Changeset ead4e6 for src

Timestamp:

Mar 12, 2010, 1:16:01 PM (15 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, 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:

745a85

Parents:

c3dbe0

Message:

Made the periodentafel use STL-containers instead of custom llists

Location:

src

Files:

• Actions/AtomsCalculation_impl.hpp (modified) (1 diff)
• Actions/Calculation_impl.hpp (modified) (1 diff)
• Descriptors/AtomTypeDescriptor.cpp (modified) (2 diffs)
• Descriptors/AtomTypeDescriptor.hpp (modified) (1 diff)
• Descriptors/AtomTypeDescriptor_impl.hpp (modified) (1 diff)
• Legacy/oldmenu.cpp (modified) (2 diffs)
• World.hpp (modified) (1 diff)
• atom.hpp (modified) (1 diff)
• atom_atominfo.cpp (modified) (1 diff)
• atom_atominfo.hpp (modified) (1 diff)
• builder.cpp (modified) (3 diffs)
• config.cpp (modified) (2 diffs)
• defs.hpp (modified) (2 diffs)
• element.cpp (modified) (4 diffs)
• element.hpp (modified) (3 diffs)
• leastsquaremin.hpp (modified) (1 diff)
• molecule.cpp (modified) (1 diff)
• moleculelist.cpp (modified) (6 diffs)
• periodentafel.cpp (modified) (20 diffs)
• periodentafel.hpp (modified) (4 diffs)
• types.hpp (added)
• unittests/AtomDescriptorTest.hpp (modified) (1 diff)
• unittests/CacheableTest.cpp (modified) (2 diffs)
• unittests/MoleculeDescriptorTest.hpp (modified) (1 diff)
• unittests/analysisbondsunittest.cpp (modified) (1 diff)
• unittests/atomsCalculationTest.cpp (modified) (4 diffs)
• unittests/atomsCalculationTest.hpp (modified) (2 diffs)
• unittests/bondgraphunittest.cpp (modified) (1 diff)

src/Actions/AtomsCalculation_impl.hpp

@@ -19 +19 @@
 AtomsCalculation<T>::AtomsCalculation(boost::function<T(atom*)> _op,std::string name,AtomDescriptor _descr) :
   Calculation<std::vector<T> >(0,name,false),
-  op(_op),
-  descr(_descr)
+  descr(_descr),
+  op(_op)
 {}
 

src/Actions/Calculation_impl.hpp

@@ -16 +16 @@
 Calculation<T>::Calculation(int _maxSteps, std::string _name, bool _doRegister) :
   Process(_maxSteps,_name,_doRegister),
-  done(false),
-  result(0)
+  result(0),
+  done(false)
 {}
 

src/Descriptors/AtomTypeDescriptor.cpp

@@ -13 +13 @@
 #include "periodentafel.hpp"
 
-AtomTypeDescriptor_impl::AtomTypeDescriptor_impl(element* _type) :
+AtomTypeDescriptor_impl::AtomTypeDescriptor_impl(const element* _type) :
   type(_type)
 {}
@@ -24 +24 @@
 }
 
-AtomDescriptor AtomByType(element *elem){
+AtomDescriptor AtomByType(const element *elem){
   return AtomDescriptor(AtomDescriptor::impl_ptr(new AtomTypeDescriptor_impl(elem)));
 }
 
 AtomDescriptor AtomByType(int Z){
-  element * elem = World::getInstance().getPeriode()->FindElement(Z);
+  const element * elem = World::getInstance().getPeriode()->FindElement(Z);
   return AtomByType(elem);
 }

src/Descriptors/AtomTypeDescriptor.hpp

@@ -13 +13 @@
 class element;
 
