Changeset 046783 for src

Timestamp:

Mar 3, 2010, 2:53:07 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:

6e8dc2, b72091

Parents:

a837d0

git-author:

Frederik Heber <heber@…> (03/03/10 14:46:13)

git-committer:

Frederik Heber <heber@…> (03/03/10 14:53:07)

Message:

Default molecule name can be set via command line, BUGFIX: molecule::DepthFirstSearchAnalysis() seg'faulted on no atoms.

Allow '-I' on empty configs:

• molecule::DepthFirstSearchAnalysis(): check whether AtomCount==0
• molecule::molecule(): name is now not 'none' but copied from World::DefaultName
• MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs():
  • Check for false from BondGraph::ConstructBondGraph()
  • Check for Subgraphs or its successor being NULL
• ParseCommandLineOptions(): first molecule only set active if molecules is not empty.

new case 'X' for setting default molecule name:

• new member variable World::DefaultName
• constructor of molecule uses this default name
• case 'X' in ParseCommandLineOptions() added for setting default name

Location:

src

Files:

• World.cpp (modified) (3 diffs)
• World.hpp (modified) (1 diff)
• builder.cpp (modified) (3 diffs)
• molecule.cpp (modified) (1 diff)
• molecule_graph.cpp (modified) (1 diff)
• moleculelist.cpp (modified) (2 diffs)

src/World.cpp

@@ -6 +6 @@
  */
 
+#include <string>
+
 #include "World.hpp"
 
 double *World::cell_size = 0;
+char *World::DefaultName = 0;
 
 /** Constructor of World.
@@ -16 +19 @@
 {
   cell_size = new double[6];
+  DefaultName = new char[6];
+  strncpy(DefaultName, "none", 4);
 };
 
@@ -24 +29 @@
 {
   delete[](cell_size);
+  delete[](DefaultName);
 };
 

src/World.hpp

@@ -32 +32 @@
 
   static double *cell_size;
+  static char *DefaultName;
 
 private:

src/builder.cpp

@@ -1480 +1480 @@
             Log() << Verbose(0) << "\t-v\t\tsets verbosity (more is more)." << endl;
             Log() << Verbose(0) << "\t-V\t\tGives version information." << endl;
+            Log() << Verbose(0) << "\t-X\t\tset default name of a molecule." << endl;
             Log() << Verbose(0) << "Note: config files must not begin with '-' !" << endl;
             return (1);
@@ -1518 +1519 @@
             Log() << Verbose(0) << "I won't parse trajectories." << endl;
             configuration.FastParsing = true;
+            break;
+          case 'X':
+            {
+              char **name = &(World::get()->DefaultName);
+              delete[](*name);
+              const int length = strlen(argv[argptr]);
+              *name = new char[length+2];
+              strncpy(*name, argv[argptr], length);
+              Log() << Verbose(0) << "Default name of new molecules set to " << *name << "." << endl;
+            }
             break;
           default:   // no match? Step on
@@ -1709 +1720 @@
                   }
               }
-              if (mol == NULL) {
+              if ((mol == NULL) && (!molecules->ListOfMolecules.empty())) {
                 mol = *(molecules->ListOfMolecules.begin());
-                mol->ActiveFlag = true;
+                if (mol != NULL)
+                  mol->ActiveFlag = true;
               }
               break;

src/molecule.cpp

@@ -46 +46 @@
   for(int i=MAX_ELEMENTS;i--;)
     ElementsInMolecule[i] = 0;
-  strcpy(name,"none");
+  strcpy(name,World::get()->DefaultName);
 };
 

src/molecule_graph.cpp

@@ -495 +495 @@
   bond *Binder = NULL;
 
+  if (AtomCount == 0)
+    return SubGraphs;
   Log() << Verbose(0) << "Begin of DepthFirstSearchAnalysis" << endl;
   DepthFirstSearchAnalysis_Init(DFS, this);

src/moleculelist.cpp

@@ -786 +786 @@
 
   // 1. dissect the molecule into connected subgraphs
-  configuration->BG->ConstructBondGraph(mol);
+  if (configuration->BG->ConstructBondGraph(mol)) {
+    delete (mol);
+    eLog() << Verbose(1) << "There are no bonds." << endl;
+    return;
+  }
 
   // 2. scan for connected subgraphs
@@ -793 +797 @@
   Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
   delete(BackEdgeStack);
+  if ((Subgraphs == NULL) || (Subgraphs->next == NULL)) {
+    delete (mol);
+    eLog() << Verbose(1) << "There are no atoms." << endl;
+    return;
+  }
 
   // 3. dissect (the following construct is needed to have the atoms not in the order of the DFS, but in