Changeset 42af9e

Timestamp:

May 31, 2010, 2:33:11 PM (15 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:

1024cb

Parents:

920c70

git-author:

Frederik Heber <heber@…> (05/31/10 14:27:12)

git-committer:

Frederik Heber <heber@…> (05/31/10 14:33:11)

Message:

MEMFIXES: no more default saving/loading of element's db, config::SaveTREMOLO(), molecule::CreateMappingLabelsToConfigSequence()

• ParseCommandLineOptions() - loading element's db only when path was given
• main() - default storing at end removed, should be handled by config::~config()
• config::SaveTREMOLO() - LocalNotoGlobalNoMap is now an STL map, id must not be continuous, so old way is very error-prone
• molecule::CreateMappingLabelsToConfigSequence() - don't delete SortIndex (is done in FragmentMolecule)
• molecule::FragmentMolecule() - dont' delete FragmentList in the block
• testsuite-simple_configuration.at - removing atoms around sphere is not broken anymore, changed testsuite accordingly.

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

Files:

• src/builder.cpp (modified) (4 diffs)
• src/config.cpp (modified) (6 diffs)
• src/molecule_fragmentation.cpp (modified) (4 diffs)
• src/periodentafel.cpp (modified) (1 diff)
• tests/regression/testsuite-simple_configuration.at (modified) (1 diff)

src/builder.cpp ¶

@@ -1513 +1513 @@
   molecule *mol = NULL;
   string BondGraphFileName("\n");
-  strncpy(configuration.databasepath, LocalPath, MAXSTRINGSIZE-1);
+  bool DatabasePathGiven = false;
 
   if (argc > 1) { // config file specified as option
@@ -1557 +1557 @@
               DoLog(0) && (Log() << Verbose(0) << "Using " << argv[argptr] << " as elements database." << endl);
               strncpy (configuration.databasepath, argv[argptr], MAXSTRINGSIZE-1);
+              DatabasePathGiven = true;
               argptr+=1;
             }
@@ -1600 +1601 @@
 
     // 3a. Parse the element database
-    if (periode->LoadPeriodentafel(configuration.databasepath)) {
-      DoLog(0) && (Log() << Verbose(0) << "Element list loaded successfully." << endl);
-      //periode->Output();
-    } else {
-      DoLog(0) && (Log() << Verbose(0) << "Element list loading failed." << endl);
-      return 1;
-    }
+    if (DatabasePathGiven)
+      if (periode->LoadPeriodentafel(configuration.databasepath)) {
+        DoLog(0) && (Log() << Verbose(0) << "Element list loaded successfully." << endl);
+        //periode->Output();
+      } else {
+        DoLog(0) && (Log() << Verbose(0) << "Element list loading failed." << endl);
+        return 1;
+      }
     // 3b. Find config file name and parse if possible, also BondGraphFileName
     if (argv[1][0] != '-') {
@@ -2522 +2524 @@
     Log() << Verbose(0) << "Saving to " << ConfigFileName << "." << endl;
     World::getInstance().getConfig()->SaveAll(ConfigFileName, World::getInstance().getPeriode(), World::getInstance().getMolecules());
-    if(World::getInstance().getPeriode()->StorePeriodentafel(configuration->databasepath))
-        Log() << Verbose(0) << "Saving of elements.db successful." << endl;
-
-    else
-        Log() << Verbose(0) << "Saving of elements.db failed." << endl;
 
   // free the new argv

src/config.cpp ¶

@@ -14 +14 @@
 #include "element.hpp"
 #include "helpers.hpp"
+#include "info.hpp"
 #include "lists.hpp"
 #include "log.hpp"
@@ -1712 +1713 @@
 bool config::SaveTREMOLO(const char * const filename, const MoleculeListClass * const MolList) const
 {
+  Info FunctionInfo(__func__);
   atom *Walker = NULL;
   ofstream *output = NULL;
@@ -1738 +1740 @@
 
   // create global to local id map
-  int **LocalNotoGlobalNoMap = new int *[MolList->ListOfMolecules.size()];
-  for (int i=0;i<MolList->ListOfMolecules.size();i++)
-    LocalNotoGlobalNoMap[i] = NULL;
+  map<int, int> LocalNotoGlobalNoMap;
   {
-    int MolCounter = 0;
-    int AtomNo = 0;
+    unsigned int MolCounter = 0;
+    int AtomNo = 1;
     for (MoleculeList::const_iterator MolWalker = MolList->ListOfMolecules.begin(); MolWalker != MolList->ListOfMolecules.end(); MolWalker++) {
-      LocalNotoGlobalNoMap[MolCounter] = new int[MolList->CountAllAtoms()];
-      for (int i=0;i<MolList->CountAllAtoms();i++)
-        LocalNotoGlobalNoMap[MolCounter][i] = NULL;
-
-      (*MolWalker)->SetIndexedArrayForEachAtomTo( LocalNotoGlobalNoMap[MolCounter], &atom::nr, IncrementalAbsoluteValue, &AtomNo);
-
+      atom *Walker = (*MolWalker)->start;
+      while (Walker->next != (*MolWalker)->end) {
+        Walker = Walker->next;
+        LocalNotoGlobalNoMap.insert( pair<int,int>(Walker->getId(), AtomNo++) );
+      }
       MolCounter++;
     }
+    ASSERT(MolCounter == MolList->ListOfMolecules.size(), "SaveTREMOLO: LocalNotoGlobalNoMap[] has not been correctly initialized for each molecule");
   }
 
@@ -1763 +1763 @@
       while (Walker->next != (*MolWalker)->end) {
         Walker = Walker->next;
-        *output << AtomNo+1 << "\t";
+        *output << LocalNotoGlobalNoMap[ Walker->getId() ] << "\t";
         *output << Walker->getName() << "\t";
         *output << (*MolWalker)->name << "\t";
@@ -1771 +1771 @@
         *output << Walker->type->symbol << "\t";
         for (BondList::iterator runner = Walker->ListOfBonds.begin(); runner != Walker->ListOfBonds.end(); runner++)
-          *output << LocalNotoGlobalNoMap[MolCounter][ (*runner)->GetOtherAtom(Walker)->nr ]+1 << "\t";
+          *output << LocalNotoGlobalNoMap[ (*runner)->GetOtherAtom(Walker)->getId() ] << "\t";
         for(int i=Walker->ListOfBonds.size(); i < MaxNeighbours; i++)
           *output << "-\t";
@@ -1786 +1786 @@
   delete(output);
   delete(fname);
-  for(size_t i=0;i<MolList->ListOfMolecules.size(); i++)
-    delete[](LocalNotoGlobalNoMap[i]);
-  delete[](LocalNotoGlobalNoMap);
 
   return true;

src/molecule_fragmentation.cpp ¶

@@ -516 +516 @@
   int AtomNo = 0;
   SetIndexedArrayForEachAtomTo( SortIndex, &atom::nr, &IncrementalAbsoluteValue, AtomNo );
-  delete[](SortIndex);
 
   return true;
@@ -542 +541 @@
 {
   MoleculeListClass *BondFragments = NULL;
-  int *SortIndex = NULL;
   int *MinimumRingSize = new int[AtomCount];
   int FragmentCounter;
@@ -685 +683 @@
   if (BondFragments->ListOfMolecules.size() != 0) {
     // create the SortIndex from BFS labels to order in the config file
+    int *SortIndex = NULL;
     CreateMappingLabelsToConfigSequence(SortIndex);
 
@@ -718 +717 @@
     // free memory for bond part
     DoLog(1) && (Log() << Verbose(1) << "Freeing bond memory" << endl);
-    delete[](FragmentList); // remove bond molecule from memory
     delete[](SortIndex);
   } else {

src/periodentafel.cpp ¶

@@ -39 +39 @@
 /** destructor for class periodentafel
  * Removes every element and afterwards deletes start and end of list.
+ * TODO: Handle when elements have changed and store databases then
  */
 periodentafel::~periodentafel()

tests/regression/testsuite-simple_configuration.at ¶

@@ -84 +84 @@
 
 # 8. Removing sphere of atoms
-AT_SETUP([Simple configuration - BROKEN: Removing sphere of atoms])
+AT_SETUP([Simple configuration - Removing sphere of atoms])
 AT_KEYWORDS([configuration])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/pre/test.* .], 0)
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -R 2 7.], 134, [stdout], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -R 2 7.], 0, [stdout], [stderr])
 AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP