Changeset db6bf74 for src

Timestamp:

Oct 15, 2009, 8:10:10 AM (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:

c144ed2

Parents:

bbc338

Message:

Fixed two memory leaks.

• FIX: if the element database could not be parsed, in LoadPeriodentafel() still one element would be allocated, Loading failure admonished and then not free'd. Fixed
• FIX: the config was allocated in main not by a new, but fixed. In its constructor Malloc calls were present. Hence, the memory was not free'd. As fixed types are free'd first at the very end of the code. Hence before any MemoryUsageObserver::getUsedMemorySize() calls ... that's why 1614 bytes were always claimed as still allocated. Fixed.
• valgrind does not admonish any leaks (however, some errors) anymore when molecuilder is started and immediately quitted.

Signed-off-by: Frederik Heber <heber@…>

Location:

src

Files:

• builder.cpp (modified) (12 diffs)
• periodentafel.cpp (modified) (1 diff)

src/builder.cpp

@@ -50 +50 @@
 using namespace std;
 
+#include "analysis_correlation.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
@@ -1375 +1376 @@
             cout << "\t-B xx xy xz yy yz zz\tBound atoms by domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl;
             cout << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl;
+            cout << "\t-C\tPair Correlation analysis." << endl;
             cout << "\t-d x1 x2 x3\tDuplicate cell along each axis by given factor." << endl;
             cout << "\t-D <bond distance>\tDepth-First-Search Analysis of the molecule, giving cycles and tree/back edges." << endl;
@@ -1575 +1577 @@
               //argptr+=1;
               break;
+            case 'C':
+              if (ExitFlag == 0) ExitFlag = 1;
+              if ((argptr+1 >= argc) || (argv[argptr+1][0] == '-') || (argv[argptr+2][0] == '-')) {
+                ExitFlag = 255;
+                cerr << "Not enough or invalid arguments given for pair correlation analysis: -C <output> <bin output>" << endl;
+              } else {
+                SaveFlag = false;
+                ofstream output(argv[argptr]);
+                ofstream binoutput(argv[argptr+1]);
+                class Tesselation T;
+                const double radius = 5.;
+                LinkedCell LCList(mol, 2.*radius);
+                element *oxygen = periode->FindElement(8);
+                FindNonConvexBorder((ofstream *)&cout, mol, &LCList, radius, NULL);
+                CorrelationToSurfaceMap *surfacemap = CorrelationToSurface( (ofstream *)&cout, mol, oxygen, mol->TesselStruct, &LCList );
+                BinPairMap *binmap = BinData( (ofstream *)&cout, surfacemap, 0.5, 0., 0. );
+                OutputCorrelation ( &binoutput, binmap );
+                output.close();
+                binoutput.close();
+                argptr+=2;
+              }
+              break;
             case 'E':
               if (ExitFlag == 0) ExitFlag = 1;
@@ -2043 +2067 @@
   MoleculeListClass *molecules = new MoleculeListClass;  // list of all molecules
   molecule *mol = NULL;
-  config configuration;
+  config *configuration = new config;
   char choice;  // menu choice char
   Vector x,y,z,n;  // coordinates for absolute point in cell volume
@@ -2053 +2077 @@
 
   // =========================== PARSE COMMAND LINE OPTIONS ====================================
-  j = ParseCommandLineOptions(argc, argv, molecules, periode, configuration, ConfigFileName);
+  j = ParseCommandLineOptions(argc, argv, molecules, periode, *configuration, ConfigFileName);
   switch(j) {
     case 255:  // something went wrong
@@ -2135 +2159 @@
 
       case 'c': // edit each field of the configuration
-       configuration.Edit();
+       configuration->Edit();
        break;
 
@@ -2143 +2167 @@
 
       case 'g': // manipulate molecules
-        ManipulateMolecules(periode, molecules, &configuration);
+        ManipulateMolecules(periode, molecules, configuration);
         break;
 
@@ -2151 +2175 @@
 
       case 'm': // manipulate atoms
-        ManipulateAtoms(periode, molecules, &configuration);
+        ManipulateAtoms(periode, molecules, configuration);
         break;
 
@@ -2158 +2182 @@
 
       case 's': // save to config file
-        SaveConfig(ConfigFileName, &configuration, periode, molecules);
+        SaveConfig(ConfigFileName, configuration, periode, molecules);
         break;
 
@@ -2171 +2195 @@
 
   // save element data base
-  if (periode->StorePeriodentafel(configuration.databasepath)) //ElementsFileName
+  if (periode->StorePeriodentafel(configuration->databasepath)) //ElementsFileName
     cout << Verbose(0) << "Saving of elements.db successful." << endl;
   else
@@ -2178 +2202 @@
   delete(molecules); // also free's all molecules contained
   delete(periode);
+  delete(configuration);
 
   cout << Verbose(0) <<  "Maximum of allocated memory: "
@@ -2183 +2208 @@
   cout << Verbose(0) <<  "Remaining non-freed memory: "
     << MemoryUsageObserver::getInstance()->getUsedMemorySize() << endl;
+  MemoryUsageObserver::purgeInstance();
 
   return (0);

src/periodentafel.cpp

@@ -215 +215 @@
         cout << "Could not parse element: ";
         neues->Output((ofstream *)&cout);
+        delete(neues);
       }
     }