Changeset 14d4d4

Timestamp:

Jun 16, 2008, 2:09:27 PM (17 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:

d427bd

Parents:

edb650

Message:

BUGFIX: If other databases could not be loaded, no error was produced, resulting in strange behaviour of the fragmentation routine.

Now an error message is produced, though we still continue. The problem was the switch in handling const char * and a huge mess in LoadPeriodenTafel() with strncat and strncpy.

Location:

src

Files:

• builder.cpp (modified) (1 diff)
• moleculelist.cpp (modified) (1 diff)
• molecules.cpp (modified) (4 diffs)
• periodentafel.cpp (modified) (8 diffs)

src/builder.cpp

@@ -805 +805 @@
       cout << Verbose(0) << "Element list loaded successfully." << endl;
       periode->Output((ofstream *)&cout);
-    } else
+    } else {
       cout << Verbose(0) << "Element list loading failed." << endl;
+      return 1;
+    }
     
     // 3. Find config file name and parse if possible

src/moleculelist.cpp

@@ -240 +240 @@
     *out << endl;
     // prepare output of config file
-    sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
+    sprintf(FragmentName, "%s/%s%s.conf", PathBackup, FRAGMENTPREFIX, FragmentNumber);
     outputFragment.open(FragmentName, ios::out);
-    strcpy(PathBackup, configuration->configpath);
-    sprintf(FragmentName, "%s/%s%s/", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
+    //strcpy(PathBackup, configuration->configpath);
+    sprintf(FragmentName, "%s/%s%s/", PathBackup, FRAGMENTPREFIX, FragmentNumber);
     
     // center on edge

src/molecules.cpp

@@ -1573 +1573 @@
             for(j=0;j<NumberOfBondsPerAtom[Walker->nr];j++)
               NoBonds += ListOfBondsPerAtom[Walker->nr][j]->BondDegree;
-                  //*out << Verbose(3) << "Walker: " << (int)Walker->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
+                  *out << Verbose(3) << "Walker: " << (int)Walker->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
                   if ((int)(Walker->type->NoValenceOrbitals) > NoBonds) { // we have a mismatch, check NoBonds of other atom
                     // count valence of second partner
@@ -1579 +1579 @@
               for(j=0;j<NumberOfBondsPerAtom[OtherWalker->nr];j++)
                 NoBonds += ListOfBondsPerAtom[OtherWalker->nr][j]->BondDegree;
-              //*out << Verbose(3) << "OtherWalker: " << (int)OtherWalker->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
+              *out << Verbose(3) << "OtherWalker: " << (int)OtherWalker->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
                     if ((int)(OtherWalker->type->NoValenceOrbitals) > NoBonds) // increase bond degree by one
                 ListOfBondsPerAtom[Walker->nr][i]->BondDegree++;
@@ -1591 +1591 @@
           *out << Verbose(1) << "I detected " << BondCount << " bonds in the molecule with distance " << bonddistance << "." << endl;
                 
-//        // output bonds for debugging (if bond chain list was correctly installed)
-//        *out << Verbose(1) << endl << "From contents of bond chain list:";
-//        bond *Binder = first;
-//    while(Binder->next != last) {
-//      Binder = Binder->next;
-//                      *out << *Binder << "\t" << endl;
-//    }
-//    *out << endl;
+          // output bonds for debugging (if bond chain list was correctly installed)
+          *out << Verbose(1) << endl << "From contents of bond chain list:";
+          bond *Binder = first;
+    while(Binder->next != last) {
+      Binder = Binder->next;
+                        *out << *Binder << "\t" << endl;
+    }
+    *out << endl;
   } else
         *out << Verbose(1) << "AtomCount is " << AtomCount << ", thus no bonds, no connections!." << endl; 
@@ -3131 +3131 @@
 //          *out << ", who has no son in this fragment molecule." << endl; 
 #ifdef ADDHYDROGEN
-//          *out << Verbose(3) << "Adding Hydrogen to " << Runner->Name << " and a bond in between." << endl;
+          //*out << Verbose(3) << "Adding Hydrogen to " << Runner->Name << " and a bond in between." << endl;
           Leaf->AddHydrogenReplacementAtom(out, ListOfBondsPerAtom[FatherOfRunner->nr][i], Runner, FatherOfRunner, OtherFather, ListOfBondsPerAtom[FatherOfRunner->nr],NumberOfBondsPerAtom[FatherOfRunner->nr], IsAngstroem);
 #endif

src/periodentafel.cpp

@@ -217 +217 @@
 
   // fill valence DB per element
-  strncat(filename, path, MAXSTRINGSIZE);
-  strncpy(filename, STANDARDVALENCEDB, MAXSTRINGSIZE-strlen(filename));
+  strncpy(filename, path, MAXSTRINGSIZE);
+  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
+  strncat(filename, STANDARDVALENCEDB, MAXSTRINGSIZE-strlen(filename));
   infile.open(filename);
   if (infile != NULL) {
@@ -226 +227 @@
         infile >> FindElement((int)tmp)->Valence;
         infile >> ws;
-        //cout << Verbose(3) << "Element " << (int)tmp << " has " << find_element((int)tmp)->Valence << " valence electrons." << endl;
+        //cout << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->Valence << " valence electrons." << endl;
     }
     infile.close();
@@ -234 +235 @@
 
   // fill valence DB per element
-  strncat(filename, path, MAXSTRINGSIZE);
-  strncpy(filename, STANDARDORBITALDB, MAXSTRINGSIZE-strlen(filename));
+  strncpy(filename, path, MAXSTRINGSIZE);
+  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
+  strncat(filename, STANDARDORBITALDB, MAXSTRINGSIZE-strlen(filename));
   infile.open(filename);
   if (infile != NULL) {
@@ -243 +245 @@
       infile >> FindElement((int)tmp)->NoValenceOrbitals;
       infile >> ws;
-      //cout << Verbose(3) << "Element " << (int)tmp << " has " << find_element((int)tmp)->NoValenceOrbitals << " number of singly occupied valence orbitals." << endl;
+      //cout << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->NoValenceOrbitals << " number of singly occupied valence orbitals." << endl;
     }
     infile.close();
@@ -251 +253 @@
   
   // fill H-BondDistance DB per element
-  strncat(filename, path, MAXSTRINGSIZE);
-  strncpy(filename, STANDARDHBONDDISTANCEDB, MAXSTRINGSIZE-strlen(filename));
+  strncpy(filename, path, MAXSTRINGSIZE);
+  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
+  strncat(filename, STANDARDHBONDDISTANCEDB, MAXSTRINGSIZE-strlen(filename));
   infile.open(filename);
   if (infile != NULL) {
@@ -263 +266 @@
       infile >> ptr->HBondDistance[2];
         infile >> ws;
-      //cout << Verbose(3) << "Element " << (int)tmp << " has " << find_element((int)tmp)->HBondDistance[0] << " Angstrom typical distance to hydrogen." << endl;
+      //cout << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->HBondDistance[0] << " Angstrom typical distance to hydrogen." << endl;
     }
     infile.close();
@@ -271 +274 @@
   
   // fill H-BondAngle DB per element
-  strncat(filename, path, MAXSTRINGSIZE);
-  strncpy(filename, STANDARDHBONDANGLEDB, MAXSTRINGSIZE-strlen(filename));
+  strncpy(filename, path, MAXSTRINGSIZE);
+  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
+  strncat(filename, STANDARDHBONDANGLEDB, MAXSTRINGSIZE-strlen(filename));
   infile.open(filename);
   if (infile != NULL) {
@@ -288 +292 @@
   } else
     otherstatus = false;
+  
+  if (!otherstatus)
+    cerr << "ERROR: Something went wrong while parsing the databases!" << endl;
   
   return status;