Changeset 5f612ee for src/molecule_dynamics.cpp

Timestamp:

Apr 27, 2010, 2:25:42 PM (16 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, 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:

632bc3

Parents:

13d5a9 (diff), c695c9 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'Analysis_PairCorrelation' into StructureRefactoring

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/World.cpp
molecuilder/src/World.hpp
molecuilder/src/boundary.cpp
molecuilder/src/builder.cpp
molecuilder/src/log.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/periodentafel.cpp
molecuilder/src/tesselation.cpp
molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp
molecuilder/src/unittests/Makefile.am
molecuilder/src/unittests/bondgraphunittest.cpp
molecuilder/src/unittests/gslvectorunittest.cpp
molecuilder/src/unittests/logunittest.cpp
molecuilder/src/unittests/tesselation_boundarytriangleunittest.hpp
molecuilder/src/vector.cpp
molecuilder/tests/Tesselations/defs.in

Conflicts have been many and too numerous to listen here, just the few general cases

• new molecule() replaced by World::getInstance().createMolecule()
• new atom() replaced by World::getInstance().createAtom() where appropriate.
• Some DoLog()s added interfered with changes to the message produced by Log() << Verbose(.) << ...
• DoLog() has been erroneously added to TestRunner.cpp as well, there cout is appropriate
• ...

Additionally, there was a bug in atom::clone(), sort was set to atom::nr of the atom to clone not of the clone itself. This caused a failure of the fragmentation.

This merge has been fully checked from a clean build directory with subsequent configure,make all install and make check.
It configures, compiles and runs all test cases and the test suite without errors.

Signed-off-by: Frederik Heber <heber@…>

File:

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

src/molecule_dynamics.cpp

@@ -208 +208 @@
     doubles++;
   if (doubles >0)
-    Log() << Verbose(2) << "Found " << doubles << " Doubles." << endl;
+    DoLog(2) && (Log() << Verbose(2) << "Found " << doubles << " Doubles." << endl);
   Free(&DoubleList);
 //  Log() << Verbose(2) << zeile1.str() << endl << zeile2.str() << endl;
@@ -250 +250 @@
     Params.DoubleList[Params.DistanceList[Walker->nr]->begin()->second->nr]++;            // increase this target's source count (>1? not injective)
     Params.DistanceIterators[Walker->nr] = Params.DistanceList[Walker->nr]->begin();    // and remember which one we picked
-    Log() << Verbose(2) << *Walker << " starts with distance " << Params.DistanceList[Walker->nr]->begin()->first << "." << endl;
+    DoLog(2) && (Log() << Verbose(2) << *Walker << " starts with distance " << Params.DistanceList[Walker->nr]->begin()->first << "." << endl);
   }
 };
@@ -278 +278 @@
       Params.DistanceIterators[Walker->nr] = NewBase;
       OldPotential = Potential;
-      Log() << Verbose(3) << "Found a new permutation, new potential is " << OldPotential << "." << endl;
+      DoLog(3) && (Log() << Verbose(3) << "Found a new permutation, new potential is " << OldPotential << "." << endl);
     }
   }
@@ -307 +307 @@
   for (int i=mol->AtomCount; i--;) // now each single entry in the DoubleList should be <=1
     if (Params.DoubleList[i] > 1) {
-      eLog() << Verbose(0) << "Failed to create an injective PermutationMap!" << endl;
+      DoeLog(0) && (eLog()<< Verbose(0) << "Failed to create an injective PermutationMap!" << endl);
       performCriticalExit();
     }
-  Log() << Verbose(1) << "done." << endl;
+  DoLog(1) && (Log() << Verbose(1) << "done." << endl);
 };
 
@@ -359 +359 @@
   Params.PenaltyConstants[2] = 1e+7;    // just a huge penalty
   // generate the distance list
-  Log() << Verbose(1) << "Allocating, initializting and filling the distance list ... " << endl;
+  DoLog(1) && (Log() << Verbose(1) << "Allocating, initializting and filling the distance list ... " << endl);
   FillDistanceList(this, Params);
 
@@ -366 +366 @@
 
   // make the PermutationMap injective by checking whether we have a non-zero constants[2] term in it
-  Log() << Verbose(1) << "Making the PermutationMap injective ... " << endl;
+  DoLog(1) && (Log() << Verbose(1) << "Making the PermutationMap injective ... " << endl);
   MakeInjectivePermutation(this, Params);
   Free(&Params.DoubleList);
 
   // argument minimise the constrained potential in this injective PermutationMap
-  Log() << Verbose(1) << "Argument minimising the PermutationMap." << endl;
+  DoLog(1) && (Log() << Verbose(1) << "Argument minimising the PermutationMap." << endl);
   OldPotential = 1e+10;
   round = 0;
   do {
-    Log() << Verbose(2) << "Starting round " << ++round << ", at current potential " << OldPotential << " ... " << endl;
+    DoLog(2) && (Log() << Verbose(2) << "Starting round " << ++round << ", at current potential " << OldPotential << " ... " << endl);
     OlderPotential = OldPotential;
     do {
@@ -425 +425 @@
             } else {
               Params.DistanceIterators[Runner->nr] = Rider;  // if successful also move the pointer in the iterator list
-              Log() << Verbose(3) << "Found a better permutation, new potential is " << Potential << " vs." << OldPotential << "." << endl;
+              DoLog(3) && (Log() << Verbose(3) << "Found a better permutation, new potential is " << Potential << " vs." << OldPotential << "." << endl);
               OldPotential = Potential;
             }
             if (Potential > Params.PenaltyConstants[2]) {
-              eLog() << Verbose(1) << "The two-step permutation procedure did not maintain injectivity!" << endl;
+              DoeLog(1) && (eLog()<< Verbose(1) << "The two-step permutation procedure did not maintain injectivity!" << endl);
               exit(255);
             }
             //Log() << Verbose(0) << endl;
           } else {
-            eLog() << Verbose(1) << *Runner << " was not the owner of " << *Sprinter << "!" << endl;
+            DoeLog(1) && (eLog()<< Verbose(1) << *Runner << " was not the owner of " << *Sprinter << "!" << endl);
             exit(255);
           }
@@ -444 +444 @@
     } while (Walker->next != end);
   } while ((OlderPotential - OldPotential) > 1e-3);
-  Log() << Verbose(1) << "done." << endl;
+  DoLog(1) && (Log() << Verbose(1) << "done." << endl);
 
 
@@ -467 +467 @@
 {
   /// evaluate forces (only the distance to target dependent part) with the final PermutationMap
-  Log() << Verbose(1) << "Calculating forces and adding onto ForceMatrix ... " << endl;
+  DoLog(1) && (Log() << Verbose(1) << "Calculating forces and adding onto ForceMatrix ... " << endl);
   ActOnAllAtoms( &atom::EvaluateConstrainedForce, startstep, endstep, PermutationMap, Force );
-  Log() << Verbose(1) << "done." << endl;
+  DoLog(1) && (Log() << Verbose(1) << "done." << endl);
 };
 
