Changeset d6f886 for src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

Timestamp:

Feb 3, 2011, 9:51:18 AM (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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

9df680

Parents:

66fd49

git-author:

Frederik Heber <heber@…> (01/10/11 10:55:48)

git-committer:

Frederik Heber <heber@…> (02/03/11 09:51:18)

Message:

changed stupid --lengths parameter of fill...-with-molecule into three distinct ones.

• in this Vector length three distinct things had been mixed, with --distance it made sense, with lengths this's been just nonsense.
• new parameters are --distance-to-molecule --random-atom-displacement and --random-molecule-displacement and all default to zero.
• moved files into regression/Filling and three files, one for each test case according to new scheme.

TESTFIXES:

• Filling/1-3: lengths mostly replaced by --distance-to-molecule

File:

• src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) (2 diffs)

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -45 +45 @@
   getParametersfromValueStorage();
 
-  DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, lengths(" << params.lengths[0] << "," << params.lengths[1] << "," << params.lengths[2] << "), distances (" << params.distances[0] << "," << params.distances[1] << "," << params.distances[2] << "), MaxDistance " << params.MaxDistance << ", DoRotate " << params.DoRotate << "." << endl);
+  DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, "
+      << " minimum distance to molecules" << params.boundary
+      << ", random atom displacement " << params.RandAtomDisplacement
+      << ", random molecule displacement " << params.RandMoleculeDisplacement
+      << ", distances between fillers (" << params.distances[0] << "," << params.distances[1] << "," << params.distances[2]
+      << "), MinDistance " << params.MaxDistance
+      << ", DoRotate " << params.DoRotate << "." << endl);
   // construct water molecule
   molecule *filler = World::getInstance().createMolecule();
@@ -74 +80 @@
   for (int i=0;i<NDIM;i++)
     distance[i] = params.distances[i];
-  Filling = FillBoxWithMolecule(World::getInstance().getMolecules(), filler, *(World::getInstance().getConfig()), params.MaxDistance, distance, params.lengths[0], params.lengths[1], params.lengths[2], params.DoRotate);
+  Filling = FillBoxWithMolecule(
+      World::getInstance().getMolecules(),
+      filler, *(World::getInstance().getConfig()),
+      params.MaxDistance,
+      distance,
+      params.boundary,
+      params.RandAtomDisplacement,
+      params.RandMoleculeDisplacement,
+      params.DoRotate);
   if (Filling != NULL) {
     Filling->ActiveFlag = false;