Changeset 560bbe for src

Timestamp:

Feb 17, 2012, 3:24:18 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:

cdaae6

Parents:

ac5c36

git-author:

Frederik Heber <heber@…> (01/06/12 16:49:11)

git-committer:

Frederik Heber <heber@…> (02/17/12 15:24:18)

Message:

AtomicInfo now also (re)stores ParticleInfo::Nr, molecule has own IdPool.

• molecule now also has an internal IdPool to be able to hand out unique ids, according to uniqueId policy.
• new functions: molecule::changeAtomNr(), molecule::setAtomName()
• molecule::erase() and ::insert() release and set the id (and the name).
• molecule::setAtomName() uses getNr() with id increased by one.
• AtomicInfo stores and sets ParticleInfo::Nr.
• atom::changeNr() is similar to changeId() only for the molecule.
• molecule::AddAtom() does not set the name anymore, is done by ::insert().
• simplified molecule::doCountAtoms() a lot, no more naming of atoms.
• SPEEDUP: This speeds up the GUI already a lot.
• TESTFIX: changed regression test Tesselation/BigNonConvex due to different ordering of node ids (due to above), surface is still the same (checked).

Location:

src

Files:

• Atom/AtomicInfo.cpp (modified) (4 diffs)
• Atom/AtomicInfo.hpp (modified) (1 diff)
• Atom/atom.cpp (modified) (1 diff)
• Atom/atom.hpp (modified) (1 diff)
• documentation/constructs/molecules.dox (modified) (1 diff)
• molecule.cpp (modified) (11 diffs)
• molecule.hpp (modified) (3 diffs)

src/Atom/AtomicInfo.cpp

@@ -35 +35 @@
     FatherId(0),
     MolId(0),
-    Id(0)
+    Id(0),
+    Nr(0)
 {}
 AtomicInfo::AtomicInfo(const atom &_atom) :
@@ -43 +44 @@
     FatherId(_atom.father->getId()),
     MolId(_atom.getMolecule()->getId()),
-    Id(_atom.getId())
+    Id(_atom.getId()),
+    Nr(_atom.getNr())
 {}
 
@@ -72 +74 @@
   if (_mol != NULL)
     _atom.setMolecule(_mol); // this is ok, mol is const within AtomicInfo, but not outside (atoms need to register)
+  _atom.changeNr(Nr);
 
   return status;
@@ -90 +93 @@
   Velocity = AI.Velocity;
   Id = AI.Id;
+  Nr = AI.Nr;
   return *this;
 }

src/Atom/AtomicInfo.hpp

@@ -41 +41 @@
   moleculeId_t MolId;
   atomId_t Id;
+  int Nr;
 };
 

src/Atom/atom.cpp

@@ -322 +322 @@
 }
 
+bool atom::changeNr(const int newNr)
+{
+  if ((mol) && (mol->changeAtomNr(getNr(),newNr,this))) {
+    return true;
+  } else{
+    return false;
+  }
+}
+
 int atom::getNr() const{
   return ParticleInfo::getNr();

src/Atom/atom.hpp

@@ -211 +211 @@
     */
    void removeFromMolecule();
+
+   /** Changes the molecule internal ParticleInfo::Nr of this atom.
+    *
+    * @param newNr new ParticleInfo::Nr to set
+    * @return true - change successful, false - changed not successful, id remains the old one
+    */
+   bool changeNr(int newNr);
 
    /** Getter for ParticleInfo::Nr of the atom.

src/documentation/constructs/molecules.dox

@@ -29 +29 @@
  * as well.
  *
+ * \section molecules-atoms Atoms
+ *
+ * Atoms are added to the molecule via molecule::AddAtom() and removed via
+ * molecule::RemoveAtom(). Therein, the atom receives a unique ParticleInfo::Nr
+ * that is useful only within the molecule and is displayed in the atoms name,
+ * i.e. atom names only vary within the molecule.
+ *
+ * The molecule only stores the atoms global id and uses a boost::transform_iterator
+ * to map the ids to the true refs obtained from the World.
+ *
  * \section molecules-formula Formula
  *

src/molecule.cpp

@@ -25 +25 @@
 #include <gsl/gsl_inline.h>
 #include <gsl/gsl_heapsort.h>
+
+#include "molecule.hpp"
 
