Changeset 560bbe for src/molecule.cpp

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).

File:

• src/molecule.cpp (modified) (11 diffs)

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)