-AtomDescriptor AtomByType(element *);
+AtomDescriptor AtomByType(const element *);
 AtomDescriptor AtomByType(int);
 

src/Descriptors/AtomTypeDescriptor_impl.hpp

@@ -14 +14 @@
 {
 public:
-  AtomTypeDescriptor_impl(element* _type);
+  AtomTypeDescriptor_impl(const element* _type);
   virtual ~AtomTypeDescriptor_impl();
 
   bool predicate(std::pair<atomId_t,atom*> atom);
 private:
-  element *type;
+  const element * const type;
 };
 

src/Legacy/oldmenu.cpp

@@ -748 +748 @@
   int axis,faktor,count,j;
   atom *first = NULL;
-  element **Elements;
+  const element **Elements;
   Vector x,y;
   Vector **vectors;
@@ -764 +764 @@
     if (mol->AtomCount != 0) {  // if there is more than none
       count = mol->AtomCount;  // is changed becausing of adding, thus has to be stored away beforehand
-      Elements = new element *[count];
+      Elements = new const element *[count];
       vectors = new Vector *[count];
       j = 0;

src/World.hpp

@@ -16 +16 @@
 #include <boost/shared_ptr.hpp>
 
-#include "defs.hpp"
+#include "types.hpp"
 #include "Patterns/Observer.hpp"
 #include "Patterns/Cacheable.hpp"

src/atom.hpp

@@ -28 +28 @@
 #include "atom_trajectoryparticle.hpp"
 #include "tesselation.hpp"
+#include "types.hpp"
 
 /****************************************** forward declarations *****************************/

src/atom_atominfo.cpp

@@ -20 +20 @@
 };
 
-element *AtomInfo::getType(){
+const element *AtomInfo::getType(){
   return type;
 }
 
-void AtomInfo::setType(element* _type) {
+void AtomInfo::setType(const element* _type) {
   type = _type;
 }
 
 void AtomInfo::setType(int Z) {
-  element *elem = World::getInstance().getPeriode()->FindElement(Z);
+  const element *elem = World::getInstance().getPeriode()->FindElement(Z);
   setType(elem);
 }

src/atom_atominfo.hpp

@@ -32 +32 @@
   Vector v;       //!< velocity vector of atom, giving last velocity within cell
   Vector F;       //!< Force vector of atom, giving last force within cell
-  element *type;  //!< pointing to element
+  const element *type;  //!< pointing to element
 
   AtomInfo();
   ~AtomInfo();
 
-  element *getType();
-  void setType(element *);
+  const element *getType();
+  void setType(const element *);
   void setType(int);
 

src/builder.cpp

@@ -1593 +1593 @@
                 }
                 LCList = new LinkedCell(Boundary, 2.*radius);
-                element *elemental = periode->FindElement((const int) atoi(argv[argptr]));
+                const element *elemental = periode->FindElement((atomicNumber_t) atoi(argv[argptr]));
                 FindNonConvexBorder(Boundary, TesselStruct, LCList, radius, NULL);
                 int ranges[NDIM] = {1,1,1};
@@ -2070 +2070 @@
                   int faktor = atoi(argv[argptr++]);
                   int count;
-                  element ** Elements;
+                  const element ** Elements;
                   Vector ** vectors;
                   if (faktor < 1) {
-                    eLog() << Verbose(1) << "Repetition factor mus be greater than 1!" << endl;
+                    eLog() << Verbose(1) << "Repetition factor must be greater than 1!" << endl;
                     faktor = 1;
                   }
@@ -2079 +2079 @@
                   if (mol->AtomCount != 0) {  // if there is more than none
                     count = mol->AtomCount;   // is changed becausing of adding, thus has to be stored away beforehand
-                    Elements = new element *[count];
+                    Elements = new const element *[count];
                     vectors = new Vector *[count];
                     j = 0;

src/config.cpp

@@ -675 +675 @@
 {
   int MaxTypes = 0;
-  element *elementhash[MAX_ELEMENTS];
+  const element *elementhash[MAX_ELEMENTS];
   char name[MAX_ELEMENTS];
   char keyword[MAX_ELEMENTS];
@@ -1107 +1107 @@
   string zeile;
   string dummy;
-  element *elementhash[128];
+  const element *elementhash[128];
   int Z = -1;
   int No = -1;

src/defs.hpp

@@ -33 +33 @@
 enum Shading { white, lightgray, darkgray, black };  //!< color in Breadth-First-Search analysis
 
-// some types that can stay abstract
-typedef unsigned int moleculeId_t;
-typedef unsigned int atomId_t;
+
 
 //enum CutCyclicBond { KeepBond,  SaturateBond }; //!< Saturation scheme either atom- or bondwise 
@@ -85 +83 @@
 #define STD_SEPERATOR_SPACER '-'
 
-// some types used to set template parameters
-struct true_type{
-  enum{value=1};
-};
-struct false_type{
-  enum{value = 0};
-};
-
 #endif /*DEFS_HPP_*/

src/element.cpp

@@ -9 +9 @@
 
 #include "element.hpp"
+
+using namespace std;
 
 /************************************* Functions for class element **********************************/
@@ -35 +37 @@
  * \param *out outstream
  */
-bool element::Output(ofstream * const out) const
+bool element::Output(ostream * const out) const
 { 
   if (out != NULL) {
@@ -50 +52 @@
  * \param NoOfAtoms total number of atom of this element type
  */
-bool element::Checkout(ofstream * const out, const int Number, const int NoOfAtoms) const
+bool element::Checkout(ostream * const out, const int Number, const int NoOfAtoms) const
 { 
   if (out != NULL) {
@@ -58 +60 @@
     return false;
 };
+
+atomicNumber_t element::getNumber() const{
+  return Z;
+}
+
+string element::getSymbol() const{
+  return string(symbol);
+}

src/element.hpp

@@ -9 +9 @@
 #define ELEMENT_HPP_
 
-using namespace std;
-
 /*********************************************** includes ***********************************/
 
@@ -19 +17 @@
 
 #include <iostream>
+#include <string>
 
 #include "defs.hpp"
+#include "types.hpp"
 
 /********************************************** declarations *******************************/
@@ -50 +50 @@
   ~element();
 
+  // accessor functions
+  atomicNumber_t getNumber() const;
+  std::string getSymbol() const;
+
   //> print element entries to screen
-  bool Output(ofstream * const out) const;
-  bool Checkout(ofstream * const out, const int No, const int NoOfAtoms) const;
+  bool Output(std::ostream * const out) const;
+  bool Checkout(std::ostream * const out, const int No, const int NoOfAtoms) const;
 
   private:

src/leastsquaremin.hpp

@@ -42 +42 @@
   gsl_vector *x;
   const molecule *mol;
-  element *type;
+  const element *type;
 };
 

src/molecule.cpp

@@ -99 +99 @@
 
 std::string molecule::calcFormula(){
-  int Counts[MAX_ELEMENTS];
+  std::map<atomicNumber_t,unsigned int> counts;
   stringstream sstr;
-  for (int j = 0; j<MAX_ELEMENTS;j++)
-    Counts[j] = 0;
+  periodentafel *periode = World::getInstance().getPeriode();
   for(atom *Walker = start; Walker != end; Walker = Walker->next) {
-    Counts[Walker->type->Z]++;
-  }
-  for(element* Elemental = elemente->end; Elemental != elemente->start; Elemental = Elemental->previous) {
-    if (Counts[Elemental->Z] != 0)
-      sstr << Elemental->symbol << Counts[Elemental->Z];
+    counts[Walker->type->getNumber()]++;
+  }
+  std::map<atomicNumber_t,unsigned int>::reverse_iterator iter;
+  for(iter = counts.rbegin(); iter != counts.rend(); ++iter) {
+    atomicNumber_t Z = (*iter).first;
+    sstr << periode->FindElement(Z)->symbol << (*iter).second;
   }
   return sstr.str();

src/moleculelist.cpp

@@ -141 +141 @@
 void MoleculeListClass::Enumerate(ostream *out)
 {
-  element* Elemental = NULL;
   atom *Walker = NULL;
-  int Counts[MAX_ELEMENTS];
+  periodentafel *periode = World::getInstance().getPeriode();
+  std::map<atomicNumber_t,unsigned int> counts;
   double size=0;
   Vector Origin;
@@ -155 +155 @@
     Origin.Zero();
     for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
-      // reset element counts
-      for (int j = 0; j<MAX_ELEMENTS;j++)
-        Counts[j] = 0;
       // count atoms per element and determine size of bounding sphere
       size=0.;
@@ -163 +160 @@
       while (Walker->next != (*ListRunner)->end) {
         Walker = Walker->next;
-        Counts[Walker->type->Z]++;
+        counts[Walker->type->getNumber()]++;
         if (Walker->x.DistanceSquared(&Origin) > size)
           size = Walker->x.DistanceSquared(&Origin);
@@ -169 +166 @@
       // output Index, Name, number of atoms, chemical formula
       (*out) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
-      Elemental = (*ListRunner)->elemente->end;
-      while(Elemental->previous != (*ListRunner)->elemente->start) {
-        Elemental = Elemental->previous;
-        if (Counts[Elemental->Z] != 0)
-          (*out) << Elemental->symbol << Counts[Elemental->Z];
+
+      std::map<atomicNumber_t,unsigned int>::reverse_iterator iter;
+      for(iter=counts.rbegin(); iter!=counts.rend();++iter){
+        atomicNumber_t Z =(*iter).first;
+        (*out) << periode->FindElement(Z)->getSymbol() << (*iter).second;
       }
       // Center and size
@@ -580 +577 @@
   stringstream line;
   atom *Walker = NULL;
-  element *runner = NULL;
+  periodentafel *periode=World::getInstance().getPeriode();
 
   // open file for the force factors
@@ -590 +587 @@
     //output << prefix << "Forces" << endl;
     for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
-      runner = (*ListRunner)->elemente->start;
-      while (runner->next != (*ListRunner)->elemente->end) { // go through every element
-        runner = runner->next;
-        if ((*ListRunner)->ElementsInMolecule[runner->Z]) { // if this element got atoms
+      periodentafel::const_iterator elemIter;
+      for(elemIter=periode->begin();elemIter!=periode->end();++elemIter){
+          if ((*ListRunner)->ElementsInMolecule[(*elemIter).first]) { // if this element got atoms
           Walker = (*ListRunner)->start;
           while (Walker->next != (*ListRunner)->end) { // go through every atom of this element
             Walker = Walker->next;
-            if (Walker->type->Z == runner->Z) {
+            if (Walker->type->getNumber() == (*elemIter).first) {
               if ((Walker->GetTrueFather() != NULL) && (Walker->GetTrueFather() != Walker)) {// if there is a rea
                 //Log() << Verbose(0) << "Walker is " << *Walker << " with true father " << *( Walker->GetTrueFather()) << ", it

src/periodentafel.cpp

@@ -10 +10 @@
 #include <fstream>
 #include <cstring>
+#include <cassert>
 
 #include "element.hpp"
@@ -18 +19 @@
 #include "verbose.hpp"
 
+using namespace std;
+
 /************************************* Functions for class periodentafel ***************************/
 
@@ -23 +26 @@
  * Initialises start and end of list and resets periodentafel::checkliste to false.
  */
-periodentafel::periodentafel() : start(new element), end(new element)
-{
-  start->previous = NULL;
-  start->next = end;
-  end->previous = start;
-  end->next = NULL;
-};
+periodentafel::periodentafel()
+{};
 
 /** destructor for class periodentafel
@@ -37 +35 @@
 {
   CleanupPeriodtable();
-  delete(end);
-  delete(start);
 };
 
@@ -45 +41 @@
  * \return true - succeeded, false - does not occur
  */
-bool periodentafel::AddElement(element * const pointer)
-{
+periodentafel::iterator periodentafel::AddElement(element * const pointer)
+{
+  atomicNumber_t Z = pointer->getNumber();
+  assert(!elements.count(Z));
   pointer->sort = &pointer->Z;
-  if (pointer->Z < 1 && pointer->Z >= MAX_ELEMENTS)
+  if (pointer->getNumber() < 1 && pointer->getNumber() >= MAX_ELEMENTS)
     Log() << Verbose(0) << "Invalid Z number!\n";
-  return add(pointer, end);
+  pair<iterator,bool> res = elements.insert(pair<atomicNumber_t,element*>(Z,pointer));
+  return res.first;
 };
 
@@ -57 +56 @@
  * \return true - succeeded, false - element not found
  */
-bool periodentafel::RemoveElement(element * const pointer)
-{
-  return remove(pointer, start, end);
+void periodentafel::RemoveElement(element * const pointer)
+{
+  atomicNumber_t Z = pointer->getNumber();
+  elements.erase(Z);
 };
 
@@ -65 +65 @@
  * \return true - succeeded, false - does not occur
  */
-bool periodentafel::CleanupPeriodtable()
-{
-  return cleanup(start,end);
+void periodentafel::CleanupPeriodtable()
+{
+  elements.clear();
 };
 
