Changeset 83f176 for src/config.cpp

Timestamp:

Aug 19, 2010, 3:23:37 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:

2a7457

Parents:

1ee380f

git-author:

Frederik Heber <heber@…> (08/17/10 17:21:25)

git-committer:

Frederik Heber <heber@…> (08/19/10 15:23:37)

Message:

Made all member variables of class element private, added accessor functions and periodentafel is friend.

File:

• src/config.cpp (modified) (7 diffs)

src/config.cpp

@@ -484 +484 @@
       ParseForParameter(verbose,FileBuffer, name, 0, 2, 1, int_type, &Z, 1, critical);
       elementhash[i] = periode->FindElement(Z);
-      DoLog(1) && (Log() << Verbose(1) << i << ". Z = " << elementhash[i]->Z << " with " << No[i] << " ions." << endl);
+      DoLog(1) && (Log() << Verbose(1) << i << ". Z = " << elementhash[i]->getAtomicNumber() << " with " << No[i] << " ions." << endl);
       NoAtoms += No[i];
     }
@@ -1352 +1352 @@
     AtomNo = 0;
     for (molecule::const_iterator iter = (*MolRunner)->begin(); iter != (*MolRunner)->end(); ++iter) {
-      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
+      sprintf(name, "%2s%2d",(*iter)->getType()->getSymbol().c_str(), elementNo[(*iter)->getType()->getAtomicNumber()]);
+      elementNo[(*iter)->getType()->getAtomicNumber()] = (elementNo[(*iter)->getType()->getAtomicNumber()]+1) % 100;   // confine to two digits
       fprintf(f,
              "ATOM %6u %-4s %4s%c%4u    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n",
@@ -1364 +1364 @@
              (*iter)->at(1),                 /* position Y in Angstroem */
              (*iter)->at(2),                 /* position Z in Angstroem */
-             (double)(*iter)->getType()->Valence,         /* occupancy */
-             (double)(*iter)->getType()->NoValenceOrbitals,          /* temperature factor */
+             (double)(*iter)->getType()->getValence(),         /* occupancy */
+             (double)(*iter)->getType()->getNoValenceOrbitals(),          /* temperature factor */
              "0",            /* segment identifier */
              (*iter)->getType()->getSymbol().c_str(),    /* element symbol */
@@ -1405 +1405 @@
   AtomNo = 0;
   for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    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
+    sprintf(name, "%2s%2d",(*iter)->getType()->getSymbol().c_str(), elementNo[(*iter)->getType()->getAtomicNumber()]);
+    elementNo[(*iter)->getType()->getAtomicNumber()] = (elementNo[(*iter)->getType()->getAtomicNumber()]+1) % 100;   // confine to two digits
     fprintf(f,
            "ATOM %6u %-4s %4s%c%4u    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n",
@@ -1417 +1417 @@
            (*iter)->at(1),                 /* position Y in Angstroem */
            (*iter)->at(2),                 /* position Z in Angstroem */
-           (double)(*iter)->getType()->Valence,         /* occupancy */
-           (double)(*iter)->getType()->NoValenceOrbitals,          /* temperature factor */
+           (double)(*iter)->getType()->getValence(),         /* occupancy */
+           (double)(*iter)->getType()->getNoValenceOrbitals(),          /* temperature factor */
            "0",            /* segment identifier */
            (*iter)->getType()->getSymbol().c_str(),    /* element symbol */
@@ -1464 +1464 @@
     *output << 0 << "\t";
     *output << (*iter)->at(0) << "\t" << (*iter)->at(1) << "\t" << (*iter)->at(2) << "\t";
-    *output << static_cast<double>((*iter)->getType()->Valence) << "\t";
+    *output << static_cast<double>((*iter)->getType()->getValence()) << "\t";
     *output << (*iter)->getType()->getSymbol() << "\t";
     for (BondList::iterator runner = (*iter)->ListOfBonds.begin(); runner != (*iter)->ListOfBonds.end(); runner++)
@@ -1536 +1536 @@
         *output << MolCounter+1 << "\t";
         *output << (*iter)->at(0) << "\t" << (*iter)->at(1) << "\t" << (*iter)->at(2) << "\t";
-        *output << (double)(*iter)->getType()->Valence << "\t";
+        *output << (double)(*iter)->getType()->getValence() << "\t";
         *output << (*iter)->getType()->getSymbol() << "\t";
         for (BondList::iterator runner = (*iter)->ListOfBonds.begin(); runner != (*iter)->ListOfBonds.end(); runner++)