Changeset 47d041 for src/Graph

Timestamp:

Nov 3, 2011, 7:44:01 PM (14 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:

41a467

Parents:

50e4e5

git-author:

Frederik Heber <heber@…> (10/27/11 11:53:58)

git-committer:

Frederik Heber <heber@…> (11/03/11 19:44:01)

Message:

HUGE: Removed all calls to Log(), eLog(), replaced by LOG() and ELOG().

• Replaced DoLog(.) && (Log() << Verbose(.) << ... << std::endl) by Log(., ...).
• Replaced Log() << Verbose(.) << .. << by Log(., ...)
• on multiline used stringstream to generate and message which was finally used in LOG(., output.str())
• there should be no more occurence of Log(). LOG() and ELOG() must be used instead.
• Eventually, this will allow for storing all errors and re-printing them on program exit which would be very helpful to ascertain error-free runs for the user.

Location:

src/Graph

Files:

• BondGraph.cpp (modified) (1 diff)
• BondGraph.hpp (modified) (2 diffs)
• BreadthFirstSearchAdd.cpp (modified) (6 diffs)
• BuildInducedSubgraph.cpp (modified) (1 diff)
• CyclicStructureAnalysis.cpp (modified) (1 diff)
• DepthFirstSearchAnalysis.cpp (modified) (1 diff)

src/Graph/BondGraph.cpp

@@ -81 +81 @@
     LOG(1, "Parsing bond length matrix successful.");
   } else {
-    DoeLog(1) && (eLog()<< Verbose(1) << "Parsing bond length matrix failed." << endl);
+    ELOG(1, "Parsing bond length matrix failed.");
     status = false;
   }

src/Graph/BondGraph.hpp

@@ -395 +395 @@
       AtomSetMixin<container_type,iterator_type,const_iterator_type> &Set) const
   {
-    //DoLog(1) && (Log() << Verbose(1) << "Correcting Bond degree of each bond ... " << endl);
+    //LOG(1, "Correcting Bond degree of each bond ... ");
     int No = 0, OldNo = -1;
     do {
@@ -404 +404 @@
       }
     } while (OldNo != No);
-    //DoLog(0) && (Log() << Verbose(0) << " done." << endl);
+    //LOG(0, " done.");
     return No;
   }

src/Graph/BreadthFirstSearchAdd.cpp

@@ -21 +21 @@
 
 #include "BreadthFirstSearchAdd.hpp"
+
+#include <sstream>
 
 #include "atom.hpp"
@@ -70 +72 @@
   PredecessorList[OtherAtom->getNr()] = Walker; // Walker is the predecessor
   ShortestPathList[OtherAtom->getNr()] = ShortestPathList[Walker->getNr()] + 1;
-  DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->getName() << " " << GraphEdge::getColorName(ColorList[OtherAtom->getNr()]) << ", its predecessor is " << Walker->getName() << " and its Shortest Path is " << ShortestPathList[OtherAtom->getNr()] << " egde(s) long." << endl);
+  LOG(2, "Coloring OtherAtom " << OtherAtom->getName() << " " << GraphEdge::getColorName(ColorList[OtherAtom->getNr()]) << ", its predecessor is " << Walker->getName() << " and its Shortest Path is " << ShortestPathList[OtherAtom->getNr()] << " egde(s) long.");
   if ((((ShortestPathList[OtherAtom->getNr()] < BondOrder) && (Binder != Bond)))) { // Check for maximum distance
-    DoLog(3) && (Log() << Verbose(3));
+    std::stringstream output;
     if (AddedAtomList[OtherAtom->getNr()] == NULL) { // add if it's not been so far
       AddedAtomList[OtherAtom->getNr()] = Mol->AddCopyAtom(OtherAtom);
-      DoLog(0) && (Log() << Verbose(0) << "Added OtherAtom " << OtherAtom->getName());
+      output << "Added OtherAtom " << OtherAtom->getName();
       AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
-      DoLog(0) && (Log() << Verbose(0) << " and bond " << *(AddedBondList[Binder]) << ", ");
+      output << " and bond " << *(AddedBondList[Binder]) << ", ";
     } else { // this code should actually never come into play (all GraphEdge::white atoms are not yet present in BondMolecule, that's why they are GraphEdge::white in the first place)
-      DoLog(0) && (Log() << Verbose(0) << "Not adding OtherAtom " << OtherAtom->getName());
+      output << "Not adding OtherAtom " << OtherAtom->getName();
       if (AddedBondList[Binder] == NULL) {
         AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
-        DoLog(0) && (Log() << Verbose(0) << ", added Bond " << *(AddedBondList[Binder]));
+        output << ", added Bond " << *(AddedBondList[Binder]);
       } else
-        DoLog(0) && (Log() << Verbose(0) << ", not added Bond ");
+        output << ", not added Bond ";
     }
-    DoLog(0) && (Log() << Verbose(0) << ", putting OtherAtom into queue." << endl);
+    output << ", putting OtherAtom into queue.";
+    LOG(0, output.str());
     BFSStack.push_front(OtherAtom);
   } else { // out of bond order, then replace
     if ((AddedAtomList[OtherAtom->getNr()] == NULL) && (Binder->Cyclic))
       ColorList[OtherAtom->getNr()] = GraphEdge::white; // unmark if it has not been queued/added, to make it available via its other bonds (cyclic)
-    if (Binder == Bond)
-      DoLog(3) && (Log() << Verbose(3) << "Not Queueing, is the Root bond");
-    else if (ShortestPathList[OtherAtom->getNr()] >= BondOrder)
-      DoLog(3) && (Log() << Verbose(3) << "Not Queueing, is out of Bond Count of " << BondOrder);
-    if (!Binder->Cyclic)
-      DoLog(0) && (Log() << Verbose(0) << ", is not part of a cyclic bond, saturating bond with Hydrogen." << endl);
+    {
+      std::stringstream output;
+      if (Binder == Bond)
+        output << "Not Queueing, is the Root bond";
+      else if (ShortestPathList[OtherAtom->getNr()] >= BondOrder)
+        output << "Not Queueing, is out of Bond Count of " << BondOrder;
+      if (!Binder->Cyclic)
+        output << ", is not part of a cyclic bond, saturating bond with Hydrogen.";
+      LOG(3, output.str());
+    }
     if (AddedBondList[Binder] == NULL) {
       if ((AddedAtomList[OtherAtom->getNr()] != NULL)) { // .. whether we add or saturate
@@ -112 +119 @@
 void BreadthFirstSearchAdd::VisitedNode(molecule *Mol, atom *&Walker, atom *&OtherAtom, bond *&Binder, bond *&Bond)
 {
-  DoLog(3) && (Log() << Verbose(3) << "Not Adding, has already been visited." << endl);
+  LOG(3, "Not Adding, has already been visited.");
   // This has to be a cyclic bond, check whether it's present ...
   if (AddedBondList[Binder] == NULL) {
@@ -147 +154 @@
     BFSStack.pop_front();
     const BondList& ListOfBonds = Walker->getListOfBonds();
-    DoLog(1) && (Log() << Verbose(1) << "Current Walker is: " << Walker->getName() << ", and has " << ListOfBonds.size() << " bonds." << endl);
+    LOG(1, "Current Walker is: " << Walker->getName() << ", and has " << ListOfBonds.size() << " bonds.");
     for (BondList::const_iterator Runner = ListOfBonds.begin();
         Runner != ListOfBonds.end();
@@ -154 +161 @@
         Binder = (*Runner);
         OtherAtom = (*Runner)->GetOtherAtom(Walker);
-        DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);
+        LOG(2, "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << ".");
         if (ColorList[OtherAtom->getNr()] == GraphEdge::white) {
           UnvisitedNode(Mol, Walker, OtherAtom, Binder, Bond);
@@ -163 +170 @@
     }
     ColorList[Walker->getNr()] = GraphEdge::black;
-    DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->getName() << " GraphEdge::black." << endl);
+    LOG(1, "Coloring Walker " << Walker->getName() << " GraphEdge::black.");
   }
 }

