Changeset cca9ef for src/Actions

Timestamp:

Dec 4, 2010, 11:54:32 PM (14 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:

0d4424

Parents:

3bc926

git-author:

Frederik Heber <heber@…> (11/15/10 12:58:27)

git-committer:

Frederik Heber <heber@…> (12/04/10 23:54:32)

Message:

Renamed Matrix to RealSpaceMatrix.

• class Matrix only represents 3x3 matrices, whereas we are now going to extend the class MatrixContent to contain arbritrary dimensions.
• renamed class and file

Location:

src/Actions

Files:

• AnalysisAction/PrincipalAxisSystemAction.cpp (modified) (2 diffs)
• MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) (2 diffs)
• SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) (3 diffs)
• SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) (3 diffs)
• ValueStorage.cpp (modified) (3 diffs)
• WorldAction/CenterOnEdgeAction.cpp (modified) (2 diffs)
• WorldAction/ChangeBoxAction.cpp (modified) (1 diff)
• WorldAction/RepeatBoxAction.cpp (modified) (2 diffs)
• WorldAction/ScaleBoxAction.cpp (modified) (2 diffs)

src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp

@@ -22 +22 @@
 #include "Helpers/Log.hpp"
 #include "Helpers/Verbose.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "element.hpp"
@@ -40 +40 @@
 /** =========== define the function ====================== */
 Action::state_ptr AnalysisPrincipalAxisSystemAction::performCall() {
-  Matrix InertiaTensor;
+  RealSpaceMatrix InertiaTensor;
 
   DoLog(0) && (Log() << Verbose(0) << "Evaluating prinicipal axis." << endl);

src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp

@@ -23 +23 @@
 #include "Helpers/Verbose.hpp"
 #include "LinearAlgebra/Line.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "element.hpp"
@@ -50 +50 @@
     mol = iter->second;
     DoLog(0) && (Log() << Verbose(0) << "Converting to prinicipal axis system." << endl);
-    Matrix InertiaTensor;
+    RealSpaceMatrix InertiaTensor;
     Vector *CenterOfGravity = mol->DetermineCenterOfGravity();
 

src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp

@@ -25 +25 @@
 #include "Helpers/Log.hpp"
 #include "Helpers/Verbose.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "Shapes/BaseShapes.hpp"
@@ -45 +45 @@
 Action::state_ptr SelectionAllAtomsInsideCuboidAction::performCall() {
   std::vector<atom *> selectedAtoms = World::getInstance().getSelectedAtoms();
-  Matrix RotationMatrix;
+  RealSpaceMatrix RotationMatrix;
 
   // obtain information
@@ -70 +70 @@
 Action::state_ptr SelectionAllAtomsInsideCuboidAction::performRedo(Action::state_ptr _state){
   SelectionAllAtomsInsideCuboidState *state = assert_cast<SelectionAllAtomsInsideCuboidState*>(_state.get());
-  Matrix RotationMatrix;
+  RealSpaceMatrix RotationMatrix;
 
   RotationMatrix.setRotation(state->params.Xangle, state->params.Yangle, state->params.Zangle);

src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp

@@ -25 +25 @@
 #include "Helpers/Log.hpp"
 #include "Helpers/Verbose.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "Shapes/BaseShapes.hpp"
@@ -45 +45 @@
 Action::state_ptr SelectionNotAllAtomsInsideCuboidAction::performCall() {
   std::vector<atom *> selectedAtoms = World::getInstance().getSelectedAtoms();
-  Matrix RotationMatrix;
+  RealSpaceMatrix RotationMatrix;
 
   // obtain information
@@ -70 +70 @@
 Action::state_ptr SelectionNotAllAtomsInsideCuboidAction::performRedo(Action::state_ptr _state){
   SelectionNotAllAtomsInsideCuboidState *state = assert_cast<SelectionNotAllAtomsInsideCuboidState*>(_state.get());
-  Matrix RotationMatrix;
+  RealSpaceMatrix RotationMatrix;
 
   RotationMatrix.setRotation(state->params.Xangle, state->params.Yangle, state->params.Zangle);

src/Actions/ValueStorage.cpp

@@ -31 +31 @@
 #include "Helpers/Verbose.hpp"
 #include "LinearAlgebra/BoxVector.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "atom.hpp"
@@ -95 +95 @@
 
 void ValueStorage::queryCurrentValue(const char * name, class Box &_T) {
-  Matrix M;
+  RealSpaceMatrix M;
   double tmp;
   if (typeid( Box ) == *(OptionRegistry_instance.getOptionByName(name)->getType())) {
@@ -254 +254 @@
 void ValueStorage::setCurrentValue(const char * name, class Box &_T)
 {
-  const Matrix &M = _T.getM();
+  const RealSpaceMatrix &M = _T.getM();
   if (typeid( Box ) == *(OptionRegistry_instance.getOptionByName(name)->getType())) {
     std::ostringstream stream;

src/Actions/WorldAction/CenterOnEdgeAction.cpp

@@ -24 +24 @@
 #include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 
 #include <iostream>
@@ -59 +59 @@
   }
   // set new box size
-  Matrix domain;
+  RealSpaceMatrix domain;
   for (int i=0;i<NDIM;i++) {
     double tmp = Max[i]-Min[i];

src/Actions/WorldAction/ChangeBoxAction.cpp

@@ -24 +24 @@
 #include "World.hpp"
 #include "Box.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 
 #include <iostream>

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -25 +25 @@
 #include "molecule.hpp"
 #include "LinearAlgebra/Vector.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "Helpers/Verbose.hpp"
 #include "World.hpp"
@@ -63 +63 @@
 
   (cout << "Repeating box " << params.Repeater << " times for (x,y,z) axis." << endl);
-  Matrix M = World::getInstance().getDomain().getM();
-  Matrix newM = M;
+  RealSpaceMatrix M = World::getInstance().getDomain().getM();
+  RealSpaceMatrix newM = M;
   Vector x,y;
   int n[NDIM];
-  Matrix repMat;
+  RealSpaceMatrix repMat;
   for (int axis = 0; axis < NDIM; axis++) {
     params.Repeater[axis] = floor(params.Repeater[axis]);

src/Actions/WorldAction/ScaleBoxAction.cpp

@@ -26 +26 @@
 #include "World.hpp"
 #include "Box.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 
 #include <iostream>
@@ -53 +53 @@
   }
 
-  Matrix M = World::getInstance().getDomain().getM();
-  Matrix scale;
+  RealSpaceMatrix M = World::getInstance().getDomain().getM();
+  RealSpaceMatrix scale;
 
   for (int i=0;i<NDIM;i++) {