Changeset 7e4d0a6

Timestamp:

Apr 4, 2018, 4:59:24 PM (7 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Adding_MD_integration_tests, Adding_StructOpt_integration_tests, AutomationFragmentation_failures, Candidate_v1.6.1, ChemicalSpaceEvaluator, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Exclude_Hydrogens_annealWithBondGraph, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_contraction-expansion, Gui_displays_atomic_force_velocity, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, PythonUI_with_named_parameters, StoppableMakroAction, TremoloParser_IncreasedPrecision

Children:

37fe17

Parents:

0aae02

git-author:

Frederik Heber <frederik.heber@…> (07/12/17 20:53:30)

git-committer:

Frederik Heber <frederik.heber@…> (04/04/18 16:59:24)

Message:

FIX: Fragmentation does no longer use getTrueFather().

• in a very early implementations saturation hydrogens were all over the place and we needed to look at the original atom. Every atom has a father member where for the saturation hydrogen the original atom (i.e. the one from the dangling bond not present in the current fragment) was stored. Now, however, we only look at the set of atoms without any hydrogens and saturation is done after the fragmentation has taken place (namely in the ExportGraph routines). Therefore, we do not need the getTrueFather() calls any longer.
• FIX: This fixes a bug where we filled the box with water molecules and intended to perform a long-range MD afterwards but only a single fragment is calculated. This is because of the getTrueFather() calls that mask every atom except for the three atoms of the original water molecule that was used to fill the box with.

File:

• src/Fragmentation/Fragmentation.cpp (modified) (4 diffs)

src/Fragmentation/Fragmentation.cpp

@@ -286 +286 @@
     atom *Walker = mol->FindAtom(RootKeyNr);
     // check cyclic lengths
-    //if ((MinimumRingSize[Walker->GetTrueFather()->getNr()] != -1) && (Walker->GetTrueFather()->getAdaptiveOrder()+1 > MinimumRingSize[Walker->GetTrueFather()->getNr()])) {
-    //  LOG(0, "Bond order " << Walker->GetTrueFather()->getAdaptiveOrder() << " of Root " << *Walker << " greater than or equal to Minimum Ring size of " << MinimumRingSize << " found is not allowed.");
+    //if ((MinimumRingSize[Walker->getNr()] != -1) && (Walker->getAdaptiveOrder()+1 > MinimumRingSize[Walker->getNr()])) {
+    //  LOG(0, "Bond order " << Walker->getAdaptiveOrder() << " of Root " << *Walker << " greater than or equal to Minimum Ring size of " << MinimumRingSize << " found is not allowed.");
     //} else
     {
       // set adaptive order to desired max order
-      Walker->GetTrueFather()->setAdaptiveOrder(Walker->GetTrueFather()->getMaxOrder());
-      Order = Walker->GetTrueFather()->getAdaptiveOrder();
+      Walker->setAdaptiveOrder(Walker->getMaxOrder());
+      Order = Walker->getAdaptiveOrder();
       Walker->setAdaptiveOrder(Order);
 
@@ -320 +320 @@
       //NumMoleculesOfOrder[Walker->getAdaptiveOrder()-1] = NumMolecules;
       TotalNumMolecules += NumMoleculesOfOrder[RootNr];
-//      LOG(1, "Number of resulting molecules for Order " << (int)Walker->GetTrueFather()->getAdaptiveOrder() << " is: " << NumMoleculesOfOrder[RootNr] << ".");
+//      LOG(1, "Number of resulting molecules for Order " << (int)Walker->getAdaptiveOrder() << " is: " << NumMoleculesOfOrder[RootNr] << ".");
       RootStack.push_back(RootKeyNr); // put back on stack
       RootNr++;
@@ -540 +540 @@
       iter != const_cast<const molecule *>(mol)->end();
       ++iter) {
-    const atom * const Father = (*iter)->GetTrueFather();
-    if (AtomMask.isTrue(Father->getNr())) // apply mask
-      if ((treatment == IncludeHydrogen) || ((*iter)->getType()->getAtomicNumber() != 1)) // skip hydrogen
-        RootStack.push_front((*iter)->getNr());
+    const atom * const Walker = (*iter);
+    if (AtomMask.isTrue(Walker->getNr())) // apply mask
+      if ((treatment == IncludeHydrogen) || (Walker->getType()->getAtomicNumber() != 1)) // skip hydrogen
+        RootStack.push_front(Walker->getNr());
   }
 }
@@ -600 +600 @@
     KeySet TempSet;
     for (KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
-      TempSet.insert((mol->FindAtom(*sprinter))->GetTrueFather()->getId());
+      TempSet.insert((mol->FindAtom(*sprinter))->getId());
     TotalGraph.insert(GraphPair(TempSet, pair<int, double> (TotalNumberOfKeySets++, (*runner).second.second)));
   }