Changeset 6e06bd for src/LinearAlgebra/MatrixContent.hpp

Timestamp:

Dec 5, 2010, 12:19:19 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:

f03705

Parents:

589112 (diff), bbf1bd (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 'MatrixVectorContentRefactoring' into stable

File:

• src/LinearAlgebra/MatrixContent.hpp (modified) (1 diff)

src/LinearAlgebra/MatrixContent.hpp

@@ -9 +9 @@
 #define MATRIXCONTENT_HPP_
 
-/**
- * !file
- * The way GSL works does not allow for forward definitions of the structures.
- * Because of this the pointer to the gsl_matrix struct is wrapped inside another
- * (dumb) object that allows for forward definitions. All methods of this class
- * are empty, to allow for a maximum of flexibility.
+/** MatrixContent is a wrapper for gsl_matrix.
+ *
+ * The GNU Scientific Library contaisn some very well written routines for
+ * linear algebra problems. However, it's syntax is C and hence it does not
+ * lend itself to readable written code, i.e. C = A * B, where A, B, and C
+ * are all matrices. Writing code this way is very convenient, concise and
+ * also in the same manner as one would type in MatLab.
+ * However, with C++ and its feature to overload functions and its operator
+ * functions such syntax is easy to create.
+ *
+ * Hence, this class is a C++ wrapper to gsl_matrix. There already some other
+ * libraries, however they fall short for the following reasons:
+ * -# gslwrap: not very well written and uses floats instead of doubles
+ * -# gslcpp: last change is from 2007 and only very few commits
+ * -# o2scl: basically, the same functionality as gsl only written in C++,
+ *    however it uses GPLv3 license which is inconvenient for MoleCuilder.
+ *
+ * <h1>Howto use MatrixContent</h1>
+ *
+ * One should not use MatrixContent directly but either have it as a member
+ * variable in a specialized class or inherit from it.
+ *
  */
 
 #include <gsl/gsl_matrix.h>
 
-struct MatrixContent{
+class Vector;
+
+class MatrixContent
+{
+  friend Vector operator*(const MatrixContent &mat,const Vector &vec);
+  friend class RealSpaceMatrix;
+  friend class LinearSystemOfEquations;
+
+  friend class MatrixContentTest;
+  friend class MatrixContentSymmetricTest;
+public:
+  MatrixContent(size_t rows, size_t columns);
+  MatrixContent(size_t rows, size_t columns, const double *src);
+  MatrixContent(gsl_matrix *&src);
+  MatrixContent(const MatrixContent &src);
+  MatrixContent(const MatrixContent *src);
+  ~MatrixContent();
+
+  // Accessing
+  double &at(size_t i, size_t j);
+  const double at(size_t i, size_t j) const;
+  void set(size_t i, size_t j, const double value);
+
+  // Initializing
+  void setFromDoubleArray(double * x);
+  void setIdentity();
+  void setValue(double _value);
+  void setZero();
+
+  // Exchanging elements
+  bool SwapRows(size_t i, size_t j);
+  bool SwapColumns(size_t i, size_t j);
+  bool SwapRowColumn(size_t i, size_t j);
+
+  // Transformations
+  MatrixContent transpose() const;
+  MatrixContent &transpose();
+  gsl_vector* transformToEigenbasis();
+
+  // Properties
+  bool IsNull() const;
+  bool IsPositive() const;
+  bool IsNegative() const;
+  bool IsNonNegative() const;
+  bool IsPositiveDefinite() const;
+  double Determinant() const;
+
+  // Operators
+  MatrixContent &operator=(const MatrixContent &src);
+  const MatrixContent &operator+=(const MatrixContent &rhs);
+  const MatrixContent &operator-=(const MatrixContent &rhs);
+  const MatrixContent &operator*=(const MatrixContent &rhs);
+  const MatrixContent operator*(const MatrixContent &rhs) const;
+  const MatrixContent &operator*=(const double factor);
+  bool operator==(const MatrixContent &rhs) const;
+
+protected:
+  double *Pointer(size_t m, size_t n);
+  const double *const_Pointer(size_t m, size_t n) const;
+
+private:
   gsl_matrix * content;
+  const size_t rows;      // store for internal purposes
+  const size_t columns;  // store for internal purposes
 };
 
+const MatrixContent operator*(const double factor,const MatrixContent& mat);
+const MatrixContent operator*(const MatrixContent &mat,const double factor);
+Vector operator*(const MatrixContent &mat,const Vector &vec);
+
 #endif /* MATRIXCONTENT_HPP_ */