Changeset 5f612ee for src/joiner.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/joiner.cpp (modified) (6 diffs)

src/joiner.cpp

@@ -47 +47 @@
   bool NoHessian = false;
 
-  Log() << Verbose(0) << "Joiner" << endl;
-  Log() << Verbose(0) << "======" << endl;
+  DoLog(0) && (Log() << Verbose(0) << "Joiner" << endl);
+  DoLog(0) && (Log() << Verbose(0) << "======" << endl);
 
   // Get the command line options
   if (argc < 3) {
-    Log() << Verbose(0) << "Usage: " << argv[0] << " <inputdir> <prefix> [elementsdb]" << endl;
-    Log() << Verbose(0) << "<inputdir>\ttherein the output of a molecuilder fragmentation is expected, each fragment with a subdir containing an energy.all and a forces.all file." << endl;
-    Log() << Verbose(0) << "<prefix>\tprefix of energy and forces file." << endl;
-    Log() << Verbose(0) << "[elementsdb]\tpath to elements database, needed for shieldings." << endl;
+    DoLog(0) && (Log() << Verbose(0) << "Usage: " << argv[0] << " <inputdir> <prefix> [elementsdb]" << endl);
+    DoLog(0) && (Log() << Verbose(0) << "<inputdir>\ttherein the output of a molecuilder fragmentation is expected, each fragment with a subdir containing an energy.all and a forces.all file." << endl);
+    DoLog(0) && (Log() << Verbose(0) << "<prefix>\tprefix of energy and forces file." << endl);
+    DoLog(0) && (Log() << Verbose(0) << "[elementsdb]\tpath to elements database, needed for shieldings." << endl);
     return 1;
   } else {
@@ -77 +77 @@
   if (!Hcorrection.ParseFragmentMatrix(argv[1], "", HCORRECTIONSUFFIX, 0,0)) {
     NoHCorrection = true;
-    Log() << Verbose(0) << "No HCorrection matrices found, skipping these." << endl;
+    DoLog(0) && (Log() << Verbose(0) << "No HCorrection matrices found, skipping these." << endl);
   }
   if (!Force.ParseFragmentMatrix(argv[1], dir, ForcesSuffix, 0,0)) return 1;
   if (!Hessian.ParseFragmentMatrix(argv[1], dir, HessianSuffix, 0,0)) {
     NoHessian = true;
-    Log() << Verbose(0) << "No hessian matrices found, skipping these." << endl;
+    DoLog(0) && (Log() << Verbose(0) << "No hessian matrices found, skipping these." << endl);
   }
   if (periode != NULL) { // also look for PAS values
@@ -146 +146 @@
   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
     // --------- sum up energy --------------------
-    Log() << Verbose(0) << "Summing energy of order " << BondOrder+1 << " ..." << endl;
+    DoLog(0) && (Log() << Verbose(0) << "Summing energy of order " << BondOrder+1 << " ..." << endl);
     if (!EnergyFragments.SumSubManyBodyTerms(Energy, KeySet, BondOrder)) return 1;
     if (!NoHCorrection) { 
@@ -155 +155 @@
       if (!Energy.SumSubEnergy(EnergyFragments, NULL, KeySet, BondOrder, 1.)) return 1;
     // --------- sum up Forces --------------------
-    Log() << Verbose(0) << "Summing forces of order " << BondOrder+1 << " ..." << endl;
+    DoLog(0) && (Log() << Verbose(0) << "Summing forces of order " << BondOrder+1 << " ..." << endl);
     if (!ForceFragments.SumSubManyBodyTerms(Force, KeySet, BondOrder)) return 1;
     if (!Force.SumSubForces(ForceFragments, KeySet, BondOrder, 1.)) return 1;
     // --------- sum up Hessian --------------------
     if (!NoHessian) {
-      Log() << Verbose(0) << "Summing Hessian of order " << BondOrder+1 << " ..." << endl;
+      DoLog(0) && (Log() << Verbose(0) << "Summing Hessian of order " << BondOrder+1 << " ..." << endl);
       if (!HessianFragments.SumSubManyBodyTerms(Hessian, KeySet, BondOrder)) return 1;
       if (!Hessian.SumSubHessians(HessianFragments, KeySet, BondOrder, 1.)) return 1;
     }
     if (periode != NULL) { // also look for PAS values
-      Log() << Verbose(0) << "Summing shieldings and susceptibilities of order " << BondOrder+1 << " ..." << endl;
+      DoLog(0) && (Log() << Verbose(0) << "Summing shieldings and susceptibilities of order " << BondOrder+1 << " ..." << endl);
       if (!ShieldingFragments.SumSubManyBodyTerms(Shielding, KeySet, BondOrder)) return 1;
       if (!Shielding.SumSubForces(ShieldingFragments, KeySet, BondOrder, 1.)) return 1;
@@ -179 +179 @@
     prefix.str(" ");
     prefix << dir << OrderSuffix << (BondOrder+1);
-    Log() << Verbose(0) << "Writing files " << argv[1] << prefix.str() << ". ..." << endl;
+    DoLog(0) && (Log() << Verbose(0) << "Writing files " << argv[1] << prefix.str() << ". ..." << endl);
     // energy
     if (!Energy.WriteLastMatrix(argv[1], (prefix.str()).c_str(), EnergySuffix)) return 1;
@@ -244 +244 @@
   delete(periode);
   Free(&dir);
-  Log() << Verbose(0) << "done." << endl;
+  DoLog(0) && (Log() << Verbose(0) << "done." << endl);
   return 0;
 };