Changeset 5f612ee for src/Legacy/oldmenu.cpp

Timestamp:

Apr 27, 2010, 2:25:42 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, 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/Legacy/oldmenu.cpp (modified) (8 diffs)

src/Legacy/oldmenu.cpp

@@ -79 +79 @@
         Log() << Verbose(0) << "Enter absolute coordinates." << endl;
         first = World::getInstance().createAtom();
-        first->x.AskPosition(mol->cell_size, false);
+        first->x.AskPosition(World::getInstance().getDomain(), false);
         first->type = periode->AskElement();  // give type
         mol->AddAtom(first);  // add to molecule
@@ -90 +90 @@
           if (!valid) eLog() << Verbose(2) << "Resulting position out of cell." << endl;
           Log() << Verbose(0) << "Enter reference coordinates." << endl;
-          x.AskPosition(mol->cell_size, true);
+          x.AskPosition(World::getInstance().getDomain(), true);
           Log() << Verbose(0) << "Enter relative coordinates." << endl;
-          first->x.AskPosition(mol->cell_size, false);
+          first->x.AskPosition(World::getInstance().getDomain(), false);
           first->x.AddVector((const Vector *)&x);
           Log() << Verbose(0) << "\n";
@@ -107 +107 @@
           second = mol->AskAtom("Enter atom number: ");
           Log() << Verbose(0) << "Enter relative coordinates." << endl;
-          first->x.AskPosition(mol->cell_size, false);
+          first->x.AskPosition(World::getInstance().getDomain(), false);
           for (int i=NDIM;i--;) {
             first->x.x[i] += second->x.x[i];
@@ -334 +334 @@
     case 'b': // normal vector of mirror plane
       Log() << Verbose(0) << "Enter normal vector of mirror plane." << endl;
-      n.AskPosition(mol->cell_size,0);
+      n.AskPosition(World::getInstance().getDomain(),0);
       n.Normalize();
       break;
@@ -401 +401 @@
     case 'b': // normal vector of mirror plane
       Log() << Verbose(0) << "Enter normal vector of mirror plane." << endl;
-      n.AskPosition(mol->cell_size,0);
+      n.AskPosition(World::getInstance().getDomain(),0);
       n.Normalize();
       break;
@@ -778 +778 @@
       x.Zero();
       y.Zero();
-      y.x[abs(axis)-1] = mol->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] * abs(axis)/axis; // last term is for sign, first is for magnitude
+      y.x[abs(axis)-1] = World::getInstance().getDomain()[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] * abs(axis)/axis; // last term is for sign, first is for magnitude
       for (int i=1;i<faktor;i++) {  // then add this list with respective translation factor times
         x.AddVector(&y); // per factor one cell width further
@@ -801 +801 @@
         mol->Translate(&x);
       }
-      mol->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= faktor;
+      World::getInstance().getDomain()[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= faktor;
     }
   }
@@ -894 +894 @@
         Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
         Log() << Verbose(0) << "Enter translation vector." << endl;
-        x.AskPosition(mol->cell_size,0);
+        x.AskPosition(World::getInstance().getDomain(),0);
         mol->Center.AddVector((const Vector *)&x);
      }