Changeset 6145577

Timestamp:

Apr 10, 2018, 6:43:12 AM (7 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

AutomationFragmentation_failures, Candidate_v1.6.1, ChemicalSpaceEvaluator, Enhanced_StructuralOptimization_continued, Exclude_Hydrogens_annealWithBondGraph, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_contraction-expansion, Gui_displays_atomic_force_velocity, PythonUI_with_named_parameters, StoppableMakroAction, TremoloParser_IncreasedPrecision

Children:

c87d6e

Parents:

8c6b68

git-author:

Frederik Heber <frederik.heber@…> (08/03/17 10:47:26)

git-committer:

Frederik Heber <frederik.heber@…> (04/10/18 06:43:12)

Message:

FIX: ForceAnnealingAction's Undo is again working.

• AtomicInfo::setAtom() and SetAtomsFromAtomicInfo() now accept a time step. This allows to undo changes to the old state (where forces might have been passed to) and the current state (modified by time integration).
• TESTFIX: ForceAnnealing's undo test.conf was no longer valid since the additional time stepping is extracted (and the tests were changed already). I.e. the extra trajectory step is because of step-world-time and not because of force-annealing. Hence, it should not be undone here.

Files:

• src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) (6 diffs)
• src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) (1 diff)
• src/Actions/UndoRedoHelpers.cpp (modified) (2 diffs)
• src/Actions/UndoRedoHelpers.hpp (modified) (2 diffs)
• src/Atom/AtomicInfo.cpp (modified) (2 diffs)
• src/Atom/AtomicInfo.hpp (modified) (2 diffs)
• tests/regression/Molecules/ForceAnnealing/post/test-undo.conf (modified) (1 diff)
• tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) (1 diff)

src/Actions/MoleculeAction/ForceAnnealingAction.cpp

@@ -71 +71 @@
     return Action::failure;
   }
+
+  size_t CurrentStep = WorldTime::getInstance().getTime();
+  if (CurrentStep == 0) {
+    ELOG(1, "WorldTime must be at least at step 1 already, use step-world-time if necessary.");
+    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)
@@ -76 +83 @@
 
   // 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)));
+  std::vector< std::vector<AtomicInfo> > UndoInfo(2);
+  for (int i=0;i<2;++i) {
+    UndoInfo[i].reserve(set.size());
+    {
+      for (World::AtomSelectionConstIterator iter = World::getInstance().beginAtomSelection();
+          iter != World::getInstance().endAtomSelection();
+          ++iter)
+        UndoInfo[i].push_back(AtomicInfo(*(iter->second), CurrentStep-i));
+    }
   }
 
@@ -93 +102 @@
       params.MaxDistance.get(),
       params.DampingFactor.get());
-  size_t CurrentStep = WorldTime::getInstance().getTime();
-  if (CurrentStep == 0) {
-    ELOG(1, "WorldTime must be at least at step 1 already, use step-world-time if necessary.");
-    return Action::failure;
-  }
 
   // parse forces into last step (assuming we stepped on already)
@@ -113 +117 @@
   STATUS("Successfully optimized structure by one step.");
 
-  std::vector<AtomicInfo> RedoInfo;
-  RedoInfo.reserve(set.size());
-  {
-    for (World::AtomSelectionConstIterator iter = World::getInstance().beginAtomSelection();
-        iter != World::getInstance().endAtomSelection();
-        ++iter)
-      RedoInfo.push_back(AtomicInfo(*(iter->second)));
+  std::vector< std::vector<AtomicInfo> > RedoInfo(2);
+  for (int i=0;i<2;++i) {
+    RedoInfo[i].reserve(set.size());
+    {
+      for (World::AtomSelectionConstIterator iter = World::getInstance().beginAtomSelection();
+          iter != World::getInstance().endAtomSelection();
+          ++iter)
+        RedoInfo[i].push_back(AtomicInfo(*(iter->second), CurrentStep-i));
+    }
   }
+
   MoleculeForceAnnealingState *UndoState =
     new MoleculeForceAnnealingState(UndoInfo, RedoInfo, params);
@@ -130 +137 @@
   MoleculeForceAnnealingState *state =
       assert_cast<MoleculeForceAnnealingState*>(_state.get());
+  const size_t CurrentStep = WorldTime::getInstance().getTime();
 
   // set stored old state
-  SetAtomsFromAtomicInfo(state->UndoInfo);
+  for (int i=0;i<2;++i)
+    SetAtomsFromAtomicInfo(state->UndoInfo[i], CurrentStep-i);
 
   return ActionState::ptr(_state);
@@ -140 +149 @@
   MoleculeForceAnnealingState *state =
       assert_cast<MoleculeForceAnnealingState*>(_state.get());
+  const size_t CurrentStep = WorldTime::getInstance().getTime();
 
   // set stored new state
-  SetAtomsFromAtomicInfo(state->RedoInfo);
+  for (int i=0;i<2;++i)
+    SetAtomsFromAtomicInfo(state->RedoInfo[i], CurrentStep-i);
 
   return ActionState::ptr(_state);

src/Actions/MoleculeAction/ForceAnnealingAction.def

@@ -32 +32 @@
 (DummyValidator<bool>())
 
-#define statetypes (std::vector<AtomicInfo>)(std::vector<AtomicInfo>)
+#define statetypes (std::vector< std::vector<AtomicInfo> >)(std::vector< std::vector<AtomicInfo> >)
 #define statereferences (UndoInfo)(RedoInfo)
 

src/Actions/UndoRedoHelpers.cpp

@@ -145 +145 @@
 }
 
-void MoleCuilder::SetAtomsFromAtomicInfo(const std::vector<AtomicInfo> &_movedatoms)
+void MoleCuilder::SetAtomsFromAtomicInfo(
+    const std::vector<AtomicInfo> &_movedatoms,
+    const unsigned int _step)
 {
   BOOST_FOREACH( const AtomicInfo &_atominfo, _movedatoms) {
@@ -153 +155 @@
         "MoleCuilder::SetAtomsFromAtomicInfo() - cannot find atom with id "
         +toString(id)+" in the world.");
-    _atominfo.setAtom( *_atom );
+    _atominfo.setAtom( *_atom, _step );
   }
 }

src/Actions/UndoRedoHelpers.hpp

@@ -19 +19 @@
 #include "Atom/AtomicInfo.hpp"
 #include "Bond/BondInfo.hpp"
+#include "WorldTime.hpp"
 
 namespace MoleCuilder {
@@ -61 +62 @@
    *
    * @param movedatoms vector of atomicInfo
+   * @param _step set state information for given world time
    */
-  void SetAtomsFromAtomicInfo(const std::vector<AtomicInfo> &_movedatoms);
+  void SetAtomsFromAtomicInfo(
+      const std::vector<AtomicInfo> &_movedatoms,
+      const unsigned int _step = WorldTime::getTime());
 
   /** Selects all atoms inside the given vector

src/Atom/AtomicInfo.cpp

@@ -58 +58 @@
 {}
 
-AtomicInfo::AtomicInfo(const atom &_atom) :
-    Position(_atom.getPosition()),
+AtomicInfo::AtomicInfo(const atom &_atom, unsigned int _step) :
+    Position(_atom.getPositionAtStep(_step)),
     Type(_atom.getType()),
     charge(_atom.getCharge()),
-    Velocity(_atom.getAtomicVelocity()),
-    Force(_atom.getAtomicForce()),
+    Velocity(_atom.getAtomicVelocityAtStep(_step)),
+    Force(_atom.getAtomicForceAtStep(_step)),
     FatherId(_atom.father->getId()),
     MolId(0),
@@ -101 +101 @@
 
 
-bool AtomicInfo::setAtom(atom &_atom) const
+bool AtomicInfo::setAtom(atom &_atom, const unsigned int _step) const
 {
-  _atom.setPosition(Position);
+  _atom.setPositionAtStep(_step, Position);
   _atom.setType(Type);
   _atom.setCharge(charge);
-  _atom.setAtomicVelocity(Velocity);
-  _atom.setAtomicForce(Force);
+  _atom.setAtomicVelocityAtStep(_step, Velocity);
+  _atom.setAtomicForceAtStep(_step, Force);
 
   // set old id

src/Atom/AtomicInfo.hpp

@@ -20 +20 @@
 
 #include "Bond/BondInfo.hpp"
+#include "WorldTime.hpp"
 
 class atom;
@@ -31 +32 @@
 public:
   AtomicInfo();
-  AtomicInfo(const atom &_atom);
+  AtomicInfo(const atom &_atom, const unsigned int _step = WorldTime::getTime());
   AtomicInfo(const AtomicInfo &_atominfo);
   ~AtomicInfo();
 
-  bool setAtom(atom &_atom) const;
+  bool setAtom(atom &_atom, const unsigned int _step = WorldTime::getTime()) const;
   atomId_t getId() const;
 

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

@@ -33 +33 @@
 AT_SETUP([Molecules - Force Annealing with Undo])
 AT_KEYWORDS([molecules force-annealing undo])
-AT_XFAIL_IF([/bin/true])
 
 file=test.conf