Changeset 47d041 for src/Dynamics

Timestamp:

Nov 3, 2011, 7:44:01 PM (13 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/Dynamics

Files:

• MinimiseConstrainedPotential.cpp (modified) (20 diffs)
• VerletForceIntegration.hpp (modified) (3 diffs)

src/Dynamics/MinimiseConstrainedPotential.cpp

@@ -73 +73 @@
   PenaltyConstants[2] = 1e+7;    // just a huge penalty
   // generate the distance list
-  DoLog(1) && (Log() << Verbose(1) << "Allocating, initializting and filling the distance list ... " << endl);
+  LOG(1, "Allocating, initializting and filling the distance list ... ");
   FillDistanceList();
 
@@ -80 +80 @@
 
   // make the PermutationMap injective by checking whether we have a non-zero constants[2] term in it
-  DoLog(1) && (Log() << Verbose(1) << "Making the PermutationMap injective ... " << endl);
+  LOG(1, "Making the PermutationMap injective ... ");
   MakeInjectivePermutation();
   DoubleList.clear();
 
   // argument minimise the constrained potential in this injective PermutationMap
-  DoLog(1) && (Log() << Verbose(1) << "Argument minimising the PermutationMap." << endl);
+  LOG(1, "Argument minimising the PermutationMap.");
   OldPotential = 1e+10;
   round = 0;
   do {
-    DoLog(2) && (Log() << Verbose(2) << "Starting round " << ++round << ", at current potential " << OldPotential << " ... " << endl);
+    LOG(2, "Starting round " << ++round << ", at current potential " << OldPotential << " ... ");
     OlderPotential = OldPotential;
     molecule::atomSet::const_iterator iter;
@@ -104 +104 @@
           break;
         }
-        //Log() << Verbose(2) << "Current Walker: " << *(*iter) << " with old/next candidate " << *Sprinter << "/" << *DistanceIterators[(*iter)]->second << "." << endl;
+        //LOG(2, "Current Walker: " << *(*iter) << " with old/next candidate " << *Sprinter << "/" << *DistanceIterators[(*iter)]->second << ".");
         // find source of the new target
         molecule::atomSet::const_iterator runner = atoms.begin();
         for (; runner != atoms.end(); ++runner) { // find the source whose toes we might be stepping on (Walker's new target should be in use by another already)
           if (PermutationMap[(*runner)] == DistanceIterators[(*iter)]->second) {
-            //Log() << Verbose(2) << "Found the corresponding owner " << *(*runner) << " to " << *PermutationMap[(*runner)] << "." << endl;
+            //LOG(2, "Found the corresponding owner " << *(*runner) << " to " << *PermutationMap[(*runner)] << ".");
             break;
           }
@@ -120 +120 @@
               break;
           if (Rider != DistanceList[(*runner)].end()) { // if we have found one
-            //Log() << Verbose(2) << "Current Other: " << *(*runner) << " with old/next candidate " << *PermutationMap[(*runner)] << "/" << *Rider->second << "." << endl;
+            //LOG(2, "Current Other: " << *(*runner) << " with old/next candidate " << *PermutationMap[(*runner)] << "/" << *Rider->second << ".");
             // exchange both
             PermutationMap[(*iter)] = DistanceIterators[(*iter)]->second; // put next farther distance into PermutationMap
@@ -127 +127 @@
             PrintPermutationMap();
             // calculate the new potential
-            //Log() << Verbose(2) << "Checking new potential ..." << endl;
+            //LOG(2, "Checking new potential ...");
             Potential = ConstrainedPotential();
             if (Potential > OldPotential) { // we made everything worse! Undo ...
-              //Log() << Verbose(3) << "Nay, made the potential worse: " << Potential << " vs. " << OldPotential << "!" << endl;
-              //Log() << Verbose(3) << "Setting " << *(*runner) << "'s source to " << *DistanceIterators[(*runner)]->second << "." << endl;
+              //LOG(3, "Nay, made the potential worse: " << Potential << " vs. " << OldPotential << "!");
+              //LOG(3, "Setting " << *(*runner) << "'s source to " << *DistanceIterators[(*runner)]->second << ".");
               // Undo for Runner (note, we haven't moved the iteration yet, we may use this)
               PermutationMap[(*runner)] = DistanceIterators[(*runner)]->second;
               // Undo for Walker
               DistanceIterators[(*iter)] = Strider;  // take next farther distance target
-              //Log() << Verbose(3) << "Setting " << *(*iter) << "'s source to " << *DistanceIterators[(*iter)]->second << "." << endl;
+              //LOG(3, "Setting " << *(*iter) << "'s source to " << *DistanceIterators[(*iter)]->second << ".");
               PermutationMap[(*iter)] = DistanceIterators[(*iter)]->second;
             } else {
               DistanceIterators[(*runner)] = Rider;  // if successful also move the pointer in the iterator list
-              DoLog(3) && (Log() << Verbose(3) << "Found a better permutation, new potential is " << Potential << " vs." << OldPotential << "." << endl);
+              LOG(3, "Found a better permutation, new potential is " << Potential << " vs." << OldPotential << ".");
               OldPotential = Potential;
             }
             if (Potential > PenaltyConstants[2]) {
-              DoeLog(1) && (eLog()<< Verbose(1) << "The two-step permutation procedure did not maintain injectivity!" << endl);
+              ELOG(1, "The two-step permutation procedure did not maintain injectivity!");
               exit(255);
             }
-            //Log() << Verbose(0) << endl;
           } else {
-            DoeLog(1) && (eLog()<< Verbose(1) << **runner << " was not the owner of " << *Sprinter << "!" << endl);
+            ELOG(1, **runner << " was not the owner of " << *Sprinter << "!");
             exit(255);
           }
@@ -159 +158 @@
     } while (++iter != atoms.end());
   } while ((OlderPotential - OldPotential) > 1e-3);
-  DoLog(1) && (Log() << Verbose(1) << "done." << endl);
+  LOG(1, "done.");
 
