Changeset 6c438f for src/Shapes/ShapeOps.cpp

Timestamp:

Aug 28, 2010, 3:21:11 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:

a6e6b5, f8982c

Parents:

2ad482 (diff), fd4905 (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.

git-author:

Frederik Heber <heber@…> (08/28/10 03:17:48)

git-committer:

Frederik Heber <heber@…> (08/28/10 03:21:11)

Message:

Merge branch 'StructureRefactoring' into Shapes

Conflicts:

src/Box.cpp
src/Box.hpp
src/Descriptors/AtomShapeDescriptor.cpp
src/Descriptors/AtomShapeDescriptor.hpp
src/Descriptors/AtomShapeDescriptor_impl.hpp
src/LinearAlgebra/Line.cpp
src/LinearAlgebra/Line.hpp
src/LinearAlgebra/Matrix.cpp
src/LinearAlgebra/Matrix.hpp
src/Makefile.am
src/Shapes/BaseShapes.cpp
src/Shapes/BaseShapes_impl.hpp
src/Shapes/Shape.cpp
src/Shapes/Shape.hpp
src/Shapes/ShapeOps_impl.hpp
src/Shapes/Shape_impl.hpp
src/unittests/ShapeUnittest.cpp

• AtomShapeDescriptor had been implemented doubly.
• LineSegment* moved to LinearAlgebra/
• BaseShapes:: Cuboid is from (0,0,0) and not from (-1,-1,-1) to (1,1,1)
  • had to fix ShapeUnittest
• some overlap in Shapes due to getHomogeneousPointsOnSurface added in stable.
• BUGFIX: Matrix::transpose() did not allocate MatrixContent::content.
• merged BaseShapesUnitTest into ShapeUnitTest.

File:

• src/Shapes/ShapeOps.cpp (modified) (11 diffs)

src/Shapes/ShapeOps.cpp

@@ +1 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2010 University of Bonn. All rights reserved.
+ * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
+ */
+
 /*
  * ShapeOps.cpp
@@ -6 +13 @@
  */
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "Helpers/MemDebug.hpp"
+
 #include "Shapes/ShapeOps.hpp"
 #include "Shapes/ShapeOps_impl.hpp"
 
+#include "LinearAlgebra/Vector.hpp"
 #include "Helpers/Assert.hpp"
 
@@ -55 +70 @@
 }
 
-Shape::impl_ptr ShapeOpsBase_impl::getArg(){
+std::vector<Vector> ShapeOpsBase_impl::getHomogeneousPointsOnSurface(const size_t N) const {
+  return getArg()->getHomogeneousPointsOnSurface(N);;
+}
+
+Shape::impl_ptr ShapeOpsBase_impl::getArg() const{
   return arg;
 }
@@ -69 +88 @@
 Resize_impl::~Resize_impl(){}
 
+bool Resize_impl::isInside(const Vector& point){
+  return getArg()->isInside((1/size) * point);
+}
+
 Vector Resize_impl::translateIn(const Vector& point){
   return (1/size) * point;
@@ -86 +109 @@
   return sstr.str();
 }
+
+std::vector<Vector> Resize_impl::getHomogeneousPointsOnSurface(const size_t N) const {
+  std::vector<Vector> PointsOnSurface = getArg()->getHomogeneousPointsOnSurface(N);
+  for(std::vector<Vector>::iterator iter = PointsOnSurface.begin(); iter != PointsOnSurface.end(); ++iter) {
+    *iter *= size;
+  }
+  return PointsOnSurface;
+}
+
 
 Shape resize(const Shape &arg,double size){
@@ -100 +132 @@
 Translate_impl::~Translate_impl(){}
 
+bool Translate_impl::isInside(const Vector& point){
+  return getArg()->isInside(point-offset);
+}
+
 Vector Translate_impl::translateIn(const Vector& point){
   return point-offset;
@@ -116 +152 @@
   sstr << "translate(" << getArg()->toString() << "," << offset << ")";
   return sstr.str();
+}
+
+std::vector<Vector> Translate_impl::getHomogeneousPointsOnSurface(const size_t N) const {
+  std::vector<Vector> PointsOnSurface = getArg()->getHomogeneousPointsOnSurface(N);
+  for(std::vector<Vector>::iterator iter = PointsOnSurface.begin(); iter != PointsOnSurface.end(); ++iter) {
+    *iter += offset;
+  }
+  return PointsOnSurface;
 }
 
@@ -138 +182 @@
 Stretch_impl::~Stretch_impl(){}
 
+bool Stretch_impl::isInside(const Vector& point){
+  Vector helper=point;
+  helper.ScaleAll(reciFactors);
+  return getArg()->isInside(helper);
+}
+
 Vector Stretch_impl::translateIn(const Vector& point){
   Vector helper=point;
@@ -168 +218 @@
 }
 
+std::vector<Vector> Stretch_impl::getHomogeneousPointsOnSurface(const size_t N) const {
+  std::vector<Vector> PointsOnSurface = getArg()->getHomogeneousPointsOnSurface(N);
+  for(std::vector<Vector>::iterator iter = PointsOnSurface.begin(); iter != PointsOnSurface.end(); ++iter) {
+    (*iter).ScaleAll(reciFactors);
+  }
+  return PointsOnSurface;
+}
+
 Shape stretch(const Shape &arg, const Vector &factors){
   Shape::impl_ptr impl = Shape::impl_ptr(new Stretch_impl(getShapeImpl(arg),factors));
@@ -183 +241 @@
 Transform_impl::~Transform_impl(){}
 
+bool Transform_impl::isInside(const Vector& point){
+  return getArg()->isInside(transformationInv * point);
+}
+
 Vector Transform_impl::translateIn(const Vector& point){
   return transformationInv * point;
@@ -202 +264 @@
 }
 
+std::vector<Vector> Transform_impl::getHomogeneousPointsOnSurface(const size_t N) const {
+  std::vector<Vector> PointsOnSurface = getArg()->getHomogeneousPointsOnSurface(N);
+  for(std::vector<Vector>::iterator iter = PointsOnSurface.begin(); iter != PointsOnSurface.end(); ++iter) {
+    *iter = transformation * (*iter);
+  }
+  return PointsOnSurface;
+}
+
 Shape transform(const Shape &arg, const Matrix &transformation){
   Shape::impl_ptr impl = Shape::impl_ptr(new Transform_impl(getShapeImpl(arg),transformation));