Changeset 49f802c for src/molecule.cpp

Timestamp:

Oct 9, 2009, 11:57:41 AM (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:

c111db

Parents:

f66195

Message:

Implementing templated iterators done for molecule.cpp

• new functions in class atom: atom::DistanceSquaredToVector(), atom::DistanceToVector() and atom::AddKineticToTemperature()
• above used with ActOnAllAtoms() in molecule.cpp: molecule::OutputTemperatureFromTrajectories(), molecule::OutputListOfBonds() (uses atom::OutputBondOfAtom() which gives slightly different output than before but rather with more info)
• new template SetIndexedArrayForEachAtomTo() which sets the contents of an index array according to a member function result.
• above used in molecule::IsEqualToWithinThreshold()

File:

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

src/molecule.cpp

@@ -779 +779 @@
 {
   *out << Verbose(2) << endl << "From Contents of ListOfBondsPerAtom, all non-hydrogen atoms:" << endl;
-  atom *Walker = start;
-  while (Walker->next != end) {
-    Walker = Walker->next;
-#ifdef ADDHYDROGEN
-    if (Walker->type->Z != 1) {   // regard only non-hydrogen
-#endif
-      *out << Verbose(2) << "Atom " << Walker->Name << " has Bonds: "<<endl;
-      for(int j=0;j<NumberOfBondsPerAtom[Walker->nr];j++) {
-        *out << Verbose(3) << *(ListOfBondsPerAtom)[Walker->nr][j] << endl;
-      }
-#ifdef ADDHYDROGEN
-    }
-#endif
-  }
+  ActOnAllAtoms (&atom::OutputBondOfAtom, out, NumberOfBondsPerAtom, ListOfBondsPerAtom);
   *out << endl;
 };
@@ -983 +970 @@
   size_t *PermMap = NULL, *OtherPermMap = NULL;
   int *PermutationMap = NULL;
-  atom *Walker = NULL;
   bool result = true; // status of comparison
 
@@ -1042 +1028 @@
     Distances = Malloc<double>(AtomCount, "molecule::IsEqualToWithinThreshold: Distances");
     OtherDistances = Malloc<double>(AtomCount, "molecule::IsEqualToWithinThreshold: OtherDistances");
-    Walker = start;
-    while (Walker->next != end) {
-      Walker = Walker->next;
-      Distances[Walker->nr] = CenterOfGravity.DistanceSquared(&Walker->x);
-    }
-    Walker = OtherMolecule->start;
-    while (Walker->next != OtherMolecule->end) {
-      Walker = Walker->next;
-      OtherDistances[Walker->nr] = OtherCenterOfGravity.DistanceSquared(&Walker->x);
-    }
+    SetIndexedArrayForEachAtomTo ( Distances, &atom::nr, &atom::DistanceSquaredToVector, CenterOfGravity);
+    SetIndexedArrayForEachAtomTo ( OtherDistances, &atom::nr, &atom::DistanceSquaredToVector, CenterOfGravity);
 
     /// ... sort each list (using heapsort (o(N log N)) from GSL)
@@ -1150 +1128 @@
 {
   double temperature;
-  atom *Walker = NULL;
   // test stream
   if (output == NULL)
@@ -1158 +1135 @@
   for (int step=startstep;step < endstep; step++) { // loop over all time steps
     temperature = 0.;
-    Walker = start;
-    while (Walker->next != end) {
-      Walker = Walker->next;
-      for (int i=NDIM;i--;)
-        temperature += Walker->type->mass * Walker->Trajectory.U.at(step).x[i]* Walker->Trajectory.U.at(step).x[i];
-    }
+    ActOnAllAtoms( &atom::AddKineticToTemperature, &temperature, step);
     *output << step << "\t" << temperature*AtomicEnergyToKelvin << "\t" << temperature << endl;
   }