Changeset 45f835 for src

Timestamp:

Oct 14, 2011, 12:10:02 PM (13 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:

9c27b0

Parents:

34fbb3

Message:

Added Undo/Redo capabilities to RepeatBoxAction.

• adapted regression tests.

Location:

src/Actions/WorldAction

Files:

• RepeatBoxAction.cpp (modified) (7 diffs)
• RepeatBoxAction.def (modified) (2 diffs)

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -31 +31 @@
 
 #include <iostream>
+#include <set>
 #include <string>
 #include <vector>
@@ -42 +43 @@
 #include "Action_impl_pre.hpp"
 /** =========== define the function ====================== */
-Action::state_ptr WorldRepeatBoxAction::performCall() {
+
+void repeatMoleculesinDomain(Vector Repeater, const std::vector<molecule *> &AllMolecules)
+{
   int count;
   const element ** Elements;
-  molecule *mol = NULL;
   int j = 0;
   atom *Walker = NULL;
   MoleculeListClass *molecules = World::getInstance().getMolecules();
 
-  // obtain information
-  getParametersfromValueStorage();
-
-  vector<molecule *> AllMolecules;
-  if (mol != NULL) {
-    DoLog(0) && (Log() << Verbose(0) << "Using molecule " << mol->name << "." << endl);
-    AllMolecules = World::getInstance().getAllMolecules(MoleculeByPtr(mol));
-  } else {
-    DoLog(0) && (Log() << Verbose(0) << "Using all molecules." << endl);
-    AllMolecules = World::getInstance().getAllMolecules();
-  }
-
-  (cout << "Repeating box " << params.Repeater << " times for (x,y,z) axis." << endl);
+  LOG(0, "STATUS: Repeating box " << Repeater << " times for (x,y,z) axis.");
+
+  // set new domain
   RealSpaceMatrix M = World::getInstance().getDomain().getM();
   RealSpaceMatrix newM = M;
@@ -69 +61 @@
   RealSpaceMatrix repMat;
   for (int axis = 0; axis < NDIM; axis++) {
-    params.Repeater[axis] = floor(params.Repeater[axis]);
-    if (params.Repeater[axis] < 1) {
-      DoeLog(1) && (eLog()<< Verbose(1) << "Repetition factor must be greater than 1!" << endl);
-      params.Repeater[axis] = 1;
+    Repeater[axis] = floor(Repeater[axis]);
+    if (Repeater[axis] < 1) {
+      ELOG(1, "Repetition factor must be greater than 1!");
+      Repeater[axis] = 1;
     }
-    repMat.at(axis,axis) = params.Repeater[axis];
+    repMat.at(axis,axis) = Repeater[axis];
   }
   newM *= repMat;
   World::getInstance().setDomain(newM);
 
+  // add molecules in each repeated domain part
   molecule *newmol = NULL;
   std::vector<Vector> vectors;
-  for (n[0] = 0; n[0] < params.Repeater[0]; n[0]++) {
+  for (n[0] = 0; n[0] < Repeater[0]; n[0]++) {
     y[0] = n[0];
-    for (n[1] = 0; n[1] < params.Repeater[1]; n[1]++) {
+    for (n[1] = 0; n[1] < Repeater[1]; n[1]++) {
       y[1] = n[1];
-      for (n[2] = 0; n[2] < params.Repeater[2]; n[2]++) {
+      for (n[2] = 0; n[2] < Repeater[2]; n[2]++) {
         y[2] = n[2];
         if ((n[0] == 0) && (n[1] == 0) && (n[2] == 0))
           continue;
-        for (vector<molecule *>::iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
-          mol = *MolRunner;
-          DoLog(1) && (Log() << Verbose(1) << "Current mol is " << mol->name << "." << endl);
+        for (vector<molecule *>::const_iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
+          const molecule *mol = *MolRunner;
+          LOG(2, "INFO: Current mol is " << mol->name << ".");
           count = mol->getAtomCount();   // is changed becausing of adding, thus has to be stored away beforehand
           if (count != 0) {  // if there is more than none
@@ -97 +90 @@
             vectors.resize(count);
             j = 0;
-            for(molecule::iterator AtomRunner = mol->begin(); AtomRunner != mol->end(); ++AtomRunner) {
+            for(molecule::const_iterator AtomRunner = mol->begin(); AtomRunner != mol->end(); ++AtomRunner) {
               Elements[j] = (*AtomRunner)->getType();
               vectors[j] = (*AtomRunner)->getPosition();
@@ -103 +96 @@
             }
             if (count != j)
-              DoeLog(1) && (eLog()<< Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl);
+              ELOG(1, "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!");
             x = y;
             x *= M;
             newmol = World::getInstance().createMolecule();
+            // TODO: Remove this when World don't has deprecated MoleculeListClass anymore
             molecules->insert(newmol);
             for (int k=count;k--;) { // go through every atom of the original cell
@@ -118 +112 @@
             delete[](Elements);
           } else {
-            DoLog(1) && (Log() << Verbose(1) << "\t ... is empty." << endl);
+            LOG(1, "\t ... is empty.");
           }
         }
@@ -124 +118 @@
     }
   }
+}
+
+Action::state_ptr WorldRepeatBoxAction::performCall() {
+  molecule *mol = NULL;
+
+  // obtain information
+  getParametersfromValueStorage();
+
+  std::vector<molecule *> AllMolecules;
+  if (mol != NULL) {
+    DoLog(0) && (Log() << Verbose(0) << "Using molecule " << mol->name << "." << endl);
+    AllMolecules = World::getInstance().getAllMolecules(MoleculeByPtr(mol));
+  } else {
+    DoLog(0) && (Log() << Verbose(0) << "Using all molecules." << endl);
+    AllMolecules = World::getInstance().getAllMolecules();
+  }
+
+  // prepare undo state
+  RealSpaceMatrix olddomain = World::getInstance().getDomain().getM();
+  std::set<molecule *> oldmolecules;
+  for(std::vector<molecule *>::const_iterator iter = AllMolecules.begin();
+      iter != AllMolecules.end();
+      ++iter)
+    oldmolecules.insert(*iter);
+  WorldRepeatBoxState *undostate = new WorldRepeatBoxState(olddomain, oldmolecules, params);
+
+  repeatMoleculesinDomain(params.Repeater, AllMolecules);
 
   // give final box size
   LOG(0, "Box domain is now " << World::getInstance().getDomain().getM());
 
-  return Action::success;
+  return Action::state_ptr(undostate);
 }
 
 Action::state_ptr WorldRepeatBoxAction::performUndo(Action::state_ptr _state) {
-//  ParserLoadXyzState *state = assert_cast<ParserLoadXyzState*>(_state.get());
-
-  return Action::failure;
-//  string newName = state->mol->getName();
-//  state->mol->setName(state->lastName);
-//
-//  return Action::state_ptr(new ParserLoadXyzState(state->mol,newName));
+  WorldRepeatBoxState *state = assert_cast<WorldRepeatBoxState*>(_state.get());
+  MoleculeListClass *molecules = World::getInstance().getMolecules();
+
+  // set old domain
+  World::getInstance().setDomain(state->olddomain);
+
+  // remove all added molecules (and their atoms)
+  std::vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
+  for (std::vector<molecule *>::iterator iter = allmolecules.begin();
+      iter != allmolecules.end();
+      ++iter) {
+    if (state->oldmolecules.find(*iter) == state->oldmolecules.end()) {
+      (*iter)->removeAtomsinMolecule();
+      // TODO: Remove this when World don't has deprecated MoleculeListClass anymore
+      molecules->erase(*iter);
+      World::getInstance().destroyMolecule(*iter);
+    }
+  }
+
+  // give final box size
+  LOG(0, "Box domain restored to " << World::getInstance().getDomain().getM());
+
+  return Action::state_ptr(_state);
 }
 
 Action::state_ptr WorldRepeatBoxAction::performRedo(Action::state_ptr _state){
-  return Action::failure;
+  WorldRepeatBoxState *state = assert_cast<WorldRepeatBoxState*>(_state.get());
+
+  std::vector<molecule *> originalmolecules;
+  for(std::set<molecule *>::const_iterator iter = state->oldmolecules.begin();
+      iter != state->oldmolecules.end();
+      ++iter)
+    originalmolecules.push_back(*iter);
+  repeatMoleculesinDomain(state->params.Repeater, originalmolecules);
+
+  // give final box size
+  LOG(0, "Box domain is again " << World::getInstance().getDomain().getM());
+
+  return Action::state_ptr(_state);
 }
 
 bool WorldRepeatBoxAction::canUndo() {
-  return false;
+  return true;
 }
 
 bool WorldRepeatBoxAction::shouldUndo() {
-  return false;
+  return true;
 }
 /** =========== end of function ====================== */

src/Actions/WorldAction/RepeatBoxAction.def

@@ -8 +8 @@
 // all includes and forward declarations necessary for non-integral types below
 #include "Actions/Values.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
+#include <set>
+
+class molecule;
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -19 +23 @@
 #define paramreferences (Repeater)
 
-#undef statetypes
-#undef statereferences
+#define statetypes (RealSpaceMatrix)(std::set< molecule *>)
+#define statereferences (olddomain)(oldmolecules)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS