  molecule::const_iterator runner = iter;
+  if (runner != begin()) {
+    runner--;
+    if (iter != end())
+      atoms.erase( key );
+    return runner;
+  } else
+    return end();
+}
+
+molecule::const_iterator molecule::find ( atom *& key ) const
+{
+  return atoms.find( key );
+}
+
+pair<molecule::iterator,bool> molecule::insert ( atom * const key )
+{
+  return atoms.insert(key);
 }
 
@@ -139 +176 @@
 bool molecule::AddAtom(atom *pointer)
 {
-  bool retval = false;
   OBSERVE;
   if (pointer != NULL) {
     pointer->sort = &pointer->nr;
-    pointer->nr = last_atom++;  // increase number within molecule
     AtomCount++;
     if (pointer->type != NULL) {
@@ -157 +192 @@
       }
     }
-    retval = add(pointer, end);
-  }
-  return retval;
+    insert(pointer);
+  }
+  return true;
 };
 
@@ -175 +210 @@
     walker->Name = Malloc<char>(strlen(pointer->Name) + 1, "atom::atom: *Name");
     strcpy (walker->Name, pointer->Name);
-    walker->nr = last_atom++;  // increase number within molecule
-    add(walker, end);
+    insert(walker);
     if ((pointer->type != NULL) && (pointer->type->Z != 1))
       NoNonHydrogen++;
@@ -701 +735 @@
     ElementCount--;
   RemoveBonds(pointer);
-  return remove(pointer, start, end);
+  erase(pointer);
+  return true;
 };
 
@@ -718 +753 @@
   if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
     ElementCount--;
-  unlink(pointer);
+  erase(pointer);
   return true;
 };
@@ -727 +762 @@
 bool molecule::CleanupMolecule()
 {
-  return (cleanup(first,last) && cleanup(start,end));
+  for (molecule::iterator iter = begin(); !empty(); iter = begin())
+      erase(iter);
+  return (cleanup(first,last));
 };
 
@@ -734 +771 @@
  * \return pointer to atom or NULL
  */
-atom * molecule::FindAtom(int Nr)  const{
-  atom * walker = find(&Nr, start,end);
-  if (walker != NULL) {
+atom * molecule::FindAtom(int Nr)  const
+{
+  molecule::const_iterator iter = begin();
+  for (; iter != end(); ++iter)
+    if ((*iter)->nr == Nr)
+      break;
+  if (iter != end()) {
     //Log() << Verbose(0) << "Found Atom Nr. " << walker->nr << endl;
-    return walker;
+    return (*iter);
   } else {
     Log() << Verbose(0) << "Atom not found in list." << endl;
@@ -896 +937 @@
 void molecule::CountAtoms()
 {
-  int i = 0;
-  atom *Walker = start;
-  while (Walker->next != end) {
-    Walker = Walker->next;
-    i++;
-  }
+  int i = size();
   if ((AtomCount == 0) || (i != AtomCount)) {
     Log() << Verbose(3) << "Mismatch in AtomCount " << AtomCount << " and recounted number " << i << ", renaming all." << endl;
@@ -910 +946 @@
       i=0;
       NoNonHydrogen = 0;
-      Walker = start;
-      while (Walker->next != end) {
-        Walker = Walker->next;
-        Walker->nr = i;   // update number in molecule (for easier referencing in FragmentMolecule lateron)
-        if (Walker->type->Z != 1) // count non-hydrogen atoms whilst at it
+      for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+        (*iter)->nr = i;   // update number in molecule (for easier referencing in FragmentMolecule lateron)
+        if ((*iter)->type->Z != 1) // count non-hydrogen atoms whilst at it
           NoNonHydrogen++;
-        Free(&Walker->Name);
-        Walker->Name = Malloc<char>(6, "molecule::CountAtoms: *walker->Name");
-        sprintf(Walker->Name, "%2s%02d", Walker->type->symbol, Walker->nr+1);
-        Log() << Verbose(3) << "Naming atom nr. " << Walker->nr << " " << Walker->Name << "." << endl;
+        Free(&(*iter)->Name);
+        (*iter)->Name = Malloc<char>(6, "molecule::CountAtoms: *walker->Name");
+        sprintf((*iter)->Name, "%2s%02d", (*iter)->type->symbol, (*iter)->nr+1);
+        Log() << Verbose(3) << "Naming atom nr. " << (*iter)->nr << " " << (*iter)->Name << "." << endl;
         i++;
       }
@@ -1092 +1126 @@
 int * molecule::GetFatherSonAtomicMap(molecule *OtherMolecule)
 {
-  atom *Walker = NULL, *OtherWalker = NULL;
   Log() << Verbose(3) << "Begin of GetFatherAtomicMap." << endl;
   int *AtomicMap = Malloc<int>(AtomCount, "molecule::GetAtomicMap: *AtomicMap");
@@ -1103 +1136 @@
   } else {
     Log() << Verbose(4) << "Map is ";
-    Walker = start;
-    while (Walker->next != end) {
-      Walker = Walker->next;
-      if (Walker->father == NULL) {
-        AtomicMap[Walker->nr] = -2;
+    for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+      if ((*iter)->father == NULL) {
+        AtomicMap[(*iter)->nr] = -2;
       } else {
-        OtherWalker = OtherMolecule->start;
-        while (OtherWalker->next != OtherMolecule->end) {
-          OtherWalker = OtherWalker->next;
+        for (molecule::const_iterator runner = OtherMolecule->begin(); runner != OtherMolecule->end(); ++runner) {
       //for (int i=0;i<AtomCount;i++) { // search atom
         //for (int j=0;j<OtherMolecule->AtomCount;j++) {
-          //Log() << Verbose(4) << "Comparing father " << Walker->father << " with the other one " << OtherWalker->father << "." << endl;
-          if (Walker->father == OtherWalker)
-            AtomicMap[Walker->nr] = OtherWalker->nr;
+          //Log() << Verbose(4) << "Comparing father " << (*iter)->father << " with the other one " << (*runner)->father << "." << endl;
+          if ((*iter)->father == (*runner))
+            AtomicMap[(*iter)->nr] = (*runner)->nr;
         }
       }
-      Log() << Verbose(0) << AtomicMap[Walker->nr] << "\t";
+      Log() << Verbose(0) << AtomicMap[(*iter)->nr] << "\t";
     }
     Log() << Verbose(0) << endl;
@@ -1153 +1182 @@
 void molecule::SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::*index) const
 {
-  atom *Walker = start;
-  while (Walker->next != end) {
-    Walker = Walker->next;
-    array[(Walker->*index)] = Walker;
+  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+    array[((*iter)->*index)] = (*iter);
   }
 };