Changeset 5ec8e3 for src/boundary.cpp

Timestamp:

Jul 2, 2010, 9:51:01 AM (16 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, Candidate_v1.7.1, 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:

36166d

Parents:

56fb09 (diff), 7ac4af (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 'VectorRefactoring' into StructureRefactoring

Conflicts:

molecuilder/src/Makefile.am

File:

• src/boundary.cpp (modified) (7 diffs)

src/boundary.cpp

@@ -22 +22 @@
 #include "World.hpp"
 #include "Plane.hpp"
+#include "Matrix.hpp"
+#include "Box.hpp"
 
 #include<gsl/gsl_poly.h>
@@ -764 +766 @@
   int N[NDIM];
   int n[NDIM];
-  double *M =  ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
-  double Rotations[NDIM*NDIM];
-  double *MInverse = InverseMatrix(M);
+  const Matrix &M = World::getInstance().getDomain().getM();
+  Matrix Rotations;
+  const Matrix &MInverse = World::getInstance().getDomain().getMinv();
   Vector AtomTranslations;
   Vector FillerTranslations;
@@ -799 +801 @@
 
   // calculate filler grid in [0,1]^3
-  FillerDistance = Vector(distance[0], distance[1], distance[2]);
-  FillerDistance.InverseMatrixMultiplication(M);
+  FillerDistance = MInverse * Vector(distance[0], distance[1], distance[2]);
   for(int i=0;i<NDIM;i++)
     N[i] = (int) ceil(1./FillerDistance[i]);
@@ -813 +814 @@
       for (n[2] = 0; n[2] < N[2]; n[2]++) {
         // calculate position of current grid vector in untransformed box
-        CurrentPosition = Vector((double)n[0]/(double)N[0], (double)n[1]/(double)N[1], (double)n[2]/(double)N[2]);
-        CurrentPosition.MatrixMultiplication(M);
+        CurrentPosition = M * Vector((double)n[0]/(double)N[0], (double)n[1]/(double)N[1], (double)n[2]/(double)N[2]);
         // create molecule random translation vector ...
         for (int i=0;i<NDIM;i++)
@@ -835 +835 @@
             }
 
-            Rotations[0] =   cos(phi[0])            *cos(phi[2]) + (sin(phi[0])*sin(phi[1])*sin(phi[2]));
-            Rotations[3] =   sin(phi[0])            *cos(phi[2]) - (cos(phi[0])*sin(phi[1])*sin(phi[2]));
-            Rotations[6] =               cos(phi[1])*sin(phi[2])                                     ;
-            Rotations[1] = - sin(phi[0])*cos(phi[1])                                                ;
-            Rotations[4] =   cos(phi[0])*cos(phi[1])                                                ;
-            Rotations[7] =               sin(phi[1])                                                ;
-            Rotations[3] = - cos(phi[0])            *sin(phi[2]) + (sin(phi[0])*sin(phi[1])*cos(phi[2]));
-            Rotations[5] = - sin(phi[0])            *sin(phi[2]) - (cos(phi[0])*sin(phi[1])*cos(phi[2]));
-            Rotations[8] =               cos(phi[1])*cos(phi[2])                                     ;
+            Rotations.set(0,0,  cos(phi[0])            *cos(phi[2]) + (sin(phi[0])*sin(phi[1])*sin(phi[2])));
+            Rotations.set(0,1,  sin(phi[0])            *cos(phi[2]) - (cos(phi[0])*sin(phi[1])*sin(phi[2])));
+            Rotations.set(0,2,              cos(phi[1])*sin(phi[2])                                        );
+            Rotations.set(1,0, -sin(phi[0])*cos(phi[1])                                                    );
+            Rotations.set(1,1,  cos(phi[0])*cos(phi[1])                                                    );
+            Rotations.set(1,2,              sin(phi[1])                                                    );
+            Rotations.set(2,0, -cos(phi[0])            *sin(phi[2]) + (sin(phi[0])*sin(phi[1])*cos(phi[2])));
+            Rotations.set(2,1, -sin(phi[0])            *sin(phi[2]) - (cos(phi[0])*sin(phi[1])*cos(phi[2])));
+            Rotations.set(2,2,              cos(phi[1])*cos(phi[2])                                        );
           }
 
@@ -849 +849 @@
           Inserter = (*iter)->x;
           if (DoRandomRotation)
-            Inserter.MatrixMultiplication(Rotations);
+            Inserter *= Rotations;
           Inserter += AtomTranslations + FillerTranslations + CurrentPosition;
 
           // check whether inserter is inside box
-          Inserter.MatrixMultiplication(MInverse);
+          Inserter *= MInverse;
           FillIt = true;
           for (int i=0;i<NDIM;i++)
             FillIt = FillIt && (Inserter[i] >= -MYEPSILON) && ((Inserter[i]-1.) <= MYEPSILON);
-          Inserter.MatrixMultiplication(M);
+          Inserter *= M;
 
           // Check whether point is in- or outside
@@ -892 +892 @@
             }
       }
-  delete[](M);
-  delete[](MInverse);
 
   return Filling;