@@ -75 +75 @@
  * \return pointer to element or NULL if not found
  */
-element * const periodentafel::FindElement(const int Z) const
-{
-  element *walker = find(&Z, start,end);
-  return(walker);
+const element * periodentafel::FindElement(atomicNumber_t Z) const
+{
+  const_iterator res = elements.find(Z);
+  return res!=elements.end()?((*res).second):0;
 };
 
@@ -86 +86 @@
  * \return pointer to element
  */
-element * const periodentafel::FindElement(const char * const shorthand) const
-{
-  element *walker =  periodentafel::start;
-  while (walker->next != periodentafel::end) {
-    walker = walker->next;
-    if (strncmp(walker->symbol, shorthand, 3) == 0)
-      return(walker);
+const element * periodentafel::FindElement(const char * const shorthand) const
+{
+  element *res = 0;
+  for(const_iterator iter=elements.begin();iter!=elements.end();++iter) {
+    if((*iter).second->getSymbol() == shorthand){
+      res = (*iter).second;
+      break;
+    }
   }
-  return (NULL);
+  return res;
 };
 
 /** Asks for element number and returns pointer to element
  */
-element * const periodentafel::AskElement() const
-{
-  element *walker = NULL;
+const element * periodentafel::AskElement() const
+{
+  const element *walker = NULL;
   int Z;
   do {
@@ -114 +115 @@
  * \return pointer to either present or newly created element
  */
-element * const periodentafel::EnterElement()
-{
-  element *walker = NULL;
-  int Z = -1;
+const element * periodentafel::EnterElement()
+{
+  const element *res = NULL;
+  atomicNumber_t Z = 0;
   Log() << Verbose(0) << "Atomic number: " << Z << endl;
   cin >> Z;
-  walker = FindElement(Z);
-  if (walker == NULL) {
+  res = FindElement(Z);
+  if (!res) {
+    // TODO: make this using the constructor
+    element *tmp;
     Log() << Verbose(0) << "Element not found in database, please enter." << endl;
-    walker = new element;
-    walker->Z = Z;
+    tmp = new element;
+    tmp->Z = Z;
     Log() << Verbose(0) << "Mass: " << endl;
-    cin >> walker->mass;
+    cin >> tmp->mass;
     Log() << Verbose(0) << "Name [max 64 chars]: " << endl;
-    cin >> walker->name;
+    cin >> tmp->name;
     Log() << Verbose(0) << "Short form [max 3 chars]: " << endl;
-    cin >> walker->symbol;
-    periodentafel::AddElement(walker);
+    cin >> tmp->symbol;
+    AddElement(tmp);
+    res = tmp;
   }
-  return(walker);
-};
+  return res;
+};
+
+
+/******************** Access to iterators ****************************/
+periodentafel::const_iterator periodentafel::begin(){
+  return elements.begin();
+}
+
+periodentafel::const_iterator periodentafel::end(){
+  return elements.end();
+}
+
+periodentafel::reverse_iterator periodentafel::rbegin(){
+  return reverse_iterator(elements.end());
+}
+
+periodentafel::reverse_iterator periodentafel::rend(){
+  return reverse_iterator(elements.begin());
+}
 
