Changeset 9df5c6 for src

Timestamp:

Jun 30, 2010, 12:20:34 PM (15 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, 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:

84c494

Parents:

4b0cbb

Message:

Made the Vector::IsInParallelepiped() method take a matrix instead of a double*

Location:

src

Files:

• atom.cpp (modified) (1 diff)
• atom.hpp (modified) (1 diff)
• molecule.cpp (modified) (2 diffs)
• molecule.hpp (modified) (1 diff)
• unittests/vectorunittest.cpp (modified) (2 diffs)
• vector.cpp (modified) (1 diff)
• vector.hpp (modified) (1 diff)

src/atom.cpp

@@ -112 +112 @@
  * \return true - is inside, false - is not
  */
-bool atom::IsInParallelepiped(const Vector offset, const double *parallelepiped) const
+bool atom::IsInParallelepiped(const Vector offset, const Matrix& parallelepiped) const
 {
   return (node->IsInParallelepiped(offset, parallelepiped));

src/atom.hpp

@@ -66 +66 @@
   double DistanceToVector(const Vector &origin) const;
   double DistanceSquaredToVector(const Vector &origin) const;
-  bool IsInParallelepiped(const Vector offset, const double *parallelepiped) const;
+  bool IsInParallelepiped(const Vector offset, const Matrix &parallelepiped) const;
 
   // getter and setter

src/molecule.cpp

@@ -9 +9 @@
 #include <cstring>
 #include <boost/bind.hpp>
+#include <boost/foreach.hpp>
 
 #include "World.hpp"
@@ -659 +660 @@
  * @param three vectors forming the matrix that defines the shape of the parallelpiped
  */
-molecule* molecule::CopyMoleculeFromSubRegion(const Vector offset, const double *parallelepiped) const {
+molecule* molecule::CopyMoleculeFromSubRegion(const Vector offset, const Matrix &parallelepiped) const {
   molecule *copy = World::getInstance().createMolecule();
 
-  ActOnCopyWithEachAtomIfTrue ( &molecule::AddCopyAtom, copy, &atom::IsInParallelepiped, offset, parallelepiped );
+  BOOST_FOREACH(atom *iter,atoms){
+    if(iter->IsInParallelepiped(offset,parallelepiped)){
+      copy->AddCopyAtom(iter);
+    }
+  }
 
   //TODO: copy->BuildInducedSubgraph(this);

src/molecule.hpp

@@ -316 +316 @@
 
   molecule *CopyMolecule();
-  molecule* CopyMoleculeFromSubRegion(const Vector offset, const double *parallelepiped) const;
+  molecule* CopyMoleculeFromSubRegion(const Vector offset, const Matrix &parallelepiped) const;
 
   /// Fragment molecule by two different approaches:

src/unittests/vectorunittest.cpp

@@ -21 +21 @@
 #include "Plane.hpp"
 #include "Exceptions/LinearDependenceException.hpp"
+#include "Matrix.hpp"
 
 #ifdef HAVE_TESTRUNNER
@@ -221 +222 @@
 void VectorTest::IsInParallelepipedTest()
 {
-  double parallelepiped[NDIM*NDIM];
-  parallelepiped[0] = 1;
-  parallelepiped[1] = 0;
-  parallelepiped[2] = 0;
-  parallelepiped[3] = 0;
-  parallelepiped[4] = 1;
-  parallelepiped[5] = 0;
-  parallelepiped[6] = 0;
-  parallelepiped[7] = 0;
-  parallelepiped[8] = 1;
+  Matrix parallelepiped;
+  parallelepiped.at(0,0) = 1;
+  parallelepiped.at(1,0) = 0;
+  parallelepiped.at(2,0) = 0;
+  parallelepiped.at(0,1) = 0;
+  parallelepiped.at(1,1) = 1;
+  parallelepiped.at(2,1) = 0;
+  parallelepiped.at(0,2) = 0;
+  parallelepiped.at(1,2) = 0;
+  parallelepiped.at(2,2) = 1;
 
   fixture = zero;

src/vector.cpp

@@ -601 +601 @@
  * @param three vectors forming the matrix that defines the shape of the parallelpiped
  */
-bool Vector::IsInParallelepiped(const Vector &offset, const double * const _parallelepiped) const
-{
-  Matrix parallelepiped = Matrix(_parallelepiped).invert();
+bool Vector::IsInParallelepiped(const Vector &offset, const Matrix& _parallelepiped) const
+{
+  Matrix parallelepiped = _parallelepiped.invert();
   Vector a = parallelepiped * ((*this)-offset);
   bool isInside = true;

src/vector.hpp

@@ -62 +62 @@
   bool GetOneNormalVector(const Vector &x1);
   bool MakeNormalTo(const Vector &y1);
-  bool IsInParallelepiped(const Vector &offset, const double * const parallelepiped) const;
+  bool IsInParallelepiped(const Vector &offset, const Matrix& _parallelepiped) const;
   void WrapPeriodically(const Matrix &M, const Matrix &Minv);
   std::pair<Vector,Vector> partition(const Vector&) const;