 #include "Atom/atom.hpp"
@@ -32 +34 @@
 #include "CodePatterns/Log.hpp"
 #include "config.hpp"
+#include "Descriptors/AtomIdDescriptor.hpp"
 #include "Element/element.hpp"
 #include "Element/periodentafel.hpp"
@@ -41 +44 @@
 #include "LinearAlgebra/Vector.hpp"
 #include "LinkedCell/linkedcell.hpp"
-#include "molecule.hpp"
+#include "IdPool_impl.hpp"
 #include "Tesselation/tesselation.hpp"
 #include "World.hpp"
@@ -63 +66 @@
   AtomCount(this,boost::bind(&molecule::doCountAtoms,this),"AtomCount"),
   BondCount(this,boost::bind(&molecule::doCountBonds,this),"BondCount"),
+  atomIdPool(0, 20, 100),
   last_atom(0)
 {
@@ -103 +107 @@
   cout << "Set name of molecule " << getId() << " to " << _name << endl;
   strncpy(name,_name.c_str(),MAXSTRINGSIZE);
+}
+
+bool molecule::changeAtomNr(int oldNr, int newNr, atom* target){
+  OBSERVE;
+  if(atomIdPool.reserveId(newNr)){
+    if (oldNr != -1)  // -1 is reserved and indicates no number
+      atomIdPool.releaseId(oldNr);
+    ASSERT (target,
+        "molecule::changeAtomNr() - given target is NULL, cannot set Nr or name.");
+    target->setNr(newNr);
+    setAtomName(target);
+    return true;
+  } else{
+    return false;
+  }
 }
 
@@ -197 +216 @@
     ++iter;
     atomIds.erase( key->getId() );
+    atomIdPool.releaseId(key->getNr());
+    key->setNr(-1);
     formula-=key->getType();
     key->removeFromMolecule();
@@ -213 +234 @@
   pair<atomIdSet::iterator,bool> res = atomIds.insert(key->getId());
   if (res.second) { // push atom if went well
+    key->setNr(atomIdPool.getNextId());
+    setAtomName(key);
     formula+=key->getType();
     return pair<iterator,bool>(iterator(res.first, FromIdToAtom()),res.second);
@@ -219 +242 @@
   }
 }
+
+void molecule::setAtomName(atom *_atom) const
+{
+  std::stringstream sstr;
+  sstr << _atom->getType()->getSymbol() << _atom->getNr()+1;
+  _atom->setName(sstr.str());
+}
+
 
 bool molecule::containsAtom(atom* key){
@@ -247 +278 @@
   OBSERVE;
   if (pointer != NULL) {
-    if (pointer->getType() != NULL) {
-      if (pointer->getType()->getAtomicNumber() != 1)
-        NoNonHydrogen++;
-      if(pointer->getName() == "Unknown"){
-        stringstream sstr;
-        sstr << pointer->getType()->getSymbol() << pointer->getNr()+1;
-        pointer->setName(sstr.str());
-      }
-    }
+    if (pointer->getType()->getAtomicNumber() != 1)
+      NoNonHydrogen++;
     insert(pointer);
     pointer->setMolecule(this);
@@ -1029 +1053 @@
 {
   int res = size();
-  int i = 0;
   NoNonHydrogen = 0;
-  for (molecule::iterator iter = begin(); iter != end(); ++iter) {
-    (*iter)->setNr(i);   // update number in molecule (for easier referencing in FragmentMolecule lateron)
+  // go through atoms and look for new ones
+  for (molecule::const_iterator iter = begin(); iter != end(); ++iter)
     if ((*iter)->getType()->getAtomicNumber() != 1) // count non-hydrogen atoms whilst at it
       NoNonHydrogen++;
-    stringstream sstr;
-    sstr << (*iter)->getType()->getSymbol() << (*iter)->getNr()+1;
-    (*iter)->setName(sstr.str());
-    LOG(3, "Naming atom nr. " << (*iter)->getNr() << " " << (*iter)->getName() << ".");
-    i++;
-  }
   return res;
 };
@@ -1106 +1123 @@
   ActiveFlag = !ActiveFlag;
 }
+
+// construct idpool
+CONSTRUCT_IDPOOL(atomId_t, continuousId)

src/molecule.hpp

@@ -33 +33 @@
 #include "Formula.hpp"
 #include "Helpers/defs.hpp"
+#include "IdPool_policy.hpp"
+#include "IdPool.hpp"
 #include "types.hpp"
 
@@ -97 +99 @@
   moleculeId_t id;
   atomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
+  IdPool<atomId_t, uniqueId> atomIdPool;  //!< pool of internal ids such that way may guarantee uniqueness
+
 protected:
 
@@ -150 +154 @@
    */
   const_iterator erase(atom * key);
+
+private:
+  friend bool atom::changeNr(int newId);
+  /**
+   * used when changing an ParticleInfo::Nr.
+   * Note that this number is local with this molecule.
+   * Unless you are calling this method from inside an atom don't fiddle with the third parameter.
+   *
+   * @param oldNr old Nr
+   * @param newNr new Nr to set
+   * @param *target ref to atom
+   * @return indicates wether the change could be done or not.
+   */
+  bool changeAtomNr(int oldNr, int newNr, atom* target=0);
+
+  /** Sets the name of the atom.
+   *
+   * The name is set via its element symbol and its internal ParticleInfo::Nr.
+   *
+   * @param _atom atom whose name to set
+   */
+  void setAtomName(atom *_atom) const;
 
 public: