Changeset 10b1ef

Timestamp:

Nov 7, 2017, 7:34:56 AM (7 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

ForceAnnealing_with_BondGraph_continued_betteresults

Children:

03d40df

Parents:

38ac25

git-author:

Frederik Heber <frederik.heber@…> (11/04/17 10:00:15)

git-committer:

Frederik Heber <frederik.heber@…> (11/07/17 07:34:56)

Message:

ForceAnnealingAction's Undo removes trajectory item if it was added.

• before Undo would not truly undo the change to the trajectory. Now, we additionally store the trajectory size and may recogniye thereby whether we added a step or not. Note that stepping the world time does not add to the trajectory, as it uses the last present map element closest to the current time step.
• TESTFIX: XFAIL removed from Undo as it is now working. Extended Undo test to cover both cases (ForceAnnealing added new step and did not add new step).

Files:

• src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) (3 diffs)
• src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) (1 diff)
• tests/regression/Molecules/ForceAnnealing/post/test-undo.conf (modified) (1 diff)
• tests/regression/Molecules/ForceAnnealing/post/test-undo2.conf (added)
• tests/regression/Molecules/ForceAnnealing/pre/test2.conf (added)
• tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) (2 diffs)

src/Actions/MoleculeAction/ForceAnnealingAction.cpp

@@ -90 +90 @@
           iter != World::getInstance().endAtomSelection();
           ++iter)
-        UndoInfo[i].push_back(AtomicInfo(*(iter->second), CurrentStep-i));
+          UndoInfo[i].push_back(AtomicInfo(*(iter->second), CurrentStep-i));
     }
   }
+  std::vector<int> UndoTrajectorySize;
+  UndoTrajectorySize.reserve(set.size());
+  for (World::AtomSelectionConstIterator iter = World::getInstance().beginAtomSelection();
+      iter != World::getInstance().endAtomSelection();
+      ++iter)
+    UndoTrajectorySize.push_back(iter->second->getTrajectorySize());
 
   // instantiate optimizer
@@ -129 +135 @@
 
   MoleculeForceAnnealingState *UndoState =
-    new MoleculeForceAnnealingState(UndoInfo, RedoInfo, params);
+    new MoleculeForceAnnealingState(UndoInfo, UndoTrajectorySize, RedoInfo, params);
 
   return ActionState::ptr(UndoState);
@@ -139 +145 @@
   const size_t CurrentStep = WorldTime::getInstance().getTime();
 
-  // set stored old state
-  for (int i=0;i<2;++i)
-    SetAtomsFromAtomicInfo(state->UndoInfo[i], CurrentStep-i);
+  // set stored old state and remove current one from trajectory if we set it
+  for (int i=0;i<2;++i) {
+    for(size_t j=0;j<state->UndoInfo[i].size();++j) {
+      const AtomicInfo &_atominfo = state->UndoInfo[i][j];
+      const atomId_t id = _atominfo.getId();
+      atom * const _atom = World::getInstance().getAtom(AtomById(id));
+      ASSERT( _atom != NULL,
+          "MoleCuilder::SetAtomsFromAtomicInfo() - cannot find atom with id "
+          +toString(id)+" in the world.");
+      if (state->UndoTrajectorySize[j] > CurrentStep-i)
+        _atominfo.setAtom( *_atom, CurrentStep-i );
+      else
+        _atom->removeSteps(state->UndoTrajectorySize[j], CurrentStep-i);
+    }
+  }
 
   return ActionState::ptr(_state);

src/Actions/MoleculeAction/ForceAnnealingAction.def

@@ -32 +32 @@
 (DummyValidator<bool>())
 
-#define statetypes (std::vector< std::vector<AtomicInfo> >)(std::vector< std::vector<AtomicInfo> >)
-#define statereferences (UndoInfo)(RedoInfo)
+#define statetypes (std::vector< std::vector<AtomicInfo> >)(std::vector<int>)(std::vector< std::vector<AtomicInfo> >)
+#define statereferences (UndoInfo)(UndoTrajectorySize)(RedoInfo)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS

tests/regression/Molecules/ForceAnnealing/post/test-undo.conf

@@ -82 +82 @@
 Ion_Type2_2     8.532785963     4.158586027     3.535886037     0       1.000000e-01    0.000000e+00    0.000000e+00     # molecule nr 9
 Ion_Type2_3     7.283585982     3.275186040     3.535886037     0       1.000000e-01    0.000000e+00    0.000000e+00     # molecule nr 10
-
-Ion_Type1_1     9.782085945     2.645886050     2.645886050     0 # molecule nr 0
-Ion_Type1_2     9.782085945     2.645886050     4.425886024     0 # molecule nr 1
-Ion_Type1_3     10.672039608    3.904536878     3.535886037     0 # molecule nr 2
-Ion_Type1_4     8.532785963     4.787886018     2.645886050     0 # molecule nr 3
-Ion_Type1_5     8.532785963     4.787886018     4.425886024     0 # molecule nr 4
-Ion_Type1_6     6.393632318     3.904536877     3.535886037     0 # molecule nr 5
-Ion_Type1_7     7.283585982     2.645886050     2.645886050     0 # molecule nr 6
-Ion_Type1_8     7.283585982     2.645886050     4.425886024     0 # molecule nr 7
-Ion_Type2_1     9.782085945     3.275186040     3.535886037     0 # molecule nr 8
-Ion_Type2_2     8.532785963     4.158586027     3.535886037     0 # molecule nr 9
-Ion_Type2_3     7.283585982     3.275186040     3.535886037     0 # molecule nr 10

tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at

@@ -31 +31 @@
 
 
-AT_SETUP([Molecules - Force Annealing with Undo])
+# here, we have only one step in the trajectories
+AT_SETUP([Molecules - Force Annealing with Undo I])
 AT_KEYWORDS([molecules force-annealing undo])
 
@@ -40 +41 @@
 AT_CHECK([../../molecuilder -i $file --select-all-atoms --step-world-time 1 --force-annealing --forces-file test.forces --steps 1 --undo], 0, [stdout], [stderr])
 AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Molecules/ForceAnnealing/post/test-undo.conf], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+
+# here two steps are present already
+AT_SETUP([Molecules - Force Annealing with Undo II])
+AT_KEYWORDS([molecules force-annealing undo])
+
+file=test2.conf
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/ForceAnnealing/pre/test2.conf $file], 0)
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/ForceAnnealing/pre/test.forces .], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file --select-all-atoms --set-world-time 1 --force-annealing --forces-file test.forces --steps 1 --undo], 0, [stdout], [stderr])
+AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Molecules/ForceAnnealing/post/test-undo2.conf], 0, [ignore], [ignore])
 
 AT_CLEANUP