Changeset 9758f7 for src/Fragmentation/MatrixContainer.cpp

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.cpp (modified) (13 diffs)

src/Fragmentation/MatrixContainer.cpp ¶

@@ -35 +35 @@
 /** Constructor of MatrixContainer class.
  */
-MatrixContainer::MatrixContainer() :
-  Indices(NULL)
-{
-  Header = new char*[1];
-  Matrix = new double**[1]; // one more each for the total molecule
-  RowCounter = new int[1];
-  ColumnCounter = new int[1];
-  Header[0] = NULL;
-  Matrix[0] = NULL;
-  RowCounter[0] = -1;
+MatrixContainer::MatrixContainer()
+{
+  Header.resize(1);
+  RowCounter.resize(1);
+  ColumnCounter.resize(1);
+  ColumnCounter[0] = -1;
   MatrixCounter = 0;
-  ColumnCounter[0] = -1;
 };
 
 /** Destructor of MatrixContainer class.
  */
-MatrixContainer::~MatrixContainer() {
-  if (Matrix != NULL) {
-    // free Matrix[MatrixCounter]
-    if ((ColumnCounter != NULL) && (RowCounter != NULL) && (Matrix[MatrixCounter] != NULL))
-      for(int j=RowCounter[MatrixCounter]+1;j--;)
-        delete[](Matrix[MatrixCounter][j]);
-    //if (MatrixCounter != 0)
-    delete[](Matrix[MatrixCounter]);
-    // free all matrices but ultimate one
-    for(int i=MatrixCounter;i--;) {
-      if ((ColumnCounter != NULL) && (RowCounter != NULL)) {
-          for(int j=RowCounter[i]+1;j--;)
-            delete[](Matrix[i][j]);
-          delete[](Matrix[i]);
-      }
-    }
-    delete[](Matrix);
-  }
-  // free indices
-  if (Indices != NULL)
-    for(int i=MatrixCounter+1;i--;) {
-      delete[](Indices[i]);
-    }
-  delete[](Indices);
-
-  // free header and counters
-  if (Header != NULL)
-    for(int i=MatrixCounter+1;i--;)
-      delete[](Header[i]);
-  delete[](Header);
-  delete[](RowCounter);
-  delete[](ColumnCounter);
-};
+MatrixContainer::~MatrixContainer()
+{}
 
 /** Either copies index matrix from another MatrixContainer or initialises with trivial mapping if NULL.
@@ -90 +54 @@
  * \return true - copy/initialisation sucessful, false - dimension false for copying
  */
-bool MatrixContainer::InitialiseIndices(class MatrixContainer *Matrix)
+bool MatrixContainer::InitialiseIndices(class MatrixContainer *_container)
 {
   DoLog(0) && (Log() << Verbose(0) << "Initialising indices");
-  if (Matrix == NULL) {
+  if (_container == NULL) {
     DoLog(0) && (Log() << Verbose(0) << " with trivial mapping." << endl);
-    Indices = new int*[MatrixCounter + 1];
+    Indices.resize(MatrixCounter + 1);
     for(int i=MatrixCounter+1;i--;) {
-      Indices[i] = new int[RowCounter[i]];
+      Indices[i].resize(RowCounter[i]);
       for(int j=RowCounter[i];j--;)
         Indices[i][j] = j;
@@ -103 +67 @@
   } else {
     DoLog(0) && (Log() << Verbose(0) << " from other MatrixContainer." << endl);
-    if (MatrixCounter != Matrix->MatrixCounter)
+    if (MatrixCounter != _container->MatrixCounter)
       return false;
-    Indices = new int*[MatrixCounter + 1];
+    Indices.resize(MatrixCounter + 1);
     for(int i=MatrixCounter+1;i--;) {
-      if (RowCounter[i] != Matrix->RowCounter[i])
+      if (RowCounter[i] != _container->RowCounter[i])
         return false;
-      Indices[i] = new int[Matrix->RowCounter[i]];
-      for(int j=Matrix->RowCounter[i];j--;) {
-        Indices[i][j] = Matrix->Indices[i][j];
+      Indices[i].resize(_container->RowCounter[i]);
+      for(int j=_container->RowCounter[i];j--;) {
+        Indices[i][j] = _container->Indices[i][j];
         //Log() << Verbose(0) << Indices[i][j] << "\t";
       }
@@ -133 +97 @@
  * \return parsing successful
  */
-bool MatrixContainer::ParseMatrix(std::istream &input, int skiplines, int skipcolumns, int MatrixNr)
+bool MatrixContainer::ParseMatrix(std::istream &input, int skiplines, int skipcolumns, size_t MatrixNr)
 {
   stringstream line;
@@ -146 +110 @@
 
