Changeset f16a4b

Timestamp:

Feb 25, 2010, 10:18:50 AM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

0e2a47

Parents:

02ee15

Message:

Added Descriptor that allows querying of atoms by their type

Location:

src

Files:

• Descriptors/AtomDescriptor_impl.hpp (modified) (2 diffs)
• Descriptors/AtomIdDescriptor.cpp (modified) (3 diffs)
• Descriptors/AtomIdDescriptor_impl.hpp (modified) (2 diffs)
• Descriptors/AtomTypeDescriptor.cpp (added)
• Descriptors/AtomTypeDescriptor.hpp (added)
• Descriptors/AtomTypeDescriptor_impl.hpp (added)
• Legacy/oldmenu.cpp (modified) (1 diff)
• Makefile.am (modified) (1 diff)
• atom_atominfo.cpp (modified) (2 diffs)
• atom_atominfo.hpp (modified) (1 diff)

src/Descriptors/AtomDescriptor_impl.hpp

@@ +1 @@
+#ifndef ATOMDESCRIPTOR_IMPL_HPP
+#define ATOMDESCRIPTOR_IMPL_HPP
+
 /************************ Declarations of implementation Objects ************************/
 
@@ -70 +73 @@
   AtomDescriptor::impl_ptr arg;
 };
+
+#endif //ATOMDESCRIPTOR_IMPL_HPP

src/Descriptors/AtomIdDescriptor.cpp

@@ -22 +22 @@
 
 bool AtomIdDescriptor_impl::predicate(std::pair<int,atom*> atom) {
-  return atom.second->getId()==id;
+  return atom.first==id;
 }
 
@@ -29 +29 @@
 }
 
-#if 0
-
-// so far the lookuptable for Atoms-by-id does not work, since atoms don't get an ID upon creation.
-// instead of this we rely on walking through all atoms.
-
-atom *AtomIdDescriptor::find(){
+atom *AtomIdDescriptor_impl::find(){
   map<int,atom*> atoms = getAtoms();
   map<int,atom*>::iterator res = atoms.find(id);
@@ -40 +35 @@
 }
 
-vector<atom*> AtomIdDescriptor::findAll(){
+vector<atom*> AtomIdDescriptor_impl::findAll(){
   atom *res = find();
   return (res)?(vector<atom*>(1,res)):(vector<atom*>());
 }
-
-#endif

src/Descriptors/AtomIdDescriptor_impl.hpp

@@ +1 @@
+#ifndef ATOMIDDESCRIPTOR_IMPL_HPP
+#define ATOMIDDESCRIPTOR_IMPL_HPP
+
 #include "Descriptors/AtomDescriptor_impl.hpp"
 
@@ -10 +13 @@
 
 protected:
-#if 0
-  atom *find();
-  std::vector<atom*> findAll();
-#endif
+  virtual atom *find();
+  virtual std::vector<atom*> findAll();
 private:
   int id;
 };
+
+#endif //ATOMIDDESCRIPTOR_IMPL_HPP

src/Legacy/oldmenu.cpp

@@ -737 +737 @@
         Log() << Verbose(0) << "New element by atomic number Z: ";
         cin >> Z;
-        first->type = periode->FindElement(Z);
+        first->setType(Z);
         Log() << Verbose(0) << "Atom " << first->nr << "'s element is " << first->type->name << "." << endl;
       }

src/Makefile.am

@@ -29 +29 @@
 LEGACYHEADER = Legacy/oldmenu.hpp
 
-DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp Descriptors/AtomIdDescriptor.cpp
-DESCRIPTORHEADER = Descriptors/AtomDescriptor.hpp Descriptors/AtomIdDescriptor.hpp
+DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp Descriptors/AtomIdDescriptor.cpp Descriptors/AtomTypeDescriptor.cpp
+DESCRIPTORHEADER = Descriptors/AtomDescriptor.hpp Descriptors/AtomIdDescriptor.hpp Descriptors/AtomTypeDescriptor.hpp
 
 SOURCE = ${ANALYSISSOURCE} ${ATOMSOURCE} ${PATTERNSOURCE} ${UISOURCE} ${DESCRIPTORSOURCE} ${LEGACYSOURCE} bond.cpp bondgraph.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp errorlogger.cpp graph.cpp helpers.cpp info.cpp leastsquaremin.cpp linkedcell.cpp lists.cpp log.cpp logger.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp World.cpp 

src/atom_atominfo.cpp

@@ -6 +6 @@
  */
 
+#include "periodentafel.hpp"
+#include "World.hpp"
 #include "atom_atominfo.hpp"
 
@@ -18 +20 @@
 };
 
+element *AtomInfo::getType(){
+  return type;
+}
+
+void AtomInfo::setType(element* _type) {
+  type = _type;
+}
+
+void AtomInfo::setType(int Z) {
+  element *elem = World::get()->getPeriode()->FindElement(Z);
+  setType(elem);
+}

src/atom_atominfo.hpp

@@ -37 +37 @@
   ~AtomInfo();
 
+  element *getType();
+  void setType(element *);
+  void setType(int);
+
 private:
 };