Changeset 8cbb97 for src/ellipsoid.cpp

Timestamp:

Apr 29, 2010, 1:55:21 PM (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, 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:

d79639

Parents:

632bc3 (diff), 753f02 (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/Legacy/oldmenu.cpp
molecuilder/src/Makefile.am
molecuilder/src/analysis_correlation.cpp
molecuilder/src/boundary.cpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/ellipsoid.cpp
molecuilder/src/linkedcell.cpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/tesselation.cpp
molecuilder/src/tesselationhelpers.cpp
molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp
molecuilder/src/unittests/bondgraphunittest.cpp
molecuilder/src/vector.cpp
molecuilder/src/vector.hpp

File:

• src/ellipsoid.cpp (modified) (13 diffs)

src/ellipsoid.cpp

@@ -42 +42 @@
 
   // 1. translate coordinate system so that ellipsoid center is in origin
-  helper.CopyVector(&x);
-  helper.SubtractVector(&EllipsoidCenter);
-  RefPoint.CopyVector(&helper);
+  RefPoint = helper = x - EllipsoidCenter;
   //Log() << Verbose(4) << "Translated given point is at " << RefPoint << "." << endl;
 
@@ -61 +59 @@
   Matrix[8] = cos(theta);
   helper.MatrixMultiplication(Matrix);
-  helper.Scale(InverseLength);
+  helper.ScaleAll(InverseLength);
   //Log() << Verbose(4) << "Transformed RefPoint is at " << helper << "." << endl;
 
@@ -72 +70 @@
   theta = -EllipsoidAngle[1];
   phi = -EllipsoidAngle[2];
-  helper.Scale(EllipsoidLength);
+  helper.ScaleAll(EllipsoidLength);
   Matrix[0] = cos(psi)*cos(phi) - sin(psi)*cos(theta)*sin(phi);
   Matrix[1] = -cos(psi)*sin(phi) - sin(psi)*cos(theta)*cos(phi);
@@ -86 +84 @@
 
   // 5. determine distance between backtransformed point and x
-  distance = RefPoint.DistanceSquared(&helper);
+  distance = RefPoint.DistanceSquared(helper);
   //Log() << Verbose(4) << "Squared distance between intersection and RefPoint is " << distance << "." << endl;
 
@@ -116 +114 @@
   // put parameters into suitable ellipsoid form
   for (int i=0;i<3;i++) {
-    Center.x[i] = gsl_vector_get(x, i+0);
+    Center[i] = gsl_vector_get(x, i+0);
     EllipsoidLength[i] = gsl_vector_get(x, i+3);
     EllipsoidAngle[i] = gsl_vector_get(x, i+6);
@@ -160 +158 @@
     x = gsl_vector_alloc (9);
     for (int i=0;i<3;i++) {
-      gsl_vector_set (x, i+0, EllipsoidCenter->x[i]);
+      gsl_vector_set (x, i+0, EllipsoidCenter->at(i));
       gsl_vector_set (x, i+3, EllipsoidLength[i]);
       gsl_vector_set (x, i+6, EllipsoidAngle[i]);
@@ -195 +193 @@
       if (status == GSL_SUCCESS) {
         for (int i=0;i<3;i++) {
-          EllipsoidCenter->x[i] = gsl_vector_get (s->x,i+0);
+          EllipsoidCenter->at(i) = gsl_vector_get (s->x,i+0);
           EllipsoidLength[i] = gsl_vector_get (s->x, i+3);
           EllipsoidAngle[i] = gsl_vector_get (s->x, i+6);
@@ -304 +302 @@
                 Candidate = (*Runner);
                 DoLog(2) && (Log() << Verbose(2) << "Current picked node is " << **Runner << " with index " << index << "." << endl);
-                x[PointsPicked++].CopyVector(Candidate->node);    // we have one more atom picked
+                x[PointsPicked++] = *Candidate->node;    // we have one more atom picked
                 current++;    // next pre-picked atom
               }
@@ -350 +348 @@
       //Log() << Verbose(3) << "Current node is " << *Runner->second->node << " with " << value << " ... " << threshold << ": ";
       if (value > threshold) {
-        x[PointsPicked].CopyVector(Runner->second->node->node);
+        x[PointsPicked] = (*Runner->second->node->node);
         PointsPicked++;
         //Log() << Verbose(0) << "IN." << endl;
@@ -387 +385 @@
   Center.Zero();
   for (PointMap::iterator Runner = T->PointsOnBoundary.begin(); Runner != T->PointsOnBoundary.end(); Runner++)
-    Center.AddVector(Runner->second->node->node);
+    Center += (*Runner->second->node->node);
   Center.Scale(1./T->PointsOnBoundaryCount);
   DoLog(1) && (Log() << Verbose(1) << "Center is at " << Center << "." << endl);
@@ -405 +403 @@
     // calculate some sensible starting values for parameter fit
     MaxDistance = 0.;
-    MinDistance = x[0].ScalarProduct(&x[0]);
+    MinDistance = x[0].ScalarProduct(x[0]);
     for (int i=0;i<N;i++) {
-      distance = x[i].ScalarProduct(&x[i]);
+      distance = x[i].ScalarProduct(x[i]);
       if (distance > MaxDistance)
         MaxDistance = distance;
@@ -414 +412 @@
     }
     //Log() << Verbose(2) << "MinDistance " << MinDistance << ", MaxDistance " << MaxDistance << "." << endl;
-    EllipsoidCenter.CopyVector(&Center);  // use Center of Gravity as initial center of ellipsoid
+    EllipsoidCenter = Center;  // use Center of Gravity as initial center of ellipsoid
     for (int i=0;i<3;i++)
       EllipsoidAngle[i] = 0.;
@@ -427 +425 @@
       output << number << "\t";
       for (int i=0;i<3;i++)
-        output << setprecision(9) << EllipsoidCenter.x[i] << "\t";
+        output << setprecision(9) << EllipsoidCenter[i] << "\t";
       for (int i=0;i<3;i++)
         output << setprecision(9) << EllipsoidLength[i] << "\t";