Changeset b40b9d for src

Timestamp:

Oct 6, 2011, 12:08:30 PM (13 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:

47812b

Parents:

29daad

git-author:

Frederik Heber <heber@…> (08/12/11 15:16:28)

git-committer:

Frederik Heber <heber@…> (10/06/11 12:08:30)

Message:

FIX: Bonds are now displayed correctly.

• using Vector::VectorProduct() to correctly create normal vectors and fixed therewith GLMoleculeView::makeCylinder().

File:

• src/UIElements/Views/Qt4/GLMoleculeView.cpp (modified) (5 diffs)

src/UIElements/Views/Qt4/GLMoleculeView.cpp

@@ -28 +28 @@
 
 #include <iostream>
+#include <boost/shared_ptr.hpp>
 
 #include "LinearAlgebra/Line.hpp"
@@ -229 +230 @@
   float blueMaterial[] = { 255./(float)color[0], 255./(float)color[1], 255./(float)color[2], 1 };  // need to recast from [0,255] with integers into [0,1] with floats
   GLUquadricObj* q = gluNewQuadric ();
+  gluQuadricOrientation(q, GLU_OUTSIDE);
 
   std::cout << "Setting sphere at " << x << " with color r"
@@ -254 +256 @@
   float blueMaterial[] = { 255./(float)color[0], 255./(float)color[1], 255./(float)color[2], 1 };
   GLUquadricObj* q = gluNewQuadric ();
+  gluQuadricOrientation(q, GLU_OUTSIDE);
   Vector a,b;
+  Vector OtherAxis;
   double alpha;
-  a = x - b;
-  b.GetOneNormalVector(a);
-  b.MakeNormalTo(Z);
+  a = x - y;
+  // construct rotation axis
+  b = a;
+  b.VectorProduct(Z);
+  Line axis(zeroVec, b);
+  // calculate rotation angle
   alpha = a.Angle(Z);
-  if (fabs(a[2]) > MYEPSILON)   // I have no idea why I need to check this, but this fixes the sign problem of the rotation angle
+  // construct other axis to check right-hand rule
+  OtherAxis = b;
+  OtherAxis.VectorProduct(Z);
+  // assure right-hand rule for the rotation
+  if (a.ScalarProduct(OtherAxis) < MYEPSILON)
     alpha = M_PI-alpha;
-  Line axis(zeroVec, b);
-  a = axis.rotateVector(a, alpha);
-  std::cout << "Setting cylinder from " << x << " to " << a << " with color r"
+  // check
+  Vector a_rotated = axis.rotateVector(a, alpha);
+  std::cout << "Setting cylinder from "// << x << " to " << y
+      << a << " to " << a_rotated << " around " << b << " by " << alpha/M_PI*180. << ", respectively, "
+      << " with color r"
       << (int)color[0] << ",g" << (int)color[1] << ",b" << (int)color[2] << "." << endl;
 
@@ -307 +320 @@
         // create atom
         const element *ptr = (*atomiter)->getType();
-        molecule::const_iterator moliter = (*Runner)->begin();
-        Position = (*atomiter)->getPosition() - (*moliter)->getPosition();
+        boost::shared_ptr<Vector> MolCenter((*Runner)->DetermineCenterOfGravity());
+        Position = (*atomiter)->getPosition() - *MolCenter;
         const unsigned char* color = NULL;
         if ((World::getInstance().isSelected(*atomiter)) || (World::getInstance().isSelected((*Runner))))
@@ -322 +335 @@
             ++bonditer) {
           if ((*bonditer)->leftatom->getId() == (*atomiter)->getId()) {
-            Position = (*bonditer)->leftatom->getPosition() - (*moliter)->getPosition();
-            OtherPosition = (*bonditer)->rightatom->getPosition() - (*moliter)->getPosition();
+            Position = (*bonditer)->leftatom->getPosition() - *MolCenter;
+            OtherPosition = (*bonditer)->rightatom->getPosition() - *MolCenter;
             const double distance = sqrt(Position.DistanceSquared(OtherPosition))/2.;
             const unsigned char *color1 = (*bonditer)->leftatom->getType()->getColor();