   // parse header
-  if (Header[MatrixNr] != NULL)
-    delete[] Header[MatrixNr];
-  Header[MatrixNr] = new char[1024];
+  if (Header.size() <= MatrixNr)
+    Header.resize(MatrixNr);
+  Header[MatrixNr] = std::string("");
+  char dummy[1024];
   for (int m=skiplines+1;m--;)
-    input.getline(Header[MatrixNr], 1023);
-
-  // scan header for number of columns
-  line.str(Header[MatrixNr]);
+    input.getline(dummy, 1023);
+  line.str(dummy);
   for(int k=skipcolumns;k--;)
     line >> Header[MatrixNr];
   Log() << Verbose(0) << line.str() << endl;
+
+  // scan header for number of columns
+  if (ColumnCounter.size() <= MatrixNr)
+    ColumnCounter.resize(MatrixNr);
   ColumnCounter[MatrixNr]=0;
   while ( getline(line,token, '\t') ) {
@@ -170 +137 @@
 
   // scan rest for number of rows/lines
+  if (RowCounter.size() <= MatrixNr)
+    RowCounter.resize(MatrixNr);
   RowCounter[MatrixNr]=-1;    // counts one line too much
   while (!input.eof()) {
@@ -186 +155 @@
 
   // allocate matrix if it's not zero dimension in one direction
-  if ((ColumnCounter[MatrixNr] > 0) && (RowCounter[MatrixNr] > -1)) {
-    if (Matrix[MatrixNr] != NULL)
-      delete[] Matrix[MatrixNr];
-    Matrix[MatrixNr] = new double*[RowCounter[MatrixNr] + 1];
-    for(int j=0;j<RowCounter[MatrixNr]+1;j++)
-      Matrix[MatrixNr][j] = 0;
-
-    // parse in each entry for this matrix
-    input.clear();
-    input.seekg(ios::beg);
-    for (int m=skiplines+1;m--;)
-      input.getline(Header[MatrixNr], 1023);    // skip header
-    line.str(Header[MatrixNr]);
-    Log() << Verbose(0) << "Header: " << line.str() << endl;
-    for(int k=skipcolumns;k--;)  // skip columns in header too
-      line >> filename;
-    strncpy(Header[MatrixNr], line.str().c_str(), 1023);
-    for(int j=0;j<RowCounter[MatrixNr];j++) {
-      if (Matrix[MatrixNr][j] != NULL)
-        delete[] Matrix[MatrixNr][j];
-      Matrix[MatrixNr][j] = new double[ColumnCounter[MatrixNr]];
-      for(int k=0;k<ColumnCounter[MatrixNr];k++)
+  if (Matrix.size() <= MatrixNr)
+    Matrix.resize(MatrixNr+1);
+  if ((Matrix[MatrixNr].size() <= (size_t)RowCounter[MatrixNr] + 1) && (RowCounter[MatrixNr] > -1)) {
+    Matrix[MatrixNr].resize(RowCounter[MatrixNr] + 2);
+    for(int j=0;j<=RowCounter[MatrixNr];j++) {
+      if ((Matrix[MatrixNr][j].size() <= (size_t)ColumnCounter[MatrixNr]) && (ColumnCounter[MatrixNr] > -1))
+        Matrix[MatrixNr][j].resize(ColumnCounter[MatrixNr]+1);
+      // clear
+      for(int k=0;k<=ColumnCounter[MatrixNr];k++)
         Matrix[MatrixNr][j][k] = 0;
-
-      input.getline(filename, 1023);
-      stringstream lines(filename);
-      Log() << Verbose(2) << "Matrix at level " << j << ":";// << filename << endl;
-      for(int k=skipcolumns;k--;)
-        lines >> filename;
-      for(int k=0;(k<ColumnCounter[MatrixNr]) && (!lines.eof());k++) {
-        lines >> Matrix[MatrixNr][j][k];
-        Log() << Verbose(1) << " " << std::setprecision(2) << Matrix[MatrixNr][j][k] << endl;
-      }
-      if (Matrix[MatrixNr][ RowCounter[MatrixNr] ] != NULL)
-        delete[] Matrix[MatrixNr][ RowCounter[MatrixNr] ];
-      Matrix[MatrixNr][ RowCounter[MatrixNr] ] = new double[ColumnCounter[MatrixNr]];
-      for(int j=ColumnCounter[MatrixNr];j--;)
-        Matrix[MatrixNr][ RowCounter[MatrixNr] ][j] = 0.;
     }
   } else {
-    DoeLog(1) && (eLog()<< Verbose(1) << "Matrix nr. " << MatrixNr << " has column and row count of (" << ColumnCounter[MatrixNr] << "," << RowCounter[MatrixNr] << "), could not allocate nor parse!" << endl);
-  }
+    ELOG(1, "Matrix nr. " << MatrixNr << " has column and row count of (" << ColumnCounter[MatrixNr] << "," << RowCounter[MatrixNr] << "), could not allocate nor parse!");
+    return false;
+  }
+
+  // parse in each entry for this matrix
+  input.clear();
+  input.seekg(ios::beg);
+  for (int m=skiplines+1;m--;)
+    input.getline(dummy, 1023);    // skip header
+  line.str(dummy);
+  Log() << Verbose(0) << "Header: " << line.str() << endl;
+  for(int k=skipcolumns;k--;)  // skip columns in header too
+    line >> filename;
+  Header[MatrixNr] = line.str();
+  for(int j=0;j<RowCounter[MatrixNr];j++) {
+    input.getline(filename, 1023);
+    stringstream lines(filename);
+    Log() << Verbose(2) << "Matrix at level " << j << ":";// << filename << endl;
+    for(int k=skipcolumns;k--;)
+      lines >> filename;
+    for(int k=0;(k<ColumnCounter[MatrixNr]) && (!lines.eof());k++) {
+      lines >> Matrix[MatrixNr][j][k];
+      Log() << Verbose(1) << " " << std::setprecision(2) << Matrix[MatrixNr][j][k] << endl;
+    }
+  }
+
   return true;
 };
@@ -249 +214 @@
  * \return parsing successful
  */
-bool MatrixContainer::ParseFragmentMatrix(const char *name, const char *prefix, string suffix, int skiplines, int skipcolumns)
+bool MatrixContainer::ParseFragmentMatrix(const std::string name, const std::string prefix, std::string suffix, int skiplines, int skipcolumns)
 {
   char filename[1023];
@@ -274 +239 @@
 
