Changeset 6d35e4 for src/atom.cpp

Timestamp:

May 7, 2008, 1:38:13 PM (18 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, 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:

8d9c38

Parents:

db066d

Message:

AtomStackClass -> template <typename T> StackClass<T> change in new file stackclass.hpp, other templates to helpers.hpp

StackClass was changed to a template and as template code may only be present in header file was moved to a new
header file stackclass.hpp. New file was added to Makefile.am
Other templates (list management et al) were moved to helpers.hpp as they are more sensibly placed there.

File:

• src/atom.cpp (modified) (1 diff)

src/atom.cpp

@@ -106 +106 @@
 };
 
-/******************************** Functions for class AtomStackClass ********************************/
-
-/** Constructor of class AtomStackClass.
- */
-AtomStackClass::AtomStackClass(int dimension)
-{
-  CurrentLastEntry = 0;
-  CurrentFirstEntry = 0;
-  NextFreeField = 0;
-  EntryCount = dimension;
-  StackList = (atom **) Malloc(sizeof(atom *)*EntryCount, "AtomStackClass::AtomStackClass: **StackList");
-};
-
-/** Destructor of class AtomStackClass.
- */
-AtomStackClass::~AtomStackClass()
-{
-  Free((void **)&StackList, "AtomStackClass::AtomStackClass: **StackList");
-};
-
-/** Pushes an object onto the stack.
- * \param *object atom to be pushed on stack
- * \return true - sucess, false - failure, meaning stack field was occupied
- */
-bool AtomStackClass::Push(atom *object)
-{
-  if (!IsFull()) {    // check whether free field is really not occupied
-    StackList[NextFreeField] = object;
-    CurrentLastEntry = NextFreeField;
-    NextFreeField = (NextFreeField + 1) % EntryCount; // step on to next free field
-    return true;
-  } else {
-    cerr << "ERROR: Stack is full, " << "Stack: CurrentLastEntry " << CurrentLastEntry<< "\tCurrentFirstEntry " << CurrentFirstEntry << "\tNextFreeField " << NextFreeField << "\tEntryCount " << EntryCount << "!" << endl;
-    return false;
-  }
-};
-
-/** Pops first/oldest atom from stack.
- * First in, last out.
- * \return atom pointer from stack, NULL - if failure (no atom pointer in field)
- */
-atom *AtomStackClass::PopFirst()
-{
-  atom *Walker = NULL;
-  if (!IsEmpty()) {
-    Walker = StackList[CurrentFirstEntry];
-    if (Walker == NULL)
-      cerr << "ERROR: Stack's field is empty!" << endl;
-    StackList[CurrentFirstEntry] = NULL;
-    if (CurrentFirstEntry != CurrentLastEntry) { // hasn't last item been popped as well?
-      CurrentFirstEntry = (CurrentFirstEntry + 1) % EntryCount; // step back from current free field to last used (somehow modulo does not work in -1)
-    } else {
-      CurrentFirstEntry = (CurrentFirstEntry + 1) % EntryCount; // step back from current free field to last used (somehow modulo does not work in -1)
-      CurrentLastEntry = CurrentFirstEntry;
-    }
-  } else
-    cerr << "ERROR: Stack is empty!" << endl; 
-  return Walker;
-};
-
-/** Pops last atom from stack.
- * First in, first out.
- * \return atom pointer from stack, NULL - if failure (no atom pointer in field)
- */
-atom *AtomStackClass::PopLast()
-{
-  atom *Walker = NULL;
-  if (!IsEmpty()) {
-    Walker = StackList[CurrentLastEntry];
-    StackList[CurrentLastEntry] = NULL;
-    if (Walker == NULL)
-      cerr << "ERROR: Stack's field is empty!" << endl;
-    NextFreeField = CurrentLastEntry;
-    if (CurrentLastEntry != CurrentFirstEntry)  // has there been more than one item on stack
-      CurrentLastEntry = (CurrentLastEntry + (EntryCount-1)) % EntryCount; // step back from current free field to last (modulo does not work in -1, thus go EntryCount-1 instead)
-  } else {
-    cerr << "ERROR: Stack is empty!" << endl;
-  } 
-  return Walker;
-};
-
-/** Removes a certain item from the stack.
- * Item is seeked between \a CurrentFirstEntry and \a CurrentLastEntry, if found, place in stack is NULL'd and
- * all subsequent items shifted by one position downward (with wrapping taken into account).
- * \param *ptr adress of item
- * \return true - item was removed, false - item was not found
- */
-bool AtomStackClass::RemoveItem(atom *ptr)
-{
-  bool found = false;
-  cout << Verbose(5) << "First " << CurrentFirstEntry<< "\tLast " << CurrentLastEntry<< "\tNext " << NextFreeField<< "\tCount " << EntryCount<< "." << endl;
-  int i=CurrentFirstEntry;
-  if (!IsEmpty())
-    do {
-      if (StackList[i] == ptr) {  // if item found, remove
-        cout << Verbose(5) << "Item " << *ptr << " was number " << i << " on stack, removing it." << endl;
-        found = true;
-        StackList[i] = NULL;
-      }
-      if ((found) && (StackList[i] != NULL)) {  // means we have to shift (and not the removed item)
-        if (i == 0) { // we are down to first item in stack, have to put onto last item
-          cout << Verbose(5) << "Shifting item 0 to place " << EntryCount-1 << "." << endl;
-          StackList[EntryCount-1] = StackList[0];
-        } else {
-          cout << Verbose(5) << "Shifting item " << i << " to place " << i-1 << "." << endl;
-          StackList[i-1] = StackList[i];
-        }
-      }
-      i=((i + 1) % EntryCount); // step on
-    } while (i!=NextFreeField);
-  else
-    cerr << "ERROR: Stack is already empty!" << endl;
-  if (found) {
-    NextFreeField = CurrentLastEntry;
-    if (CurrentLastEntry != CurrentFirstEntry)  // has there been more than one item on stack
-      CurrentLastEntry = (CurrentLastEntry + (EntryCount-1)) % EntryCount;
-  }
-  return found;
-};
-
-/** Test the functionality of the stack.
- * \param *out ofstream for debugging
- * \param *test one item to put on stack  
- * \return true - all tests worked correctly
- */
-void AtomStackClass::TestImplementation(ofstream *out, atom *test)
-{
-  atom *Walker = test;
-  *out << Verbose(1) << "Testing the snake stack..." << endl;
-  for (int i=0;i<EntryCount;i++) {
-    *out << Verbose(2) << "Filling " << i << "th element of stack." << endl; 
-    Push(Walker);
-    Walker=Walker->next;
-  }
-  *out << endl;
-  Output(out);
-  if (IsFull())
-    *out << "Stack is full as supposed to be!" << endl;
-  else
-    *out << "ERROR: Stack is not as full as supposed to be!" << endl;
-  //if (StackList[(EntryCount+1)/2] != NULL) {
-    *out << "Removing element in the middle ..." << endl;
-    RemoveItem(StackList[(EntryCount+1)/2]);
-    Output(out);
-  //}
-  //if (StackList[CurrentFirstEntry] != NULL) {
-    *out << "Removing first element  ..." << endl;
-    RemoveItem(StackList[CurrentFirstEntry]);
-    Output(out);
-  //}
-  //if (StackList[CurrentLastEntry] != NULL) {
-    *out << "Removing last element ..." << endl;
-    RemoveItem(StackList[CurrentLastEntry]);
-    Output(out);
-  //}
-  *out << "Clearing stack ... " << endl;  
-  ClearStack();
-  Output(out);
-  if (IsEmpty())
-    *out << "Stack is empty as supposed to be!" << endl;
-  else
-    *out << "ERROR: Stack is not as empty as supposed to be!" << endl;
-  *out << "done." << endl;
-};
-
-/** Puts contents of stack into ofstream \a *out.
- * \param *out ofstream for output
- */
-void AtomStackClass::Output(ofstream *out) const
-{
-  *out << "Contents of Stack: ";
-  for(int i=0;i<EntryCount;i++) {
-    *out << "\t";
-    if (i == CurrentFirstEntry)
-      *out << " 1";
-    if  (i == CurrentLastEntry)
-      *out << " "<< EntryCount;
-    if (i ==  NextFreeField)
-      *out << " F";
-    *out << ": " << StackList[i];
-  }
-  *out << endl;
-};
-
-/** Checks whether stack is empty.
- * Simply checks whether AtomStackClass::NextFreeField is equal to AtomStackClass::CurrentFirstEntry and
- * AtomStackClass::CurrentFirstEntry is equal to AtomStackClass::CurrentLastEntry.
- * \return true - empty, false - not
- */
-bool AtomStackClass::IsEmpty()
-{
-  return((NextFreeField == CurrentFirstEntry) && (CurrentLastEntry == CurrentFirstEntry));
-};
-
-/** Checks whether stack is full.
- * Simply checks whether AtomStackClass::NextFreeField is equal to AtomStackClass::CurrentFirstEntry and
- * AtomStackClass::CurrentFirstEntry is _not_ equal to AtomStackClass::CurrentLastEntry.
- * \return true - full, false - not
- */
-bool AtomStackClass::IsFull()
-{
-  return((NextFreeField == CurrentFirstEntry) && (CurrentLastEntry != CurrentFirstEntry));
-};
-
-/** Returns number of items on stack.
- * Simply returns difference between AtomStackClass::Stacklist entry AtomStackClass::CurrentEntry-1.
- * \return number of items on stack
- * \warning will never return correct item count if stack is full, i.e. count would be AtomStackClass::EntryCount.
- */
-int AtomStackClass::ItemCount()
-{
-  //cout << "Stack: CurrentLastEntry " << CurrentLastEntry<< "\tCurrentFirstEntry " << CurrentFirstEntry << "\tEntryCount " << EntryCount << "." << endl;
-  return((NextFreeField + (EntryCount - CurrentFirstEntry)) % EntryCount);
-};
-
-/** Clears the stack from all atoms.
- * \return true - sucess, false - failure
- */
-void AtomStackClass::ClearStack()
-{
-  for(int i=0;i<EntryCount; i++)
-    StackList[i] = NULL;
-  CurrentFirstEntry = 0;
-  CurrentLastEntry = 0;
-  NextFreeField = 0;
-};
-