Changeset a58c16 for src/Parser

Timestamp:

Jul 24, 2015, 4:44:35 PM (9 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:

99db9b

Parents:

f01769

git-author:

Frederik Heber <heber@…> (06/01/15 19:16:02)

git-committer:

Frederik Heber <heber@…> (07/24/15 16:44:35)

Message:

Replaced World::getAllAtoms() by const version where possible.

Location:

src/Parser

Files:

• MpqcParser.cpp (modified) (1 diff)
• PdbParser.cpp (modified) (3 diffs)
• XmlParser.cpp (modified) (1 diff)
• XyzParser.cpp (modified) (1 diff)
• unittests/ParserPsi3UnitTest.cpp (modified) (1 diff)
• unittests/ParserXyzUnitTest.cpp (modified) (2 diffs)

src/Parser/MpqcParser.cpp

@@ -294 +294 @@
 {
   Vector center;
-//  vector<atom *> allatoms = World::getInstance().getAllAtoms();
+//  vector<const atom *> allatoms = const_cast<const World &>(World::getInstance()).
+//      getAllAtoms();
 
   // calculate center
-//  for (std::vector<atom *>::const_iterator runner = atoms.begin();runner != atoms.end(); ++runner)
+//  for (std::vector<const atom *>::const_iterator runner = atoms.begin();runner != atoms.end(); ++runner)
 //    center += (*runner)->getPosition();
 //  center.Scale(1./(double)atoms.size());

src/Parser/PdbParser.cpp

@@ -200 +200 @@
   // check for maximum number of time steps
   size_t max_timesteps = 0;
-  BOOST_FOREACH(atom *_atom, World::getInstance().getAllAtoms()) {
-    LOG(4, "INFO: Atom " << _atom->getName() << " " << *dynamic_cast<AtomInfo *>(_atom) << ".");
+  BOOST_FOREACH(const atom * _atom, const_cast<const World &>(World::getInstance()).getAllAtoms()) {
+    LOG(4, "INFO: Atom " << _atom->getName() << " " << *dynamic_cast<const AtomInfo *>(_atom) << ".");
     if (_atom->getTrajectorySize() > max_timesteps)
       max_timesteps = _atom->getTrajectorySize();
@@ -546 +546 @@
     newAtom = World::getInstance().getAtom(AtomById(AtomID_global));
     LOG(5, "INFO: Listing all present atoms with id.");
-    BOOST_FOREACH(atom *_atom, World::getInstance().getAllAtoms())
+    BOOST_FOREACH(const atom *_atom, const_cast<const World &>(World::getInstance()).getAllAtoms())
       LOG(5, "INFO: " << *_atom << " with id " << _atom->getId());
   }
@@ -842 +842 @@
 {
   bool status = true;
-  World::AtomComposite atoms = World::getInstance().getAllAtoms();
-  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  World::ConstAtomComposite atoms = const_cast<const World &>(World::getInstance()).
+      getAllAtoms();
+  for (World::ConstAtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     if ((additionalAtomData.find((*iter)->getId()) != additionalAtomData.end())
         && (b.additionalAtomData.find((*iter)->getId()) != b.additionalAtomData.end())) {

src/Parser/XmlParser.cpp

@@ -202 +202 @@
   }
 
-  BOOST_FOREACH(atom *_atom, World::getInstance().getAllAtoms())
-    LOG(3, "INFO: Atom " << _atom->getName() << " " << *dynamic_cast<AtomInfo *>(_atom) << ".");
+  BOOST_FOREACH(const atom *_atom, const_cast<const World &>(World::getInstance()).getAllAtoms())
+    LOG(3, "INFO: Atom " << _atom->getName() << " " << *dynamic_cast<const AtomInfo *>(_atom) << ".");
 
   // refresh atom::nr and atom::name

src/Parser/XyzParser.cpp

@@ -143 +143 @@
     ++step;
   }
-  BOOST_FOREACH(atom *_atom, World::getInstance().getAllAtoms())
-    LOG(3, "INFO: Atom " << _atom->getName() << " " << *dynamic_cast<AtomInfo *>(_atom) << ".");
+  BOOST_FOREACH(const atom *_atom, const_cast<const World &>(World::getInstance()).getAllAtoms())
+    LOG(3, "INFO: Atom " << _atom->getName() << " " << *dynamic_cast<const AtomInfo *>(_atom) << ".");
 
   // refresh atom::nr and atom::name

src/Parser/unittests/ParserPsi3UnitTest.cpp

@@ -303 +303 @@
   // check that positions are right
   Vector PositionSum;
-  std::vector<atom *> atoms = World::getInstance().getAllAtoms();
-  for (std::vector<atom *>::const_iterator iter = atoms.begin();
+  std::vector<const atom *> atoms = const_cast<const World &>(World::getInstance()).
+      getAllAtoms();
+  for (std::vector<const atom *>::const_iterator iter = atoms.begin();
       iter != atoms.end();
       ++iter)

src/Parser/unittests/ParserXyzUnitTest.cpp

@@ -143 +143 @@
 
   // 3 not 6 atoms!
-  CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
+  CPPUNIT_ASSERT_EQUAL(3, const_cast<const World &>(World::getInstance()).numAtoms());
 
   // check for trajectory size
-  BOOST_FOREACH (atom *_atom, World::getInstance().getAllAtoms())
+  BOOST_FOREACH (const atom *_atom, const_cast<const World &>(World::getInstance()).getAllAtoms())
     CPPUNIT_ASSERT_EQUAL((size_t) 2, _atom->getTrajectorySize());
 }
@@ -172 +172 @@
 
   // check for trajectory size of all 6! atoms
-  BOOST_FOREACH (atom *_atom, World::getInstance().getAllAtoms())
+  BOOST_FOREACH (const atom *_atom, const_cast<const World &>(World::getInstance()).getAllAtoms())
     CPPUNIT_ASSERT_EQUAL((size_t) 2, _atom->getTrajectorySize());
 
   // check every atom
-  std::vector<atom *> atoms = World::getInstance().getAllAtoms();
-  std::vector<atom *>::const_iterator firstiter = atoms.begin();
-  std::vector<atom *>::const_iterator seconditer = atoms.begin();
+  std::vector<const atom *> atoms = const_cast<const World &>(World::getInstance()).
+      getAllAtoms();
+  std::vector<const atom *>::const_iterator firstiter = atoms.begin();
+  std::vector<const atom *>::const_iterator seconditer = atoms.begin();
   for (size_t i=0;i<3;i++)
     ++seconditer;