Changeset ed26ae

Timestamp:

Apr 4, 2012, 11:30:11 AM (13 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:

613da6

Parents:

47ed3d

git-author:

Frederik Heber <heber@…> (03/26/12 08:06:19)

git-committer:

Frederik Heber <heber@…> (04/04/12 11:30:11)

Message:

Renamed calls to element::getNumber() -> ::getAtomicNumber().

• dropped element::getNumber() as getAtomicNumber has same functionality.

Location:

src

Files:

• Atom/atom.cpp (modified) (1 diff)
• Atom/atom_atominfo.cpp (modified) (1 diff)
• Element/element.cpp (modified) (3 diffs)
• Element/element.hpp (modified) (3 diffs)
• Element/periodentafel.cpp (modified) (3 diffs)
• Element/unittests/ElementUnitTest.cpp (modified) (2 diffs)
• Element/unittests/PeriodentafelUnitTest.cpp (modified) (1 diff)
• Formula.cpp (modified) (5 diffs)
• UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) (1 diff)
• UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) (2 diffs)
• moleculelist.cpp (modified) (2 diffs)

src/Atom/atom.cpp

@@ -291 +291 @@
 
 bool compareAtomElements(atom* atom1,atom* atom2){
-  return atom1->getType()->getNumber() < atom2->getType()->getNumber();
-}
+  return atom1->getType()->getAtomicNumber() < atom2->getType()->getAtomicNumber();
+}

src/Atom/atom_atominfo.cpp

@@ -164 +164 @@
 void AtomInfo::setType(const element* _type)
 {
-  if (_type->getNumber() != AtomicElement) {
+  if (_type->getAtomicNumber() != AtomicElement) {
     OBSERVE;
     NOTIFY(AtomObservable::ElementChanged);
-    AtomicElement = _type->getNumber();
+    AtomicElement = _type->getAtomicNumber();
   }
 }

src/Element/element.cpp

@@ -104 +104 @@
 }
 
-atomicNumber_t element::getNumber() const{
-  return Z;
-}
-
 double element::getMass() const
 {
@@ -133 +129 @@
 }
 
-int element::getAtomicNumber() const
+atomicNumber_t element::getAtomicNumber() const
 {
   return Z;
@@ -207 +203 @@
 
 std::ostream &operator<<(std::ostream &ost,const element &elem){
-  ost << elem.getName() << "(" << elem.getNumber() << ")";
+  ost << elem.getName() << "(" << elem.getAtomicNumber() << ")";
   return ost;
 }

src/Element/element.hpp

@@ -41 +41 @@
 
     // accessor functions
-    atomicNumber_t getNumber() const;
     double getMass() const;
     const unsigned char *getColor() const;
@@ -47 +46 @@
     double getElectronegativity() const;
     double getVanDerWaalsRadius() const;
-    int getAtomicNumber() const;
+    atomicNumber_t getAtomicNumber() const;
     double getValence() const;
     int getNoValenceOrbitals() const;
@@ -92 +91 @@
     double Electronegativity; //!< electronegativity in Pauling units
     double VanDerWaalsRadius;  //!< can-der-Waals radius
-    int Z;          //!< atomic number
+    atomicNumber_t Z;          //!< atomic number
     std::string period;    //!< period: n quantum number
     std::string group;    //!< group: l quantum number

src/Element/periodentafel.cpp

@@ -60 +60 @@
 periodentafel::iterator periodentafel::AddElement(element * pointer)
 {
-  atomicNumber_t Z = pointer->getNumber();
+  atomicNumber_t Z = pointer->getAtomicNumber();
   ASSERT(!elements.count(Z), "Element is already present.");
-  if (pointer->getNumber() < 1 && pointer->getNumber() >= MAX_ELEMENTS)
+  if (pointer->getAtomicNumber() < 1 && pointer->getAtomicNumber() >= MAX_ELEMENTS)
     ELOG(0, "Invalid Z number!");
   pair<iterator,bool> res = elements.insert(pair<atomicNumber_t,element*>(Z,pointer));
@@ -73 +73 @@
 size_t periodentafel::RemoveElement(const element * pointer)
 {
-  return RemoveElement(pointer->getNumber());
+  return RemoveElement(pointer->getAtomicNumber());
 };
 
@@ -406 +406 @@
       input >> ws;
       //neues->Output((ofstream *)&cout);
-      if ((neues->getNumber() > 0) && (neues->getNumber() < MAX_ELEMENTS)) {
+      if ((neues->getAtomicNumber() > 0) && (neues->getAtomicNumber() < MAX_ELEMENTS)) {
         parsedElements[neues->Z] = neues;
 //        parsedelements << " " << *neues);

src/Element/unittests/ElementUnitTest.cpp

@@ -82 +82 @@
 void ElementTest::GetterTest()
 {
-  CPPUNIT_ASSERT_EQUAL( (atomId_t)0, testelement->getNumber() );
+  CPPUNIT_ASSERT_EQUAL( (atomId_t)0, testelement->getAtomicNumber() );
   CPPUNIT_ASSERT_EQUAL( 0., testelement->getMass() );
   const unsigned char * color = testelement->getColor();
@@ -90 +90 @@
   CPPUNIT_ASSERT_EQUAL( 0., testelement->getElectronegativity() );
   CPPUNIT_ASSERT_EQUAL( 0., testelement->getVanDerWaalsRadius() );
-  CPPUNIT_ASSERT_EQUAL( 0, testelement->getAtomicNumber() );
   CPPUNIT_ASSERT_EQUAL( 0., testelement->getValence() );
   CPPUNIT_ASSERT_EQUAL( 0, testelement->getNoValenceOrbitals() );

src/Element/unittests/PeriodentafelUnitTest.cpp

@@ -103 +103 @@
   atomicNumber_t Z = 1;
   for(periodentafel::const_iterator ElementRunner = tafel->begin(); ElementRunner != tafel->end(); ++ElementRunner)
-    CPPUNIT_ASSERT( (ElementRunner->second->getNumber() == Z++) && "element is missing in sequence");
+    CPPUNIT_ASSERT( (ElementRunner->second->getAtomicNumber() == Z++) && "element is missing in sequence");
 };
 

src/Formula.cpp

@@ -135 +135 @@
 bool Formula::hasElement(const element *element) const{
   ASSERT(element,"Invalid pointer in Formula::hasElement(element*)");
-  return hasElement(element->getNumber());
+  return hasElement(element->getAtomicNumber());
 }
 
@@ -151 +151 @@
 void Formula::operator+=(const element *element){
   ASSERT(element,"Invalid pointer in increment of Formula");
-  operator+=(element->getNumber());
+  operator+=(element->getAtomicNumber());
 }
 
@@ -172 +172 @@
 void Formula::operator-=(const element *element){
   ASSERT(element,"Invalid pointer in decrement of Formula");
-  operator-=(element->getNumber());
+  operator-=(element->getAtomicNumber());
 }
 
@@ -203 +203 @@
 void Formula::addElements(const element *element,unsigned int count){
   ASSERT(element,"Invalid pointer in Formula::addElements(element*)");
-  addElements(element->getNumber(),count);
+  addElements(element->getAtomicNumber(),count);
 }
 
@@ -239 +239 @@
 const unsigned int Formula::operator[](const element *element) const{
   ASSERT(element,"Invalid pointer in access of Formula");
-  return operator[](element->getNumber());
+  return operator[](element->getAtomicNumber());
 }
 

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp

@@ -93 +93 @@
   size_t elementno = 0;
   if (_atom->getType() != NULL) {
-    elementno = _atom->getType()->getNumber();
+    elementno = _atom->getType()->getAtomicNumber();
   } else { // if no element yet, set to hydrogen
     elementno = 1;

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp

@@ -70 +70 @@
       OtherPosition = _bond->rightatom->getPosition();
       if (_bond->leftatom->getType() != NULL) {
-        elementno = _bond->leftatom->getType()->getNumber();
+        elementno = _bond->leftatom->getType()->getAtomicNumber();
       } else { // if not element yet set, set to hydrogen
         elementno = 1;
@@ -79 +79 @@
       OtherPosition = _bond->leftatom->getPosition();
       if (_bond->rightatom->getType() != NULL) {
-        elementno = _bond->rightatom->getType()->getNumber();
+        elementno = _bond->rightatom->getType()->getAtomicNumber();
       } else { // if not element yet set, set to hydrogen
         elementno = 1;

src/moleculelist.cpp

@@ -200 +200 @@
       size=0.;
       for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
-        counts[(*iter)->getType()->getNumber()]++;
+        counts[(*iter)->getType()->getAtomicNumber()]++;
         if ((*iter)->DistanceSquared(Origin) > size)
           size = (*iter)->DistanceSquared(Origin);
@@ -494 +494 @@
         if ((*ListRunner)->hasElement((*elemIter).first)) { // if this element got atoms
           for(molecule::iterator atomIter = (*ListRunner)->begin(); atomIter !=(*ListRunner)->end();++atomIter){
-            if ((*atomIter)->getType()->getNumber() == (*elemIter).first) {
+            if ((*atomIter)->getType()->getAtomicNumber() == (*elemIter).first) {
               if (((*atomIter)->GetTrueFather() != NULL) && ((*atomIter)->GetTrueFather() != (*atomIter))) {// if there is a rea
                 ForcesFile << SortIndex[(*atomIter)->GetTrueFather()->getNr()] << "\t";