@@ -504 +504 @@
 
   // go through all steps and add the molecular configuration to the list and to the Trajectories of \a this molecule
-  Log() << Verbose(1) << "Filling intermediate " << MaxSteps << " steps with MDSteps of " << MDSteps << "." << endl;
+  DoLog(1) && (Log() << Verbose(1) << "Filling intermediate " << MaxSteps << " steps with MDSteps of " << MDSteps << "." << endl);
   for (int step = 0; step <= MaxSteps; step++) {
     mol = World::getInstance().createMolecule();
@@ -569 +569 @@
     // parse file into ForceMatrix
     if (!Force.ParseMatrix(file, 0,0,0)) {
-      eLog() << Verbose(0) << "Could not parse Force Matrix file " << file << "." << endl;
+      DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse Force Matrix file " << file << "." << endl);
       performCriticalExit();
       return false;
     }
     if (Force.RowCounter[0] != AtomCount) {
-      eLog() << Verbose(0) << "Mismatch between number of atoms in file " << Force.RowCounter[0] << " and in molecule " << AtomCount << "." << endl;
+      DoeLog(0) && (eLog()<< Verbose(0) << "Mismatch between number of atoms in file " << Force.RowCounter[0] << " and in molecule " << AtomCount << "." << endl);
       performCriticalExit();
       return false;
@@ -653 +653 @@
   switch(Thermostat) {
      case None:
-      Log() << Verbose(2) <<  "Applying no thermostat..." << endl;
+      DoLog(2) && (Log() << Verbose(2) <<  "Applying no thermostat..." << endl);
       break;
      case Woodcock:
       if ((configuration.ScaleTempStep > 0) && ((MDSteps-1) % configuration.ScaleTempStep == 0)) {
-        Log() << Verbose(2) <<  "Applying Woodcock thermostat..." << endl;
+        DoLog(2) && (Log() << Verbose(2) <<  "Applying Woodcock thermostat..." << endl);
         ActOnAllAtoms( &atom::Thermostat_Woodcock, sqrt(ScaleTempFactor), MDSteps, &ekin );
       }
       break;
      case Gaussian:
-      Log() << Verbose(2) <<  "Applying Gaussian thermostat..." << endl;
+      DoLog(2) && (Log() << Verbose(2) <<  "Applying Gaussian thermostat..." << endl);
       ActOnAllAtoms( &atom::Thermostat_Gaussian_init, MDSteps, &G, &E );
 
-      Log() << Verbose(1) << "Gaussian Least Constraint constant is " << G/E << "." << endl;
+      DoLog(1) && (Log() << Verbose(1) << "Gaussian Least Constraint constant is " << G/E << "." << endl);
       ActOnAllAtoms( &atom::Thermostat_Gaussian_least_constraint, MDSteps, G/E, &ekin, &configuration);
 
       break;
      case Langevin:
-      Log() << Verbose(2) <<  "Applying Langevin thermostat..." << endl;
+      DoLog(2) && (Log() << Verbose(2) <<  "Applying Langevin thermostat..." << endl);
       // init random number generator
       gsl_rng_env_setup();
@@ -680 +680 @@
 
      case Berendsen:
-      Log() << Verbose(2) <<  "Applying Berendsen-VanGunsteren thermostat..." << endl;
+      DoLog(2) && (Log() << Verbose(2) <<  "Applying Berendsen-VanGunsteren thermostat..." << endl);
       ActOnAllAtoms( &atom::Thermostat_Berendsen, MDSteps, ScaleTempFactor, &ekin, &configuration );
       break;
 
      case NoseHoover:
-      Log() << Verbose(2) <<  "Applying Nose-Hoover thermostat..." << endl;
+      DoLog(2) && (Log() << Verbose(2) <<  "Applying Nose-Hoover thermostat..." << endl);
       // dynamically evolve alpha (the additional degree of freedom)
       delta_alpha = 0.;
@@ -691 +691 @@
       delta_alpha = (delta_alpha - (3.*AtomCount+1.) * configuration.TargetTemp)/(configuration.HooverMass*Units2Electronmass);
       configuration.alpha += delta_alpha*configuration.Deltat;
-      Log() << Verbose(3) << "alpha = " << delta_alpha << " * " << configuration.Deltat << " = " << configuration.alpha << "." << endl;
+      DoLog(3) && (Log() << Verbose(3) << "alpha = " << delta_alpha << " * " << configuration.Deltat << " = " << configuration.alpha << "." << endl);
       // apply updated alpha as additional force
       ActOnAllAtoms( &atom::Thermostat_NoseHoover_scale, MDSteps, &ekin, &configuration );
       break;
   }
-  Log() << Verbose(1) << "Kinetic energy is " << ekin << "." << endl;
-};
+  DoLog(1) && (Log() << Verbose(1) << "Kinetic energy is " << ekin << "." << endl);
+};