Changeset b34306 for src/molecule.cpp

Timestamp:

Mar 3, 2010, 10:13:19 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, 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:

70378e, a837d0, fd179f

Parents:

c5805a

Message:

singleton class World introduced, contains only cell_size from class molecule.

• class World is actually code from Till Crueger from his branch StructureRefactoring.
• has been introduced here in minimalistic form to allow molecule::cell_size to be outsourced to World::cell_size
• access to cell_size can be obtained from anyhwere by invoking World::get()->cell_size
• INFO: cell_size was placed in class molecule for the fragmentation procedure where the cell_size had to be individually adapted to each fragment.

• all appearances have been changed accordingly. Where appropriate we have employed a const pointer onto cell_size.

Signed-off-by: Frederik Heber <heber@…>

File:

• src/molecule.cpp (modified) (5 diffs)

src/molecule.cpp

@@ -23 +23 @@
 #include "tesselation.hpp"
 #include "vector.hpp"
+#include "World.hpp"
 
 /************************************* Functions for class molecule *********************************/
@@ -45 +46 @@
   for(int i=MAX_ELEMENTS;i--;)
     ElementsInMolecule[i] = 0;
-  cell_size[0] = cell_size[2] = cell_size[5]= 20.;
-  cell_size[1] = cell_size[3] = cell_size[4]= 0.;
   strcpy(name,"none");
 };
@@ -159 +158 @@
   double *matrix = NULL;
   bond *Binder = NULL;
+  double * const cell_size = World::get()->cell_size;
 
 //  Log() << Verbose(3) << "Begin of AddHydrogenReplacementAtom." << endl;
@@ -603 +603 @@
 void molecule::SetBoxDimension(Vector *dim)
 {
+  double * const cell_size = World::get()->cell_size;
   cell_size[0] = dim->x[0];
   cell_size[1] = 0.;
@@ -693 +694 @@
 bool molecule::CheckBounds(const Vector *x) const
 {
+  double * const cell_size = World::get()->cell_size;
   bool result = true;
   int j =-1;