Changeset e420f9

Timestamp:

Oct 6, 2011, 7:17:46 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:

7a0340

Parents:

d2bac9

git-author:

Frederik Heber <heber@…> (04/23/11 19:38:12)

git-committer:

Frederik Heber <heber@…> (10/06/11 07:17:46)

Message:

Added read/write capability of VectorContent from stream.

• this is all taken and adapted from MatrixContent.
• Unit test function added on this.

Location:

LinearAlgebra/src

Files:

• LinearAlgebra/VectorContent.cpp (modified) (3 diffs)
• LinearAlgebra/VectorContent.hpp (modified) (2 diffs)
• unittests/VectorContentUnitTest.cpp (modified) (1 diff)
• unittests/VectorContentUnitTest.hpp (modified) (2 diffs)

LinearAlgebra/src/LinearAlgebra/VectorContent.cpp

@@ -25 +25 @@
 #include <iostream>
 #include <limits>
+#include <vector>
 
 #include "CodePatterns/Assert.hpp"
@@ -77 +78 @@
 };
 
-/** Copy constructor of class VectorContent.
+/** Constructor that parses vector from a stream.
+ *
+ * \param _dimension size of vector
+ * \param &inputstream stream to parse from
+ */
+VectorContent::VectorContent(const size_t _dimension, std::istream &inputstream) :
+  dimension(_dimension),
+  content(NULL),
+  free_content_on_exit(true)
+{
+   // allocate vector and set contents
+  content = gsl_vector_alloc(dimension);
+
+  size_t row = 0;
+  size_t index = 0;
+  do {
+    std::string line;
+    getline(inputstream, line);
+    //std::cout << line << std::endl;
+    std::stringstream parseline(line);
+    // skip comments
+    if ((parseline.peek() == '#') || (parseline.str().empty()))
+      continue;
+    // break on empty lines
+    if (parseline.peek() == '\n')
+      break;
+
+    // parse line with values
+    std::vector<double> line_of_values;
+    do {
+      double value;
+      parseline >> value >> ws;
+      line_of_values.push_back(value);
+    } while (parseline.good());
+
+    // check number of columns parsed
+    ASSERT(line_of_values.size()+index <= dimension,
+        "VectorContent::VectorContent() - exceedingly many entries in row "
+        +toString(row)+": current number is "
+        +toString(index)+" and expecting now "
+        +toString(line_of_values.size())+" which exceeds "+toString(dimension)+".");
+
+    for (std::vector<double>::const_iterator iter = line_of_values.begin();
+        iter != line_of_values.end();++iter, ++index)
+      at(index) = *iter;
+    ++row;
+  } while (inputstream.good());
+  // check number of rows parsed
+  ASSERT(index == dimension,
+      "VectorContent::VectorContent() - insufficent number of components "
+      +toString(index)+" < "+toString(dimension)+" read.");
+}
+
+
+/** Constructor of class VectorContent.
  * No allocation, we just take over gsl_vector.
  * \param *src source gsl_vector
@@ -463 +518 @@
 }
 
+/** Preparses a vector in an input stream for component count.
+ *
+ *  \note This does not change the get position within the stream.
+ *
+ * @param inputstream to parse vector from
+ * @return number of present entries
+ */
+size_t VectorContent::preparseVectorDimensions(std::istream &inputstream)
+{
+  const std::streampos initial_position(inputstream.tellg());
+//  std::cout << "We are at position "
+//      +toString((int)inputstream.tellg())+" from start of stream." << std::endl;
+  size_t index = 0;
+  do {
+    std::string line;
+    getline(inputstream, line);
+    std::stringstream parseline(line);
+    // skip comments
+    if ((parseline.peek() == '#') || (line.empty()))
+      continue;
+    // break on empty lines
+    if (parseline.peek() == '\n')
+      break;
+
+    // parse line with values
+    std::vector<double> line_of_values;
+    do {
+      double value;
+      parseline >> value >> ws;
+      line_of_values.push_back(value);
+    } while (parseline.good());
+
+    index += line_of_values.size();
+  } while (inputstream.good());
+  // clear end of file flags
+  inputstream.clear();
+
+  // reset to initial position
+  inputstream.seekg(initial_position);
+//  std::cout << "We are again at position "
+//      +toString((int)inputstream.tellg())+" from start of stream." << std::endl;
+
+  return index;
+}
+
+/** Writes vector content to ostream in such a manner that it can be re-parsed
+ * by the code in the constructor.
+ *
+ * @param ost stream to write to
+ */
+void VectorContent::write(std::ostream &ost) const
+{
+  for (size_t index = 0; index < dimension; ++index)
+    ost << at(index) << "\t";
+  ost << std::endl;
+}
+
+
 /* ======================== Properties ============================= */
 /** Calculates scalar product between \a *this and \a b.

LinearAlgebra/src/LinearAlgebra/VectorContent.hpp

@@ -55 +55 @@
   VectorContent(const VectorContent & src);
   VectorContent(gsl_vector * _src, bool _free_content_on_exit = false);
+  VectorContent(const size_t _dimension, std::istream &inputstream);
   virtual ~VectorContent();
 
@@ -107 +108 @@
   const size_t getDimension() const;
 
+  static size_t preparseVectorDimensions(std::istream &inputstream);
+  void write(std::ostream &ost) const;
+
   size_t dimension;
   gsl_vector *content;

LinearAlgebra/src/unittests/VectorContentUnitTest.cpp

@@ -175 +175 @@
   CPPUNIT_ASSERT_EQUAL( true, unit.IsOne() );
 };
+
+/** Unit test for reading from and writing vector to stream
+ *
+ */
+void VectorContentTest::ReadWriteTest()
+{
+  // set up matrix
+  VectorContent v((size_t)3);
+  for (size_t i=0; i<3;++i)
+    v.at(i) = i+1.;
+
+  // write to stream
+  std::stringstream vectorstream;
+  v.write(vectorstream);
+
+  // parse in dimensions and check
+  size_t vectordimension = VectorContent::preparseVectorDimensions(vectorstream);
+  CPPUNIT_ASSERT_EQUAL( (size_t)3, vectordimension );
+  // parse in vector and check
+  VectorContent w(3, vectorstream);
+  CPPUNIT_ASSERT_EQUAL( v, w );
+}

LinearAlgebra/src/unittests/VectorContentUnitTest.hpp

@@ -30 +30 @@
     CPPUNIT_TEST (OperatorAlgebraTest );
     CPPUNIT_TEST (OperatorIsTest );
+    CPPUNIT_TEST (ReadWriteTest );
     CPPUNIT_TEST_SUITE_END();
 
@@ -42 +43 @@
     void OperatorIsTest();
     void OperatorAlgebraTest();
+    void ReadWriteTest();
 
 private: