Changeset fefe0d

Timestamp:

Jul 21, 2010, 3:47:47 PM (14 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

9f632c

Parents:

add42a

Message:

FIX: Bug with vector resizing in Formula

File:

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

src/Formula.cpp

@@ -9 +9 @@
 
 #include <sstream>
-#include <iostream>
 
 #include "World.hpp"
@@ -73 +72 @@
       throw(ParseError(__FILE__,__LINE__));
     shorthand+=(*it++);
-    cout << "Beginning of shorthand read: " << shorthand << endl;
     // the rest of the name follows
     while(it!=end && isInRange(SmallLetters,(*it)))
       shorthand+=(*it++);
-    cout << "Full shorthand read: " << shorthand << endl;
     // now we can count the occurences
     int count = 0;
     while(it!=end && isInRange(Numbers,(*it)))
       count = (count*10) + ((*it++)-Numbers.first);
-    cout << "Count read: " << count << endl;
     // one is implicit
     count = (count!=0)?count:1;
-    cout << "Corrected implicit count: " << count << endl;
+    // test if the shorthand exists
+    if(!World::getInstance().getPeriode()->FindElement(shorthand))
+      throw(ParseError(__FILE__,__LINE__));
     // done, we can get the next one
     addElements(shorthand,count);
@@ -135 +133 @@
   ASSERT(Z>0,"Invalid atomic Number");
   ASSERT(World::getInstance().getPeriode()->FindElement(Z),"No Element with this number in Periodentafel");
-  elementCounts.resize(Z); // No-op when we already have the right size
+  elementCounts.resize(max<atomicNumber_t>(Z,elementCounts.size()),0); // No-op when we already have the right size
   // might need to update number of elements
   if(!elementCounts[Z-1]){
@@ -178 +176 @@
   ASSERT(Z>0,"Invalid atomic Number");
   ASSERT(World::getInstance().getPeriode()->FindElement(Z),"No Element with this number in Periodentafel");
-  elementCounts.resize(Z); // No-op when we already have the right size
-  cout << "Adding " << count << " to element with number " << Z << endl;
+  elementCounts.resize(max<atomicNumber_t>(Z,elementCounts.size()),0); // No-op when we already have the right size
   // might need to update number of elements
   if(!elementCounts[Z-1]){
@@ -185 +182 @@
   }
   elementCounts[Z-1]+=count;
-  cout << "Element ist now " << elementCounts[Z-1] << endl;
 }