Changeset 6e06bd for src/Box.cpp

Timestamp:

Dec 5, 2010, 12:19:19 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, 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:

f03705

Parents:

589112 (diff), bbf1bd (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 'MatrixVectorContentRefactoring' into stable

File:

• src/Box.cpp (modified) (7 diffs)

src/Box.cpp

@@ -26 +26 @@
 #include <cstdlib>
 
-#include "LinearAlgebra/Matrix.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "LinearAlgebra/Plane.hpp"
@@ -38 +38 @@
 Box::Box()
 {
-  M= new Matrix();
-  M->one();
-  Minv = new Matrix();
-  Minv->one();
+  M= new RealSpaceMatrix();
+  M->setIdentity();
+  Minv = new RealSpaceMatrix();
+  Minv->setIdentity();
   conditions.resize(3);
   conditions[0] = conditions[1] = conditions[2] = Wrap;
@@ -47 +47 @@
 
 Box::Box(const Box& src){
-  M=new Matrix(*src.M);
-  Minv = new Matrix(*src.Minv);
+  M=new RealSpaceMatrix(*src.M);
+  Minv = new RealSpaceMatrix(*src.Minv);
   conditions = src.conditions;
 }
@@ -58 +58 @@
 }
 
-const Matrix &Box::getM() const{
+const RealSpaceMatrix &Box::getM() const{
   return *M;
 }
-const Matrix &Box::getMinv() const{
+const RealSpaceMatrix &Box::getMinv() const{
   return *Minv;
 }
 
-void Box::setM(Matrix _M){
+void Box::setM(RealSpaceMatrix _M){
   ASSERT(_M.determinant()!=0,"Matrix in Box construction was not invertible");
   *M    =_M;
@@ -253 +253 @@
 void Box::setCuboid(const Vector &endpoint){
   ASSERT(endpoint[0]>0 && endpoint[1]>0 && endpoint[2]>0,"Vector does not define a full cuboid");
-  M->one();
+  M->setIdentity();
   M->diagonal()=endpoint;
   Vector &dinv = Minv->diagonal();
@@ -264 +264 @@
     delete M;
     delete Minv;
-    M    = new Matrix(*src.M);
-    Minv = new Matrix(*src.Minv);
+    M    = new RealSpaceMatrix(*src.M);
+    Minv = new RealSpaceMatrix(*src.Minv);
     conditions = src.conditions;
   }
@@ -271 +271 @@
 }
 
-Box &Box::operator=(const Matrix &mat){
+Box &Box::operator=(const RealSpaceMatrix &mat){
   setM(mat);
   return *this;