Changeset a6b7fb

Timestamp:

Sep 6, 2008, 3:08:32 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:

deac6c

Parents:

d1fc7f

Message:

BUGFIX: config::SaveMPQC() used molecule::DetermineCenter() which relies on the created bond structure, causing segfault.

When storing a newly created configuration file, the bond structure needs not be present yet. Hence, we created the function molecule:DetermineCenterOfAll(), similar to molecule::DetermineCenterOfGravity() just without scaling by masses. This new function is now used instead.

Location:

src

Files:

• config.cpp (modified) (3 diffs)
• molecules.cpp (modified) (1 diff)
• molecules.hpp (modified) (1 diff)

src/config.cpp

@@ -1072 +1072 @@
 bool config::SaveMPQC(ofstream *output, molecule *mol) const
 {
-  int ElementNo;
+  int ElementNo = 0;
   int AtomNo;
   atom *Walker = NULL;
-  element *runner;
-  Vector center;
+  element *runner = mol->elemente->start;
+  Vector *center = NULL;
 
   *output << "% Created by MoleCuilder" << endl;
@@ -1086 +1086 @@
   *output << "\t\t\tunit = " << (IsAngstroem ? "angstrom" : "bohr" ) << endl;
   *output << "\t\t\t{ atoms geometry } = {" << endl;
-  mol->DetermineCenter(center);
+  center = mol->DetermineCenterOfAll(output);
   // output of atoms
-  ElementNo = 0;
-  runner = mol->elemente->start;
   while (runner->next != mol->elemente->end) { // go through every element
     runner = runner->next;
@@ -1100 +1098 @@
         if (Walker->type == runner) { // if this atom fits to element
           AtomNo++;
-          *output << "\t\t\t\t" << Walker->type->symbol << " [ " << Walker->x.x[0]-center.x[0] << "\t" << Walker->x.x[1]-center.x[1] << "\t" << Walker->x.x[2]-center.x[2] << " ]" << endl;
+          *output << "\t\t\t\t" << Walker->type->symbol << " [ " << Walker->x.x[0]-center->x[0] << "\t" << Walker->x.x[1]-center->x[1] << "\t" << Walker->x.x[2]-center->x[2] << " ]" << endl;
         }
       }
     }
   }
+  delete(center);
   *output << "\t\t\t}" << endl;
   *output << "\t\t)" << endl;

src/molecules.cpp

@@ -720 +720 @@
   }
 }; 
+
+/** Returns vector pointing to center of gravity.
+ * \param *out output stream for debugging
+ * \return pointer to center of gravity vector
+ */
+Vector * molecule::DetermineCenterOfAll(ofstream *out)
+{
+  atom *ptr = start->next;  // start at first in list
+  Vector *a = new Vector();
+  Vector tmp;
+  double Num = 0;
+  
+  a->Zero();
+
+  if (ptr != end) {   //list not empty?
+    while (ptr->next != end) {  // continue with second if present
+      ptr = ptr->next;
+      Num += 1.;
+      tmp.CopyVector(&ptr->x);
+      a->AddVector(&tmp);       
+    }
+    a->Scale(-1./Num); // divide through total mass (and sign for direction)
+  }
+  //cout << Verbose(1) << "Resulting center of gravity: ";
+  //a->Output(out);
+  //cout << endl;
+  return a;
+};
 
 /** Returns vector pointing to center of gravity.

src/molecules.hpp

@@ -253 +253 @@
   void DetermineCenter(Vector &center);
   Vector * DetermineCenterOfGravity(ofstream *out);
+  Vector * DetermineCenterOfAll(ofstream *out);
   void SetBoxDimension(Vector *dim);
   double * ReturnFullMatrixforSymmetric(double *cell_size);