 /** Prints period table to given stream.
  * \param output stream
  */
-bool periodentafel::Output(ofstream * const output) const
+bool periodentafel::Output(ostream * const output) const
 {
   bool result = true;
-  element *walker = start;
   if (output != NULL) {
-    while (walker->next != end) {
-      walker = walker->next;
-      result = result && walker->Output(output);
+    for(const_iterator iter=elements.begin(); iter !=elements.end();++iter){
+      result = result && (*iter).second->Output(output);
     }
     return result;
@@ -157 +177 @@
  * \param *checkliste elements table for this molecule
  */
-bool periodentafel::Checkout(ofstream * const output, const int * const checkliste) const
-{
-  element *walker = start;
+bool periodentafel::Checkout(ostream * const output, const int * const checkliste) const
+{
   bool result = true;
   int No = 1;
@@ -166 +185 @@
     *output << "# Ion type data (PP = PseudoPotential, Z = atomic number)" << endl;
     *output << "#Ion_TypeNr.\tAmount\tZ\tRGauss\tL_Max(PP)L_Loc(PP)IonMass\t# chemical name, symbol" << endl;
-    while (walker->next != end) {
-      walker = walker->next;
-      if ((walker != NULL) && (walker->Z > 0) && (walker->Z < MAX_ELEMENTS) && (checkliste[walker->Z])) {
-        walker->No = No;
-        result = result && walker->Checkout(output, No++, checkliste[walker->Z]);
+    for(const_iterator iter=elements.begin(); iter!=elements.end();++iter){
+      if (((*iter).first < MAX_ELEMENTS) && (checkliste[(*iter).first])) {
+        (*iter).second->No = No;
+        result = result && (*iter).second->Checkout(output, No++, checkliste[(*iter).first]);
       }
     }
@@ -184 +202 @@
 {
   ifstream infile;
-  double tmp;
   element *ptr;
+  map<atomicNumber_t,element*> parsedElems;
   bool status = true;
   bool otherstatus = true;
@@ -223 +241 @@
       //neues->Output((ofstream *)&cout);
       if ((neues->Z > 0) && (neues->Z < MAX_ELEMENTS))
-        periodentafel::AddElement(neues);
+        parsedElems[neues->getNumber()] = neues;
       else {
         Log() << Verbose(0) << "Could not parse element: ";
@@ -243 +261 @@
   if (infile != NULL) {
     while (!infile.eof()) {
-      infile >> tmp;
-      infile >> ws;
-      infile >> FindElement((int)tmp)->Valence;
+      atomicNumber_t Z;
+      infile >> Z;
+      infile >> ws;
+      infile >> parsedElems[Z]->Valence;
       infile >> ws;
       //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->Valence << " valence electrons." << endl;
@@ -261 +280 @@
   if (infile != NULL) {
     while (!infile.eof()) {
-      infile >> tmp;
-      infile >> ws;
-      infile >> FindElement((int)tmp)->NoValenceOrbitals;
+      atomicNumber_t Z;
+      infile >> Z;
+      infile >> ws;
+      infile >> parsedElems[Z]->NoValenceOrbitals;
       infile >> ws;
       //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->NoValenceOrbitals << " number of singly occupied valence orbitals." << endl;
@@ -279 +299 @@
   if (infile != NULL) {
     while (!infile.eof()) {
-      infile >> tmp;
-      ptr = FindElement((int)tmp);
+      atomicNumber_t Z;
+      infile >> Z;
+      ptr = parsedElems[Z];
       infile >> ws;
       infile >> ptr->HBondDistance[0];
@@ -300 +321 @@
   if (infile != NULL) {
     while (!infile.eof()) {
-      infile >> tmp;
-      ptr = FindElement((int)tmp);
+      atomicNumber_t Z;
+      infile >> Z;
+      ptr = parsedElems[Z];
       infile >> ws;
       infile >> ptr->HBondAngle[0];
@@ -313 +335 @@
     otherstatus = false;
 
-  if (!otherstatus)
+  if (otherstatus){
+    map<atomicNumber_t,element*>::iterator iter;
+    for(iter=parsedElems.begin();iter!=parsedElems.end();++iter){
+      AddElement((*iter).second);
+    }
+  }
+  else{
     eLog() << Verbose(2) << "Something went wrong while parsing the other databases!" << endl;
+  }
 
   return status;
@@ -334 +363 @@
     f << header1 << endl;
     f << header2 << endl;
-    element *walker = periodentafel::start;
-    while (walker->next != periodentafel::end) {
-      walker = walker->next;
-      result = result && walker->Output(&f);
+    for(const_iterator iter=elements.begin();iter!=elements.end();++iter){
+         result = result && (*iter).second->Output(&f);
     }
     f.close();

src/periodentafel.hpp

@@ -1 +1 @@
 #ifndef PERIODENTAFEL_HPP_
 #define PERIODENTAFEL_HPP_
-
-using namespace std;
 
 /*********************************************** includes ***********************************/
@@ -12 +10 @@
 
 #include <iostream>
+#include <map>
+#include <iterator>
 
 #include "defs.hpp"
+#include "types.hpp"
 
