Changeset 84c494 for src/molecule.cpp

Timestamp:

Jun 30, 2010, 1:55:42 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, Candidate_v1.7.0, 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:

4907a3

Parents:

9df5c6

Message:

Made the world store the cell_size within a Box object.

File:

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

src/molecule.cpp

@@ -30 +30 @@
 #include "Matrix.hpp"
 #include "World.hpp"
+#include "Box.hpp"
 #include "Plane.hpp"
 #include "Exceptions/LinearDependenceException.hpp"
@@ -286 +287 @@
   Vector Orthovector1, Orthovector2;  // temporary vectors in coordination construction
   Vector InBondvector;    // vector in direction of *Bond
-  Matrix matrix;
+  const Matrix &matrix =  World::getInstance().getDomain().getM();
   bond *Binder = NULL;
-  double * const cell_size = World::getInstance().getDomain();
 
 //  Log() << Verbose(3) << "Begin of AddHydrogenReplacementAtom." << endl;
@@ -309 +309 @@
       } // (signs are correct, was tested!)
     }
-    matrix = ReturnFullMatrixforSymmetric(cell_size);
     Orthovector1 *= matrix;
     InBondvector -= Orthovector1; // subtract just the additional translation
@@ -754 +753 @@
 void molecule::SetBoxDimension(Vector *dim)
 {
-  double * const cell_size = World::getInstance().getDomain();
-  cell_size[0] = dim->at(0);
-  cell_size[1] = 0.;
-  cell_size[2] = dim->at(1);
-  cell_size[3] = 0.;
-  cell_size[4] = 0.;
-  cell_size[5] = dim->at(2);
+  Matrix domain;
+  for(int i =0; i<NDIM;++i)
+    domain.at(i,i) = dim->at(i);
+  World::getInstance().setDomain(domain);
 };
 
@@ -853 +849 @@
 bool molecule::CheckBounds(const Vector *x) const
 {
-  double * const cell_size = World::getInstance().getDomain();
+  const Matrix &domain = World::getInstance().getDomain().getM();
   bool result = true;
-  int j =-1;
   for (int i=0;i<NDIM;i++) {
-    j += i+1;
-    result = result && ((x->at(i) >= 0) && (x->at(i) < cell_size[j]));
+    result = result && ((x->at(i) >= 0) && (x->at(i) < domain.at(i,i)));
   }
   //return result;