   DoLog(0) && (Log() << Verbose(0) << "Parsing through each fragment and retrieving " << prefix << suffix << "." << endl);
-  delete[](Header);
-  delete[](Matrix);
-  delete[](RowCounter);
-  delete[](ColumnCounter);
-  Header = new char*[MatrixCounter + 1]; // one more each for the total molecule
-  Matrix = new double**[MatrixCounter + 1]; // one more each for the total molecule
-  RowCounter = new int[MatrixCounter + 1];
-  ColumnCounter = new int[MatrixCounter + 1];
-  for(int i=MatrixCounter+1;i--;) {
-    Matrix[i] = NULL;
-    Header[i] = NULL;
-    RowCounter[i] = -1;
-    ColumnCounter[i] = -1;
-  }
+  Header.clear();
+  Matrix.clear();
+  RowCounter.clear();
+  ColumnCounter.clear();
+  Header.resize(MatrixCounter + 1); // one more each for the total molecule
+  Matrix.resize(MatrixCounter + 1); // one more each for the total molecule
+  RowCounter.resize(MatrixCounter + 1);
+  ColumnCounter.resize(MatrixCounter + 1);
   for(int i=0; i < MatrixCounter;i++) {
     // open matrix file
@@ -312 +271 @@
  * \return Allocation successful
  */
-bool MatrixContainer::AllocateMatrix(char **GivenHeader, int MCounter, int *RCounter, int *CCounter)
+bool MatrixContainer::AllocateMatrix(StringVector GivenHeader, int MCounter, IntVector RCounter, IntVector CCounter)
 {
   MatrixCounter = MCounter;
-  Header = new char*[MatrixCounter + 1];
-  Matrix = new double**[MatrixCounter + 1]; // one more each for the total molecule
-  RowCounter = new int[MatrixCounter + 1];
-  ColumnCounter = new int[MatrixCounter + 1];
+  Header.resize(MatrixCounter + 1);
+  Matrix.resize(MatrixCounter + 1); // one more each for the total molecule
+  RowCounter.resize(MatrixCounter + 1);
+  ColumnCounter.resize(MatrixCounter + 1);
   for(int i=MatrixCounter+1;i--;) {
-    Header[i] = new char[1024];
-    strncpy(Header[i], GivenHeader[i], 1023);
+    Header[i] = GivenHeader[i];
     RowCounter[i] = RCounter[i];
     ColumnCounter[i] = CCounter[i];
-    Matrix[i] = new double*[RowCounter[i] + 1];
-    for(int j=RowCounter[i]+1;j--;) {
-      Matrix[i][j] = new double[ColumnCounter[i]];
-      for(int k=ColumnCounter[i];k--;)
-        Matrix[i][j][k] = 0.;
-    }
+    if (Matrix[i].size() <= RowCounter[i] + 2)
+      Matrix[i].resize(RowCounter[i] + 1);
+    for(int j=0;j<=RowCounter[i];j++)
+      if (Matrix[i][j].size() <= ColumnCounter[i]+1)
+        Matrix[i][j].resize(ColumnCounter[i]);
+    // allocation with 0 is guaranted by STL
   }
   return true;
@@ -396 +354 @@
  * \return true if successful
  */
-bool MatrixContainer::SetLastMatrix(double **values, int skipcolumns)
+bool MatrixContainer::SetLastMatrix(const MatrixArray &values, int skipcolumns)
 {
   for(int j=RowCounter[MatrixCounter]+1;j--;)
@@ -466 +424 @@
  * \return file was written
  */
-bool MatrixContainer::WriteTotalFragments(const char *name, const char *prefix)
+bool MatrixContainer::WriteTotalFragments(const std::string name, const std::string prefix)
 {
   ofstream output;
@@ -500 +458 @@
  * \return file was written
  */
-bool MatrixContainer::WriteLastMatrix(const char *name, const char *prefix, const char *suffix)
+bool MatrixContainer::WriteLastMatrix(const std::string name, const std::string prefix, const std::string suffix)
 {
   ofstream output;