src/Graph/BuildInducedSubgraph.cpp

@@ -45 +45 @@
 {
   // fill parent list with sons
-  DoLog(3) && (Log() << Verbose(3) << "Filling Parent List." << endl);
+  LOG(3, "Filling Parent List.");
   for (molecule::const_iterator iter = Son->begin(); iter != Son->end(); ++iter) {
     ParentList[(*iter)->father] = (*iter);

src/Graph/CyclicStructureAnalysis.cpp

@@ -321 +321 @@
   int MinRingSize = -1;
 
-  //Log() << Verbose(1) << "Back edge list - ";
-  //BackEdgeStack->Output(out);
+  //std::stringstream output;
+  //output << "Back edge list - ";
+  //BackEdgeStack->Output(output);
+  //LOG(0, output.str());
 
   LOG(1, "STATUS: Analysing cycles ... " << endl);

src/Graph/DepthFirstSearchAnalysis.cpp

@@ -163 +163 @@
         const bond *Binder = *BondRunner;
         if (DoLog(2)) {
-          ostream &out = (Log() << Verbose(2));
-          out << ((Binder->Type == GraphEdge::TreeEdge) ? "TreeEdge " : "BackEdge ") << *Binder << ": <";
-          out << ((Binder->leftatom->SeparationVertex) ? "SP," : "") << "L" << Binder->leftatom->LowpointNr << " G" << Binder->leftatom->GraphNr << " Comp.";
-          Binder->leftatom->OutputComponentNumber(&out);
-          out << " ===  ";
-          out << ((Binder->rightatom->SeparationVertex) ? "SP," : "") << "L" << Binder->rightatom->LowpointNr << " G" << Binder->rightatom->GraphNr << " Comp.";
-          Binder->rightatom->OutputComponentNumber(&out);
-          out << ">." << endl;
+          std::stringstream output;
+          output << ((Binder->Type == GraphEdge::TreeEdge) ? "TreeEdge " : "BackEdge ") << *Binder << ": <";
+          output << ((Binder->leftatom->SeparationVertex) ? "SP," : "") << "L" << Binder->leftatom->LowpointNr << " G" << Binder->leftatom->GraphNr << " Comp.";
+          Binder->leftatom->OutputComponentNumber(&output);
+          output << " ===  ";
+          output << ((Binder->rightatom->SeparationVertex) ? "SP," : "") << "L" << Binder->rightatom->LowpointNr << " G" << Binder->rightatom->GraphNr << " Comp.";
+          Binder->rightatom->OutputComponentNumber(&output);
+          output << ">.";
+          LOG(2, output.str());
         }
         if (Binder->Cyclic) // cyclic ??