Changeset d74077 for src/moleculelist.cpp

Timestamp:

Jul 31, 2010, 3:23:10 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, 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:

8f4df1

Parents:

5fbaeb

Message:

Member variable Vector and element of class atom are now private.

• renamed to AtomicPosition
• created interface class VectorInterface with alle functions from class Vector as virtual ones
• implemented in AtomInfo
• everywhere direct access to AtomicPosition has been replaced by get/setPosition() and others
• for element get/setType() have been present already, direct access has been replaced by calling of these.
• class TesselPoint now derives from AtomInfo and ParticleInfo
• tesselation.cpp split up
  • new files for the classes: BoundaryLineSet, BoundaryPointSet, BoundaryPolygonSet, BoundaryTriangleSet, CandidateForTesselation, PointCloud, TesselPoint
  • all defines are in BoundaryMaps.hpp

File:

• src/moleculelist.cpp (modified) (5 diffs)

src/moleculelist.cpp

@@ -182 +182 @@
       size=0.;
       for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
-        counts[(*iter)->type->getNumber()]++;
-        if ((*iter)->x.DistanceSquared(Origin) > size)
-          size = (*iter)->x.DistanceSquared(Origin);
+        counts[(*iter)->getType()->getNumber()]++;
+        if ((*iter)->DistanceSquared(Origin) > size)
+          size = (*iter)->DistanceSquared(Origin);
       }
       // output Index, Name, number of atoms, chemical formula
@@ -354 +354 @@
   for (molecule::const_iterator iter = srcmol->begin(); iter != srcmol->end(); ++iter) {
     DoLog(2) && (Log() << Verbose(2) << "INFO: Current Walker is " << **iter << "." << endl);
-    if (!TesselStruct->IsInnerPoint((*iter)->x, LCList)) {
+    if (!TesselStruct->IsInnerPoint((*iter)->getPosition(), LCList)) {
       CopyAtoms[(*iter)->nr] = (*iter)->clone();
       mol->AddAtom(CopyAtoms[(*iter)->nr]);
@@ -501 +501 @@
     for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
       //Log() << Verbose(1) << "(*iter): " << *(*iter) << " with first bond " << *((*iter)->ListOfBonds.begin()) << "." << endl;
-      if (((*iter)->type->Z == 1) && (((*iter)->father == NULL)
-          || ((*iter)->father->type->Z != 1))) { // if it's a hydrogen
+      if (((*iter)->getType()->Z == 1) && (((*iter)->father == NULL)
+          || ((*iter)->father->getType()->Z != 1))) { // if it's a hydrogen
         for (molecule::const_iterator runner = (*ListRunner)->begin(); runner != (*ListRunner)->end(); ++runner) {
           //Log() << Verbose(2) << "Runner: " << *(*runner) << " with first bond " << *((*iter)->ListOfBonds.begin()) << "." << endl;
           // 3. take every other hydrogen that is the not the first and not bound to same bonding partner
           Binder = *((*runner)->ListOfBonds.begin());
-          if (((*runner)->type->Z == 1) && ((*runner)->nr > (*iter)->nr) && (Binder->GetOtherAtom((*runner)) != Binder->GetOtherAtom((*iter)))) { // (hydrogens have only one bonding partner!)
+          if (((*runner)->getType()->Z == 1) && ((*runner)->nr > (*iter)->nr) && (Binder->GetOtherAtom((*runner)) != Binder->GetOtherAtom((*iter)))) { // (hydrogens have only one bonding partner!)
             // 4. evaluate the morse potential for each matrix component and add up
-            distance = (*runner)->x.distance((*iter)->x);
+            distance = (*runner)->distance(*(*iter));
             //Log() << Verbose(0) << "Fragment " << (*ListRunner)->name << ": " << *(*runner) << "<= " << distance << "=>" << *(*iter) << ":" << endl;
             for (int k = 0; k < a; k++) {
@@ -599 +599 @@
         if ((*ListRunner)->hasElement((*elemIter).first)) { // if this element got atoms
           for(molecule::iterator atomIter = (*ListRunner)->begin(); atomIter !=(*ListRunner)->end();++atomIter){
-            if ((*atomIter)->type->getNumber() == (*elemIter).first) {
+            if ((*atomIter)->getType()->getNumber() == (*elemIter).first) {
               if (((*atomIter)->GetTrueFather() != NULL) && ((*atomIter)->GetTrueFather() != (*atomIter))) {// if there is a rea
                 //Log() << Verbose(0) << "Walker is " << *Walker << " with true father " << *( Walker->GetTrueFather()) << ", it
@@ -1089 +1089 @@
         if (AtomMask[Father->nr]) // apply mask
 #ifdef ADDHYDROGEN
-          if ((*iter)->type->Z != 1) // skip hydrogen
+          if ((*iter)->getType()->Z != 1) // skip hydrogen
 #endif
           RootStack[FragmentCounter].push_front((*iter)->nr);