Changeset efe516 for src/moleculelist.cpp

Timestamp:

Mar 2, 2011, 9:53:09 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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

7d8aa0

Parents:

2fa1dc

git-author:

Frederik Heber <heber@…> (03/01/11 14:16:44)

git-committer:

Frederik Heber <heber@…> (03/02/11 21:53:09)

Message:

Removed bond::nr.

• has only been used by BreadthFirstSearchAdd.
• changed BreadthFirstSearchAdd::AddedBonds into map<bond*,bond*>.

File:

• src/moleculelist.cpp (modified) (5 diffs)

src/moleculelist.cpp

@@ -512 +512 @@
       strcpy(PathBackup, path);
     else {
-      DoeLog(0) && (eLog()<< Verbose(0) << "OutputConfigForListOfFragments: NULL default path obtained from config!" << endl);
+      ELOG(0, "OutputConfigForListOfFragments: NULL default path obtained from config!");
       performCriticalExit();
     }
@@ -521 +521 @@
     }
 
-    // output xyz file
-    FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), FragmentCounter++);
-    FragmentName = prefix + FragmentNumber + ".conf.xyz";
-    outputFragment.open(FragmentName.c_str(), ios::out);
-    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ...");
-    if ((intermediateResult = (*ListRunner)->OutputXYZ(&outputFragment)))
-      DoLog(0) && (Log() << Verbose(0) << " done." << endl);
-    else
-      DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
-    result = result && intermediateResult;
-    outputFragment.close();
-    outputFragment.clear();
-
-    // list atoms in fragment for debugging
-    DoLog(2) && (Log() << Verbose(2) << "Contained atoms: ");
-    for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
-      DoLog(0) && (Log() << Verbose(0) << (*iter)->getName() << " ");
-    }
-    DoLog(0) && (Log() << Verbose(0) << endl);
+    {
+      // list atoms in fragment for debugging
+      std::stringstream output;
+      output << "Contained atoms: ";
+      for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
+        output << (*iter)->getName() << " ";
+      }
+      LOG(2, output.str());
+    }
+
+    {
+      // output xyz file
+      FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), FragmentCounter++);
+      FragmentName = prefix + FragmentNumber + ".conf.xyz";
+      outputFragment.open(FragmentName.c_str(), ios::out);
+      std::stringstream output;
+      output << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ... ";
+      if ((intermediateResult = (*ListRunner)->OutputXYZ(&outputFragment)))
+        output << " done.";
+      else
+        output << " failed.";
+      LOG(3, output.str());
+      result = result && intermediateResult;
+      outputFragment.close();
+      outputFragment.clear();
+    }
 
     // center on edge
@@ -554 +561 @@
     (*ListRunner)->Translate(&BoxDimension);
 
-    // also calculate necessary orbitals
-    //(*ListRunner)->CalculateOrbitals(*World::getInstance().getConfig);
-
     // change path in config
     FragmentName = PathBackup;
@@ -565 +569 @@
     World::getInstance().getConfig()->SetDefaultPath(FragmentName.c_str());
 
-    // and save as config
-    FragmentName = prefix + FragmentNumber + ".conf";
-    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ...");
-    if ((intermediateResult = World::getInstance().getConfig()->Save(FragmentName.c_str(), (*ListRunner)->elemente, (*ListRunner))))
-      DoLog(0) && (Log() << Verbose(0) << " done." << endl);
-    else
-      DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
-    result = result && intermediateResult;
+    {
+      // and save as config
+      FragmentName = prefix + FragmentNumber + ".conf";
+      std::stringstream output;
+      output << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ... ";
+      if ((intermediateResult = World::getInstance().getConfig()->Save(FragmentName.c_str(), (*ListRunner)->elemente, (*ListRunner))))
+        output << " done.";
+      else
+        output << " failed.";
+      LOG(3, output.str());
+      result = result && intermediateResult;
+    }
 
     // restore old config
     World::getInstance().getConfig()->SetDefaultPath(PathBackup);
 
-    // and save as mpqc input file
-    FragmentName = prefix + FragmentNumber + ".conf";
-    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ...");
-    if ((intermediateResult = World::getInstance().getConfig()->SaveMPQC(FragmentName.c_str(), (*ListRunner))))
-      DoLog(2) && (Log() << Verbose(2) << " done." << endl);
-    else
-      DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
+    {
+      // and save as mpqc input file
+      stringstream output;
+      FragmentName = prefix + FragmentNumber + ".conf";
+      output << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ... ";
+      if ((intermediateResult = World::getInstance().getConfig()->SaveMPQC(FragmentName.c_str(), (*ListRunner))))
+        output << " done.";
+      else
+        output << " failed.";
+      LOG(3, output.str());
+    }
 
     result = result && intermediateResult;
@@ -590 +602 @@
     delete[](FragmentNumber);
   }
-  DoLog(0) && (Log() << Verbose(0) << " done." << endl);
+  LOG(0, "STATUS: done.");
 
   // printing final number
-  DoLog(2) && (Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl);
+  LOG(2, "INFO: Final number of fragments: " << FragmentCounter << ".");
 
   // printing final number
-  DoLog(0) && (Log() << Verbose(0) << "For " << count << " fragments periodic correction would have been necessary." << endl);
+  LOG(2, "INFO: For " << count << " fragments periodic correction would have been necessary.");
 
   // restore cell_size