Changeset 66dc36

Timestamp:

Sep 26, 2012, 5:24:47 PM (13 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:

c3ecde

Parents:

52cac0

git-author:

Frederik Heber <heber@…> (08/10/12 13:28:06)

git-committer:

Frederik Heber <heber@…> (09/26/12 17:24:47)

Message:

FIX: Written fragments are not centered on edge and stored.

• this would prevent the sampled electron densities from matching up.

File:

• src/moleculelist.cpp (modified) (1 diff)

src/moleculelist.cpp

@@ -556 +556 @@
 
     {
-      // center on edge
-      (*ListRunner)->CenterEdge(&BoxDimension);
-      for (int k = 0; k < NDIM; k++)  // if one edge is to small, set at least to 1 angstroem
-        if (BoxDimension[k] < 1.)
-          BoxDimension[k] += 1.;
-      (*ListRunner)->SetBoxDimension(&BoxDimension); // update Box of atoms by boundary
-      for (int k = 0; k < NDIM; k++) {
-        BoxDimension[k] = 2.5 * (World::getInstance().getConfig()->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
-        cell_size.at(k,k) = BoxDimension[k] * 2.;
-      }
-      World::getInstance().setDomain(cell_size);
-      (*ListRunner)->Translate(&BoxDimension);
+//      // center on edge
+//      (*ListRunner)->CenterEdge(&BoxDimension);
+//      for (int k = 0; k < NDIM; k++)  // if one edge is to small, set at least to 1 angstroem
+//        if (BoxDimension[k] < 1.)
+//          BoxDimension[k] += 1.;
+//      (*ListRunner)->SetBoxDimension(&BoxDimension); // update Box of atoms by boundary
+//      for (int k = 0; k < NDIM; k++) {
+//        BoxDimension[k] = 2.5 * (World::getInstance().getConfig()->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
+//        cell_size.at(k,k) = BoxDimension[k] * 2.;
+//      }
+//      World::getInstance().setDomain(cell_size);
+//      (*ListRunner)->Translate(&BoxDimension);
 
       // output file