Changeset 76096d for src

Timestamp:

Sep 19, 2013, 8:23:52 PM (11 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:

46b181

Parents:

f54cda

git-author:

Frederik Heber <heber@…> (08/22/13 10:48:24)

git-committer:

Frederik Heber <heber@…> (09/19/13 20:23:52)

Message:

FIX: Several fixes found through CppCheck.

• strncpy does not always cap with \0.
• mismatch in new[] with delete.
• division by zero.
• NULL pointer not checked.

Location:

src

Files:

• Element/periodentafel.cpp (modified) (3 diffs)
• Fragmentation/EnergyMatrix.cpp (modified) (3 diffs)
• Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (modified) (1 diff)
• Fragmentation/analyzer.cpp (modified) (1 diff)
• Parser/PcpParser_helper.cpp (modified) (1 diff)
• Tesselation/BoundaryPolygonSet.cpp (modified) (1 diff)
• Tesselation/boundary.cpp (modified) (1 diff)

src/Element/periodentafel.cpp

@@ -44 +44 @@
 #include "element.hpp"
 #include "elements_db.hpp"
+#include "Helpers/defs.hpp"
 #include "periodentafel.hpp"
 
@@ -296 +297 @@
   bool status = true;
   bool otherstatus = true;
-  char filename[255];
+  char filename[MAXSTRINGSIZE];
 
   // fill elements DB
-  strncpy(filename, path, MAXSTRINGSIZE);
+  if (strlen(path)+1+strlen(STANDARDELEMENTSDB) > MAXSTRINGSIZE-1)
+    ELOG(2, "Generated path '" << path << "' will be too long.");
+  filename[0] = '\0';
+  strncat(filename, path, MAXSTRINGSIZE);
   strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
   strncat(filename, STANDARDELEMENTSDB, MAXSTRINGSIZE-strlen(filename));
@@ -633 +637 @@
   char filename[MAXSTRINGSIZE];
 
-  strncpy(filename, path, MAXSTRINGSIZE);
+  if (strlen(path)+1+strlen(STANDARDELEMENTSDB) > MAXSTRINGSIZE-1)
+    ELOG(2, "Generated path '" << path << "' will be too long.");
+  filename[0] = '\0';
+  strncat(filename, path, MAXSTRINGSIZE);
   strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
   strncat(filename, STANDARDELEMENTSDB, MAXSTRINGSIZE-strlen(filename));

src/Fragmentation/EnergyMatrix.cpp

@@ -39 +39 @@
 
 #include "CodePatterns/Log.hpp"
+#include "Helpers/defs.hpp"
 #include "KeySetsContainer.hpp"
 
@@ -94 +95 @@
 bool EnergyMatrix::ParseFragmentMatrix(const char *name, const char *prefix, std::string suffix, int skiplines, int skipcolumns)
 {
-  char filename[1024];
+  char filename[MAXSTRINGSIZE];
   bool status = MatrixContainer::ParseFragmentMatrix(name, prefix, suffix, skiplines, skipcolumns);
 
@@ -115 +116 @@
 
     // try independently to parse global energysuffix file if present
-    strncpy(filename, name, 1023);
-    strncat(filename, prefix, 1023-strlen(filename));
-    strncat(filename, suffix.c_str(), 1023-strlen(filename));
+    if (strlen(name)+strlen(prefix)+suffix.size() > MAXSTRINGSIZE-1)
+      ELOG(2, "Generated path '" << name << "' will be too long.");
+    filename[0] = '\0';
+    strncat(filename, name, MAXSTRINGSIZE);
+    strncat(filename, prefix, MAXSTRINGSIZE-strlen(filename));
+    strncat(filename, suffix.c_str(), MAXSTRINGSIZE-strlen(filename));
     std::ifstream input(filename);
     ParseMatrix(input, skiplines, skipcolumns, MatrixCounter);

src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp

@@ -505 +505 @@
   ia >> samefragment;
 
+  CPPUNIT_ASSERT( samefragment != NULL );
   CPPUNIT_ASSERT( *fragment == *samefragment );
 

src/Fragmentation/analyzer.cpp

@@ -119 +119 @@
   // Test the given directory
   if (!TestParams(argc, argv)) {
-    delete dir;
+    delete[] dir;
     delete periode;
     return 1;

src/Parser/PcpParser_helper.cpp

@@ -163 +163 @@
               line++;
             } while ((dummy1[0] == '#') || (dummy1[0] == '\n'));
-            if (dummy1 == NULL){
-              if (verbose) fprintf(stderr,"Error reading line %i\n", line);
-            } else {
-              //fprintf(stderr,"Reading next line %i: %s\n", line, dummy1);
-            }
+//            if (dummy1 == NULL){
+//              if (verbose) fprintf(stderr,"Error reading line %i\n", line);
+//            } else {
+//              //fprintf(stderr,"Reading next line %i: %s\n", line, dummy1);
+//            }
           } else { // simple int, strings or doubles start in the same line
             while ((*dummy == '\t') || (*dummy == ' '))   // skip interjacent tabs and spaces

src/Tesselation/BoundaryPolygonSet.cpp

@@ -107 +107 @@
     (*TotalNormal) += TemporaryNormal;
   }
-  TotalNormal->Scale(1. / (double) counter);
+  if (counter != 0.)
+    TotalNormal->Scale(1. / (double) counter);
 
   // make it always point inward (any offset vector onto plane projected onto normal vector suffices)

src/Tesselation/boundary.cpp

@@ -752 +752 @@
     mol->CenterInBox();
   }
-  delete GreatestDiameter;
+  delete[] GreatestDiameter;
   // update Box of atoms by boundary
   mol->SetBoxDimension(&BoxLengths);