Changeset b5c53d for src/config.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, 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/config.cpp (modified) (6 diffs)

src/config.cpp

@@ -1339 +1339 @@
     AtomNo = 0;
     for (molecule::const_iterator iter = (*MolRunner)->begin(); iter != (*MolRunner)->end(); ++iter) {
-      sprintf(name, "%2s%2d",(*iter)->getType()->symbol, elementNo[(*iter)->getType()->Z]);
+      sprintf(name, "%2s%2d",(*iter)->getType()->getSymbol().c_str(), elementNo[(*iter)->getType()->Z]);
       elementNo[(*iter)->getType()->Z] = (elementNo[(*iter)->getType()->Z]+1) % 100;   // confine to two digits
       fprintf(f,
@@ -1354 +1354 @@
              (double)(*iter)->getType()->NoValenceOrbitals,          /* temperature factor */
              "0",            /* segment identifier */
-             (*iter)->getType()->symbol,    /* element symbol */
+             (*iter)->getType()->getSymbol().c_str(),    /* element symbol */
              "0");           /* charge */
       AtomNo++;
@@ -1392 +1392 @@
   AtomNo = 0;
   for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    sprintf(name, "%2s%2d",(*iter)->getType()->symbol, elementNo[(*iter)->getType()->Z]);
+    sprintf(name, "%2s%2d",(*iter)->getType()->getSymbol().c_str(), elementNo[(*iter)->getType()->Z]);
     elementNo[(*iter)->getType()->Z] = (elementNo[(*iter)->getType()->Z]+1) % 100;   // confine to two digits
     fprintf(f,
@@ -1407 +1407 @@
            (double)(*iter)->getType()->NoValenceOrbitals,          /* temperature factor */
            "0",            /* segment identifier */
-           (*iter)->getType()->symbol,    /* element symbol */
+           (*iter)->getType()->getSymbol().c_str(),    /* element symbol */
            "0");           /* charge */
     AtomNo++;
@@ -1452 +1452 @@
     *output << (*iter)->at(0) << "\t" << (*iter)->at(1) << "\t" << (*iter)->at(2) << "\t";
     *output << static_cast<double>((*iter)->getType()->Valence) << "\t";
-    *output << (*iter)->getType()->symbol << "\t";
+    *output << (*iter)->getType()->getSymbol() << "\t";
     for (BondList::iterator runner = (*iter)->ListOfBonds.begin(); runner != (*iter)->ListOfBonds.end(); runner++)
       *output << (*runner)->GetOtherAtom(*iter)->nr << "\t";
@@ -1524 +1524 @@
         *output << (*iter)->at(0) << "\t" << (*iter)->at(1) << "\t" << (*iter)->at(2) << "\t";
         *output << (double)(*iter)->getType()->Valence << "\t";
-        *output << (*iter)->getType()->symbol << "\t";
+        *output << (*iter)->getType()->getSymbol() << "\t";
         for (BondList::iterator runner = (*iter)->ListOfBonds.begin(); runner != (*iter)->ListOfBonds.end(); runner++)
           *output << LocalNotoGlobalNoMap[ (*runner)->GetOtherAtom((*iter))->getId() ] << "\t";