Changeset b5c53d for src/periodentafel.cpp

Timestamp:

Aug 9, 2010, 6:33:29 PM (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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

353e82

Parents:

458447 (diff), e588312 (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 stable

Conflicts:

src/Actions/AtomAction/AddAction.cpp
src/Actions/AtomAction/ChangeElementAction.cpp
src/Parser/XyzParser.cpp
src/analysis_correlation.cpp
src/atom.cpp
src/config.cpp
src/molecule.cpp

• AtomInfo::element were privatized in stable and element::symbol, ::name in StructureRefactoring (overlapped in various lines).

File:

• src/periodentafel.cpp (modified) (13 diffs)

src/periodentafel.cpp

@@ -34 +34 @@
   {
     stringstream input(elementsDB,ios_base::in);
-    bool status = LoadElementsDatabase(&input);
+    bool status = LoadElementsDatabase(input);
     ASSERT(status,  "General element initialization failed");
   }
@@ -72 +72 @@
  * \return iterator to added element
  */
-periodentafel::iterator periodentafel::AddElement(element * const pointer)
+periodentafel::iterator periodentafel::AddElement(element * pointer)
 {
   atomicNumber_t Z = pointer->getNumber();
   ASSERT(!elements.count(Z), "Element is already present.");
-  pointer->sort = &pointer->Z;
   if (pointer->getNumber() < 1 && pointer->getNumber() >= MAX_ELEMENTS)
     DoeLog(0) && (eLog() << Verbose(0) << "Invalid Z number!\n");
@@ -86 +85 @@
  * \param *pointer element to be removed
  */
-size_t periodentafel::RemoveElement(element * const pointer)
+size_t periodentafel::RemoveElement(const element * pointer)
 {
   return RemoveElement(pointer->getNumber());
@@ -114 +113 @@
  * \return pointer to element or NULL if not found
  */
-element * const periodentafel::FindElement(atomicNumber_t Z) const
+const element * periodentafel::FindElement(atomicNumber_t Z) const
 {
   const_iterator res = elements.find(Z);
@@ -125 +124 @@
  * \return pointer to element
  */
-element * const periodentafel::FindElement(const string &shorthand) const
+const element * periodentafel::FindElement(const string &shorthand) const
 {
   element *res = 0;
@@ -140 +139 @@
  * \return desired element or NULL
  */
-element * const periodentafel::AskElement() const
-{
-  element * walker = NULL;
+const element * periodentafel::AskElement() const
+{
+  const element * walker = NULL;
   int Z;
   do {
@@ -155 +154 @@
  * \return pointer to either present or newly created element
  */
-element * const periodentafel::EnterElement()
+const element * periodentafel::EnterElement()
 {
   atomicNumber_t Z = 0;
   DoLog(0) && (Log() << Verbose(0) << "Atomic number: " << Z << endl);
   cin >> Z;
-  element * const res = FindElement(Z);
+  const element *res = FindElement(Z);
   if (!res) {
     // TODO: make this using the constructor
@@ -169 +168 @@
     cin >> tmp->mass;
     DoLog(0) && (Log() << Verbose(0) << "Name [max 64 chars]: " << endl);
-    cin >> tmp->name;
+    cin >> tmp->getName();
     DoLog(0) && (Log() << Verbose(0) << "Short form [max 3 chars]: " << endl);
-    cin >> tmp->symbol;
+    cin >> tmp->getSymbol();
     AddElement(tmp);
     return tmp;
@@ -180 +179 @@
 
 /******************** Access to iterators ****************************/
-periodentafel::const_iterator periodentafel::begin(){
+periodentafel::const_iterator periodentafel::begin() const{
   return elements.begin();
 }
 
-periodentafel::const_iterator periodentafel::end(){
+periodentafel::const_iterator periodentafel::end() const{
   return elements.end();
 }
 
-periodentafel::reverse_iterator periodentafel::rbegin(){
+periodentafel::reverse_iterator periodentafel::rbegin() const{
   return reverse_iterator(elements.end());
 }
 
-periodentafel::reverse_iterator periodentafel::rend(){
+periodentafel::reverse_iterator periodentafel::rend() const{
   return reverse_iterator(elements.begin());
 }
@@ -228 +227 @@
   if (!input.fail())
     DoLog(0) && (Log() << Verbose(0) << "Using " << filename << " as elements database." << endl);
-  status = status && LoadElementsDatabase(&input);
+  status = status && LoadElementsDatabase(input);
   input.close();
   input.clear();
@@ -287 +286 @@
  * \return true - parsing successful, false - something went wrong
  */
-bool periodentafel::LoadElementsDatabase(istream *input)
+bool periodentafel::LoadElementsDatabase(istream &input)
 {
   bool status = true;
-  int counter = 0;
-  pair< std::map<atomicNumber_t,element*>::iterator, bool > InserterTest;
-  if (!(*input).fail()) {
-    (*input).getline(header1, MAXSTRINGSIZE);
-    (*input).getline(header2, MAXSTRINGSIZE); // skip first two header lines
+  string header1tmp,header2tmp;
+  // first parse into a map, so we can revert to old status in case something goes wront
+  map<atomicNumber_t,element*> parsedElements;
+  if (!input.fail()) {
+    getline(input,header1tmp);
+    getline(input,header2tmp); // skip first two header lines
+    cout << "First header: " << header1tmp << endl;
+    cout << "Second header: " << header2tmp << endl;
     DoLog(0) && (Log() << Verbose(0) <<  "Parsed elements:");
-    while (!(*input).eof()) {
+    while (!input.eof()) {
       element *neues = new element;
-      (*input) >> neues->name;
-      //(*input) >> ws;
-      (*input) >> neues->symbol;
-      //(*input) >> ws;
-      (*input) >> neues->period;
-      //(*input) >> ws;
-      (*input) >> neues->group;
-      //(*input) >> ws;
-      (*input) >> neues->block;
-      //(*input) >> ws;
-      (*input) >> neues->Z;
-      //(*input) >> ws;
-      (*input) >> neues->mass;
-      //(*input) >> ws;
-      (*input) >> neues->CovalentRadius;
-      //(*input) >> ws;
-      (*input) >> neues->VanDerWaalsRadius;
-      //(*input) >> ws;
-      (*input) >> ws;
+      input >> neues->getName();;
+      //(*input) >> ws;
+      input >> neues->getSymbol();
+      //(*input) >> ws;
+      input >> neues->period;
+      //(*input) >> ws;
+      input >> neues->group;
+      //(*input) >> ws;
+      input >> neues->block;
+      //(*input) >> ws;
+      input >> neues->Z;
+      //(*input) >> ws;
+      input >> neues->mass;
+      //(*input) >> ws;
+      input >> neues->CovalentRadius;
+      //(*input) >> ws;
+      input >> neues->VanDerWaalsRadius;
+      //(*input) >> ws;
+      input >> ws;
       //neues->Output((ofstream *)&cout);
       if ((neues->getNumber() > 0) && (neues->getNumber() < MAX_ELEMENTS)) {
-        if (elements.count(neues->getNumber())) {// if element already present, remove and delete old one (i.e. replace it)
-          //cout << neues->symbol << " is present already." << endl;
-          element * const Elemental = FindElement(neues->getNumber());
-          ASSERT(Elemental != NULL, "element should be present but is not??");
-          *Elemental = *neues;
-          delete(neues);
-          neues = Elemental;
-        } else {
-          InserterTest = elements.insert(pair <atomicNumber_t,element*> (neues->getNumber(), neues));
-          ASSERT(InserterTest.second, "Could not insert new element into periodentafel on LoadElementsDatabase().");
-        }
-        DoLog(0) && (Log() << Verbose(0) << " " << elements[neues->getNumber()]->symbol);
-        counter++;
+        parsedElements[neues->Z] = neues;
+        DoLog(0) && (Log() << Verbose(0) << " " << *neues);
       } else {
         DoeLog(2) && (eLog() << Verbose(2) << "Detected empty line or invalid element in elements db, discarding." << endl);
@@ -337 +328 @@
         delete(neues);
       }
+      // when the input is in failed state, we most likely just read garbage
+      if(input.fail()) {
+        DoeLog(2) && (eLog() << Verbose(2) << "Error parsing elements db." << endl);
+        status = false;
+        break;
+      }
     }
     DoLog(0) && (Log() << Verbose(0) << endl);
@@ -344 +341 @@
   }
 
-  if (counter == 0)
+  if (!parsedElements.size())
     status = false;
+
+  if(status){
+    for(map<atomicNumber_t,element*>::iterator iter=parsedElements.begin();
+                                               iter!=parsedElements.end();
+                                               ++iter){
+      if (elements.count(iter->first)) {
+        // if element already present, replace the old one
+        // pointer to old element might still be in use, so we have to replace into the old element
+        *(elements[iter->first])=*iter->second;
+      }
+      else {
+        // no such element in periodentafel... we can just insert
+        elements[iter->first] = iter->second;
+      }
+    }
+    // all went well.. we now copy the header
+    strncpy(header1,header1tmp.c_str(),MAXSTRINGSIZE);
+    header1[MAXSTRINGSIZE-1]=0;
+    strncpy(header2,header2tmp.c_str(),MAXSTRINGSIZE);
+    header2[MAXSTRINGSIZE-1]=0;
+  }
 
   return status;