Changeset c459c4

Timestamp:

Nov 5, 2017, 1:55:28 AM (7 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

ForceAnnealing_with_BondGraph_continued_betteresults

Children:

1c8a80

Parents:

d79ef32

git-author:

Frederik Heber <frederik.heber@…> (06/27/17 21:02:47)

git-committer:

Frederik Heber <frederik.heber@…> (11/05/17 01:55:28)

Message:

Sorting given selected atoms by ids in ForceAnnealing.

Location:

src

Files:

• Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) (2 diffs)
• Dynamics/AtomicForceManipulator.hpp (modified) (1 diff)

src/Actions/MoleculeAction/ForceAnnealingAction.cpp

@@ -71 +71 @@
     return Action::failure;
   }
+  // first, we need to sort the mixin according to their ids (as selected atoms are sorted
+  // according to their arbitrary address in memory)
+  set.sortByIds();
+
+  // create undo state for all selected atoms (undo info)
+  std::vector<AtomicInfo> UndoInfo;
+  UndoInfo.reserve(set.size());
+  {
+    for (World::AtomSelectionConstIterator iter = World::getInstance().beginAtomSelection();
+        iter != World::getInstance().endAtomSelection();
+        ++iter)
+      UndoInfo.push_back(AtomicInfo(*(iter->second)));
+  }
+
   // we always operate relative to current time step, except on single debug output
   size_t CurrentStep = WorldTime::getInstance().getTime();
@@ -103 +117 @@
     else
       LOG(2, "File " << params.forcesfile.get() << " found and parsed.");
-  }
-
-  // create undo state for all selected atoms (undo info)
-  std::vector<AtomicInfo> UndoInfo;
-  UndoInfo.reserve(set.size());
-  {
-    for (World::AtomSelectionConstIterator iter = World::getInstance().beginAtomSelection();
-        iter != World::getInstance().endAtomSelection();
-        ++iter)
-      UndoInfo.push_back(AtomicInfo(*(iter->second)));
   }
 

src/Dynamics/AtomicForceManipulator.hpp

@@ -82 +82 @@
     Vector tempVector;
     size_t i=0;
+
     for(typename AtomSetMixin<T>::iterator iter = atoms.begin(); iter != atoms.end(); ++iter,++i) {
       for(size_t d=0;d<NDIM;d++) {
         tempVector[d] = Force.Matrix[0][i][d+offset]*(IsAngstroem ? AtomicLengthToAngstroem : 1.);
       }
+      LOG(3, "DEBUG: Adding force vector " << tempVector << " to atom " << **iter);
+      ASSERT( ((*iter)->getId()+1) == Force.Matrix[0][i][0],
+          "AtomicForceManipulator::addForceMatrixToAtomicForce() - mismatch in ids "
+          +toString(((*iter)->getId()+1))+" and file "+toString(Force.Matrix[0][i][0])+".");
       tempVector += (*iter)->getAtomicForceAtStep(TimeStep);
       (*iter)->setAtomicForceAtStep(TimeStep, tempVector);