Changeset 7adf0f

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:

715b67

Parents:

e7350d4

git-author:

Frederik Heber <heber@…> (02/18/11 14:28:52)

git-committer:

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

Message:

Removed molecule::BondDistance, replaced by BondGraph::getMinMaxDistance().

• changed in:
  • molecule::AddHydrogenReplacementAtom()
  • StoreFragmentFromKeySet_Init()
  • molecule::DeterminePeriodicCenter()
  • molecule::CreateAdjacencyList()

Location:

src

Files:

• molecule.cpp (modified) (5 diffs)
• molecule.hpp (modified) (1 diff)
• molecule_fragmentation.cpp (modified) (5 diffs)
• molecule_geometry.cpp (modified) (3 diffs)
• molecule_graph.cpp (modified) (2 diffs)

src/molecule.cpp

@@ -28 +28 @@
 #include "atom.hpp"
 #include "bond.hpp"
+#include "bondgraph.hpp"
 #include "Box.hpp"
 #include "CodePatterns/enumeration.hpp"
@@ -56 +57 @@
   Observable("molecule"),
   elemente(teil),  MDSteps(0),  BondCount(0), NoNonHydrogen(0), NoNonBonds(0),
-  NoCyclicBonds(0), BondDistance(0.),  ActiveFlag(false), IndexNr(-1),
+  NoCyclicBonds(0),  ActiveFlag(false), IndexNr(-1),
   AtomCount(this,boost::bind(&molecule::doCountAtoms,this),"AtomCount"), last_atom(0)
 {
@@ -324 +325 @@
    // the problem is not the H being out of the box, but InBondvector have the wrong direction
    // due to TopReplacement or Origin being on the wrong side!
-  if (bondlength > BondDistance) {
+  double MinBondDistance;
+  double MaxBondDistance;
+  World::getInstance().getBondGraph()->getMinMaxDistance(
+      TopOrigin,
+      TopReplacement,
+      MinBondDistance,MaxBondDistance,IsAngstroem);
+  std::cout << "bondlength > MaxBondDistance: " << bondlength << " > " <<  MaxBondDistance << std::endl;
+  std::cout << "bondlength < MinBondDistance: " << bondlength << " < " <<  MinBondDistance << std::endl;
+  if ((bondlength < MinBondDistance) || (bondlength > MaxBondDistance)) {
 //    Log() << Verbose(4) << "InBondvector is: ";
 //    InBondvector.Output(out);
@@ -331 +340 @@
     for (int i=NDIM;i--;) {
       l = TopReplacement->at(i) - TopOrigin->at(i);
-      if (fabs(l) > BondDistance) { // is component greater than bond distance
+      if (fabs(l) > MaxBondDistance) { // is component greater than bond distance (check against min not useful here)
         Orthovector1[i] = (l < 0) ? -1. : +1.;
       } // (signs are correct, was tested!)
@@ -669 +678 @@
   for_each(atoms.begin(),atoms.end(),mem_fun(&atom::CorrectFather));
 
-  // copy values
-  if (hasBondStructure()) {  // if adjaceny list is present
-    copy->BondDistance = BondDistance;
-  }
-
   return copy;
 };

src/molecule.hpp

@@ -103 +103 @@
   mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
   mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
-  double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
+  //double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
   bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
   //Vector Center;      //!< Center of molecule in a global box

src/molecule_fragmentation.cpp

@@ -25 +25 @@
 #include "atom.hpp"
 #include "bond.hpp"
+#include "bondgraph.hpp"
 #include "config.hpp"
 #include "element.hpp"
@@ -974 +975 @@
 {
   atom *FatherOfRunner = NULL;
-
-  Leaf->BondDistance = mol->BondDistance;
 
   // first create the minimal set of atoms from the KeySet
@@ -1802 +1801 @@
   std::deque<atom *> *AtomStack = new std::deque<atom *>; // (getAtomCount());
   bool flag = true;
+  BondGraph *BG = World::getInstance().getBondGraph();
 
   DoLog(2) && (Log() << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl);
@@ -1822 +1822 @@
           tmp = fabs(Binder->leftatom->at(i) - Binder->rightatom->at(i));
           //Log() << Verbose(3) << "Checking " << i << "th distance of " << *Binder->leftatom << " to " << *Binder->rightatom << ": " << tmp << "." << endl;
-          if (tmp > BondDistance) {
+          double MinBondDistance;
+          double MaxBondDistance;
+          BG->getMinMaxDistance(Binder->leftatom, Binder->rightatom, MinBondDistance, MaxBondDistance, true);
+          if ((tmp < MinBondDistance) || ((tmp > MaxBondDistance))) {
             DoLog(2) && (Log() << Verbose(2) << "Correcting at bond " << *Binder << "." << endl);
             flag = true;
@@ -1835 +1838 @@
       for (int i=NDIM;i--;) {
         tmp = Binder->leftatom->at(i) - Binder->rightatom->at(i);
-        if (fabs(tmp) > BondDistance)
+        double MinBondDistance;
+        double MaxBondDistance;
+        BG->getMinMaxDistance(Binder->leftatom, Binder->rightatom, MinBondDistance, MaxBondDistance, true);
+        if (fabs(tmp) > MaxBondDistance)  // check against Min is not useful for components
           Translationvector[i] = (tmp < 0) ? +1. : -1.;
       }

src/molecule_geometry.cpp

@@ -29 +29 @@
 #include "atom.hpp"
 #include "bond.hpp"
+#include "bondgraph.hpp"
 #include "config.hpp"
 #include "element.hpp"
@@ -374 +375 @@
   Vector Testvector, Translationvector;
   Vector Center;
+  BondGraph *BG = World::getInstance().getBondGraph();
 
   do {
@@ -391 +393 @@
             for (int j=0;j<NDIM;j++) {
               tmp = (*iter)->at(j) - (*Runner)->GetOtherAtom(*iter)->at(j);
-              if ((fabs(tmp)) > BondDistance) {
+              double MinBondDistance;
+              double MaxBondDistance;
+              BG->getMinMaxDistance((*iter), (*Runner)->GetOtherAtom(*iter), MinBondDistance, MaxBondDistance, true);
+              if (fabs(tmp) > MaxBondDistance) {  // check against Min is not useful for components
                 flag = false;
                 DoLog(0) && (Log() << Verbose(0) << "Hit: atom " << (*iter)->getName() << " in bond " << *(*Runner) << " has to be shifted due to " << tmp << "." << endl);

src/molecule_graph.cpp

@@ -139 +139 @@
   Box &domain = World::getInstance().getDomain();
 
-  BondDistance = bonddistance; // * ((IsAngstroem) ? 1. : 1./AtomicLengthToAngstroem);
   DoLog(0) && (Log() << Verbose(0) << "Begin of CreateAdjacencyList." << endl);
   // remove every bond from the list
@@ -215 +214 @@
         }
     delete (LC);
-    DoLog(1) && (Log() << Verbose(1) << "I detected " << BondCount << " bonds in the molecule with distance " << BondDistance << "." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "I detected " << BondCount << " bonds in the molecule." << endl);
 
     // correct bond degree by comparing valence and bond degree