Changeset 9758f7 for src/Fragmentation/MatrixContainer.hpp

Timestamp:

Oct 18, 2011, 8:07:37 AM (14 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:

1b145f

Parents:

a9b86d

git-author:

Frederik Heber <heber@…> (09/16/11 16:24:18)

git-committer:

Frederik Heber <heber@…> (10/18/11 08:07:37)

Message:

Removed C arrays in KeySetsContainer and MatrixContainer.

• replaced by std::vector<>s.
• transition is so far very minimal, external (range) counters are still present.
• extracted allocation of memory into own block in MatrixContainer::parseMatrix().

File:

• src/Fragmentation/MatrixContainer.hpp (modified) (3 diffs)

src/Fragmentation/MatrixContainer.hpp

@@ -14 +14 @@
 #endif
 
-#include "boost/serialization/array.hpp"
-
-#include "boost/multi_array.hpp"
+#include <vector>
 
 /** Contains a sequence of matrices parsed from file.
@@ -23 +21 @@
 class MatrixContainer {
   public:
-    double ***Matrix;
-    int **Indices;
-    char **Header;
+    typedef std::vector<std::vector<double> > MatrixArray;
+    typedef std::vector<MatrixArray> ArrayOfMatrices;
+    typedef std::vector<std::string> StringVector;
+    typedef std::vector<int> IntVector;
+    typedef std::vector<IntVector> VectorOfIntVectors;
+
+    ArrayOfMatrices Matrix;
+    VectorOfIntVectors Indices;
+    StringVector Header;
     int MatrixCounter;
-    int *RowCounter;
-    int *ColumnCounter;
+    IntVector RowCounter;
+    IntVector ColumnCounter;
 
   MatrixContainer();
@@ -34 +38 @@
 
   bool InitialiseIndices(class MatrixContainer *Matrix = NULL);
-  bool ParseMatrix(std::istream &input, int skiplines, int skipcolumns, int MatrixNr);
-  virtual bool ParseFragmentMatrix(const char *name, const char *prefix, std::string suffix, int skiplines, int skipcolumns);
-  bool AllocateMatrix(char **GivenHeader, int MCounter, int *RCounter, int *CCounter);
+  bool ParseMatrix(std::istream &input, int skiplines, int skipcolumns, size_t MatrixNr);
+  virtual bool ParseFragmentMatrix(const std::string name, const std::string prefix, std::string suffix, int skiplines, int skipcolumns);
+  bool AllocateMatrix(StringVector GivenHeader, int MCounter, IntVector RCounter, IntVector CCounter);
   bool ResetMatrix();
   double FindMinValue();
   double FindMaxValue();
   bool SetLastMatrix(double value, int skipcolumns);
-  bool SetLastMatrix(double **values, int skipcolumns);
+  bool SetLastMatrix(const MatrixArray &values, int skipcolumns);
   //bool ParseIndices();
   //bool SumSubValues();
   bool SumSubManyBodyTerms(class MatrixContainer &Matrix, class KeySetsContainer &KeySets, int Order);
-  bool WriteTotalFragments(const char *name, const char *prefix);
-  bool WriteLastMatrix(const char *name, const char *prefix, const char *suffix);
+  bool WriteTotalFragments(const std::string name, const std::string prefix);
+  bool WriteLastMatrix(const std::string name, const std::string prefix, const std::string suffix);
 };