Changeset 16876c for src/Parameters/StreamOperators.hpp

Timestamp:

Jun 13, 2012, 5:38:39 PM (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:

bf72ec

Parents:

7b1a19

git-author:

Frederik Heber <heber@…> (05/31/12 13:24:04)

git-committer:

Frederik Heber <heber@…> (06/13/12 17:38:39)

Message:

Implemented all stream operator >> functions in StreamOperators.hpp.

• also added operators for const atom* and vector<const atom *>.

File:

• src/Parameters/StreamOperators.hpp (modified) (9 diffs)

src/Parameters/StreamOperators.hpp

@@ -3 +3 @@
  *
  *  Created on: Apr 16, 2012
- *      Author: ankele
+ *      Author: ankele, heber
  */
 
 #ifndef STREAMOPERATORS_HPP_
 #define STREAMOPERATORS_HPP_
-
-
-
 
 // include config.h
@@ -17 +14 @@
 #endif
 
+#include <boost/tokenizer.hpp>
 #include <string>
+#include <sstream>
 #include <iosfwd>
 
@@ -23 +22 @@
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "Box.hpp"
-#include "Element/element.hpp"
-#include "molecule.hpp"
+#include "Descriptors/AtomIdDescriptor.hpp"
+#include "Descriptors/MoleculeIdDescriptor.hpp"
+#include "Element/periodentafel.hpp"
+#include "World.hpp"
 
 #include "CodePatterns/Assert.hpp"
 
-class Vector;
-class Box;
-class RealSpaceMatrix;
+class atom;
+class element;
 class molecule;
-class element;
-
-inline std::istream& operator>>(std::istream& ist, Vector& m)
-{
-
+
+/** Returns a single line from \a ist without leading and ending brackets.
+ *
+ * @param ist stream to get line from
+ * @return line as string without ()
+ */
+inline std::string getLine(std::istream& ist)
+{
   std::string line;
   getline(ist,line);
@@ -44 +47 @@
   if (!line.empty() && line[line.size() - 1] == ')')
     line.erase(line.size() - 1, 1);
-  Vector temp_vector;
-
-  // dissect by ","
-  double coord = 0.;
-  int counter = 0;
-  std::string::iterator olditer = line.begin();
-  for(std::string::iterator iter = line.begin(); (iter != line.end()) && (counter != 3); ++iter) {
-    if ((*iter == ',') || (*iter == ' ')) {
-      std::istringstream stream(std::string(olditer, iter));
-
-      stream >> coord;
-
-      temp_vector[counter++] = coord;
-
-      olditer = iter + 1;
-    }
-  }
-  if ((olditer != line.begin()) && (counter != 3)) { // insert last part also
-
-    std::istringstream stream(std::string(olditer, line.end()));
-    stream >> coord;
-    temp_vector[counter++] = coord;
-  }
-  m = temp_vector;
+
+  return line;
+}
+
+inline std::istream& operator>>(std::istream& ist, Vector& m)
+{
+  std::string line = getLine(ist);
+
+  // dissect by " " or ","
+  ConvertTo<double> converter;
+  std::vector<double> temp_vector;
+  boost::char_separator<char> sep(", ");
+  boost::tokenizer<boost::char_separator<char> > tok(line, sep);
+  for(boost::tokenizer<boost::char_separator<char> >::const_iterator iter = tok.begin();
+      iter != tok.end(); ++iter)
+    temp_vector.push_back(converter(*iter));
+  ASSERT (temp_vector.size() == (size_t)NDIM,
+      "operator>>(std::istream& ist, Vector& m) - not "+toString((size_t)NDIM)+" but "
+      +toString(temp_vector.size())+" components given.");
+  for (size_t i=0;i<NDIM;++i)
+    m[i] = temp_vector[i];
   return ist;
 };
@@ -73 +73 @@
 inline std::istream& operator>>(std::istream& ist, RealSpaceMatrix& m)
 {
-
-  std::string line;
-  getline(ist,line);
-
-  if (!line.empty() && line[0] == '(')
-    line.erase(0, 1);
-  if (!line.empty() && line[line.size() - 1] == ')')
-    line.erase(line.size() - 1, 1);
-  double temp[6];
-
-  // dissect by ","
-  double coord = 0.;
-  int counter = 0;
-  std::string::iterator olditer = line.begin();
-  for(std::string::iterator iter = line.begin(); (iter != line.end()) && (counter != 6); ++iter) {
-    if ((*iter == ',') || (*iter == ' ')) {
-      std::istringstream stream(std::string(olditer, iter));
-
-      stream >> coord;
-
-      temp[counter++] = coord;
-
-      olditer = iter + 1;
-    }
-  }
-  if ((olditer != line.begin()) && (counter != 6)) { // insert last part also
-
-    std::istringstream stream(std::string(olditer, line.end()));
-    stream >> coord;
-    temp[counter++] = coord;
-  }
-  m.set(0,0, temp[0]);
-  m.set(0,1, temp[1]);
-  m.set(0,2, temp[2]);
-  m.set(1,0, temp[1]);
-  m.set(1,1, temp[3]);
-  m.set(1,2, temp[4]);
-  m.set(2,0, temp[2]);
-  m.set(2,1, temp[4]);
-  m.set(2,2, temp[5]);
+  std::string line = getLine(ist);
+
+  // dissect by " " or ","
+  ConvertTo<double> converter;
+  std::vector<double> temp_vector;
+  boost::char_separator<char> sep(", ");
+  boost::tokenizer<boost::char_separator<char> > tok(line, sep);
+  for(boost::tokenizer<boost::char_separator<char> >::const_iterator iter = tok.begin();
+      iter != tok.end(); ++iter)
+    temp_vector.push_back(converter(*iter));
+  ASSERT (temp_vector.size() == (size_t)NDIM*(NDIM+1)/2,
+      "operator>>(std::istream& ist, RealSpaceMatrix& m) - not "+toString((size_t)NDIM*((size_t)NDIM+1)/2)+" but "
+      +toString(temp_vector.size())+" components given.");
+  m.set(0,0, temp_vector[0]);
+  m.set(0,1, temp_vector[1]);
+  m.set(0,2, temp_vector[2]);
+  m.set(1,0, temp_vector[1]);
+  m.set(1,1, temp_vector[3]);
+  m.set(1,2, temp_vector[4]);
+  m.set(2,0, temp_vector[2]);
+  m.set(2,1, temp_vector[4]);
+  m.set(2,2, temp_vector[5]);
   return ist;
 };
@@ -125 +107 @@
 
 
+inline std::istream& operator>>(std::istream& ist, const atom* & m)
+{
+  std::string line = getLine(ist);
+
+  ConvertTo<unsigned int> converter;
+  const atomId_t temp_value = converter(line);
+  const atom *a = World::getInstance().getAtom(AtomById(temp_value));
+  ASSERT( a != NULL,
+      "operator>>(std::istream& ist, const atom* & m) - atom molecule id "
+      +toString(temp_value)+".");
+  m = a;
+  return ist;
+}
+
 inline std::istream& operator>>(std::istream& ist, const molecule* & m)
 {
-  std::cout << "===============   operator >> (istream, const element *) not implemented!\n";
-  ASSERT(0, "operator >> (istream, const element *) not implemented!");
+  std::string line = getLine(ist);
+
+  ConvertTo<unsigned int> converter;
+  const moleculeId_t temp_value = converter(line);
+  const molecule *mol = World::getInstance().getMolecule(MoleculeById(temp_value));
+  ASSERT( mol != NULL,
+      "operator>>(std::istream& ist, const molecule* & m) - invalid molecule id "
+      +toString(temp_value)+".");
+  m = mol;
   return ist;
 }
@@ -135 +138 @@
 inline std::istream& operator>>(std::istream& ist, const element* & m)
 {
-  std::cout << "===============   operator >> (istream, const element *) not implemented!\n";
-  ASSERT(0, "operator >> (istream, const element *) not implemented!");
+  std::string line = getLine(ist);
+
+  ConvertTo<unsigned int> converter;
+  const atomicNumber_t temp_value = converter(line);
+  const element *elem = World::getInstance().getPeriode()->FindElement(temp_value);
+  ASSERT( elem != NULL,
+      "operator>>(std::istream& ist, const element* & m) - invalid atomic number "
+      +toString(temp_value)+".");
+  m = elem;
   return ist;
 }
@@ -143 +153 @@
 inline std::istream& operator>>(std::istream& ist, std::vector<const molecule*> & m)
 {
-  std::cout << "===============   operator >> (istream, std::vector<const element *>) not implemented!\n";
-  ASSERT(0, "operator >> (istream, std::vector<const element *>) not implemented!");
-  return ist;
-}
-
+  std::string line = getLine(ist);
+
+  // dissect by " " or ","
+  boost::char_separator<char> sep(", ");
+  boost::tokenizer<boost::char_separator<char> > tok(line, sep);
+  ConvertTo<unsigned int> converter;
+  for(boost::tokenizer<boost::char_separator<char> >::const_iterator iter = tok.begin();
+      iter != tok.end(); ++iter) {
+    const moleculeId_t temp_value = converter(*iter);
+    const molecule *mol = World::getInstance().getMolecule(MoleculeById(temp_value));
+    ASSERT( mol != NULL,
+        "operator>>(std::istream& ist, std::vector<const molecule*> & m) - invalid molecule id "
+        +toString(temp_value)+".");
+    m.push_back(mol);
+  }
+  return ist;
+}
+
+
+inline std::istream& operator>>(std::istream& ist, std::vector<const atom*> & m)
+{
+  std::string line = getLine(ist);
+
+  // dissect by " " or ","
+  boost::char_separator<char> sep(", ");
+  boost::tokenizer<boost::char_separator<char> > tok(line, sep);
+  ConvertTo<unsigned int> converter;
+  for(boost::tokenizer<boost::char_separator<char> >::const_iterator iter = tok.begin();
+      iter != tok.end(); ++iter) {
+    const atomId_t temp_value = converter(line);
+    const atom *a = World::getInstance().getAtom(AtomById(temp_value));
+    ASSERT( a != NULL,
+        "operator>>(std::istream& ist, std::vector<const atom*> & m) - invalid atom id "
+        +toString(temp_value)+".");
+    m.push_back(a);
+  }
+  return ist;
+}
 
 inline std::istream& operator>>(std::istream& ist, std::vector<const element*> & m)
 {
-  std::cout << "===============   operator >> (istream, std::vector<const element *>) not implemented!\n";
-  ASSERT(0, "operator >> (istream, std::vector<const element *>) not implemented!");
+  std::string line = getLine(ist);
+
+  // dissect by " " or ","
+  boost::char_separator<char> sep(", ");
+  boost::tokenizer<boost::char_separator<char> > tok(line, sep);
+  ConvertTo<unsigned int> converter;
+  for(boost::tokenizer<boost::char_separator<char> >::const_iterator iter = tok.begin();
+      iter != tok.end(); ++iter) {
+    const atomicNumber_t temp_value = converter(*iter);
+    const element *elem = World::getInstance().getPeriode()->FindElement(temp_value);
+    ASSERT( elem != NULL,
+        "operator>>(std::istream& ist, std::vector<const element*> & m) - invalid atomic number "
+        +toString(temp_value)+".");
+    m.push_back(elem);
+  }
   return ist;
 }
@@ -159 +215 @@
 inline std::istream& operator>>(std::istream& ist, std::vector<std::string> & m)
 {
-  std::cout << "===============   operator >> (istream, std::vector<std::string>) not implemented!\n";
-  ASSERT(0, "operator >> (istream, std::vector<std::string>) not implemented!");
+  std::string line = getLine(ist);
+
+  // dissect by " " or ","
+  boost::char_separator<char> sep(", ");
+  boost::tokenizer<boost::char_separator<char> > tok(line, sep);
+  for(boost::tokenizer<boost::char_separator<char> >::const_iterator iter = tok.begin();
+      iter != tok.end(); ++iter)
+    m.push_back(*iter);
+  return ist;
+}
+
+inline std::istream& operator>>(std::istream& ist, std::vector<unsigned int> & m)
+{
+  std::string line = getLine(ist);
+
+  // dissect by " " or ","
+  boost::char_separator<char> sep(", ");
+  boost::tokenizer<boost::char_separator<char> > tok(line, sep);
+  ConvertTo<unsigned int> converter;
+  for(boost::tokenizer<boost::char_separator<char> >::const_iterator iter = tok.begin();
+      iter != tok.end(); ++iter)
+    m.push_back(converter(*iter));
   return ist;
 }