 
@@ -181 +180 @@
     DoubleList[DistanceList[(*iter)].begin()->second]++;            // increase this target's source count (>1? not injective)
     DistanceIterators[(*iter)] = DistanceList[(*iter)].begin();    // and remember which one we picked
-    DoLog(2) && (Log() << Verbose(2) << **iter << " starts with distance " << DistanceList[(*iter)].begin()->first << "." << endl);
+    LOG(2, **iter << " starts with distance " << DistanceList[(*iter)].begin()->first << ".");
   }
 };
@@ -192 +191 @@
 
   if (atoms.empty()) {
-    eLog() << Verbose(1) << "Molecule is empty." << endl;
+    ELOG(1, "Molecule is empty.");
     return;
   }
@@ -209 +208 @@
     // now each single entry in the DoubleList should be <=1
     if (DoubleList[*iter] > 1) {
-      DoeLog(0) && (eLog()<< Verbose(0) << "Failed to create an injective PermutationMap!" << endl);
+      ELOG(0, "Failed to create an injective PermutationMap!");
       performCriticalExit();
     }
   }
-  DoLog(1) && (Log() << Verbose(1) << "done." << endl);
+  LOG(1, "done.");
 };
 
@@ -227 +226 @@
       doubles++;
   if (doubles >0)
-    DoLog(2) && (Log() << Verbose(2) << "Found " << doubles << " Doubles." << endl);
+    LOG(2, "Found " << doubles << " Doubles.");
   return doubles;
 };
@@ -247 +246 @@
   }
   if (doubles >0)
-    DoLog(2) && (Log() << Verbose(2) << "Found " << doubles << " Doubles." << endl);
-//  Log() << Verbose(2) << zeile1.str() << endl << zeile2.str() << endl;
+    LOG(2, "Found " << doubles << " Doubles.");
+//  LOG(2, zeile1.str() << endl << zeile2.str());
 };
 
@@ -263 +262 @@
     tmp *= IsAngstroem ? 1. : 1./AtomicLengthToAngstroem;
     result += PenaltyConstants[0] * tmp;
-    //Log() << Verbose(4) << "Adding " << tmp*constants[0] << "." << endl;
+    //LOG(4, "Adding " << tmp*constants[0] << ".");
 
