Changeset 5309ba for src/molecule_fragmentation.cpp

Timestamp:

Mar 1, 2011, 10:16:39 AM (14 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:

f71baf

Parents:

735b1c

git-author:

Frederik Heber <heber@…> (02/22/11 09:59:11)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:39)

Message:

Renamed ParticleInfo_nr back to Nr.

• Note that this mostly affected comments.

File:

• src/molecule_fragmentation.cpp (modified) (9 diffs)

src/molecule_fragmentation.cpp

@@ -351 +351 @@
 
   if (CountLinesinFile(InputFile) > 0) {
-    // each line represents a fragment root (Atom::ParticleInfo_nr) id and its energy contribution
+    // each line represents a fragment root (Atom::Nr) id and its energy contribution
     InputFile.getline(buffer, MAXSTRINGSIZE); // skip comment lines
     InputFile.getline(buffer, MAXSTRINGSIZE);
@@ -411 +411 @@
  * Picks a given number of highest values and set *AtomMask to true.
  * \param *out output stream for debugging
- * \param *AtomMask defines true/false per global Atom::ParticleInfo_nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
+ * \param *AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
  * \param FinalRootCandidates list candidates to check
  * \param Order desired order
@@ -437 +437 @@
 /** print atom mask for debugging.
  * \param *out output stream for debugging
- * \param *AtomMask defines true/false per global Atom::ParticleInfo_nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
+ * \param *AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
  * \param AtomCount number of entries in \a *AtomMask
  */
@@ -453 +453 @@
 
 /** Checks whether the OrderAtSite is still below \a Order at some site.
- * \param *AtomMask defines true/false per global Atom::ParticleInfo_nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
+ * \param *AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
  * \param *GlobalKeySetList list of keysets with global ids (valid in "this" molecule) needed for adaptive increase
  * \param Order desired Order if positive, desired exponent in threshold criteria if negative (0 is single-step)
@@ -574 +574 @@
   // count them
   if (count == 0) {
-    for (molecule::iterator iter = begin(); iter != end(); ++iter) { // create a lookup table (Atom::ParticleInfo_nr -> atom) used as a marker table lateron
+    for (molecule::iterator iter = begin(); iter != end(); ++iter) { // create a lookup table (Atom::Nr -> atom) used as a marker table lateron
       count = (count < (*iter)->GetTrueFather()->getNr()) ? (*iter)->GetTrueFather()->getNr() : count;
     }
@@ -655 +655 @@
   // ===== 1. Check whether bond structure is same as stored in files ====
 
-  // create lookup table for Atom::ParticleInfo_nr
+  // create lookup table for Atom::Nr
   FragmentationToDo = FragmentationToDo && CreateFatherLookupTable(ListOfAtoms, getAtomCount());
 
@@ -854 +854 @@
 
 
-/** Stores pairs (Atom::ParticleInfo_nr, Atom::AdaptiveOrder) into file.
+/** Stores pairs (Atom::Nr, Atom::AdaptiveOrder) into file.
  * Atoms not present in the file get "-1".
  * \param &path path to file ORDERATSITEFILE
@@ -878 +878 @@
 };
 
-/** Parses pairs(Atom::ParticleInfo_nr, Atom::AdaptiveOrder) from file and stores in molecule's Atom's.
+/** Parses pairs(Atom::Nr, Atom::AdaptiveOrder) from file and stores in molecule's Atom's.
  * Atoms not present in the file get "0".
  * \param &path path to file ORDERATSITEFILEe
@@ -1018 +1018 @@
         if (SonList[OtherFather->getNr()] != NULL) {
 //          Log() << Verbose(0) << ", whose son is " << *SonList[OtherFather->getNr()] << "." << endl;
-          if (OtherFather->getNr() > FatherOfRunner->getNr()) { // add bond (ParticleInfo_nr check is for adding only one of both variants: ab, ba)
+          if (OtherFather->getNr() > FatherOfRunner->getNr()) { // add bond (Nr check is for adding only one of both variants: ab, ba)
 //            Log() << Verbose(3) << "Adding Bond: ";
 //            Log() << Verbose(0) <<