Changeset 89c8b2 for src

Timestamp:

Aug 20, 2009, 3:40:49 PM (15 years ago)

Author:

Saskia Metzler <metzler@…>

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:

0227a9, 29812d

Parents:

78b73c

Message:

Ticket 17: Write new function molecule::CopyMoleculeFromSubRegion()

Location:

src

Files:

• atom.cpp (modified) (2 diffs)
• molecules.cpp (modified) (2 diffs)
• molecules.hpp (modified) (1 diff)
• vector.cpp (modified) (1 diff)
• vector.hpp (modified) (1 diff)
• vectorunittest.cpp (modified) (1 diff)
• vectorunittest.hpp (modified) (2 diffs)

src/atom.cpp

@@ -38 +38 @@
   previous = NULL;
   next = NULL;
-  father = this;  // generally, father is itself
+  father = pointer;  // generally, father is itself
   Ancestor = NULL;
   GraphNr = -1;
@@ -53 +53 @@
   nr = -1;
   sort = &nr;
+  node = &x;
 }
 

src/molecules.cpp

@@ -176 +176 @@
  * Increases molecule::last_atom and gives last number to added atom.
  * \param *pointer allocated and set atom
- * \return true - succeeded, false - atom not found in list
+ * \return pointer to the newly added atom
  */
 atom * molecule::AddCopyAtom(atom *pointer)
@@ -612 +612 @@
   return copy;
 };
+
+
+/**
+ * Copies all atoms of a molecule which are within the defined parallelepiped.
+ *
+ * @param offest for the origin of the parallelepiped
+ * @param three vectors forming the matrix that defines the shape of the parallelpiped
+ */
+molecule* molecule::CopyMoleculeFromSubRegion(Vector offset, double *parallelepiped) {
+  molecule *copy = new molecule(elemente);
+  atom *Walker = start;
+
+  while(Walker->next != end) {
+    Walker = Walker->next;
+    if (Walker->x.IsInParallelepiped(offset, parallelepiped)) {
+      cout << "Adding atom " << *Walker << endl;
+      copy->AddCopyAtom(Walker);
+    }
+  }
+
+  //TODO: copy->BuildInducedSubgraph((ofstream *)&cout, this);
+
+  return copy;
+}
 
 /** Adds a bond to a the molecule specified by two atoms, \a *first and \a *second.

src/molecules.hpp

@@ -207 +207 @@
 
   molecule *CopyMolecule();
+  molecule* CopyMoleculeFromSubRegion(Vector offset, double *parallelepiped);
 
   /// Fragment molecule by two different approaches:

src/vector.cpp

@@ -1221 +1221 @@
   return true;
 };
+
+/**
+ * Checks whether this vector is within the parallelepiped defined by the given three vectors and
+ * their offset.
+ *
+ * @param offest for the origin of the parallelepiped
+ * @param three vectors forming the matrix that defines the shape of the parallelpiped
+ */
+bool Vector::IsInParallelepiped(Vector offset, double *parallelepiped)
+{
+  Vector a;
+  a.CopyVector(this);
+  a.SubtractVector(&offset);
+  a.InverseMatrixMultiplication(parallelepiped);
+  bool isInside = true;
+
+  for (int i=NDIM;i--;)
+    isInside = isInside && ((a.x[i] <= 1) && (a.x[i] >= 0));
+
+  return isInside;
+}

src/vector.hpp

@@ -68 +68 @@
   void AskPosition(double *cell_size, bool check);
   bool Output(ofstream *out) const;
+  bool IsInParallelepiped(Vector offset, double *parallelepiped);
 };
 

src/vectorunittest.cpp

@@ -258 +258 @@
 }
 
+/**
+ * UnitTest for Vector::IsInParallelepiped().
+ */
+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;
+
+  fixture.CopyVector(zero);
+  CPPUNIT_ASSERT_EQUAL( false, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
+  fixture.Init(2.5,2.5,2.5);
+  CPPUNIT_ASSERT_EQUAL( true, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
+  fixture.Init(1.,1.,1.);
+  CPPUNIT_ASSERT_EQUAL( false, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
+  fixture.Init(3.5,3.5,3.5);
+  CPPUNIT_ASSERT_EQUAL( false, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
+  fixture.Init(2.,2.,2.);
+  CPPUNIT_ASSERT_EQUAL( true, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
+  fixture.Init(2.,3.,2.);
+  CPPUNIT_ASSERT_EQUAL( true, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
+  fixture.Init(-2.,2.,-1.);
+  CPPUNIT_ASSERT_EQUAL( false, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
+}
+
 
 /********************************************** Main routine **************************************/

src/vectorunittest.hpp

@@ -28 +28 @@
     CPPUNIT_TEST ( LineIntersectionTest );
     CPPUNIT_TEST ( VectorRotationTest );
+    CPPUNIT_TEST ( IsInParallelepipedTest );
     CPPUNIT_TEST_SUITE_END();
 
@@ -44 +45 @@
     void LineIntersectionTest();
     void VectorRotationTest();
+    void IsInParallelepipedTest();
 
 private: