Changeset a2d653

Timestamp:

Jul 2, 2012, 7:54:12 AM (13 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:

e11611

Parents:

d7bb9b1

git-author:

Frederik Heber <heber@…> (04/19/12 18:22:48)

git-committer:

Frederik Heber <heber@…> (07/02/12 07:54:12)

Message:

Added MatrixContainer::AddMatrix() which takes of the functionality of ::ParseMatrix().

• AddMatrix simply adds a received MatrixArray to the internal matrix. Also, we restructured the function a bit: check preconditions, allocate, then set.
• ParseMatrix() creates first such a MatrixArray which it parses from a file.

Location:

src/Fragmentation

Files:

• MatrixContainer.cpp (modified) (5 diffs)
• MatrixContainer.hpp (modified) (1 diff)

src/Fragmentation/MatrixContainer.cpp

@@ -88 +88 @@
  *    -# scan header lines for number of columns
  *    -# scan lines for number of rows
- *    -# allocate matrix
+ *    -# allocate a temporary matrix
  *    -# loop over found column and row counts and parse in each entry
+ *    -# use MatrixContainer::AddMatrix() to add the parsed matrix to the internal
  * \param &input input stream
  * \param skiplines number of inital lines to skip
@@ -109 +110 @@
 
   // parse header
-  if (Header.size() <= MatrixNr)
-    Header.resize(MatrixNr);
-  Header[MatrixNr] = std::string("");
+  std::string header;
   char dummy[1024];
   for (int m=skiplines+1;m--;)
@@ -117 +116 @@
   line.str(dummy);
   for(int k=skipcolumns;k--;)
-    line >> Header[MatrixNr];
+    line >> header;
   LOG(3, "INFO: Header of Matrix " << MatrixNr << " :" << line.str());
 
   // scan header for number of columns
-  if (ColumnCounter.size() <= MatrixNr)
-    ColumnCounter.resize(MatrixNr);
-  ColumnCounter[MatrixNr]=0;
+  size_t ColumnCounter = 0;
   while ( getline(line,token, '\t') ) {
     if (token.length() > 0)
-      ColumnCounter[MatrixNr]++;
+      ColumnCounter++;
   }
   LOG(3, "INFO: "+line.str());
-  LOG(4, "INFO: ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << ".");
-  if (ColumnCounter[MatrixNr] == 0) {
-    ELOG(0, "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << " from ostream.");
-    performCriticalExit();
-  }
 
   // scan rest for number of rows/lines
-  if (RowCounter.size() <= MatrixNr)
-    RowCounter.resize(MatrixNr);
-  RowCounter[MatrixNr]=-1;    // counts one line too much
+  size_t RowCounter = -1;
   while (!input.eof()) {
     input.getline(filename, 1023);
     LOG(3, "INFO: Comparing: " << strncmp(filename,"MeanForce",9));
-    RowCounter[MatrixNr]++; // then line was not last MeanForce
+    RowCounter++; // then line was not last MeanForce
     if (strncmp(filename,"MeanForce", 9) == 0) {
       break;
     }
   }
-  LOG(4, "INFO: RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from input stream.");
-  if (RowCounter[MatrixNr] == 0) {
-    ELOG(0, "INFO: RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from input stream.");
-    performCriticalExit();
-  }
-
-  // allocate matrix if it's not zero dimension in one direction
-  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;
-    }
-  } else {
-    ELOG(1, "Matrix nr. " << MatrixNr << " has column and row count of (" << ColumnCounter[MatrixNr] << "," << RowCounter[MatrixNr] << "), could not allocate nor parse!");
-    return false;
-  }
+
+  // allocate temporary matrix
+  MatrixArray temp_matrix;
+  temp_matrix.resize(RowCounter);
+  for(MatrixArray::iterator iter = temp_matrix.begin(); iter != temp_matrix.end(); ++iter)
+    (*iter).resize(ColumnCounter);
 
   // parse in each entry for this matrix
@@ -179 +153 @@
   for(int k=skipcolumns;k--;)  // skip columns in header too
     line >> filename;
-  Header[MatrixNr] = line.str();
-  for(int j=0;j<RowCounter[MatrixNr];j++) {
+  header = line.str();
+  for(size_t j=0;j<RowCounter;j++) {
     input.getline(filename, 1023);
     std::stringstream lines(filename);
@@ -187 +161 @@
     for(int k=skipcolumns;k--;)
       lines >> filename;
-    for(int k=0;(k<ColumnCounter[MatrixNr]) && (!lines.eof());k++) {
-      lines >> Matrix[MatrixNr][j][k];
-      output << " " << std::setprecision(2) << Matrix[MatrixNr][j][k] << endl;
+    for(size_t k=0;(k<ColumnCounter) && (!lines.eof());k++) {
+      lines >> temp_matrix[j][k];
+      output << " " << std::setprecision(2) << temp_matrix[j][k] << endl;
     }
     LOG(3, output.str());
   }
 
-  return true;
-};
+  // finally add the matrix
+  return AddMatrix(header, temp_matrix, MatrixNr);
+}
+
+/** Adds a matrix at position \a MatrixNr to MatrixContainer::Matrix.
+ *
+ * @param header header to add for this matrix
+ * @param matrix to add
+ * @param MatrixNr position in MatrixContainer::Matrix.
+ * @return true - insertion ok, false - invalid matrix
+ */
+bool MatrixContainer::AddMatrix(const std::string &header, const MatrixArray &matrix, size_t MatrixNr)
+{
+  // make some pre-checks
+  if (header.size() == 0)
+    ELOG(2, "The given header of the matrix to add is empty.");
+  if (matrix.size() == 0) {
+    ELOG(1, "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from input stream.");
+    return false;
+  }
+  if (matrix[0].size() == 0) {
+    ELOG(1, "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << " from ostream.");
+    return false;
+  }
+
+  // add header
+  if (Header.size() <= MatrixNr)
+    Header.resize(MatrixNr+1);
+  Header[MatrixNr] = header;
+
+  // row count
+  if (RowCounter.size() <= MatrixNr)
+    RowCounter.resize(MatrixNr+1);
+  RowCounter[MatrixNr] = matrix.size();
+  LOG(4, "INFO: RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from input stream.");
+
+  // column count
+  if (ColumnCounter.size() <= MatrixNr)
+    ColumnCounter.resize(MatrixNr+1);
+  ColumnCounter[MatrixNr] = matrix[0].size();
+  LOG(4, "INFO: ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << ".");
+
+  // allocate matrix ...
+  if (Matrix.size() <= MatrixNr)
+    Matrix.resize(MatrixNr+1);
+  MatrixCounter = Matrix.size()-1;
+  Matrix[MatrixNr].resize(RowCounter[MatrixNr] + 1);
+  for(int j=0;j<=RowCounter[MatrixNr];++j)
+    Matrix[MatrixNr][j].resize(ColumnCounter[MatrixNr]+1);
+
+  // .. and copy values
+  for(int j=0;j<RowCounter[MatrixNr];++j)
+    for(int k=0;k<ColumnCounter[MatrixNr];++k)
+      Matrix[MatrixNr][j][k] = matrix[j][k];
+  // reset last column
+  for(int j=0;j<RowCounter[MatrixNr];++j)
+    Matrix[MatrixNr][j][ ColumnCounter[MatrixNr] ] = 0.;
+  // reset last row
+  for(int k=0;k<=ColumnCounter[MatrixNr];++k)
+    Matrix[MatrixNr][ RowCounter[MatrixNr] ][ k ] = 0.;
+
+  return true;
+}
 
 /** Parsing a number of matrices.

src/Fragmentation/MatrixContainer.hpp

@@ -41 +41 @@
   bool InitialiseIndices(class MatrixContainer *Matrix = NULL);
   bool ParseMatrix(std::istream &input, int skiplines, int skipcolumns, size_t MatrixNr);
+  bool AddMatrix(const std::string &header, const MatrixArray &matrix, 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);