Changeset 23b830

Timestamp:

Oct 7, 2009, 1:18:59 PM (16 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:

e41951

Parents:

681a8a

Message:

molecule::CountElements() changed to use SetIndexedArrayForEachAtomTo(), molecule::OutputXYZ() fixed

• in molecule::OutputXYZ() AtomCount is used
• molecule::CountElements() now uses SetIndexedArrayForEachAtomTo() to get the number of atoms per element counted

File:

• src/molecule.cpp (modified) (2 diffs)

src/molecule.cpp

@@ -822 +822 @@
   time_t now;
 
-  now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
-  walker = start;
-  while (walker->next != end) { // go through every atom and count
-    walker = walker->next;
-    AtomNo++;
-  }
   if (out != NULL) {
-    *out << AtomNo << "\n\tCreated by molecuilder on " << ctime(&now);
+    now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
+    *out << AtomCount << "\n\tCreated by molecuilder on " << ctime(&now);
     ActOnAllAtoms( &atom::OutputXYZLine, out );
     return true;
@@ -876 +871 @@
 void molecule::CountElements()
 {
-  int i = 0;
-  for(i=MAX_ELEMENTS;i--;)
+  for(int i=MAX_ELEMENTS;i--;)
     ElementsInMolecule[i] = 0;
   ElementCount = 0;
 
-  atom *walker = start;
-  while (walker->next != end) {
-    walker = walker->next;
-    ElementsInMolecule[walker->type->Z]++;
-    i++;
-  }
-  for(i=MAX_ELEMENTS;i--;)
+  SetIndexedArrayForEachAtomTo ( ElementsInMolecule, &element::Z, &Increment, 1);
+
+  for(int i=MAX_ELEMENTS;i--;)
     ElementCount += (ElementsInMolecule[i] != 0 ? 1 : 0);
 };
-