Changeset caf5d6 for src/molecules.cpp

Timestamp:

Dec 11, 2008, 3:23:01 PM (16 years ago)

Author:

Christian Neuen <neuen@…>

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:

e4ea46

Parents:

f714979

Message:

Atom indices are now correctly processed.

File:

• src/molecules.cpp (modified) (3 diffs)

src/molecules.cpp

@@ -1518 +1518 @@
 {
   atom *walker = NULL;
-  int No = 0;
+  int AtomNo = 0, ElementNo;
   time_t now;
+  element *runner = NULL;
 
   now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
@@ -1525 +1526 @@
   while (walker->next != end) { // go through every atom and count
     walker = walker->next;
-    No++;
+    AtomNo++;
   }
   if (out != NULL) {
-    *out << No << "\n\tCreated by molecuilder on " << ctime(&now);
-    walker = start;
-    while (walker->next != end) { // go through every atom of this element
-      walker = walker->next;
-      walker->OutputXYZLine(out);
+    *out << AtomNo << "\n\tCreated by molecuilder on " << ctime(&now);
+    ElementNo = 0;
+    runner = elemente->start;
+    while (runner->next != elemente->end) { // go through every element
+                runner = runner->next;
+      if (ElementsInMolecule[runner->Z]) { // if this element got atoms
+        ElementNo++;
+        walker = start;
+        while (walker->next != end) { // go through every atom of this element
+          walker = walker->next;
+          if (walker->type == runner) { // if this atom fits to element
+            walker->OutputXYZLine(out);
+          }
+        }
+      }
     }
     return true;
@@ -1716 +1727 @@
                         };
                         AddBond(Walker, OtherWalker); //Add the bond between the two atoms with respective indices.
-                        BondCount++; //Increase bond count of molecule
+                        
                 }