Changeset 3c4f04 for src

Timestamp:

Jul 27, 2009, 2:22:20 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:

fcc9b0

Parents:

b6d8a9

git-author:

Frederik Heber <heber@…> (07/27/09 14:19:12)

git-committer:

Frederik Heber <heber@…> (07/27/09 14:22:20)

Message:

BUGFIX: config::Load() added atoms in wrong order, hence resulting in wrong names.

• config::Load() - int in LinearList should have been mapped not original one

File:

• src/config.cpp (modified) (5 diffs)

src/config.cpp

@@ -936 +936 @@
     map<int, atom *> AtomList[config::MaxTypes];
     map<int, atom *> LinearList;
+    atom *neues = NULL;
     if (!FastParsing) {
       // parse in trajectories
       bool status = true;
-      atom *neues = NULL;
       while (status) {
         cout << "Currently parsing MD step " << repetition << "." << endl;
@@ -949 +949 @@
               neues = new atom();
               AtomList[i][j] = neues;
-              LinearList[FileBuffer->CurrentLine] = neues;
+              LinearList[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ] = neues;
               neues->type = elementhash[i]; // find element type
             } else
@@ -1005 +1005 @@
         }
         repetition++;
-      }
-      // put atoms into the molecule in their original order
-      for(map<int, atom*>::iterator runner = LinearList.begin(); runner != LinearList.end(); ++runner) {
-        mol->AddAtom(runner->second);
       }
       repetition--;
@@ -1026 +1022 @@
         for(int j=0;j<No[i];j++) {
           sprintf(keyword,"%s_%i",name, j+1);
-          atom *neues = new atom();
+          if (repetition == 0) {
+            neues = new atom();
+            AtomList[i][j] = neues;
+            LinearList[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ] = neues;
+            neues->type = elementhash[i]; // find element type
+          } else
+            neues = AtomList[i][j];
           // then parse for each atom the coordinates as often as present
           ParseForParameter(verbose,FileBuffer, keyword, 0, 1, 1, double_type, &neues->x.x[0], repetition,critical);
@@ -1043 +1045 @@
         }
       }
+    }
+    // put atoms into the molecule in their original order
+    for(map<int, atom*>::iterator runner = LinearList.begin(); runner != LinearList.end(); ++runner) {
+      mol->AddAtom(runner->second);
     }
   }