Changeset be97a8 for src/Actions/WorldAction/CenterOnEdgeAction.cpp

Timestamp:

Jul 20, 2010, 1:01:11 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:

3d078d, 4b6777, c644a5

Parents:

ba9f5b (diff), 818eda (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 'StructureRefactoring' into stable

Conflicts:

test_all.sh

• test_all.sh was modified by Till in StructureRefactoring (these changes taken over).
• World::setDomain() was missing OBSERVE macro.
• MapOfActions: "molecule-by-name" needs String not Molecule.
• TESTFIX: Tesselations/defs.in - paths changed such that @srcdir@ may be absolute.
• TESTFIX: Tesselations/heptan/1.5/NonConvexEnvelope.dat - exchanged due to same surface but different polygon triangulation.
• TESTFIX: Domain/4 molecule-by-id changed from 208 to 207 due to different handling of molecule ids.

File:

• src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) (3 diffs)

src/Actions/WorldAction/CenterOnEdgeAction.cpp

@@ -13 +13 @@
 #include "vector.hpp"
 #include "World.hpp"
+#include "Matrix.hpp"
 
 #include <iostream>
@@ -37 +38 @@
   Vector Min;
   Vector Max;
-  int j=0;
 
   dialog->queryEmpty(NAME, MapOfActions::getInstance().getDescription(NAME));
@@ -57 +57 @@
     }
     // set new box size
-    double * const cell_size = World::getInstance().getDomain();
-    for (j=0;j<6;j++)
-      cell_size[j] = 0.;
-    j=-1;
+    Matrix domain;
     for (int i=0;i<NDIM;i++) {
-      j += i+1;
-      cell_size[j] = (Max[i]-Min[i]);
+      double tmp = Max[i]-Min[i];
+      tmp = fabs(tmp)>=1. ? tmp : 1.0;
+      domain.at(i,i) = tmp;
     }
-    World::getInstance().setDomain(cell_size);
+    World::getInstance().setDomain(domain);
     // translate all atoms, such that Min is aty (0,0,0)
     for (vector<atom*>::iterator AtomRunner = AllAtoms.begin(); AtomRunner != AllAtoms.end(); ++AtomRunner)