     // second term: sum of distances to other trajectories
@@ -292 +291 @@
       DistanceIterators[Walker] = NewBase;
       OldPotential = Potential;
-      DoLog(3) && (Log() << Verbose(3) << "Found a new permutation, new potential is " << OldPotential << "." << endl);
+      LOG(3, "Found a new permutation, new potential is " << OldPotential << ".");
     }
   }
@@ -303 +302 @@
   for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     if ((PermutationMap[Walker] == PermutationMap[(*iter)]) && (Walker < (*iter))) {
-  //    atom *Sprinter = PermutationMap[Walker->nr];
-  //        Log() << Verbose(0) << *Walker << " and " << *(*iter) << " are heading to the same target at ";
-  //        Log() << Verbose(0) << Sprinter->getPosition(endstep);
-  //        Log() << Verbose(0) << ", penalting." << endl;
+//    atom *Sprinter = PermutationMap[Walker->nr];
+//    if (DoLog(0)) {
+//        std::stringstream output;
+//        output << *Walker << " and " << *(*iter) << " are heading to the same target at ";
+//        output << Sprinter->getPosition(endstep);
+//        output << ", penalting.";
+//        LOG(0, output.str());
+//    }
       result += PenaltyConstants[2];
-      //Log() << Verbose(4) << "Adding " << constants[2] << "." << endl;
+      //LOG(4, "INFO: Adding " << constants[2] << ".");
     }
   }
@@ -350 +353 @@
       tmp = trajectory2.Norm();  // remaining norm is distance
     } else if ((fabs(trajectory1.ScalarProduct(trajectory2)/Norm1/Norm2) - 1.) < MYEPSILON) { // check whether they're linear dependent
-  //        Log() << Verbose(3) << "Both trajectories of " << *Walker << " and " << *Runner << " are linear dependent: ";
-  //        Log() << Verbose(0) << trajectory1;
-  //        Log() << Verbose(0) << " and ";
-  //        Log() << Verbose(0) << trajectory2;
+//      std::stringstream output;
+//      output << "Both trajectories of " << *Walker << " and " << *Runner << " are linear dependent: ";
+//      output << trajectory1 << " and " << trajectory2;
+//      LOG(3, output.str());
       tmp = Walker->getPositionAtStep(startstep).distance((*iter)->getPositionAtStep(startstep));
-  //        Log() << Verbose(0) << " with distance " << tmp << "." << endl;
+//        LOG(0, " with distance " << tmp << ".");
     } else { // determine distance by finding minimum distance
-  //        Log() << Verbose(3) << "Both trajectories of " << *Walker << " and " << *(*iter) << " are linear independent ";
-  //        Log() << Verbose(0) << endl;
-  //        Log() << Verbose(0) << "First Trajectory: ";
-  //        Log() << Verbose(0) << trajectory1 << endl;
-  //        Log() << Verbose(0) << "Second Trajectory: ";
-  //        Log() << Verbose(0) << trajectory2 << endl;
+//      std::stringstream output;
+//      output "Both trajectories of " << *Walker << " and " << *(*iter) << " are linear independent -- ";
+//      output "First Trajectory: " << trajectory1 << ". Second Trajectory: " << trajectory2);
+//      LOG(3, output.str());
       // determine normal vector for both
       normal = Plane(trajectory1, trajectory2,0).getNormal();
       // print all vectors for debugging
-  //        Log() << Verbose(0) << "Normal vector in between: ";
-  //        Log() << Verbose(0) << normal << endl;
+//        LOG(3, "INFO: Normal vector in between: " << normal);
       // setup matrix
       for (int i=NDIM;i--;) {
@@ -379 +379 @@
       // distance from last component
       tmp = gsl_vector_get(x,2);
-  //        Log() << Verbose(0) << " with distance " << tmp << "." << endl;
+//      LOG(0, " with distance " << tmp << ".");
       // test whether we really have the intersection (by checking on c_1 and c_2)
       trajectory1.Scale(gsl_vector_get(x,0));
@@ -387 +387 @@
                    - (Walker->getPositionAtStep(startstep) + trajectory1);
       if (TestVector.Norm() < MYEPSILON) {
-  //          Log() << Verbose(2) << "Test: ok.\tDistance of " << tmp << " is correct." << endl;
+//        LOG(2, "Test: ok.\tDistance of " << tmp << " is correct.");
       } else {
-  //          Log() << Verbose(2) << "Test: failed.\tIntersection is off by ";
-  //          Log() << Verbose(0) << TestVector;
-  //          Log() << Verbose(0) << "." << endl;
+//        LOG(2, "Test: failed.\tIntersection is off by " << TestVector << ".");
       }
     }
@@ -398 +396 @@
     if (fabs(tmp) > MYEPSILON) {
       result += PenaltyConstants[1] * 1./tmp;
-      //Log() << Verbose(4) << "Adding " << 1./tmp*constants[1] << "." << endl;
+      //LOG(4, "Adding " << 1./tmp*constants[1] << ".");
     }
   }
@@ -409 +407 @@
 
   /// evaluate forces (only the distance to target dependent part) with the final PermutationMap
-  DoLog(1) && (Log() << Verbose(1) << "Calculating forces and adding onto ForceMatrix ... " << endl);
+  LOG(1, "Calculating forces and adding onto ForceMatrix ... ");
   for(molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     atom *Sprinter = PermutationMap[(*iter)];
@@ -416 +414 @@
       Force->Matrix[0][(*iter)->getNr()][5+i] += 2.*constant*sqrt((*iter)->getPositionAtStep(startstep).distance(Sprinter->getPositionAtStep(endstep)));
   }
-  DoLog(1) && (Log() << Verbose(1) << "done." << endl);
-};
-
+  LOG(1, "done.");
+};
+

src/Dynamics/VerletForceIntegration.hpp

@@ -65 +65 @@
     std::ifstream input(file);
     if ((input.good()) && (!Force.ParseMatrix(input, 0,0,0))) {
-      DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse Force Matrix file " << file << "." << endl);
+      ELOG(0, "Could not parse Force Matrix file " << file << ".");
       performCriticalExit();
       return false;
@@ -71 +71 @@
     input.close();
     if (Force.RowCounter[0] != AtomCount) {
-      DoeLog(0) && (eLog()<< Verbose(0) << "Mismatch between number of atoms in file " << Force.RowCounter[0] << " and in molecule " << atoms.size() << "." << endl);
+      ELOG(0, "Mismatch between number of atoms in file " << Force.RowCounter[0] << " and in molecule " << atoms.size() << ".");
       performCriticalExit();
       return false;
@@ -135 +135 @@
     ActualTemp = atoms.totalTemperatureAtStep(MDSteps+1);
     LOG(3, "INFO: New temperature after thermostat is " << ActualTemp);
-    DoLog(1) && (Log() << Verbose(1) << "Kinetic energy is " << ekin << "." << endl);
+    LOG(1, "Kinetic energy is " << ekin << ".");
 
     // next step