 /****************************************** forward declarations *****************************/
@@ -25 +26 @@
  */
 class periodentafel {
+  /******* Types *********/
+  private:
+    typedef std::map<atomicNumber_t,element*> elementSet;
   public:
-    element *start; //!< start of element list
-    element *end;   //!< end of element list
+    typedef elementSet::iterator iterator;
+    typedef elementSet::const_iterator const_iterator;
+    typedef std::reverse_iterator<const_iterator> reverse_iterator;
+  public:
+
     char header1[MAXSTRINGSIZE]; //!< store first header line
     char header2[MAXSTRINGSIZE]; //!< store second header line
@@ -34 +41 @@
   ~periodentafel();
 
-  bool AddElement(element * const pointer);
-  bool RemoveElement(element * const pointer);
-  bool CleanupPeriodtable();
-  element * const FindElement(const int Z) const;
-  element * const FindElement(const char * const shorthand) const;
-  element * const AskElement() const;
-  element * const EnterElement();
-  bool Output(ofstream * const output) const;
-  bool Checkout(ofstream * const output, const int * const checkliste) const;
+  iterator AddElement(element * const pointer);
+  void RemoveElement(element * const pointer);
+  void CleanupPeriodtable();
+  const element *FindElement(atomicNumber_t) const;
+  const element *FindElement(const char * const shorthand) const;
+  const element *AskElement() const;
+  const element *EnterElement();
+
+  const_iterator begin();
+  const_iterator end();
+  reverse_iterator rbegin();
+  reverse_iterator rend();
+  bool Output(std::ostream * const output) const;
+  bool Checkout(std::ostream * const output, const int * const checkliste) const;
   bool LoadPeriodentafel(const char * const path);
   bool StorePeriodentafel(const char * const path) const;
 
   private:
+    elementSet elements;
 };
 

src/unittests/AtomDescriptorTest.hpp

@@ -11 +11 @@
 #include <cppunit/extensions/HelperMacros.h>
 
-#include "defs.hpp"
+#include "types.hpp"
 
 #define ATOM_COUNT (10)

src/unittests/CacheableTest.cpp

@@ -27 +27 @@
 class threeNumbers : public Observable {
 public:
-  bool hasRecalced;
   int x;
   int y;
   int z;
+  Cacheable<int> sum;
+  bool hasRecalced;
 
   void setX(int _x){
@@ -54 +55 @@
 
   threeNumbers(int _x,int _y, int _z) :
+    x(_x),y(_y),z(_z),
     sum(this,boost::bind(&threeNumbers::calcSum,this)),
-    x(_x),y(_y),z(_z),
     hasRecalced(false)
   {}
-
-  Cacheable<int> sum;
 };
 

src/unittests/MoleculeDescriptorTest.hpp

@@ -11 +11 @@
 #include <cppunit/extensions/HelperMacros.h>
 
-#include "defs.hpp"
+#include "types.hpp"
 
 #define MOLECULE_COUNT (10)

src/unittests/analysisbondsunittest.cpp

@@ -53 +53 @@
   strcpy(hydrogen->symbol, "H");
   carbon = new element;
-  carbon->Z = 1;
+  carbon->Z = 2;
   carbon->Valence = 4;
   carbon->NoValenceOrbitals = 4;

src/unittests/atomsCalculationTest.cpp

@@ -31 +31 @@
 CPPUNIT_TEST_SUITE_REGISTRATION( atomsCalculationTest );
 
-// some stubs
-class AtomStub : public atom {
-public:
-  AtomStub(atomId_t _id) :
-  atom(),
-  id(_id),
-  manipulated(false)
-  {}
-
-  virtual atomId_t getId(){
-    return id;
-  }
-
-  virtual void doSomething(){
-    manipulated = true;
-  }
-
-  bool manipulated;
-private:
-  atomId_t id;
-};
-
 // set up and tear down
 void atomsCalculationTest::setUp(){
   World::getInstance();
   for(int i=0;i<ATOM_COUNT;++i){
-    atoms[i]= new AtomStub(i);
-    World::getInstance().registerAtom(atoms[i]);
+    atoms[i]= World::getInstance().createAtom();
+    atomIds[i]= atoms[i]->getId();
   }
 }
@@ -67 +45 @@
 
 // some helper functions
-static bool hasAll(std::vector<int> ids,int min, int max, std::set<int> excluded = std::set<int>()){
-  for(int i=min;i<max;++i){
-    if(!excluded.count(i)){
-      std::vector<int>::iterator iter;
+static bool hasAllIds(std::vector<atomId_t> atoms,atomId_t ids[ATOM_COUNT], std::set<atomId_t> excluded = std::set<atomId_t>()){
+  for(int i=0;i<ATOM_COUNT;++i){
+    atomId_t id = ids[i];
+    if(!excluded.count(id)){
+      std::vector<atomId_t>::iterator iter;
       bool res=false;
-      for(iter=ids.begin();iter!=ids.end();++iter){
-        res |= (*iter) == i;
+      for(iter=atoms.begin();iter!=atoms.end();++iter){
+        res |= (*iter) == id;
       }
       if(!res) {
-        cout << "Atom " << i << " missing in returned list" << endl;
+        cout << "Atom " << id << " missing in returned list" << endl;
         return false;
       }
@@ -84 +63 @@
 }
 
-static bool hasNoDuplicates(std::vector<int> ids){
-  std::set<int> found;
-  std::vector<int>::iterator iter;
+static bool hasNoDuplicates(std::vector<atomId_t> ids){
+  std::set<atomId_t> found;
+  std::vector<atomId_t>::iterator iter;
   for(iter=ids.begin();iter!=ids.end();++iter){
     int id = (*iter);
@@ -97 +76 @@
 
 void atomsCalculationTest::testCalculateSimple(){
-  AtomsCalculation<int> *calc = World::getInstance().calcOnAtoms<int>(boost::bind(&atom::getId,_1),"FOO",AllAtoms());
-  std::vector<int> allIds = (*calc)();
-  CPPUNIT_ASSERT(hasAll(allIds,0,ATOM_COUNT));
+  AtomsCalculation<atomId_t> *calc = World::getInstance().calcOnAtoms<atomId_t>(boost::bind(&atom::getId,_1),"FOO",AllAtoms());
+  std::vector<atomId_t> allIds = (*calc)();
+  CPPUNIT_ASSERT(hasAllIds(allIds,atomIds));
   CPPUNIT_ASSERT(hasNoDuplicates(allIds));
 }
 
 void atomsCalculationTest::testCalculateExcluded(){
-  int excluded = ATOM_COUNT/2;
-  AtomsCalculation<int> *calc = World::getInstance().calcOnAtoms<int>(boost::bind(&atom::getId,_1),"FOO",AllAtoms() && !AtomById(excluded));
-  std::vector<int> allIds = (*calc)();
-  std::set<int> excluded_set;
+  atomId_t excluded = atomIds[ATOM_COUNT/2];
+  AtomsCalculation<atomId_t> *calc = World::getInstance().calcOnAtoms<atomId_t>(boost::bind(&atom::getId,_1),"FOO",AllAtoms() && !AtomById(excluded));
+  std::vector<atomId_t> allIds = (*calc)();
+  std::set<atomId_t> excluded_set;
   excluded_set.insert(excluded);
-  CPPUNIT_ASSERT(hasAll(allIds,0,ATOM_COUNT,excluded_set));
+  CPPUNIT_ASSERT(hasAllIds(allIds,atomIds,excluded_set));
   CPPUNIT_ASSERT(hasNoDuplicates(allIds));
   CPPUNIT_ASSERT_EQUAL((size_t)(ATOM_COUNT-1),allIds.size());

src/unittests/atomsCalculationTest.hpp

@@ -12 +12 @@
 
 #define ATOM_COUNT (10)
+
+#include "types.hpp"
 
 class atom;
@@ -31 +33 @@
 private:
   atom *atoms [ATOM_COUNT];
-  int atomIds [ATOM_COUNT];
+  atomId_t atomIds [ATOM_COUNT];
 };
 

src/unittests/bondgraphunittest.cpp

@@ -51 +51 @@
   strcpy(hydrogen->symbol, "H");
   carbon = new element;
-  carbon->Z = 1;
+  carbon->Z = 2;
   strcpy(carbon->name, "carbon");
   strcpy(carbon->symbol, "C");