Changeset e6317b for src/Actions/MoleculeAction

Timestamp:

Jun 16, 2010, 12:24:21 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

492279

Parents:

f8e486 (diff), 980dd6 (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:

Broken: Merge commit 'Gitosis/stable' into stable

Conflicts:

molecuilder/src/Actions/AnalysisAction/PairCorrelationToPointAction.cpp
molecuilder/src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp
molecuilder/src/Makefile.am

Location:

src/Actions/MoleculeAction

Files:

• FillWithMoleculeAction.cpp (modified) (1 diff)
• LinearInterpolationofTrajectoriesAction.cpp (modified) (1 diff)
• TranslateAction.cpp (modified) (1 diff)

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -68 +68 @@
 
   if(dialog->display()) {
+    DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, lengths(" << lengths[0] << "," << lengths[1] << "," << lengths[2] << "), distances (" << distances[0] << "," << distances[1] << "," << distances[2] << "), MaxDistance " << MaxDistance << ", DoRotate " << DoRotate << "." << endl);
     // construct water molecule
     molecule *filler = World::getInstance().createMolecule();
-//    if (!filler->AddXYZFile(filename)) {
-//      DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse filler molecule from " << filename << "." << endl);
-//    }
-//    filler->SetNameFromFilename(filename);
+    if (!filler->AddXYZFile(filename)) {
+      DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse filler molecule from " << filename << "." << endl);
+    }
+    filler->SetNameFromFilename(filename.c_str());
     molecule *Filling = NULL;
-    atom *first = NULL, *second = NULL, *third = NULL;
-    first = World::getInstance().createAtom();
-    first->type = World::getInstance().getPeriode()->FindElement(1);
-    first->x = Vector(0.441, -0.143, 0.);
-    filler->AddAtom(first);
-    second = World::getInstance().createAtom();
-    second->type = World::getInstance().getPeriode()->FindElement(1);
-    second->x = Vector(-0.464, 1.137, 0.0);
-    filler->AddAtom(second);
-    third = World::getInstance().createAtom();
-    third->type = World::getInstance().getPeriode()->FindElement(8);
-    third->x = Vector(-0.464, 0.177, 0.);
-    filler->AddAtom(third);
-    filler->AddBond(first, third, 1);
-    filler->AddBond(second, third, 1);
+//    atom *first = NULL, *second = NULL, *third = NULL;
+//    first = World::getInstance().createAtom();
+//    first->type = World::getInstance().getPeriode()->FindElement(1);
+//    first->x = Vector(0.441, -0.143, 0.);
+//    filler->AddAtom(first);
+//    second = World::getInstance().createAtom();
+//    second->type = World::getInstance().getPeriode()->FindElement(1);
+//    second->x = Vector(-0.464, 1.137, 0.0);
+//    filler->AddAtom(second);
+//    third = World::getInstance().createAtom();
+//    third->type = World::getInstance().getPeriode()->FindElement(8);
+//    third->x = Vector(-0.464, 0.177, 0.);
+//    filler->AddAtom(third);
+//    filler->AddBond(first, third, 1);
+//    filler->AddBond(second, third, 1);
     World::getInstance().getConfig()->BG->ConstructBondGraph(filler);
-    filler->SetNameFromFilename("water");
+//    filler->SetNameFromFilename("water");
     // call routine
     double distance[NDIM];

src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp

@@ -60 +60 @@
 
   dialog->queryString(NAME, &filename, MapOfActions::getInstance().getDescription(NAME));
-  dialog->queryInt("start-mol", &start, MapOfActions::getInstance().getDescription("start"));
-  dialog->queryInt("end-mol", &start, MapOfActions::getInstance().getDescription("end"));
+  dialog->queryInt("start-step", &start, MapOfActions::getInstance().getDescription("start-step"));
+  dialog->queryInt("end-step", &end, MapOfActions::getInstance().getDescription("end-step"));
   dialog->queryMolecule("molecule-by-id", &mol, MapOfActions::getInstance().getDescription("molecule-by-id"));
   dialog->queryBoolean("id-mapping", &IdMapping, MapOfActions::getInstance().getDescription("id-mapping"));

src/Actions/MoleculeAction/TranslateAction.cpp

@@ -58 +58 @@
   dialog->queryMolecule("molecule-by-id", &mol, MapOfActions::getInstance().getDescription("molecule-by-id"));
   dialog->queryBoolean("periodic", &periodic, MapOfActions::getInstance().getDescription("periodic"));
+  cout << "pre-dialog" << endl;
 
   if(dialog->display()) {
+    cout << "post-dialog" << endl;
     DoLog(1) && (Log() << Verbose(1) << "Translating all ions by given vector." << endl);
     if (periodic)