Changeset 47d041 for src/molecule_geometry.cpp

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.

File:

• src/molecule_geometry.cpp (modified) (14 diffs)

src/molecule_geometry.cpp

@@ -89 +89 @@
 void molecule::CenterEdge(Vector *max)
 {
+//  Info info(__func__);
   Vector *min = new Vector;
 
-//  Log() << Verbose(3) << "Begin of CenterEdge." << endl;
   molecule::const_iterator iter = begin();  // start at first in list
   if (iter != end()) { //list not empty?
@@ -105 +105 @@
       }
     }
-//    Log() << Verbose(4) << "Maximum is ";
-//    max->Output(out);
-//    Log() << Verbose(0) << ", Minimum is ";
-//    min->Output(out);
-//    Log() << Verbose(0) << endl;
+    LOG(1, "INFO: Maximum is " << *max << ", Minimum is " << *min << ".");
     min->Scale(-1.);
     (*max) += (*min);
@@ -115 +111 @@
   }
   delete(min);
-//  Log() << Verbose(3) << "End of CenterEdge." << endl;
 };
 
@@ -192 +187 @@
     a->Scale(1./Num); // divide through total mass
   }
-//  Log() << Verbose(1) << "Resulting center of gravity: ";
-//  a->Output(out);
-//  Log() << Verbose(0) << endl;
+  LOG(1, "INFO: Resulting center of gravity: " << *a << ".");
   return a;
 };
@@ -253 +246 @@
   }
   // print InertiaTensor
-  DoLog(0) && (Log() << Verbose(0) << "The inertia tensor of molecule "
-      << getName() <<  " is:"
-      << InertiaTensor << endl);
+  LOG(1, "INFO: The inertia tensor of molecule " << getName() <<  " is:" << InertiaTensor);
 
   delete CenterOfGravity;
@@ -275 +266 @@
 
   for(int i=0;i<NDIM;i++)
-    DoLog(0) && (Log() << Verbose(0) << "eigenvalue = " << Eigenvalues[i] << ", eigenvector = " << InertiaTensor.column(i) << endl);
-
-  DoLog(0) && (Log() << Verbose(0) << "Transforming to PAS ... ");
+    LOG(0, "eigenvalue = " << Eigenvalues[i] << ", eigenvector = " << InertiaTensor.column(i));
+
+  LOG(0, "STATUS: Transforming to PAS ... ");
 
   // obtain first column, eigenvector to biggest eigenvalue
@@ -290 +281 @@
   const double alpha = BiggestEigenvector.Angle(Axis);
 
-  DoLog(0) && (Log() << Verbose(0) << "Rotation angle is " << alpha << endl);
+  LOG(1, "INFO: Rotation angle is " << alpha);
 
   // and rotate
@@ -298 +289 @@
     *(*iter) += *CenterOfGravity;
   }
-  DoLog(0) && (Log() << Verbose(0) << "done." << endl);
+  LOG(0, "STATUS: done.");
 
   delete CenterOfGravity;
@@ -393 +384 @@
               if (fabs(tmp) > MinMaxBondDistance.last) {  // check against Min is not useful for components
                 flag = false;
-                DoLog(0) && (Log() << Verbose(0) << "Hit: atom " << (*iter)->getName() << " in bond " << *(*Runner) << " has to be shifted due to " << tmp << "." << endl);
+                LOG(0, "Hit: atom " << (*iter)->getName() << " in bond " << *(*Runner) << " has to be shifted due to " << tmp << ".");
                 if (tmp > 0)
                   Translationvector[j] -= 1.;
@@ -404 +395 @@
         Testvector *= matrix;
         Center += Testvector;
-        Log() << Verbose(1) << "vector is: " << Testvector << endl;
+        LOG(1, "vector is: " << Testvector);
         if (saturation == DoSaturate) {
           // now also change all hydrogens
@@ -415 +406 @@
               Testvector *= matrix;
               Center += Testvector;
-              Log() << Verbose(1) << "Hydrogen vector is: " << Testvector << endl;
+              LOG(1, "Hydrogen vector is: " << Testvector);
             }
           }
@@ -439 +430 @@
 
   // rotate on z-x plane
-  DoLog(0) && (Log() << Verbose(0) << "Begin of Aligning all atoms." << endl);
+  LOG(0, "Begin of Aligning all atoms.");
   alpha = atan(-n->at(0)/n->at(2));
-  DoLog(1) && (Log() << Verbose(1) << "Z-X-angle: " << alpha << " ... ");
+  LOG(1, "INFO: Z-X-angle: " << alpha << " ... ");
   for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
     tmp = (*iter)->at(0);
@@ -457 +448 @@
   n->at(0) =  cos(alpha) * tmp +  sin(alpha) * n->at(2);
   n->at(2) = -sin(alpha) * tmp +  cos(alpha) * n->at(2);
-  DoLog(1) && (Log() << Verbose(1) << "alignment vector after first rotation: " << n << endl);
+  LOG(1, "alignment vector after first rotation: " << n);
 
   // rotate on z-y plane
   alpha = atan(-n->at(1)/n->at(2));
-  DoLog(1) && (Log() << Verbose(1) << "Z-Y-angle: " << alpha << " ... ");
+  LOG(1, "INFO: Z-Y-angle: " << alpha << " ... ");
   for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
     tmp = (*iter)->at(1);
@@ -479 +470 @@
 
 
-  DoLog(1) && (Log() << Verbose(1) << "alignment vector after second rotation: " << n << endl);
-  DoLog(0) && (Log() << Verbose(0) << "End of Aligning all atoms." << endl);
+  LOG(1, "alignment vector after second rotation: " << n);
+  LOG(0, "End of Aligning all atoms.");
 };